Query 009896
Match_columns 523
No_of_seqs 125 out of 273
Neff 8.0
Searched_HMMs 46136
Date Thu Mar 28 18:37:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009896.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009896hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2587 RNA polymerase III (C) 100.0 3E-81 6.6E-86 631.4 41.5 500 2-523 1-551 (551)
2 PF05645 RNA_pol_Rpc82: RNA po 99.9 3.9E-25 8.5E-30 218.8 9.9 115 252-366 98-258 (258)
3 PF08221 HTH_9: RNA polymerase 99.8 1.7E-19 3.8E-24 137.5 6.2 61 8-68 1-61 (62)
4 PF02002 TFIIE_alpha: TFIIE al 99.5 2.3E-14 4.9E-19 122.2 4.7 103 370-474 2-104 (105)
5 TIGR00373 conserved hypothetic 98.9 1.5E-08 3.3E-13 92.4 11.5 106 370-477 3-108 (158)
6 PRK06266 transcription initiat 98.8 3.4E-08 7.5E-13 91.7 11.4 108 367-476 6-115 (178)
7 COG1675 TFA1 Transcription ini 98.6 3.8E-07 8.3E-12 83.6 11.1 97 380-478 17-113 (176)
8 smart00531 TFIIE Transcription 98.3 1.1E-06 2.3E-11 79.5 7.1 92 384-476 4-97 (147)
9 PF02002 TFIIE_alpha: TFIIE al 98.2 3.8E-06 8.2E-11 71.5 5.9 89 8-96 1-89 (105)
10 TIGR00373 conserved hypothetic 97.4 0.00076 1.6E-08 61.7 9.1 88 9-96 3-90 (158)
11 PF08221 HTH_9: RNA polymerase 97.2 0.00051 1.1E-08 52.4 4.6 60 370-430 2-61 (62)
12 KOG2587 RNA polymerase III (C) 97.2 0.025 5.5E-07 59.4 17.6 60 96-162 8-67 (551)
13 PRK06266 transcription initiat 96.8 0.0072 1.6E-07 56.3 9.4 77 19-95 21-97 (178)
14 PF01978 TrmB: Sugar-specific 95.7 0.021 4.6E-07 44.2 5.1 46 20-65 8-53 (68)
15 smart00550 Zalpha Z-DNA-bindin 95.7 0.015 3.3E-07 45.2 4.0 44 384-428 9-54 (68)
16 PHA02943 hypothetical protein; 95.6 0.08 1.7E-06 47.1 8.7 74 385-468 15-88 (165)
17 KOG2593 Transcription initiati 95.3 0.073 1.6E-06 55.1 8.7 142 369-515 17-198 (436)
18 smart00531 TFIIE Transcription 95.3 0.044 9.4E-07 49.5 6.3 72 24-95 5-79 (147)
19 PF13601 HTH_34: Winged helix 95.0 0.095 2.1E-06 42.1 6.9 75 24-103 4-78 (80)
20 PF13412 HTH_24: Winged helix- 94.9 0.04 8.7E-07 39.4 3.9 43 384-427 6-48 (48)
21 smart00550 Zalpha Z-DNA-bindin 94.3 0.11 2.4E-06 40.3 5.5 45 21-65 7-53 (68)
22 PHA02943 hypothetical protein; 94.0 1.2 2.6E-05 39.8 11.8 101 23-153 14-117 (165)
23 PF04703 FaeA: FaeA-like prote 93.4 0.13 2.9E-06 39.0 4.3 56 386-447 5-61 (62)
24 PF01978 TrmB: Sugar-specific 93.2 0.12 2.6E-06 39.9 3.8 46 384-430 11-56 (68)
25 PF13412 HTH_24: Winged helix- 92.8 0.28 6E-06 34.9 5.1 43 22-64 5-47 (48)
26 TIGR02702 SufR_cyano iron-sulf 92.8 1.9 4.2E-05 40.9 12.3 66 22-88 3-68 (203)
27 PF09339 HTH_IclR: IclR helix- 92.5 0.2 4.4E-06 36.4 4.1 44 22-65 5-49 (52)
28 COG3355 Predicted transcriptio 92.0 0.92 2E-05 39.5 8.1 78 10-88 15-96 (126)
29 PF04337 DUF480: Protein of un 91.4 3.1 6.7E-05 37.0 10.7 121 21-163 4-143 (148)
30 COG3355 Predicted transcriptio 91.3 2.3 5.1E-05 37.1 9.9 95 371-468 15-116 (126)
31 PRK10141 DNA-binding transcrip 91.2 2.2 4.7E-05 36.9 9.5 64 17-86 12-76 (117)
32 PF09339 HTH_IclR: IclR helix- 91.1 0.19 4E-06 36.6 2.5 46 382-427 4-49 (52)
33 COG1675 TFA1 Transcription ini 91.0 1.6 3.4E-05 40.5 9.0 80 14-93 11-91 (176)
34 smart00418 HTH_ARSR helix_turn 90.9 0.95 2.1E-05 33.5 6.4 57 25-88 2-58 (66)
35 COG5647 Cullin, a subunit of E 90.4 1.5 3.3E-05 48.5 9.6 138 24-163 612-764 (773)
36 KOG2593 Transcription initiati 90.3 1.1 2.3E-05 46.8 7.9 97 7-105 16-116 (436)
37 PF09012 FeoC: FeoC like trans 89.7 0.61 1.3E-05 36.1 4.4 46 24-69 4-49 (69)
38 PF10771 DUF2582: Protein of u 89.5 0.56 1.2E-05 36.0 4.0 55 15-70 3-57 (65)
39 smart00420 HTH_DEOR helix_turn 89.3 0.93 2E-05 32.3 5.0 42 24-65 4-45 (53)
40 PF01022 HTH_5: Bacterial regu 89.3 0.7 1.5E-05 32.8 4.2 42 23-65 5-46 (47)
41 cd00090 HTH_ARSR Arsenical Res 89.0 2.2 4.7E-05 32.5 7.3 59 20-85 7-65 (78)
42 PF05645 RNA_pol_Rpc82: RNA po 88.9 0.75 1.6E-05 45.6 5.6 42 353-394 102-143 (258)
43 smart00347 HTH_MARR helix_turn 88.7 4 8.7E-05 33.2 9.2 68 18-88 8-75 (101)
44 PF03965 Penicillinase_R: Peni 88.3 5.6 0.00012 34.0 10.0 100 19-127 2-106 (115)
45 PRK11239 hypothetical protein; 88.0 9.2 0.0002 36.3 11.7 123 18-163 5-153 (215)
46 COG2345 Predicted transcriptio 88.0 8 0.00017 37.1 11.6 93 17-120 8-100 (218)
47 COG1378 Predicted transcriptio 87.6 4.4 9.4E-05 39.9 9.9 48 18-65 14-61 (247)
48 PF12840 HTH_20: Helix-turn-he 87.5 1.1 2.5E-05 33.6 4.6 51 381-432 10-60 (61)
49 smart00344 HTH_ASNC helix_turn 87.5 3.1 6.8E-05 34.9 7.8 63 384-447 6-72 (108)
50 COG1510 Predicted transcriptio 87.4 1.8 4E-05 39.6 6.5 69 20-93 26-95 (177)
51 TIGR02698 CopY_TcrY copper tra 87.0 8.8 0.00019 33.8 10.6 98 21-127 5-107 (130)
52 PF14947 HTH_45: Winged helix- 86.7 5.3 0.00012 31.6 8.2 70 20-100 6-75 (77)
53 smart00346 HTH_ICLR helix_turn 86.7 1.7 3.7E-05 35.2 5.6 44 22-65 7-51 (91)
54 PF12840 HTH_20: Helix-turn-he 86.5 3 6.4E-05 31.3 6.4 46 20-65 10-55 (61)
55 PF03962 Mnd1: Mnd1 family; I 86.4 8.3 0.00018 36.3 10.7 84 388-477 3-92 (188)
56 PF08220 HTH_DeoR: DeoR-like h 86.3 1.6 3.6E-05 32.4 4.8 43 23-65 3-45 (57)
57 COG3388 Predicted transcriptio 85.6 1.3 2.8E-05 36.2 4.0 42 24-65 18-59 (101)
58 COG3132 Uncharacterized protei 85.1 17 0.00036 33.5 11.3 121 19-163 6-151 (215)
59 PRK00135 scpB segregation and 85.0 19 0.00041 33.9 12.3 121 21-163 5-135 (188)
60 smart00344 HTH_ASNC helix_turn 84.4 1.9 4.1E-05 36.2 5.0 43 23-65 6-48 (108)
61 PF06163 DUF977: Bacterial pro 83.9 2.6 5.6E-05 36.6 5.4 46 20-65 12-57 (127)
62 PRK00135 scpB segregation and 83.8 9.5 0.00021 35.9 9.7 135 288-447 7-149 (188)
63 PF12802 MarR_2: MarR family; 82.5 4.1 8.9E-05 30.2 5.6 46 20-65 5-52 (62)
64 PF02082 Rrf2: Transcriptional 82.5 3.3 7.2E-05 33.2 5.4 41 25-65 13-56 (83)
65 PF01047 MarR: MarR family; I 82.4 2.5 5.4E-05 31.2 4.3 50 383-433 5-54 (59)
66 PF10557 Cullin_Nedd8: Cullin 82.4 4 8.6E-05 31.5 5.5 57 107-163 8-64 (68)
67 PF09824 ArsR: ArsR transcript 82.3 10 0.00022 34.3 8.6 112 16-132 12-132 (160)
68 PF04703 FaeA: FaeA-like prote 81.7 5.3 0.00011 30.4 5.8 56 25-84 5-61 (62)
69 PF01638 HxlR: HxlR-like helix 81.6 16 0.00035 29.7 9.3 63 22-88 7-70 (90)
70 TIGR02702 SufR_cyano iron-sulf 81.6 3.5 7.5E-05 39.2 6.0 63 384-449 4-66 (203)
71 PHA02701 ORF020 dsRNA-binding 81.0 2.1 4.5E-05 39.7 4.1 46 383-429 6-52 (183)
72 COG2345 Predicted transcriptio 80.9 7.2 0.00016 37.4 7.9 66 381-449 11-76 (218)
73 PF01022 HTH_5: Bacterial regu 80.0 2.4 5.2E-05 30.0 3.3 42 384-427 5-46 (47)
74 COG3682 Predicted transcriptio 79.9 4.8 0.0001 35.0 5.6 55 105-163 4-58 (123)
75 PF01047 MarR: MarR family; I 79.8 3.5 7.5E-05 30.4 4.3 46 24-69 7-52 (59)
76 PRK11169 leucine-responsive tr 79.8 4.2 9.1E-05 37.2 5.8 43 384-427 17-59 (164)
77 TIGR01889 Staph_reg_Sar staphy 79.0 38 0.00082 28.5 11.3 92 366-461 8-106 (109)
78 PF12802 MarR_2: MarR family; 78.5 3.3 7.2E-05 30.8 3.9 51 382-433 6-58 (62)
79 PF13463 HTH_27: Winged helix 78.4 9 0.0002 28.9 6.4 57 25-84 8-65 (68)
80 PF13463 HTH_27: Winged helix 78.0 6.5 0.00014 29.7 5.5 50 384-434 6-56 (68)
81 PRK11179 DNA-binding transcrip 78.0 8.3 0.00018 34.8 7.1 66 381-447 9-78 (153)
82 smart00346 HTH_ICLR helix_turn 77.7 3.3 7.2E-05 33.4 4.0 46 382-428 6-52 (91)
83 PRK13777 transcriptional regul 77.4 39 0.00086 31.6 11.5 62 384-449 48-109 (185)
84 PRK15090 DNA-binding transcrip 77.3 4.9 0.00011 39.6 5.8 42 24-65 18-59 (257)
85 PHA00738 putative HTH transcri 77.1 8.3 0.00018 32.6 6.1 61 23-89 15-75 (108)
86 PF10771 DUF2582: Protein of u 76.9 2.3 5.1E-05 32.6 2.6 55 377-432 4-58 (65)
87 TIGR02337 HpaR homoprotocatech 76.7 45 0.00098 28.3 11.1 65 20-87 28-92 (118)
88 smart00420 HTH_DEOR helix_turn 76.6 4.3 9.3E-05 28.7 3.9 43 385-428 4-46 (53)
89 cd00092 HTH_CRP helix_turn_hel 75.4 7.3 0.00016 29.3 5.1 35 31-65 22-56 (67)
90 PF08220 HTH_DeoR: DeoR-like h 74.8 4.6 0.0001 30.0 3.7 41 385-426 4-44 (57)
91 PF03965 Penicillinase_R: Peni 74.4 8 0.00017 33.0 5.7 53 106-162 2-54 (115)
92 COG1414 IclR Transcriptional r 74.3 7 0.00015 38.4 6.0 42 24-65 8-50 (246)
93 PF02082 Rrf2: Transcriptional 74.1 4.4 9.5E-05 32.5 3.7 47 382-428 9-57 (83)
94 PF02295 z-alpha: Adenosine de 73.6 3.3 7.1E-05 31.9 2.7 43 385-428 8-52 (66)
95 PF08784 RPA_C: Replication pr 73.1 9.1 0.0002 31.9 5.6 53 17-70 44-100 (102)
96 PRK06474 hypothetical protein; 72.8 9.9 0.00021 35.4 6.3 68 21-89 12-81 (178)
97 COG3682 Predicted transcriptio 72.6 51 0.0011 28.7 10.0 101 18-126 4-108 (123)
98 COG1522 Lrp Transcriptional re 72.6 5 0.00011 36.0 4.1 68 380-448 7-78 (154)
99 TIGR01610 phage_O_Nterm phage 72.1 7.7 0.00017 32.1 4.8 49 17-65 19-78 (95)
100 smart00418 HTH_ARSR helix_turn 72.0 5.2 0.00011 29.3 3.5 42 385-428 1-42 (66)
101 PRK11512 DNA-binding transcrip 72.0 34 0.00073 30.3 9.4 42 24-65 44-85 (144)
102 TIGR02698 CopY_TcrY copper tra 71.8 50 0.0011 29.0 10.2 70 384-461 7-82 (130)
103 PF09904 HTH_43: Winged helix- 71.6 6.8 0.00015 31.9 4.1 63 27-91 14-76 (90)
104 PF08679 DsrD: Dissimilatory s 70.9 10 0.00022 29.0 4.7 42 36-83 21-63 (67)
105 COG3398 Uncharacterized protei 70.8 53 0.0011 31.6 10.4 119 21-161 102-220 (240)
106 COG1378 Predicted transcriptio 70.2 32 0.0007 33.8 9.5 71 382-460 17-87 (247)
107 smart00347 HTH_MARR helix_turn 70.1 31 0.00066 27.8 8.1 48 381-429 10-57 (101)
108 PRK03902 manganese transport t 69.8 10 0.00022 33.7 5.5 45 21-65 9-53 (142)
109 TIGR02787 codY_Gpos GTP-sensin 69.5 8.5 0.00018 37.4 5.0 59 7-65 170-229 (251)
110 PF13404 HTH_AsnC-type: AsnC-t 69.2 12 0.00026 25.9 4.5 36 23-58 6-41 (42)
111 TIGR02337 HpaR homoprotocatech 69.1 27 0.00059 29.7 7.8 49 380-429 27-75 (118)
112 PF04079 DUF387: Putative tran 67.4 11 0.00023 34.5 5.1 130 289-443 2-138 (159)
113 PF13601 HTH_34: Winged helix 67.3 14 0.0003 29.5 5.2 48 384-432 3-50 (80)
114 PHA02701 ORF020 dsRNA-binding 67.0 14 0.00031 34.3 5.7 46 20-65 4-50 (183)
115 PF08279 HTH_11: HTH domain; 66.9 13 0.00029 26.8 4.7 48 384-432 3-50 (55)
116 PRK11169 leucine-responsive tr 66.8 9.5 0.0002 34.9 4.7 46 20-65 14-59 (164)
117 PF06163 DUF977: Bacterial pro 66.6 19 0.00041 31.4 6.0 49 107-163 12-60 (127)
118 PRK15431 ferrous iron transpor 66.6 15 0.00032 29.3 5.0 45 24-68 6-50 (78)
119 PRK10163 DNA-binding transcrip 66.1 22 0.00047 35.4 7.5 42 24-65 29-71 (271)
120 PF05402 PqqD: Coenzyme PQQ sy 65.6 9.1 0.0002 29.1 3.7 55 104-160 14-68 (68)
121 PF08280 HTH_Mga: M protein tr 65.4 14 0.0003 27.6 4.5 36 24-59 9-44 (59)
122 cd07377 WHTH_GntR Winged helix 65.2 10 0.00022 28.2 3.9 47 19-65 4-56 (66)
123 PF10007 DUF2250: Uncharacteri 65.1 27 0.00058 28.8 6.4 51 20-70 7-57 (92)
124 TIGR01610 phage_O_Nterm phage 64.4 9.3 0.0002 31.6 3.8 36 393-429 45-80 (95)
125 PRK09834 DNA-binding transcrip 64.4 15 0.00032 36.4 5.9 43 23-65 14-57 (263)
126 smart00419 HTH_CRP helix_turn_ 64.3 10 0.00023 26.2 3.6 32 34-65 8-39 (48)
127 PRK11512 DNA-binding transcrip 64.0 31 0.00066 30.6 7.4 63 382-448 41-103 (144)
128 TIGR02010 IscR iron-sulfur clu 63.9 11 0.00024 33.2 4.5 49 380-428 7-57 (135)
129 COG2512 Predicted membrane-ass 63.4 9.8 0.00021 37.6 4.4 52 384-435 198-249 (258)
130 PF13730 HTH_36: Helix-turn-he 62.9 10 0.00023 27.4 3.4 29 36-64 27-55 (55)
131 TIGR02944 suf_reg_Xantho FeS a 62.5 9 0.00019 33.4 3.6 51 378-428 6-57 (130)
132 PRK11179 DNA-binding transcrip 62.5 15 0.00033 33.1 5.1 46 20-65 9-54 (153)
133 PRK13777 transcriptional regul 62.4 1.4E+02 0.003 28.0 11.6 43 23-65 48-90 (185)
134 PRK15090 DNA-binding transcrip 62.1 8.6 0.00019 37.9 3.8 45 382-427 15-59 (257)
135 TIGR01889 Staph_reg_Sar staphy 61.6 34 0.00073 28.8 6.9 71 14-87 17-93 (109)
136 cd00090 HTH_ARSR Arsenical Res 61.4 13 0.00028 28.0 4.0 45 382-428 8-52 (78)
137 smart00419 HTH_CRP helix_turn_ 61.4 8.6 0.00019 26.6 2.7 32 398-429 10-41 (48)
138 PRK11569 transcriptional repre 61.1 18 0.00039 36.0 5.9 41 25-65 33-74 (274)
139 TIGR02844 spore_III_D sporulat 60.7 16 0.00034 29.3 4.3 34 21-55 7-40 (80)
140 PF00392 GntR: Bacterial regul 60.6 10 0.00022 28.6 3.1 32 34-65 23-55 (64)
141 COG1733 Predicted transcriptio 60.2 67 0.0015 27.8 8.5 82 19-123 22-104 (120)
142 PF08784 RPA_C: Replication pr 59.9 9 0.00019 31.9 3.0 48 379-427 45-96 (102)
143 COG5625 Predicted transcriptio 59.7 9.4 0.0002 31.7 2.9 43 23-65 24-67 (113)
144 PHA03103 double-strand RNA-bin 59.6 9.7 0.00021 35.5 3.3 43 385-428 17-59 (183)
145 cd07153 Fur_like Ferric uptake 59.5 28 0.0006 29.4 6.1 51 111-164 5-56 (116)
146 PF01325 Fe_dep_repress: Iron 59.5 30 0.00064 26.0 5.4 44 22-65 10-53 (60)
147 PF01726 LexA_DNA_bind: LexA D 59.4 25 0.00055 26.8 5.1 46 20-65 10-57 (65)
148 cd00092 HTH_CRP helix_turn_hel 59.3 21 0.00045 26.7 4.7 55 94-163 5-59 (67)
149 PF09012 FeoC: FeoC like trans 59.3 16 0.00035 28.0 4.1 49 385-434 4-52 (69)
150 PF12793 SgrR_N: Sugar transpo 59.2 29 0.00064 29.8 6.0 55 34-89 19-73 (115)
151 TIGR02431 pcaR_pcaU beta-ketoa 58.6 16 0.00034 35.8 4.9 41 25-65 14-55 (248)
152 TIGR02944 suf_reg_Xantho FeS a 58.2 27 0.00058 30.4 5.8 34 33-66 24-57 (130)
153 PRK10163 DNA-binding transcrip 58.0 12 0.00027 37.1 4.1 47 382-428 26-72 (271)
154 TIGR00738 rrf2_super rrf2 fami 57.9 14 0.00031 32.1 4.0 46 382-427 9-56 (132)
155 PRK11569 transcriptional repre 57.8 12 0.00027 37.2 4.1 46 382-427 29-74 (274)
156 COG4190 Predicted transcriptio 57.7 39 0.00085 29.7 6.4 51 19-70 63-113 (144)
157 PRK03573 transcriptional regul 57.6 1.3E+02 0.0029 26.3 11.6 61 383-447 33-94 (144)
158 PRK09834 DNA-binding transcrip 57.5 13 0.00028 36.8 4.1 46 382-428 12-58 (263)
159 PF01325 Fe_dep_repress: Iron 57.1 18 0.00038 27.2 3.8 43 386-429 13-55 (60)
160 COG1386 scpB Chromosome segreg 56.7 1.1E+02 0.0023 28.8 9.7 135 286-443 9-148 (184)
161 smart00345 HTH_GNTR helix_turn 56.4 15 0.00033 26.5 3.4 32 34-65 19-51 (60)
162 COG1414 IclR Transcriptional r 56.4 14 0.0003 36.3 4.1 92 382-480 5-98 (246)
163 COG1846 MarR Transcriptional r 56.4 1.1E+02 0.0024 25.3 9.4 52 18-69 20-71 (126)
164 TIGR00281 segregation and cond 56.3 1.4E+02 0.0031 27.9 10.6 134 288-446 4-145 (186)
165 PF04079 DUF387: Putative tran 56.1 77 0.0017 28.9 8.6 117 24-163 2-127 (159)
166 TIGR02431 pcaR_pcaU beta-ketoa 56.0 13 0.00028 36.4 3.8 46 382-427 10-55 (248)
167 TIGR01884 cas_HTH CRISPR locus 55.6 21 0.00045 33.8 5.1 48 18-65 141-188 (203)
168 TIGR00738 rrf2_super rrf2 fami 55.6 34 0.00074 29.7 6.1 34 33-66 24-57 (132)
169 TIGR02010 IscR iron-sulfur clu 55.2 33 0.0007 30.2 5.9 33 33-65 24-56 (135)
170 cd07153 Fur_like Ferric uptake 54.7 41 0.00089 28.4 6.3 57 24-85 5-67 (116)
171 PRK03573 transcriptional regul 54.7 1.5E+02 0.0032 26.0 11.4 41 25-65 36-77 (144)
172 PF05584 Sulfolobus_pRN: Sulfo 54.0 40 0.00088 26.4 5.4 46 23-69 8-54 (72)
173 PRK11050 manganese transport r 53.6 31 0.00067 31.1 5.6 42 24-65 41-82 (152)
174 PF09756 DDRGK: DDRGK domain; 53.4 11 0.00024 35.3 2.7 85 21-132 100-184 (188)
175 PRK10870 transcriptional repre 53.3 1.7E+02 0.0037 27.0 10.6 49 17-65 50-102 (176)
176 TIGR01884 cas_HTH CRISPR locus 52.6 18 0.00039 34.3 4.0 51 378-429 140-190 (203)
177 COG4738 Predicted transcriptio 51.5 1.6E+02 0.0034 25.3 10.1 105 8-119 15-119 (124)
178 COG4344 Uncharacterized protei 51.2 17 0.00036 32.4 3.2 50 38-87 35-95 (175)
179 PHA03103 double-strand RNA-bin 51.1 32 0.0007 32.1 5.3 46 20-65 13-58 (183)
180 COG4189 Predicted transcriptio 50.6 40 0.00087 32.6 5.9 51 384-435 26-76 (308)
181 PF04492 Phage_rep_O: Bacterio 50.4 25 0.00055 29.4 4.1 51 368-427 35-85 (100)
182 PRK11014 transcriptional repre 50.0 23 0.0005 31.4 4.1 47 382-428 9-57 (141)
183 PF07848 PaaX: PaaX-like prote 49.8 44 0.00095 26.0 5.1 47 33-85 19-68 (70)
184 PRK09462 fur ferric uptake reg 49.8 46 0.00099 29.8 6.1 54 107-163 17-72 (148)
185 PF09681 Phage_rep_org_N: N-te 49.7 41 0.00088 29.2 5.4 48 33-88 52-99 (121)
186 TIGR00122 birA_repr_reg BirA b 49.7 30 0.00066 26.4 4.2 41 24-65 4-44 (69)
187 PF08279 HTH_11: HTH domain; 48.9 47 0.001 23.9 5.0 40 23-62 3-43 (55)
188 PF11994 DUF3489: Protein of u 48.2 70 0.0015 25.1 5.9 43 23-65 13-57 (72)
189 COG0735 Fur Fe2+/Zn2+ uptake r 47.1 53 0.0011 29.4 6.0 55 107-164 21-76 (145)
190 COG1522 Lrp Transcriptional re 46.9 37 0.0008 30.2 5.0 49 21-69 9-57 (154)
191 PF10007 DUF2250: Uncharacteri 46.7 33 0.00071 28.3 4.1 46 381-427 7-52 (92)
192 COG1777 Predicted transcriptio 45.8 2.4E+02 0.0052 27.0 10.1 133 16-161 10-209 (217)
193 PF02796 HTH_7: Helix-turn-hel 45.3 36 0.00079 23.7 3.7 31 23-55 12-42 (45)
194 PF07381 DUF1495: Winged helix 45.1 76 0.0016 26.0 6.0 60 23-87 12-83 (90)
195 PRK11014 transcriptional repre 45.0 31 0.00068 30.5 4.2 32 34-65 25-56 (141)
196 PRK09462 fur ferric uptake reg 44.8 72 0.0016 28.5 6.5 60 20-84 17-83 (148)
197 PRK09954 putative kinase; Prov 44.6 23 0.00049 36.7 3.7 43 384-427 6-48 (362)
198 PRK10434 srlR DNA-bindng trans 44.6 35 0.00076 33.7 4.8 44 22-65 7-50 (256)
199 COG1959 Predicted transcriptio 44.5 31 0.00067 31.1 4.1 55 379-433 6-62 (150)
200 PF00392 GntR: Bacterial regul 44.4 23 0.00049 26.7 2.7 35 394-428 21-56 (64)
201 PF14947 HTH_45: Winged helix- 44.1 27 0.00059 27.5 3.2 41 384-426 9-49 (77)
202 PF01638 HxlR: HxlR-like helix 43.3 44 0.00096 27.0 4.5 47 109-163 7-53 (90)
203 PF04337 DUF480: Protein of un 43.1 54 0.0012 29.3 5.1 49 17-65 85-140 (148)
204 PRK04424 fatty acid biosynthes 42.5 33 0.00071 32.1 4.1 44 22-65 9-52 (185)
205 PRK10857 DNA-binding transcrip 42.3 33 0.00071 31.5 3.9 50 380-429 7-58 (164)
206 PF04492 Phage_rep_O: Bacterio 42.0 89 0.0019 26.2 6.1 32 34-65 54-85 (100)
207 PRK10906 DNA-binding transcrip 41.5 42 0.00092 33.0 4.8 43 23-65 8-50 (252)
208 TIGR03879 near_KaiC_dom probab 41.1 42 0.0009 26.4 3.7 46 20-65 18-63 (73)
209 COG0735 Fur Fe2+/Zn2+ uptake r 40.7 82 0.0018 28.2 6.2 60 23-87 24-89 (145)
210 COG1510 Predicted transcriptio 40.5 1E+02 0.0022 28.5 6.6 69 364-432 5-77 (177)
211 PRK10344 DNA-binding transcrip 40.4 57 0.0012 26.7 4.4 34 22-56 10-43 (92)
212 COG2238 RPS19A Ribosomal prote 40.3 90 0.0019 27.7 6.0 57 107-163 53-115 (147)
213 PF13730 HTH_36: Helix-turn-he 40.2 22 0.00048 25.6 2.0 29 398-426 27-55 (55)
214 PF01726 LexA_DNA_bind: LexA D 39.7 1.1E+02 0.0024 23.3 5.9 48 109-163 12-60 (65)
215 PF04157 EAP30: EAP30/Vps36 fa 39.3 1.1E+02 0.0024 29.4 7.3 106 308-427 110-221 (223)
216 cd07377 WHTH_GntR Winged helix 39.2 25 0.00055 25.9 2.3 31 398-428 27-57 (66)
217 PF13545 HTH_Crp_2: Crp-like h 39.2 31 0.00066 26.6 2.8 33 395-428 28-60 (76)
218 COG1802 GntR Transcriptional r 39.0 1.5E+02 0.0031 28.5 8.2 54 393-453 36-89 (230)
219 TIGR01714 phage_rep_org_N phag 38.8 59 0.0013 28.2 4.7 47 33-87 50-96 (119)
220 PF09743 DUF2042: Uncharacteri 38.4 1.5E+02 0.0032 29.7 8.1 52 14-65 110-161 (272)
221 COG1959 Predicted transcriptio 38.3 90 0.002 28.1 6.1 50 19-68 7-59 (150)
222 PRK11534 DNA-binding transcrip 38.0 51 0.0011 31.5 4.7 49 17-65 12-61 (224)
223 smart00345 HTH_GNTR helix_turn 37.8 32 0.00069 24.8 2.6 31 398-428 22-52 (60)
224 PRK09775 putative DNA-binding 37.7 65 0.0014 34.6 5.8 43 25-69 4-46 (442)
225 COG1321 TroR Mn-dependent tran 37.3 44 0.00096 30.3 3.9 42 386-428 15-56 (154)
226 TIGR02787 codY_Gpos GTP-sensin 36.8 37 0.00079 33.1 3.4 48 384-432 186-234 (251)
227 PRK09802 DNA-binding transcrip 36.6 55 0.0012 32.5 4.9 45 21-65 18-62 (269)
228 KOG2165 Anaphase-promoting com 36.0 5.9E+02 0.013 28.9 12.7 138 23-162 605-757 (765)
229 PRK11534 DNA-binding transcrip 36.0 61 0.0013 30.9 4.9 59 102-164 5-65 (224)
230 COG3888 Predicted transcriptio 35.9 70 0.0015 31.6 5.1 42 385-426 8-50 (321)
231 PRK10141 DNA-binding transcrip 35.8 2.9E+02 0.0062 23.8 10.2 58 384-449 19-76 (117)
232 PF13404 HTH_AsnC-type: AsnC-t 35.5 56 0.0012 22.6 3.3 36 384-420 6-41 (42)
233 PF02295 z-alpha: Adenosine de 35.4 39 0.00084 26.0 2.7 46 20-65 4-51 (66)
234 TIGR03859 PQQ_PqqD coenzyme PQ 35.2 91 0.002 24.8 5.0 52 106-160 30-81 (81)
235 PRK10857 DNA-binding transcrip 35.2 61 0.0013 29.7 4.5 34 33-66 24-57 (164)
236 COG1349 GlpR Transcriptional r 35.1 62 0.0013 31.9 4.9 47 109-163 7-53 (253)
237 PF13814 Replic_Relax: Replica 35.1 76 0.0016 29.3 5.3 61 388-449 2-65 (191)
238 PRK11920 rirA iron-responsive 34.9 1E+02 0.0023 27.7 6.0 35 34-68 24-58 (153)
239 PRK11920 rirA iron-responsive 34.7 43 0.00092 30.3 3.4 52 379-430 6-58 (153)
240 COG3423 Nlp Predicted transcri 34.6 76 0.0016 25.1 4.1 33 23-56 11-43 (82)
241 PRK03902 manganese transport t 34.2 51 0.0011 29.1 3.8 41 386-427 13-53 (142)
242 PF14502 HTH_41: Helix-turn-he 33.6 61 0.0013 23.3 3.2 31 35-65 7-37 (48)
243 PRK04172 pheS phenylalanyl-tRN 33.1 5.4E+02 0.012 28.0 12.2 113 21-161 7-119 (489)
244 PLN02853 Probable phenylalanyl 32.9 5.5E+02 0.012 28.0 11.8 112 22-162 5-117 (492)
245 PF01475 FUR: Ferric uptake re 32.5 1E+02 0.0023 26.1 5.4 53 109-164 10-63 (120)
246 KOG4562 Uncharacterized conser 32.4 43 0.00093 34.3 3.2 56 384-446 223-279 (329)
247 PF09397 Ftsk_gamma: Ftsk gamm 32.4 1.3E+02 0.0028 23.1 5.1 48 19-66 5-52 (65)
248 PRK11050 manganese transport r 32.2 1.5E+02 0.0032 26.7 6.5 42 385-427 41-82 (152)
249 COG2512 Predicted membrane-ass 32.0 72 0.0016 31.6 4.7 55 15-69 190-245 (258)
250 COG5625 Predicted transcriptio 31.3 1.5E+02 0.0033 24.8 5.6 86 377-466 15-103 (113)
251 PRK12423 LexA repressor; Provi 31.3 1E+02 0.0023 29.0 5.6 45 21-65 11-57 (202)
252 PF14394 DUF4423: Domain of un 31.0 1.1E+02 0.0025 28.1 5.6 50 16-65 19-72 (171)
253 PRK13509 transcriptional repre 31.0 88 0.0019 30.7 5.2 44 22-65 7-50 (251)
254 TIGR00122 birA_repr_reg BirA b 31.0 71 0.0015 24.2 3.7 42 384-427 3-44 (69)
255 PRK13509 transcriptional repre 30.7 57 0.0012 32.1 3.8 43 384-427 8-50 (251)
256 COG1349 GlpR Transcriptional r 30.6 75 0.0016 31.3 4.6 43 23-65 8-50 (253)
257 PF09202 Rio2_N: Rio2, N-termi 30.3 54 0.0012 26.4 2.9 47 382-428 7-56 (82)
258 TIGR03879 near_KaiC_dom probab 30.1 41 0.00089 26.5 2.1 44 382-426 19-62 (73)
259 PF09202 Rio2_N: Rio2, N-termi 30.0 61 0.0013 26.0 3.2 36 31-66 21-56 (82)
260 TIGR03882 cyclo_dehyd_2 bacter 29.7 1.2E+02 0.0026 28.6 5.6 49 106-162 29-77 (193)
261 PF10668 Phage_terminase: Phag 29.6 69 0.0015 24.2 3.1 25 29-53 17-41 (60)
262 PRK09464 pdhR transcriptional 29.5 3.2E+02 0.007 26.4 9.0 36 394-429 31-67 (254)
263 PHA02591 hypothetical protein; 29.5 1.2E+02 0.0026 24.1 4.5 34 21-55 47-80 (83)
264 TIGR00281 segregation and cond 29.5 4.8E+02 0.01 24.5 10.6 121 22-163 3-132 (186)
265 PF00325 Crp: Bacterial regula 29.4 79 0.0017 20.6 3.0 31 34-64 2-32 (32)
266 PF00888 Cullin: Cullin family 29.1 42 0.00092 37.1 2.9 56 30-85 530-585 (588)
267 KOG2166 Cullins [Cell cycle co 28.9 3.1E+02 0.0068 31.5 9.6 127 32-162 578-717 (725)
268 PF03428 RP-C: Replication pro 28.6 4.8E+02 0.01 24.2 10.5 78 398-480 72-156 (177)
269 COG5124 Protein predicted to b 27.9 3.1E+02 0.0067 25.4 7.5 42 403-450 35-76 (209)
270 PRK06474 hypothetical protein; 27.9 1.5E+02 0.0032 27.5 5.9 49 384-433 14-64 (178)
271 TIGR03338 phnR_burk phosphonat 27.9 70 0.0015 30.2 3.8 32 34-65 34-65 (212)
272 PRK10402 DNA-binding transcrip 27.6 1.6E+02 0.0035 28.0 6.4 58 8-65 138-200 (226)
273 PRK11639 zinc uptake transcrip 27.4 1.4E+02 0.003 27.4 5.5 54 107-163 26-80 (169)
274 PF13693 HTH_35: Winged helix- 27.0 56 0.0012 26.0 2.4 32 23-55 5-36 (78)
275 TIGR03338 phnR_burk phosphonat 27.0 3.7E+02 0.0081 25.1 8.7 35 394-428 32-66 (212)
276 PF03551 PadR: Transcriptional 26.8 1.5E+02 0.0032 22.9 4.8 48 116-163 4-51 (75)
277 COG4189 Predicted transcriptio 26.7 1E+02 0.0023 29.8 4.5 43 23-65 26-68 (308)
278 PF01399 PCI: PCI domain; Int 26.7 1.8E+02 0.0038 23.5 5.6 36 30-65 56-91 (105)
279 PF01454 MAGE: MAGE family; I 26.6 84 0.0018 29.4 4.0 59 385-449 125-185 (195)
280 COG1321 TroR Mn-dependent tran 26.5 4.8E+02 0.01 23.5 9.7 44 25-69 15-58 (154)
281 PF10415 FumaraseC_C: Fumarase 26.5 1.2E+02 0.0025 22.4 3.9 41 14-55 5-47 (55)
282 PRK13918 CRP/FNR family transc 26.2 4.4E+02 0.0095 24.1 9.0 51 309-366 147-198 (202)
283 TIGR03882 cyclo_dehyd_2 bacter 26.1 1.4E+02 0.003 28.1 5.4 45 19-65 29-75 (193)
284 COG1733 Predicted transcriptio 25.8 2.4E+02 0.0052 24.4 6.3 48 109-164 25-72 (120)
285 PF04182 B-block_TFIIIC: B-blo 25.6 3.2E+02 0.007 21.2 7.0 50 398-447 20-71 (75)
286 PRK10906 DNA-binding transcrip 25.5 75 0.0016 31.3 3.6 42 384-426 8-49 (252)
287 PF08672 APC2: Anaphase promot 25.4 1.4E+02 0.003 22.5 4.1 47 311-357 11-60 (60)
288 PF14394 DUF4423: Domain of un 25.2 2.5E+02 0.0055 25.8 6.8 33 398-430 41-75 (171)
289 PRK09990 DNA-binding transcrip 25.1 4E+02 0.0088 25.7 8.8 37 393-429 27-64 (251)
290 PRK09333 30S ribosomal protein 25.0 2.4E+02 0.0051 25.5 6.3 56 108-163 54-115 (150)
291 PF05379 Peptidase_C23: Carlav 25.0 2.3E+02 0.0049 23.2 5.7 55 270-343 2-56 (89)
292 PF09382 RQC: RQC domain; Int 24.3 2.9E+02 0.0063 22.6 6.6 56 107-162 4-75 (106)
293 PRK03837 transcriptional regul 24.2 1E+02 0.0023 29.5 4.4 33 34-66 36-69 (241)
294 PRK11414 colanic acid/biofilm 24.2 92 0.002 29.6 3.9 32 34-65 34-65 (221)
295 TIGR02147 Fsuc_second hypothet 24.1 1.5E+02 0.0033 29.5 5.5 50 16-65 117-170 (271)
296 COG1846 MarR Transcriptional r 24.1 1E+02 0.0022 25.5 3.8 65 379-447 20-84 (126)
297 PRK09954 putative kinase; Prov 24.0 1.3E+02 0.0029 31.0 5.3 99 23-121 6-108 (362)
298 PF12793 SgrR_N: Sugar transpo 23.7 3.2E+02 0.007 23.4 6.7 60 397-458 20-79 (115)
299 PRK11239 hypothetical protein; 23.6 1.6E+02 0.0035 28.2 5.1 48 18-65 95-150 (215)
300 PRK10411 DNA-binding transcrip 23.4 1.5E+02 0.0032 28.9 5.2 43 23-65 7-49 (240)
301 PF12324 HTH_15: Helix-turn-he 23.2 2.9E+02 0.0063 22.0 5.7 56 3-58 3-62 (77)
302 smart00753 PAM PCI/PINT associ 23.2 1.5E+02 0.0032 23.5 4.4 41 26-66 16-56 (88)
303 smart00088 PINT motif in prote 23.2 1.5E+02 0.0032 23.5 4.4 41 26-66 16-56 (88)
304 PF04157 EAP30: EAP30/Vps36 fa 23.1 1E+02 0.0023 29.6 4.1 48 18-65 172-221 (223)
305 PRK03837 transcriptional regul 23.0 1.4E+02 0.0031 28.6 5.0 36 394-429 34-70 (241)
306 PRK10402 DNA-binding transcrip 22.5 2.7E+02 0.0058 26.4 6.8 47 381-428 150-201 (226)
307 TIGR00498 lexA SOS regulatory 22.3 1.2E+02 0.0025 28.4 4.2 31 35-65 26-57 (199)
308 PF03428 RP-C: Replication pro 22.3 3.6E+02 0.0077 25.1 7.2 88 14-104 35-146 (177)
309 PRK04984 fatty acid metabolism 22.3 1.1E+02 0.0024 29.4 4.0 54 106-163 9-65 (239)
310 PF10330 Stb3: Putative Sin3 b 22.1 1.4E+02 0.0031 24.4 3.9 34 25-58 11-52 (92)
311 PF05732 RepL: Firmicute plasm 21.9 1.3E+02 0.0029 27.5 4.2 65 16-89 51-121 (165)
312 PF01475 FUR: Ferric uptake re 21.6 2.5E+02 0.0054 23.7 5.8 57 24-85 12-74 (120)
313 COG4190 Predicted transcriptio 21.6 5.4E+02 0.012 22.8 7.5 69 349-431 45-113 (144)
314 PF05158 RNA_pol_Rpc34: RNA po 21.4 1E+02 0.0022 31.7 3.7 45 24-68 88-134 (327)
315 COG4742 Predicted transcriptio 21.3 6E+02 0.013 25.2 8.8 79 13-101 5-83 (260)
316 COG4860 Uncharacterized protei 21.2 6E+02 0.013 22.7 8.0 108 17-130 20-137 (170)
317 PLN00104 MYST -like histone ac 21.2 2.9E+02 0.0062 29.7 7.0 44 23-69 362-406 (450)
318 COG3398 Uncharacterized protei 21.1 3.2E+02 0.007 26.4 6.6 65 16-86 170-234 (240)
319 PF03444 HrcA_DNA-bdg: Winged 21.0 1.6E+02 0.0035 23.5 3.9 38 392-429 19-56 (78)
320 PF01090 Ribosomal_S19e: Ribos 21.0 2.3E+02 0.005 25.3 5.3 57 107-163 52-114 (139)
321 PF10557 Cullin_Nedd8: Cullin 20.9 1.9E+02 0.0041 22.1 4.3 46 20-65 8-61 (68)
322 TIGR02812 fadR_gamma fatty aci 20.9 1.7E+02 0.0037 28.0 5.1 61 357-429 2-63 (235)
323 PRK09333 30S ribosomal protein 20.7 1.6E+02 0.0035 26.6 4.3 45 21-65 54-112 (150)
324 PF05584 Sulfolobus_pRN: Sulfo 20.6 1.6E+02 0.0035 23.1 3.8 58 385-447 9-66 (72)
325 PF09105 SelB-wing_1: Elongati 20.6 2.3E+02 0.0049 20.3 4.1 37 395-432 17-53 (61)
326 PF03551 PadR: Transcriptional 20.5 1.9E+02 0.0041 22.3 4.3 55 32-87 7-69 (75)
327 TIGR02277 PaaX_trns_reg phenyl 20.4 1.3E+02 0.0027 30.3 4.1 60 16-88 5-68 (280)
328 PRK14165 winged helix-turn-hel 20.3 2.9E+02 0.0064 26.6 6.4 63 395-467 21-83 (217)
329 PRK00215 LexA repressor; Valid 20.1 2.2E+02 0.0048 26.7 5.6 43 23-65 11-55 (205)
No 1
>KOG2587 consensus RNA polymerase III (C) subunit [Transcription]
Probab=100.00 E-value=3e-81 Score=631.37 Aligned_cols=500 Identities=26% Similarity=0.413 Sum_probs=386.0
Q ss_pred ccHHHHHHHHHHHHhhhchhHHHHHHHHHhcCCCc-HHHHHhhcCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceE
Q 009896 2 LTEYGTKHAVHVITNHFGDLVAKVCECLLRKGPLT-RQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQ 80 (523)
Q Consensus 2 ~~~~~~~Lc~~iv~~~FG~~v~~V~~~Ll~~G~lt-l~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~ 80 (523)
||+|+++||.+||++|||++|++|+.+|++.|++| ..-+...++++..+||.+|++|||||||.|+...... +..++
T Consensus 1 msq~eielc~~lie~~FGeivakV~~~Llr~G~lss~~~~~~~t~i~~~kVk~aL~sLiQh~~V~y~~~~~~~--g~vt~ 78 (551)
T KOG2587|consen 1 MSQYEIELCSILIEEHFGEIVAKVGEHLLRTGRLSSLRVIAKDTGISLDKVKKALVSLIQHNCVSYQVHTRNS--GKVTT 78 (551)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCcchhHHHHhhcCCChHHHHHHHHHHHHhcceEEEEecCCC--CceEE
Confidence 79999999999999999999999999999999999 7777888999999999999999999999988776433 35799
Q ss_pred EEechhhHHHHhchhhHHHHHHHHhhHHHHHHHHHHHHcCcCCHHHHHHHhhhcccCCCccC-----HHHHHHHHHHHHh
Q 009896 81 YVVLFDNILHRVRFAKFLTILSQEFDQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVD-----LDSLRETLVKLVT 155 (523)
Q Consensus 81 Y~~~~~~il~rlR~p~~i~~i~~~~G~~a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~-----~~~i~~~f~~Lv~ 155 (523)
|++.+++|+++||||+|+..++++||+.|+.|+++|+.+|++|++++++++.++.......+ ...+.+.|..++.
T Consensus 79 Y~~~~~ei~hilry~r~~~i~~~~~~q~~~sIv~~Lls~GrLTv~e~i~rv~~~~~~~~~ss~~~ql~~lv~q~F~~~~~ 158 (551)
T KOG2587|consen 79 YEAQCSEILHILRYPRYIYITKTLYSQTAESIVEELLSNGRLTVSEVIKRVADRLTTTMESSKTMQLCALVSQTFVELAD 158 (551)
T ss_pred EEehhhHHHHHHhcccceeeHHHHhhhHHHHHHHHHHhcCceeHHHHHHHHHhcccccchhhHHHHHHHHHHHHHHHhhC
Confidence 99999999999999999999999999999999999999999999999999887643322111 1335666666666
Q ss_pred c---ccceecCCCCCCCCCCCCCCCcccccCCCCccccCCchhhhHHHHHHhCccchhhhhhhhcccccccccccCCCCC
Q 009896 156 A---HYVERCPASEPLLMPISEEEGPARKKGSKSAKKIGEPETIEQQVVEAALPMEAMRFSVVTNVESDVGEKEKNSNNV 232 (523)
Q Consensus 156 ~---~fi~~v~~~~~~~~p~~~~~~~~~~~g~~~~k~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~ 232 (523)
. ||..++|.+.+. .+.+.++.+.++-+........++..+...++.+....+++. ..+..
T Consensus 159 ~~ekH~~~r~~e~~~~-------------~~~~a~~~~~e~~~~~~~~~q~lt~~pkis~~~~~~~~s~s~----~~d~~ 221 (551)
T KOG2587|consen 159 PLEKHFVNRCPESVPT-------------VENSAAGPPPEAPTLVINEKQILTLVPKISLPGKGKRRSSSD----EDDRG 221 (551)
T ss_pred chhhHhhccCCCcccc-------------cccccCCCCcccccchhhhccccccccccccCCCCCcccccc----ccccc
Confidence 6 666666532211 112222222222222222222223333333333221111111 11112
Q ss_pred CCCCccccccccccccCcCCCCceEEEeehhhHHHHhchhHHHHHHHhhcCccHHHHHHHHHhccch-hcc-ccc---c-
Q 009896 233 TPGEKRKHDVLELDECGVADEQSVVYRANFEGFIRRLRHKGCIDHVRAHLDDGAANVLSAMLQATSS-AEK-KVK---T- 306 (523)
Q Consensus 233 ~~~~krk~~~~~~d~~~~~~~~~~~~rvN~e~f~~~lR~~~iv~~v~~r~~~~a~~v~~~~L~~~~~-~~~-~~~---~- 306 (523)
.++.++|.- ..|......+.+++||+|+++|+.++||++|+++|.+|.+++++.++++||..... -++ .+. .
T Consensus 222 ~~~~~~k~l--~~D~~~~~~d~ga~wr~N~~rf~~~lRd~~~v~~v~~r~~e~ts~v~~a~Lt~~tie~~r~~~~~l~~e 299 (551)
T KOG2587|consen 222 EKKAKRKKL--TTDNKTPDPDDGAYWRINLDRFHQHLRDQAIVSAVANRMDEGTSEVLRAMLTRMTIELTRHSPAPLDTE 299 (551)
T ss_pred Ccccccccc--ccccCCCCCCCceeEehhhHHhhHHhhhHHHHHHHHhcccchhHHHHHHHHHhhhhhhccCCchhhhch
Confidence 233333321 01111223467899999999999999999999999999999999999999944321 111 110 0
Q ss_pred ------cCCcc------ccHHHHHHHhhh-----hccCCCCCHHHHHHHHHHhccCC------CCCCCCCeEEEehHHHH
Q 009896 307 ------KNSVP------LSLSSIYEEVIK-----SEAGRNMTLDHVRASLVQLGELS------FVDASSDSYSIDFEKII 363 (523)
Q Consensus 307 ------~~s~~------~s~~~I~~~l~~-----~~~~~~~~~~~i~~~L~~La~~~------~~~~~~~~y~V~~~~i~ 363 (523)
..|.+ .+...+-+.+.. ++++.+...+.+..|+..|++++ +++.|||+|.|||++++
T Consensus 300 ~si~~~~~s~n~~s~~~~~~esl~~~~~l~Er~~~ee~~nl~~~~~~~ac~~l~d~slk~l~klges~~G~yiV~y~k~i 379 (551)
T KOG2587|consen 300 LSINEIFRSLNVGSNGSISMESLDQYLTLLERGDTEEEENLDADTEDPACASLADDSLKFLGKLGESGGGMYIVNYHKAI 379 (551)
T ss_pred hhhhhhccCcccccchHHHHHhhhhHHHHHhhccchhhccccccchhhHHHHhhcchHHHHHHhccCCCCEEEEEHHHHH
Confidence 01111 111111111111 12344556677889999999888 77999999999999999
Q ss_pred HHHHHHHHHHHHHHHcCCchHHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCC--CCceEE
Q 009896 364 EIAQNEEVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTG--ARQSQF 441 (523)
Q Consensus 364 ~~lr~~~le~~v~~~~G~~a~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQEvpk~~--~~~~t~ 441 (523)
..++...+|++|.++||..|.|+||+|..+|++ |||||++.|||+.||+|..||+|+++||+++||||||+ +|+|||
T Consensus 380 ~vl~~~~~E~vI~~rfG~rAiRl~R~l~~k~~v-eekqv~~~Alm~~Kd~r~~L~~m~~~g~v~lQeVprTaD~~psrtF 458 (551)
T KOG2587|consen 380 AVLATATYESVIQERFGSRAIRLFRLLLQKKHV-EEKQVEDFALMPAKDARDMLYKMLEEGYVELQEVPRTADRAPSRTF 458 (551)
T ss_pred HHHHHHHHHHHHHHHhhHHHHHHHHHHHhcccc-hHHHHHHhhccccccHHHHHHHHHHcCceeeeecCCCCCCCCcceE
Confidence 999999999999999999999999999999866 99999999999999999999999999999999999998 999999
Q ss_pred EEEEEchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhccccccCCC-----------hhhHHHHHHHHHHHHHHHHHH
Q 009896 442 LLWKVNRQILWKHVLDEMFHAALNLSLRVSYELDREKELLNLPADKRT-----------GPLQDRYNRIRKVRILLESSQ 510 (523)
Q Consensus 442 ~lw~v~~~~~~~~~l~~~~k~~~nl~~R~~~e~~~~k~ll~k~~~~~~-----------~~e~~~l~~~~~~~~~L~~~~ 510 (523)
|||+||+..+++++++++||++.||+.|++||+.+++.||+|.++.+. +.+..+++++...+..++...
T Consensus 459 ~L~~v~~~~a~~~lld~ly~~iaNL~~R~~~eraEn~~LL~Ka~rve~~Ik~~e~~~~k~~qlael~~~~~~ql~lf~r~ 538 (551)
T KOG2587|consen 459 YLYTVNILRAYRMLLDELYKSIANLIERLRHERAENKRLLEKAQRVEAIIKGREATGAKEAQLAELEEMYTAQLNLFKRA 538 (551)
T ss_pred EEEEeccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcccHhhhhhHHhhhhHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999765551 778888899999999999999
Q ss_pred hhhhhhhhcccCC
Q 009896 511 MKLDDAILLFHDF 523 (523)
Q Consensus 511 ~rlD~~l~ll~d~ 523 (523)
.|+|+++++|++|
T Consensus 539 s~l~~~~~vf~~~ 551 (551)
T KOG2587|consen 539 SQLDETILVFESY 551 (551)
T ss_pred HHHHHHHHHHhcC
Confidence 9999999999987
No 2
>PF05645 RNA_pol_Rpc82: RNA polymerase III subunit RPC82; InterPro: IPR008806 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and 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 []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This entry describes the C-terminal region of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In Saccharomyces cerevisiae, the enzyme is composed of 15 subunits, ranging from 160 to about 10 kDa [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2XV4_S 2XUB_A.
