Query 034427
Match_columns 95
No_of_seqs 120 out of 578
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 02:44:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034427.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034427hhsearch_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 1.7E-14 3.7E-19 84.5 6.5 46 8-56 2-47 (48)
2 smart00717 SANT SANT SWI3, AD 99.3 4.1E-12 8.9E-17 71.3 6.0 46 8-57 2-47 (49)
3 cd00167 SANT 'SWI3, ADA2, N-Co 99.3 1.5E-11 3.3E-16 68.2 5.9 44 9-56 1-44 (45)
4 PF13921 Myb_DNA-bind_6: Myb-l 99.1 2.4E-10 5.3E-15 68.8 5.3 42 10-56 1-43 (60)
5 PLN03212 Transcription repress 99.0 1E-09 2.2E-14 84.6 5.4 53 6-61 24-77 (249)
6 PLN03212 Transcription repress 98.8 3.2E-08 6.9E-13 76.4 8.7 50 6-60 77-126 (249)
7 PLN03091 hypothetical protein; 98.8 3.8E-09 8.2E-14 87.0 3.6 51 7-60 14-65 (459)
8 KOG0048 Transcription factor, 98.8 7.8E-09 1.7E-13 77.9 4.1 52 7-61 9-61 (238)
9 PLN03091 hypothetical protein; 98.6 7.7E-08 1.7E-12 79.4 7.0 50 6-60 66-115 (459)
10 TIGR01557 myb_SHAQKYF myb-like 98.6 1.9E-07 4.2E-12 57.4 6.0 47 8-57 4-54 (57)
11 KOG0048 Transcription factor, 98.5 2.9E-07 6.3E-12 69.4 7.0 51 7-62 62-113 (238)
12 KOG0724 Zuotin and related mol 98.4 4.6E-07 9.9E-12 70.4 5.4 68 8-76 32-104 (335)
13 KOG0457 Histone acetyltransfer 98.4 6.6E-07 1.4E-11 73.6 5.9 47 7-57 72-118 (438)
14 COG5259 RSC8 RSC chromatin rem 98.2 1.9E-06 4E-11 71.9 4.5 44 8-56 280-323 (531)
15 KOG1279 Chromatin remodeling f 98.1 6.3E-06 1.4E-10 69.0 5.4 46 6-56 252-297 (506)
16 KOG0049 Transcription factor, 97.8 3.4E-05 7.3E-10 67.0 5.9 46 6-55 359-404 (939)
17 COG5114 Histone acetyltransfer 97.7 6.6E-05 1.4E-09 60.8 5.6 57 8-73 64-120 (432)
18 KOG4167 Predicted DNA-binding 97.6 0.00013 2.7E-09 63.9 6.0 45 6-55 618-662 (907)
19 PF13837 Myb_DNA-bind_4: Myb/S 97.5 0.00039 8.4E-09 44.0 5.4 59 8-66 2-73 (90)
20 PF13873 Myb_DNA-bind_5: Myb/S 97.4 0.00094 2E-08 41.7 6.2 55 8-62 3-74 (78)
21 KOG0050 mRNA splicing protein 97.1 0.00087 1.9E-08 57.0 4.8 54 7-64 7-61 (617)
22 KOG0051 RNA polymerase I termi 96.5 0.0039 8.5E-08 53.5 4.8 46 6-57 383-428 (607)
23 KOG0050 mRNA splicing protein 96.4 0.0092 2E-07 50.9 6.3 53 8-66 60-112 (617)
24 KOG0049 Transcription factor, 96.3 0.0083 1.8E-07 52.6 5.5 55 7-66 412-467 (939)
25 PF09111 SLIDE: SLIDE; InterP 96.2 0.026 5.5E-07 39.2 6.6 55 6-61 48-114 (118)
26 PF12776 Myb_DNA-bind_3: Myb/S 95.9 0.037 8E-07 35.2 5.8 57 9-65 1-70 (96)
27 COG5147 REB1 Myb superfamily p 95.8 0.013 2.8E-07 49.5 4.5 51 7-62 72-122 (512)
28 PLN03142 Probable chromatin-re 95.8 0.025 5.5E-07 51.1 6.4 55 8-66 825-889 (1033)
29 COG5118 BDP1 Transcription ini 95.2 0.037 8.1E-07 46.0 5.0 44 7-55 365-408 (507)
30 TIGR02894 DNA_bind_RsfA transc 94.9 0.056 1.2E-06 39.7 4.6 49 8-58 5-56 (161)
31 KOG0051 RNA polymerase I termi 94.7 0.052 1.1E-06 46.8 4.7 52 6-58 435-508 (607)
32 KOG1194 Predicted DNA-binding 94.7 0.065 1.4E-06 45.3 5.0 43 8-55 188-230 (534)
33 smart00595 MADF subfamily of S 93.9 0.09 2E-06 33.1 3.5 26 31-58 28-53 (89)
34 KOG4468 Polycomb-group transcr 93.9 0.15 3.2E-06 44.6 5.7 60 7-71 88-158 (782)
35 KOG4329 DNA-binding protein [G 93.9 0.11 2.5E-06 42.9 4.8 45 6-55 276-321 (445)
36 KOG3554 Histone deacetylase co 93.3 0.19 4.1E-06 43.0 5.3 68 6-78 284-364 (693)
37 KOG4282 Transcription factor G 93.2 0.7 1.5E-05 36.2 8.1 61 7-67 54-123 (345)
38 PRK13923 putative spore coat p 93.1 0.22 4.7E-06 36.8 4.8 46 8-55 6-54 (170)
39 PF10545 MADF_DNA_bdg: Alcohol 93.0 0.21 4.4E-06 30.5 3.9 31 30-60 26-56 (85)
40 KOG2656 DNA methyltransferase 92.9 0.11 2.5E-06 43.1 3.3 78 8-92 131-213 (445)
41 PF11035 SnAPC_2_like: Small n 92.6 0.52 1.1E-05 38.2 6.6 54 8-62 22-75 (344)
42 COG5147 REB1 Myb superfamily p 92.4 0.082 1.8E-06 44.8 2.0 49 8-60 21-70 (512)
43 PF08914 Myb_DNA-bind_2: Rap1 91.8 0.55 1.2E-05 29.4 4.8 48 8-55 3-55 (65)
44 PF13404 HTH_AsnC-type: AsnC-t 91.0 1.2 2.7E-05 25.3 5.3 38 15-57 5-42 (42)
45 PF05263 DUF722: Protein of un 85.8 2.6 5.5E-05 29.8 5.2 48 9-61 81-128 (130)
46 PF13325 MCRS_N: N-terminal re 84.3 5.8 0.00012 30.0 6.8 52 6-59 72-128 (199)
47 KOG3841 TEF-1 and related tran 82.6 6.3 0.00014 33.0 6.9 54 6-59 75-144 (455)
48 PRK11179 DNA-binding transcrip 82.1 5.1 0.00011 27.9 5.5 41 13-58 9-49 (153)
49 cd00086 homeodomain Homeodomai 82.0 7.2 0.00015 22.0 6.1 50 7-58 4-53 (59)
50 PF00046 Homeobox: Homeobox do 81.4 7.9 0.00017 22.1 6.5 50 7-58 4-53 (57)
51 PF04504 DUF573: Protein of un 79.4 8 0.00017 25.7 5.5 53 8-60 5-65 (98)
52 PLN03142 Probable chromatin-re 78.3 8.3 0.00018 35.4 6.8 51 7-61 926-988 (1033)
53 KOG2009 Transcription initiati 78.1 1.9 4E-05 37.4 2.6 45 6-55 408-452 (584)
54 PRK11169 leucine-responsive tr 76.2 8.7 0.00019 27.1 5.2 41 14-59 15-55 (164)
55 PF04545 Sigma70_r4: Sigma-70, 74.7 13 0.00028 20.9 6.2 44 11-61 6-49 (50)
56 PF06461 DUF1086: Domain of Un 73.0 26 0.00057 25.4 7.0 50 9-60 40-89 (145)
57 PF00674 DUP: DUP family; Int 72.9 5 0.00011 26.7 3.2 27 15-41 44-70 (108)
58 smart00344 HTH_ASNC helix_turn 71.6 17 0.00037 23.2 5.4 42 13-59 3-44 (108)
59 PF07750 GcrA: GcrA cell cycle 71.5 8 0.00017 27.9 4.1 42 9-56 2-43 (162)
60 smart00426 TEA TEA domain. 69.3 5.4 0.00012 25.5 2.5 21 8-28 4-24 (68)
61 smart00389 HOX Homeodomain. DN 67.5 20 0.00043 20.1 6.1 47 8-56 5-51 (56)
62 PF01466 Skp1: Skp1 family, di 64.8 7.8 0.00017 24.3 2.6 22 32-54 35-56 (78)
63 PF08281 Sigma70_r4_2: Sigma-7 63.5 25 0.00054 19.8 5.7 25 32-58 28-52 (54)
64 KOG1194 Predicted DNA-binding 62.8 5.3 0.00012 34.1 2.0 47 8-60 471-517 (534)
65 TIGR02937 sigma70-ECF RNA poly 62.0 38 0.00082 21.4 5.7 30 31-62 127-156 (158)
66 COG1522 Lrp Transcriptional re 61.4 28 0.00061 23.4 5.1 40 15-59 10-49 (154)
67 PF11626 Rap1_C: TRF2-interact 58.5 8.1 0.00018 24.8 1.9 14 6-19 46-59 (87)
68 PF01285 TEA: TEA/ATTS domain 57.2 20 0.00043 29.9 4.4 50 7-56 49-112 (431)
69 PF13325 MCRS_N: N-terminal re 56.7 30 0.00066 26.1 5.0 45 9-58 1-47 (199)
70 PF00196 GerE: Bacterial regul 52.0 45 0.00097 19.2 4.4 44 10-61 4-47 (58)
71 PRK11924 RNA polymerase sigma 50.7 73 0.0016 21.3 5.8 29 31-61 142-170 (179)
72 PLN03162 golden-2 like transcr 49.6 50 0.0011 27.9 5.5 52 8-61 238-291 (526)
73 COG5269 ZUO1 Ribosome-associat 49.5 34 0.00073 27.9 4.4 52 8-60 246-303 (379)
74 smart00501 BRIGHT BRIGHT, ARID 48.3 69 0.0015 20.3 5.6 41 18-59 37-86 (93)
75 PF01388 ARID: ARID/BRIGHT DNA 47.6 37 0.00081 21.3 3.7 40 18-58 41-89 (92)
76 KOG4559 Uncharacterized conser 47.1 73 0.0016 22.2 5.2 47 12-65 50-100 (120)
77 KOG0385 Chromatin remodeling c 47.0 54 0.0012 30.1 5.6 44 8-56 796-839 (971)
78 PF07030 DUF1320: Protein of u 44.3 84 0.0018 21.4 5.3 28 46-73 84-111 (130)
79 PF04282 DUF438: Family of unk 44.1 19 0.00041 23.0 1.8 22 42-63 11-32 (71)
80 PRK12516 RNA polymerase sigma 43.5 1E+02 0.0023 21.7 5.8 65 14-82 106-181 (187)
81 PF12451 VPS11_C: Vacuolar pro 41.2 21 0.00045 20.9 1.6 25 13-41 19-43 (49)
82 COG4281 ACB Acyl-CoA-binding p 40.9 63 0.0014 21.4 4.0 30 31-62 54-83 (87)
83 KOG2941 Beta-1,4-mannosyltrans 40.7 13 0.00029 31.1 0.9 21 6-26 260-281 (444)
84 cd08307 Death_Pelle Death doma 40.1 30 0.00065 23.2 2.4 18 31-49 22-39 (97)
85 PF10743 Phage_Cox: Regulatory 40.1 58 0.0013 21.7 3.8 48 21-81 4-52 (87)
86 PRK09648 RNA polymerase sigma 38.6 1.3E+02 0.0029 20.8 5.8 44 16-61 131-184 (189)
87 PRK09646 RNA polymerase sigma 37.0 1.2E+02 0.0026 21.2 5.3 47 13-61 131-187 (194)
88 PRK12541 RNA polymerase sigma 34.9 1.4E+02 0.003 20.0 5.5 47 16-64 104-160 (161)
89 PF02954 HTH_8: Bacterial regu 34.7 82 0.0018 17.2 4.5 34 14-53 6-39 (42)
90 PF00887 ACBP: Acyl CoA bindin 34.0 46 0.00099 21.0 2.5 22 39-61 62-83 (87)
91 PF11842 DUF3362: Domain of un 33.6 57 0.0012 23.7 3.2 27 13-41 41-67 (150)
92 smart00386 HAT HAT (Half-A-TPR 33.1 61 0.0013 15.2 3.0 24 15-39 7-30 (33)
93 cd00435 ACBP Acyl CoA binding 33.0 68 0.0015 20.6 3.2 22 39-61 60-81 (85)
94 TIGR02985 Sig70_bacteroi1 RNA 32.4 1.4E+02 0.0031 19.3 5.8 28 32-61 131-158 (161)
95 PRK12522 RNA polymerase sigma 32.4 1.5E+02 0.0032 20.2 5.1 48 12-61 107-164 (173)
96 TIGR02950 SigM_subfam RNA poly 31.9 1.5E+02 0.0033 19.4 6.3 44 16-61 97-150 (154)
97 TIGR02952 Sig70_famx2 RNA poly 31.1 1.6E+02 0.0035 19.6 5.6 44 16-61 114-167 (170)
98 PRK04654 sec-independent trans 31.1 86 0.0019 24.1 3.9 39 18-61 13-51 (214)
99 PF13560 HTH_31: Helix-turn-he 31.0 61 0.0013 18.9 2.6 29 43-71 14-42 (64)
100 PTZ00458 acyl CoA binding prot 30.7 78 0.0017 20.8 3.3 21 40-61 63-83 (90)
101 PRK09643 RNA polymerase sigma 29.0 2.1E+02 0.0045 20.1 5.7 44 15-60 125-178 (192)
102 PF11112 PyocinActivator: Pyoc 28.7 94 0.002 19.8 3.3 33 46-78 17-52 (76)
103 PF15508 NAAA-beta: beta subun 28.5 66 0.0014 20.8 2.6 27 31-59 16-42 (95)
104 PRK11922 RNA polymerase sigma 27.8 2.4E+02 0.0052 20.5 5.9 44 16-61 141-194 (231)
105 KOG1724 SCF ubiquitin ligase, 27.8 55 0.0012 23.8 2.3 40 14-54 97-140 (162)
106 PRK09642 RNA polymerase sigma 27.3 1.9E+02 0.0042 19.2 5.7 44 16-61 98-151 (160)
107 TIGR01636 phage_rinA phage tra 27.3 2.1E+02 0.0045 19.5 6.0 46 11-61 84-129 (134)
108 TIGR02939 RpoE_Sigma70 RNA pol 26.9 2.1E+02 0.0045 19.5 5.6 43 17-61 131-183 (190)
109 PF13174 TPR_6: Tetratricopept 26.7 71 0.0015 15.3 2.0 13 15-27 20-32 (33)
110 cd08308 Death_Tube Death domai 26.2 28 0.00061 24.5 0.5 17 30-48 22-38 (125)
111 PF10046 BLOC1_2: Biogenesis o 26.1 1.2E+02 0.0026 19.9 3.5 47 11-64 19-69 (99)
112 PF09420 Nop16: Ribosome bioge 26.0 1.9E+02 0.004 20.5 4.8 45 8-56 115-162 (164)
113 PF08259 Periviscerokin: Periv 25.7 33 0.00072 14.7 0.5 8 65-72 3-10 (11)
114 PF14966 DNA_repr_REX1B: DNA r 25.5 1.2E+02 0.0025 20.1 3.4 44 16-67 20-63 (97)
115 cd08777 Death_RIP1 Death Domai 25.2 1.9E+02 0.0042 18.5 4.7 30 11-49 1-30 (86)
116 COG4387 Mu-like prophage prote 25.0 1.1E+02 0.0023 22.1 3.3 28 43-70 80-107 (139)
117 KOG2527 Sorting nexin SNX11 [I 24.8 93 0.002 22.6 3.0 30 48-78 55-87 (144)
118 PRK12524 RNA polymerase sigma 24.6 2.5E+02 0.0054 19.6 6.6 45 16-62 128-182 (196)
119 PF05256 UPF0223: Uncharacteri 24.5 2.2E+02 0.0048 18.9 4.9 40 8-58 9-48 (88)
120 PRK14857 tatA twin arginine tr 24.3 1.7E+02 0.0037 19.4 4.0 41 18-63 15-55 (90)
121 PRK00575 tatA twin arginine tr 24.3 1.6E+02 0.0034 19.8 3.8 44 17-65 12-55 (92)
122 PF13991 BssS: BssS protein fa 24.1 1.7E+02 0.0037 18.8 3.8 30 44-73 42-71 (73)
123 PRK12534 RNA polymerase sigma 24.1 2.4E+02 0.0053 19.3 5.5 45 15-61 128-182 (187)
124 PRK04387 hypothetical protein; 23.4 2.4E+02 0.0051 18.9 5.2 38 8-56 9-46 (90)
125 TIGR03001 Sig-70_gmx1 RNA poly 23.3 2.6E+02 0.0057 20.9 5.4 39 16-56 153-201 (244)
126 PTZ00370 STEVOR; Provisional 23.2 2.3E+02 0.005 22.9 5.2 76 17-93 66-169 (296)
127 PRK15411 rcsA colanic acid cap 23.1 2.9E+02 0.0063 19.8 5.5 44 10-61 138-181 (207)
128 cd04517 TLF TBP-like factors ( 22.7 1.4E+02 0.003 21.7 3.6 35 42-76 62-96 (174)
129 PF13748 ABC_membrane_3: ABC t 22.6 99 0.0021 24.0 3.0 27 30-57 170-196 (237)
130 KOG0488 Transcription factor B 22.6 2.4E+02 0.0052 22.4 5.2 53 6-61 175-228 (309)
131 PRK09649 RNA polymerase sigma 22.4 2.8E+02 0.006 19.3 5.6 48 13-62 119-176 (185)
132 PRK10430 DNA-binding transcrip 22.3 3E+02 0.0065 19.6 5.8 47 9-58 158-204 (239)
133 KOG2251 Homeobox transcription 22.1 1.5E+02 0.0032 23.1 3.7 42 6-49 40-83 (228)
134 TIGR02943 Sig70_famx1 RNA poly 21.9 2.9E+02 0.0062 19.3 5.6 42 16-59 123-174 (188)
135 KOG3411 40S ribosomal protein 21.8 96 0.0021 22.4 2.6 36 40-76 1-36 (143)
136 PRK09641 RNA polymerase sigma 21.7 2.7E+02 0.0058 18.9 5.9 30 30-61 152-181 (187)
137 PRK09645 RNA polymerase sigma 21.5 2.7E+02 0.0058 18.8 5.5 44 16-61 110-163 (173)
138 TIGR03830 CxxCG_CxxCG_HTH puta 21.4 2.4E+02 0.0052 18.2 5.9 59 9-69 41-104 (127)
139 PF11084 DUF2621: Protein of u 21.4 1E+02 0.0022 22.2 2.6 22 6-27 55-76 (141)
140 PF10124 Mu-like_gpT: Mu-like 21.4 29 0.00063 27.7 -0.2 29 15-48 9-37 (291)
141 PRK09652 RNA polymerase sigma 21.3 2.6E+02 0.0056 18.6 5.6 29 31-61 145-173 (182)
142 PRK14858 tatA twin arginine tr 20.9 2.1E+02 0.0046 19.6 4.0 39 17-60 12-50 (108)
143 cd06257 DnaJ DnaJ domain or J- 20.7 1.3E+02 0.0028 16.4 2.6 18 43-60 11-28 (55)
144 TIGR02947 SigH_actino RNA poly 20.7 3E+02 0.0065 19.0 5.5 43 16-60 123-175 (193)
145 PF09197 Rap1-DNA-bind: Rap1, 20.6 2.9E+02 0.0063 18.8 5.8 46 10-56 2-74 (105)
146 PF05524 PEP-utilisers_N: PEP- 20.5 98 0.0021 20.4 2.3 47 12-60 34-80 (123)
147 PRK00295 hypothetical protein; 20.4 2E+02 0.0044 17.7 3.6 27 47-73 36-68 (68)
148 PRK00404 tatB sec-independent 20.2 1.9E+02 0.0042 20.8 3.9 38 19-61 14-51 (141)
149 PF06163 DUF977: Bacterial pro 20.2 3.3E+02 0.0071 19.3 5.6 59 7-73 2-61 (127)
150 PF08165 FerA: FerA (NUC095) d 20.0 2.3E+02 0.005 17.5 4.9 32 43-76 6-37 (66)
151 PF14775 NYD-SP28_assoc: Sperm 20.0 1.8E+02 0.0038 17.7 3.2 23 32-55 2-30 (60)
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=99.55 E-value=1.7e-14 Score=84.49 Aligned_cols=46 Identities=33% Similarity=0.725 Sum_probs=41.9
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHHH
Q 034427 8 STWTPKENKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEIL 56 (95)
Q Consensus 8 ~~WT~eEdklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~L 56 (95)
..||.||+++|.+++.+|+.+ +|..||..||+|||..||+.||..+
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 579999999999999999886 8999999999889999999999986
No 2
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.34 E-value=4.1e-12 Score=71.30 Aligned_cols=46 Identities=30% Similarity=0.694 Sum_probs=42.3
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 034427 8 STWTPKENKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEILV 57 (95)
Q Consensus 8 ~~WT~eEdklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~L~ 57 (95)
..||.+|+.+|..++.+|+.. +|..||..|| +||..+|+.||..+.
