Query 034697
Match_columns 86
No_of_seqs 111 out of 681
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 05:33:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034697.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034697hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00249 Myb_DNA-binding: Myb- 99.6 1.1E-15 2.4E-20 87.1 5.8 45 14-61 2-47 (48)
2 smart00717 SANT SANT SWI3, AD 99.4 5E-13 1.1E-17 73.3 6.1 46 14-62 2-47 (49)
3 cd00167 SANT 'SWI3, ADA2, N-Co 99.4 2E-12 4.4E-17 70.0 6.0 44 15-61 1-44 (45)
4 PF13921 Myb_DNA-bind_6: Myb-l 99.3 1.4E-11 3E-16 72.3 5.3 41 16-60 1-41 (60)
5 PLN03212 Transcription repress 99.1 9.3E-11 2E-15 87.5 5.2 47 12-61 24-71 (249)
6 PLN03212 Transcription repress 99.1 2E-10 4.2E-15 85.8 6.8 51 11-65 76-126 (249)
7 KOG0048 Transcription factor, 99.0 1.2E-09 2.7E-14 79.9 6.9 46 12-61 61-106 (238)
8 PLN03091 hypothetical protein; 99.0 1.4E-09 3E-14 86.7 7.5 49 12-64 66-114 (459)
9 PLN03091 hypothetical protein; 99.0 5.3E-10 1.1E-14 89.0 4.7 47 12-61 13-60 (459)
10 KOG0048 Transcription factor, 98.9 5.9E-10 1.3E-14 81.6 2.6 51 13-66 9-61 (238)
11 KOG0457 Histone acetyltransfer 98.8 9.8E-09 2.1E-13 81.5 6.6 51 8-61 67-117 (438)
12 TIGR01557 myb_SHAQKYF myb-like 98.6 1.2E-07 2.7E-12 56.5 5.9 48 13-63 3-55 (57)
13 COG5259 RSC8 RSC chromatin rem 98.6 7.3E-08 1.6E-12 77.6 4.3 45 13-61 279-323 (531)
14 KOG0049 Transcription factor, 98.4 5E-07 1.1E-11 75.6 6.0 52 10-64 357-408 (939)
15 KOG1279 Chromatin remodeling f 98.3 8.9E-07 1.9E-11 71.7 5.6 49 9-61 249-297 (506)
16 COG5114 Histone acetyltransfer 98.1 6.2E-06 1.3E-10 64.5 6.3 48 12-62 62-109 (432)
17 KOG0724 Zuotin and related mol 98.1 6.6E-06 1.4E-10 62.2 5.3 68 14-81 32-104 (335)
18 PF13837 Myb_DNA-bind_4: Myb/S 98.0 1.9E-05 4.1E-10 48.7 5.0 57 14-70 2-72 (90)
19 KOG4167 Predicted DNA-binding 97.9 2.5E-05 5.4E-10 66.0 6.1 44 12-59 618-661 (907)
20 KOG0050 mRNA splicing protein 97.6 8.9E-05 1.9E-09 60.8 4.6 52 13-67 7-59 (617)
21 PF13873 Myb_DNA-bind_5: Myb/S 97.5 0.00036 7.7E-09 42.5 5.8 54 14-67 3-74 (78)
22 KOG0050 mRNA splicing protein 97.4 0.00021 4.6E-09 58.6 4.6 53 12-69 58-110 (617)
23 COG5147 REB1 Myb superfamily p 97.3 0.00037 8.1E-09 56.8 4.8 52 12-67 71-122 (512)
24 KOG0049 Transcription factor, 97.2 0.00058 1.3E-08 57.7 5.4 45 10-57 409-453 (939)
25 KOG0051 RNA polymerase I termi 97.2 0.0006 1.3E-08 56.6 4.8 47 12-63 383-429 (607)
26 PF09111 SLIDE: SLIDE; InterP 97.2 0.002 4.3E-08 43.4 6.6 57 10-66 46-114 (118)
27 PF12776 Myb_DNA-bind_3: Myb/S 96.9 0.0035 7.5E-08 39.0 5.6 54 15-68 1-68 (96)
28 TIGR02894 DNA_bind_RsfA transc 96.9 0.0011 2.4E-08 47.1 3.5 50 13-63 4-56 (161)
29 KOG0051 RNA polymerase I termi 96.5 0.005 1.1E-07 51.2 5.2 52 11-62 434-507 (607)
30 KOG4282 Transcription factor G 96.4 0.014 3.1E-07 44.4 6.7 59 14-72 55-123 (345)
31 PF08914 Myb_DNA-bind_2: Rap1 95.9 0.021 4.5E-07 34.8 4.4 49 13-61 2-56 (65)
32 KOG4468 Polycomb-group transcr 95.8 0.023 4.9E-07 47.9 5.7 54 13-70 88-151 (782)
33 COG5147 REB1 Myb superfamily p 95.8 0.0055 1.2E-07 50.2 2.1 45 13-60 20-64 (512)
34 COG5118 BDP1 Transcription ini 95.8 0.024 5.2E-07 45.6 5.5 45 12-60 364-408 (507)
35 PRK13923 putative spore coat p 95.5 0.022 4.9E-07 40.7 4.1 48 13-61 5-55 (170)
36 KOG1194 Predicted DNA-binding 95.3 0.056 1.2E-06 44.2 6.1 44 13-60 187-230 (534)
37 PLN03142 Probable chromatin-re 95.2 0.052 1.1E-06 47.7 6.2 45 12-59 823-867 (1033)
38 smart00595 MADF subfamily of S 95.1 0.043 9.3E-07 33.7 4.0 27 37-64 28-54 (89)
39 KOG4329 DNA-binding protein [G 94.8 0.064 1.4E-06 42.9 5.0 47 10-59 274-320 (445)
40 KOG3841 TEF-1 and related tran 94.4 0.21 4.7E-06 40.1 7.2 59 12-70 75-151 (455)
41 PF11035 SnAPC_2_like: Small n 94.3 0.24 5.2E-06 38.9 7.2 55 12-66 20-74 (344)
42 PF13404 HTH_AsnC-type: AsnC-t 93.6 0.37 7.9E-06 26.7 5.2 39 20-62 4-42 (42)
43 PF10545 MADF_DNA_bdg: Alcohol 93.1 0.18 3.9E-06 29.9 3.7 30 37-66 27-57 (85)
44 KOG2656 DNA methyltransferase 91.9 0.13 2.8E-06 41.4 2.4 51 14-68 131-187 (445)
45 smart00426 TEA TEA domain. 91.3 0.4 8.7E-06 29.7 3.7 23 12-34 2-24 (68)
46 PF04504 DUF573: Protein of un 91.2 0.89 1.9E-05 29.4 5.5 54 13-66 4-66 (98)
47 PF07750 GcrA: GcrA cell cycle 90.0 0.53 1.1E-05 33.1 3.9 42 15-61 2-43 (162)
48 PF04545 Sigma70_r4: Sigma-70, 89.9 2.1 4.5E-05 23.6 5.8 44 17-66 6-49 (50)
49 PRK11179 DNA-binding transcrip 89.5 1.4 2.9E-05 29.9 5.5 42 19-64 9-50 (153)
50 PLN03142 Probable chromatin-re 88.6 2 4.4E-05 38.1 7.1 53 11-66 924-988 (1033)
51 PF13325 MCRS_N: N-terminal re 87.5 3.4 7.4E-05 30.2 6.7 55 9-64 69-128 (199)
52 PRK11169 leucine-responsive tr 87.4 1.9 4.1E-05 29.6 5.2 42 19-64 14-55 (164)
53 KOG3554 Histone deacetylase co 87.4 0.8 1.7E-05 38.1 3.8 43 13-59 285-328 (693)
54 PF13325 MCRS_N: N-terminal re 86.0 1.8 3.8E-05 31.7 4.6 43 15-62 1-46 (199)
55 PF01285 TEA: TEA/ATTS domain 84.4 2 4.2E-05 34.7 4.6 50 12-61 48-112 (431)
56 PF05263 DUF722: Protein of un 83.8 3.6 7.8E-05 28.2 5.1 36 30-66 93-128 (130)
57 PF00046 Homeobox: Homeobox do 83.3 5.9 0.00013 22.0 5.9 50 13-63 4-53 (57)
58 KOG1194 Predicted DNA-binding 81.8 0.87 1.9E-05 37.4 1.6 47 14-65 471-517 (534)
59 smart00344 HTH_ASNC helix_turn 80.9 7.1 0.00015 24.3 5.4 42 19-64 3-44 (108)
60 KOG2009 Transcription initiati 79.3 1.9 4.2E-05 36.1 2.9 45 12-60 408-452 (584)
61 PF08281 Sigma70_r4_2: Sigma-7 79.0 8.6 0.00019 21.1 5.7 26 37-63 27-52 (54)
62 PF06461 DUF1086: Domain of Un 77.8 19 0.00041 25.3 7.1 52 14-66 39-90 (145)
63 COG1522 Lrp Transcriptional re 77.4 8.2 0.00018 25.3 5.1 41 20-64 9-49 (154)
64 cd00086 homeodomain Homeodomai 75.6 11 0.00024 20.6 6.4 50 13-63 4-53 (59)
65 PF11626 Rap1_C: TRF2-interact 74.8 4.5 9.8E-05 25.2 3.1 14 12-25 46-59 (87)
66 TIGR02937 sigma70-ECF RNA poly 74.4 18 0.00039 22.4 6.0 31 36-67 126-156 (158)
67 PRK11924 RNA polymerase sigma 73.5 17 0.00036 23.8 5.8 31 36-67 141-171 (179)
68 PF00674 DUP: DUP family; Int 73.1 5.1 0.00011 25.9 3.1 44 21-64 44-101 (108)
69 smart00501 BRIGHT BRIGHT, ARID 72.7 12 0.00026 23.2 4.7 42 23-64 36-86 (93)
70 TIGR02950 SigM_subfam RNA poly 71.4 25 0.00053 22.7 6.2 45 22-67 97-151 (154)
71 smart00389 HOX Homeodomain. DN 70.3 15 0.00033 19.9 5.7 47 14-61 5-51 (56)
72 PF01388 ARID: ARID/BRIGHT DNA 69.1 9.8 0.00021 23.3 3.7 41 23-63 40-89 (92)
73 PF01466 Skp1: Skp1 family, di 69.1 5.5 0.00012 24.3 2.5 21 39-59 36-56 (78)
74 PLN03162 golden-2 like transcr 67.0 18 0.00038 29.6 5.5 52 14-66 238-291 (526)
75 PRK12541 RNA polymerase sigma 66.6 28 0.0006 22.9 5.7 47 22-69 104-160 (161)
76 TIGR02985 Sig70_bacteroi1 RNA 66.6 31 0.00067 22.0 5.9 31 36-67 129-159 (161)
77 PRK09648 RNA polymerase sigma 65.8 29 0.00064 23.4 5.9 44 23-67 132-185 (189)
78 PRK09646 RNA polymerase sigma 63.6 28 0.0006 23.8 5.4 48 19-67 131-188 (194)
79 TIGR02952 Sig70_famx2 RNA poly 62.7 35 0.00075 22.3 5.6 45 22-67 114-168 (170)
80 PRK09642 RNA polymerase sigma 62.0 39 0.00085 22.0 5.8 45 22-67 98-152 (160)
81 PRK06759 RNA polymerase factor 59.5 42 0.00091 21.7 5.5 45 22-67 98-152 (154)
82 PRK12522 RNA polymerase sigma 59.4 32 0.0007 22.9 5.1 51 16-67 105-165 (173)
83 PF00887 ACBP: Acyl CoA bindin 59.4 12 0.00026 23.1 2.7 24 44-67 61-84 (87)
84 cd00435 ACBP Acyl CoA binding 58.7 16 0.00035 22.8 3.3 23 45-67 60-82 (85)
85 TIGR02939 RpoE_Sigma70 RNA pol 58.4 45 0.00097 22.3 5.7 44 23-67 131-184 (190)
86 PRK09645 RNA polymerase sigma 57.3 46 0.001 22.0 5.5 44 23-67 111-164 (173)
87 PRK09643 RNA polymerase sigma 57.0 48 0.001 22.7 5.7 46 21-67 125-180 (192)
88 PTZ00458 acyl CoA binding prot 56.8 19 0.00041 23.1 3.3 23 45-67 62-84 (90)
89 PRK09641 RNA polymerase sigma 56.4 55 0.0012 21.8 5.8 43 23-66 129-181 (187)
90 KOG0385 Chromatin remodeling c 56.2 35 0.00076 30.3 5.7 44 12-59 794-837 (971)
91 PRK12516 RNA polymerase sigma 56.2 48 0.001 22.8 5.6 47 20-67 106-162 (187)
92 TIGR02954 Sig70_famx3 RNA poly 56.2 50 0.0011 21.8 5.6 47 20-67 109-165 (169)
93 COG5269 ZUO1 Ribosome-associat 55.5 22 0.00048 28.0 4.1 48 14-61 246-299 (379)
94 cd08307 Death_Pelle Death doma 54.7 14 0.0003 24.0 2.5 20 36-55 21-40 (97)
95 PRK09047 RNA polymerase factor 54.0 58 0.0013 21.1 5.6 45 22-67 98-152 (161)
96 TIGR02943 Sig70_famx1 RNA poly 53.4 60 0.0013 22.2 5.7 44 22-66 123-176 (188)
97 PRK11922 RNA polymerase sigma 53.2 64 0.0014 22.8 6.0 44 23-67 142-195 (231)
98 PRK09649 RNA polymerase sigma 53.0 62 0.0013 22.0 5.7 47 20-67 120-176 (185)
99 PF14775 NYD-SP28_assoc: Sperm 52.4 26 0.00057 20.7 3.3 31 38-68 2-38 (60)
100 PRK12530 RNA polymerase sigma 51.7 66 0.0014 21.9 5.7 44 23-67 127-180 (189)
101 TIGR02947 SigH_actino RNA poly 50.9 66 0.0014 21.8 5.6 44 22-66 123-176 (193)
102 TIGR02983 SigE-fam_strep RNA p 50.5 68 0.0015 20.9 5.7 46 22-68 102-157 (162)
103 PF07030 DUF1320: Protein of u 50.4 35 0.00076 22.6 4.0 28 51-78 84-111 (130)
104 PRK11923 algU RNA polymerase s 50.3 76 0.0017 21.4 5.8 44 22-66 130-183 (193)
105 PRK09640 RNA polymerase sigma 49.8 79 0.0017 21.4 6.5 51 16-67 120-180 (188)
106 PRK12534 RNA polymerase sigma 49.5 71 0.0015 21.4 5.5 46 21-67 128-183 (187)
107 PF11842 DUF3362: Domain of un 49.4 22 0.00048 25.0 3.0 27 19-47 41-67 (150)
108 PRK09637 RNA polymerase sigma 47.7 84 0.0018 21.4 5.7 31 36-67 122-152 (181)
109 PRK12514 RNA polymerase sigma 47.5 78 0.0017 21.1 5.5 45 22-67 121-175 (179)
110 TIGR02948 SigW_bacill RNA poly 47.4 82 0.0018 20.9 5.9 45 22-67 128-182 (187)
111 PRK09652 RNA polymerase sigma 47.2 78 0.0017 20.6 6.1 31 36-67 144-174 (182)
112 PRK05602 RNA polymerase sigma 47.0 86 0.0019 21.0 6.0 45 22-67 120-174 (186)
113 PRK12524 RNA polymerase sigma 46.1 94 0.002 21.2 6.6 45 22-67 128-182 (196)
114 KOG2941 Beta-1,4-mannosyltrans 45.9 9.9 0.00022 30.8 0.9 21 12-32 260-281 (444)
115 TIGR03001 Sig-70_gmx1 RNA poly 45.5 74 0.0016 23.2 5.4 43 22-65 153-205 (244)
116 PRK12542 RNA polymerase sigma 45.3 93 0.002 20.9 5.8 45 22-67 114-168 (185)
117 cd08777 Death_RIP1 Death Domai 45.0 72 0.0016 19.9 4.6 31 17-55 1-31 (86)
118 PRK12536 RNA polymerase sigma 44.7 90 0.0019 21.0 5.5 45 22-67 121-175 (181)
119 PRK12543 RNA polymerase sigma 44.6 95 0.0021 20.8 5.7 45 21-66 108-162 (179)
120 PRK12547 RNA polymerase sigma 44.1 92 0.002 20.5 5.6 45 22-67 104-158 (164)
121 TIGR02984 Sig-70_plancto1 RNA 43.7 95 0.0021 20.6 5.6 44 23-67 133-186 (189)
122 PRK12532 RNA polymerase sigma 43.5 1E+02 0.0022 20.9 5.6 43 23-66 129-181 (195)
123 PRK12537 RNA polymerase sigma 42.7 1E+02 0.0022 20.7 5.5 44 23-67 126-179 (182)
124 COG4281 ACB Acyl-CoA-binding p 42.0 55 0.0012 21.0 3.7 30 37-67 54-83 (87)
125 COG1497 Predicted transcriptio 41.9 76 0.0017 24.3 5.1 39 22-64 14-52 (260)
126 PRK12523 RNA polymerase sigma 41.5 1E+02 0.0023 20.4 5.7 44 22-66 111-164 (172)
127 PRK12515 RNA polymerase sigma 41.3 1.1E+02 0.0024 20.6 5.7 43 23-66 124-176 (189)
128 PF08784 RPA_C: Replication pr 40.9 88 0.0019 19.4 5.2 41 22-63 50-91 (102)
129 PRK06811 RNA polymerase factor 40.9 1.1E+02 0.0025 20.6 5.6 45 21-66 122-176 (189)
130 PRK12518 RNA polymerase sigma 40.8 1E+02 0.0023 20.2 5.6 45 22-67 112-166 (175)
131 COG5352 Uncharacterized protei 40.5 27 0.00058 24.8 2.3 42 15-61 2-43 (169)
132 PF12451 VPS11_C: Vacuolar pro 39.1 33 0.00071 19.4 2.2 24 20-47 20-43 (49)
133 TIGR02989 Sig-70_gvs1 RNA poly 38.0 1.1E+02 0.0024 19.7 5.6 49 17-66 98-156 (159)
134 PRK13919 putative RNA polymera 38.0 1.2E+02 0.0026 20.2 5.6 45 22-67 127-181 (186)
135 TIGR02859 spore_sigH RNA polym 38.0 1.2E+02 0.0027 20.3 6.3 30 37-67 166-195 (198)
136 cd00580 CHMI 5-carboxymethyl-2 37.8 54 0.0012 21.0 3.3 22 46-67 68-89 (113)
137 PRK09651 RNA polymerase sigma 37.4 1.2E+02 0.0027 20.1 5.9 44 22-66 111-164 (172)
138 PRK12527 RNA polymerase sigma 37.2 1.2E+02 0.0025 19.8 5.7 38 23-61 98-145 (159)
139 PRK12540 RNA polymerase sigma 36.5 1.4E+02 0.003 20.3 5.7 45 22-67 103-157 (182)
140 PF13496 DUF4120: Domain of un 36.4 36 0.00078 22.2 2.2 25 39-63 11-35 (95)
141 PRK10430 DNA-binding transcrip 36.3 1.3E+02 0.0028 20.9 5.3 62 15-78 158-222 (239)
142 PRK12538 RNA polymerase sigma 36.3 1.5E+02 0.0033 21.3 5.8 43 23-66 164-216 (233)
143 PRK12545 RNA polymerase sigma 35.5 1.5E+02 0.0032 20.4 5.7 43 23-66 132-184 (201)
144 PRK12511 RNA polymerase sigma 35.3 1.5E+02 0.0031 20.3 5.6 49 22-71 103-161 (182)
145 cd06171 Sigma70_r4 Sigma70, re 35.0 66 0.0014 16.2 5.4 42 16-63 11-52 (55)
146 PF01726 LexA_DNA_bind: LexA D 34.9 99 0.0022 18.2 4.4 48 16-63 4-52 (65)
147 KOG0843 Transcription factor E 34.8 1.4E+02 0.003 22.0 5.3 56 13-69 106-161 (197)
148 PF02954 HTH_8: Bacterial regu 34.4 77 0.0017 16.8 4.3 33 20-57 6-38 (42)
149 PF04282 DUF438: Family of unk 34.3 33 0.00071 21.2 1.8 22 47-68 11-32 (71)
150 PRK02220 4-oxalocrotonate taut 34.2 80 0.0017 17.5 3.3 23 45-67 8-30 (61)
151 PRK12528 RNA polymerase sigma 34.0 1.3E+02 0.0029 19.5 5.6 44 22-66 105-158 (161)
152 PRK09636 RNA polymerase sigma 34.0 1.9E+02 0.0041 21.2 6.2 44 23-67 108-161 (293)
153 PRK12533 RNA polymerase sigma 33.9 1.7E+02 0.0038 20.7 5.8 45 22-67 126-180 (216)
154 PRK12535 RNA polymerase sigma 33.8 1.6E+02 0.0035 20.3 5.5 45 22-67 125-179 (196)
155 cd08318 Death_NMPP84 Death dom 33.7 1.2E+02 0.0025 18.7 4.7 17 37-54 19-35 (86)
156 KOG0488 Transcription factor B 33.7 1.1E+02 0.0024 23.6 4.9 49 12-62 175-224 (309)
157 TIGR02960 SigX5 RNA polymerase 33.5 1.7E+02 0.0037 21.4 5.8 44 23-67 135-188 (324)
158 PRK04217 hypothetical protein; 33.4 1.4E+02 0.0031 19.6 6.2 30 37-67 59-88 (110)
159 PRK12519 RNA polymerase sigma 33.2 1.5E+02 0.0033 19.9 5.9 44 23-67 134-187 (194)
160 PRK09635 sigI RNA polymerase s 33.2 1.8E+02 0.0038 21.7 5.9 46 22-68 110-165 (290)
161 PRK12520 RNA polymerase sigma 33.1 1.5E+02 0.0033 19.9 5.6 43 23-66 124-176 (191)
162 PF09420 Nop16: Ribosome bioge 32.9 1.5E+02 0.0033 20.3 5.1 45 13-61 114-162 (164)
163 cd07216 Pat17_PNPLA8_PNPLA9_li 32.7 58 0.0013 24.3 3.2 27 41-67 54-82 (309)
164 PRK12526 RNA polymerase sigma 32.5 1.7E+02 0.0037 20.2 5.7 45 22-67 145-199 (206)
165 PF09197 Rap1-DNA-bind: Rap1, 32.5 1.5E+02 0.0033 19.6 5.8 46 16-61 2-74 (105)
166 COG0193 Pth Peptidyl-tRNA hydr 30.4 1E+02 0.0022 22.5 4.0 38 14-59 150-187 (190)
167 PF09905 DUF2132: Uncharacteri 30.3 83 0.0018 19.2 3.0 22 21-48 12-33 (64)
168 PRK07408 RNA polymerase sigma 30.3 2E+02 0.0044 20.8 5.7 48 19-67 192-249 (256)
169 PF00196 GerE: Bacterial regul 30.3 1E+02 0.0022 17.0 5.0 44 16-66 4-47 (58)
170 PF10743 Phage_Cox: Regulatory 29.9 1.4E+02 0.0031 19.2 4.2 40 28-79 5-44 (87)
171 KOG1724 SCF ubiquitin ligase, 29.2 49 0.0011 23.3 2.2 22 38-59 119-140 (162)
172 PRK06288 RNA polymerase sigma 29.1 2.2E+02 0.0049 20.6 5.8 38 22-60 204-251 (268)
173 PRK06986 fliA flagellar biosyn 29.1 2.1E+02 0.0045 20.2 5.8 44 22-66 176-229 (236)
174 PRK12525 RNA polymerase sigma 29.1 1.7E+02 0.0038 19.3 5.5 44 22-66 110-163 (168)
175 COG4387 Mu-like prophage prote 29.0 82 0.0018 21.9 3.2 36 40-75 70-107 (139)
176 TIGR01636 phage_rinA phage tra 28.7 1.8E+02 0.0039 19.2 6.3 29 37-66 101-129 (134)
177 KOG2251 Homeobox transcription 28.3 83 0.0018 23.7 3.3 43 12-54 40-83 (228)
178 PF11084 DUF2621: Protein of u 28.3 68 0.0015 22.4 2.7 21 13-33 56-76 (141)
179 PRK07670 RNA polymerase sigma 28.2 2.2E+02 0.0048 20.4 5.6 30 36-66 217-246 (251)
180 PRK15411 rcsA colanic acid cap 27.9 2.2E+02 0.0047 19.9 5.6 45 15-66 137-181 (207)
181 PTZ00397 macrophage migration 27.9 94 0.002 19.8 3.2 22 46-67 66-87 (116)
182 PRK12529 RNA polymerase sigma 27.8 1.9E+02 0.0042 19.3 5.6 41 23-64 120-170 (178)
183 COG3695 Predicted methylated D 27.7 1.5E+02 0.0033 19.6 4.2 36 21-56 8-44 (103)
184 PRK08241 RNA polymerase factor 27.4 2.2E+02 0.0049 21.1 5.6 44 23-67 146-199 (339)
185 TIGR02957 SigX4 RNA polymerase 27.4 2.2E+02 0.0047 20.9 5.5 31 36-67 124-154 (281)
186 KOG4031 Vesicle coat protein c 26.9 1.9E+02 0.004 21.6 4.9 46 19-66 161-210 (216)
187 cd08780 Death_TRADD Death Doma 26.6 1.1E+02 0.0023 19.9 3.2 24 17-47 1-24 (90)
188 PRK09638 RNA polymerase sigma 26.3 2E+02 0.0042 18.9 5.3 43 23-66 119-171 (176)
189 PRK08301 sporulation sigma fac 26.2 2.3E+02 0.0051 19.8 5.8 43 23-66 171-227 (234)
190 PF01086 Clathrin_lg_ch: Clath 26.1 24 0.00051 25.8 0.1 48 19-67 167-218 (225)
191 PRK15372 pathogenicity island 25.8 1.1E+02 0.0023 23.7 3.6 18 47-64 31-48 (292)
192 PRK12531 RNA polymerase sigma 25.7 2.2E+02 0.0048 19.3 6.3 45 22-67 133-187 (194)
193 PRK12544 RNA polymerase sigma 25.6 2.4E+02 0.0052 19.7 5.6 44 23-67 141-194 (206)
194 KOG0847 Transcription factor, 25.6 2.1E+02 0.0045 21.9 5.1 52 13-67 171-224 (288)
195 COG1223 Predicted ATPase (AAA+ 25.2 2.7E+02 0.0058 22.2 5.7 40 21-60 290-329 (368)
196 PRK00575 tatA twin arginine tr 25.0 1.6E+02 0.0035 19.1 3.8 41 23-67 12-52 (92)
197 PRK04654 sec-independent trans 25.0 1.2E+02 0.0027 22.5 3.7 38 24-65 13-50 (214)
198 TIGR02479 FliA_WhiG RNA polyme 24.5 2.5E+02 0.0055 19.6 5.7 28 38-66 193-220 (224)
199 cd08779 Death_PIDD Death Domai 24.3 1.4E+02 0.0031 18.4 3.5 22 36-58 13-37 (86)
200 cd06257 DnaJ DnaJ domain or J- 24.2 1.3E+02 0.0027 16.0 2.9 20 47-66 10-29 (55)
201 PF13412 HTH_24: Winged helix- 24.1 1.3E+02 0.0027 15.9 5.6 40 21-64 5-44 (48)
202 PRK09415 RNA polymerase factor 23.9 2.3E+02 0.005 18.9 6.1 44 23-67 120-173 (179)
203 PF14552 Tautomerase_2: Tautom 23.7 1.1E+02 0.0024 18.9 2.9 30 38-67 28-58 (82)
204 PRK13719 conjugal transfer tra 23.5 3E+02 0.0065 20.4 5.5 45 14-65 142-186 (217)
205 KOG1878 Nuclear receptor coreg 23.3 44 0.00095 31.5 1.3 27 36-62 373-399 (1672)
206 PRK14857 tatA twin arginine tr 23.2 1.7E+02 0.0038 18.7 3.8 41 23-67 14-54 (90)
207 TIGR02959 SigZ RNA polymerase 23.2 2.3E+02 0.0051 18.8 5.6 43 23-66 93-145 (170)
208 TIGR02787 codY_Gpos GTP-sensin 23.0 3.3E+02 0.0071 20.8 5.7 47 16-63 177-224 (251)
209 PF07638 Sigma70_ECF: ECF sigm 23.0 2.6E+02 0.0056 19.1 6.1 30 36-66 151-180 (185)
210 PF09862 DUF2089: Protein of u 22.8 2.4E+02 0.0053 18.8 5.5 44 19-67 36-79 (113)
211 PF08285 DPM3: Dolichol-phosph 22.8 40 0.00086 21.6 0.7 22 49-70 61-82 (91)
212 smart00005 DEATH DEATH domain, 22.7 1.7E+02 0.0037 17.2 3.5 17 36-53 17-33 (88)
213 PRK09647 RNA polymerase sigma 22.4 2.8E+02 0.006 19.3 5.7 44 23-67 131-184 (203)
214 PF11740 KfrA_N: Plasmid repli 22.4 2.1E+02 0.0046 17.9 6.1 54 24-77 7-61 (120)
215 PRK12546 RNA polymerase sigma 22.4 2.7E+02 0.0058 19.1 5.9 44 23-67 106-159 (188)
216 PF02416 MttA_Hcf106: mttA/Hcf 22.4 1.5E+02 0.0033 16.8 3.1 39 24-66 10-48 (53)
217 cd07018 S49_SppA_67K_type Sign 22.2 2.5E+02 0.0055 19.9 4.9 57 14-74 151-208 (222)
218 PRK15201 fimbriae regulatory p 22.2 3.3E+02 0.0071 20.1 5.5 45 15-66 133-177 (198)
219 KOG3493 Ubiquitin-like protein 22.2 1E+02 0.0022 19.2 2.4 28 37-64 26-53 (73)
220 PF01035 DNA_binding_1: 6-O-me 22.1 2E+02 0.0044 17.6 4.3 36 21-56 4-40 (85)
221 PF13725 tRNA_bind_2: Possible 21.9 91 0.002 19.2 2.2 24 19-47 71-94 (101)
222 PRK12517 RNA polymerase sigma 21.4 2.8E+02 0.006 18.9 5.6 44 22-66 120-173 (188)
223 PF13748 ABC_membrane_3: ABC t 21.3 1E+02 0.0023 23.2 2.8 28 36-63 170-197 (237)
224 KOG4051 Uncharacterized conser 21.2 1.3E+02 0.0029 22.4 3.3 36 12-47 31-73 (214)
225 COG5622 Protein required for a 20.8 71 0.0015 22.3 1.6 57 8-66 56-116 (139)
226 smart00441 FF Contains two con 20.7 1.6E+02 0.0035 15.9 3.0 26 22-47 5-31 (55)
227 PRK12513 RNA polymerase sigma 20.7 2.8E+02 0.006 18.6 6.0 43 23-66 132-184 (194)
228 PRK09413 IS2 repressor TnpA; R 20.1 89 0.0019 20.2 2.0 24 22-48 95-118 (121)
229 KOG0817 Acyl-CoA-binding prote 20.0 3.1E+02 0.0067 18.9 6.8 33 35-67 47-86 (142)
No 1
>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=99.62 E-value=1.1e-15 Score=87.12 Aligned_cols=45 Identities=29% Similarity=0.686 Sum_probs=40.6
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcC-CCCHHHHHHHHHHH
Q 034697 14 SSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVS-GKTVEDVKKHYELL 61 (86)
Q Consensus 14 ~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vp-gRT~~qc~~ry~~L 61 (86)
..||.+|+.+|.++|.+|+.+ +|..||..|| |||..||+.||..+
T Consensus 2 ~~Wt~eE~~~l~~~v~~~g~~---~W~~Ia~~~~~~Rt~~qc~~~~~~~ 47 (48)
T PF00249_consen 2 GPWTEEEDEKLLEAVKKYGKD---NWKKIAKRMPGGRTAKQCRSRYQNL 47 (48)
T ss_dssp -SS-HHHHHHHHHHHHHSTTT---HHHHHHHHHSSSSTHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHhCCc---HHHHHHHHcCCCCCHHHHHHHHHhh
Confidence 589999999999999999854 7999999999 99999999999876
No 2
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.43 E-value=5e-13 Score=73.31 Aligned_cols=46 Identities=24% Similarity=0.632 Sum_probs=42.2
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHH
Q 034697 14 SSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLV 62 (86)
Q Consensus 14 ~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~ 62 (86)
..||.+|+.+|+.++.+|+. .+|..||..||+||..+|+.||..+.
