Query 041937
Match_columns 88
No_of_seqs 105 out of 640
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 12:16:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041937.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041937hhsearch_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 1.3E-15 2.9E-20 87.3 6.1 45 14-61 2-47 (48)
2 smart00717 SANT SANT SWI3, AD 99.4 4.9E-13 1.1E-17 73.7 6.1 46 14-62 2-47 (49)
3 cd00167 SANT 'SWI3, ADA2, N-Co 99.4 2.1E-12 4.6E-17 70.3 6.0 44 15-61 1-44 (45)
4 PF13921 Myb_DNA-bind_6: Myb-l 99.2 3E-11 6.6E-16 71.3 5.3 41 16-60 1-41 (60)
5 PLN03212 Transcription repress 99.2 1.4E-10 3.1E-15 87.1 8.1 57 5-65 70-126 (249)
6 PLN03212 Transcription repress 99.1 1.6E-10 3.5E-15 86.8 5.6 52 11-65 23-76 (249)
7 PLN03091 hypothetical protein; 99.0 7.1E-10 1.5E-14 88.9 7.5 55 6-64 60-114 (459)
8 KOG0048 Transcription factor, 99.0 1.9E-09 4E-14 79.4 7.3 58 5-66 54-112 (238)
9 PLN03091 hypothetical protein; 98.9 1.5E-09 3.2E-14 87.1 4.7 47 11-60 12-59 (459)
10 KOG0048 Transcription factor, 98.8 1.6E-09 3.6E-14 79.7 2.6 52 12-66 8-61 (238)
11 KOG0457 Histone acetyltransfer 98.8 8.1E-09 1.7E-13 82.5 6.5 50 8-60 67-116 (438)
12 TIGR01557 myb_SHAQKYF myb-like 98.6 1.5E-07 3.3E-12 56.5 6.0 46 14-62 4-54 (57)
13 COG5259 RSC8 RSC chromatin rem 98.5 1.3E-07 2.9E-12 76.6 4.6 45 13-61 279-323 (531)
14 KOG0049 Transcription factor, 98.4 4.1E-07 8.8E-12 76.5 6.3 55 6-63 353-407 (939)
15 KOG1279 Chromatin remodeling f 98.3 1E-06 2.2E-11 71.8 5.4 47 11-61 251-297 (506)
16 KOG0724 Zuotin and related mol 98.2 2.9E-06 6.2E-11 64.5 5.6 68 14-81 32-104 (335)
17 COG5114 Histone acetyltransfer 98.2 5.2E-06 1.1E-10 65.3 6.2 49 11-62 61-109 (432)
18 KOG0049 Transcription factor, 97.8 5.1E-05 1.1E-09 64.3 6.6 61 6-69 246-307 (939)
19 PF13837 Myb_DNA-bind_4: Myb/S 97.8 7.1E-05 1.5E-09 46.4 5.5 58 14-71 2-73 (90)
20 KOG4167 Predicted DNA-binding 97.7 6.7E-05 1.4E-09 63.9 6.1 44 13-60 619-662 (907)
21 KOG0050 mRNA splicing protein 97.6 8.6E-05 1.9E-09 61.3 4.7 47 13-62 7-53 (617)
22 PF13873 Myb_DNA-bind_5: Myb/S 97.3 0.0011 2.3E-08 40.6 6.2 54 14-67 3-74 (78)
23 KOG0050 mRNA splicing protein 97.3 0.00027 5.8E-09 58.4 4.0 59 7-70 53-111 (617)
24 COG5147 REB1 Myb superfamily p 97.2 0.00057 1.2E-08 56.1 4.6 58 6-67 65-122 (512)
25 PF09111 SLIDE: SLIDE; InterP 97.1 0.0032 6.8E-08 42.7 6.8 57 10-66 46-114 (118)
26 KOG0051 RNA polymerase I termi 97.0 0.0014 2.9E-08 54.9 5.0 47 12-63 383-429 (607)
27 PF12776 Myb_DNA-bind_3: Myb/S 96.8 0.0042 9.1E-08 38.8 5.4 53 15-67 1-67 (96)
28 KOG0051 RNA polymerase I termi 96.4 0.0059 1.3E-07 51.1 4.8 53 11-63 434-508 (607)
29 COG5118 BDP1 Transcription ini 96.3 0.011 2.4E-07 47.7 5.8 44 13-60 365-408 (507)
30 TIGR02894 DNA_bind_RsfA transc 96.1 0.0085 1.8E-07 42.8 3.8 50 13-63 4-56 (161)
31 KOG1194 Predicted DNA-binding 96.0 0.022 4.8E-07 46.8 6.2 46 12-61 186-231 (534)
32 COG5147 REB1 Myb superfamily p 95.7 0.0068 1.5E-07 49.9 2.3 45 13-60 20-64 (512)
33 PF08914 Myb_DNA-bind_2: Rap1 95.5 0.04 8.7E-07 33.7 4.7 47 14-60 3-55 (65)
34 KOG4282 Transcription factor G 95.5 0.084 1.8E-06 40.4 7.3 60 13-72 54-123 (345)
35 PLN03142 Probable chromatin-re 95.4 0.039 8.4E-07 48.7 6.0 43 14-59 825-867 (1033)
36 KOG4468 Polycomb-group transcr 95.2 0.045 9.7E-07 46.4 5.5 55 13-71 88-152 (782)
37 PF11035 SnAPC_2_like: Small n 94.9 0.17 3.7E-06 39.9 7.5 54 13-66 21-74 (344)
38 smart00595 MADF subfamily of S 94.6 0.074 1.6E-06 32.8 4.1 26 37-63 28-53 (89)
39 PRK13923 putative spore coat p 94.3 0.11 2.4E-06 37.5 4.8 49 13-62 5-56 (170)
40 KOG4329 DNA-binding protein [G 94.0 0.14 2.9E-06 41.4 5.3 47 10-60 274-321 (445)
41 KOG3554 Histone deacetylase co 93.7 0.14 3.1E-06 42.6 5.1 66 12-81 284-362 (693)
42 PF13404 HTH_AsnC-type: AsnC-t 93.1 0.53 1.2E-05 26.1 5.4 37 21-61 5-41 (42)
43 KOG2656 DNA methyltransferase 92.8 0.078 1.7E-06 42.9 2.3 52 13-68 130-187 (445)
44 PF10545 MADF_DNA_bdg: Alcohol 92.3 0.28 6.1E-06 29.2 3.8 28 37-64 27-55 (85)
45 PF04504 DUF573: Protein of un 91.2 1.1 2.3E-05 29.2 5.9 62 13-74 4-78 (98)
46 PF13325 MCRS_N: N-terminal re 88.8 2.6 5.6E-05 31.0 6.9 54 10-64 70-128 (199)
47 PRK11179 DNA-binding transcrip 88.7 1.7 3.7E-05 29.6 5.6 41 19-63 9-49 (153)
48 PRK11169 leucine-responsive tr 87.4 1.6 3.4E-05 30.2 4.8 41 19-63 14-54 (164)
49 smart00426 TEA TEA domain. 86.7 1.6 3.4E-05 27.2 4.0 22 13-34 3-24 (68)
50 PLN03142 Probable chromatin-re 86.7 3.2 7E-05 37.1 7.3 52 12-66 925-988 (1033)
51 PF05263 DUF722: Protein of un 84.7 3.2 6.9E-05 28.6 5.2 47 17-67 83-129 (130)
52 PF11626 Rap1_C: TRF2-interact 83.3 1.4 2.9E-05 27.8 2.7 21 5-25 39-59 (87)
53 KOG3841 TEF-1 and related tran 82.7 6.1 0.00013 32.2 6.7 53 11-63 74-143 (455)
54 KOG2009 Transcription initiati 82.6 1.3 2.9E-05 37.3 3.1 47 10-60 406-452 (584)
55 PF06461 DUF1086: Domain of Un 82.4 5.9 0.00013 27.9 5.8 51 15-66 40-90 (145)
56 PF04545 Sigma70_r4: Sigma-70, 82.3 6.4 0.00014 21.7 6.3 44 17-66 6-49 (50)
57 PF07750 GcrA: GcrA cell cycle 82.1 2.4 5.1E-05 29.9 3.8 42 15-61 2-43 (162)
58 KOG1194 Predicted DNA-binding 79.8 1.3 2.8E-05 36.7 2.0 47 14-65 471-517 (534)
59 smart00344 HTH_ASNC helix_turn 79.1 9 0.0002 24.0 5.5 41 19-63 3-43 (108)
60 PF00046 Homeobox: Homeobox do 79.0 9 0.0002 21.4 6.4 49 13-62 4-52 (57)
61 COG1522 Lrp Transcriptional re 78.1 7.8 0.00017 25.6 5.2 40 20-63 9-48 (154)
62 PF00674 DUP: DUP family; Int 75.0 4.4 9.5E-05 26.4 3.2 43 21-63 44-100 (108)
63 PF13325 MCRS_N: N-terminal re 74.1 7.1 0.00015 28.7 4.4 43 15-62 1-46 (199)
64 cd00086 homeodomain Homeodomai 73.8 13 0.00028 20.5 6.8 49 13-62 4-52 (59)
65 PF01285 TEA: TEA/ATTS domain 71.5 6.9 0.00015 31.8 4.1 50 12-61 48-112 (431)
66 PF01466 Skp1: Skp1 family, di 70.2 5.5 0.00012 24.4 2.7 21 39-59 36-56 (78)
67 TIGR02937 sigma70-ECF RNA poly 69.8 23 0.0005 22.0 5.6 30 37-67 127-156 (158)
68 smart00389 HOX Homeodomain. DN 68.2 18 0.00038 19.8 6.0 46 14-60 5-50 (56)
69 smart00501 BRIGHT BRIGHT, ARID 67.8 17 0.00036 22.7 4.6 42 23-64 36-86 (93)
70 PRK11924 RNA polymerase sigma 66.0 28 0.00061 22.8 5.7 44 22-66 117-170 (179)
71 PF01388 ARID: ARID/BRIGHT DNA 62.8 14 0.00031 22.7 3.6 41 23-63 40-89 (92)
72 TIGR02950 SigM_subfam RNA poly 62.7 39 0.00085 21.8 6.1 44 22-66 97-150 (154)
73 COG5269 ZUO1 Ribosome-associat 62.6 15 0.00033 29.0 4.3 50 14-63 246-301 (379)
74 PF08281 Sigma70_r4_2: Sigma-7 62.4 24 0.00053 19.3 5.7 26 37-63 27-52 (54)
75 PF09197 Rap1-DNA-bind: Rap1, 60.6 47 0.001 22.1 5.9 45 16-60 2-73 (105)
76 COG4281 ACB Acyl-CoA-binding p 59.7 20 0.00044 23.1 3.8 31 37-68 54-84 (87)
77 PF11842 DUF3362: Domain of un 57.8 15 0.00032 26.1 3.2 28 18-47 40-67 (150)
78 PRK09648 RNA polymerase sigma 56.9 48 0.0011 22.5 5.7 45 22-67 131-185 (189)
79 PRK12541 RNA polymerase sigma 56.1 54 0.0012 21.6 5.7 48 21-69 103-160 (161)
80 PLN03162 golden-2 like transcr 55.9 37 0.0008 27.9 5.6 52 14-66 238-291 (526)
81 PRK09642 RNA polymerase sigma 54.5 58 0.0012 21.4 5.6 44 22-66 98-151 (160)
82 PRK09646 RNA polymerase sigma 53.9 46 0.001 22.9 5.3 49 18-67 130-188 (194)
83 PRK12522 RNA polymerase sigma 53.6 43 0.00094 22.4 5.0 50 16-66 105-164 (173)
84 PF07030 DUF1320: Protein of u 53.0 26 0.00056 23.4 3.7 27 51-77 84-110 (130)
85 TIGR02952 Sig70_famx2 RNA poly 52.8 60 0.0013 21.3 5.5 45 22-67 114-168 (170)
86 PF00887 ACBP: Acyl CoA bindin 49.5 18 0.00039 22.4 2.3 22 45-66 62-83 (87)
87 cd00435 ACBP Acyl CoA binding 49.3 28 0.0006 21.9 3.2 22 45-66 60-81 (85)
88 TIGR02985 Sig70_bacteroi1 RNA 48.9 69 0.0015 20.5 5.8 30 37-67 130-159 (161)
89 PRK12516 RNA polymerase sigma 47.7 72 0.0016 22.0 5.5 47 19-66 105-161 (187)
90 PRK09645 RNA polymerase sigma 47.4 76 0.0016 21.1 5.4 44 22-66 110-163 (173)
91 TIGR02939 RpoE_Sigma70 RNA pol 47.2 82 0.0018 21.1 5.6 44 22-66 130-183 (190)
92 PRK09641 RNA polymerase sigma 47.1 84 0.0018 21.0 5.7 43 23-66 129-181 (187)
93 PRK09643 RNA polymerase sigma 47.0 79 0.0017 21.7 5.6 45 21-66 125-179 (192)
94 KOG2941 Beta-1,4-mannosyltrans 46.6 9.5 0.00021 31.1 0.9 50 12-63 260-313 (444)
95 cd08307 Death_Pelle Death doma 46.4 22 0.00048 23.2 2.5 19 37-55 22-40 (97)
96 PRK12524 RNA polymerase sigma 46.2 79 0.0017 21.7 5.5 45 22-67 128-182 (196)
97 PTZ00458 acyl CoA binding prot 45.6 35 0.00076 21.9 3.3 22 45-66 62-83 (90)
98 PRK11922 RNA polymerase sigma 45.6 91 0.002 22.2 5.8 44 22-66 141-194 (231)
99 TIGR02954 Sig70_famx3 RNA poly 44.7 91 0.002 20.6 5.5 48 19-67 108-165 (169)
100 TIGR02943 Sig70_famx1 RNA poly 43.8 94 0.002 21.3 5.5 43 22-65 123-175 (188)
101 PRK09047 RNA polymerase factor 43.8 89 0.0019 20.3 5.3 44 22-66 98-151 (161)
102 PRK06759 RNA polymerase factor 43.6 89 0.0019 20.2 5.4 45 21-66 97-151 (154)
103 PRK12530 RNA polymerase sigma 42.1 1E+02 0.0023 21.0 5.6 43 23-66 127-179 (189)
104 TIGR02947 SigH_actino RNA poly 42.0 1E+02 0.0022 21.0 5.4 43 22-65 123-175 (193)
105 PRK09649 RNA polymerase sigma 41.7 1.1E+02 0.0024 20.8 5.6 48 19-67 119-176 (185)
106 PRK12534 RNA polymerase sigma 41.6 1E+02 0.0022 20.8 5.4 46 21-67 128-183 (187)
107 KOG0385 Chromatin remodeling c 41.6 73 0.0016 28.6 5.5 40 13-56 795-834 (971)
108 PF14775 NYD-SP28_assoc: Sperm 41.6 42 0.00091 19.9 3.0 27 38-64 2-34 (60)
109 TIGR02983 SigE-fam_strep RNA p 41.3 1E+02 0.0022 20.2 5.5 48 20-68 100-157 (162)
110 PF14164 YqzH: YqzH-like prote 39.7 24 0.00051 21.7 1.7 27 21-47 7-39 (64)
111 cd08777 Death_RIP1 Death Domai 39.7 95 0.0021 19.4 4.7 30 17-54 1-30 (86)
112 KOG0843 Transcription factor E 39.0 1.5E+02 0.0033 21.9 6.1 72 13-85 106-181 (197)
113 KOG1724 SCF ubiquitin ligase, 38.9 29 0.00063 24.6 2.3 40 20-59 97-140 (162)
114 TIGR03001 Sig-70_gmx1 RNA poly 38.1 1E+02 0.0023 22.5 5.3 41 22-63 153-203 (244)
115 PRK11923 algU RNA polymerase s 37.5 1.3E+02 0.0028 20.3 5.7 44 22-66 130-183 (193)
116 PRK09637 RNA polymerase sigma 37.4 1.3E+02 0.0029 20.5 5.5 44 22-66 98-151 (181)
117 PRK09652 RNA polymerase sigma 37.1 1.2E+02 0.0026 19.8 5.5 30 36-66 144-173 (182)
118 TIGR02948 SigW_bacill RNA poly 37.0 1.3E+02 0.0027 20.1 5.7 44 22-66 128-181 (187)
119 PF12451 VPS11_C: Vacuolar pro 36.7 36 0.00078 19.4 2.1 25 19-47 19-43 (49)
120 cd00580 CHMI 5-carboxymethyl-2 36.2 56 0.0012 21.0 3.2 23 45-67 67-89 (113)
121 PF09420 Nop16: Ribosome bioge 36.1 1.2E+02 0.0025 21.0 5.0 45 13-61 114-162 (164)
122 PRK12543 RNA polymerase sigma 36.1 1.4E+02 0.0029 20.1 5.4 44 21-65 108-161 (179)
123 KOG0488 Transcription factor B 35.9 1.1E+02 0.0023 23.8 5.2 50 12-63 175-225 (309)
124 PF04282 DUF438: Family of unk 35.2 30 0.00064 21.5 1.7 21 47-67 11-31 (71)
125 PRK12547 RNA polymerase sigma 35.0 1.4E+02 0.0029 19.8 5.4 46 21-67 103-158 (164)
126 PRK12527 RNA polymerase sigma 34.8 1.3E+02 0.0029 19.6 5.7 48 23-71 98-159 (159)
127 COG0193 Pth Peptidyl-tRNA hydr 34.6 87 0.0019 23.0 4.3 39 14-60 150-188 (190)
128 PF01726 LexA_DNA_bind: LexA D 34.5 1E+02 0.0022 18.3 4.8 47 16-63 4-52 (65)
129 PRK12514 RNA polymerase sigma 33.8 1.5E+02 0.0032 19.8 5.3 44 22-66 121-174 (179)
130 PRK12536 RNA polymerase sigma 33.8 1.5E+02 0.0032 20.0 5.4 46 21-67 120-175 (181)
131 PF08784 RPA_C: Replication pr 33.8 1.2E+02 0.0026 18.9 4.9 41 22-63 50-91 (102)
132 PRK12523 RNA polymerase sigma 33.7 1.5E+02 0.0032 19.8 5.6 43 22-65 111-163 (172)
133 PRK05602 RNA polymerase sigma 33.6 1.5E+02 0.0033 19.9 5.9 44 22-66 120-173 (186)
134 PRK09640 RNA polymerase sigma 33.3 1.6E+02 0.0034 20.0 6.4 52 15-67 119-180 (188)
135 PRK12542 RNA polymerase sigma 32.9 1.6E+02 0.0034 19.9 5.6 45 22-67 114-168 (185)
136 PRK02220 4-oxalocrotonate taut 32.4 84 0.0018 17.5 3.2 22 45-66 8-29 (61)
137 PF05524 PEP-utilisers_N: PEP- 32.2 32 0.0007 22.2 1.6 42 18-64 34-79 (123)
138 PRK12515 RNA polymerase sigma 31.2 1.7E+02 0.0037 19.8 5.5 44 22-66 123-176 (189)
139 COG5201 SKP1 SCF ubiquitin lig 31.2 50 0.0011 23.4 2.5 21 39-59 115-135 (158)
140 PRK12531 RNA polymerase sigma 31.2 1.7E+02 0.0038 19.9 5.4 44 22-66 133-186 (194)
141 PRK15411 rcsA colanic acid cap 30.8 1.8E+02 0.004 20.4 5.4 45 15-66 137-181 (207)
142 cd07216 Pat17_PNPLA8_PNPLA9_li 30.6 68 0.0015 24.1 3.3 26 41-66 54-81 (309)
143 PF00196 GerE: Bacterial regul 30.5 1E+02 0.0023 17.1 5.1 44 16-66 4-47 (58)
144 PRK12532 RNA polymerase sigma 29.9 1.8E+02 0.0039 19.7 5.5 42 23-65 129-180 (195)
145 PRK14857 tatA twin arginine tr 29.6 1.2E+02 0.0027 19.5 4.0 41 23-67 14-54 (90)
146 cd08318 Death_NMPP84 Death dom 29.2 1.5E+02 0.0031 18.4 4.7 30 17-54 6-35 (86)
147 TIGR02984 Sig-70_plancto1 RNA 29.0 1.8E+02 0.0038 19.3 5.4 44 23-67 133-186 (189)
148 PF02416 MttA_Hcf106: mttA/Hcf 28.9 1E+02 0.0023 17.6 3.2 38 24-65 10-47 (53)
149 PRK10430 DNA-binding transcrip 28.8 2.1E+02 0.0045 20.0 5.8 47 15-63 158-204 (239)
150 PRK06930 positive control sigm 28.5 1.9E+02 0.0041 20.2 5.1 50 16-66 100-159 (170)
151 PRK06811 RNA polymerase factor 28.2 2E+02 0.0042 19.6 5.4 45 21-66 122-176 (189)
152 PRK12540 RNA polymerase sigma 27.7 2E+02 0.0044 19.6 5.5 44 22-66 103-156 (182)
153 COG3053 CitC Citrate lyase syn 27.6 93 0.002 24.8 3.7 29 38-66 317-345 (352)
154 PRK09413 IS2 repressor TnpA; R 27.5 43 0.00094 21.9 1.6 24 22-48 95-118 (121)
155 PRK12537 RNA polymerase sigma 27.4 2E+02 0.0043 19.4 5.4 44 22-66 125-178 (182)
156 PRK12518 RNA polymerase sigma 27.4 1.9E+02 0.0041 19.1 5.6 44 22-66 112-165 (175)
157 KOG0721 Molecular chaperone (D 27.2 71 0.0015 24.2 2.8 20 47-66 109-128 (230)
158 PRK04654 sec-independent trans 27.0 1.1E+02 0.0025 22.8 3.9 39 23-65 12-50 (214)
159 PRK12511 RNA polymerase sigma 27.0 2.1E+02 0.0046 19.6 5.5 49 22-71 103-161 (182)
160 cd06257 DnaJ DnaJ domain or J- 26.9 1E+02 0.0022 16.4 2.9 20 47-66 10-29 (55)
161 KOG4031 Vesicle coat protein c 26.8 1.7E+02 0.0036 22.0 4.7 46 19-66 161-210 (216)
162 COG1497 Predicted transcriptio 26.3 1.9E+02 0.0042 22.3 5.1 39 22-64 14-52 (260)
163 PTZ00397 macrophage migration 26.3 1E+02 0.0022 19.7 3.2 21 46-66 66-86 (116)
164 PRK09651 RNA polymerase sigma 26.2 2.1E+02 0.0045 19.1 5.7 43 22-65 111-163 (172)
165 TIGR02960 SigX5 RNA polymerase 26.1 2.1E+02 0.0045 21.1 5.2 44 23-67 135-188 (324)
166 TIGR02859 spore_sigH RNA polym 26.0 2.1E+02 0.0046 19.2 6.1 43 23-66 142-194 (198)
167 KOG2251 Homeobox transcription 26.0 1.2E+02 0.0027 22.9 3.9 43 12-54 40-83 (228)
168 COG5158 SEC1 Proteins involved 26.0 56 0.0012 27.8 2.3 26 57-82 239-264 (582)
169 PRK12538 RNA polymerase sigma 25.8 2.6E+02 0.0056 20.1 5.7 43 23-66 164-216 (233)
170 COG4387 Mu-like prophage prote 25.7 94 0.002 21.7 3.0 36 40-75 70-107 (139)
171 PRK00575 tatA twin arginine tr 25.1 1.9E+02 0.004 18.9 4.2 41 23-67 12-52 (92)
172 PRK09635 sigI RNA polymerase s 25.1 2.8E+02 0.0061 20.8 5.8 46 22-68 110-165 (290)
173 PRK12519 RNA polymerase sigma 25.1 2.2E+02 0.0048 19.2 5.7 44 22-66 133-186 (194)
174 PF08259 Periviscerokin: Periv 25.1 33 0.00072 14.2 0.4 8 70-77 3-10 (11)
175 PRK12520 RNA polymerase sigma 24.8 2.3E+02 0.0049 19.2 5.5 43 22-65 123-175 (191)
176 PF13748 ABC_membrane_3: ABC t 24.7 87 0.0019 23.7 2.9 29 35-63 169-197 (237)
177 PF01086 Clathrin_lg_ch: Clath 24.1 27 0.00059 25.7 0.1 48 19-68 167-219 (225)
178 PRK13719 conjugal transfer tra 24.0 2.8E+02 0.0061 20.7 5.5 46 14-66 142-187 (217)
179 PRK09636 RNA polymerase sigma 24.0 2.8E+02 0.006 20.4 5.5 44 23-67 108-161 (293)
180 PF08424 NRDE-2: NRDE-2, neces 23.8 3.1E+02 0.0067 20.8 5.9 58 14-72 77-139 (321)
181 PRK12528 RNA polymerase sigma 23.7 2.2E+02 0.0047 18.6 5.4 44 22-66 105-158 (161)
182 PRK15201 fimbriae regulatory p 23.5 3.1E+02 0.0067 20.4 5.5 45 15-66 133-177 (198)
183 PRK12526 RNA polymerase sigma 23.2 2.6E+02 0.0057 19.3 5.6 45 22-67 145-199 (206)
184 PRK13919 putative RNA polymera 23.2 2.4E+02 0.0052 18.8 5.5 44 22-66 127-180 (186)
185 PRK12545 RNA polymerase sigma 23.1 2.6E+02 0.0057 19.3 5.5 42 23-65 132-183 (201)
186 PF02954 HTH_8: Bacterial regu 22.8 1.4E+02 0.003 15.9 4.6 33 20-57 6-38 (42)
187 PRK01371 sec-independent trans 22.7 1.4E+02 0.0031 20.7 3.5 40 23-66 12-51 (137)
188 KOG0384 Chromodomain-helicase 22.7 62 0.0013 30.2 2.1 55 13-70 1133-1199(1373)
189 PF14552 Tautomerase_2: Tautom 22.6 1.2E+02 0.0025 18.9 2.8 20 47-66 38-57 (82)
190 PF13496 DUF4120: Domain of un 22.3 92 0.002 20.4 2.3 24 39-62 11-34 (95)
191 PF01035 DNA_binding_1: 6-O-me 22.2 1.7E+02 0.0036 18.1 3.5 36 21-56 4-40 (85)
192 PRK14858 tatA twin arginine tr 22.0 2E+02 0.0043 19.2 4.0 39 23-65 12-50 (108)
193 PRK00846 hypothetical protein; 22.0 2.2E+02 0.0047 17.9 4.0 17 55-71 47-63 (77)
194 PRK07408 RNA polymerase sigma 22.0 3.2E+02 0.007 19.9 5.6 47 19-66 192-248 (256)
195 PRK07670 RNA polymerase sigma 21.6 3.2E+02 0.0069 19.7 5.4 43 23-66 194-246 (251)
196 PRK12546 RNA polymerase sigma 21.6 2.8E+02 0.0061 19.1 5.7 44 22-66 105-158 (188)
197 TIGR02989 Sig-70_gvs1 RNA poly 21.5 2.4E+02 0.0051 18.2 5.4 49 17-66 98-156 (159)
198 KOG1878 Nuclear receptor coreg 21.5 18 0.00039 34.0 -1.5 43 13-59 225-267 (1672)
199 PRK12533 RNA polymerase sigma 21.3 3.1E+02 0.0068 19.5 5.6 46 21-67 125-180 (216)
200 PF09127 Leuk-A4-hydro_C: Leuk 21.1 2.7E+02 0.0059 18.8 4.7 53 10-62 25-79 (143)
201 PRK12525 RNA polymerase sigma 20.9 2.6E+02 0.0057 18.5 5.3 42 22-64 110-161 (168)
202 PF08074 CHDCT2: CHDCT2 (NUC03 20.9 75 0.0016 23.1 1.9 55 14-71 4-75 (173)
203 PRK10360 DNA-binding transcrip 20.8 2.5E+02 0.0054 18.2 5.5 45 15-66 137-181 (196)
204 smart00271 DnaJ DnaJ molecular 20.6 1.6E+02 0.0035 16.0 2.9 18 48-65 12-29 (60)
205 cd08780 Death_TRADD Death Doma 20.5 1.8E+02 0.0038 19.0 3.4 24 17-47 1-24 (90)
206 TIGR00695 uxuA mannonate dehyd 20.4 1.9E+02 0.0041 23.4 4.2 51 12-66 36-93 (394)
207 PF11740 KfrA_N: Plasmid repli 20.2 2.4E+02 0.0052 17.8 6.1 44 33-76 16-60 (120)
208 PRK06288 RNA polymerase sigma 20.2 3.5E+02 0.0077 19.7 5.6 49 22-71 204-266 (268)
209 PF13174 TPR_6: Tetratricopept 20.0 1.2E+02 0.0025 14.1 2.0 13 21-33 20-32 (33)
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=1.3e-15 Score=87.29 Aligned_cols=45 Identities=31% Similarity=0.661 Sum_probs=41.0
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCChhHHHHHHHcC-CCCHHHHHHHHHHH
Q 041937 14 SSWTAKKNKLFENALAIYDKDTPDRWQIIAKIVG-GTSEEEVKRRYEML 61 (88)
Q Consensus 14 ~~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~vp-gRT~~qc~~ry~~L 61 (88)
..||.+|+.+|.+|+.+|+.+ +|..||..|| |||..||+.||+.+
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 589999999999999999876 8999999999 99999999999876
No 2
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.43 E-value=4.9e-13 Score=73.74 Aligned_cols=46 Identities=28% Similarity=0.649 Sum_probs=42.3
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHHHH
Q 041937 14 SSWTAKKNKLFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEMLV 62 (88)
Q Consensus 14 ~~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~L~ 62 (88)
..||.+|+.+|..++.+|+. .+|..||..||+||..+|+.||..+.