T Consensus 2 ~~Wt~~E~~~l~~~~~~~g~~---~w~~Ia~~~~-~rt~~~~~~~~~~~~ 47 (49)
T smart00717 2 GEWTEEEDELLIELVKKYGKN---NWEKIAKELP-GRTAEQCRERWNNLL 47 (49)
T ss_pred CCCCHHHHHHHHHHHHHHCcC---CHHHHHHHcC-CCCHHHHHHHHHHHc
Confidence 579999999999999999842 6999999999 999999999999865
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=99.28 E-value=1.5e-11 Score=68.15 Aligned_cols=44 Identities=32% Similarity=0.711 Sum_probs=40.6
Q ss_pred CCCHHHHHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHHH
Q 034427 9 TWTPKENKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEIL 56 (95)
Q Consensus 9 ~WT~eEdklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~L 56 (95)
+||.+|++.|..++.+|+. .+|..||..|| +||..||+.||..+
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~---~~w~~Ia~~~~-~rs~~~~~~~~~~~ 44 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGK---NNWEKIAKELP-GRTPKQCRERWRNL 44 (45)
T ss_pred CCCHHHHHHHHHHHHHHCc---CCHHHHHhHcC-CCCHHHHHHHHHHh
Confidence 5999999999999999984 27999999999 89999999999875
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=99.09 E-value=2.4e-10 Score=68.83 Aligned_cols=42 Identities=26% Similarity=0.662 Sum_probs=36.9
Q ss_pred CCHHHHHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHH-H
Q 034427 10 WTPKENKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEI-L 56 (95)
Q Consensus 10 WT~eEdklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~-L 56 (95)
||.||+.+|..++.+|+. .|..||..|| .||..+|+.||.. |
T Consensus 1 WT~eEd~~L~~~~~~~g~----~W~~Ia~~l~-~Rt~~~~~~r~~~~l 43 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGN----DWKKIAEHLG-NRTPKQCRNRWRNHL 43 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-----HHHHHHHST-TS-HHHHHHHHHHTT
T ss_pred CCHHHHHHHHHHHHHHCc----CHHHHHHHHC-cCCHHHHHHHHHHHC
Confidence 999999999999999964 6999999998 8999999999999 5
No 5
>PLN03212 Transcription repressor MYB5; Provisional
Probab=98.96 E-value=1e-09 Score=84.64 Aligned_cols=53 Identities=15% Similarity=0.317 Sum_probs=44.9
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHH-HHHHHH
Q 034427 6 LSSTWTPKENKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEI-LVDDLN 61 (95)
Q Consensus 6 ~~~~WT~eEdklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~-L~~dV~ 61 (95)
...+||+|||++|.+++.+|+.. +|..||..++.|||.+||++||.+ |..+|.
T Consensus 24 KRg~WT~EEDe~L~~lV~kyG~~---nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~ 77 (249)
T PLN03212 24 KRGPWTVEEDEILVSFIKKEGEG---RWRSLPKRAGLLRCGKSCRLRWMNYLRPSVK 77 (249)
T ss_pred cCCCCCHHHHHHHHHHHHHhCcc---cHHHHHHhhhcCCCcchHHHHHHHhhchhcc
Confidence 45689999999999999999764 799999998438999999999997 555544
No 6
>PLN03212 Transcription repressor MYB5; Provisional
Probab=98.80 E-value=3.2e-08 Score=76.42 Aligned_cols=50 Identities=24% Similarity=0.353 Sum_probs=44.0
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHHHHHHH
Q 034427 6 LSSTWTPKENKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEILVDDL 60 (95)
Q Consensus 6 ~~~~WT~eEdklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~L~~dV 60 (95)
..++||.||+.+|..+...|+. +|.+||..|| |||..+|+.||..+....
T Consensus 77 ~kgpWT~EED~lLlel~~~~Gn----KWs~IAk~Lp-GRTDnqIKNRWns~LrK~ 126 (249)
T PLN03212 77 KRGGITSDEEDLILRLHRLLGN----RWSLIAGRIP-GRTDNEIKNYWNTHLRKK 126 (249)
T ss_pred ccCCCChHHHHHHHHHHHhccc----cHHHHHhhcC-CCCHHHHHHHHHHHHhHH
Confidence 4578999999999999888875 7999999999 999999999999865543
No 7
>PLN03091 hypothetical protein; Provisional
Probab=98.79 E-value=3.8e-09 Score=86.96 Aligned_cols=51 Identities=20% Similarity=0.456 Sum_probs=43.8
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHH-HHHHH
Q 034427 7 SSTWTPKENKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEI-LVDDL 60 (95)
Q Consensus 7 ~~~WT~eEdklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~-L~~dV 60 (95)
...||.|||++|..+|.+|+.. .|..||..++.|||.+||++||.+ |..+|
T Consensus 14 Kg~WTpEEDe~L~~~V~kyG~~---nWs~IAk~~g~gRT~KQCRERW~NyLdP~I 65 (459)
T PLN03091 14 KGLWSPEEDEKLLRHITKYGHG---CWSSVPKQAGLQRCGKSCRLRWINYLRPDL 65 (459)
T ss_pred CCCCCHHHHHHHHHHHHHhCcC---CHHHHhhhhccCcCcchHhHHHHhccCCcc
Confidence 4679999999999999999764 799999988548999999999996 54444
No 8
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=98.76 E-value=7.8e-09 Score=77.89 Aligned_cols=52 Identities=17% Similarity=0.285 Sum_probs=48.1
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHH-HHHHHH
Q 034427 7 SSTWTPKENKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEI-LVDDLN 61 (95)
Q Consensus 7 ~~~WT~eEdklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~-L~~dV~ 61 (95)
.++||.|||..|...|.+|+++ +|..||..+|=||+.++||.||-+ |..+|+
T Consensus 9 kGpWt~EED~~L~~~V~~~G~~---~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ik 61 (238)
T KOG0048|consen 9 KGPWTQEEDLTQIRSIKSFGKH---NGTALPKLAGLRRCGKSCRLRWTNYLRPDLK 61 (238)
T ss_pred CCCCChHHHHHHHHHHHHhCCC---CcchhhhhcCCCccchHHHHHhhcccCCCcc
Confidence 3899999999999999999887 899999999867999999999996 888887
No 9
>PLN03091 hypothetical protein; Provisional
Probab=98.65 E-value=7.7e-08 Score=79.37 Aligned_cols=50 Identities=24% Similarity=0.432 Sum_probs=44.5
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHHHHHHH
Q 034427 6 LSSTWTPKENKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEILVDDL 60 (95)
Q Consensus 6 ~~~~WT~eEdklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~L~~dV 60 (95)
..++||.|||.+|..+.++|+. +|.+||..|| |||..+|+.||..+....
T Consensus 66 kKgpWT~EED~lLLeL~k~~Gn----KWskIAk~LP-GRTDnqIKNRWnslLKKk 115 (459)
T PLN03091 66 KRGTFSQQEENLIIELHAVLGN----RWSQIAAQLP-GRTDNEIKNLWNSCLKKK 115 (459)
T ss_pred cCCCCCHHHHHHHHHHHHHhCc----chHHHHHhcC-CCCHHHHHHHHHHHHHHH
Confidence 4578999999999999999875 7999999999 999999999999865543
No 10
>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=98.59 E-value=1.9e-07 Score=57.43 Aligned_cols=47 Identities=19% Similarity=0.304 Sum_probs=41.5
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCChHH---HHHHHHcCCCC-CHHHHHHHHHHHH
Q 034427 8 STWTPKENKLFEKALALYDKETPDRW---QNIAKAVGGGK-TVEEVKKHYEILV 57 (95)
Q Consensus 8 ~~WT~eEdklle~aL~~~~~~~~~rW---~kIA~~vpggR-T~~qv~~ry~~L~ 57 (95)
-.||.||...|..||..|+.+ .| .+|+++|...+ |..||+.|++..+
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 59 99999886346 9999999999865
No 11
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=98.54 E-value=2.9e-07 Score=69.38 Aligned_cols=51 Identities=33% Similarity=0.525 Sum_probs=44.5
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHH-HHHHHHH
Q 034427 7 SSTWTPKENKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEI-LVDDLNR 62 (95)
Q Consensus 7 ~~~WT~eEdklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~-L~~dV~~ 62 (95)
.+.||.||+.++.++-+.|+- ||..||.+|| |||..+|+.||.. |...+..
T Consensus 62 rg~fT~eEe~~Ii~lH~~~GN----rWs~IA~~LP-GRTDNeIKN~Wnt~lkkkl~~ 113 (238)
T KOG0048|consen 62 RGNFSDEEEDLIIKLHALLGN----RWSLIAGRLP-GRTDNEVKNHWNTHLKKKLLK 113 (238)
T ss_pred CCCCCHHHHHHHHHHHHHHCc----HHHHHHhhCC-CcCHHHHHHHHHHHHHHHHHH
Confidence 468999999999999999876 7999999999 9999999999986 5555543
No 12
>KOG0724 consensus Zuotin and related molecular chaperones (DnaJ superfamily), contains DNA-binding domains [Posttranslational modification, protein turnover, chaperones]
Probab=98.41 E-value=4.6e-07 Score=70.42 Aligned_cols=68 Identities=43% Similarity=0.656 Sum_probs=63.6
Q ss_pred CCCCHHHHHHHHHHHHhcCCC----CChHHHHHHHHcCCC-CCHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q 034427 8 STWTPKENKLFEKALALYDKE----TPDRWQNIAKAVGGG-KTVEEVKKHYEILVDDLNRIEAGRVPIPNYKSP 76 (95)
Q Consensus 8 ~~WT~eEdklle~aL~~~~~~----~~~rW~kIA~~vpgg-RT~~qv~~ry~~L~~dV~~iesg~v~~P~y~~~ 76 (95)
..|+.++.+.|++|+..|... ++++|.+++..+| + ++..++..+|..++.+|..+++|.++||.|...
T Consensus 32 ~~~~~~~~k~i~ka~~i~~~~~~~~t~~~~~~~~~~l~-~~~~~~~~~~~~~~~~~~v~~~~~~~~~~p~~~~~ 104 (335)
T KOG0724|consen 32 SLWTEEEFKKIEKALAILDDDEPRRTPDSWDKFAEALP-LEKRLEDKIEEYIGLVFDVNIRESGQKPFPKYGKS 104 (335)
T ss_pred hhhHHHHHHHHHHHHHHHhccccccchhhhhHHHhcCc-cccccchhHHhhhhhHHHHhhhhccCCCccccCcc
Confidence 559999999999999999754 7899999999999 8 999999999999999999999999999999764
No 13
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=98.38 E-value=6.6e-07 Score=73.59 Aligned_cols=47 Identities=38% Similarity=0.619 Sum_probs=43.5
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 034427 7 SSTWTPKENKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEILV 57 (95)
Q Consensus 7 ~~~WT~eEdklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~L~ 57 (95)
...||.+|.-+|..|+..|+-| +|+.||.+|+ .||.+||++||.+..
T Consensus 72 ~~~WtadEEilLLea~~t~G~G---NW~dIA~hIG-tKtkeeck~hy~k~f 118 (438)
T KOG0457|consen 72 DPSWTADEEILLLEAAETYGFG---NWQDIADHIG-TKTKEECKEHYLKHF 118 (438)
T ss_pred CCCCChHHHHHHHHHHHHhCCC---cHHHHHHHHc-ccchHHHHHHHHHHH
Confidence 4579999999999999999988 8999999999 999999999999753
No 14
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=98.19 E-value=1.9e-06 Score=71.89 Aligned_cols=44 Identities=30% Similarity=0.619 Sum_probs=41.1
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHHH
Q 034427 8 STWTPKENKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEIL 56 (95)
Q Consensus 8 ~~WT~eEdklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~L 56 (95)
..||.+|.-+|.++|.+|+. .|.+||.+|+ .||++||+-||..|
T Consensus 280 k~WS~qE~~LLLEGIe~ygD----dW~kVA~HVg-tKt~EqCIl~FL~L 323 (531)
T COG5259 280 KNWSRQELLLLLEGIEMYGD----DWDKVARHVG-TKTKEQCILHFLQL 323 (531)
T ss_pred ccccHHHHHHHHHHHHHhhh----hHHHHHHHhC-CCCHHHHHHHHHcC
Confidence 47999999999999999976 5999999999 99999999999875
No 15
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=98.07 E-value=6.3e-06 Score=69.03 Aligned_cols=46 Identities=28% Similarity=0.568 Sum_probs=42.8
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHHH
Q 034427 6 LSSTWTPKENKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEIL 56 (95)
Q Consensus 6 ~~~~WT~eEdklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~L 56 (95)
....||.+|.-+|..+|.+|.. .|.+||.+|+ +||.+||..||..|
T Consensus 252 ~~~~WT~qE~lLLLE~ie~y~d----dW~kVa~hVg-~ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 252 ARPNWTEQETLLLLEAIEMYGD----DWNKVADHVG-TKSQEQCILKFLRL 297 (506)
T ss_pred CCCCccHHHHHHHHHHHHHhcc----cHHHHHhccC-CCCHHHHHHHHHhc
Confidence 5678999999999999999987 4999999999 99999999999986
No 16
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=97.84 E-value=3.4e-05 Score=67.04 Aligned_cols=46 Identities=22% Similarity=0.496 Sum_probs=42.8
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHH
Q 034427 6 LSSTWTPKENKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEI 55 (95)
Q Consensus 6 ~~~~WT~eEdklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~ 55 (95)
.-+.||.+||.+|..|+++|+.. .|-+|-+.|| |||.-||+.||-+
T Consensus 359 khg~wt~~ED~~L~~AV~~Yg~k---dw~k~R~~vP-nRSdsQcR~RY~n 404 (939)
T KOG0049|consen 359 KHGRWTDQEDVLLVCAVSRYGAK---DWAKVRQAVP-NRSDSQCRERYTN 404 (939)
T ss_pred cCCCCCCHHHHHHHHHHHHhCcc---chhhHHHhcC-CccHHHHHHHHHH
Confidence 45789999999999999999875 7999999999 9999999999986
No 17
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.73 E-value=6.6e-05 Score=60.82 Aligned_cols=57 Identities=28% Similarity=0.559 Sum_probs=47.5
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhcCCCCCCCC
Q 034427 8 STWTPKENKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEILVDDLNRIEAGRVPIPNY 73 (95)
Q Consensus 8 ~~WT~eEdklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~L~~dV~~iesg~v~~P~y 73 (95)
..|+.+|.-+|..++...+-| +|+-||.+|| .|+.+||++||.++. +||.-.|+|+-
T Consensus 64 e~WgadEEllli~~~~TlGlG---NW~dIadyiG-sr~kee~k~HylK~y-----~es~~ypl~~i 120 (432)
T COG5114 64 EGWGADEELLLIECLDTLGLG---NWEDIADYIG-SRAKEEIKSHYLKMY-----DESKYYPLPDI 120 (432)
T ss_pred CCcCchHHHHHHHHHHhcCCC---cHHHHHHHHh-hhhhHHHHHHHHHHH-----hhccccccccc
Confidence 469999999999999998877 8999999999 999999999998754 34444555444
No 18
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=97.61 E-value=0.00013 Score=63.94 Aligned_cols=45 Identities=42% Similarity=0.587 Sum_probs=40.8
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHH
Q 034427 6 LSSTWTPKENKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEI 55 (95)
Q Consensus 6 ~~~~WT~eEdklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~ 55 (95)
.+..||..|.++|.+||..|.++ +..|+.+|+ |||++||.+.|-.
T Consensus 618 gSd~WTp~E~~lF~kA~y~~~KD----F~~v~km~~-~KtVaqCVeyYYt 662 (907)
T KOG4167|consen 618 GSDKWTPLERKLFNKALYTYSKD----FIFVQKMVK-SKTVAQCVEYYYT 662 (907)
T ss_pred CcccccHHHHHHHHHHHHHhccc----HHHHHHHhc-cccHHHHHHHHHH
Confidence 35789999999999999999885 999999999 9999999998753
No 19
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=97.47 E-value=0.00039 Score=43.97 Aligned_cols=59 Identities=22% Similarity=0.459 Sum_probs=41.7
Q ss_pred CCCCHHHHHHHHHHHHh------cC--CCC--ChHHHHHHHHcC---CCCCHHHHHHHHHHHHHHHHHHhcC
Q 034427 8 STWTPKENKLFEKALAL------YD--KET--PDRWQNIAKAVG---GGKTVEEVKKHYEILVDDLNRIEAG 66 (95)
Q Consensus 8 ~~WT~eEdklle~aL~~------~~--~~~--~~rW~kIA~~vp---ggRT~~qv~~ry~~L~~dV~~iesg 66 (95)
..||.+|..+|..+... |. ... ..-|+.||..|. -.||+.||+.+|++|..+-+.+...
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 46999999999988777 21 121 247999999973 2499999999999999988866554
No 20
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=97.36 E-value=0.00094 Score=41.74 Aligned_cols=55 Identities=15% Similarity=0.396 Sum_probs=45.2
Q ss_pred CCCCHHHHHHHHHHHHhcCC---C----------CChHHHHHHHHc----CCCCCHHHHHHHHHHHHHHHHH
Q 034427 8 STWTPKENKLFEKALALYDK---E----------TPDRWQNIAKAV----GGGKTVEEVKKHYEILVDDLNR 62 (95)
Q Consensus 8 ~~WT~eEdklle~aL~~~~~---~----------~~~rW~kIA~~v----pggRT~~qv~~ry~~L~~dV~~ 62 (95)
..||.+|..+|...|.+|+. + ...-|+.|+..| |+.||.+||+..|..|...++.
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 57999999999999998742 1 146799999988 2249999999999999888764
No 21
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=97.07 E-value=0.00087 Score=56.97 Aligned_cols=54 Identities=26% Similarity=0.540 Sum_probs=46.7
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHH-HHHHHHHHh
Q 034427 7 SSTWTPKENKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEI-LVDDLNRIE 64 (95)
Q Consensus 7 ~~~WT~eEdklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~-L~~dV~~ie 64 (95)
++.|+.-||..|..++.+|+.+ .|.+||+.++ -||+.||+.||.. |-+.|+..|
T Consensus 7 ggvwrntEdeilkaav~kyg~n---qws~i~sll~-~kt~rqC~~rw~e~ldp~i~~te 61 (617)
T KOG0050|consen 7 GGVWRNTEDEVLKAAVMKYGKN---QWSRIASLLN-RKTARQCKARWEEWLDPAIKKTE 61 (617)
T ss_pred cceecccHHHHHHHHHHHcchH---HHHHHHHHHh-hcchhHHHHHHHHHhCHHHhhhh
Confidence 4789999999999999999886 8999999999 9999999999986 555555443
No 22
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=96.54 E-value=0.0039 Score=53.53 Aligned_cols=46 Identities=24% Similarity=0.546 Sum_probs=41.3
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 034427 6 LSSTWTPKENKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEILV 57 (95)
Q Consensus 6 ~~~~WT~eEdklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~L~ 57 (95)
..+.||+||++.|.....+++. .|..|+..|+ |.+..|+.||+..+
T Consensus 383 ~rg~wt~ee~eeL~~l~~~~g~----~W~~Ig~~lg--r~P~~crd~wr~~~ 428 (607)
T KOG0051|consen 383 KRGKWTPEEEEELKKLVVEHGN----DWKEIGKALG--RMPMDCRDRWRQYV 428 (607)
T ss_pred ccCCCCcchHHHHHHHHHHhcc----cHHHHHHHHc--cCcHHHHHHHHHhh
Confidence 4578999999999999999876 6999999997 99999999999764
No 23
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=96.43 E-value=0.0092 Score=50.91 Aligned_cols=53 Identities=21% Similarity=0.419 Sum_probs=44.6
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhcC
Q 034427 8 STWTPKENKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEILVDDLNRIEAG 66 (95)
Q Consensus 8 ~~WT~eEdklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~L~~dV~~iesg 66 (95)
..||.|||..|..+..-+|. .|--||..|+ ||..||.+||.+|+..-.....+
T Consensus 60 tews~eederlLhlakl~p~----qwrtIa~i~g--r~~~qc~eRy~~ll~~~~s~~~~ 112 (617)
T KOG0050|consen 60 TEWSREEDERLLHLAKLEPT----QWRTIADIMG--RTSQQCLERYNNLLDVYVSYHYH 112 (617)
T ss_pred hhhhhhHHHHHHHHHHhcCC----ccchHHHHhh--hhHHHHHHHHHHHHHHHHhhhcc
Confidence 46999999998887776665 6999999997 99999999999998777655554
No 24
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=96.30 E-value=0.0083 Score=52.63 Aligned_cols=55 Identities=24% Similarity=0.424 Sum_probs=43.5
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHH-HHHHHHHHhcC
Q 034427 7 SSTWTPKENKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEI-LVDDLNRIEAG 66 (95)
Q Consensus 7 ~~~WT~eEdklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~-L~~dV~~iesg 66 (95)
...||-.||..|..++.+|+.+ .|.+||..+| .||.+|.++|-.. ++..+. .++|
T Consensus 412 ~~rW~l~edeqL~~~V~~YG~g---~WakcA~~Lp-~~t~~q~~rrR~R~~~~k~r-l~~~ 467 (939)
T KOG0049|consen 412 VERWTLVEDEQLLYAVKVYGKG---NWAKCAMLLP-KKTSRQLRRRRLRLIAAKLR-LAAG 467 (939)
T ss_pred cCceeecchHHHHHHHHHHccc---hHHHHHHHcc-ccchhHHHHHHHHHHHHHHH-HhcC
Confidence 4679999999999999999987 8999999999 9999886554443 444433 4554
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=96.20 E-value=0.026 Score=39.20 Aligned_cols=55 Identities=15% Similarity=0.401 Sum_probs=46.3
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCCChHHHHHHHHc------------CCCCCHHHHHHHHHHHHHHHH
Q 034427 6 LSSTWTPKENKLFEKALALYDKETPDRWQNIAKAV------------GGGKTVEEVKKHYEILVDDLN 61 (95)
Q Consensus 6 ~~~~WT~eEdklle~aL~~~~~~~~~rW~kIA~~v------------pggRT~~qv~~ry~~L~~dV~ 61 (95)
....+|.+||..|...+.+|+-++++.|++|-..+ - +||+.++.+|-..|..-|.