T Consensus 2 ~~Wt~~E~~~l~~~~~~~g~---~~w~~Ia~~~~~rt~~~~~~~~~~~~ 47 (49)
T smart00717 2 GEWTEEEDELLIELVKKYGK---NNWEKIAKELPGRTAEQCRERWNNLL 47 (49)
T ss_pred CCCCHHHHHHHHHHHHHHCc---CCHHHHHHHcCCCCHHHHHHHHHHHc
Confidence 58999999999999999973 47999999999999999999998764
No 3
>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=99.38 E-value=2e-12 Score=70.02 Aligned_cols=44 Identities=25% Similarity=0.635 Sum_probs=40.6
Q ss_pred CCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHH
Q 034697 15 SWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELL 61 (86)
Q Consensus 15 ~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L 61 (86)
.||.+|++.|..++.+|+. .+|..||+.||+||..||+.||..+
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~---~~w~~Ia~~~~~rs~~~~~~~~~~~ 44 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGK---NNWEKIAKELPGRTPKQCRERWRNL 44 (45)
T ss_pred CCCHHHHHHHHHHHHHHCc---CCHHHHHhHcCCCCHHHHHHHHHHh
Confidence 5999999999999999973 4799999999999999999999875
No 4
>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=99.26 E-value=1.4e-11 Score=72.34 Aligned_cols=41 Identities=15% Similarity=0.494 Sum_probs=35.9
Q ss_pred CCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHH
Q 034697 16 WTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYEL 60 (86)
Q Consensus 16 WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~ 60 (86)
||.+||.+|..++.+|+ ..|..||+.||.||..+|+.||..
T Consensus 1 WT~eEd~~L~~~~~~~g----~~W~~Ia~~l~~Rt~~~~~~r~~~ 41 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYG----NDWKKIAEHLGNRTPKQCRNRWRN 41 (60)
T ss_dssp S-HHHHHHHHHHHHHHT----S-HHHHHHHSTTS-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHC----cCHHHHHHHHCcCCHHHHHHHHHH
Confidence 99999999999999995 379999999977999999999998
No 5
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.12 E-value=9.3e-11 Score=87.51 Aligned_cols=47 Identities=13% Similarity=0.304 Sum_probs=42.0
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcC-CCCHHHHHHHHHHH
Q 034697 12 SGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVS-GKTVEDVKKHYELL 61 (86)
Q Consensus 12 ~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vp-gRT~~qc~~ry~~L 61 (86)
....||+|||++|.+++.+|+. .+|..||+.++ |||.+||++||..+
T Consensus 24 KRg~WT~EEDe~L~~lV~kyG~---~nW~~IAk~~g~gRT~KQCReRW~N~ 71 (249)
T PLN03212 24 KRGPWTVEEDEILVSFIKKEGE---GRWRSLPKRAGLLRCGKSCRLRWMNY 71 (249)
T ss_pred cCCCCCHHHHHHHHHHHHHhCc---ccHHHHHHhhhcCCCcchHHHHHHHh
Confidence 4678999999999999999974 48999999994 89999999999764
No 6
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.11 E-value=2e-10 Score=85.79 Aligned_cols=51 Identities=14% Similarity=0.296 Sum_probs=45.1
Q ss_pred CCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHH
Q 034697 11 SSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDI 65 (86)
Q Consensus 11 ~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv 65 (86)
-..++||.|||.+|.+++..|+ .+|..||+.|||||..+|++||..+....
T Consensus 76 I~kgpWT~EED~lLlel~~~~G----nKWs~IAk~LpGRTDnqIKNRWns~LrK~ 126 (249)
T PLN03212 76 VKRGGITSDEEDLILRLHRLLG----NRWSLIAGRIPGRTDNEIKNYWNTHLRKK 126 (249)
T ss_pred cccCCCChHHHHHHHHHHHhcc----ccHHHHHhhcCCCCHHHHHHHHHHHHhHH
Confidence 4568999999999999999985 58999999999999999999998766554
No 7
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.00 E-value=1.2e-09 Score=79.90 Aligned_cols=46 Identities=20% Similarity=0.417 Sum_probs=42.2
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHH
Q 034697 12 SGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELL 61 (86)
Q Consensus 12 ~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L 61 (86)
..+.||+|||.++.++.+.++ +||..||++|||||+.+|++||...
T Consensus 61 krg~fT~eEe~~Ii~lH~~~G----NrWs~IA~~LPGRTDNeIKN~Wnt~ 106 (238)
T KOG0048|consen 61 KRGNFSDEEEDLIIKLHALLG----NRWSLIAGRLPGRTDNEVKNHWNTH 106 (238)
T ss_pred cCCCCCHHHHHHHHHHHHHHC----cHHHHHHhhCCCcCHHHHHHHHHHH
Confidence 467999999999999999985 6899999999999999999999754
No 8
>PLN03091 hypothetical protein; Provisional
Probab=98.99 E-value=1.4e-09 Score=86.67 Aligned_cols=49 Identities=16% Similarity=0.407 Sum_probs=44.4
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHH
Q 034697 12 SGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKD 64 (86)
Q Consensus 12 ~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~d 64 (86)
..++||.|||++|.+++..|+ .+|.+||+.|||||..+|++||..++..
T Consensus 66 kKgpWT~EED~lLLeL~k~~G----nKWskIAk~LPGRTDnqIKNRWnslLKK 114 (459)
T PLN03091 66 KRGTFSQQEENLIIELHAVLG----NRWSQIAAQLPGRTDNEIKNLWNSCLKK 114 (459)
T ss_pred cCCCCCHHHHHHHHHHHHHhC----cchHHHHHhcCCCCHHHHHHHHHHHHHH
Confidence 467999999999999999986 4899999999999999999999976654
No 9
>PLN03091 hypothetical protein; Provisional
Probab=98.98 E-value=5.3e-10 Score=89.05 Aligned_cols=47 Identities=11% Similarity=0.323 Sum_probs=41.9
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcC-CCCHHHHHHHHHHH
Q 034697 12 SGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVS-GKTVEDVKKHYELL 61 (86)
Q Consensus 12 ~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vp-gRT~~qc~~ry~~L 61 (86)
....||.|||++|..+|.+|+. ..|..||+.++ |||.+||++||.++
T Consensus 13 rKg~WTpEEDe~L~~~V~kyG~---~nWs~IAk~~g~gRT~KQCRERW~Ny 60 (459)
T PLN03091 13 RKGLWSPEEDEKLLRHITKYGH---GCWSSVPKQAGLQRCGKSCRLRWINY 60 (459)
T ss_pred cCCCCCHHHHHHHHHHHHHhCc---CCHHHHhhhhccCcCcchHhHHHHhc
Confidence 3568999999999999999975 48999999986 89999999999863
No 10
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=98.92 E-value=5.9e-10 Score=81.60 Aligned_cols=51 Identities=12% Similarity=0.244 Sum_probs=45.9
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcC-CCCHHHHHHHHH-HHHHHHh
Q 034697 13 GSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVS-GKTVEDVKKHYE-LLVKDIN 66 (86)
Q Consensus 13 ~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vp-gRT~~qc~~ry~-~L~~dv~ 66 (86)
.++||.|||.+|...|.+|+++ +|..||+.+| ||+.++|+.||. +|..+|+
T Consensus 9 kGpWt~EED~~L~~~V~~~G~~---~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ik 61 (238)
T KOG0048|consen 9 KGPWTQEEDLTQIRSIKSFGKH---NGTALPKLAGLRRCGKSCRLRWTNYLRPDLK 61 (238)
T ss_pred CCCCChHHHHHHHHHHHHhCCC---CcchhhhhcCCCccchHHHHHhhcccCCCcc
Confidence 5899999999999999999764 8999999999 999999999996 4666665
No 11
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=98.82 E-value=9.8e-09 Score=81.51 Aligned_cols=51 Identities=27% Similarity=0.414 Sum_probs=45.5
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHH
Q 034697 8 SSRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELL 61 (86)
Q Consensus 8 ~~~~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L 61 (86)
|..-....||.+|+.+|.+|+..|+-| +|+.||.+||.||.++|++||.+.
T Consensus 67 s~~i~~~~WtadEEilLLea~~t~G~G---NW~dIA~hIGtKtkeeck~hy~k~ 117 (438)
T KOG0457|consen 67 SFPILDPSWTADEEILLLEAAETYGFG---NWQDIADHIGTKTKEECKEHYLKH 117 (438)
T ss_pred CCCCCCCCCChHHHHHHHHHHHHhCCC---cHHHHHHHHcccchHHHHHHHHHH
Confidence 344467889999999999999999865 899999999999999999999864
No 12
>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=98.63 E-value=1.2e-07 Score=56.53 Aligned_cols=48 Identities=17% Similarity=0.293 Sum_probs=41.3
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCCchH---HHHHHHcC-CC-CHHHHHHHHHHHHH
Q 034697 13 GSSWTVKQNKQFETALAFYDKDTPDRW---DNVAKAVS-GK-TVEDVKKHYELLVK 63 (86)
Q Consensus 13 ~~~WT~eEdk~Le~al~~~~~~~~~rW---~~IA~~vp-gR-T~~qc~~ry~~L~~ 63 (86)
.-.||.||...|..||..|+.+ .| .+|++.|. .+ |..||+.|++++..
T Consensus 3 r~~WT~eeh~~Fl~ai~~~G~g---~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~~ 55 (57)
T TIGR01557 3 RVVWTEDLHDRFLQAVQKLGGP---DWATPKRILELMVVDGLTRDQVASHLQKYRL 55 (57)
T ss_pred CCCCCHHHHHHHHHHHHHhCCC---cccchHHHHHHcCCCCCCHHHHHHHHHHHHc
Confidence 3579999999999999999754 69 99999986 35 99999999987653
No 13
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=98.55 E-value=7.3e-08 Score=77.56 Aligned_cols=45 Identities=29% Similarity=0.539 Sum_probs=41.6
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHH
Q 034697 13 GSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELL 61 (86)
Q Consensus 13 ~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L 61 (86)
...||.+|..+|.++|..|+ +.|.+||.+|+.||++||+.||.+|
T Consensus 279 dk~WS~qE~~LLLEGIe~yg----DdW~kVA~HVgtKt~EqCIl~FL~L 323 (531)
T COG5259 279 DKNWSRQELLLLLEGIEMYG----DDWDKVARHVGTKTKEQCILHFLQL 323 (531)
T ss_pred cccccHHHHHHHHHHHHHhh----hhHHHHHHHhCCCCHHHHHHHHHcC
Confidence 35899999999999999996 5699999999999999999999875
No 14
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=98.42 E-value=5e-07 Score=75.56 Aligned_cols=52 Identities=17% Similarity=0.413 Sum_probs=45.9
Q ss_pred CCCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHH
Q 034697 10 RSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKD 64 (86)
Q Consensus 10 ~~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~d 64 (86)
+-+.+.||.+||..|..|+.+|+. ..|-+|-+.|||||..||+.||.+.+..
T Consensus 357 sikhg~wt~~ED~~L~~AV~~Yg~---kdw~k~R~~vPnRSdsQcR~RY~nvL~~ 408 (939)
T KOG0049|consen 357 SVKHGRWTDQEDVLLVCAVSRYGA---KDWAKVRQAVPNRSDSQCRERYTNVLNR 408 (939)
T ss_pred cccCCCCCCHHHHHHHHHHHHhCc---cchhhHHHhcCCccHHHHHHHHHHHHHH
Confidence 345689999999999999999974 4899999999999999999999876544
No 15
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=98.34 E-value=8.9e-07 Score=71.75 Aligned_cols=49 Identities=27% Similarity=0.484 Sum_probs=44.8
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHH
Q 034697 9 SRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELL 61 (86)
Q Consensus 9 ~~~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L 61 (86)
..+....||.+|.-+|.++|..|+ +.|.+||.+|++||.+||..||.+|
T Consensus 249 ~~~~~~~WT~qE~lLLLE~ie~y~----ddW~kVa~hVg~ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 249 GESARPNWTEQETLLLLEAIEMYG----DDWNKVADHVGTKSQEQCILKFLRL 297 (506)
T ss_pred cccCCCCccHHHHHHHHHHHHHhc----ccHHHHHhccCCCCHHHHHHHHHhc
Confidence 456678999999999999999996 4699999999999999999999886
No 16
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=98.14 E-value=6.2e-06 Score=64.53 Aligned_cols=48 Identities=17% Similarity=0.446 Sum_probs=43.7
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHH
Q 034697 12 SGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLV 62 (86)
Q Consensus 12 ~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~ 62 (86)
....|+.+|+-+|.+++...+.| +|+.||.+||.|+.++|+.||.+..
T Consensus 62 ~~e~WgadEEllli~~~~TlGlG---NW~dIadyiGsr~kee~k~HylK~y 109 (432)
T COG5114 62 GEEGWGADEELLLIECLDTLGLG---NWEDIADYIGSRAKEEIKSHYLKMY 109 (432)
T ss_pred cCCCcCchHHHHHHHHHHhcCCC---cHHHHHHHHhhhhhHHHHHHHHHHH
Confidence 56789999999999999999865 8999999999999999999998754
No 17
>KOG0724 consensus Zuotin and related molecular chaperones (DnaJ superfamily), contains DNA-binding domains [Posttranslational modification, protein turnover, chaperones]
Probab=98.09 E-value=6.6e-06 Score=62.19 Aligned_cols=68 Identities=44% Similarity=0.677 Sum_probs=63.1
Q ss_pred CCCCHHHHHHHHHHHHhcCCC----CCchHHHHHHHcCC-CCHHHHHHHHHHHHHHHhhhhcCCCCCCCCCCC
Q 034697 14 SSWTVKQNKQFETALAFYDKD----TPDRWDNVAKAVSG-KTVEDVKKHYELLVKDINDIEAGRYPHPNYRST 81 (86)
Q Consensus 14 ~~WT~eEdk~Le~al~~~~~~----~~~rW~~IA~~vpg-RT~~qc~~ry~~L~~dv~~ie~g~v~~P~y~~~ 81 (86)
..|+.++.+.|++|+..|... .+++|.+++..||+ .+..+.+.+|..++.++..++++.+++|.|...
T Consensus 32 ~~~~~~~~k~i~ka~~i~~~~~~~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~p~~~~~ 104 (335)
T KOG0724|consen 32 SLWTEEEFKKIEKALAILDDDEPRRTPDSWDKFAEALPLEKRLEDKIEEYIGLVFDVNIRESGQKPFPKYGKS 104 (335)
T ss_pred hhhHHHHHHHHHHHHHHHhccccccchhhhhHHHhcCccccccchhHHhhhhhHHHHhhhhccCCCccccCcc
Confidence 569999999999999999753 68999999999999 999999999999999999999999999999763
No 18
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=97.97 E-value=1.9e-05 Score=48.74 Aligned_cols=57 Identities=19% Similarity=0.414 Sum_probs=41.3
Q ss_pred CCCCHHHHHHHHHHHHh------cC--CC-CC-chHHHHHHHcC----CCCHHHHHHHHHHHHHHHhhhhc
Q 034697 14 SSWTVKQNKQFETALAF------YD--KD-TP-DRWDNVAKAVS----GKTVEDVKKHYELLVKDINDIEA 70 (86)
Q Consensus 14 ~~WT~eEdk~Le~al~~------~~--~~-~~-~rW~~IA~~vp----gRT~~qc~~ry~~L~~dv~~ie~ 70 (86)
..||.+|-..|+.++.. |. .. .. .-|..||..|. .||+.||+.+|+.|..+-+.+..
T Consensus 2 ~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~~Yk~~k~ 72 (90)
T PF13837_consen 2 RNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLKKKYKKIKD 72 (90)
T ss_dssp -SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHHHHHHCSSS
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence 57999999999998777 21 12 22 37999999984 49999999999999999887654
No 19
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=97.91 E-value=2.5e-05 Score=66.04 Aligned_cols=44 Identities=36% Similarity=0.476 Sum_probs=40.4
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHH
Q 034697 12 SGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYE 59 (86)
Q Consensus 12 ~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~ 59 (86)
++..||..|-++|.+||-.|.++ +..|+++|+|||+.||.+.|.
T Consensus 618 gSd~WTp~E~~lF~kA~y~~~KD----F~~v~km~~~KtVaqCVeyYY 661 (907)
T KOG4167|consen 618 GSDKWTPLERKLFNKALYTYSKD----FIFVQKMVKSKTVAQCVEYYY 661 (907)
T ss_pred CcccccHHHHHHHHHHHHHhccc----HHHHHHHhccccHHHHHHHHH
Confidence 57799999999999999999764 999999999999999999875
No 20
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=97.60 E-value=8.9e-05 Score=60.79 Aligned_cols=52 Identities=23% Similarity=0.498 Sum_probs=44.6
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHH-HHHHhh
Q 034697 13 GSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELL-VKDIND 67 (86)
Q Consensus 13 ~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L-~~dv~~ 67 (86)
.+.|+..||.+|..++.+|+.+ .|.+||+.++-+|+.||+.||.+. -+.|+.
T Consensus 7 ggvwrntEdeilkaav~kyg~n---qws~i~sll~~kt~rqC~~rw~e~ldp~i~~ 59 (617)
T KOG0050|consen 7 GGVWRNTEDEVLKAAVMKYGKN---QWSRIASLLNRKTARQCKARWEEWLDPAIKK 59 (617)
T ss_pred cceecccHHHHHHHHHHHcchH---HHHHHHHHHhhcchhHHHHHHHHHhCHHHhh
Confidence 4689999999999999999864 899999999999999999999764 344443
No 21
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=97.54 E-value=0.00036 Score=42.49 Aligned_cols=54 Identities=9% Similarity=0.302 Sum_probs=45.1
Q ss_pred CCCCHHHHHHHHHHHHhcCC---C----------CCchHHHHHHHc----C-CCCHHHHHHHHHHHHHHHhh
Q 034697 14 SSWTVKQNKQFETALAFYDK---D----------TPDRWDNVAKAV----S-GKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 14 ~~WT~eEdk~Le~al~~~~~---~----------~~~rW~~IA~~v----p-gRT~~qc~~ry~~L~~dv~~ 67 (86)
..||.+|..+|.+.|.+|+. + ...-|+.|+..| | .||..||+..|..+...++.
T Consensus 3 ~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~~~Kk 74 (78)
T PF13873_consen 3 PNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKSKAKK 74 (78)
T ss_pred CCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHH
Confidence 47999999999999999851 1 346799999988 2 49999999999999888764
No 22
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=97.41 E-value=0.00021 Score=58.63 Aligned_cols=53 Identities=13% Similarity=0.373 Sum_probs=45.0
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhhhh
Q 034697 12 SGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDINDIE 69 (86)
Q Consensus 12 ~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ie 69 (86)
....|+.+||..|..+...+| ..|.-||..| |||..||.+||..|+.......
T Consensus 58 ~~tews~eederlLhlakl~p----~qwrtIa~i~-gr~~~qc~eRy~~ll~~~~s~~ 110 (617)
T KOG0050|consen 58 KKTEWSREEDERLLHLAKLEP----TQWRTIADIM-GRTSQQCLERYNNLLDVYVSYH 110 (617)
T ss_pred hhhhhhhhHHHHHHHHHHhcC----CccchHHHHh-hhhHHHHHHHHHHHHHHHHhhh
Confidence 346899999999999988875 4799999999 7999999999999887655433
No 23
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=97.30 E-value=0.00037 Score=56.84 Aligned_cols=52 Identities=13% Similarity=0.338 Sum_probs=46.2
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 12 SGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 12 ~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
....|+.+|+..|..+-.+++ .+|.-||..+||||..+|.++|..+..+...
T Consensus 71 k~~~~~~eed~~li~l~~~~~----~~wstia~~~d~rt~~~~~ery~~~~~~~~s 122 (512)
T COG5147 71 KKKNWSEEEDEQLIDLDKELG----TQWSTIADYKDRRTAQQCVERYVNTLEDLSS 122 (512)
T ss_pred ccccccHHHHHHHHHHHHhcC----chhhhhccccCccchHHHHHHHHHHhhhhhc
Confidence 457899999999999988875 4699999999999999999999988777665
No 24
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=97.24 E-value=0.00058 Score=57.69 Aligned_cols=45 Identities=22% Similarity=0.478 Sum_probs=39.1
Q ss_pred CCCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHH
Q 034697 10 RSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKH 57 (86)
Q Consensus 10 ~~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~r 57 (86)
+.....||-.||..|..+|.+|+.+ .|.+||..+|.||.+|...|
T Consensus 409 s~K~~rW~l~edeqL~~~V~~YG~g---~WakcA~~Lp~~t~~q~~rr 453 (939)
T KOG0049|consen 409 SAKVERWTLVEDEQLLYAVKVYGKG---NWAKCAMLLPKKTSRQLRRR 453 (939)
T ss_pred hhccCceeecchHHHHHHHHHHccc---hHHHHHHHccccchhHHHHH
Confidence 3456889999999999999999876 89999999999999775544
No 25
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=97.19 E-value=0.0006 Score=56.59 Aligned_cols=47 Identities=19% Similarity=0.502 Sum_probs=41.9
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHH
Q 034697 12 SGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVK 63 (86)
Q Consensus 12 ~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~ 63 (86)
..+.||++|++.|-..+.+++ ..|..|++.| ||.+..|+.||..++.
T Consensus 383 ~rg~wt~ee~eeL~~l~~~~g----~~W~~Ig~~l-gr~P~~crd~wr~~~~ 429 (607)
T KOG0051|consen 383 KRGKWTPEEEEELKKLVVEHG----NDWKEIGKAL-GRMPMDCRDRWRQYVK 429 (607)
T ss_pred ccCCCCcchHHHHHHHHHHhc----ccHHHHHHHH-ccCcHHHHHHHHHhhc
Confidence 567999999999999999975 5799999999 7999999999987653
No 26
>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=97.18 E-value=0.002 Score=43.39 Aligned_cols=57 Identities=14% Similarity=0.387 Sum_probs=47.9
Q ss_pred CCCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHc------------CCCCHHHHHHHHHHHHHHHh
Q 034697 10 RSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAV------------SGKTVEDVKKHYELLVKDIN 66 (86)
Q Consensus 10 ~~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~v------------pgRT~~qc~~ry~~L~~dv~ 66 (86)
+.+...+|.+||..|.-.+.+|+-+.++.|++|-..+ -.||+.++..|...|+.-|.
T Consensus 46 ~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~tLi~~i~ 114 (118)
T PF09111_consen 46 NNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCNTLIKLIE 114 (118)
T ss_dssp TSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHHHHHHHHH
T ss_pred CCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHHHHHHHHH
Confidence 5667899999999999999999987788999999876 57999999999998887665
No 27
>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=96.94 E-value=0.0035 Score=39.01 Aligned_cols=54 Identities=22% Similarity=0.344 Sum_probs=41.7
Q ss_pred CCCHHHHHHHHHHHHhcC-------CC--CCchHHHHHHHcC-----CCCHHHHHHHHHHHHHHHhhh
Q 034697 15 SWTVKQNKQFETALAFYD-------KD--TPDRWDNVAKAVS-----GKTVEDVKKHYELLVKDINDI 68 (86)
Q Consensus 15 ~WT~eEdk~Le~al~~~~-------~~--~~~rW~~IA~~vp-----gRT~~qc~~ry~~L~~dv~~i 68 (86)
.||.++++.|.+++...- .+ ++..|..|++.|- ..|..||++||..|..+-+.+
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk~~y~~~ 68 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLKKDYRIW 68 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHHHHHHHH
Confidence 599999999999876651 11 3457999999883 378999999999887766554
No 28
>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=96.91 E-value=0.0011 Score=47.08 Aligned_cols=50 Identities=12% Similarity=0.289 Sum_probs=41.5
Q ss_pred CCCCCHHHHHHHHHHHHhcCCC---CCchHHHHHHHcCCCCHHHHHHHHHHHHH
Q 034697 13 GSSWTVKQNKQFETALAFYDKD---TPDRWDNVAKAVSGKTVEDVKKHYELLVK 63 (86)
Q Consensus 13 ~~~WT~eEdk~Le~al~~~~~~---~~~rW~~IA~~vpgRT~~qc~~ry~~L~~ 63 (86)
.+.||.|||.+|-+.|.+|-.. .-.-++.|+..+ +||.-.|-=||+.++.
T Consensus 4 QDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L-~RTsAACGFRWNs~VR 56 (161)
T TIGR02894 4 QDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL-NRTAAACGFRWNAYVR 56 (161)
T ss_pred ccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH-cccHHHhcchHHHHHH
Confidence 3589999999999999888422 246799999999 7999999999987654
No 29
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=96.53 E-value=0.005 Score=51.24 Aligned_cols=52 Identities=8% Similarity=0.266 Sum_probs=42.5
Q ss_pred CCCCCCCHHHHHHHHHHHH-------hc------------CCC---CCchHHHHHHHcCCCCHHHHHHHHHHHH
Q 034697 11 SSGSSWTVKQNKQFETALA-------FY------------DKD---TPDRWDNVAKAVSGKTVEDVKKHYELLV 62 (86)
Q Consensus 11 ~~~~~WT~eEdk~Le~al~-------~~------------~~~---~~~rW~~IA~~vpgRT~~qc~~ry~~L~ 62 (86)
...+.||.||+..|.+++. +| |.+ .+-.|..|++.+++|+..||+.+|.+|+
T Consensus 434 ~~r~~Ws~eEe~~Llk~V~~~~~~~~q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~ 507 (607)
T KOG0051|consen 434 RNRGAWSIEEEEKLLKTVNEMIREALQPQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLT 507 (607)
T ss_pred cccCcchHHHHHHHHHHHHHHHHHhhcccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHH
Confidence 4678999999999999984 33 111 3457999999999999999999998875
No 30
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=96.40 E-value=0.014 Score=44.41 Aligned_cols=59 Identities=19% Similarity=0.291 Sum_probs=46.1
Q ss_pred CCCCHHHHHHHHHHHHhcC------CCCCchHHHHHHHcC----CCCHHHHHHHHHHHHHHHhhhhcCC
Q 034697 14 SSWTVKQNKQFETALAFYD------KDTPDRWDNVAKAVS----GKTVEDVKKHYELLVKDINDIEAGR 72 (86)
Q Consensus 14 ~~WT~eEdk~Le~al~~~~------~~~~~rW~~IA~~vp----gRT~~qc~~ry~~L~~dv~~ie~g~ 72 (86)
..|+.+|=..|+.+..... .....-|+.||..+. -||..||+.+|..|....+....+.
