Query 008455
Match_columns 565
No_of_seqs 268 out of 1162
Neff 6.4
Searched_HMMs 46136
Date Thu Mar 28 12:22:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008455.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008455hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1598 Transcription initiati 100.0 1.3E-82 2.8E-87 674.8 27.9 482 2-547 1-493 (521)
2 PRK00423 tfb transcription ini 100.0 4E-53 8.7E-58 439.4 26.7 250 2-260 12-302 (310)
3 COG1405 SUA7 Transcription ini 100.0 8.8E-53 1.9E-57 428.3 24.0 253 1-262 1-279 (285)
4 KOG1597 Transcription initiati 100.0 4E-47 8.6E-52 377.6 24.1 265 2-274 1-299 (308)
5 PF07741 BRF1: Brf1-like TBP-b 100.0 6.6E-30 1.4E-34 221.9 1.3 96 421-541 1-97 (97)
6 PF00382 TFIIB: Transcription 99.7 2.5E-16 5.3E-21 129.1 9.3 71 78-150 1-71 (71)
7 PF00382 TFIIB: Transcription 99.6 3.3E-15 7.2E-20 122.4 9.2 71 179-251 1-71 (71)
8 TIGR00569 ccl1 cyclin ccl1. Un 99.4 3.6E-11 7.7E-16 124.8 19.6 164 67-237 51-226 (305)
9 KOG0835 Cyclin L [General func 99.3 5.3E-11 1.1E-15 121.2 18.4 189 66-261 18-231 (367)
10 PRK00423 tfb transcription ini 99.3 1E-11 2.2E-16 129.7 11.7 89 74-164 219-307 (310)
11 KOG0834 CDK9 kinase-activating 99.2 3.5E-11 7.7E-16 125.0 11.3 158 72-236 40-214 (323)
12 PF08271 TF_Zn_Ribbon: TFIIB z 99.2 9.2E-12 2E-16 92.3 2.4 43 2-44 1-43 (43)
13 COG5333 CCL1 Cdk activating ki 99.1 1.5E-09 3.3E-14 110.6 13.1 158 72-236 46-211 (297)
14 COG1405 SUA7 Transcription ini 99.0 1.9E-09 4.2E-14 110.8 10.2 91 73-165 193-283 (285)
15 cd00043 CYCLIN Cyclin box fold 98.8 3.4E-08 7.3E-13 81.6 10.8 83 73-157 4-87 (88)
16 cd00043 CYCLIN Cyclin box fold 98.8 2.9E-08 6.3E-13 82.0 9.9 84 173-258 3-87 (88)
17 KOG1597 Transcription initiati 98.8 2.1E-08 4.6E-13 101.4 10.2 88 73-162 202-289 (308)
18 smart00385 CYCLIN domain prese 98.8 3.7E-08 8E-13 80.6 9.5 81 177-259 1-82 (83)
19 smart00385 CYCLIN domain prese 98.7 6.1E-08 1.3E-12 79.2 8.7 79 77-158 2-82 (83)
20 KOG0794 CDK8 kinase-activating 98.7 2.2E-07 4.7E-12 91.1 13.4 176 74-258 44-234 (264)
21 KOG0656 G1/S-specific cyclin D 98.5 3.5E-06 7.6E-11 88.1 16.9 178 72-256 79-268 (335)
22 KOG1598 Transcription initiati 98.3 5.5E-07 1.2E-11 97.9 5.2 159 77-235 169-335 (521)
23 KOG4557 Origin recognition com 97.6 0.0026 5.6E-08 62.2 14.8 159 77-249 2-168 (262)
24 PF00134 Cyclin_N: Cyclin, N-t 97.5 0.00095 2.1E-08 59.7 11.3 92 71-164 31-125 (127)
25 KOG2496 Cdk activating kinase 97.5 0.0021 4.5E-08 66.0 13.7 147 78-228 63-219 (325)
26 KOG0653 Cyclin B and related k 97.3 0.0027 5.7E-08 68.8 13.4 153 74-235 161-317 (391)