T Consensus 48 ~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~k-SRt~~el~rR~~tLi~~i~ 114 (118)
T PF09111_consen 48 KKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFK-SRTPQELQRRCNTLIKLIE 114 (118)
T ss_dssp S-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHH-TS-HHHHHHHHHHHHHHHH
T ss_pred CCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcc-cCCHHHHHHHHHHHHHHHH
Confidence 45789999999999999999998889999999875 4 6999999999999987665
No 26
>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=95.86 E-value=0.037 Score=35.23 Aligned_cols=57 Identities=21% Similarity=0.400 Sum_probs=42.4
Q ss_pred CCCHHHHHHHHHHHHhc------C-CC--CChHHHHHHHHcC----CCCCHHHHHHHHHHHHHHHHHHhc
Q 034427 9 TWTPKENKLFEKALALY------D-KE--TPDRWQNIAKAVG----GGKTVEEVKKHYEILVDDLNRIEA 65 (95)
Q Consensus 9 ~WT~eEdklle~aL~~~------~-~~--~~~rW~kIA~~vp----ggRT~~qv~~ry~~L~~dV~~ies 65 (95)
.||.++++.|..+|... + .+ ++.-|..|+..|. ...|.+||+.||+.|..+-..+..
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk~~y~~~~~ 70 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLKKDYRIWKE 70 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHHHHHHHHHH
Confidence 49999999998887654 2 11 3578999998874 125789999999998777665443
No 27
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=95.84 E-value=0.013 Score=49.54 Aligned_cols=51 Identities=18% Similarity=0.375 Sum_probs=44.0
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHH
Q 034427 7 SSTWTPKENKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEILVDDLNR 62 (95)
Q Consensus 7 ~~~WT~eEdklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~L~~dV~~ 62 (95)
...||.+|++.+..+=..++. +|.-||..+| |+|..+|.++|..+..+...
T Consensus 72 ~~~~~~eed~~li~l~~~~~~----~wstia~~~d-~rt~~~~~ery~~~~~~~~s 122 (512)
T COG5147 72 KKNWSEEEDEQLIDLDKELGT----QWSTIADYKD-RRTAQQCVERYVNTLEDLSS 122 (512)
T ss_pred cccccHHHHHHHHHHHHhcCc----hhhhhccccC-ccchHHHHHHHHHHhhhhhc
Confidence 457999999999777666655 6999999999 99999999999988777765
No 28
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=95.81 E-value=0.025 Score=51.13 Aligned_cols=55 Identities=31% Similarity=0.549 Sum_probs=45.1
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHHHHHH----------HHHHhcC
Q 034427 8 STWTPKENKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEILVDD----------LNRIEAG 66 (95)
Q Consensus 8 ~~WT~eEdklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~L~~d----------V~~iesg 66 (95)
..||..+=..|.+|..+|+.+ .-+.||..|. |||.+||++.++..-+. ++.||.|
T Consensus 825 ~~w~~~~f~~f~~~~~~~gr~---~~~~i~~~~~-~k~~~ev~~y~~~f~~~~~~~~~~~~~~~~ie~~ 889 (1033)
T PLN03142 825 STWSRRDFNAFIRACEKYGRN---DIKSIASEME-GKTEEEVERYAKVFWERYKELNDYDRIIKNIERG 889 (1033)
T ss_pred CcccHHHHHHHHHHHHHhCHh---HHHHHHHHhc-CCCHHHHHHHHHHHHHhhhhhccHHHHHHHHHHH
Confidence 469999999999999999886 7999999999 89999998655543322 5667766
No 29
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=95.24 E-value=0.037 Score=46.00 Aligned_cols=44 Identities=20% Similarity=0.424 Sum_probs=40.6
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHH
Q 034427 7 SSTWTPKENKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEI 55 (95)
Q Consensus 7 ~~~WT~eEdklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~ 55 (95)
..+||.+|...|-+||.+++-+ +.-|++.+| .|+-+||+..|.+
T Consensus 365 ~~~Ws~~e~ekFYKALs~wGtd----F~LIs~lfP-~R~RkqIKaKfi~ 408 (507)
T COG5118 365 ALRWSKKEIEKFYKALSIWGTD----FSLISSLFP-NRERKQIKAKFIK 408 (507)
T ss_pred CCcccHHHHHHHHHHHHHhcch----HHHHHHhcC-chhHHHHHHHHHH
Confidence 4579999999999999999774 999999999 9999999999985
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=94.88 E-value=0.056 Score=39.70 Aligned_cols=49 Identities=16% Similarity=0.345 Sum_probs=40.6
Q ss_pred CCCCHHHHHHHHHHHHhcCCCC---ChHHHHHHHHcCCCCCHHHHHHHHHHHHH
Q 034427 8 STWTPKENKLFEKALALYDKET---PDRWQNIAKAVGGGKTVEEVKKHYEILVD 58 (95)
Q Consensus 8 ~~WT~eEdklle~aL~~~~~~~---~~rW~kIA~~vpggRT~~qv~~ry~~L~~ 58 (95)
..||.|||.+|-..+-.|-..+ -.-++.|+..++ ||..-|-=||...+.
T Consensus 5 DAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L~--RTsAACGFRWNs~VR 56 (161)
T TIGR02894 5 DAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRALN--RTAAACGFRWNAYVR 56 (161)
T ss_pred cccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHc--ccHHHhcchHHHHHH
Confidence 4699999999999988884322 367999999998 999999888887554
No 31
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=94.73 E-value=0.052 Score=46.81 Aligned_cols=52 Identities=12% Similarity=0.264 Sum_probs=41.9
Q ss_pred CCCCCCHHHHHHHHHHHH-------hc------------CCC---CChHHHHHHHHcCCCCCHHHHHHHHHHHHH
Q 034427 6 LSSTWTPKENKLFEKALA-------LY------------DKE---TPDRWQNIAKAVGGGKTVEEVKKHYEILVD 58 (95)
Q Consensus 6 ~~~~WT~eEdklle~aL~-------~~------------~~~---~~~rW~kIA~~vpggRT~~qv~~ry~~L~~ 58 (95)
.+..||.||...|.+++. +| |.+ .+..|..|++.++ +|+.-||+.+|..|..
T Consensus 435 ~r~~Ws~eEe~~Llk~V~~~~~~~~q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~-TR~~~qCr~Kw~kl~~ 508 (607)
T KOG0051|consen 435 NRGAWSIEEEEKLLKTVNEMIREALQPQASNTDTGLQESPESTLKDDINWTLVSEMLG-TRSRIQCRYKWYKLTT 508 (607)
T ss_pred ccCcchHHHHHHHHHHHHHHHHHhhcccccccchhhhcCccccccCCcchhhhhHhhc-CCCcchHHHHHHHHHh
Confidence 567899999999998884 23 121 4568999999888 9999999999998753
No 32
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=94.66 E-value=0.065 Score=45.26 Aligned_cols=43 Identities=23% Similarity=0.526 Sum_probs=39.3
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHH
Q 034427 8 STWTPKENKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEI 55 (95)
Q Consensus 8 ~~WT~eEdklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~ 55 (95)
..||.||.-+|++|...|++ ++.+|-++|| -||...++..|-.
T Consensus 188 d~WT~Ed~vlFe~aF~~~GK----~F~kIrq~LP-~rsLaSlvqyYy~ 230 (534)
T KOG1194|consen 188 DEWTAEDIVLFEQAFQFFGK----DFHKIRQALP-HRSLASLVQYYYS 230 (534)
T ss_pred ccchHHHHHHHHHHHHHhcc----cHHHHHHHcc-CccHHHHHHHHHH
Confidence 46999999999999999988 5999999999 9999999887764
No 33
>smart00595 MADF subfamily of SANT domain.
Probab=93.95 E-value=0.09 Score=33.12 Aligned_cols=26 Identities=42% Similarity=0.755 Sum_probs=23.0
Q ss_pred hHHHHHHHHcCCCCCHHHHHHHHHHHHH
Q 034427 31 DRWQNIAKAVGGGKTVEEVKKHYEILVD 58 (95)
Q Consensus 31 ~rW~kIA~~vpggRT~~qv~~ry~~L~~ 58 (95)
.-|..||..|+ .|+++|+.+|+.|..
T Consensus 28 ~aW~~Ia~~l~--~~~~~~~~kw~~LR~ 53 (89)
T smart00595 28 KAWEEIAEELG--LSVEECKKRWKNLRD 53 (89)
T ss_pred HHHHHHHHHHC--cCHHHHHHHHHHHHH
Confidence 46999999998 599999999998854
No 34
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=93.89 E-value=0.15 Score=44.58 Aligned_cols=60 Identities=27% Similarity=0.485 Sum_probs=47.9
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCChHHHHH----------HHHcCCCCCHHHHHHHHHHHHHHHHHHhcCC-CCCC
Q 034427 7 SSTWTPKENKLFEKALALYDKETPDRWQNI----------AKAVGGGKTVEEVKKHYEILVDDLNRIEAGR-VPIP 71 (95)
Q Consensus 7 ~~~WT~eEdklle~aL~~~~~~~~~rW~kI----------A~~vpggRT~~qv~~ry~~L~~dV~~iesg~-v~~P 71 (95)
...||..|...|-.||.+|+++ +++| -..+- -||..||+.+|-.++..+...-.|. ++.|
T Consensus 88 ktaWt~~E~~~Ffdal~~~GKd----Fe~VinaklKRrna~s~~~-~Ktkdqvr~~yY~~~~~m~k~~F~~~l~~d 158 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGKD----FEKVINAKLKRRNATSRVQ-SKTKDQVRHYYYRLVRRMNKLLFGPDLSLD 158 (782)
T ss_pred ccccchhhHHHHHHHHHHhccc----HHHHHHHHHHhcccccchh-hhhhHHHHHHHHHHHHHHHhhhcccccCcc
Confidence 4579999999999999999985 8898 45566 6899999999998887777655552 4443
No 35
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=93.87 E-value=0.11 Score=42.92 Aligned_cols=45 Identities=33% Similarity=0.551 Sum_probs=38.1
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCCChHHHHH-HHHcCCCCCHHHHHHHHHH
Q 034427 6 LSSTWTPKENKLFEKALALYDKETPDRWQNI-AKAVGGGKTVEEVKKHYEI 55 (95)
Q Consensus 6 ~~~~WT~eEdklle~aL~~~~~~~~~rW~kI-A~~vpggRT~~qv~~ry~~ 55 (95)
....||.+|=+.||..|..|+++ +..| |..|+ .||+-+|...|-.
T Consensus 276 ~l~~wsEeEcr~FEegl~~yGKD----F~lIr~nkvr-tRsvgElVeyYYl 321 (445)
T KOG4329|consen 276 DLSGWSEEECRNFEEGLELYGKD----FHLIRANKVR-TRSVGELVEYYYL 321 (445)
T ss_pred ccccCCHHHHHHHHHHHHHhccc----HHHHHhcccc-cchHHHHHHHHHH
Confidence 45679999999999999999985 5555 67899 9999999987753
No 36
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=93.27 E-value=0.19 Score=43.01 Aligned_cols=68 Identities=29% Similarity=0.529 Sum_probs=48.7
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCCChHHHHH-HHHcCCCCCHHHHHHHHHHH--------HHHHHHHhcC----CCCCCC
Q 034427 6 LSSTWTPKENKLFEKALALYDKETPDRWQNI-AKAVGGGKTVEEVKKHYEIL--------VDDLNRIEAG----RVPIPN 72 (95)
Q Consensus 6 ~~~~WT~eEdklle~aL~~~~~~~~~rW~kI-A~~vpggRT~~qv~~ry~~L--------~~dV~~iesg----~v~~P~ 72 (95)
.+..||..|-.+||.||.+|+++ +..| +..+| =||...+.+.|-.. +..++.-|.. .|-+|.
T Consensus 284 emEEWSasEanLFEeALeKyGKD----FndIrqdfLP-WKSl~sIveyYYmwKttdRYvqqKrlKaaeadsKlkqvYIP~ 358 (693)
T KOG3554|consen 284 EMEEWSASEANLFEEALEKYGKD----FNDIRQDFLP-WKSLTSIVEYYYMWKTTDRYVQQKRLKAAEADSKLKQVYIPT 358 (693)
T ss_pred hhhhccchhhHHHHHHHHHhccc----HHHHHHhhcc-hHHHHHHHHHHHHHhhhhHHHHHHhhhhhhhhhhhheeeccC
Confidence 46789999999999999999986 5555 45677 79988888776532 2233333333 477899
Q ss_pred CCCCCC
Q 034427 73 YKSPGS 78 (95)
Q Consensus 73 y~~~~~ 78 (95)
|.-+.+
T Consensus 359 ynKPnp 364 (693)
T KOG3554|consen 359 YNKPNP 364 (693)
T ss_pred CCCCCc
Confidence 966655
No 37
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=93.19 E-value=0.7 Score=36.20 Aligned_cols=61 Identities=15% Similarity=0.302 Sum_probs=44.9
Q ss_pred CCCCCHHHHHHHHHHHHhc----CCC--CChHHHHHHHHc---CCCCCHHHHHHHHHHHHHHHHHHhcCC
Q 034427 7 SSTWTPKENKLFEKALALY----DKE--TPDRWQNIAKAV---GGGKTVEEVKKHYEILVDDLNRIEAGR 67 (95)
Q Consensus 7 ~~~WT~eEdklle~aL~~~----~~~--~~~rW~kIA~~v---pggRT~~qv~~ry~~L~~dV~~iesg~ 67 (95)
...||.+|-..|..+.... ..+ ...-|+.||..+ +.-||..||+.+|.+|....+....+.
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 4689999999998775442 111 234699999832 223999999999999998888766653
No 38
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=93.10 E-value=0.22 Score=36.84 Aligned_cols=46 Identities=13% Similarity=0.298 Sum_probs=38.5
Q ss_pred CCCCHHHHHHHHHHHHhcCCCC---ChHHHHHHHHcCCCCCHHHHHHHHHH
Q 034427 8 STWTPKENKLFEKALALYDKET---PDRWQNIAKAVGGGKTVEEVKKHYEI 55 (95)
Q Consensus 8 ~~WT~eEdklle~aL~~~~~~~---~~rW~kIA~~vpggRT~~qv~~ry~~ 55 (95)
..||.|+|.+|.+.+..|-... -.-.+.++..+. ||.-.|.-||..
T Consensus 6 dawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L~--rt~aac~fRwNs 54 (170)
T PRK13923 6 DAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDALK--RTAAACGFRWNS 54 (170)
T ss_pred hhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHHh--hhHHHHHhHHHH
Confidence 4699999999999988886433 366888889998 999999999964
No 39
>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=92.96 E-value=0.21 Score=30.49 Aligned_cols=31 Identities=32% Similarity=0.623 Sum_probs=25.5
Q ss_pred ChHHHHHHHHcCCCCCHHHHHHHHHHHHHHH
Q 034427 30 PDRWQNIAKAVGGGKTVEEVKKHYEILVDDL 60 (95)
Q Consensus 30 ~~rW~kIA~~vpggRT~~qv~~ry~~L~~dV 60 (95)
..-|+.||..++..-++++|+.+|..|+...
T Consensus 26 ~~aw~~Ia~~l~~~~~~~~~~~~w~~Lr~~y 56 (85)
T PF10545_consen 26 EEAWQEIARELGKEFSVDDCKKRWKNLRDRY 56 (85)
T ss_pred HHHHHHHHHHHccchhHHHHHHHHHHHHHHH
Confidence 3579999999985578999999999886543
No 40
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=92.87 E-value=0.11 Score=43.08 Aligned_cols=78 Identities=24% Similarity=0.346 Sum_probs=51.3
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCChHHHHHHHH-----cCCCCCHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCcc
Q 034427 8 STWTPKENKLFEKALALYDKETPDRWQNIAKA-----VGGGKTVEEVKKHYEILVDDLNRIEAGRVPIPNYKSPGSSYNA 82 (95)
Q Consensus 8 ~~WT~eEdklle~aL~~~~~~~~~rW~kIA~~-----vpggRT~~qv~~ry~~L~~dV~~iesg~v~~P~y~~~~~~~~~ 82 (95)
..||.+|-..|=..-..|+- ||-.||.. .+..||++|+++||-..+..+.+. +-|.+.-.-......+
T Consensus 131 n~WskeETD~LF~lck~fDL----Rf~VIaDRyd~qq~~~sRTvEdLKeRyY~v~r~l~kA---r~~s~sdllk~~~yd~ 203 (445)
T KOG2656|consen 131 NSWSKEETDYLFDLCKRFDL----RFFVIADRYDNQQYKKSRTVEDLKERYYSVCRKLLKA---RAPSNSDLLKSLVYDA 203 (445)
T ss_pred ccccHHHHHHHHHHHHhcCe----eEEEEeeccchhhccccccHHHHHHHHHHHHHHHHHc---cCCCchhhhhccccch
Confidence 45999999988788888876 66666665 673499999999999988887632 2222111112233445
Q ss_pred chHHHHHhhc
Q 034427 83 ANEERILKNL 92 (95)
Q Consensus 83 ~~~~~~~~~~ 92 (95)
.-|.+|-+.|
T Consensus 204 e~Er~RKk~L 213 (445)
T KOG2656|consen 204 EHERERKKYL 213 (445)
T ss_pred HHHHHHHHHH
Confidence 5555555544
No 41
>PF11035 SnAPC_2_like: Small nuclear RNA activating complex subunit 2-like; InterPro: IPR021281 This family of proteins is SnAPC subunit 2-like. SnAPC allows the transcription of human small nuclear RNA genes to occur by recognition of the proximal sequence element [].
Probab=92.57 E-value=0.52 Score=38.24 Aligned_cols=54 Identities=17% Similarity=0.364 Sum_probs=42.7
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHH
Q 034427 8 STWTPKENKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEILVDDLNR 62 (95)
Q Consensus 8 ~~WT~eEdklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~L~~dV~~ 62 (95)
..||..|.+.|.++|..........-..|+..|+ |||..|++.-.+.|...|.+
T Consensus 22 ~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~-~Rs~aEI~~fl~~LK~rvar 75 (344)
T PF11035_consen 22 AAWSAREKRQLLRLLQARRGQPEPDAAELAKELP-GRSEAEIRDFLQQLKGRVAR 75 (344)
T ss_pred ccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhcc-CcCHHHHHHHHHHHHHHHHH
Confidence 4699999999999988653322234556999999 99999999988888777764
No 42
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=92.36 E-value=0.082 Score=44.80 Aligned_cols=49 Identities=14% Similarity=0.329 Sum_probs=41.1
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHH-HHHHH
Q 034427 8 STWTPKENKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEI-LVDDL 60 (95)
Q Consensus 8 ~~WT~eEdklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~-L~~dV 60 (95)
+.|+..||..+..++..|... .|.+||+.++ -++.+||+.|+.. +-..+
T Consensus 21 gsw~~~EDe~l~~~vk~l~~n---nws~vas~~~-~~~~kq~~~rw~~~lnp~l 70 (512)
T COG5147 21 GSWKRTEDEDLKALVKKLGPN---NWSKVASLLI-SSTGKQSSNRWNNHLNPQL 70 (512)
T ss_pred CCCCCcchhHHHHHHhhcccc---cHHHHHHHhc-ccccccccchhhhhhchhc
Confidence 579999999999999888664 6999999999 8899999999943 43333
No 43
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=91.75 E-value=0.55 Score=29.38 Aligned_cols=48 Identities=8% Similarity=0.204 Sum_probs=33.6
Q ss_pred CCCCHHHHHHHHHHHHhcCC-----CCChHHHHHHHHcCCCCCHHHHHHHHHH
Q 034427 8 STWTPKENKLFEKALALYDK-----ETPDRWQNIAKAVGGGKTVEEVKKHYEI 55 (95)
Q Consensus 8 ~~WT~eEdklle~aL~~~~~-----~~~~rW~kIA~~vpggRT~~qv~~ry~~ 55 (95)
.++|.+||.+|..-|+.+.. .+..-|..+++.-|...|-.--++||..
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 46899999999999977632 2467899999998856888889999975
No 44
>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=90.97 E-value=1.2 Score=25.31 Aligned_cols=38 Identities=13% Similarity=0.256 Sum_probs=28.2
Q ss_pred HHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 034427 15 NKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEILV 57 (95)
Q Consensus 15 dklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~L~ 57 (95)
|..+..+|..-+. -.|..||+.++ -|...|.+|.+.|.
T Consensus 5 D~~Il~~Lq~d~r---~s~~~la~~lg--lS~~~v~~Ri~rL~ 42 (42)
T PF13404_consen 5 DRKILRLLQEDGR---RSYAELAEELG--LSESTVRRRIRRLE 42 (42)
T ss_dssp HHHHHHHHHH-TT---S-HHHHHHHHT--S-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCC---ccHHHHHHHHC--cCHHHHHHHHHHhC
Confidence 5566667776544 47999999997 99999999998873
No 45
>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=85.77 E-value=2.6 Score=29.83 Aligned_cols=48 Identities=17% Similarity=0.373 Sum_probs=37.3
Q ss_pred CCCHHHHHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHHHHHHHH
Q 034427 9 TWTPKENKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEILVDDLN 61 (95)
Q Consensus 9 ~WT~eEdklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~L~~dV~ 61 (95)
.++.++.++| -..|.......|..||..+. .+..+|++.+....++|.