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 58999999999999999974 27999999999999999999999764
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=99.37 E-value=2.1e-12 Score=70.34 Aligned_cols=44 Identities=30% Similarity=0.664 Sum_probs=40.7
Q ss_pred CCCHHHHHHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHHH
Q 041937 15 SWTAKKNKLFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEML 61 (88)
Q Consensus 15 ~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~L 61 (88)
.||.+|++.|..++.+|+. .+|..||+.||+||..+|+.||..+
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 5999999999999999974 3799999999999999999999875
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=99.21 E-value=3e-11 Score=71.28 Aligned_cols=41 Identities=22% Similarity=0.604 Sum_probs=36.0
Q ss_pred CCHHHHHHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHH
Q 041937 16 WTAKKNKLFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEM 60 (88)
Q Consensus 16 WT~eE~k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~ 60 (88)
||.+|+.+|..++.+|+. +|..||++||.||..+|+.||..
T Consensus 1 WT~eEd~~L~~~~~~~g~----~W~~Ia~~l~~Rt~~~~~~r~~~ 41 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGN----DWKKIAEHLGNRTPKQCRNRWRN 41 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-----HHHHHHHSTTS-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHCc----CHHHHHHHHCcCCHHHHHHHHHH
Confidence 999999999999999964 69999999977999999999998
No 5
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.16 E-value=1.4e-10 Score=87.08 Aligned_cols=57 Identities=16% Similarity=0.336 Sum_probs=50.3
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHHHHHHH
Q 041937 5 GQRTSTISGSSWTAKKNKLFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEMLVDDI 65 (88)
Q Consensus 5 ~~~~~~~s~~~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv 65 (88)
-++.|.+...+||.||+.+|..++..|+. +|..||+.|||||..+|++||..++...
T Consensus 70 N~L~P~I~kgpWT~EED~lLlel~~~~Gn----KWs~IAk~LpGRTDnqIKNRWns~LrK~ 126 (249)
T PLN03212 70 NYLRPSVKRGGITSDEEDLILRLHRLLGN----RWSLIAGRIPGRTDNEIKNYWNTHLRKK 126 (249)
T ss_pred HhhchhcccCCCChHHHHHHHHHHHhccc----cHHHHHhhcCCCCHHHHHHHHHHHHhHH
Confidence 45678889999999999999999999864 7999999999999999999999766543
No 6
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.09 E-value=1.6e-10 Score=86.80 Aligned_cols=52 Identities=13% Similarity=0.321 Sum_probs=44.4
Q ss_pred CCCCCCCHHHHHHHHHHHHhcCCCCChhHHHHHHHc-CCCCHHHHHHHHHH-HHHHH
Q 041937 11 ISGSSWTAKKNKLFENALAIYDKDTPDRWQIIAKIV-GGTSEEEVKRRYEM-LVDDI 65 (88)
Q Consensus 11 ~s~~~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~v-pgRT~~qc~~ry~~-L~~dv 65 (88)
.....||.|||++|..++.+|+.. +|..||+.+ +|||.+||++||.. |...|
T Consensus 23 lKRg~WT~EEDe~L~~lV~kyG~~---nW~~IAk~~g~gRT~KQCReRW~N~L~P~I 76 (249)
T PLN03212 23 MKRGPWTVEEDEILVSFIKKEGEG---RWRSLPKRAGLLRCGKSCRLRWMNYLRPSV 76 (249)
T ss_pred CcCCCCCHHHHHHHHHHHHHhCcc---cHHHHHHhhhcCCCcchHHHHHHHhhchhc
Confidence 456789999999999999999754 899999998 59999999999986 43443
No 7
>PLN03091 hypothetical protein; Provisional
Probab=99.04 E-value=7.1e-10 Score=88.86 Aligned_cols=55 Identities=16% Similarity=0.376 Sum_probs=49.8
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHHHHHH
Q 041937 6 QRTSTISGSSWTAKKNKLFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEMLVDD 64 (88)
Q Consensus 6 ~~~~~~s~~~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~L~~d 64 (88)
++.|.+..++||.|||++|..++.+|+. +|.+||..|||||..+|++||..++..
T Consensus 60 yLdP~IkKgpWT~EED~lLLeL~k~~Gn----KWskIAk~LPGRTDnqIKNRWnslLKK 114 (459)
T PLN03091 60 YLRPDLKRGTFSQQEENLIIELHAVLGN----RWSQIAAQLPGRTDNEIKNLWNSCLKK 114 (459)
T ss_pred ccCCcccCCCCCHHHHHHHHHHHHHhCc----chHHHHHhcCCCCHHHHHHHHHHHHHH
Confidence 5678889999999999999999999864 799999999999999999999986654
No 8
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=98.98 E-value=1.9e-09 Score=79.42 Aligned_cols=58 Identities=19% Similarity=0.407 Sum_probs=50.4
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHH-HHHHHh
Q 041937 5 GQRTSTISGSSWTAKKNKLFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEM-LVDDIK 66 (88)
Q Consensus 5 ~~~~~~~s~~~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~-L~~dv~ 66 (88)
.++-|.+-.+.||.||+.++.++.+.++- ||..||++|||||..+|++||.. |...+.
T Consensus 54 NyLrP~ikrg~fT~eEe~~Ii~lH~~~GN----rWs~IA~~LPGRTDNeIKN~Wnt~lkkkl~ 112 (238)
T KOG0048|consen 54 NYLRPDLKRGNFSDEEEDLIIKLHALLGN----RWSLIAGRLPGRTDNEVKNHWNTHLKKKLL 112 (238)
T ss_pred cccCCCccCCCCCHHHHHHHHHHHHHHCc----HHHHHHhhCCCcCHHHHHHHHHHHHHHHHH
Confidence 46778888999999999999999999754 89999999999999999999985 444443
No 9
>PLN03091 hypothetical protein; Provisional
Probab=98.91 E-value=1.5e-09 Score=87.10 Aligned_cols=47 Identities=13% Similarity=0.383 Sum_probs=42.2
Q ss_pred CCCCCCCHHHHHHHHHHHHhcCCCCChhHHHHHHHcC-CCCHHHHHHHHHH
Q 041937 11 ISGSSWTAKKNKLFENALAIYDKDTPDRWQIIAKIVG-GTSEEEVKRRYEM 60 (88)
Q Consensus 11 ~s~~~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~vp-gRT~~qc~~ry~~ 60 (88)
.....||.|||++|..++.+|+.. +|..||+.++ |||.+||++||..
T Consensus 12 lrKg~WTpEEDe~L~~~V~kyG~~---nWs~IAk~~g~gRT~KQCRERW~N 59 (459)
T PLN03091 12 LRKGLWSPEEDEKLLRHITKYGHG---CWSSVPKQAGLQRCGKSCRLRWIN 59 (459)
T ss_pred CcCCCCCHHHHHHHHHHHHHhCcC---CHHHHhhhhccCcCcchHhHHHHh
Confidence 345789999999999999999764 8999999985 8999999999985
No 10
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=98.84 E-value=1.6e-09 Score=79.72 Aligned_cols=52 Identities=17% Similarity=0.333 Sum_probs=47.0
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCCChhHHHHHHHcC-CCCHHHHHHHHHH-HHHHHh
Q 041937 12 SGSSWTAKKNKLFENALAIYDKDTPDRWQIIAKIVG-GTSEEEVKRRYEM-LVDDIK 66 (88)
Q Consensus 12 s~~~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~vp-gRT~~qc~~ry~~-L~~dv~ 66 (88)
..++||.|||.+|...|.+|+++ +|..||+.+| ||+.++||.||.. |..+|+
T Consensus 8 ~kGpWt~EED~~L~~~V~~~G~~---~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ik 61 (238)
T KOG0048|consen 8 VKGPWTQEEDLTQIRSIKSFGKH---NGTALPKLAGLRRCGKSCRLRWTNYLRPDLK 61 (238)
T ss_pred cCCCCChHHHHHHHHHHHHhCCC---CcchhhhhcCCCccchHHHHHhhcccCCCcc
Confidence 35899999999999999999876 9999999999 9999999999974 666766
No 11
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=98.83 E-value=8.1e-09 Score=82.50 Aligned_cols=50 Identities=34% Similarity=0.514 Sum_probs=45.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHH
Q 041937 8 TSTISGSSWTAKKNKLFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEM 60 (88)
Q Consensus 8 ~~~~s~~~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~ 60 (88)
+..+-...||++|+-+|.+|+..|+-| +|+.||.+|+.||.++|++||.+
T Consensus 67 s~~i~~~~WtadEEilLLea~~t~G~G---NW~dIA~hIGtKtkeeck~hy~k 116 (438)
T KOG0457|consen 67 SFPILDPSWTADEEILLLEAAETYGFG---NWQDIADHIGTKTKEECKEHYLK 116 (438)
T ss_pred CCCCCCCCCChHHHHHHHHHHHHhCCC---cHHHHHHHHcccchHHHHHHHHH
Confidence 445556789999999999999999887 99999999999999999999976
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=98.62 E-value=1.5e-07 Score=56.48 Aligned_cols=46 Identities=15% Similarity=0.287 Sum_probs=40.7
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCChhH---HHHHHHcCC-C-CHHHHHHHHHHHH
Q 041937 14 SSWTAKKNKLFENALAIYDKDTPDRW---QIIAKIVGG-T-SEEEVKRRYEMLV 62 (88)
Q Consensus 14 ~~WT~eE~k~Le~al~~~~~~~~~rW---~kIA~~vpg-R-T~~qc~~ry~~L~ 62 (88)
-.||.||...|..||..|+.+ .| .+|+++|.. + |..||+.|++...
T Consensus 4 ~~WT~eeh~~Fl~ai~~~G~g---~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~ 54 (57)
T TIGR01557 4 VVWTEDLHDRFLQAVQKLGGP---DWATPKRILELMVVDGLTRDQVASHLQKYR 54 (57)
T ss_pred CCCCHHHHHHHHHHHHHhCCC---cccchHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence 579999999999999999875 69 999999863 5 9999999998754
No 13
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=98.50 E-value=1.3e-07 Score=76.57 Aligned_cols=45 Identities=20% Similarity=0.515 Sum_probs=41.4
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHHH
Q 041937 13 GSSWTAKKNKLFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEML 61 (88)
Q Consensus 13 ~~~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~L 61 (88)
...||.+|..+|.++|..|+. .|.+||.+|++||++||.-||.+|
T Consensus 279 dk~WS~qE~~LLLEGIe~ygD----dW~kVA~HVgtKt~EqCIl~FL~L 323 (531)
T COG5259 279 DKNWSRQELLLLLEGIEMYGD----DWDKVARHVGTKTKEQCILHFLQL 323 (531)
T ss_pred cccccHHHHHHHHHHHHHhhh----hHHHHHHHhCCCCHHHHHHHHHcC
Confidence 358999999999999999976 599999999999999999999874
No 14
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=98.45 E-value=4.1e-07 Score=76.53 Aligned_cols=55 Identities=18% Similarity=0.469 Sum_probs=49.7
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHHHHH
Q 041937 6 QRTSTISGSSWTAKKNKLFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEMLVD 63 (88)
Q Consensus 6 ~~~~~~s~~~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~L~~ 63 (88)
-+.|+++-+.||.+||.+|..|+.+|+.. .|-+|-+.|||||.-||+.||...+.
T Consensus 353 ~LdPsikhg~wt~~ED~~L~~AV~~Yg~k---dw~k~R~~vPnRSdsQcR~RY~nvL~ 407 (939)
T KOG0049|consen 353 TLDPSVKHGRWTDQEDVLLVCAVSRYGAK---DWAKVRQAVPNRSDSQCRERYTNVLN 407 (939)
T ss_pred ccCccccCCCCCCHHHHHHHHHHHHhCcc---chhhHHHhcCCccHHHHHHHHHHHHH
Confidence 35678889999999999999999999765 89999999999999999999987554
No 15
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=98.31 E-value=1e-06 Score=71.85 Aligned_cols=47 Identities=26% Similarity=0.533 Sum_probs=42.9
Q ss_pred CCCCCCCHHHHHHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHHH
Q 041937 11 ISGSSWTAKKNKLFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEML 61 (88)
Q Consensus 11 ~s~~~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~L 61 (88)
+....||.+|.-+|..+|.+|+. .|.+||.+|++||.+||..||..|
T Consensus 251 ~~~~~WT~qE~lLLLE~ie~y~d----dW~kVa~hVg~ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 251 SARPNWTEQETLLLLEAIEMYGD----DWNKVADHVGTKSQEQCILKFLRL 297 (506)
T ss_pred cCCCCccHHHHHHHHHHHHHhcc----cHHHHHhccCCCCHHHHHHHHHhc
Confidence 45678999999999999999976 499999999999999999999873
No 16
>KOG0724 consensus Zuotin and related molecular chaperones (DnaJ superfamily), contains DNA-binding domains [Posttranslational modification, protein turnover, chaperones]
Probab=98.21 E-value=2.9e-06 Score=64.53 Aligned_cols=68 Identities=38% Similarity=0.569 Sum_probs=63.9
Q ss_pred CCCCHHHHHHHHHHHHhcCCC----CChhHHHHHHHcCC-CCHHHHHHHHHHHHHHHhhhcCCCCCCCCCCCC
Q 041937 14 SSWTAKKNKLFENALAIYDKD----TPDRWQIIAKIVGG-TSEEEVKRRYEMLVDDIKSIESDRVPLPDYAQN 81 (88)
Q Consensus 14 ~~WT~eE~k~Le~al~~~~~~----~~~rW~kIA~~vpg-RT~~qc~~ry~~L~~dv~~ie~g~v~~P~y~~~ 81 (88)
..|+.++.+.+++||..|... ++++|.+++..+|+ ++..+...+|..++.++..++++.+++|.|...
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 559999999999999999854 78999999999999 999999999999999999999999999999875
No 17
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=98.16 E-value=5.2e-06 Score=65.31 Aligned_cols=49 Identities=27% Similarity=0.519 Sum_probs=44.0
Q ss_pred CCCCCCCHHHHHHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHHHH
Q 041937 11 ISGSSWTAKKNKLFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEMLV 62 (88)
Q Consensus 11 ~s~~~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~L~ 62 (88)
+-...|+++|+.+|..++...+-+ +|+.||.+++.|+.++|+.||.++.
T Consensus 61 I~~e~WgadEEllli~~~~TlGlG---NW~dIadyiGsr~kee~k~HylK~y 109 (432)
T COG5114 61 IGEEGWGADEELLLIECLDTLGLG---NWEDIADYIGSRAKEEIKSHYLKMY 109 (432)
T ss_pred ccCCCcCchHHHHHHHHHHhcCCC---cHHHHHHHHhhhhhHHHHHHHHHHH
Confidence 455689999999999999999776 9999999999999999999997643
No 18
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=97.83 E-value=5.1e-05 Score=64.25 Aligned_cols=61 Identities=13% Similarity=0.242 Sum_probs=48.7
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCChhHHHHHHHcCC-CCHHHHHHHHHHHHHHHhhhc
Q 041937 6 QRTSTISGSSWTAKKNKLFENALAIYDKDTPDRWQIIAKIVGG-TSEEEVKRRYEMLVDDIKSIE 69 (88)
Q Consensus 6 ~~~~~~s~~~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~vpg-RT~~qc~~ry~~L~~dv~~ie 69 (88)
++.|..+...||.||++.|...-.... -..|++||..+++ ||.=||..+|+..+..+..+|
T Consensus 246 ~l~P~~nk~~WS~EE~E~L~AiA~A~~---~~~W~~IA~~Lgt~RS~yQC~~kF~t~~~~L~eke 307 (939)
T KOG0049|consen 246 ELNPKWNKEHWSNEEVEKLKALAEAPK---FVSWPMIALNLGTNRSSYQCMEKFKTEVSQLSEKE 307 (939)
T ss_pred hcCCccchhccChHHHHHHHHHHhccc---cccHHHHHHHhCCCcchHHHHHHHHHHHHHHHhhh
Confidence 456778899999999999865444432 3479999999998 999999999998777666543
No 19
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=97.80 E-value=7.1e-05 Score=46.43 Aligned_cols=58 Identities=21% Similarity=0.437 Sum_probs=41.8
Q ss_pred CCCCHHHHHHHHHHHHh------cC--CC-CC-hhHHHHHHHcC----CCCHHHHHHHHHHHHHHHhhhcCC
Q 041937 14 SSWTAKKNKLFENALAI------YD--KD-TP-DRWQIIAKIVG----GTSEEEVKRRYEMLVDDIKSIESD 71 (88)
Q Consensus 14 ~~WT~eE~k~Le~al~~------~~--~~-~~-~rW~kIA~~vp----gRT~~qc~~ry~~L~~dv~~ie~g 71 (88)
..||.+|-..|..++.. |. .. .. .-|..||..|. .||+.||+.+|+.|...-+.+...
T Consensus 2 ~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~~Yk~~k~~ 73 (90)
T PF13837_consen 2 RNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLKKKYKKIKDR 73 (90)
T ss_dssp -SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHHHHHHCSSSS
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 57999999999998777 21 11 22 37999999984 499999999999999988876554
No 20
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=97.75 E-value=6.7e-05 Score=63.92 Aligned_cols=44 Identities=30% Similarity=0.530 Sum_probs=40.5
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHH
Q 041937 13 GSSWTAKKNKLFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEM 60 (88)
Q Consensus 13 ~~~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~ 60 (88)
+..||..|.++|.+||-.|.++ +.+|+.+|+|||+.||.+-|..
T Consensus 619 Sd~WTp~E~~lF~kA~y~~~KD----F~~v~km~~~KtVaqCVeyYYt 662 (907)
T KOG4167|consen 619 SDKWTPLERKLFNKALYTYSKD----FIFVQKMVKSKTVAQCVEYYYT 662 (907)
T ss_pred cccccHHHHHHHHHHHHHhccc----HHHHHHHhccccHHHHHHHHHH
Confidence 4689999999999999999875 9999999999999999998864
No 21
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=97.61 E-value=8.6e-05 Score=61.26 Aligned_cols=47 Identities=23% Similarity=0.608 Sum_probs=43.2
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHHHH
Q 041937 13 GSSWTAKKNKLFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEMLV 62 (88)
Q Consensus 13 ~~~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~L~ 62 (88)
++.|+.-||.+|..|+.+|+.+ .|.+||+.++-+|+.||+.||.+.+
T Consensus 7 ggvwrntEdeilkaav~kyg~n---qws~i~sll~~kt~rqC~~rw~e~l 53 (617)
T KOG0050|consen 7 GGVWRNTEDEVLKAAVMKYGKN---QWSRIASLLNRKTARQCKARWEEWL 53 (617)
T ss_pred cceecccHHHHHHHHHHHcchH---HHHHHHHHHhhcchhHHHHHHHHHh
Confidence 5789999999999999999876 8999999999999999999998643
No 22
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=97.34 E-value=0.0011 Score=40.57 Aligned_cols=54 Identities=13% Similarity=0.312 Sum_probs=45.2
Q ss_pred CCCCHHHHHHHHHHHHhcCC---C----------CChhHHHHHHHc----C-CCCHHHHHHHHHHHHHHHhh
Q 041937 14 SSWTAKKNKLFENALAIYDK---D----------TPDRWQIIAKIV----G-GTSEEEVKRRYEMLVDDIKS 67 (88)
Q Consensus 14 ~~WT~eE~k~Le~al~~~~~---~----------~~~rW~kIA~~v----p-gRT~~qc~~ry~~L~~dv~~ 67 (88)
..||.+|..+|...|.+|+. + ...-|+.||..| | .||..||+..|..|...++.
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 57999999999999999852 1 245799999988 2 39999999999999887764
No 23
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=97.30 E-value=0.00027 Score=58.40 Aligned_cols=59 Identities=20% Similarity=0.423 Sum_probs=49.2
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHHHHHHHhhhcC
Q 041937 7 RTSTISGSSWTAKKNKLFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIKSIES 70 (88)
Q Consensus 7 ~~~~~s~~~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~~ie~ 70 (88)
..|++....||.+||..|..+...+|. .|.-||..| |||..||.+||..|+........
T Consensus 53 ldp~i~~tews~eederlLhlakl~p~----qwrtIa~i~-gr~~~qc~eRy~~ll~~~~s~~~ 111 (617)
T KOG0050|consen 53 LDPAIKKTEWSREEDERLLHLAKLEPT----QWRTIADIM-GRTSQQCLERYNNLLDVYVSYHY 111 (617)
T ss_pred hCHHHhhhhhhhhHHHHHHHHHHhcCC----ccchHHHHh-hhhHHHHHHHHHHHHHHHHhhhc
Confidence 456677889999999999998888654 699999999 79999999999998876554433
No 24
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=97.18 E-value=0.00057 Score=56.12 Aligned_cols=58 Identities=14% Similarity=0.345 Sum_probs=49.5
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 041937 6 QRTSTISGSSWTAKKNKLFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIKS 67 (88)
Q Consensus 6 ~~~~~~s~~~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (88)
...|......||.+|+..|..+-.+++. +|.-||..+||+|..+|.++|..+..+...