27 PF01857 RB_B: Retinoblastoma- 97.3 0.0017 3.7E-08 60.1 9.7 84 70-155 10-95 (135)
28 PF02984 Cyclin_C: Cyclin, C-t 97.1 0.0014 3.1E-08 57.5 6.8 86 174-261 2-88 (118)
29 COG5024 Cyclin [Cell division 96.6 0.012 2.5E-07 64.3 10.6 148 76-233 218-369 (440)
30 PF11781 RRN7: RNA polymerase 96.3 0.0025 5.4E-08 45.5 1.8 27 3-31 10-36 (36)
31 PF09862 DUF2089: Protein of u 96.2 0.07 1.5E-06 47.8 11.1 55 135-193 51-106 (113)
32 KOG0835 Cyclin L [General func 95.8 0.056 1.2E-06 56.3 9.8 105 74-186 141-246 (367)
33 PRK00415 rps27e 30S ribosomal 94.8 0.015 3.2E-07 46.0 1.4 31 2-32 12-42 (59)
34 COG2051 RPS27A Ribosomal prote 94.7 0.016 3.5E-07 46.6 1.6 31 2-32 20-50 (67)
35 PF01667 Ribosomal_S27e: Ribos 94.6 0.016 3.5E-07 45.2 1.3 31 2-32 8-38 (55)
36 KOG0655 G1/S-specific cyclin E 94.2 0.61 1.3E-05 48.9 11.9 170 74-258 148-331 (408)
37 TIGR01206 lysW lysine biosynth 94.2 0.029 6.3E-07 43.7 1.9 31 1-31 2-33 (54)
38 PF02150 RNA_POL_M_15KD: RNA p 94.0 0.03 6.5E-07 39.7 1.5 31 1-31 1-31 (35)
39 PF13248 zf-ribbon_3: zinc-rib 94.0 0.028 6.1E-07 37.1 1.3 24 1-29 2-25 (26)
40 PLN00209 ribosomal protein S27 93.8 0.034 7.3E-07 47.0 1.7 31 2-32 37-67 (86)
41 PF02984 Cyclin_C: Cyclin, C-t 93.8 0.32 6.9E-06 42.5 8.1 86 75-162 4-90 (118)
42 PF13240 zinc_ribbon_2: zinc-r 93.8 0.033 7.2E-07 35.8 1.2 22 3-29 1-22 (23)
43 PF14803 Nudix_N_2: Nudix N-te 93.8 0.028 6.1E-07 39.6 1.0 28 3-30 2-32 (34)
44 PTZ00083 40S ribosomal protein 93.6 0.039 8.4E-07 46.6 1.8 31 2-32 36-66 (85)
45 PRK00420 hypothetical protein; 93.6 0.047 1E-06 48.9 2.4 27 3-31 25-51 (112)
46 PF00134 Cyclin_N: Cyclin, N-t 93.4 0.27 5.9E-06 43.7 7.0 67 176-244 35-102 (127)
47 PF08792 A2L_zn_ribbon: A2L zi 93.4 0.06 1.3E-06 37.7 2.1 27 3-30 5-31 (33)
48 PHA00626 hypothetical protein 93.3 0.061 1.3E-06 41.8 2.3 30 2-31 1-34 (59)
49 TIGR02098 MJ0042_CXXC MJ0042 f 92.8 0.061 1.3E-06 38.4 1.5 30 2-31 3-36 (38)
50 TIGR00569 ccl1 cyclin ccl1. Un 92.5 0.52 1.1E-05 49.5 8.7 69 177-245 61-129 (305)
51 PF08274 PhnA_Zn_Ribbon: PhnA 92.3 0.11 2.3E-06 35.6 2.1 28 1-30 2-29 (30)
52 COG1645 Uncharacterized Zn-fin 92.1 0.085 1.9E-06 48.3 2.0 23 3-28 30-52 (131)
53 smart00342 HTH_ARAC helix_turn 91.2 1.7 3.7E-05 34.9 8.7 75 133-259 1-76 (84)
54 KOG0834 CDK9 kinase-activating 90.7 0.49 1.1E-05 50.0 6.2 82 176-259 43-128 (323)
55 PF03966 Trm112p: Trm112p-like 90.7 0.19 4.2E-06 40.8 2.5 17 14-30 47-63 (68)
56 COG1997 RPL43A Ribosomal prote 90.2 0.2 4.3E-06 42.6 2.2 30 3-33 37-66 (89)