T Consensus 81 ~l~de~k~Ii---~lry~~r~~~TW~~IA~~l~--i~erta~r~~~~fK~~i~ 128 (130)
T PF05263_consen 81 TLIDEEKRII---KLRYDRRSRRTWYQIAQKLH--ISERTARRWRDRFKNDIY 128 (130)
T ss_pred hhCHHHHHHH---HHHHcccccchHHHHHHHhC--ccHHHHHHHHHHHHHHhc
Confidence 3556666666 44566555568999999998 999999999998888875
No 46
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=84.34 E-value=5.8 Score=29.99 Aligned_cols=52 Identities=10% Similarity=0.268 Sum_probs=38.2
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCCChHHHHHHHH-----cCCCCCHHHHHHHHHHHHHH
Q 034427 6 LSSTWTPKENKLFEKALALYDKETPDRWQNIAKA-----VGGGKTVEEVKKHYEILVDD 59 (95)
Q Consensus 6 ~~~~WT~eEdklle~aL~~~~~~~~~rW~kIA~~-----vpggRT~~qv~~ry~~L~~d 59 (95)
+...||.+|+.+|-.......+ +...+++|=.. -+ +||+++...||+.|..-
T Consensus 72 ~kalfS~~EE~lL~~v~s~~~p-~le~Fq~LL~~n~~vFh~-sRTak~L~~HW~lmkqy 128 (199)
T PF13325_consen 72 SKALFSKEEEQLLGTVASSSQP-SLETFQELLDKNRSVFHP-SRTAKSLQDHWRLMKQY 128 (199)
T ss_pred ccCCCCHHHHHHHHhhhhccCC-cHHHHHHHHHhChhhhcc-ccCHHHHHHHHHHHHHh
Confidence 5678999999999886554433 35678887543 34 69999999999976543
No 47
>KOG3841 consensus TEF-1 and related transcription factor, TEAD family [Transcription]
Probab=82.57 E-value=6.3 Score=33.01 Aligned_cols=54 Identities=26% Similarity=0.442 Sum_probs=43.0
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCC------------ChHHHHHHHHcC----CCCCHHHHHHHHHHHHHH
Q 034427 6 LSSTWTPKENKLFEKALALYDKET------------PDRWQNIAKAVG----GGKTVEEVKKHYEILVDD 59 (95)
Q Consensus 6 ~~~~WT~eEdklle~aL~~~~~~~------------~~rW~kIA~~vp----ggRT~~qv~~ry~~L~~d 59 (95)
+.+.||++=+..|.+||+.||+.+ =.|=+-||.++. -.||.+||-.|-+.|...
T Consensus 75 aegvWSpdIEqsFqEALaiyppcGrrKIilsdegkmyGRNELIarYIKlrtgktRTrKQVSSHIQVlarr 144 (455)
T KOG3841|consen 75 AEGVWSPDIEQSFQEALAIYPPCGRRKIILSDEGKMYGRNELIARYIKLRTGKTRTRKQVSSHIQVLARR 144 (455)
T ss_pred cccccChhHHHHHHHHHhhcCCCCceeEEEccCccccchHHHHHHHHHHhcCCchhHHHHHHHHHHHHHH
Confidence 456799999999999999998752 257789998873 247889999999987443
No 48
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=82.13 E-value=5.1 Score=27.87 Aligned_cols=41 Identities=15% Similarity=0.187 Sum_probs=32.7
Q ss_pred HHHHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHHHHH
Q 034427 13 KENKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEILVD 58 (95)
Q Consensus 13 eEdklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~L~~ 58 (95)
+-|..+..+|.+=+. -.|..||+.++ -|...|++|++.|.+
T Consensus 9 ~~D~~Il~~Lq~d~R---~s~~eiA~~lg--lS~~tV~~Ri~rL~~ 49 (153)
T PRK11179 9 NLDRGILEALMENAR---TPYAELAKQFG--VSPGTIHVRVEKMKQ 49 (153)
T ss_pred HHHHHHHHHHHHcCC---CCHHHHHHHHC--cCHHHHHHHHHHHHH
Confidence 346666677776544 36999999997 999999999998864
No 49
>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=82.00 E-value=7.2 Score=22.04 Aligned_cols=50 Identities=20% Similarity=0.284 Sum_probs=42.1
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHHHHH
Q 034427 7 SSTWTPKENKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEILVD 58 (95)
Q Consensus 7 ~~~WT~eEdklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~L~~ 58 (95)
...+|.++...|+......+.-+...=+.||..++ -|..+|..=|.+-..
T Consensus 4 r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~--l~~~qV~~WF~nrR~ 53 (59)
T cd00086 4 RTRFTPEQLEELEKEFEKNPYPSREEREELAKELG--LTERQVKIWFQNRRA 53 (59)
T ss_pred CCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHC--cCHHHHHHHHHHHHH
Confidence 45789999999999999877666778899999997 999999988776543
No 50
>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=81.37 E-value=7.9 Score=22.13 Aligned_cols=50 Identities=18% Similarity=0.261 Sum_probs=41.6
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHHHHH
Q 034427 7 SSTWTPKENKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEILVD 58 (95)
Q Consensus 7 ~~~WT~eEdklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~L~~ 58 (95)
...+|.++.+.|+.....-+.-+...-+.||..++ -|..+|..=|.+-..
T Consensus 4 r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~--l~~~~V~~WF~nrR~ 53 (57)
T PF00046_consen 4 RTRFTKEQLKVLEEYFQENPYPSKEEREELAKELG--LTERQVKNWFQNRRR 53 (57)
T ss_dssp SSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHT--SSHHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHhcccccccccccccccc--ccccccccCHHHhHH
Confidence 35689999999999988866556788999999997 999999887776543
No 51
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=79.44 E-value=8 Score=25.66 Aligned_cols=53 Identities=8% Similarity=0.111 Sum_probs=34.9
Q ss_pred CCCCHHHHHHHHHHHHhcCC--C--CChHHHHHHHHc----CCCCCHHHHHHHHHHHHHHH
Q 034427 8 STWTPKENKLFEKALALYDK--E--TPDRWQNIAKAV----GGGKTVEEVKKHYEILVDDL 60 (95)
Q Consensus 8 ~~WT~eEdklle~aL~~~~~--~--~~~rW~kIA~~v----pggRT~~qv~~ry~~L~~dV 60 (95)
..||.++.-.|.++|..|-. | ....|..+-..| .-.=|..|+.+..+.|....
T Consensus 5 R~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~KirrLK~Ky 65 (98)
T PF04504_consen 5 RLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRRLKKKY 65 (98)
T ss_pred CCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHH
Confidence 56999999999999988821 2 123455555544 32247888888777765443
No 52
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=78.34 E-value=8.3 Score=35.41 Aligned_cols=51 Identities=10% Similarity=0.272 Sum_probs=43.9
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCChHHHHHHHHc------------CCCCCHHHHHHHHHHHHHHHH
Q 034427 7 SSTWTPKENKLFEKALALYDKETPDRWQNIAKAV------------GGGKTVEEVKKHYEILVDDLN 61 (95)
Q Consensus 7 ~~~WT~eEdklle~aL~~~~~~~~~rW~kIA~~v------------pggRT~~qv~~ry~~L~~dV~ 61 (95)
...+|.+||..|.-.+.+|+-+ +|++|-..+ - .||+.++.+|...|..-|.
T Consensus 926 ~~~~~~~~d~~~~~~~~~~g~~---~~~~~~~~i~~~~~f~fd~~~~-srt~~~~~~r~~~l~~~~~ 988 (1033)
T PLN03142 926 GKLYNEECDRFMLCMVHKLGYG---NWDELKAAFRTSPLFRFDWFVK-SRTPQELARRCDTLIRLIE 988 (1033)
T ss_pred CCcCCHHHHHHHHHHHHHhccc---hHHHHHHHHHhCCceeeehhhc-cCCHHHHHHHHHHHHHHHH
Confidence 4579999999999999999875 699997765 3 5999999999999887775
No 53
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=78.12 E-value=1.9 Score=37.38 Aligned_cols=45 Identities=20% Similarity=0.375 Sum_probs=40.6
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHH
Q 034427 6 LSSTWTPKENKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEI 55 (95)
Q Consensus 6 ~~~~WT~eEdklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~ 55 (95)
....||.+|-.+|..+|..++.+ ..-|++..| +|+.++++..|..
T Consensus 408 ~~~~w~~se~e~fyka~~~~gs~----~slis~l~p-~R~rk~iK~K~~~ 452 (584)
T KOG2009|consen 408 ETDKWDASETELFYKALSERGSD----FSLISNLFP-LRDRKQIKAKFKK 452 (584)
T ss_pred ccCcccchhhHHhhhHHhhhccc----ccccccccc-cccHHHHHHHHhh
Confidence 45689999999999999999875 778999999 9999999999984
No 54
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=76.17 E-value=8.7 Score=27.05 Aligned_cols=41 Identities=12% Similarity=0.039 Sum_probs=31.7
Q ss_pred HHHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHHHHHH
Q 034427 14 ENKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEILVDD 59 (95)
Q Consensus 14 Edklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~L~~d 59 (95)
-|..+..+|.+-+. -.|..||+.++ -|..-|.+|++.|.+.
T Consensus 15 ~D~~IL~~Lq~d~R---~s~~eiA~~lg--lS~~tv~~Ri~rL~~~ 55 (164)
T PRK11169 15 IDRNILNELQKDGR---ISNVELSKRVG--LSPTPCLERVRRLERQ 55 (164)
T ss_pred HHHHHHHHhccCCC---CCHHHHHHHHC--cCHHHHHHHHHHHHHC
Confidence 35555566666444 47999999997 9999999999998653
No 55
>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=74.69 E-value=13 Score=20.91 Aligned_cols=44 Identities=18% Similarity=0.317 Sum_probs=32.0
Q ss_pred CHHHHHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHHHHHHHH
Q 034427 11 TPKENKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEILVDDLN 61 (95)
Q Consensus 11 T~eEdklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~L~~dV~ 61 (95)
|++|...|..- |..+ ..+..||..++ -|...|+.+.......++
T Consensus 6 ~~~er~vi~~~---y~~~--~t~~eIa~~lg--~s~~~V~~~~~~al~kLR 49 (50)
T PF04545_consen 6 PPREREVIRLR---YFEG--LTLEEIAERLG--ISRSTVRRILKRALKKLR 49 (50)
T ss_dssp -HHHHHHHHHH---HTST---SHHHHHHHHT--SCHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHH---hcCC--CCHHHHHHHHC--CcHHHHHHHHHHHHHHhc
Confidence 56777777443 3332 36999999997 999999999988776664
No 56
>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=72.96 E-value=26 Score=25.37 Aligned_cols=50 Identities=20% Similarity=0.412 Sum_probs=40.3
Q ss_pred CCCHHHHHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHHHHHHH
Q 034427 9 TWTPKENKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEILVDDL 60 (95)
Q Consensus 9 ~WT~eEdklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~L~~dV 60 (95)
.++..|.+.|.+++..|+-+ .-.|.-+...+. +||.++++..-.....-|
T Consensus 40 GFn~rQR~~Fln~vMR~G~~-~f~~~w~~~~Lr-~Ks~~ei~aY~~LFm~HL 89 (145)
T PF06461_consen 40 GFNPRQRKAFLNAVMRYGMG-AFDWKWFVPRLR-GKSEKEIRAYGSLFMRHL 89 (145)
T ss_pred ccCHHHHHHHHHHHHHHCcC-cccchHHhhhhc-cccHHHHHHHHHHHHHHh
Confidence 48899999999999999874 336888899999 999999987666544444
No 57
>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=72.92 E-value=5 Score=26.72 Aligned_cols=27 Identities=15% Similarity=0.327 Sum_probs=20.5
Q ss_pred HHHHHHHHHhcCCCCChHHHHHHHHcC
Q 034427 15 NKLFEKALALYDKETPDRWQNIAKAVG 41 (95)
Q Consensus 15 dklle~aL~~~~~~~~~rW~kIA~~vp 41 (95)
.++|.+.++.-|......|+.||..|.
T Consensus 44 ~kfl~eIi~~~P~~d~~~Wd~IA~~mN 70 (108)
T PF00674_consen 44 MKFLKEIIEVKPGVDMKKWDIIASRMN 70 (108)
T ss_pred HHHHHHHHhcCCCCCcccHHHHHHHHH
Confidence 456666666666667889999999986
No 58
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=71.59 E-value=17 Score=23.22 Aligned_cols=42 Identities=17% Similarity=0.195 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHHHHHH
Q 034427 13 KENKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEILVDD 59 (95)
Q Consensus 13 eEdklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~L~~d 59 (95)
+.|..+..+|...+. -.+..||..++ -|...|+++.+.|.+.
T Consensus 3 ~~D~~il~~L~~~~~---~~~~~la~~l~--~s~~tv~~~l~~L~~~ 44 (108)
T smart00344 3 EIDRKILEELQKDAR---ISLAELAKKVG--LSPSTVHNRVKRLEEE 44 (108)
T ss_pred HHHHHHHHHHHHhCC---CCHHHHHHHHC--cCHHHHHHHHHHHHHC
Confidence 345666677777654 35999999997 9999999999998763
No 59
>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=71.45 E-value=8 Score=27.93 Aligned_cols=42 Identities=24% Similarity=0.298 Sum_probs=34.1
Q ss_pred CCCHHHHHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHHH
Q 034427 9 TWTPKENKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEIL 56 (95)
Q Consensus 9 ~WT~eEdklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~L 56 (95)
.||.|+...|.++... |. .=.+||..|+ |.|-.-|+-+...|
T Consensus 2 ~Wtde~~~~L~~lw~~---G~--SasqIA~~lg-~vsRnAViGk~hRl 43 (162)
T PF07750_consen 2 SWTDERVERLRKLWAE---GL--SASQIARQLG-GVSRNAVIGKAHRL 43 (162)
T ss_pred CCCHHHHHHHHHHHHc---CC--CHHHHHHHhC-Ccchhhhhhhhhcc
Confidence 4999999999887654 32 3579999999 89999999887765
No 60
>smart00426 TEA TEA domain.
Probab=69.31 E-value=5.4 Score=25.51 Aligned_cols=21 Identities=33% Similarity=0.757 Sum_probs=18.8
Q ss_pred CCCCHHHHHHHHHHHHhcCCC
Q 034427 8 STWTPKENKLFEKALALYDKE 28 (95)
Q Consensus 8 ~~WT~eEdklle~aL~~~~~~ 28 (95)
.-|+.+=...|.+||..|++.
T Consensus 4 ~vWp~~lE~Af~~aL~~~~~~ 24 (68)
T smart00426 4 GVWSPDIEQAFQEALAIYPPC 24 (68)
T ss_pred CcCcHHHHHHHHHHHHHcCcc
Confidence 569999999999999999875
No 61
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=67.50 E-value=20 Score=20.09 Aligned_cols=47 Identities=17% Similarity=0.298 Sum_probs=38.8
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHHH
Q 034427 8 STWTPKENKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEIL 56 (95)
Q Consensus 8 ~~WT~eEdklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~L 56 (95)
..+|.++...|+......+.-+...=+.||..++ -|..+|..=|.+-
T Consensus 5 ~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~--l~~~qV~~WF~nr 51 (56)
T smart00389 5 TSFTPEQLEELEKEFQKNPYPSREEREELAAKLG--LSERQVKVWFQNR 51 (56)
T ss_pred CcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHC--cCHHHHHHhHHHH
Confidence 4589999999999988876556677889999997 9999998776654
No 62
>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=64.84 E-value=7.8 Score=24.32 Aligned_cols=22 Identities=32% Similarity=0.504 Sum_probs=18.0
Q ss_pred HHHHHHHHcCCCCCHHHHHHHHH
Q 034427 32 RWQNIAKAVGGGKTVEEVKKHYE 54 (95)
Q Consensus 32 rW~kIA~~vpggRT~~qv~~ry~ 54 (95)
--..||..+. |||++|++..|.
T Consensus 35 ~~~~iA~~i~-gks~eeir~~fg 56 (78)
T PF01466_consen 35 CCKYIANMIK-GKSPEEIRKYFG 56 (78)
T ss_dssp HHHHHHHHHT-TS-HHHHHHHHT
T ss_pred HHHHHHHHhc-CCCHHHHHHHcC
Confidence 3568999999 999999999874
No 63
>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=63.48 E-value=25 Score=19.80 Aligned_cols=25 Identities=20% Similarity=0.303 Sum_probs=19.7
Q ss_pred HHHHHHHHcCCCCCHHHHHHHHHHHHH
Q 034427 32 RWQNIAKAVGGGKTVEEVKKHYEILVD 58 (95)
Q Consensus 32 rW~kIA~~vpggRT~~qv~~ry~~L~~ 58 (95)
.|..||..++ .|...|+.++..-..
T Consensus 28 s~~eIa~~l~--~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 28 SYAEIAEILG--ISESTVKRRLRRARK 52 (54)
T ss_dssp -HHHHHHHCT--S-HHHHHHHHHHHHH
T ss_pred CHHHHHHHHC--cCHHHHHHHHHHHHh
Confidence 6999999997 999999998876443
No 64
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=62.83 E-value=5.3 Score=34.09 Aligned_cols=47 Identities=28% Similarity=0.409 Sum_probs=34.7
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHHHHHHH
Q 034427 8 STWTPKENKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEILVDDL 60 (95)
Q Consensus 8 ~~WT~eEdklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~L~~dV 60 (95)
..||++|-+ ++.=|+-- .+.++.||..+. .||+.|+..+|-.-..-|
T Consensus 471 ~~wSp~e~s----~ircf~~y-~~~fe~ia~l~~-tktp~Q~~~fy~~n~k~i 517 (534)
T KOG1194|consen 471 YGWSPEEKS----AIRCFHWY-KDNFELIAELMA-TKTPEQIKKFYMDNEKLI 517 (534)
T ss_pred CCCCCcccc----cccCchhh-ccchHHHHHHhc-CCCHHHHHHHhcCchhhh
Confidence 469999988 33333322 236999999999 999999999997644433
No 65
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=61.96 E-value=38 Score=21.41 Aligned_cols=30 Identities=23% Similarity=0.341 Sum_probs=24.7
Q ss_pred hHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHH
Q 034427 31 DRWQNIAKAVGGGKTVEEVKKHYEILVDDLNR 62 (95)
Q Consensus 31 ~rW~kIA~~vpggRT~~qv~~ry~~L~~dV~~ 62 (95)
..+..||+.++ -|...|+.+.......++.
T Consensus 127 ~s~~eIA~~l~--~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 127 LSYKEIAEILG--ISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred CCHHHHHHHHC--CCHHHHHHHHHHHHHHHHh
Confidence 36889999997 8999999998888777653
No 66
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=61.37 E-value=28 Score=23.38 Aligned_cols=40 Identities=15% Similarity=0.167 Sum_probs=30.3
Q ss_pred HHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHHHHHH
Q 034427 15 NKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEILVDD 59 (95)
Q Consensus 15 dklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~L~~d 59 (95)
|..+.+.|..-.. ..+..||+.++ .|...|.+|-+.|.++
T Consensus 10 D~~IL~~L~~d~r---~~~~eia~~lg--lS~~~v~~Ri~~L~~~ 49 (154)
T COG1522 10 DRRILRLLQEDAR---ISNAELAERVG--LSPSTVLRRIKRLEEE 49 (154)
T ss_pred HHHHHHHHHHhCC---CCHHHHHHHHC--CCHHHHHHHHHHHHHC
Confidence 4445555555333 46999999997 9999999999998754
No 67
>PF11626 Rap1_C: TRF2-interacting telomeric protein/Rap1 - C terminal domain; InterPro: IPR021661 This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres []. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C-terminal domain []. ; PDB: 3K6G_C 3CZ6_A 3OWT_A.
Probab=58.45 E-value=8.1 Score=24.84 Aligned_cols=14 Identities=21% Similarity=0.947 Sum_probs=8.2
Q ss_pred CCCCCCHHHHHHHH
Q 034427 6 LSSTWTPKENKLFE 19 (95)
Q Consensus 6 ~~~~WT~eEdklle 19 (95)
..+-||.++|..|.