T Consensus 65 ~lnp~lk~~~~~~eed~~li~l~~~~~~----~wstia~~~d~rt~~~~~ery~~~~~~~~s 122 (512)
T COG5147 65 HLNPQLKKKNWSEEEDEQLIDLDKELGT----QWSTIADYKDRRTAQQCVERYVNTLEDLSS 122 (512)
T ss_pred hhchhcccccccHHHHHHHHHHHHhcCc----hhhhhccccCccchHHHHHHHHHHhhhhhc
Confidence 4456667789999999999888888755 699999999999999999999987776654
No 25
>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=97.08 E-value=0.0032 Score=42.68 Aligned_cols=57 Identities=18% Similarity=0.376 Sum_probs=48.0
Q ss_pred CCCCCCCCHHHHHHHHHHHHhcCCCCChhHHHHHHHc------------CCCCHHHHHHHHHHHHHHHh
Q 041937 10 TISGSSWTAKKNKLFENALAIYDKDTPDRWQIIAKIV------------GGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 10 ~~s~~~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~v------------pgRT~~qc~~ry~~L~~dv~ 66 (88)
+.+...||.+||..|...+.+|+-+.++.|++|-+.+ -.||+.++..|-..|+.-|.
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 5567899999999999999999998888999999864 57999999999999888765
No 26
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=96.97 E-value=0.0014 Score=54.86 Aligned_cols=47 Identities=17% Similarity=0.427 Sum_probs=41.7
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHHHHH
Q 041937 12 SGSSWTAKKNKLFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEMLVD 63 (88)
Q Consensus 12 s~~~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~L~~ 63 (88)
..+.||++|++.|...+.+++. .|..|+..| ||.+..|+.||...+.
T Consensus 383 ~rg~wt~ee~eeL~~l~~~~g~----~W~~Ig~~l-gr~P~~crd~wr~~~~ 429 (607)
T KOG0051|consen 383 KRGKWTPEEEEELKKLVVEHGN----DWKEIGKAL-GRMPMDCRDRWRQYVK 429 (607)
T ss_pred ccCCCCcchHHHHHHHHHHhcc----cHHHHHHHH-ccCcHHHHHHHHHhhc
Confidence 4678999999999999999754 699999999 7999999999987654
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=96.82 E-value=0.0042 Score=38.85 Aligned_cols=53 Identities=21% Similarity=0.439 Sum_probs=40.6
Q ss_pred CCCHHHHHHHHHHHHhcC-------CC--CChhHHHHHHHcC---C--CCHHHHHHHHHHHHHHHhh
Q 041937 15 SWTAKKNKLFENALAIYD-------KD--TPDRWQIIAKIVG---G--TSEEEVKRRYEMLVDDIKS 67 (88)
Q Consensus 15 ~WT~eE~k~Le~al~~~~-------~~--~~~rW~kIA~~vp---g--RT~~qc~~ry~~L~~dv~~ 67 (88)
.||.++++.|..+|...- .+ .+.-|..|++.|- | .|..||++||+.|..+-+.
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk~~y~~ 67 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLKKDYRI 67 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHHHHHHH
Confidence 599999999999886651 11 3567999999883 3 6889999999987765443
No 28
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=96.37 E-value=0.0059 Score=51.13 Aligned_cols=53 Identities=9% Similarity=0.325 Sum_probs=43.1
Q ss_pred CCCCCCCHHHHHHHHHHHH-------hc------------CCC---CChhHHHHHHHcCCCCHHHHHHHHHHHHH
Q 041937 11 ISGSSWTAKKNKLFENALA-------IY------------DKD---TPDRWQIIAKIVGGTSEEEVKRRYEMLVD 63 (88)
Q Consensus 11 ~s~~~WT~eE~k~Le~al~-------~~------------~~~---~~~rW~kIA~~vpgRT~~qc~~ry~~L~~ 63 (88)
...+.||.+|+..|.+++. +| |.+ .+-.|..|++.+++|+..||+.+|..|+.
T Consensus 434 ~~r~~Ws~eEe~~Llk~V~~~~~~~~q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~~ 508 (607)
T KOG0051|consen 434 RNRGAWSIEEEEKLLKTVNEMIREALQPQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLTT 508 (607)
T ss_pred cccCcchHHHHHHHHHHHHHHHHHhhcccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHHh
Confidence 3678999999999999984 33 111 34579999999999999999999988764
No 29
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=96.28 E-value=0.011 Score=47.72 Aligned_cols=44 Identities=20% Similarity=0.501 Sum_probs=40.5
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHH
Q 041937 13 GSSWTAKKNKLFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEM 60 (88)
Q Consensus 13 ~~~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~ 60 (88)
...||.+|...|-+||.+++-+ +..||..+|.|+-+||+-.|.+
T Consensus 365 ~~~Ws~~e~ekFYKALs~wGtd----F~LIs~lfP~R~RkqIKaKfi~ 408 (507)
T COG5118 365 ALRWSKKEIEKFYKALSIWGTD----FSLISSLFPNRERKQIKAKFIK 408 (507)
T ss_pred CCcccHHHHHHHHHHHHHhcch----HHHHHHhcCchhHHHHHHHHHH
Confidence 3789999999999999999764 9999999999999999999974
No 30
>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=96.10 E-value=0.0085 Score=42.85 Aligned_cols=50 Identities=10% Similarity=0.276 Sum_probs=41.4
Q ss_pred CCCCCHHHHHHHHHHHHhcCCC---CChhHHHHHHHcCCCCHHHHHHHHHHHHH
Q 041937 13 GSSWTAKKNKLFENALAIYDKD---TPDRWQIIAKIVGGTSEEEVKRRYEMLVD 63 (88)
Q Consensus 13 ~~~WT~eE~k~Le~al~~~~~~---~~~rW~kIA~~vpgRT~~qc~~ry~~L~~ 63 (88)
...||.|||.+|-..+.+|-.. ...-++.|+..+ +||+-.|-=||+..+.
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 3689999999999999998543 246789999999 6999999988887554
No 31
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=95.98 E-value=0.022 Score=46.75 Aligned_cols=46 Identities=24% Similarity=0.356 Sum_probs=41.3
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHHH
Q 041937 12 SGSSWTAKKNKLFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEML 61 (88)
Q Consensus 12 s~~~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~L 61 (88)
-...||.||.-+|++|...|++ ++.+|-++||.||...++.-|...
T Consensus 186 ~~d~WT~Ed~vlFe~aF~~~GK----~F~kIrq~LP~rsLaSlvqyYy~~ 231 (534)
T KOG1194|consen 186 FPDEWTAEDIVLFEQAFQFFGK----DFHKIRQALPHRSLASLVQYYYSW 231 (534)
T ss_pred CcccchHHHHHHHHHHHHHhcc----cHHHHHHHccCccHHHHHHHHHHH
Confidence 3468999999999999999987 599999999999999999988653
No 32
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=95.71 E-value=0.0068 Score=49.92 Aligned_cols=45 Identities=13% Similarity=0.423 Sum_probs=40.2
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHH
Q 041937 13 GSSWTAKKNKLFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEM 60 (88)
Q Consensus 13 ~~~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~ 60 (88)
.+.|+..||..|..++..|+.. +|.+||+.+.-++.+||+.|+..
T Consensus 20 ~gsw~~~EDe~l~~~vk~l~~n---nws~vas~~~~~~~kq~~~rw~~ 64 (512)
T COG5147 20 GGSWKRTEDEDLKALVKKLGPN---NWSKVASLLISSTGKQSSNRWNN 64 (512)
T ss_pred CCCCCCcchhHHHHHHhhcccc---cHHHHHHHhcccccccccchhhh
Confidence 3589999999999999998654 79999999998999999999954
No 33
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=95.52 E-value=0.04 Score=33.70 Aligned_cols=47 Identities=9% Similarity=0.186 Sum_probs=33.7
Q ss_pred CCCCHHHHHHHHHHHHhcCC-----CCChhHHHHHHHcC-CCCHHHHHHHHHH
Q 041937 14 SSWTAKKNKLFENALAIYDK-----DTPDRWQIIAKIVG-GTSEEEVKRRYEM 60 (88)
Q Consensus 14 ~~WT~eE~k~Le~al~~~~~-----~~~~rW~kIA~~vp-gRT~~qc~~ry~~ 60 (88)
.++|.+||.+|..-|+.+.. .++.=|+.+|+.-| .+|-..-++||..
T Consensus 3 ~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K 55 (65)
T PF08914_consen 3 TPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLK 55 (65)
T ss_dssp ----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence 57899999999999977642 25778999999999 7999999999965
No 34
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=95.46 E-value=0.084 Score=40.44 Aligned_cols=60 Identities=17% Similarity=0.286 Sum_probs=46.3
Q ss_pred CCCCCHHHHHHHHHHHHhcCC------CCChhHHHHHHHcC--C--CCHHHHHHHHHHHHHHHhhhcCCC
Q 041937 13 GSSWTAKKNKLFENALAIYDK------DTPDRWQIIAKIVG--G--TSEEEVKRRYEMLVDDIKSIESDR 72 (88)
Q Consensus 13 ~~~WT~eE~k~Le~al~~~~~------~~~~rW~kIA~~vp--g--RT~~qc~~ry~~L~~dv~~ie~g~ 72 (88)
...||.+|=..|..+...... ....-|+.||..+. | ||+.||+.+|..|....+....+.
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k~Yk~~k~~~ 123 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKKKYKKEKAKK 123 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHhccc
Confidence 478999999999887654421 12446999999553 3 999999999999998888766664
No 35
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=95.43 E-value=0.039 Score=48.74 Aligned_cols=43 Identities=30% Similarity=0.485 Sum_probs=38.3
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHH
Q 041937 14 SSWTAKKNKLFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYE 59 (88)
Q Consensus 14 ~~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~ 59 (88)
..||..+=..|.+|..+|+.. ....||..|.|||.+||+.-.+
T Consensus 825 ~~w~~~~f~~f~~~~~~~gr~---~~~~i~~~~~~k~~~ev~~y~~ 867 (1033)
T PLN03142 825 STWSRRDFNAFIRACEKYGRN---DIKSIASEMEGKTEEEVERYAK 867 (1033)
T ss_pred CcccHHHHHHHHHHHHHhCHh---HHHHHHHHhcCCCHHHHHHHHH
Confidence 469999999999999999876 8999999999999999986444
No 36
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=95.23 E-value=0.045 Score=46.44 Aligned_cols=55 Identities=22% Similarity=0.405 Sum_probs=45.6
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCChhHHHH----------HHHcCCCCHHHHHHHHHHHHHHHhhhcCC
Q 041937 13 GSSWTAKKNKLFENALAIYDKDTPDRWQII----------AKIVGGTSEEEVKRRYEMLVDDIKSIESD 71 (88)
Q Consensus 13 ~~~WT~eE~k~Le~al~~~~~~~~~rW~kI----------A~~vpgRT~~qc~~ry~~L~~dv~~ie~g 71 (88)
...||-.|...|-.||.+++++ +++| -..+.-||..||+.+|.+++..+...-.|
T Consensus 88 ktaWt~~E~~~Ffdal~~~GKd----Fe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~~m~k~~F~ 152 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGKD----FEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVRRMNKLLFG 152 (782)
T ss_pred ccccchhhHHHHHHHHHHhccc----HHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHHHHHhhhcc
Confidence 5689999999999999999885 8888 44566699999999999888777655544
No 37
>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=94.90 E-value=0.17 Score=39.93 Aligned_cols=54 Identities=19% Similarity=0.280 Sum_probs=42.6
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 041937 13 GSSWTAKKNKLFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 13 ~~~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
...||..|.+.|.++|..........-..|++.|+|||..||+...+.|...|.
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~fl~~LK~rva 74 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDFLQQLKGRVA 74 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHHHHHHHHHHH
Confidence 478999999999999887532233346679999999999999998887766554
No 38
>smart00595 MADF subfamily of SANT domain.
Probab=94.58 E-value=0.074 Score=32.79 Aligned_cols=26 Identities=42% Similarity=0.680 Sum_probs=22.5
Q ss_pred hhHHHHHHHcCCCCHHHHHHHHHHHHH
Q 041937 37 DRWQIIAKIVGGTSEEEVKRRYEMLVD 63 (88)
Q Consensus 37 ~rW~kIA~~vpgRT~~qc~~ry~~L~~ 63 (88)
.-|..||..|+ .|+++|+.+|+.|..
T Consensus 28 ~aW~~Ia~~l~-~~~~~~~~kw~~LR~ 53 (89)
T smart00595 28 KAWEEIAEELG-LSVEECKKRWKNLRD 53 (89)
T ss_pred HHHHHHHHHHC-cCHHHHHHHHHHHHH
Confidence 46999999995 599999999998754
No 39
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=94.26 E-value=0.11 Score=37.46 Aligned_cols=49 Identities=10% Similarity=0.281 Sum_probs=38.9
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCC---hhHHHHHHHcCCCCHHHHHHHHHHHH
Q 041937 13 GSSWTAKKNKLFENALAIYDKDTP---DRWQIIAKIVGGTSEEEVKRRYEMLV 62 (88)
Q Consensus 13 ~~~WT~eE~k~Le~al~~~~~~~~---~rW~kIA~~vpgRT~~qc~~ry~~L~ 62 (88)
...||.|+|.+|...+..|..... .-.+.++..+ +||.-.|--||+..+
T Consensus 5 qdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRwNs~v 56 (170)
T PRK13923 5 QDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRWNSVV 56 (170)
T ss_pred hhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHHHHHH
Confidence 367999999999999999875433 4466677788 699999999996543
No 40
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=93.97 E-value=0.14 Score=41.37 Aligned_cols=47 Identities=30% Similarity=0.489 Sum_probs=39.4
Q ss_pred CCCCCCCCHHHHHHHHHHHHhcCCCCChhHHHH-HHHcCCCCHHHHHHHHHH
Q 041937 10 TISGSSWTAKKNKLFENALAIYDKDTPDRWQII-AKIVGGTSEEEVKRRYEM 60 (88)
Q Consensus 10 ~~s~~~WT~eE~k~Le~al~~~~~~~~~rW~kI-A~~vpgRT~~qc~~ry~~ 60 (88)
......||.+|=+.|+..|..|+++ +..| |..|+.||+-+|..-|..
T Consensus 274 rd~l~~wsEeEcr~FEegl~~yGKD----F~lIr~nkvrtRsvgElVeyYYl 321 (445)
T KOG4329|consen 274 RDDLSGWSEEECRNFEEGLELYGKD----FHLIRANKVRTRSVGELVEYYYL 321 (445)
T ss_pred ccccccCCHHHHHHHHHHHHHhccc----HHHHHhcccccchHHHHHHHHHH
Confidence 3455789999999999999999886 5555 668999999999998864
No 41
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=93.73 E-value=0.14 Score=42.59 Aligned_cols=66 Identities=30% Similarity=0.493 Sum_probs=47.8
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCCChhHHHH-HHHcCCCCHHHHHHHHHHHH--------HHHhhhcCC----CCCCCCC
Q 041937 12 SGSSWTAKKNKLFENALAIYDKDTPDRWQII-AKIVGGTSEEEVKRRYEMLV--------DDIKSIESD----RVPLPDY 78 (88)
Q Consensus 12 s~~~WT~eE~k~Le~al~~~~~~~~~rW~kI-A~~vpgRT~~qc~~ry~~L~--------~dv~~ie~g----~v~~P~y 78 (88)
-...||..|--+||.||.+|+++ +..| +..+|=||...+.+-|.... ..++..|+. .|-+|.|
T Consensus 284 emEEWSasEanLFEeALeKyGKD----FndIrqdfLPWKSl~sIveyYYmwKttdRYvqqKrlKaaeadsKlkqvYIP~y 359 (693)
T KOG3554|consen 284 EMEEWSASEANLFEEALEKYGKD----FNDIRQDFLPWKSLTSIVEYYYMWKTTDRYVQQKRLKAAEADSKLKQVYIPTY 359 (693)
T ss_pred hhhhccchhhHHHHHHHHHhccc----HHHHHHhhcchHHHHHHHHHHHHHhhhhHHHHHHhhhhhhhhhhhheeeccCC
Confidence 45789999999999999999986 4455 55678899999988876422 234444444 2667777
Q ss_pred CCC
Q 041937 79 AQN 81 (88)
Q Consensus 79 ~~~ 81 (88)
.-+
T Consensus 360 nKP 362 (693)
T KOG3554|consen 360 NKP 362 (693)
T ss_pred CCC
Confidence 543
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=93.10 E-value=0.53 Score=26.14 Aligned_cols=37 Identities=24% Similarity=0.327 Sum_probs=28.6
Q ss_pred HHHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHHH
Q 041937 21 NKLFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEML 61 (88)
Q Consensus 21 ~k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~L 61 (88)
|..+..+|..-+. .-|..||+.+ |=|...|.+|.+.|
T Consensus 5 D~~Il~~Lq~d~r---~s~~~la~~l-glS~~~v~~Ri~rL 41 (42)
T PF13404_consen 5 DRKILRLLQEDGR---RSYAELAEEL-GLSESTVRRRIRRL 41 (42)
T ss_dssp HHHHHHHHHH-TT---S-HHHHHHHH-TS-HHHHHHHHHHH
T ss_pred HHHHHHHHHHcCC---ccHHHHHHHH-CcCHHHHHHHHHHh
Confidence 5677788888644 3699999999 79999999999876
No 43
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=92.84 E-value=0.078 Score=42.86 Aligned_cols=52 Identities=19% Similarity=0.360 Sum_probs=41.7
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCChhHHHHHHH-----cCC-CCHHHHHHHHHHHHHHHhhh
Q 041937 13 GSSWTAKKNKLFENALAIYDKDTPDRWQIIAKI-----VGG-TSEEEVKRRYEMLVDDIKSI 68 (88)
Q Consensus 13 ~~~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~-----vpg-RT~~qc~~ry~~L~~dv~~i 68 (88)
.+.||.+|-.-|=+....|.- ||--||.. .+. ||+++.++||...+..+.+.
T Consensus 130 dn~WskeETD~LF~lck~fDL----Rf~VIaDRyd~qq~~~sRTvEdLKeRyY~v~r~l~kA 187 (445)
T KOG2656|consen 130 DNSWSKEETDYLFDLCKRFDL----RFFVIADRYDNQQYKKSRTVEDLKERYYSVCRKLLKA 187 (445)
T ss_pred cccccHHHHHHHHHHHHhcCe----eEEEEeeccchhhccccccHHHHHHHHHHHHHHHHHc
Confidence 467999999988888888864 56666655 776 99999999999988777643
No 44
>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=92.28 E-value=0.28 Score=29.23 Aligned_cols=28 Identities=36% Similarity=0.639 Sum_probs=23.6
Q ss_pred hhHHHHHHHcCC-CCHHHHHHHHHHHHHH
Q 041937 37 DRWQIIAKIVGG-TSEEEVKRRYEMLVDD 64 (88)
Q Consensus 37 ~rW~kIA~~vpg-RT~~qc~~ry~~L~~d 64 (88)
.-|..||..++. -++++|+.+++.|...
T Consensus 27 ~aw~~Ia~~l~~~~~~~~~~~~w~~Lr~~ 55 (85)
T PF10545_consen 27 EAWQEIARELGKEFSVDDCKKRWKNLRDR 55 (85)
T ss_pred HHHHHHHHHHccchhHHHHHHHHHHHHHH
Confidence 469999999974 6889999999987653
No 45
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=91.16 E-value=1.1 Score=29.15 Aligned_cols=62 Identities=13% Similarity=0.263 Sum_probs=40.9
Q ss_pred CCCCCHHHHHHHHHHHHhcCC--C--CChhHHHHHHHcCC-----CCHHHHHHHHHHHHHH----HhhhcCCCCC
Q 041937 13 GSSWTAKKNKLFENALAIYDK--D--TPDRWQIIAKIVGG-----TSEEEVKRRYEMLVDD----IKSIESDRVP 74 (88)
Q Consensus 13 ~~~WT~eE~k~Le~al~~~~~--~--~~~rW~kIA~~vpg-----RT~~qc~~ry~~L~~d----v~~ie~g~v~ 74 (88)
...||.+++-.|.++|..|-. + ....|..+...|.+ =|..|+.+..+.|... +..+..|..+
T Consensus 4 qR~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~KirrLK~Ky~~~~~k~~~g~~~ 78 (98)
T PF04504_consen 4 QRLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRRLKKKYRNAVKKSKNGKDP 78 (98)
T ss_pred cCCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHhhhcccCcCC
Confidence 467999999999999999932 1 22456666666543 3788887777765543 3334455443
No 46
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=88.82 E-value=2.6 Score=31.04 Aligned_cols=54 Identities=6% Similarity=0.151 Sum_probs=40.6
Q ss_pred CCCCCCCCHHHHHHHHHHHHhcCCCCChhHHHHHHHc-----CCCCHHHHHHHHHHHHHH
Q 041937 10 TISGSSWTAKKNKLFENALAIYDKDTPDRWQIIAKIV-----GGTSEEEVKRRYEMLVDD 64 (88)
Q Consensus 10 ~~s~~~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~v-----pgRT~~qc~~ry~~L~~d 64 (88)
..+...||.+|+.+|........+ +...+++|=..= ++||+++...||..|..-
T Consensus 70 iq~kalfS~~EE~lL~~v~s~~~p-~le~Fq~LL~~n~~vFh~sRTak~L~~HW~lmkqy 128 (199)
T PF13325_consen 70 IQSKALFSKEEEQLLGTVASSSQP-SLETFQELLDKNRSVFHPSRTAKSLQDHWRLMKQY 128 (199)
T ss_pred ccccCCCCHHHHHHHHhhhhccCC-cHHHHHHHHHhChhhhccccCHHHHHHHHHHHHHh
Confidence 446788999999999886655433 346788875433 579999999999976543
No 47
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=88.72 E-value=1.7 Score=29.62 Aligned_cols=41 Identities=20% Similarity=0.214 Sum_probs=34.5
Q ss_pred HHHHHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHHHHH
Q 041937 19 KKNKLFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEMLVD 63 (88)
Q Consensus 19 eE~k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~L~~ 63 (88)
+-|..+..+|++-+.- .|..||+.+ |-|...|..|++.|.+
T Consensus 9 ~~D~~Il~~Lq~d~R~---s~~eiA~~l-glS~~tV~~Ri~rL~~ 49 (153)
T PRK11179 9 NLDRGILEALMENART---PYAELAKQF-GVSPGTIHVRVEKMKQ 49 (153)
T ss_pred HHHHHHHHHHHHcCCC---CHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 4577788888886543 699999999 7999999999999876
No 48
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=87.42 E-value=1.6 Score=30.19 Aligned_cols=41 Identities=20% Similarity=0.094 Sum_probs=33.6
Q ss_pred HHHHHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHHHHH
Q 041937 19 KKNKLFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEMLVD 63 (88)
Q Consensus 19 eE~k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~L~~ 63 (88)
+-|..+..+|++-+.- .|..||+.+ |-|..-|.+|++.|.+
T Consensus 14 ~~D~~IL~~Lq~d~R~---s~~eiA~~l-glS~~tv~~Ri~rL~~ 54 (164)
T PRK11169 14 RIDRNILNELQKDGRI---SNVELSKRV-GLSPTPCLERVRRLER 54 (164)
T ss_pred HHHHHHHHHhccCCCC---CHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 3466777788876543 799999999 7999999999999876
No 49
>smart00426 TEA TEA domain.
Probab=86.69 E-value=1.6 Score=27.24 Aligned_cols=22 Identities=32% Similarity=0.605 Sum_probs=19.4
Q ss_pred CCCCCHHHHHHHHHHHHhcCCC
Q 041937 13 GSSWTAKKNKLFENALAIYDKD 34 (88)
Q Consensus 13 ~~~WT~eE~k~Le~al~~~~~~ 34 (88)
...|+.+=+..|.+||..|++.
T Consensus 3 ~~vWp~~lE~Af~~aL~~~~~~ 24 (68)
T smart00426 3 EGVWSPDIEQAFQEALAIYPPC 24 (68)
T ss_pred CCcCcHHHHHHHHHHHHHcCcc
Confidence 4679999999999999999864
No 50
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=86.66 E-value=3.2 Score=37.08 Aligned_cols=52 Identities=13% Similarity=0.307 Sum_probs=44.6
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCCChhHHHHHHHc------------CCCCHHHHHHHHHHHHHHHh
Q 041937 12 SGSSWTAKKNKLFENALAIYDKDTPDRWQIIAKIV------------GGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 12 s~~~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~v------------pgRT~~qc~~ry~~L~~dv~ 66 (88)
....+|.+||..|...+.+|+-+ +|++|-..+ ..||+.++..|-..|+.-|.