Probab=99.92 E-value=3.9e-25 Score=218.76 Aligned_cols=115 Identities=27% Similarity=0.398 Sum_probs=84.5
Q ss_pred CCCceEEEeehhhHHHHhchhHHHHHHHhhcCccHHHHHHHHHhccchhccccccc--------CCccccHHHHHHHhhh
Q 009896 252 DEQSVVYRANFEGFIRRLRHKGCIDHVRAHLDDGAANVLSAMLQATSSAEKKVKTK--------NSVPLSLSSIYEEVIK 323 (523)
Q Consensus 252 ~~~~~~~rvN~e~f~~~lR~~~iv~~v~~r~~~~a~~v~~~~L~~~~~~~~~~~~~--------~s~~~s~~~I~~~l~~ 323 (523)
.+++++|||||++|+++|||+.|+++|+.|+|..||+||++||++++..++....+ .|.|+|+.+|.+.|.+
T Consensus 98 ~d~~v~~rvN~erF~~~lRn~~lv~~a~~r~g~~ta~Vy~~~L~~~e~~~~~~~~~~~~~~~~~~s~~is~~dI~~~l~~ 177 (258)
T PF05645_consen 98 LDPDVVWRVNYERFLVHLRNQRLVDLAERRIGSVTAEVYRAMLKLSESKTPSCRDPPSGEEEKQPSVPISANDIARHLPK 177 (258)
T ss_dssp --TTTSEEE-HHHHHHHHHHHHHHHHHHHHT-CHHHHHHHHHHHCTTTTS-TT-SB------------EEHHHHHHTS-T
T ss_pred CCCCeEEEEEHHHHHHHHHHHHHHHHHHHhhCchHHHHHHHHHhhccccCCcccccccccccccCCceecHHHHHHHCcc
Confidence 35789999999999999999999999999999999999999999998877665555 6899999999999843
Q ss_pred hcc---C-----------------------------CCCCHHHHHHHHHHhccCC--C----CCCCCCeEEEehHHHHHH
Q 009896 324 SEA---G-----------------------------RNMTLDHVRASLVQLGELS--F----VDASSDSYSIDFEKIIEI 365 (523)
Q Consensus 324 ~~~---~-----------------------------~~~~~~~i~~~L~~La~~~--~----~~~~~~~y~V~~~~i~~~ 365 (523)
.-+ + .+.++++|++||++||+++ | +.+|+|+|+|||+++++.
T Consensus 178 ~~dl~~~i~K~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~i~qhL~LLa~~~~~Fl~~~~~~g~g~~~V~f~~l~~~ 257 (258)
T PF05645_consen 178 DLDLSGSIGKRPSSNSSPPNPKKLKTEDSDDDDEDNDPSRLSLIDQHLKLLAEDPLPFLRKCGPSGGGQYTVDFKKLAEQ 257 (258)
T ss_dssp T---HHH-----------------------------------HHHHHHHHHCSTTT-BEEE----SS-EEEEBHHHHHHH
T ss_pred ccCcccccccccccccccccccccccccccccccccchhhHHHHHHHHHHHhCCChhhhheecCCCCcEEEeEHHHHHhh
Confidence 211 1 1223569999999999999 4 478899999999999987
Q ss_pred H
Q 009896 366 A 366 (523)
Q Consensus 366 l 366 (523)
|
T Consensus 258 L 258 (258)
T PF05645_consen 258 L 258 (258)
T ss_dssp H
T ss_pred C
Confidence 5
No 3
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and 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 []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=99.78 E-value=1.7e-19 Score=137.51 Aligned_cols=61 Identities=51% Similarity=0.695 Sum_probs=56.3
Q ss_pred HHHHHHHHhhhchhHHHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhccccccc
Q 009896 8 KHAVHVITNHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFT 68 (523)
Q Consensus 8 ~Lc~~iv~~~FG~~v~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~ 68 (523)
+||+.|++++||++|++|+++|+++|++|+++|++.|++|+++||+||++|||||||.|+.
T Consensus 1 ~L~~~ii~~~fG~~~~~V~~~Ll~~G~ltl~~i~~~t~l~~~~Vk~~L~~LiQh~~v~y~~ 61 (62)
T PF08221_consen 1 ELCTLIIEEHFGEIVAKVGEVLLSRGRLTLREIVRRTGLSPKQVKKALVVLIQHNLVQYFE 61 (62)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHC-SEEHHHHHHHHT--HHHHHHHHHHHHHTTSEEEEE
T ss_pred CHHHHHHHHHcChHHHHHHHHHHHcCCcCHHHHHHHhCCCHHHHHHHHHHHHHcCCeeeec
Confidence 6999999999999999999999999999999999999999999999999999999999765
No 4
>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits, TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF []. This entry represents a helix-turn-helix (HTH) domain found in eukaryotic TFIIE-alpha []. It is also found in proteins from archaebacteria that are presumed to be TFIIE-alpha subunits [], the transcriptional regulator SarR, and also DNA-directed RNA polymerase III subunit Rpc3.; PDB: 1VD4_A 1Q1H_A.
Probab=99.48 E-value=2.3e-14 Score=122.16 Aligned_cols=103 Identities=23% Similarity=0.401 Sum_probs=60.9
Q ss_pred HHHHHHHHHcCCchHHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCceEEEEEEEchH
Q 009896 370 EVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQ 449 (523)
Q Consensus 370 ~le~~v~~~~G~~a~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQEvpk~~~~~~t~~lw~v~~~ 449 (523)
.+..+++..||..|.+|+++|..+|.+ ++++|++.++|+.+++|++|++|...|||..+..+.. .++++.|+|++|.+
T Consensus 2 L~~~v~r~~yg~~~~~Il~~L~~~~~l-~de~la~~~~l~~~~vRkiL~~L~~~~lv~~~~~~d~-~~~~~~~yw~i~~~ 79 (105)
T PF02002_consen 2 LLKEVVRAFYGEEAVRILDALLRKGEL-TDEDLAKKLGLKPKEVRKILYKLYEDGLVSYRRRKDD-ERGWTRYYWYIDYD 79 (105)
T ss_dssp ----HHHTTS-STTHHHHHHHHHH--B--HHHHHHTT-S-HHHHHHHHHHHHHHSS-EEEEE---------EEEEE-THH
T ss_pred hHHHHHHHHcCchHHHHHHHHHHcCCc-CHHHHHHHhCCCHHHHHHHHHHHHHCCCeEEEEEEcC-CCcEEEEEEEEcHH
Confidence 577899999999999999999999998 9999999999999999999999999999999876553 77899999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 009896 450 ILWKHVLDEMFHAALNLSLRVSYEL 474 (523)
Q Consensus 450 ~~~~~~l~~~~k~~~nl~~R~~~e~ 474 (523)
.+...+...++++..++..|++.|.
T Consensus 80 ~~~~~ik~r~~~~~~~l~~~l~~e~ 104 (105)
T PF02002_consen 80 QIIDVIKYRIYKMREKLKKRLEFEE 104 (105)
T ss_dssp HH------------------SSS--
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 9999999999999999999988775
No 5
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=98.89 E-value=1.5e-08 Score=92.42 Aligned_cols=106 Identities=16% Similarity=0.188 Sum_probs=93.2
Q ss_pred HHHHHHHHHcCCchHHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCceEEEEEEEchH
Q 009896 370 EVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQ 449 (523)
Q Consensus 370 ~le~~v~~~~G~~a~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQEvpk~~~~~~t~~lw~v~~~ 449 (523)
.+..++..-+|..+..|+..|..+|.+ .+++||+...|+.+++|++||+|.+.|+|. ..-.+....+|.-|+|++|.+
T Consensus 3 ~~~~~~~~~~g~~~v~Vl~aL~~~~~~-tdEeLa~~Lgi~~~~VRk~L~~L~e~~Lv~-~~r~r~~~~gw~~Y~w~i~~~ 80 (158)
T TIGR00373 3 LLNEVVGRAAEEEVGLVLFSLGIKGEF-TDEEISLELGIKLNEVRKALYALYDAGLAD-YKRRKDDETGWYEYTWRINYE 80 (158)
T ss_pred HHHHHHHHHcChhHHHHHHHHhccCCC-CHHHHHHHHCCCHHHHHHHHHHHHHCCCce-eeeeeecCCCcEEEEEEeCHH
Confidence 456789999999999999999989888 999999999999999999999999999997 332222256889999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 009896 450 ILWKHVLDEMFHAALNLSLRVSYELDRE 477 (523)
Q Consensus 450 ~~~~~~l~~~~k~~~nl~~R~~~e~~~~ 477 (523)
.+...+..++.+.+.++..++++|.+..
T Consensus 81 ~i~d~Ik~~~~~~~~~lk~~l~~e~~~~ 108 (158)
T TIGR00373 81 KALDVLKRKLEETAKKLREKLEFETNNM 108 (158)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhccCCC
Confidence 9999999999999999999998876543
No 6
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=98.82 E-value=3.4e-08 Score=91.72 Aligned_cols=108 Identities=18% Similarity=0.246 Sum_probs=92.5
Q ss_pred HHHHHHHHHHHHc--CCchHHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCceEEEEE
Q 009896 367 QNEEVESVVSKRY--GRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLW 444 (523)
Q Consensus 367 r~~~le~~v~~~~--G~~a~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQEvpk~~~~~~t~~lw 444 (523)
....+.+++.+-. |..+.+|+..|..+|.+ .+++|++...|+.+++|++||+|.++|+|........ ..+|..|+|
T Consensus 6 ~~~~v~~~l~~~~~~~~~~~~Vl~~L~~~g~~-tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~~~r~r~~-~~Gr~~y~w 83 (178)
T PRK06266 6 NNPLVQKVLFEIMEGDEEGFEVLKALIKKGEV-TDEEIAEQTGIKLNTVRKILYKLYDARLADYKREKDE-ETNWYTYTW 83 (178)
T ss_pred cCHHHHHHHHHHhcCCccHhHHHHHHHHcCCc-CHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEeeeecc-CCCcEEEEE
Confidence 3344445555555 77799999999998888 9999999999999999999999999999986554332 568999999
Q ss_pred EEchHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 009896 445 KVNRQILWKHVLDEMFHAALNLSLRVSYELDR 476 (523)
Q Consensus 445 ~v~~~~~~~~~l~~~~k~~~nl~~R~~~e~~~ 476 (523)
++|.+++...+..++++...++..|+++|.+.
T Consensus 84 ~l~~~~i~d~ik~~~~~~~~klk~~l~~e~~~ 115 (178)
T PRK06266 84 KPELEKLPEIIKKKKMEELKKLKEQLEEEENN 115 (178)
T ss_pred EeCHHHHHHHHHHHHHHHHHHHHHHhhhccCC
Confidence 99999999999999999999999999987765
No 7
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=98.60 E-value=3.8e-07 Score=83.56 Aligned_cols=97 Identities=18% Similarity=0.287 Sum_probs=87.5
Q ss_pred CCchHHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCceEEEEEEEchHHHHHHHHHHH
Q 009896 380 GRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQILWKHVLDEM 459 (523)
Q Consensus 380 G~~a~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQEvpk~~~~~~t~~lw~v~~~~~~~~~l~~~ 459 (523)
|+.|.+|+..|.++|.+ ++++|++...|..+++|.+||.|+..|+|..--.... .+.+..|+|+++.+.+..++....
T Consensus 17 g~~~~~v~~~l~~kge~-tDeela~~l~i~~~~vrriL~~L~e~~li~~~k~rd~-~~~~~~y~w~~~~~~v~~~l~~~~ 94 (176)
T COG1675 17 GDEAVLVVDALLEKGEL-TDEELAELLGIKKNEVRRILYALYEDGLISYRKKRDE-ESGWEEYTWYINYEKVLEVLKGKK 94 (176)
T ss_pred CchhhHHHHHHHhcCCc-ChHHHHHHhCccHHHHHHHHHHHHhCCceEEEeeccc-CCCcEEEEEEechHHHHHHHHHHH
Confidence 99999999999999877 9999999999999999999999999999966333222 667999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhhh
Q 009896 460 FHAALNLSLRVSYELDREK 478 (523)
Q Consensus 460 ~k~~~nl~~R~~~e~~~~k 478 (523)
.+.+-+|..++++|.++.-
T Consensus 95 ~~~le~Lk~~le~~~~~~~ 113 (176)
T COG1675 95 RKILEKLKRKLEKETENNY 113 (176)
T ss_pred HHHHHHHHHHHHhhccCCc
Confidence 9999999999999887763
No 8
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=98.35 E-value=1.1e-06 Score=79.53 Aligned_cols=92 Identities=15% Similarity=0.255 Sum_probs=77.0
Q ss_pred HHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCC-C-CceEEEEEEEchHHHHHHHHHHHHH
Q 009896 384 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTG-A-RQSQFLLWKVNRQILWKHVLDEMFH 461 (523)
Q Consensus 384 ~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQEvpk~~-~-~~~t~~lw~v~~~~~~~~~l~~~~k 461 (523)
.-|+..|..+|.+ .+++|++...|+.|++|++||+|.+++++...-....+ . .+++.|+|++|.+.+...+...+++
T Consensus 4 ~~v~d~L~~~~~~-~dedLa~~l~i~~n~vRkiL~~L~ed~~~~~~~~~e~~~~~~~~~~~yw~i~y~~~~~vik~r~~~ 82 (147)
T smart00531 4 FLVLDALMRNGCV-TEEDLAELLGIKQKQLRKILYLLYDEKLIKIDYKREKDPETKTWYRYYWYINYDTLLDVVKYKLDK 82 (147)
T ss_pred EeehHHHHhcCCc-CHHHHHHHhCCCHHHHHHHHHHHHhhhcchhheeeeeCCCCceEEEEEEEecHHHHHHHHHHHHHH
Confidence 4567778788887 99999999999999999999999998886544333222 3 3389999999999999999999999
Q ss_pred HHHHHHHHHHHHHHh
Q 009896 462 AALNLSLRVSYELDR 476 (523)
Q Consensus 462 ~~~nl~~R~~~e~~~ 476 (523)
...++-.|+++|.+.
T Consensus 83 ~~~~L~~~l~~e~~~ 97 (147)
T smart00531 83 MRKRLEDKLEDETNN 97 (147)
T ss_pred HHHHHHHHHhcccCC
Confidence 999999998887654
No 9
>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits, TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF []. This entry represents a helix-turn-helix (HTH) domain found in eukaryotic TFIIE-alpha []. It is also found in proteins from archaebacteria that are presumed to be TFIIE-alpha subunits [], the transcriptional regulator SarR, and also DNA-directed RNA polymerase III subunit Rpc3.; PDB: 1VD4_A 1Q1H_A.
Probab=98.15 E-value=3.8e-06 Score=71.46 Aligned_cols=89 Identities=18% Similarity=0.348 Sum_probs=56.5
Q ss_pred HHHHHHHHhhhchhHHHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEechhh
Q 009896 8 KHAVHVITNHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFDN 87 (523)
Q Consensus 8 ~Lc~~iv~~~FG~~v~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~~~~ 87 (523)
+|...+++..||+-+..|..+|+.+|.++=.+|...++++++.||..|..|.+.++|.+....+++.....++|.+|++.
T Consensus 1 ~L~~~v~r~~yg~~~~~Il~~L~~~~~l~de~la~~~~l~~~~vRkiL~~L~~~~lv~~~~~~d~~~~~~~~yw~i~~~~ 80 (105)
T PF02002_consen 1 ELLKEVVRAFYGEEAVRILDALLRKGELTDEDLAKKLGLKPKEVRKILYKLYEDGLVSYRRRKDDERGWTRYYWYIDYDQ 80 (105)
T ss_dssp -----HHHTTS-STTHHHHHHHHHH--B-HHHHHHTT-S-HHHHHHHHHHHHHHSS-EEEEE--------EEEEE-THHH
T ss_pred ChHHHHHHHHcCchHHHHHHHHHHcCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeEEEEEEcCCCcEEEEEEEEcHHH
Confidence 46678999999999999999999999999999999999999999999999999999986554433323456899999999
Q ss_pred HHHHhchhh
Q 009896 88 ILHRVRFAK 96 (523)
Q Consensus 88 il~rlR~p~ 96 (523)
+...+.+-.
T Consensus 81 ~~~~ik~r~ 89 (105)
T PF02002_consen 81 IIDVIKYRI 89 (105)
T ss_dssp H--------
T ss_pred HHHHHHHHH
Confidence 887776543
No 10
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=97.44 E-value=0.00076 Score=61.65 Aligned_cols=88 Identities=14% Similarity=0.097 Sum_probs=72.4
Q ss_pred HHHHHHHhhhchhHHHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEechhhH
Q 009896 9 HAVHVITNHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFDNI 88 (523)
Q Consensus 9 Lc~~iv~~~FG~~v~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~~~~i 88 (523)
|.-..+...+|+..-.|...|+.+|.+|-.+|+..+|++.+.||.+|..|.-.|+|.|....++++....++|.++.+.+
T Consensus 3 ~~~~~~~~~~g~~~v~Vl~aL~~~~~~tdEeLa~~Lgi~~~~VRk~L~~L~e~~Lv~~~r~r~~~~gw~~Y~w~i~~~~i 82 (158)
T TIGR00373 3 LLNEVVGRAAEEEVGLVLFSLGIKGEFTDEEISLELGIKLNEVRKALYALYDAGLADYKRRKDDETGWYEYTWRINYEKA 82 (158)
T ss_pred HHHHHHHHHcChhHHHHHHHHhccCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCceeeeeeecCCCcEEEEEEeCHHHH
Confidence 45567888999999999999999999999999999999999999999999999999855533322223345667999998
Q ss_pred HHHhchhh
Q 009896 89 LHRVRFAK 96 (523)
Q Consensus 89 l~rlR~p~ 96 (523)
+..+++-.
T Consensus 83 ~d~Ik~~~ 90 (158)
T TIGR00373 83 LDVLKRKL 90 (158)
T ss_pred HHHHHHHH
Confidence 88777653
No 11
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and 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 []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=97.22 E-value=0.00051 Score=52.38 Aligned_cols=60 Identities=18% Similarity=0.218 Sum_probs=52.9
Q ss_pred HHHHHHHHHcCCchHHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEE
Q 009896 370 EVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEK 430 (523)
Q Consensus 370 ~le~~v~~~~G~~a~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQE 430 (523)
....+|++-||+.+.+|+..|..+|.+ .-.+|.+.+-+|.+.+|+.|..|.+.|+|...+
T Consensus 2 L~~~ii~~~fG~~~~~V~~~Ll~~G~l-tl~~i~~~t~l~~~~Vk~~L~~LiQh~~v~y~~ 61 (62)
T PF08221_consen 2 LCTLIIEEHFGEIVAKVGEVLLSRGRL-TLREIVRRTGLSPKQVKKALVVLIQHNLVQYFE 61 (62)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHC-SE-EHHHHHHHHT--HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHcChHHHHHHHHHHHcCCc-CHHHHHHHhCCCHHHHHHHHHHHHHcCCeeeec
Confidence 346789999999999999999999999 999999999999999999999999999998754
No 12
>KOG2587 consensus RNA polymerase III (C) subunit [Transcription]
Probab=97.16 E-value=0.025 Score=59.43 Aligned_cols=60 Identities=20% Similarity=0.360 Sum_probs=49.1
Q ss_pred hHHHHHHHHhhHHHHHHHHHHHHcCcCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccceec
Q 009896 96 KFLTILSQEFDQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERC 162 (523)
Q Consensus 96 ~~i~~i~~~~G~~a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~~~~i~~~f~~Lv~~~fi~~v 162 (523)
-+..+|+..||+.++.|++.||.+|+++...+++.-. ..+...|++++..|++.|++.-.
T Consensus 8 lc~~lie~~FGeivakV~~~Llr~G~lss~~~~~~~t-------~i~~~kVk~aL~sLiQh~~V~y~ 67 (551)
T KOG2587|consen 8 LCSILIEEHFGEIVAKVGEHLLRTGRLSSLRVIAKDT-------GISLDKVKKALVSLIQHNCVSYQ 67 (551)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCcchhHHHHhhc-------CCChHHHHHHHHHHHHhcceEEE
Confidence 3577899999999999999999999999755544422 23567899999999999998665
No 13
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=96.83 E-value=0.0072 Score=56.32 Aligned_cols=77 Identities=12% Similarity=0.145 Sum_probs=62.5
Q ss_pred chhHHHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEechhhHHHHhchh
Q 009896 19 GDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFDNILHRVRFA 95 (523)
Q Consensus 19 G~~v~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~~~~il~rlR~p 95 (523)
|+..-.|...|..+|.+|-.+|+..++++...||..|..|...|+|.|....+++..+...+|.++.+.+...+.+-
T Consensus 21 ~~~~~~Vl~~L~~~g~~tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~~~r~r~~~~Gr~~y~w~l~~~~i~d~ik~~ 97 (178)
T PRK06266 21 DEEGFEVLKALIKKGEVTDEEIAEQTGIKLNTVRKILYKLYDARLADYKREKDEETNWYTYTWKPELEKLPEIIKKK 97 (178)
T ss_pred CccHhHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEeeeeccCCCcEEEEEEeCHHHHHHHHHHH
Confidence 77889999999999999999999999999999999999999999999555333222344556777777777666554
No 14
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=95.73 E-value=0.021 Score=44.16 Aligned_cols=46 Identities=30% Similarity=0.361 Sum_probs=44.3
Q ss_pred hhHHHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 20 DLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 20 ~~v~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
+.=++|..+|+.+|+.|..+|++.++++.+.|..+|-.|.+.|+|.
T Consensus 8 ~~E~~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~ 53 (68)
T PF01978_consen 8 ENEAKVYLALLKNGPATAEEIAEELGISRSTVYRALKSLEEKGLVE 53 (68)
T ss_dssp HHHHHHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 6678999999999999999999999999999999999999999997
No 15
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=95.65 E-value=0.015 Score=45.17 Aligned_cols=44 Identities=25% Similarity=0.382 Sum_probs=40.4
Q ss_pred HHHHHHHHhhCC--CcchhhhhhhcCCCcccHHHHHHHHhhcccceE
Q 009896 384 YRIFRLLSKSGR--LLETDKISDTTFVEKKDAPKILYKLWKDGYLLM 428 (523)
Q Consensus 384 ~RI~r~L~~k~~--l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~l 428 (523)
-+|+.+|...|. + ..++|++...|+.++++..||+|.++|||.-
T Consensus 9 ~~IL~~L~~~g~~~~-ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~ 54 (68)
T smart00550 9 EKILEFLENSGDETS-TALQLAKNLGLPKKEVNRVLYSLEKKGKVCK 54 (68)
T ss_pred HHHHHHHHHCCCCCc-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence 478999988877 7 9999999999999999999999999999954
No 16
>PHA02943 hypothetical protein; Provisional
Probab=95.61 E-value=0.08 Score=47.09 Aligned_cols=74 Identities=23% Similarity=0.374 Sum_probs=61.3
Q ss_pred HHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCceEEEEEEEchHHHHHHHHHHHHHHHH
Q 009896 385 RIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQILWKHVLDEMFHAAL 464 (523)
Q Consensus 385 RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQEvpk~~~~~~t~~lw~v~~~~~~~~~l~~~~k~~~ 464 (523)
-|+++| +.|.. ...+|++...++-..|+-.||.|.++|.| ++|+++ .+=+|.++.+ .+...+.++++.+.
T Consensus 15 eILE~L-k~G~~-TtseIAkaLGlS~~qa~~~LyvLErEG~V--krV~~G-----~~tyw~l~~d-ay~~~v~~~~Relw 84 (165)
T PHA02943 15 KTLRLL-ADGCK-TTSRIANKLGVSHSMARNALYQLAKEGMV--LKVEIG-----RAAIWCLDED-AYTNLVFEIKRELW 84 (165)
T ss_pred HHHHHH-hcCCc-cHHHHHHHHCCCHHHHHHHHHHHHHcCce--EEEeec-----ceEEEEEChH-HHHHHHHHHHHHHH
Confidence 367777 76777 99999999999999999999999999999 558877 3568999974 66666888888887
Q ss_pred HHHH
Q 009896 465 NLSL 468 (523)
Q Consensus 465 nl~~ 468 (523)
.++.
T Consensus 85 rlv~ 88 (165)
T PHA02943 85 RLVC 88 (165)
T ss_pred HHHH
Confidence 7653
No 17
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=95.34 E-value=0.073 Score=55.13 Aligned_cols=142 Identities=14% Similarity=0.188 Sum_probs=101.3
Q ss_pred HHHHHHHHHHcCCchHHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCceE---EEEEE
Q 009896 369 EEVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQ---FLLWK 445 (523)
Q Consensus 369 ~~le~~v~~~~G~~a~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQEvpk~~~~~~t---~~lw~ 445 (523)
..+.-+|+-.||..++=|+..|+.++.+ -|+++++..-++.|++|.++.+|-.+.||.++--.-++..+|+ .-+|+
T Consensus 17 ~l~k~vvr~fy~~~~~lild~llr~~~v-~Eedl~~llk~~~KqLR~li~~LredKlI~~~~r~E~~~nGr~~~~~~Yyy 95 (436)
T KOG2593|consen 17 DLLKKVVRGFYGGEHVLILDALLRRQCV-REEDLKELLKFNKKQLRKLIASLREDKLIKIRTRTETAENGRAVDKHTYYY 95 (436)
T ss_pred HHHHHHHHhcccchhHHHHHHHHHhhhc-chHHHHHHhcccHHHHHHHHHHhhhhhhhhhhhhhhcCCCCcceeeeEEEE
Confidence 3455678889999999999999999898 9999999999999999999999999999988744333322333 35778
Q ss_pred EchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh--------------------ccc---------------cccCCCh
Q 009896 446 VNRQILWKHVLDEMFHAALNLSLRVSYELDREKEL--------------------LNL---------------PADKRTG 490 (523)
Q Consensus 446 v~~~~~~~~~l~~~~k~~~nl~~R~~~e~~~~k~l--------------------l~k---------------~~~~~~~ 490 (523)
+|+.+++..+.=.+. .+..|++.+....... ++- ...+..|
T Consensus 96 InY~~~idvVKyKlh----~m~krled~~~d~t~~~~Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~gelveDe~~~~ 171 (436)
T KOG2593|consen 96 INYAQVIDVVKYKLH----QMRKRLEDRLRDDTNVAGYVCPNCQKKYTSLEALQLLDNETGEFHCENCGGELVEDENKLP 171 (436)
T ss_pred eehHHHHHHHHHHHH----HHHHHHHHHhhhccccccccCCccccchhhhHHHHhhcccCceEEEecCCCchhcccccCc
Confidence 999987777554444 5556665554433221 110 0011113
Q ss_pred hhH--HHHHHHHHHHHHHHHHHhhhhh
Q 009896 491 PLQ--DRYNRIRKVRILLESSQMKLDD 515 (523)
Q Consensus 491 ~e~--~~l~~~~~~~~~L~~~~~rlD~ 515 (523)
++- ..|.++....+-|...+.++|.
T Consensus 172 ~~e~~~~l~~~~~Q~~pi~d~Lk~~e~ 198 (436)
T KOG2593|consen 172 SKESRTALNRLMEQLEPIIDLLKELEG 198 (436)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 333 3588899989999888888887
No 18
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=95.31 E-value=0.044 Score=49.51 Aligned_cols=72 Identities=17% Similarity=0.373 Sum_probs=53.7
Q ss_pred HHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcc--cccccccCCC-CCCcceEEEechhhHHHHhchh
Q 009896 24 KVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNC--VQAFTTEQPD-GPKANTQYVVLFDNILHRVRFA 95 (523)
Q Consensus 24 ~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~--V~~~~~~~~~-~~~~~~~Y~~~~~~il~rlR~p 95 (523)
.|...|+.+|.+|=.+|+..++++.+.||..|..|-.+++ +.|-..-+++ |....+||.+|.+.+...+++-
T Consensus 5 ~v~d~L~~~~~~~dedLa~~l~i~~n~vRkiL~~L~ed~~~~~~~~~e~~~~~~~~~~~yw~i~y~~~~~vik~r 79 (147)
T smart00531 5 LVLDALMRNGCVTEEDLAELLGIKQKQLRKILYLLYDEKLIKIDYKREKDPETKTWYRYYWYINYDTLLDVVKYK 79 (147)
T ss_pred eehHHHHhcCCcCHHHHHHHhCCCHHHHHHHHHHHHhhhcchhheeeeeCCCCceEEEEEEEecHHHHHHHHHHH
Confidence 4778899999999999999999999999999999999555 4433322222 2234556678877777766654
No 19
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=95.05 E-value=0.095 Score=42.08 Aligned_cols=75 Identities=17% Similarity=0.199 Sum_probs=57.2
Q ss_pred HHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEechhhHHHHhchhhHHHHHHH
Q 009896 24 KVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFDNILHRVRFAKFLTILSQ 103 (523)
Q Consensus 24 ~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~~~~il~rlR~p~~i~~i~~ 103 (523)
.|..+|...+.+++.+|...++++...+..-|-.|...|+|...... .+ .++.++|++-..+ +-.|.+|+..++.
T Consensus 4 ~Il~~L~~~~~~~f~~L~~~l~lt~g~Ls~hL~~Le~~GyV~~~k~~-~~-~~p~t~~~lT~~G---r~~~~~~~~~L~~ 78 (80)
T PF13601_consen 4 AILALLYANEEATFSELKEELGLTDGNLSKHLKKLEEAGYVEVEKEF-EG-RRPRTWYSLTDKG---REAFERYVAALRE 78 (80)
T ss_dssp HHHHHHHHHSEEEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEE--SS-S--EEEEEE-HHH---HHHHHHHHHHHHH
T ss_pred HHHHHHhhcCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEEEec-cC-CCCeEEEEECHHH---HHHHHHHHHHHHH
Confidence 47888999999999999999999999999999999999999944333 22 2346899998887 6677777776654
No 20
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=94.89 E-value=0.04 Score=39.39 Aligned_cols=43 Identities=16% Similarity=0.321 Sum_probs=38.7
Q ss_pred HHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccce
Q 009896 384 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 427 (523)
Q Consensus 384 ~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~ 427 (523)
.+|+.+|.+++.+ ..++|++...++...+...|.+|.++|+|+
T Consensus 6 ~~Il~~l~~~~~~-t~~ela~~~~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 6 RKILNYLRENPRI-TQKELAEKLGISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHCTTS--HHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHcCCC-CHHHHHHHhCCCHHHHHHHHHHHHHCcCcC
Confidence 5899999998888 999999999999999999999999999985
No 21
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=94.33 E-value=0.11 Score=40.27 Aligned_cols=45 Identities=24% Similarity=0.261 Sum_probs=42.4
Q ss_pred hHHHHHHHHHhcCC--CcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 21 LVAKVCECLLRKGP--LTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 21 ~v~~V~~~Ll~~G~--ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
.-.+|..+|..+|. +|..+|++..+++.+.|+..|..|..+|+|.
T Consensus 7 ~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~ 53 (68)
T smart00550 7 LEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVC 53 (68)
T ss_pred HHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 45689999999988 9999999999999999999999999999997
No 22
>PHA02943 hypothetical protein; Provisional
Probab=94.02 E-value=1.2 Score=39.79 Aligned_cols=101 Identities=15% Similarity=0.132 Sum_probs=69.9
Q ss_pred HHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEechhhHHHHhchhhHHHHHH
Q 009896 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFDNILHRVRFAKFLTILS 102 (523)
Q Consensus 23 ~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~~~~il~rlR~p~~i~~i~ 102 (523)
-.|.++| ..|..|..+|++.+|++..+++..|.+|-.-|+|.-..- +..++|.++.++..+. +.
T Consensus 14 ~eILE~L-k~G~~TtseIAkaLGlS~~qa~~~LyvLErEG~VkrV~~------G~~tyw~l~~day~~~---------v~ 77 (165)
T PHA02943 14 IKTLRLL-ADGCKTTSRIANKLGVSHSMARNALYQLAKEGMVLKVEI------GRAAIWCLDEDAYTNL---------VF 77 (165)
T ss_pred HHHHHHH-hcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCceEEEee------cceEEEEEChHHHHHH---------HH
Confidence 3566677 889999999999999999999999999999999983222 2468999998765554 22
Q ss_pred HHhhHHHHHHHHHHHHcCc---CCHHHHHHHhhhcccCCCccCHHHHHHHHHHH
Q 009896 103 QEFDQQCVELVQGLLEHGR---LTLKQMFDRAKSSEKEGNLVDLDSLRETLVKL 153 (523)
Q Consensus 103 ~~~G~~a~~I~~~lL~~G~---~~~~~li~~~~~~~~~~~~~~~~~i~~~f~~L 153 (523)
+-+-+ +..++.+-+ ++++++..-+..+ .+.++.|.++
T Consensus 78 ~~~Re-----lwrlv~s~~~kfi~p~~l~~li~kd---------~~a~~~~ak~ 117 (165)
T PHA02943 78 EIKRE-----LWRLVCNSRLKFITPSRLLRLIAKD---------TEAHNIFAKY 117 (165)
T ss_pred HHHHH-----HHHHHHhccccccChHHHHHHHHhC---------HHHHHHHHHh
Confidence 22211 233444554 4577877776654 2355666554
No 23
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=93.42 E-value=0.13 Score=39.01 Aligned_cols=56 Identities=25% Similarity=0.340 Sum_probs=41.1
Q ss_pred HHHHHHh-hCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCceEEEEEEEc
Q 009896 386 IFRLLSK-SGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVN 447 (523)
Q Consensus 386 I~r~L~~-k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQEvpk~~~~~~t~~lw~v~ 447 (523)
|+.+|.. ++-+ ...+||+.+.|+...||..|..|.++|.|+-.++.|++ + + +|+++
T Consensus 5 Il~~i~~~~~p~-~T~eiA~~~gls~~~aR~yL~~Le~eG~V~~~~~~rG~--~-~--~W~l~ 61 (62)
T PF04703_consen 5 ILEYIKEQNGPL-KTREIADALGLSIYQARYYLEKLEKEGKVERSPVRRGK--S-T--YWRLN 61 (62)
T ss_dssp HHHHHHHHTS-E-EHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEES-SSSS--S----EEEES
T ss_pred HHHHHHHcCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCCCc--c-e--eeeec
Confidence 5556655 4455 99999999999999999999999999999655555542 2 2 59876
No 24
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=93.19 E-value=0.12 Score=39.91 Aligned_cols=46 Identities=17% Similarity=0.281 Sum_probs=42.8
Q ss_pred HHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEE
Q 009896 384 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEK 430 (523)
Q Consensus 384 ~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQE 430 (523)
.+|+..|+.+|.. +.++|++..-+|...+...|.+|.+.|+|+..+
T Consensus 11 ~~vy~~Ll~~~~~-t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~~ 56 (68)
T PF01978_consen 11 AKVYLALLKNGPA-TAEEIAEELGISRSTVYRALKSLEEKGLVEREE 56 (68)
T ss_dssp HHHHHHHHHHCHE-EHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHcCCC-CHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEc
Confidence 6899999999898 999999999999999999999999999997655
No 25
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=92.82 E-value=0.28 Score=34.94 Aligned_cols=43 Identities=16% Similarity=0.190 Sum_probs=38.4
Q ss_pred HHHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhccc
Q 009896 22 VAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCV 64 (523)
Q Consensus 22 v~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V 64 (523)
-.+|..+|..+|++|..+|++.++++...|...|--|...|+|
T Consensus 5 ~~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~~~g~I 47 (48)
T PF13412_consen 5 QRKILNYLRENPRITQKELAEKLGISRSTVNRYLKKLEEKGLI 47 (48)
T ss_dssp HHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHCcCc
Confidence 3578899999999999999999999999999999999999987
No 26
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=92.76 E-value=1.9 Score=40.94 Aligned_cols=66 Identities=17% Similarity=0.185 Sum_probs=51.8
Q ss_pred HHHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEechhhH
Q 009896 22 VAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFDNI 88 (523)
Q Consensus 22 v~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~~~~i 88 (523)
-..|...|..+|++|..+|...+++++..|+..|-.|.+.|+|.......+.| +....|.+...+.
T Consensus 3 r~~IL~~L~~~~~~t~~eLA~~lgis~~tV~~~L~~Le~~GlV~r~~~~~~~g-Rp~~~y~LT~~G~ 68 (203)
T TIGR02702 3 KEDILSYLLKQGQATAAALAEALAISPQAVRRHLKDLETEGLIEYEAVVQGMG-RPQYHYQLSRQGR 68 (203)
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEeecccCCC-CCceEEEECcchh
Confidence 35788899999999999999999999999999999999999998332222222 3346778776653
No 27
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=92.51 E-value=0.2 Score=36.43 Aligned_cols=44 Identities=25% Similarity=0.382 Sum_probs=37.9
Q ss_pred HHHHHHHHHhcCC-CcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 22 VAKVCECLLRKGP-LTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 22 v~~V~~~Ll~~G~-ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
+-.|.++|...+. +|+.+|++.+++|.+.+..-|-.|.++|+|.
T Consensus 5 al~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~ 49 (52)
T PF09339_consen 5 ALRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVEEGYVE 49 (52)
T ss_dssp HHHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCee
Confidence 4467777777765 7999999999999999999999999999996
No 28
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=92.01 E-value=0.92 Score=39.54 Aligned_cols=78 Identities=23% Similarity=0.301 Sum_probs=58.5
Q ss_pred HHHHHHhhhc--hhHHHHHHHHH-hcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEE-Eech
Q 009896 10 AVHVITNHFG--DLVAKVCECLL-RKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQY-VVLF 85 (523)
Q Consensus 10 c~~iv~~~FG--~~v~~V~~~Ll-~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y-~~~~ 85 (523)
|..+++=.|| +.=-.|...|+ .+|++|.-+|+...+.+.+.|..||--|+.-|+|.--..+-.+| +....| -+++
T Consensus 15 ~~dvl~c~~GLs~~Dv~v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~~~~G-gy~yiY~~i~~ 93 (126)
T COG3355 15 CEDVLKCVYGLSELDVEVYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVNLKGG-GYYYLYKPIDP 93 (126)
T ss_pred HHHHHHHHhCCcHHHHHHHHHHHhhcCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeeccCCC-ceeEEEecCCH
Confidence 5567777788 55667889999 79999999999999999999999999999999998333332222 223455 3444
Q ss_pred hhH
Q 009896 86 DNI 88 (523)
Q Consensus 86 ~~i 88 (523)
+++
T Consensus 94 ee~ 96 (126)
T COG3355 94 EEI 96 (126)
T ss_pred HHH
Confidence 443
No 29
>PF04337 DUF480: Protein of unknown function, DUF480; InterPro: IPR007432 This family consists of several proteins of uncharacterised function.; PDB: 3BZ6_A.
Probab=91.37 E-value=3.1 Score=37.03 Aligned_cols=121 Identities=25% Similarity=0.305 Sum_probs=81.9
Q ss_pred hHHHHHHHHHhc-------CCCcHHHHHhhc----------CCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEe
Q 009896 21 LVAKVCECLLRK-------GPLTRQNVKRYT----------ELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVV 83 (523)
Q Consensus 21 ~v~~V~~~Ll~~-------G~ltl~~l~~~t----------~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~ 83 (523)
.-++|..||+.+ -++||..|...+ +++...|..+|=.|...++|.. ... + . -+..|+=
T Consensus 4 ~E~RVLG~LiEK~~TTPd~YPLtLNaL~~aCNQKsnR~PVm~l~e~eV~~ald~L~~~~Lv~~-~~~--g-s-Rv~ky~H 78 (148)
T PF04337_consen 4 VEARVLGCLIEKEVTTPDQYPLTLNALTTACNQKSNREPVMNLSESEVQAALDELRAKGLVRE-SGF--G-S-RVAKYEH 78 (148)
T ss_dssp HHHHHHHHHHHHHHH-GGG-SEEHHHHHHHHT-SSS-SS-----HHHHHHHHHHHHHTTSEEE--E-----S-S--EEEE
T ss_pred hHhhHHHhhheecccCCCcCcchHHHHHHHhccccccCccccCCHHHHHHHHHHHHHCcCeee-cCC--C-c-chHHHHh
Confidence 446777777754 478999997654 3778999999999999999973 221 2 2 2568887
Q ss_pred chhhHHHHhchhhHHHHHHHHhhHHHHHHHHHHHHcCcCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcc--ccee
Q 009896 84 LFDNILHRVRFAKFLTILSQEFDQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAH--YVER 161 (523)
Q Consensus 84 ~~~~il~rlR~p~~i~~i~~~~G~~a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~~~~i~~~f~~Lv~~~--fi~~ 161 (523)
+..+. -.+......|+-.||..|--|+.++-.+..- + -+..+.++++..+..|++.+ ++.+
T Consensus 79 r~~~~--------------l~l~~~e~All~~LlLRGpQT~GELR~Rs~R-l--~~F~d~~~Ve~~L~~L~~r~~plV~~ 141 (148)
T PF04337_consen 79 RFCNT--------------LQLSPQELALLCLLLLRGPQTPGELRTRSER-L--HEFADVAEVEAVLERLAEREPPLVVK 141 (148)
T ss_dssp -HHHH--------------HT--HHHHHHHHHHHHH-SB-HHHHHHHHTT-T--S--SSHHHHHHHHHHHHHTT--SEEE
T ss_pred hhhhh--------------cCCCHHHHHHHHHHHHcCCCchhHHHhhhcc-c--cCCCCHHHHHHHHHHHHhccchhhee
Confidence 66665 1345677889999999999999999877532 1 12447889999999999999 8877
Q ss_pred cC
Q 009896 162 CP 163 (523)
Q Consensus 162 v~ 163 (523)
.|
T Consensus 142 Lp 143 (148)
T PF04337_consen 142 LP 143 (148)
T ss_dssp E-
T ss_pred cC
Confidence 75
No 30
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=91.34 E-value=2.3 Score=37.05 Aligned_cols=95 Identities=19% Similarity=0.330 Sum_probs=68.7
Q ss_pred HHHHHHHHcCCch--HHHHHHHH-hhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCceEEEEE-EE
Q 009896 371 VESVVSKRYGRDA--YRIFRLLS-KSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLW-KV 446 (523)
Q Consensus 371 le~~v~~~~G~~a--~RI~r~L~-~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQEvpk~~~~~~t~~lw-~v 446 (523)
+++++.=-||-.- ..++-.|+ ..|.+ +.++||+..-.+...|-+.|.+|...|+|+=--++- ..++..|+| -+
T Consensus 15 ~~dvl~c~~GLs~~Dv~v~~~LL~~~~~~-tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~~--~~Ggy~yiY~~i 91 (126)
T COG3355 15 CEDVLKCVYGLSELDVEVYKALLEENGPL-TVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVNL--KGGGYYYLYKPI 91 (126)
T ss_pred HHHHHHHHhCCcHHHHHHHHHHHhhcCCc-CHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeecc--CCCceeEEEecC
Confidence 4455555555544 35677777 57777 999999999999999999999999999994433332 446778888 89
Q ss_pred chHHHHHHHHH---HHHHHHHHHHH
Q 009896 447 NRQILWKHVLD---EMFHAALNLSL 468 (523)
Q Consensus 447 ~~~~~~~~~l~---~~~k~~~nl~~ 468 (523)
|++.+...++. ++|..+..+++
T Consensus 92 ~~ee~k~~i~~~l~~w~~~~~~~i~ 116 (126)
T COG3355 92 DPEEIKKKILKDLDEWYDKMKQLIE 116 (126)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99998866655 44544444444
No 31
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=91.18 E-value=2.2 Score=36.92 Aligned_cols=64 Identities=13% Similarity=0.072 Sum_probs=51.8
Q ss_pred hhch-hHHHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEechh
Q 009896 17 HFGD-LVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFD 86 (523)
Q Consensus 17 ~FG~-~v~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~~~ 86 (523)
.+|+ .=-+|...|...|.++..+|...++++++.|-+=|-+|.+-|+|...... ...+|.+|.+
T Consensus 12 aLadptRl~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~~L~~AGLV~~~r~G------r~~~Y~l~~~ 76 (117)
T PRK10141 12 ILSDETRLGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLRESGLLLDRKQG------KWVHYRLSPH 76 (117)
T ss_pred HhCCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEEEc------CEEEEEECch
Confidence 3443 33478888888899999999999999999999999999999999733332 2579999876
No 32
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=91.06 E-value=0.19 Score=36.65 Aligned_cols=46 Identities=28% Similarity=0.416 Sum_probs=40.6
Q ss_pred chHHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccce
Q 009896 382 DAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 427 (523)
Q Consensus 382 ~a~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~ 427 (523)
.|++|+++|...+.-+.-.+|++...+|...+..+|..|...|||+
T Consensus 4 ral~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~ 49 (52)
T PF09339_consen 4 RALRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVEEGYVE 49 (52)
T ss_dssp HHHHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCee
Confidence 4788999998777644999999999999999999999999999995
No 33
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=90.99 E-value=1.6 Score=40.47 Aligned_cols=80 Identities=16% Similarity=0.331 Sum_probs=61.2
Q ss_pred HHhhh-chhHHHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEechhhHHHHh
Q 009896 14 ITNHF-GDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFDNILHRV 92 (523)
Q Consensus 14 v~~~F-G~~v~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~~~~il~rl 92 (523)
+.+.+ |+-+-.|+.+|+.+|-.|=.+|+..+++....||..|..|--.|++.|-..-++...-..++|.++.+.+...+
T Consensus 11 ~~~i~~g~~~~~v~~~l~~kge~tDeela~~l~i~~~~vrriL~~L~e~~li~~~k~rd~~~~~~~y~w~~~~~~v~~~l 90 (176)
T COG1675 11 LKSIVRGDEAVLVVDALLEKGELTDEELAELLGIKKNEVRRILYALYEDGLISYRKKRDEESGWEEYTWYINYEKVLEVL 90 (176)
T ss_pred HHHHccCchhhHHHHHHHhcCCcChHHHHHHhCccHHHHHHHHHHHHhCCceEEEeecccCCCcEEEEEEechHHHHHHH
Confidence 33434 99999999999999999999999999999999999999999999999544332211123456666666665544
Q ss_pred c
Q 009896 93 R 93 (523)
Q Consensus 93 R 93 (523)
+
T Consensus 91 ~ 91 (176)
T COG1675 91 K 91 (176)
T ss_pred H
Confidence 3
No 34
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=90.87 E-value=0.95 Score=33.47 Aligned_cols=57 Identities=18% Similarity=0.197 Sum_probs=44.8
Q ss_pred HHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEechhhH
Q 009896 25 VCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFDNI 88 (523)
Q Consensus 25 V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~~~~i 88 (523)
|..+|. .+++|+.+|.+.+++++..++..|-.|.+.|++...... ...+|.++.+..
T Consensus 2 il~~l~-~~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~~~~~------~~~~~~~~~~~~ 58 (66)
T smart00418 2 ILKLLA-EGELCVCELAEILGLSQSTVSHHLKKLREAGLVESRREG------KRVYYSLTDEKV 58 (66)
T ss_pred HHHHhh-cCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeeecC------CEEEEEEchHHH
Confidence 456666 889999999999999999999999999999999733221 135777777533
No 35
>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.45 E-value=1.5 Score=48.49 Aligned_cols=138 Identities=16% Similarity=0.189 Sum_probs=97.9
Q ss_pred HHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEechh--hHHHHhchhhHHHHH
Q 009896 24 KVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFD--NILHRVRFAKFLTIL 101 (523)
Q Consensus 24 ~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~~~--~il~rlR~p~~i~~i 101 (523)
.|+.....+..+|+.+|...|+++...++..|..|+--+++.--.++.. +.+.+.|.+|.+ ....|++++-...-.
T Consensus 612 ~vfll~n~~e~lt~eei~e~T~l~~~dl~~~L~sl~~ak~~~l~~~~~~--~~p~~~fy~ne~f~~~~~rIki~~~~~~~ 689 (773)
T COG5647 612 LVFLLFNDHEELTFEEILELTKLSTDDLKRVLQSLSCAKLVVLLKDDKL--VSPNTKFYVNENFSSKLERIKINYIAESE 689 (773)
T ss_pred HHHHHhcCccceeHHHHHhhcCCChhhHHHHHHHHHhhheeeecccccc--CCCCceEEEccccccccceeeecccccch
Confidence 4444455566899999999999999999999999999998872222111 122345555544 677777777664332
Q ss_pred HHH--------hh-----HHHHHHHHHHHHcCcCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccceecC
Q 009896 102 SQE--------FD-----QQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 163 (523)
Q Consensus 102 ~~~--------~G-----~~a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~~~~i~~~f~~Lv~~~fi~~v~ 163 (523)
... +. ..-++|+--.=..++++-.++++.+......--..++..++.++..|++.+||+|..
T Consensus 690 ~~q~~~~~h~~v~edR~~~lqA~IVRIMK~rk~l~H~~Lv~e~i~q~~~Rf~p~vsmvKr~Ie~LiEKeYLeR~~ 764 (773)
T COG5647 690 CMQDNLDTHETVEEDRQAELQACIVRIMKARKKLKHGDLVKEVIAQHKSRFEPKVSMVKRAIETLIEKEYLERQA 764 (773)
T ss_pred hhccchhhHHHHHHHHHHHHHHHHHHHHHHhccCcHHHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHHHhcc
Confidence 221 11 235778888888999999999988765422111236889999999999999999974
No 36
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=90.34 E-value=1.1 Score=46.81 Aligned_cols=97 Identities=14% Similarity=0.338 Sum_probs=78.7
Q ss_pred HHHHHHHHHhhhchhHHHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccc--cCCCC-CC-cceEEE
Q 009896 7 TKHAVHVITNHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTT--EQPDG-PK-ANTQYV 82 (523)
Q Consensus 7 ~~Lc~~iv~~~FG~~v~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~--~~~~~-~~-~~~~Y~ 82 (523)
.+|.-..|+..||.-+.-|..+|++++++.=-+|....+++.+++|.-|..|--..+|...+- ..++| .. .++||.
T Consensus 16 ~~l~k~vvr~fy~~~~~lild~llr~~~v~Eedl~~llk~~~KqLR~li~~LredKlI~~~~r~E~~~nGr~~~~~~Yyy 95 (436)
T KOG2593|consen 16 NDLLKKVVRGFYGGEHVLILDALLRRQCVREEDLKELLKFNKKQLRKLIASLREDKLIKIRTRTETAENGRAVDKHTYYY 95 (436)
T ss_pred HHHHHHHHHhcccchhHHHHHHHHHhhhcchHHHHHHhcccHHHHHHHHHHhhhhhhhhhhhhhhcCCCCcceeeeEEEE
Confidence 367777899999999999999999999999999999999999999999999998888883331 11222 22 258999
Q ss_pred echhhHHHHhchhhHHHHHHHHh
Q 009896 83 VLFDNILHRVRFAKFLTILSQEF 105 (523)
Q Consensus 83 ~~~~~il~rlR~p~~i~~i~~~~ 105 (523)
+|+..++..+||- |+++++++
T Consensus 96 InY~~~idvVKyK--lh~m~krl 116 (436)
T KOG2593|consen 96 INYAQVIDVVKYK--LHQMRKRL 116 (436)
T ss_pred eehHHHHHHHHHH--HHHHHHHH
Confidence 9999999999885 45555555
No 37
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=89.65 E-value=0.61 Score=36.14 Aligned_cols=46 Identities=20% Similarity=0.311 Sum_probs=38.7
Q ss_pred HHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccc
Q 009896 24 KVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTT 69 (523)
Q Consensus 24 ~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~ 69 (523)
.|-++|-.+|+.|+.+|++..++++..|+.-|-.|++-|-|.-...
T Consensus 4 ~i~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~~~ 49 (69)
T PF09012_consen 4 EIRDYLRERGRVSLAELAREFGISPEAVEAMLEQLIRKGYIRKVDM 49 (69)
T ss_dssp HHHHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEEEEE
T ss_pred HHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEecC
Confidence 5778899999999999999999999999999999999999984433
No 38
>PF10771 DUF2582: Protein of unknown function (DUF2582); InterPro: IPR019707 This entry represents conserved proteins found in bacteria and archaea. The function is not known. ; PDB: 2L02_B 2L01_A.
Probab=89.48 E-value=0.56 Score=35.98 Aligned_cols=55 Identities=27% Similarity=0.376 Sum_probs=48.8
Q ss_pred HhhhchhHHHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhccccccccc
Q 009896 15 TNHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTE 70 (523)
Q Consensus 15 ~~~FG~~v~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~~ 70 (523)
++..|..++.|-+.|..+|.+|+++|.+.++++...+-.|+==|.+-|=|. +...
T Consensus 3 ~~~IG~nAG~Vw~~L~~~~~~s~~el~k~~~l~~~~~~~AiGWLarE~KI~-~~~~ 57 (65)
T PF10771_consen 3 KENIGENAGKVWQLLNENGEWSVSELKKATGLSDKEVYLAIGWLARENKIE-FEEK 57 (65)
T ss_dssp HHHHHHHHHHHHHHHCCSSSEEHHHHHHHCT-SCHHHHHHHHHHHCTTSEE-EEEE
T ss_pred hhHHHHHHHHHHHHHhhCCCcCHHHHHHHhCcCHHHHHHHHHHHhccCcee-EEee
Confidence 356899999999999999999999999999999999999999999999886 5543
No 39
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=89.34 E-value=0.93 Score=32.29 Aligned_cols=42 Identities=17% Similarity=0.294 Sum_probs=38.7
Q ss_pred HHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 24 KVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 24 ~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
.|..+|..+|..+..+|.+..++++..|+..|-.|.+.|+|.
T Consensus 4 ~il~~l~~~~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~ 45 (53)
T smart00420 4 QILELLAQQGKVSVEELAELLGVSEMTIRRDLNKLEEQGLLT 45 (53)
T ss_pred HHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 467778888999999999999999999999999999999987
No 40
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=89.28 E-value=0.7 Score=32.81 Aligned_cols=42 Identities=26% Similarity=0.322 Sum_probs=36.4
Q ss_pred HHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 23 ~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
.+|...|.. |+++..+|++.++++.+.|..-|-.|...|+|.
T Consensus 5 ~~Il~~L~~-~~~~~~el~~~l~~s~~~vs~hL~~L~~~glV~ 46 (47)
T PF01022_consen 5 LRILKLLSE-GPLTVSELAEELGLSQSTVSHHLKKLREAGLVE 46 (47)
T ss_dssp HHHHHHHTT-SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHh-CCCchhhHHHhccccchHHHHHHHHHHHCcCee
Confidence 356666665 999999999999999999999999999999986
No 41
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=89.04 E-value=2.2 Score=32.52 Aligned_cols=59 Identities=19% Similarity=0.127 Sum_probs=47.3
Q ss_pred hhHHHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEech
Q 009896 20 DLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLF 85 (523)
Q Consensus 20 ~~v~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~~ 85 (523)
+....|..++...+ .+..+|.+.++++...++..|-.|.++|++...... ...+|.++.
T Consensus 7 ~~~~~il~~l~~~~-~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~~~~------~~~~~~~~~ 65 (78)
T cd00090 7 PTRLRILRLLLEGP-LTVSELAERLGLSQSTVSRHLKKLEEAGLVESRREG------RRVYYSLTD 65 (78)
T ss_pred hHHHHHHHHHHHCC-cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEEEec------cEEEEEeCC
Confidence 45667888887766 999999999999999999999999999999844332 135777764
No 42
>PF05645 RNA_pol_Rpc82: RNA polymerase III subunit RPC82; InterPro: IPR008806 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and 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 []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This entry describes the C-terminal region of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In Saccharomyces cerevisiae, the enzyme is composed of 15 subunits, ranging from 160 to about 10 kDa [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2XV4_S 2XUB_A.