T Consensus 46 ~~GiWT~eDD~~L~ 59 (87)
T PF11626_consen 46 MPGIWTPEDDEMLR 59 (87)
T ss_dssp -TT---HHHHHHHT
T ss_pred CCCCcCHHHHHHHH
Confidence 34569999999993
No 68
>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=57.24 E-value=20 Score=29.85 Aligned_cols=50 Identities=28% Similarity=0.528 Sum_probs=32.6
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCC----------hHHHHHHHHc----CCCCCHHHHHHHHHHH
Q 034427 7 SSTWTPKENKLFEKALALYDKETP----------DRWQNIAKAV----GGGKTVEEVKKHYEIL 56 (95)
Q Consensus 7 ~~~WT~eEdklle~aL~~~~~~~~----------~rW~kIA~~v----pggRT~~qv~~ry~~L 56 (95)
..-|+.+=...|.+||+.||+.+- .|=+-|+.+| |-.||.+||-.|.+.|
T Consensus 49 ~~vw~~~~e~af~~al~~~~~~g~~k~~~~~~~~grn~li~~yi~~~tg~~rt~kqvsshiqvl 112 (431)
T PF01285_consen 49 EGVWPPDIEQAFQEALAIYPPCGRRKLSDEGKMYGRNELISDYIKLKTGKTRTRKQVSSHIQVL 112 (431)
T ss_dssp S--S-HHHHHHHHHHHHHS-SSS---HHHH-----THHHHHHHHHHHHS----SHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHhCCCCCCcccccccccccchhHHHHHHHHHhCcccchhHHHHHHHHH
Confidence 456999999999999999987642 3334566655 2238899999999999
No 69
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=56.72 E-value=30 Score=26.13 Aligned_cols=45 Identities=18% Similarity=0.373 Sum_probs=34.5
Q ss_pred CCCHHHHHHHHHHHHhcCCCCChHHHHHHHHcC--CCCCHHHHHHHHHHHHH
Q 034427 9 TWTPKENKLFEKALALYDKETPDRWQNIAKAVG--GGKTVEEVKKHYEILVD 58 (95)
Q Consensus 9 ~WT~eEdklle~aL~~~~~~~~~rW~kIA~~vp--ggRT~~qv~~ry~~L~~ 58 (95)
.|++.+|-+|..|+..-. .-+.|+..|. ..-|..|+.+||..|.-
T Consensus 1 rW~~~DDl~Li~av~~~~-----~L~~v~~gvkFS~~fT~~Ei~~RW~~lly 47 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQTN-----DLESVHLGVKFSCKFTLQEIEERWYALLY 47 (199)
T ss_pred CCCchhhHHHHHHHHHhc-----CHHHHHccCCcCCcCcHHHHHHHHHHHHc
Confidence 499999999999988632 3677776654 33689999999998643
No 70
>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=52.00 E-value=45 Score=19.19 Aligned_cols=44 Identities=20% Similarity=0.249 Sum_probs=33.3
Q ss_pred CCHHHHHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHHHHHHHH
Q 034427 10 WTPKENKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEILVDDLN 61 (95)
Q Consensus 10 WT~eEdklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~L~~dV~ 61 (95)
-|+.|-..|.-....+ .=..||..++ .|..-|+.|...+...+.
T Consensus 4 LT~~E~~vl~~l~~G~------~~~eIA~~l~--is~~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 4 LTERELEVLRLLAQGM------SNKEIAEELG--ISEKTVKSHRRRIMKKLG 47 (58)
T ss_dssp S-HHHHHHHHHHHTTS-------HHHHHHHHT--SHHHHHHHHHHHHHHHHT
T ss_pred cCHHHHHHHHHHHhcC------CcchhHHhcC--cchhhHHHHHHHHHHHhC
Confidence 5777888776666544 3468999997 999999999998887764
No 71
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=50.70 E-value=73 Score=21.26 Aligned_cols=29 Identities=24% Similarity=0.251 Sum_probs=22.0
Q ss_pred hHHHHHHHHcCCCCCHHHHHHHHHHHHHHHH
Q 034427 31 DRWQNIAKAVGGGKTVEEVKKHYEILVDDLN 61 (95)
Q Consensus 31 ~rW~kIA~~vpggRT~~qv~~ry~~L~~dV~ 61 (95)
-.+..||..++ .|...|+.+.......++
T Consensus 142 ~~~~eIA~~lg--is~~tv~~~~~ra~~~lr 170 (179)
T PRK11924 142 LSYREIAEILG--VPVGTVKSRLRRARQLLR 170 (179)
T ss_pred CCHHHHHHHHC--CCHHHHHHHHHHHHHHHH
Confidence 46889999997 888888888776555544
No 72
>PLN03162 golden-2 like transcription factor; Provisional
Probab=49.61 E-value=50 Score=27.94 Aligned_cols=52 Identities=21% Similarity=0.321 Sum_probs=40.5
Q ss_pred CCCCHHHHHHHHHHHHhcCCC--CChHHHHHHHHcCCCCCHHHHHHHHHHHHHHHH
Q 034427 8 STWTPKENKLFEKALALYDKE--TPDRWQNIAKAVGGGKTVEEVKKHYEILVDDLN 61 (95)
Q Consensus 8 ~~WT~eEdklle~aL~~~~~~--~~~rW~kIA~~vpggRT~~qv~~ry~~L~~dV~ 61 (95)
-.||.|=.+.|.+||.+.+.+ +|.+--++= .|+ |-|-..|+.|-++++-.++
T Consensus 238 LrWTpELH~rFVeAV~qLG~dKATPK~ILelM-nV~-GLTRenVKSHLQKYRl~rk 291 (526)
T PLN03162 238 VDWTPELHRRFVHAVEQLGVEKAFPSRILELM-GVQ-CLTRHNIASHLQKYRSHRR 291 (526)
T ss_pred ccCCHHHHHHHHHHHHHhCcCccchHHHHHHc-CCC-CcCHHHHHHHHHHHHHhcc
Confidence 369999999999999998743 566655553 478 8999999999887665544
No 73
>COG5269 ZUO1 Ribosome-associated chaperone zuotin [Translation, ribosomal structure and biogenesis / Posttranslational modification, protein turnover, chaperones]
Probab=49.53 E-value=34 Score=27.91 Aligned_cols=52 Identities=19% Similarity=0.215 Sum_probs=40.0
Q ss_pred CCCCHHHHHHHHHHHHhcCCCC-ChHHHHHHHHcCCC-----CCHHHHHHHHHHHHHHH
Q 034427 8 STWTPKENKLFEKALALYDKET-PDRWQNIAKAVGGG-----KTVEEVKKHYEILVDDL 60 (95)
Q Consensus 8 ~~WT~eEdklle~aL~~~~~~~-~~rW~kIA~~vpgg-----RT~~qv~~ry~~L~~dV 60 (95)
..|+.++-..++.+++.+.+.. ..+|+.+|+.+- + |+.++++...+..-..+
T Consensus 246 rkWereagar~~a~aa~k~kae~k~kae~ea~a~a-sa~a~kkkaKE~~kka~k~~Kk~ 303 (379)
T COG5269 246 RKWEREAGARLKALAALKGKAEAKNKAEIEAEALA-SATAVKKKAKEVMKKALKMEKKA 303 (379)
T ss_pred hccchhhhhhHHHHHHHhhhhHHHhHHHHHHHHhh-hhHHHHHhHHHHHHHHHHHHHHH
Confidence 5699999999999999987654 689999998876 4 56777777766554433
No 74
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=48.32 E-value=69 Score=20.29 Aligned_cols=41 Identities=20% Similarity=0.375 Sum_probs=27.2
Q ss_pred HHHHHHhcCCC----CChHHHHHHHHcCCCCC-----HHHHHHHHHHHHHH
Q 034427 18 FEKALALYDKE----TPDRWQNIAKAVGGGKT-----VEEVKKHYEILVDD 59 (95)
Q Consensus 18 le~aL~~~~~~----~~~rW~kIA~~vpggRT-----~~qv~~ry~~L~~d 59 (95)
|-.++.+++.. ....|..||..++ -.. ..+++.+|....-.
T Consensus 37 Ly~~V~~~GG~~~v~~~~~W~~Va~~lg-~~~~~~~~~~~lk~~Y~k~L~~ 86 (93)
T smart00501 37 LYRLVQERGGYDQVTKDKKWKEIARELG-IPDTSTSAASSLRKHYERYLLP 86 (93)
T ss_pred HHHHHHHccCHHHHcCCCCHHHHHHHhC-CCcccchHHHHHHHHHHHHhHH
Confidence 44456665432 3468999999998 432 56788888875443
No 75
>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=47.55 E-value=37 Score=21.26 Aligned_cols=40 Identities=20% Similarity=0.412 Sum_probs=25.4
Q ss_pred HHHHHHhcCCC----CChHHHHHHHHcCCCCC-----HHHHHHHHHHHHH
Q 034427 18 FEKALALYDKE----TPDRWQNIAKAVGGGKT-----VEEVKKHYEILVD 58 (95)
Q Consensus 18 le~aL~~~~~~----~~~rW~kIA~~vpggRT-----~~qv~~ry~~L~~ 58 (95)
|-.++.+++.. ....|..||..++ --+ ..+++.+|.....
T Consensus 41 Ly~~V~~~GG~~~V~~~~~W~~va~~lg-~~~~~~~~~~~L~~~Y~~~L~ 89 (92)
T PF01388_consen 41 LYKAVMKRGGFDKVTKNKKWREVARKLG-FPPSSTSAAQQLRQHYEKYLL 89 (92)
T ss_dssp HHHHHHHHTSHHHHHHHTTHHHHHHHTT-S-TTSCHHHHHHHHHHHHHTH
T ss_pred HHHHHHhCcCcccCcccchHHHHHHHhC-CCCCCCcHHHHHHHHHHHHhH
Confidence 34455555432 1346999999997 322 4789999987543
No 76
>KOG4559 consensus Uncharacterized conserved protein [Function unknown]
Probab=47.09 E-value=73 Score=22.21 Aligned_cols=47 Identities=32% Similarity=0.509 Sum_probs=35.4
Q ss_pred HHHHHHHHHH----HHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhc
Q 034427 12 PKENKLFEKA----LALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEILVDDLNRIEA 65 (95)
Q Consensus 12 ~eEdklle~a----L~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~L~~dV~~ies 65 (95)
-||-|+||.. +++|. .-..||+.|. |+ ..++-..|++|...+..|+.
T Consensus 50 iEdYKLLEeMNkaTaakY~-----DMk~iAEkla-~k-~deLn~KfenL~P~lqQIDa 100 (120)
T KOG4559|consen 50 IEDYKLLEEMNKATAAKYK-----DMKQIAEKLA-GK-LDELNLKFENLAPMLQQIDA 100 (120)
T ss_pred HHHHHHHHHHHHHHHHHHH-----HHHHHHHHHc-cc-hHHHHHHHHHHHHHHHHHHH
Confidence 4677888875 45553 3678999999 55 56888999999888877764
No 77
>KOG0385 consensus Chromatin remodeling complex WSTF-ISWI, small subunit [Transcription]
Probab=46.99 E-value=54 Score=30.14 Aligned_cols=44 Identities=34% Similarity=0.522 Sum_probs=36.4
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHHH
Q 034427 8 STWTPKENKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEIL 56 (95)
Q Consensus 8 ~~WT~eEdklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~L 56 (95)
..||..+-..|..|-.+|+.+ .-+.||+.|- | |++||..--+.+
T Consensus 796 t~w~k~df~~fi~a~eKygr~---di~~ia~~~e-~-~~eev~~y~rvf 839 (971)
T KOG0385|consen 796 TNWTKRDFNQFIKANEKYGRD---DIENIAAEVE-G-TPEEVGEYARVF 839 (971)
T ss_pred cchhhhhHHHHHHHhhccCcc---hhhhhHHhhc-C-CHHHHHHHHHHH
Confidence 459999999999999999886 6899999999 5 999986544433
No 78
>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=44.33 E-value=84 Score=21.38 Aligned_cols=28 Identities=21% Similarity=0.353 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCCCCCCC
Q 034427 46 VEEVKKHYEILVDDLNRIEAGRVPIPNY 73 (95)
Q Consensus 46 ~~qv~~ry~~L~~dV~~iesg~v~~P~y 73 (95)
.++++.+|+.-+..++.|-.|++.++--
T Consensus 84 ~e~~~~rY~~A~~~L~~ia~G~~~L~~~ 111 (130)
T PF07030_consen 84 TEPVRERYKDAIKWLEDIAKGKISLGLP 111 (130)
T ss_pred cHHHHHHHHHHHHHHHHHHCCCccCCCC
Confidence 8899999999999999999998776443
No 79
>PF04282 DUF438: Family of unknown function (DUF438); InterPro: IPR007380 This is a a group of uncharacterised proteins.
Probab=44.05 E-value=19 Score=23.01 Aligned_cols=22 Identities=32% Similarity=0.522 Sum_probs=18.0
Q ss_pred CCCCHHHHHHHHHHHHHHHHHH
Q 034427 42 GGKTVEEVKKHYEILVDDLNRI 63 (95)
Q Consensus 42 ggRT~~qv~~ry~~L~~dV~~i 63 (95)
.|.+.++|+++|..++.+|...
T Consensus 11 ~G~~~e~vk~~F~~~~~~Vs~~ 32 (71)
T PF04282_consen 11 EGEDPEEVKEEFKKLFSDVSAS 32 (71)
T ss_pred CCCCHHHHHHHHHHHHCCCCHH
Confidence 3789999999999988777643
No 80
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=43.48 E-value=1e+02 Score=21.68 Aligned_cols=65 Identities=17% Similarity=0.209 Sum_probs=40.2
Q ss_pred HHHHHHHHHHhcCCC----------CChHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHH-HhcCCCCCCCCCCCCCCCcc
Q 034427 14 ENKLFEKALALYDKE----------TPDRWQNIAKAVGGGKTVEEVKKHYEILVDDLNR-IEAGRVPIPNYKSPGSSYNA 82 (95)
Q Consensus 14 Edklle~aL~~~~~~----------~~~rW~kIA~~vpggRT~~qv~~ry~~L~~dV~~-iesg~v~~P~y~~~~~~~~~ 82 (95)
+...|..+|.+.|+. .......||+.++ -|..-|+.|.......++. ++.+. ...+...+.++++
T Consensus 106 ~~~~l~~~L~~Lp~~~r~i~~L~~~~g~s~~EIA~~Lg--is~~tVk~~l~Rar~~Lr~~l~~~~--~~~~~~~~~~~~~ 181 (187)
T PRK12516 106 DLQDFRAALDQLPDDQREAIILVGASGFAYEEAAEICG--CAVGTIKSRVNRARQRLQEILQIEG--EADYGPDADSARA 181 (187)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHC--CCHHHHHHHHHHHHHHHHHHHHhhc--ccccCccchhhHH
Confidence 344577777776543 1346789999997 9999999887765555543 33322 2455555555543
No 81
>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=41.22 E-value=21 Score=20.92 Aligned_cols=25 Identities=40% Similarity=0.610 Sum_probs=19.4
Q ss_pred HHHHHHHHHHHhcCCCCChHHHHHHHHcC
Q 034427 13 KENKLFEKALALYDKETPDRWQNIAKAVG 41 (95)
Q Consensus 13 eEdklle~aL~~~~~~~~~rW~kIA~~vp 41 (95)
+...+|..+|. ...|+...||..++
T Consensus 19 ~~~d~F~~~L~----~s~D~F~vIaeyfG 43 (49)
T PF12451_consen 19 DQHDLFFKQLE----ESEDRFSVIAEYFG 43 (49)
T ss_pred hcHHHHHHHHH----hCCCCchhHHHHHc
Confidence 44568888883 45679999999997
No 82
>COG4281 ACB Acyl-CoA-binding protein [Lipid metabolism]
Probab=40.93 E-value=63 Score=21.44 Aligned_cols=30 Identities=27% Similarity=0.531 Sum_probs=25.0
Q ss_pred hHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHH
Q 034427 31 DRWQNIAKAVGGGKTVEEVKKHYEILVDDLNR 62 (95)
Q Consensus 31 ~rW~kIA~~vpggRT~~qv~~ry~~L~~dV~~ 62 (95)
..|+.-|. +. |||.+|.+..|..|++.++.
T Consensus 54 ~K~eAW~~-LK-GksqedA~qeYialVeeLka 83 (87)
T COG4281 54 YKYEAWAG-LK-GKSQEDARQEYIALVEELKA 83 (87)
T ss_pred hhHHHHhh-cc-CccHHHHHHHHHHHHHHHHh
Confidence 56777775 44 69999999999999999884
No 83
>KOG2941 consensus Beta-1,4-mannosyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=40.71 E-value=13 Score=31.11 Aligned_cols=21 Identities=38% Similarity=0.847 Sum_probs=17.3
Q ss_pred CCCCCCHHHHH-HHHHHHHhcC
Q 034427 6 LSSTWTPKENK-LFEKALALYD 26 (95)
Q Consensus 6 ~~~~WT~eEdk-lle~aL~~~~ 26 (95)
+|.+||++||= +|..||..|.
T Consensus 260 sSTswTpDEdf~ILL~AL~~y~ 281 (444)
T KOG2941|consen 260 SSTSWTPDEDFGILLEALVIYE 281 (444)
T ss_pred ecCCCCCcccHHHHHHHHHhhh
Confidence 56889999986 8888888774
No 84
>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=40.11 E-value=30 Score=23.16 Aligned_cols=18 Identities=22% Similarity=0.551 Sum_probs=14.1
Q ss_pred hHHHHHHHHcCCCCCHHHH
Q 034427 31 DRWQNIAKAVGGGKTVEEV 49 (95)
Q Consensus 31 ~rW~kIA~~vpggRT~~qv 49 (95)
+.|+++|..++ +=|..+|
T Consensus 22 ~~W~~LA~~i~-~ys~~~v 39 (97)
T cd08307 22 NVWEELAFVMM-GYSNDDV 39 (97)
T ss_pred CcHHHHHHHHh-cCCHHHH
Confidence 58999999998 5555554
No 85
>PF10743 Phage_Cox: Regulatory phage protein cox; InterPro: IPR019679 Phage Cox proteins are expressed by Enterobacteria phages. The Cox protein is a 79-residue basic protein with a predicted strong helix-turn-helix DNA-binding motif. It inhibits integrative recombination and it activates site-specific excision of the HP1 genome from the Haemophilus influenzae chromosome, Hp1. Cox appears to function as a tetramer. Cox binding sites consist of two direct repeats of the consensus motif 5'-GGTMAWWWWA, one Cox tetramer binding to each motif. Cox binding interferes with the interaction of HP1 integrase with one of its binding sites, IBS5. This competition is central to directional control. Both Cox binding sites are needed for full inhibition of integration and for activating excision, because it plays a positive role in assembling the nucleoprotein complexes that produce excisive recombination, by inducing the formation of a critical conformation in those complexes [].
Probab=40.08 E-value=58 Score=21.73 Aligned_cols=48 Identities=25% Similarity=0.504 Sum_probs=33.2
Q ss_pred HHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCC-CCCCc
Q 034427 21 ALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEILVDDLNRIEAGRVPIPNYKSP-GSSYN 81 (95)
Q Consensus 21 aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~L~~dV~~iesg~v~~P~y~~~-~~~~~ 81 (95)
-+..||.+. -.=+++|..+| ||..-|+. .|+.|++|+=...++ .+++.
T Consensus 4 ~~~~~p~d~-v~~~~FA~~IG--Kt~sAVr~----------Mi~~gKLP~i~~~dP~~p~~r 52 (87)
T PF10743_consen 4 QVSEYPSDA-VTYEKFAEYIG--KTPSAVRK----------MIKAGKLPVIEMRDPEKPNGR 52 (87)
T ss_pred hHHhhhccc-cCHHHHHHHHC--CCHHHHHH----------HHHcCCCCeEeccCCCCCCCc
Confidence 345565542 24689999997 99998875 467999887766655 33444
No 86
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=38.64 E-value=1.3e+02 Score=20.75 Aligned_cols=44 Identities=18% Similarity=0.135 Sum_probs=29.1
Q ss_pred HHHHHHHHhcCCC----------CChHHHHHHHHcCCCCCHHHHHHHHHHHHHHHH
Q 034427 16 KLFEKALALYDKE----------TPDRWQNIAKAVGGGKTVEEVKKHYEILVDDLN 61 (95)
Q Consensus 16 klle~aL~~~~~~----------~~~rW~kIA~~vpggRT~~qv~~ry~~L~~dV~ 61 (95)
+.+..+|.+.|+. .....+.||..++ -|..-|+.+...-...++
T Consensus 131 ~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lg--is~~tV~~~l~Ra~~~Lr 184 (189)
T PRK09648 131 NRMRELLDTLPEKQREILILRVVVGLSAEETAEAVG--STPGAVRVAQHRALARLR 184 (189)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHC--CCHHHHHHHHHHHHHHHH
Confidence 3466666666543 1345788888886 888888887766555544
No 87
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=37.01 E-value=1.2e+02 Score=21.20 Aligned_cols=47 Identities=13% Similarity=0.100 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHhcCCC----------CChHHHHHHHHcCCCCCHHHHHHHHHHHHHHHH
Q 034427 13 KENKLFEKALALYDKE----------TPDRWQNIAKAVGGGKTVEEVKKHYEILVDDLN 61 (95)
Q Consensus 13 eEdklle~aL~~~~~~----------~~~rW~kIA~~vpggRT~~qv~~ry~~L~~dV~ 61 (95)
++...|..+|...|+. ..-....||+.++ .|..-|+.+-..-...++
T Consensus 131 ~~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~EIA~~Lg--is~~tVk~~l~ra~~~Lr 187 (194)
T PRK09646 131 LERERVRDCLDALTDTQRESVTLAYYGGLTYREVAERLA--VPLGTVKTRMRDGLIRLR 187 (194)
T ss_pred hHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhC--CChHhHHHHHHHHHHHHH
Confidence 4455677777766543 1345778888887 788888877766555554
No 88
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=34.94 E-value=1.4e+02 Score=19.99 Aligned_cols=47 Identities=17% Similarity=0.159 Sum_probs=33.1
Q ss_pred HHHHHHHHhcCCC----------CChHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHh
Q 034427 16 KLFEKALALYDKE----------TPDRWQNIAKAVGGGKTVEEVKKHYEILVDDLNRIE 64 (95)
Q Consensus 16 klle~aL~~~~~~----------~~~rW~kIA~~vpggRT~~qv~~ry~~L~~dV~~ie 64 (95)
..+..+|...|+. ..-....||..++ -|...|+.|.......++.+.