T Consensus 55 ~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k~Yk~~k~~~ 123 (345)
T KOG4282|consen 55 PRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKKKYKKEKAKK 123 (345)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHhccc
Confidence 7899999999999855432 123567999999553 2999999999999988888766553
No 31
>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=95.90 E-value=0.021 Score=34.76 Aligned_cols=49 Identities=8% Similarity=0.168 Sum_probs=33.9
Q ss_pred CCCCCHHHHHHHHHHHHhcCC-----CCCchHHHHHHHcC-CCCHHHHHHHHHHH
Q 034697 13 GSSWTVKQNKQFETALAFYDK-----DTPDRWDNVAKAVS-GKTVEDVKKHYELL 61 (86)
Q Consensus 13 ~~~WT~eEdk~Le~al~~~~~-----~~~~rW~~IA~~vp-gRT~~qc~~ry~~L 61 (86)
..++|.+||.+|...|..+.. ..+.=|..+++.-| ..|-+.-++||.+-
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~ 56 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKH 56 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHH
Confidence 457999999999999976631 24678999999999 89999999999653
No 32
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=95.83 E-value=0.023 Score=47.86 Aligned_cols=54 Identities=30% Similarity=0.487 Sum_probs=44.2
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCCchHHHH----------HHHcCCCCHHHHHHHHHHHHHHHhhhhc
Q 034697 13 GSSWTVKQNKQFETALAFYDKDTPDRWDNV----------AKAVSGKTVEDVKKHYELLVKDINDIEA 70 (86)
Q Consensus 13 ~~~WT~eEdk~Le~al~~~~~~~~~rW~~I----------A~~vpgRT~~qc~~ry~~L~~dv~~ie~ 70 (86)
...||..|...|-.||.+|+++ +++| -..+.-||..||+.+|.+++..+.+-..
T Consensus 88 ktaWt~~E~~~Ffdal~~~GKd----Fe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~~m~k~~F 151 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGKD----FEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVRRMNKLLF 151 (782)
T ss_pred ccccchhhHHHHHHHHHHhccc----HHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHHHHHhhhc
Confidence 3579999999999999999864 8888 4445569999999999988877766543
No 33
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=95.81 E-value=0.0055 Score=50.15 Aligned_cols=45 Identities=18% Similarity=0.468 Sum_probs=40.0
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHH
Q 034697 13 GSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYEL 60 (86)
Q Consensus 13 ~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~ 60 (86)
.+.|+..||..|..++..|+ ++.|.+||+.++-++.+||+.||..
T Consensus 20 ~gsw~~~EDe~l~~~vk~l~---~nnws~vas~~~~~~~kq~~~rw~~ 64 (512)
T COG5147 20 GGSWKRTEDEDLKALVKKLG---PNNWSKVASLLISSTGKQSSNRWNN 64 (512)
T ss_pred CCCCCCcchhHHHHHHhhcc---cccHHHHHHHhcccccccccchhhh
Confidence 35899999999999999986 4579999999998999999999854
No 34
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=95.77 E-value=0.024 Score=45.58 Aligned_cols=45 Identities=13% Similarity=0.364 Sum_probs=41.0
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHH
Q 034697 12 SGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYEL 60 (86)
Q Consensus 12 ~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~ 60 (86)
....||.+|-..|-+||..++- .+..||..+|.|..+||+..|.+
T Consensus 364 ~~~~Ws~~e~ekFYKALs~wGt----dF~LIs~lfP~R~RkqIKaKfi~ 408 (507)
T COG5118 364 GALRWSKKEIEKFYKALSIWGT----DFSLISSLFPNRERKQIKAKFIK 408 (507)
T ss_pred CCCcccHHHHHHHHHHHHHhcc----hHHHHHHhcCchhHHHHHHHHHH
Confidence 4578999999999999999974 59999999999999999999975
No 35
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=95.53 E-value=0.022 Score=40.72 Aligned_cols=48 Identities=10% Similarity=0.237 Sum_probs=38.8
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCC---CchHHHHHHHcCCCCHHHHHHHHHHH
Q 034697 13 GSSWTVKQNKQFETALAFYDKDT---PDRWDNVAKAVSGKTVEDVKKHYELL 61 (86)
Q Consensus 13 ~~~WT~eEdk~Le~al~~~~~~~---~~rW~~IA~~vpgRT~~qc~~ry~~L 61 (86)
...||.|+|.+|.+.+..|.... -.-.+.++..+ +||.-+|--||+.+
T Consensus 5 qdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRwNs~ 55 (170)
T PRK13923 5 QDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRWNSV 55 (170)
T ss_pred hhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHHHHH
Confidence 35899999999999988886432 35577888889 69999999999654
No 36
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=95.32 E-value=0.056 Score=44.19 Aligned_cols=44 Identities=20% Similarity=0.476 Sum_probs=39.7
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHH
Q 034697 13 GSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYEL 60 (86)
Q Consensus 13 ~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~ 60 (86)
...||.||--+|++|...|++ ++.+|-++||.||...++..|..
T Consensus 187 ~d~WT~Ed~vlFe~aF~~~GK----~F~kIrq~LP~rsLaSlvqyYy~ 230 (534)
T KOG1194|consen 187 PDEWTAEDIVLFEQAFQFFGK----DFHKIRQALPHRSLASLVQYYYS 230 (534)
T ss_pred cccchHHHHHHHHHHHHHhcc----cHHHHHHHccCccHHHHHHHHHH
Confidence 357999999999999999975 69999999999999999988764
No 37
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=95.25 E-value=0.052 Score=47.68 Aligned_cols=45 Identities=24% Similarity=0.414 Sum_probs=39.2
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHH
Q 034697 12 SGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYE 59 (86)
Q Consensus 12 ~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~ 59 (86)
+=..||..+=..|..|..+|+.+ ..+.||..|.|||.+||+..++
T Consensus 823 gf~~w~~~~f~~f~~~~~~~gr~---~~~~i~~~~~~k~~~ev~~y~~ 867 (1033)
T PLN03142 823 GFSTWSRRDFNAFIRACEKYGRN---DIKSIASEMEGKTEEEVERYAK 867 (1033)
T ss_pred CcCcccHHHHHHHHHHHHHhCHh---HHHHHHHHhcCCCHHHHHHHHH
Confidence 34579999999999999999864 7999999999999999986443
No 38
>smart00595 MADF subfamily of SANT domain.
Probab=95.12 E-value=0.043 Score=33.67 Aligned_cols=27 Identities=26% Similarity=0.583 Sum_probs=22.9
Q ss_pred chHHHHHHHcCCCCHHHHHHHHHHHHHH
Q 034697 37 DRWDNVAKAVSGKTVEDVKKHYELLVKD 64 (86)
Q Consensus 37 ~rW~~IA~~vpgRT~~qc~~ry~~L~~d 64 (86)
.-|..||..|+ .|+++|+.+|+.|...
T Consensus 28 ~aW~~Ia~~l~-~~~~~~~~kw~~LR~~ 54 (89)
T smart00595 28 KAWEEIAEELG-LSVEECKKRWKNLRDR 54 (89)
T ss_pred HHHHHHHHHHC-cCHHHHHHHHHHHHHH
Confidence 46999999995 5999999999987533
No 39
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=94.78 E-value=0.064 Score=42.92 Aligned_cols=47 Identities=28% Similarity=0.432 Sum_probs=39.0
Q ss_pred CCCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHH
Q 034697 10 RSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYE 59 (86)
Q Consensus 10 ~~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~ 59 (86)
......||++|=+.|++.|..|+++ +-..=|..|+.||+-+|...|.
T Consensus 274 rd~l~~wsEeEcr~FEegl~~yGKD---F~lIr~nkvrtRsvgElVeyYY 320 (445)
T KOG4329|consen 274 RDDLSGWSEEECRNFEEGLELYGKD---FHLIRANKVRTRSVGELVEYYY 320 (445)
T ss_pred ccccccCCHHHHHHHHHHHHHhccc---HHHHHhcccccchHHHHHHHHH
Confidence 3456789999999999999999875 4444477899999999998765
No 40
>KOG3841 consensus TEF-1 and related transcription factor, TEAD family [Transcription]
Probab=94.43 E-value=0.21 Score=40.10 Aligned_cols=59 Identities=24% Similarity=0.454 Sum_probs=45.8
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCC------------CchHHHHHHHcC-----CCCHHHHHHHHHHHHH-HHhhhhc
Q 034697 12 SGSSWTVKQNKQFETALAFYDKDT------------PDRWDNVAKAVS-----GKTVEDVKKHYELLVK-DINDIEA 70 (86)
Q Consensus 12 ~~~~WT~eEdk~Le~al~~~~~~~------------~~rW~~IA~~vp-----gRT~~qc~~ry~~L~~-dv~~ie~ 70 (86)
+.+.|+++=++.|.+||+.||+.. -+|=+.||.++. .||.+||-.|-+.|.. .++.|.+
T Consensus 75 aegvWSpdIEqsFqEALaiyppcGrrKIilsdegkmyGRNELIarYIKlrtgktRTrKQVSSHIQVlarrk~reiq~ 151 (455)
T KOG3841|consen 75 AEGVWSPDIEQSFQEALAIYPPCGRRKIILSDEGKMYGRNELIARYIKLRTGKTRTRKQVSSHIQVLARRKLREIQA 151 (455)
T ss_pred cccccChhHHHHHHHHHhhcCCCCceeEEEccCccccchHHHHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHHHHh
Confidence 567899999999999999998541 368899999984 4899999999887643 3334444
No 41
>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=94.35 E-value=0.24 Score=38.86 Aligned_cols=55 Identities=13% Similarity=0.312 Sum_probs=43.0
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697 12 SGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDIN 66 (86)
Q Consensus 12 ~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~ 66 (86)
+...||..|.+.|.++|..........-..|++.|+||+..||++..+.|...|.
T Consensus 20 gp~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~fl~~LK~rva 74 (344)
T PF11035_consen 20 GPAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDFLQQLKGRVA 74 (344)
T ss_pred CcccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHHHHHHHHHHH
Confidence 3468999999999999886533233456679999999999999998877765554
No 42
>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=93.57 E-value=0.37 Score=26.65 Aligned_cols=39 Identities=13% Similarity=0.226 Sum_probs=29.5
Q ss_pred HHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHH
Q 034697 20 QNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLV 62 (86)
Q Consensus 20 Edk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~ 62 (86)
=|..|..+|..-+. .-|..||+.+ |-|...|..|.+.|.
T Consensus 4 ~D~~Il~~Lq~d~r---~s~~~la~~l-glS~~~v~~Ri~rL~ 42 (42)
T PF13404_consen 4 LDRKILRLLQEDGR---RSYAELAEEL-GLSESTVRRRIRRLE 42 (42)
T ss_dssp HHHHHHHHHHH-TT---S-HHHHHHHH-TS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHcCC---ccHHHHHHHH-CcCHHHHHHHHHHhC
Confidence 36677788777643 5799999999 699999999998873
No 43
>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=93.12 E-value=0.18 Score=29.93 Aligned_cols=30 Identities=23% Similarity=0.529 Sum_probs=24.7
Q ss_pred chHHHHHHHcCC-CCHHHHHHHHHHHHHHHh
Q 034697 37 DRWDNVAKAVSG-KTVEDVKKHYELLVKDIN 66 (86)
Q Consensus 37 ~rW~~IA~~vpg-RT~~qc~~ry~~L~~dv~ 66 (86)
.-|..||..++. -++++|+.+|..|....+
T Consensus 27 ~aw~~Ia~~l~~~~~~~~~~~~w~~Lr~~y~ 57 (85)
T PF10545_consen 27 EAWQEIARELGKEFSVDDCKKRWKNLRDRYR 57 (85)
T ss_pred HHHHHHHHHHccchhHHHHHHHHHHHHHHHH
Confidence 569999999974 689999999998765443
No 44
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=91.89 E-value=0.13 Score=41.40 Aligned_cols=51 Identities=22% Similarity=0.360 Sum_probs=41.7
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCCchHHHHHHH-----cCC-CCHHHHHHHHHHHHHHHhhh
Q 034697 14 SSWTVKQNKQFETALAFYDKDTPDRWDNVAKA-----VSG-KTVEDVKKHYELLVKDINDI 68 (86)
Q Consensus 14 ~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~-----vpg-RT~~qc~~ry~~L~~dv~~i 68 (86)
+.||.+|-.-|-+....|.. ||--||.. .+. ||+++.++||......+.+.
T Consensus 131 n~WskeETD~LF~lck~fDL----Rf~VIaDRyd~qq~~~sRTvEdLKeRyY~v~r~l~kA 187 (445)
T KOG2656|consen 131 NSWSKEETDYLFDLCKRFDL----RFFVIADRYDNQQYKKSRTVEDLKERYYSVCRKLLKA 187 (445)
T ss_pred ccccHHHHHHHHHHHHhcCe----eEEEEeeccchhhccccccHHHHHHHHHHHHHHHHHc
Confidence 68999999999999999864 67777766 676 99999999998876666543
No 45
>smart00426 TEA TEA domain.
Probab=91.32 E-value=0.4 Score=29.68 Aligned_cols=23 Identities=26% Similarity=0.524 Sum_probs=20.0
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCC
Q 034697 12 SGSSWTVKQNKQFETALAFYDKD 34 (86)
Q Consensus 12 ~~~~WT~eEdk~Le~al~~~~~~ 34 (86)
+...|..+=+..|++||..|++.
T Consensus 2 g~~vWp~~lE~Af~~aL~~~~~~ 24 (68)
T smart00426 2 AEGVWSPDIEQAFQEALAIYPPC 24 (68)
T ss_pred CCCcCcHHHHHHHHHHHHHcCcc
Confidence 45689999999999999999854
No 46
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=91.18 E-value=0.89 Score=29.37 Aligned_cols=54 Identities=9% Similarity=0.119 Sum_probs=36.1
Q ss_pred CCCCCHHHHHHHHHHHHhcCC--C--CCchHHHHHH----HcC-CCCHHHHHHHHHHHHHHHh
Q 034697 13 GSSWTVKQNKQFETALAFYDK--D--TPDRWDNVAK----AVS-GKTVEDVKKHYELLVKDIN 66 (86)
Q Consensus 13 ~~~WT~eEdk~Le~al~~~~~--~--~~~rW~~IA~----~vp-gRT~~qc~~ry~~L~~dv~ 66 (86)
...||++++-.|.++|..|-. | ....|..+-. .+. .=|..|+.+..+.|.....
T Consensus 4 qR~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~KirrLK~Ky~ 66 (98)
T PF04504_consen 4 QRLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRRLKKKYR 66 (98)
T ss_pred cCCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHH
Confidence 357999999999999999931 1 1234544444 443 2488898888777655544
No 47
>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=90.05 E-value=0.53 Score=33.06 Aligned_cols=42 Identities=19% Similarity=0.209 Sum_probs=35.1
Q ss_pred CCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHH
Q 034697 15 SWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELL 61 (86)
Q Consensus 15 ~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L 61 (86)
.||.|+...|.++..+ +-.=.+||..|||.|-..|+-+...|
T Consensus 2 ~Wtde~~~~L~~lw~~-----G~SasqIA~~lg~vsRnAViGk~hRl 43 (162)
T PF07750_consen 2 SWTDERVERLRKLWAE-----GLSASQIARQLGGVSRNAVIGKAHRL 43 (162)
T ss_pred CCCHHHHHHHHHHHHc-----CCCHHHHHHHhCCcchhhhhhhhhcc
Confidence 5999999988888654 34578999999989999999887765
No 48
>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=89.93 E-value=2.1 Score=23.57 Aligned_cols=44 Identities=9% Similarity=0.225 Sum_probs=32.2
Q ss_pred CHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697 17 TVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDIN 66 (86)
Q Consensus 17 T~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~ 66 (86)
+++|.++|.... | .+..+..||..+ |-|...|+.+....+..++
T Consensus 6 ~~~er~vi~~~y--~---~~~t~~eIa~~l-g~s~~~V~~~~~~al~kLR 49 (50)
T PF04545_consen 6 PPREREVIRLRY--F---EGLTLEEIAERL-GISRSTVRRILKRALKKLR 49 (50)
T ss_dssp -HHHHHHHHHHH--T---ST-SHHHHHHHH-TSCHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHh--c---CCCCHHHHHHHH-CCcHHHHHHHHHHHHHHhc
Confidence 456666665554 2 235799999999 6999999999888777765
No 49
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=89.48 E-value=1.4 Score=29.93 Aligned_cols=42 Identities=14% Similarity=0.194 Sum_probs=35.1
Q ss_pred HHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHH
Q 034697 19 KQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKD 64 (86)
Q Consensus 19 eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~d 64 (86)
+-|..|..+|.+-+. -.|..||+.+ |-|...|..|++.|.+.
T Consensus 9 ~~D~~Il~~Lq~d~R---~s~~eiA~~l-glS~~tV~~Ri~rL~~~ 50 (153)
T PRK11179 9 NLDRGILEALMENAR---TPYAELAKQF-GVSPGTIHVRVEKMKQA 50 (153)
T ss_pred HHHHHHHHHHHHcCC---CCHHHHHHHH-CcCHHHHHHHHHHHHHC
Confidence 467788888888653 4799999999 79999999999998754
No 50
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=88.57 E-value=2 Score=38.07 Aligned_cols=53 Identities=13% Similarity=0.322 Sum_probs=44.5
Q ss_pred CCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHc------------CCCCHHHHHHHHHHHHHHHh
Q 034697 11 SSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAV------------SGKTVEDVKKHYELLVKDIN 66 (86)
Q Consensus 11 ~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~v------------pgRT~~qc~~ry~~L~~dv~ 66 (86)
.....+|.+||..|.-.+.+|+-+ +|++|-..+ ..||+.++..|...|+.-|.
T Consensus 924 ~~~~~~~~~~d~~~~~~~~~~g~~---~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l~~~~~ 988 (1033)
T PLN03142 924 NKGKLYNEECDRFMLCMVHKLGYG---NWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTLIRLIE 988 (1033)
T ss_pred CCCCcCCHHHHHHHHHHHHHhccc---hHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHHHHHHH
Confidence 456689999999999999999754 699997665 57999999999998876664
No 51
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=87.47 E-value=3.4 Score=30.23 Aligned_cols=55 Identities=9% Similarity=0.225 Sum_probs=40.8
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHc-----CCCCHHHHHHHHHHHHHH
Q 034697 9 SRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAV-----SGKTVEDVKKHYELLVKD 64 (86)
Q Consensus 9 ~~~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~v-----pgRT~~qc~~ry~~L~~d 64 (86)
+..+...||.+|+.+|........+ ....+++|=..= ++||+++...||..+..-
T Consensus 69 ~iq~kalfS~~EE~lL~~v~s~~~p-~le~Fq~LL~~n~~vFh~sRTak~L~~HW~lmkqy 128 (199)
T PF13325_consen 69 AIQSKALFSKEEEQLLGTVASSSQP-SLETFQELLDKNRSVFHPSRTAKSLQDHWRLMKQY 128 (199)
T ss_pred cccccCCCCHHHHHHHHhhhhccCC-cHHHHHHHHHhChhhhccccCHHHHHHHHHHHHHh
Confidence 4456789999999999997655533 346788775433 589999999999965433
No 52
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=87.42 E-value=1.9 Score=29.60 Aligned_cols=42 Identities=12% Similarity=0.088 Sum_probs=34.0
Q ss_pred HHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHH
Q 034697 19 KQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKD 64 (86)
Q Consensus 19 eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~d 64 (86)
+-|..+..+|.+-+. -.|..||+.+ |-|...|..|+++|.+.
T Consensus 14 ~~D~~IL~~Lq~d~R---~s~~eiA~~l-glS~~tv~~Ri~rL~~~ 55 (164)
T PRK11169 14 RIDRNILNELQKDGR---ISNVELSKRV-GLSPTPCLERVRRLERQ 55 (164)
T ss_pred HHHHHHHHHhccCCC---CCHHHHHHHH-CcCHHHHHHHHHHHHHC
Confidence 446677778777543 4799999999 79999999999998754
No 53
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=87.35 E-value=0.8 Score=38.06 Aligned_cols=43 Identities=23% Similarity=0.485 Sum_probs=35.7
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCCchHHHH-HHHcCCCCHHHHHHHHH
Q 034697 13 GSSWTVKQNKQFETALAFYDKDTPDRWDNV-AKAVSGKTVEDVKKHYE 59 (86)
Q Consensus 13 ~~~WT~eEdk~Le~al~~~~~~~~~rW~~I-A~~vpgRT~~qc~~ry~ 59 (86)
...||..|--+||+||.+|+++ +..| +.++|=||...+.+.|.
T Consensus 285 mEEWSasEanLFEeALeKyGKD----FndIrqdfLPWKSl~sIveyYY 328 (693)
T KOG3554|consen 285 MEEWSASEANLFEEALEKYGKD----FNDIRQDFLPWKSLTSIVEYYY 328 (693)
T ss_pred hhhccchhhHHHHHHHHHhccc----HHHHHHhhcchHHHHHHHHHHH
Confidence 4679999999999999999875 4455 66788899999988764
No 54
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=86.01 E-value=1.8 Score=31.73 Aligned_cols=43 Identities=14% Similarity=0.297 Sum_probs=37.1
Q ss_pred CCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcC---CCCHHHHHHHHHHHH
Q 034697 15 SWTVKQNKQFETALAFYDKDTPDRWDNVAKAVS---GKTVEDVKKHYELLV 62 (86)
Q Consensus 15 ~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vp---gRT~~qc~~ry~~L~ 62 (86)
.|++.+|-+|..|+.+- ..-+.|+..|+ .-|..++.+||..|.
T Consensus 1 rW~~~DDl~Li~av~~~-----~~L~~v~~gvkFS~~fT~~Ei~~RW~~ll 46 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQT-----NDLESVHLGVKFSCKFTLQEIEERWYALL 46 (199)
T ss_pred CCCchhhHHHHHHHHHh-----cCHHHHHccCCcCCcCcHHHHHHHHHHHH
Confidence 59999999999999983 46888988886 479999999999864
No 55
>PF01285 TEA: TEA/ATTS domain family; InterPro: IPR000818 Transcriptional enhancer activators are nuclear proteins that contain a TEA/ATTSdomain, a DNA-binding region of 66-68 amino acids. The TEA/ATTS domain is found in the N-termini of certain gene regulatory proteins, such as the Simian virus 40 (SV40) enhancer factor TEF-1, yeast trans-acting factor TEC-1 (which is required for TY1 enhancer activity), and the Aspergillus abaA regulatory gene product. SV40 and retroviral enhancers, and those to which TEF-1, TEC-1 and abaA proteins bind, contain GT-IIC sites: the TEA/ATTS domain may therefore recognise and bind such sites. Secondary structure predictions suggest the presence of 3 helices, but have not confirmed the presence of the helix-turn-helix motif characteristic of many DNA-binding proteins: DNA-binding may therefore be effected by a different mechanism [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3L15_B 2HZD_A 3KYS_A 3JUA_C 4EAZ_B.
Probab=84.37 E-value=2 Score=34.65 Aligned_cols=50 Identities=22% Similarity=0.381 Sum_probs=34.0
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCC----------CchHHHHHHHcC-----CCCHHHHHHHHHHH
Q 034697 12 SGSSWTVKQNKQFETALAFYDKDT----------PDRWDNVAKAVS-----GKTVEDVKKHYELL 61 (86)
Q Consensus 12 ~~~~WT~eEdk~Le~al~~~~~~~----------~~rW~~IA~~vp-----gRT~~qc~~ry~~L 61 (86)
+...|+.+=+..|++||+.||+.. -.|=+-||.+|- .||.+||-.|.+.|
T Consensus 48 ~~~vw~~~~e~af~~al~~~~~~g~~k~~~~~~~~grn~li~~yi~~~tg~~rt~kqvsshiqvl 112 (431)
T PF01285_consen 48 GEGVWPPDIEQAFQEALAIYPPCGRRKLSDEGKMYGRNELISDYIKLKTGKTRTRKQVSSHIQVL 112 (431)
T ss_dssp GS--S-HHHHHHHHHHHHHS-SSS---HHHH-----THHHHHHHHHHHHS----SHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHHHhCCCCCCcccccccccccchhHHHHHHHHHhCcccchhHHHHHHHHH
Confidence 467899999999999999998652 234456777772 39999999999988
No 56
>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=83.76 E-value=3.6 Score=28.15 Aligned_cols=36 Identities=17% Similarity=0.377 Sum_probs=28.6
Q ss_pred hcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697 30 FYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDIN 66 (86)
Q Consensus 30 ~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~ 66 (86)
.|......-|..||..+ ..+..+|+..+....++|.
T Consensus 93 ry~~r~~~TW~~IA~~l-~i~erta~r~~~~fK~~i~ 128 (130)
T PF05263_consen 93 RYDRRSRRTWYQIAQKL-HISERTARRWRDRFKNDIY 128 (130)
T ss_pred HHcccccchHHHHHHHh-CccHHHHHHHHHHHHHHhc
Confidence 34443456899999999 5999999998888887765
No 57
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=83.33 E-value=5.9 Score=22.01 Aligned_cols=50 Identities=20% Similarity=0.229 Sum_probs=40.3
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHH
Q 034697 13 GSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVK 63 (86)
Q Consensus 13 ~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~ 63 (86)
...+|.++...|+......+--....-+.||..+ |-|..+|..=|.+-..
T Consensus 4 r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l-~l~~~~V~~WF~nrR~ 53 (57)
T PF00046_consen 4 RTRFTKEQLKVLEEYFQENPYPSKEEREELAKEL-GLTERQVKNWFQNRRR 53 (57)
T ss_dssp SSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHH-TSSHHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHhccccccccccccccc-cccccccccCHHHhHH
Confidence 3568999999999998876544567899999999 7999999887765443
No 58
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=81.77 E-value=0.87 Score=37.44 Aligned_cols=47 Identities=26% Similarity=0.376 Sum_probs=35.4
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHH
Q 034697 14 SSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDI 65 (86)
Q Consensus 14 ~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv 65 (86)
-.||++|-. ++.-|+- -...++.||..++.+|+.|++.+|..-..-|
T Consensus 471 ~~wSp~e~s----~ircf~~-y~~~fe~ia~l~~tktp~Q~~~fy~~n~k~i 517 (534)
T KOG1194|consen 471 YGWSPEEKS----AIRCFHW-YKDNFELIAELMATKTPEQIKKFYMDNEKLI 517 (534)
T ss_pred CCCCCcccc----cccCchh-hccchHHHHHHhcCCCHHHHHHHhcCchhhh
Confidence 469999988 4444432 3467999999999999999999997644433
No 59
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=80.85 E-value=7.1 Score=24.32 Aligned_cols=42 Identities=17% Similarity=0.192 Sum_probs=34.3
Q ss_pred HHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHH
Q 034697 19 KQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKD 64 (86)
Q Consensus 19 eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~d 64 (86)
+.|..+..+|.+.+. -.+..||+.+ |-+...|..|.+.|.+.
T Consensus 3 ~~D~~il~~L~~~~~---~~~~~la~~l-~~s~~tv~~~l~~L~~~ 44 (108)
T smart00344 3 EIDRKILEELQKDAR---ISLAELAKKV-GLSPSTVHNRVKRLEEE 44 (108)
T ss_pred HHHHHHHHHHHHhCC---CCHHHHHHHH-CcCHHHHHHHHHHHHHC
Confidence 456777788887653 4699999999 79999999999998764
No 60
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=79.27 E-value=1.9 Score=36.10 Aligned_cols=45 Identities=11% Similarity=0.272 Sum_probs=40.4
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHH
Q 034697 12 SGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYEL 60 (86)
Q Consensus 12 ~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~ 60 (86)
....||.+|-.+|..++..++. ...-|+...|+|+.+|++..|..
T Consensus 408 ~~~~w~~se~e~fyka~~~~gs----~~slis~l~p~R~rk~iK~K~~~ 452 (584)
T KOG2009|consen 408 ETDKWDASETELFYKALSERGS----DFSLISNLFPLRDRKQIKAKFKK 452 (584)
T ss_pred ccCcccchhhHHhhhHHhhhcc----cccccccccccccHHHHHHHHhh
Confidence 4678999999999999999865 48899999999999999999864
No 61
>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=78.97 E-value=8.6 Score=21.12 Aligned_cols=26 Identities=19% Similarity=0.279 Sum_probs=19.6
Q ss_pred chHHHHHHHcCCCCHHHHHHHHHHHHH
Q 034697 37 DRWDNVAKAVSGKTVEDVKKHYELLVK 63 (86)
Q Consensus 37 ~rW~~IA~~vpgRT~~qc~~ry~~L~~ 63 (86)
-.|..||..+ |.|...|+.++..-..
T Consensus 27 ~s~~eIa~~l-~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 27 MSYAEIAEIL-GISESTVKRRLRRARK 52 (54)
T ss_dssp --HHHHHHHC-TS-HHHHHHHHHHHHH
T ss_pred cCHHHHHHHH-CcCHHHHHHHHHHHHh
Confidence 5799999999 6999999998766443
No 62
>PF06461 DUF1086: Domain of Unknown Function (DUF1086); InterPro: IPR009462 This entry represents several eukaryotic domains of unknown function, which are present in chromodomain helicase DNA binding proteins. This domain is often found in conjunction with IPR000330 from INTERPRO, IPR001650 from INTERPRO, IPR009463 from INTERPRO, IPR000953 from INTERPRO and IPR001965 from INTERPRO.