Probab=88.88 E-value=0.75 Score=45.55 Aligned_cols=42 Identities=14% Similarity=0.382 Sum_probs=37.5
Q ss_pred CeEEEehHHHHHHHHHHHHHHHHHHHcCCchHHHHHHHHhhC
Q 009896 353 DSYSIDFEKIIEIAQNEEVESVVSKRYGRDAYRIFRLLSKSG 394 (523)
Q Consensus 353 ~~y~V~~~~i~~~lr~~~le~~v~~~~G~~a~RI~r~L~~k~ 394 (523)
-.|.|||++....+|...+-++++.|+|..++.|++.+++-.
T Consensus 102 v~~rvN~erF~~~lRn~~lv~~a~~r~g~~ta~Vy~~~L~~~ 143 (258)
T PF05645_consen 102 VVWRVNYERFLVHLRNQRLVDLAERRIGSVTAEVYRAMLKLS 143 (258)
T ss_dssp TSEEE-HHHHHHHHHHHHHHHHHHHHT-CHHHHHHHHHHHCT
T ss_pred eEEEEEHHHHHHHHHHHHHHHHHHHhhCchHHHHHHHHHhhc
Confidence 369999999999999999999999999999999999998754
No 43
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=88.74 E-value=4 Score=33.20 Aligned_cols=68 Identities=13% Similarity=0.164 Sum_probs=53.1
Q ss_pred hchhHHHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEechhhH
Q 009896 18 FGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFDNI 88 (523)
Q Consensus 18 FG~~v~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~~~~i 88 (523)
....--.|...|..+|..+..+|.+.++++...|...|-.|.+.|+|...... + ++...+|.+...+.
T Consensus 8 l~~~~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~~~~--~-~~r~~~~~lT~~g~ 75 (101)
T smart00347 8 LTPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRLPSP--E-DRRSVLVSLTEEGR 75 (101)
T ss_pred CCHHHHHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEecCCC--C-CCCeEEEEECHhHH
Confidence 34556678888988999999999999999999999999999999999844332 1 12345777766653
No 44
>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea. Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....
Probab=88.33 E-value=5.6 Score=34.02 Aligned_cols=100 Identities=19% Similarity=0.250 Sum_probs=70.2
Q ss_pred chhHHHHHHHHHhcCCCcHHHHHhhc----CCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEechh-hHHHHhc
Q 009896 19 GDLVAKVCECLLRKGPLTRQNVKRYT----ELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFD-NILHRVR 93 (523)
Q Consensus 19 G~~v~~V~~~Ll~~G~ltl~~l~~~t----~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~~~-~il~rlR 93 (523)
|+.=..|-.+|=.+|++|..+|.... +.++..|+..|-.|.+-|+|...... + ..+|.+... +-+..-.
T Consensus 2 s~~E~~IM~~lW~~~~~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~~~~~g-----r-~~~Y~p~is~~e~~~~~ 75 (115)
T PF03965_consen 2 SDLELEIMEILWESGEATVREIHEALPEERSWAYSTVQTLLNRLVEKGFLTREKIG-----R-AYVYSPLISREEYLAQE 75 (115)
T ss_dssp -HHHHHHHHHHHHHSSEEHHHHHHHHCTTSS--HHHHHHHHHHHHHTTSEEEEEET-----T-CEEEEESSSHHHHHHHH
T ss_pred CHHHHHHHHHHHhCCCCCHHHHHHHHHhccccchhHHHHHHHHHHhCCceeEeecC-----C-ceEEEeCCcHHHHHHHH
Confidence 44456788999999999999998774 47799999999999999999844332 1 346665444 3333333
Q ss_pred hhhHHHHHHHHhhHHHHHHHHHHHHcCcCCHHHH
Q 009896 94 FAKFLTILSQEFDQQCVELVQGLLEHGRLTLKQM 127 (523)
Q Consensus 94 ~p~~i~~i~~~~G~~a~~I~~~lL~~G~~~~~~l 127 (523)
. -.+++..||.....++..|+....++.+++
T Consensus 76 ~---~~~l~~~~~gs~~~l~~~l~~~~~ls~~el 106 (115)
T PF03965_consen 76 L---RQFLDRLFDGSIPQLVAALVESEELSPEEL 106 (115)
T ss_dssp H---HHHHHHHSTTHHHHHHHHHHHCT-S-HHHH
T ss_pred H---HHHHHHHhCCCHHHHHHHHHhcCCCCHHHH
Confidence 3 334566788888999999999998887775
No 45
>PRK11239 hypothetical protein; Provisional
Probab=88.00 E-value=9.2 Score=36.31 Aligned_cols=123 Identities=27% Similarity=0.381 Sum_probs=89.2
Q ss_pred hchhHHHHHHHHHhcC-------CCcHHHHHhhc----------CCCHHHHHHHHHHHHhhcccccccccCCCCCCcceE
Q 009896 18 FGDLVAKVCECLLRKG-------PLTRQNVKRYT----------ELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQ 80 (523)
Q Consensus 18 FG~~v~~V~~~Ll~~G-------~ltl~~l~~~t----------~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~ 80 (523)
+-+.-++|..||+.+- ++||..|...+ .++...|..+|=.|...++|.-.... | .
T Consensus 5 Ls~~EaRVlG~LiEKe~TTPd~YPLSLNaL~~aCNQKsnRePVm~lsE~eV~~ald~L~~~~Lv~~~~~~--g-s----- 76 (215)
T PRK11239 5 LTALEARVIGCLLEKQVTTPEQYPLSVNGVVTACNQKTNREPVMNLSESEVQEQLDNLVKRHYLRTVSGF--G-N----- 76 (215)
T ss_pred cCHHHHHHHHHhhhhcccCCCcCcchHHHHHHHhccccccCccccCCHHHHHHHHHHHHhCcCeeeecCC--C-c-----
Confidence 5567788999999763 78888887654 37889999999999999999622111 1 1
Q ss_pred EEechhhHHHHhchhhHHHHH-HHHhh-----HHHHHHHHHHHHcCcCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHH
Q 009896 81 YVVLFDNILHRVRFAKFLTIL-SQEFD-----QQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLV 154 (523)
Q Consensus 81 Y~~~~~~il~rlR~p~~i~~i-~~~~G-----~~a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~~~~i~~~f~~Lv 154 (523)
|.+||=+.. .++|| .....|+-.||..|--|+.++..+..- + -...+.++++..+..|+
T Consensus 77 ------------Rv~Ky~Hr~~~~ef~~l~l~~~~~All~~LlLRGPQT~gELRtRs~R-l--~~F~dv~~Ve~~L~~L~ 141 (215)
T PRK11239 77 ------------RVTKYEQRFCNSEFGDLKLSAAEVALITTLLLRGAQTPGELRSRAAR-M--YEFSDMAEVESTLEQLA 141 (215)
T ss_pred ------------chHHHHHhcccccccccCCCHHHHHHHHHHHhcCCCChHHHHHhHhc-C--CcCCCHHHHHHHHHHHH
Confidence 334554433 23333 668889999999999999999877432 1 12446889999999999
Q ss_pred hcc---cceecC
Q 009896 155 TAH---YVERCP 163 (523)
Q Consensus 155 ~~~---fi~~v~ 163 (523)
... ++.+.|
T Consensus 142 ~r~~~plV~~Lp 153 (215)
T PRK11239 142 NREDGPFVVRLA 153 (215)
T ss_pred hccCCceeeecC
Confidence 874 677765
No 46
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=87.97 E-value=8 Score=37.14 Aligned_cols=93 Identities=17% Similarity=0.243 Sum_probs=66.5
Q ss_pred hhchhHHHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEechhhHHHHhchhh
Q 009896 17 HFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFDNILHRVRFAK 96 (523)
Q Consensus 17 ~FG~~v~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~~~~il~rlR~p~ 96 (523)
.=|..-.+|-..|..+|+.|+.+|....++++-.||.=|-.|.--|+|.+.......| ++...|.+-....=
T Consensus 8 ~~~~tr~~il~lL~~~g~~sa~elA~~Lgis~~avR~HL~~Le~~Glv~~~~~~~g~G-RP~~~y~Lt~~g~~------- 79 (218)
T COG2345 8 PSGSTRERILELLKKSGPVSADELAEELGISPMAVRRHLDDLEAEGLVEVERQQGGRG-RPAKLYRLTEKGRE------- 79 (218)
T ss_pred CCccHHHHHHHHHhccCCccHHHHHHHhCCCHHHHHHHHHHHHhCcceeeeeccCCCC-CCceeeeecccchh-------
Confidence 4467778889999999999999999999999999999999999999999553332223 33456665444321
Q ss_pred HHHHHHHHhhHHHHHHHHHHHHcC
Q 009896 97 FLTILSQEFDQQCVELVQGLLEHG 120 (523)
Q Consensus 97 ~i~~i~~~~G~~a~~I~~~lL~~G 120 (523)
.....||+.+..++..|=..|
T Consensus 80 ---~f~~~y~~l~~~~l~~l~~~~ 100 (218)
T COG2345 80 ---QFPKRYGELALALLDALEETG 100 (218)
T ss_pred ---hcchhhHHHHHHHHHHHHHhc
Confidence 334456666655555555544
No 47
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=87.62 E-value=4.4 Score=39.90 Aligned_cols=48 Identities=23% Similarity=0.269 Sum_probs=45.8
Q ss_pred hchhHHHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 18 FGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 18 FG~~v~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
|++-=++|..+|+.+|+.|..+|++.+++|..+|-..|=.|..-|+|.
T Consensus 14 lt~yEa~vY~aLl~~g~~tA~eis~~sgvP~~kvY~vl~sLe~kG~v~ 61 (247)
T COG1378 14 LTEYEAKVYLALLCLGEATAKEISEASGVPRPKVYDVLRSLEKKGLVE 61 (247)
T ss_pred CCHHHHHHHHHHHHhCCccHHHHHHHcCCCchhHHHHHHHHHHCCCEE
Confidence 447789999999999999999999999999999999999999999998
No 48
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=87.48 E-value=1.1 Score=33.58 Aligned_cols=51 Identities=22% Similarity=0.324 Sum_probs=43.4
Q ss_pred CchHHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEe
Q 009896 381 RDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLV 432 (523)
Q Consensus 381 ~~a~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQEvp 432 (523)
+.-.+|++.|...+.+ .-.+|++...+|...+..-|..|.+.|+|+.....
T Consensus 10 p~R~~Il~~L~~~~~~-t~~ela~~l~~~~~t~s~hL~~L~~aGli~~~~~g 60 (61)
T PF12840_consen 10 PTRLRILRLLASNGPM-TVSELAEELGISQSTVSYHLKKLEEAGLIEVEREG 60 (61)
T ss_dssp HHHHHHHHHHHHCSTB-EHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEET
T ss_pred HHHHHHHHHHhcCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEeccC
Confidence 3446889999777788 99999999999999999999999999999876543
No 49
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=87.46 E-value=3.1 Score=34.92 Aligned_cols=63 Identities=11% Similarity=0.187 Sum_probs=50.8
Q ss_pred HHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccce-EEEEec-CC--CCceEEEEEEEc
Q 009896 384 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL-MEKLVV-TG--ARQSQFLLWKVN 447 (523)
Q Consensus 384 ~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~-lQEvpk-~~--~~~~t~~lw~v~ 447 (523)
.+|++.|...+.+ .-.+|++...++...+++.+.+|.+.|+|. ..-... .. .+...+..|.++
T Consensus 6 ~~il~~L~~~~~~-~~~~la~~l~~s~~tv~~~l~~L~~~g~i~~~~~~~~~~~~g~~~~~~v~i~~~ 72 (108)
T smart00344 6 RKILEELQKDARI-SLAELAKKVGLSPSTVHNRVKRLEEEGVIKGYTAVINPKKLGLSVTAFVGVDLE 72 (108)
T ss_pred HHHHHHHHHhCCC-CHHHHHHHHCcCHHHHHHHHHHHHHCCCeeceEEEeCHHHcCCCEEEEEEEEEC
Confidence 5899999888888 999999999999999999999999999997 332222 21 445667778887
No 50
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=87.40 E-value=1.8 Score=39.55 Aligned_cols=69 Identities=19% Similarity=0.224 Sum_probs=51.8
Q ss_pred hhHHHHHHHHHh-cCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEechhhHHHHhc
Q 009896 20 DLVAKVCECLLR-KGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFDNILHRVR 93 (523)
Q Consensus 20 ~~v~~V~~~Ll~-~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~~~~il~rlR 93 (523)
..|+.|..+|.- ++++|+.+|...+|++.+.|-.+|-.|.--|+|.....+ |.+. .||++ .++.+...|
T Consensus 26 rtVG~iYgilyls~~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~~~lV~~~~~~---G~Rk-~~F~a-~~df~~~f~ 95 (177)
T COG1510 26 RTVGQIYGILYLSRKPLTLDEIAEALGMSKSNVSMGLKKLQDWNLVKKVFEK---GDRK-DYFEA-EKDFSQIFR 95 (177)
T ss_pred chHHHHhhhheecCCCccHHHHHHHHCCCcchHHHHHHHHHhcchHHhhhcc---Ccch-hhhcc-cchHHHHHH
Confidence 457778777766 899999999999999999999999999999999843332 1232 35554 565555444
No 51
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=86.95 E-value=8.8 Score=33.75 Aligned_cols=98 Identities=17% Similarity=0.283 Sum_probs=69.4
Q ss_pred hHHHHHHHHHhcCCCcHHHHHhh----cCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEechh-hHHHHhchh
Q 009896 21 LVAKVCECLLRKGPLTRQNVKRY----TELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFD-NILHRVRFA 95 (523)
Q Consensus 21 ~v~~V~~~Ll~~G~ltl~~l~~~----t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~~~-~il~rlR~p 95 (523)
.=-.|-.+|-..|+.|..+|... .++++..|...|-.|.+.|+|.. ... | + ...|++... +-+..-...
T Consensus 5 ~E~~VM~vlW~~~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~KG~v~~-~k~--g--r-~~~Y~p~vs~ee~~~~~~~ 78 (130)
T TIGR02698 5 AEWEVMRVVWTLGETTSRDIIRILAEKKDWSDSTIKTLLGRLVDKGCLTT-EKE--G--R-KFIYTALVSEDEAVENAAQ 78 (130)
T ss_pred HHHHHHHHHHcCCCCCHHHHHHHHhhccCCcHHHHHHHHHHHHHCCceee-ecC--C--C-cEEEEecCCHHHHHHHHHH
Confidence 33467788888999999997655 47899999999999999999973 322 1 2 346764333 322222233
Q ss_pred hHHHHHHHHhhHHHHHHHHHHHHcCcCCHHHH
Q 009896 96 KFLTILSQEFDQQCVELVQGLLEHGRLTLKQM 127 (523)
Q Consensus 96 ~~i~~i~~~~G~~a~~I~~~lL~~G~~~~~~l 127 (523)
.+++..||.....++..|+....++.+++
T Consensus 79 ---~~~~~~f~gs~~~ll~~l~~~~~ls~eel 107 (130)
T TIGR02698 79 ---ELFSRICSRKVGAVIADLIEESPLSQTDI 107 (130)
T ss_pred ---HHHHHHHCCCHHHHHHHHHhcCCCCHHHH
Confidence 34455788888889999999888887765
No 52
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=86.72 E-value=5.3 Score=31.60 Aligned_cols=70 Identities=11% Similarity=0.193 Sum_probs=46.9
Q ss_pred hhHHHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEechhhHHHHhchhhHHH
Q 009896 20 DLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFDNILHRVRFAKFLT 99 (523)
Q Consensus 20 ~~v~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~~~~il~rlR~p~~i~ 99 (523)
+++..|-..|. .|+.+..+|+..++++++.+..-|--|++.|+|. . . ...|.+-..+--..-.+-++..
T Consensus 6 ~Ii~~IL~~l~-~~~~~~t~i~~~~~L~~~~~~~yL~~L~~~gLI~-~--~-------~~~Y~lTekG~~~l~~l~~~~~ 74 (77)
T PF14947_consen 6 EIIFDILKILS-KGGAKKTEIMYKANLNYSTLKKYLKELEEKGLIK-K--K-------DGKYRLTEKGKEFLEELEELIE 74 (77)
T ss_dssp HHHHHHHHHH--TT-B-HHHHHTTST--HHHHHHHHHHHHHTTSEE-E--E-------TTEEEE-HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHH-cCCCCHHHHHHHhCcCHHHHHHHHHHHHHCcCee-C--C-------CCEEEECccHHHHHHHHHHHHH
Confidence 34555556655 7999999999999999999999999999999994 1 1 1378877666555555544444
Q ss_pred H
Q 009896 100 I 100 (523)
Q Consensus 100 ~ 100 (523)
+
T Consensus 75 ~ 75 (77)
T PF14947_consen 75 L 75 (77)
T ss_dssp H
T ss_pred H
Confidence 3
No 53
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=86.66 E-value=1.7 Score=35.17 Aligned_cols=44 Identities=23% Similarity=0.192 Sum_probs=40.0
Q ss_pred HHHHHHHHHhc-CCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 22 VAKVCECLLRK-GPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 22 v~~V~~~Ll~~-G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
+-.|..+|..+ |++|+.+|++.++++...|..-|-.|.++|++.
T Consensus 7 ~~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~ 51 (91)
T smart00346 7 GLAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQELGYVE 51 (91)
T ss_pred HHHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCee
Confidence 45677778777 899999999999999999999999999999997
No 54
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=86.49 E-value=3 Score=31.29 Aligned_cols=46 Identities=17% Similarity=0.227 Sum_probs=42.2
Q ss_pred hhHHHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 20 DLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 20 ~~v~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
|.--+|...|...|++|..+|...++++...+..-|-.|...|+|.
T Consensus 10 p~R~~Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli~ 55 (61)
T PF12840_consen 10 PTRLRILRLLASNGPMTVSELAEELGISQSTVSYHLKKLEEAGLIE 55 (61)
T ss_dssp HHHHHHHHHHHHCSTBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeE
Confidence 6677888889889999999999999999999999999999999997
No 55
>PF03962 Mnd1: Mnd1 family; InterPro: IPR005647 This family of proteins includes meiotic nuclear division protein 1 (MND1) from Saccharomyces cerevisiae (Baker's yeast). The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair [].
Probab=86.45 E-value=8.3 Score=36.28 Aligned_cols=84 Identities=14% Similarity=0.229 Sum_probs=50.3
Q ss_pred HHHHhhCCCcchhhh----hhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCceEEEEEEEchHH--HHHHHHHHHHH
Q 009896 388 RLLSKSGRLLETDKI----SDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQI--LWKHVLDEMFH 461 (523)
Q Consensus 388 r~L~~k~~l~eek~i----~~~ami~~k~~R~~L~~L~~~g~v~lQEvpk~~~~~~t~~lw~v~~~~--~~~~~l~~~~k 461 (523)
.++...+....-|+| .+.+.|....++.+|..|..+|.|+.--+ +.+.|+|...-.. ....-++.+-+
T Consensus 3 ~~f~e~~~~y~lKELEK~~pK~~gI~~~~VKdvlq~LvDDglV~~EKi------Gssn~YWsFps~~~~~~~~~~~~l~~ 76 (188)
T PF03962_consen 3 EIFHESKDFYTLKELEKLAPKEKGIVSMSVKDVLQSLVDDGLVHVEKI------GSSNYYWSFPSQAKQKRQNKLEKLQK 76 (188)
T ss_pred HHHhhcCCcccHHHHHHHcccccCCchhhHHHHHHHHhccccchhhhc------cCeeEEEecChHHHHHHHHHHHHHHH
Confidence 344444443354444 45589999999999999999999965333 3356777766443 33344444444
Q ss_pred HHHHHHHHHHHHHHhh
Q 009896 462 AALNLSLRVSYELDRE 477 (523)
Q Consensus 462 ~~~nl~~R~~~e~~~~ 477 (523)
.+.++..++....+..
T Consensus 77 ~~~~~~~~i~~l~~~i 92 (188)
T PF03962_consen 77 EIEELEKKIEELEEKI 92 (188)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 4444444444433333
No 56
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=86.26 E-value=1.6 Score=32.38 Aligned_cols=43 Identities=19% Similarity=0.274 Sum_probs=40.5
Q ss_pred HHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 23 ~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
..|..+|-.+|.+++.+|+...+++...||.=|..|-+.|++.
T Consensus 3 ~~Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~i~ 45 (57)
T PF08220_consen 3 QQILELLKEKGKVSVKELAEEFGVSEMTIRRDLNKLEKQGLIK 45 (57)
T ss_pred HHHHHHHHHcCCEEHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 4688899999999999999999999999999999999999986
No 57
>COG3388 Predicted transcriptional regulator [Transcription]
Probab=85.61 E-value=1.3 Score=36.18 Aligned_cols=42 Identities=24% Similarity=0.370 Sum_probs=39.8
Q ss_pred HHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 24 KVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 24 ~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
.|..+++..++.-+-.|+.-||+|...||.+|-||-|-|++.
T Consensus 18 ~Vl~~v~eeqPiGI~klS~~TGmp~HKVRYSLRVLEq~~iI~ 59 (101)
T COG3388 18 SVLKVVLEEQPIGIIKLSDETGMPEHKVRYSLRVLEQENIIS 59 (101)
T ss_pred HHHHHHHHhCCceeEeechhcCCchhhhhhhhhhhhhcCccC
Confidence 578889999999999999999999999999999999999996
No 58
>COG3132 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=85.13 E-value=17 Score=33.46 Aligned_cols=121 Identities=29% Similarity=0.362 Sum_probs=87.4
Q ss_pred chhHHHHHHHHHhc-------CCCcHHHHHhhc----------CCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEE
Q 009896 19 GDLVAKVCECLLRK-------GPLTRQNVKRYT----------ELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQY 81 (523)
Q Consensus 19 G~~v~~V~~~Ll~~-------G~ltl~~l~~~t----------~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y 81 (523)
-++=++|..||+.+ -++|+..++-.+ +|+..+|..+|=-|++.++|. +.+. .+ .+.|
T Consensus 6 ~a~eARViGcLlEKqvtTPe~YPLtlN~l~~AcNQKT~RdPVmnLse~eVq~~l~~L~~r~lvr--~~sg---sR-v~ky 79 (215)
T COG3132 6 TALEARVIGCLLEKQVTTPEQYPLTLNGLVTACNQKTNRDPVMNLSESEVQEQLDNLEKRHLVR--TVSG---SR-VTKY 79 (215)
T ss_pred chHHHHHHHHhhhcccCCcccccchHHHHHHHHhccccccchhcCCHHHHHHHHHHHHHhhhHH--Hhhc---ch-HHHH
Confidence 36678899999876 367888886553 478899999999999999997 2221 11 2333
Q ss_pred EechhhHHHHhchhhHHHHHHHHhhH-----HHHHHHHHHHHcCcCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhc
Q 009896 82 VVLFDNILHRVRFAKFLTILSQEFDQ-----QCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTA 156 (523)
Q Consensus 82 ~~~~~~il~rlR~p~~i~~i~~~~G~-----~a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~~~~i~~~f~~Lv~~ 156 (523)
+ . .+...+||+ .-..++-.||..|--|+.++..+..--. +..+..+++..+.+|+..
T Consensus 80 e----h-----------rfcnsefgdlkl~~~evali~lLlLRGaQTpgELrtRanRm~---~Fsdv~e~e~~Le~La~R 141 (215)
T COG3132 80 E----H-----------RFCNSEFGDLKLSAAEVALITLLLLRGAQTPGELRTRANRMY---EFSDVAEVEHTLERLANR 141 (215)
T ss_pred H----H-----------HHhhccccceeechHHHHHHHHHHHcCCCChhHHHHHHHhhh---ccchHHHHHHHHHHHhcC
Confidence 3 1 234456663 3456788999999999999998754311 133578899999999999
Q ss_pred c---cceecC
Q 009896 157 H---YVERCP 163 (523)
Q Consensus 157 ~---fi~~v~ 163 (523)
+ |+++.|
T Consensus 142 ~~gplvv~l~ 151 (215)
T COG3132 142 EDGPLVVRLA 151 (215)
T ss_pred CCCceeeecC
Confidence 8 888875
No 59
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=85.04 E-value=19 Score=33.87 Aligned_cols=121 Identities=14% Similarity=0.197 Sum_probs=81.8
Q ss_pred hHHHHHHHHHhcCC--CcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEechhhHHHHhchhhHH
Q 009896 21 LVAKVCECLLRKGP--LTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFDNILHRVRFAKFL 98 (523)
Q Consensus 21 ~v~~V~~~Ll~~G~--ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~~~~il~rlR~p~~i 98 (523)
..+.|=.+|+..|. +|+.+|.+.++++...|+.+|--|.++ |...+ .| .--....+-|.+.--|.|-
T Consensus 5 ~~~~iEA~LF~sg~pgls~~~La~~l~~~~~~v~~~l~~L~~~-----y~~~~-~g-----i~i~~~~~~y~l~tk~e~~ 73 (188)
T PRK00135 5 YKSIIEALLFVSGEEGLSLEQLAEILELEPTEVQQLLEELQEK-----YEGDD-RG-----LKLIEFNDVYKLVTKEENA 73 (188)
T ss_pred HHHHHHHHHHHcCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH-----HhhCC-CC-----EEEEEECCEEEEEEcHHHH
Confidence 34567778888883 899999999999999999999999775 11111 00 1111112222222333444
Q ss_pred HHHHH--------HhhHHHHHHHHHHHHcCcCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccceecC
Q 009896 99 TILSQ--------EFDQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 163 (523)
Q Consensus 99 ~~i~~--------~~G~~a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~~~~i~~~f~~Lv~~~fi~~v~ 163 (523)
.+++. .+...+-+++..+..+|-+|-.++.+.-... ....+.+|+..|||..+.
T Consensus 74 ~~v~~~~~~~~~~~LS~aaLEtLaiIay~qPiTr~eI~~irGv~-----------~~~ii~~L~~~gLI~e~g 135 (188)
T PRK00135 74 DYLQKLVKTPIKQSLSQAALEVLAIIAYKQPITRIEIDEIRGVN-----------SDGALQTLLAKGLIKEVG 135 (188)
T ss_pred HHHHHHhcccccCCCCHHHHHHHHHHHHcCCcCHHHHHHHHCCC-----------HHHHHHHHHHCCCeEEcC
Confidence 44433 4667799999999999999999987663221 268899999999998764
No 60
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=84.43 E-value=1.9 Score=36.24 Aligned_cols=43 Identities=19% Similarity=0.268 Sum_probs=40.8
Q ss_pred HHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 23 ~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
.+|...|...|+.|..+|.+.+++++..|+..+-.|.+.|+|.
T Consensus 6 ~~il~~L~~~~~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~ 48 (108)
T smart00344 6 RKILEELQKDARISLAELAKKVGLSPSTVHNRVKRLEEEGVIK 48 (108)
T ss_pred HHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence 4788899999999999999999999999999999999999997
No 61
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=83.94 E-value=2.6 Score=36.56 Aligned_cols=46 Identities=24% Similarity=0.275 Sum_probs=43.2
Q ss_pred hhHHHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 20 DLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 20 ~~v~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
++.++|.+.+=.+|+.|+.++...|+++...++.-+-.|+-.|-|+
T Consensus 12 eLk~rIvElVRe~GRiTi~ql~~~TGasR~Tvk~~lreLVa~G~l~ 57 (127)
T PF06163_consen 12 ELKARIVELVREHGRITIKQLVAKTGASRNTVKRYLRELVARGDLY 57 (127)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCCeE
Confidence 5678899999999999999999999999999999999999999886
No 62
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=83.83 E-value=9.5 Score=35.88 Aligned_cols=135 Identities=15% Similarity=0.164 Sum_probs=90.3
Q ss_pred HHHHHHHhccchhcccccccCCcc-ccHHHHHHHhhhhccCCCCCHHHHHHHHHHhccC----C--C-CCCCCCeEEEeh
Q 009896 288 NVLSAMLQATSSAEKKVKTKNSVP-LSLSSIYEEVIKSEAGRNMTLDHVRASLVQLGEL----S--F-VDASSDSYSIDF 359 (523)
Q Consensus 288 ~v~~~~L~~~~~~~~~~~~~~s~~-~s~~~I~~~l~~~~~~~~~~~~~i~~~L~~La~~----~--~-~~~~~~~y~V~~ 359 (523)
.+++|+|-.+ ..| +|+.+|...+.. ..+.+...|..|..+ . + ...-+|.|.+-.
T Consensus 7 ~~iEA~LF~s-----------g~pgls~~~La~~l~~-------~~~~v~~~l~~L~~~y~~~~~gi~i~~~~~~y~l~t 68 (188)
T PRK00135 7 SIIEALLFVS-----------GEEGLSLEQLAEILEL-------EPTEVQQLLEELQEKYEGDDRGLKLIEFNDVYKLVT 68 (188)
T ss_pred HHHHHHHHHc-----------CCCCCCHHHHHHHHCC-------CHHHHHHHHHHHHHHHhhCCCCEEEEEECCEEEEEE
Confidence 4577777764 234 999999987742 234566666666433 1 1 133356688877
Q ss_pred HHHHHHHHHHHHHHHHHHHcCCchHHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCce
Q 009896 360 EKIIEIAQNEEVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQS 439 (523)
Q Consensus 360 ~~i~~~lr~~~le~~v~~~~G~~a~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQEvpk~~~~~~ 439 (523)
+.-..-.....+..--..++...++.++.++.-++-+ ...+|++.-.++. -.++.+|...|+|. |..+...+++
T Consensus 69 k~e~~~~v~~~~~~~~~~~LS~aaLEtLaiIay~qPi-Tr~eI~~irGv~~---~~ii~~L~~~gLI~--e~gr~~~~Gr 142 (188)
T PRK00135 69 KEENADYLQKLVKTPIKQSLSQAALEVLAIIAYKQPI-TRIEIDEIRGVNS---DGALQTLLAKGLIK--EVGRKEVPGR 142 (188)
T ss_pred cHHHHHHHHHHhcccccCCCCHHHHHHHHHHHHcCCc-CHHHHHHHHCCCH---HHHHHHHHHCCCeE--EcCcCCCCCC
Confidence 7666555544444433447899999999999888777 9999999998885 79999999999994 3444333443
Q ss_pred EEEEEEEc
Q 009896 440 QFLLWKVN 447 (523)
Q Consensus 440 t~~lw~v~ 447 (523)
-++|.+.
T Consensus 143 -p~ly~tT 149 (188)
T PRK00135 143 -PILYGTT 149 (188)
T ss_pred -Ceeeehh
Confidence 3444444
No 63
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=82.51 E-value=4.1 Score=30.23 Aligned_cols=46 Identities=20% Similarity=0.169 Sum_probs=40.5
Q ss_pred hhHHHHHHHHHhcCC--CcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 20 DLVAKVCECLLRKGP--LTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 20 ~~v~~V~~~Ll~~G~--ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
+.-..|..+|..+|+ +|..+|++.+++++..|-..+--|++.|+|.
T Consensus 5 ~~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~ 52 (62)
T PF12802_consen 5 PSQFRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKKGLVE 52 (62)
T ss_dssp HHHHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 344567788888988 9999999999999999999999999999998
No 64
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=82.45 E-value=3.3 Score=33.19 Aligned_cols=41 Identities=15% Similarity=0.262 Sum_probs=33.4
Q ss_pred HHHHHHhcC---CCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 25 VCECLLRKG---PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 25 V~~~Ll~~G---~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
+.-+|..++ ++|..+|+..+++|++.+++.|-.|.++|+|.
T Consensus 13 ~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~ 56 (83)
T PF02082_consen 13 ILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIE 56 (83)
T ss_dssp HHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeE
Confidence 334444444 38999999999999999999999999999997
No 65
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=82.40 E-value=2.5 Score=31.20 Aligned_cols=50 Identities=20% Similarity=0.400 Sum_probs=44.0
Q ss_pred hHHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEec
Q 009896 383 AYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVV 433 (523)
Q Consensus 383 a~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQEvpk 433 (523)
-++++.+|..++.+ ...+|++..-++...+-..+.+|.+.|||.-+.-|.
T Consensus 5 q~~iL~~l~~~~~~-~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~~~~~ 54 (59)
T PF01047_consen 5 QFRILRILYENGGI-TQSELAEKLGISRSTVTRIIKRLEKKGLIERERDPD 54 (59)
T ss_dssp HHHHHHHHHHHSSE-EHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETT
T ss_pred HHHHHHHHHHcCCC-CHHHHHHHHCCChhHHHHHHHHHHHCCCEEeccCCC
Confidence 35788888888898 999999999999999999999999999998877664
No 66
>PF10557 Cullin_Nedd8: Cullin protein neddylation domain; InterPro: IPR019559 This is the neddylation site of cullin proteins, which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae (Baker's yeast), and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue []. ; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_B 1U6G_A 3O6B_J 3O2P_E 4A0K_A 2HYE_C ....
Probab=82.35 E-value=4 Score=31.53 Aligned_cols=57 Identities=14% Similarity=0.251 Sum_probs=45.3
Q ss_pred HHHHHHHHHHHHcCcCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccceecC
Q 009896 107 QQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 163 (523)
Q Consensus 107 ~~a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~~~~i~~~f~~Lv~~~fi~~v~ 163 (523)
..-+.|+..+=..+.++..+|+..+.+.....-..+...++.++..|++.+||.|-+
T Consensus 8 ~I~AaIVrimK~~k~~~~~~L~~~v~~~l~~~f~~~~~~ik~~Ie~LIekeyi~Rd~ 64 (68)
T PF10557_consen 8 QIDAAIVRIMKQEKKLSHDELINEVIEELKKRFPPSVSDIKKRIESLIEKEYIERDE 64 (68)
T ss_dssp HHHHHHHHHHHHSSEEEHHHHHHHHHHHTTTTS---HHHHHHHHHHHHHTTSEEEES
T ss_pred hhhhheehhhhhcCceeHHHHHHHHHHHhcCCcCCCHHHHHHHHHHHHHhhhhhcCC
Confidence 345788899999999999999999877544322347889999999999999999975
No 67
>PF09824 ArsR: ArsR transcriptional regulator; InterPro: IPR014517 Members of this family of archaeal proteins are conserved transcriptional regulators belonging to the ArsR family.
Probab=82.25 E-value=10 Score=34.26 Aligned_cols=112 Identities=19% Similarity=0.269 Sum_probs=68.4
Q ss_pred hhhchhHHHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc-cccccCCCC-CC--cceEEE---echhhH
Q 009896 16 NHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ-AFTTEQPDG-PK--ANTQYV---VLFDNI 88 (523)
Q Consensus 16 ~~FG~~v~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~-~~~~~~~~~-~~--~~~~Y~---~~~~~i 88 (523)
..||.-+-+=.--++..|.+|..+|....+-.. +.||.+|=+-|+|. -|..+.+|+ |. .+++|+ +|..--
T Consensus 12 ~~f~s~~~kkV~~~Ls~~W~T~~El~e~~G~d~---~~~L~~LkK~gLiE~qWrmP~pG~kPeKEYhtsYs~vqaNFqcs 88 (160)
T PF09824_consen 12 QTFNSEVYKKVYDELSKGWMTEEELEEKYGKDV---RESLLILKKGGLIESQWRMPEPGEKPEKEYHTSYSKVQANFQCS 88 (160)
T ss_pred HHhCCHHHHHHHHHHHhccCCHHHHHHHHCcCH---HHHHHHHHHcCchhhccccCCCCCCchHHHHhhHhheeeeeEee
Confidence 467755544444445699999999999887655 89999999999998 677776553 21 122222 222111
Q ss_pred HHHhchhhHHHHHHHHhh--HHHHHHHHHHHHcCcCCHHHHHHHhh
Q 009896 89 LHRVRFAKFLTILSQEFD--QQCVELVQGLLEHGRLTLKQMFDRAK 132 (523)
Q Consensus 89 l~rlR~p~~i~~i~~~~G--~~a~~I~~~lL~~G~~~~~~li~~~~ 132 (523)
+ -=.+.+|..+-..+. .+.+.-++..+..|.+++.++.....
T Consensus 89 ~--~DLsdii~i~f~~deel~~~~e~i~~~v~~Gn~Sl~~lsr~l~ 132 (160)
T PF09824_consen 89 M--EDLSDIIYIAFMSDEELRDYVEKIEKEVEAGNTSLSDLSRKLG 132 (160)
T ss_pred H--HHHHHHHheeecCHHHHHHHHHHHHHHHHcCCCcHHHHHHHhC
Confidence 1 112333443332232 23445556666779999999877643
No 68
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=81.71 E-value=5.3 Score=30.35 Aligned_cols=56 Identities=21% Similarity=0.240 Sum_probs=41.0
Q ss_pred HHHHHHh-cCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEec
Q 009896 25 VCECLLR-KGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVL 84 (523)
Q Consensus 25 V~~~Ll~-~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~ 84 (523)
|..+|-. +++++-.+|+..++++..++|.=|..|.+.|.|. ..+.. .| ..+++.+|
T Consensus 5 Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~-~~~~~-rG--~~~~W~l~ 61 (62)
T PF04703_consen 5 ILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLEKEGKVE-RSPVR-RG--KSTYWRLN 61 (62)
T ss_dssp HHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEE-EES-S-SS--SS-EEEES
T ss_pred HHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE-EecCC-CC--cceeeeec
Confidence 5556666 8999999999999999999999999999999997 33321 22 23577765
No 69
>PF01638 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002577 The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure. The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde []. The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH []. The crystal structure of ytfH resembles the DNA-binding domains of winged helix proteins, containing a three helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-H2-B1-H3-H4-B2-B3-H5-H6. This topology corresponds with that of the marR-type DNA-binding domain, wherein helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. ; PDB: 2F2E_B 3DF8_A 1Z7U_B 1YYV_A 4A5M_D 4A5N_B 2FSW_A 2HZT_D.
Probab=81.58 E-value=16 Score=29.65 Aligned_cols=63 Identities=16% Similarity=0.231 Sum_probs=45.7
Q ss_pred HHHHHHHHHhcCCCcHHHHHhhc-CCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEechhhH
Q 009896 22 VAKVCECLLRKGPLTRQNVKRYT-ELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFDNI 88 (523)
Q Consensus 22 v~~V~~~Ll~~G~ltl~~l~~~t-~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~~~~i 88 (523)
...|...|.. |+..+.+|.+.. +++++.+-..|-.|..+|+|.- ...+.. + ..+.|.+-..+.
T Consensus 7 ~~~IL~~l~~-g~~rf~el~~~l~~is~~~L~~~L~~L~~~GLv~r-~~~~~~-p-~~v~Y~LT~~G~ 70 (90)
T PF01638_consen 7 TLLILRALFQ-GPMRFSELQRRLPGISPKVLSQRLKELEEAGLVER-RVYPEV-P-PRVEYSLTEKGK 70 (90)
T ss_dssp HHHHHHHHTT-SSEEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEE-EEESSS-S-SEEEEEE-HHHH
T ss_pred HHHHHHHHHh-CCCcHHHHHHhcchhHHHHHHHHHHHHHHcchhhc-ccccCC-C-CCCccCCCcCHH
Confidence 4456667766 999999999987 8999999999999999999972 222111 2 346888755543
No 70
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=81.55 E-value=3.5 Score=39.22 Aligned_cols=63 Identities=17% Similarity=0.251 Sum_probs=50.9
Q ss_pred HHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCceEEEEEEEchH
Q 009896 384 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQ 449 (523)
Q Consensus 384 ~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQEvpk~~~~~~t~~lw~v~~~ 449 (523)
.+|+..|..+|.+ ...+|++...++...++..|..|.+.|+|+-...+.+ ..|..++|++...
T Consensus 4 ~~IL~~L~~~~~~-t~~eLA~~lgis~~tV~~~L~~Le~~GlV~r~~~~~~--~gRp~~~y~LT~~ 66 (203)
T TIGR02702 4 EDILSYLLKQGQA-TAAALAEALAISPQAVRRHLKDLETEGLIEYEAVVQG--MGRPQYHYQLSRQ 66 (203)
T ss_pred HHHHHHHHHcCCC-CHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEeecccC--CCCCceEEEECcc
Confidence 4788889888887 9999999999999999999999999999976544332 3455667777643
No 71
>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional
Probab=80.99 E-value=2.1 Score=39.69 Aligned_cols=46 Identities=33% Similarity=0.471 Sum_probs=41.8
Q ss_pred hHHHHHHHHhhC-CCcchhhhhhhcCCCcccHHHHHHHHhhcccceEE
Q 009896 383 AYRIFRLLSKSG-RLLETDKISDTTFVEKKDAPKILYKLWKDGYLLME 429 (523)
Q Consensus 383 a~RI~r~L~~k~-~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQ 429 (523)
+.||+-+|..+| ++ .-.+|++...|...++-+.||+|++.|+|..-
T Consensus 6 ~~~i~~~l~~~~~~~-~a~~i~k~l~i~k~~vNr~LY~L~~~~~v~~~ 52 (183)
T PHA02701 6 ASLILTLLSSSGDKL-PAKRIAKELGISKHEANRCLYRLLESDAVSCE 52 (183)
T ss_pred HHHHHHHHHhcCCCC-cHHHHHHHhCccHHHHHHHHHHHhhcCcEecC
Confidence 568999999988 65 99999999999999999999999999999653
No 72
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=80.94 E-value=7.2 Score=37.45 Aligned_cols=66 Identities=21% Similarity=0.303 Sum_probs=54.1
Q ss_pred CchHHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCceEEEEEEEchH
Q 009896 381 RDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQ 449 (523)
Q Consensus 381 ~~a~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQEvpk~~~~~~t~~lw~v~~~ 449 (523)
.---+|..+|.+.|-+ .-.+|++...|+...+|.-|-.|..+|+|+.+..+.. .+|..++|+....
T Consensus 11 ~tr~~il~lL~~~g~~-sa~elA~~Lgis~~avR~HL~~Le~~Glv~~~~~~~g--~GRP~~~y~Lt~~ 76 (218)
T COG2345 11 STRERILELLKKSGPV-SADELAEELGISPMAVRRHLDDLEAEGLVEVERQQGG--RGRPAKLYRLTEK 76 (218)
T ss_pred cHHHHHHHHHhccCCc-cHHHHHHHhCCCHHHHHHHHHHHHhCcceeeeeccCC--CCCCceeeeeccc
Confidence 3345788888778888 9999999999999999999999999999999955543 4677777776543
No 73
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=80.01 E-value=2.4 Score=30.03 Aligned_cols=42 Identities=26% Similarity=0.419 Sum_probs=37.4
Q ss_pred HHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccce
Q 009896 384 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 427 (523)
Q Consensus 384 ~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~ 427 (523)
.+|+..|.. |.+ .-.+|++...++...+..-|..|.+.|+|+
T Consensus 5 ~~Il~~L~~-~~~-~~~el~~~l~~s~~~vs~hL~~L~~~glV~ 46 (47)
T PF01022_consen 5 LRILKLLSE-GPL-TVSELAEELGLSQSTVSHHLKKLREAGLVE 46 (47)
T ss_dssp HHHHHHHTT-SSE-EHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHh-CCC-chhhHHHhccccchHHHHHHHHHHHCcCee
Confidence 578888855 788 999999999999999999999999999985
No 74
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=79.86 E-value=4.8 Score=34.96 Aligned_cols=55 Identities=15% Similarity=0.241 Sum_probs=47.8
Q ss_pred hhHHHHHHHHHHHHcCcCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccceecC
Q 009896 105 FDQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 163 (523)
Q Consensus 105 ~G~~a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~~~~i~~~f~~Lv~~~fi~~v~ 163 (523)
.|+.-..||+.+=.+|-+|.+++++.+..+.+. +...|+..+.+|++.|+|.+.-
T Consensus 4 Is~aE~eVM~ilW~~~~~t~~eI~~~l~~~~ew----s~sTV~TLl~RL~KKg~l~~~k 58 (123)
T COG3682 4 ISAAEWEVMEILWSRGPATVREIIEELPADREW----SYSTVKTLLNRLVKKGLLTRKK 58 (123)
T ss_pred ccHHHHHHHHHHHHcCCccHHHHHHHHhhcccc----cHHHHHHHHHHHHhccchhhhh
Confidence 467788999999999999999999999876443 6778999999999999998763
No 75
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=79.83 E-value=3.5 Score=30.41 Aligned_cols=46 Identities=13% Similarity=0.213 Sum_probs=39.1
Q ss_pred HHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccc
Q 009896 24 KVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTT 69 (523)
Q Consensus 24 ~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~ 69 (523)
.|-.+|-.+|++|..+|.+..+++...+-..+--|++.|+|.-...
T Consensus 7 ~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~~~ 52 (59)
T PF01047_consen 7 RILRILYENGGITQSELAEKLGISRSTVTRIIKRLEKKGLIERERD 52 (59)
T ss_dssp HHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE
T ss_pred HHHHHHHHcCCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEeccC
Confidence 3556677899999999999999999999999999999999983333
No 76
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=79.82 E-value=4.2 Score=37.25 Aligned_cols=43 Identities=19% Similarity=0.310 Sum_probs=41.1
Q ss_pred HHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccce
Q 009896 384 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 427 (523)
Q Consensus 384 ~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~ 427 (523)
.+|++.|...+.+ .-.+|++...++...++.-+.+|.+.|+|.
T Consensus 17 ~~IL~~Lq~d~R~-s~~eiA~~lglS~~tv~~Ri~rL~~~GvI~ 59 (164)
T PRK11169 17 RNILNELQKDGRI-SNVELSKRVGLSPTPCLERVRRLERQGFIQ 59 (164)
T ss_pred HHHHHHhccCCCC-CHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence 5899999999999 999999999999999999999999999996
No 77
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=79.04 E-value=38 Score=28.53 Aligned_cols=92 Identities=18% Similarity=0.270 Sum_probs=61.1
Q ss_pred HHHHHHHHHHHHHcCCch--HHHHHHHH----hhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCce
Q 009896 366 AQNEEVESVVSKRYGRDA--YRIFRLLS----KSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQS 439 (523)
Q Consensus 366 lr~~~le~~v~~~~G~~a--~RI~r~L~----~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQEvpk~~~~~~ 439 (523)
..-..+.+.+...||-.. ++|+.+|. ..|.+ ..++|++...++...+=..+.+|.+.|||.=+.-| ...|
T Consensus 8 ~~~~~~~~~l~~~~~ls~~q~~vL~~l~~~~~~~~~~-t~~eL~~~l~~~~stvs~~i~~Le~kg~I~r~~~~---~D~R 83 (109)
T TIGR01889 8 LYIKSLKRYLKKEFNLSLEELLILYYLGKLENNEGKL-TLKEIIKEILIKQSALVKIIKKLSKKGYLSKERSE---DDER 83 (109)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHHhhhccCCcC-cHHHHHHHHCCCHHHHHHHHHHHHHCCCEeccCCc---ccCC
Confidence 334456666776666544 56777776 34567 99999999999999999999999999999322111 4466
Q ss_pred EEEEEEEchH-HHHHHHHHHHHH
Q 009896 440 QFLLWKVNRQ-ILWKHVLDEMFH 461 (523)
Q Consensus 440 t~~lw~v~~~-~~~~~~l~~~~k 461 (523)
.+++.-...- .....+.+.+++
T Consensus 84 ~~~i~lT~~G~~~~~~~~~~~~~ 106 (109)
T TIGR01889 84 KVIISINKEQRSKIESLISEIEQ 106 (109)
T ss_pred eEEEEECHHHHHHHHHHHHHHHH
Confidence 6655544332 233444444443
No 78
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=78.51 E-value=3.3 Score=30.76 Aligned_cols=51 Identities=18% Similarity=0.286 Sum_probs=43.1
Q ss_pred chHHHHHHHHhhCC--CcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEec
Q 009896 382 DAYRIFRLLSKSGR--LLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVV 433 (523)
Q Consensus 382 ~a~RI~r~L~~k~~--l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQEvpk 433 (523)
.-++|+..|...+. + ...+|++...+++..+-.++.+|.+.|||+-..-|.
T Consensus 6 ~q~~vL~~l~~~~~~~~-t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~~~~~ 58 (62)
T PF12802_consen 6 SQFRVLMALARHPGEEL-TQSELAERLGISKSTVSRIVKRLEKKGLVERERDPG 58 (62)
T ss_dssp HHHHHHHHHHHSTTSGE-EHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE-SS
T ss_pred HHHHHHHHHHHCCCCCc-CHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCCC
Confidence 45788888888777 7 999999999999999999999999999998765543
No 79
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=78.38 E-value=9 Score=28.91 Aligned_cols=57 Identities=18% Similarity=0.280 Sum_probs=39.5
Q ss_pred HHHHHH-hcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEec
Q 009896 25 VCECLL-RKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVL 84 (523)
Q Consensus 25 V~~~Ll-~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~ 84 (523)
|-.+|. ..|++|..+|+..++++...+...+-.|+.+|+|.-...+.++ ...+|.+-
T Consensus 8 vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~~~~~d~---R~~~~~LT 65 (68)
T PF13463_consen 8 VLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLVEKERDPHDK---RSKRYRLT 65 (68)
T ss_dssp HHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEESSCT---TSEEEEE-
T ss_pred HHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecCCCCcC---CeeEEEeC
Confidence 444555 6899999999999999999999999999999999733333322 23566653
No 80
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=77.99 E-value=6.5 Score=29.73 Aligned_cols=50 Identities=18% Similarity=0.341 Sum_probs=39.4
Q ss_pred HHHHHHHH-hhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecC
Q 009896 384 YRIFRLLS-KSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVT 434 (523)
Q Consensus 384 ~RI~r~L~-~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQEvpk~ 434 (523)
+.|++.|. .++.+ ...+|++...++...+...+.+|.+.|||+-+.-|..
T Consensus 6 ~~vL~~l~~~~~~~-t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~~~~~d 56 (68)
T PF13463_consen 6 WQVLRALAHSDGPM-TQSDLAERLGISKSTVSRIIKKLEEKGLVEKERDPHD 56 (68)
T ss_dssp HHHHHHHT--TS-B-EHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEESSC
T ss_pred HHHHHHHHccCCCc-CHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecCCCCc
Confidence 56777776 56777 9999999999999999999999999999977666543
No 81
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=77.95 E-value=8.3 Score=34.80 Aligned_cols=66 Identities=12% Similarity=-0.009 Sum_probs=50.5
Q ss_pred CchHHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceE-EEEecCC---CCceEEEEEEEc
Q 009896 381 RDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLM-EKLVVTG---ARQSQFLLWKVN 447 (523)
Q Consensus 381 ~~a~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~l-QEvpk~~---~~~~t~~lw~v~ 447 (523)
..=.+|++.|...|.. .-.+|++...++...++.-+-+|.+.|+|.- .-+.... .+...+..+.++
T Consensus 9 ~~D~~Il~~Lq~d~R~-s~~eiA~~lglS~~tV~~Ri~rL~~~GvI~~~~~~v~~~~lg~~~~a~v~v~v~ 78 (153)
T PRK11179 9 NLDRGILEALMENART-PYAELAKQFGVSPGTIHVRVEKMKQAGIITGTRVDVNPKQLGYDVCCFIGIILK 78 (153)
T ss_pred HHHHHHHHHHHHcCCC-CHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeEEEEECHHHcCCCEEEEEEEEEc
Confidence 3446899999999999 9999999999999999999999999999973 3232222 333444555564
No 82
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=77.68 E-value=3.3 Score=33.41 Aligned_cols=46 Identities=22% Similarity=0.359 Sum_probs=40.7
Q ss_pred chHHHHHHHHhh-CCCcchhhhhhhcCCCcccHHHHHHHHhhcccceE
Q 009896 382 DAYRIFRLLSKS-GRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLM 428 (523)
Q Consensus 382 ~a~RI~r~L~~k-~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~l 428 (523)
.+.+|+.+|... +.+ .-.+|++..-+|...++..|..|.+.|||.-
T Consensus 6 r~~~Il~~l~~~~~~~-t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~ 52 (91)
T smart00346 6 RGLAVLRALAEEPGGL-TLAELAERLGLSKSTAHRLLNTLQELGYVEQ 52 (91)
T ss_pred HHHHHHHHHHhCCCCc-CHHHHHHHhCCCHHHHHHHHHHHHHCCCeee
Confidence 467888888776 566 9999999999999999999999999999953
No 83
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=77.43 E-value=39 Score=31.64 Aligned_cols=62 Identities=15% Similarity=0.100 Sum_probs=48.7
Q ss_pred HHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCceEEEEEEEchH
Q 009896 384 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQ 449 (523)
Q Consensus 384 ~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQEvpk~~~~~~t~~lw~v~~~ 449 (523)
++|+-+|..++.+ .+++|++...++...+-.++.+|.+.|||.-+.-| ...|..+++-.+.=
T Consensus 48 ~~iL~~L~~~~~i-tq~eLa~~l~l~~sTvtr~l~rLE~kGlI~R~~~~---~DrR~~~I~LTekG 109 (185)
T PRK13777 48 HHILWIAYHLKGA-SISEIAKFGVMHVSTAFNFSKKLEERGYLTFSKKE---DDKRNTYIELTEKG 109 (185)
T ss_pred HHHHHHHHhCCCc-CHHHHHHHHCCCHhhHHHHHHHHHHCCCEEecCCC---CCCCeeEEEECHHH
Confidence 4777777777777 99999999999999999999999999999432222 55777777766543
No 84
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=77.32 E-value=4.9 Score=39.64 Aligned_cols=42 Identities=12% Similarity=0.096 Sum_probs=37.6
Q ss_pred HHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 24 KVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 24 ~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
.|-++|...+++|+.+|++.+++|.+.+..-|-.|.++|+|.
T Consensus 18 ~IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~ 59 (257)
T PRK15090 18 GILQALGEEREIGITELSQRVMMSKSTVYRFLQTMKTLGYVA 59 (257)
T ss_pred HHHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 455556677889999999999999999999999999999997
No 85
>PHA00738 putative HTH transcription regulator
Probab=77.07 E-value=8.3 Score=32.63 Aligned_cols=61 Identities=15% Similarity=0.074 Sum_probs=49.7
Q ss_pred HHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEechhhHH
Q 009896 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFDNIL 89 (523)
Q Consensus 23 ~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~~~~il 89 (523)
-+|...|...+.++..+|....+++...|-+=|-+|-+-|+|...... ...||+++.+.-.