T Consensus 925 ~~~~~~~~~d~~~~~~~~~~g~~---~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l~~~~~ 988 (1033)
T PLN03142 925 KGKLYNEECDRFMLCMVHKLGYG---NWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTLIRLIE 988 (1033)
T ss_pred CCCcCCHHHHHHHHHHHHHhccc---hHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHHHHHHH
Confidence 45679999999999999999875 699997654 47999999999999887775
No 51
>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=84.69 E-value=3.2 Score=28.60 Aligned_cols=47 Identities=21% Similarity=0.387 Sum_probs=33.8
Q ss_pred CHHHHHHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 041937 17 TAKKNKLFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIKS 67 (88)
Q Consensus 17 T~eE~k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (88)
+.++.++| -..|.......|..||..+ ..+..+|+..+....++|.+
T Consensus 83 ~de~k~Ii---~lry~~r~~~TW~~IA~~l-~i~erta~r~~~~fK~~i~~ 129 (130)
T PF05263_consen 83 IDEEKRII---KLRYDRRSRRTWYQIAQKL-HISERTARRWRDRFKNDIYR 129 (130)
T ss_pred CHHHHHHH---HHHHcccccchHHHHHHHh-CccHHHHHHHHHHHHHHhcC
Confidence 34444444 3455544456899999999 59999999999888877753
No 52
>PF11626 Rap1_C: TRF2-interacting telomeric protein/Rap1 - C terminal domain; InterPro: IPR021661 This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres []. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C-terminal domain []. ; PDB: 3K6G_C 3CZ6_A 3OWT_A.
Probab=83.35 E-value=1.4 Score=27.83 Aligned_cols=21 Identities=14% Similarity=0.430 Sum_probs=11.5
Q ss_pred CCCCCCCCCCCCCHHHHHHHH
Q 041937 5 GQRTSTISGSSWTAKKNKLFE 25 (88)
Q Consensus 5 ~~~~~~~s~~~WT~eE~k~Le 25 (88)
|.+-|..-.+-||.++|..|.
T Consensus 39 g~~~P~n~~GiWT~eDD~~L~ 59 (87)
T PF11626_consen 39 GKGIPDNMPGIWTPEDDEMLR 59 (87)
T ss_dssp TTSS-TT-TT---HHHHHHHT
T ss_pred CCCCCCCCCCCcCHHHHHHHH
Confidence 444455566789999999993
No 53
>KOG3841 consensus TEF-1 and related transcription factor, TEAD family [Transcription]
Probab=82.69 E-value=6.1 Score=32.22 Aligned_cols=53 Identities=23% Similarity=0.394 Sum_probs=43.4
Q ss_pred CCCCCCCHHHHHHHHHHHHhcCCC------------CChhHHHHHHHcC-----CCCHHHHHHHHHHHHH
Q 041937 11 ISGSSWTAKKNKLFENALAIYDKD------------TPDRWQIIAKIVG-----GTSEEEVKRRYEMLVD 63 (88)
Q Consensus 11 ~s~~~WT~eE~k~Le~al~~~~~~------------~~~rW~kIA~~vp-----gRT~~qc~~ry~~L~~ 63 (88)
.+.+.||.+=++.|.+||+.||+- .-+|=+.||..+. .||.+||-.|-+.|..
T Consensus 74 daegvWSpdIEqsFqEALaiyppcGrrKIilsdegkmyGRNELIarYIKlrtgktRTrKQVSSHIQVlar 143 (455)
T KOG3841|consen 74 DAEGVWSPDIEQSFQEALAIYPPCGRRKIILSDEGKMYGRNELIARYIKLRTGKTRTRKQVSSHIQVLAR 143 (455)
T ss_pred ccccccChhHHHHHHHHHhhcCCCCceeEEEccCccccchHHHHHHHHHHhcCCchhHHHHHHHHHHHHH
Confidence 456789999999999999999852 1368899999884 4889999999987654
No 54
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=82.58 E-value=1.3 Score=37.26 Aligned_cols=47 Identities=19% Similarity=0.466 Sum_probs=41.4
Q ss_pred CCCCCCCCHHHHHHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHH
Q 041937 10 TISGSSWTAKKNKLFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEM 60 (88)
Q Consensus 10 ~~s~~~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~ 60 (88)
......||.+|-.+|..+|..++.+ ..-|++.+|+|+.++++..|..
T Consensus 406 ~~~~~~w~~se~e~fyka~~~~gs~----~slis~l~p~R~rk~iK~K~~~ 452 (584)
T KOG2009|consen 406 KLETDKWDASETELFYKALSERGSD----FSLISNLFPLRDRKQIKAKFKK 452 (584)
T ss_pred ccccCcccchhhHHhhhHHhhhccc----ccccccccccccHHHHHHHHhh
Confidence 3355789999999999999998764 7889999999999999999974
No 55
>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=82.42 E-value=5.9 Score=27.95 Aligned_cols=51 Identities=20% Similarity=0.391 Sum_probs=41.8
Q ss_pred CCCHHHHHHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 041937 15 SWTAKKNKLFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 15 ~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
.++..|-+.|.+++..|+.+.- .|.-+...+.+||.++++..-.-....|.
T Consensus 40 GFn~rQR~~Fln~vMR~G~~~f-~~~w~~~~Lr~Ks~~ei~aY~~LFm~HL~ 90 (145)
T PF06461_consen 40 GFNPRQRKAFLNAVMRYGMGAF-DWKWFVPRLRGKSEKEIRAYGSLFMRHLC 90 (145)
T ss_pred ccCHHHHHHHHHHHHHHCcCcc-cchHHhhhhccccHHHHHHHHHHHHHHhc
Confidence 4889999999999999998533 68888999999999999876655555554
No 56
>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=82.26 E-value=6.4 Score=21.67 Aligned_cols=44 Identities=14% Similarity=0.184 Sum_probs=31.8
Q ss_pred CHHHHHHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 041937 17 TAKKNKLFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 17 T~eE~k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
+.+|.++|.... . .+-.+..||+.+ |-|...|+.+....+..++
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 456666664433 2 233699999999 6999999999988777765
No 57
>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=82.15 E-value=2.4 Score=29.93 Aligned_cols=42 Identities=26% Similarity=0.320 Sum_probs=34.6
Q ss_pred CCCHHHHHHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHHH
Q 041937 15 SWTAKKNKLFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEML 61 (88)
Q Consensus 15 ~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~L 61 (88)
.||.|....|.+...+ + -.=..||+.|+|.|-+.|.-+...|
T Consensus 2 ~Wtde~~~~L~~lw~~-G----~SasqIA~~lg~vsRnAViGk~hRl 43 (162)
T PF07750_consen 2 SWTDERVERLRKLWAE-G----LSASQIARQLGGVSRNAVIGKAHRL 43 (162)
T ss_pred CCCHHHHHHHHHHHHc-C----CCHHHHHHHhCCcchhhhhhhhhcc
Confidence 6999999998777655 2 2468999999889999999888765
No 58
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=79.80 E-value=1.3 Score=36.71 Aligned_cols=47 Identities=17% Similarity=0.260 Sum_probs=34.9
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHHHHHHH
Q 041937 14 SSWTAKKNKLFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEMLVDDI 65 (88)
Q Consensus 14 ~~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv 65 (88)
-.||++|-. +.++++--....+.||+.+.++|+.|++.+|..-...|
T Consensus 471 ~~wSp~e~s-----~ircf~~y~~~fe~ia~l~~tktp~Q~~~fy~~n~k~i 517 (534)
T KOG1194|consen 471 YGWSPEEKS-----AIRCFHWYKDNFELIAELMATKTPEQIKKFYMDNEKLI 517 (534)
T ss_pred CCCCCcccc-----cccCchhhccchHHHHHHhcCCCHHHHHHHhcCchhhh
Confidence 469999887 33443323347999999999999999999997644333
No 59
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=79.07 E-value=9 Score=23.98 Aligned_cols=41 Identities=22% Similarity=0.195 Sum_probs=33.7
Q ss_pred HHHHHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHHHHH
Q 041937 19 KKNKLFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEMLVD 63 (88)
Q Consensus 19 eE~k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~L~~ 63 (88)
+.|..+..+|.+.+. -.+..||+.+ |-|...|.+|.+.|.+
T Consensus 3 ~~D~~il~~L~~~~~---~~~~~la~~l-~~s~~tv~~~l~~L~~ 43 (108)
T smart00344 3 EIDRKILEELQKDAR---ISLAELAKKV-GLSPSTVHNRVKRLEE 43 (108)
T ss_pred HHHHHHHHHHHHhCC---CCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 356777788888654 3699999999 7999999999999876
No 60
>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=78.98 E-value=9 Score=21.35 Aligned_cols=49 Identities=18% Similarity=0.249 Sum_probs=40.8
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHHHH
Q 041937 13 GSSWTAKKNKLFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEMLV 62 (88)
Q Consensus 13 ~~~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~L~ 62 (88)
...+|.++...|+......+.-+...-+.||..+ |-|..+|..=|..-.
T Consensus 4 r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l-~l~~~~V~~WF~nrR 52 (57)
T PF00046_consen 4 RTRFTKEQLKVLEEYFQENPYPSKEEREELAKEL-GLTERQVKNWFQNRR 52 (57)
T ss_dssp SSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHH-TSSHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHhccccccccccccccc-cccccccccCHHHhH
Confidence 3578999999999999987765677899999999 799999988776543
No 61
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=78.08 E-value=7.8 Score=25.58 Aligned_cols=40 Identities=23% Similarity=0.143 Sum_probs=31.9
Q ss_pred HHHHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHHHHH
Q 041937 20 KNKLFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEMLVD 63 (88)
Q Consensus 20 E~k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~L~~ 63 (88)
=|..+.+.|++-+. ..+..||+.+ |-|...|.+|-+.|.+
T Consensus 9 ~D~~IL~~L~~d~r---~~~~eia~~l-glS~~~v~~Ri~~L~~ 48 (154)
T COG1522 9 IDRRILRLLQEDAR---ISNAELAERV-GLSPSTVLRRIKRLEE 48 (154)
T ss_pred HHHHHHHHHHHhCC---CCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 35566677777544 4699999999 6999999999999876
No 62
>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=75.01 E-value=4.4 Score=26.37 Aligned_cols=43 Identities=21% Similarity=0.387 Sum_probs=29.4
Q ss_pred HHHHHHHHHhcCCCCChhHHHHHHHcC------C--CC------HHHHHHHHHHHHH
Q 041937 21 NKLFENALAIYDKDTPDRWQIIAKIVG------G--TS------EEEVKRRYEMLVD 63 (88)
Q Consensus 21 ~k~Le~al~~~~~~~~~rW~kIA~~vp------g--RT------~~qc~~ry~~L~~ 63 (88)
.++|.+.+..-|......|+.||..|. | +| .++|..-|+.++.
T Consensus 44 ~kfl~eIi~~~P~~d~~~Wd~IA~~mN~yly~~~~w~t~~~FyDG~~C~~~Fr~~v~ 100 (108)
T PF00674_consen 44 MKFLKEIIEVKPGVDMKKWDIIASRMNQYLYEEGLWNTPYFFYDGKDCYRFFRRLVL 100 (108)
T ss_pred HHHHHHHHhcCCCCCcccHHHHHHHHHHHHHhCCCCCCcCcccCcHHHHHHHHHHhc
Confidence 355555666656557789999999984 2 33 4778888876543
No 63
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=74.12 E-value=7.1 Score=28.75 Aligned_cols=43 Identities=21% Similarity=0.341 Sum_probs=36.0
Q ss_pred CCCHHHHHHHHHHHHhcCCCCChhHHHHHHHcC---CCCHHHHHHHHHHHH
Q 041937 15 SWTAKKNKLFENALAIYDKDTPDRWQIIAKIVG---GTSEEEVKRRYEMLV 62 (88)
Q Consensus 15 ~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~vp---gRT~~qc~~ry~~L~ 62 (88)
.|++.+|-+|..|+.+ + ..-+.|+..|+ .-|..++.+||..|.
T Consensus 1 rW~~~DDl~Li~av~~----~-~~L~~v~~gvkFS~~fT~~Ei~~RW~~ll 46 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQ----T-NDLESVHLGVKFSCKFTLQEIEERWYALL 46 (199)
T ss_pred CCCchhhHHHHHHHHH----h-cCHHHHHccCCcCCcCcHHHHHHHHHHHH
Confidence 4999999999999998 2 25788887775 479999999999765
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=73.78 E-value=13 Score=20.46 Aligned_cols=49 Identities=16% Similarity=0.208 Sum_probs=40.8
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHHHH
Q 041937 13 GSSWTAKKNKLFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEMLV 62 (88)
Q Consensus 13 ~~~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~L~ 62 (88)
...+|.++..+|+......+.-+...=..||+.+ |-|..+|..=|..-.
T Consensus 4 r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~-~l~~~qV~~WF~nrR 52 (59)
T cd00086 4 RTRFTPEQLEELEKEFEKNPYPSREEREELAKEL-GLTERQVKIWFQNRR 52 (59)
T ss_pred CCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 3578999999999999998765667789999999 699999998776543
No 65
>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=71.50 E-value=6.9 Score=31.75 Aligned_cols=50 Identities=24% Similarity=0.461 Sum_probs=34.6
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCC----------ChhHHHHHHHcC---C--CCHHHHHHHHHHH
Q 041937 12 SGSSWTAKKNKLFENALAIYDKDT----------PDRWQIIAKIVG---G--TSEEEVKRRYEML 61 (88)
Q Consensus 12 s~~~WT~eE~k~Le~al~~~~~~~----------~~rW~kIA~~vp---g--RT~~qc~~ry~~L 61 (88)
....|+.+=+..|.+||+.||+.+ -+|=+-||..+- | ||.+||-.|.+.|
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 556799999999999999998642 234566777763 3 8999999999998
No 66
>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=70.20 E-value=5.5 Score=24.41 Aligned_cols=21 Identities=29% Similarity=0.605 Sum_probs=17.5
Q ss_pred HHHHHHHcCCCCHHHHHHHHH
Q 041937 39 WQIIAKIVGGTSEEEVKRRYE 59 (88)
Q Consensus 39 W~kIA~~vpgRT~~qc~~ry~ 59 (88)
-..||..+-|||++|++..+.
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 567899999999999999774
No 67
>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=69.83 E-value=23 Score=22.00 Aligned_cols=30 Identities=30% Similarity=0.407 Sum_probs=24.2
Q ss_pred hhHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 041937 37 DRWQIIAKIVGGTSEEEVKRRYEMLVDDIKS 67 (88)
Q Consensus 37 ~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (88)
..+..||+.+ |-|...|+.+.......++.
T Consensus 127 ~s~~eIA~~l-~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 127 LSYKEIAEIL-GISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred CCHHHHHHHH-CCCHHHHHHHHHHHHHHHHh
Confidence 4688999999 57899999988887777653
No 68
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=68.20 E-value=18 Score=19.81 Aligned_cols=46 Identities=20% Similarity=0.261 Sum_probs=37.9
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHH
Q 041937 14 SSWTAKKNKLFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEM 60 (88)
Q Consensus 14 ~~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~ 60 (88)
..+|.++..+|+......+.-+...=..||+.+ |-|..+|..=|..
T Consensus 5 ~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~-~l~~~qV~~WF~n 50 (56)
T smart00389 5 TSFTPEQLEELEKEFQKNPYPSREEREELAAKL-GLSERQVKVWFQN 50 (56)
T ss_pred CcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHH-CcCHHHHHHhHHH
Confidence 458999999999999888755566788999999 6999998876654
No 69
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=67.84 E-value=17 Score=22.67 Aligned_cols=42 Identities=14% Similarity=0.248 Sum_probs=28.8
Q ss_pred HHHHHHHhcCCC----CChhHHHHHHHcCCCC-----HHHHHHHHHHHHHH
Q 041937 23 LFENALAIYDKD----TPDRWQIIAKIVGGTS-----EEEVKRRYEMLVDD 64 (88)
Q Consensus 23 ~Le~al~~~~~~----~~~rW~kIA~~vpgRT-----~~qc~~ry~~L~~d 64 (88)
.|-.++.+.+.. ....|..||..++-.. ..+++.+|..++-.
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 455667776532 3468999999996532 56788899875543
No 70
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=65.96 E-value=28 Score=22.84 Aligned_cols=44 Identities=18% Similarity=0.203 Sum_probs=29.9
Q ss_pred HHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 041937 22 KLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
..|..+|.+.|+. ..-.+..||+.+ |.|...|+.+.......++
T Consensus 117 ~~l~~~l~~L~~~~r~i~~l~~~~~~~~~eIA~~l-gis~~tv~~~~~ra~~~lr 170 (179)
T PRK11924 117 ARIDRCLDALPVKQREVFLLRYVEGLSYREIAEIL-GVPVGTVKSRLRRARQLLR 170 (179)
T ss_pred HHHHHHHHhCCHHHHHHhhHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 3566666665532 244689999999 6888888888776555544
No 71
>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=62.83 E-value=14 Score=22.66 Aligned_cols=41 Identities=15% Similarity=0.287 Sum_probs=26.3
Q ss_pred HHHHHHHhcCCC----CChhHHHHHHHcCCCC-----HHHHHHHHHHHHH
Q 041937 23 LFENALAIYDKD----TPDRWQIIAKIVGGTS-----EEEVKRRYEMLVD 63 (88)
Q Consensus 23 ~Le~al~~~~~~----~~~rW~kIA~~vpgRT-----~~qc~~ry~~L~~ 63 (88)
.|-.++.+.+.. ....|..||..++--+ ..+++.+|..++.
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 344555555432 1346999999996422 4789999987543
No 72
>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=62.67 E-value=39 Score=21.85 Aligned_cols=44 Identities=16% Similarity=0.168 Sum_probs=34.0
Q ss_pred HHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 041937 22 KLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
..|..+|.+.|+. ..-.++.||+.+ |-|...|+.+.......++
T Consensus 97 ~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~l-gis~~tv~~~l~Ra~~~Lr 150 (154)
T TIGR02950 97 EEITHHLSRLPENYRTVLILREFKEFSYKEIAELL-NLSLAKVKSNLFRARKELK 150 (154)
T ss_pred HHHHHHHHhCCHhheeeeeehhhccCcHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 4577888888743 245799999999 6999999999887666655
No 73
>COG5269 ZUO1 Ribosome-associated chaperone zuotin [Translation, ribosomal structure and biogenesis / Posttranslational modification, protein turnover, chaperones]
Probab=62.63 E-value=15 Score=29.02 Aligned_cols=50 Identities=14% Similarity=0.236 Sum_probs=39.3
Q ss_pred CCCCHHHHHHHHHHHHhcCCCC-ChhHHHHHHHcCC-----CCHHHHHHHHHHHHH
Q 041937 14 SSWTAKKNKLFENALAIYDKDT-PDRWQIIAKIVGG-----TSEEEVKRRYEMLVD 63 (88)
Q Consensus 14 ~~WT~eE~k~Le~al~~~~~~~-~~rW~kIA~~vpg-----RT~~qc~~ry~~L~~ 63 (88)
..|+.++-..+..+++.+++.. ..+|+.+|+.+-+ |+.+++++.-+.+-.
T Consensus 246 rkWereagar~~a~aa~k~kae~k~kae~ea~a~asa~a~kkkaKE~~kka~k~~K 301 (379)
T COG5269 246 RKWEREAGARLKALAALKGKAEAKNKAEIEAEALASATAVKKKAKEVMKKALKMEK 301 (379)
T ss_pred hccchhhhhhHHHHHHHhhhhHHHhHHHHHHHHhhhhHHHHHhHHHHHHHHHHHHH
Confidence 5799999999999999988653 6899999988765 667777776665433
No 74
>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=62.42 E-value=24 Score=19.35 Aligned_cols=26 Identities=38% Similarity=0.454 Sum_probs=19.5
Q ss_pred hhHHHHHHHcCCCCHHHHHHHHHHHHH
Q 041937 37 DRWQIIAKIVGGTSEEEVKRRYEMLVD 63 (88)
Q Consensus 37 ~rW~kIA~~vpgRT~~qc~~ry~~L~~ 63 (88)
-.|..||+.+ |.|...|+.++..-..
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 3699999999 6999999998876443
No 75
>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=60.57 E-value=47 Score=22.14 Aligned_cols=45 Identities=18% Similarity=0.177 Sum_probs=33.2
Q ss_pred CCHHHHHHHHHHHHhcC--------CC-C------------------ChhHHHHHHHcCCCCHHHHHHHHHH
Q 041937 16 WTAKKNKLFENALAIYD--------KD-T------------------PDRWQIIAKIVGGTSEEEVKRRYEM 60 (88)
Q Consensus 16 WT~eE~k~Le~al~~~~--------~~-~------------------~~rW~kIA~~vpgRT~~qc~~ry~~ 60 (88)
+|++||-.|+.++.+|- .+ . -.-....+...|..|...=+.||++
T Consensus 2 fTA~dDY~Lc~~i~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~fF~~~~~~~p~HT~~sWRDR~RK 73 (105)
T PF09197_consen 2 FTADDDYALCKAIKKQFYRDIYQKDPDTGSSLISDGDSKEFIPKRDMRSFFKDLARKNPRHTENSWRDRYRK 73 (105)
T ss_dssp --HHHHHHHHHHHHHHHHHHHHSB-TTSS-B----------------TTHHHHHHHHTTTS-HHHHHHHHHH
T ss_pred CChHHHHHHHHHHHHHHHHHHHhhCcccccccccCCCccccccchhhHHHHHHHHHcCCccchhHHHHHHHH
Confidence 69999999999987661 11 0 2347788999999999999999986
No 76
>COG4281 ACB Acyl-CoA-binding protein [Lipid metabolism]
Probab=59.70 E-value=20 Score=23.10 Aligned_cols=31 Identities=26% Similarity=0.490 Sum_probs=25.7
Q ss_pred hhHHHHHHHcCCCCHHHHHHHHHHHHHHHhhh
Q 041937 37 DRWQIIAKIVGGTSEEEVKRRYEMLVDDIKSI 68 (88)
Q Consensus 37 ~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~~i 68 (88)
-.|+.-| -+.|||.++.++.|..|++.++..
T Consensus 54 ~K~eAW~-~LKGksqedA~qeYialVeeLkak 84 (87)
T COG4281 54 YKYEAWA-GLKGKSQEDARQEYIALVEELKAK 84 (87)
T ss_pred hhHHHHh-hccCccHHHHHHHHHHHHHHHHhh
Confidence 4677777 466999999999999999998753
No 77
>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=57.81 E-value=15 Score=26.07 Aligned_cols=28 Identities=18% Similarity=0.623 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHHhcCCCCChhHHHHHHHcC
Q 041937 18 AKKNKLFENALAIYDKDTPDRWQIIAKIVG 47 (88)
Q Consensus 18 ~eE~k~Le~al~~~~~~~~~rW~kIA~~vp 47 (88)
.++++.|-+||.+|- .+.+|..|-++|-
T Consensus 40 ~~~er~lqkAll~Y~--~PeN~~lvreAL~ 67 (150)
T PF11842_consen 40 GERERRLQKALLRYH--DPENWPLVREALK 67 (150)
T ss_pred CHHHHHHHHHHHhhc--ChhhHHHHHHHHH
Confidence 367899999999994 4568999988873
No 78
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=56.89 E-value=48 Score=22.48 Aligned_cols=45 Identities=11% Similarity=0.113 Sum_probs=32.0
Q ss_pred HHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 041937 22 KLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIKS 67 (88)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (88)
..|..+|.+.|+. .....+.||+.+ |-|..-|+.+...-...++.
T Consensus 131 ~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~Lr~ 185 (189)
T PRK09648 131 NRMRELLDTLPEKQREILILRVVVGLSAEETAEAV-GSTPGAVRVAQHRALARLRA 185 (189)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence 3566777777643 245688899998 68888888888766665553
No 79
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=56.12 E-value=54 Score=21.58 Aligned_cols=48 Identities=21% Similarity=0.160 Sum_probs=34.8
Q ss_pred HHHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHhhhc
Q 041937 21 NKLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIKSIE 69 (88)
Q Consensus 21 ~k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~~ie 69 (88)
...+..+|...|+. ..-....||..+ |-|...|+.|.......++.+.