T Consensus 104 ~~~~~~l~~L~~~~r~v~~l~~~~~~s~~eIA~~lg--is~~tv~~~l~Rar~~L~~~~ 160 (161)
T PRK12541 104 ASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTG--LSLAKVKIELHRGRKETKSIK 160 (161)
T ss_pred HHHHHHHHHCCHHHHHHhhhHHhcCCCHHHHHHHHC--CCHHHHHHHHHHHHHHHHhhc
Confidence 3455566666542 1235689999997 899999999888877777553
No 89
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=34.70 E-value=82 Score=17.25 Aligned_cols=34 Identities=18% Similarity=0.260 Sum_probs=24.8
Q ss_pred HHHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHH
Q 034427 14 ENKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHY 53 (95)
Q Consensus 14 Edklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry 53 (95)
|...++.+|..+.. +..+.|..++ -|...+..+-
T Consensus 6 E~~~i~~aL~~~~g----n~~~aA~~Lg--isr~tL~~kl 39 (42)
T PF02954_consen 6 EKQLIRQALERCGG----NVSKAARLLG--ISRRTLYRKL 39 (42)
T ss_dssp HHHHHHHHHHHTTT-----HHHHHHHHT--S-HHHHHHHH
T ss_pred HHHHHHHHHHHhCC----CHHHHHHHHC--CCHHHHHHHH
Confidence 66788899998866 5889999997 7776665543
No 90
>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=34.02 E-value=46 Score=21.03 Aligned_cols=22 Identities=36% Similarity=0.508 Sum_probs=19.0
Q ss_pred HcCCCCCHHHHHHHHHHHHHHHH
Q 034427 39 AVGGGKTVEEVKKHYEILVDDLN 61 (95)
Q Consensus 39 ~vpggRT~~qv~~ry~~L~~dV~ 61 (95)
.+. |.|.+|.+++|..++.++.
T Consensus 62 ~l~-gms~~eA~~~Yi~~v~~~~ 83 (87)
T PF00887_consen 62 ALK-GMSKEEAMREYIELVEELI 83 (87)
T ss_dssp TTT-TTHHHHHHHHHHHHHHHHH
T ss_pred Hcc-CCCHHHHHHHHHHHHHHHH
Confidence 356 8999999999999988775
No 91
>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=33.63 E-value=57 Score=23.71 Aligned_cols=27 Identities=26% Similarity=0.612 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHhcCCCCChHHHHHHHHcC
Q 034427 13 KENKLFEKALALYDKETPDRWQNIAKAVG 41 (95)
Q Consensus 13 eEdklle~aL~~~~~~~~~rW~kIA~~vp 41 (95)
++++.|.+||..| ..|..|..|-++|-
T Consensus 41 ~~er~lqkAll~Y--~~PeN~~lvreAL~ 67 (150)
T PF11842_consen 41 ERERRLQKALLRY--HDPENWPLVREALK 67 (150)
T ss_pred HHHHHHHHHHHhh--cChhhHHHHHHHHH
Confidence 5788999999999 34568999988886
No 92
>smart00386 HAT HAT (Half-A-TPR) repeats. Present in several RNA-binding proteins. Structurally and sequentially thought to be similar to TPRs.
Probab=33.12 E-value=61 Score=15.24 Aligned_cols=24 Identities=25% Similarity=0.581 Sum_probs=18.2
Q ss_pred HHHHHHHHHhcCCCCChHHHHHHHH
Q 034427 15 NKLFEKALALYDKETPDRWQNIAKA 39 (95)
Q Consensus 15 dklle~aL~~~~~~~~~rW~kIA~~ 39 (95)
..+|+++|..+| ..++-|..-+..
T Consensus 7 r~i~e~~l~~~~-~~~~~W~~y~~~ 30 (33)
T smart00386 7 RKIYERALEKFP-KSVELWLKYAEF 30 (33)
T ss_pred HHHHHHHHHHCC-CChHHHHHHHHH
Confidence 468999999988 456788876654
No 93
>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=33.00 E-value=68 Score=20.59 Aligned_cols=22 Identities=27% Similarity=0.401 Sum_probs=19.1
Q ss_pred HcCCCCCHHHHHHHHHHHHHHHH
Q 034427 39 AVGGGKTVEEVKKHYEILVDDLN 61 (95)
Q Consensus 39 ~vpggRT~~qv~~ry~~L~~dV~ 61 (95)
.++ |-|.+++++.|..+++.+.
T Consensus 60 ~l~-~ms~~eA~~~YV~~~~~l~ 81 (85)
T cd00435 60 SLK-GMSKEDAMKAYIAKVEELI 81 (85)
T ss_pred HcC-CCCHHHHHHHHHHHHHHHh
Confidence 356 8999999999999998874
No 94
>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=32.37 E-value=1.4e+02 Score=19.34 Aligned_cols=28 Identities=25% Similarity=0.479 Sum_probs=23.7
Q ss_pred HHHHHHHHcCCCCCHHHHHHHHHHHHHHHH
Q 034427 32 RWQNIAKAVGGGKTVEEVKKHYEILVDDLN 61 (95)
Q Consensus 32 rW~kIA~~vpggRT~~qv~~ry~~L~~dV~ 61 (95)
.+..||+.++ .|...|+.+.......++
T Consensus 131 ~~~eIA~~lg--is~~tv~~~~~ra~~~Lr 158 (161)
T TIGR02985 131 SYKEIAEELG--ISVKTVEYHISKALKELR 158 (161)
T ss_pred CHHHHHHHHC--CCHHHHHHHHHHHHHHHH
Confidence 5889999997 899999998888777765
No 95
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=32.35 E-value=1.5e+02 Score=20.17 Aligned_cols=48 Identities=8% Similarity=0.235 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHHhcCCCC----------ChHHHHHHHHcCCCCCHHHHHHHHHHHHHHHH
Q 034427 12 PKENKLFEKALALYDKET----------PDRWQNIAKAVGGGKTVEEVKKHYEILVDDLN 61 (95)
Q Consensus 12 ~eEdklle~aL~~~~~~~----------~~rW~kIA~~vpggRT~~qv~~ry~~L~~dV~ 61 (95)
.++...+.++|...|+.. .-.-+.||+.++ .|..-|+.|.......++
T Consensus 107 ~~~~~~l~~~l~~L~~~~r~i~~l~~~~~~s~~EIA~~lg--is~~tV~~~l~Ra~~~Lr 164 (173)
T PRK12522 107 KVEAEMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILN--IPIGTVKYRLNYAKKQMR 164 (173)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhC--CCHHHHHHHHHHHHHHHH
Confidence 344456777777776531 223467787776 777788877665554444
No 96
>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=31.94 E-value=1.5e+02 Score=19.44 Aligned_cols=44 Identities=14% Similarity=0.170 Sum_probs=32.5
Q ss_pred HHHHHHHHhcCCC----------CChHHHHHHHHcCCCCCHHHHHHHHHHHHHHHH
Q 034427 16 KLFEKALALYDKE----------TPDRWQNIAKAVGGGKTVEEVKKHYEILVDDLN 61 (95)
Q Consensus 16 klle~aL~~~~~~----------~~~rW~kIA~~vpggRT~~qv~~ry~~L~~dV~ 61 (95)
..|..+|.+.|+. ..-.++.||+.++ .|...|+.+.......++
T Consensus 97 ~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lg--is~~tv~~~l~Ra~~~Lr 150 (154)
T TIGR02950 97 EEITHHLSRLPENYRTVLILREFKEFSYKEIAELLN--LSLAKVKSNLFRARKELK 150 (154)
T ss_pred HHHHHHHHhCCHhheeeeeehhhccCcHHHHHHHHC--CCHHHHHHHHHHHHHHHH
Confidence 4567777777643 1357999999997 999999888876665554
No 97
>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=31.15 E-value=1.6e+02 Score=19.57 Aligned_cols=44 Identities=23% Similarity=0.184 Sum_probs=28.7
Q ss_pred HHHHHHHHhcCCC----------CChHHHHHHHHcCCCCCHHHHHHHHHHHHHHHH
Q 034427 16 KLFEKALALYDKE----------TPDRWQNIAKAVGGGKTVEEVKKHYEILVDDLN 61 (95)
Q Consensus 16 klle~aL~~~~~~----------~~~rW~kIA~~vpggRT~~qv~~ry~~L~~dV~ 61 (95)
..|..+|.+.|+. ....-..||+.++ .|..-|+.+.......++
T Consensus 114 ~~l~~~l~~L~~~~r~vl~l~~~~g~s~~eIA~~l~--is~~tv~~~l~ra~~~Lr 167 (170)
T TIGR02952 114 EKLLKALKILTPKQQHVIALRFGQNLPIAEVARILG--KTEGAVKILQFRAIKKLA 167 (170)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHhcCCCHHHHHHHHC--CCHHHHHHHHHHHHHHHH
Confidence 4566776665542 1235678888886 777778777776665554
No 98
>PRK04654 sec-independent translocase; Provisional
Probab=31.06 E-value=86 Score=24.11 Aligned_cols=39 Identities=18% Similarity=0.281 Sum_probs=28.5
Q ss_pred HHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHHHHHHHH
Q 034427 18 FEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEILVDDLN 61 (95)
Q Consensus 18 le~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~L~~dV~ 61 (95)
+.-+|..|++ +|+-+++..++ |...++|+.+....+++.
T Consensus 13 ~VVALlV~GP---erLPe~aRtlG--k~irk~R~~~~~vk~El~ 51 (214)
T PRK04654 13 AVVALVVLGP---ERLPKAARFAG--LWVRRARMQWDSVKQELE 51 (214)
T ss_pred HHHHHHhcCc---hHHHHHHHHHH--HHHHHHHHHHHHHHHHHH
Confidence 3445666654 59999999997 888888877776666553
No 99
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=31.03 E-value=61 Score=18.88 Aligned_cols=29 Identities=28% Similarity=0.511 Sum_probs=20.0
Q ss_pred CCCHHHHHHHHHHHHHHHHHHhcCCCCCC
Q 034427 43 GKTVEEVKKHYEILVDDLNRIEAGRVPIP 71 (95)
Q Consensus 43 gRT~~qv~~ry~~L~~dV~~iesg~v~~P 71 (95)
|-|..|+-.+-..=...|.+||.|..+.|
T Consensus 14 gls~~~lA~~~g~s~s~v~~iE~G~~~~p 42 (64)
T PF13560_consen 14 GLSQAQLADRLGVSQSTVSRIERGRRPRP 42 (64)
T ss_dssp TS-HHHHHHHHTS-HHHHHHHHTTSSSS-
T ss_pred CCCHHHHHHHHCcCHHHHHHHHCCCCCCC
Confidence 46777777777677788899999987544
No 100
>PTZ00458 acyl CoA binding protein; Provisional
Probab=30.75 E-value=78 Score=20.81 Aligned_cols=21 Identities=29% Similarity=0.406 Sum_probs=18.6
Q ss_pred cCCCCCHHHHHHHHHHHHHHHH
Q 034427 40 VGGGKTVEEVKKHYEILVDDLN 61 (95)
Q Consensus 40 vpggRT~~qv~~ry~~L~~dV~ 61 (95)
++ |-|.++.+++|..|+.++.
T Consensus 63 l~-~ms~~eA~~~YI~l~~~l~ 83 (90)
T PTZ00458 63 IE-NLNREDAKKRYVEIVTELF 83 (90)
T ss_pred cC-CCCHHHHHHHHHHHHHHHh
Confidence 46 8999999999999998874
No 101
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=29.02 E-value=2.1e+02 Score=20.08 Aligned_cols=44 Identities=18% Similarity=0.077 Sum_probs=29.6
Q ss_pred HHHHHHHHHhcCCC----------CChHHHHHHHHcCCCCCHHHHHHHHHHHHHHH
Q 034427 15 NKLFEKALALYDKE----------TPDRWQNIAKAVGGGKTVEEVKKHYEILVDDL 60 (95)
Q Consensus 15 dklle~aL~~~~~~----------~~~rW~kIA~~vpggRT~~qv~~ry~~L~~dV 60 (95)
...++.+|...|+. .......||..++ -|...|+.|.......+
T Consensus 125 ~~~l~~~l~~Lp~~~r~i~~l~~~~g~s~~EIA~~lg--~s~~tV~~rl~rar~~L 178 (192)
T PRK09643 125 ALAVQRALMRLPVEQRAALVAVDMQGYSVADAARMLG--VAEGTVKSRCARGRARL 178 (192)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHC--cCHHHHHHHHHHHHHHH
Confidence 34666777766543 1345788999997 88888988875544433
No 102
>PF11112 PyocinActivator: Pyocin activator protein PrtN
Probab=28.67 E-value=94 Score=19.85 Aligned_cols=33 Identities=30% Similarity=0.508 Sum_probs=22.5
Q ss_pred HHHHHHHHH-HH--HHHHHHHhcCCCCCCCCCCCCC
Q 034427 46 VEEVKKHYE-IL--VDDLNRIEAGRVPIPNYKSPGS 78 (95)
Q Consensus 46 ~~qv~~ry~-~L--~~dV~~iesg~v~~P~y~~~~~ 78 (95)
.++|..+|- .| ..-..++-+|.+|+|-+.-+++
T Consensus 17 L~~v~~~yf~~lt~~~a~rk~~~g~lplPv~rl~~S 52 (76)
T PF11112_consen 17 LEEVCEDYFPHLTPKTAKRKANAGELPLPVFRLDDS 52 (76)
T ss_pred HHHHHHHHHccCCHHHHHHHHHCCCCCCceeecCCc
Confidence 667777775 32 3344557799999999976643
No 103
>PF15508 NAAA-beta: beta subunit of N-acylethanolamine-hydrolyzing acid amidase
Probab=28.55 E-value=66 Score=20.75 Aligned_cols=27 Identities=26% Similarity=0.481 Sum_probs=19.3
Q ss_pred hHHHHHHHHcCCCCCHHHHHHHHHHHHHH
Q 034427 31 DRWQNIAKAVGGGKTVEEVKKHYEILVDD 59 (95)
Q Consensus 31 ~rW~kIA~~vpggRT~~qv~~ry~~L~~d 59 (95)
+||..|+.... .....+...++.+...
T Consensus 16 eRw~~i~~~~k--~~i~~l~~~~~~~~~~ 42 (95)
T PF15508_consen 16 ERWVQIAKDYK--DEIRELIEVLKDLLQS 42 (95)
T ss_pred HHHHHHHHHHH--HHHHHHHHHHHHHHHH
Confidence 79999999887 5555666666665443
No 104
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=27.85 E-value=2.4e+02 Score=20.46 Aligned_cols=44 Identities=23% Similarity=0.202 Sum_probs=30.9
Q ss_pred HHHHHHHHhcCCC----------CChHHHHHHHHcCCCCCHHHHHHHHHHHHHHHH
Q 034427 16 KLFEKALALYDKE----------TPDRWQNIAKAVGGGKTVEEVKKHYEILVDDLN 61 (95)
Q Consensus 16 klle~aL~~~~~~----------~~~rW~kIA~~vpggRT~~qv~~ry~~L~~dV~ 61 (95)
..+..+|...|+. .....+.||+.++ .|...|+.++......++
T Consensus 141 ~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIAe~lg--is~~tVk~~l~Rar~kLr 194 (231)
T PRK11922 141 ALLERAIDALPDAFRAVFVLRVVEELSVEETAQALG--LPEETVKTRLHRARRLLR 194 (231)
T ss_pred HHHHHHHHhCCHHHhhhheeehhcCCCHHHHHHHHC--cCHHHHHHHHHHHHHHHH
Confidence 3466676665532 2456899999997 999999988876554444
No 105
>KOG1724 consensus SCF ubiquitin ligase, Skp1 component [Posttranslational modification, protein turnover, chaperones]
Probab=27.82 E-value=55 Score=23.83 Aligned_cols=40 Identities=25% Similarity=0.386 Sum_probs=27.6
Q ss_pred HHHHHHHHHHhcCCCC----ChHHHHHHHHcCCCCCHHHHHHHHH
Q 034427 14 ENKLFEKALALYDKET----PDRWQNIAKAVGGGKTVEEVKKHYE 54 (95)
Q Consensus 14 Edklle~aL~~~~~~~----~~rW~kIA~~vpggRT~~qv~~ry~ 54 (95)
+.-+|+-.++.+--+- .-.=..||.++- |||++|+|..|.
T Consensus 97 ~~tLfdli~AAnyLdi~gLl~~~ck~va~mik-gktpeEir~~f~ 140 (162)
T KOG1724|consen 97 QGTLFDLILAANYLDIKGLLDLTCKTVANMIK-GKTPEEIREIFN 140 (162)
T ss_pred HHHHHHHHHHhhhcccHHHHHHHHHHHHHHHc-cCCHHHHHHHcC
Confidence 3456666666643332 234578999999 999999999854
No 106
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=27.26 E-value=1.9e+02 Score=19.20 Aligned_cols=44 Identities=16% Similarity=0.087 Sum_probs=29.2
Q ss_pred HHHHHHHHhcCCC----------CChHHHHHHHHcCCCCCHHHHHHHHHHHHHHHH
Q 034427 16 KLFEKALALYDKE----------TPDRWQNIAKAVGGGKTVEEVKKHYEILVDDLN 61 (95)
Q Consensus 16 klle~aL~~~~~~----------~~~rW~kIA~~vpggRT~~qv~~ry~~L~~dV~ 61 (95)
..|..+|.+.|+. ..-.-..||..++ .|..-|+.|.......++
T Consensus 98 ~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lg--is~~tV~~~l~Rar~~Lr 151 (160)
T PRK09642 98 LLIAQKLRELPENYRDVVLAHYLEEKSYQEIALQEK--IEVKTVEMKLYRARKWIK 151 (160)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHHC--CCHHHHHHHHHHHHHHHH
Confidence 3566777776654 1345678888887 888888887665444443
No 107
>TIGR01636 phage_rinA phage transcriptional activator, RinA family. This model represents a family of phage proteins, including RinA, a transcriptional activator in staphylococcal phage phi 11. This family shows similarity to ArpU, a phage-related putative autolysin regulator, and to some sporulation-specific sigma factors.
Probab=27.25 E-value=2.1e+02 Score=19.53 Aligned_cols=46 Identities=11% Similarity=0.199 Sum_probs=28.9
Q ss_pred CHHHHHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHHHHHHHH
Q 034427 11 TPKENKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEILVDDLN 61 (95)
Q Consensus 11 T~eEdklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~L~~dV~ 61 (95)
+.+|.++|+. .|.......|..||..++ -|...|.++=+.....+.
T Consensus 84 d~~er~II~~---rY~~~~~~t~~~Ia~~l~--iS~~t~~r~r~~~l~kla 129 (134)
T TIGR01636 84 DEQTRVIIQE---LYMKKRPLTLVGLAQQLF--ISKSTAYRLRNHIIEAVA 129 (134)
T ss_pred CHHHHHHHHH---HHccCCCCCHHHHHHHhC--CCHHHHHHHHHHHHHHHH
Confidence 4444444432 243332347999999997 999998766555555554
No 108
>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=26.86 E-value=2.1e+02 Score=19.46 Aligned_cols=43 Identities=12% Similarity=0.150 Sum_probs=29.8
Q ss_pred HHHHHHHhcCCC----------CChHHHHHHHHcCCCCCHHHHHHHHHHHHHHHH
Q 034427 17 LFEKALALYDKE----------TPDRWQNIAKAVGGGKTVEEVKKHYEILVDDLN 61 (95)
Q Consensus 17 lle~aL~~~~~~----------~~~rW~kIA~~vpggRT~~qv~~ry~~L~~dV~ 61 (95)
.|..+|...|+. .......||+.++ -|..-|+.+.......++
T Consensus 131 ~l~~~l~~L~~~~r~v~~l~~~~~~s~~EIA~~lg--is~~tv~~~l~rar~~Lr 183 (190)
T TIGR02939 131 TVMRAVEALPEDLRTAITLRELEGLSYEDIARIMD--CPVGTVRSRIFRAREAIA 183 (190)
T ss_pred HHHHHHHcCCHHHhhhhhhhhhcCCCHHHHHHHHC--cCHHHHHHHHHHHHHHHH
Confidence 466677766542 1345788999997 888888888776655554
No 109
>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A.
Probab=26.71 E-value=71 Score=15.28 Aligned_cols=13 Identities=15% Similarity=0.422 Sum_probs=8.8
Q ss_pred HHHHHHHHHhcCC
Q 034427 15 NKLFEKALALYDK 27 (95)
Q Consensus 15 dklle~aL~~~~~ 27 (95)
.+.|++.+..||.
T Consensus 20 ~~~~~~~~~~~P~ 32 (33)
T PF13174_consen 20 IEYFQRLIKRYPD 32 (33)
T ss_dssp HHHHHHHHHHSTT
T ss_pred HHHHHHHHHHCcC
Confidence 4567777777775
No 110
>cd08308 Death_Tube Death domain of Tube. Death domains (DDs) similar to the DD in the protein Tube from Drosophila melanogaster. 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 also in mediating innate immune response to pathogens. Tube and Pelle transmit the signal from the Toll receptor to the Dorsal/Cactus complex. Some members of this subfamily contain a C-terminal kinase domain, like Pelle, in addition to the DD. Tube has no counterpart in vertebrates. It contains an N-terminal DD and a C-terminal region with five copies of the Tube repeat, an 8-amino acid motif. 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 (D
Probab=26.16 E-value=28 Score=24.53 Aligned_cols=17 Identities=12% Similarity=0.477 Sum_probs=13.1
Q ss_pred ChHHHHHHHHcCCCCCHHH
Q 034427 30 PDRWQNIAKAVGGGKTVEE 48 (95)
Q Consensus 30 ~~rW~kIA~~vpggRT~~q 48 (95)
.+.|++++..+| |...+
T Consensus 22 ~d~Wk~L~~~Ip--~~~~~ 38 (125)
T cd08308 22 NDGWKKLMAIIP--SDDDD 38 (125)
T ss_pred cccHHHHHHhcC--Ccccc
Confidence 368999999999 55444
No 111
>PF10046 BLOC1_2: Biogenesis of lysosome-related organelles complex-1 subunit 2 ; InterPro: IPR019269 This entry represents a family of proteins that play a role in cellular proliferation, as well as in the biogenesis of specialised organelles of the endosomal-lysosomal system [].