57 PF13404 HTH_AsnC-type: AsnC-t 90.0 0.59 1.3E-05 34.4 4.3 32 228-259 11-42 (42)
58 smart00778 Prim_Zn_Ribbon Zinc 89.9 0.23 5E-06 35.7 2.0 27 2-28 4-33 (37)
59 smart00661 RPOL9 RNA polymeras 89.9 0.23 5.1E-06 37.7 2.2 29 3-31 2-31 (52)
60 PF14354 Lar_restr_allev: Rest 89.8 0.27 5.9E-06 38.7 2.6 27 2-28 4-37 (61)
61 PRK00432 30S ribosomal protein 89.8 0.23 4.9E-06 38.1 2.0 26 3-30 22-47 (50)
62 PF08613 Cyclin: Cyclin; Inte 89.1 5.6 0.00012 37.2 11.3 89 74-164 54-148 (149)
63 PF13719 zinc_ribbon_5: zinc-r 88.7 0.25 5.4E-06 35.4 1.5 28 3-30 4-35 (37)
64 PRK00398 rpoP DNA-directed RNA 88.3 0.36 7.8E-06 36.1 2.2 27 3-30 5-31 (46)
65 PRK00464 nrdR transcriptional 88.0 0.33 7.2E-06 45.9 2.3 29 2-30 1-38 (154)
66 smart00342 HTH_ARAC helix_turn 87.2 2 4.3E-05 34.5 6.2 71 78-157 4-75 (84)
67 PF09538 FYDLN_acid: Protein o 87.1 0.34 7.3E-06 43.2 1.6 29 3-33 11-39 (108)
68 KOG2496 Cdk activating kinase 86.9 1.6 3.4E-05 45.4 6.5 71 175-245 59-129 (325)
69 PRK05657 RNA polymerase sigma 86.6 35 0.00076 36.2 16.8 27 233-259 281-307 (325)
70 TIGR03655 anti_R_Lar restricti 86.6 0.49 1.1E-05 36.5 2.1 31 2-32 2-38 (53)
71 PRK11827 hypothetical protein; 86.5 0.54 1.2E-05 37.5 2.3 27 3-30 10-36 (60)
72 PF05460 ORC6: Origin recognit 86.3 0.22 4.7E-06 53.4 0.0 86 80-165 3-89 (353)
73 PF10571 UPF0547: Uncharacteri 86.0 0.44 9.5E-06 31.6 1.3 24 3-31 2-25 (26)
74 KOG4164 Cyclin ik3-1/CABLES [C 85.9 2.5 5.3E-05 45.4 7.4 91 74-166 385-480 (497)
75 TIGR02393 RpoD_Cterm RNA polym 85.9 40 0.00087 33.7 18.2 27 233-259 195-221 (238)
76 COG1594 RPB9 DNA-directed RNA 85.4 0.52 1.1E-05 42.4 2.0 33 1-33 2-35 (113)
77 PF01857 RB_B: Retinoblastoma- 85.2 3.2 6.9E-05 38.5 7.1 64 179-244 18-83 (135)
78 PF13412 HTH_24: Winged helix- 85.0 1.7 3.6E-05 32.3 4.3 29 232-260 15-43 (48)
79 COG1998 RPS31 Ribosomal protei 84.4 0.61 1.3E-05 35.5 1.6 26 3-29 21-46 (51)
80 PRK09210 RNA polymerase sigma 84.3 57 0.0012 35.2 17.3 92 65-156 129-255 (367)
81 COG4888 Uncharacterized Zn rib 84.1 0.54 1.2E-05 41.0 1.4 29 3-31 24-57 (104)
82 COG2835 Uncharacterized conser 84.0 0.71 1.5E-05 36.7 1.9 28 2-30 9-36 (60)
83 PRK14892 putative transcriptio 83.8 0.7 1.5E-05 40.6 2.0 30 3-32 23-54 (99)
84 COG4640 Predicted membrane pro 83.1 0.62 1.3E-05 49.8 1.6 26 1-31 1-26 (465)
85 PRK09678 DNA-binding transcrip 82.9 0.93 2E-05 37.5 2.3 31 1-31 1-40 (72)
86 TIGR02300 FYDLN_acid conserved 82.9 0.72 1.6E-05 42.1 1.7 29 3-33 11-39 (129)
87 PF07282 OrfB_Zn_ribbon: Putat 82.4 0.92 2E-05 36.6 2.1 28 3-31 30-57 (69)