T Consensus 103 ~~~~~~~l~~L~~~~r~v~~l~~~~~~s~~eIA~~l-gis~~tv~~~l~Rar~~L~~~~ 160 (161)
T PRK12541 103 IASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMT-GLSLAKVKIELHRGRKETKSIK 160 (161)
T ss_pred HHHHHHHHHHCCHHHHHHhhhHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHhhc
Confidence 34455677666642 234568999999 6999999999988888887654
No 80
>PLN03162 golden-2 like transcription factor; Provisional
Probab=55.90 E-value=37 Score=27.94 Aligned_cols=52 Identities=13% Similarity=0.215 Sum_probs=39.4
Q ss_pred CCCCHHHHHHHHHHHHhcCCC--CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 041937 14 SSWTAKKNKLFENALAIYDKD--TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 14 ~~WT~eE~k~Le~al~~~~~~--~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
-.||.+=.+.|.+|+.+.+.+ +|.+--++ ..|+|-|-..|+.|-+++...++
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 359999999999999999843 45444433 23679999999999887665554
No 81
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=54.51 E-value=58 Score=21.37 Aligned_cols=44 Identities=18% Similarity=0.071 Sum_probs=30.8
Q ss_pred HHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 041937 22 KLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
..|..+|.+.|+. ..-.-..||+.+ |.|..-|+.|.......++
T Consensus 98 ~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~l-gis~~tV~~~l~Rar~~Lr 151 (160)
T PRK09642 98 LLIAQKLRELPENYRDVVLAHYLEEKSYQEIALQE-KIEVKTVEMKLYRARKWIK 151 (160)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 4577788877743 234578899988 6888889888766554444
No 82
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=53.93 E-value=46 Score=22.85 Aligned_cols=49 Identities=10% Similarity=0.079 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 041937 18 AKKNKLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIKS 67 (88)
Q Consensus 18 ~eE~k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (88)
.++...|..+|.+.|+. ..-....||+.+ |.|...|+.+-......|+.
T Consensus 130 ~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~EIA~~L-gis~~tVk~~l~ra~~~Lr~ 188 (194)
T PRK09646 130 RLERERVRDCLDALTDTQRESVTLAYYGGLTYREVAERL-AVPLGTVKTRMRDGLIRLRD 188 (194)
T ss_pred HhHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHh-CCChHhHHHHHHHHHHHHHH
Confidence 34556788888877642 234678899888 57888888887766655543
No 83
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=53.63 E-value=43 Score=22.39 Aligned_cols=50 Identities=8% Similarity=0.224 Sum_probs=32.9
Q ss_pred CCHHHHHHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 041937 16 WTAKKNKLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 16 WT~eE~k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
+..++...|..+|...|+. ..-.-+.||+.+ |.|..-|+.|.......++
T Consensus 105 ~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~~~s~~EIA~~l-gis~~tV~~~l~Ra~~~Lr 164 (173)
T PRK12522 105 IQKVEAEMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEIL-NIPIGTVKYRLNYAKKQMR 164 (173)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHh-CCCHHHHHHHHHHHHHHHH
Confidence 4445556788888887752 233456788888 5788888888765555544
No 84
>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=53.00 E-value=26 Score=23.39 Aligned_cols=27 Identities=22% Similarity=0.380 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHHHHHhhhcCCCCCCCC
Q 041937 51 EEEVKRRYEMLVDDIKSIESDRVPLPD 77 (88)
Q Consensus 51 ~~qc~~ry~~L~~dv~~ie~g~v~~P~ 77 (88)
.+++++||+.-+..++.|-.|++.++-
T Consensus 84 ~e~~~~rY~~A~~~L~~ia~G~~~L~~ 110 (130)
T PF07030_consen 84 TEPVRERYKDAIKWLEDIAKGKISLGL 110 (130)
T ss_pred cHHHHHHHHHHHHHHHHHHCCCccCCC
Confidence 889999999999999999999977553
No 85
>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=52.82 E-value=60 Score=21.26 Aligned_cols=45 Identities=20% Similarity=0.175 Sum_probs=31.3
Q ss_pred HHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 041937 22 KLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIKS 67 (88)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (88)
..|..+|.+.|+. ..-....||+.+ |-|..-|+.+.......++.
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 4577777776642 244578888888 68888888888776666653
No 86
>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=49.48 E-value=18 Score=22.41 Aligned_cols=22 Identities=36% Similarity=0.560 Sum_probs=19.3
Q ss_pred HcCCCCHHHHHHHHHHHHHHHh
Q 041937 45 IVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 45 ~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
.+.|.|.++.+.+|..+++.+.
T Consensus 62 ~l~gms~~eA~~~Yi~~v~~~~ 83 (87)
T PF00887_consen 62 ALKGMSKEEAMREYIELVEELI 83 (87)
T ss_dssp TTTTTHHHHHHHHHHHHHHHHH
T ss_pred HccCCCHHHHHHHHHHHHHHHH
Confidence 4689999999999999888774
No 87
>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=49.35 E-value=28 Score=21.89 Aligned_cols=22 Identities=23% Similarity=0.413 Sum_probs=19.5
Q ss_pred HcCCCCHHHHHHHHHHHHHHHh
Q 041937 45 IVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 45 ~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
.++|-|.++++.+|..+++.+.
T Consensus 60 ~l~~ms~~eA~~~YV~~~~~l~ 81 (85)
T cd00435 60 SLKGMSKEDAMKAYIAKVEELI 81 (85)
T ss_pred HcCCCCHHHHHHHHHHHHHHHh
Confidence 4689999999999999998874
No 88
>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=48.91 E-value=69 Score=20.46 Aligned_cols=30 Identities=17% Similarity=0.315 Sum_probs=24.7
Q ss_pred hhHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 041937 37 DRWQIIAKIVGGTSEEEVKRRYEMLVDDIKS 67 (88)
Q Consensus 37 ~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (88)
-.+..||+.+ |.|...|+.+.......++.
T Consensus 130 ~~~~eIA~~l-gis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 130 KSYKEIAEEL-GISVKTVEYHISKALKELRK 159 (161)
T ss_pred CCHHHHHHHH-CCCHHHHHHHHHHHHHHHHh
Confidence 3689999998 68999999999888777763
No 89
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=47.69 E-value=72 Score=21.98 Aligned_cols=47 Identities=19% Similarity=0.203 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 041937 19 KKNKLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 19 eE~k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
++...|..+|.+.|+. ..-....||+.+ |-|..-|+.|.......|+
T Consensus 105 ~~~~~l~~~L~~Lp~~~r~i~~L~~~~g~s~~EIA~~L-gis~~tVk~~l~Rar~~Lr 161 (187)
T PRK12516 105 LDLQDFRAALDQLPDDQREAIILVGASGFAYEEAAEIC-GCAVGTIKSRVNRARQRLQ 161 (187)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 3445677888877642 245688999999 6999999998876555444
No 90
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=47.42 E-value=76 Score=21.06 Aligned_cols=44 Identities=25% Similarity=0.235 Sum_probs=30.2
Q ss_pred HHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 041937 22 KLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
..|..+|.+.|+. ..-.-+.||+.+ |.|..-|+.|...-...++
T Consensus 110 ~~l~~~l~~L~~~~r~vl~L~~~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~Lr 163 (173)
T PRK09645 110 LLVADALAQLSPEHRAVLVRSYYRGWSTAQIAADL-GIPEGTVKSRLHYALRALR 163 (173)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHH
Confidence 3577888877643 233567888888 6888888888776555444
No 91
>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=47.19 E-value=82 Score=21.07 Aligned_cols=44 Identities=18% Similarity=0.171 Sum_probs=31.5
Q ss_pred HHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 041937 22 KLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
..|..+|.+.|+. ..-....||+.+ |-|...|+.+.......++
T Consensus 130 ~~l~~~l~~L~~~~r~v~~l~~~~~~s~~EIA~~l-gis~~tv~~~l~rar~~Lr 183 (190)
T TIGR02939 130 QTVMRAVEALPEDLRTAITLRELEGLSYEDIARIM-DCPVGTVRSRIFRAREAIA 183 (190)
T ss_pred HHHHHHHHcCCHHHhhhhhhhhhcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHH
Confidence 3577777777642 244688999999 6889999888877666554
No 92
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=47.15 E-value=84 Score=20.95 Aligned_cols=43 Identities=14% Similarity=0.139 Sum_probs=29.9
Q ss_pred HHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 041937 23 LFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 23 ~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
.+..+|...|.. ....++.||+.+ |-|..-|+.+.......++
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 466666666532 245688999999 6888888888776555554
No 93
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=47.03 E-value=79 Score=21.72 Aligned_cols=45 Identities=18% Similarity=0.107 Sum_probs=31.3
Q ss_pred HHHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 041937 21 NKLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 21 ~k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
...|..+|...|+. ..-....||+.+ |-|...|+.|.......++
T Consensus 125 ~~~l~~~l~~Lp~~~r~i~~l~~~~g~s~~EIA~~l-g~s~~tV~~rl~rar~~Lr 179 (192)
T PRK09643 125 ALAVQRALMRLPVEQRAALVAVDMQGYSVADAARML-GVAEGTVKSRCARGRARLA 179 (192)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHH
Confidence 45677788777642 244688899999 6888889888865444433
No 94
>KOG2941 consensus Beta-1,4-mannosyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=46.61 E-value=9.5 Score=31.09 Aligned_cols=50 Identities=24% Similarity=0.503 Sum_probs=29.3
Q ss_pred CCCCCCHHHHH-HHHHHHHhcCCC---CChhHHHHHHHcCCCCHHHHHHHHHHHHH
Q 041937 12 SGSSWTAKKNK-LFENALAIYDKD---TPDRWQIIAKIVGGTSEEEVKRRYEMLVD 63 (88)
Q Consensus 12 s~~~WT~eE~k-~Le~al~~~~~~---~~~rW~kIA~~vpgRT~~qc~~ry~~L~~ 63 (88)
++.+||++||- +|..||..|.+. ....--++--.+.||-+ .+++|...++
T Consensus 260 sSTswTpDEdf~ILL~AL~~y~~~~~~~~~~lP~llciITGKGP--lkE~Y~~~I~ 313 (444)
T KOG2941|consen 260 SSTSWTPDEDFGILLEALVIYEEQLYDKTHNLPSLLCIITGKGP--LKEKYSQEIH 313 (444)
T ss_pred ecCCCCCcccHHHHHHHHHhhhhhhhhccCCCCcEEEEEcCCCc--hhHHHHHHHH
Confidence 67899999987 899999977421 11111122222345544 3666665544
No 95
>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=46.40 E-value=22 Score=23.17 Aligned_cols=19 Identities=26% Similarity=0.602 Sum_probs=14.8
Q ss_pred hhHHHHHHHcCCCCHHHHH
Q 041937 37 DRWQIIAKIVGGTSEEEVK 55 (88)
Q Consensus 37 ~rW~kIA~~vpgRT~~qc~ 55 (88)
+.|+++|..+++=|..+++
T Consensus 22 ~~W~~LA~~i~~ys~~~v~ 40 (97)
T cd08307 22 NVWEELAFVMMGYSNDDVE 40 (97)
T ss_pred CcHHHHHHHHhcCCHHHHH
Confidence 5899999999866666654
No 96
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=46.19 E-value=79 Score=21.70 Aligned_cols=45 Identities=16% Similarity=0.077 Sum_probs=32.6
Q ss_pred HHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 041937 22 KLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIKS 67 (88)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (88)
+.|..+|.+.|+. ..-.++.||+.+ |-|..-|+.+...-...++.
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 4566777776632 245699999999 69999998888775555554
No 97
>PTZ00458 acyl CoA binding protein; Provisional
Probab=45.60 E-value=35 Score=21.91 Aligned_cols=22 Identities=23% Similarity=0.459 Sum_probs=19.4
Q ss_pred HcCCCCHHHHHHHHHHHHHHHh
Q 041937 45 IVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 45 ~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
.++|-|.++++++|..+++.+.
T Consensus 62 ~l~~ms~~eA~~~YI~l~~~l~ 83 (90)
T PTZ00458 62 SIENLNREDAKKRYVEIVTELF 83 (90)
T ss_pred HcCCCCHHHHHHHHHHHHHHHh
Confidence 4589999999999999998874
No 98
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=45.57 E-value=91 Score=22.17 Aligned_cols=44 Identities=23% Similarity=0.226 Sum_probs=31.7
Q ss_pred HHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 041937 22 KLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
..|..+|...|+. ..-..+.||+.+ |.|...|+.++......++
T Consensus 141 ~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIAe~l-gis~~tVk~~l~Rar~kLr 194 (231)
T PRK11922 141 ALLERAIDALPDAFRAVFVLRVVEELSVEETAQAL-GLPEETVKTRLHRARRLLR 194 (231)
T ss_pred HHHHHHHHhCCHHHhhhheeehhcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHH
Confidence 3577777776632 345789999999 6999999999876544444
No 99
>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=44.74 E-value=91 Score=20.64 Aligned_cols=48 Identities=15% Similarity=0.149 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 041937 19 KKNKLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIKS 67 (88)
Q Consensus 19 eE~k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (88)
++...|..+|.+.|.. ..-....||+.+ |-|...|+.+.......++.
T Consensus 108 ~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eiA~~l-gis~~tv~~~l~Ra~~~Lr~ 165 (169)
T TIGR02954 108 DSRLDLYKAIDTLNDKYQTAIILRYYHDLTIKEIAEVM-NKPEGTVKTYLHRALKKLKK 165 (169)
T ss_pred HHHHHHHHHHHhCCHHHhHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence 3444677787777632 234678888888 58888888888776665553
No 100
>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=43.84 E-value=94 Score=21.31 Aligned_cols=43 Identities=12% Similarity=-0.015 Sum_probs=28.6
Q ss_pred HHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHH
Q 041937 22 KLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDI 65 (88)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv 65 (88)
..|..+|.+.|+. ..-..+.||+.+ |.|..-|+.|.......+
T Consensus 123 ~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~l-gis~~tvk~rl~Rar~~L 175 (188)
T TIGR02943 123 EVFEACLYHLPEQTARVFMMREVLGFESDEICQEL-EISTSNCHVLLYRARLSL 175 (188)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHh-CCCHHHHHHHHHHHHHHH
Confidence 4566777776642 234578888888 688888888876544443
No 101
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=43.82 E-value=89 Score=20.28 Aligned_cols=44 Identities=20% Similarity=0.174 Sum_probs=30.9
Q ss_pred HHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 041937 22 KLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
..|..+|.+.|+. ..-.-..||+.+ |-|..-|+.|.......++
T Consensus 98 ~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~Lr 151 (161)
T PRK09047 98 QLIEEAIQKLPARQREAFLLRYWEDMDVAETAAAM-GCSEGSVKTHCSRATHALA 151 (161)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHhcCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 4566777777643 234578899999 6899999888876555554
No 102
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=43.63 E-value=89 Score=20.19 Aligned_cols=45 Identities=11% Similarity=0.167 Sum_probs=29.7
Q ss_pred HHHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 041937 21 NKLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 21 ~k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
...|..+|.+.|+. ..-....||+.+ |.|...|+.+.......++
T Consensus 97 ~~~l~~~l~~L~~~~r~ii~l~~~~~~s~~EIA~~l-~is~~tV~~~~~ra~~~Lr 151 (154)
T PRK06759 97 EMKVKDFMSVLDEKEKYIIFERFFVGKTMGEIALET-EMTYYQVRWIYRQALEKMR 151 (154)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHh
Confidence 35577777766542 233577788888 6888888887776666554
No 103
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=42.11 E-value=1e+02 Score=21.05 Aligned_cols=43 Identities=12% Similarity=0.027 Sum_probs=31.0
Q ss_pred HHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 041937 23 LFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 23 ~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
.|..+|.+.|+. ..-....||+.+ |-|..-|+.|...-...++
T Consensus 127 ~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~l-gis~~tVk~~l~RAr~~Lr 179 (189)
T PRK12530 127 IFEACLNHLPAQQARVFMMREYLELSSEQICQEC-DISTSNLHVLLYRARLQLQ 179 (189)
T ss_pred HHHHHHHhCCHHHHHHHhHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 466778877642 245689999999 6999999888765444444
No 104
>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=41.98 E-value=1e+02 Score=21.00 Aligned_cols=43 Identities=21% Similarity=0.196 Sum_probs=31.3
Q ss_pred HHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHH
Q 041937 22 KLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDI 65 (88)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv 65 (88)
..|..+|.+.|+. ..-.-..||+.+ |-|..-|+.|...-...+
T Consensus 123 ~~l~~~l~~Lp~~~r~i~~L~~~~g~s~~EIA~~l-gis~~tVk~~l~Rar~~L 175 (193)
T TIGR02947 123 QDIKDALQGLPEEFRQAVYLADVEGFAYKEIAEIM-GTPIGTVMSRLHRGRKQL 175 (193)
T ss_pred HHHHHHHHhCCHHHhhheeehhhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 5677888887743 245678999999 699999998886544433
No 105
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=41.71 E-value=1.1e+02 Score=20.84 Aligned_cols=48 Identities=13% Similarity=0.084 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 041937 19 KKNKLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIKS 67 (88)
Q Consensus 19 eE~k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (88)
++...|..+|.+.|+. ..-....||+.+ |.|..-|+.|...-...++.
T Consensus 119 e~~~~l~~~l~~Lp~~~r~v~~L~~~~g~s~~EIA~~l-gis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 119 EDLVEVTTMIADLTTDQREALLLTQLLGLSYADAAAVC-GCPVGTIRSRVARARDALLA 176 (185)
T ss_pred HHHHHHHHHHHhCCHHHhHHhhhHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHh
Confidence 3345677888887743 234578999999 69999999998877776664
No 106
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=41.62 E-value=1e+02 Score=20.76 Aligned_cols=46 Identities=15% Similarity=0.133 Sum_probs=33.0
Q ss_pred HHHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 041937 21 NKLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIKS 67 (88)
Q Consensus 21 ~k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (88)
...|..+|...|+. ..-..+.||..+ |-|...|+.|-......++.
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 45777788887642 245678899888 68888888888776665553
No 107
>KOG0385 consensus Chromatin remodeling complex WSTF-ISWI, small subunit [Transcription]
Probab=41.61 E-value=73 Score=28.60 Aligned_cols=40 Identities=33% Similarity=0.424 Sum_probs=34.8
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHH
Q 041937 13 GSSWTAKKNKLFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKR 56 (88)
Q Consensus 13 ~~~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ 56 (88)
-..||..+=..|..|-.+|+.+ .-+.||+.|-| |+++|..
T Consensus 795 ft~w~k~df~~fi~a~eKygr~---di~~ia~~~e~-~~eev~~ 834 (971)
T KOG0385|consen 795 FTNWTKRDFNQFIKANEKYGRD---DIENIAAEVEG-TPEEVGE 834 (971)
T ss_pred ccchhhhhHHHHHHHhhccCcc---hhhhhHHhhcC-CHHHHHH
Confidence 4579999999999999999876 78899999988 9999864
No 108
>PF14775 NYD-SP28_assoc: Sperm tail C-terminal domain
Probab=41.60 E-value=42 Score=19.95 Aligned_cols=27 Identities=19% Similarity=0.470 Sum_probs=18.5
Q ss_pred hHHHHHHHcCCCCHH------HHHHHHHHHHHH
Q 041937 38 RWQIIAKIVGGTSEE------EVKRRYEMLVDD 64 (88)
Q Consensus 38 rW~kIA~~vpgRT~~------qc~~ry~~L~~d 64 (88)
-|+++|..+|..+.. .-.+||...+.+
T Consensus 2 yW~~~~~vip~~~~~~W~~L~~~l~rY~~vL~~ 34 (60)
T PF14775_consen 2 YWERLANVIPDEKIRLWDALENFLKRYNKVLLD 34 (60)
T ss_pred HHHHHhhcCChHHHHHHHHHHHHHHHHHHHHHH
Confidence 499999999975544 356777664443
No 109
>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=41.29 E-value=1e+02 Score=20.16 Aligned_cols=48 Identities=17% Similarity=0.146 Sum_probs=32.6
Q ss_pred HHHHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHhhh
Q 041937 20 KNKLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIKSI 68 (88)
Q Consensus 20 E~k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~~i 68 (88)
....|..+|.+.|+. ..-.-+.||+.+ |-|...|+.|.......++..
T Consensus 100 ~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~l-gis~~tV~~~l~ra~~~Lr~~ 157 (162)
T TIGR02983 100 LRAALARALRRLPARQRAVVVLRYYEDLSEAQVAEAL-GISVGTVKSRLSRALARLREL 157 (162)
T ss_pred HHHHHHHHHHhCCHHHHHHhhhHHHhcCCHHHHHHHh-CCCHHHHHHHHHHHHHHHHHH
Confidence 334566677666532 123467888888 688888888888877777653
No 110
>PF14164 YqzH: YqzH-like protein
Probab=39.69 E-value=24 Score=21.70 Aligned_cols=27 Identities=26% Similarity=0.556 Sum_probs=15.6
Q ss_pred HHHHHHHHHhcCCC------CChhHHHHHHHcC
Q 041937 21 NKLFENALAIYDKD------TPDRWQIIAKIVG 47 (88)
Q Consensus 21 ~k~Le~al~~~~~~------~~~rW~kIA~~vp 47 (88)
+|.+.+.|.+|+.+ ++.-|+.+.+.+.
T Consensus 7 ~Kmi~~~l~QYg~d~~~~pls~~E~~~L~~~i~ 39 (64)
T PF14164_consen 7 EKMIINCLRQYGYDVECMPLSDEEWEELCKHIQ 39 (64)
T ss_pred HHHHHHHHHHhCCcccCCCCCHHHHHHHHHHHH
Confidence 35566677777543 3455666655553
No 111
>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=39.67 E-value=95 Score=19.44 Aligned_cols=30 Identities=30% Similarity=0.548 Sum_probs=20.0
Q ss_pred CHHHHHHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHH
Q 041937 17 TAKKNKLFENALAIYDKDTPDRWQIIAKIVGGTSEEEV 54 (88)
Q Consensus 17 T~eE~k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc 54 (88)
|.++-..|...|.. +|..+|..+ |=|..++
T Consensus 1 ~~~~l~~l~~~lG~-------~Wk~lar~L-G~s~~eI 30 (86)
T cd08777 1 TEKHLDLLRENLGK-------KWKRCARKL-GFTESEI 30 (86)
T ss_pred CHHHHHHHHHHHHH-------HHHHHHHHc-CCCHHHH
Confidence 44555556555555 799999999 4665554
No 112
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=39.04 E-value=1.5e+02 Score=21.93 Aligned_cols=72 Identities=14% Similarity=0.154 Sum_probs=49.2
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHHHHHHHhhhcC---CCCC-CCCCCCCCCCc
Q 041937 13 GSSWTAKKNKLFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIKSIES---DRVP-LPDYAQNDTSN 85 (88)
Q Consensus 13 ~~~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~~ie~---g~v~-~P~y~~~~~~~ 85 (88)
...+|.++-.+||.+.....--...-=+++|..+ +-|..||+-=|++-....+++.. |..+ .++-.+..+.|
T Consensus 106 RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L-~LsetQVkvWFQNRRtk~kr~~~e~k~s~~~~~~~~~~~~~d 181 (197)
T KOG0843|consen 106 RTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSL-SLSETQVKVWFQNRRTKHKRMQQEDKGSDPRAEKKSDEEDKD 181 (197)
T ss_pred ccccCHHHHHHHHHHHhcCCeeechHHHHHHHHc-CCChhHhhhhhhhhhHHHHHHHHHhhccCccccccccccccc
Confidence 4679999999999998876432334568899999 69999999888876655555443 3222 44444444443
No 113
>KOG1724 consensus SCF ubiquitin ligase, Skp1 component [Posttranslational modification, protein turnover, chaperones]
Probab=38.95 E-value=29 Score=24.63 Aligned_cols=40 Identities=23% Similarity=0.383 Sum_probs=26.4
Q ss_pred HHHHHHHHHHhcCCCC----ChhHHHHHHHcCCCCHHHHHHHHH
Q 041937 20 KNKLFENALAIYDKDT----PDRWQIIAKIVGGTSEEEVKRRYE 59 (88)
Q Consensus 20 E~k~Le~al~~~~~~~----~~rW~kIA~~vpgRT~~qc~~ry~ 59 (88)
+..+|+-.++.+--+. .-.=+.||.++-|||++|++..|.
T Consensus 97 ~~tLfdli~AAnyLdi~gLl~~~ck~va~mikgktpeEir~~f~ 140 (162)
T KOG1724|consen 97 QGTLFDLILAANYLDIKGLLDLTCKTVANMIKGKTPEEIREIFN 140 (162)
T ss_pred HHHHHHHHHHhhhcccHHHHHHHHHHHHHHHccCCHHHHHHHcC
Confidence 3345555555443221 234578999999999999999864
No 114
>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=38.10 E-value=1e+02 Score=22.50 Aligned_cols=41 Identities=15% Similarity=0.112 Sum_probs=30.2
Q ss_pred HHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHH
Q 041937 22 KLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVD 63 (88)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~ 63 (88)
..|.++|.+.|+. ..-..+.||+.+ |-|..-|+.|...-..