Probab=77.82 E-value=19 Score=25.29 Aligned_cols=52 Identities=17% Similarity=0.338 Sum_probs=42.3
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697 14 SSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDIN 66 (86)
Q Consensus 14 ~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~ 66 (86)
=.++..|-+.|.+++-.|+.+ .-.|.-....+.+||.++++..-.-....|.
T Consensus 39 lGFn~rQR~~Fln~vMR~G~~-~f~~~w~~~~Lr~Ks~~ei~aY~~LFm~HL~ 90 (145)
T PF06461_consen 39 LGFNPRQRKAFLNAVMRYGMG-AFDWKWFVPRLRGKSEKEIRAYGSLFMRHLC 90 (145)
T ss_pred eccCHHHHHHHHHHHHHHCcC-cccchHHhhhhccccHHHHHHHHHHHHHHhc
Confidence 358899999999999999985 3479999999999999999876554455554
No 63
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=77.43 E-value=8.2 Score=25.34 Aligned_cols=41 Identities=15% Similarity=0.127 Sum_probs=32.2
Q ss_pred HHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHH
Q 034697 20 QNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKD 64 (86)
Q Consensus 20 Edk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~d 64 (86)
-|..+.+.|..-.. ..+..||+.+ |.|...|.+|-++|.+.
T Consensus 9 ~D~~IL~~L~~d~r---~~~~eia~~l-glS~~~v~~Ri~~L~~~ 49 (154)
T COG1522 9 IDRRILRLLQEDAR---ISNAELAERV-GLSPSTVLRRIKRLEEE 49 (154)
T ss_pred HHHHHHHHHHHhCC---CCHHHHHHHH-CCCHHHHHHHHHHHHHC
Confidence 45566666666433 5799999999 69999999999988754
No 64
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=75.61 E-value=11 Score=20.60 Aligned_cols=50 Identities=18% Similarity=0.216 Sum_probs=40.1
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHH
Q 034697 13 GSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVK 63 (86)
Q Consensus 13 ~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~ 63 (86)
...+|.++...|+......+--....=..||+.+ |-|..+|..=|..-..
T Consensus 4 r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~-~l~~~qV~~WF~nrR~ 53 (59)
T cd00086 4 RTRFTPEQLEELEKEFEKNPYPSREEREELAKEL-GLTERQVKIWFQNRRA 53 (59)
T ss_pred CCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 4578999999999998887644556788999999 6999999987765443
No 65
>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=74.82 E-value=4.5 Score=25.25 Aligned_cols=14 Identities=14% Similarity=0.416 Sum_probs=8.3
Q ss_pred CCCCCCHHHHHHHH
Q 034697 12 SGSSWTVKQNKQFE 25 (86)
Q Consensus 12 ~~~~WT~eEdk~Le 25 (86)
-.+-||+++|..|+
T Consensus 46 ~~GiWT~eDD~~L~ 59 (87)
T PF11626_consen 46 MPGIWTPEDDEMLR 59 (87)
T ss_dssp -TT---HHHHHHHT
T ss_pred CCCCcCHHHHHHHH
Confidence 35679999999993
No 66
>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=74.39 E-value=18 Score=22.40 Aligned_cols=31 Identities=19% Similarity=0.337 Sum_probs=25.3
Q ss_pred CchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 36 PDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 36 ~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
+..+..||+.+ |-|...|+.+.......++.
T Consensus 126 g~s~~eIA~~l-~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 126 GLSYKEIAEIL-GISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHh
Confidence 35799999999 58999999988888777664
No 67
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=73.48 E-value=17 Score=23.80 Aligned_cols=31 Identities=16% Similarity=0.215 Sum_probs=24.0
Q ss_pred CchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 36 PDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 36 ~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
+..+..||+.+ |.|...|+.+.......++.
T Consensus 141 ~~~~~eIA~~l-gis~~tv~~~~~ra~~~lr~ 171 (179)
T PRK11924 141 GLSYREIAEIL-GVPVGTVKSRLRRARQLLRE 171 (179)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence 45789999999 69999998887766555553
No 68
>PF00674 DUP: DUP family; InterPro: IPR001142 A number of uncharacterised integral membrane proteins from yeast contain an internal duplication due to duplicated genes. Duplicated copies of genes may be classified in two types of cluster organisation. The first type includes genes sharing a significant level of identity in the amino acid sequences of their predicted protein product. They are recovered on two different chromosomes, transcribed in the same orientation and the distance between them is conserved. The second type of cluster is based on one gene unit tandemly repeated. This duplication is itself repeated elsewhere in the genome. The basic gene unit is recovered many times in the genome and is a component of a multigene family of unknown function. These organisations in clusters of genes suggest a 'Lego organisation' of the yeast chromosomes []. The proteins belonging to this family are of unknown function.
Probab=73.10 E-value=5.1 Score=25.90 Aligned_cols=44 Identities=18% Similarity=0.311 Sum_probs=29.9
Q ss_pred HHHHHHHHHhcCCCCCchHHHHHHHcC------C--C------CHHHHHHHHHHHHHH
Q 034697 21 NKQFETALAFYDKDTPDRWDNVAKAVS------G--K------TVEDVKKHYELLVKD 64 (86)
Q Consensus 21 dk~Le~al~~~~~~~~~rW~~IA~~vp------g--R------T~~qc~~ry~~L~~d 64 (86)
.++|.+.+..-|......|+.||..|. | + ..++|...|+.++..
T Consensus 44 ~kfl~eIi~~~P~~d~~~Wd~IA~~mN~yly~~~~w~t~~~FyDG~~C~~~Fr~~v~~ 101 (108)
T PF00674_consen 44 MKFLKEIIEVKPGVDMKKWDIIASRMNQYLYEEGLWNTPYFFYDGKDCYRFFRRLVLK 101 (108)
T ss_pred HHHHHHHHhcCCCCCcccHHHHHHHHHHHHHhCCCCCCcCcccCcHHHHHHHHHHhcc
Confidence 345556666556556789999999983 1 3 347888888776543
No 69
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=72.74 E-value=12 Score=23.18 Aligned_cols=42 Identities=14% Similarity=0.301 Sum_probs=27.9
Q ss_pred HHHHHHHhcCCC----CCchHHHHHHHcCCCC-----HHHHHHHHHHHHHH
Q 034697 23 QFETALAFYDKD----TPDRWDNVAKAVSGKT-----VEDVKKHYELLVKD 64 (86)
Q Consensus 23 ~Le~al~~~~~~----~~~rW~~IA~~vpgRT-----~~qc~~ry~~L~~d 64 (86)
.|-.++.+.+.- ...+|..||..++-.. ..+++.+|.+++-.
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 455566666531 3578999999997432 46678888776543
No 70
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=71.39 E-value=25 Score=22.71 Aligned_cols=45 Identities=11% Similarity=0.192 Sum_probs=34.1
Q ss_pred HHHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 22 KQFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
..|..+|.+.|+. .+-.++.||+.+ |-|...|+.+.......++.
T Consensus 97 ~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~l-gis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 97 EEITHHLSRLPENYRTVLILREFKEFSYKEIAELL-NLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred HHHHHHHHhCCHhheeeeeehhhccCcHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence 4577778777632 356799999999 69999999988776666653
No 71
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=70.32 E-value=15 Score=19.94 Aligned_cols=47 Identities=17% Similarity=0.237 Sum_probs=37.3
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHH
Q 034697 14 SSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELL 61 (86)
Q Consensus 14 ~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L 61 (86)
..+|.++...|+..+...+--....=..||+.+ |-|..+|..=|..-
T Consensus 5 ~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~-~l~~~qV~~WF~nr 51 (56)
T smart00389 5 TSFTPEQLEELEKEFQKNPYPSREEREELAAKL-GLSERQVKVWFQNR 51 (56)
T ss_pred CcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHH-CcCHHHHHHhHHHH
Confidence 458999999999998877643456778999999 69999998866543
No 72
>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=69.10 E-value=9.8 Score=23.30 Aligned_cols=41 Identities=17% Similarity=0.321 Sum_probs=26.0
Q ss_pred HHHHHHHhcCCC----CCchHHHHHHHcCCCC-----HHHHHHHHHHHHH
Q 034697 23 QFETALAFYDKD----TPDRWDNVAKAVSGKT-----VEDVKKHYELLVK 63 (86)
Q Consensus 23 ~Le~al~~~~~~----~~~rW~~IA~~vpgRT-----~~qc~~ry~~L~~ 63 (86)
.|-.+|.+++.. ....|..||..++--+ ..+++.+|.+++.
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 344555555421 1356999999996422 4678888987654
No 73
>PF01466 Skp1: Skp1 family, dimerisation domain; InterPro: IPR016072 SKP1 (together with SKP2) was identified as an essential component of the cyclin A-CDK2 S phase kinase complex []. It was found to bind several F-box containing proteins (e.g., Cdc4, Skp2, cyclin F) and to be involved in the ubiquitin protein degradation pathway. A yeast homologue of SKP1 (P52286) was identified in the centromere bound kinetochore complex [] and is also involved in the ubiquitin pathway []. In Dictyostelium discoideum (Slime mold) FP21 was shown to be glycosylated in the cytosol and has homology to SKP1 []. This entry represents a dimerisation domain found at the C-terminal of SKP1 proteins [], as well as in subunit D of the centromere DNA-binding protein complex Cbf3 []. This domain is multi-helical in structure, and consists of an interlocked herterodimer in F-box proteins.; GO: 0006511 ubiquitin-dependent protein catabolic process; PDB: 2P1O_A 3OGL_G 3OGM_A 3C6O_A 2P1N_A 2P1Q_A 3OGK_I 3C6N_A 3C6P_A 2P1P_A ....
Probab=69.05 E-value=5.5 Score=24.28 Aligned_cols=21 Identities=24% Similarity=0.537 Sum_probs=17.5
Q ss_pred HHHHHHHcCCCCHHHHHHHHH
Q 034697 39 WDNVAKAVSGKTVEDVKKHYE 59 (86)
Q Consensus 39 W~~IA~~vpgRT~~qc~~ry~ 59 (86)
-..||..+.|||++|++..|.
T Consensus 36 ~~~iA~~i~gks~eeir~~fg 56 (78)
T PF01466_consen 36 CKYIANMIKGKSPEEIRKYFG 56 (78)
T ss_dssp HHHHHHHHTTS-HHHHHHHHT
T ss_pred HHHHHHHhcCCCHHHHHHHcC
Confidence 567899999999999999874
No 74
>PLN03162 golden-2 like transcription factor; Provisional
Probab=67.04 E-value=18 Score=29.59 Aligned_cols=52 Identities=17% Similarity=0.264 Sum_probs=38.8
Q ss_pred CCCCHHHHHHHHHHHHhcCCC--CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697 14 SSWTVKQNKQFETALAFYDKD--TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIN 66 (86)
Q Consensus 14 ~~WT~eEdk~Le~al~~~~~~--~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~ 66 (86)
-.||.|=.+.|.+||.+.+.+ .+.+--++ .-|+|-|.+.|+.|.++++-.++
T Consensus 238 LrWTpELH~rFVeAV~qLG~dKATPK~ILel-MnV~GLTRenVKSHLQKYRl~rk 291 (526)
T PLN03162 238 VDWTPELHRRFVHAVEQLGVEKAFPSRILEL-MGVQCLTRHNIASHLQKYRSHRR 291 (526)
T ss_pred ccCCHHHHHHHHHHHHHhCcCccchHHHHHH-cCCCCcCHHHHHHHHHHHHHhcc
Confidence 569999999999999999843 34443333 23569999999999887665554
No 75
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=66.65 E-value=28 Score=22.87 Aligned_cols=47 Identities=15% Similarity=0.172 Sum_probs=34.3
Q ss_pred HHHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhhhh
Q 034697 22 KQFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDINDIE 69 (86)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ie 69 (86)
..+..+|...|.. .+-....||..+ |-|...|+.|....+..++.++
T Consensus 104 ~~~~~~l~~L~~~~r~v~~l~~~~~~s~~eIA~~l-gis~~tv~~~l~Rar~~L~~~~ 160 (161)
T PRK12541 104 ASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMT-GLSLAKVKIELHRGRKETKSIK 160 (161)
T ss_pred HHHHHHHHHCCHHHHHHhhhHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHhhc
Confidence 3455566666531 245678999999 6999999999888888887654
No 76
>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=66.64 E-value=31 Score=22.03 Aligned_cols=31 Identities=19% Similarity=0.424 Sum_probs=25.8
Q ss_pred CchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 36 PDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 36 ~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
+-.+..||+.+ |.|...|+.+.......++.
T Consensus 129 ~~~~~eIA~~l-gis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 129 GKSYKEIAEEL-GISVKTVEYHISKALKELRK 159 (161)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHh
Confidence 35799999999 69999999998888777764
No 77
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=65.79 E-value=29 Score=23.44 Aligned_cols=44 Identities=16% Similarity=0.134 Sum_probs=31.6
Q ss_pred HHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 23 QFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 23 ~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
.|..+|.+.|.. .+...+.||..+ |-|..-|+.+.......++.
T Consensus 132 ~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~Lr~ 185 (189)
T PRK09648 132 RMRELLDTLPEKQREILILRVVVGLSAEETAEAV-GSTPGAVRVAQHRALARLRA 185 (189)
T ss_pred HHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence 466677766632 346788999999 68888888887766666654
No 78
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=63.60 E-value=28 Score=23.84 Aligned_cols=48 Identities=13% Similarity=0.125 Sum_probs=33.6
Q ss_pred HHHHHHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 19 KQNKQFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 19 eEdk~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
++...|..+|.+.|.. .+-....||+.+ |.|...|+.|-...+..++.
T Consensus 131 ~~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~EIA~~L-gis~~tVk~~l~ra~~~Lr~ 188 (194)
T PRK09646 131 LERERVRDCLDALTDTQRESVTLAYYGGLTYREVAERL-AVPLGTVKTRMRDGLIRLRD 188 (194)
T ss_pred hHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHh-CCChHhHHHHHHHHHHHHHH
Confidence 4455677777776632 345688899999 58888888887666665553
No 79
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 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 a limited number of Gram-positive bacterial lineages.
Probab=62.75 E-value=35 Score=22.31 Aligned_cols=45 Identities=22% Similarity=0.175 Sum_probs=31.6
Q ss_pred HHHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 22 KQFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
..|..+|.+.|+. .+-....||+.+ |.|..-|+.+.......++.
T Consensus 114 ~~l~~~l~~L~~~~r~vl~l~~~~g~s~~eIA~~l-~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 114 EKLLKALKILTPKQQHVIALRFGQNLPIAEVARIL-GKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence 4566777666531 345678888888 68888888887777766654
No 80
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=61.99 E-value=39 Score=22.05 Aligned_cols=45 Identities=13% Similarity=0.049 Sum_probs=31.5
Q ss_pred HHHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 22 KQFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
..|..+|.+.|+. .+-.-..||+.+ |.|...|+.|.......++.
T Consensus 98 ~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~l-gis~~tV~~~l~Rar~~Lr~ 152 (160)
T PRK09642 98 LLIAQKLRELPENYRDVVLAHYLEEKSYQEIALQE-KIEVKTVEMKLYRARKWIKK 152 (160)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence 3567777777643 345678899999 68999998887665555543
No 81
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=59.46 E-value=42 Score=21.65 Aligned_cols=45 Identities=11% Similarity=0.175 Sum_probs=29.9
Q ss_pred HHHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 22 KQFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
..|..+|.+.|+. .+-....||+.+ |.|...|+.+.......++.
T Consensus 98 ~~l~~~l~~L~~~~r~ii~l~~~~~~s~~EIA~~l-~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 98 MKVKDFMSVLDEKEKYIIFERFFVGKTMGEIALET-EMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHhh
Confidence 4566666665532 234578888888 68888888887766666553
No 82
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=59.40 E-value=32 Score=22.90 Aligned_cols=51 Identities=6% Similarity=0.177 Sum_probs=33.0
Q ss_pred CCHHHHHHHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 16 WTVKQNKQFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 16 WT~eEdk~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
+..++...|..+|...|.. .+..-+.||+.+ |.|...|+.|.......++.
T Consensus 105 ~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~~~s~~EIA~~l-gis~~tV~~~l~Ra~~~Lr~ 165 (173)
T PRK12522 105 IQKVEAEMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEIL-NIPIGTVKYRLNYAKKQMRE 165 (173)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHh-CCCHHHHHHHHHHHHHHHHH
Confidence 3334445677788777642 234567788888 58888888887665555553
No 83
>PF00887 ACBP: Acyl CoA binding protein; InterPro: IPR000582 Acyl-CoA-binding protein (ACBP) is a small (10 Kd) protein that binds medium- and long-chain acyl-CoA esters with very high affinity and may function as an intracellular carrier of acyl-CoA esters []. ACBP is also known as diazepam binding inhibitor (DBI) or endozepine (EP) because of its ability to displace diazepam from the benzodiazepine (BZD) recognition site located on the GABA type A receptor. It is therefore possible that this protein also acts as a neuropeptide to modulate the action of the GABA receptor []. ACBP is a highly conserved protein of about 90 residues that is found in all four eukaryotic kingdoms, Animalia, Plantae, Fungi and Protista, and in some eubacterial species []. Although ACBP occurs as a completely independent protein, intact ACB domains have been identified in a number of large, multifunctional proteins in a variety of eukaryotic species. These include large membrane-associated proteins with N-terminal ACB domains, multifunctional enzymes with both ACB and peroxisomal enoyl-CoA Delta(3), Delta(2)-enoyl-CoA isomerase domains, and proteins with both an ACB domain and ankyrin repeats (IPR002110 from INTERPRO) []. The ACB domain consists of four alpha-helices arranged in a bowl shape with a highly exposed acyl-CoA-binding site. The ligand is bound through specific interactions with residues on the protein, most notably several conserved positive charges that interact with the phosphate group on the adenosine-3'phosphate moiety, and the acyl chain is sandwiched between the hydrophobic surfaces of CoA and the protein []. Other proteins containing an ACB domain include: Endozepine-like peptide (ELP) (gene DBIL5) from mouse []. ELP is a testis-specific ACBP homologue that may be involved in the energy metabolism of the mature sperm. MA-DBI, a transmembrane protein of unknown function which has been found in mammals. MA-DBI contains a N-terminal ACB domain. DRS-1 [], a human protein of unknown function that contains a N-terminal ACB domain and a C-terminal enoyl-CoA isomerase/hydratase domain. ; GO: 0000062 fatty-acyl-CoA binding; PDB: 2CB8_A 2FJ9_A 2LBB_A 1ST7_A 3EPY_B 2FDQ_C 1NTI_A 1HB8_A 1ACA_A 1NVL_A ....
Probab=59.37 E-value=12 Score=23.07 Aligned_cols=24 Identities=29% Similarity=0.466 Sum_probs=20.3
Q ss_pred HHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 44 KAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 44 ~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
+.++|.|.++++.+|..+++++..
T Consensus 61 ~~l~gms~~eA~~~Yi~~v~~~~~ 84 (87)
T PF00887_consen 61 KALKGMSKEEAMREYIELVEELIP 84 (87)
T ss_dssp HTTTTTHHHHHHHHHHHHHHHHHH
T ss_pred HHccCCCHHHHHHHHHHHHHHHHH
Confidence 346899999999999999888753
No 84
>cd00435 ACBP Acyl CoA binding protein (ACBP) binds thiol esters of long fatty acids and coenzyme A in a one-to-one binding mode with high specificity and affinity. Acyl-CoAs are important intermediates in fatty lipid synthesis and fatty acid degradation and play a role in regulation of intermediary metabolism and gene regulation. The suggested role of ACBP is to act as a intracellular acyl-CoA transporter and pool former. ACBPs are present in a large group of eukaryotic species and several tissue-specific isoforms have been detected.
Probab=58.72 E-value=16 Score=22.83 Aligned_cols=23 Identities=26% Similarity=0.381 Sum_probs=20.0
Q ss_pred HcCCCCHHHHHHHHHHHHHHHhh
Q 034697 45 AVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 45 ~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
.++|.|.++++.+|..+++.+..
T Consensus 60 ~l~~ms~~eA~~~YV~~~~~l~~ 82 (85)
T cd00435 60 SLKGMSKEDAMKAYIAKVEELIA 82 (85)
T ss_pred HcCCCCHHHHHHHHHHHHHHHhh
Confidence 46899999999999999988753
No 85
>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=58.42 E-value=45 Score=22.26 Aligned_cols=44 Identities=14% Similarity=0.114 Sum_probs=31.6
Q ss_pred HHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 23 QFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 23 ~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
.|..+|.+.|.. .+.....||+.+ |-|...|+.+.......++.
T Consensus 131 ~l~~~l~~L~~~~r~v~~l~~~~~~s~~EIA~~l-gis~~tv~~~l~rar~~Lr~ 184 (190)
T TIGR02939 131 TVMRAVEALPEDLRTAITLRELEGLSYEDIARIM-DCPVGTVRSRIFRAREAIAI 184 (190)
T ss_pred HHHHHHHcCCHHHhhhhhhhhhcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHHH
Confidence 466677766532 345689999999 68899999887766666553
No 86
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=57.32 E-value=46 Score=22.00 Aligned_cols=44 Identities=16% Similarity=0.118 Sum_probs=31.0
Q ss_pred HHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 23 QFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 23 ~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
.|..+|.+.|+. .+-.-+.||+.+ |.|..-|+.|....+..++.
T Consensus 111 ~l~~~l~~L~~~~r~vl~L~~~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~Lr~ 164 (173)
T PRK09645 111 LVADALAQLSPEHRAVLVRSYYRGWSTAQIAADL-GIPEGTVKSRLHYALRALRL 164 (173)
T ss_pred HHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHHH
Confidence 577777776632 244578889999 68888898887766555553
No 87
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=56.97 E-value=48 Score=22.70 Aligned_cols=46 Identities=13% Similarity=0.063 Sum_probs=32.2
Q ss_pred HHHHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 21 NKQFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 21 dk~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
...|..+|...|+. .+-..+.||..+ |.|...|+.|.......++.
T Consensus 125 ~~~l~~~l~~Lp~~~r~i~~l~~~~g~s~~EIA~~l-g~s~~tV~~rl~rar~~Lr~ 180 (192)
T PRK09643 125 ALAVQRALMRLPVEQRAALVAVDMQGYSVADAARML-GVAEGTVKSRCARGRARLAE 180 (192)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHHH
Confidence 34677777776632 345788999999 69999999987665555543
No 88
>PTZ00458 acyl CoA binding protein; Provisional
Probab=56.77 E-value=19 Score=23.05 Aligned_cols=23 Identities=26% Similarity=0.403 Sum_probs=19.9
Q ss_pred HcCCCCHHHHHHHHHHHHHHHhh
Q 034697 45 AVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 45 ~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
.++|.|.++++.+|..++.++..
T Consensus 62 ~l~~ms~~eA~~~YI~l~~~l~~ 84 (90)
T PTZ00458 62 SIENLNREDAKKRYVEIVTELFP 84 (90)
T ss_pred HcCCCCHHHHHHHHHHHHHHHhh
Confidence 45899999999999999988753
No 89
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=56.43 E-value=55 Score=21.75 Aligned_cols=43 Identities=9% Similarity=0.081 Sum_probs=30.1
Q ss_pred HHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697 23 QFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIN 66 (86)
Q Consensus 23 ~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~ 66 (86)
.+..+|...|.. .+..++.||..+ |.|..-|+.+.......++
T Consensus 129 ~l~~~l~~L~~~~r~il~l~~~~~~s~~eIA~~l-gis~~~v~~~l~Rar~~Lr 181 (187)
T PRK09641 129 TIQEAILQLPEKYRTVIVLKYIEDLSLKEISEIL-DLPVGTVKTRIHRGREALR 181 (187)
T ss_pred HHHHHHHhCCHHHHHHhhhHHhhCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 455566655421 346789999999 6999999888776666555
No 90
>KOG0385 consensus Chromatin remodeling complex WSTF-ISWI, small subunit [Transcription]
Probab=56.19 E-value=35 Score=30.30 Aligned_cols=44 Identities=32% Similarity=0.445 Sum_probs=37.3
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHH
Q 034697 12 SGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYE 59 (86)
Q Consensus 12 ~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~ 59 (86)
+-..||.-+=..|..|..+|+.+ .-+.||+.|-| |+++|...-+
T Consensus 794 gft~w~k~df~~fi~a~eKygr~---di~~ia~~~e~-~~eev~~y~r 837 (971)
T KOG0385|consen 794 GFTNWTKRDFNQFIKANEKYGRD---DIENIAAEVEG-TPEEVGEYAR 837 (971)
T ss_pred cccchhhhhHHHHHHHhhccCcc---hhhhhHHhhcC-CHHHHHHHHH
Confidence 55779999999999999999764 68999999988 9999976433
No 91
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=56.18 E-value=48 Score=22.76 Aligned_cols=47 Identities=17% Similarity=0.268 Sum_probs=33.5
Q ss_pred HHHHHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 20 QNKQFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 20 Edk~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
+...|..+|.+.|.. .+-....||+.+ |.|...|+.|....+..++.
T Consensus 106 ~~~~l~~~L~~Lp~~~r~i~~L~~~~g~s~~EIA~~L-gis~~tVk~~l~Rar~~Lr~ 162 (187)
T PRK12516 106 DLQDFRAALDQLPDDQREAIILVGASGFAYEEAAEIC-GCAVGTIKSRVNRARQRLQE 162 (187)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence 345577777776632 356789999999 69999999987665555553
No 92
>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=56.18 E-value=50 Score=21.80 Aligned_cols=47 Identities=13% Similarity=0.140 Sum_probs=33.0
Q ss_pred HHHHHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 20 QNKQFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 20 Edk~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
+...|..+|.+.|.. .+.....||+.+ |.|...|+.+.......++.
T Consensus 109 ~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eiA~~l-gis~~tv~~~l~Ra~~~Lr~ 165 (169)
T TIGR02954 109 SRLDLYKAIDTLNDKYQTAIILRYYHDLTIKEIAEVM-NKPEGTVKTYLHRALKKLKK 165 (169)
T ss_pred HHHHHHHHHHhCCHHHhHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence 344677777776532 345788899999 58999999887776666654
No 93
>COG5269 ZUO1 Ribosome-associated chaperone zuotin [Translation, ribosomal structure and biogenesis / Posttranslational modification, protein turnover, chaperones]
Probab=55.53 E-value=22 Score=27.97 Aligned_cols=48 Identities=17% Similarity=0.265 Sum_probs=37.5
Q ss_pred CCCCHHHHHHHHHHHHhcCCCC-CchHHHHHHHcCC-----CCHHHHHHHHHHH
Q 034697 14 SSWTVKQNKQFETALAFYDKDT-PDRWDNVAKAVSG-----KTVEDVKKHYELL 61 (86)
Q Consensus 14 ~~WT~eEdk~Le~al~~~~~~~-~~rW~~IA~~vpg-----RT~~qc~~ry~~L 61 (86)
..|+.++-..+..+++.+++.. .++|+.+|+.+-+ |..+++++..++.
T Consensus 246 rkWereagar~~a~aa~k~kae~k~kae~ea~a~asa~a~kkkaKE~~kka~k~ 299 (379)
T COG5269 246 RKWEREAGARLKALAALKGKAEAKNKAEIEAEALASATAVKKKAKEVMKKALKM 299 (379)
T ss_pred hccchhhhhhHHHHHHHhhhhHHHhHHHHHHHHhhhhHHHHHhHHHHHHHHHHH
Confidence 5799999999999999887543 6899999998754 5667777665543
No 94
>cd08307 Death_Pelle Death domain of the protein kinase Pelle. Death domain (DD) of the protein kinase Pelle from Drosophila melanogaster and simlar proteins. In Drosophila, interaction between the DDs of Tube and Pelle is an important component of the Toll pathway, which functions in establishing dorsoventral polarity in embryos and in mediating innate immune responses to pathogens. Tube and Pelle transmit the signal from the Toll receptor to the Dorsal/Cactus complex. Pelle also functions in photoreceptor axon targeting. 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=54.72 E-value=14 Score=24.00 Aligned_cols=20 Identities=25% Similarity=0.572 Sum_probs=15.7
Q ss_pred CchHHHHHHHcCCCCHHHHH
Q 034697 36 PDRWDNVAKAVSGKTVEDVK 55 (86)
Q Consensus 36 ~~rW~~IA~~vpgRT~~qc~ 55 (86)
.+.|+++|..+++-|..+++
T Consensus 21 ~~~W~~LA~~i~~ys~~~v~ 40 (97)
T cd08307 21 DNVWEELAFVMMGYSNDDVE 40 (97)
T ss_pred cCcHHHHHHHHhcCCHHHHH
Confidence 46899999999866666654
No 95
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=53.96 E-value=58 Score=21.07 Aligned_cols=45 Identities=18% Similarity=0.150 Sum_probs=31.3
Q ss_pred HHHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 22 KQFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
..|..+|.+.|+. .+-.-..||+.+ |.|..-|+.|....+..++.