T Consensus 15 r~IL~lL~~~e~~~V~eLae~l~lSQptVS~HLKvLreAGLV~srK~G------r~vyY~Ln~~~~~ 75 (108)
T PHA00738 15 RKILELIAENYILSASLISHTLLLSYTTVLRHLKILNEQGYIELYKEG------RTLYAKIRENSKE 75 (108)
T ss_pred HHHHHHHHHcCCccHHHHHHhhCCCHHHHHHHHHHHHHCCceEEEEEC------CEEEEEECCCccH
Confidence 357777776678999999999999999999999999999999833222 3579999988643
No 86
>PF10771 DUF2582: Protein of unknown function (DUF2582); InterPro: IPR019707 This entry represents conserved proteins found in bacteria and archaea. The function is not known. ; PDB: 2L02_B 2L01_A.
Probab=76.92 E-value=2.3 Score=32.60 Aligned_cols=55 Identities=16% Similarity=0.267 Sum_probs=48.4
Q ss_pred HHcCCchHHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEe
Q 009896 377 KRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLV 432 (523)
Q Consensus 377 ~~~G~~a~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQEvp 432 (523)
+..|..|..||++|..+|.+ +-++|.+.+-++.+++--.+-=|.++|=|.+.+..
T Consensus 4 ~~IG~nAG~Vw~~L~~~~~~-s~~el~k~~~l~~~~~~~AiGWLarE~KI~~~~~~ 58 (65)
T PF10771_consen 4 ENIGENAGKVWQLLNENGEW-SVSELKKATGLSDKEVYLAIGWLARENKIEFEEKN 58 (65)
T ss_dssp HHHHHHHHHHHHHHCCSSSE-EHHHHHHHCT-SCHHHHHHHHHHHCTTSEEEEEET
T ss_pred hHHHHHHHHHHHHHhhCCCc-CHHHHHHHhCcCHHHHHHHHHHHhccCceeEEeeC
Confidence 44788999999999887777 99999999999999999999999999999887654
No 87
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=76.66 E-value=45 Score=28.32 Aligned_cols=65 Identities=8% Similarity=0.088 Sum_probs=50.1
Q ss_pred hhHHHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEechhh
Q 009896 20 DLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFDN 87 (523)
Q Consensus 20 ~~v~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~~~~ 87 (523)
..--.|..+|..+|++|..+|++.++++...|-..|-.|...|+|.-...+.+ .+ ...|.+...+
T Consensus 28 ~~q~~iL~~l~~~~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~~~~D--~R-~~~v~LT~~G 92 (118)
T TIGR02337 28 EQQWRILRILAEQGSMEFTQLANQACILRPSLTGILARLERDGLVTRLKASND--QR-RVYISLTPKG 92 (118)
T ss_pred HHHHHHHHHHHHcCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeccCCCC--CC-eeEEEECHhH
Confidence 33446888888999999999999999999999999999999999983333322 12 3566666554
No 88
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=76.63 E-value=4.3 Score=28.71 Aligned_cols=43 Identities=23% Similarity=0.377 Sum_probs=37.7
Q ss_pred HHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceE
Q 009896 385 RIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLM 428 (523)
Q Consensus 385 RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~l 428 (523)
.|++.|..++.+ ...+|++..-++...++..|..|.+.|+|.-
T Consensus 4 ~il~~l~~~~~~-s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~ 46 (53)
T smart00420 4 QILELLAQQGKV-SVEELAELLGVSEMTIRRDLNKLEEQGLLTR 46 (53)
T ss_pred HHHHHHHHcCCc-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 466777677776 9999999999999999999999999999964
No 89
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=75.39 E-value=7.3 Score=29.25 Aligned_cols=35 Identities=31% Similarity=0.436 Sum_probs=33.3
Q ss_pred hcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 31 RKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 31 ~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
..+++|..+|+..++++...|...|-.|.+.|+|.
T Consensus 22 ~~~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~ 56 (67)
T cd00092 22 VQLPLTRQEIADYLGLTRETVSRTLKELEEEGLIS 56 (67)
T ss_pred ccCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 46889999999999999999999999999999997
No 90
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=74.81 E-value=4.6 Score=29.95 Aligned_cols=41 Identities=24% Similarity=0.400 Sum_probs=38.3
Q ss_pred HHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccc
Q 009896 385 RIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYL 426 (523)
Q Consensus 385 RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v 426 (523)
.|+.+|..++.+ .-+++++.--++...+|.-|..|.+.|+|
T Consensus 4 ~Il~~l~~~~~~-s~~ela~~~~VS~~TiRRDl~~L~~~g~i 44 (57)
T PF08220_consen 4 QILELLKEKGKV-SVKELAEEFGVSEMTIRRDLNKLEKQGLI 44 (57)
T ss_pred HHHHHHHHcCCE-EHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence 578888888888 99999999999999999999999999997
No 91
>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea. Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....
Probab=74.42 E-value=8 Score=33.05 Aligned_cols=53 Identities=17% Similarity=0.304 Sum_probs=43.5
Q ss_pred hHHHHHHHHHHHHcCcCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccceec
Q 009896 106 DQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERC 162 (523)
Q Consensus 106 G~~a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~~~~i~~~f~~Lv~~~fi~~v 162 (523)
|+.-..||+.|-.+|.++..++.+.+....+ -+...+...+.+|++.|||.+-
T Consensus 2 s~~E~~IM~~lW~~~~~t~~eI~~~l~~~~~----~~~sTv~t~L~rL~~Kg~l~~~ 54 (115)
T PF03965_consen 2 SDLELEIMEILWESGEATVREIHEALPEERS----WAYSTVQTLLNRLVEKGFLTRE 54 (115)
T ss_dssp -HHHHHHHHHHHHHSSEEHHHHHHHHCTTSS------HHHHHHHHHHHHHTTSEEEE
T ss_pred CHHHHHHHHHHHhCCCCCHHHHHHHHHhccc----cchhHHHHHHHHHHhCCceeEe
Confidence 5666789999999999999999999765422 2678899999999999999886
No 92
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=74.32 E-value=7 Score=38.37 Aligned_cols=42 Identities=17% Similarity=0.208 Sum_probs=35.9
Q ss_pred HHHHHHHhcCC-CcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 24 KVCECLLRKGP-LTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 24 ~V~~~Ll~~G~-ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
.|-.+|...+. +++.+|.+.+++|++.+..-|..|+++|+|.
T Consensus 8 ~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL~~~G~v~ 50 (246)
T COG1414 8 AILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTLVELGYVE 50 (246)
T ss_pred HHHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEE
Confidence 45556665443 6799999999999999999999999999998
No 93
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=74.10 E-value=4.4 Score=32.49 Aligned_cols=47 Identities=26% Similarity=0.264 Sum_probs=38.4
Q ss_pred chHHHHHHHHhhCC--CcchhhhhhhcCCCcccHHHHHHHHhhcccceE
Q 009896 382 DAYRIFRLLSKSGR--LLETDKISDTTFVEKKDAPKILYKLWKDGYLLM 428 (523)
Q Consensus 382 ~a~RI~r~L~~k~~--l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~l 428 (523)
-|.|++-.|...+. .+.-++|++..-+|...+++++.+|.+.|+|+.
T Consensus 9 ~Al~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s 57 (83)
T PF02082_consen 9 YALRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIES 57 (83)
T ss_dssp HHHHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEe
Confidence 47788888865543 249999999999999999999999999999844
No 94
>PF02295 z-alpha: Adenosine deaminase z-alpha domain; InterPro: IPR000607 Double-stranded RNA-specific adenosine deaminase (3.5 from EC) converts multiple adenosines to inosines and creates I/U mismatched base pairs in double-helical RNA substrates without apparent sequence specificity. DRADA has been found to modify adenosines in AU-rich regions more frequently, probably due to the relative ease of melting A/U base pairs compared to G/C base pairs. The protein functions to modify viral RNA genomes, and may be responsible for hypermutation of certain negative-stranded viruses. DRADA edits the mRNAs for the glutamate receptor subunits by site-selective adenosine deamination. The DRADA repeat is also found in viral E3 proteins, which contain a double-stranded RNA-binding domain.; GO: 0003723 RNA binding, 0003726 double-stranded RNA adenosine deaminase activity; PDB: 1OYI_A 3EYI_A 2L4M_A 2HEO_D 1J75_A 1SFU_B 3IRR_B 2ACJ_C 3F22_B 2L54_A ....
Probab=73.59 E-value=3.3 Score=31.90 Aligned_cols=43 Identities=26% Similarity=0.420 Sum_probs=33.4
Q ss_pred HHHHHHHhhCCCcchhhhhhhcCC--CcccHHHHHHHHhhcccceE
Q 009896 385 RIFRLLSKSGRLLETDKISDTTFV--EKKDAPKILYKLWKDGYLLM 428 (523)
Q Consensus 385 RI~r~L~~k~~l~eek~i~~~ami--~~k~~R~~L~~L~~~g~v~l 428 (523)
||+.+|...|.. .-..++....+ |.|++-..||+|.+.|.|.-
T Consensus 8 ~Il~~L~~~g~~-~a~~ia~~~~L~~~kk~VN~~LY~L~k~g~v~k 52 (66)
T PF02295_consen 8 KILDFLKELGGS-TATAIAKALGLSVPKKEVNRVLYRLEKQGKVCK 52 (66)
T ss_dssp HHHHHHHHHTSS-EEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHhcCCc-cHHHHHHHhCcchhHHHHHHHHHHHHHCCCEee
Confidence 688888877744 66666665554 58999999999999999953
No 95
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=73.08 E-value=9.1 Score=31.89 Aligned_cols=53 Identities=17% Similarity=0.234 Sum_probs=43.2
Q ss_pred hhchhHHHHHHHHHh----cCCCcHHHHHhhcCCCHHHHHHHHHHHHhhccccccccc
Q 009896 17 HFGDLVAKVCECLLR----KGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTE 70 (523)
Q Consensus 17 ~FG~~v~~V~~~Ll~----~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~~ 70 (523)
..+++-.+|..+|-. .-.+++.+|.+.++++..+||.+|--|+-.|.|+ .+.+
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IY-sTiD 100 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNEGHIY-STID 100 (102)
T ss_dssp -S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTTSEE-ESSS
T ss_pred CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhCCeEe-cccC
Confidence 467888899999987 3358999999999999999999999999999996 5443
No 96
>PRK06474 hypothetical protein; Provisional
Probab=72.80 E-value=9.9 Score=35.40 Aligned_cols=68 Identities=12% Similarity=0.284 Sum_probs=51.1
Q ss_pred hHHHHHHHHHhcCC-CcHHHHHhhc-CCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEechhhHH
Q 009896 21 LVAKVCECLLRKGP-LTRQNVKRYT-ELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFDNIL 89 (523)
Q Consensus 21 ~v~~V~~~Ll~~G~-ltl~~l~~~t-~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~~~~il 89 (523)
.=-+|..+|..+|. +|..+|.... +++...|-.-|-.|.++|+|.......-+| ...-+|.++.+.+-
T Consensus 12 ~R~~Il~~L~~~~~~~ta~el~~~l~~is~aTvYrhL~~L~e~GLI~~~~~~~~~~-~~ek~y~~~~~~~~ 81 (178)
T PRK06474 12 VRMKICQVLMRNKEGLTPLELVKILKDVPQATLYRHLQTMVDSGILHVVKEKKVRS-VSEKYYAINEEDAK 81 (178)
T ss_pred HHHHHHHHHHhCCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEEeecccccC-ceeEEEEeccceee
Confidence 34578888988876 9999998887 799999999999999999998443322111 22358888887643
No 97
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=72.57 E-value=51 Score=28.69 Aligned_cols=101 Identities=21% Similarity=0.196 Sum_probs=67.6
Q ss_pred hchhHHHHHHHHHhcCCCcHHHHHhh----cCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEechhhHHHHhc
Q 009896 18 FGDLVAKVCECLLRKGPLTRQNVKRY----TELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFDNILHRVR 93 (523)
Q Consensus 18 FG~~v~~V~~~Ll~~G~ltl~~l~~~----t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~~~~il~rlR 93 (523)
-|++=..|-.+|=.+|+.|..+|... ...+++.|+.-|-.|..-|+|...... ....|++..+.--++-
T Consensus 4 Is~aE~eVM~ilW~~~~~t~~eI~~~l~~~~ews~sTV~TLl~RL~KKg~l~~~kdg------r~~~y~pL~~~~~~~~- 76 (123)
T COG3682 4 ISAAEWEVMEILWSRGPATVREIIEELPADREWSYSTVKTLLNRLVKKGLLTRKKDG------RAFRYSPLLTRDQYVA- 76 (123)
T ss_pred ccHHHHHHHHHHHHcCCccHHHHHHHHhhcccccHHHHHHHHHHHHhccchhhhhcC------CeeeeecccCHHHHHH-
Confidence 47777899999999999999999766 458899999999999999999833332 2467887766543321
Q ss_pred hhhHHHHHHHHhhHHHHHHHHHHHHcCcCCHHH
Q 009896 94 FAKFLTILSQEFDQQCVELVQGLLEHGRLTLKQ 126 (523)
Q Consensus 94 ~p~~i~~i~~~~G~~a~~I~~~lL~~G~~~~~~ 126 (523)
+.--.++.+-|+.....++.++..+-.++..+
T Consensus 77 -~~~~~~l~k~~d~~~~~lv~~F~~~~~l~~~e 108 (123)
T COG3682 77 -GESQDLLDKICDGGLASLVAHFAEKEKLTADE 108 (123)
T ss_pred -HHHHHHHHHHHcccchHHHHHHHHhccCCHHH
Confidence 22223333444444455555555555555443
No 98
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=72.55 E-value=5 Score=35.95 Aligned_cols=68 Identities=18% Similarity=0.253 Sum_probs=53.1
Q ss_pred CCchHHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCC----CCceEEEEEEEch
Q 009896 380 GRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTG----ARQSQFLLWKVNR 448 (523)
Q Consensus 380 G~~a~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQEvpk~~----~~~~t~~lw~v~~ 448 (523)
...-.||+++|...+.. ...+|++...+++..++..+.+|.+.|+|.--..--.. .+-..|..+.+..
T Consensus 7 D~~D~~IL~~L~~d~r~-~~~eia~~lglS~~~v~~Ri~~L~~~GiI~~~~~~v~~~~lg~~~~a~v~v~~~~ 78 (154)
T COG1522 7 DDIDRRILRLLQEDARI-SNAELAERVGLSPSTVLRRIKRLEEEGVIKGYTAVLDPEKLGLDLTAFVEVKLER 78 (154)
T ss_pred cHHHHHHHHHHHHhCCC-CHHHHHHHHCCCHHHHHHHHHHHHHCCceeeEEEEECHHHcCCCEEEEEEEEecC
Confidence 34557999999998887 99999999999999999999999999999655443221 1112677777775
No 99
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=72.08 E-value=7.7 Score=32.07 Aligned_cols=49 Identities=22% Similarity=0.282 Sum_probs=40.6
Q ss_pred hhchhHHHHHHHHH-----------hcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 17 HFGDLVAKVCECLL-----------RKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 17 ~FG~~v~~V~~~Ll-----------~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
.|-++.++++.+|+ ...++|-.+|+..+++++..|..+|-.|.+.|+|.
T Consensus 19 ~~~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~ 78 (95)
T TIGR01610 19 PGADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSDAIKSLARRRIIF 78 (95)
T ss_pred HhCCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence 35566666666555 35688999999999999999999999999999997
No 100
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=72.04 E-value=5.2 Score=29.30 Aligned_cols=42 Identities=21% Similarity=0.329 Sum_probs=36.2
Q ss_pred HHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceE
Q 009896 385 RIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLM 428 (523)
Q Consensus 385 RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~l 428 (523)
+|+++|. .+.. ...+|++...++...++..|.+|.+.|+|..
T Consensus 1 ~il~~l~-~~~~-~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~ 42 (66)
T smart00418 1 KILKLLA-EGEL-CVCELAEILGLSQSTVSHHLKKLREAGLVES 42 (66)
T ss_pred CHHHHhh-cCCc-cHHHHHHHHCCCHHHHHHHHHHHHHCCCeee
Confidence 3667775 5666 8899999999999999999999999999963
No 101
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=71.99 E-value=34 Score=30.33 Aligned_cols=42 Identities=17% Similarity=0.116 Sum_probs=37.9
Q ss_pred HHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 24 KVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 24 ~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
.|...|...|++|..+|+...++++..|-..+-.|.+.|+|.
T Consensus 44 ~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~ 85 (144)
T PRK11512 44 KVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCKGWVE 85 (144)
T ss_pred HHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 455566678899999999999999999999999999999998
No 102
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=71.82 E-value=50 Score=28.98 Aligned_cols=70 Identities=16% Similarity=0.257 Sum_probs=48.5
Q ss_pred HHHHHHHHhhCCCcchhhhhhhc----CCCcccHHHHHHHHhhcccceEEEEecCCCCceEEEEEE--EchHHHHHHHHH
Q 009896 384 YRIFRLLSKSGRLLETDKISDTT----FVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWK--VNRQILWKHVLD 457 (523)
Q Consensus 384 ~RI~r~L~~k~~l~eek~i~~~a----mi~~k~~R~~L~~L~~~g~v~lQEvpk~~~~~~t~~lw~--v~~~~~~~~~l~ 457 (523)
.-|+++|-..|.. ..++|.+.. -+....++.+|.+|.+.|||..+ +. +|+ |+|+ ++.+........
T Consensus 7 ~~VM~vlW~~~~~-t~~eI~~~l~~~~~~~~tTv~T~L~rL~~KG~v~~~---k~---gr~-~~Y~p~vs~ee~~~~~~~ 78 (130)
T TIGR02698 7 WEVMRVVWTLGET-TSRDIIRILAEKKDWSDSTIKTLLGRLVDKGCLTTE---KE---GRK-FIYTALVSEDEAVENAAQ 78 (130)
T ss_pred HHHHHHHHcCCCC-CHHHHHHHHhhccCCcHHHHHHHHHHHHHCCceeee---cC---CCc-EEEEecCCHHHHHHHHHH
Confidence 3467777677776 777755542 57788999999999999999654 22 343 3455 777777666666
Q ss_pred HHHH
Q 009896 458 EMFH 461 (523)
Q Consensus 458 ~~~k 461 (523)
++..
T Consensus 79 ~~~~ 82 (130)
T TIGR02698 79 ELFS 82 (130)
T ss_pred HHHH
Confidence 5554
No 103
>PF09904 HTH_43: Winged helix-turn helix; InterPro: IPR017162 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.; PDB: 3KE2_B.
Probab=71.65 E-value=6.8 Score=31.95 Aligned_cols=63 Identities=11% Similarity=0.132 Sum_probs=39.5
Q ss_pred HHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEechhhHHHH
Q 009896 27 ECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFDNILHR 91 (523)
Q Consensus 27 ~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~~~~il~r 91 (523)
..|+.+|.-+++.|...|++|.+.++.+|..|--.++..-|.-+ |...+.-||.+.-=+++.+
T Consensus 14 a~li~~~~~nvp~L~~~TGmPrRT~Qd~i~aL~~~~I~~~Fvq~--G~R~~~GyY~i~~WG~id~ 76 (90)
T PF09904_consen 14 AYLIDSGERNVPALMEATGMPRRTIQDTIKALPELGIECEFVQD--GERNNAGYYRISDWGPIDR 76 (90)
T ss_dssp HHHHHHS-B-HHHHHHHH---HHHHHHHHHGGGGGT-EEEEE----TTS-S--EEEEEE-TTB-H
T ss_pred HHHHhcCCccHHHHHHHhCCCHhHHHHHHHHhhcCCeEEEEEec--CccCCCCcEEeeecCCCCH
Confidence 46788888899999999999999999999999999988766652 2222344888765455443
No 104
>PF08679 DsrD: Dissimilatory sulfite reductase D (DsrD); InterPro: IPR014793 The structure of the dissimilatory sulphite reductase D (DsrD) protein has shown it to contain a winged-helix motif similar to those found in DNA binding proteins []. The structure suggests a possible role for DsrD in transcription or translation of genes, which catalyse dissimilatory sulphite reduction. ; PDB: 1WQ2_B 1UCR_B.
Probab=70.85 E-value=10 Score=29.01 Aligned_cols=42 Identities=12% Similarity=0.276 Sum_probs=34.1
Q ss_pred cHHHHHh-hcCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEe
Q 009896 36 TRQNVKR-YTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVV 83 (523)
Q Consensus 36 tl~~l~~-~t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~ 83 (523)
=+.++.+ .....++.||+++-.||+-+.+.||... +.|+|-+
T Consensus 21 YfkD~~k~~pd~k~R~vKKi~~~LV~Eg~l~yWSSG------STTmYgl 63 (67)
T PF08679_consen 21 YFKDFYKAFPDAKPREVKKIVNELVNEGKLEYWSSG------STTMYGL 63 (67)
T ss_dssp EHHHHHHH-TTS-HHHHHHHHHHHHHTTSEEEEEET------TEEEEEE
T ss_pred eHHHHHHHCCCcCHHHHHHHHHHHHhhCeEEEEcCC------CcEEecC
Confidence 4788877 6789999999999999999999989874 4578865
No 105
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=70.76 E-value=53 Score=31.55 Aligned_cols=119 Identities=8% Similarity=-0.006 Sum_probs=88.0
Q ss_pred hHHHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEechhhHHHHhchhhHHHH
Q 009896 21 LVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFDNILHRVRFAKFLTI 100 (523)
Q Consensus 21 ~v~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~~~~il~rlR~p~~i~~ 100 (523)
.=..|.++...+++..+.++....+++.+..|-=|-+|-.|+++....... ..-||-+|.+- .+.=
T Consensus 102 ~R~~Iy~~i~~nPG~~lsEl~~nl~i~R~TlRyhlriLe~~~li~a~~~~g-----~~~yfpa~~t~------~~~e--- 167 (240)
T COG3398 102 KRDGIYNYIKPNPGFSLSELRANLYINRSTLRYHLRILESNPLIEAGRVGG-----ALRYFPADMTY------GEAE--- 167 (240)
T ss_pred hHHHHHHHhccCCCccHHHHHHhcCCChHHHHHHHHHHHhCcchhhhccCC-----ceEEccCCCCc------ccch---
Confidence 345789999999999999999999999999999999999999998555532 12233332210 0000
Q ss_pred HHHHhhHHHHHHHHHHHHcCcCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhccccee
Q 009896 101 LSQEFDQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVER 161 (523)
Q Consensus 101 i~~~~G~~a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~~~~i~~~f~~Lv~~~fi~~ 161 (523)
+-..=|.....|+.++..++..+..++-.... .+.+.+.=...+|-+-|+|..
T Consensus 168 ~~~Lkn~~~k~I~~eiq~~~~~t~~~ia~~l~--------ls~aTV~~~lk~l~~~Gii~~ 220 (240)
T COG3398 168 VLSLKNETSKAIIYEIQENKCNTNLLIAYELN--------LSVATVAYHLKKLEELGIIPE 220 (240)
T ss_pred HHHhhchhHHHHHHHHhcCCcchHHHHHHHcC--------ccHHHHHHHHHHHHHcCCCcc
Confidence 22234677899999999999999888765532 356778888899998888743
No 106
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=70.19 E-value=32 Score=33.82 Aligned_cols=71 Identities=17% Similarity=0.158 Sum_probs=56.0
Q ss_pred chHHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCceEEEEEEEchHHHHHHHHHHHH
Q 009896 382 DAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQILWKHVLDEMF 460 (523)
Q Consensus 382 ~a~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQEvpk~~~~~~t~~lw~v~~~~~~~~~l~~~~ 460 (523)
-=++++..|+..|.. .-++|++.+.+|..-+=++|-.|-..|||+.| +++.-.+--++++.+.....+++-
T Consensus 17 yEa~vY~aLl~~g~~-tA~eis~~sgvP~~kvY~vl~sLe~kG~v~~~-------~g~P~~y~av~p~~~i~~~~~~~~ 87 (247)
T COG1378 17 YEAKVYLALLCLGEA-TAKEISEASGVPRPKVYDVLRSLEKKGLVEVI-------EGRPKKYRAVPPEELIERIKEELQ 87 (247)
T ss_pred HHHHHHHHHHHhCCc-cHHHHHHHcCCCchhHHHHHHHHHHCCCEEee-------CCCCceEEeCCHHHHHHHHHHHHH
Confidence 347889999999999 99999999999999999999999999999876 233444556777765554444443
No 107
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=70.07 E-value=31 Score=27.78 Aligned_cols=48 Identities=19% Similarity=0.323 Sum_probs=42.4
Q ss_pred CchHHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEE
Q 009896 381 RDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLME 429 (523)
Q Consensus 381 ~~a~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQ 429 (523)
....+|+.+|...+.+ ..++|++..-++...+...+.+|.+.|+|...
T Consensus 10 ~~~~~il~~l~~~~~~-~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~ 57 (101)
T smart00347 10 PTQFLVLRILYEEGPL-SVSELAKRLGVSPSTVTRVLDRLEKKGLIRRL 57 (101)
T ss_pred HHHHHHHHHHHHcCCc-CHHHHHHHHCCCchhHHHHHHHHHHCCCeEec
Confidence 4457889999877777 99999999999999999999999999999654
No 108
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=69.82 E-value=10 Score=33.71 Aligned_cols=45 Identities=9% Similarity=0.114 Sum_probs=41.0
Q ss_pred hHHHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 21 LVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 21 ~v~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
....|...+-..|..++.+|++..++++..|...|-.|.+.|+|.
T Consensus 9 yL~~I~~l~~~~~~~~~~ela~~l~vs~~svs~~l~~L~~~Gli~ 53 (142)
T PRK03902 9 YIEQIYLLIEEKGYARVSDIAEALSVHPSSVTKMVQKLDKDEYLI 53 (142)
T ss_pred HHHHHHHHHhcCCCcCHHHHHHHhCCChhHHHHHHHHHHHCCCEE
Confidence 456677778888999999999999999999999999999999997
No 109
>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY. This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.
Probab=69.50 E-value=8.5 Score=37.41 Aligned_cols=59 Identities=17% Similarity=0.201 Sum_probs=48.6
Q ss_pred HHHHHHHHHhhhchhHHHHHHHHHh-cCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 7 TKHAVHVITNHFGDLVAKVCECLLR-KGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 7 ~~Lc~~iv~~~FG~~v~~V~~~Ll~-~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
+++|..-+...==+.+.+|.+.|-. .|+++-.+|+...++++..|++++-.|-+-|++.
T Consensus 170 Vq~Ai~tLSySEleAv~~IL~~L~~~egrlse~eLAerlGVSRs~ireAlrkLE~aGvIe 229 (251)
T TIGR02787 170 VQMAINTLSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIE 229 (251)
T ss_pred HHHHHHhccHhHHHHHHHHHHHhccccccccHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 3444433322222678999999998 4999999999999999999999999999999998
No 110
>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=69.16 E-value=12 Score=25.89 Aligned_cols=36 Identities=19% Similarity=0.231 Sum_probs=28.3
Q ss_pred HHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHH
Q 009896 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVL 58 (523)
Q Consensus 23 ~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vL 58 (523)
.+|...|...|+.|+.+|.+.+|+++..|..-+--|
T Consensus 6 ~~Il~~Lq~d~r~s~~~la~~lglS~~~v~~Ri~rL 41 (42)
T PF13404_consen 6 RKILRLLQEDGRRSYAELAEELGLSESTVRRRIRRL 41 (42)
T ss_dssp HHHHHHHHH-TTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHcCCccHHHHHHHHCcCHHHHHHHHHHh
Confidence 467888999999999999999999999998766543
No 111
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=69.12 E-value=27 Score=29.71 Aligned_cols=49 Identities=22% Similarity=0.448 Sum_probs=42.1
Q ss_pred CCchHHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEE
Q 009896 380 GRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLME 429 (523)
Q Consensus 380 G~~a~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQ 429 (523)
+..-.+|+.+|..++.+ ...+|++...++...+-..+.+|.+.|||.-+
T Consensus 27 t~~q~~iL~~l~~~~~~-t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~ 75 (118)
T TIGR02337 27 TEQQWRILRILAEQGSM-EFTQLANQACILRPSLTGILARLERDGLVTRL 75 (118)
T ss_pred CHHHHHHHHHHHHcCCc-CHHHHHHHhCCCchhHHHHHHHHHHCCCEEec
Confidence 34445788888777777 99999999999999999999999999999554
No 112
>PF04079 DUF387: Putative transcriptional regulators (Ypuh-like); InterPro: IPR005234 This family represents ScpB, which along with ScpA (IPR003768 from INTERPRO) interacts with SMC in vivo forming a complex that is required for chromosome condensation and segregation [, ]. The SMC-Scp complex appears to be similar to the MukB-MukE-Muk-F complex in Escherichia coli [], where MukB (IPR007406 from INTERPRO) is the homologue of SMC. ScpA and ScpB have little sequence similarity to MukE (IPR007385 from INTERPRO) or MukF (IPR005582 from INTERPRO), they are predicted to be structurally similar, being predominantly alpha-helical with coiled coil regions. In general scpA and scpB form an operon in most bacterial genomes. Flanking genes are highly variable suggesting that the operon has moved throughout evolution. Bacteria containing an smc gene also contain scpA or scpB but not necessarily both. An exception is found in Deinococcus radiodurans, which contains scpB but neither smc nor scpA. In the archaea the gene order SMC-ScpA is conserved in nearly all species, as is the very short distance between the two genes, indicating co-transcription of the both in different archaeal genera and arguing that interaction of the gene products is not confined to the homologues in Bacillus subtilis. It would seem probable that, in light of all the studies, SMC, ScpA and ScpB proteins or homologues act together in chromosome condensation and segregation in all prokaryotes []. ; GO: 0051304 chromosome separation; PDB: 1T6S_B 2Z99_A.
Probab=67.35 E-value=11 Score=34.48 Aligned_cols=130 Identities=15% Similarity=0.191 Sum_probs=77.6
Q ss_pred HHHHHHhccchhcccccccCCccccHHHHHHHhhhhccCCCCCHHHHHHHHHHhccC----C---CCCCCCCeEEEehHH
Q 009896 289 VLSAMLQATSSAEKKVKTKNSVPLSLSSIYEEVIKSEAGRNMTLDHVRASLVQLGEL----S---FVDASSDSYSIDFEK 361 (523)
Q Consensus 289 v~~~~L~~~~~~~~~~~~~~s~~~s~~~I~~~l~~~~~~~~~~~~~i~~~L~~La~~----~---~~~~~~~~y~V~~~~ 361 (523)
+++|+|-.+ +.|++..+|.+.+. + .+.+...|..|... + -...-+|.|.+-.+.
T Consensus 2 ~iEAlLF~s-----------~~pvs~~~La~~l~-~-------~~~v~~~l~~L~~~y~~~~~gl~l~~~~~~y~l~tk~ 62 (159)
T PF04079_consen 2 IIEALLFAS-----------GEPVSIEELAEILG-S-------EDEVEEALEELQEEYNEEDRGLELVEVGGGYRLQTKP 62 (159)
T ss_dssp HHHHHHHH------------SS-B-HHHHHHHCT---------HHHHHHHHHHHHHHHHHCT-SEEEEEETTEEEEEE-G
T ss_pred hhHhhHHHc-----------CCCCCHHHHHHHhC-C-------HHHHHHHHHHHHHHhccCCCCEEEEEECCEEEEEEhH
Confidence 466666654 34799999988884 2 34555555544332 1 113336777766555
Q ss_pred HHHHHHHHHHHHHHHHHcCCchHHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCceEE
Q 009896 362 IIEIAQNEEVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQF 441 (523)
Q Consensus 362 i~~~lr~~~le~~v~~~~G~~a~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQEvpk~~~~~~t~ 441 (523)
-..-.....+..--..++...++.++-++.-+.-+ ...+|.+.=... +...+.+|.+.|+|. ++.+...|+|.+
T Consensus 63 ~~~~~v~~~~~~~~~~~LS~aalEtLAiIAY~QPi-Tr~eIe~IRGv~---s~~~i~~L~e~glI~--~~gr~~~~Grp~ 136 (159)
T PF04079_consen 63 EYAEYVEKLFKKPKPPKLSQAALETLAIIAYKQPI-TRAEIEEIRGVN---SDSVIKTLLERGLIE--EVGRKDTPGRPI 136 (159)
T ss_dssp GGHHHHHHHHCTCCCHHHHHHHHHHHHHHHHH-SE-EHHHHHHHHTS-----HCHHHHHHHTTSEE--EEEE-TTTT--E
T ss_pred HHHHHHHHHhccCccCCCCHHHHHHHHHHHhcCCc-CHHHHHHHcCCC---hHHHHHHHHHCCCEE--ecCcCCCCCCCe
Confidence 44433333333322347777889999999777555 999998887766 788999999999994 456555678765
Q ss_pred EE
Q 009896 442 LL 443 (523)
Q Consensus 442 ~l 443 (523)
.+
T Consensus 137 ly 138 (159)
T PF04079_consen 137 LY 138 (159)
T ss_dssp EE
T ss_pred Ee
Confidence 53
No 113
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=67.33 E-value=14 Score=29.50 Aligned_cols=48 Identities=23% Similarity=0.255 Sum_probs=39.8
Q ss_pred HHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEe
Q 009896 384 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLV 432 (523)
Q Consensus 384 ~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQEvp 432 (523)
+.|+-+|...+.+ +-++|.+..-++.-.....|..|.++|||+.....
T Consensus 3 l~Il~~L~~~~~~-~f~~L~~~l~lt~g~Ls~hL~~Le~~GyV~~~k~~ 50 (80)
T PF13601_consen 3 LAILALLYANEEA-TFSELKEELGLTDGNLSKHLKKLEEAGYVEVEKEF 50 (80)
T ss_dssp HHHHHHHHHHSEE-EHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEE-
T ss_pred HHHHHHHhhcCCC-CHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEEEec
Confidence 3577788777888 99999999999999999999999999999876544
No 114
>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional
Probab=66.95 E-value=14 Score=34.33 Aligned_cols=46 Identities=17% Similarity=0.308 Sum_probs=42.8
Q ss_pred hhHHHHHHHHHhcC-CCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 20 DLVAKVCECLLRKG-PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 20 ~~v~~V~~~Ll~~G-~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
+..++|+..|-++| ++|..+|.+..+++.+.|=..|..|.+-+.|+
T Consensus 4 ~~~~~i~~~l~~~~~~~~a~~i~k~l~i~k~~vNr~LY~L~~~~~v~ 50 (183)
T PHA02701 4 DCASLILTLLSSSGDKLPAKRIAKELGISKHEANRCLYRLLESDAVS 50 (183)
T ss_pred hHHHHHHHHHHhcCCCCcHHHHHHHhCccHHHHHHHHHHHhhcCcEe
Confidence 34678999999999 89999999999999999999999999999997
No 115
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=66.90 E-value=13 Score=26.84 Aligned_cols=48 Identities=17% Similarity=0.246 Sum_probs=37.3
Q ss_pred HHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEe
Q 009896 384 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLV 432 (523)
Q Consensus 384 ~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQEvp 432 (523)
.+|+.+|...+..+.-++|++..-++...++.-+..|-..| +.+.-.|
T Consensus 3 ~~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~-~~I~~~~ 50 (55)
T PF08279_consen 3 KQILKLLLESKEPITAKELAEELGVSRRTIRRDIKELREWG-IPIESKR 50 (55)
T ss_dssp HHHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT--EEEEET
T ss_pred HHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC-CeEEeeC
Confidence 36788886655545999999999999999999999999988 5554443
No 116
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=66.76 E-value=9.5 Score=34.90 Aligned_cols=46 Identities=15% Similarity=0.208 Sum_probs=42.6
Q ss_pred hhHHHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 20 DLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 20 ~~v~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
++=.+|...|...||.|..+|.+.++++...|+.=+--|.+.|++.
T Consensus 14 ~~D~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~GvI~ 59 (164)
T PRK11169 14 RIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQGFIQ 59 (164)
T ss_pred HHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence 3446788999999999999999999999999999999999999997
No 117
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=66.64 E-value=19 Score=31.37 Aligned_cols=49 Identities=24% Similarity=0.369 Sum_probs=42.2
Q ss_pred HHHHHHHHHHHHcCcCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccceecC
Q 009896 107 QQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 163 (523)
Q Consensus 107 ~~a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~~~~i~~~f~~Lv~~~fi~~v~ 163 (523)
+..+.|++-+=++|++|+.|+...... +...++..|.+||..|-|.+..
T Consensus 12 eLk~rIvElVRe~GRiTi~ql~~~TGa--------sR~Tvk~~lreLVa~G~l~~~G 60 (127)
T PF06163_consen 12 ELKARIVELVREHGRITIKQLVAKTGA--------SRNTVKRYLRELVARGDLYRHG 60 (127)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHCC--------CHHHHHHHHHHHHHcCCeEeCC
Confidence 457889999999999999999877543 5778999999999999998864
No 118
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=66.62 E-value=15 Score=29.28 Aligned_cols=45 Identities=11% Similarity=0.130 Sum_probs=41.5
Q ss_pred HHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhccccccc
Q 009896 24 KVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFT 68 (523)
Q Consensus 24 ~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~ 68 (523)
.|-++|-.+|+.++.+|++..+.|+.-|..=|-.|+.-|-|....
T Consensus 6 qlRd~l~~~gr~s~~~Ls~~~~~p~~~VeaMLe~l~~kGkverv~ 50 (78)
T PRK15431 6 QVRDLLALRGRMEAAQISQTLNTPQPMINAMLQQLESMGKAVRIQ 50 (78)
T ss_pred HHHHHHHHcCcccHHHHHHHHCcCHHHHHHHHHHHHHCCCeEeec
Confidence 577899999999999999999999999999999999999998443
No 119
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=66.12 E-value=22 Score=35.39 Aligned_cols=42 Identities=17% Similarity=0.166 Sum_probs=36.2
Q ss_pred HHHHHHHhc-CCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 24 KVCECLLRK-GPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 24 ~V~~~Ll~~-G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
.|.+++-.. +.+|+.+|++.+++|.+.+..-|-.|.++|+|.
T Consensus 29 ~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~ 71 (271)
T PRK10163 29 AILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQAADFVY 71 (271)
T ss_pred HHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 345555544 469999999999999999999999999999997
No 120
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=65.65 E-value=9.1 Score=29.10 Aligned_cols=55 Identities=15% Similarity=0.154 Sum_probs=34.2
Q ss_pred HhhHHHHHHHHHHHHcCcCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccce
Q 009896 104 EFDQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVE 160 (523)
Q Consensus 104 ~~G~~a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~~~~i~~~f~~Lv~~~fi~ 160 (523)
...+.|..|.+.+ .|..|++++++.+.+..+.........+..-+.+|.+.|+|+
T Consensus 14 ~Ln~~a~~Iw~~~--~g~~t~~ei~~~l~~~y~~~~~~~~~dv~~fl~~L~~~glIe 68 (68)
T PF05402_consen 14 TLNETAAFIWELL--DGPRTVEEIVDALAEEYDVDPEEAEEDVEEFLEQLREKGLIE 68 (68)
T ss_dssp ---THHHHHHHH----SSS-HHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT---
T ss_pred cccHHHHHHHHHc--cCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHCcCcC
Confidence 3445666676666 789999999999887654322224677899999999999874
No 121
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=65.38 E-value=14 Score=27.57 Aligned_cols=36 Identities=25% Similarity=0.326 Sum_probs=31.0
Q ss_pred HHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHH
Q 009896 24 KVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLI 59 (523)
Q Consensus 24 ~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLi 59 (523)
.+...|+..+..|+.+|+..++++.+.|++-+--|-
T Consensus 9 ~Ll~~L~~~~~~~~~ela~~l~~S~rti~~~i~~L~ 44 (59)
T PF08280_consen 9 KLLELLLKNKWITLKELAKKLNISERTIKNDINELN 44 (59)
T ss_dssp HHHHHHHHHTSBBHHHHHHHCTS-HHHHHHHHHHHH
T ss_pred HHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHHHHHH
Confidence 567888899999999999999999999999887653
No 122
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=65.18 E-value=10 Score=28.16 Aligned_cols=47 Identities=19% Similarity=0.275 Sum_probs=35.7
Q ss_pred chhHHHHHHHHHh----cCC--CcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 19 GDLVAKVCECLLR----KGP--LTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 19 G~~v~~V~~~Ll~----~G~--ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
.++...+...+.. .|. .|..+|++..+++...|+++|..|.+.|+|.
T Consensus 4 ~~~~~~i~~~i~~~~~~~~~~~~~~~~la~~~~is~~~v~~~l~~L~~~G~i~ 56 (66)
T cd07377 4 EQIADQLREAILSGELKPGDRLPSERELAEELGVSRTTVREALRELEAEGLVE 56 (66)
T ss_pred HHHHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 3444455555443 232 3488999999999999999999999999986
No 123
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=65.07 E-value=27 Score=28.83 Aligned_cols=51 Identities=22% Similarity=0.273 Sum_probs=44.0
Q ss_pred hhHHHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhccccccccc
Q 009896 20 DLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTE 70 (523)
Q Consensus 20 ~~v~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~~ 70 (523)
++.-.|...|-..|+=.-..|++.++++...|+..|--|.+-|+|..+...
T Consensus 7 ~l~~~IL~hl~~~~~Dy~k~ia~~l~~~~~~v~~~l~~Le~~GLler~~g~ 57 (92)
T PF10007_consen 7 PLDLKILQHLKKAGPDYAKSIARRLKIPLEEVREALEKLEEMGLLERVEGK 57 (92)
T ss_pred hhHHHHHHHHHHHCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEecCc
Confidence 445578888888898888899999999999999999999999999965533
No 124
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=64.40 E-value=9.3 Score=31.55 Aligned_cols=36 Identities=11% Similarity=0.201 Sum_probs=32.1
Q ss_pred hCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEE
Q 009896 393 SGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLME 429 (523)
Q Consensus 393 k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQ 429 (523)
...+ .+.+|++.+.++...+.+.|.+|.+.|+|..+
T Consensus 45 ~~~i-s~~eLa~~~g~sr~tVsr~L~~Le~~GlI~r~ 80 (95)
T TIGR01610 45 QDRV-TATVIAELTGLSRTHVSDAIKSLARRRIIFRQ 80 (95)
T ss_pred CCcc-CHHHHHHHHCcCHHHHHHHHHHHHHCCCeeee
Confidence 3456 99999999999999999999999999999643
No 125
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=64.39 E-value=15 Score=36.39 Aligned_cols=43 Identities=23% Similarity=0.166 Sum_probs=37.4
Q ss_pred HHHHHHHHhcC-CCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 23 AKVCECLLRKG-PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 23 ~~V~~~Ll~~G-~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
-.|..+|..++ ++++.+|.+.++++.+.+...|-.|.++|+|.
T Consensus 14 l~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~~~g~v~ 57 (263)
T PRK09834 14 LMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQEEGYVR 57 (263)
T ss_pred HHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 34556666655 59999999999999999999999999999997
No 126
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=64.34 E-value=10 Score=26.20 Aligned_cols=32 Identities=31% Similarity=0.451 Sum_probs=30.4
Q ss_pred CCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 34 PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 34 ~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
+.|..+|++.++++...+...|-.|.++|+|.
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~ 39 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLEKEGLIS 39 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 57899999999999999999999999999997
No 127
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=63.98 E-value=31 Score=30.59 Aligned_cols=63 Identities=8% Similarity=0.095 Sum_probs=48.1
Q ss_pred chHHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCceEEEEEEEch
Q 009896 382 DAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNR 448 (523)
Q Consensus 382 ~a~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQEvpk~~~~~~t~~lw~v~~ 448 (523)
.-++|+..|...+.+ .+++|++...+++..+=..+.+|.+.|||.-+.-| ...|..+++-.+.
T Consensus 41 ~q~~vL~~l~~~~~~-t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~~~~---~DrR~~~l~LT~~ 103 (144)
T PRK11512 41 AQFKVLCSIRCAACI-TPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNP---NDKRGVLVKLTTS 103 (144)
T ss_pred HHHHHHHHHHHcCCC-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCc---ccCCeeEeEEChh
Confidence 335667777666677 99999999999999999999999999999432222 4567777765553
No 128
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=63.87 E-value=11 Score=33.19 Aligned_cols=49 Identities=20% Similarity=0.152 Sum_probs=41.2
Q ss_pred CCchHHHHHHHHhh--CCCcchhhhhhhcCCCcccHHHHHHHHhhcccceE
Q 009896 380 GRDAYRIFRLLSKS--GRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLM 428 (523)
Q Consensus 380 G~~a~RI~r~L~~k--~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~l 428 (523)
..-|+|++-.|..+ +..+.-++|++..-+|..-++++|.+|.+.|+|..
T Consensus 7 ~~YAl~~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s 57 (135)
T TIGR02010 7 GRYAVTAMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKAGLVKS 57 (135)
T ss_pred HHHHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEE
Confidence 34578888888643 33459999999999999999999999999999964
No 129
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=63.43 E-value=9.8 Score=37.65 Aligned_cols=52 Identities=23% Similarity=0.274 Sum_probs=45.3
Q ss_pred HHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCC
Q 009896 384 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTG 435 (523)
Q Consensus 384 ~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQEvpk~~ 435 (523)
.-|+.+|+.+|.-+.|.+|.+...+|.-.+..+|.+|-+.|+|+.+-.-+++
T Consensus 198 ~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LEk~GlIe~~K~G~~n 249 (258)
T COG2512 198 KEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLEKRGLIEKEKKGRTN 249 (258)
T ss_pred HHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHHHHHhCCceEEEEeCCee
Confidence 3467788888876699999999999999999999999999999998776663
No 130
>PF13730 HTH_36: Helix-turn-helix domain
Probab=62.86 E-value=10 Score=27.41 Aligned_cols=29 Identities=14% Similarity=0.248 Sum_probs=27.1
Q ss_pred cHHHHHhhcCCCHHHHHHHHHHHHhhccc
Q 009896 36 TRQNVKRYTELSDEQVKNALLVLIQQNCV 64 (523)
Q Consensus 36 tl~~l~~~t~l~~~~vr~aL~vLiQhn~V 64 (523)
+...|+..++++.+.|+.++-.|.++|++
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHCcCC
Confidence 68999999999999999999999999975
No 131
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=62.49 E-value=9 Score=33.43 Aligned_cols=51 Identities=18% Similarity=0.200 Sum_probs=42.9
Q ss_pred HcCCchHHHHHHHHhh-CCCcchhhhhhhcCCCcccHHHHHHHHhhcccceE
Q 009896 378 RYGRDAYRIFRLLSKS-GRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLM 428 (523)
Q Consensus 378 ~~G~~a~RI~r~L~~k-~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~l 428 (523)
+...-|.|++..|... +..+.-++|++...+|...++++|..|.+.|+|.-
T Consensus 6 ~~~~yal~~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~ 57 (130)
T TIGR02944 6 KLTDYATLVLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTS 57 (130)
T ss_pred hHHhHHHHHHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEe
Confidence 3456688999999754 34449999999999999999999999999999954
No 132
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=62.47 E-value=15 Score=33.10 Aligned_cols=46 Identities=11% Similarity=0.135 Sum_probs=42.9
Q ss_pred hhHHHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 20 DLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 20 ~~v~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
++=.+|...|...||.|..+|++..++++..|+.-+-.|...|++.
T Consensus 9 ~~D~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI~ 54 (153)
T PRK11179 9 NLDRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQAGIIT 54 (153)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence 4456788999999999999999999999999999999999999997
No 133
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=62.45 E-value=1.4e+02 Score=28.03 Aligned_cols=43 Identities=5% Similarity=-0.031 Sum_probs=39.8
Q ss_pred HHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 23 ~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
..|-.+|..+|++|..+|++.+.++...|-..|-.|...|+|.
T Consensus 48 ~~iL~~L~~~~~itq~eLa~~l~l~~sTvtr~l~rLE~kGlI~ 90 (185)
T PRK13777 48 HHILWIAYHLKGASISEIAKFGVMHVSTAFNFSKKLEERGYLT 90 (185)
T ss_pred HHHHHHHHhCCCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCEE
Confidence 3677788888999999999999999999999999999999998
No 134
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=62.06 E-value=8.6 Score=37.88 Aligned_cols=45 Identities=16% Similarity=0.333 Sum_probs=40.1
Q ss_pred chHHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccce
Q 009896 382 DAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 427 (523)
Q Consensus 382 ~a~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~ 427 (523)
.+++|+++|...+.+ .-.+|++...||...+..+|..|...|||+
T Consensus 15 r~l~IL~~l~~~~~l-~l~eia~~lgl~kstv~Rll~tL~~~G~l~ 59 (257)
T PRK15090 15 KVFGILQALGEEREI-GITELSQRVMMSKSTVYRFLQTMKTLGYVA 59 (257)
T ss_pred HHHHHHHHhhcCCCC-CHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 467888888766666 999999999999999999999999999994
No 135
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=61.60 E-value=34 Score=28.84 Aligned_cols=71 Identities=10% Similarity=0.113 Sum_probs=49.3
Q ss_pred HHhhhchhHH--HHHHHHH----hcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEechhh
Q 009896 14 ITNHFGDLVA--KVCECLL----RKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFDN 87 (523)
Q Consensus 14 v~~~FG~~v~--~V~~~Ll----~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~~~~ 87 (523)
++..||-... .|..+|. ..|++|..+|+..++++++.|-..+-.|.++|+|.-...+.+ +-..+..+...+
T Consensus 17 l~~~~~ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~r~~~~~D---~R~~~i~lT~~G 93 (109)
T TIGR01889 17 LKKEFNLSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLSKKGYLSKERSEDD---ERKVIISINKEQ 93 (109)
T ss_pred HHHHcCCCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEeccCCccc---CCeEEEEECHHH
Confidence 4445664443 4456665 458899999999999999999999999999999983333222 223455554443
No 136
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=61.39 E-value=13 Score=28.00 Aligned_cols=45 Identities=22% Similarity=0.303 Sum_probs=38.3
Q ss_pred chHHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceE
Q 009896 382 DAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLM 428 (523)
Q Consensus 382 ~a~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~l 428 (523)
....|+..+...+ . ..++|++...++...++..|..|...|+|..
T Consensus 8 ~~~~il~~l~~~~-~-~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~ 52 (78)
T cd00090 8 TRLRILRLLLEGP-L-TVSELAERLGLSQSTVSRHLKKLEEAGLVES 52 (78)
T ss_pred HHHHHHHHHHHCC-c-CHHHHHHHHCcCHhHHHHHHHHHHHCCCeEE
Confidence 4466777776654 5 9999999999999999999999999999954
No 137
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=61.35 E-value=8.6 Score=26.65 Aligned_cols=32 Identities=19% Similarity=0.308 Sum_probs=29.9
Q ss_pred chhhhhhhcCCCcccHHHHHHHHhhcccceEE
Q 009896 398 ETDKISDTTFVEKKDAPKILYKLWKDGYLLME 429 (523)
Q Consensus 398 eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQ 429 (523)
..++|++...++...+.+.|.+|.+.|+|..+
T Consensus 10 s~~~la~~l~~s~~tv~~~l~~L~~~g~l~~~ 41 (48)
T smart00419 10 TRQEIAELLGLTRETVSRTLKRLEKEGLISRE 41 (48)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 78899999999999999999999999999754
No 138
>PRK11569 transcriptional repressor IclR; Provisional
Probab=61.07 E-value=18 Score=36.01 Aligned_cols=41 Identities=17% Similarity=0.284 Sum_probs=35.3
Q ss_pred HHHHHHh-cCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 25 VCECLLR-KGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 25 V~~~Ll~-~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
|-++|.. .+++++.+|++.+++|.+.+..-|..|.++|+|.
T Consensus 33 IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~~G~l~ 74 (274)
T PRK11569 33 LLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQQGFVR 74 (274)
T ss_pred HHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 3344444 4679999999999999999999999999999997
No 139
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=60.72 E-value=16 Score=29.35 Aligned_cols=34 Identities=12% Similarity=0.171 Sum_probs=30.9
Q ss_pred hHHHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHH
Q 009896 21 LVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNAL 55 (523)
Q Consensus 21 ~v~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL 55 (523)
-...|...|.. |..|+.+|++.+|++...|+.+|
T Consensus 7 R~~~I~e~l~~-~~~ti~dvA~~~gvS~~TVsr~L 40 (80)
T TIGR02844 7 RVLEIGKYIVE-TKATVRETAKVFGVSKSTVHKDV 40 (80)
T ss_pred HHHHHHHHHHH-CCCCHHHHHHHhCCCHHHHHHHh
Confidence 45678899999 99999999999999999999966
No 140
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=60.59 E-value=10 Score=28.57 Aligned_cols=32 Identities=19% Similarity=0.252 Sum_probs=28.4
Q ss_pred CC-cHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 34 PL-TRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 34 ~l-tl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
++ +..+|++..+++...|+.||-.|.+.|+|.
T Consensus 23 ~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~ 55 (64)
T PF00392_consen 23 RLPSERELAERYGVSRTTVREALRRLEAEGLIE 55 (64)
T ss_dssp BE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred EeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEE
Confidence 56 789999999999999999999999999997
No 141
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=60.16 E-value=67 Score=27.79 Aligned_cols=82 Identities=17% Similarity=0.251 Sum_probs=57.5
Q ss_pred chhHHHHHHHHHhcCCCcHHHHHhhcC-CCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEechhhHHHHhchhhH
Q 009896 19 GDLVAKVCECLLRKGPLTRQNVKRYTE-LSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFDNILHRVRFAKF 97 (523)
Q Consensus 19 G~~v~~V~~~Ll~~G~ltl~~l~~~t~-l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~~~~il~rlR~p~~ 97 (523)
|.-..-|...|.. |..-+.+|.+..+ ++.+-+-+.|-.|.++|+|. -...+.. | ..++|++-
T Consensus 22 ~kW~~lIl~~L~~-g~~RF~eL~r~i~~Is~k~Ls~~Lk~Le~~Glv~-R~~~~~~-P-prveY~LT------------- 84 (120)
T COG1733 22 GKWTLLILRDLFD-GPKRFNELRRSIGGISPKMLSRRLKELEEDGLVE-RVVYPEE-P-PRVEYRLT------------- 84 (120)
T ss_pred CccHHHHHHHHhc-CCCcHHHHHHHccccCHHHHHHHHHHHHHCCCEE-eeecCCC-C-ceeEEEEh-------------
Confidence 3556667777776 9999999999977 99999999999999999998 2221111 1 24788873
Q ss_pred HHHHHHHhhHHHHHHHHHHHHcCcCC
Q 009896 98 LTILSQEFDQQCVELVQGLLEHGRLT 123 (523)
Q Consensus 98 i~~i~~~~G~~a~~I~~~lL~~G~~~ 123 (523)
..|..-..++..+..-|..-
T Consensus 85 ------~~G~~L~~vl~~l~~Wg~~~ 104 (120)
T COG1733 85 ------EKGRDLLPVLLALADWGEKW 104 (120)
T ss_pred ------hhHHHHHHHHHHHHHHHHHH
Confidence 35555555555555555433
No 142
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=59.86 E-value=9 Score=31.94 Aligned_cols=48 Identities=13% Similarity=0.213 Sum_probs=36.0
Q ss_pred cCCchHHHHHHHHh----hCCCcchhhhhhhcCCCcccHHHHHHHHhhcccce
Q 009896 379 YGRDAYRIFRLLSK----SGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 427 (523)
Q Consensus 379 ~G~~a~RI~r~L~~----k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~ 427 (523)
++...-+||++|.. ...+ .-++|++..-++.+++|+.|..|..+|+|.