T Consensus 153 ~~l~~aL~~Lp~~~R~v~~L~~~eg~S~~EIA~~L-gis~~TVk~rl~RAr~ 203 (244)
T TIGR03001 153 QALREALAALSERERHLLRLHFVDGLSMDRIGAMY-QVHRSTVSRWVAQARE 203 (244)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 4577888887753 244689999999 6888888888865333
No 115
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=37.47 E-value=1.3e+02 Score=20.34 Aligned_cols=44 Identities=14% Similarity=0.126 Sum_probs=27.8
Q ss_pred HHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 041937 22 KLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
..|..+|...|.. .+-..+.||+.+ |-|..-|+.|.......|+
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 3566777766532 133467788888 5777778887765444443
No 116
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=37.42 E-value=1.3e+02 Score=20.46 Aligned_cols=44 Identities=16% Similarity=0.043 Sum_probs=29.7
Q ss_pred HHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 041937 22 KLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
..|..+|...|+. .+-....||+.+ |.|..-|+.+.......++
T Consensus 98 ~~l~~~l~~L~~~~r~i~~l~~~~g~~~~EIA~~l-gis~~tV~~~l~Rar~~Lr 151 (181)
T PRK09637 98 PCLRPFIDALPEKYAEALRLTELEGLSQKEIAEKL-GLSLSGAKSRVQRGRVKLK 151 (181)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHhcCCCHHHHHHHh-CCCHHHHHHHHHHHHHHHH
Confidence 3555666666532 244688999999 6888899888876544444
No 117
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=37.13 E-value=1.2e+02 Score=19.82 Aligned_cols=30 Identities=20% Similarity=0.251 Sum_probs=22.0
Q ss_pred ChhHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 041937 36 PDRWQIIAKIVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 36 ~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
.-.+..||+.+ |.|..-|+.+.......++
T Consensus 144 ~~s~~eIA~~l-gis~~tV~~~l~ra~~~Lr 173 (182)
T PRK09652 144 GLSYEEIAEIM-GCPIGTVRSRIFRAREALR 173 (182)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 34689999999 6888888877765555444
No 118
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=36.99 E-value=1.3e+02 Score=20.07 Aligned_cols=44 Identities=11% Similarity=0.122 Sum_probs=29.5
Q ss_pred HHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 041937 22 KLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
..|..+|.+.|+. ..-..+.||+.+ |.|..-|+.+-......++
T Consensus 128 ~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~l-gis~~~v~~~l~Rar~~Lr 181 (187)
T TIGR02948 128 DTIQQEIQALPPKYRMVIVLKYMEDLSLKEISEIL-DLPVGTVKTRIHRGREALR 181 (187)
T ss_pred HHHHHHHHhCCHHHhHHhhhHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 4577777776532 234577888888 5788888887766555554
No 119
>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=36.71 E-value=36 Score=19.36 Aligned_cols=25 Identities=32% Similarity=0.582 Sum_probs=18.9
Q ss_pred HHHHHHHHHHHhcCCCCChhHHHHHHHcC
Q 041937 19 KKNKLFENALAIYDKDTPDRWQIIAKIVG 47 (88)
Q Consensus 19 eE~k~Le~al~~~~~~~~~rW~kIA~~vp 47 (88)
+...+|..+|.. ..++..-||..++
T Consensus 19 ~~~d~F~~~L~~----s~D~F~vIaeyfG 43 (49)
T PF12451_consen 19 DQHDLFFKQLEE----SEDRFSVIAEYFG 43 (49)
T ss_pred hcHHHHHHHHHh----CCCCchhHHHHHc
Confidence 345678788844 6679999999994
No 120
>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=36.17 E-value=56 Score=21.00 Aligned_cols=23 Identities=30% Similarity=0.502 Sum_probs=19.2
Q ss_pred HcCCCCHHHHHHHHHHHHHHHhh
Q 041937 45 IVGGTSEEEVKRRYEMLVDDIKS 67 (88)
Q Consensus 45 ~vpgRT~~qc~~ry~~L~~dv~~ 67 (88)
.++|||.+|-+.-|+.+.+.+..
T Consensus 67 l~~GRs~eqK~~l~~~i~~~l~~ 89 (113)
T cd00580 67 ILAGRSEEQKQELSEALLAALRA 89 (113)
T ss_pred EcCCCCHHHHHHHHHHHHHHHHH
Confidence 36899999999999988877753
No 121
>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=36.11 E-value=1.2e+02 Score=21.05 Aligned_cols=45 Identities=7% Similarity=0.137 Sum_probs=34.7
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCChhHHHHHHHcC----CCCHHHHHHHHHHH
Q 041937 13 GSSWTAKKNKLFENALAIYDKDTPDRWQIIAKIVG----GTSEEEVKRRYEML 61 (88)
Q Consensus 13 ~~~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~vp----gRT~~qc~~ry~~L 61 (88)
...=|..|...+...|.+|+. .++.+|.-.- -.|..||+.++...
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 445688899999999999985 4888886554 27999998877653
No 122
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=36.08 E-value=1.4e+02 Score=20.14 Aligned_cols=44 Identities=14% Similarity=0.105 Sum_probs=26.6
Q ss_pred HHHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHH
Q 041937 21 NKLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDI 65 (88)
Q Consensus 21 ~k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv 65 (88)
...|..+|...|+. ..-.-..||+.+ |-|..-|+.|.......+
T Consensus 108 ~~~l~~~l~~Lp~~~r~i~~l~~~e~~s~~EIA~~l-gis~~tV~~~l~ra~~~L 161 (179)
T PRK12543 108 NQELIELIHKLPYKLRQVIILRYLHDYSQEEIAQLL-QIPIGTVKSRIHAALKKL 161 (179)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHccCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 45777888877643 122456777777 566666766665433333
No 123
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=35.93 E-value=1.1e+02 Score=23.81 Aligned_cols=50 Identities=16% Similarity=0.207 Sum_probs=39.5
Q ss_pred CCCCCCHHHHHHHHHHHHhcCC-CCChhHHHHHHHcCCCCHHHHHHHHHHHHH
Q 041937 12 SGSSWTAKKNKLFENALAIYDK-DTPDRWQIIAKIVGGTSEEEVKRRYEMLVD 63 (88)
Q Consensus 12 s~~~WT~eE~k~Le~al~~~~~-~~~~rW~kIA~~vpgRT~~qc~~ry~~L~~ 63 (88)
+...+|.-+-+.||+-..+..- ...+| .+||+.| |-|..||+-=|++-..
T Consensus 175 sRTaFT~~Ql~~LEkrF~~QKYLS~~DR-~~LA~~L-gLTdaQVKtWfQNRRt 225 (309)
T KOG0488|consen 175 SRTAFSDHQLFELEKRFEKQKYLSVADR-IELAASL-GLTDAQVKTWFQNRRT 225 (309)
T ss_pred chhhhhHHHHHHHHHHHHHhhcccHHHH-HHHHHHc-CCchhhHHHHHhhhhH
Confidence 4567999999999997665542 24678 9999999 7999999998876443
No 124
>PF04282 DUF438: Family of unknown function (DUF438); InterPro: IPR007380 This is a a group of uncharacterised proteins.
Probab=35.20 E-value=30 Score=21.50 Aligned_cols=21 Identities=33% Similarity=0.616 Sum_probs=16.8
Q ss_pred CCCCHHHHHHHHHHHHHHHhh
Q 041937 47 GGTSEEEVKRRYEMLVDDIKS 67 (88)
Q Consensus 47 pgRT~~qc~~ry~~L~~dv~~ 67 (88)
.|.+.++|+++|..+..+|..
T Consensus 11 ~G~~~e~vk~~F~~~~~~Vs~ 31 (71)
T PF04282_consen 11 EGEDPEEVKEEFKKLFSDVSA 31 (71)
T ss_pred CCCCHHHHHHHHHHHHCCCCH
Confidence 478899999999888876654
No 125
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=35.01 E-value=1.4e+02 Score=19.83 Aligned_cols=46 Identities=20% Similarity=0.258 Sum_probs=32.5
Q ss_pred HHHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 041937 21 NKLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIKS 67 (88)
Q Consensus 21 ~k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (88)
...|..+|.+.|+. ..-....||+.+ |-|...|+.+.......++.
T Consensus 103 ~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~l-gis~~tV~~~l~Rar~~Lr~ 158 (164)
T PRK12547 103 LQDFKKALNLLSADQREAIILIGASGFSYEDAAAIC-GCAVGTIKSRVSRARNRLQE 158 (164)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHh-CCCHHHHHHHHHHHHHHHHH
Confidence 34567777777642 234578899888 68888888888776666654
No 126
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=34.82 E-value=1.3e+02 Score=19.63 Aligned_cols=48 Identities=25% Similarity=0.180 Sum_probs=30.6
Q ss_pred HHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHH----HHHHHhhhcCC
Q 041937 23 LFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEM----LVDDIKSIESD 71 (88)
Q Consensus 23 ~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~----L~~dv~~ie~g 71 (88)
.|..+|.+.|+. ..-.-..||+.+ |-|..-|+.|... |...+...++|
T Consensus 98 ~l~~~l~~L~~~~r~v~~l~~~~~~s~~eIA~~l-gis~~tv~~~l~ra~~~Lr~~l~~~~~~ 159 (159)
T PRK12527 98 LLQRALAELPPACRDSFLLRKLEGLSHQQIAEHL-GISRSLVEKHIVNAMKHCRVRMRQWESG 159 (159)
T ss_pred HHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHh-CCCHHHHHHHHHHHHHHHHHHHHhccCC
Confidence 567777777643 123457888888 6888888887654 44555444443
No 127
>COG0193 Pth Peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis]
Probab=34.64 E-value=87 Score=22.96 Aligned_cols=39 Identities=10% Similarity=0.273 Sum_probs=30.7
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHH
Q 041937 14 SSWTAKKNKLFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEM 60 (88)
Q Consensus 14 ~~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~ 60 (88)
+.+|.+|.+.|+.++.+ -++.+...+.+ ..+..+++|..
T Consensus 150 ~~f~~~E~~~l~~~~~~-------a~~~~~~~~~~-~~~~~mn~~~~ 188 (190)
T COG0193 150 GKFSKEERELLDKAIDK-------AADALELLLEG-DFEKAMNKLNA 188 (190)
T ss_pred CCCCHHHHHHHHHHHHH-------HHHHHHHHHHH-hHHHHHHHHhc
Confidence 46999999999999988 47778877776 67777776653
No 128
>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=34.51 E-value=1e+02 Score=18.29 Aligned_cols=47 Identities=23% Similarity=0.309 Sum_probs=29.5
Q ss_pred CCHHHHHHHHHHHHhcC--CCCChhHHHHHHHcCCCCHHHHHHHHHHHHH
Q 041937 16 WTAKKNKLFENALAIYD--KDTPDRWQIIAKIVGGTSEEEVKRRYEMLVD 63 (88)
Q Consensus 16 WT~eE~k~Le~al~~~~--~~~~~rW~kIA~~vpgRT~~qc~~ry~~L~~ 63 (88)
=|..|.+.|+- |..|- .+-+.--..||+.|+=+|..-|..|-+.|.+
T Consensus 4 LT~rQ~~vL~~-I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~ 52 (65)
T PF01726_consen 4 LTERQKEVLEF-IREYIEENGYPPTVREIAEALGLKSTSTVQRHLKALER 52 (65)
T ss_dssp --HHHHHHHHH-HHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHH-HHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 35666666543 33332 1234468999999977999999998877764
No 129
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=33.77 E-value=1.5e+02 Score=19.82 Aligned_cols=44 Identities=9% Similarity=0.120 Sum_probs=29.3
Q ss_pred HHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 041937 22 KLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
..|..+|.+.|+. .+-.-+.||+.+ |.|...|+.+.......++
T Consensus 121 ~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~l-gis~~tV~~~l~Rar~~Lr 174 (179)
T PRK12514 121 QRIDACLEELEKDRAAAVRRAYLEGLSYKELAERH-DVPLNTMRTWLRRSLLKLR 174 (179)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHH-CCChHHHHHHHHHHHHHHH
Confidence 3466677766532 133577889888 6888888888776555544
No 130
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=33.76 E-value=1.5e+02 Score=19.96 Aligned_cols=46 Identities=15% Similarity=0.076 Sum_probs=31.5
Q ss_pred HHHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 041937 21 NKLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIKS 67 (88)
Q Consensus 21 ~k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (88)
...|.++|...|+. ..-..+.||+.+ |.|..-|+.+.......++.
T Consensus 120 ~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~l-~is~~tV~~~l~rar~~Lr~ 175 (181)
T PRK12536 120 RRDLGKLLEQLPDRQRLPIVHVKLEGLSVAETAQLT-GLSESAVKVGIHRGLKALAA 175 (181)
T ss_pred HHHHHHHHHHCCHHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence 33577777777642 234678888888 68888888887765555543
No 131
>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=33.75 E-value=1.2e+02 Score=18.87 Aligned_cols=41 Identities=22% Similarity=0.270 Sum_probs=27.3
Q ss_pred HHHHHHHHh-cCCCCChhHHHHHHHcCCCCHHHHHHHHHHHHH
Q 041937 22 KLFENALAI-YDKDTPDRWQIIAKIVGGTSEEEVKRRYEMLVD 63 (88)
Q Consensus 22 k~Le~al~~-~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~L~~ 63 (88)
+.+...|.. ......-.-..|++.| +-+..+|+..-..|..
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 344455665 3333455688999999 9999999998777765
No 132
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=33.67 E-value=1.5e+02 Score=19.79 Aligned_cols=43 Identities=16% Similarity=0.120 Sum_probs=29.2
Q ss_pred HHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHH
Q 041937 22 KLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDI 65 (88)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv 65 (88)
..|..+|.+.|+. ..-....||+.+ |.|..-|+.+...-+..+
T Consensus 111 ~~l~~~l~~Lp~~~r~v~~L~~~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~~ 163 (172)
T PRK12523 111 KAIDRLLGKLSSKARAAFLYNRLDGMGHAEIAERL-GVSVSRVRQYLAQGLRQC 163 (172)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 4577777777643 234678888888 688888888776544433
No 133
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=33.63 E-value=1.5e+02 Score=19.94 Aligned_cols=44 Identities=14% Similarity=0.040 Sum_probs=30.0
Q ss_pred HHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 041937 22 KLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
..|..+|...|+. ..-..+.||+.+ |-|..-|+.+.......++
T Consensus 120 ~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~l-gis~~tV~~~l~Rar~~Lr 173 (186)
T PRK05602 120 RRVEQALAALPERQREAIVLQYYQGLSNIEAAAVM-DISVDALESLLARGRRALR 173 (186)
T ss_pred HHHHHHHHhCCHHHHHHhhHHHhcCCCHHHHHHHh-CcCHHHHHHHHHHHHHHHH
Confidence 4577777776632 234578888888 6888888888776555554
No 134
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=33.25 E-value=1.6e+02 Score=20.01 Aligned_cols=52 Identities=17% Similarity=0.176 Sum_probs=37.7
Q ss_pred CCCHHHHHHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 041937 15 SWTAKKNKLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIKS 67 (88)
Q Consensus 15 ~WT~eE~k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (88)
.+..+....|..+|.+.|+. ..-..+.||..+ |-|..-|+.|.......++.
T Consensus 119 ~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~Lr~ 180 (188)
T PRK09640 119 APKPEERGGLDRWLVHVNPIDREILVLRFVAELEFQEIADIM-HMGLSATKMRYKRALDKLRE 180 (188)
T ss_pred cccHHHHHHHHHHHHhcChhheeeeeeHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence 34556667788888888743 245689999999 68889998888765555543
No 135
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=32.88 E-value=1.6e+02 Score=19.90 Aligned_cols=45 Identities=16% Similarity=0.322 Sum_probs=31.6
Q ss_pred HHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 041937 22 KLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIKS 67 (88)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (88)
..|..+|.+.|+. ..-.-+.||+.+ |-|..-|+.|.......++.
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 3566777776642 234678999999 69999999988765555543
No 136
>PRK02220 4-oxalocrotonate tautomerase; Provisional
Probab=32.40 E-value=84 Score=17.53 Aligned_cols=22 Identities=18% Similarity=0.389 Sum_probs=16.9
Q ss_pred HcCCCCHHHHHHHHHHHHHHHh
Q 041937 45 IVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 45 ~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
.++|||.+|-++-++.+.+.+.
T Consensus 8 ~~~Grs~eqk~~l~~~it~~l~ 29 (61)
T PRK02220 8 LIEGRTEEQLKALVKDVTAAVS 29 (61)
T ss_pred EcCCCCHHHHHHHHHHHHHHHH
Confidence 3578999998888887766664
No 137
>PF05524 PEP-utilisers_N: PEP-utilising enzyme, N-terminal; InterPro: IPR008731 This sequence identifies proteins which are a component of the phosphoenolpyruvate:sugar phosphotransferase system (PTS), a major carbohydrate active transport system. The PTS system is found throughout the bacterial kingdom, and is responsible for the coupled phosphorylation and translocation of numerous sugars across the cytoplasmic membrane []. This entry represents the N-terminal domain of enzyme I (EIN) which transfers the phosphoryl group from phosphoenolpyruvate (PEP) to the phosphoryl carrier protein (HPr) which in turn phosphorylates a group of membrane-associated proteins, known as enzyme II. The N-terminal domain of EI (EIN) extends from residues 1 to 259 and can be phosphorylated in a fully reversible manner by phosphorylated HPr. EIN, however, cannot be autophosphorylated by PEP [, ].; GO: 0005351 sugar:hydrogen symporter activity, 0008965 phosphoenolpyruvate-protein phosphotransferase activity, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0005737 cytoplasm; PDB: 2WQD_A 2XDF_B 2HWG_A 3EZB_A 2L5H_A 3EZA_A 1EZB_A 2EZA_A 1EZA_A 1EZC_A ....
Probab=32.21 E-value=32 Score=22.22 Aligned_cols=42 Identities=17% Similarity=0.227 Sum_probs=28.4
Q ss_pred HHHHHHHHHHHHhcCCCCChhHHHHHHH----cCCCCHHHHHHHHHHHHHH
Q 041937 18 AKKNKLFENALAIYDKDTPDRWQIIAKI----VGGTSEEEVKRRYEMLVDD 64 (88)
Q Consensus 18 ~eE~k~Le~al~~~~~~~~~rW~kIA~~----vpgRT~~qc~~ry~~L~~d 64 (88)
..|...|..||.+.-. ....+++. ++.... ++.+-+..|++|
T Consensus 34 ~~E~~rl~~Al~~~~~----eL~~l~~~~~~~~~~~~a-~If~ah~~~L~D 79 (123)
T PF05524_consen 34 EAEIERLEQALEKARE----ELEQLAERAESKLGEEEA-AIFEAHLMMLED 79 (123)
T ss_dssp HHHHHHHHHHHHHHHH----HHHHHHHHHHHHCHSSCT-HHHHHHHHHHT-
T ss_pred HHHHHHHHHHHHHHHH----HHHHHHHHHHHhccccHH-HHHHHHHHHhcC
Confidence 5677899999998543 34555544 443443 899999887776
No 138
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=31.23 E-value=1.7e+02 Score=19.79 Aligned_cols=44 Identities=20% Similarity=0.230 Sum_probs=29.4
Q ss_pred HHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 041937 22 KLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
..|..+|...|+. ..-....||+.+ |.|...|+.+.......++
T Consensus 123 ~~l~~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~l-gis~~tV~~~l~Rar~~Lr 176 (189)
T PRK12515 123 AALRACLAKLSPAHREIIDLVYYHEKSVEEVGEIV-GIPESTVKTRMFYARKKLA 176 (189)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHH
Confidence 3466666666532 234688999999 6899999888765444443
No 139
>COG5201 SKP1 SCF ubiquitin ligase, SKP1 component [Posttranslational modification, protein turnover, chaperones]
Probab=31.21 E-value=50 Score=23.38 Aligned_cols=21 Identities=29% Similarity=0.689 Sum_probs=18.6
Q ss_pred HHHHHHHcCCCCHHHHHHHHH
Q 041937 39 WQIIAKIVGGTSEEEVKRRYE 59 (88)
Q Consensus 39 W~kIA~~vpgRT~~qc~~ry~ 59 (88)
=..||+.+.|||++++++.+.
T Consensus 115 CKivaemirgkSpeeir~tfn 135 (158)
T COG5201 115 CKIVAEMIRGKSPEEIRETFN 135 (158)
T ss_pred HHHHHHHHccCCHHHHHHHhC
Confidence 567999999999999998775
No 140
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=31.15 E-value=1.7e+02 Score=19.92 Aligned_cols=44 Identities=18% Similarity=0.191 Sum_probs=29.2
Q ss_pred HHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 041937 22 KLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
..|..+|.+.|+. ..-..+.||+.+ |-|..-|+.|.......++
T Consensus 133 ~~l~~~l~~Lp~~~r~v~~l~~~eg~s~~EIA~~l-gis~~tVk~rl~ra~~~Lr 186 (194)
T PRK12531 133 EQVMKFLDRLPKAQRDVLQAVYLEELPHQQVAEMF-DIPLGTVKSRLRLAVEKLR 186 (194)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHh-CcCHHHHHHHHHHHHHHHH
Confidence 4566677666532 133577888888 6888888888776555554
No 141
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=30.83 E-value=1.8e+02 Score=20.40 Aligned_cols=45 Identities=13% Similarity=0.065 Sum_probs=34.2
Q ss_pred CCCHHHHHHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 041937 15 SWTAKKNKLFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 15 ~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
.-|..|.+.|.-...-+ .-..||+.+ +-|..-|+.|-..+...+.
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 47888888875444433 468999999 6999999998888777664
No 142
>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=30.58 E-value=68 Score=24.06 Aligned_cols=26 Identities=27% Similarity=0.400 Sum_probs=21.5
Q ss_pred HHHHHcC--CCCHHHHHHHHHHHHHHHh
Q 041937 41 IIAKIVG--GTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 41 kIA~~vp--gRT~~qc~~ry~~L~~dv~ 66 (88)
.||..+. +.|.+||.+.|..+..++-
T Consensus 54 iiA~~l~~~~~t~~e~~~~y~~~~~~iF 81 (309)
T cd07216 54 LIAIMLGRLRMTVDECIDAYTRLAKKIF 81 (309)
T ss_pred HHHHHhcccCCCHHHHHHHHHHHhHHhC
Confidence 5677774 6799999999999888775
No 143
>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=30.54 E-value=1e+02 Score=17.13 Aligned_cols=44 Identities=18% Similarity=0.179 Sum_probs=31.7
Q ss_pred CCHHHHHHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 041937 16 WTAKKNKLFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 16 WT~eE~k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
-|..|-..|.-...-+ .=..||..+ |.|..-|+.|...+...+.
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 4667777665555443 457899999 6999999999888877664
No 144
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=29.88 E-value=1.8e+02 Score=19.74 Aligned_cols=42 Identities=10% Similarity=0.098 Sum_probs=27.8
Q ss_pred HHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHH
Q 041937 23 LFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDI 65 (88)
Q Consensus 23 ~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv 65 (88)
.|..+|.+.|+. ..-.-..||+.+ |-|..-|+.|...-...+
T Consensus 129 ~l~~~l~~L~~~~r~i~~L~~~~g~s~~EIA~~l-gis~~tVk~~l~Rar~~L 180 (195)
T PRK12532 129 ILQSCLYNLPENTARVFTLKEILGFSSDEIQQMC-GISTSNYHTIMHRARESL 180 (195)
T ss_pred HHHHHHHhCCHHHHHHhhhHHHhCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 466677776632 133568899988 688888888876544433
No 145
>PRK14857 tatA twin arginine translocase protein A; Provisional
Probab=29.58 E-value=1.2e+02 Score=19.54 Aligned_cols=41 Identities=15% Similarity=0.297 Sum_probs=30.4
Q ss_pred HHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 041937 23 LFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIKS 67 (88)
Q Consensus 23 ~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (88)
++.-+|.-|+++ |+-.++..| ||...+.++-.....+++..
T Consensus 14 IlvVaLlvfGP~---KLP~lar~l-Gk~i~~fkk~~~~~~~e~~~ 54 (90)
T PRK14857 14 ILVIALLVFGPK---KLPEIGRSL-GKTLKGFQEASKEFENEIKR 54 (90)
T ss_pred HHHHHHHHcCch---HHHHHHHHH-HHHHHHHHHHHHHHHHHHHH
Confidence 455577787654 999999999 68888888777666655554
No 146
>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=29.24 E-value=1.5e+02 Score=18.40 Aligned_cols=30 Identities=23% Similarity=0.504 Sum_probs=19.8
Q ss_pred CHHHHHHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHH
Q 041937 17 TAKKNKLFENALAIYDKDTPDRWQIIAKIVGGTSEEEV 54 (88)
Q Consensus 17 T~eE~k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc 54 (88)
|.++-..+...|-. .|.++|..+ |-|..++
T Consensus 6 t~~~l~~ia~~iG~-------~Wk~Lar~L-Gls~~dI 35 (86)
T cd08318 6 TGEQITVFANKLGE-------DWKTLAPHL-EMKDKEI 35 (86)
T ss_pred CHHHHHHHHHHHhh-------hHHHHHHHc-CCCHHHH
Confidence 55555555444433 799999999 5666665
No 147
>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=28.98 E-value=1.8e+02 Score=19.32 Aligned_cols=44 Identities=18% Similarity=0.158 Sum_probs=28.6
Q ss_pred HHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 041937 23 LFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIKS 67 (88)
Q Consensus 23 ~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (88)
.|..+|.+.|+. ..-....||+.+ |-|..-|+.+.......++.
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 566666665532 234577888888 58888888877766665543
No 148
>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=28.86 E-value=1e+02 Score=17.64 Aligned_cols=38 Identities=18% Similarity=0.328 Sum_probs=26.4
Q ss_pred HHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHHHHHHH
Q 041937 24 FENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEMLVDDI 65 (88)
Q Consensus 24 Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv 65 (88)
+.-+|.-|+++ +.-.+|..+ |++..+.++..+...++.