T Consensus 98 ~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~Lr~ 152 (161)
T PRK09047 98 QLIEEAIQKLPARQREAFLLRYWEDMDVAETAAAM-GCSEGSVKTHCSRATHALAK 152 (161)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHhcCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence 3466666666532 245678999999 68999999887766655553
No 96
>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=53.40 E-value=60 Score=22.20 Aligned_cols=44 Identities=9% Similarity=0.064 Sum_probs=29.5
Q ss_pred HHHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697 22 KQFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIN 66 (86)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~ 66 (86)
..|..+|.+.|.. .+...+.||+.+ |.|..-|+.|....+..++
T Consensus 123 ~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~l-gis~~tvk~rl~Rar~~Lr 176 (188)
T TIGR02943 123 EVFEACLYHLPEQTARVFMMREVLGFESDEICQEL-EISTSNCHVLLYRARLSLR 176 (188)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHh-CCCHHHHHHHHHHHHHHHH
Confidence 3466666666532 245688899999 6888888888765554444
No 97
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=53.21 E-value=64 Score=22.85 Aligned_cols=44 Identities=18% Similarity=0.178 Sum_probs=31.8
Q ss_pred HHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 23 QFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 23 ~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
.|..+|...|.. .+...+.||+.+ |.|...|+.++......++.
T Consensus 142 ~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIAe~l-gis~~tVk~~l~Rar~kLr~ 195 (231)
T PRK11922 142 LLERAIDALPDAFRAVFVLRVVEELSVEETAQAL-GLPEETVKTRLHRARRLLRE 195 (231)
T ss_pred HHHHHHHhCCHHHhhhheeehhcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHHH
Confidence 466677666522 356789999999 69999999987765555553
No 98
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=53.00 E-value=62 Score=22.00 Aligned_cols=47 Identities=13% Similarity=0.091 Sum_probs=34.9
Q ss_pred HHHHHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 20 QNKQFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 20 Edk~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
+...|..+|.+.|.. .+-....||+.+ |.|...|+.|...-+..+++
T Consensus 120 ~~~~l~~~l~~Lp~~~r~v~~L~~~~g~s~~EIA~~l-gis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 120 DLVEVTTMIADLTTDQREALLLTQLLGLSYADAAAVC-GCPVGTIRSRVARARDALLA 176 (185)
T ss_pred HHHHHHHHHHhCCHHHhHHhhhHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHh
Confidence 345677787777633 245678999999 69999999998777777665
No 99
>PF14775 NYD-SP28_assoc: Sperm tail C-terminal domain
Probab=52.39 E-value=26 Score=20.73 Aligned_cols=31 Identities=16% Similarity=0.424 Sum_probs=21.3
Q ss_pred hHHHHHHHcCCCCHHH------HHHHHHHHHHHHhhh
Q 034697 38 RWDNVAKAVSGKTVED------VKKHYELLVKDINDI 68 (86)
Q Consensus 38 rW~~IA~~vpgRT~~q------c~~ry~~L~~dv~~i 68 (86)
.|+++|..+|..+.+. -.+||...+.+...+
T Consensus 2 yW~~~~~vip~~~~~~W~~L~~~l~rY~~vL~~R~~l 38 (60)
T PF14775_consen 2 YWERLANVIPDEKIRLWDALENFLKRYNKVLLDRAAL 38 (60)
T ss_pred HHHHHhhcCChHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6999999999866554 456777655554443
No 100
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=51.73 E-value=66 Score=21.95 Aligned_cols=44 Identities=7% Similarity=0.055 Sum_probs=31.5
Q ss_pred HHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 23 QFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 23 ~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
.|..+|.+.|.. .+-....||+.+ |.|..-|+.|...-...++.
T Consensus 127 ~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~l-gis~~tVk~~l~RAr~~Lr~ 180 (189)
T PRK12530 127 IFEACLNHLPAQQARVFMMREYLELSSEQICQEC-DISTSNLHVLLYRARLQLQA 180 (189)
T ss_pred HHHHHHHhCCHHHHHHHhHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence 466777776632 356789999999 69999999887665555543
No 101
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 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 (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=50.88 E-value=66 Score=21.81 Aligned_cols=44 Identities=14% Similarity=0.197 Sum_probs=31.9
Q ss_pred HHHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697 22 KQFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIN 66 (86)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~ 66 (86)
..|..+|.+.|.. .+-.-..||+.+ |.|...|+.|.......++
T Consensus 123 ~~l~~~l~~Lp~~~r~i~~L~~~~g~s~~EIA~~l-gis~~tVk~~l~Rar~~Lr 176 (193)
T TIGR02947 123 QDIKDALQGLPEEFRQAVYLADVEGFAYKEIAEIM-GTPIGTVMSRLHRGRKQLR 176 (193)
T ss_pred HHHHHHHHhCCHHHhhheeehhhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 5677788777632 346688999999 6999999998765444444
No 102
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=50.48 E-value=68 Score=20.86 Aligned_cols=46 Identities=20% Similarity=0.198 Sum_probs=31.6
Q ss_pred HHHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhhh
Q 034697 22 KQFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDINDI 68 (86)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~i 68 (86)
..|..+|.+.|.. .+-.-+.||..+ |.|...|+.|....+..++..
T Consensus 102 ~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~l-gis~~tV~~~l~ra~~~Lr~~ 157 (162)
T TIGR02983 102 AALARALRRLPARQRAVVVLRYYEDLSEAQVAEAL-GISVGTVKSRLSRALARLREL 157 (162)
T ss_pred HHHHHHHHhCCHHHHHHhhhHHHhcCCHHHHHHHh-CCCHHHHHHHHHHHHHHHHHH
Confidence 3455666555422 234567888888 688888999888877777754
No 103
>PF07030 DUF1320: Protein of unknown function (DUF1320); InterPro: IPR009752 This entry is represented by the Bacteriophage Mu, Gp36. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=50.42 E-value=35 Score=22.59 Aligned_cols=28 Identities=25% Similarity=0.324 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHHHHHhhhhcCCCCCCCC
Q 034697 51 VEDVKKHYELLVKDINDIEAGRYPHPNY 78 (86)
Q Consensus 51 ~~qc~~ry~~L~~dv~~ie~g~v~~P~y 78 (86)
.++++.||+.-+..++.|-.|++.++--
T Consensus 84 ~e~~~~rY~~A~~~L~~ia~G~~~L~~~ 111 (130)
T PF07030_consen 84 TEPVRERYKDAIKWLEDIAKGKISLGLP 111 (130)
T ss_pred cHHHHHHHHHHHHHHHHHHCCCccCCCC
Confidence 8899999999999999999998776433
No 104
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=50.28 E-value=76 Score=21.38 Aligned_cols=44 Identities=11% Similarity=0.141 Sum_probs=28.7
Q ss_pred HHHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697 22 KQFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIN 66 (86)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~ 66 (86)
..|..+|...|.. .+...+.||+.+ |.|..-|+.|.......++
T Consensus 130 ~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~l-gis~~tv~~~l~Rar~~Lr 183 (193)
T PRK11923 130 GTVHRTIQQLPEDLRTALTLREFDGLSYEDIASVM-QCPVGTVRSRIFRAREAID 183 (193)
T ss_pred HHHHHHHHhCCHHHhHHHhhHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 3566666665532 234577888888 5888888888766555544
No 105
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=49.79 E-value=79 Score=21.38 Aligned_cols=51 Identities=8% Similarity=0.127 Sum_probs=37.3
Q ss_pred CCHHHHHHHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 16 WTVKQNKQFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 16 WT~eEdk~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
+..+....|..+|.+.|.. .+-..+.||..+ |-|...|+.|.......++.
T Consensus 120 ~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~Lr~ 180 (188)
T PRK09640 120 PKPEERGGLDRWLVHVNPIDREILVLRFVAELEFQEIADIM-HMGLSATKMRYKRALDKLRE 180 (188)
T ss_pred ccHHHHHHHHHHHHhcChhheeeeeeHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence 4445556788888887732 346789999999 69999999987766665554
No 106
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=49.51 E-value=71 Score=21.42 Aligned_cols=46 Identities=11% Similarity=0.178 Sum_probs=32.9
Q ss_pred HHHHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 21 NKQFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 21 dk~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
...|..+|..+|+. .+-..+.||..+ |-|...|+.|-......++.
T Consensus 128 ~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~l-gis~~~v~~~l~Rar~~Lr~ 183 (187)
T PRK12534 128 RRRIDHCLAELEPPRSELIRTAFFEGITYEELAART-DTPIGTVKSWIRRGLAKLKA 183 (187)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHh-CCChhHHHHHHHHHHHHHHH
Confidence 34677777777632 345788999999 68888888887766666553
No 107
>PF11842 DUF3362: Domain of unknown function (DUF3362); InterPro: IPR024560 This domain tends to occur to the C terminus of a radical SAM domain (PF04055 from PFAM) in members of the uncharacterised protein family UPF0313. Radical SAM proteins catalyse diverse reactions, including unusual methylations, isomerization, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation. Evidence exists that these proteins generate a radical species by reductive cleavage of S:-adenosylmethionine (SAM) through an unusual Fe-S centre [, ].
Probab=49.36 E-value=22 Score=25.03 Aligned_cols=27 Identities=26% Similarity=0.633 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHhcCCCCCchHHHHHHHcC
Q 034697 19 KQNKQFETALAFYDKDTPDRWDNVAKAVS 47 (86)
Q Consensus 19 eEdk~Le~al~~~~~~~~~rW~~IA~~vp 47 (86)
++++.|..||.+|- .+.+|..|-++|-
T Consensus 41 ~~er~lqkAll~Y~--~PeN~~lvreAL~ 67 (150)
T PF11842_consen 41 ERERRLQKALLRYH--DPENWPLVREALK 67 (150)
T ss_pred HHHHHHHHHHHhhc--ChhhHHHHHHHHH
Confidence 67899999999995 4678999988883
No 108
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=47.74 E-value=84 Score=21.37 Aligned_cols=31 Identities=10% Similarity=0.112 Sum_probs=23.9
Q ss_pred CchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 36 PDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 36 ~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
+-..+.||..+ |.|..-|+.+.......++.
T Consensus 122 g~~~~EIA~~l-gis~~tV~~~l~Rar~~Lr~ 152 (181)
T PRK09637 122 GLSQKEIAEKL-GLSLSGAKSRVQRGRVKLKE 152 (181)
T ss_pred CCCHHHHHHHh-CCCHHHHHHHHHHHHHHHHH
Confidence 45789999999 69999999887665555553
No 109
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=47.50 E-value=78 Score=21.05 Aligned_cols=45 Identities=9% Similarity=0.208 Sum_probs=30.0
Q ss_pred HHHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 22 KQFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
..|..+|.+.|.. .+-.-+.||+.+ |.|...|+.+.......++.
T Consensus 121 ~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~l-gis~~tV~~~l~Rar~~Lr~ 175 (179)
T PRK12514 121 QRIDACLEELEKDRAAAVRRAYLEGLSYKELAERH-DVPLNTMRTWLRRSLLKLRE 175 (179)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHH-CCChHHHHHHHHHHHHHHHH
Confidence 3455666665522 234678899999 69999998887665555543
No 110
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=47.41 E-value=82 Score=20.89 Aligned_cols=45 Identities=7% Similarity=0.065 Sum_probs=30.1
Q ss_pred HHHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 22 KQFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
..|..+|.+.|.. .+...+.||+.+ |.|...|+.+.......++.
T Consensus 128 ~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~l-gis~~~v~~~l~Rar~~Lr~ 182 (187)
T TIGR02948 128 DTIQQEIQALPPKYRMVIVLKYMEDLSLKEISEIL-DLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred HHHHHHHHhCCHHHhHHhhhHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence 4566777666422 245678888888 58888888887666655553
No 111
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=47.18 E-value=78 Score=20.60 Aligned_cols=31 Identities=10% Similarity=0.175 Sum_probs=23.4
Q ss_pred CchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 36 PDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 36 ~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
+-.+..||+.+ |.|...|+.+.......++.
T Consensus 144 ~~s~~eIA~~l-gis~~tV~~~l~ra~~~Lr~ 174 (182)
T PRK09652 144 GLSYEEIAEIM-GCPIGTVRSRIFRAREALRA 174 (182)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence 45799999999 68999888876665555543
No 112
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=47.03 E-value=86 Score=21.03 Aligned_cols=45 Identities=13% Similarity=0.071 Sum_probs=30.5
Q ss_pred HHHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 22 KQFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
..|..+|...|+. .+...+.||+.+ |.|...|+.+.......++.
T Consensus 120 ~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~l-gis~~tV~~~l~Rar~~Lr~ 174 (186)
T PRK05602 120 RRVEQALAALPERQREAIVLQYYQGLSNIEAAAVM-DISVDALESLLARGRRALRA 174 (186)
T ss_pred HHHHHHHHhCCHHHHHHhhHHHhcCCCHHHHHHHh-CcCHHHHHHHHHHHHHHHHH
Confidence 4566676666522 245678889988 68888888887666555553
No 113
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=46.12 E-value=94 Score=21.20 Aligned_cols=45 Identities=16% Similarity=0.102 Sum_probs=32.2
Q ss_pred HHHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 22 KQFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
+.|..+|.+.|+. .+-.++.||+.+ |-|..-|+.+...-...++.
T Consensus 128 ~~l~~~l~~L~~~~r~i~~L~~~~g~s~~eIA~~l-gis~~tV~~~l~Ra~~~Lr~ 182 (196)
T PRK12524 128 RALDAALAALPERQRQAVVLRHIEGLSNPEIAEVM-EIGVEAVESLTARGKRALAA 182 (196)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHHH
Confidence 4466666666522 346799999999 69999999888776666654
No 114
>KOG2941 consensus Beta-1,4-mannosyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=45.86 E-value=9.9 Score=30.80 Aligned_cols=21 Identities=33% Similarity=0.596 Sum_probs=17.8
Q ss_pred CCCCCCHHHHH-HHHHHHHhcC
Q 034697 12 SGSSWTVKQNK-QFETALAFYD 32 (86)
Q Consensus 12 ~~~~WT~eEdk-~Le~al~~~~ 32 (86)
++..||++||- +|.+||..|.
T Consensus 260 sSTswTpDEdf~ILL~AL~~y~ 281 (444)
T KOG2941|consen 260 SSTSWTPDEDFGILLEALVIYE 281 (444)
T ss_pred ecCCCCCcccHHHHHHHHHhhh
Confidence 56789999997 8889999774
No 115
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=45.49 E-value=74 Score=23.16 Aligned_cols=43 Identities=12% Similarity=0.076 Sum_probs=30.9
Q ss_pred HHHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHH
Q 034697 22 KQFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDI 65 (86)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv 65 (86)
..|.++|.+.|.. .+-..+.||..+ |-|..-|+.|...-...+
T Consensus 153 ~~l~~aL~~Lp~~~R~v~~L~~~eg~S~~EIA~~L-gis~~TVk~rl~RAr~~L 205 (244)
T TIGR03001 153 QALREALAALSERERHLLRLHFVDGLSMDRIGAMY-QVHRSTVSRWVAQARERL 205 (244)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 4577778777643 345789999999 699999988876544333
No 116
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=45.28 E-value=93 Score=20.91 Aligned_cols=45 Identities=20% Similarity=0.331 Sum_probs=32.0
Q ss_pred HHHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 22 KQFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
..|..+|.+.|+. .+-.-+.||..+ |.|..-|+.|....+..++.
T Consensus 114 ~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~l-gis~~tVk~~l~Rar~~Lr~ 168 (185)
T PRK12542 114 VQIDTLLKELNESNRQVFKYKVFYNLTYQEISSVM-GITEANVRKQFERARKRVQN 168 (185)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence 3466676666532 245678999999 69999999988776666654
No 117
>cd08777 Death_RIP1 Death Domain of Receptor-Interacting Protein 1. Death domain (DD) found in Receptor-Interacting Protein 1 (RIP1) and related proteins. RIP kinases serve as essential sensors of cellular stress. Vertebrates contain several types containing a homologous N-terminal kinase domain and varying C-terminal domains. RIP1 harbors a C-terminal DD, which binds death receptors (DRs) including TNF receptor 1, Fas, TNF-related apoptosis-inducing ligand receptor 1 (TRAILR1), and TRAILR2. It also interacts with other DD-containing adaptor proteins such as TRADD and FADD. RIP1 plays a crucial role in determining a cell's fate, between survival or death, following exposure to stress signals. It is important in the signaling of NF-kappaB and MAPKs, and it links DR-associated signaling to reactive oxygen species (ROS) production. Abnormal RIP1 function may result in ROS accumulation affecting inflammatory responses, innate immunity, stress responses, and cell survival. In general, DDs ar
Probab=44.99 E-value=72 Score=19.89 Aligned_cols=31 Identities=23% Similarity=0.425 Sum_probs=20.1
Q ss_pred CHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHH
Q 034697 17 TVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVK 55 (86)
Q Consensus 17 T~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~ 55 (86)
|.++-..|...|.. .|..+|..+ |=|..++.
T Consensus 1 ~~~~l~~l~~~lG~-------~Wk~lar~L-G~s~~eI~ 31 (86)
T cd08777 1 TEKHLDLLRENLGK-------KWKRCARKL-GFTESEIE 31 (86)
T ss_pred CHHHHHHHHHHHHH-------HHHHHHHHc-CCCHHHHH
Confidence 34455555555444 799999999 46666653
No 118
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=44.75 E-value=90 Score=20.95 Aligned_cols=45 Identities=13% Similarity=0.054 Sum_probs=31.3
Q ss_pred HHHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 22 KQFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
..|.++|...|+. .+-..+.||+.+ |.|...|+.+....+..++.
T Consensus 121 ~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~l-~is~~tV~~~l~rar~~Lr~ 175 (181)
T PRK12536 121 RDLGKLLEQLPDRQRLPIVHVKLEGLSVAETAQLT-GLSESAVKVGIHRGLKALAA 175 (181)
T ss_pred HHHHHHHHHCCHHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence 3467777776532 345678889999 68888888887666655553
No 119
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=44.57 E-value=95 Score=20.80 Aligned_cols=45 Identities=11% Similarity=0.138 Sum_probs=27.8
Q ss_pred HHHHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697 21 NKQFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIN 66 (86)
Q Consensus 21 dk~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~ 66 (86)
...|..+|...|+. .+-.-..||+.+ |.|..-|+.|.......++
T Consensus 108 ~~~l~~~l~~Lp~~~r~i~~l~~~e~~s~~EIA~~l-gis~~tV~~~l~ra~~~Lr 162 (179)
T PRK12543 108 NQELIELIHKLPYKLRQVIILRYLHDYSQEEIAQLL-QIPIGTVKSRIHAALKKLR 162 (179)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHccCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 45677777777632 233567788888 5777777777655444433
No 120
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=44.12 E-value=92 Score=20.54 Aligned_cols=45 Identities=18% Similarity=0.324 Sum_probs=32.1
Q ss_pred HHHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 22 KQFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
..|..+|.+.|.. .+-..+.||..+ |.|...|+.+.......++.
T Consensus 104 ~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~l-gis~~tV~~~l~Rar~~Lr~ 158 (164)
T PRK12547 104 QDFKKALNLLSADQREAIILIGASGFSYEDAAAIC-GCAVGTIKSRVSRARNRLQE 158 (164)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHh-CCCHHHHHHHHHHHHHHHHH
Confidence 4566777766532 345688899999 68888898888777666664
No 121
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=43.68 E-value=95 Score=20.55 Aligned_cols=44 Identities=16% Similarity=0.174 Sum_probs=29.2
Q ss_pred HHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 23 QFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 23 ~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
.|..+|.+.++. .+-....||..+ |-|..-|+.+....+..+++
T Consensus 133 ~l~~~l~~L~~~~r~vi~l~~~~g~s~~eIA~~l-gis~~~v~~~l~Ra~~~Lr~ 186 (189)
T TIGR02984 133 RLAQALAKLPEDYREVILLRHLEGLSFAEVAERM-DRSEGAVSMLWVRGLARLRQ 186 (189)
T ss_pred HHHHHHHcCCHHHHHHHHHHHhcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHHH
Confidence 455566555421 245678888888 68888888887766666654
No 122
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=43.50 E-value=1e+02 Score=20.89 Aligned_cols=43 Identities=7% Similarity=0.072 Sum_probs=28.7
Q ss_pred HHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697 23 QFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIN 66 (86)
Q Consensus 23 ~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~ 66 (86)
.|..+|.+.|.. .+-.-+.||+.+ |.|..-|+.|...-+..++
T Consensus 129 ~l~~~l~~L~~~~r~i~~L~~~~g~s~~EIA~~l-gis~~tVk~~l~Rar~~Lr 181 (195)
T PRK12532 129 ILQSCLYNLPENTARVFTLKEILGFSSDEIQQMC-GISTSNYHTIMHRARESLR 181 (195)
T ss_pred HHHHHHHhCCHHHHHHhhhHHHhCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 466666666532 235678899999 6888888888665444444
No 123
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=42.72 E-value=1e+02 Score=20.69 Aligned_cols=44 Identities=14% Similarity=0.220 Sum_probs=28.3
Q ss_pred HHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 23 QFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 23 ~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
.+..+|.+.|+. .+..-+.||+.+ |-|..-|+.|....+..++.
T Consensus 126 ~l~~~l~~L~~~~r~i~~l~~~~~~s~~eIA~~l-gis~~tV~~~l~ra~~~Lr~ 179 (182)
T PRK12537 126 KIHRCLEQLEPARRNCILHAYVDGCSHAEIAQRL-GAPLGTVKAWIKRSLKALRE 179 (182)
T ss_pred HHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHH-CCChhhHHHHHHHHHHHHHH
Confidence 466666665532 234567788888 57788888877766665553
No 124
>COG4281 ACB Acyl-CoA-binding protein [Lipid metabolism]
Probab=42.04 E-value=55 Score=20.96 Aligned_cols=30 Identities=27% Similarity=0.537 Sum_probs=24.6
Q ss_pred chHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 37 DRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 37 ~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
-+|+.-|. +.|+|.++.+..|..|++.++.
T Consensus 54 ~K~eAW~~-LKGksqedA~qeYialVeeLka 83 (87)
T COG4281 54 YKYEAWAG-LKGKSQEDARQEYIALVEELKA 83 (87)
T ss_pred hhHHHHhh-ccCccHHHHHHHHHHHHHHHHh
Confidence 35776665 4589999999999999999875
No 125
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=41.94 E-value=76 Score=24.28 Aligned_cols=39 Identities=23% Similarity=0.321 Sum_probs=29.5
Q ss_pred HHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHH
Q 034697 22 KQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKD 64 (86)
Q Consensus 22 k~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~d 64 (86)
+.|-.....+|. .+=..||+.| |-|++.|.+|.++|+.+
T Consensus 14 qIL~ei~~~qp~---v~q~eIA~~l-giT~QaVsehiK~Lv~e 52 (260)
T COG1497 14 QILSEIAVRQPR---VKQKEIAKKL-GITLQAVSEHIKELVKE 52 (260)
T ss_pred HHHHHHHHhCCC---CCHHHHHHHc-CCCHHHHHHHHHHHHhc
Confidence 344444444453 4778999999 79999999999999865
No 126
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=41.47 E-value=1e+02 Score=20.39 Aligned_cols=44 Identities=14% Similarity=0.166 Sum_probs=29.2
Q ss_pred HHHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697 22 KQFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIN 66 (86)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~ 66 (86)
..|..+|.+.|.. .+-....||+.+ |.|..-|+.|...-+..++
T Consensus 111 ~~l~~~l~~Lp~~~r~v~~L~~~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~~~ 164 (172)
T PRK12523 111 KAIDRLLGKLSSKARAAFLYNRLDGMGHAEIAERL-GVSVSRVRQYLAQGLRQCY 164 (172)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 3566777776632 345688888888 6888888887655444433
No 127
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=41.28 E-value=1.1e+02 Score=20.61 Aligned_cols=43 Identities=19% Similarity=0.183 Sum_probs=29.4
Q ss_pred HHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697 23 QFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIN 66 (86)
Q Consensus 23 ~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~ 66 (86)
.|..+|...|.. .+.....||..+ |.|...|+.+.......++
T Consensus 124 ~l~~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~l-gis~~tV~~~l~Rar~~Lr 176 (189)
T PRK12515 124 ALRACLAKLSPAHREIIDLVYYHEKSVEEVGEIV-GIPESTVKTRMFYARKKLA 176 (189)
T ss_pred HHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHH
Confidence 455666655522 345688999999 6899999888766555554
No 128
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=40.90 E-value=88 Score=19.39 Aligned_cols=41 Identities=15% Similarity=0.263 Sum_probs=27.0
Q ss_pred HHHHHHHHh-cCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHH
Q 034697 22 KQFETALAF-YDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVK 63 (86)
Q Consensus 22 k~Le~al~~-~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~ 63 (86)
+.+...|.. .....+-.-..|++.| +.+..+|+..-..|..
T Consensus 50 ~~Vl~~i~~~~~~~~Gv~v~~I~~~l-~~~~~~v~~al~~L~~ 91 (102)
T PF08784_consen 50 DKVLNFIKQQPNSEEGVHVDEIAQQL-GMSENEVRKALDFLSN 91 (102)
T ss_dssp HHHHHHHHC----TTTEEHHHHHHHS-TS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHhcCCCCCcccHHHHHHHh-CcCHHHHHHHHHHHHh
Confidence 344445555 3334567899999999 8999999997666654
No 129
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=40.88 E-value=1.1e+02 Score=20.65 Aligned_cols=45 Identities=13% Similarity=0.178 Sum_probs=27.1
Q ss_pred HHHHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697 21 NKQFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIN 66 (86)
Q Consensus 21 dk~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~ 66 (86)
...|..+|.+.|+. .+..-..||+.+ |.|...|+.|.......++
T Consensus 122 ~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIAe~l-gis~~~V~~~l~Ra~~~Lr 176 (189)
T PRK06811 122 KEEILKLINDLEKLDREIFIRRYLLGEKIEEIAKKL-GLTRSAIDNRLSRGRKKLQ 176 (189)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHccCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 34566666666532 123456777777 5777778777655444444
No 130
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=40.80 E-value=1e+02 Score=20.23 Aligned_cols=45 Identities=11% Similarity=0.099 Sum_probs=31.9
Q ss_pred HHHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 22 KQFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
..|..+|...|.. .+-.-+.||+.+ |-|..-|+.+.......++.
T Consensus 112 ~~l~~~l~~L~~~~r~vl~l~~~~g~s~~eIA~~l-g~s~~tv~~~l~Rar~~L~~ 166 (175)
T PRK12518 112 DLVQQGLQTLSLEHRAVLVLHDLEDLPQKEIAEIL-NIPVGTVKSRLFYARRQLRK 166 (175)
T ss_pred HHHHHHHHhCCHHHeeeeeehHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence 3466677776632 345688999999 68899999887766666554
No 131
>COG5352 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=40.50 E-value=27 Score=24.85 Aligned_cols=42 Identities=14% Similarity=0.181 Sum_probs=31.3
Q ss_pred CCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHH
Q 034697 15 SWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELL 61 (86)
Q Consensus 15 ~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L 61 (86)
.||.|--..|.++-.. | -.=..||+++||-|-..|+-....|
T Consensus 2 nWtdERve~LkKLWse---G--LSASQIAaQLGGVsRnAVIGKVHRL 43 (169)
T COG5352 2 NWTDERVETLKKLWSE---G--LSASQIAAQLGGVSRNAVIGKVHRL 43 (169)
T ss_pred CchHHHHHHHHHHHHc---c--cCHHHHHHHhcCcchhhhheeeeec
Confidence 5999888887776333 2 2457999999999999988765554
No 132
>PF12451 VPS11_C: Vacuolar protein sorting protein 11 C terminal; InterPro: IPR024763 Vps 11 is one of the evolutionarily conserved class C vacuolar protein sorting genes (c-vps: vps11, vps16, vps18, and vps33), whose products physically associate to form the c-vps protein complex required for vesicle docking and fusion. This entry represents the C-terminal domain of vps11.
Probab=39.14 E-value=33 Score=19.41 Aligned_cols=24 Identities=25% Similarity=0.324 Sum_probs=18.1
Q ss_pred HHHHHHHHHHhcCCCCCchHHHHHHHcC
Q 034697 20 QNKQFETALAFYDKDTPDRWDNVAKAVS 47 (86)
Q Consensus 20 Edk~Le~al~~~~~~~~~rW~~IA~~vp 47 (86)
...+|..+|.. ..++..-||.++|
T Consensus 20 ~~d~F~~~L~~----s~D~F~vIaeyfG 43 (49)
T PF12451_consen 20 QHDLFFKQLEE----SEDRFSVIAEYFG 43 (49)
T ss_pred cHHHHHHHHHh----CCCCchhHHHHHc
Confidence 34577777744 5689999999995
No 133
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=37.99 E-value=1.1e+02 Score=19.67 Aligned_cols=49 Identities=18% Similarity=0.190 Sum_probs=30.0
Q ss_pred CHHHHHHHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697 17 TVKQNKQFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIN 66 (86)
Q Consensus 17 T~eEdk~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~ 66 (86)
..++...|..++.+.|.. .+..-..||+.+ |-|...|+.|.......++
T Consensus 98 ~~~~~~~l~~~i~~L~~~~r~v~~l~~~~g~~~~eIA~~l-~is~~tv~~~l~Rar~~Lr 156 (159)
T TIGR02989 98 SEDELQALEGCLEKLPERQRELLQLRYQRGVSLTALAEQL-GRTVNAVYKALSRLRVRLR 156 (159)
T ss_pred HHHHHHHHHHHHHHCCHHHHHHHHHHHhcCCCHHHHHHHh-CCCHHHHHHHHHHHHHHHH
Confidence 344445677777777632 234566777777 5777777777665555544
No 134
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=37.96 E-value=1.2e+02 Score=20.17 Aligned_cols=45 Identities=11% Similarity=0.170 Sum_probs=31.0
Q ss_pred HHHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 22 KQFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
..|..+|...|.. .+-.-+.||+.+ |.|...|+.+.......++.