T Consensus 45 ~~~~~~~Vl~~i~~~~~~~~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IY 96 (102)
T PF08784_consen 45 LSPLQDKVLNFIKQQPNSEEGV-HVDEIAQQLGMSENEVRKALDFLSNEGHIY 96 (102)
T ss_dssp S-HHHHHHHHHHHC----TTTE-EHHHHHHHSTS-HHHHHHHHHHHHHTTSEE
T ss_pred CCHHHHHHHHHHHhcCCCCCcc-cHHHHHHHhCcCHHHHHHHHHHHHhCCeEe
Confidence 34445567777755 1234 778899999999999999999999999985
No 143
>COG5625 Predicted transcription regulator containing HTH domain [Transcription]
Probab=59.73 E-value=9.4 Score=31.67 Aligned_cols=43 Identities=21% Similarity=0.435 Sum_probs=39.3
Q ss_pred HHHHHHHHhcCC-CcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 23 AKVCECLLRKGP-LTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 23 ~~V~~~Ll~~G~-ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
-.|.+.|+.+|+ +-+++|.+..+++...|+.++.+|...|++-
T Consensus 24 I~IY~lLve~~~~mri~ei~rEl~is~rtvr~~v~~l~rrGll~ 67 (113)
T COG5625 24 IRIYSLLVEKGRGMRIREIQRELGISERTVRAAVAVLLRRGLLA 67 (113)
T ss_pred hhhhhHHHHhcCCchHHHHHHHHhHHHHHHHHHHHHHHHhhHHH
Confidence 578899999987 9999999999999999999999999888886
No 144
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=59.60 E-value=9.7 Score=35.50 Aligned_cols=43 Identities=28% Similarity=0.392 Sum_probs=36.3
Q ss_pred HHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceE
Q 009896 385 RIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLM 428 (523)
Q Consensus 385 RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~l 428 (523)
++.-.|...++. .-.+|++...|+.+++-..||+|++.|.|..
T Consensus 17 ~~~~~l~~~~~~-~a~~i~~~l~~~k~~vNr~LY~l~~~~~v~~ 59 (183)
T PHA03103 17 KEVKNLGLGEGI-TAIEISRKLNIEKSEVNKQLYKLQREGMVYM 59 (183)
T ss_pred HHHHHhccCCCc-cHHHHHHHhCCCHHHHHHHHHHHHhcCceec
Confidence 345556555566 9999999999999999999999999999954
No 145
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=59.50 E-value=28 Score=29.45 Aligned_cols=51 Identities=25% Similarity=0.391 Sum_probs=40.4
Q ss_pred HHHHHHHH-cCcCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccceecCC
Q 009896 111 ELVQGLLE-HGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCPA 164 (523)
Q Consensus 111 ~I~~~lL~-~G~~~~~~li~~~~~~~~~~~~~~~~~i~~~f~~Lv~~~fi~~v~~ 164 (523)
.|++.|.. .++++++++.+.+....+ ..+...+-.++..|++.|+|.++..
T Consensus 5 ~Il~~l~~~~~~~sa~ei~~~l~~~~~---~i~~~TVYR~L~~L~~~Gli~~~~~ 56 (116)
T cd07153 5 AILEVLLESDGHLTAEEIYERLRKKGP---SISLATVYRTLELLEEAGLVREIEL 56 (116)
T ss_pred HHHHHHHhCCCCCCHHHHHHHHHhcCC---CCCHHHHHHHHHHHHhCCCEEEEEe
Confidence 46677766 468999999999865422 3467889999999999999999853
No 146
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=59.47 E-value=30 Score=25.96 Aligned_cols=44 Identities=18% Similarity=0.270 Sum_probs=38.0
Q ss_pred HHHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 22 VAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 22 v~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
...|+..--..+..+..+|++..++++..|-..|-.|...|+|.
T Consensus 10 L~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV~ 53 (60)
T PF01325_consen 10 LKAIYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLAEKGLVE 53 (60)
T ss_dssp HHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHHHCCCEE
Confidence 34566666678899999999999999999999999999999998
No 147
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=59.39 E-value=25 Score=26.85 Aligned_cols=46 Identities=17% Similarity=0.301 Sum_probs=38.0
Q ss_pred hhHHHHHHHHHhcC-CCcHHHHHhhcCCC-HHHHHHHHHHHHhhcccc
Q 009896 20 DLVAKVCECLLRKG-PLTRQNVKRYTELS-DEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 20 ~~v~~V~~~Ll~~G-~ltl~~l~~~t~l~-~~~vr~aL~vLiQhn~V~ 65 (523)
++-..|..++..+| +-|+.+|.+..+++ ++.|..-|-.|..-|++.
T Consensus 10 ~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~kG~I~ 57 (65)
T PF01726_consen 10 EVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKALERKGYIR 57 (65)
T ss_dssp HHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCcCcc
Confidence 45566777888888 55799999999997 999999999999999997
No 148
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=59.28 E-value=21 Score=26.67 Aligned_cols=55 Identities=25% Similarity=0.262 Sum_probs=39.2
Q ss_pred hhhHHHHHHHHhhHHHHHHHHHHHHcCcCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccceecC
Q 009896 94 FAKFLTILSQEFDQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 163 (523)
Q Consensus 94 ~p~~i~~i~~~~G~~a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~~~~i~~~f~~Lv~~~fi~~v~ 163 (523)
...|+...-+.||. ....++.++..++.+.+.- +...+...+..|.+.|+|...+
T Consensus 5 ia~~l~~l~~~~~~-------~~~~~~~~s~~ela~~~g~--------s~~tv~r~l~~L~~~g~i~~~~ 59 (67)
T cd00092 5 LASFLLNLSLRYGA-------GDLVQLPLTRQEIADYLGL--------TRETVSRTLKELEEEGLISRRG 59 (67)
T ss_pred HHHHHHHHHHHcCC-------CccccCCcCHHHHHHHHCC--------CHHHHHHHHHHHHHCCCEEecC
Confidence 34445544445653 2345778888888777542 5778999999999999998875
No 149
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=59.25 E-value=16 Score=28.05 Aligned_cols=49 Identities=16% Similarity=0.278 Sum_probs=38.9
Q ss_pred HHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecC
Q 009896 385 RIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVT 434 (523)
Q Consensus 385 RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQEvpk~ 434 (523)
.|..+|..+|.. +-.+|+...-+++..++..|-.|.+.|+|.-.+.+..
T Consensus 4 ~i~~~l~~~~~~-S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~~~~~~ 52 (69)
T PF09012_consen 4 EIRDYLRERGRV-SLAELAREFGISPEAVEAMLEQLIRKGYIRKVDMSSC 52 (69)
T ss_dssp HHHHHHHHS-SE-EHHHHHHHTT--HHHHHHHHHHHHCCTSCEEEEEE--
T ss_pred HHHHHHHHcCCc-CHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEecCCCC
Confidence 466778777777 9999999999999999999999999999987766653
No 150
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=59.24 E-value=29 Score=29.81 Aligned_cols=55 Identities=9% Similarity=0.194 Sum_probs=47.3
Q ss_pred CCcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEechhhHH
Q 009896 34 PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFDNIL 89 (523)
Q Consensus 34 ~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~~~~il 89 (523)
..||.+|+....-+.+.+|.-|--|.+.|.+. |.+..+.|..+......+++.++
T Consensus 19 ~vtl~elA~~l~cS~Rn~r~lLkkm~~~gWi~-W~pg~GRG~~S~L~~l~~~~~~~ 73 (115)
T PF12793_consen 19 EVTLDELAELLFCSRRNARTLLKKMQEEGWIT-WQPGRGRGNRSQLTFLKSPEELL 73 (115)
T ss_pred ceeHHHHHHHhCCCHHHHHHHHHHHHHCCCee-eeCCCCCCCCCeeEEeeCHHHHH
Confidence 57999999999999999999999999999998 89887777777777777776654
No 151
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=58.62 E-value=16 Score=35.78 Aligned_cols=41 Identities=27% Similarity=0.305 Sum_probs=35.3
Q ss_pred HHHHHHh-cCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 25 VCECLLR-KGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 25 V~~~Ll~-~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
|-+++.. .+++++.+|++.+++|.+.+..-|..|.++|+|.
T Consensus 14 IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~~G~l~ 55 (248)
T TIGR02431 14 VIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVELGYVT 55 (248)
T ss_pred HHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 3344443 5679999999999999999999999999999997
No 152
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=58.15 E-value=27 Score=30.39 Aligned_cols=34 Identities=21% Similarity=0.232 Sum_probs=32.0
Q ss_pred CCCcHHHHHhhcCCCHHHHHHHHHHHHhhccccc
Q 009896 33 GPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQA 66 (523)
Q Consensus 33 G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~ 66 (523)
++.+..+|++..++|++.|.+.|-.|.+.|+|..
T Consensus 24 ~~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~ 57 (130)
T TIGR02944 24 QPYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTS 57 (130)
T ss_pred CCccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEe
Confidence 5789999999999999999999999999999973
No 153
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=57.99 E-value=12 Score=37.12 Aligned_cols=47 Identities=19% Similarity=0.171 Sum_probs=40.5
Q ss_pred chHHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceE
Q 009896 382 DAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLM 428 (523)
Q Consensus 382 ~a~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~l 428 (523)
.+++|+++|...+.-+.-.+|++...||...+..+|..|...|||.-
T Consensus 26 r~l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~~ 72 (271)
T PRK10163 26 RGIAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQAADFVYQ 72 (271)
T ss_pred HHHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence 46788889876654449999999999999999999999999999943
No 154
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=57.89 E-value=14 Score=32.10 Aligned_cols=46 Identities=20% Similarity=0.195 Sum_probs=38.7
Q ss_pred chHHHHHHHHhh--CCCcchhhhhhhcCCCcccHHHHHHHHhhcccce
Q 009896 382 DAYRIFRLLSKS--GRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 427 (523)
Q Consensus 382 ~a~RI~r~L~~k--~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~ 427 (523)
.|++++-.|... +..+.-++|++..-+|...++++|..|.+.|+|.
T Consensus 9 ~al~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~ 56 (132)
T TIGR00738 9 YALRALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRRAGLVE 56 (132)
T ss_pred HHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEE
Confidence 467777777643 2245999999999999999999999999999984
No 155
>PRK11569 transcriptional repressor IclR; Provisional
Probab=57.83 E-value=12 Score=37.22 Aligned_cols=46 Identities=7% Similarity=0.270 Sum_probs=40.0
Q ss_pred chHHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccce
Q 009896 382 DAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 427 (523)
Q Consensus 382 ~a~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~ 427 (523)
.+++|+++|.+.+.-+.-.+|++...+|...+..+|..|...||+.
T Consensus 29 ral~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~~G~l~ 74 (274)
T PRK11569 29 RGLKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQQGFVR 74 (274)
T ss_pred HHHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 4678888887654434999999999999999999999999999995
No 156
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=57.70 E-value=39 Score=29.67 Aligned_cols=51 Identities=12% Similarity=0.164 Sum_probs=44.9
Q ss_pred chhHHHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhccccccccc
Q 009896 19 GDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTE 70 (523)
Q Consensus 19 G~~v~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~~ 70 (523)
-|-.-.....+..+++.++.++.+.++=.++.|...|..|+..|+|. |...
T Consensus 63 sp~nleLl~~Ia~~~P~Si~ElAe~vgRdv~nvhr~Ls~l~~~GlI~-fe~~ 113 (144)
T COG4190 63 SPRNLELLELIAQEEPASINELAELVGRDVKNVHRTLSTLADLGLIF-FEED 113 (144)
T ss_pred ChhHHHHHHHHHhcCcccHHHHHHHhCcchHHHHHHHHHHHhcCeEE-EecC
Confidence 44555677788889999999999999999999999999999999998 7663
No 157
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=57.63 E-value=1.3e+02 Score=26.32 Aligned_cols=61 Identities=7% Similarity=0.048 Sum_probs=45.4
Q ss_pred hHHHHHHHHhhC-CCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCceEEEEEEEc
Q 009896 383 AYRIFRLLSKSG-RLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVN 447 (523)
Q Consensus 383 a~RI~r~L~~k~-~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQEvpk~~~~~~t~~lw~v~ 447 (523)
-+.++..|...+ .. .+.+|++...++...+-..+.+|.+.|||+-..-| ...|..+++-.+
T Consensus 33 q~~vL~~l~~~~~~~-t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~~~---~DrR~~~l~LT~ 94 (144)
T PRK03573 33 HWVTLHNIHQLPPEQ-SQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQTCA---SDRRAKRIKLTE 94 (144)
T ss_pred HHHHHHHHHHcCCCC-CHHHHHHHhCCChhhHHHHHHHHHHCCCEeeecCC---CCcCeeeeEECh
Confidence 345666665544 46 89999999999999999999999999999443222 446666665554
No 158
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=57.45 E-value=13 Score=36.80 Aligned_cols=46 Identities=15% Similarity=0.289 Sum_probs=40.9
Q ss_pred chHHHHHHHHhhCC-CcchhhhhhhcCCCcccHHHHHHHHhhcccceE
Q 009896 382 DAYRIFRLLSKSGR-LLETDKISDTTFVEKKDAPKILYKLWKDGYLLM 428 (523)
Q Consensus 382 ~a~RI~r~L~~k~~-l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~l 428 (523)
.+++|+++|..++. + ...+|++...+|...+..+|..|.+.|||+-
T Consensus 12 ral~iL~~l~~~~~~l-s~~eia~~lgl~kstv~RlL~tL~~~g~v~~ 58 (263)
T PRK09834 12 RGLMVLRALNRLDGGA-TVGLLAELTGLHRTTVRRLLETLQEEGYVRR 58 (263)
T ss_pred HHHHHHHHHHhcCCCC-CHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence 57889999976655 6 9999999999999999999999999999953
No 159
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=57.12 E-value=18 Score=27.21 Aligned_cols=43 Identities=23% Similarity=0.342 Sum_probs=36.4
Q ss_pred HHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEE
Q 009896 386 IFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLME 429 (523)
Q Consensus 386 I~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQ 429 (523)
||++-. ++..+..++||+..-+++..+-+.+.+|.+.|||..+
T Consensus 13 Iy~l~~-~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV~~~ 55 (60)
T PF01325_consen 13 IYELSE-EGGPVRTKDIAERLGVSPPTVTEMLKRLAEKGLVEYE 55 (60)
T ss_dssp HHHHHH-CTSSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHc-CCCCccHHHHHHHHCCChHHHHHHHHHHHHCCCEEec
Confidence 666664 5566699999999999999999999999999999764
No 160
>COG1386 scpB Chromosome segregation and condensation protein B [DNA replication, recombination and repair]
Probab=56.75 E-value=1.1e+02 Score=28.78 Aligned_cols=135 Identities=15% Similarity=0.188 Sum_probs=90.0
Q ss_pred HHHHHHHHHhccchhcccccccCCccccHHHHHHHhhhhccCCCCCHHHHHHHHHHhccCC-----CCCCCCCeEEEehH
Q 009896 286 AANVLSAMLQATSSAEKKVKTKNSVPLSLSSIYEEVIKSEAGRNMTLDHVRASLVQLGELS-----FVDASSDSYSIDFE 360 (523)
Q Consensus 286 a~~v~~~~L~~~~~~~~~~~~~~s~~~s~~~I~~~l~~~~~~~~~~~~~i~~~L~~La~~~-----~~~~~~~~y~V~~~ 360 (523)
.+.+++++|-+. ..|+|..++..-++.. ....+...|..|..+- -...-++.|..-..
T Consensus 9 ~~~~vEall~a~-----------~~pls~~~L~~il~~~------~~~~~~~~l~~l~~~y~~rg~~L~~~~~~~r~~t~ 71 (184)
T COG1386 9 LKALIEALLFAG-----------GEPLSLKELAEILGIV------SADAIIDALAELKEEYEDRGLELVEVAEGWRLQTK 71 (184)
T ss_pred HHHHHHHHHHhc-----------CCCCCHHHHHHHhCCC------chHHHHHHHHHHHHhhcCCCeeEEEEcCceeEEeh
Confidence 355677777754 3489999999888532 2234444444444332 11333455666666
Q ss_pred HHHHHHHHHHHHHHHHHHcCCchHHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCceE
Q 009896 361 KIIEIAQNEEVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQ 440 (523)
Q Consensus 361 ~i~~~lr~~~le~~v~~~~G~~a~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQEvpk~~~~~~t 440 (523)
....-.-....+.-....++..+++++-++.-+.- +..-+|.+.-..... ..+..|...|+| .++++...|+|+
T Consensus 72 ~~~~~~~~~l~~~~~~~~LSraalEtLAiIAY~QP-iTR~eI~~iRGv~~~---~~i~~L~e~glI--~~~g~~~~~Grp 145 (184)
T COG1386 72 QEYAEYLEKLQEQRPKRELSRAALETLAIIAYKQP-VTRSEIEEIRGVAVS---QVISTLLERGLI--REVGRRDTPGRP 145 (184)
T ss_pred HHHHHHHHHHhcccccccccHHHHHHHHHHHHcCC-ccHHHHHHHhCccHH---HHHHHHHHCCCe--EecCCCCCCCCc
Confidence 66655555666666666789999999999976644 488888887776654 489999999999 457776677776
Q ss_pred EEE
Q 009896 441 FLL 443 (523)
Q Consensus 441 ~~l 443 (523)
+.+
T Consensus 146 ~ly 148 (184)
T COG1386 146 YLY 148 (184)
T ss_pred eee
Confidence 544
No 161
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=56.43 E-value=15 Score=26.53 Aligned_cols=32 Identities=25% Similarity=0.266 Sum_probs=30.0
Q ss_pred CC-cHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 34 PL-TRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 34 ~l-tl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
++ |..+|++..+++...|+.+|-.|.+.|+|.
T Consensus 19 ~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i~ 51 (60)
T smart00345 19 KLPSERELAAQLGVSRTTVREALSRLEAEGLVQ 51 (60)
T ss_pred cCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 46 799999999999999999999999999986
No 162
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=56.40 E-value=14 Score=36.32 Aligned_cols=92 Identities=18% Similarity=0.158 Sum_probs=62.3
Q ss_pred chHHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCceEEEEEEEchHHHHHHHHHH--H
Q 009896 382 DAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQILWKHVLDE--M 459 (523)
Q Consensus 382 ~a~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQEvpk~~~~~~t~~lw~v~~~~~~~~~l~~--~ 459 (523)
.|++|+.+|........-.+|++...+|...++.+|..|.+.|||.- . ....+|+|.--- -.+-...+.. +
T Consensus 5 ral~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL~~~G~v~~-----d-~~~g~Y~Lg~~~-~~lg~~~l~~~~l 77 (246)
T COG1414 5 RALAILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTLVELGYVEQ-----D-PEDGRYRLGPRL-LELGAAALSSLDL 77 (246)
T ss_pred HHHHHHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEE-----c-CCCCcEeehHHH-HHHHHHHHhcCCH
Confidence 57889999976444237999999999999999999999999999943 1 112334443222 2233344443 7
Q ss_pred HHHHHHHHHHHHHHHHhhhhh
Q 009896 460 FHAALNLSLRVSYELDREKEL 480 (523)
Q Consensus 460 ~k~~~nl~~R~~~e~~~~k~l 480 (523)
.+.+.-.+.++..+..+...|
T Consensus 78 ~~~a~p~l~~L~~~tgetv~L 98 (246)
T COG1414 78 VSLARPLLEELAEETGETVHL 98 (246)
T ss_pred HHHhHHHHHHHHHHhCCcEEE
Confidence 777777777777766644433
No 163
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=56.39 E-value=1.1e+02 Score=25.33 Aligned_cols=52 Identities=15% Similarity=0.152 Sum_probs=42.9
Q ss_pred hchhHHHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccc
Q 009896 18 FGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTT 69 (523)
Q Consensus 18 FG~~v~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~ 69 (523)
+++.--.|..+|...|+.+..+|....+++++.|-..+-.|.+.|+|.-...
T Consensus 20 lt~~q~~~L~~l~~~~~~~~~~la~~l~i~~~~vt~~l~~Le~~glv~r~~~ 71 (126)
T COG1846 20 LTPPQYQVLLALYEAGGITVKELAERLGLDRSTVTRLLKRLEDKGLIERLRD 71 (126)
T ss_pred CCHHHHHHHHHHHHhCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCeeecCC
Confidence 4455566777778888877799999999999999999999999999983333
No 164
>TIGR00281 segregation and condensation protein B. Shown to be required for chromosome segregation and condensation in B. subtilis.
Probab=56.32 E-value=1.4e+02 Score=27.95 Aligned_cols=134 Identities=13% Similarity=0.218 Sum_probs=87.1
Q ss_pred HHHHHHHhccchhcccccccCCcc-ccHHHHHHHhhhhccCCCCCHHHHHHHHHHhccC----CC---CCCCCCeEEEeh
Q 009896 288 NVLSAMLQATSSAEKKVKTKNSVP-LSLSSIYEEVIKSEAGRNMTLDHVRASLVQLGEL----SF---VDASSDSYSIDF 359 (523)
Q Consensus 288 ~v~~~~L~~~~~~~~~~~~~~s~~-~s~~~I~~~l~~~~~~~~~~~~~i~~~L~~La~~----~~---~~~~~~~y~V~~ 359 (523)
.+++|+|-.+ +.| +|..+|.+-+.... .+.+...+..|... +. ...-+|.|.+-.
T Consensus 4 ~~iEAlLF~s-----------g~pgls~~~La~il~~~~------~~~~~~~l~~l~~~~~~~~~gl~l~~~~~~y~l~t 66 (186)
T TIGR00281 4 AIIEALLFVS-----------GEPGVTLAELVRILGKEK------AEKLNAIMELLEDYLSRDTAGIEIIKFGQSYSLVT 66 (186)
T ss_pred HHHHHHHHHc-----------CCCCCCHHHHHHHhCCCc------hHHHHHHHHHHHHHHhcCCCCEEEEEECCEEEEEE
Confidence 4577777764 246 99999998874211 12344444444322 21 134468888887
Q ss_pred HHHHHHHHHHHHHHHHHHHcCCchHHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCce
Q 009896 360 EKIIEIAQNEEVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQS 439 (523)
Q Consensus 360 ~~i~~~lr~~~le~~v~~~~G~~a~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQEvpk~~~~~~ 439 (523)
+.-..-.....+..-.. ++...++..+-++.-+.-+ ...+|.+.-.+. +...+.+|.+.|+|.. +.+...|+|
T Consensus 67 k~e~~~~i~~~~~~~~~-~LS~aaLEtLAIIAY~QPI-Tr~eIe~IRGv~---s~~~l~~L~ergLI~~--~Gr~~~~Gr 139 (186)
T TIGR00281 67 KPAFADYIHRFLPAKLK-NLNSASLEVLAIIAYKQPI-TRARINEIRGVK---SYQIVDDLVEKGLVVE--LGRKDTPGR 139 (186)
T ss_pred hHHHHHHHHHHhccccc-cCCHHHHHHHHHHHHcCCc-CHHHHHHHcCCC---HHHHHHHHHHCCCeEe--cCcCCCCCC
Confidence 77666555555544322 3778999999999776555 999999888777 6789999999999954 333335666
Q ss_pred EEEEEEE
Q 009896 440 QFLLWKV 446 (523)
Q Consensus 440 t~~lw~v 446 (523)
.+ +|.+
T Consensus 140 p~-ly~T 145 (186)
T TIGR00281 140 SF-IYET 145 (186)
T ss_pred Ce-eehh
Confidence 54 4443
No 165
>PF04079 DUF387: Putative transcriptional regulators (Ypuh-like); InterPro: IPR005234 This family represents ScpB, which along with ScpA (IPR003768 from INTERPRO) interacts with SMC in vivo forming a complex that is required for chromosome condensation and segregation [, ]. The SMC-Scp complex appears to be similar to the MukB-MukE-Muk-F complex in Escherichia coli [], where MukB (IPR007406 from INTERPRO) is the homologue of SMC. ScpA and ScpB have little sequence similarity to MukE (IPR007385 from INTERPRO) or MukF (IPR005582 from INTERPRO), they are predicted to be structurally similar, being predominantly alpha-helical with coiled coil regions. In general scpA and scpB form an operon in most bacterial genomes. Flanking genes are highly variable suggesting that the operon has moved throughout evolution. Bacteria containing an smc gene also contain scpA or scpB but not necessarily both. An exception is found in Deinococcus radiodurans, which contains scpB but neither smc nor scpA. In the archaea the gene order SMC-ScpA is conserved in nearly all species, as is the very short distance between the two genes, indicating co-transcription of the both in different archaeal genera and arguing that interaction of the gene products is not confined to the homologues in Bacillus subtilis. It would seem probable that, in light of all the studies, SMC, ScpA and ScpB proteins or homologues act together in chromosome condensation and segregation in all prokaryotes []. ; GO: 0051304 chromosome separation; PDB: 1T6S_B 2Z99_A.
Probab=56.11 E-value=77 Score=28.93 Aligned_cols=117 Identities=13% Similarity=0.154 Sum_probs=73.9
Q ss_pred HHHHHHHhcC-CCcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEechhhHHHHhchhhHHHHHH
Q 009896 24 KVCECLLRKG-PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFDNILHRVRFAKFLTILS 102 (523)
Q Consensus 24 ~V~~~Ll~~G-~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~~~~il~rlR~p~~i~~i~ 102 (523)
.|=..|+..| ++++.+|.+.++ +...|+.+|--|.++- ...+ . ..--....+-|.+.--|.|-.+++
T Consensus 2 ~iEAlLF~s~~pvs~~~La~~l~-~~~~v~~~l~~L~~~y-----~~~~-~-----gl~l~~~~~~y~l~tk~~~~~~v~ 69 (159)
T PF04079_consen 2 IIEALLFASGEPVSIEELAEILG-SEDEVEEALEELQEEY-----NEED-R-----GLELVEVGGGYRLQTKPEYAEYVE 69 (159)
T ss_dssp HHHHHHHH-SS-B-HHHHHHHCT--HHHHHHHHHHHHHHH-----HHCT-------SEEEEEETTEEEEEE-GGGHHHHH
T ss_pred hhHhhHHHcCCCCCHHHHHHHhC-CHHHHHHHHHHHHHHh-----ccCC-C-----CEEEEEECCEEEEEEhHHHHHHHH
Confidence 3445677775 899999999999 9999999999998763 2221 1 122333345555555666666666
Q ss_pred HHhhH--------HHHHHHHHHHHcCcCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccceecC
Q 009896 103 QEFDQ--------QCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 163 (523)
Q Consensus 103 ~~~G~--------~a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~~~~i~~~f~~Lv~~~fi~~v~ 163 (523)
+.++. .+-+++.-+.-++=+|-.++-+-=.. .-...+.+|.+.|||..+.
T Consensus 70 ~~~~~~~~~~LS~aalEtLAiIAY~QPiTr~eIe~IRGv-----------~s~~~i~~L~e~glI~~~g 127 (159)
T PF04079_consen 70 KLFKKPKPPKLSQAALETLAIIAYKQPITRAEIEEIRGV-----------NSDSVIKTLLERGLIEEVG 127 (159)
T ss_dssp HHHCTCCCHHHHHHHHHHHHHHHHH-SEEHHHHHHHHTS-------------HCHHHHHHHTTSEEEEE
T ss_pred HHhccCccCCCCHHHHHHHHHHHhcCCcCHHHHHHHcCC-----------ChHHHHHHHHHCCCEEecC
Confidence 66654 56667777777887887776433111 1356889999999999885
No 166
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=55.99 E-value=13 Score=36.38 Aligned_cols=46 Identities=15% Similarity=0.258 Sum_probs=39.7
Q ss_pred chHHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccce
Q 009896 382 DAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 427 (523)
Q Consensus 382 ~a~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~ 427 (523)
.+++|+.++...+.-+.-.+|++...+|...+..+|..|...|||+
T Consensus 10 ral~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~~G~l~ 55 (248)
T TIGR02431 10 RGLAVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVELGYVT 55 (248)
T ss_pred HHHHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 4678888886544333999999999999999999999999999995
No 167
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.
Probab=55.65 E-value=21 Score=33.84 Aligned_cols=48 Identities=21% Similarity=0.173 Sum_probs=43.2
Q ss_pred hchhHHHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 18 FGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 18 FG~~v~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
..+.-..|...|..+|+.++.+|++.++++++.+..-|-.|.+.|+|.
T Consensus 141 ls~~~~~IL~~l~~~g~~s~~eia~~l~is~stv~r~L~~Le~~GlI~ 188 (203)
T TIGR01884 141 LSREELKVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLRELEKKGLVE 188 (203)
T ss_pred CCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 345556788888888999999999999999999999999999999998
No 168
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=55.58 E-value=34 Score=29.66 Aligned_cols=34 Identities=18% Similarity=0.339 Sum_probs=32.0
Q ss_pred CCCcHHHHHhhcCCCHHHHHHHHHHHHhhccccc
Q 009896 33 GPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQA 66 (523)
Q Consensus 33 G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~ 66 (523)
++.|..+|+..+++|+..|++.|-.|.+.|+|..
T Consensus 24 ~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~ 57 (132)
T TIGR00738 24 GPVSVKEIAERQGISRSYLEKILRTLRRAGLVES 57 (132)
T ss_pred CcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEe
Confidence 4899999999999999999999999999999973
No 169
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=55.25 E-value=33 Score=30.20 Aligned_cols=33 Identities=18% Similarity=0.275 Sum_probs=31.4
Q ss_pred CCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 33 GPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 33 G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
++.|..+|+...++|+.-+++.|-.|.+.|+|.
T Consensus 24 ~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~ 56 (135)
T TIGR02010 24 GPVTLADISERQGISLSYLEQLFAKLRKAGLVK 56 (135)
T ss_pred CcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceE
Confidence 468999999999999999999999999999997
No 170
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=54.74 E-value=41 Score=28.38 Aligned_cols=57 Identities=21% Similarity=0.260 Sum_probs=43.4
Q ss_pred HHHHHHHhc-CCCcHHHHHhhc-----CCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEech
Q 009896 24 KVCECLLRK-GPLTRQNVKRYT-----ELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLF 85 (523)
Q Consensus 24 ~V~~~Ll~~-G~ltl~~l~~~t-----~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~~ 85 (523)
.|..+|... +.+|..+|.... +++...|-.+|-.|.+.|+|.-+..++ ..++|..+.
T Consensus 5 ~Il~~l~~~~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~~~~~-----~~~~y~~~~ 67 (116)
T cd07153 5 AILEVLLESDGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREIELGD-----GKARYELNT 67 (116)
T ss_pred HHHHHHHhCCCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEEEeCC-----CceEEEeCC
Confidence 567777764 579999997765 689999999999999999998554432 136787653
No 171
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=54.71 E-value=1.5e+02 Score=26.00 Aligned_cols=41 Identities=5% Similarity=0.050 Sum_probs=35.9
Q ss_pred HHHHHHhc-CCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 25 VCECLLRK-GPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 25 V~~~Ll~~-G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
|-..|... +.+|..+|++.+++++..|-..+-.|.+.|+|.
T Consensus 36 vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~ 77 (144)
T PRK03573 36 TLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLEEKGLIS 77 (144)
T ss_pred HHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHHCCCEe
Confidence 45555555 468999999999999999999999999999998
No 172
>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=54.00 E-value=40 Score=26.38 Aligned_cols=46 Identities=17% Similarity=0.156 Sum_probs=37.7
Q ss_pred HHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc-cccc
Q 009896 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ-AFTT 69 (523)
Q Consensus 23 ~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~-~~~~ 69 (523)
..|-.+|. ++.+|+.+|...|+++.+.+--.|.-|...|+|. .|..
T Consensus 8 ~~IL~~ls-~~c~TLeeL~ekTgi~k~~LlV~LsrL~k~GiI~Rkw~~ 54 (72)
T PF05584_consen 8 QKILIILS-KRCCTLEELEEKTGISKNTLLVYLSRLAKRGIIERKWRK 54 (72)
T ss_pred HHHHHHHH-hccCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeeeEE
Confidence 34444454 5599999999999999999999999999999998 3443
No 173
>PRK11050 manganese transport regulator MntR; Provisional
Probab=53.60 E-value=31 Score=31.14 Aligned_cols=42 Identities=14% Similarity=0.201 Sum_probs=37.8
Q ss_pred HHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 24 KVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 24 ~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
.|...+...|+.+..+|++..+++++.|...|-.|.+.|+|.
T Consensus 41 ~I~~~l~~~~~~t~~eLA~~l~is~stVsr~l~~Le~~GlI~ 82 (152)
T PRK11050 41 LIADLIAEVGEARQVDIAARLGVSQPTVAKMLKRLARDGLVE 82 (152)
T ss_pred HHHHHHHhcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 455666677999999999999999999999999999999986
No 174
>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues. They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.
Probab=53.41 E-value=11 Score=35.32 Aligned_cols=85 Identities=13% Similarity=0.264 Sum_probs=40.3
Q ss_pred hHHHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEechhhHHHHhchhhHHHH
Q 009896 21 LVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFDNILHRVRFAKFLTI 100 (523)
Q Consensus 21 ~v~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~~~~il~rlR~p~~i~~ 100 (523)
+......++-.+--++|.+|+...+|+...+.+-+-.|...|.++=.-++ . |+||++
T Consensus 100 lL~~Fi~yIK~~Kvv~ledla~~f~l~t~~~i~ri~~L~~~g~ltGv~Dd--r---------------------GkfIyI 156 (188)
T PF09756_consen 100 LLQEFINYIKEHKVVNLEDLAAEFGLRTQDVINRIQELEAEGRLTGVIDD--R---------------------GKFIYI 156 (188)
T ss_dssp HHHHHHHHHHH-SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-T--T-----------------------EEE-
T ss_pred HHHHHHHHHHHcceeeHHHHHHHcCCCHHHHHHHHHHHHHCCCceeeEcC--C---------------------CCeEEe
Confidence 67778889999999999999999999999999999999999999722221 1 566666
Q ss_pred HHHHhhHHHHHHHHHHHHcCcCCHHHHHHHhh
Q 009896 101 LSQEFDQQCVELVQGLLEHGRLTLKQMFDRAK 132 (523)
Q Consensus 101 i~~~~G~~a~~I~~~lL~~G~~~~~~li~~~~ 132 (523)
-.+.+. .|...+-+.|++++++|...+.
T Consensus 157 s~eE~~----~va~fi~~rGRvsi~el~~~~N 184 (188)
T PF09756_consen 157 SEEEME----AVAKFIKQRGRVSISELAQESN 184 (188)
T ss_dssp --------------------------------
T ss_pred cHHHHH----HHHHHHHHcCCccHHHHHHHHH
Confidence 666664 4556677899999999987653
No 175
>PRK10870 transcriptional repressor MprA; Provisional
Probab=53.34 E-value=1.7e+02 Score=26.97 Aligned_cols=49 Identities=8% Similarity=-0.067 Sum_probs=38.6
Q ss_pred hhchhHH--HHHHHHHh--cCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 17 HFGDLVA--KVCECLLR--KGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 17 ~FG~~v~--~V~~~Ll~--~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
.+|-..+ .|...|.. .|++|..+|++..+++...|-..+-.|.+.|+|.
T Consensus 50 ~~gLt~~q~~iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe~kGlV~ 102 (176)
T PRK10870 50 AQGINETLFMALITLESQENHSIQPSELSCALGSSRTNATRIADELEKRGWIE 102 (176)
T ss_pred HCCCCHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 4553333 34444443 3568999999999999999999999999999998
No 176
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.
Probab=52.56 E-value=18 Score=34.32 Aligned_cols=51 Identities=16% Similarity=0.234 Sum_probs=44.2
Q ss_pred HcCCchHHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEE
Q 009896 378 RYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLME 429 (523)
Q Consensus 378 ~~G~~a~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQ 429 (523)
.......+|+..|..+|.+ ..++|++..-++...++..|.+|.+.|+|.-.
T Consensus 140 ~ls~~~~~IL~~l~~~g~~-s~~eia~~l~is~stv~r~L~~Le~~GlI~r~ 190 (203)
T TIGR01884 140 GLSREELKVLEVLKAEGEK-SVKNIAKKLGKSLSTISRHLRELEKKGLVEQK 190 (203)
T ss_pred CCCHHHHHHHHHHHHcCCc-CHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence 3455566888888777787 99999999999999999999999999999754
No 177
>COG4738 Predicted transcriptional regulator [Transcription]
Probab=51.53 E-value=1.6e+02 Score=25.29 Aligned_cols=105 Identities=14% Similarity=0.183 Sum_probs=80.7
Q ss_pred HHHHHHHHhhhchhHHHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEechhh
Q 009896 8 KHAVHVITNHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFDN 87 (523)
Q Consensus 8 ~Lc~~iv~~~FG~~v~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~~~~ 87 (523)
++...+=.-..---+|...-||...+-.+=.+|-+.+||--..|--|+--|-..|-|.--.....|..+++-.|.+-
T Consensus 15 ~~ie~L~~lgi~R~vA~tlv~L~~~~E~sS~~IE~~sgLRQPEVSiAMr~Lre~gWV~~R~eKKkGKGRPik~Y~Lt--- 91 (124)
T COG4738 15 EIIELLRILGIPRNVATTLVCLAKGDEASSREIERVSGLRQPEVSIAMRYLRENGWVDEREEKKKGKGRPIKLYRLT--- 91 (124)
T ss_pred HHHHHHHHcCCCchHHHHHHHHhcCcchhhhhhHHhhcCCCchhHHHHHHHHHccccchHHhcccCCCCCceEEEec---
Confidence 44444444455567888889999999999999999999999999999999999999984443333434567788873
Q ss_pred HHHHhchhhHHHHHHHHhhHHHHHHHHHHHHc
Q 009896 88 ILHRVRFAKFLTILSQEFDQQCVELVQGLLEH 119 (523)
Q Consensus 88 il~rlR~p~~i~~i~~~~G~~a~~I~~~lL~~ 119 (523)
.-|+.++..+.+.+-.+...|+.++=..
T Consensus 92 ----~~~~eIvs~iee~~~ke~k~i~~~ierL 119 (124)
T COG4738 92 ----VPFDEIVSEIEEEIIKESKEIIYNIERL 119 (124)
T ss_pred ----CcHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4578889999999988888888776443
No 178
>COG4344 Uncharacterized protein conserved in archaea [Function unknown]
Probab=51.18 E-value=17 Score=32.44 Aligned_cols=50 Identities=20% Similarity=0.299 Sum_probs=39.6
Q ss_pred HHHHhhcCCCHHHHHHHHHHHHhhcccccccccCCCC-----------CCcceEEEechhh
Q 009896 38 QNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDG-----------PKANTQYVVLFDN 87 (523)
Q Consensus 38 ~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~-----------~~~~~~Y~~~~~~ 87 (523)
..|.+.|++|...|+..|--|..-|++.+++...-+. ....|||.+|-++
T Consensus 35 K~i~r~tkiPl~~i~e~l~dL~elGLier~tgttiKrteAKfKksaEVHKHHTYYrl~reg 95 (175)
T COG4344 35 KNITRYTKIPLPRIREYLKDLKELGLIERYTGTTIKRTEAKFKKSAEVHKHHTYYRLNREG 95 (175)
T ss_pred HHHHHHccCChHHHHHHHHHHHHcCCeeeccCchhhhhHHHHHHhHHHHhchhhheechhH
Confidence 4678899999999999999999999999877653221 2347899988764
No 179
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=51.15 E-value=32 Score=32.08 Aligned_cols=46 Identities=22% Similarity=0.237 Sum_probs=43.7
Q ss_pred hhHHHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 20 DLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 20 ~~v~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
++|-+++..|-..|..|..+|.+..+++.+.|=..|..|.+-+.|+
T Consensus 13 ~lv~~~~~~l~~~~~~~a~~i~~~l~~~k~~vNr~LY~l~~~~~v~ 58 (183)
T PHA03103 13 ELVKKEVKNLGLGEGITAIEISRKLNIEKSEVNKQLYKLQREGMVY 58 (183)
T ss_pred HHHHHHHHHhccCCCccHHHHHHHhCCCHHHHHHHHHHHHhcCcee
Confidence 6788899999989999999999999999999999999999999996
No 180
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=50.55 E-value=40 Score=32.57 Aligned_cols=51 Identities=20% Similarity=0.279 Sum_probs=47.2
Q ss_pred HHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCC
Q 009896 384 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTG 435 (523)
Q Consensus 384 ~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQEvpk~~ 435 (523)
.+|+.+|..||-+ .-.+|++...+|...+-.-+..|.+.|+|+..-++-++
T Consensus 26 v~Il~lL~~k~pl-NvneiAe~lgLpqst~s~~ik~Le~aGlirT~t~kark 76 (308)
T COG4189 26 VAILQLLHRKGPL-NVNEIAEALGLPQSTMSANIKVLEKAGLIRTETVKARK 76 (308)
T ss_pred HHHHHHHHHhCCC-CHHHHHHHhCCchhhhhhhHHHHHhcCceeeeeecccc
Confidence 5789999999999 99999999999999999999999999999998888654
No 181
>PF04492 Phage_rep_O: Bacteriophage replication protein O ; InterPro: IPR006497 This entry is represented by the N-terminal domain of Bacteriophage lambda, GpO. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0006260 DNA replication
Probab=50.37 E-value=25 Score=29.43 Aligned_cols=51 Identities=20% Similarity=0.360 Sum_probs=44.7
Q ss_pred HHHHHHHHHHHcCCchHHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccce
Q 009896 368 NEEVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 427 (523)
Q Consensus 368 ~~~le~~v~~~~G~~a~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~ 427 (523)
..++..+++..||-. ++...+...|+++...++...+.+.+..|.+.|+|.
T Consensus 35 ~ki~~ai~RkTyG~n---------Kk~d~Is~sq~~e~tg~~~~~V~~al~~Li~~~vI~ 85 (100)
T PF04492_consen 35 LKILLAIIRKTYGWN---------KKMDRISNSQIAEMTGLSRDHVSKALNELIRRGVII 85 (100)
T ss_pred HHHHHHHHHHccCCC---------CccceeeHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 367888888888876 555666999999999999999999999999999993
No 182
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=49.97 E-value=23 Score=31.38 Aligned_cols=47 Identities=19% Similarity=0.371 Sum_probs=37.4
Q ss_pred chHHHHHHHHh--hCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceE
Q 009896 382 DAYRIFRLLSK--SGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLM 428 (523)
Q Consensus 382 ~a~RI~r~L~~--k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~l 428 (523)
-|.|..=.+.. .|..+.+++|++...+|..-+|++|.+|.++|+|..
T Consensus 9 YAl~~~i~la~~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s 57 (141)
T PRK11014 9 YGLRALIYMASLPEGRMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTA 57 (141)
T ss_pred HHHHHHHHHhcCCCCCccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEE
Confidence 34555544432 345669999999999999999999999999999965
No 183
>PF07848 PaaX: PaaX-like protein; InterPro: IPR012906 This entry describes the N-terminal region of proteins that are similar to, and nclude, the product of the paaX gene of Escherichia coli (P76086 from SWISSPROT). PaaX is a transcriptional regulator that is always found in association with operons believed to be involved in the degradation of phenylacetic acid []. The gene product has been shown to bind to the promoter sites and repress their transcription []. ; PDB: 3KFW_X 3L09_B.
Probab=49.83 E-value=44 Score=26.01 Aligned_cols=47 Identities=17% Similarity=0.197 Sum_probs=32.9
Q ss_pred CCCcHHHHHhh---cCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEech
Q 009896 33 GPLTRQNVKRY---TELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLF 85 (523)
Q Consensus 33 G~ltl~~l~~~---t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~~ 85 (523)
|.++...|+.. .+++...+|.||.-|.+.|.+...... ..++|.+-.
T Consensus 19 ~~i~~~~Li~ll~~~Gv~e~avR~alsRl~~~G~L~~~r~G------r~~~Y~Lt~ 68 (70)
T PF07848_consen 19 GWIWVASLIRLLAAFGVSESAVRTALSRLVRRGWLESERRG------RRSYYRLTE 68 (70)
T ss_dssp S-EEHHHHHHHHCCTT--HHHHHHHHHHHHHTTSEEEECCC------TEEEEEE-H
T ss_pred CceeHHHHHHHHHHcCCChHHHHHHHHHHHHcCceeeeecC------ccceEeeCC
Confidence 56788888766 689999999999999999999722221 257887643
No 184
>PRK09462 fur ferric uptake regulator; Provisional
Probab=49.82 E-value=46 Score=29.75 Aligned_cols=54 Identities=15% Similarity=0.212 Sum_probs=42.5
Q ss_pred HHHHHHHHHHHHc--CcCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccceecC
Q 009896 107 QQCVELVQGLLEH--GRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 163 (523)
Q Consensus 107 ~~a~~I~~~lL~~--G~~~~~~li~~~~~~~~~~~~~~~~~i~~~f~~Lv~~~fi~~v~ 163 (523)
..=..|++.|... +++++.+|.+.+....+ ..+...|-.++..|.+.|+|.++.
T Consensus 17 ~qR~~Il~~l~~~~~~h~sa~eI~~~l~~~~~---~i~~aTVYR~L~~L~e~Gli~~~~ 72 (148)
T PRK09462 17 LPRLKILEVLQEPDNHHVSAEDLYKRLIDMGE---EIGLATVYRVLNQFDDAGIVTRHN 72 (148)
T ss_pred HHHHHHHHHHHhCCCCCCCHHHHHHHHHhhCC---CCCHHHHHHHHHHHHHCCCEEEEE
Confidence 3445677777753 69999999999865432 346788999999999999999875
No 185
>PF09681 Phage_rep_org_N: N-terminal phage replisome organiser (Phage_rep_org_N); InterPro: IPR010056 This entry is represented by the N-terminal domain of Bacteriophage A500, Gp45. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. The proteins in this entry contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The low-complexity region is adjacent to this N-terminal domain.
Probab=49.73 E-value=41 Score=29.25 Aligned_cols=48 Identities=15% Similarity=0.196 Sum_probs=38.8
Q ss_pred CCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEechhhH
Q 009896 33 GPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFDNI 88 (523)
Q Consensus 33 G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~~~~i 88 (523)
.+-|...|+..++-+...|+.||.+|.+.|++. ...+ .++|-.++.+.
T Consensus 52 ipy~~e~LA~~~~~~~~~V~~AL~~f~k~glIe-~~ed-------~~i~i~~~~~~ 99 (121)
T PF09681_consen 52 IPYTAEMLALEFDRPVDTVRLALAVFQKLGLIE-IDED-------GVIYIPNWEKH 99 (121)
T ss_pred CCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEE-EecC-------CeEEeecHHHH
Confidence 366788888889999999999999999999998 4432 26787777654
No 186
>TIGR00122 birA_repr_reg BirA biotin operon repressor domain. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.
Probab=49.71 E-value=30 Score=26.37 Aligned_cols=41 Identities=12% Similarity=0.178 Sum_probs=35.5
Q ss_pred HHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 24 KVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 24 ~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
++... +..|+.+..+|+...+++.+.|++.+..|-+.|+..
T Consensus 4 ~il~~-L~~~~~~~~eLa~~l~vS~~tv~~~l~~L~~~g~~i 44 (69)
T TIGR00122 4 RLLAL-LADNPFSGEKLGEALGMSRTAVNKHIQTLREWGVDV 44 (69)
T ss_pred HHHHH-HHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeE
Confidence 45555 457788999999999999999999999999999975
No 187
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=48.86 E-value=47 Score=23.86 Aligned_cols=40 Identities=18% Similarity=0.285 Sum_probs=33.5
Q ss_pred HHHHHHHH-hcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhc
Q 009896 23 AKVCECLL-RKGPLTRQNVKRYTELSDEQVKNALLVLIQQN 62 (523)
Q Consensus 23 ~~V~~~Ll-~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn 62 (523)
.+|...|+ ..++.|..+|+...+++.+.|++-|-.|-..+
T Consensus 3 ~~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 3 KQILKLLLESKEPITAKELAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp HHHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 35677784 55679999999999999999999999998887
No 188
>PF11994 DUF3489: Protein of unknown function (DUF3489); InterPro: IPR021880 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 84 to 211 amino acids in length. This protein has a single completely conserved residue W that may be functionally important.
Probab=48.24 E-value=70 Score=25.09 Aligned_cols=43 Identities=21% Similarity=0.099 Sum_probs=37.7
Q ss_pred HHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHH--Hhhcccc
Q 009896 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVL--IQQNCVQ 65 (523)
Q Consensus 23 ~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vL--iQhn~V~ 65 (523)
+.|...|...+.-|+.+|+..|+-.+..||-+|.-+ =+.|+..
T Consensus 13 a~li~mL~rp~GATi~ei~~atGWq~HTvRgalsg~~kKklGl~i 57 (72)
T PF11994_consen 13 AQLIAMLRRPEGATIAEICEATGWQPHTVRGALSGLLKKKLGLTI 57 (72)
T ss_pred HHHHHHHcCCCCCCHHHHHHhhCCchhhHHHHHHHHHHHhcCcEE
Confidence 678889999999999999999999999999999999 4555554
No 189
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=47.07 E-value=53 Score=29.39 Aligned_cols=55 Identities=24% Similarity=0.331 Sum_probs=43.8
Q ss_pred HHHHHHHHHHHHc-CcCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccceecCC
Q 009896 107 QQCVELVQGLLEH-GRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCPA 164 (523)
Q Consensus 107 ~~a~~I~~~lL~~-G~~~~~~li~~~~~~~~~~~~~~~~~i~~~f~~Lv~~~fi~~v~~ 164 (523)
+.=..|++-|..+ |++++.++...+....+ ..+.+.|-+++..|.+.|+|.++..
T Consensus 21 ~qR~~vl~~L~~~~~~~sAeei~~~l~~~~p---~islaTVYr~L~~l~e~Glv~~~~~ 76 (145)
T COG0735 21 PQRLAVLELLLEADGHLSAEELYEELREEGP---GISLATVYRTLKLLEEAGLVHRLEF 76 (145)
T ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHHHHhCC---CCCHhHHHHHHHHHHHCCCEEEEEe
Confidence 4446778888866 77999999998876432 3568899999999999999999753
No 190
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=46.87 E-value=37 Score=30.17 Aligned_cols=49 Identities=12% Similarity=0.231 Sum_probs=43.6
Q ss_pred hHHHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccc
Q 009896 21 LVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTT 69 (523)
Q Consensus 21 ~v~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~ 69 (523)
.=.+|-..|...|+.|+.+|++..++++..|+.=+--|...|++.-|..
T Consensus 9 ~D~~IL~~L~~d~r~~~~eia~~lglS~~~v~~Ri~~L~~~GiI~~~~~ 57 (154)
T COG1522 9 IDRRILRLLQEDARISNAELAERVGLSPSTVLRRIKRLEEEGVIKGYTA 57 (154)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCceeeEEE
Confidence 3457888999999999999999999999999999999999999984443
No 191
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=46.73 E-value=33 Score=28.31 Aligned_cols=46 Identities=22% Similarity=0.190 Sum_probs=39.1
Q ss_pred CchHHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccce
Q 009896 381 RDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 427 (523)
Q Consensus 381 ~~a~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~ 427 (523)
+....|+..|.+-|-= -.+.|+....+|..+++..|-+|.+.|+|+
T Consensus 7 ~l~~~IL~hl~~~~~D-y~k~ia~~l~~~~~~v~~~l~~Le~~GLle 52 (92)
T PF10007_consen 7 PLDLKILQHLKKAGPD-YAKSIARRLKIPLEEVREALEKLEEMGLLE 52 (92)
T ss_pred hhHHHHHHHHHHHCCC-cHHHHHHHHCCCHHHHHHHHHHHHHCCCeE
Confidence 4567788888666555 678899999999999999999999999994
No 192
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=45.78 E-value=2.4e+02 Score=26.97 Aligned_cols=133 Identities=17% Similarity=0.293 Sum_probs=83.4
Q ss_pred hhhchhHH-HHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEE-------------
Q 009896 16 NHFGDLVA-KVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQY------------- 81 (523)
Q Consensus 16 ~~FG~~v~-~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y------------- 81 (523)
+..|.-.. +|.+.| .+-++-..+|++..+++++.|=.=|-.|-+-|+|..+-...+.|+.. -||
T Consensus 10 dvLGNetRR~Il~lL-t~~p~yvsEiS~~lgvsqkAVl~HL~~LE~AGlveS~ie~~~Rg~~r-KYY~Is~~~rleV~ls 87 (217)
T COG1777 10 DVLGNETRRRILQLL-TRRPCYVSEISRELGVSQKAVLKHLRILERAGLVESRIEKIPRGRPR-KYYMISRNLRLEVTLS 87 (217)
T ss_pred HHHcCcHHHHHHHHH-hcCchHHHHHHhhcCcCHHHHHHHHHHHHHcCCchhhccccccCCCc-ceeeccCCeEEEEEec
Confidence 55674444 455555 55558999999999999999999999999999999633332222100 011
Q ss_pred ---------Eec--------------------hhhHHHHh-------------------chhhHHHHHHHHhh-----HH
Q 009896 82 ---------VVL--------------------FDNILHRV-------------------RFAKFLTILSQEFD-----QQ 108 (523)
Q Consensus 82 ---------~~~--------------------~~~il~rl-------------------R~p~~i~~i~~~~G-----~~ 108 (523)
.++ ..+.+.++ ++..++..+++.++ .+
T Consensus 88 p~~f~~~~~~~~~~~l~~~r~~~~~~~~s~~~~~~l~srl~~~~~~~e~l~~~~~~L~~~~~el~~rik~~ied~~~~~~ 167 (217)
T COG1777 88 PNFFGAERFDLEEDDLESERSEVSKLFKSPEGISELISRLLEINREIEELSRAQTELQKQLNELMDRIKEEIEDKDGDMT 167 (217)
T ss_pred CcccceeccCccccchhhhhcchhhhcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccchHH
Confidence 111 12233332 23334455555554 34
Q ss_pred HHHHHHHHHHcCcCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhccccee
Q 009896 109 CVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVER 161 (523)
Q Consensus 109 a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~~~~i~~~f~~Lv~~~fi~~ 161 (523)
-..|++.|+.||-.++.+.... +...+...+..|...||+..