T Consensus 10 ~vvalllfGp~---kLP~~~r~l-G~~ir~fk~~~~~~~~~~ 47 (53)
T PF02416_consen 10 LVVALLLFGPK---KLPELARSL-GKAIREFKKAINEAKEEI 47 (53)
T ss_dssp HHHHHHHS-TT---THHHHHHHH-HHHHHHHHHHHHHHHH--
T ss_pred HHHHHHHhCch---HHHHHHHHH-HHHHHHHHHHHHhhhhhh
Confidence 44567777654 899999999 688888887777666654
No 149
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=28.85 E-value=2.1e+02 Score=20.01 Aligned_cols=47 Identities=15% Similarity=0.074 Sum_probs=34.1
Q ss_pred CCCHHHHHHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHHHHH
Q 041937 15 SWTAKKNKLFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEMLVD 63 (88)
Q Consensus 15 ~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~L~~ 63 (88)
.-|..|-..|...+.... ...-..+.||+.| +-|..-|+.|-..|+.
T Consensus 158 ~Lt~re~~~l~~~i~~~~-~~g~s~~eIA~~l-~iS~~Tv~~~~~~~~~ 204 (239)
T PRK10430 158 GLTPQTLRTLCQWIDAHQ-DYEFSTDELANAV-NISRVSCRKYLIWLVN 204 (239)
T ss_pred CCCHHHHHHHHHHHHhCC-CCCcCHHHHHHHh-CchHHHHHHHHHHHHh
Confidence 478888766666565432 1234689999999 6999999998888755
No 150
>PRK06930 positive control sigma-like factor; Validated
Probab=28.46 E-value=1.9e+02 Score=20.23 Aligned_cols=50 Identities=16% Similarity=0.137 Sum_probs=30.2
Q ss_pred CCHHHHHHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 041937 16 WTAKKNKLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 16 WT~eE~k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
.+.++...|..+|...++. ..-....||+.+ |-|..-|+.+.......++
T Consensus 100 ~~~e~~~~l~~al~~L~~rer~V~~L~~~eg~s~~EIA~~l-giS~~tVk~~l~Ra~~kLr 159 (170)
T PRK06930 100 ISEWDKIRIEDALSVLTEREKEVYLMHRGYGLSYSEIADYL-NIKKSTVQSMIERAEKKIA 159 (170)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHH
Confidence 3444555666676666531 233567788777 5777777777766555444
No 151
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=28.23 E-value=2e+02 Score=19.57 Aligned_cols=45 Identities=13% Similarity=0.150 Sum_probs=27.3
Q ss_pred HHHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 041937 21 NKLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 21 ~k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
...|..+|.+.|+. ..-.-..||+.+ |.|..-|+.+.......++
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 45577777776643 122346777777 5777777777665444444
No 152
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=27.66 E-value=2e+02 Score=19.59 Aligned_cols=44 Identities=20% Similarity=0.240 Sum_probs=29.7
Q ss_pred HHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 041937 22 KLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
..|..+|.+.|+. ..-.-..||+.+ |-|..-|+.|.......|+
T Consensus 103 ~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~L-gis~~tV~~~l~RAr~~Lr 156 (182)
T PRK12540 103 EEFRAALDKLPQDQREALILVGASGFSYEDAAAIC-GCAVGTIKSRVNRARSKLS 156 (182)
T ss_pred HHHHHHHHhCCHHHHHHhhHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 4577788877642 234577888888 5888888888765555554
No 153
>COG3053 CitC Citrate lyase synthetase [Energy production and conversion]
Probab=27.62 E-value=93 Score=24.85 Aligned_cols=29 Identities=21% Similarity=0.240 Sum_probs=23.1
Q ss_pred hHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 041937 38 RWQIIAKIVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 38 rW~kIA~~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
+|+.||..||--|-.=..+|+.....++.
T Consensus 317 ~~~~ia~lVP~tTl~Yl~~~~a~~~~~~~ 345 (352)
T COG3053 317 DLEAIANLVPATTLNYLQQHLAEHIIDIA 345 (352)
T ss_pred CHHHHHhhCcHHHHHHHHHHHHHhHHHHh
Confidence 79999999997777777777777666554
No 154
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=27.52 E-value=43 Score=21.87 Aligned_cols=24 Identities=21% Similarity=0.445 Sum_probs=12.7
Q ss_pred HHHHHHHHhcCCCCChhHHHHHHHcCC
Q 041937 22 KLFENALAIYDKDTPDRWQIIAKIVGG 48 (88)
Q Consensus 22 k~Le~al~~~~~~~~~rW~kIA~~vpg 48 (88)
.+|.+|+.-|... .|..++.++||
T Consensus 95 diLKKa~~~~~~~---~~~~~~~~~~~ 118 (121)
T PRK09413 95 ELLKEAVEYGRAK---KWIAHAPLLPG 118 (121)
T ss_pred HHHHHHHHHhchh---hhhhcCCCCCC
Confidence 3444444444332 67777666665
No 155
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=27.39 E-value=2e+02 Score=19.37 Aligned_cols=44 Identities=14% Similarity=0.108 Sum_probs=27.0
Q ss_pred HHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 041937 22 KLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
..+..+|.+.|+. ..-.-+.||+.+ |-|..-|+.+.......++
T Consensus 125 ~~l~~~l~~L~~~~r~i~~l~~~~~~s~~eIA~~l-gis~~tV~~~l~ra~~~Lr 178 (182)
T PRK12537 125 GKIHRCLEQLEPARRNCILHAYVDGCSHAEIAQRL-GAPLGTVKAWIKRSLKALR 178 (182)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHH-CCChhhHHHHHHHHHHHHH
Confidence 3566677776542 123456677777 5777777777766555554
No 156
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=27.36 E-value=1.9e+02 Score=19.09 Aligned_cols=44 Identities=18% Similarity=0.175 Sum_probs=30.7
Q ss_pred HHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 041937 22 KLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
..|.++|...|+. .+-.-+.||+.+ |-|..-|+.+.......++
T Consensus 112 ~~l~~~l~~L~~~~r~vl~l~~~~g~s~~eIA~~l-g~s~~tv~~~l~Rar~~L~ 165 (175)
T PRK12518 112 DLVQQGLQTLSLEHRAVLVLHDLEDLPQKEIAEIL-NIPVGTVKSRLFYARRQLR 165 (175)
T ss_pred HHHHHHHHhCCHHHeeeeeehHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 3466777777632 234578999999 6888888888876555544
No 157
>KOG0721 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=27.17 E-value=71 Score=24.19 Aligned_cols=20 Identities=35% Similarity=0.513 Sum_probs=16.2
Q ss_pred CCCCHHHHHHHHHHHHHHHh
Q 041937 47 GGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 47 pgRT~~qc~~ry~~L~~dv~ 66 (88)
||-|..|+++||+.|.-...
T Consensus 109 pgas~~eIKkaYR~LSik~H 128 (230)
T KOG0721|consen 109 PGASEKEIKKAYRRLSIKYH 128 (230)
T ss_pred CCCCHHHHHHHHHHhhhhhC
Confidence 78899999999998775543
No 158
>PRK04654 sec-independent translocase; Provisional
Probab=27.03 E-value=1.1e+02 Score=22.84 Aligned_cols=39 Identities=13% Similarity=0.264 Sum_probs=27.1
Q ss_pred HHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHHHHHHH
Q 041937 23 LFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEMLVDDI 65 (88)
Q Consensus 23 ~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv 65 (88)
++.-+|.-|++ .|+=+|+..+ ||...++|+.+....+++
T Consensus 12 I~VVALlV~GP---erLPe~aRtl-Gk~irk~R~~~~~vk~El 50 (214)
T PRK04654 12 IAVVALVVLGP---ERLPKAARFA-GLWVRRARMQWDSVKQEL 50 (214)
T ss_pred HHHHHHHhcCc---hHHHHHHHHH-HHHHHHHHHHHHHHHHHH
Confidence 44456777754 4999999999 688888776665554444
No 159
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=27.02 E-value=2.1e+02 Score=19.56 Aligned_cols=49 Identities=12% Similarity=0.135 Sum_probs=33.9
Q ss_pred HHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHhhhcCC
Q 041937 22 KLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIKSIESD 71 (88)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~~ie~g 71 (88)
..|..+|.+.|+. ..-.-..||+.+ |-|..-|+.+.......++.+-.+
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 4567777777642 234578888888 688888888887766666665553
No 160
>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=26.95 E-value=1e+02 Score=16.43 Aligned_cols=20 Identities=30% Similarity=0.449 Sum_probs=15.6
Q ss_pred CCCCHHHHHHHHHHHHHHHh
Q 041937 47 GGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 47 pgRT~~qc~~ry~~L~~dv~ 66 (88)
++-|.++++.+|+.|.....
T Consensus 10 ~~~~~~~ik~~y~~l~~~~H 29 (55)
T cd06257 10 PDASDEEIKKAYRKLALKYH 29 (55)
T ss_pred CCCCHHHHHHHHHHHHHHHC
Confidence 35788999999998876553
No 161
>KOG4031 consensus Vesicle coat protein clathrin, light chain [Intracellular trafficking, secretion, and vesicular transport]
Probab=26.81 E-value=1.7e+02 Score=22.00 Aligned_cols=46 Identities=17% Similarity=0.289 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHhcCCCCChhHHHHHHHcCC--CCHHHHH--HHHHHHHHHHh
Q 041937 19 KKNKLFENALAIYDKDTPDRWQIIAKIVGG--TSEEEVK--RRYEMLVDDIK 66 (88)
Q Consensus 19 eE~k~Le~al~~~~~~~~~rW~kIA~~vpg--RT~~qc~--~ry~~L~~dv~ 66 (88)
.|+..|+.-...+..+ .-|++|++.+-- |+-++|+ .|.+.|+-.|+
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 3344444444444444 579999999842 6677775 44555555444
No 162
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=26.34 E-value=1.9e+02 Score=22.27 Aligned_cols=39 Identities=18% Similarity=0.246 Sum_probs=30.0
Q ss_pred HHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHHHHHH
Q 041937 22 KLFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEMLVDD 64 (88)
Q Consensus 22 k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~L~~d 64 (88)
+.|-.....+|.- +=..||+.| |=|++-|-+|.++|+.+
T Consensus 14 qIL~ei~~~qp~v---~q~eIA~~l-giT~QaVsehiK~Lv~e 52 (260)
T COG1497 14 QILSEIAVRQPRV---KQKEIAKKL-GITLQAVSEHIKELVKE 52 (260)
T ss_pred HHHHHHHHhCCCC---CHHHHHHHc-CCCHHHHHHHHHHHHhc
Confidence 4444444555654 678999999 79999999999999874
No 163
>PTZ00397 macrophage migration inhibition factor-like protein; Provisional
Probab=26.29 E-value=1e+02 Score=19.73 Aligned_cols=21 Identities=14% Similarity=0.219 Sum_probs=17.1
Q ss_pred cCCCCHHHHHHHHHHHHHHHh
Q 041937 46 VGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 46 vpgRT~~qc~~ry~~L~~dv~ 66 (88)
++||+.++.++.|+.+.+.+.
T Consensus 66 ~g~~~~e~k~~l~~~i~~~l~ 86 (116)
T PTZ00397 66 IGGISRSNNSSIAAAITKILA 86 (116)
T ss_pred ecCCCHHHHHHHHHHHHHHHH
Confidence 578999999999998766554
No 164
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=26.20 E-value=2.1e+02 Score=19.15 Aligned_cols=43 Identities=19% Similarity=0.210 Sum_probs=30.2
Q ss_pred HHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHH
Q 041937 22 KLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDI 65 (88)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv 65 (88)
..+..+|.+.|+. ..-....||+.+ |.|..-|+.|...-...+
T Consensus 111 ~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~~ 163 (172)
T PRK09651 111 QLLDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKL-GVSVSSVKKYVAKATEHC 163 (172)
T ss_pred HHHHHHHHhCCHHHhHHhhhhhccCCCHHHHHHHh-CCCHHHHHHHHHHHHHHH
Confidence 4566677777642 245688999999 699999998887644433
No 165
>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=26.10 E-value=2.1e+02 Score=21.08 Aligned_cols=44 Identities=18% Similarity=0.145 Sum_probs=31.8
Q ss_pred HHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 041937 23 LFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIKS 67 (88)
Q Consensus 23 ~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (88)
.|..+|.+.|+. ..-.-..||+.+ |.|..-|+.|.......|+.
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 466677777643 234578999999 69999999998765555554
No 166
>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=26.04 E-value=2.1e+02 Score=19.21 Aligned_cols=43 Identities=12% Similarity=0.105 Sum_probs=26.7
Q ss_pred HHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 041937 23 LFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 23 ~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
.|.++|.+.+.. ..-.-..||+.+ |.|...|+.+...+...++
T Consensus 142 ~l~~~l~~Ll~~~~~~i~~~~~~~~s~~eIA~~l-~~s~~tV~~~l~r~r~~L~ 194 (198)
T TIGR02859 142 DIESKMNELLSDLEWKVLQSYLDGKSYQEIACDL-NRHVKSIDNALQRVKRKLE 194 (198)
T ss_pred HHHHHHHHhcCHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 466677664322 133456777777 5777777777777666655
No 167
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=25.96 E-value=1.2e+02 Score=22.86 Aligned_cols=43 Identities=16% Similarity=0.071 Sum_probs=31.9
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCCChhHHHHHHHcCC-CCHHHH
Q 041937 12 SGSSWTAKKNKLFENALAIYDKDTPDRWQIIAKIVGG-TSEEEV 54 (88)
Q Consensus 12 s~~~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~vpg-RT~~qc 54 (88)
....+|.++...||..+++--.-....|+++|..+.= .+..+|
T Consensus 40 ERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqV 83 (228)
T KOG2251|consen 40 ERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQV 83 (228)
T ss_pred ccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhh
Confidence 3456999999999998887443345799999999853 555554
No 168
>COG5158 SEC1 Proteins involved in synaptic transmission and general secretion, Sec1 family [Intracellular trafficking and secretion]
Probab=25.95 E-value=56 Score=27.77 Aligned_cols=26 Identities=23% Similarity=0.526 Sum_probs=23.0
Q ss_pred HHHHHHHHHhhhcCCCCCCCCCCCCC
Q 041937 57 RYEMLVDDIKSIESDRVPLPDYAQND 82 (88)
Q Consensus 57 ry~~L~~dv~~ie~g~v~~P~y~~~~ 82 (88)
.|+.|++|+..+..+.|.+|.+...|
T Consensus 239 TYqaml~Dl~~~~~~~v~~~~~~~~g 264 (582)
T COG5158 239 TYQAMLHDLLGINNNIVTIPSSSVNG 264 (582)
T ss_pred HHHHHHHHHHHhhcCeEEeccccccc
Confidence 48889999999999999999887744
No 169
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=25.76 E-value=2.6e+02 Score=20.15 Aligned_cols=43 Identities=16% Similarity=0.149 Sum_probs=29.3
Q ss_pred HHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 041937 23 LFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 23 ~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
.|..+|.+.|.. ..-.-..||+.+ |.|..-|+.|...-...++
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 467777776642 234578899999 6888888888765444443
No 170
>COG4387 Mu-like prophage protein gp36 [Function unknown]
Probab=25.71 E-value=94 Score=21.72 Aligned_cols=36 Identities=25% Similarity=0.337 Sum_probs=26.9
Q ss_pred HHHHHHc--CCCCHHHHHHHHHHHHHHHhhhcCCCCCC
Q 041937 40 QIIAKIV--GGTSEEEVKRRYEMLVDDIKSIESDRVPL 75 (88)
Q Consensus 40 ~kIA~~v--pgRT~~qc~~ry~~L~~dv~~ie~g~v~~ 75 (88)
..||-.. -+|-.+|.++||+.-+.-++..-+|.|++
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 3456543 36889999999998777777777888775
No 171
>PRK00575 tatA twin arginine translocase protein A; Provisional
Probab=25.15 E-value=1.9e+02 Score=18.92 Aligned_cols=41 Identities=17% Similarity=0.190 Sum_probs=32.0
Q ss_pred HHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 041937 23 LFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIKS 67 (88)
Q Consensus 23 ~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (88)
++.-+|.-|+.+ |--.++..| ||+..+.|+--+.+.++...
T Consensus 12 Ilvi~LllFGpk---KLPel~r~l-Gk~ir~fK~a~~~~~~e~~~ 52 (92)
T PRK00575 12 LAVVVILLFGAK---KLPDAARSL-GKSLRIFKSEVKEMQSDNKA 52 (92)
T ss_pred HHHHHHHhccch---HHHHHHHHH-HHHHHHHHHHHhhhhhcccc
Confidence 455577888655 889999999 69999999887777776654
No 172
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=25.09 E-value=2.8e+02 Score=20.76 Aligned_cols=46 Identities=13% Similarity=0.042 Sum_probs=34.1
Q ss_pred HHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHhhh
Q 041937 22 KLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIKSI 68 (88)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~~i 68 (88)
..|..+|...++. ..-.-..||+.+ |.|..-|+.+...-...++..
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 4566667666532 234578999999 799999999998877777653
No 173
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=25.08 E-value=2.2e+02 Score=19.17 Aligned_cols=44 Identities=23% Similarity=0.134 Sum_probs=29.3
Q ss_pred HHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 041937 22 KLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
..|..+|...|+. ..-.-..||+.+ |.|..-|+.+.......++
T Consensus 133 ~~l~~~l~~L~~~~~~v~~l~~~~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~Lr 186 (194)
T PRK12519 133 QRVQTALAQLPESQRQVLELAYYEGLSQSEIAKRL-GIPLGTVKARARQGLLKLR 186 (194)
T ss_pred HHHHHHHHhCCHHHhhhhhhhhhcCCCHHHHHHHh-CCCHHHHHHHHHHHHHHHH
Confidence 3466677776632 234567888888 5888888888776555554
No 174
>PF08259 Periviscerokin: Periviscerokinin family; InterPro: IPR013231 Perviscerokinin neuropeptides are found in the abdominal perisympathetic organs of insects. They mediate visceral muscle contractile activity (myotropic activity). CAPA, which are in the periviscerokinin and pyrokinin peptide families, has potential medical importance. This is due to its myotropic effects on, for example, heart muscles and due to its occurrence in the Ixodoidea (ticks), which are important vectors in the transmission of many animal diseases []. These peptides also have a strong diuretic or anti-diuretic effect, suggesting they have significant medical implications [].
Probab=25.07 E-value=33 Score=14.21 Aligned_cols=8 Identities=38% Similarity=0.837 Sum_probs=5.9
Q ss_pred CCCCCCCC
Q 041937 70 SDRVPLPD 77 (88)
Q Consensus 70 ~g~v~~P~ 77 (88)
+|.++||.
T Consensus 3 sGlI~fpR 10 (11)
T PF08259_consen 3 SGLIPFPR 10 (11)
T ss_pred ccccccCC
Confidence 57788884
No 175
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=24.81 E-value=2.3e+02 Score=19.18 Aligned_cols=43 Identities=2% Similarity=-0.116 Sum_probs=28.3
Q ss_pred HHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHH
Q 041937 22 KLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDI 65 (88)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv 65 (88)
..|..+|.+.|+. ..-.-..||+.+ |-|..-|+.|.......+
T Consensus 123 ~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~l-gis~~tV~~~l~Rar~~L 175 (191)
T PRK12520 123 EVLQACVDRLPPRTGRVFMMREWLELETEEICQEL-QITATNAWVLLYRARMRL 175 (191)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 3466777777642 133467888888 688888888876544433
No 176
>PF13748 ABC_membrane_3: ABC transporter transmembrane region
Probab=24.71 E-value=87 Score=23.74 Aligned_cols=29 Identities=17% Similarity=0.294 Sum_probs=25.4
Q ss_pred CChhHHHHHHHcCCCCHHHHHHHHHHHHH
Q 041937 35 TPDRWQIIAKIVGGTSEEEVKRRYEMLVD 63 (88)
Q Consensus 35 ~~~rW~kIA~~vpgRT~~qc~~ry~~L~~ 63 (88)
-++|+|+=...+.+++..++++||..|..
T Consensus 169 LNnrlE~eV~~i~~~~~~~l~rHy~~L~~ 197 (237)
T PF13748_consen 169 LNNRLEKEVDIIERRKPASLRRHYRRLSR 197 (237)
T ss_pred HhHHHHHHccHhhcCChHHHHHHHHHHHh
Confidence 36699999999999999999999997654
No 177
>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=24.11 E-value=27 Score=25.65 Aligned_cols=48 Identities=15% Similarity=0.265 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHhcCCCCChhHHHHHHHcC--CCC---HHHHHHHHHHHHHHHhhh
Q 041937 19 KKNKLFENALAIYDKDTPDRWQIIAKIVG--GTS---EEEVKRRYEMLVDDIKSI 68 (88)
Q Consensus 19 eE~k~Le~al~~~~~~~~~rW~kIA~~vp--gRT---~~qc~~ry~~L~~dv~~i 68 (88)
++++.|......+. ....-|++|+++|- .+. ..+ +.|++.|+-.|+..
T Consensus 167 ~~ee~fl~~~~~~~-~~~t~WerV~~Lid~~~~~~~~~kD-~sRmR~iLl~LK~~ 219 (225)
T PF01086_consen 167 EEEEEFLAKREEFL-QPGTEWERVAKLIDFNPKSSKSGKD-VSRMREILLKLKGD 219 (225)
T ss_dssp -------------------------------------------------------
T ss_pred HHHHHHHHcccccC-CCCCcHHHHHHHhCCCCCCCCCCCc-HHHHHHHHHHhhhh
Confidence 44455555555542 13457999999992 222 222 56777777767643
No 178
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=24.04 E-value=2.8e+02 Score=20.68 Aligned_cols=46 Identities=13% Similarity=0.117 Sum_probs=33.9
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 041937 14 SSWTAKKNKLFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 14 ~~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
..=|+.|.+.|.-...-+ ....||+.+ +-|..-|+.|-..+...+.
T Consensus 142 ~~LS~RE~eVL~Lia~G~------SnkEIA~~L-~IS~~TVk~hvs~I~~KLg 187 (217)
T PRK13719 142 NKVTKYQNDVFILYSFGF------SHEYIAQLL-NITVGSSKNKISEILKFFG 187 (217)
T ss_pred CCCCHHHHHHHHHHHCCC------CHHHHHHHh-CCCHHHHHHHHHHHHHHhC
Confidence 456888888875544332 588999999 6999999988877766543
No 179
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=24.03 E-value=2.8e+02 Score=20.45 Aligned_cols=44 Identities=14% Similarity=0.067 Sum_probs=32.8
Q ss_pred HHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 041937 23 LFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIKS 67 (88)
Q Consensus 23 ~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (88)
.|..+|.+.|+. ..-.-+.||+.+ |.|..-|+.+...-...++.
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 466777777643 234578899999 79999999998877766664
No 180
>PF08424 NRDE-2: NRDE-2, necessary for RNA interference; InterPro: IPR013633 This is domain is found in eukaryotic proteins of unknown function.
Probab=23.83 E-value=3.1e+02 Score=20.75 Aligned_cols=58 Identities=21% Similarity=0.369 Sum_probs=41.9
Q ss_pred CCCCHHH-HHHHHHHHHhcCCCCChhHHHHHHHcCC----CCHHHHHHHHHHHHHHHhhhcCCC
Q 041937 14 SSWTAKK-NKLFENALAIYDKDTPDRWQIIAKIVGG----TSEEEVKRRYEMLVDDIKSIESDR 72 (88)
Q Consensus 14 ~~WT~eE-~k~Le~al~~~~~~~~~rW~kIA~~vpg----RT~~qc~~ry~~L~~dv~~ie~g~ 72 (88)
..|+.++ .+.++++|..+|. ...=|..--...-+ =|..+|+.-|..++..+.....+.
T Consensus 77 ~~~~~~~l~~~we~~l~~~~~-~~~LW~~yL~~~q~~~~~f~v~~~~~~y~~~l~~L~~~~~~~ 139 (321)
T PF08424_consen 77 KVWDSEKLAKKWEELLFKNPG-SPELWREYLDFRQSNFASFTVSDVRDVYEKCLRALSRRRSGR 139 (321)
T ss_pred HhCCHHHHHHHHHHHHHHCCC-ChHHHHHHHHHHHHHhccCcHHHHHHHHHHHHHHHHHhhccc
Confidence 3476666 4577777887765 35567766555544 478999999999999888887775
No 181
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=23.67 E-value=2.2e+02 Score=18.58 Aligned_cols=44 Identities=18% Similarity=0.000 Sum_probs=29.7
Q ss_pred HHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 041937 22 KLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
..|..+|.+.|+. ..-..+.||+.+ |-|..-|+.|...-...++
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 4566777776642 234577888888 5888888888776555543
No 182
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=23.50 E-value=3.1e+02 Score=20.35 Aligned_cols=45 Identities=13% Similarity=0.171 Sum_probs=33.4
Q ss_pred CCCHHHHHHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 041937 15 SWTAKKNKLFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 15 ~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
.-|..|-+.|.-...- .....||+.+ +-|..-|+.+-..+...+.