T Consensus 127 ~~l~~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~l-gis~~~V~~~l~ra~~~Lr~ 181 (186)
T PRK13919 127 TRLGRALKALSPEERRVIEVLYYQGYTHREAAQLL-GLPLGTLKTRARRALSRLKE 181 (186)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHHH
Confidence 4577777776532 234567888888 68888888887766666553
No 135
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=37.96 E-value=1.2e+02 Score=20.25 Aligned_cols=30 Identities=7% Similarity=0.323 Sum_probs=21.4
Q ss_pred chHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 37 DRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 37 ~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
-.-..||+.+ |.|...|+.+...+...++.
T Consensus 166 ~s~~eIA~~l-~~s~~tV~~~l~r~r~~L~~ 195 (198)
T TIGR02859 166 KSYQEIACDL-NRHVKSIDNALQRVKRKLEK 195 (198)
T ss_pred CCHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence 4567788888 57777788877777666653
No 136
>cd00580 CHMI 5-carboxymethyl-2-hydroxymuconate isomerase (CHMI) is a trimeric enzyme catalyzing the isomerization of the unsaturated ketone 5-(carboxymethyl)-2-hydroxymuconate to 5-(carboxymethyl)-2-oxo-3-hexene-1,6-dionate. This is one step in the homoprotocatechuate pathway, one of the microbial meta-fission pathways that degrade aromatic carbon sources to citric acid cycle intermediates. Despite the structural similarity of CHMI with 4-oxalocrotonate tautomerase (4-OT) and macrophage migration inhibitory factor (MIF), there is no significant sequence similarity among these protein families, and therefore, they are not combined in one hierarchy.
Probab=37.80 E-value=54 Score=20.96 Aligned_cols=22 Identities=18% Similarity=0.362 Sum_probs=18.9
Q ss_pred cCCCCHHHHHHHHHHHHHHHhh
Q 034697 46 VSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 46 vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
++|||.+|-+.-|+.+.+.+..
T Consensus 68 ~~GRs~eqK~~l~~~i~~~l~~ 89 (113)
T cd00580 68 LAGRSEEQKQELSEALLAALRA 89 (113)
T ss_pred cCCCCHHHHHHHHHHHHHHHHH
Confidence 5899999999999988877764
No 137
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=37.43 E-value=1.2e+02 Score=20.12 Aligned_cols=44 Identities=16% Similarity=0.183 Sum_probs=30.8
Q ss_pred HHHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697 22 KQFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIN 66 (86)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~ 66 (86)
..+..+|.+.|+. .+-..+.||+.+ |.|..-|+.|...-....+
T Consensus 111 ~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~~~ 164 (172)
T PRK09651 111 QLLDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKL-GVSVSSVKKYVAKATEHCL 164 (172)
T ss_pred HHHHHHHHhCCHHHhHHhhhhhccCCCHHHHHHHh-CCCHHHHHHHHHHHHHHHH
Confidence 3456666666532 345789999999 6999999998776555544
No 138
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=37.21 E-value=1.2e+02 Score=19.76 Aligned_cols=38 Identities=21% Similarity=0.134 Sum_probs=26.0
Q ss_pred HHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHH
Q 034697 23 QFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELL 61 (86)
Q Consensus 23 ~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L 61 (86)
.|..+|.+.|.. .+-.-+.||..+ |.|..-|+.|...-
T Consensus 98 ~l~~~l~~L~~~~r~v~~l~~~~~~s~~eIA~~l-gis~~tv~~~l~ra 145 (159)
T PRK12527 98 LLQRALAELPPACRDSFLLRKLEGLSHQQIAEHL-GISRSLVEKHIVNA 145 (159)
T ss_pred HHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHh-CCCHHHHHHHHHHH
Confidence 466777776632 234567888888 68888888876543
No 139
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=36.53 E-value=1.4e+02 Score=20.34 Aligned_cols=45 Identities=18% Similarity=0.276 Sum_probs=30.5
Q ss_pred HHHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 22 KQFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
..|..+|.+.|.. .+-.-..||+.+ |.|..-|+.|.......++.
T Consensus 103 ~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~L-gis~~tV~~~l~RAr~~Lr~ 157 (182)
T PRK12540 103 EEFRAALDKLPQDQREALILVGASGFSYEDAAAIC-GCAVGTIKSRVNRARSKLSA 157 (182)
T ss_pred HHHHHHHHhCCHHHHHHhhHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence 3467777776532 244578888888 68888888887665555554
No 140
>PF13496 DUF4120: Domain of unknown function (DUF4120)
Probab=36.40 E-value=36 Score=22.18 Aligned_cols=25 Identities=12% Similarity=0.121 Sum_probs=19.9
Q ss_pred HHHHHHHcCCCCHHHHHHHHHHHHH
Q 034697 39 WDNVAKAVSGKTVEDVKKHYELLVK 63 (86)
Q Consensus 39 W~~IA~~vpgRT~~qc~~ry~~L~~ 63 (86)
=.++|+.++..|.+.|.+|-++-.+
T Consensus 11 vv~yA~sI~D~tl~~ClerLk~We~ 35 (95)
T PF13496_consen 11 VVQYAESIGDSTLQKCLERLKQWEK 35 (95)
T ss_pred HHHHHHHhcchHHHHHHHHHHHHHh
Confidence 3567999999999999998765443
No 141
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=36.28 E-value=1.3e+02 Score=20.94 Aligned_cols=62 Identities=21% Similarity=0.089 Sum_probs=41.0
Q ss_pred CCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh---hhcCCCCCCCC
Q 034697 15 SWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND---IEAGRYPHPNY 78 (86)
Q Consensus 15 ~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~---ie~g~v~~P~y 78 (86)
.-|..|-..|...+.... ..+-..+.||+.+ +-|..-|+.|-..|+.-... +.-|.+.=|.|
T Consensus 158 ~Lt~re~~~l~~~i~~~~-~~g~s~~eIA~~l-~iS~~Tv~~~~~~~~~~~~~~~~~~~~~~~~~~~ 222 (239)
T PRK10430 158 GLTPQTLRTLCQWIDAHQ-DYEFSTDELANAV-NISRVSCRKYLIWLVNCHILFTSIHYGVTGRPVY 222 (239)
T ss_pred CCCHHHHHHHHHHHHhCC-CCCcCHHHHHHHh-CchHHHHHHHHHHHHhCCEEEEEeeccCCCCCCe
Confidence 478888666666665432 1245789999999 69999999988887654333 22344444554
No 142
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=36.28 E-value=1.5e+02 Score=21.25 Aligned_cols=43 Identities=14% Similarity=0.127 Sum_probs=29.5
Q ss_pred HHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697 23 QFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIN 66 (86)
Q Consensus 23 ~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~ 66 (86)
.|..+|.+.|.. .+-.-..||..+ |.|..-|+.|....+..++
T Consensus 164 ~l~~~L~~Lp~~~R~v~~L~~~eg~s~~EIA~~L-gis~~tVk~~l~RAr~kLr 216 (233)
T PRK12538 164 LLEAAMQRLPEQQRIAVILSYHENMSNGEIAEVM-DTTVAAVESLLKRGRQQLR 216 (233)
T ss_pred HHHHHHHhCCHHHHHHhhhHHhcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHH
Confidence 466677766532 245678999999 6888888888765554444
No 143
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=35.52 E-value=1.5e+02 Score=20.43 Aligned_cols=43 Identities=14% Similarity=0.107 Sum_probs=30.0
Q ss_pred HHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697 23 QFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIN 66 (86)
Q Consensus 23 ~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~ 66 (86)
.|..+|.+.|.. .+-.-..||..+ |.|..-|+.|...-...++
T Consensus 132 ~l~~~L~~Lp~~~r~v~~L~~~eg~s~~EIA~~l-gis~~tVk~~l~RAr~~Lr 184 (201)
T PRK12545 132 LFETCLDHLPEQIGRVFMMREFLDFEIDDICTEL-TLTANHCSVLLYRARTRLR 184 (201)
T ss_pred HHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHH
Confidence 466677776532 245688999999 6999999988766555544
No 144
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=35.32 E-value=1.5e+02 Score=20.27 Aligned_cols=49 Identities=12% Similarity=0.158 Sum_probs=33.8
Q ss_pred HHHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhhhhcC
Q 034697 22 KQFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDINDIEAG 71 (86)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ie~g 71 (86)
..|..+|.+.|.. .+-.-..||+.+ |.|..-|+.+.......++.+-.+
T Consensus 103 ~~l~~~l~~Lp~~~R~v~~L~~~eg~s~~EIA~~l-gis~~tV~~~l~Rar~~Lr~~~~~ 161 (182)
T PRK12511 103 AQIRDAFFDLPEEQRAALHLVAIEGLSYQEAAAVL-GIPIGTLMSRIGRARAALRAFEEG 161 (182)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHh-CcCHHHHHHHHHHHHHHHHHHHHh
Confidence 3466777766532 245678889888 688888888887777777665443
No 145
>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=34.96 E-value=66 Score=16.21 Aligned_cols=42 Identities=10% Similarity=0.207 Sum_probs=25.0
Q ss_pred CCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHH
Q 034697 16 WTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVK 63 (86)
Q Consensus 16 WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~ 63 (86)
.+.++...|..... . +..+..||+.+ |-|...|..+-.....
T Consensus 11 l~~~~~~~~~~~~~---~--~~~~~~ia~~~-~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 11 LPEREREVILLRFG---E--GLSYEEIAEIL-GISRSTVRQRLHRALK 52 (55)
T ss_pred CCHHHHHHHHHHHh---c--CCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 45555555544321 1 24688999998 5777777665554443
No 146
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=34.92 E-value=99 Score=18.25 Aligned_cols=48 Identities=21% Similarity=0.329 Sum_probs=29.0
Q ss_pred CCHHHHHHHHHHHHhcC-CCCCchHHHHHHHcCCCCHHHHHHHHHHHHH
Q 034697 16 WTVKQNKQFETALAFYD-KDTPDRWDNVAKAVSGKTVEDVKKHYELLVK 63 (86)
Q Consensus 16 WT~eEdk~Le~al~~~~-~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~ 63 (86)
=|+.|.++|+-....+. .+-+.--..||+.+|=+|..-|..|-+.|.+
T Consensus 4 LT~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~ 52 (65)
T PF01726_consen 4 LTERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKALER 52 (65)
T ss_dssp --HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 35666665554332221 1235578999999987899999887777653
No 147
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=34.76 E-value=1.4e+02 Score=21.99 Aligned_cols=56 Identities=13% Similarity=0.106 Sum_probs=41.6
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhhhh
Q 034697 13 GSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDINDIE 69 (86)
Q Consensus 13 ~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ie 69 (86)
...+|.++-.+||.+.....=-.+.-=+++|..+ +-|..||+--|++-....+++.
T Consensus 106 RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L-~LsetQVkvWFQNRRtk~kr~~ 161 (197)
T KOG0843|consen 106 RTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSL-SLSETQVKVWFQNRRTKHKRMQ 161 (197)
T ss_pred ccccCHHHHHHHHHHHhcCCeeechHHHHHHHHc-CCChhHhhhhhhhhhHHHHHHH
Confidence 5679999999999997764311234568999999 6999999988877655555443
No 148
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=34.37 E-value=77 Score=16.80 Aligned_cols=33 Identities=12% Similarity=0.193 Sum_probs=23.1
Q ss_pred HHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHH
Q 034697 20 QNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKH 57 (86)
Q Consensus 20 Edk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~r 57 (86)
|-..|+.+|..+. .+..+.|+.+ |-+......+
T Consensus 6 E~~~i~~aL~~~~----gn~~~aA~~L-gisr~tL~~k 38 (42)
T PF02954_consen 6 EKQLIRQALERCG----GNVSKAARLL-GISRRTLYRK 38 (42)
T ss_dssp HHHHHHHHHHHTT----T-HHHHHHHH-TS-HHHHHHH
T ss_pred HHHHHHHHHHHhC----CCHHHHHHHH-CCCHHHHHHH
Confidence 5668888999974 4689999999 5666655544
No 149
>PF04282 DUF438: Family of unknown function (DUF438); InterPro: IPR007380 This is a a group of uncharacterised proteins.
Probab=34.32 E-value=33 Score=21.17 Aligned_cols=22 Identities=27% Similarity=0.542 Sum_probs=17.3
Q ss_pred CCCCHHHHHHHHHHHHHHHhhh
Q 034697 47 SGKTVEDVKKHYELLVKDINDI 68 (86)
Q Consensus 47 pgRT~~qc~~ry~~L~~dv~~i 68 (86)
.|.+.++++++|..++.+|...
T Consensus 11 ~G~~~e~vk~~F~~~~~~Vs~~ 32 (71)
T PF04282_consen 11 EGEDPEEVKEEFKKLFSDVSAS 32 (71)
T ss_pred CCCCHHHHHHHHHHHHCCCCHH
Confidence 4788999999999887776543
No 150
>PRK02220 4-oxalocrotonate tautomerase; Provisional
Probab=34.15 E-value=80 Score=17.50 Aligned_cols=23 Identities=17% Similarity=0.304 Sum_probs=17.8
Q ss_pred HcCCCCHHHHHHHHHHHHHHHhh
Q 034697 45 AVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 45 ~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
.++|||.+|-++-++.+.+.+..
T Consensus 8 ~~~Grs~eqk~~l~~~it~~l~~ 30 (61)
T PRK02220 8 LIEGRTEEQLKALVKDVTAAVSK 30 (61)
T ss_pred EcCCCCHHHHHHHHHHHHHHHHH
Confidence 35789999999888877766654
No 151
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=34.00 E-value=1.3e+02 Score=19.50 Aligned_cols=44 Identities=11% Similarity=0.086 Sum_probs=29.8
Q ss_pred HHHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697 22 KQFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIN 66 (86)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~ 66 (86)
..|..+|.+.|+. .+-..+.||+.+ |-|..-|+.|...-...++
T Consensus 105 ~~l~~~l~~L~~~~r~v~~L~~~~g~s~~EIA~~l-~is~~tV~~~l~ra~~~~~ 158 (161)
T PRK12528 105 VELDQLLDGLPPLVKRAFLLAQVDGLGYGEIATEL-GISLATVKRYLNKAAMRCY 158 (161)
T ss_pred HHHHHHHHHCCHHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 3566666666532 345678888888 6888888888776665554
No 152
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=33.97 E-value=1.9e+02 Score=21.19 Aligned_cols=44 Identities=14% Similarity=0.135 Sum_probs=32.5
Q ss_pred HHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 23 QFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 23 ~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
.|..+|.+.|+. .+-.-+.||+.+ |.|..-|+.+...-...++.
T Consensus 108 ~l~~~l~~L~~~~R~v~~L~~~~g~s~~EIA~~l-g~s~~tVk~~l~RAr~~Lr~ 161 (293)
T PRK09636 108 ALMLALERLSPLERAAFLLHDVFGVPFDEIASTL-GRSPAACRQLASRARKHVRA 161 (293)
T ss_pred HHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHh
Confidence 466777776532 245678999999 69999999998776666664
No 153
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=33.89 E-value=1.7e+02 Score=20.73 Aligned_cols=45 Identities=13% Similarity=0.125 Sum_probs=30.5
Q ss_pred HHHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 22 KQFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
..|..+|...|.. .+-.-+.||+.| |-|..-|+.|....+..++.
T Consensus 126 ~~l~~al~~Lp~~~R~v~~L~y~eg~s~~EIAe~L-giS~~tVk~~L~RAr~~Lr~ 180 (216)
T PRK12533 126 RLVNAALAKLPVEYREVLVLRELEDMSYREIAAIA-DVPVGTVMSRLARARRRLAA 180 (216)
T ss_pred HHHHHHHHcCCHHHHhHhhhHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence 4677777766532 234578889999 68888888887665555554
No 154
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=33.78 E-value=1.6e+02 Score=20.30 Aligned_cols=45 Identities=11% Similarity=0.104 Sum_probs=30.8
Q ss_pred HHHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 22 KQFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
..|..+|.+.|.. .+..-..||+.+ |.|..-|+.|....+..++.
T Consensus 125 ~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIAe~l-gis~~tV~~~l~Rar~~Lr~ 179 (196)
T PRK12535 125 IDVRTLIDALPPERREALILTQVLGYTYEEAAKIA-DVRVGTIRSRVARARADLIA 179 (196)
T ss_pred HHHHHHHHcCCHHHHHHhhhHHHhCCCHHHHHHHh-CCCHHHHHHHHHHHHHHHHH
Confidence 4577777777632 234567888888 68888888887665555553
No 155
>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=33.68 E-value=1.2e+02 Score=18.71 Aligned_cols=17 Identities=12% Similarity=0.475 Sum_probs=13.4
Q ss_pred chHHHHHHHcCCCCHHHH
Q 034697 37 DRWDNVAKAVSGKTVEDV 54 (86)
Q Consensus 37 ~rW~~IA~~vpgRT~~qc 54 (86)
..|.++|..+ |-|..++
T Consensus 19 ~~Wk~Lar~L-Gls~~dI 35 (86)
T cd08318 19 EDWKTLAPHL-EMKDKEI 35 (86)
T ss_pred hhHHHHHHHc-CCCHHHH
Confidence 4799999999 5666665
No 156
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=33.67 E-value=1.1e+02 Score=23.60 Aligned_cols=49 Identities=20% Similarity=0.204 Sum_probs=37.3
Q ss_pred CCCCCCHHHHHHHHHHHHhcC-CCCCchHHHHHHHcCCCCHHHHHHHHHHHH
Q 034697 12 SGSSWTVKQNKQFETALAFYD-KDTPDRWDNVAKAVSGKTVEDVKKHYELLV 62 (86)
Q Consensus 12 ~~~~WT~eEdk~Le~al~~~~-~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~ 62 (86)
++..+|.-+-+.||+-..+.. .-..+| .+||+.| |-|..||+-=|++-+
T Consensus 175 sRTaFT~~Ql~~LEkrF~~QKYLS~~DR-~~LA~~L-gLTdaQVKtWfQNRR 224 (309)
T KOG0488|consen 175 SRTAFSDHQLFELEKRFEKQKYLSVADR-IELAASL-GLTDAQVKTWFQNRR 224 (309)
T ss_pred chhhhhHHHHHHHHHHHHHhhcccHHHH-HHHHHHc-CCchhhHHHHHhhhh
Confidence 456799999999999754432 114678 9999999 699999998777643
No 157
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 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=33.51 E-value=1.7e+02 Score=21.43 Aligned_cols=44 Identities=14% Similarity=0.211 Sum_probs=31.9
Q ss_pred HHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 23 QFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 23 ~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
.|..+|.+.|.. .+-.-..||+.+ |.|..-|+.|....+..++.
T Consensus 135 ~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~l-gis~~tV~~~l~Rar~~Lr~ 188 (324)
T TIGR02960 135 AFVAAIQYLPPRQRAVLLLRDVLGWRAAETAELL-GTSTASVNSALQRARATLDE 188 (324)
T ss_pred HHHHHHHhCCHHHhhHhhhHHHhCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence 356677776532 245678999999 69999999997766666654
No 158
>PRK04217 hypothetical protein; Provisional
Probab=33.35 E-value=1.4e+02 Score=19.62 Aligned_cols=30 Identities=13% Similarity=0.101 Sum_probs=24.0
Q ss_pred chHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 37 DRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 37 ~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
-..+.||+.+ |.|..-|..++......++.
T Consensus 59 lS~~EIAk~L-GIS~sTV~r~L~RArkkLre 88 (110)
T PRK04217 59 LTQEEAGKRM-GVSRGTVWRALTSARKKVAQ 88 (110)
T ss_pred CCHHHHHHHH-CcCHHHHHHHHHHHHHHHHH
Confidence 3689999999 69999999888776666553
No 159
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=33.23 E-value=1.5e+02 Score=19.89 Aligned_cols=44 Identities=20% Similarity=0.201 Sum_probs=29.4
Q ss_pred HHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 23 QFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 23 ~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
.|..+|...|.. .+-.-..||..+ |.|..-|+.|....+..++.
T Consensus 134 ~l~~~l~~L~~~~~~v~~l~~~~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~Lr~ 187 (194)
T PRK12519 134 RVQTALAQLPESQRQVLELAYYEGLSQSEIAKRL-GIPLGTVKARARQGLLKLRE 187 (194)
T ss_pred HHHHHHHhCCHHHhhhhhhhhhcCCCHHHHHHHh-CCCHHHHHHHHHHHHHHHHH
Confidence 456666666522 245567888888 58888888887666555553
No 160
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=33.20 E-value=1.8e+02 Score=21.74 Aligned_cols=46 Identities=11% Similarity=0.117 Sum_probs=33.5
Q ss_pred HHHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhhh
Q 034697 22 KQFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDINDI 68 (86)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~i 68 (86)
..|..+|...++. .+-.-..||+.+ |.|..-|+.+...-...++..
T Consensus 110 ~al~~~L~~L~p~~R~vf~L~~~~g~s~~EIA~~L-gis~~tVr~~l~RAr~~Lr~~ 165 (290)
T PRK09635 110 LALLIMLERLGPAERVVFVLHEIFGLPYQQIATTI-GSQASTCRQLAHRARRKINES 165 (290)
T ss_pred HHHHHHHHhCCHHHHHHhhHHHHhCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHHhh
Confidence 3566666665422 245688999999 699999999988777777653
No 161
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=33.11 E-value=1.5e+02 Score=19.91 Aligned_cols=43 Identities=2% Similarity=-0.079 Sum_probs=28.7
Q ss_pred HHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697 23 QFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIN 66 (86)
Q Consensus 23 ~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~ 66 (86)
.|..+|.+.|.. .+-.-..||..+ |.|..-|+.|.......++
T Consensus 124 ~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~l-gis~~tV~~~l~Rar~~Lr 176 (191)
T PRK12520 124 VLQACVDRLPPRTGRVFMMREWLELETEEICQEL-QITATNAWVLLYRARMRLR 176 (191)
T ss_pred HHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 466777776632 234568888888 6888888888665544444
No 162
>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=32.86 E-value=1.5e+02 Score=20.35 Aligned_cols=45 Identities=7% Similarity=0.089 Sum_probs=34.1
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcC----CCCHHHHHHHHHHH
Q 034697 13 GSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVS----GKTVEDVKKHYELL 61 (86)
Q Consensus 13 ~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vp----gRT~~qc~~ry~~L 61 (86)
...=|..|...++.+|.+|+. .++.+|.=.- -.|..||+.++..+
T Consensus 114 ~~~ls~~e~~~i~~Li~KhGd----Dy~aMarD~KLN~~Q~T~~qlrrki~~~ 162 (164)
T PF09420_consen 114 PRRLSEREIEYIEYLIEKHGD----DYKAMARDRKLNYMQHTPGQLRRKIRKY 162 (164)
T ss_pred CCCCCHHHHHHHHHHHHHHCc----cHHHHhccCCCCcccCCHHHHHHHHHHh
Confidence 445688899999999999974 4787776553 37999998876653
No 163
>cd07216 Pat17_PNPLA8_PNPLA9_like3 Patatin-like phospholipase. Patatin is a storage protein of the potato tuber that shows Phospholipase A2 activity (PLA2; EC 3.1.1.4). Patatin catalyzes the nonspecific hydrolysis of phospholipids, glycolipids, sulfolipids, and mono- and diacylglycerols, thereby showing lipid acyl hydrolase activity. The active site includes an oxyanion hole with a conserved GGxR motif; it is found in almost all the members of this family. The catalytic dyad is formed by a serine and an aspartate. Patatin belongs to the alpha-beta hydrolase family which is identified by a characteristic nucleophile elbow with a consensus sequence of Sm-X-Nu-Sm (Sm = small residue, X = any residue and Nu = nucleophile). Members of this family have been found also in vertebrates. This family includes subfamily of PNPLA8 (iPLA2-gamma) and PNPLA9 (iPLA2-beta) like phospholipases from human as well as the Pat17 isozyme from Solanum cardiophyllum.
Probab=32.74 E-value=58 Score=24.27 Aligned_cols=27 Identities=26% Similarity=0.287 Sum_probs=21.6
Q ss_pred HHHHHcC--CCCHHHHHHHHHHHHHHHhh
Q 034697 41 NVAKAVS--GKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 41 ~IA~~vp--gRT~~qc~~ry~~L~~dv~~ 67 (86)
-||..+. +.|.+||.+.|..+..++-.
T Consensus 54 iiA~~l~~~~~t~~e~~~~y~~~~~~iF~ 82 (309)
T cd07216 54 LIAIMLGRLRMTVDECIDAYTRLAKKIFS 82 (309)
T ss_pred HHHHHhcccCCCHHHHHHHHHHHhHHhCC
Confidence 4677774 67999999999998877753
No 164
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=32.54 E-value=1.7e+02 Score=20.21 Aligned_cols=45 Identities=13% Similarity=0.145 Sum_probs=30.1
Q ss_pred HHHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 22 KQFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
..|..+|...|.. .+-.-+.||..+ |.|...|+.+....+..++.
T Consensus 145 ~~l~~~l~~L~~~~r~vl~l~~~~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~Lr~ 199 (206)
T PRK12526 145 KQILSYIEKLPEAQQTVVKGVYFQELSQEQLAQQL-NVPLGTVKSRLRLALAKLKV 199 (206)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence 3466666666532 234567899999 68888888887666555553
No 165
>PF09197 Rap1-DNA-bind: Rap1, DNA-binding; InterPro: IPR015280 Members of this entry, which are predominantly found in the yeast protein Rap1, assume a secondary structure consisting of a three-helix bundle and an N-terminal arm. They contain an Arg-Asp-Arg-Lys sequence that interacts with an ACAregion in the 3, region of the DNA-binding site []. ; PDB: 1IGN_A 3UKG_A.
Probab=32.48 E-value=1.5e+02 Score=19.59 Aligned_cols=46 Identities=15% Similarity=0.235 Sum_probs=33.4
Q ss_pred CCHHHHHHHHHHHHhc------CCC------C---------------CchHHHHHHHcCCCCHHHHHHHHHHH
Q 034697 16 WTVKQNKQFETALAFY------DKD------T---------------PDRWDNVAKAVSGKTVEDVKKHYELL 61 (86)
Q Consensus 16 WT~eEdk~Le~al~~~------~~~------~---------------~~rW~~IA~~vpgRT~~qc~~ry~~L 61 (86)
+|.+||-.|..+|.+| ..+ . -..+...+...|.-|...=++||++.
T Consensus 2 fTA~dDY~Lc~~i~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~fF~~~~~~~p~HT~~sWRDR~RKf 74 (105)
T PF09197_consen 2 FTADDDYALCKAIKKQFYRDIYQKDPDTGSSLISDGDSKEFIPKRDMRSFFKDLARKNPRHTENSWRDRYRKF 74 (105)
T ss_dssp --HHHHHHHHHHHHHHHHHHHHSB-TTSS-B----------------TTHHHHHHHHTTTS-HHHHHHHHHHT
T ss_pred CChHHHHHHHHHHHHHHHHHHHhhCcccccccccCCCccccccchhhHHHHHHHHHcCCccchhHHHHHHHHH
Confidence 6899999999988665 111 1 24688899999999999999999873
No 166
>COG0193 Pth Peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis]
Probab=30.39 E-value=1e+02 Score=22.46 Aligned_cols=38 Identities=11% Similarity=0.226 Sum_probs=29.8
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHH
Q 034697 14 SSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYE 59 (86)
Q Consensus 14 ~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~ 59 (86)
+.++.+|.+.|+.++.+ -++.+...+.+ ..+..+++|.
T Consensus 150 ~~f~~~E~~~l~~~~~~-------a~~~~~~~~~~-~~~~~mn~~~ 187 (190)
T COG0193 150 GKFSKEERELLDKAIDK-------AADALELLLEG-DFEKAMNKLN 187 (190)
T ss_pred CCCCHHHHHHHHHHHHH-------HHHHHHHHHHH-hHHHHHHHHh
Confidence 68999999999999887 47777777766 6666666664
No 167
>PF09905 DUF2132: Uncharacterized conserved protein (DUF2132); InterPro: IPR018668 This entry contains proteins that have no known function. ; PDB: 2JVW_A.
Probab=30.34 E-value=83 Score=19.22 Aligned_cols=22 Identities=9% Similarity=0.448 Sum_probs=17.4
Q ss_pred HHHHHHHHHhcCCCCCchHHHHHHHcCC
Q 034697 21 NKQFETALAFYDKDTPDRWDNVAKAVSG 48 (86)
Q Consensus 21 dk~Le~al~~~~~~~~~rW~~IA~~vpg 48 (86)
+.+|.+.+..|+ |+..++.|+=
T Consensus 12 e~il~~Lv~~yG------W~~L~~~i~i 33 (64)
T PF09905_consen 12 ETILTELVEHYG------WEELGERINI 33 (64)
T ss_dssp HHHHHHHHHHT-------HHHHHHHTTS
T ss_pred HHHHHHHHHHhC------HHHHHhhccc
Confidence 467788888884 9999999963
No 168
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=30.30 E-value=2e+02 Score=20.80 Aligned_cols=48 Identities=13% Similarity=0.167 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 19 KQNKQFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 19 eEdk~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
++...|..+|...+.. .+.....||..+ |-|...|+.+....+..++.