Probab=26.09 E-value=1.2e+02 Score=19.86 Aligned_cols=47 Identities=28% Similarity=0.480 Sum_probs=33.3
Q ss_pred CHHHHHHHHHH----HHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHh
Q 034427 11 TPKENKLFEKA----LALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEILVDDLNRIE 64 (95)
Q Consensus 11 T~eEdklle~a----L~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~L~~dV~~ie 64 (95)
|.++-++|++. ..+| .....++..+. ++.++....|..|.+-+..|.
T Consensus 19 t~~d~~LLe~mN~~~~~kY-----~~~~~~~~~l~--~~~~~l~~k~~~l~~~l~~Id 69 (99)
T PF10046_consen 19 TNEDYNLLENMNKATSLKY-----KKMKDIAAGLE--KNLEDLNQKYEELQPYLQQID 69 (99)
T ss_pred HHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHH
Confidence 34566666654 3334 35888888887 999999999998776666554
No 112
>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=26.02 E-value=1.9e+02 Score=20.50 Aligned_cols=45 Identities=9% Similarity=0.181 Sum_probs=31.6
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCChHHHHHHHHcC-C--CCCHHHHHHHHHHH
Q 034427 8 STWTPKENKLFEKALALYDKETPDRWQNIAKAVG-G--GKTVEEVKKHYEIL 56 (95)
Q Consensus 8 ~~WT~eEdklle~aL~~~~~~~~~rW~kIA~~vp-g--gRT~~qv~~ry~~L 56 (95)
..=|..|...++.+|.+|+.+ ++.+|.-.- + -.|..||+.++...
T Consensus 115 ~~ls~~e~~~i~~Li~KhGdD----y~aMarD~KLN~~Q~T~~qlrrki~~~ 162 (164)
T PF09420_consen 115 RRLSEREIEYIEYLIEKHGDD----YKAMARDRKLNYMQHTPGQLRRKIRKY 162 (164)
T ss_pred CCCCHHHHHHHHHHHHHHCcc----HHHHhccCCCCcccCCHHHHHHHHHHh
Confidence 346788999999999999864 676663221 0 16888888877653
No 113
>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=25.68 E-value=33 Score=14.70 Aligned_cols=8 Identities=38% Similarity=1.045 Sum_probs=5.9
Q ss_pred cCCCCCCC
Q 034427 65 AGRVPIPN 72 (95)
Q Consensus 65 sg~v~~P~ 72 (95)
+|.++||.
T Consensus 3 sGlI~fpR 10 (11)
T PF08259_consen 3 SGLIPFPR 10 (11)
T ss_pred ccccccCC
Confidence 57888874
No 114
>PF14966 DNA_repr_REX1B: DNA repair REX1-B
Probab=25.47 E-value=1.2e+02 Score=20.14 Aligned_cols=44 Identities=20% Similarity=0.401 Sum_probs=34.1
Q ss_pred HHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhcCC
Q 034427 16 KLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEILVDDLNRIEAGR 67 (95)
Q Consensus 16 klle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~L~~dV~~iesg~ 67 (95)
..|+.++..|-.+.+. ...+ ....+|..-|..+-.+|..||...
T Consensus 20 ~~~~~gf~~yl~~~~~------~~y~--~~~~~iT~~f~~~S~ei~~ie~~L 63 (97)
T PF14966_consen 20 NRFEEGFKKYLRSGPE------EAYR--QLCHEITQEFSAISKEILAIEAEL 63 (97)
T ss_pred HHHHHHHHHHHhcCCh------HHHH--HHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4688889999776654 3343 556678899999999999999875
No 115
>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=25.16 E-value=1.9e+02 Score=18.49 Aligned_cols=30 Identities=30% Similarity=0.531 Sum_probs=19.6
Q ss_pred CHHHHHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHH
Q 034427 11 TPKENKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEV 49 (95)
Q Consensus 11 T~eEdklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv 49 (95)
|.++...|...|.. .|..+|..++ =|..++
T Consensus 1 ~~~~l~~l~~~lG~-------~Wk~lar~LG--~s~~eI 30 (86)
T cd08777 1 TEKHLDLLRENLGK-------KWKRCARKLG--FTESEI 30 (86)
T ss_pred CHHHHHHHHHHHHH-------HHHHHHHHcC--CCHHHH
Confidence 44555555544443 7999999998 665554
No 116
>COG4387 Mu-like prophage protein gp36 [Function unknown]
Probab=24.95 E-value=1.1e+02 Score=22.05 Aligned_cols=28 Identities=21% Similarity=0.506 Sum_probs=22.7
Q ss_pred CCCHHHHHHHHHHHHHHHHHHhcCCCCC
Q 034427 43 GKTVEEVKKHYEILVDDLNRIEAGRVPI 70 (95)
Q Consensus 43 gRT~~qv~~ry~~L~~dV~~iesg~v~~ 70 (95)
+|-.+|.+.||+.-+.-++..-+|.|++
T Consensus 80 ~r~Tdq~r~rYe~av~~L~~va~G~V~l 107 (139)
T COG4387 80 NRATDQARQRYEDAVRFLEKVASGAVSL 107 (139)
T ss_pred hhhhHHHHHHHHHHHHHHHHHHcCCCcc
Confidence 5788999999998666666677998876
No 117
>KOG2527 consensus Sorting nexin SNX11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=24.82 E-value=93 Score=22.57 Aligned_cols=30 Identities=27% Similarity=0.447 Sum_probs=21.5
Q ss_pred HHHHHHHH---HHHHHHHHhcCCCCCCCCCCCCC
Q 034427 48 EVKKHYEI---LVDDLNRIEAGRVPIPNYKSPGS 78 (95)
Q Consensus 48 qv~~ry~~---L~~dV~~iesg~v~~P~y~~~~~ 78 (95)
-|++||.. |...+. -++|+|.+|......-
T Consensus 55 ~VRRRYsdFewlr~~Le-r~s~kvvvP~LPgK~~ 87 (144)
T KOG2527|consen 55 CVRRRYSDFEWLRKRLE-RESGKVVVPELPGKAL 87 (144)
T ss_pred HHHHHHHHHHHHHHHHH-HhcccccCCCCCcHHH
Confidence 47899985 555554 7889999998854433
No 118
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=24.59 E-value=2.5e+02 Score=19.59 Aligned_cols=45 Identities=20% Similarity=0.096 Sum_probs=31.8
Q ss_pred HHHHHHHHhcCCC----------CChHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHH
Q 034427 16 KLFEKALALYDKE----------TPDRWQNIAKAVGGGKTVEEVKKHYEILVDDLNR 62 (95)
Q Consensus 16 klle~aL~~~~~~----------~~~rW~kIA~~vpggRT~~qv~~ry~~L~~dV~~ 62 (95)
+.+..+|...|+. ..-.++.||..++ -|..-|+.+...-...++.
T Consensus 128 ~~l~~~l~~L~~~~r~i~~L~~~~g~s~~eIA~~lg--is~~tV~~~l~Ra~~~Lr~ 182 (196)
T PRK12524 128 RALDAALAALPERQRQAVVLRHIEGLSNPEIAEVME--IGVEAVESLTARGKRALAA 182 (196)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHC--cCHHHHHHHHHHHHHHHHH
Confidence 4566666665532 2346999999997 9999998888876655554
No 119
>PF05256 UPF0223: Uncharacterised protein family (UPF0223); InterPro: IPR007920 This family of proteins is functionally uncharacterised.; PDB: 2OY9_B.
Probab=24.51 E-value=2.2e+02 Score=18.89 Aligned_cols=40 Identities=20% Similarity=0.276 Sum_probs=23.3
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHHHHH
Q 034427 8 STWTPKENKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEILVD 58 (95)
Q Consensus 8 ~~WT~eEdklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~L~~ 58 (95)
..||.||.-.... -|+.|..+-..|-..+++..+|+....
T Consensus 9 ~dWsteEii~Vi~-----------F~~~VE~AYE~gV~r~~ll~~Y~~FK~ 48 (88)
T PF05256_consen 9 PDWSTEEIIDVIN-----------FFNAVEKAYEKGVDREELLDAYRRFKK 48 (88)
T ss_dssp ----HHHHHHHHH-----------HHHHHHHHHTT-EEHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHH-----------HHHHHHHHHHccCcHHHHHHHHHHHHH
Confidence 4699999765422 366676666667777788777776544
No 120
>PRK14857 tatA twin arginine translocase protein A; Provisional
Probab=24.32 E-value=1.7e+02 Score=19.38 Aligned_cols=41 Identities=17% Similarity=0.386 Sum_probs=30.9
Q ss_pred HHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHH
Q 034427 18 FEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEILVDDLNRI 63 (95)
Q Consensus 18 le~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~L~~dV~~i 63 (95)
+.-+|..|++. ++-.++..|+ |...+.++......+++..-
T Consensus 15 lvVaLlvfGP~---KLP~lar~lG--k~i~~fkk~~~~~~~e~~~~ 55 (90)
T PRK14857 15 LVIALLVFGPK---KLPEIGRSLG--KTLKGFQEASKEFENEIKRE 55 (90)
T ss_pred HHHHHHHcCch---HHHHHHHHHH--HHHHHHHHHHHHHHHHHHHH
Confidence 34456667654 9999999997 99999888877777766643
No 121
>PRK00575 tatA twin arginine translocase protein A; Provisional
Probab=24.29 E-value=1.6e+02 Score=19.83 Aligned_cols=44 Identities=16% Similarity=0.268 Sum_probs=33.4
Q ss_pred HHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhc
Q 034427 17 LFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEILVDDLNRIEA 65 (95)
Q Consensus 17 lle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~L~~dV~~ies 65 (95)
++.-+|.-|+.+ +--.++..|+ |+.++.++-.+.+.++...-+.
T Consensus 12 Ilvi~LllFGpk---KLPel~r~lG--k~ir~fK~a~~~~~~e~~~~~~ 55 (92)
T PRK00575 12 LAVVVILLFGAK---KLPDAARSLG--KSLRIFKSEVKEMQSDNKAEAS 55 (92)
T ss_pred HHHHHHHhccch---HHHHHHHHHH--HHHHHHHHHHhhhhhccccccc
Confidence 344466777664 8999999997 9999999888888777764433
No 122
>PF13991 BssS: BssS protein family
Probab=24.15 E-value=1.7e+02 Score=18.85 Aligned_cols=30 Identities=27% Similarity=0.459 Sum_probs=24.2
Q ss_pred CCHHHHHHHHHHHHHHHHHHhcCCCCCCCC
Q 034427 44 KTVEEVKKHYEILVDDLNRIEAGRVPIPNY 73 (95)
Q Consensus 44 RT~~qv~~ry~~L~~dV~~iesg~v~~P~y 73 (95)
-|.++.+.--..|..-|..||++.+.-|.|
T Consensus 42 lT~e~Ar~Li~~L~~~I~kiE~se~~~~~~ 71 (73)
T PF13991_consen 42 LTTEMARQLISILEAGIDKIESSEYQKPDY 71 (73)
T ss_pred ecHHHHHHHHHHHHHHHHHHHhCCcccccc
Confidence 356777777778999999999998877776
No 123
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=24.15 E-value=2.4e+02 Score=19.29 Aligned_cols=45 Identities=13% Similarity=0.180 Sum_probs=30.8
Q ss_pred HHHHHHHHHhcCCC----------CChHHHHHHHHcCCCCCHHHHHHHHHHHHHHHH
Q 034427 15 NKLFEKALALYDKE----------TPDRWQNIAKAVGGGKTVEEVKKHYEILVDDLN 61 (95)
Q Consensus 15 dklle~aL~~~~~~----------~~~rW~kIA~~vpggRT~~qv~~ry~~L~~dV~ 61 (95)
...|+.+|...|+. ..-..+.||..++ -|..-|+.+-......++
T Consensus 128 ~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lg--is~~~v~~~l~Rar~~Lr 182 (187)
T PRK12534 128 RRRIDHCLAELEPPRSELIRTAFFEGITYEELAARTD--TPIGTVKSWIRRGLAKLK 182 (187)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhC--CChhHHHHHHHHHHHHHH
Confidence 45677777776643 2345788888887 888888877776655554
No 124
>PRK04387 hypothetical protein; Provisional
Probab=23.45 E-value=2.4e+02 Score=18.87 Aligned_cols=38 Identities=21% Similarity=0.316 Sum_probs=22.2
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHHH
Q 034427 8 STWTPKENKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEIL 56 (95)
Q Consensus 8 ~~WT~eEdklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~L 56 (95)
..||.||.-.... -|+.|..+-..|-..+++..+|+..
T Consensus 9 ~dWsteEii~Vi~-----------F~~~VE~aYE~gv~re~ll~~Y~~F 46 (90)
T PRK04387 9 LDWSTEEMISVLH-----------FFNAVEKAYEKGVDAEELLDAYRRF 46 (90)
T ss_pred CCCCHHHHHHHHH-----------HHHHHHHHHHcCCcHHHHHHHHHHH
Confidence 4699999764422 2455555554455566666666544
No 125
>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=23.26 E-value=2.6e+02 Score=20.86 Aligned_cols=39 Identities=13% Similarity=0.059 Sum_probs=28.8
Q ss_pred HHHHHHHHhcCCC----------CChHHHHHHHHcCCCCCHHHHHHHHHHH
Q 034427 16 KLFEKALALYDKE----------TPDRWQNIAKAVGGGKTVEEVKKHYEIL 56 (95)
Q Consensus 16 klle~aL~~~~~~----------~~~rW~kIA~~vpggRT~~qv~~ry~~L 56 (95)
..++++|.+.|+. ..-....||..++ -|..-|+.|...-
T Consensus 153 ~~l~~aL~~Lp~~~R~v~~L~~~eg~S~~EIA~~Lg--is~~TVk~rl~RA 201 (244)
T TIGR03001 153 QALREALAALSERERHLLRLHFVDGLSMDRIGAMYQ--VHRSTVSRWVAQA 201 (244)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHC--cCHHHHHHHHHHH
Confidence 4577788877654 2346889999997 8888888887753
No 126
>PTZ00370 STEVOR; Provisional
Probab=23.19 E-value=2.3e+02 Score=22.85 Aligned_cols=76 Identities=28% Similarity=0.405 Sum_probs=46.8
Q ss_pred HHHHHHHhcCCCCChHHHHHHHHcCCCCC--------------HHHHHHHHHHHHHHHHH--HhcCCCCCCCCCCCCCCC
Q 034427 17 LFEKALALYDKETPDRWQNIAKAVGGGKT--------------VEEVKKHYEILVDDLNR--IEAGRVPIPNYKSPGSSY 80 (95)
Q Consensus 17 lle~aL~~~~~~~~~rW~kIA~~vpggRT--------------~~qv~~ry~~L~~dV~~--iesg~v~~P~y~~~~~~~ 80 (95)
+=++||++|-. +.+|.+..-+.|...|+ .+|..+.|.+++.|-.. +.||+.|=.+.+++.+++
T Consensus 66 ~n~eaikkyqq-T~~~f~e~~e~~~k~~~K~k~~~d~e~k~klEKel~e~~ee~fg~~~~imlksg~~~n~d~~~d~ss~ 144 (296)
T PTZ00370 66 MNEEAIKKYQQ-THDPYEQLKEVVEKNGTKYTGGNDAEPMSTLEKELLETYEEMFGDESDIMLKSGMYPNDDDKSDKSST 144 (296)
T ss_pred HhHHHhhhhhh-hcchHHHHHHHHHhcCCccccccCcchhHHHHHHHHHHHHHHhcCccchhhhcCCCCCccccccCCCc
Confidence 33457777755 56788888877752222 35677778777665554 678886665555555556
Q ss_pred ccc------------hHHHHHhhcc
Q 034427 81 NAA------------NEERILKNLK 93 (95)
Q Consensus 81 ~~~------------~~~~~~~~~~ 93 (95)
|.- --|+-|+|||
T Consensus 145 cectd~n~~~l~~~kg~DkYLkhLK 169 (296)
T PTZ00370 145 CECTDINNVKLAKTKGRDKYLKHLK 169 (296)
T ss_pred eeeeecccchhhhcccchHHHhhhh
Confidence 521 3456666664
No 127
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=23.12 E-value=2.9e+02 Score=19.82 Aligned_cols=44 Identities=11% Similarity=0.105 Sum_probs=33.0
Q ss_pred CCHHHHHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHHHHHHHH
Q 034427 10 WTPKENKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEILVDDLN 61 (95)
Q Consensus 10 WT~eEdklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~L~~dV~ 61 (95)
=|+.|.+.|.-...-+ .-..||+.+. -|..=|+.|-..+..++.
T Consensus 138 LT~RE~eVL~lla~G~------snkeIA~~L~--iS~~TVk~h~~~I~~KL~ 181 (207)
T PRK15411 138 LSRTESSMLRMWMAGQ------GTIQISDQMN--IKAKTVSSHKGNIKRKIK 181 (207)
T ss_pred CCHHHHHHHHHHHcCC------CHHHHHHHcC--CCHHHHHHHHHHHHHHhC
Confidence 6778877775444322 3689999997 999999999888877765
No 128
>cd04517 TLF TBP-like factors (TLF; also called TLP, TRF, TRP), which are found in most metazoans. TLFs and TBPs have well-conserved core domains; however, they only share about 60% similarity. TLFs, like TBPs, interact with TFIIA and TFIIB, which are part of the basal transcription machinery. Yet, in contrast to TBPs, TLFs seem not to interact with the TATA-box and even have a negative effect on the transcription of TATA-containing promoters. Recent results indicate that TLFs are involved in the transcription via TATA-less promoters.
Probab=22.68 E-value=1.4e+02 Score=21.67 Aligned_cols=35 Identities=20% Similarity=0.241 Sum_probs=26.5
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q 034427 42 GGKTVEEVKKHYEILVDDLNRIEAGRVPIPNYKSP 76 (95)
Q Consensus 42 ggRT~~qv~~ry~~L~~dV~~iesg~v~~P~y~~~ 76 (95)
|+||.++++.-.+.+.+.++.+.-..+.+|++.-.
T Consensus 62 Gaks~~~~~~a~~~~~~~l~~~g~~~~~~~~f~v~ 96 (174)
T cd04517 62 GATSEEEAKQAARRAARLLQKLGFKVVRFSNFRVV 96 (174)
T ss_pred ccCCHHHHHHHHHHHHHHHHHcCCCcccCCceEEE
Confidence 48999999999999988887665444456776443
No 129
>PF13748 ABC_membrane_3: ABC transporter transmembrane region
Probab=22.57 E-value=99 Score=24.04 Aligned_cols=27 Identities=15% Similarity=0.364 Sum_probs=24.4
Q ss_pred ChHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 034427 30 PDRWQNIAKAVGGGKTVEEVKKHYEILV 57 (95)
Q Consensus 30 ~~rW~kIA~~vpggRT~~qv~~ry~~L~ 57 (95)
++|+|+=...+. +++..++++||..|.
T Consensus 170 NnrlE~eV~~i~-~~~~~~l~rHy~~L~ 196 (237)
T PF13748_consen 170 NNRLEKEVDIIE-RRKPASLRRHYRRLS 196 (237)
T ss_pred hHHHHHHccHhh-cCChHHHHHHHHHHH
Confidence 579999999999 999999999999864
No 130
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=22.56 E-value=2.4e+02 Score=22.39 Aligned_cols=53 Identities=17% Similarity=0.196 Sum_probs=40.1
Q ss_pred CCCCCCHHHHHHHHHHHHhcC-CCCChHHHHHHHHcCCCCCHHHHHHHHHHHHHHHH
Q 034427 6 LSSTWTPKENKLFEKALALYD-KETPDRWQNIAKAVGGGKTVEEVKKHYEILVDDLN 61 (95)
Q Consensus 6 ~~~~WT~eEdklle~aL~~~~-~~~~~rW~kIA~~vpggRT~~qv~~ry~~L~~dV~ 61 (95)
+...+|.-+.+.||+-..+.. -..+|| ..+|+.++ -|..||+-=|++-+.+-+
T Consensus 175 sRTaFT~~Ql~~LEkrF~~QKYLS~~DR-~~LA~~Lg--LTdaQVKtWfQNRRtKWK 228 (309)
T KOG0488|consen 175 SRTAFSDHQLFELEKRFEKQKYLSVADR-IELAASLG--LTDAQVKTWFQNRRTKWK 228 (309)
T ss_pred chhhhhHHHHHHHHHHHHHhhcccHHHH-HHHHHHcC--CchhhHHHHHhhhhHHHH
Confidence 445699999999999755432 224678 99999997 999999999987444333
No 131
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=22.41 E-value=2.8e+02 Score=19.29 Aligned_cols=48 Identities=13% Similarity=0.079 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHhcCCC----------CChHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHH
Q 034427 13 KENKLFEKALALYDKE----------TPDRWQNIAKAVGGGKTVEEVKKHYEILVDDLNR 62 (95)
Q Consensus 13 eEdklle~aL~~~~~~----------~~~rW~kIA~~vpggRT~~qv~~ry~~L~~dV~~ 62 (95)
++...|..+|.+.|+. ..-.-..||..++ .|..-|+.|...-...++.