T Consensus 133 ~LSpRErEVLrLLAqG------kTnKEIAe~L-~IS~rTVkth~srImkKLg 177 (198)
T PRK15201 133 HFSVTERHLLKLIASG------YHLSETAALL-SLSEEQTKSLRRSIMRKLH 177 (198)
T ss_pred CCCHHHHHHHHHHHCC------CCHHHHHHHh-CCCHHHHHHHHHHHHHHhC
Confidence 3678888777544332 2589999999 6999999988887776654
No 183
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=23.19 E-value=2.6e+02 Score=19.34 Aligned_cols=45 Identities=13% Similarity=0.118 Sum_probs=29.9
Q ss_pred HHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 041937 22 KLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIKS 67 (88)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (88)
..|..+|...|+. ..-.-+.||+.+ |.|..-|+.+.......++.
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 3566777776632 233467888888 68888888887765555543
No 184
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=23.16 E-value=2.4e+02 Score=18.83 Aligned_cols=44 Identities=16% Similarity=0.177 Sum_probs=29.6
Q ss_pred HHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 041937 22 KLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
..|..+|...|+. ..-.-+.||+.+ |-|..-|+.+-......++
T Consensus 127 ~~l~~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~l-gis~~~V~~~l~ra~~~Lr 180 (186)
T PRK13919 127 TRLGRALKALSPEERRVIEVLYYQGYTHREAAQLL-GLPLGTLKTRARRALSRLK 180 (186)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHH
Confidence 4577777776632 233467888888 6888888887776555554
No 185
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=23.10 E-value=2.6e+02 Score=19.28 Aligned_cols=42 Identities=12% Similarity=0.023 Sum_probs=29.1
Q ss_pred HHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHH
Q 041937 23 LFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDI 65 (88)
Q Consensus 23 ~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv 65 (88)
.|..+|.+.|+. ..-.-..||+.+ |.|..-|+.|...-...+
T Consensus 132 ~l~~~L~~Lp~~~r~v~~L~~~eg~s~~EIA~~l-gis~~tVk~~l~RAr~~L 183 (201)
T PRK12545 132 LFETCLDHLPEQIGRVFMMREFLDFEIDDICTEL-TLTANHCSVLLYRARTRL 183 (201)
T ss_pred HHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 466777776642 234578899999 688888988876544444
No 186
>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=22.79 E-value=1.4e+02 Score=15.89 Aligned_cols=33 Identities=21% Similarity=0.333 Sum_probs=22.5
Q ss_pred HHHHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHH
Q 041937 20 KNKLFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRR 57 (88)
Q Consensus 20 E~k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~r 57 (88)
|-..+..+|..+.. +..+.|+.+ |-|...+..+
T Consensus 6 E~~~i~~aL~~~~g----n~~~aA~~L-gisr~tL~~k 38 (42)
T PF02954_consen 6 EKQLIRQALERCGG----NVSKAARLL-GISRRTLYRK 38 (42)
T ss_dssp HHHHHHHHHHHTTT-----HHHHHHHH-TS-HHHHHHH
T ss_pred HHHHHHHHHHHhCC----CHHHHHHHH-CCCHHHHHHH
Confidence 56688889999643 688999999 5665555443
No 187
>PRK01371 sec-independent translocase; Provisional
Probab=22.74 E-value=1.4e+02 Score=20.72 Aligned_cols=40 Identities=15% Similarity=0.260 Sum_probs=28.2
Q ss_pred HHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 041937 23 LFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 23 ~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
++.-+|.-|++ .|+-.+++.+ ||...++|+-.....++++
T Consensus 12 IlvVallvfGP---eKLP~~ar~l-g~~ir~~R~~~~~ak~~i~ 51 (137)
T PRK01371 12 LVVLAVLVFGP---DKLPKAARDA-GRTLRQLREMANNARNDLR 51 (137)
T ss_pred HHHHHhheeCc---hHHHHHHHHH-HHHHHHHHHHHHHHHHHHH
Confidence 44456777754 4999999999 6888888876555555554
No 188
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=22.66 E-value=62 Score=30.21 Aligned_cols=55 Identities=13% Similarity=0.318 Sum_probs=40.0
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCChhHHHHHH---------Hc---CCCCHHHHHHHHHHHHHHHhhhcC
Q 041937 13 GSSWTAKKNKLFENALAIYDKDTPDRWQIIAK---------IV---GGTSEEEVKRRYEMLVDDIKSIES 70 (88)
Q Consensus 13 ~~~WT~eE~k~Le~al~~~~~~~~~rW~kIA~---------~v---pgRT~~qc~~ry~~L~~dv~~ie~ 70 (88)
...|..++|+.|.-.+-+|+-+ +|+.|-. .+ +.=++.+...|-..|...++....
T Consensus 1133 ~~~W~~e~Ds~LLiGI~khGyg---swe~Ir~Dp~L~l~dKi~~~e~~P~a~~L~~R~~yLls~~~~~~~ 1199 (1373)
T KOG0384|consen 1133 DCDWGSEDDSMLLIGIFKHGYG---SWEAIRLDPDLGLTDKIFLVETVPQAKHLQRRADYLLSLLRKHDK 1199 (1373)
T ss_pred ccCCCchhhhhHhhhhhhcccc---cHHHhccCccccchhhhcccccCCchHHHHHHHHHHHHHHhhccc
Confidence 4579999999999999999877 8998842 11 023566777777777777765543
No 189
>PF14552 Tautomerase_2: Tautomerase enzyme; PDB: 2AAG_C 2AAL_A 2AAJ_A 1MWW_C.
Probab=22.62 E-value=1.2e+02 Score=18.93 Aligned_cols=20 Identities=30% Similarity=0.491 Sum_probs=15.0
Q ss_pred CCCCHHHHHHHHHHHHHHHh
Q 041937 47 GGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 47 pgRT~~qc~~ry~~L~~dv~ 66 (88)
+|||.++=+.-|+.|.+.+.
T Consensus 38 ~gRs~e~K~~ly~~l~~~L~ 57 (82)
T PF14552_consen 38 AGRSTEQKKALYRALAERLA 57 (82)
T ss_dssp S---HHHHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHHH
Confidence 48999999999999998885
No 190
>PF13496 DUF4120: Domain of unknown function (DUF4120)
Probab=22.26 E-value=92 Score=20.42 Aligned_cols=24 Identities=13% Similarity=0.122 Sum_probs=19.4
Q ss_pred HHHHHHHcCCCCHHHHHHHHHHHH
Q 041937 39 WQIIAKIVGGTSEEEVKRRYEMLV 62 (88)
Q Consensus 39 W~kIA~~vpgRT~~qc~~ry~~L~ 62 (88)
=.++|+.++..|.+.|.+|-++-.
T Consensus 11 vv~yA~sI~D~tl~~ClerLk~We 34 (95)
T PF13496_consen 11 VVQYAESIGDSTLQKCLERLKQWE 34 (95)
T ss_pred HHHHHHHhcchHHHHHHHHHHHHH
Confidence 346789999999999999877644
No 191
>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=22.21 E-value=1.7e+02 Score=18.06 Aligned_cols=36 Identities=14% Similarity=0.166 Sum_probs=25.6
Q ss_pred HHHHHHHHHhcCCCCChhHHHHHHHcCC-CCHHHHHH
Q 041937 21 NKLFENALAIYDKDTPDRWQIIAKIVGG-TSEEEVKR 56 (88)
Q Consensus 21 ~k~Le~al~~~~~~~~~rW~kIA~~vpg-RT~~qc~~ 56 (88)
+..+.++|.+.|.+.-.....||+.++. ++...|-.
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 4556677888999988899999999963 66666554
No 192
>PRK14858 tatA twin arginine translocase protein A; Provisional
Probab=22.04 E-value=2e+02 Score=19.22 Aligned_cols=39 Identities=15% Similarity=0.253 Sum_probs=26.0
Q ss_pred HHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHHHHHHH
Q 041937 23 LFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEMLVDDI 65 (88)
Q Consensus 23 ~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv 65 (88)
+|.-+|.-|++ .++-.++..+ ||...+.++....+..++
T Consensus 12 IlvVallvfGP---kKLPelar~l-Gk~i~~fk~~~~d~k~~i 50 (108)
T PRK14858 12 ILVIALIVIGP---QKLPDLARSL-GRGLAEFKKATDDFKQSM 50 (108)
T ss_pred HHHHHHHhcCc---hHHHHHHHHH-HHHHHHHHHHHHHHHHHH
Confidence 45556777754 4899999999 577777776655444333
No 193
>PRK00846 hypothetical protein; Provisional
Probab=22.01 E-value=2.2e+02 Score=17.90 Aligned_cols=17 Identities=18% Similarity=0.333 Sum_probs=10.1
Q ss_pred HHHHHHHHHHHhhhcCC
Q 041937 55 KRRYEMLVDDIKSIESD 71 (88)
Q Consensus 55 ~~ry~~L~~dv~~ie~g 71 (88)
+..-+.|.+.++.++++
T Consensus 47 ~~ql~~L~~rL~~~~~s 63 (77)
T PRK00846 47 AELIRHLLEDLGKVRST 63 (77)
T ss_pred HHHHHHHHHHHHHhccc
Confidence 34445567777776654
No 194
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=21.95 E-value=3.2e+02 Score=19.87 Aligned_cols=47 Identities=23% Similarity=0.229 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 041937 19 KKNKLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 19 eE~k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
++...|..+|...|+. ..-....||+.+ |-|...|+.+....+..++
T Consensus 192 ~~~~~l~~~l~~L~~~~r~vl~l~y~~~~s~~eIA~~l-gvs~~~V~~~~~ra~~kLr 248 (256)
T PRK07408 192 EDRIRLQQALAQLEERTREVLEFVFLHDLTQKEAAERL-GISPVTVSRRVKKGLDQLK 248 (256)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHCCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHH
Confidence 3445677777776632 234578888888 6888888888776555554
No 195
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=21.60 E-value=3.2e+02 Score=19.67 Aligned_cols=43 Identities=7% Similarity=0.067 Sum_probs=26.8
Q ss_pred HHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 041937 23 LFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 23 ~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
.|..+|.+.|+. ..-....||+.+ |-|..-|+.+.......++
T Consensus 194 ~l~~~l~~L~~~~r~vl~l~~~~~~s~~EIA~~l-gis~~tV~~~~~ra~~~Lr 246 (251)
T PRK07670 194 ELAEKIKQLSEKEQLVISLFYKEELTLTEIGQVL-NLSTSRISQIHSKALFKLK 246 (251)
T ss_pred HHHHHHhcCCHHHHHHHHHHHhcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHH
Confidence 455666665532 233567788777 5777777777766555544
No 196
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=21.59 E-value=2.8e+02 Score=19.08 Aligned_cols=44 Identities=18% Similarity=0.197 Sum_probs=31.0
Q ss_pred HHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 041937 22 KLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
..|..+|.+.|+. ..-....||..+ |-|...|+.|.......++
T Consensus 105 ~~l~~~L~~Lp~~~r~v~~L~~~~g~s~~EIA~~L-giS~~tVk~~l~Rar~~Lr 158 (188)
T PRK12546 105 SDFRAAFAQLPDEQREALILVGASGFSYEEAAEMC-GVAVGTVKSRANRARARLA 158 (188)
T ss_pred HHHHHHHHhCCHHHhHHhhhHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 3566777776642 244688999999 6889999888876555444
No 197
>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=21.53 E-value=2.4e+02 Score=18.17 Aligned_cols=49 Identities=12% Similarity=0.152 Sum_probs=28.6
Q ss_pred CHHHHHHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 041937 17 TAKKNKLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 17 T~eE~k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
..++...|..+|.+.|+. ..-.-..||+.+ |-|...|+.|.......++
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 444556678888877643 123455666666 4666666666655554443
No 198
>KOG1878 consensus Nuclear receptor coregulator SMRT/SMRTER, contains Myb-like domains [Transcription]
Probab=21.51 E-value=18 Score=34.04 Aligned_cols=43 Identities=21% Similarity=0.342 Sum_probs=37.1
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHH
Q 041937 13 GSSWTAKKNKLFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYE 59 (88)
Q Consensus 13 ~~~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~ 59 (88)
+..|+.+|-++|..-+.++++ +...||..+-.||+.+|.--|.
T Consensus 225 ~n~Ws~~Ek~~fk~rf~~H~k----nf~~~as~~erkSv~d~vlfyy 267 (1672)
T KOG1878|consen 225 MNEWSPEEKELFKSRFAQHVK----NFGLIASFFERKSVSDCVLFYY 267 (1672)
T ss_pred hhhccccccccccchhhhcCc----chhhhhhhhcccchhhceeeee
Confidence 367999999999999999765 6899999999999999976553
No 199
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=21.28 E-value=3.1e+02 Score=19.50 Aligned_cols=46 Identities=20% Similarity=0.172 Sum_probs=30.5
Q ss_pred HHHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 041937 21 NKLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIKS 67 (88)
Q Consensus 21 ~k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~~ 67 (88)
...|..+|...|+. ..-.-+.||+.| |-|..-|+.|.......|+.
T Consensus 125 ~~~l~~al~~Lp~~~R~v~~L~y~eg~s~~EIAe~L-giS~~tVk~~L~RAr~~Lr~ 180 (216)
T PRK12533 125 VRLVNAALAKLPVEYREVLVLRELEDMSYREIAAIA-DVPVGTVMSRLARARRRLAA 180 (216)
T ss_pred HHHHHHHHHcCCHHHHhHhhhHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence 35677777776642 123467888888 68888888887765544443
No 200
>PF09127 Leuk-A4-hydro_C: Leukotriene A4 hydrolase, C-terminal; InterPro: IPR015211 This C-terminal domain is found in peptidases belonging to MEROPS peptidase family M1, particularly: aminopeptidase-1 of Caenorhabditis elegans, aminopeptidase O, aminopeptidase B and the bifunctional leukotriene A4 hydrolase/aminopeptidase. The domain adopts a structure consisting of two layers of parallel alpha-helices, five in the inner layer and four in the outer, arranged in an antiparallel manner, with perpendicular loops containing short helical segments on top. It is required for the formation of a deep cleft harbouring the catalytic Zn2+ site in leukotriene A4 hydrolase []. ; GO: 0008237 metallopeptidase activity, 0008270 zinc ion binding, 0019370 leukotriene biosynthetic process; PDB: 3FUJ_A 3FU3_A 3FTX_A 3FTS_A 3B7R_L 2VJ8_A 3FTW_A 3FUF_A 3FU0_A 3CHO_A ....
Probab=21.13 E-value=2.7e+02 Score=18.78 Aligned_cols=53 Identities=17% Similarity=0.319 Sum_probs=35.7
Q ss_pred CCCCCCCCHHHHHHHHHHHHhcCCCCChhHHHHHHHc--CCCCHHHHHHHHHHHH
Q 041937 10 TISGSSWTAKKNKLFENALAIYDKDTPDRWQIIAKIV--GGTSEEEVKRRYEMLV 62 (88)
Q Consensus 10 ~~s~~~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~v--pgRT~~qc~~ry~~L~ 62 (88)
...-..|+..|-..|.+.|.....-.+..-+.+.+.. ..-+.-|++-||..|.
T Consensus 25 ~~d~~~~~~~Q~~~FL~~L~~~~~l~~~~l~~Ld~~y~l~~s~NaEI~~rW~~l~ 79 (143)
T PF09127_consen 25 AEDIKDWSSNQWVVFLDQLLEPKPLSPEKLQALDKVYKLSNSKNAEIRFRWLRLA 79 (143)
T ss_dssp GGGGTT--HHHHHHHHHHHHTCCG-CHHHHHHHHHHHCHCT-SSHHHHHHHHHHH
T ss_pred HHHHHhCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCCCCCHHHHHHHHHHH
Confidence 3455789999999999999665544556777777766 3456688888887654
No 201
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=20.92 E-value=2.6e+02 Score=18.48 Aligned_cols=42 Identities=10% Similarity=0.001 Sum_probs=25.1
Q ss_pred HHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHHHHHH
Q 041937 22 KLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEMLVDD 64 (88)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~L~~d 64 (88)
..|+.+|...|+. ..-..+.||+.+ |-|..-|+.+...-...
T Consensus 110 ~~l~~~l~~L~~~~r~v~~L~~~eg~s~~EIA~~l-~is~~tV~~~l~ra~~~ 161 (168)
T PRK12525 110 LAIDRLLDGLSGKARAAFLMSQLEGLTYVEIGERL-GVSLSRIHQYMVEAFKC 161 (168)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3466677776643 233567777777 56777777666554433
No 202
>PF08074 CHDCT2: CHDCT2 (NUC038) domain; InterPro: IPR012957 The CHDCT2 C-terminal domain is found in PHD/RING fingers and chromo domain-associated CHD-like helicases [].; GO: 0003677 DNA binding, 0005524 ATP binding, 0008270 zinc ion binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=20.89 E-value=75 Score=23.06 Aligned_cols=55 Identities=20% Similarity=0.301 Sum_probs=40.3
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCChhHHHHHHHc-------CCCCH------HHHHHHHH----HHHHHHhhhcCC
Q 041937 14 SSWTAKKNKLFENALAIYDKDTPDRWQIIAKIV-------GGTSE------EEVKRRYE----MLVDDIKSIESD 71 (88)
Q Consensus 14 ~~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~v-------pgRT~------~qc~~ry~----~L~~dv~~ie~g 71 (88)
.-|-..-|.-|..++..|+.+ ||+.|...- |=|+. -|.+++|. +|++...-||..
T Consensus 4 ~iw~r~hdywll~gi~~hgy~---rwqdi~nd~~f~IiNEPFk~e~~kgnfle~KNkFLaRRfKLLEQaLvIEEq 75 (173)
T PF08074_consen 4 EIWHRRHDYWLLAGIVKHGYG---RWQDIQNDPRFAIINEPFKTESQKGNFLEMKNKFLARRFKLLEQALVIEEQ 75 (173)
T ss_pred hhhhhhhhHHHHhHHhhccch---hHHHHhcCCceeeecccccccccccchHHHHHHHHHHHHHHHHHHHhhhcc
Confidence 358888899999999999887 999997532 11333 48888875 366776678876
No 203
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=20.83 E-value=2.5e+02 Score=18.16 Aligned_cols=45 Identities=18% Similarity=0.165 Sum_probs=32.8
Q ss_pred CCCHHHHHHHHHHHHhcCCCCChhHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 041937 15 SWTAKKNKLFENALAIYDKDTPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 15 ~WT~eE~k~Le~al~~~~~~~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
..|..|.++|.-...-+ .-+.||..+ +-|..-++.|...+...+.
T Consensus 137 ~Lt~~E~~il~~l~~g~------~~~~Ia~~l-~~s~~tv~~~~~~l~~Kl~ 181 (196)
T PRK10360 137 PLTKRERQVAEKLAQGM------AVKEIAAEL-GLSPKTVHVHRANLMEKLG 181 (196)
T ss_pred CCCHHHHHHHHHHHCCC------CHHHHHHHh-CCCHHHHHHHHHHHHHHhC
Confidence 57777877776544332 578999999 5788888888888777664
No 204
>smart00271 DnaJ DnaJ molecular chaperone homology domain.
Probab=20.60 E-value=1.6e+02 Score=16.01 Aligned_cols=18 Identities=28% Similarity=0.399 Sum_probs=14.1
Q ss_pred CCCHHHHHHHHHHHHHHH
Q 041937 48 GTSEEEVKRRYEMLVDDI 65 (88)
Q Consensus 48 gRT~~qc~~ry~~L~~dv 65 (88)
+-|.++|+..|+.|....
T Consensus 12 ~~~~~~ik~ay~~l~~~~ 29 (60)
T smart00271 12 DASLDEIKKAYRKLALKY 29 (60)
T ss_pred CCCHHHHHHHHHHHHHHH
Confidence 468889999998877655
No 205
>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=20.48 E-value=1.8e+02 Score=19.02 Aligned_cols=24 Identities=13% Similarity=0.465 Sum_probs=17.7
Q ss_pred CHHHHHHHHHHHHhcCCCCChhHHHHHHHcC
Q 041937 17 TAKKNKLFENALAIYDKDTPDRWQIIAKIVG 47 (88)
Q Consensus 17 T~eE~k~Le~al~~~~~~~~~rW~kIA~~vp 47 (88)
|+++.+.|...|-+ .|.++|..++
T Consensus 1 ~~~~~q~~~~nvGr-------~WK~laR~Lg 24 (90)
T cd08780 1 TPADQQHFAKSVGK-------KWKPVGRSLQ 24 (90)
T ss_pred CHHHHHHHHHHHhH-------HHHHHHHHHc
Confidence 45666666666555 7999999995
No 206
>TIGR00695 uxuA mannonate dehydratase. This Fe2+-requiring enzyme plays a role in D-glucuronate catabolism in Escherichia coli. Mannonate dehydratase converts D-mannonate to 2-dehydro-3-deoxy-D-gluconate. An apparent equivalog is found in a glucuronate utilization operon in Bacillus stearothermophilus T-6.
Probab=20.41 E-value=1.9e+02 Score=23.41 Aligned_cols=51 Identities=10% Similarity=0.277 Sum_probs=36.1
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCCChhHHHHH-------HHcCCCCHHHHHHHHHHHHHHHh
Q 041937 12 SGSSWTAKKNKLFENALAIYDKDTPDRWQIIA-------KIVGGTSEEEVKRRYEMLVDDIK 66 (88)
Q Consensus 12 s~~~WT~eE~k~Le~al~~~~~~~~~rW~kIA-------~~vpgRT~~qc~~ry~~L~~dv~ 66 (88)
....||.++.+.+.+.+..++- +|.-|. =.+++-.-++-.+.|++++..+.
T Consensus 36 ~gevW~~~~i~~~k~~ie~~GL----~~~vvEs~pv~e~Ik~g~~~rd~~Ienyk~~irNla 93 (394)
T TIGR00695 36 NGEVWEKEEIRKRKEYIESAGL----HWSVVESVPVHEAIKTGTGNYGRWIENYKQTLRNLA 93 (394)
T ss_pred CCCCCCHHHHHHHHHHHHHcCC----eEEEEeCCCccHHHHcCCCcHHHHHHHHHHHHHHHH
Confidence 3578999999999999999874 344431 12344556677888888777664
No 207
>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=20.17 E-value=2.4e+02 Score=17.77 Aligned_cols=44 Identities=11% Similarity=0.190 Sum_probs=31.6
Q ss_pred CCCChhHHHHHHHcCCCCHHHHHHHHHHHHHHHhhhc-CCCCCCC
Q 041937 33 KDTPDRWQIIAKIVGGTSEEEVKRRYEMLVDDIKSIE-SDRVPLP 76 (88)
Q Consensus 33 ~~~~~rW~kIA~~vpgRT~~qc~~ry~~L~~dv~~ie-~g~v~~P 76 (88)
.|.......|-+.+++=|...|..+++.......... ....++|
T Consensus 16 ~G~~pT~~~Vr~~lG~GS~~ti~~~l~~w~~~~~~~~~~~~~~lP 60 (120)
T PF11740_consen 16 AGKKPTVRAVRERLGGGSMSTISKHLKEWREEREAQVSEAAPDLP 60 (120)
T ss_pred cCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHhhhccccccccCCC
Confidence 3444579999999998899999999988777665444 2234455
No 208
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=20.15 E-value=3.5e+02 Score=19.66 Aligned_cols=49 Identities=14% Similarity=0.246 Sum_probs=28.2
Q ss_pred HHHHHHHHhcCCC----------CChhHHHHHHHcCCCCHHHHHHHHHH----HHHHHhhhcCC
Q 041937 22 KLFENALAIYDKD----------TPDRWQIIAKIVGGTSEEEVKRRYEM----LVDDIKSIESD 71 (88)
Q Consensus 22 k~Le~al~~~~~~----------~~~rW~kIA~~vpgRT~~qc~~ry~~----L~~dv~~ie~g 71 (88)
..|..+|...|+. ..-.-..||+.+ |.|..-|+.+... |...+..+..|
T Consensus 204 ~~l~~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~l-gis~~tV~~~~~ra~~~Lr~~l~~~~~~ 266 (268)
T PRK06288 204 RVIVEAIKTLPEREKKVLILYYYEDLTLKEIGKVL-GVTESRISQLHTKAVLQLRAKLAEIKKG 266 (268)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 4577777776532 123456777777 5777777766543 44444444444
No 209
>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A.
Probab=20.04 E-value=1.2e+02 Score=14.07 Aligned_cols=13 Identities=15% Similarity=0.355 Sum_probs=8.0
Q ss_pred HHHHHHHHHhcCC
Q 041937 21 NKLFENALAIYDK 33 (88)
Q Consensus 21 ~k~Le~al~~~~~ 33 (88)
...|++.+.+||.
T Consensus 20 ~~~~~~~~~~~P~ 32 (33)
T PF13174_consen 20 IEYFQRLIKRYPD 32 (33)
T ss_dssp HHHHHHHHHHSTT
T ss_pred HHHHHHHHHHCcC
Confidence 3456666777664
Done!