T Consensus 192 ~~~~~l~~~l~~L~~~~r~vl~l~y~~~~s~~eIA~~l-gvs~~~V~~~~~ra~~kLr~ 249 (256)
T PRK07408 192 EDRIRLQQALAQLEERTREVLEFVFLHDLTQKEAAERL-GISPVTVSRRVKKGLDQLKK 249 (256)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHCCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHHH
Confidence 3344677777766522 245678888888 58888888887766655553
No 169
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=30.26 E-value=1e+02 Score=17.03 Aligned_cols=44 Identities=16% Similarity=0.198 Sum_probs=31.3
Q ss_pred CCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697 16 WTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDIN 66 (86)
Q Consensus 16 WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~ 66 (86)
-|+.|-..|.-...-+ .=..||..+ |.+..-|+.|...+...+.
T Consensus 4 LT~~E~~vl~~l~~G~------~~~eIA~~l-~is~~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 4 LTERELEVLRLLAQGM------SNKEIAEEL-GISEKTVKSHRRRIMKKLG 47 (58)
T ss_dssp S-HHHHHHHHHHHTTS-------HHHHHHHH-TSHHHHHHHHHHHHHHHHT
T ss_pred cCHHHHHHHHHHHhcC------CcchhHHhc-CcchhhHHHHHHHHHHHhC
Confidence 4666777666655443 467999999 6999999998888776654
No 170
>PF10743 Phage_Cox: Regulatory phage protein cox; InterPro: IPR019679 Phage Cox proteins are expressed by Enterobacteria phages. The Cox protein is a 79-residue basic protein with a predicted strong helix-turn-helix DNA-binding motif. It inhibits integrative recombination and it activates site-specific excision of the HP1 genome from the Haemophilus influenzae chromosome, Hp1. Cox appears to function as a tetramer. Cox binding sites consist of two direct repeats of the consensus motif 5'-GGTMAWWWWA, one Cox tetramer binding to each motif. Cox binding interferes with the interaction of HP1 integrase with one of its binding sites, IBS5. This competition is central to directional control. Both Cox binding sites are needed for full inhibition of integration and for activating excision, because it plays a positive role in assembling the nucleoprotein complexes that produce excisive recombination, by inducing the formation of a critical conformation in those complexes [].
Probab=29.94 E-value=1.4e+02 Score=19.21 Aligned_cols=40 Identities=33% Similarity=0.520 Sum_probs=27.2
Q ss_pred HHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhhhhcCCCCCCCCC
Q 034697 28 LAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDINDIEAGRYPHPNYR 79 (86)
Q Consensus 28 l~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ie~g~v~~P~y~ 79 (86)
+.+||.+ .-.-++.|.++ |||...|+. -|+.|+.|+=...
T Consensus 5 ~~~~p~d-~v~~~~FA~~I-GKt~sAVr~----------Mi~~gKLP~i~~~ 44 (87)
T PF10743_consen 5 VSEYPSD-AVTYEKFAEYI-GKTPSAVRK----------MIKAGKLPVIEMR 44 (87)
T ss_pred HHhhhcc-ccCHHHHHHHH-CCCHHHHHH----------HHHcCCCCeEecc
Confidence 5556544 34578899999 799999887 3556766654443
No 171
>KOG1724 consensus SCF ubiquitin ligase, Skp1 component [Posttranslational modification, protein turnover, chaperones]
Probab=29.24 E-value=49 Score=23.32 Aligned_cols=22 Identities=27% Similarity=0.554 Sum_probs=18.8
Q ss_pred hHHHHHHHcCCCCHHHHHHHHH
Q 034697 38 RWDNVAKAVSGKTVEDVKKHYE 59 (86)
Q Consensus 38 rW~~IA~~vpgRT~~qc~~ry~ 59 (86)
.=..||..+-|||++|++..|.
T Consensus 119 ~ck~va~mikgktpeEir~~f~ 140 (162)
T KOG1724|consen 119 TCKTVANMIKGKTPEEIREIFN 140 (162)
T ss_pred HHHHHHHHHccCCHHHHHHHcC
Confidence 4468999999999999999864
No 172
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=29.14 E-value=2.2e+02 Score=20.60 Aligned_cols=38 Identities=11% Similarity=0.101 Sum_probs=22.9
Q ss_pred HHHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHH
Q 034697 22 KQFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYEL 60 (86)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~ 60 (86)
..|..+|...|+. .+..-..||..+ |.|..-|+.+...
T Consensus 204 ~~l~~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~l-gis~~tV~~~~~r 251 (268)
T PRK06288 204 RVIVEAIKTLPEREKKVLILYYYEDLTLKEIGKVL-GVTESRISQLHTK 251 (268)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHH
Confidence 4566777666532 234566777777 5777777766543
No 173
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=29.13 E-value=2.1e+02 Score=20.20 Aligned_cols=44 Identities=9% Similarity=0.128 Sum_probs=28.4
Q ss_pred HHHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697 22 KQFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIN 66 (86)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~ 66 (86)
..|..+|...|.. .+-....||+.+ |.|..-|+.+....+..++
T Consensus 176 ~~l~~~l~~L~~~~r~vl~l~~~~g~s~~EIA~~l-gis~~tV~~~~~ra~~~Lr 229 (236)
T PRK06986 176 EALVEAIESLPEREQLVLSLYYQEELNLKEIGAVL-GVSESRVSQIHSQAIKRLR 229 (236)
T ss_pred HHHHHHHHhCCHHHHHHHHhHhccCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 3456666665522 234678888888 6888888887666555554
No 174
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=29.12 E-value=1.7e+02 Score=19.26 Aligned_cols=44 Identities=7% Similarity=0.027 Sum_probs=26.4
Q ss_pred HHHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697 22 KQFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIN 66 (86)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~ 66 (86)
..|..+|...|+. .+-..+.||..+ |-|..-|+.+...-...++
T Consensus 110 ~~l~~~l~~L~~~~r~v~~L~~~eg~s~~EIA~~l-~is~~tV~~~l~ra~~~~~ 163 (168)
T PRK12525 110 LAIDRLLDGLSGKARAAFLMSQLEGLTYVEIGERL-GVSLSRIHQYMVEAFKCCY 163 (168)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 3455666666532 234677788888 5777777777655444443
No 175
>COG4387 Mu-like prophage protein gp36 [Function unknown]
Probab=29.04 E-value=82 Score=21.86 Aligned_cols=36 Identities=14% Similarity=0.325 Sum_probs=27.5
Q ss_pred HHHHHHc--CCCCHHHHHHHHHHHHHHHhhhhcCCCCC
Q 034697 40 DNVAKAV--SGKTVEDVKKHYELLVKDINDIEAGRYPH 75 (86)
Q Consensus 40 ~~IA~~v--pgRT~~qc~~ry~~L~~dv~~ie~g~v~~ 75 (86)
..||.+. -+|--+|++.||+.-+.-++..-+|.|++
T Consensus 70 C~IA~Y~L~~~r~Tdq~r~rYe~av~~L~~va~G~V~l 107 (139)
T COG4387 70 CDIARYRLCKNRATDQARQRYEDAVRFLEKVASGAVSL 107 (139)
T ss_pred HHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHcCCCcc
Confidence 4566554 46888999999998777777777888775
No 176
>TIGR01636 phage_rinA phage transcriptional activator, RinA family. This model represents a family of phage proteins, including RinA, a transcriptional activator in staphylococcal phage phi 11. This family shows similarity to ArpU, a phage-related putative autolysin regulator, and to some sporulation-specific sigma factors.
Probab=28.68 E-value=1.8e+02 Score=19.25 Aligned_cols=29 Identities=3% Similarity=-0.018 Sum_probs=21.5
Q ss_pred chHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697 37 DRWDNVAKAVSGKTVEDVKKHYELLVKDIN 66 (86)
Q Consensus 37 ~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~ 66 (86)
..|..||..+ |-|...|..+=+..+..+.
T Consensus 101 ~t~~~Ia~~l-~iS~~t~~r~r~~~l~kla 129 (134)
T TIGR01636 101 LTLVGLAQQL-FISKSTAYRLRNHIIEAVA 129 (134)
T ss_pred CCHHHHHHHh-CCCHHHHHHHHHHHHHHHH
Confidence 4799999999 6898888765445555444
No 177
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=28.29 E-value=83 Score=23.66 Aligned_cols=43 Identities=16% Similarity=0.067 Sum_probs=31.8
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCC-CCHHHH
Q 034697 12 SGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSG-KTVEDV 54 (86)
Q Consensus 12 ~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpg-RT~~qc 54 (86)
.+..+|.++...||.++++-.--.-..|+++|..|.= .+..||
T Consensus 40 ERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqV 83 (228)
T KOG2251|consen 40 ERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQV 83 (228)
T ss_pred ccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhh
Confidence 3577999999999999876432235789999999952 455554
No 178
>PF11084 DUF2621: Protein of unknown function (DUF2621); InterPro: IPR020203 This entry represents a group of uncharacterised proteins.
Probab=28.28 E-value=68 Score=22.38 Aligned_cols=21 Identities=19% Similarity=0.256 Sum_probs=17.4
Q ss_pred CCCCCHHHHHHHHHHHHhcCC
Q 034697 13 GSSWTVKQNKQFETALAFYDK 33 (86)
Q Consensus 13 ~~~WT~eEdk~Le~al~~~~~ 33 (86)
..-||.|+-.+|++++.-.|.
T Consensus 56 rhlW~de~K~lL~eLV~PVPe 76 (141)
T PF11084_consen 56 RHLWTDEQKALLEELVSPVPE 76 (141)
T ss_pred HhhcCHHHHHHHHHHhhcCcH
Confidence 456999999999999887764
No 179
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=28.23 E-value=2.2e+02 Score=20.36 Aligned_cols=30 Identities=0% Similarity=0.025 Sum_probs=20.0
Q ss_pred CchHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697 36 PDRWDNVAKAVSGKTVEDVKKHYELLVKDIN 66 (86)
Q Consensus 36 ~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~ 66 (86)
+.....||..+ |.|..-|+.+.......++
T Consensus 217 ~~s~~EIA~~l-gis~~tV~~~~~ra~~~Lr 246 (251)
T PRK07670 217 ELTLTEIGQVL-NLSTSRISQIHSKALFKLK 246 (251)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHHHHHH
Confidence 34567778777 5777777777665555544
No 180
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=27.87 E-value=2.2e+02 Score=19.93 Aligned_cols=45 Identities=11% Similarity=0.079 Sum_probs=33.2
Q ss_pred CCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697 15 SWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDIN 66 (86)
Q Consensus 15 ~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~ 66 (86)
.=|+.|-+.|.-...-+ .-..||+.+ +-|..-|+.|-..+..++.
T Consensus 137 ~LT~RE~eVL~lla~G~------snkeIA~~L-~iS~~TVk~h~~~I~~KL~ 181 (207)
T PRK15411 137 SLSRTESSMLRMWMAGQ------GTIQISDQM-NIKAKTVSSHKGNIKRKIK 181 (207)
T ss_pred cCCHHHHHHHHHHHcCC------CHHHHHHHc-CCCHHHHHHHHHHHHHHhC
Confidence 47888888776654443 579999999 5888888888777666554
No 181
>PTZ00397 macrophage migration inhibition factor-like protein; Provisional
Probab=27.86 E-value=94 Score=19.78 Aligned_cols=22 Identities=9% Similarity=0.116 Sum_probs=17.3
Q ss_pred cCCCCHHHHHHHHHHHHHHHhh
Q 034697 46 VSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 46 vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
++||+.+|.++.|..+.+-+..
T Consensus 66 ~g~~~~e~k~~l~~~i~~~l~~ 87 (116)
T PTZ00397 66 IGGISRSNNSSIAAAITKILAS 87 (116)
T ss_pred ecCCCHHHHHHHHHHHHHHHHH
Confidence 4889999999999887655553
No 182
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=27.83 E-value=1.9e+02 Score=19.34 Aligned_cols=41 Identities=15% Similarity=0.132 Sum_probs=28.4
Q ss_pred HHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHH
Q 034697 23 QFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKD 64 (86)
Q Consensus 23 ~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~d 64 (86)
.|..+|.+.|+. .+-..+.||+.+ |-|..-|+.|...-+..
T Consensus 120 ~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~l-gis~~tVk~~l~rAl~~ 170 (178)
T PRK12529 120 EIDALLDTLRPRVKQAFLMATLDGMKQKDIAQAL-DIALPTVKKYIHQAYVT 170 (178)
T ss_pred HHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 466677776633 245688899999 68888888886654433
No 183
>COG3695 Predicted methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]
Probab=27.66 E-value=1.5e+02 Score=19.64 Aligned_cols=36 Identities=11% Similarity=0.222 Sum_probs=28.9
Q ss_pred HHHHHHHHHhcCCCCCchHHHHHHHcC-CCCHHHHHH
Q 034697 21 NKQFETALAFYDKDTPDRWDNVAKAVS-GKTVEDVKK 56 (86)
Q Consensus 21 dk~Le~al~~~~~~~~~rW~~IA~~vp-gRT~~qc~~ 56 (86)
-+.+...+...|.|.-.-...||+.+| ++.+.||=.
T Consensus 8 ~~~v~~vv~~IP~GkV~TYGdIA~laG~p~~ARqVG~ 44 (103)
T COG3695 8 TQRVLDVVAAIPEGKVSTYGDIAKLAGLPRAARQVGR 44 (103)
T ss_pred HHHHHHHHHhCCCCceeeHHHHHHHhCCChhHHHHHH
Confidence 346667788899998888999999998 477888754
No 184
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=27.42 E-value=2.2e+02 Score=21.09 Aligned_cols=44 Identities=16% Similarity=0.121 Sum_probs=32.8
Q ss_pred HHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 23 QFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 23 ~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
.|..+|.+.|.. .+-.-..||+.+ |.|..-|+.|...-+..++.
T Consensus 146 ~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~l-gis~~tVk~~l~RAr~~Lr~ 199 (339)
T PRK08241 146 AFVAALQHLPPRQRAVLILRDVLGWSAAEVAELL-DTSVAAVNSALQRARATLAE 199 (339)
T ss_pred HHHHHHHhCCHHHhhhhhhHHhhCCCHHHHHHHh-CCCHHHHHHHHHHHHHHHhh
Confidence 466777776632 245678999999 69999999988777776665
No 185
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=27.42 E-value=2.2e+02 Score=20.88 Aligned_cols=31 Identities=13% Similarity=0.291 Sum_probs=25.7
Q ss_pred CchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 36 PDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 36 ~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
+-.-..||+.+ |.|...|+.+.......++.
T Consensus 124 g~s~~EIA~~l-g~s~~tVr~~l~RAr~~Lr~ 154 (281)
T TIGR02957 124 DYPYEEIASIV-GKSEANCRQLVSRARRHLDA 154 (281)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHh
Confidence 34678999999 59999999998887777765
No 186
>KOG4031 consensus Vesicle coat protein clathrin, light chain [Intracellular trafficking, secretion, and vesicular transport]
Probab=26.95 E-value=1.9e+02 Score=21.63 Aligned_cols=46 Identities=15% Similarity=0.283 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHhcCCCCCchHHHHHHHcC--CCCHHHHHH--HHHHHHHHHh
Q 034697 19 KQNKQFETALAFYDKDTPDRWDNVAKAVS--GKTVEDVKK--HYELLVKDIN 66 (86)
Q Consensus 19 eEdk~Le~al~~~~~~~~~rW~~IA~~vp--gRT~~qc~~--ry~~L~~dv~ 66 (86)
.|+..|+.-...+..+ .-|++|++.+- -++-++|+. |.+.|+-.++
T Consensus 161 ~eee~~~~e~~~~~~g--TeWErv~kL~D~n~k~sk~gkD~SRlrslL~~LK 210 (216)
T KOG4031|consen 161 AEEEALVKENEEFSPG--TEWERVAKLCDFNPKSSKQGKDVSRLRSLLISLK 210 (216)
T ss_pred HHHHHHHHhhcccCCC--chHHHHHHHHcCCccchhccccHHHHHHHHHHhh
Confidence 3444444444444444 68999999995 377778764 5666655544
No 187
>cd08780 Death_TRADD Death Domain of Tumor Necrosis Factor Receptor 1-Associated Death Domain protein. Death domain (DD) of TRADD (TNF Receptor 1-Associated Death Domain or TNFRSF1A-associated via death domain) protein. TRADD is a central signaling adaptor for TNF-receptor 1 (TNFR1), mediating activation of Nuclear Factor -kappaB (NF-kB) and c-Jun N-terminal kinase (JNK), as well as caspase-dependent apoptosis. It also carries important immunological roles including germinal center formation, DR3-mediated T-cell stimulation, and TNFalpha-mediated inflammatory responses. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into s
Probab=26.62 E-value=1.1e+02 Score=19.94 Aligned_cols=24 Identities=17% Similarity=0.529 Sum_probs=17.6
Q ss_pred CHHHHHHHHHHHHhcCCCCCchHHHHHHHcC
Q 034697 17 TVKQNKQFETALAFYDKDTPDRWDNVAKAVS 47 (86)
Q Consensus 17 T~eEdk~Le~al~~~~~~~~~rW~~IA~~vp 47 (86)
|+++.+.|.+-|-+ .|.++|..++
T Consensus 1 ~~~~~q~~~~nvGr-------~WK~laR~Lg 24 (90)
T cd08780 1 TPADQQHFAKSVGK-------KWKPVGRSLQ 24 (90)
T ss_pred CHHHHHHHHHHHhH-------HHHHHHHHHc
Confidence 45666666666544 7999999995
No 188
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=26.30 E-value=2e+02 Score=18.92 Aligned_cols=43 Identities=19% Similarity=0.225 Sum_probs=29.8
Q ss_pred HHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697 23 QFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIN 66 (86)
Q Consensus 23 ~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~ 66 (86)
.|..+|...|+. .+...+.||+.+ |.|...|+.+.....+.++
T Consensus 119 ~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~l-~is~~~V~~~l~ra~~~l~ 171 (176)
T PRK09638 119 EMLDALSKLDPEFRAPVILKHYYGYTYEEIAKML-NIPEGTVKSRVHHGIKQLR 171 (176)
T ss_pred HHHHHHHcCCHHHhheeeehhhcCCCHHHHHHHH-CCChhHHHHHHHHHHHHHH
Confidence 455566665522 356789999999 6899989888766555554
No 189
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=26.21 E-value=2.3e+02 Score=19.81 Aligned_cols=43 Identities=14% Similarity=0.200 Sum_probs=29.1
Q ss_pred HHHHHHHhcCCC--------------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697 23 QFETALAFYDKD--------------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIN 66 (86)
Q Consensus 23 ~Le~al~~~~~~--------------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~ 66 (86)
.|..+|.+.|.. .+-....||+.+ |-|..-|+.+....+..++
T Consensus 171 ~l~~al~~Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~l-gis~~tVk~~~~rA~~~Lr 227 (234)
T PRK08301 171 LLKKALKKLSDREKQIMELRFGLNGGEEKTQKEVADML-GISQSYISRLEKRIIKRLK 227 (234)
T ss_pred HHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 566676666521 245688999999 6888888887665555554
No 190
>PF01086 Clathrin_lg_ch: Clathrin light chain; InterPro: IPR000996 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport []. Clathrin coats contain both clathrin (acts as a scaffold) and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [, ]. Clathrin is a trimer composed of three heavy chains and three light chains, each monomer projecting outwards like a leg; this three-legged structure is known as a triskelion [, ]. The heavy chains form the legs, their N-terminal beta-propeller regions extending outwards, while their C-terminal alpha-alpha-superhelical regions form the central hub of the triskelion. Peptide motifs can bind between the beta-propeller blades. The light chains appear to have a regulatory role, and may help orient the assembly and disassembly of clathrin coats as they interact with hsc70 uncoating ATPase []. Clathrin triskelia self-polymerise into a curved lattice by twisting individual legs together. The clathrin lattice forms around a vesicle as it buds from the TGN, plasma membrane or endosomes, acting to stabilise the vesicle and facilitate the budding process []. The multiple blades created when the triskelia polymerise are involved in multiple protein interactions, enabling the recruitment of different cargo adaptors and membrane attachment proteins []. This entry represents clathrin light chains, which are more divergent in sequence than the heavy chains []. In higher eukaryotes, two genes encode distinct but related light chains, each of which can yield two separate forms via alternative splicing. In yeast there is a single light chain whose sequence is only distantly related to that of higher eukaryotes. Clathrin light chains have a conserved acidic N-terminal domain, a central coiled-coil domain and a conserved C-terminal domain. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030130 clathrin coat of trans-Golgi network vesicle, 0030132 clathrin coat of coated pit; PDB: 3LVG_E 3LVH_D.
Probab=26.07 E-value=24 Score=25.81 Aligned_cols=48 Identities=13% Similarity=0.270 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHhcCCCCCchHHHHHHHcC--CCCHHHH--HHHHHHHHHHHhh
Q 034697 19 KQNKQFETALAFYDKDTPDRWDNVAKAVS--GKTVEDV--KKHYELLVKDIND 67 (86)
Q Consensus 19 eEdk~Le~al~~~~~~~~~rW~~IA~~vp--gRT~~qc--~~ry~~L~~dv~~ 67 (86)
++++.|+.....+.. .+.-|++|++.|- ++..+.- +.|++.|+-.++.
T Consensus 167 ~~ee~fl~~~~~~~~-~~t~WerV~~Lid~~~~~~~~~kD~sRmR~iLl~LK~ 218 (225)
T PF01086_consen 167 EEEEEFLAKREEFLQ-PGTEWERVAKLIDFNPKSSKSGKDVSRMREILLKLKG 218 (225)
T ss_dssp -----------------------------------------------------
T ss_pred HHHHHHHHcccccCC-CCCcHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhhh
Confidence 455556555555532 3567999999992 2222122 3577777766664
No 191
>PRK15372 pathogenicity island 2 effector protein SseI; Provisional
Probab=25.76 E-value=1.1e+02 Score=23.73 Aligned_cols=18 Identities=44% Similarity=0.553 Sum_probs=14.4
Q ss_pred CCCCHHHHHHHHHHHHHH
Q 034697 47 SGKTVEDVKKHYELLVKD 64 (86)
Q Consensus 47 pgRT~~qc~~ry~~L~~d 64 (86)
.|-|.++|+.+|.+|..-
T Consensus 31 ~gtTpe~I~s~Fe~Lr~L 48 (292)
T PRK15372 31 AGTTREDVVSRFELLRTL 48 (292)
T ss_pred CCCCHHHHHHHHHHHHHH
Confidence 368999999999988643
No 192
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=25.67 E-value=2.2e+02 Score=19.29 Aligned_cols=45 Identities=20% Similarity=0.168 Sum_probs=30.9
Q ss_pred HHHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 22 KQFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
..|.++|.+.|.. .+-..+.||+.+ |.|...|+.|.......++.
T Consensus 133 ~~l~~~l~~Lp~~~r~v~~l~~~eg~s~~EIA~~l-gis~~tVk~rl~ra~~~Lr~ 187 (194)
T PRK12531 133 EQVMKFLDRLPKAQRDVLQAVYLEELPHQQVAEMF-DIPLGTVKSRLRLAVEKLRH 187 (194)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHh-CcCHHHHHHHHHHHHHHHHH
Confidence 4466666665532 234678899999 68899999887776666653
No 193
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=25.62 E-value=2.4e+02 Score=19.68 Aligned_cols=44 Identities=14% Similarity=0.095 Sum_probs=30.1
Q ss_pred HHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 23 QFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 23 ~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
.|..+|.+.|.. .+-.-..||+.+ |.|..-|+.|....+..++.
T Consensus 141 ~l~~~L~~L~~~~r~v~~L~~~~g~s~~EIAe~l-gis~~tV~~~l~RAr~~Lr~ 194 (206)
T PRK12544 141 IFEACLDGLPAKYARVFMMREFIELETNEICHAV-DLSVSNLNVLLYRARLRLRE 194 (206)
T ss_pred HHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHHH
Confidence 466667766522 234568999999 68999998887765555554
No 194
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=25.58 E-value=2.1e+02 Score=21.90 Aligned_cols=52 Identities=17% Similarity=0.141 Sum_probs=39.1
Q ss_pred CCCCCHHHHHHHHHHHH--hcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 13 GSSWTVKQNKQFETALA--FYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 13 ~~~WT~eEdk~Le~al~--~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
...|+-.|...|+.-.. +|+.+ ..|.+.|..+ |.|.-||+--|++.+..-++
T Consensus 171 rPTf~g~qi~~le~~feqtkylaG--~~ra~lA~~l-gmteSqvkVWFQNRRTKWRK 224 (288)
T KOG0847|consen 171 RPTFTGHQIYQLERKFEQTKYLAG--ADRAQLAQEL-NMTESQVKVWFQNRRTKWRK 224 (288)
T ss_pred CCCccchhhhhhhhhhhhhhcccc--hhHHHhhccc-cccHHHHHHHHhcchhhhhh
Confidence 34599999888887644 45543 5799999888 79999999888776555544
No 195
>COG1223 Predicted ATPase (AAA+ superfamily) [General function prediction only]
Probab=25.17 E-value=2.7e+02 Score=22.15 Aligned_cols=40 Identities=13% Similarity=0.043 Sum_probs=33.6
Q ss_pred HHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHH
Q 034697 21 NKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYEL 60 (86)
Q Consensus 21 dk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~ 60 (86)
.++|+..+.+||..-..+-..+++.-.|-|..+++++..+
T Consensus 290 ~~ile~y~k~~Plpv~~~~~~~~~~t~g~SgRdikekvlK 329 (368)
T COG1223 290 LEILEYYAKKFPLPVDADLRYLAAKTKGMSGRDIKEKVLK 329 (368)
T ss_pred HHHHHHHHHhCCCccccCHHHHHHHhCCCCchhHHHHHHH
Confidence 4577788999987656679999999999999999998764
No 196
>PRK00575 tatA twin arginine translocase protein A; Provisional
Probab=25.02 E-value=1.6e+02 Score=19.11 Aligned_cols=41 Identities=12% Similarity=0.246 Sum_probs=30.9
Q ss_pred HHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 23 QFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 23 ~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
++.-+|.-|+ +.|--.+++.| ||+..+.|+--+.+.++...
T Consensus 12 Ilvi~LllFG---pkKLPel~r~l-Gk~ir~fK~a~~~~~~e~~~ 52 (92)
T PRK00575 12 LAVVVILLFG---AKKLPDAARSL-GKSLRIFKSEVKEMQSDNKA 52 (92)
T ss_pred HHHHHHHhcc---chHHHHHHHHH-HHHHHHHHHHHhhhhhcccc
Confidence 4455677775 45899999999 69999998877777666654
No 197
>PRK04654 sec-independent translocase; Provisional
Probab=24.98 E-value=1.2e+02 Score=22.51 Aligned_cols=38 Identities=18% Similarity=0.342 Sum_probs=26.1
Q ss_pred HHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHH
Q 034697 24 FETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDI 65 (86)
Q Consensus 24 Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv 65 (86)
+.-+|.-|+ +.|+=+|++.+ ||...+.|..+....+++
T Consensus 13 ~VVALlV~G---PerLPe~aRtl-Gk~irk~R~~~~~vk~El 50 (214)
T PRK04654 13 AVVALVVLG---PERLPKAARFA-GLWVRRARMQWDSVKQEL 50 (214)
T ss_pred HHHHHHhcC---chHHHHHHHHH-HHHHHHHHHHHHHHHHHH
Confidence 344566664 57999999999 688888776665544433
No 198
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=24.47 E-value=2.5e+02 Score=19.56 Aligned_cols=28 Identities=14% Similarity=0.232 Sum_probs=17.9
Q ss_pred hHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697 38 RWDNVAKAVSGKTVEDVKKHYELLVKDIN 66 (86)
Q Consensus 38 rW~~IA~~vpgRT~~qc~~ry~~L~~dv~ 66 (86)
.-..||..+ |.|..-|+.+.......++
T Consensus 193 s~~eIA~~l-gis~~tV~~~~~ra~~~Lr 220 (224)
T TIGR02479 193 NLKEIGEVL-GLTESRVSQIHSQALKKLR 220 (224)
T ss_pred CHHHHHHHh-CCCHHHHHHHHHHHHHHHH
Confidence 456667777 4666667777666555554
No 199
>cd08779 Death_PIDD Death Domain of p53-induced protein with a death domain. Death domain (DD) found in PIDD (p53-induced protein with a death domain) and similar proteins. PIDD is a component of the PIDDosome complex, which is an oligomeric caspase-activating complex involved in caspase-2 activation and plays a role in mediating stress-induced apoptosis. The PIDDosome complex is composed of three components, PIDD, RAIDD and caspase-2, which interact through their DDs and DD-like domains. The DD of PIDD interacts with the DD of RAIDD, which also contains a Caspase Activation and Recruitment Domain (CARD) that interacts with the caspase-2 CARD. Autoproteolysis of PIDD determines the downstream signaling event, between pro-survival NF-kB or pro-death caspase-2 activation. 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
Probab=24.30 E-value=1.4e+02 Score=18.38 Aligned_cols=22 Identities=9% Similarity=0.237 Sum_probs=14.8
Q ss_pred CchHHHHHHHcCCCCH---HHHHHHH
Q 034697 36 PDRWDNVAKAVSGKTV---EDVKKHY 58 (86)
Q Consensus 36 ~~rW~~IA~~vpgRT~---~qc~~ry 58 (86)
+..|..+|..+| =|. +.|+.+|
T Consensus 13 G~~Wk~lar~LG-lse~~Id~Ie~~~ 37 (86)
T cd08779 13 GLDWQAIGLHLG-LSYRELQRIKYNN 37 (86)
T ss_pred hHHHHHHHHHcC-CCHHHHHHHHHHC
Confidence 358999999995 333 3455555
No 200
>cd06257 DnaJ DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification.