T Consensus 168 ~~~vl~~l~~n~~~~v~E~~r~-----------~~~~i~~vle~l~e~g~v~i 209 (217)
T COG1777 168 ERIVLEYLLKNGAADVEETSRR-----------TVLKIEEVLEILAEKGFVEI 209 (217)
T ss_pred HHHHHHHHHhhhhhHHHHHHhc-----------cchhHHHHHHHHhhccceee
Confidence 5678888888885555555444 33457889999999997644
No 193
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=45.28 E-value=36 Score=23.69 Aligned_cols=31 Identities=19% Similarity=0.291 Sum_probs=22.1
Q ss_pred HHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHH
Q 009896 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNAL 55 (523)
Q Consensus 23 ~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL 55 (523)
..|.. |+..| .|+.+|++.++++...|...|
T Consensus 12 ~~i~~-l~~~G-~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 12 EEIKE-LYAEG-MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp HHHHH-HHHTT---HHHHHHHTTS-HHHHHHHH
T ss_pred HHHHH-HHHCC-CCHHHHHHHHCcCHHHHHHHH
Confidence 34444 67788 899999999999999987654
No 194
>PF07381 DUF1495: Winged helix DNA-binding domain (DUF1495); InterPro: IPR010863 This family consists of several hypothetical archaeal proteins of around 110 residues in length. The function of this family is unknown, although one sequence (Q8U3W1 from SWISSPROT) is described as a putative HTH transcription regulator.
Probab=45.11 E-value=76 Score=26.05 Aligned_cols=60 Identities=20% Similarity=0.123 Sum_probs=45.6
Q ss_pred HHHHHHHHhc--CCCcHHHHHhhcCCCHHHHHHHHH----------HHHhhcccccccccCCCCCCcceEEEechhh
Q 009896 23 AKVCECLLRK--GPLTRQNVKRYTELSDEQVKNALL----------VLIQQNCVQAFTTEQPDGPKANTQYVVLFDN 87 (523)
Q Consensus 23 ~~V~~~Ll~~--G~ltl~~l~~~t~l~~~~vr~aL~----------vLiQhn~V~~~~~~~~~~~~~~~~Y~~~~~~ 87 (523)
.+|..+|... .+.++.+|++.++.+++.|+-||. .|+..|+|....... ...+|.+....
T Consensus 12 ~~vl~~L~~~yp~~~~~~eIar~v~~~~snV~GaL~G~g~rY~~e~SLv~lGLV~~~~~~~-----g~k~Y~lT~~G 83 (90)
T PF07381_consen 12 KKVLEYLCSIYPEPAYPSEIARSVGSDYSNVLGALRGDGKRYNKEDSLVGLGLVEEEEEKG-----GFKYYRLTEKG 83 (90)
T ss_pred HHHHHHHHHcCCCcCCHHHHHHHHCCCHHHHHHHHhcCCCCcCcchhHHHcCCeeEeeecC-----CeeEEEeChhh
Confidence 5678888887 356788999999999999999996 799999994222221 23588887654
No 195
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=45.02 E-value=31 Score=30.53 Aligned_cols=32 Identities=13% Similarity=0.079 Sum_probs=30.5
Q ss_pred CCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 34 PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 34 ~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
+.+..+|+...++|+.-|+++|..|.++|+|.
T Consensus 25 ~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~ 56 (141)
T PRK11014 25 MTSISEVTEVYGVSRNHMVKIINQLSRAGYVT 56 (141)
T ss_pred ccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEE
Confidence 56889999999999999999999999999998
No 196
>PRK09462 fur ferric uptake regulator; Provisional
Probab=44.81 E-value=72 Score=28.45 Aligned_cols=60 Identities=13% Similarity=0.094 Sum_probs=45.3
Q ss_pred hhHHHHHHHHHhc--CCCcHHHHHhh-----cCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEec
Q 009896 20 DLVAKVCECLLRK--GPLTRQNVKRY-----TELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVL 84 (523)
Q Consensus 20 ~~v~~V~~~Ll~~--G~ltl~~l~~~-----t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~ 84 (523)
+-=..|.++|... +.+|..+|... .++++..|-.+|-.|.+.|+|.-+...+ ...+|..+
T Consensus 17 ~qR~~Il~~l~~~~~~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~Gli~~~~~~~-----~~~~y~~~ 83 (148)
T PRK09462 17 LPRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRHNFEG-----GKSVFELT 83 (148)
T ss_pred HHHHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCCEEEEEcCC-----CcEEEEeC
Confidence 3445788889863 69999999765 3588999999999999999998554432 13578764
No 197
>PRK09954 putative kinase; Provisional
Probab=44.59 E-value=23 Score=36.70 Aligned_cols=43 Identities=14% Similarity=0.325 Sum_probs=39.3
Q ss_pred HHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccce
Q 009896 384 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 427 (523)
Q Consensus 384 ~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~ 427 (523)
.+|+++|.+.+.+ ...+|++..-++...++..+.+|.++|+|.
T Consensus 6 ~~il~~l~~~~~~-s~~~la~~l~~s~~~v~~~i~~L~~~g~i~ 48 (362)
T PRK09954 6 KEILAILRRNPLI-QQNEIADILQISRSRVAAHIMDLMRKGRIK 48 (362)
T ss_pred HHHHHHHHHCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHCCCcC
Confidence 3689999887777 999999999999999999999999999984
No 198
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=44.56 E-value=35 Score=33.67 Aligned_cols=44 Identities=18% Similarity=0.372 Sum_probs=41.1
Q ss_pred HHHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 22 VAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 22 v~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
=.+|...|-.+|+.++.+|++..+++...||.=|-.|-+.|+|.
T Consensus 7 ~~~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~Le~~g~l~ 50 (256)
T PRK10434 7 QAAILEYLQKQGKTSVEELAQYFDTTGTTIRKDLVILEHAGTVI 50 (256)
T ss_pred HHHHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 35788999999999999999999999999999999999999886
No 199
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=44.52 E-value=31 Score=31.12 Aligned_cols=55 Identities=22% Similarity=0.144 Sum_probs=45.8
Q ss_pred cCCchHHHHHHHHhhCC--CcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEec
Q 009896 379 YGRDAYRIFRLLSKSGR--LLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVV 433 (523)
Q Consensus 379 ~G~~a~RI~r~L~~k~~--l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQEvpk 433 (523)
.|.-|+|++=.|..+.. ++.-++|++.--+|+.-.++++.+|-+.|+|+-..=|+
T Consensus 6 ~~~yal~~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~kaGlV~S~rG~~ 62 (150)
T COG1959 6 KGEYALRALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLRKAGLVKSVRGKG 62 (150)
T ss_pred hHhHHHHHHHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHHcCCEEeecCCC
Confidence 46678888888865543 66899999999999999999999999999998864444
No 200
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=44.44 E-value=23 Score=26.66 Aligned_cols=35 Identities=17% Similarity=0.251 Sum_probs=30.1
Q ss_pred CCCc-chhhhhhhcCCCcccHHHHHHHHhhcccceE
Q 009896 394 GRLL-ETDKISDTTFVEKKDAPKILYKLWKDGYLLM 428 (523)
Q Consensus 394 ~~l~-eek~i~~~ami~~k~~R~~L~~L~~~g~v~l 428 (523)
|..+ .+.+|++.--++...+|+.|..|..+|+|+.
T Consensus 21 g~~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~~ 56 (64)
T PF00392_consen 21 GDRLPSERELAERYGVSRTTVREALRRLEAEGLIER 56 (64)
T ss_dssp TSBE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred CCEeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEEE
Confidence 4555 8999999999999999999999999999976
No 201
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=44.05 E-value=27 Score=27.49 Aligned_cols=41 Identities=22% Similarity=0.345 Sum_probs=31.7
Q ss_pred HHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccc
Q 009896 384 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYL 426 (523)
Q Consensus 384 ~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v 426 (523)
..|+..+. +|.. .-.+|+..+-++.+.+.+.|..|.+.|+|
T Consensus 9 ~~IL~~l~-~~~~-~~t~i~~~~~L~~~~~~~yL~~L~~~gLI 49 (77)
T PF14947_consen 9 FDILKILS-KGGA-KKTEIMYKANLNYSTLKKYLKELEEKGLI 49 (77)
T ss_dssp HHHHHHH--TT-B--HHHHHTTST--HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHH-cCCC-CHHHHHHHhCcCHHHHHHHHHHHHHCcCe
Confidence 34566663 6777 88999999999999999999999999999
No 202
>PF01638 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002577 The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure. The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde []. The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH []. The crystal structure of ytfH resembles the DNA-binding domains of winged helix proteins, containing a three helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-H2-B1-H3-H4-B2-B3-H5-H6. This topology corresponds with that of the marR-type DNA-binding domain, wherein helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. ; PDB: 2F2E_B 3DF8_A 1Z7U_B 1YYV_A 4A5M_D 4A5N_B 2FSW_A 2HZT_D.
Probab=43.31 E-value=44 Score=27.05 Aligned_cols=47 Identities=21% Similarity=0.345 Sum_probs=37.6
Q ss_pred HHHHHHHHHHcCcCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccceecC
Q 009896 109 CVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 163 (523)
Q Consensus 109 a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~~~~i~~~f~~Lv~~~fi~~v~ 163 (523)
...|+..|.. |..+.+++.+.+.. .+...+.+.+..|.++|+|.+..
T Consensus 7 ~~~IL~~l~~-g~~rf~el~~~l~~-------is~~~L~~~L~~L~~~GLv~r~~ 53 (90)
T PF01638_consen 7 TLLILRALFQ-GPMRFSELQRRLPG-------ISPKVLSQRLKELEEAGLVERRV 53 (90)
T ss_dssp HHHHHHHHTT-SSEEHHHHHHHSTT-------S-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHh-CCCcHHHHHHhcch-------hHHHHHHHHHHHHHHcchhhccc
Confidence 4566777776 99999999888632 25678999999999999999974
No 203
>PF04337 DUF480: Protein of unknown function, DUF480; InterPro: IPR007432 This family consists of several proteins of uncharacterised function.; PDB: 3BZ6_A.
Probab=43.11 E-value=54 Score=29.34 Aligned_cols=49 Identities=22% Similarity=0.263 Sum_probs=36.7
Q ss_pred hhchhHHHHHHHHHhcCCCcHHHHHhhcC-C----CHHHHHHHHHHHHhhc--ccc
Q 009896 17 HFGDLVAKVCECLLRKGPLTRQNVKRYTE-L----SDEQVKNALLVLIQQN--CVQ 65 (523)
Q Consensus 17 ~FG~~v~~V~~~Ll~~G~ltl~~l~~~t~-l----~~~~vr~aL~vLiQhn--~V~ 65 (523)
.|.+--..|.-.|+-||++|..+|-..++ + +...|...|--|++++ +|.
T Consensus 85 ~l~~~e~All~~LlLRGpQT~GELR~Rs~Rl~~F~d~~~Ve~~L~~L~~r~~plV~ 140 (148)
T PF04337_consen 85 QLSPQELALLCLLLLRGPQTPGELRTRSERLHEFADVAEVEAVLERLAEREPPLVV 140 (148)
T ss_dssp T--HHHHHHHHHHHHH-SB-HHHHHHHHTTTS--SSHHHHHHHHHHHHHTT--SEE
T ss_pred CCCHHHHHHHHHHHHcCCCchhHHHhhhccccCCCCHHHHHHHHHHHHhccchhhe
Confidence 45566667888889999999999976654 2 6789999999999999 664
No 204
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=42.54 E-value=33 Score=32.09 Aligned_cols=44 Identities=9% Similarity=-0.006 Sum_probs=41.2
Q ss_pred HHHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 22 VAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 22 v~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
=..|...|..+|..++.+|++..+.+...||.=|..|-+.|.|.
T Consensus 9 ~~~Il~~l~~~~~~~~~~La~~~~vS~~TiRRDl~~L~~~g~~~ 52 (185)
T PRK04424 9 QKALQELIEENPFITDEELAEKFGVSIQTIRLDRMELGIPELRE 52 (185)
T ss_pred HHHHHHHHHHCCCEEHHHHHHHHCcCHHHHHHHHHHHhcchHHH
Confidence 35788899999999999999999999999999999999999887
No 205
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=42.30 E-value=33 Score=31.50 Aligned_cols=50 Identities=16% Similarity=0.145 Sum_probs=41.3
Q ss_pred CCchHHHHHHHHhh--CCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEE
Q 009896 380 GRDAYRIFRLLSKS--GRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLME 429 (523)
Q Consensus 380 G~~a~RI~r~L~~k--~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQ 429 (523)
..-|+|++-.|..+ +..+.-++|++.-.+|.+-++++|.+|.+.|+|.-+
T Consensus 7 ~~yAl~~l~~lA~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s~ 58 (164)
T PRK10857 7 GRYAVTAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSV 58 (164)
T ss_pred HHHHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeC
Confidence 34577888777643 235699999999999999999999999999999753
No 206
>PF04492 Phage_rep_O: Bacteriophage replication protein O ; InterPro: IPR006497 This entry is represented by the N-terminal domain of Bacteriophage lambda, GpO. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0006260 DNA replication
Probab=42.02 E-value=89 Score=26.15 Aligned_cols=32 Identities=25% Similarity=0.391 Sum_probs=30.5
Q ss_pred CCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 34 PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 34 ~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
+.|..++...|++++..|..++-.|+.-|++.
T Consensus 54 ~Is~sq~~e~tg~~~~~V~~al~~Li~~~vI~ 85 (100)
T PF04492_consen 54 RISNSQIAEMTGLSRDHVSKALNELIRRGVII 85 (100)
T ss_pred eeeHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 78999999999999999999999999999995
No 207
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=41.46 E-value=42 Score=33.02 Aligned_cols=43 Identities=16% Similarity=0.239 Sum_probs=40.7
Q ss_pred HHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 23 ~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
.+|.+.|-.+|.+++.+|.+..+++...||.=|..|-+.|++.
T Consensus 8 ~~Il~~l~~~~~~~~~ela~~l~vS~~TiRRdL~~Le~~g~l~ 50 (252)
T PRK10906 8 DAIIELVKQQGYVSTEELVEHFSVSPQTIRRDLNDLAEQNKIL 50 (252)
T ss_pred HHHHHHHHHcCCEeHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence 5788899999999999999999999999999999999999986
No 208
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=41.13 E-value=42 Score=26.41 Aligned_cols=46 Identities=11% Similarity=0.057 Sum_probs=36.2
Q ss_pred hhHHHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 20 DLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 20 ~~v~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
+.+..++...-....+|..+|++.+++|.+.|++-+..+.+.+.+.
T Consensus 18 ~~~r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~~~~~~~~~ 63 (73)
T TIGR03879 18 SLAEAAAALAREEAGKTASEIAEELGRTEQTVRNHLKGETKAGGLV 63 (73)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcCcccchHH
Confidence 4455555555444778999999999999999999998888877554
No 209
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=40.73 E-value=82 Score=28.17 Aligned_cols=60 Identities=23% Similarity=0.246 Sum_probs=45.0
Q ss_pred HHHHHHHHhc-CCCcHHHHHhh-----cCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEechhh
Q 009896 23 AKVCECLLRK-GPLTRQNVKRY-----TELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFDN 87 (523)
Q Consensus 23 ~~V~~~Ll~~-G~ltl~~l~~~-----t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~~~~ 87 (523)
..|.++|... +++|..+|.+. .++++..|-++|=.|...|+|.-+...+ ..+.|+.+...
T Consensus 24 ~~vl~~L~~~~~~~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~~~~~~-----~~~~y~~~~~~ 89 (145)
T COG0735 24 LAVLELLLEADGHLSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHRLEFEG-----GKTRYELNSEP 89 (145)
T ss_pred HHHHHHHHhcCCCCCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCCCEEEEEeCC-----CEEEEecCCCC
Confidence 3577888865 67888888655 4689999999999999999998555542 24677766553
No 210
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=40.51 E-value=1e+02 Score=28.47 Aligned_cols=69 Identities=22% Similarity=0.178 Sum_probs=51.6
Q ss_pred HHHHHHHHHHHHH--HHcCCc--hHHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEe
Q 009896 364 EIAQNEEVESVVS--KRYGRD--AYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLV 432 (523)
Q Consensus 364 ~~lr~~~le~~v~--~~~G~~--a~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQEvp 432 (523)
+..++..++.+-+ .+||.. ..+|+-+|.-..+-..-.+|++...|+..-+=..+-+|...|+|+.+-.|
T Consensus 5 eqak~~~Ie~fae~m~r~G~nrtVG~iYgilyls~~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~~~lV~~~~~~ 77 (177)
T COG1510 5 EQAKDIFIEHFAETMSRWGINRTVGQIYGILYLSRKPLTLDEIAEALGMSKSNVSMGLKKLQDWNLVKKVFEK 77 (177)
T ss_pred HHHHHHHHHHHHHHHHHhCCcchHHHHhhhheecCCCccHHHHHHHHCCCcchHHHHHHHHHhcchHHhhhcc
Confidence 3444555555543 556643 45777788664454499999999999999999999999999999776666
No 211
>PRK10344 DNA-binding transcriptional regulator Nlp; Provisional
Probab=40.41 E-value=57 Score=26.68 Aligned_cols=34 Identities=29% Similarity=0.302 Sum_probs=29.0
Q ss_pred HHHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHH
Q 009896 22 VAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALL 56 (523)
Q Consensus 22 v~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~ 56 (523)
.+.|...|-.+| .||..|++..|++.+.++++|.
T Consensus 10 ~adI~AaL~KrG-~sLa~lsr~~Gls~~TL~nAL~ 43 (92)
T PRK10344 10 PADIIAGLRKKG-TSMAAESRRNGLSSSTLANALS 43 (92)
T ss_pred HHHHHHHHHHcC-CcHHHHHHHcCCChHHHHHHHc
Confidence 356777888888 5999999999999999999874
No 212
>COG2238 RPS19A Ribosomal protein S19E (S16A) [Translation, ribosomal structure and biogenesis]
Probab=40.32 E-value=90 Score=27.74 Aligned_cols=57 Identities=16% Similarity=0.271 Sum_probs=44.1
Q ss_pred HHHHHHHHHHHHcCcCCHHHHHHHhhhcccCCC------ccCHHHHHHHHHHHHhcccceecC
Q 009896 107 QQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGN------LVDLDSLRETLVKLVTAHYVERCP 163 (523)
Q Consensus 107 ~~a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~------~~~~~~i~~~f~~Lv~~~fi~~v~ 163 (523)
.-||.|+-.+..+|.+.++-+-........-|. .-+.+-++.+|.+|-+.|||+..|
T Consensus 53 ~RaASilRkiyi~gpvGi~rL~t~YGg~k~rG~rP~~~~~gsgsI~RkilqqLE~~G~V~k~~ 115 (147)
T COG2238 53 VRAASILRKIYIDGPVGIERLRTAYGGRKNRGSRPEKFRKGSGSIIRKVLQQLEKAGLVEKTP 115 (147)
T ss_pred HHHHHHHHHHHhcCchhHHHHHHHHCccccCCCCchhhhcCCchHHHHHHHHHHHCCceeecC
Confidence 348889999999999998888777665433222 125677899999999999999986
No 213
>PF13730 HTH_36: Helix-turn-helix domain
Probab=40.18 E-value=22 Score=25.63 Aligned_cols=29 Identities=10% Similarity=0.282 Sum_probs=27.7
Q ss_pred chhhhhhhcCCCcccHHHHHHHHhhcccc
Q 009896 398 ETDKISDTTFVEKKDAPKILYKLWKDGYL 426 (523)
Q Consensus 398 eek~i~~~ami~~k~~R~~L~~L~~~g~v 426 (523)
..++|++...++.+.+++.+..|.+.|||
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHCcCC
Confidence 78999999999999999999999999986
No 214
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=39.75 E-value=1.1e+02 Score=23.31 Aligned_cols=48 Identities=15% Similarity=0.196 Sum_probs=34.7
Q ss_pred HHHHHHHHHHcCcCC-HHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccceecC
Q 009896 109 CVELVQGLLEHGRLT-LKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 163 (523)
Q Consensus 109 a~~I~~~lL~~G~~~-~~~li~~~~~~~~~~~~~~~~~i~~~f~~Lv~~~fi~~v~ 163 (523)
-..|.+.+-.+|... +.+|.+.+.- .|...+...+..|.+.|||.+.|
T Consensus 12 L~~I~~~~~~~G~~Pt~rEIa~~~g~-------~S~~tv~~~L~~Le~kG~I~r~~ 60 (65)
T PF01726_consen 12 LEFIREYIEENGYPPTVREIAEALGL-------KSTSTVQRHLKALERKGYIRRDP 60 (65)
T ss_dssp HHHHHHHHHHHSS---HHHHHHHHTS-------SSHHHHHHHHHHHHHTTSEEEGC
T ss_pred HHHHHHHHHHcCCCCCHHHHHHHhCC-------CChHHHHHHHHHHHHCcCccCCC
Confidence 345666677788775 4666665432 26788999999999999999986
No 215
>PF04157 EAP30: EAP30/Vps36 family; InterPro: IPR007286 EAP30 is a subunit of the ELL complex. The ELL is an 80kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity. ; PDB: 2ZME_A 3CUQ_A 1W7P_D 1U5T_B.
Probab=39.27 E-value=1.1e+02 Score=29.44 Aligned_cols=106 Identities=18% Similarity=0.212 Sum_probs=70.2
Q ss_pred CCccccHHHHHHHhhhhc-cCCCCCHHHHHHHHHHhccCC----CCCCCCCeEEEehHHHHHHHHHHHHHHHHHHHcCCc
Q 009896 308 NSVPLSLSSIYEEVIKSE-AGRNMTLDHVRASLVQLGELS----FVDASSDSYSIDFEKIIEIAQNEEVESVVSKRYGRD 382 (523)
Q Consensus 308 ~s~~~s~~~I~~~l~~~~-~~~~~~~~~i~~~L~~La~~~----~~~~~~~~y~V~~~~i~~~lr~~~le~~v~~~~G~~ 382 (523)
++.-+++.++...+.+.- ....++++.+.+.++.|..-. ....++|...|-...-.+. +..
T Consensus 110 ~GGii~L~dl~~~~nr~R~g~~lISp~Di~~A~~~l~~lg~g~~l~~~~sg~~vv~s~~~~e~--------------~~~ 175 (223)
T PF04157_consen 110 NGGIISLSDLYCRYNRARGGSELISPEDILRACKLLEVLGLGFRLRKFGSGVKVVQSVPYSEL--------------SKD 175 (223)
T ss_dssp TTSEEEHHHHHHHHHHCTTTSST--HHHHHHHHHHHCCCTSSEEEEEETTTEEEEECST-CHH---------------HH
T ss_pred CCCEEEHHHHHHHHHHhcccCCCcCHHHHHHHHHHHHHcCCCeEEEEeCCCcEEEEeCCchhh--------------hHH
Confidence 445789999999888754 233578889999998886554 1244455655554442221 222
Q ss_pred hHHHHHHH-HhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccce
Q 009896 383 AYRIFRLL-SKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 427 (523)
Q Consensus 383 a~RI~r~L-~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~ 427 (523)
+.+|+.++ ...+..++..++++....+..-|++.|..|..+|++-
T Consensus 176 ~~~il~~~~~~~~g~vt~~~l~~~~~ws~~~a~~~L~~~~~~G~l~ 221 (223)
T PF04157_consen 176 QSRILELAEEENGGGVTASELAEKLGWSVERAKEALEELEREGLLW 221 (223)
T ss_dssp HHHHHHHH--TTTSEEEHHHHHHHHTB-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHhhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCEe
Confidence 34555555 2333444999999999999999999999999999984
No 216
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=39.21 E-value=25 Score=25.89 Aligned_cols=31 Identities=13% Similarity=0.177 Sum_probs=28.7
Q ss_pred chhhhhhhcCCCcccHHHHHHHHhhcccceE
Q 009896 398 ETDKISDTTFVEKKDAPKILYKLWKDGYLLM 428 (523)
Q Consensus 398 eek~i~~~ami~~k~~R~~L~~L~~~g~v~l 428 (523)
...+|++...++...+++.|.+|.+.|+|..
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L~~~G~i~~ 57 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELEAEGLVER 57 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence 4889999999999999999999999999854
No 217
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=39.16 E-value=31 Score=26.60 Aligned_cols=33 Identities=24% Similarity=0.406 Sum_probs=30.6
Q ss_pred CCcchhhhhhhcCCCcccHHHHHHHHhhcccceE
Q 009896 395 RLLETDKISDTTFVEKKDAPKILYKLWKDGYLLM 428 (523)
Q Consensus 395 ~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~l 428 (523)
.+ ..++||+.+.++...+-..|.+|.++|+|+.
T Consensus 28 ~l-t~~~iA~~~g~sr~tv~r~l~~l~~~g~I~~ 60 (76)
T PF13545_consen 28 PL-TQEEIADMLGVSRETVSRILKRLKDEGIIEV 60 (76)
T ss_dssp ES-SHHHHHHHHTSCHHHHHHHHHHHHHTTSEEE
T ss_pred cC-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 35 8999999999999999999999999999975
No 218
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=39.01 E-value=1.5e+02 Score=28.47 Aligned_cols=54 Identities=13% Similarity=0.181 Sum_probs=42.6
Q ss_pred hCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCceEEEEEEEchHHHHH
Q 009896 393 SGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQILWK 453 (523)
Q Consensus 393 k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQEvpk~~~~~~t~~lw~v~~~~~~~ 453 (523)
-|.-+.|.+|++.-.++..-+|+.|.+|..+|+|... |++-++.=.++...+..
T Consensus 36 pG~~l~e~~La~~~gvSrtPVReAL~rL~~eGlv~~~-------p~rG~~V~~~~~~~~~e 89 (230)
T COG1802 36 PGERLSEEELAEELGVSRTPVREALRRLEAEGLVEIE-------PNRGAFVAPLSLAEARE 89 (230)
T ss_pred CCCCccHHHHHHHhCCCCccHHHHHHHHHHCCCeEec-------CCCCCeeCCCCHHHHHH
Confidence 3544499999999999999999999999999999773 44456666666665554
No 219
>TIGR01714 phage_rep_org_N phage replisome organizer, putative, N-terminal region. This model represents the N-terminal domain of a small family of phage proteins. The protein contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The region covered by this model is N-terminal to the low-complexity region.
Probab=38.84 E-value=59 Score=28.15 Aligned_cols=47 Identities=6% Similarity=0.133 Sum_probs=36.7
Q ss_pred CCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEechhh
Q 009896 33 GPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFDN 87 (523)
Q Consensus 33 G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~~~~ 87 (523)
.+-|...|+.-++-+...|+.||.+|.+.|++. ...+ .++|-.|++.
T Consensus 50 ipy~~e~LA~~~~~~~~~V~~Al~~f~k~glIe-~~d~-------g~i~i~~~~~ 96 (119)
T TIGR01714 50 APYNAEMLATMFNRNVGDIRITLQTLESLGLIE-KKNN-------GDIFLENWEK 96 (119)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE-EecC-------CcEEehhHHH
Confidence 355677778888999999999999999999998 4432 1577777764
No 220
>PF09743 DUF2042: Uncharacterized conserved protein (DUF2042); InterPro: IPR018611 The ubiquitin fold modifier 1 (Ufm1) is the most recently discovered ubiquitin-like modifier whose conjugation (ufmylation) system is conserved in multicellular organisms. Ufm1 is known to covalently attach with cellular protein(s) via a specific E1-activating enzyme (Uba5), an E2-conjugating enzyme (Ufc1), and a E3-ligating enzyme []. This entry represents E3 UFM1-protein ligase 1.
Probab=38.35 E-value=1.5e+02 Score=29.65 Aligned_cols=52 Identities=15% Similarity=0.241 Sum_probs=43.2
Q ss_pred HHhhhchhHHHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 14 ITNHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 14 v~~~FG~~v~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
=++++-.++..|-+.|-.+|..++.+|++..+||..-+++.++.-.-...+.
T Consensus 110 t~~Yld~l~~Eine~Lqe~G~vsi~eLa~~~~Lp~efl~~~li~~~lg~~I~ 161 (272)
T PF09743_consen 110 TDSYLDSLAEEINEKLQESGQVSISELAKQYDLPSEFLKEELISKRLGKIIK 161 (272)
T ss_pred cHHHHHHHHHHHHHHHHHcCeEeHHHHHHhcCCcHHHHHHHHhhhhcCccee
Confidence 3457778899999999999999999999999999998887777665455544
No 221
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=38.26 E-value=90 Score=28.09 Aligned_cols=50 Identities=14% Similarity=0.193 Sum_probs=39.3
Q ss_pred chhHHHHHHHHHhcC---CCcHHHHHhhcCCCHHHHHHHHHHHHhhccccccc
Q 009896 19 GDLVAKVCECLLRKG---PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFT 68 (523)
Q Consensus 19 G~~v~~V~~~Ll~~G---~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~ 68 (523)
|+.+=.+--+|..++ ..|+.+|+...++|+.-+++.|.-|-+.|+|....
T Consensus 7 ~~yal~~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~kaGlV~S~r 59 (150)
T COG1959 7 GEYALRALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLRKAGLVKSVR 59 (150)
T ss_pred HhHHHHHHHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHHcCCEEeec
Confidence 344444555555443 57899999999999999999999999999998333
No 222
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=37.98 E-value=51 Score=31.49 Aligned_cols=49 Identities=14% Similarity=0.115 Sum_probs=37.8
Q ss_pred hhchhHHHHHHHHHhcC-CCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 17 HFGDLVAKVCECLLRKG-PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 17 ~FG~~v~~V~~~Ll~~G-~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
.|..+-..|.+-=+.-| ++|-.+|+...+++..-||.||..|.+-|+|.
T Consensus 12 vy~~i~~~I~~g~l~pG~~L~e~eLae~lgVSRtpVREAL~~L~~eGlv~ 61 (224)
T PRK11534 12 GYRWLKNDIIRGNFQPDEKLRMSLLTSRYALGVGPLREALSQLVAERLVT 61 (224)
T ss_pred HHHHHHHHHHhCCCCCCCcCCHHHHHHHHCCChHHHHHHHHHHHHCCCEE
Confidence 33334444444434445 77889999999999999999999999999998
No 223
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=37.77 E-value=32 Score=24.76 Aligned_cols=31 Identities=13% Similarity=0.174 Sum_probs=28.9
Q ss_pred chhhhhhhcCCCcccHHHHHHHHhhcccceE
Q 009896 398 ETDKISDTTFVEKKDAPKILYKLWKDGYLLM 428 (523)
Q Consensus 398 eek~i~~~ami~~k~~R~~L~~L~~~g~v~l 428 (523)
.+.+|++..-++...+++.|.+|.++|+|..
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~L~~~g~i~~ 52 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSRLEAEGLVQR 52 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 7889999999999999999999999999853
No 224
>PRK09775 putative DNA-binding transcriptional regulator; Provisional
Probab=37.72 E-value=65 Score=34.60 Aligned_cols=43 Identities=23% Similarity=0.332 Sum_probs=37.5
Q ss_pred HHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccc
Q 009896 25 VCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTT 69 (523)
Q Consensus 25 V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~ 69 (523)
...+++..|+.|..+|....+++...|-+-|.+| .++|.....
T Consensus 4 ~~~~~L~~g~~~~~eL~~~l~~sq~~~s~~L~~L--~~~V~~~~~ 46 (442)
T PRK09775 4 LLTTLLLQGPLSAAELAARLGVSQATLSRLLAAL--GDQVVRFGK 46 (442)
T ss_pred HHHHHHhcCCCCHHHHHHHhCCCHHHHHHHHHHh--hcceeEecc
Confidence 4567888999999999999999999999999999 888874443
No 225
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=37.32 E-value=44 Score=30.32 Aligned_cols=42 Identities=24% Similarity=0.345 Sum_probs=36.7
Q ss_pred HHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceE
Q 009896 386 IFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLM 428 (523)
Q Consensus 386 I~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~l 428 (523)
|+.+...+|.. -.++||+.--+++..+.+.+.+|.+.|||..
T Consensus 15 Iy~l~~~~~~~-~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~~ 56 (154)
T COG1321 15 IYELLEEKGFA-RTKDIAERLKVSPPSVTEMLKRLERLGLVEY 56 (154)
T ss_pred HHHHHhccCcc-cHHHHHHHhCCCcHHHHHHHHHHHHCCCeEE
Confidence 55566556566 9999999999999999999999999999966
No 226
>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY. This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.
Probab=36.76 E-value=37 Score=33.15 Aligned_cols=48 Identities=27% Similarity=0.250 Sum_probs=42.4
Q ss_pred HHHHHHHHh-hCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEe
Q 009896 384 YRIFRLLSK-SGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLV 432 (523)
Q Consensus 384 ~RI~r~L~~-k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQEvp 432 (523)
-+|++.|-. .|.+ .+.+|++...++..-+|+.+-+|...|+|+.+...
T Consensus 186 ~~IL~~L~~~egrl-se~eLAerlGVSRs~ireAlrkLE~aGvIe~r~LG 234 (251)
T TIGR02787 186 EHIFEELDGNEGLL-VASKIADRVGITRSVIVNALRKLESAGVIESRSLG 234 (251)
T ss_pred HHHHHHhccccccc-cHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCC
Confidence 368888866 4788 99999999999999999999999999999887644
No 227
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=36.65 E-value=55 Score=32.54 Aligned_cols=45 Identities=16% Similarity=0.221 Sum_probs=42.1
Q ss_pred hHHHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 21 LVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 21 ~v~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
--.+|...|-.+|..++.+|++..+++...||.=|..|-+.|++.
T Consensus 18 R~~~Il~~L~~~~~vtv~eLa~~l~VS~~TIRRDL~~Le~~G~l~ 62 (269)
T PRK09802 18 RREQIIQRLRQQGSVQVNDLSALYGVSTVTIRNDLAFLEKQGIAV 62 (269)
T ss_pred HHHHHHHHHHHcCCEeHHHHHHHHCCCHHHHHHHHHHHHhCCCeE
Confidence 456788999999999999999999999999999999999999987
No 228
>KOG2165 consensus Anaphase-promoting complex (APC), subunit 2 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=36.02 E-value=5.9e+02 Score=28.88 Aligned_cols=138 Identities=15% Similarity=0.123 Sum_probs=83.2
Q ss_pred HHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhccccccccc-CCCC------------CCcceEEEechhhHH
Q 009896 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTE-QPDG------------PKANTQYVVLFDNIL 89 (523)
Q Consensus 23 ~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~~-~~~~------------~~~~~~Y~~~~~~il 89 (523)
+.|...-......|+.+++..+++|+..++.=|-..||||++.--+.. +++. ..+.+.-++..++
T Consensus 605 A~iI~~Fqek~twt~eelse~l~ip~~~lrrrL~fWi~~GvL~e~~~~s~tgt~T~iEse~d~~q~~~~~~~e~eee~-- 682 (765)
T KOG2165|consen 605 AAIINLFQEKNTWTLEELSESLGIPVPALRRRLSFWIQKGVLREEPIISDTGTLTVIESEMDFDQAEGTVLLEAEEEN-- 682 (765)
T ss_pred HHHHHHhcCcccccHHHHHHHhCCCHHHHHHHHHHHHHcCeeecCCCCCCCceeeeccccccccccCCCccccccccc--
Confidence 344444455677999999999999999999999999999999722210 0000 0011111111111
Q ss_pred HHhchhhHHHHHHHHhhHHHHHHHHHHHHcCcCCHHHHHHHhhhcc-cCCC-ccCHHHHHHHHHHHHhcccceec
Q 009896 90 HRVRFAKFLTILSQEFDQQCVELVQGLLEHGRLTLKQMFDRAKSSE-KEGN-LVDLDSLRETLVKLVTAHYVERC 162 (523)
Q Consensus 90 ~rlR~p~~i~~i~~~~G~~a~~I~~~lL~~G~~~~~~li~~~~~~~-~~~~-~~~~~~i~~~f~~Lv~~~fi~~v 162 (523)
.=.+-..++..-+++++-.-.-|+--|-..|.+.++-+-..+.=-. +.+. ..+..+++.-+..+|..|-++-.
T Consensus 683 ~e~~~as~vdqle~el~~~~~fI~gMLTNlgsm~leRIHnmLkmF~~~~~~~~~TlqeL~~fLq~kV~e~kL~f~ 757 (765)
T KOG2165|consen 683 YESHNASEVDQLEEELTLFRSFIVGMLTNLGSMKLERIHNMLKMFVPPDGSAEITLQELQGFLQRKVREGKLEFI 757 (765)
T ss_pred chhhhhhHHHHHHHHHHHHHHHHHHHhcCcccchHHHHHHHHeeeecCCCCCcccHHHHHHHHHHHhhccceEEe
Confidence 1122334555566666644444544444449998766644332111 2223 34788999999999999988654
No 229
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=35.99 E-value=61 Score=30.92 Aligned_cols=59 Identities=17% Similarity=0.156 Sum_probs=43.7
Q ss_pred HHHhhHHHHHHHHHHHHcCcCCHHHHHHH--hhhcccCCCccCHHHHHHHHHHHHhcccceecCC
Q 009896 102 SQEFDQQCVELVQGLLEHGRLTLKQMFDR--AKSSEKEGNLVDLDSLRETLVKLVTAHYVERCPA 164 (523)
Q Consensus 102 ~~~~G~~a~~I~~~lL~~G~~~~~~li~~--~~~~~~~~~~~~~~~i~~~f~~Lv~~~fi~~v~~ 164 (523)
+...++.+..-+.+-+..|.+.+++-+.. +.+.. ..|+.-|++++..|...|+|+..|.
T Consensus 5 ~~~~~~~vy~~i~~~I~~g~l~pG~~L~e~eLae~l----gVSRtpVREAL~~L~~eGlv~~~~~ 65 (224)
T PRK11534 5 MQITALDGYRWLKNDIIRGNFQPDEKLRMSLLTSRY----ALGVGPLREALSQLVAERLVTVVNQ 65 (224)
T ss_pred HHhhhHHHHHHHHHHHHhCCCCCCCcCCHHHHHHHH----CCChHHHHHHHHHHHHCCCEEEeCC
Confidence 45567777888888888998887765532 11111 2377889999999999999998864
No 230
>COG3888 Predicted transcriptional regulator [Transcription]
Probab=35.91 E-value=70 Score=31.59 Aligned_cols=42 Identities=21% Similarity=0.359 Sum_probs=37.0
Q ss_pred HHHHHHHhhCC-CcchhhhhhhcCCCcccHHHHHHHHhhcccc
Q 009896 385 RIFRLLSKSGR-LLETDKISDTTFVEKKDAPKILYKLWKDGYL 426 (523)
Q Consensus 385 RI~r~L~~k~~-l~eek~i~~~ami~~k~~R~~L~~L~~~g~v 426 (523)
.+.|.|...|- -++|-+|.+...++...+-+.|..|.+.|.|
T Consensus 8 klir~Lk~a~~~GI~Q~eIeel~GlSKStvSEaLs~LE~~giv 50 (321)
T COG3888 8 KLIRELKRAGPEGIDQTEIEELMGLSKSTVSEALSELEKQGIV 50 (321)
T ss_pred HHHHHHHhcCCCCccHHHHHHHhCcchhHHHHHHHHHHhcCee
Confidence 47788877664 2399999999999999999999999999999
No 231
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=35.76 E-value=2.9e+02 Score=23.81 Aligned_cols=58 Identities=21% Similarity=0.237 Sum_probs=45.3
Q ss_pred HHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCceEEEEEEEchH
Q 009896 384 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQ 449 (523)
Q Consensus 384 ~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQEvpk~~~~~~t~~lw~v~~~ 449 (523)
.+|+++|...|.+ .-.+|++..-++...+=.-|-.|.+.|+|...-..+ .-+|++|.+
T Consensus 19 l~IL~~L~~~~~~-~v~ela~~l~lsqstvS~HL~~L~~AGLV~~~r~Gr-------~~~Y~l~~~ 76 (117)
T PRK10141 19 LGIVLLLRESGEL-CVCDLCTALDQSQPKISRHLALLRESGLLLDRKQGK-------WVHYRLSPH 76 (117)
T ss_pred HHHHHHHHHcCCc-CHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEEEcC-------EEEEEECch
Confidence 4788888766676 888999999999999999999999999996543322 234666754
No 232
>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=35.52 E-value=56 Score=22.57 Aligned_cols=36 Identities=19% Similarity=0.374 Sum_probs=29.9
Q ss_pred HHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHH
Q 009896 384 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKL 420 (523)
Q Consensus 384 ~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L 420 (523)
.+|++.|...+.. .-.+|++...++...++.-+.+|
T Consensus 6 ~~Il~~Lq~d~r~-s~~~la~~lglS~~~v~~Ri~rL 41 (42)
T PF13404_consen 6 RKILRLLQEDGRR-SYAELAEELGLSESTVRRRIRRL 41 (42)
T ss_dssp HHHHHHHHH-TTS--HHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHcCCc-cHHHHHHHHCcCHHHHHHHHHHh
Confidence 4789999888898 99999999999999999988777
No 233
>PF02295 z-alpha: Adenosine deaminase z-alpha domain; InterPro: IPR000607 Double-stranded RNA-specific adenosine deaminase (3.5 from EC) converts multiple adenosines to inosines and creates I/U mismatched base pairs in double-helical RNA substrates without apparent sequence specificity. DRADA has been found to modify adenosines in AU-rich regions more frequently, probably due to the relative ease of melting A/U base pairs compared to G/C base pairs. The protein functions to modify viral RNA genomes, and may be responsible for hypermutation of certain negative-stranded viruses. DRADA edits the mRNAs for the glutamate receptor subunits by site-selective adenosine deamination. The DRADA repeat is also found in viral E3 proteins, which contain a double-stranded RNA-binding domain.; GO: 0003723 RNA binding, 0003726 double-stranded RNA adenosine deaminase activity; PDB: 1OYI_A 3EYI_A 2L4M_A 2HEO_D 1J75_A 1SFU_B 3IRR_B 2ACJ_C 3F22_B 2L54_A ....
Probab=35.35 E-value=39 Score=25.96 Aligned_cols=46 Identities=28% Similarity=0.289 Sum_probs=39.8
Q ss_pred hhHHHHHHHHHhcCCCcHHHHHhhcCCC--HHHHHHHHHHHHhhcccc
Q 009896 20 DLVAKVCECLLRKGPLTRQNVKRYTELS--DEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 20 ~~v~~V~~~Ll~~G~ltl~~l~~~t~l~--~~~vr~aL~vLiQhn~V~ 65 (523)
+.-.+|..+|...|+.|...|....+|+ .+.|=..|..|...|.|.
T Consensus 4 ~~ee~Il~~L~~~g~~~a~~ia~~~~L~~~kk~VN~~LY~L~k~g~v~ 51 (66)
T PF02295_consen 4 DLEEKILDFLKELGGSTATAIAKALGLSVPKKEVNRVLYRLEKQGKVC 51 (66)
T ss_dssp HHHHHHHHHHHHHTSSEEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred hHHHHHHHHHHhcCCccHHHHHHHhCcchhHHHHHHHHHHHHHCCCEe
Confidence 3457899999999988988888876654 899999999999999996
No 234
>TIGR03859 PQQ_PqqD coenzyme PQQ biosynthesis protein PqqD. This model identifies PqqD, a protein involved in the final steps of the biosynthesis of pyrroloquinoline quinone, coenzyme PQQ.
Probab=35.25 E-value=91 Score=24.82 Aligned_cols=52 Identities=13% Similarity=0.151 Sum_probs=39.2
Q ss_pred hHHHHHHHHHHHHcCcCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccce
Q 009896 106 DQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVE 160 (523)
Q Consensus 106 G~~a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~~~~i~~~f~~Lv~~~fi~ 160 (523)
.+.|..|.+.+ .|.-|+++++..+.+..+. ......++..-+.+|.+.|+|.
T Consensus 30 n~~g~~Iw~ll--dg~~tv~eI~~~L~~~Y~~-~e~~~~dV~~fL~~L~~~gli~ 81 (81)
T TIGR03859 30 NDSAGEILELC--DGKRSLAEIIQELAQRFPA-AEEIEDDVIAFLAVARAKHWLE 81 (81)
T ss_pred ChHHHHHHHHc--cCCCcHHHHHHHHHHHcCC-hhhHHHHHHHHHHHHHHCcCcC
Confidence 35677777655 7888999999998877654 3335677888888899999873
No 235
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=35.17 E-value=61 Score=29.72 Aligned_cols=34 Identities=15% Similarity=0.239 Sum_probs=32.1
Q ss_pred CCCcHHHHHhhcCCCHHHHHHHHHHHHhhccccc
Q 009896 33 GPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQA 66 (523)
Q Consensus 33 G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~ 66 (523)
++.|+.+|+...++|+.-+.+.|-.|-+.|+|..
T Consensus 24 ~~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s 57 (164)
T PRK10857 24 GPVPLADISERQGISLSYLEQLFSRLRKNGLVSS 57 (164)
T ss_pred CcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe
Confidence 4789999999999999999999999999999983
No 236
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=35.14 E-value=62 Score=31.86 Aligned_cols=47 Identities=17% Similarity=0.249 Sum_probs=41.5
Q ss_pred HHHHHHHHHHcCcCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccceecC
Q 009896 109 CVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 163 (523)
Q Consensus 109 a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~~~~i~~~f~~Lv~~~fi~~v~ 163 (523)
...|++.|-++|.++++++.+.+. .|...|+.=+..|.+.|+|.|++
T Consensus 7 ~~~Il~~l~~~g~v~v~eLa~~~~--------VS~~TIRRDL~~Le~~g~l~R~h 53 (253)
T COG1349 7 HQKILELLKEKGKVSVEELAELFG--------VSEMTIRRDLNELEEQGLLLRVH 53 (253)
T ss_pred HHHHHHHHHHcCcEEHHHHHHHhC--------CCHHHHHHhHHHHHHCCcEEEEe
Confidence 468999999999999999988864 26778999999999999999985
No 237
>PF13814 Replic_Relax: Replication-relaxation
Probab=35.06 E-value=76 Score=29.29 Aligned_cols=61 Identities=26% Similarity=0.249 Sum_probs=46.2
Q ss_pred HHHHhhCCCcchhhhhhhcCCCcc---cHHHHHHHHhhcccceEEEEecCCCCceEEEEEEEchH
Q 009896 388 RLLSKSGRLLETDKISDTTFVEKK---DAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQ 449 (523)
Q Consensus 388 r~L~~k~~l~eek~i~~~ami~~k---~~R~~L~~L~~~g~v~lQEvpk~~~~~~t~~lw~v~~~ 449 (523)
++|-+.+.+ +.+||+...-.+.+ .++..|.+|.+.|+|.--..+.+......-+.|++...
T Consensus 2 ~~L~~~r~l-t~~Qi~~l~~~~~~~~~~~~rrL~~L~~~glv~~~~~~~~~~~g~~~~vy~Lt~~ 65 (191)
T PF13814_consen 2 RLLARHRFL-TTDQIARLLFPSSKSERTARRRLKRLRELGLVDRFRRRVGARGGSQPYVYYLTPA 65 (191)
T ss_pred hhHHHhcCc-CHHHHHHHHcCCCcchHHHHHHHHHHhhCCcEEeecccccccCCCcceEEEECHH
Confidence 456566666 99999999999998 79999999999999977666532223444577777755
No 238
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=34.92 E-value=1e+02 Score=27.73 Aligned_cols=35 Identities=14% Similarity=0.095 Sum_probs=31.7
Q ss_pred CCcHHHHHhhcCCCHHHHHHHHHHHHhhccccccc
Q 009896 34 PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFT 68 (523)
Q Consensus 34 ~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~ 68 (523)
..|..+|+...++|+.-+++.|..|.+.|+|....
T Consensus 24 ~~s~~eIA~~~~is~~~L~kIl~~L~~aGlv~S~r 58 (153)
T PRK11920 24 LSRIPEIARAYGVSELFLFKILQPLVEAGLVETVR 58 (153)
T ss_pred cCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeec
Confidence 46899999999999999999999999999998333
No 239
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=34.74 E-value=43 Score=30.30 Aligned_cols=52 Identities=21% Similarity=0.156 Sum_probs=43.0
Q ss_pred cCCchHHHHHHHHhh-CCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEE
Q 009896 379 YGRDAYRIFRLLSKS-GRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEK 430 (523)
Q Consensus 379 ~G~~a~RI~r~L~~k-~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQE 430 (523)
...-|+|++-.|... +..+.-++|++.--+|.+-.+++|..|.+.|+|+-..
T Consensus 6 ~~~YAlr~L~~LA~~~~~~~s~~eIA~~~~is~~~L~kIl~~L~~aGlv~S~r 58 (153)
T PRK11920 6 QTNYAIRMLMYCAANDGKLSRIPEIARAYGVSELFLFKILQPLVEAGLVETVR 58 (153)
T ss_pred HHhHHHHHHHHHHhCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeec
Confidence 345678888888543 4445889999999999999999999999999997654
No 240
>COG3423 Nlp Predicted transcriptional regulator [Transcription]
Probab=34.63 E-value=76 Score=25.10 Aligned_cols=33 Identities=30% Similarity=0.374 Sum_probs=28.0
Q ss_pred HHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHH
Q 009896 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNALL 56 (523)
Q Consensus 23 ~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~ 56 (523)
+.|...|-.+|- ||..|++..+++++.++++|.
T Consensus 11 adI~A~Lkk~G~-Sl~~LS~~agls~~tL~n~L~ 43 (82)
T COG3423 11 ADIIAALKKKGT-SLAALSREAGLSSSTLANALD 43 (82)
T ss_pred HHHHHHHHHccc-cHHHHHHHcCCCHHHHHHHHc
Confidence 556777777775 999999999999999999874
No 241
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=34.24 E-value=51 Score=29.14 Aligned_cols=41 Identities=29% Similarity=0.472 Sum_probs=35.6
Q ss_pred HHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccce
Q 009896 386 IFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 427 (523)
Q Consensus 386 I~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~ 427 (523)
|++++..+|.. ..++|++...+++..+...+.+|.+.|||.
T Consensus 13 I~~l~~~~~~~-~~~ela~~l~vs~~svs~~l~~L~~~Gli~ 53 (142)
T PRK03902 13 IYLLIEEKGYA-RVSDIAEALSVHPSSVTKMVQKLDKDEYLI 53 (142)
T ss_pred HHHHHhcCCCc-CHHHHHHHhCCChhHHHHHHHHHHHCCCEE
Confidence 56666555555 899999999999999999999999999996
No 242
>PF14502 HTH_41: Helix-turn-helix domain
Probab=33.61 E-value=61 Score=23.27 Aligned_cols=31 Identities=19% Similarity=0.196 Sum_probs=28.9
Q ss_pred CcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 35 LTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 35 ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
.|+.++....+++...|.+||-.|-..++|.
T Consensus 7 ~tI~e~~~~~~vs~GtiQ~Alk~Le~~gaI~ 37 (48)
T PF14502_consen 7 PTISEYSEKFGVSRGTIQNALKFLEENGAIK 37 (48)
T ss_pred CCHHHHHHHhCcchhHHHHHHHHHHHCCcEE
Confidence 3788999999999999999999999999996
No 243
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=33.14 E-value=5.4e+02 Score=27.97 Aligned_cols=113 Identities=16% Similarity=0.117 Sum_probs=77.6
Q ss_pred hHHHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEechhhHHHHhchhhHHHH
Q 009896 21 LVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFDNILHRVRFAKFLTI 100 (523)
Q Consensus 21 ~v~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~~~~il~rlR~p~~i~~ 100 (523)
.-..|-..|-.+|.++..+|+..+++++..|-.++-.|-..|+|. .... ....|++-.++- .+
T Consensus 7 ~e~~vL~~L~~~~~~s~~eLA~~l~l~~~tVt~~i~~Le~kGlV~-~~~~------~~~~i~LTeeG~----------~~ 69 (489)
T PRK04172 7 NEKKVLKALKELKEATLEELAEKLGLPPEAVMRAAEWLEEKGLVK-VEER------VEEVYVLTEEGK----------KY 69 (489)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHHHhCCCEE-EEee------eEEEEEECHHHH----------HH
Confidence 335667778788999999999999999999999999999999998 3322 124666544431 11
Q ss_pred HHHHhhHHHHHHHHHHHHcCcCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhccccee
Q 009896 101 LSQEFDQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVER 161 (523)
Q Consensus 101 i~~~~G~~a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~~~~i~~~f~~Lv~~~fi~~ 161 (523)
++ =|.....+++.+...|-.+++++...+. + .......+..|.+.||+..