T Consensus 119 e~~~~l~~~l~~Lp~~~r~v~~L~~~~g~s~~EIA~~lg--is~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 119 EDLVEVTTMIADLTTDQREALLLTQLLGLSYADAAAVCG--CPVGTIRSRVARARDALLA 176 (185)
T ss_pred HHHHHHHHHHHhCCHHHhHHhhhHHHcCCCHHHHHHHHC--CCHHHHHHHHHHHHHHHHh
Confidence 3345677777777654 1345788999997 9999999988876666653
No 132
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=22.25 E-value=3e+02 Score=19.61 Aligned_cols=47 Identities=17% Similarity=0.113 Sum_probs=33.4
Q ss_pred CCCHHHHHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHHHHH
Q 034427 9 TWTPKENKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEILVD 58 (95)
Q Consensus 9 ~WT~eEdklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~L~~ 58 (95)
.-|..|...+...+.... ...-....||+.+. -|..-|+.|-..|+.
T Consensus 158 ~Lt~re~~~l~~~i~~~~-~~g~s~~eIA~~l~--iS~~Tv~~~~~~~~~ 204 (239)
T PRK10430 158 GLTPQTLRTLCQWIDAHQ-DYEFSTDELANAVN--ISRVSCRKYLIWLVN 204 (239)
T ss_pred CCCHHHHHHHHHHHHhCC-CCCcCHHHHHHHhC--chHHHHHHHHHHHHh
Confidence 367777666655554331 12236899999997 999999999988754
No 133
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=22.10 E-value=1.5e+02 Score=23.11 Aligned_cols=42 Identities=19% Similarity=0.167 Sum_probs=31.9
Q ss_pred CCCCCCHHHHHHHHHHHHh--cCCCCChHHHHHHHHcCCCCCHHHH
Q 034427 6 LSSTWTPKENKLFEKALAL--YDKETPDRWQNIAKAVGGGKTVEEV 49 (95)
Q Consensus 6 ~~~~WT~eEdklle~aL~~--~~~~~~~rW~kIA~~vpggRT~~qv 49 (95)
....+|.++...||..+++ ||. -..|+++|..|.=-.+..+|
T Consensus 40 ERTtFtr~QlevLe~LF~kTqYPD--v~~rEelAlklnLpeSrVqV 83 (228)
T KOG2251|consen 40 ERTTFTRKQLEVLEALFAKTQYPD--VFMREELALKLNLPESRVQV 83 (228)
T ss_pred ccceecHHHHHHHHHHHHhhcCcc--HHHHHHHHHHhCCchhhhhh
Confidence 4557999999999999987 553 36899999987622555555
No 134
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=21.93 E-value=2.9e+02 Score=19.30 Aligned_cols=42 Identities=10% Similarity=0.002 Sum_probs=26.4
Q ss_pred HHHHHHHHhcCCC----------CChHHHHHHHHcCCCCCHHHHHHHHHHHHHH
Q 034427 16 KLFEKALALYDKE----------TPDRWQNIAKAVGGGKTVEEVKKHYEILVDD 59 (95)
Q Consensus 16 klle~aL~~~~~~----------~~~rW~kIA~~vpggRT~~qv~~ry~~L~~d 59 (95)
..|+.+|.+.|+. .......||+.++ .|..-|+.|.......
T Consensus 123 ~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~lg--is~~tvk~rl~Rar~~ 174 (188)
T TIGR02943 123 EVFEACLYHLPEQTARVFMMREVLGFESDEICQELE--ISTSNCHVLLYRARLS 174 (188)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHhC--CCHHHHHHHHHHHHHH
Confidence 3566677666543 1235677888886 7888787776644333
No 135
>KOG3411 consensus 40S ribosomal protein S19 [Translation, ribosomal structure and biogenesis]
Probab=21.81 E-value=96 Score=22.44 Aligned_cols=36 Identities=22% Similarity=0.263 Sum_probs=23.8
Q ss_pred cCCCCCHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q 034427 40 VGGGKTVEEVKKHYEILVDDLNRIEAGRVPIPNYKSP 76 (95)
Q Consensus 40 vpggRT~~qv~~ry~~L~~dV~~iesg~v~~P~y~~~ 76 (95)
+| |.|++||..|--.-.-......+|++.+|.+.+.
T Consensus 1 m~-gvtVkdV~~~~f~~a~asfLK~sgkv~vp~~~Di 36 (143)
T KOG3411|consen 1 MP-GVTVKDVDPHKFTKAYASFLKRSGKVEVPQWVDI 36 (143)
T ss_pred CC-ccchhhcCHHHHHHHHHHHHHhcCCccCcchhhh
Confidence 46 7899998766543222333467898888887554
No 136
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=21.74 E-value=2.7e+02 Score=18.87 Aligned_cols=30 Identities=17% Similarity=0.109 Sum_probs=22.2
Q ss_pred ChHHHHHHHHcCCCCCHHHHHHHHHHHHHHHH
Q 034427 30 PDRWQNIAKAVGGGKTVEEVKKHYEILVDDLN 61 (95)
Q Consensus 30 ~~rW~kIA~~vpggRT~~qv~~ry~~L~~dV~ 61 (95)
...++.||..++ -|..-|+.+.......++
T Consensus 152 ~~s~~eIA~~lg--is~~~v~~~l~Rar~~Lr 181 (187)
T PRK09641 152 DLSLKEISEILD--LPVGTVKTRIHRGREALR 181 (187)
T ss_pred CCCHHHHHHHHC--CCHHHHHHHHHHHHHHHH
Confidence 346889999997 888888888766555444
No 137
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=21.54 E-value=2.7e+02 Score=18.78 Aligned_cols=44 Identities=25% Similarity=0.181 Sum_probs=28.4
Q ss_pred HHHHHHHHhcCCC----------CChHHHHHHHHcCCCCCHHHHHHHHHHHHHHHH
Q 034427 16 KLFEKALALYDKE----------TPDRWQNIAKAVGGGKTVEEVKKHYEILVDDLN 61 (95)
Q Consensus 16 klle~aL~~~~~~----------~~~rW~kIA~~vpggRT~~qv~~ry~~L~~dV~ 61 (95)
..|..+|.+.|+. ..-.-+.||+.++ .|..-|+.|...-...++
T Consensus 110 ~~l~~~l~~L~~~~r~vl~L~~~~g~s~~EIA~~lg--is~~tV~~~l~ra~~~Lr 163 (173)
T PRK09645 110 LLVADALAQLSPEHRAVLVRSYYRGWSTAQIAADLG--IPEGTVKSRLHYALRALR 163 (173)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHC--cCHHHHHHHHHHHHHHHH
Confidence 3577777776643 1234678888886 888888877665444443
No 138
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=21.42 E-value=2.4e+02 Score=18.21 Aligned_cols=59 Identities=29% Similarity=0.309 Sum_probs=43.1
Q ss_pred CCCHHHHHHHHHHHHhc-----CCCCChHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhcCCCC
Q 034427 9 TWTPKENKLFEKALALY-----DKETPDRWQNIAKAVGGGKTVEEVKKHYEILVDDLNRIEAGRVP 69 (95)
Q Consensus 9 ~WT~eEdklle~aL~~~-----~~~~~~rW~kIA~~vpggRT~~qv~~ry~~L~~dV~~iesg~v~ 69 (95)
-+|.+..+.+..++..+ ..-.+.+...+-...+ -|..++-+....=..-|.++|+|...
T Consensus 41 ~~~~e~~~~~~~~i~~~~~~~~~~~~~~~i~~~r~~~g--ltq~~lA~~lg~~~~tis~~e~g~~~ 104 (127)
T TIGR03830 41 LLDPEESKRNSAALADFYRKVDGLLTPPEIRRIRKKLG--LSQREAAELLGGGVNAFSRYERGEVR 104 (127)
T ss_pred EEcHHHHHHHHHHHHHHHHHccCCcCHHHHHHHHHHcC--CCHHHHHHHhCCCHHHHHHHHCCCCC
Confidence 36777777777776554 2335678887777765 88888887776667888999999864
No 139
>PF11084 DUF2621: Protein of unknown function (DUF2621); InterPro: IPR020203 This entry represents a group of uncharacterised proteins.
Probab=21.41 E-value=1e+02 Score=22.24 Aligned_cols=22 Identities=18% Similarity=0.394 Sum_probs=17.8
Q ss_pred CCCCCCHHHHHHHHHHHHhcCC
Q 034427 6 LSSTWTPKENKLFEKALALYDK 27 (95)
Q Consensus 6 ~~~~WT~eEdklle~aL~~~~~ 27 (95)
+...||.|+..+|++.+.--|.
T Consensus 55 trhlW~de~K~lL~eLV~PVPe 76 (141)
T PF11084_consen 55 TRHLWTDEQKALLEELVSPVPE 76 (141)
T ss_pred hHhhcCHHHHHHHHHHhhcCcH
Confidence 3457999999999999886664
No 140
>PF10124 Mu-like_gpT: Mu-like prophage major head subunit gpT; InterPro: IPR018774 This entry represents a conserved domain found in various caudoviral prophage proteins, including the bacteriophage Mu major head subunit GpT and related prophage.
Probab=21.40 E-value=29 Score=27.70 Aligned_cols=29 Identities=28% Similarity=0.473 Sum_probs=22.5
Q ss_pred HHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHH
Q 034427 15 NKLFEKALALYDKETPDRWQNIAKAVGGGKTVEE 48 (95)
Q Consensus 15 dklle~aL~~~~~~~~~rW~kIA~~vpggRT~~q 48 (95)
.+.|.++|...++ .|.+||..|| .-|..+
T Consensus 9 ~~~F~~~l~~a~~----~~~~iA~~Vp-Stt~~n 37 (291)
T PF10124_consen 9 KTAFQKGLEAAPP----QWNKIATEVP-STTASN 37 (291)
T ss_pred HHHHHHHHhhCCC----hhheEEEEcc-CCCCcc
Confidence 4678888888766 6999999999 655543
No 141
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=21.26 E-value=2.6e+02 Score=18.55 Aligned_cols=29 Identities=17% Similarity=0.235 Sum_probs=21.3
Q ss_pred hHHHHHHHHcCCCCCHHHHHHHHHHHHHHHH
Q 034427 31 DRWQNIAKAVGGGKTVEEVKKHYEILVDDLN 61 (95)
Q Consensus 31 ~rW~kIA~~vpggRT~~qv~~ry~~L~~dV~ 61 (95)
..+..||..++ .|..-|+.+.......++
T Consensus 145 ~s~~eIA~~lg--is~~tV~~~l~ra~~~Lr 173 (182)
T PRK09652 145 LSYEEIAEIMG--CPIGTVRSRIFRAREALR 173 (182)
T ss_pred CCHHHHHHHHC--CCHHHHHHHHHHHHHHHH
Confidence 36889999997 888888777665544444
No 142
>PRK14858 tatA twin arginine translocase protein A; Provisional
Probab=20.88 E-value=2.1e+02 Score=19.60 Aligned_cols=39 Identities=18% Similarity=0.373 Sum_probs=27.6
Q ss_pred HHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHHHHHHH
Q 034427 17 LFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEILVDDL 60 (95)
Q Consensus 17 lle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~L~~dV 60 (95)
+|.-+|..|++ .++-.++..++ |...+.++....+..++
T Consensus 12 IlvVallvfGP---kKLPelar~lG--k~i~~fk~~~~d~k~~i 50 (108)
T PRK14858 12 ILVIALIVIGP---QKLPDLARSLG--RGLAEFKKATDDFKQSM 50 (108)
T ss_pred HHHHHHHhcCc---hHHHHHHHHHH--HHHHHHHHHHHHHHHHH
Confidence 34445666754 48999999997 88888877766555555
No 143
>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=20.70 E-value=1.3e+02 Score=16.43 Aligned_cols=18 Identities=33% Similarity=0.388 Sum_probs=15.2
Q ss_pred CCCHHHHHHHHHHHHHHH
Q 034427 43 GKTVEEVKKHYEILVDDL 60 (95)
Q Consensus 43 gRT~~qv~~ry~~L~~dV 60 (95)
+-|.++|+++|+.|....
T Consensus 11 ~~~~~~ik~~y~~l~~~~ 28 (55)
T cd06257 11 DASDEEIKKAYRKLALKY 28 (55)
T ss_pred CCCHHHHHHHHHHHHHHH
Confidence 578999999999987654
No 144
>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=20.69 E-value=3e+02 Score=19.04 Aligned_cols=43 Identities=19% Similarity=0.179 Sum_probs=30.4
Q ss_pred HHHHHHHHhcCCC----------CChHHHHHHHHcCCCCCHHHHHHHHHHHHHHH
Q 034427 16 KLFEKALALYDKE----------TPDRWQNIAKAVGGGKTVEEVKKHYEILVDDL 60 (95)
Q Consensus 16 klle~aL~~~~~~----------~~~rW~kIA~~vpggRT~~qv~~ry~~L~~dV 60 (95)
..+..+|.+.|+. ..-.-..||..++ .|..-|+.|...-...+
T Consensus 123 ~~l~~~l~~Lp~~~r~i~~L~~~~g~s~~EIA~~lg--is~~tVk~~l~Rar~~L 175 (193)
T TIGR02947 123 QDIKDALQGLPEEFRQAVYLADVEGFAYKEIAEIMG--TPIGTVMSRLHRGRKQL 175 (193)
T ss_pred HHHHHHHHhCCHHHhhheeehhhcCCCHHHHHHHHC--CCHHHHHHHHHHHHHHH
Confidence 5677788877653 1345789999997 99999988876543333
No 145
>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=20.62 E-value=2.9e+02 Score=18.85 Aligned_cols=46 Identities=17% Similarity=0.284 Sum_probs=33.0
Q ss_pred CCHHHHHHHHHHHHhc--------CCCC-------------------ChHHHHHHHHcCCCCCHHHHHHHHHHH
Q 034427 10 WTPKENKLFEKALALY--------DKET-------------------PDRWQNIAKAVGGGKTVEEVKKHYEIL 56 (95)
Q Consensus 10 WT~eEdklle~aL~~~--------~~~~-------------------~~rW~kIA~~vpggRT~~qv~~ry~~L 56 (95)
.|.+||-.|..++.+| ..++ -.-....+...| ..|...=+.||++.
T Consensus 2 fTA~dDY~Lc~~i~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~fF~~~~~~~p-~HT~~sWRDR~RKf 74 (105)
T PF09197_consen 2 FTADDDYALCKAIKKQFYRDIYQKDPDTGSSLISDGDSKEFIPKRDMRSFFKDLARKNP-RHTENSWRDRYRKF 74 (105)
T ss_dssp --HHHHHHHHHHHHHHHHHHHHSB-TTSS-B----------------TTHHHHHHHHTT-TS-HHHHHHHHHHT
T ss_pred CChHHHHHHHHHHHHHHHHHHHhhCcccccccccCCCccccccchhhHHHHHHHHHcCC-ccchhHHHHHHHHH
Confidence 6899999999988664 1110 235778899999 99999999999973
No 146
>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=20.50 E-value=98 Score=20.37 Aligned_cols=47 Identities=15% Similarity=0.157 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHHHHHHH
Q 034427 12 PKENKLFEKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEILVDDL 60 (95)
Q Consensus 12 ~eEdklle~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~L~~dV 60 (95)
.+|...|.+||.+.-..-..--+++...++ ....++.+-+..|.+|=
T Consensus 34 ~~E~~rl~~Al~~~~~eL~~l~~~~~~~~~--~~~a~If~ah~~~L~D~ 80 (123)
T PF05524_consen 34 EAEIERLEQALEKAREELEQLAERAESKLG--EEEAAIFEAHLMMLEDP 80 (123)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHCH--SSCTHHHHHHHHHHT-H
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcc--ccHHHHHHHHHHHhcCH
Confidence 578889999999865432222333333455 33448999998887773
No 147
>PRK00295 hypothetical protein; Provisional
Probab=20.40 E-value=2e+02 Score=17.70 Aligned_cols=27 Identities=19% Similarity=0.428 Sum_probs=15.7
Q ss_pred HHHHHHHHHHHHHHHHHhcC------CCCCCCC
Q 034427 47 EEVKKHYEILVDDLNRIEAG------RVPIPNY 73 (95)
Q Consensus 47 ~qv~~ry~~L~~dV~~iesg------~v~~P~y 73 (95)
.......+.|...++..+++ .-|.|+|
T Consensus 36 ~~L~~ql~~L~~rl~~~~~~~~~~~~e~~PPHY 68 (68)
T PRK00295 36 ERLQLQMAALIKRQEEMVGQFGSFEEEAPPPHY 68 (68)
T ss_pred HHHHHHHHHHHHHHHHhhccCCCCCCCCCcCCC
Confidence 34455666666666666654 2355666
No 148
>PRK00404 tatB sec-independent translocase; Provisional
Probab=20.22 E-value=1.9e+02 Score=20.77 Aligned_cols=38 Identities=16% Similarity=0.332 Sum_probs=26.2
Q ss_pred HHHHHhcCCCCChHHHHHHHHcCCCCCHHHHHHHHHHHHHHHH
Q 034427 19 EKALALYDKETPDRWQNIAKAVGGGKTVEEVKKHYEILVDDLN 61 (95)
Q Consensus 19 e~aL~~~~~~~~~rW~kIA~~vpggRT~~qv~~ry~~L~~dV~ 61 (95)
.-+|..|++ .|+=.++..++ +...++++.++...+++.
T Consensus 14 VVaLlV~GP---kkLP~laR~lG--~~i~~~rr~~~~~k~ei~ 51 (141)
T PRK00404 14 LVALLVLGP---ERLPGAARTAG--LWIGRLKRSFNAIKQEVE 51 (141)
T ss_pred HHHHHhcCc---hHHHHHHHHHH--HHHHHHHHHHHHHHHHHH
Confidence 345555654 48999999997 877777777766555544
No 149
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=20.20 E-value=3.3e+02 Score=19.32 Aligned_cols=59 Identities=15% Similarity=0.200 Sum_probs=39.5
Q ss_pred CCCCCHHHHHHHHHHHHhcCC-CCChHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhcCCCCCCCC
Q 034427 7 SSTWTPKENKLFEKALALYDK-ETPDRWQNIAKAVGGGKTVEEVKKHYEILVDDLNRIEAGRVPIPNY 73 (95)
Q Consensus 7 ~~~WT~eEdklle~aL~~~~~-~~~~rW~kIA~~vpggRT~~qv~~ry~~L~~dV~~iesg~v~~P~y 73 (95)
+...|+||...|..-|..+-. +...--..+....+ =|-..|+.+++.|+. +|.+-..+|
T Consensus 2 a~~~T~eer~eLk~rIvElVRe~GRiTi~ql~~~TG--asR~Tvk~~lreLVa------~G~l~~~G~ 61 (127)
T PF06163_consen 2 ARVFTPEEREELKARIVELVREHGRITIKQLVAKTG--ASRNTVKRYLRELVA------RGDLYRHGR 61 (127)
T ss_pred CCcCCHHHHHHHHHHHHHHHHHcCCccHHHHHHHHC--CCHHHHHHHHHHHHH------cCCeEeCCC
Confidence 467899999988776665532 22234666777765 888888888887763 565555444
No 150
>PF08165 FerA: FerA (NUC095) domain; InterPro: IPR012560 The ferlin gene family are characterised by multiple tandem C2 domains and a C-terminal transmembrane domain. They are found in a wide range of species and their function remains unknown, however, mutations in its two most well-characterised members, dysferlin and otoferlin, have been implicated in human disease []. This is central domain A in proteins of the Ferlin family [].; GO: 0016021 integral to membrane
Probab=20.03 E-value=2.3e+02 Score=17.46 Aligned_cols=32 Identities=28% Similarity=0.468 Sum_probs=24.0
Q ss_pred CCCHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q 034427 43 GKTVEEVKKHYEILVDDLNRIEAGRVPIPNYKSP 76 (95)
Q Consensus 43 gRT~~qv~~ry~~L~~dV~~iesg~v~~P~y~~~ 76 (95)
+-+..++-..|..|.+++ ||.-.-|+|.....
T Consensus 6 ~~~~~~l~~~~~~lLdql--IeD~~~pLP~~~~~ 37 (66)
T PF08165_consen 6 KDSEEELAELWLKLLDQL--IEDCSKPLPSLEGK 37 (66)
T ss_pred cCCHHHHHHHHHHHHHHH--HHHhcCCCCCCCCC
Confidence 456788889999988877 56655599988554
No 151
>PF14775 NYD-SP28_assoc: Sperm tail C-terminal domain
Probab=20.02 E-value=1.8e+02 Score=17.70 Aligned_cols=23 Identities=17% Similarity=0.525 Sum_probs=15.6
Q ss_pred HHHHHHHHcCCCCCHH------HHHHHHHH
Q 034427 32 RWQNIAKAVGGGKTVE------EVKKHYEI 55 (95)
Q Consensus 32 rW~kIA~~vpggRT~~------qv~~ry~~ 55 (95)
-|+++|..|| ..+.+ .-.+||..
T Consensus 2 yW~~~~~vip-~~~~~~W~~L~~~l~rY~~ 30 (60)
T PF14775_consen 2 YWERLANVIP-DEKIRLWDALENFLKRYNK 30 (60)
T ss_pred HHHHHhhcCC-hHHHHHHHHHHHHHHHHHH
Confidence 5999999999 55443 34556665
Done!