Probab=24.23 E-value=1.3e+02 Score=15.98 Aligned_cols=20 Identities=25% Similarity=0.381 Sum_probs=15.2
Q ss_pred CCCCHHHHHHHHHHHHHHHh
Q 034697 47 SGKTVEDVKKHYELLVKDIN 66 (86)
Q Consensus 47 pgRT~~qc~~ry~~L~~dv~ 66 (86)
++-|.++++.+|+.|.....
T Consensus 10 ~~~~~~~ik~~y~~l~~~~H 29 (55)
T cd06257 10 PDASDEEIKKAYRKLALKYH 29 (55)
T ss_pred CCCCHHHHHHHHHHHHHHHC
Confidence 35788999999998866543
No 201
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=24.11 E-value=1.3e+02 Score=15.94 Aligned_cols=40 Identities=13% Similarity=0.125 Sum_probs=28.6
Q ss_pred HHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHH
Q 034697 21 NKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKD 64 (86)
Q Consensus 21 dk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~d 64 (86)
+..+..+|...|. -....||+.+ |-|..-+..+.+.|.+.
T Consensus 5 ~~~Il~~l~~~~~---~t~~ela~~~-~is~~tv~~~l~~L~~~ 44 (48)
T PF13412_consen 5 QRKILNYLRENPR---ITQKELAEKL-GISRSTVNRYLKKLEEK 44 (48)
T ss_dssp HHHHHHHHHHCTT---S-HHHHHHHH-TS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHcCC---CCHHHHHHHh-CCCHHHHHHHHHHHHHC
Confidence 3455566777553 4689999999 69999999988887653
No 202
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=23.88 E-value=2.3e+02 Score=18.92 Aligned_cols=44 Identities=11% Similarity=0.110 Sum_probs=28.8
Q ss_pred HHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 23 QFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 23 ~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
.|..+|.+.|.. .+-.-+.||+.+ |-|...|+.|.......++.
T Consensus 120 ~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~l-~is~~tv~~~l~Ra~~~Lr~ 173 (179)
T PRK09415 120 RLASAVMSLPIKYREVIYLFYYEELSIKEIAEVT-GVNENTVKTRLKKAKELLKK 173 (179)
T ss_pred HHHHHHHhCCHHHhhHhHhHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence 456666665522 234567888888 57888888887766666654
No 203
>PF14552 Tautomerase_2: Tautomerase enzyme; PDB: 2AAG_C 2AAL_A 2AAJ_A 1MWW_C.
Probab=23.66 E-value=1.1e+02 Score=18.91 Aligned_cols=30 Identities=17% Similarity=0.336 Sum_probs=18.8
Q ss_pred hHHHHHHHcC-CCCHHHHHHHHHHHHHHHhh
Q 034697 38 RWDNVAKAVS-GKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 38 rW~~IA~~vp-gRT~~qc~~ry~~L~~dv~~ 67 (86)
++--|.=.+. |||.+|=+.-|+.|.+.+..
T Consensus 28 ~~v~I~It~~~gRs~e~K~~ly~~l~~~L~~ 58 (82)
T PF14552_consen 28 DFVIIQITSGAGRSTEQKKALYRALAERLAE 58 (82)
T ss_dssp T-EEEEEEECS---HHHHHHHHHHHHHHHHH
T ss_pred CEEEEEEEECCCCCHHHHHHHHHHHHHHHHH
Confidence 3434444444 89999999999999888864
No 204
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=23.52 E-value=3e+02 Score=20.41 Aligned_cols=45 Identities=20% Similarity=0.045 Sum_probs=32.5
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHH
Q 034697 14 SSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDI 65 (86)
Q Consensus 14 ~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv 65 (86)
..=|+.|.+.|+-...- ..-..||+.+ +-|..-|+.|-..+...+
T Consensus 142 ~~LS~RE~eVL~Lia~G------~SnkEIA~~L-~IS~~TVk~hvs~I~~KL 186 (217)
T PRK13719 142 NKVTKYQNDVFILYSFG------FSHEYIAQLL-NITVGSSKNKISEILKFF 186 (217)
T ss_pred CCCCHHHHHHHHHHHCC------CCHHHHHHHh-CCCHHHHHHHHHHHHHHh
Confidence 45688888877655433 3689999999 688888888776655443
No 205
>KOG1878 consensus Nuclear receptor coregulator SMRT/SMRTER, contains Myb-like domains [Transcription]
Probab=23.35 E-value=44 Score=31.46 Aligned_cols=27 Identities=22% Similarity=0.327 Sum_probs=23.5
Q ss_pred CchHHHHHHHcCCCCHHHHHHHHHHHH
Q 034697 36 PDRWDNVAKAVSGKTVEDVKKHYELLV 62 (86)
Q Consensus 36 ~~rW~~IA~~vpgRT~~qc~~ry~~L~ 62 (86)
.++|..|+..++.+|..||++.|.+..
T Consensus 373 ~R~~aai~p~vvt~tes~c~na~a~~~ 399 (1672)
T KOG1878|consen 373 GREWAAILPKVVTKTESQCKNAYAKYK 399 (1672)
T ss_pred hhhHHHhcCccceecccchhhHHHhhh
Confidence 579999999999999999998876543
No 206
>PRK14857 tatA twin arginine translocase protein A; Provisional
Probab=23.25 E-value=1.7e+02 Score=18.72 Aligned_cols=41 Identities=17% Similarity=0.404 Sum_probs=30.3
Q ss_pred HHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 23 QFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 23 ~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
++.-+|.-|+ +.|+-.+++.| ||...+.++-.....+++..
T Consensus 14 IlvVaLlvfG---P~KLP~lar~l-Gk~i~~fkk~~~~~~~e~~~ 54 (90)
T PRK14857 14 ILVIALLVFG---PKKLPEIGRSL-GKTLKGFQEASKEFENEIKR 54 (90)
T ss_pred HHHHHHHHcC---chHHHHHHHHH-HHHHHHHHHHHHHHHHHHHH
Confidence 3444667775 56999999999 68888888877766666654
No 207
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=23.23 E-value=2.3e+02 Score=18.76 Aligned_cols=43 Identities=9% Similarity=0.089 Sum_probs=26.9
Q ss_pred HHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697 23 QFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIN 66 (86)
Q Consensus 23 ~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~ 66 (86)
.|+.+|.+.+.. .+-.=+.||..+ |.|...|+.+.......++
T Consensus 93 ~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~l-gis~~tV~~~l~Rar~~Lr 145 (170)
T TIGR02959 93 CIPPMIKELPDEYREAIRLTELEGLSQQEIAEKL-GLSLSGAKSRVQRGRKKLK 145 (170)
T ss_pred HHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 466666666522 234567788888 5788888777655444444
No 208
>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY. This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.
Probab=23.02 E-value=3.3e+02 Score=20.77 Aligned_cols=47 Identities=15% Similarity=0.058 Sum_probs=36.1
Q ss_pred CCHHHHHHHHHHHHhcCC-CCCchHHHHHHHcCCCCHHHHHHHHHHHHH
Q 034697 16 WTVKQNKQFETALAFYDK-DTPDRWDNVAKAVSGKTVEDVKKHYELLVK 63 (86)
Q Consensus 16 WT~eEdk~Le~al~~~~~-~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~ 63 (86)
=|..|-+..++.|..... +.--.=..||+.+ |=|.--|++|.+.|..
T Consensus 177 LSySEleAv~~IL~~L~~~egrlse~eLAerl-GVSRs~ireAlrkLE~ 224 (251)
T TIGR02787 177 LSYSELEAVEHIFEELDGNEGLLVASKIADRV-GITRSVIVNALRKLES 224 (251)
T ss_pred ccHhHHHHHHHHHHHhccccccccHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 356678888888888765 2344578999999 6888899999998854
No 209
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=22.98 E-value=2.6e+02 Score=19.12 Aligned_cols=30 Identities=10% Similarity=0.108 Sum_probs=22.4
Q ss_pred CchHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697 36 PDRWDNVAKAVSGKTVEDVKKHYELLVKDIN 66 (86)
Q Consensus 36 ~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~ 66 (86)
+-.++.||+.+ |-|..-|+.++......++
T Consensus 151 Gls~~EIA~~l-giS~~tV~r~l~~aR~~l~ 180 (185)
T PF07638_consen 151 GLSVEEIAERL-GISERTVRRRLRRARAWLR 180 (185)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHHHHHH
Confidence 34688888888 6888888888877665554
No 210
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=22.80 E-value=2.4e+02 Score=18.79 Aligned_cols=44 Identities=9% Similarity=0.217 Sum_probs=33.8
Q ss_pred HHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 19 KQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 19 eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
+||..|...+.+. .++-..|++.+ |-|=-=+|.|...++..+..
T Consensus 36 ~E~~~Fi~~Fi~~----rGnlKe~e~~l-giSYPTvR~rLd~ii~~lg~ 79 (113)
T PF09862_consen 36 PEQLEFIKLFIKN----RGNLKEMEKEL-GISYPTVRNRLDKIIEKLGY 79 (113)
T ss_pred HHHHHHHHHHHHh----cCCHHHHHHHH-CCCcHHHHHHHHHHHHHhCC
Confidence 4556666665553 34799999999 68988999999998888775
No 211
>PF08285 DPM3: Dolichol-phosphate mannosyltransferase subunit 3 (DPM3); InterPro: IPR013174 This family corresponds to subunit 3 of dolichol-phosphate mannosyltransferase, an enzyme which generates mannosyl donors for glycosylphosphatidylinositols, N-glycan and protein O- and C-mannosylation. DPM3 is an integral membrane protein and plays a role in stabilising the dolichol-phosphate mannosyl transferase complex [].
Probab=22.77 E-value=40 Score=21.59 Aligned_cols=22 Identities=27% Similarity=0.342 Sum_probs=19.0
Q ss_pred CCHHHHHHHHHHHHHHHhhhhc
Q 034697 49 KTVEDVKKHYELLVKDINDIEA 70 (86)
Q Consensus 49 RT~~qc~~ry~~L~~dv~~ie~ 70 (86)
-|-++|-+.|++|.++|+..+.
T Consensus 61 ~tFnDcpeA~~eL~~eI~eAK~ 82 (91)
T PF08285_consen 61 ATFNDCPEAAKELQKEIKEAKA 82 (91)
T ss_pred hccCCCHHHHHHHHHHHHHHHH
Confidence 6888999999999999987654
No 212
>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=22.68 E-value=1.7e+02 Score=17.22 Aligned_cols=17 Identities=18% Similarity=0.390 Sum_probs=12.7
Q ss_pred CchHHHHHHHcCCCCHHH
Q 034697 36 PDRWDNVAKAVSGKTVED 53 (86)
Q Consensus 36 ~~rW~~IA~~vpgRT~~q 53 (86)
+..|..+|..+| -+..+
T Consensus 17 g~~W~~la~~Lg-~~~~~ 33 (88)
T smart00005 17 GLDWRELARKLG-LSEAD 33 (88)
T ss_pred chHHHHHHHHcC-CCHHH
Confidence 468999999996 44444
No 213
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=22.44 E-value=2.8e+02 Score=19.30 Aligned_cols=44 Identities=11% Similarity=0.216 Sum_probs=26.2
Q ss_pred HHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 23 QFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 23 ~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
.|..+|.+.+.. .+-.-..||+.+ |.|..-|+.+.......++.
T Consensus 131 ~l~~~L~~L~~~~r~v~~L~~~~g~s~~EIA~~L-gis~~tV~~~l~RArk~Lr~ 184 (203)
T PRK09647 131 DLQAALDSLPPEFRAAVVLCDIEGLSYEEIAATL-GVKLGTVRSRIHRGRQQLRA 184 (203)
T ss_pred HHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence 455566665422 234556777777 57777777776655555543
No 214
>PF11740 KfrA_N: Plasmid replication region DNA-binding N-term; InterPro: IPR021104 The KfrA family of protiens are encoded on plasmids, generally in or near gene clusters invloved in stable inheritance functions. These proteins are thought to form an all-helical structure, consisting of an N-terminal helix-turn-helix DNA binding domain and an extended coiled-coil tail. The best-characterised KfrA protein, encoded on the broad host-range Plasmid RK2, is a site-specific DNA-binding protein whose operator overlaps its own promoter. The DNA-binding domain is essential for function, while the coiled-coil domain is probably responsible for formation of multimers, and may provide an example of a bridge to host structures required for plasmid partitioning []. This entry represents the N-terminal DNA-binding domain.
Probab=22.39 E-value=2.1e+02 Score=17.94 Aligned_cols=54 Identities=13% Similarity=0.150 Sum_probs=35.5
Q ss_pred HHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhhhh-cCCCCCCC
Q 034697 24 FETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDINDIE-AGRYPHPN 77 (86)
Q Consensus 24 Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ie-~g~v~~P~ 77 (86)
+.-+-..+..|.......|-+.+|+=|..-|..+++.......... ....++|.
T Consensus 7 ~~Aa~~L~~~G~~pT~~~Vr~~lG~GS~~ti~~~l~~w~~~~~~~~~~~~~~lP~ 61 (120)
T PF11740_consen 7 IEAADELLAAGKKPTVRAVRERLGGGSMSTISKHLKEWREEREAQVSEAAPDLPE 61 (120)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHhhhccccccccCCCh
Confidence 3333333444555689999999998888899988888777665433 22344553
No 215
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=22.37 E-value=2.7e+02 Score=19.09 Aligned_cols=44 Identities=18% Similarity=0.265 Sum_probs=30.9
Q ss_pred HHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697 23 QFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 23 ~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
.|..+|.+.|.. .+.....||..+ |-|...|+.|.......++.
T Consensus 106 ~l~~~L~~Lp~~~r~v~~L~~~~g~s~~EIA~~L-giS~~tVk~~l~Rar~~Lr~ 159 (188)
T PRK12546 106 DFRAAFAQLPDEQREALILVGASGFSYEEAAEMC-GVAVGTVKSRANRARARLAE 159 (188)
T ss_pred HHHHHHHhCCHHHhHHhhhHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence 466676666532 345789999999 69999999887665555543
No 216
>PF02416 MttA_Hcf106: mttA/Hcf106 family; InterPro: IPR003369 Members of this protein family are involved in a sec-independent translocation mechanism. This pathway has been called the DeltapH pathway in chloroplasts []. Members of this family in Escherichia coli are involved in export of redox proteins with a "twin arginine" leader motif (S/T-R-R-X-F-L-K) []. This sec-independent pathway is termed TAT for twin-arginine translocation system. This system mainly transports proteins with bound cofactors that require folding prior to export.; GO: 0008565 protein transporter activity, 0015031 protein transport; PDB: 2L16_A.
Probab=22.36 E-value=1.5e+02 Score=16.82 Aligned_cols=39 Identities=23% Similarity=0.498 Sum_probs=25.4
Q ss_pred HHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697 24 FETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDIN 66 (86)
Q Consensus 24 Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~ 66 (86)
+.-+|.-|+ +.|.-.+|+.+ |++..+.++......++.+
T Consensus 10 ~vvalllfG---p~kLP~~~r~l-G~~ir~fk~~~~~~~~~~~ 48 (53)
T PF02416_consen 10 LVVALLLFG---PKKLPELARSL-GKAIREFKKAINEAKEEIE 48 (53)
T ss_dssp HHHHHHHS----TTTHHHHHHHH-HHHHHHHHHHHHHHHH---
T ss_pred HHHHHHHhC---chHHHHHHHHH-HHHHHHHHHHHHhhhhhhh
Confidence 344566675 46899999999 5887777776666655533
No 217
>cd07018 S49_SppA_67K_type Signal peptide peptidase A (SppA) 67K type, a serine protease, has catalytic Ser-Lys dyad. Signal peptide peptidase A (SppA; Peptidase S49; Protease IV) 67K type: SppA is found in all three domains of life and is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. Members in this subfamily contain an amino-terminal domain in addition to the carboxyl-terminal protease domain that is conserved in all the S49 family members (sometimes referred to as 67K type), similar to E. coli and Arabidopsis thaliana SppA peptidases. Unlike the eukaryotic functional homologs that are proposed to be aspartic proteases, site-directed mutagenesis and sequence analysis have shown that members in this subfamily, mostly bacterial, are serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain. Mutagenesis studies also suggest that the catalytic center comprises a Ser-Lys
Probab=22.23 E-value=2.5e+02 Score=19.87 Aligned_cols=57 Identities=14% Similarity=0.063 Sum_probs=39.1
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHH-HHHHHHhhhhcCCCC
Q 034697 14 SSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYE-LLVKDINDIEAGRYP 74 (86)
Q Consensus 14 ~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~-~L~~dv~~ie~g~v~ 74 (86)
..+|+++.+.++..|...- ......||+.- +.+.++++..+. .........+.|.|+
T Consensus 151 ~~~s~~~r~~~~~~l~~~~---~~f~~~Va~~R-~~~~~~~~~~~~~~~~~~~~A~~~GLvD 208 (222)
T cd07018 151 DDMSPEAREQTQALLDSLW---DQYLADVAASR-GLSPDALEALIDLGGDSAEEALEAGLVD 208 (222)
T ss_pred ccCCHHHHHHHHHHHHHHH---HHHHHHHHHHc-CCCHHHHHHHHHcCCcHHHHHHHCCCCC
Confidence 4689999999988887753 24677777776 478888877663 334444455667766
No 218
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=22.21 E-value=3.3e+02 Score=20.08 Aligned_cols=45 Identities=9% Similarity=0.164 Sum_probs=32.5
Q ss_pred CCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697 15 SWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDIN 66 (86)
Q Consensus 15 ~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~ 66 (86)
.-|+.|-+.|.-... +.....||+.+ +.|..-|+.+-..+...+.
T Consensus 133 ~LSpRErEVLrLLAq------GkTnKEIAe~L-~IS~rTVkth~srImkKLg 177 (198)
T PRK15201 133 HFSVTERHLLKLIAS------GYHLSETAALL-SLSEEQTKSLRRSIMRKLH 177 (198)
T ss_pred CCCHHHHHHHHHHHC------CCCHHHHHHHh-CCCHHHHHHHHHHHHHHhC
Confidence 357777776665433 24689999999 6888888888777665544
No 219
>KOG3493 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=22.19 E-value=1e+02 Score=19.15 Aligned_cols=28 Identities=21% Similarity=0.181 Sum_probs=23.2
Q ss_pred chHHHHHHHcCCCCHHHHHHHHHHHHHH
Q 034697 37 DRWDNVAKAVSGKTVEDVKKHYELLVKD 64 (86)
Q Consensus 37 ~rW~~IA~~vpgRT~~qc~~ry~~L~~d 64 (86)
+.=.-||++.|++-.+-|.++|..++.|
T Consensus 26 D~KKliaaQtGT~~~kivl~k~~~i~kd 53 (73)
T KOG3493|consen 26 DLKKLIAAQTGTRPEKIVLKKWYTIFKD 53 (73)
T ss_pred CHHHHHHHhhCCChhHhHHHhhhhhhhc
Confidence 4456789999999999999999887766
No 220
>PF01035 DNA_binding_1: 6-O-methylguanine DNA methyltransferase, DNA binding domain; InterPro: IPR014048 Synonym(s): 6-O-methylguanine-DNA methyltransferase, O-6-methylguanine-DNA-alkyltransferase This entry represents the DNA binding region of 6-O-methylguanine-DNA methyltransferases. The repair of DNA containing O6-alkylated guanine is carried out by DNA-[protein]-cysteine S-methyltransferase (2.1.1.63 from EC). The major mutagenic and carcinogenic effect of methylating agents in DNA is the formation of O6-alkylguanine. The alkyl group at the O-6 position is transferred to a cysteine residue in the enzyme []. This is a suicide reaction since the enzyme is irreversibly inactivated and the methylated protein accumulates as a dead-end product. Most, but not all of the methyltransferases are also able to repair O-4-methylthymine. DNA-[protein]-cysteine S-methyltransferases are widely distributed and are found in various prokaryotic and eukaryotic sources [].; GO: 0003824 catalytic activity, 0006281 DNA repair; PDB: 1SFE_A 1T39_B 1T38_A 1EH7_A 1EH6_A 1YFH_C 1EH8_A 1QNT_A 2KIM_A 2KIF_A ....
Probab=22.14 E-value=2e+02 Score=17.59 Aligned_cols=36 Identities=11% Similarity=0.150 Sum_probs=25.5
Q ss_pred HHHHHHHHHhcCCCCCchHHHHHHHcCC-CCHHHHHH
Q 034697 21 NKQFETALAFYDKDTPDRWDNVAKAVSG-KTVEDVKK 56 (86)
Q Consensus 21 dk~Le~al~~~~~~~~~rW~~IA~~vpg-RT~~qc~~ 56 (86)
+..+.++|.+.|.|.--....||+.++. +.+.+|-.
T Consensus 4 ~~~V~~~v~~IP~G~v~TYg~iA~~~g~p~~ar~Vg~ 40 (85)
T PF01035_consen 4 QRRVWEAVRQIPYGKVTTYGEIARLLGRPKAARAVGS 40 (85)
T ss_dssp HHHHHHHHTTS-TT-BEEHHHHHHHTT-TTCHHHHHH
T ss_pred HHHHHHHHHcCCCCceEeHHHHHHHHhhcccHHHHHH
Confidence 4456667888999888899999999972 66666654
No 221
>PF13725 tRNA_bind_2: Possible tRNA binding domain; PDB: 2ZPA_B.
Probab=21.93 E-value=91 Score=19.20 Aligned_cols=24 Identities=21% Similarity=0.223 Sum_probs=11.7
Q ss_pred HHHHHHHHHHHhcCCCCCchHHHHHHHcC
Q 034697 19 KQNKQFETALAFYDKDTPDRWDNVAKAVS 47 (86)
Q Consensus 19 eEdk~Le~al~~~~~~~~~rW~~IA~~vp 47 (86)
.+..+|...+.+. ..|+.||+.++
T Consensus 71 ~q~~lLi~k~LQ~-----ksw~~~a~~l~ 94 (101)
T PF13725_consen 71 LQQALLIAKGLQG-----KSWEEVAKELG 94 (101)
T ss_dssp S--HHHHHHHCS--------HHHHHHHCT
T ss_pred HHHHHHHHHHHCC-----CCHHHHHHHcC
Confidence 3444555444442 36888888775
No 222
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=21.36 E-value=2.8e+02 Score=18.88 Aligned_cols=44 Identities=9% Similarity=0.044 Sum_probs=28.4
Q ss_pred HHHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697 22 KQFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIN 66 (86)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~ 66 (86)
..|..+|...|.. .+-.-..||+.+ |-|..-|+.|....+..++
T Consensus 120 ~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~l-gis~~tV~~~l~Rar~~Lr 173 (188)
T PRK12517 120 EWLRRQIAKLDPEYREPLLLQVIGGFSGEEIAEIL-DLNKNTVMTRLFRARNQLK 173 (188)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 3577777777632 234567788888 5777778777655444444
No 223
>PF13748 ABC_membrane_3: ABC transporter transmembrane region
Probab=21.29 E-value=1e+02 Score=23.15 Aligned_cols=28 Identities=14% Similarity=0.423 Sum_probs=25.1
Q ss_pred CchHHHHHHHcCCCCHHHHHHHHHHHHH
Q 034697 36 PDRWDNVAKAVSGKTVEDVKKHYELLVK 63 (86)
Q Consensus 36 ~~rW~~IA~~vpgRT~~qc~~ry~~L~~ 63 (86)
++|+|+=...+.+++..++++||..|..
T Consensus 170 NnrlE~eV~~i~~~~~~~l~rHy~~L~~ 197 (237)
T PF13748_consen 170 NNRLEKEVDIIERRKPASLRRHYRRLSR 197 (237)
T ss_pred hHHHHHHccHhhcCChHHHHHHHHHHHh
Confidence 6799999999999999999999998654
No 224
>KOG4051 consensus Uncharacterized conserved protein [Function unknown]
Probab=21.23 E-value=1.3e+02 Score=22.35 Aligned_cols=36 Identities=8% Similarity=0.171 Sum_probs=26.0
Q ss_pred CCCCCCHHHHHHHHHHHHhc-CCCCCchH------HHHHHHcC
Q 034697 12 SGSSWTVKQNKQFETALAFY-DKDTPDRW------DNVAKAVS 47 (86)
Q Consensus 12 ~~~~WT~eEdk~Le~al~~~-~~~~~~rW------~~IA~~vp 47 (86)
....|++.|+-.|..|+.-+ |.|.+..+ .++.+-++
T Consensus 31 ~~~~Ws~~eE~~L~~ai~g~kPvGiNkhF~mi~I~~~~~k~~~ 73 (214)
T KOG4051|consen 31 EQDFWSPLEELGLLHAICGLKPVGINKHFHMIGIMNEKSKTIP 73 (214)
T ss_pred ccccccHHHHHHHHHHHHccCCCCcccchhhhhhHHHHhhccc
Confidence 45679999999999999988 44544444 44566665
No 225
>COG5622 Protein required for attachment to host cells [Cell motility and secretion]
Probab=20.81 E-value=71 Score=22.30 Aligned_cols=57 Identities=18% Similarity=0.229 Sum_probs=36.6
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHh----cCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697 8 SSRSSGSSWTVKQNKQFETALAF----YDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDIN 66 (86)
Q Consensus 8 ~~~~~~~~WT~eEdk~Le~al~~----~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~ 66 (86)
+++++...|+.+|+..|-..+.. +-.+ .+.+.+-=.-+-||.=++|++|.+-+.++.
T Consensus 56 ~s~~~~pd~~~e~~~~fa~~~a~~l~r~v~~--g~~~~LvIiAaPrtLG~lRK~lh~~lk~~~ 116 (139)
T COG5622 56 SSSSSNPDSSREEEDSFAAEIAKELNRSVHG--GKFKNLVIIAAPRTLGELRKELHKGLKEKL 116 (139)
T ss_pred hhccCCCccccccchhHHHHHHHHHHHHHhh--cccceeEEEeCchhHHHHHHHHHHHHHHHH
Confidence 45566788999999988775433 2221 233333333356999999999976555443
No 226
>smart00441 FF Contains two conserved F residues. A novel motif that often accompanies WW domains. Often contains two conserved Phe (F) residues.
Probab=20.69 E-value=1.6e+02 Score=15.93 Aligned_cols=26 Identities=15% Similarity=0.279 Sum_probs=19.1
Q ss_pred HHHHHHHHhcCCC-CCchHHHHHHHcC
Q 034697 22 KQFETALAFYDKD-TPDRWDNVAKAVS 47 (86)
Q Consensus 22 k~Le~al~~~~~~-~~~rW~~IA~~vp 47 (86)
..|..+|..+... ...+|..+...+.
T Consensus 5 ~~F~~LL~e~~~~~~~~~W~~~~~~~~ 31 (55)
T smart00441 5 EAFKELLKEHEVITPDTTWSEARKKLK 31 (55)
T ss_pred HHHHHHHHhCCCCCCCCcHHHHHHHHh
Confidence 3577788887654 4678999988774
No 227
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=20.65 E-value=2.8e+02 Score=18.64 Aligned_cols=43 Identities=16% Similarity=0.278 Sum_probs=29.3
Q ss_pred HHHHHHHhcCCC----------CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697 23 QFETALAFYDKD----------TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIN 66 (86)
Q Consensus 23 ~Le~al~~~~~~----------~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~ 66 (86)
.|..+|...|.. .+.....||+.+ |-|..-|+.+.......++
T Consensus 132 ~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~Lr 184 (194)
T PRK12513 132 RLQAALETLPDEQREVFLLREHGDLELEEIAELT-GVPEETVKSRLRYALQKLR 184 (194)
T ss_pred HHHHHHHhCCHhHhhheeeehccCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 466677766522 346789999999 5898888887654444444
No 228
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=20.15 E-value=89 Score=20.23 Aligned_cols=24 Identities=17% Similarity=0.390 Sum_probs=12.9
Q ss_pred HHHHHHHHhcCCCCCchHHHHHHHcCC
Q 034697 22 KQFETALAFYDKDTPDRWDNVAKAVSG 48 (86)
Q Consensus 22 k~Le~al~~~~~~~~~rW~~IA~~vpg 48 (86)
.+|.+++.-|.. ..|..++..+||
T Consensus 95 diLKKa~~~~~~---~~~~~~~~~~~~ 118 (121)
T PRK09413 95 ELLKEAVEYGRA---KKWIAHAPLLPG 118 (121)
T ss_pred HHHHHHHHHhch---hhhhhcCCCCCC
Confidence 344445444432 357776666665
No 229
>KOG0817 consensus Acyl-CoA-binding protein [Lipid transport and metabolism]
Probab=20.02 E-value=3.1e+02 Score=18.94 Aligned_cols=33 Identities=21% Similarity=0.374 Sum_probs=26.1
Q ss_pred CCchHHHHHH-------HcCCCCHHHHHHHHHHHHHHHhh
Q 034697 35 TPDRWDNVAK-------AVSGKTVEDVKKHYELLVKDIND 67 (86)
Q Consensus 35 ~~~rW~~IA~-------~vpgRT~~qc~~ry~~L~~dv~~ 67 (86)
.|.-|..+++ .++|.|..++++.|..++..+..
T Consensus 47 kPg~~d~~~k~Kw~AW~~l~~~s~~eA~~~Yv~~~~~l~~ 86 (142)
T KOG0817|consen 47 KPGFFDEEGKAKWQAWNSLGGMSKEEAMEAYVEKVEELIP 86 (142)
T ss_pred CCchhhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHH
Confidence 4566777775 47899999999999988777664
Done!