T Consensus 70 ~~--~g~pE~rl~~~l~~~~g~~~~el~~~aL---~------~~~~~i~~~~l~k~g~i~i 119 (489)
T PRK04172 70 AE--EGLPERRLLNALKDGGEVSLDELKEALL---D------KKEVGIALGNLARKGWAKI 119 (489)
T ss_pred HH--hcCHHHHHHHhhHhcCCcCHHHHHHhhc---c------chhHHHHHHHHHHCCCeec
Confidence 11 1223455666666556678888765421 1 1235677888889999976
No 244
>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain
Probab=32.85 E-value=5.5e+02 Score=28.00 Aligned_cols=112 Identities=9% Similarity=0.063 Sum_probs=78.8
Q ss_pred HHHHHHHHHhcCC-CcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEechhhHHHHhchhhHHHH
Q 009896 22 VAKVCECLLRKGP-LTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFDNILHRVRFAKFLTI 100 (523)
Q Consensus 22 v~~V~~~Ll~~G~-ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~~~~il~rlR~p~~i~~ 100 (523)
-.+|-..|...|. .+..+|...++++...|..++..|-..|+|. +... ....|++..++-- +
T Consensus 5 e~~iL~~l~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kg~v~-~~~~------~~~~~~LT~eG~~----------~ 67 (492)
T PLN02853 5 EEALLGALSNNEEISDSGQFAASHGLDHNEVVGVIKSLHGFRYVD-AQDI------KRETWVLTEEGKK----------Y 67 (492)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHHHhCCCEE-EEEE------EEEEEEECHHHHH----------H
Confidence 4566777777775 8999999999999999999999999999998 4433 2468888666511 1
Q ss_pred HHHHhhHHHHHHHHHHHHcCcCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccceec
Q 009896 101 LSQEFDQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERC 162 (523)
Q Consensus 101 i~~~~G~~a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~~~~i~~~f~~Lv~~~fi~~v 162 (523)
++ =|.--+.|+..|-..|-+.++++...+. ...+.-+|-.+.+.|||..-
T Consensus 68 l~--~G~PE~rl~~~l~~~~~~~~~eL~~~l~----------~~~~~i~~g~a~k~gwi~i~ 117 (492)
T PLN02853 68 AA--EGSPEVQLFAAVPAEGSISKDELQKKLD----------PAVFDIGFKQAMKNKWLEMG 117 (492)
T ss_pred HH--cCCHHHHHHHHHhhcCCccHHHHHHhhC----------chhHHHHHHHHHHCCcEEEC
Confidence 11 2434445555555557778888765431 12356788899999999764
No 245
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=32.50 E-value=1e+02 Score=26.14 Aligned_cols=53 Identities=19% Similarity=0.276 Sum_probs=40.4
Q ss_pred HHHHHHHHHHc-CcCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccceecCC
Q 009896 109 CVELVQGLLEH-GRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCPA 164 (523)
Q Consensus 109 a~~I~~~lL~~-G~~~~~~li~~~~~~~~~~~~~~~~~i~~~f~~Lv~~~fi~~v~~ 164 (523)
-..|++.|..+ +++++.++.+.+.... ...+.+.|-.++..|.+.|+|.+++.
T Consensus 10 R~~Il~~l~~~~~~~ta~ei~~~l~~~~---~~is~~TVYR~L~~L~e~Gli~~~~~ 63 (120)
T PF01475_consen 10 RLAILELLKESPEHLTAEEIYDKLRKKG---PRISLATVYRTLDLLEEAGLIRKIEF 63 (120)
T ss_dssp HHHHHHHHHHHSSSEEHHHHHHHHHHTT---TT--HHHHHHHHHHHHHTTSEEEEEE
T ss_pred HHHHHHHHHcCCCCCCHHHHHHHhhhcc---CCcCHHHHHHHHHHHHHCCeEEEEEc
Confidence 35667777775 5999999999887532 23477889999999999999999853
No 246
>KOG4562 consensus Uncharacterized conserved protein (tumor-rejection antigen MAGE in humans) [Function unknown]
Probab=32.39 E-value=43 Score=34.33 Aligned_cols=56 Identities=20% Similarity=0.280 Sum_probs=38.6
Q ss_pred HHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHH-HHHhhcccceEEEEecCCCCceEEEEEEE
Q 009896 384 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKIL-YKLWKDGYLLMEKLVVTGARQSQFLLWKV 446 (523)
Q Consensus 384 ~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L-~~L~~~g~v~lQEvpk~~~~~~t~~lw~v 446 (523)
.-||.+|..-|-. +.+.-. ---+.|+++ ..|.+++|++.+.||.+ .|.+..|+|--
T Consensus 223 e~iWe~L~~lGv~-~g~~H~-----ifGeprkLiT~dlVqq~YLeYr~Vp~s-dP~~YEFlWGp 279 (329)
T KOG4562|consen 223 EEIWEVLRRLGVY-DGREHS-----IFGEPRKLLTQDLVQEKYLEYRQVPDS-DPPRYEFLWGP 279 (329)
T ss_pred HHHHHHHHHhcCC-CCcccc-----ccCChHHHHHHHHHHhhceeeeecCCC-CCCceEEeecc
Confidence 3466666555544 322221 124556655 68889999999999999 89999999963
No 247
>PF09397 Ftsk_gamma: Ftsk gamma domain; InterPro: IPR018541 This domain directs oriented DNA translocation and forms a winged helix structure []. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding []. ; PDB: 2VE9_B 2VE8_E 2J5O_A 2J5P_A.
Probab=32.36 E-value=1.3e+02 Score=23.10 Aligned_cols=48 Identities=13% Similarity=0.176 Sum_probs=41.3
Q ss_pred chhHHHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhccccc
Q 009896 19 GDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQA 66 (523)
Q Consensus 19 G~~v~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~ 66 (523)
.++-..+..+++..|..+...|.|..++.+..--..+=.|-+.|+|..
T Consensus 5 D~ly~~a~~~V~~~~~~S~S~lQR~~rIGynrAariid~LE~~GiVs~ 52 (65)
T PF09397_consen 5 DPLYEEAVEFVIEEGKASISLLQRKFRIGYNRAARIIDQLEEEGIVSP 52 (65)
T ss_dssp STTHHHHHHHHHHCTCECHHHHHHHHT--HHHHHHHHHHHHHCTSBE-
T ss_pred cHHHHHHHHHHHHcCCccHHHHHHHhCCCHHHHHHHHHHHHHCCCCCC
Confidence 466778888899999999999999999999999999999999999973
No 248
>PRK11050 manganese transport regulator MntR; Provisional
Probab=32.20 E-value=1.5e+02 Score=26.66 Aligned_cols=42 Identities=24% Similarity=0.301 Sum_probs=36.5
Q ss_pred HHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccce
Q 009896 385 RIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 427 (523)
Q Consensus 385 RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~ 427 (523)
-|.+++...+.. ...+|++...++...+...+.+|.+.|+|.
T Consensus 41 ~I~~~l~~~~~~-t~~eLA~~l~is~stVsr~l~~Le~~GlI~ 82 (152)
T PRK11050 41 LIADLIAEVGEA-RQVDIAARLGVSQPTVAKMLKRLARDGLVE 82 (152)
T ss_pred HHHHHHHhcCCC-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 366677666666 999999999999999999999999999984
No 249
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=32.03 E-value=72 Score=31.60 Aligned_cols=55 Identities=15% Similarity=0.225 Sum_probs=47.9
Q ss_pred HhhhchhHHHHHHHHHhcC-CCcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccc
Q 009896 15 TNHFGDLVAKVCECLLRKG-PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTT 69 (523)
Q Consensus 15 ~~~FG~~v~~V~~~Ll~~G-~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~ 69 (523)
+..|-+.=..|..+|..+| +.+-.+|.+.+++|...|-..|.-|-+-|+|.-+..
T Consensus 190 ~~~L~~~e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LEk~GlIe~~K~ 245 (258)
T COG2512 190 EYDLNEDEKEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLEKRGLIEKEKK 245 (258)
T ss_pred cCCCCHHHHHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHHHHHhCCceEEEEe
Confidence 3566777788999999996 599999999999999999999999999999984443
No 250
>COG5625 Predicted transcription regulator containing HTH domain [Transcription]
Probab=31.35 E-value=1.5e+02 Score=24.79 Aligned_cols=86 Identities=16% Similarity=0.227 Sum_probs=60.6
Q ss_pred HHcCCch--HHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCceEEEEEE-EchHHHHH
Q 009896 377 KRYGRDA--YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWK-VNRQILWK 453 (523)
Q Consensus 377 ~~~G~~a--~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQEvpk~~~~~~t~~lw~-v~~~~~~~ 453 (523)
+..|-+. .||+++|.+++.-+--.+|+-.-.|+.-.+|..+..|++.||+.=.=| ..++-=|.|. +.++....
T Consensus 15 ~~~glk~~eI~IY~lLve~~~~mri~ei~rEl~is~rtvr~~v~~l~rrGll~relv----qkgWvGYiya~~~P~k~le 90 (113)
T COG5625 15 EAIGLKKNEIRIYSLLVEKGRGMRIREIQRELGISERTVRAAVAVLLRRGLLARELV----QKGWVGYIYATTPPPKPLE 90 (113)
T ss_pred HHcCCCcchhhhhhHHHHhcCCchHHHHHHHHhHHHHHHHHHHHHHHHhhHHHHHHH----hccceeeEecCCCCchHHH
Confidence 3456666 899999998876338899999999999999999999999999831111 3345556554 44555555
Q ss_pred HHHHHHHHHHHHH
Q 009896 454 HVLDEMFHAALNL 466 (523)
Q Consensus 454 ~~l~~~~k~~~nl 466 (523)
.+-+++.+.+..+
T Consensus 91 ei~~~i~keiEel 103 (113)
T COG5625 91 EIEEEIMKEIEEL 103 (113)
T ss_pred HHHHHHHHHHHHH
Confidence 5555555554444
No 251
>PRK12423 LexA repressor; Provisional
Probab=31.32 E-value=1e+02 Score=29.05 Aligned_cols=45 Identities=13% Similarity=0.251 Sum_probs=36.8
Q ss_pred hHHHHHHHHHhcC-CCcHHHHHhhcCC-CHHHHHHHHHHHHhhcccc
Q 009896 21 LVAKVCECLLRKG-PLTRQNVKRYTEL-SDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 21 ~v~~V~~~Ll~~G-~ltl~~l~~~t~l-~~~~vr~aL~vLiQhn~V~ 65 (523)
+...+.+.+..+| +-|..+|++..++ ++..|+..|-.|.+-|+|.
T Consensus 11 il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~~l~~L~~~G~l~ 57 (202)
T PRK12423 11 ILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKHVQALAEAGLIE 57 (202)
T ss_pred HHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEE
Confidence 3445555666566 3599999999996 8999999999999999997
No 252
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=31.00 E-value=1.1e+02 Score=28.14 Aligned_cols=50 Identities=14% Similarity=0.147 Sum_probs=40.0
Q ss_pred hhhchhHHHHHHHHHhc--CCCcHHHHHhhc--CCCHHHHHHHHHHHHhhcccc
Q 009896 16 NHFGDLVAKVCECLLRK--GPLTRQNVKRYT--ELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 16 ~~FG~~v~~V~~~Ll~~--G~ltl~~l~~~t--~l~~~~vr~aL~vLiQhn~V~ 65 (523)
++|.....-|..-|+.- |.-+...|.+.+ +++..+|++||-.|.+.|++.
T Consensus 19 ~~~~~W~~~~ir~l~~l~~~~~d~~~iak~l~p~is~~ev~~sL~~L~~~gli~ 72 (171)
T PF14394_consen 19 EYYSSWYHPAIRELLPLMPFAPDPEWIAKRLRPKISAEEVRDSLEFLEKLGLIK 72 (171)
T ss_pred HHHhhhHHHHHHHHhhcCCCCCCHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeE
Confidence 45666666666666554 333899999998 999999999999999999997
No 253
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=30.97 E-value=88 Score=30.72 Aligned_cols=44 Identities=16% Similarity=0.107 Sum_probs=40.9
Q ss_pred HHHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 22 VAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 22 v~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
-.+|...|..+|..++.+|.+..+++...||.=|-.|-+.|++.
T Consensus 7 ~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le~~g~i~ 50 (251)
T PRK13509 7 HQILLELLAQLGFVTVEKVIERLGISPATARRDINKLDESGKLK 50 (251)
T ss_pred HHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 35688899999999999999999999999999999999999986
No 254
>TIGR00122 birA_repr_reg BirA biotin operon repressor domain. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.
Probab=30.95 E-value=71 Score=24.24 Aligned_cols=42 Identities=17% Similarity=0.259 Sum_probs=36.9
Q ss_pred HHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccce
Q 009896 384 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 427 (523)
Q Consensus 384 ~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~ 427 (523)
.+|+++|. .+.. .-++|++..-++...++..+..|...|+.-
T Consensus 3 ~~il~~L~-~~~~-~~~eLa~~l~vS~~tv~~~l~~L~~~g~~i 44 (69)
T TIGR00122 3 LRLLALLA-DNPF-SGEKLGEALGMSRTAVNKHIQTLREWGVDV 44 (69)
T ss_pred HHHHHHHH-cCCc-CHHHHHHHHCCCHHHHHHHHHHHHHCCCeE
Confidence 47888874 5677 799999999999999999999999999964
No 255
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=30.74 E-value=57 Score=32.05 Aligned_cols=43 Identities=21% Similarity=0.251 Sum_probs=38.8
Q ss_pred HHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccce
Q 009896 384 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 427 (523)
Q Consensus 384 ~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~ 427 (523)
.+|.++|.++|.+ ..++|++..-++...+|.-|..|.+.|.|.
T Consensus 8 ~~Il~~l~~~~~~-~~~ela~~l~vS~~TirRdL~~Le~~g~i~ 50 (251)
T PRK13509 8 QILLELLAQLGFV-TVEKVIERLGISPATARRDINKLDESGKLK 50 (251)
T ss_pred HHHHHHHHHcCCc-CHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 3588888887777 999999999999999999999999999993
No 256
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=30.63 E-value=75 Score=31.28 Aligned_cols=43 Identities=21% Similarity=0.275 Sum_probs=41.3
Q ss_pred HHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 23 ~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
.+|.+.|-.+|..++.+|+...+.+...||.=|-.|-+.|++.
T Consensus 8 ~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l~ 50 (253)
T COG1349 8 QKILELLKEKGKVSVEELAELFGVSEMTIRRDLNELEEQGLLL 50 (253)
T ss_pred HHHHHHHHHcCcEEHHHHHHHhCCCHHHHHHhHHHHHHCCcEE
Confidence 5788999999999999999999999999999999999999997
No 257
>PF09202 Rio2_N: Rio2, N-terminal; InterPro: IPR015285 This N-terminal domain is found in RIO2 kinases, and is structurally homologous to the winged helix (wHTH) domain. It adopts a structure consisting of four alpha helices followed by two beta strands and a fifth alpha helix. The domain confers DNA binding properties to the protein, as per other winged helix domains []. ; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1TQP_A 1ZAR_A 1TQI_A 1ZAO_A 1TQM_A.
Probab=30.30 E-value=54 Score=26.35 Aligned_cols=47 Identities=17% Similarity=0.246 Sum_probs=36.5
Q ss_pred chHHHHHHHH---hhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceE
Q 009896 382 DAYRIFRLLS---KSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLM 428 (523)
Q Consensus 382 ~a~RI~r~L~---~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~l 428 (523)
.-.||++.+- ++...+-.+.|.+.+-++..++...|.+|.+.++|.-
T Consensus 7 ~d~rvL~aiE~gmk~hE~VP~~~I~~~s~l~~~~~~~~L~~L~~~kLv~~ 56 (82)
T PF09202_consen 7 EDFRVLRAIEMGMKNHEWVPLELIEKISGLSEGEVEKRLKRLVKLKLVSR 56 (82)
T ss_dssp HHHHHHHHHHTTTTT-SSEEHHHHHHHHT--HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHHHcccCCccCCHHHHHHHhCcCHHHHHHHHHHHHhcCCccc
Confidence 4567777762 3346778999999999999999999999999999955
No 258
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=30.12 E-value=41 Score=26.46 Aligned_cols=44 Identities=16% Similarity=-0.008 Sum_probs=35.6
Q ss_pred chHHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccc
Q 009896 382 DAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYL 426 (523)
Q Consensus 382 ~a~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v 426 (523)
....+|-+.+....+ +.++|++..-+|.+.++..+..+..+|.+
T Consensus 19 ~~r~af~L~R~~eGl-S~kEIAe~LGIS~~TVk~~l~~~~~~~~~ 62 (73)
T TIGR03879 19 LAEAAAALAREEAGK-TASEIAEELGRTEQTVRNHLKGETKAGGL 62 (73)
T ss_pred HHHHHHHHHHHHcCC-CHHHHHHHHCcCHHHHHHHHhcCcccchH
Confidence 344556555545678 99999999999999999999999988764
No 259
>PF09202 Rio2_N: Rio2, N-terminal; InterPro: IPR015285 This N-terminal domain is found in RIO2 kinases, and is structurally homologous to the winged helix (wHTH) domain. It adopts a structure consisting of four alpha helices followed by two beta strands and a fifth alpha helix. The domain confers DNA binding properties to the protein, as per other winged helix domains []. ; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1TQP_A 1ZAR_A 1TQI_A 1ZAO_A 1TQM_A.
Probab=29.97 E-value=61 Score=26.05 Aligned_cols=36 Identities=17% Similarity=0.227 Sum_probs=30.4
Q ss_pred hcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhccccc
Q 009896 31 RKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQA 66 (523)
Q Consensus 31 ~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~ 66 (523)
.+--.|+..|.+.++++.+.+...|-.|+.|++|.+
T Consensus 21 ~hE~VP~~~I~~~s~l~~~~~~~~L~~L~~~kLv~~ 56 (82)
T PF09202_consen 21 NHEWVPLELIEKISGLSEGEVEKRLKRLVKLKLVSR 56 (82)
T ss_dssp T-SSEEHHHHHHHHT--HHHHHHHHHHHHHTTSEEE
T ss_pred CCccCCHHHHHHHhCcCHHHHHHHHHHHHhcCCccc
Confidence 345679999999999999999999999999999996
No 260
>TIGR03882 cyclo_dehyd_2 bacteriocin biosynthesis cyclodehydratase domain. This model describes a ThiF-like domain of a fusion protein found in clusters associated with the production of TOMMs (thiazole/oxazole-modified microcins), small bacteriocins with characteristic heterocycle modifications. This domain is presumed to act as a cyclodehydratase, as do members of the SagC family modeled by TIGR03603.
Probab=29.74 E-value=1.2e+02 Score=28.57 Aligned_cols=49 Identities=18% Similarity=0.187 Sum_probs=37.3
Q ss_pred hHHHHHHHHHHHHcCcCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccceec
Q 009896 106 DQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERC 162 (523)
Q Consensus 106 G~~a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~~~~i~~~f~~Lv~~~fi~~v 162 (523)
|.....|+. +..|+-|++++++.+.... +..++.+++.+|.+.|||+..
T Consensus 29 ~~~~~~L~~--lLdG~rt~~eI~~~l~~~~------p~~~v~~~L~~L~~~G~l~~~ 77 (193)
T TIGR03882 29 GALYCQLAP--LLDGRRTLDEIIAALAGRF------PAEEVLYALDRLERRGYLVED 77 (193)
T ss_pred chhHHHHHH--HHcCCCCHHHHHHHhhccC------CHHHHHHHHHHHHHCCCEecc
Confidence 333444554 5689999999999876532 467799999999999999764
No 261
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=29.57 E-value=69 Score=24.18 Aligned_cols=25 Identities=8% Similarity=0.248 Sum_probs=21.8
Q ss_pred HHhcCCCcHHHHHhhcCCCHHHHHH
Q 009896 29 LLRKGPLTRQNVKRYTELSDEQVKN 53 (523)
Q Consensus 29 Ll~~G~ltl~~l~~~t~l~~~~vr~ 53 (523)
+-..|.+++.+|+...++++++|+.
T Consensus 17 ~~~~g~i~lkdIA~~Lgvs~~tIr~ 41 (60)
T PF10668_consen 17 KESNGKIKLKDIAEKLGVSESTIRK 41 (60)
T ss_pred HHhCCCccHHHHHHHHCCCHHHHHH
Confidence 4457899999999999999999984
No 262
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=29.49 E-value=3.2e+02 Score=26.43 Aligned_cols=36 Identities=19% Similarity=0.264 Sum_probs=32.4
Q ss_pred CCCc-chhhhhhhcCCCcccHHHHHHHHhhcccceEE
Q 009896 394 GRLL-ETDKISDTTFVEKKDAPKILYKLWKDGYLLME 429 (523)
Q Consensus 394 ~~l~-eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQ 429 (523)
|.-+ .|.+|++.-.++..-+|+.|..|..+|+|++.
T Consensus 31 G~~LpsE~eLa~~lgVSRtpVREAL~~L~~eGlv~~~ 67 (254)
T PRK09464 31 GEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRR 67 (254)
T ss_pred CCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 5444 89999999999999999999999999999873
No 263
>PHA02591 hypothetical protein; Provisional
Probab=29.47 E-value=1.2e+02 Score=24.12 Aligned_cols=34 Identities=26% Similarity=0.308 Sum_probs=29.3
Q ss_pred hHHHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHH
Q 009896 21 LVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNAL 55 (523)
Q Consensus 21 ~v~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL 55 (523)
..-.|+.-|...| +|..+|++..+++...|++-|
T Consensus 47 d~~~vA~eL~eqG-lSqeqIA~~LGVsqetVrKYL 80 (83)
T PHA02591 47 DLISVTHELARKG-FTVEKIASLLGVSVRKVRRYL 80 (83)
T ss_pred hHHHHHHHHHHcC-CCHHHHHHHhCCCHHHHHHHH
Confidence 4456888999999 599999999999999999865
No 264
>TIGR00281 segregation and condensation protein B. Shown to be required for chromosome segregation and condensation in B. subtilis.
Probab=29.45 E-value=4.8e+02 Score=24.45 Aligned_cols=121 Identities=15% Similarity=0.177 Sum_probs=70.4
Q ss_pred HHHHHHHHHhcC-C-CcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEechhhHHHHhchhhHHH
Q 009896 22 VAKVCECLLRKG-P-LTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFDNILHRVRFAKFLT 99 (523)
Q Consensus 22 v~~V~~~Ll~~G-~-ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~~~~il~rlR~p~~i~ 99 (523)
.+.|=.+|+..| + +|+.+|...++.+......+++-+++.. |..+. .| .--....+-|.+.--|.|-.
T Consensus 3 ~~~iEAlLF~sg~pgls~~~La~il~~~~~~~~~~~l~~l~~~----~~~~~-~g-----l~l~~~~~~y~l~tk~e~~~ 72 (186)
T TIGR00281 3 KAIIEALLFVSGEPGVTLAELVRILGKEKAEKLNAIMELLEDY----LSRDT-AG-----IEIIKFGQSYSLVTKPAFAD 72 (186)
T ss_pred HHHHHHHHHHcCCCCCCHHHHHHHhCCCchHHHHHHHHHHHHH----HhcCC-CC-----EEEEEECCEEEEEEhHHHHH
Confidence 455667888887 3 9999999999998554444455544432 11110 00 11111122222223334444
Q ss_pred HHHHH-------hhHHHHHHHHHHHHcCcCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccceecC
Q 009896 100 ILSQE-------FDQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 163 (523)
Q Consensus 100 ~i~~~-------~G~~a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~~~~i~~~f~~Lv~~~fi~~v~ 163 (523)
+++.. +...+-+.+--+.-++=+|-.++-+-=.. .-...+.+|++.|||..+.
T Consensus 73 ~i~~~~~~~~~~LS~aaLEtLAIIAY~QPITr~eIe~IRGv-----------~s~~~l~~L~ergLI~~~G 132 (186)
T TIGR00281 73 YIHRFLPAKLKNLNSASLEVLAIIAYKQPITRARINEIRGV-----------KSYQIVDDLVEKGLVVELG 132 (186)
T ss_pred HHHHHhccccccCCHHHHHHHHHHHHcCCcCHHHHHHHcCC-----------CHHHHHHHHHHCCCeEecC
Confidence 44333 44467777777788888887776443110 1357899999999998874
No 265
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=29.39 E-value=79 Score=20.61 Aligned_cols=31 Identities=35% Similarity=0.539 Sum_probs=24.0
Q ss_pred CCcHHHHHhhcCCCHHHHHHHHHHHHhhccc
Q 009896 34 PLTRQNVKRYTELSDEQVKNALLVLIQQNCV 64 (523)
Q Consensus 34 ~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V 64 (523)
++|-.+|...+++++..|-..|-.|-+.|++
T Consensus 2 ~mtr~diA~~lG~t~ETVSR~l~~l~~~glI 32 (32)
T PF00325_consen 2 PMTRQDIADYLGLTRETVSRILKKLERQGLI 32 (32)
T ss_dssp E--HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred CcCHHHHHHHhCCcHHHHHHHHHHHHHcCCC
Confidence 3577889999999999999999999888764
No 266
>PF00888 Cullin: Cullin family; InterPro: IPR001373 Cullins are a family of hydrophobic proteins that act as scaffolds for ubiquitin ligases (E3). Cullins are found throughout eukaryotes. Humans express seven cullins (Cul1, 2, 3, 4A, 4B, 5 and 7), each forming part of a multi-subunit ubiquitin complex. Cullin-RING ubiquitin ligases (CRLs), such as Cul1 (SCF) [], play an essential role in targeting proteins for ubiquitin-mediated destruction; as such, they are diverse in terms of composition and function, regulating many different processes from glucose sensing and DNA replication to limb patterning and circadian rhythms. The catalytic core of CRLs consists of a RING protein and a cullin family member. For Cul1, the C-terminal cullin-homology domain binds the RING protein. The RING protein appears to function as a docking site for ubiquitin-conjugating enzymes (E2s). Other proteins contain a cullin-homology domain, such as the APC2 subunit of the anaphase-promoting complex/cyclosome and the p53 cytoplasmic anchor PARC; both APC2 and PARC have ubiquitin ligase activity. The N-terminal region of cullins is more variable, and is used to interact with specific adaptor proteins [, , ]. This entry represents the N-terminal region of cullin proteins, which consists of several domains, including cullin repeat domain, a 4-helical bundle domain, an alpha+beta domain, and a winged helix-like domain.; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 2WZK_A 3DQV_D 3DPL_C 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_A 1U6G_A 4A0K_A ....
Probab=29.09 E-value=42 Score=37.09 Aligned_cols=56 Identities=20% Similarity=0.256 Sum_probs=36.5
Q ss_pred HhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEech
Q 009896 30 LRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLF 85 (523)
Q Consensus 30 l~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~~ 85 (523)
...+.+|+.+|...|+++...++.+|..|++++++.....+..........+++|.
T Consensus 530 n~~~~~t~~ei~~~~~~~~~~l~~~L~~l~~~~~l~~~~~~~~~~~~~~~~f~~N~ 585 (588)
T PF00888_consen 530 NDNDSLTVEEISEKTGISEEELKRALKSLVKSKILILLKEPNSKSFSDNDEFSVNE 585 (588)
T ss_dssp GSSSEEEHHHHHHHC---HHHHHHHHHCCCTTTTCSEEETTTSSS--TT-EEEE-T
T ss_pred ccCCCccHHHHHHHHCcCHHHHHHHHHHHHhCCcceeecCCccCCCCCCCEEEeCC
Confidence 34668899999999999999999999999999999733222211112235677764
No 267
>KOG2166 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=28.90 E-value=3.1e+02 Score=31.47 Aligned_cols=127 Identities=16% Similarity=0.210 Sum_probs=81.2
Q ss_pred cCCCcHHHHHhhcCCCHHHHHHHHHHH--HhhcccccccccCCCCCCcceEEEechh--hHHHHhchhh----HHHHHHH
Q 009896 32 KGPLTRQNVKRYTELSDEQVKNALLVL--IQQNCVQAFTTEQPDGPKANTQYVVLFD--NILHRVRFAK----FLTILSQ 103 (523)
Q Consensus 32 ~G~ltl~~l~~~t~l~~~~vr~aL~vL--iQhn~V~~~~~~~~~~~~~~~~Y~~~~~--~il~rlR~p~----~i~~i~~ 103 (523)
+-++|+.+|...|+++.+.+..+|-+| +...+.. . +.+.. .....+++|.+ .-..|+.-|. --..+.+
T Consensus 578 ~d~lt~~eI~~~t~i~~~~l~~~L~Sl~~~K~~v~~--~-~~s~~-~~~~~~~~N~~f~sk~~Rv~i~~~~~~e~~~~~~ 653 (725)
T KOG2166|consen 578 TEKLTYEEILEQTNLGHEDLARLLQSLSCLKYKILL--K-PMSRT-SPNDEFAFNSKFTSKMRRVKIPLPPMDERKKVVE 653 (725)
T ss_pred hhhccHHHHHHHhCCCHHHHHHHHHHHHHHhHhhcc--C-ccccC-CCCcEEEeeccccCcceeeccCCCCchhHHHHHh
Confidence 368999999999999999999999999 5522222 1 11100 11245555554 4455554442 2233344
Q ss_pred HhhH-----HHHHHHHHHHHcCcCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccceec
Q 009896 104 EFDQ-----QCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERC 162 (523)
Q Consensus 104 ~~G~-----~a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~~~~i~~~f~~Lv~~~fi~~v 162 (523)
..++ .-|+|+--.=..+++.=.+++..+.+.....=..++..|+.++..|++.+||+|-
T Consensus 654 ~ve~dRk~~i~AaIVRIMK~rK~l~h~~Lv~Ev~~ql~~RF~p~v~~IKk~Ie~LIEkeYleR~ 717 (725)
T KOG2166|consen 654 DVDKDRKYAIDAAIVRIMKSRKVLGHQQLVSEVVEQLSERFKPDIKMIKKRIEDLIEREYLERD 717 (725)
T ss_pred hhhhHHHHHHHHHHHHHHHhhccccHHHHHHHHHHHHhhhcCCCHHHHHHHHHHHHHHHHHhcc
Confidence 4443 2567777777788888777777766422110012578899999999999999995
No 268
>PF03428 RP-C: Replication protein C N-terminal domain; InterPro: IPR005090 Proteins in this group have homology with the RepC protein of Agrobacterium Ri and Ti plasmids []. They may be involved in plasmid replication and stabilisation functions.
Probab=28.57 E-value=4.8e+02 Score=24.22 Aligned_cols=78 Identities=9% Similarity=0.035 Sum_probs=56.0
Q ss_pred chhhhhhhc-CCCcccHHHHHHHHhhcccceEEEEecCC------CCceEEEEEEEchHHHHHHHHHHHHHHHHHHHHHH
Q 009896 398 ETDKISDTT-FVEKKDAPKILYKLWKDGYLLMEKLVVTG------ARQSQFLLWKVNRQILWKHVLDEMFHAALNLSLRV 470 (523)
Q Consensus 398 eek~i~~~a-mi~~k~~R~~L~~L~~~g~v~lQEvpk~~------~~~~t~~lw~v~~~~~~~~~l~~~~k~~~nl~~R~ 470 (523)
.-.+|+... .|+...+|..|-.|.+.|+|..+.-|... ..++-..-|-+|+.-+....- -+..+-++.
T Consensus 72 SN~~La~r~~G~s~~tlrR~l~~LveaGLI~rrDS~NgkRy~~R~~~G~I~~A~GfdLsPL~~R~~-----El~~~a~~~ 146 (177)
T PF03428_consen 72 SNAQLAERLNGMSERTLRRHLARLVEAGLIVRRDSPNGKRYARRDRGGRIVEAFGFDLSPLIARAE-----ELAALAEAA 146 (177)
T ss_pred CHHHHHHHHcCCCHHHHHHHHHHHHHCCCeeeccCCCCCccCccCCCCCEEeEeCcCHHHHHHHHH-----HHHHHHHHH
Confidence 667889999 99999999999999999999888777643 344566788888887665532 233344444
Q ss_pred HHHHHhhhhh
Q 009896 471 SYELDREKEL 480 (523)
Q Consensus 471 ~~e~~~~k~l 480 (523)
..|....+.+
T Consensus 147 ~~~~~~~r~l 156 (177)
T PF03428_consen 147 RAERRALRRL 156 (177)
T ss_pred HHHHHHHHHH
Confidence 4544445544
No 269
>COG5124 Protein predicted to be involved in meiotic recombination [Cell division and chromosome partitioning / General function prediction only]
Probab=27.93 E-value=3.1e+02 Score=25.45 Aligned_cols=42 Identities=19% Similarity=0.281 Sum_probs=30.2
Q ss_pred hhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCceEEEEEEEchHH
Q 009896 403 SDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQI 450 (523)
Q Consensus 403 ~~~ami~~k~~R~~L~~L~~~g~v~lQEvpk~~~~~~t~~lw~v~~~~ 450 (523)
...--|-...++.+|.+|..+|+|...-+.. +.|+|+..-+.
T Consensus 35 GSKK~IVl~tVKd~lQqlVDDgvV~~EK~Gt------sN~YWsF~s~~ 76 (209)
T COG5124 35 GSKKQIVLMTVKDLLQQLVDDGVVSVEKCGT------SNIYWSFKSQT 76 (209)
T ss_pred ccccccHHHHHHHHHHHHhhcCceeeeeecc------ceeEEecchHH
Confidence 3333445578999999999999997655533 46888887553
No 270
>PRK06474 hypothetical protein; Provisional
Probab=27.91 E-value=1.5e+02 Score=27.49 Aligned_cols=49 Identities=16% Similarity=0.139 Sum_probs=39.8
Q ss_pred HHHHHHHHhhCC-Ccchhhhhhhc-CCCcccHHHHHHHHhhcccceEEEEec
Q 009896 384 YRIFRLLSKSGR-LLETDKISDTT-FVEKKDAPKILYKLWKDGYLLMEKLVV 433 (523)
Q Consensus 384 ~RI~r~L~~k~~-l~eek~i~~~a-mi~~k~~R~~L~~L~~~g~v~lQEvpk 433 (523)
.+|+++|...+. + .-++|++.. -+|...+-..|..|.+.|+|+.-+.++
T Consensus 14 ~~Il~~L~~~~~~~-ta~el~~~l~~is~aTvYrhL~~L~e~GLI~~~~~~~ 64 (178)
T PRK06474 14 MKICQVLMRNKEGL-TPLELVKILKDVPQATLYRHLQTMVDSGILHVVKEKK 64 (178)
T ss_pred HHHHHHHHhCCCCC-CHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEEeeccc
Confidence 478888877665 7 999998877 588888999999999999998655543
No 271
>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Probab=27.86 E-value=70 Score=30.15 Aligned_cols=32 Identities=19% Similarity=0.246 Sum_probs=30.1
Q ss_pred CCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 34 PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 34 ~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
++|-.+|+...+++..-||.||..|-+.|+|.
T Consensus 34 ~L~e~~La~~lgVSRtpVReAL~~L~~eGlv~ 65 (212)
T TIGR03338 34 KLNESDIAARLGVSRGPVREAFRALEEAGLVR 65 (212)
T ss_pred EecHHHHHHHhCCChHHHHHHHHHHHHCCCEE
Confidence 66778899999999999999999999999998
No 272
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=27.61 E-value=1.6e+02 Score=27.99 Aligned_cols=58 Identities=16% Similarity=0.193 Sum_probs=46.1
Q ss_pred HHHHHHHHhhhchhHHHHHHHHHhc---C--CCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 8 KHAVHVITNHFGDLVAKVCECLLRK---G--PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 8 ~Lc~~iv~~~FG~~v~~V~~~Ll~~---G--~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
.+...+......++-.+|+.+|+.. + +.|-.+|+...++++..|-..|--|.+.|++.
T Consensus 138 ~~~~~~~~~~~~~~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvsR~L~~L~~~G~I~ 200 (226)
T PRK10402 138 RNIVSLTQNQSFPLENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLLYVLAQFIQDGYLK 200 (226)
T ss_pred HHHHHHHHhccChHHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHHHHHHHHHHCCCEE
Confidence 3344444445557889999999853 2 35779999999999999999999999999997
No 273
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=27.43 E-value=1.4e+02 Score=27.42 Aligned_cols=54 Identities=15% Similarity=0.222 Sum_probs=41.3
Q ss_pred HHHHHHHHHHHH-cCcCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccceecC
Q 009896 107 QQCVELVQGLLE-HGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 163 (523)
Q Consensus 107 ~~a~~I~~~lL~-~G~~~~~~li~~~~~~~~~~~~~~~~~i~~~f~~Lv~~~fi~~v~ 163 (523)
..=..|++.|.. .+++++.+|.+.+.+..+ ..+...|-.++..|++.|+|.++.
T Consensus 26 ~qR~~IL~~l~~~~~hlSa~eI~~~L~~~~~---~is~aTVYRtL~~L~e~Glv~~~~ 80 (169)
T PRK11639 26 PQRLEVLRLMSLQPGAISAYDLLDLLREAEP---QAKPPTVYRALDFLLEQGFVHKVE 80 (169)
T ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHHHhhCC---CCCcchHHHHHHHHHHCCCEEEEe
Confidence 344556666664 479999999999865432 346788999999999999999985
No 274
>PF13693 HTH_35: Winged helix-turn-helix DNA-binding; PDB: 1NEQ_A 1NER_A.
Probab=27.00 E-value=56 Score=26.05 Aligned_cols=32 Identities=28% Similarity=0.421 Sum_probs=24.1
Q ss_pred HHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHH
Q 009896 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNAL 55 (523)
Q Consensus 23 ~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL 55 (523)
+.|...|-.+| .||..|.+..+++.+.++++|
T Consensus 5 adI~AaL~krG-~sL~~lsr~~Gl~~~tl~nal 36 (78)
T PF13693_consen 5 ADIKAALRKRG-TSLAALSREAGLSSSTLRNAL 36 (78)
T ss_dssp HHHHHHHCTTS---HHHHHHHHSS-HHHHHHTT
T ss_pred HHHHHHHHHcC-CCHHHHHHHcCCCHHHHHHHH
Confidence 45666776677 699999999999999999886
No 275
>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Probab=26.95 E-value=3.7e+02 Score=25.06 Aligned_cols=35 Identities=17% Similarity=0.157 Sum_probs=31.7
Q ss_pred CCCcchhhhhhhcCCCcccHHHHHHHHhhcccceE
Q 009896 394 GRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLM 428 (523)
Q Consensus 394 ~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~l 428 (523)
|.-+.|.+|++.-.++..-+|+.|..|..+|+|+.
T Consensus 32 G~~L~e~~La~~lgVSRtpVReAL~~L~~eGlv~~ 66 (212)
T TIGR03338 32 GAKLNESDIAARLGVSRGPVREAFRALEEAGLVRN 66 (212)
T ss_pred CCEecHHHHHHHhCCChHHHHHHHHHHHHCCCEEE
Confidence 44448999999999999999999999999999976
No 276
>PF03551 PadR: Transcriptional regulator PadR-like family; InterPro: IPR005149 Phenolic acids, also called substituted hydroxycinnamic acids, are abundant in the plant kingdom because they are involved in the structure of plant cell walls and are present in some vacuoles. In plant-soil ecosystems they are released as free acids by hemicellulases produced by several fungi and bacteria. Of these weak acids, the most abundant are p-coumaric, ferulic, and caffeic acids, considered to be natural toxins that inhibit the growth of microorganisms, especially at low pHs. In spite of this chemical stress, some bacteria can use phenolic acids as a sole source of carbon. For other microorganisms, these compounds induce a specific response by which the organism adapts to its environment. The ubiquitous lactic acid bacterium Lactobacillus plantarum exhibits an inducible phenolic acid decarboxylase (PAD) activity which converts these substrates into less-toxic vinyl phenol derivatives. PadR acts as a repressor of padA gene expression in the phenolic acid stress response [].; PDB: 1XMA_B 2ESH_A 2DQL_B 3L9F_C 3ELK_B 4EJO_B 3L7W_A 3HHH_A 1YG2_A 3F8B_A ....
Probab=26.82 E-value=1.5e+02 Score=22.91 Aligned_cols=48 Identities=17% Similarity=0.075 Sum_probs=32.9
Q ss_pred HHHcCcCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccceecC
Q 009896 116 LLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 163 (523)
Q Consensus 116 lL~~G~~~~~~li~~~~~~~~~~~~~~~~~i~~~f~~Lv~~~fi~~v~ 163 (523)
+|..|-++.-++.+.+......--..+...|-.++.+|.++|||....
T Consensus 4 ~L~~~~~~Gyei~~~l~~~~~~~~~i~~g~lY~~L~~Le~~gli~~~~ 51 (75)
T PF03551_consen 4 LLSEGPMHGYEIKQELEERTGGFWKISPGSLYPALKRLEEEGLIESRW 51 (75)
T ss_dssp HHHHS-EEHHHHHHHHHHCSTTTEETTHHHHHHHHHHHHHTTSEEEEE
T ss_pred hhccCCCcHHHHHHHHHHHhCCCcccChhHHHHHHHHHHhCCCEEEee
Confidence 444477777777777655321101346889999999999999998863
No 277
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=26.67 E-value=1e+02 Score=29.84 Aligned_cols=43 Identities=21% Similarity=0.353 Sum_probs=40.1
Q ss_pred HHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 23 ~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
-+|.+.|-++|++.+.+|+...+||-+.+-..+-+|..-|++.
T Consensus 26 v~Il~lL~~k~plNvneiAe~lgLpqst~s~~ik~Le~aGlir 68 (308)
T COG4189 26 VAILQLLHRKGPLNVNEIAEALGLPQSTMSANIKVLEKAGLIR 68 (308)
T ss_pred HHHHHHHHHhCCCCHHHHHHHhCCchhhhhhhHHHHHhcCcee
Confidence 3577888889999999999999999999999999999999998
No 278
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=26.66 E-value=1.8e+02 Score=23.47 Aligned_cols=36 Identities=19% Similarity=0.349 Sum_probs=33.4
Q ss_pred HhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 30 LRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 30 l~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
..+.++++.+|++..+++...|..-|+-+|..|.+.
T Consensus 56 ~~y~~i~~~~ia~~l~~~~~~vE~~l~~~I~~~~i~ 91 (105)
T PF01399_consen 56 KPYSSISISEIAKALQLSEEEVESILIDLISNGLIK 91 (105)
T ss_dssp HC-SEEEHHHHHHHHTCCHHHHHHHHHHHHHTTSSE
T ss_pred HHhcccchHHHHHHhccchHHHHHHHHHHHHCCCEE
Confidence 377899999999999999999999999999999998
No 279
>PF01454 MAGE: MAGE family; InterPro: IPR002190 The first mammalian members of the MAGE (melanoma-associated antigen) gene family were originally described as completely silent in normal adult tissues, with the exception of male germ cells and, for some of them, placenta. By contrast, these genes were expressed in various kinds of tumors. However, other members of the family were recently found to be expressed in normal cells, indicating that the family is larger and more disparate than initially expected. MAGE-like genes have also been identified in non-mammalian species, including Drosophila melanogaster (Fruit fly) and Danio rerio (Zebrafish). Although no MAGE homologous sequences have been identified in Caenorhabditis elegans, Saccharomyces cerevisiae (Baker's yeast) or Schizosaccharomyces pombe (Fission yeast), MAGE sequences have been found in several vegetal species, including Arabidopsis thaliana (Mouse-ear cress) []. The only region of homology shared by all of the members of the family is a stretch of about 200 amino acids which has been named the MAGE conserved domain. The MAGE conserved domain is usually located close to the C-terminal, although it can also be found in a more central position in some proteins. The MAGE conserved domain is generally present as a single copy but it is duplicated in some proteins. It has been proposed that the MAGE conserved domain of MAGE-D proteins might interact with p75 neurotrophin or related receptors [].; PDB: 3NW0_B 2WA0_A 1I4F_C.
Probab=26.57 E-value=84 Score=29.38 Aligned_cols=59 Identities=14% Similarity=0.322 Sum_probs=27.0
Q ss_pred HHHHHHHhhCCCcchhhhhhhcCCCcccHHHHH-HHHhhcccc-eEEEEecCCCCceEEEEEEEchH
Q 009896 385 RIFRLLSKSGRLLETDKISDTTFVEKKDAPKIL-YKLWKDGYL-LMEKLVVTGARQSQFLLWKVNRQ 449 (523)
Q Consensus 385 RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L-~~L~~~g~v-~lQEvpk~~~~~~t~~lw~v~~~ 449 (523)
.+|+.|..= .+ ++.. ..+.... +.++++ ..|.+.||+ +..++|.+ +|....|.|++-+.
T Consensus 125 ~L~~~L~~l-gi-~~~~--~~~~~g~-~~~~~i~~~~vkq~YL~~~k~~~~~-~~~~~~~~y~~G~R 185 (195)
T PF01454_consen 125 DLWKFLRRL-GI-DEDE--KHPILGM-DIKKLILKEFVKQGYLVRYKQVPNS-DPEEYEFSYSWGPR 185 (195)
T ss_dssp HHHHHHHHT-T---TTS---BTTTB---HHHHHHCHHHHCTSE-EEE-----------EEEE---HH
T ss_pred HHHHHHHhc-CC-Cccc--cCccCCC-CHHHHHHHHHHHhcCHHheeecCCC-CCCceEEEeCCcCc
Confidence 477777443 33 3332 4444442 455555 999999999 87778877 45566777987654
No 280
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=26.53 E-value=4.8e+02 Score=23.54 Aligned_cols=44 Identities=20% Similarity=0.248 Sum_probs=38.0
Q ss_pred HHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccc
Q 009896 25 VCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTT 69 (523)
Q Consensus 25 V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~ 69 (523)
|....-..|.....+|++..+++++.|...|--|..-|+|. |.+
T Consensus 15 Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~-~~~ 58 (154)
T COG1321 15 IYELLEEKGFARTKDIAERLKVSPPSVTEMLKRLERLGLVE-YEP 58 (154)
T ss_pred HHHHHhccCcccHHHHHHHhCCCcHHHHHHHHHHHHCCCeE-Eec
Confidence 33344478999999999999999999999999999999998 544
No 281
>PF10415 FumaraseC_C: Fumarase C C-terminus; InterPro: IPR018951 Fumarase C catalyses the stereo-specific interconversion of fumarate to L-malate as part of the Krebs cycle. The full-length protein forms a tetramer with visible globular shape. FumaraseC_C is the C-terminal 65 residues referred to as domain 3. The core of the molecule consists of a bundle of 20 alpha-helices from the five-helix bundle of domain 2. The projections from the core of the tetramer are generated from domains 1 and 3 of each subunit []. This entry does not appear to be part of either the active site or the activation site but is helical in structure forming a little bundle. ; GO: 0016829 lyase activity, 0006099 tricarboxylic acid cycle; PDB: 3RRP_A 3OCE_D 3OCF_D 3E04_B 3GTD_A 3R6V_F 3R6Q_F 1J3U_B 1FUR_A 1YFE_A ....
Probab=26.52 E-value=1.2e+02 Score=22.40 Aligned_cols=41 Identities=20% Similarity=0.329 Sum_probs=30.7
Q ss_pred HHhhhc-hhHHHHHHHHHhcCCCcHHHHHhhcC-CCHHHHHHHH
Q 009896 14 ITNHFG-DLVAKVCECLLRKGPLTRQNVKRYTE-LSDEQVKNAL 55 (523)
Q Consensus 14 v~~~FG-~~v~~V~~~Ll~~G~ltl~~l~~~t~-l~~~~vr~aL 55 (523)
+.-++| +.+++|+..=+..|+ |+++++...+ ++..++...|
T Consensus 5 L~p~iGYe~aa~iAk~A~~~g~-svre~v~~~g~lt~ee~d~ll 47 (55)
T PF10415_consen 5 LNPYIGYEKAAEIAKEALAEGR-SVREVVLEEGLLTEEELDELL 47 (55)
T ss_dssp GHHHHHHHHHHHHHHHHHHHT---HHHHHHHTTSS-HHHHHHHT
T ss_pred ccchhccHHHHHHHHHHHHcCC-CHHHHHHHcCCCCHHHHHHHc
Confidence 446778 889999999888997 9999988877 6888777654
No 282
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=26.25 E-value=4.4e+02 Score=24.13 Aligned_cols=51 Identities=12% Similarity=0.164 Sum_probs=37.6
Q ss_pred CccccHHHHHHHhhhhccCCCCCHHHHHHHHHHhccCCCCCCCCCeE-EEehHHHHHHH
Q 009896 309 SVPLSLSSIYEEVIKSEAGRNMTLDHVRASLVQLGELSFVDASSDSY-SIDFEKIIEIA 366 (523)
Q Consensus 309 s~~~s~~~I~~~l~~~~~~~~~~~~~i~~~L~~La~~~~~~~~~~~y-~V~~~~i~~~l 366 (523)
..|+|-.+|.+.++ ++.+.+.+.|+.|.+.+....+++.. ..|++++.+..
T Consensus 147 ~~~~t~~~iA~~lG-------~tretvsR~l~~l~~~g~I~~~~~~i~I~d~~~L~~~~ 198 (202)
T PRK13918 147 MIYATHDELAAAVG-------SVRETVTKVIGELSREGYIRSGYGKIQLLDLKGLEELA 198 (202)
T ss_pred EecCCHHHHHHHhC-------ccHHHHHHHHHHHHHCCCEEcCCCEEEEECHHHHHHHH
Confidence 45788899998884 67788999999999888555555544 44787776543
No 283
>TIGR03882 cyclo_dehyd_2 bacteriocin biosynthesis cyclodehydratase domain. This model describes a ThiF-like domain of a fusion protein found in clusters associated with the production of TOMMs (thiazole/oxazole-modified microcins), small bacteriocins with characteristic heterocycle modifications. This domain is presumed to act as a cyclodehydratase, as do members of the SagC family modeled by TIGR03603.
Probab=26.11 E-value=1.4e+02 Score=28.08 Aligned_cols=45 Identities=22% Similarity=0.232 Sum_probs=38.5
Q ss_pred chhHHHHHHHHHhcCCCcHHHHHhhc--CCCHHHHHHHHHHHHhhcccc
Q 009896 19 GDLVAKVCECLLRKGPLTRQNVKRYT--ELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 19 G~~v~~V~~~Ll~~G~ltl~~l~~~t--~l~~~~vr~aL~vLiQhn~V~ 65 (523)
|+.+..+...| .|+.|+.+|.... .++...|.++|..|.+.|++.
T Consensus 29 ~~~~~~L~~lL--dG~rt~~eI~~~l~~~~p~~~v~~~L~~L~~~G~l~ 75 (193)
T TIGR03882 29 GALYCQLAPLL--DGRRTLDEIIAALAGRFPAEEVLYALDRLERRGYLV 75 (193)
T ss_pred chhHHHHHHHH--cCCCCHHHHHHHhhccCCHHHHHHHHHHHHHCCCEe
Confidence 67778888866 7889999998764 468899999999999999997
No 284
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=25.76 E-value=2.4e+02 Score=24.37 Aligned_cols=48 Identities=17% Similarity=0.243 Sum_probs=37.1
Q ss_pred HHHHHHHHHHcCcCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccceecCC
Q 009896 109 CVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCPA 164 (523)
Q Consensus 109 a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~~~~i~~~f~~Lv~~~fi~~v~~ 164 (523)
...|+-.|.. |..+.+++...+.. .+...+.+.+..|.++|+|.|...
T Consensus 25 ~~lIl~~L~~-g~~RF~eL~r~i~~-------Is~k~Ls~~Lk~Le~~Glv~R~~~ 72 (120)
T COG1733 25 TLLILRDLFD-GPKRFNELRRSIGG-------ISPKMLSRRLKELEEDGLVERVVY 72 (120)
T ss_pred HHHHHHHHhc-CCCcHHHHHHHccc-------cCHHHHHHHHHHHHHCCCEEeeec
Confidence 4445555555 99999999877542 356779999999999999999753
No 285
>PF04182 B-block_TFIIIC: B-block binding subunit of TFIIIC; InterPro: IPR007309 Yeast transcription factor IIIC (TFIIIC) is a multisubunit protein complex that interacts with two control elements of class III promoters called the A and B blocks. This family represents the subunit within TFIIIC involved in B-block binding []. Although defined as a yeast protein, it is also found in a number of other organisms.
Probab=25.55 E-value=3.2e+02 Score=21.18 Aligned_cols=50 Identities=16% Similarity=0.154 Sum_probs=39.7
Q ss_pred chhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCC--CCceEEEEEEEc
Q 009896 398 ETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTG--ARQSQFLLWKVN 447 (523)
Q Consensus 398 eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQEvpk~~--~~~~t~~lw~v~ 447 (523)
-+.++++..-++++.+-..+-.|...|+|.=|.++... ...+|..+|...
T Consensus 20 ~q~~L~~~~~~D~r~i~~~~k~L~~~gLI~k~~~~~~~~~~~~~t~ll~l~r 71 (75)
T PF04182_consen 20 TQSDLSKLLGIDPRSIFYRLKKLEKKGLIVKQSVISSSNSKGTRTNLLHLKR 71 (75)
T ss_pred ehhHHHHHhCCCchHHHHHHHHHHHCCCEEEEEeccccCCCceEEEEEEEec
Confidence 78888999999999999999999999999999995322 455566666543
No 286
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=25.51 E-value=75 Score=31.25 Aligned_cols=42 Identities=17% Similarity=0.243 Sum_probs=38.4
Q ss_pred HHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccc
Q 009896 384 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYL 426 (523)
Q Consensus 384 ~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v 426 (523)
.+|..+|.+++.+ ..++|++.--++...+|.-|..|.+.|++
T Consensus 8 ~~Il~~l~~~~~~-~~~ela~~l~vS~~TiRRdL~~Le~~g~l 49 (252)
T PRK10906 8 DAIIELVKQQGYV-STEELVEHFSVSPQTIRRDLNDLAEQNKI 49 (252)
T ss_pred HHHHHHHHHcCCE-eHHHHHHHhCCCHHHHHHHHHHHHHCCCE
Confidence 3578888787777 99999999999999999999999999998
No 287
>PF08672 APC2: Anaphase promoting complex (APC) subunit 2; InterPro: IPR014786 The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome. Anaphase is initiated when the APC triggers the destruction of securin, thereby allowing the protease, separase, to disrupt sister-chromatid cohesion. Securin ubiquitination by the APC is inhibited by cyclin-dependent kinase 1 (Cdk1)-dependent phosphorylation []. Forkhead Box M1 (FoxM1), which is a transcription factor that is over-expressed in many cancers, is degraded in late mitosis and early G1 phase by the APC/cyclosome (APC/C) E3 ubiquitin ligase []. The APC/C targets mitotic cyclins for destruction in mitosis and G1 phase and is then inactivated at S phase. It thereby generates alternating states of high and low cyclin-Cdk activity, which is required for the alternation of mitosis and DNA replication []. The APC/C is composed of at least 13 subunits that stay tightly associated throughout the cell cycle: APC1, APC2, APC4, APC5, APC9, APC11, CDC16, CDC23, CDC26, CDC27, DOC1, MND2 and SWM1[], []. In fission yeast the 13 subunits are known as: Apc1, Apc2, Nuc2, Apc4, Apc5, Cut9, Apc8, Apc10, Apc11, Hcn1, Apc13, Apc14 and Apc15 []. This entry represents a C-terminal domain found in APC subunit 2. ; PDB: 1LDD_A.
Probab=25.41 E-value=1.4e+02 Score=22.51 Aligned_cols=47 Identities=26% Similarity=0.376 Sum_probs=30.1
Q ss_pred cccHHHHHHHhh---hhccCCCCCHHHHHHHHHHhccCCCCCCCCCeEEE
Q 009896 311 PLSLSSIYEEVI---KSEAGRNMTLDHVRASLVQLGELSFVDASSDSYSI 357 (523)
Q Consensus 311 ~~s~~~I~~~l~---~~~~~~~~~~~~i~~~L~~La~~~~~~~~~~~y~V 357 (523)
+++++.|+.-+. ..+.+.+.+.+.+.++|..+.++.-..-.+|.|.+
T Consensus 11 sl~l~RIh~mLkmf~~~~~~~~~s~~eL~~fL~~lv~e~~L~~~~G~YkL 60 (60)
T PF08672_consen 11 SLPLDRIHSMLKMFPKDPGGYDISLEELQEFLDRLVEEGKLECSGGSYKL 60 (60)
T ss_dssp SEEHHHHHHHHHHH-GGG--TT--HHHHHHHHHHHHHTTSEE--TTEEEE
T ss_pred CCCHHHHHHHHHhccCCCCCCCCCHHHHHHHHHHHHHCCcEEecCCEEeC
Confidence 467777776553 23456778899999999999988844444888864
No 288
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=25.15 E-value=2.5e+02 Score=25.80 Aligned_cols=33 Identities=15% Similarity=0.123 Sum_probs=30.3
Q ss_pred chhhhhhhc--CCCcccHHHHHHHHhhcccceEEE
Q 009896 398 ETDKISDTT--FVEKKDAPKILYKLWKDGYLLMEK 430 (523)
Q Consensus 398 eek~i~~~a--mi~~k~~R~~L~~L~~~g~v~lQE 430 (523)
+...|++.+ -||..++++.|-.|.+.|||+-.+
T Consensus 41 d~~~iak~l~p~is~~ev~~sL~~L~~~gli~k~~ 75 (171)
T PF14394_consen 41 DPEWIAKRLRPKISAEEVRDSLEFLEKLGLIKKDG 75 (171)
T ss_pred CHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEECC
Confidence 899999999 999999999999999999995443
No 289
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=25.07 E-value=4e+02 Score=25.66 Aligned_cols=37 Identities=14% Similarity=0.144 Sum_probs=33.0
Q ss_pred hCCCc-chhhhhhhcCCCcccHHHHHHHHhhcccceEE
Q 009896 393 SGRLL-ETDKISDTTFVEKKDAPKILYKLWKDGYLLME 429 (523)
Q Consensus 393 k~~l~-eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQ 429 (523)
-|.-+ .|.+|++.-.++..-+|+.|-.|..+|+|++.
T Consensus 27 pG~~LPsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~ 64 (251)
T PRK09990 27 VGQALPSERRLCEKLGFSRSALREGLTVLRGRGIIETA 64 (251)
T ss_pred CCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 35555 89999999999999999999999999999873
No 290
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=25.05 E-value=2.4e+02 Score=25.54 Aligned_cols=56 Identities=14% Similarity=0.202 Sum_probs=42.6
Q ss_pred HHHHHHHHHHHcCcCCHHHHHHHhhhcccCC------CccCHHHHHHHHHHHHhcccceecC
Q 009896 108 QCVELVQGLLEHGRLTLKQMFDRAKSSEKEG------NLVDLDSLRETLVKLVTAHYVERCP 163 (523)
Q Consensus 108 ~a~~I~~~lL~~G~~~~~~li~~~~~~~~~~------~~~~~~~i~~~f~~Lv~~~fi~~v~ 163 (523)
-|+.|+..|..+|-+.+..+-.....+...| ...+..-++.+|.+|-+.|||+..|
T Consensus 54 R~AsIlR~vY~~gpvGV~~L~~~yGg~k~~G~~P~h~~~~sg~iiR~~LqqLE~~glVek~~ 115 (150)
T PRK09333 54 RAASILRKVYIDGPVGVERLRTAYGGRKNRGVRPEHFVKGSGSIIRKILQQLEKAGLVEKTK 115 (150)
T ss_pred HHHHHHHHHHHcCCccHHHHHHHHCCCcCCCCCCCccccCccHHHHHHHHHHHHCCCeeeCC
Confidence 4889999999999999888877765532211 1125567999999999999998764
No 291
>PF05379 Peptidase_C23: Carlavirus endopeptidase ; InterPro: IPR008041 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to the MEROPS peptidase family C23 (clan CA). The type example is Carlavirus (apple stem pitting virus) endopeptidase, this thought to play a role in the post-translational cleavage of the high molecular weight primary translation products of the virus.; GO: 0003968 RNA-directed RNA polymerase activity, 0016817 hydrolase activity, acting on acid anhydrides
Probab=25.00 E-value=2.3e+02 Score=23.16 Aligned_cols=55 Identities=15% Similarity=0.290 Sum_probs=41.4
Q ss_pred chhHHHHHHHhhcCccHHHHHHHHHhccchhcccccccCCccccHHHHHHHhhhhccCCCCCHHHHHHHHHHhc
Q 009896 270 RHKGCIDHVRAHLDDGAANVLSAMLQATSSAEKKVKTKNSVPLSLSSIYEEVIKSEAGRNMTLDHVRASLVQLG 343 (523)
Q Consensus 270 R~~~iv~~v~~r~~~~a~~v~~~~L~~~~~~~~~~~~~~s~~~s~~~I~~~l~~~~~~~~~~~~~i~~~L~~La 343 (523)
||..++.++.+-+|.....|++.+-+... .++.+.+ ..|..++.+.+...++.+.
T Consensus 2 kN~Cvi~AiA~aL~R~~~dVl~Vl~~~~~----------------~~~~~~l---~~G~Gl~l~~le~~f~~F~ 56 (89)
T PF05379_consen 2 KNGCVIRAIAEALGRREQDVLAVLSRKCG----------------EELLEEL---WSGEGLDLEDLEELFELFD 56 (89)
T ss_pred CccchhHHHHHHhCCCHHHHHHHHHhccC----------------HHHHHHH---HcCCCcCHHHHHHHHHHcC
Confidence 67788889999999998888888776441 3566666 3467788888888887664
No 292
>PF09382 RQC: RQC domain; InterPro: IPR018982 This entry represents the RQC domain, which is a DNA-binding domain found only in RecQ family enzymes. RecQ family helicases can unwind G4 DNA, and play important roles at G-rich domains of the genome, including the telomeres, rDNA, and immunoglobulin switch regions. This domain has a helix-turn-helix structure and acts as a high affinity G4 DNA binding domain []. Binding of RecQ to Holliday junctions involves both the RQC and the HRDC domains.; GO: 0043140 ATP-dependent 3'-5' DNA helicase activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1OYW_A 1OYY_A 3AAF_A 2AXL_A 2V1X_B 2WWY_B.
Probab=24.34 E-value=2.9e+02 Score=22.64 Aligned_cols=56 Identities=16% Similarity=0.265 Sum_probs=37.5
Q ss_pred HHHHHHHHHHHHc-CcCCHHHHHHHhhhcc---------------cCCCccCHHHHHHHHHHHHhcccceec
Q 009896 107 QQCVELVQGLLEH-GRLTLKQMFDRAKSSE---------------KEGNLVDLDSLRETLVKLVTAHYVERC 162 (523)
Q Consensus 107 ~~a~~I~~~lL~~-G~~~~~~li~~~~~~~---------------~~~~~~~~~~i~~~f~~Lv~~~fi~~v 162 (523)
++|..|+..+-.. |+.+...++.-+.... ..+...+...++..+.+|+..|||...
T Consensus 4 ~~a~~il~~V~~~~~~~~~~~ivdvlrGs~~~~i~~~~~~~l~~yG~gk~~~~~~~~~li~~Li~~g~L~~~ 75 (106)
T PF09382_consen 4 EEAKKILSCVQRLKQRFGLSQIVDVLRGSKSKKIREKGHDQLPTYGIGKDMSKDDWERLIRQLILEGYLSED 75 (106)
T ss_dssp HHHHHHHHHHHHTTT-S-HHHHHHHHTT-S-CCCHHTTGGGSTTTTTTTTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHHHHhccccHHHHHHHHHhccchhhhhcCCCcCcccCCcccCCHHHHHHHHHHHHHcCCceec
Confidence 4677777777775 6677777777654320 112345789999999999999999555
No 293
>PRK03837 transcriptional regulator NanR; Provisional
Probab=24.22 E-value=1e+02 Score=29.55 Aligned_cols=33 Identities=21% Similarity=0.327 Sum_probs=30.5
Q ss_pred CC-cHHHHHhhcCCCHHHHHHHHHHHHhhccccc
Q 009896 34 PL-TRQNVKRYTELSDEQVKNALLVLIQQNCVQA 66 (523)
Q Consensus 34 ~l-tl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~ 66 (523)
++ +-.+|+...+++...||.||..|-+.|+|..
T Consensus 36 ~Lp~E~~Lae~~gVSRt~VREAL~~L~~eGlv~~ 69 (241)
T PRK03837 36 QLPSERELMAFFGVGRPAVREALQALKRKGLVQI 69 (241)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE
Confidence 56 6889999999999999999999999999983
No 294
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=24.16 E-value=92 Score=29.62 Aligned_cols=32 Identities=28% Similarity=0.355 Sum_probs=30.4
Q ss_pred CCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 34 PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 34 ~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
++|-.+|+...+++...||.||..|.+-|+|.
T Consensus 34 ~L~e~~La~~lgVSRtpVREAL~~L~~eGLV~ 65 (221)
T PRK11414 34 RLITKNLAEQLGMSITPVREALLRLVSVNALS 65 (221)
T ss_pred ccCHHHHHHHHCCCchhHHHHHHHHHHCCCEE
Confidence 67888999999999999999999999999998
No 295
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147. This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.
Probab=24.10 E-value=1.5e+02 Score=29.55 Aligned_cols=50 Identities=20% Similarity=0.155 Sum_probs=41.9
Q ss_pred hhhchhHHHHHHHHHhc--CCCcHHHHHhhcC--CCHHHHHHHHHHHHhhcccc
Q 009896 16 NHFGDLVAKVCECLLRK--GPLTRQNVKRYTE--LSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 16 ~~FG~~v~~V~~~Ll~~--G~ltl~~l~~~t~--l~~~~vr~aL~vLiQhn~V~ 65 (523)
++|.....-|..-|+.- |..+...|.+.++ ++..+|+.||-.|.+.|++.
T Consensus 117 ~y~~~W~~~virel~~~~~~~~~~~~ia~~l~p~is~~ev~~sL~~L~~~glik 170 (271)
T TIGR02147 117 EYYRHWYNSVIRELLGVMPFADDPEELAKRCFPKISAEQVKESLDLLERLGLIK 170 (271)
T ss_pred HHHHHHHHHHHHHHhhcCCCCCCHHHHHHHhCCCCCHHHHHHHHHHHHHCCCee
Confidence 35667777788888854 6657888999976 89999999999999999997
No 296
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=24.05 E-value=1e+02 Score=25.52 Aligned_cols=65 Identities=11% Similarity=0.225 Sum_probs=47.7
Q ss_pred cCCchHHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCceEEEEEEEc
Q 009896 379 YGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVN 447 (523)
Q Consensus 379 ~G~~a~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQEvpk~~~~~~t~~lw~v~ 447 (523)
++..-.+++.+|...+.. ...+|++...++...+-..+.+|.+.|||.-+.-| ...|..++.-.+
T Consensus 20 lt~~q~~~L~~l~~~~~~-~~~~la~~l~i~~~~vt~~l~~Le~~glv~r~~~~---~DrR~~~l~lT~ 84 (126)
T COG1846 20 LTPPQYQVLLALYEAGGI-TVKELAERLGLDRSTVTRLLKRLEDKGLIERLRDP---EDRRAVLVRLTE 84 (126)
T ss_pred CCHHHHHHHHHHHHhCCC-cHHHHHHHHCCCHHHHHHHHHHHHHCCCeeecCCc---cccceeeEEECc
Confidence 455667777777776655 33999999999999999999999999999443322 235555555444
No 297
>PRK09954 putative kinase; Provisional
Probab=23.95 E-value=1.3e+02 Score=30.97 Aligned_cols=99 Identities=10% Similarity=0.076 Sum_probs=63.9
Q ss_pred HHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEechhhHHHHh-chhhH---H
Q 009896 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFDNILHRV-RFAKF---L 98 (523)
Q Consensus 23 ~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~~~~il~rl-R~p~~---i 98 (523)
.+|.+.|..+++.|..+|.+..+++.+.|+.-|--|.+-|++..+...-+....-.+.=.++.|-++..- ++|.- .
T Consensus 6 ~~il~~l~~~~~~s~~~la~~l~~s~~~v~~~i~~L~~~g~i~~~~~~l~~~~~v~viG~~~vD~~~~~~~~~p~~~~~~ 85 (362)
T PRK09954 6 KEILAILRRNPLIQQNEIADILQISRSRVAAHIMDLMRKGRIKGKGYILTEQEYCVVVGAINMDIRGMADIRYPQAASHP 85 (362)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCcCCcEEEEcCCccEEEEEEEEEEEEEeeCCcCcCCCCCC
Confidence 4688999999999999999999999999999999999999986333211000111123344444432211 22321 2
Q ss_pred HHHHHHhhHHHHHHHHHHHHcCc
Q 009896 99 TILSQEFDQQCVELVQGLLEHGR 121 (523)
Q Consensus 99 ~~i~~~~G~~a~~I~~~lL~~G~ 121 (523)
..+....|-.+.-+...+-..|.
T Consensus 86 ~~~~~~~GG~~~NvA~~larLG~ 108 (362)
T PRK09954 86 GTIHCSAGGVGRNIAHNLALLGR 108 (362)
T ss_pred ceEEEecCcHHHHHHHHHHHcCC
Confidence 22344467777777777777775
No 298
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=23.73 E-value=3.2e+02 Score=23.36 Aligned_cols=60 Identities=15% Similarity=0.271 Sum_probs=47.2
Q ss_pred cchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCceEEEEEEEchHHHHHHHHHH
Q 009896 397 LETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQILWKHVLDE 458 (523)
Q Consensus 397 ~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQEvpk~~~~~~t~~lw~v~~~~~~~~~l~~ 458 (523)
+.-.+||+..--+.+-||.+|-+|.+.|.|.-|.=+- =.+++-.-|..+++.+....+.+
T Consensus 20 vtl~elA~~l~cS~Rn~r~lLkkm~~~gWi~W~pg~G--RG~~S~L~~l~~~~~~~~~~~~~ 79 (115)
T PF12793_consen 20 VTLDELAELLFCSRRNARTLLKKMQEEGWITWQPGRG--RGNRSQLTFLKSPEELLEQQAEE 79 (115)
T ss_pred eeHHHHHHHhCCCHHHHHHHHHHHHHCCCeeeeCCCC--CCCCCeeEEeeCHHHHHHHHHHH
Confidence 3778899999999999999999999999997753221 24677788889988776555443
No 299
>PRK11239 hypothetical protein; Provisional
Probab=23.60 E-value=1.6e+02 Score=28.16 Aligned_cols=48 Identities=17% Similarity=0.221 Sum_probs=38.3
Q ss_pred hchhHHHHHHHHHhcCCCcHHHHHhhcC----C-CHHHHHHHHHHHHhhc---ccc
Q 009896 18 FGDLVAKVCECLLRKGPLTRQNVKRYTE----L-SDEQVKNALLVLIQQN---CVQ 65 (523)
Q Consensus 18 FG~~v~~V~~~Ll~~G~ltl~~l~~~t~----l-~~~~vr~aL~vLiQhn---~V~ 65 (523)
|.+--..|.-.|+-||++|..+|-..++ + +...|...|--|+++. +|.
T Consensus 95 l~~~~~All~~LlLRGPQT~gELRtRs~Rl~~F~dv~~Ve~~L~~L~~r~~~plV~ 150 (215)
T PRK11239 95 LSAAEVALITTLLLRGAQTPGELRSRAARMYEFSDMAEVESTLEQLANREDGPFVV 150 (215)
T ss_pred CCHHHHHHHHHHHhcCCCChHHHHHhHhcCCcCCCHHHHHHHHHHHHhccCCceee
Confidence 4455667778888999999999966553 2 6789999999999995 564
No 300
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=23.42 E-value=1.5e+02 Score=28.90 Aligned_cols=43 Identities=21% Similarity=0.282 Sum_probs=39.6
Q ss_pred HHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 23 ~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
.+|...|..+|..+..+|.+..+++...||.=|-.|...|.+.
T Consensus 7 ~~Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~~L~~~~~l~ 49 (240)
T PRK10411 7 QAIVDLLLNHTSLTTEALAEQLNVSKETIRRDLNELQTQGKIL 49 (240)
T ss_pred HHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 4578889999999999999999999999999999999988776
No 301
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=23.19 E-value=2.9e+02 Score=21.99 Aligned_cols=56 Identities=21% Similarity=0.213 Sum_probs=33.5
Q ss_pred cHHHHHHHHHHHHhhhchhHH----HHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHH
Q 009896 3 TEYGTKHAVHVITNHFGDLVA----KVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVL 58 (523)
Q Consensus 3 ~~~~~~Lc~~iv~~~FG~~v~----~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vL 58 (523)
+++..+|...+-.-.-++-.. .+.+.|..-.+.|..+|...++.+..+|+.+|..+
T Consensus 3 ~~l~~~l~~~L~~~~~~~~~~~L~r~LLr~LA~G~PVt~~~LA~a~g~~~e~v~~~L~~~ 62 (77)
T PF12324_consen 3 TELATRLAERLTSGNRPGGFAWLLRPLLRLLAKGQPVTVEQLAAALGWPVEEVRAALAAM 62 (77)
T ss_dssp -TTHHHHHHHHHHHHSSTTHHHHHHHHHHHHTTTS-B-HHHHHHHHT--HHHHHHHHHH-
T ss_pred hHHHHHHHHHhcCCCCCCccHHHHHHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHhC
Confidence 345555555555553333333 34444544459999999999999999999999765
No 302
>smart00753 PAM PCI/PINT associated module.
Probab=23.17 E-value=1.5e+02 Score=23.47 Aligned_cols=41 Identities=12% Similarity=0.109 Sum_probs=35.7
Q ss_pred HHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhccccc
Q 009896 26 CECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQA 66 (523)
Q Consensus 26 ~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~ 66 (523)
.++.-.+..+++.+|.+..+++...+-..++-+|..|.+..
T Consensus 16 ~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~ 56 (88)
T smart00753 16 LQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISA 56 (88)
T ss_pred HHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEE
Confidence 33444578999999999999999999999999999999973
No 303
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=23.17 E-value=1.5e+02 Score=23.47 Aligned_cols=41 Identities=12% Similarity=0.109 Sum_probs=35.7
Q ss_pred HHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhccccc
Q 009896 26 CECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQA 66 (523)
Q Consensus 26 ~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~ 66 (523)
.++.-.+..+++.+|.+..+++...+-..++-+|..|.+..
T Consensus 16 ~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~ 56 (88)
T smart00088 16 LQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISA 56 (88)
T ss_pred HHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEE
Confidence 33444578999999999999999999999999999999973
No 304
>PF04157 EAP30: EAP30/Vps36 family; InterPro: IPR007286 EAP30 is a subunit of the ELL complex. The ELL is an 80kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity. ; PDB: 2ZME_A 3CUQ_A 1W7P_D 1U5T_B.
Probab=23.14 E-value=1e+02 Score=29.57 Aligned_cols=48 Identities=19% Similarity=0.138 Sum_probs=42.1
Q ss_pred hchhHHHHHHHH--HhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc
Q 009896 18 FGDLVAKVCECL--LRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 18 FG~~v~~V~~~L--l~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~ 65 (523)
.+....+|...+ -..|..|..+|....+.++...+..|-.+++.|+++
T Consensus 172 ~~~~~~~il~~~~~~~~g~vt~~~l~~~~~ws~~~a~~~L~~~~~~G~l~ 221 (223)
T PF04157_consen 172 LSKDQSRILELAEEENGGGVTASELAEKLGWSVERAKEALEELEREGLLW 221 (223)
T ss_dssp H-HHHHHHHHHH--TTTSEEEHHHHHHHHTB-HHHHHHHHHHHHHTTSEE
T ss_pred hhHHHHHHHHHHHhhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCEe
Confidence 356778888888 888999999999999999999999999999999986
No 305
>PRK03837 transcriptional regulator NanR; Provisional
Probab=22.97 E-value=1.4e+02 Score=28.61 Aligned_cols=36 Identities=17% Similarity=0.190 Sum_probs=32.9
Q ss_pred CCCc-chhhhhhhcCCCcccHHHHHHHHhhcccceEE
Q 009896 394 GRLL-ETDKISDTTFVEKKDAPKILYKLWKDGYLLME 429 (523)
Q Consensus 394 ~~l~-eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQ 429 (523)
|..+ .|.+|++.-.++..-+|+.|-.|..+|+|++.
T Consensus 34 G~~Lp~E~~Lae~~gVSRt~VREAL~~L~~eGlv~~~ 70 (241)
T PRK03837 34 GDQLPSERELMAFFGVGRPAVREALQALKRKGLVQIS 70 (241)
T ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 5555 89999999999999999999999999999883
No 306
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=22.53 E-value=2.7e+02 Score=26.44 Aligned_cols=47 Identities=15% Similarity=0.158 Sum_probs=36.6
Q ss_pred CchHHHHHHHHhh---C--CCcchhhhhhhcCCCcccHHHHHHHHhhcccceE
Q 009896 381 RDAYRIFRLLSKS---G--RLLETDKISDTTFVEKKDAPKILYKLWKDGYLLM 428 (523)
Q Consensus 381 ~~a~RI~r~L~~k---~--~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~l 428 (523)
..--||.++|... + .+ ..++||+...++...+-..|.+|.++|+|+.
T Consensus 150 ~~~~Rla~~L~~~~~~~~~~~-t~~~lA~~lG~sretvsR~L~~L~~~G~I~~ 201 (226)
T PRK10402 150 PLENRLAAFILLTQEGDLYHE-KHTQAAEYLGVSYRHLLYVLAQFIQDGYLKK 201 (226)
T ss_pred hHHHHHHHHHHhcccCCcccc-hHHHHHHHHCCcHHHHHHHHHHHHHCCCEEe
Confidence 3445666665421 1 23 7899999999999999999999999999966
No 307
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=22.34 E-value=1.2e+02 Score=28.45 Aligned_cols=31 Identities=13% Similarity=0.207 Sum_probs=29.6
Q ss_pred CcHHHHHhhcCCC-HHHHHHHHHHHHhhcccc
Q 009896 35 LTRQNVKRYTELS-DEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 35 ltl~~l~~~t~l~-~~~vr~aL~vLiQhn~V~ 65 (523)
.|+.+|++.++++ ++.|...|-.|.+.|++.
T Consensus 26 ~~~~ela~~~~~~s~~tv~~~l~~L~~~g~i~ 57 (199)
T TIGR00498 26 PSIREIARAVGLRSPSAAEEHLKALERKGYIE 57 (199)
T ss_pred CcHHHHHHHhCCCChHHHHHHHHHHHHCCCEe
Confidence 6789999999998 999999999999999997
No 308
>PF03428 RP-C: Replication protein C N-terminal domain; InterPro: IPR005090 Proteins in this group have homology with the RepC protein of Agrobacterium Ri and Ti plasmids []. They may be involved in plasmid replication and stabilisation functions.
Probab=22.34 E-value=3.6e+02 Score=25.09 Aligned_cols=88 Identities=13% Similarity=0.146 Sum_probs=56.1
Q ss_pred HHhhhc--hhHHHHHHHHHhcCCC-------------cHHHHHhhc-CCCHHHHHHHHHHHHhhcccccccccCCCC---
Q 009896 14 ITNHFG--DLVAKVCECLLRKGPL-------------TRQNVKRYT-ELSDEQVKNALLVLIQQNCVQAFTTEQPDG--- 74 (523)
Q Consensus 14 v~~~FG--~~v~~V~~~Ll~~G~l-------------tl~~l~~~t-~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~--- 74 (523)
....|| +-+-.|-..|++.-+- +=.+|...+ +++.+.|+..|..|+.-|+|. ..+++.|.
T Consensus 35 a~~~lgl~~~~l~vL~aLls~~~~~d~~~~~~piVfpSN~~La~r~~G~s~~tlrR~l~~LveaGLI~-rrDS~NgkRy~ 113 (177)
T PF03428_consen 35 ARPALGLSDRALAVLDALLSFTPPDDWEPGRRPIVFPSNAQLAERLNGMSERTLRRHLARLVEAGLIV-RRDSPNGKRYA 113 (177)
T ss_pred HHHhcCCChhHHHHHHHHHHhCCcccccCCCCceeecCHHHHHHHHcCCCHHHHHHHHHHHHHCCCee-eccCCCCCccC
Confidence 445555 5566666777665332 236777778 999999999999999999998 44433221
Q ss_pred ---C--CcceEEEechhhHHHHhchhhHHHHHHHH
Q 009896 75 ---P--KANTQYVVLFDNILHRVRFAKFLTILSQE 104 (523)
Q Consensus 75 ---~--~~~~~Y~~~~~~il~rlR~p~~i~~i~~~ 104 (523)
. ....-|-+ +=.-...|++.+...+++.
T Consensus 114 ~R~~~G~I~~A~Gf--dLsPL~~R~~El~~~a~~~ 146 (177)
T PF03428_consen 114 RRDRGGRIVEAFGF--DLSPLIARAEELAALAEAA 146 (177)
T ss_pred ccCCCCCEEeEeCc--CHHHHHHHHHHHHHHHHHH
Confidence 1 11123444 3344567778877776644
No 309
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=22.25 E-value=1.1e+02 Score=29.45 Aligned_cols=54 Identities=13% Similarity=0.093 Sum_probs=0.0
Q ss_pred hHHHHHHHHHHHHcCcCCHHHHHH---HhhhcccCCCccCHHHHHHHHHHHHhcccceecC
Q 009896 106 DQQCVELVQGLLEHGRLTLKQMFD---RAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 163 (523)
Q Consensus 106 G~~a~~I~~~lL~~G~~~~~~li~---~~~~~~~~~~~~~~~~i~~~f~~Lv~~~fi~~v~ 163 (523)
.+.+...+.+-+..|.+.+++-+- .+.+.... |+.-+++++..|...|+|...|
T Consensus 9 ~~~~~~~l~~~I~~g~l~pG~~LPsE~eLae~~gV----SRt~VReAL~~L~~eGlv~~~~ 65 (239)
T PRK04984 9 AGFAEEYIIESIWNNRFPPGSILPAERELSELIGV----TRTTLREVLQRLARDGWLTIQH 65 (239)
T ss_pred HHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEeC
No 310
>PF10330 Stb3: Putative Sin3 binding protein; InterPro: IPR018818 This entry represents Sin3 binding proteins conserved in fungi. Sin3p does not bind DNA directly even though the yeast SIN3 gene functions as a transcriptional repressor. Sin3p is part of a large multiprotein complex []. Stb3 appears to bind directly to ribosomal RNA Processing Elements (RRPE) although there are no obvious domains which would accord with this, implying that Stb3 may be a novel RNA-binding protein [].
Probab=22.09 E-value=1.4e+02 Score=24.39 Aligned_cols=34 Identities=26% Similarity=0.544 Sum_probs=24.3
Q ss_pred HHHHHHhcCCCcHHHHHhh--------cCCCHHHHHHHHHHH
Q 009896 25 VCECLLRKGPLTRQNVKRY--------TELSDEQVKNALLVL 58 (523)
Q Consensus 25 V~~~Ll~~G~ltl~~l~~~--------t~l~~~~vr~aL~vL 58 (523)
+-+.|+.+|+++++.|..+ .++++++-|.-++.-
T Consensus 11 Lp~iLl~~GPLaIRhI~~~Lt~~vPgF~~ls~sKqRRLi~~A 52 (92)
T PF10330_consen 11 LPEILLNHGPLAIRHITGYLTTSVPGFSDLSPSKQRRLIMAA 52 (92)
T ss_pred hHHHHHhcCcHHHHHHHHHHhccCCCcccCCHHHHHHHHHHH
Confidence 3459999999999999776 247776655544443
No 311
>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This entry consists of proteins thought to be involved in plasmid replication. ; GO: 0006260 DNA replication, 0006276 plasmid maintenance
Probab=21.92 E-value=1.3e+02 Score=27.54 Aligned_cols=65 Identities=17% Similarity=0.241 Sum_probs=50.6
Q ss_pred hhhchhHHHHHHHHHhcC------CCcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEechhhHH
Q 009896 16 NHFGDLVAKVCECLLRKG------PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFDNIL 89 (523)
Q Consensus 16 ~~FG~~v~~V~~~Ll~~G------~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~~~~il 89 (523)
+..|.-..+|..+|+.+= -+|..+|+..++++...|..++-.|...+++. ... .-.|.+|++-+.
T Consensus 51 ~l~g~k~~~Vl~~il~~~d~~N~v~~t~~~ia~~l~iS~~Tv~r~ik~L~e~~iI~--k~~-------~G~Y~iNP~~~~ 121 (165)
T PF05732_consen 51 DLIGNKAFRVLMYILENMDKDNAVVATQKEIAEKLGISKPTVSRAIKELEEKNIIK--KIR-------NGAYMINPNFFF 121 (165)
T ss_pred hhhchhHHHHHHHHHHhcCCCCeEEeeHHHHHHHhCCCHHHHHHHHHHHHhCCcEE--Ecc-------CCeEEECcHHhe
Confidence 345666778888888652 35788999999999999999999999999996 221 137999998654
No 312
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=21.59 E-value=2.5e+02 Score=23.74 Aligned_cols=57 Identities=16% Similarity=0.171 Sum_probs=40.2
Q ss_pred HHHHHHHhc-CCCcHHHHHhh-----cCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEech
Q 009896 24 KVCECLLRK-GPLTRQNVKRY-----TELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLF 85 (523)
Q Consensus 24 ~V~~~Ll~~-G~ltl~~l~~~-----t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~~ 85 (523)
.|..+|... +..|..+|.+. .+++...|-.+|-.|...|+|.-...++ ....|..+.
T Consensus 12 ~Il~~l~~~~~~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~~~~~~-----~~~~Y~~~~ 74 (120)
T PF01475_consen 12 AILELLKESPEHLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRKIEFGD-----GESRYELST 74 (120)
T ss_dssp HHHHHHHHHSSSEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEETT-----SEEEEEESS
T ss_pred HHHHHHHcCCCCCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEEEEcCC-----CcceEeecC
Confidence 456666665 47788888655 3688899999999999999998555442 246777765
No 313
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=21.56 E-value=5.4e+02 Score=22.78 Aligned_cols=69 Identities=13% Similarity=0.266 Sum_probs=52.1
Q ss_pred CCCCCeEEEehHHHHHHHHHHHHHHHHHHHcCCchHHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceE
Q 009896 349 DASSDSYSIDFEKIIEIAQNEEVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLM 428 (523)
Q Consensus 349 ~~~~~~y~V~~~~i~~~lr~~~le~~v~~~~G~~a~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~l 428 (523)
+..+.-|+-.|+.+.+.|--. -.+++++|..++-. .-.++++...=..|.+...|..|...|+|.+
T Consensus 45 ~~~Ptl~F~Sye~la~vLsp~-------------nleLl~~Ia~~~P~-Si~ElAe~vgRdv~nvhr~Ls~l~~~GlI~f 110 (144)
T COG4190 45 DATPTLWFTSYEDLARVLSPR-------------NLELLELIAQEEPA-SINELAELVGRDVKNVHRTLSTLADLGLIFF 110 (144)
T ss_pred cCCceeccccHHHHHHHhChh-------------HHHHHHHHHhcCcc-cHHHHHHHhCcchHHHHHHHHHHHhcCeEEE
Confidence 455566666666666655443 45788888777555 7777888888888888999999999999999
Q ss_pred EEE
Q 009896 429 EKL 431 (523)
Q Consensus 429 QEv 431 (523)
|+=
T Consensus 111 e~~ 113 (144)
T COG4190 111 EED 113 (144)
T ss_pred ecC
Confidence 993
No 314
>PF05158 RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; InterPro: IPR007832 The family comprises a subunit specific to RNA Pol III, the tRNA specific polymerase. The C34 subunit of Saccharomyces cerevisiae RNA Pol III is part of a subcomplex of three subunits which have no counterpart in the other two nuclear RNA polymerases. This subunit interacts with TFIIIB70 and therefore participates in Pol III recruitment [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2DK8_A 2DK5_A 2YU3_A.
Probab=21.37 E-value=1e+02 Score=31.73 Aligned_cols=45 Identities=18% Similarity=0.279 Sum_probs=33.9
Q ss_pred HHHHHHHhcC--CCcHHHHHhhcCCCHHHHHHHHHHHHhhccccccc
Q 009896 24 KVCECLLRKG--PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFT 68 (523)
Q Consensus 24 ~V~~~Ll~~G--~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~ 68 (523)
.|.+++-.-| ..-.++|...|+|+..+|.++|-.|.+.+++....
T Consensus 88 lvy~~I~~ag~~GIw~~~i~~~t~l~~~~~~k~lk~Le~k~lIK~vk 134 (327)
T PF05158_consen 88 LVYQLIEEAGNKGIWTKDIKKKTNLHQTQLTKILKSLESKKLIKSVK 134 (327)
T ss_dssp HHHHHHHHHTTT-EEHHHHHHHCT--HHHHHHHHHHHHHTTSEEEE-
T ss_pred HHHHHHHHhCCCCCcHHHHHHHcCCCHHHHHHHHHHHHhCCCEEEec
Confidence 4555555544 46789999999999999999999999999998543
No 315
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=21.27 E-value=6e+02 Score=25.23 Aligned_cols=79 Identities=18% Similarity=0.168 Sum_probs=60.8
Q ss_pred HHHhhhchhHHHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEechhhHHHHh
Q 009896 13 VITNHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFDNILHRV 92 (523)
Q Consensus 13 iv~~~FG~~v~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~~~~il~rl 92 (523)
++.-.|..-..+=.=.|+..|+.|+.+|....+.++..|-.-|-.|.-.|+|. ... -.|++-.-+-+...
T Consensus 5 ll~~if~SekRk~lLllL~egPkti~EI~~~l~vs~~ai~pqiKkL~~~~LV~--~~~--------~~Y~LS~~G~iiv~ 74 (260)
T COG4742 5 LLDLLFLSEKRKDLLLLLKEGPKTIEEIKNELNVSSSAILPQIKKLKDKGLVV--QEG--------DRYSLSSLGKIIVE 74 (260)
T ss_pred HHHHHHccHHHHHHHHHHHhCCCCHHHHHHHhCCCcHHHHHHHHHHhhCCCEE--ecC--------CEEEecchHHHHHH
Confidence 45556666666666677788999999999999999999999999999999997 332 38888777666666
Q ss_pred chhhHHHHH
Q 009896 93 RFAKFLTIL 101 (523)
Q Consensus 93 R~p~~i~~i 101 (523)
....++..+
T Consensus 75 km~~ll~tl 83 (260)
T COG4742 75 KMEPLLDTL 83 (260)
T ss_pred HHHHHHHHH
Confidence 665555443
No 316
>COG4860 Uncharacterized protein conserved in archaea [Function unknown]
Probab=21.17 E-value=6e+02 Score=22.72 Aligned_cols=108 Identities=18% Similarity=0.260 Sum_probs=64.5
Q ss_pred hhc-hhHHHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccc-cccccCCCC-CC--cceEEE---echhhH
Q 009896 17 HFG-DLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ-AFTTEQPDG-PK--ANTQYV---VLFDNI 88 (523)
Q Consensus 17 ~FG-~~v~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~-~~~~~~~~~-~~--~~~~Y~---~~~~~i 88 (523)
.|| ++-.+++..| ..|..|+++|-+.-|-.. +.||.+|=.-+++. .|..+..|+ |. .+++|+ +|...-
T Consensus 20 ~~~set~rKl~~aL-stgW~T~~eiee~iG~eg---~RaL~iLkkagmlEtqWr~p~~G~kPeKeYHtsYt~VqiNf~~S 95 (170)
T COG4860 20 AADSETKRKLLLAL-STGWITLPEIEEKIGKEG---RRALLILKKAGMLETQWRTPSNGQKPEKEYHTSYTNVQINFMGS 95 (170)
T ss_pred HcccHHHHHHHHHH-hhcceeHHHHHHHhchhh---HHHHHHHHhhcchhheeeccCCCCCchhhhhhheeeEEEEEEEe
Confidence 344 4555666666 589999999988766433 34999999999987 455554442 22 233443 333333
Q ss_pred HHHhchhhHHHHHHHHhh--HHHHHHHHHHHHcCcCCHHHHHHH
Q 009896 89 LHRVRFAKFLTILSQEFD--QQCVELVQGLLEHGRLTLKQMFDR 130 (523)
Q Consensus 89 l~rlR~p~~i~~i~~~~G--~~a~~I~~~lL~~G~~~~~~li~~ 130 (523)
+.=| ..+|..+-.-+. .++..=+..++..|..++.++-..
T Consensus 96 l~dL--~dii~~~f~sdeev~ey~~ei~~l~e~g~ts~~~vt~~ 137 (170)
T COG4860 96 LSDL--ADIIYAAFLSDEEVKEYEDEIKALMEEGNTSFLDVTDT 137 (170)
T ss_pred HHHH--HHHHHHHhCCHHHHHHHHHHHHHHHHcCCceEeehhhh
Confidence 3222 333333333332 456666777888888887765443
No 317
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=21.15 E-value=2.9e+02 Score=29.68 Aligned_cols=44 Identities=18% Similarity=0.217 Sum_probs=34.0
Q ss_pred HHHHHHHHhc-CCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccc
Q 009896 23 AKVCECLLRK-GPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTT 69 (523)
Q Consensus 23 ~~V~~~Ll~~-G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~ 69 (523)
..|..+|..+ |.+|+.+|++.|++....|- ..|-+.|++.|+..
T Consensus 362 ~~i~~~L~~~~~~~si~~is~~T~i~~~Dii---~tL~~l~~l~~~kg 406 (450)
T PLN00104 362 RVLLEILKKHKGNISIKELSDMTAIKAEDIV---STLQSLNLIQYRKG 406 (450)
T ss_pred HHHHHHHHhcCCCccHHHHHHHhCCCHHHHH---HHHHHCCCEEecCC
Confidence 4556666666 69999999999999998775 45677899986543
No 318
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=21.05 E-value=3.2e+02 Score=26.38 Aligned_cols=65 Identities=12% Similarity=-0.038 Sum_probs=52.8
Q ss_pred hhhchhHHHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEechh
Q 009896 16 NHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFD 86 (523)
Q Consensus 16 ~~FG~~v~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~~~ 86 (523)
..=|+....|+..+...++.|...|.+..+++...|.-.+--|---|++. -+.. | ....|++|+.
T Consensus 170 ~Lkn~~~k~I~~eiq~~~~~t~~~ia~~l~ls~aTV~~~lk~l~~~Gii~-~~~~--G---r~iiy~in~s 234 (240)
T COG3398 170 SLKNETSKAIIYEIQENKCNTNLLIAYELNLSVATVAYHLKKLEELGIIP-EDRE--G---RSIIYSINPS 234 (240)
T ss_pred HhhchhHHHHHHHHhcCCcchHHHHHHHcCccHHHHHHHHHHHHHcCCCc-cccc--C---ceEEEEeCHH
Confidence 34467778999999999999999999999999999999999999999986 2221 1 2468888864
No 319
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=21.02 E-value=1.6e+02 Score=23.50 Aligned_cols=38 Identities=11% Similarity=0.083 Sum_probs=33.1
Q ss_pred hhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEE
Q 009896 392 KSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLME 429 (523)
Q Consensus 392 ~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQ 429 (523)
+.|.-+--+.|++..-+++-.+|+.+..|...|||+=|
T Consensus 19 ~~~~PVgSk~ia~~l~~s~aTIRN~M~~Le~lGlve~~ 56 (78)
T PF03444_consen 19 ETGEPVGSKTIAEELGRSPATIRNEMADLEELGLVESQ 56 (78)
T ss_pred hcCCCcCHHHHHHHHCCChHHHHHHHHHHHHCCCccCC
Confidence 55677788999999888999999999999999999643
No 320
>PF01090 Ribosomal_S19e: Ribosomal protein S19e; InterPro: IPR001266 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family includes a number of eukaryotic and archaebacterial ribosomal proteins; mammalian S19, Drosophila S19, Ascaris lumbricoides S19g (ALEP-1) and S19s, yeast YS16 (RP55A and RP55B), Aspergillus S16 and Haloarcula marismortui HS12.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZ6_S 3U5G_T 3U5C_T 3O30_M 3O2Z_M 3IZB_S 2XZN_T 2XZM_T 2V7F_A.
Probab=20.98 E-value=2.3e+02 Score=25.26 Aligned_cols=57 Identities=18% Similarity=0.244 Sum_probs=42.1
Q ss_pred HHHHHHHHHHHHcCcCCHHHHHHHhhhcccCCC------ccCHHHHHHHHHHHHhcccceecC
Q 009896 107 QQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGN------LVDLDSLRETLVKLVTAHYVERCP 163 (523)
Q Consensus 107 ~~a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~------~~~~~~i~~~f~~Lv~~~fi~~v~ 163 (523)
--||.|+-.|..+|-+.++.+-.........|. ..+..-++.+|.+|-..|||+..|
T Consensus 52 ~RaASilRklY~~g~~GV~~lr~~YGg~k~~G~~p~h~~~asg~iiR~~LqqLE~~glv~k~~ 114 (139)
T PF01090_consen 52 IRAASILRKLYIRGPVGVGRLRKIYGGRKRRGVRPSHFVKASGSIIRKILQQLEKAGLVEKDP 114 (139)
T ss_dssp HHHHHHHHHHHHCTSB-HHHHHHHH--EEEETSSCCEE--CHHHHHHHHHHHHHHTTSEEEET
T ss_pred eeHHHHHHHHHHhcCcchHHHHHHhCCCCCCCCCCCCCCCCCcHHHHHHHHHHHHCCCEEecC
Confidence 348999999999999999998877665432221 124567999999999999999885
No 321
>PF10557 Cullin_Nedd8: Cullin protein neddylation domain; InterPro: IPR019559 This is the neddylation site of cullin proteins, which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae (Baker's yeast), and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue []. ; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_B 1U6G_A 3O6B_J 3O2P_E 4A0K_A 2HYE_C ....
Probab=20.91 E-value=1.9e+02 Score=22.09 Aligned_cols=46 Identities=13% Similarity=0.231 Sum_probs=37.0
Q ss_pred hhHHHHHHHHHhcCCCcHHHHHhhc--------CCCHHHHHHHHHHHHhhcccc
Q 009896 20 DLVAKVCECLLRKGPLTRQNVKRYT--------ELSDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 20 ~~v~~V~~~Ll~~G~ltl~~l~~~t--------~l~~~~vr~aL~vLiQhn~V~ 65 (523)
.+=|.|.+++=.++.++..+|...+ ..+...|+.+|-.||..+++.
T Consensus 8 ~I~AaIVrimK~~k~~~~~~L~~~v~~~l~~~f~~~~~~ik~~Ie~LIekeyi~ 61 (68)
T PF10557_consen 8 QIDAAIVRIMKQEKKLSHDELINEVIEELKKRFPPSVSDIKKRIESLIEKEYIE 61 (68)
T ss_dssp HHHHHHHHHHHHSSEEEHHHHHHHHHHHTTTTS---HHHHHHHHHHHHHTTSEE
T ss_pred hhhhheehhhhhcCceeHHHHHHHHHHHhcCCcCCCHHHHHHHHHHHHHhhhhh
Confidence 4557888999999999999997652 356789999999999999987
No 322
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR. Members of this family are FadR, a transcriptional regulator of fatty acid metabolism, including both biosynthesis and beta-oxidation. It is found exclusively in a subset of Gammaproteobacteria, with strictly one copy per genome. It has an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR from this family heterologously expressed in Escherichia coli show differences in regulatory response and fatty acid binding profiles. The family is nevertheless designated equivalog, as all member proteins have at least nominally the same function.
Probab=20.88 E-value=1.7e+02 Score=27.97 Aligned_cols=61 Identities=25% Similarity=0.394 Sum_probs=0.0
Q ss_pred EehHHHHHHHHHHHHHHHHHHHcCCchHHHHHHHHhhCCCc-chhhhhhhcCCCcccHHHHHHHHhhcccceEE
Q 009896 357 IDFEKIIEIAQNEEVESVVSKRYGRDAYRIFRLLSKSGRLL-ETDKISDTTFVEKKDAPKILYKLWKDGYLLME 429 (523)
Q Consensus 357 V~~~~i~~~lr~~~le~~v~~~~G~~a~RI~r~L~~k~~l~-eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQ 429 (523)
+.-....+..-....+.|+..+|.+ |.-+ .|.+|++.-.++..-+|+.|..|..+|+|+++
T Consensus 2 ~~~~~~~~~v~~~l~~~I~~g~l~p------------G~~LpsE~~La~~lgVSRtpVREAL~~Le~eGlV~~~ 63 (235)
T TIGR02812 2 IKAKSPAGFAEEYIVESIWNNRFPP------------GSILPAERELSELIGVTRTTLREVLQRLARDGWLTIQ 63 (235)
T ss_pred cchhhhHHHHHHHHHHHHHcCCCCC------------CCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
No 323
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=20.73 E-value=1.6e+02 Score=26.60 Aligned_cols=45 Identities=16% Similarity=0.175 Sum_probs=39.2
Q ss_pred hHHHHHHHHHhcCCCcHHHHHhhcCC--------------CHHHHHHHHHHHHhhcccc
Q 009896 21 LVAKVCECLLRKGPLTRQNVKRYTEL--------------SDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 21 ~v~~V~~~Ll~~G~ltl~~l~~~t~l--------------~~~~vr~aL~vLiQhn~V~ 65 (523)
-++.|.+.+--+|+..+..|.+..+. +.+.||.+|-.|-+-++|.
T Consensus 54 R~AsIlR~vY~~gpvGV~~L~~~yGg~k~~G~~P~h~~~~sg~iiR~~LqqLE~~glVe 112 (150)
T PRK09333 54 RAASILRKVYIDGPVGVERLRTAYGGRKNRGVRPEHFVKGSGSIIRKILQQLEKAGLVE 112 (150)
T ss_pred HHHHHHHHHHHcCCccHHHHHHHHCCCcCCCCCCCccccCccHHHHHHHHHHHHCCCee
Confidence 37889999999999999999888765 3456999999999999998
No 324
>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=20.61 E-value=1.6e+02 Score=23.06 Aligned_cols=58 Identities=14% Similarity=0.134 Sum_probs=42.7
Q ss_pred HHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCceEEEEEEEc
Q 009896 385 RIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVN 447 (523)
Q Consensus 385 RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQEvpk~~~~~~t~~lw~v~ 447 (523)
+|+-++ .++.. .-+.+.+...++.+..--.|.+|.+.|.|.=.... -+++.+=.|.+.
T Consensus 9 ~IL~~l-s~~c~-TLeeL~ekTgi~k~~LlV~LsrL~k~GiI~Rkw~~---~~gkk~R~YclK 66 (72)
T PF05584_consen 9 KILIIL-SKRCC-TLEELEEKTGISKNTLLVYLSRLAKRGIIERKWRK---FGGKKYREYCLK 66 (72)
T ss_pred HHHHHH-HhccC-CHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeeeEE---ecCeEEEEEEec
Confidence 455555 44577 99999999999999999999999999999432222 345556556554
No 325
>PF09105 SelB-wing_1: Elongation factor SelB, winged helix ; InterPro: IPR015189 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []. Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 1". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; PDB: 2V9V_A 1LVA_A 2PLY_A.
Probab=20.60 E-value=2.3e+02 Score=20.28 Aligned_cols=37 Identities=11% Similarity=0.188 Sum_probs=29.9
Q ss_pred CCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEe
Q 009896 395 RLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLV 432 (523)
Q Consensus 395 ~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQEvp 432 (523)
.+ |=.+-+..|-++..++|++|..|...|-|.+-.|.
T Consensus 17 gl-dwqeaatraslsleetrkllqsmaaagqvtllrve 53 (61)
T PF09105_consen 17 GL-DWQEAATRASLSLEETRKLLQSMAAAGQVTLLRVE 53 (61)
T ss_dssp -E-EHHHHHHHHT--HHHHHHHHHHHHHTTSEEEEEET
T ss_pred cC-cHHHHHHHhhccHHHHHHHHHHHHhcCceEEEEec
Confidence 45 88888999999999999999999999999876554
No 326
>PF03551 PadR: Transcriptional regulator PadR-like family; InterPro: IPR005149 Phenolic acids, also called substituted hydroxycinnamic acids, are abundant in the plant kingdom because they are involved in the structure of plant cell walls and are present in some vacuoles. In plant-soil ecosystems they are released as free acids by hemicellulases produced by several fungi and bacteria. Of these weak acids, the most abundant are p-coumaric, ferulic, and caffeic acids, considered to be natural toxins that inhibit the growth of microorganisms, especially at low pHs. In spite of this chemical stress, some bacteria can use phenolic acids as a sole source of carbon. For other microorganisms, these compounds induce a specific response by which the organism adapts to its environment. The ubiquitous lactic acid bacterium Lactobacillus plantarum exhibits an inducible phenolic acid decarboxylase (PAD) activity which converts these substrates into less-toxic vinyl phenol derivatives. PadR acts as a repressor of padA gene expression in the phenolic acid stress response [].; PDB: 1XMA_B 2ESH_A 2DQL_B 3L9F_C 3ELK_B 4EJO_B 3L7W_A 3HHH_A 1YG2_A 3F8B_A ....
Probab=20.46 E-value=1.9e+02 Score=22.28 Aligned_cols=55 Identities=18% Similarity=0.276 Sum_probs=36.5
Q ss_pred cCCCcHHHHHhh--------cCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEechhh
Q 009896 32 KGPLTRQNVKRY--------TELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFDN 87 (523)
Q Consensus 32 ~G~ltl~~l~~~--------t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~~~~ 87 (523)
.|+.+-.+|.+. .++++..|-.+|-.|.+.|+|........++ +...+|.+...+
T Consensus 7 ~~~~~Gyei~~~l~~~~~~~~~i~~g~lY~~L~~Le~~gli~~~~~~~~~~-~~rk~Y~iT~~G 69 (75)
T PF03551_consen 7 EGPMHGYEIKQELEERTGGFWKISPGSLYPALKRLEEEGLIESRWEEEGNG-RPRKYYRITEKG 69 (75)
T ss_dssp HS-EEHHHHHHHHHHCSTTTEETTHHHHHHHHHHHHHTTSEEEEEEEETTS-SEEEEEEESHHH
T ss_pred cCCCcHHHHHHHHHHHhCCCcccChhHHHHHHHHHHhCCCEEEeeeccCCC-CCCEEEEECHHH
Confidence 355555555433 3588999999999999999999444432222 345688876543
No 327
>TIGR02277 PaaX_trns_reg phenylacetic acid degradation operon negative regulatory protein PaaX. This transcriptional regulator is always found in association with operons believed to be involved in the degradation of phenylacetic acid. The gene product has been shown to bind to the promoter sites and repress their transcription.
Probab=20.38 E-value=1.3e+02 Score=30.26 Aligned_cols=60 Identities=17% Similarity=0.300 Sum_probs=43.9
Q ss_pred hhhchhHHHHHHHHHhc-CCCcHHHHHhh---cCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEEEechhhH
Q 009896 16 NHFGDLVAKVCECLLRK-GPLTRQNVKRY---TELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFDNI 88 (523)
Q Consensus 16 ~~FG~~v~~V~~~Ll~~-G~ltl~~l~~~---t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y~~~~~~i 88 (523)
..||+.+. .+ |.+++..|++. .+++...|+.+|.-|.+.|++..... |. ..+|.+.....
T Consensus 5 T~~Gd~~~-------~~gg~i~~~~Li~l~~~~gi~~~~vr~al~RL~~~G~l~~~~~----gr--r~~Y~LT~~g~ 68 (280)
T TIGR02277 5 TLYGDAIR-------PRGGAIWLGSLIEFLAGLGINERLVRTAVSRLVAQGWLQSERK----GR--RSFYSLTDKGR 68 (280)
T ss_pred Eehhhhcc-------CCCCceeHHHHHHHHHhcCCCcchHHHHHHHHHHCCCEEeeec----CC--CCEEEECHHHH
Confidence 45666555 44 46888888766 68999999999999999999983322 11 36898876654
No 328
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=20.35 E-value=2.9e+02 Score=26.57 Aligned_cols=63 Identities=17% Similarity=0.226 Sum_probs=46.2
Q ss_pred CCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCceEEEEEEEchHHHHHHHHHHHHHHHHHHH
Q 009896 395 RLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQILWKHVLDEMFHAALNLS 467 (523)
Q Consensus 395 ~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQEvpk~~~~~~t~~lw~v~~~~~~~~~l~~~~k~~~nl~ 467 (523)
++ ...+|++...++...+-..|-+|.+.|||.-+..|+. +.|++... -..+++..|....+++
T Consensus 21 ~I-S~~eLA~~L~iS~~Tvsr~Lk~LEe~GlI~R~~~~r~-------~~v~LTek--G~~ll~~~~~d~~~if 83 (217)
T PRK14165 21 KI-SSSEFANHTGTSSKTAARILKQLEDEGYITRTIVPRG-------QLITITEK--GLDVLYNEYADYSRIF 83 (217)
T ss_pred Cc-CHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEEcCCc-------eEEEECHH--HHHHHHHHHHHHHHHh
Confidence 45 8999999999999999999999999999976555432 45555533 2344466666555554
No 329
>PRK00215 LexA repressor; Validated
Probab=20.11 E-value=2.2e+02 Score=26.69 Aligned_cols=43 Identities=19% Similarity=0.295 Sum_probs=35.4
Q ss_pred HHHHHHHHhcC-CCcHHHHHhhcCC-CHHHHHHHHHHHHhhcccc
Q 009896 23 AKVCECLLRKG-PLTRQNVKRYTEL-SDEQVKNALLVLIQQNCVQ 65 (523)
Q Consensus 23 ~~V~~~Ll~~G-~ltl~~l~~~t~l-~~~~vr~aL~vLiQhn~V~ 65 (523)
..|..+...+| +.|+.+|++.+++ +.+.+..-|-.|.+.|++.
T Consensus 11 ~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~~~g~i~ 55 (205)
T PRK00215 11 DFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALERKGFIR 55 (205)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEE
Confidence 33444444455 5789999999999 9999999999999999997
Done!