88 PF09297 zf-NADH-PPase: NADH p 82.4 1.1 2.4E-05 30.9 2.2 26 3-29 5-30 (32)
89 KOG1779 40s ribosomal protein 82.3 0.62 1.3E-05 38.8 1.0 30 2-31 35-64 (84)
90 PRK11169 leucine-responsive tr 82.2 1.9 4E-05 41.0 4.4 38 226-263 20-57 (164)
91 PF13730 HTH_36: Helix-turn-he 82.1 2.9 6.2E-05 31.9 4.7 26 236-261 27-52 (55)
92 PRK12495 hypothetical protein; 81.7 0.9 1.9E-05 45.1 2.1 27 3-32 44-70 (226)
93 PF08273 Prim_Zn_Ribbon: Zinc- 81.1 1.3 2.8E-05 32.4 2.2 27 3-29 5-35 (40)
94 PF04967 HTH_10: HTH DNA bindi 80.9 3.3 7.1E-05 32.2 4.5 35 225-259 9-48 (53)
95 PRK10219 DNA-binding transcrip 80.9 36 0.00078 29.4 12.0 39 118-157 7-45 (107)
96 PF12760 Zn_Tnp_IS1595: Transp 80.7 1.4 3.1E-05 32.9 2.4 26 3-28 20-45 (46)
97 KOG1010 Rb (Retinoblastoma tum 80.1 4.2 9E-05 47.7 6.9 85 71-157 677-763 (920)
98 PF13936 HTH_38: Helix-turn-he 80.0 2.4 5.2E-05 31.3 3.4 30 227-256 13-42 (44)
99 PRK09710 lar restriction allev 79.9 1.3 2.8E-05 35.6 2.0 28 3-30 8-37 (64)
100 PF13717 zinc_ribbon_4: zinc-r 79.8 1.1 2.3E-05 32.0 1.4 28 3-30 4-35 (36)
101 smart00440 ZnF_C2C2 C2C2 Zinc 79.6 1.2 2.7E-05 32.4 1.7 27 3-29 2-37 (40)
102 PF08613 Cyclin: Cyclin; Inte 79.1 13 0.00027 34.8 8.8 79 173-253 52-136 (149)
103 PF13384 HTH_23: Homeodomain-l 79.1 2.7 5.9E-05 31.3 3.6 29 234-262 17-45 (50)
104 PF08279 HTH_11: HTH domain; 78.9 3.6 7.8E-05 31.3 4.3 31 231-261 12-42 (55)
105 PRK06266 transcription initiat 78.9 0.62 1.3E-05 45.2 -0.1 30 3-32 119-148 (178)
106 PF01780 Ribosomal_L37ae: Ribo 78.9 0.99 2.1E-05 38.9 1.2 32 3-35 37-68 (90)
107 PF13542 HTH_Tnp_ISL3: Helix-t 78.7 7.4 0.00016 29.2 5.9 25 234-258 27-51 (52)
108 PRK07405 RNA polymerase sigma 78.6 93 0.002 32.8 17.2 25 232-256 274-298 (317)
109 PRK11179 DNA-binding transcrip 78.5 2.9 6.3E-05 39.1 4.4 38 226-263 15-52 (153)
110 PF06677 Auto_anti-p27: Sjogre 78.4 1.7 3.6E-05 32.0 2.1 23 3-27 19-41 (41)
111 KOG4557 Origin recognition com 78.2 6.9 0.00015 38.9 6.8 83 76-161 94-181 (262)
112 TIGR00244 transcriptional regu 78.1 1.7 3.7E-05 40.7 2.6 29 2-30 1-38 (147)
113 PF05191 ADK_lid: Adenylate ki 77.9 0.61 1.3E-05 33.3 -0.3 28 3-30 3-31 (36)
114 PRK14559 putative protein seri 77.0 1.3 2.8E-05 51.1 1.8 25 1-30 1-25 (645)
115 PRK10220 hypothetical protein; 77.0 1.8 3.9E-05 38.4 2.2 28 3-32 5-32 (111)
116 PF13545 HTH_Crp_2: Crp-like h 76.7 4.3 9.4E-05 32.8 4.4 29 233-261 27-55 (76)
117 PF01325 Fe_dep_repress: Iron 76.6 5.6 0.00012 31.5 4.8 38 223-261 12-49 (60)
118 PF12773 DZR: Double zinc ribb 76.1 1.5 3.3E-05 33.0 1.4 12 20-31 12-23 (50)
119 TIGR00686 phnA alkylphosphonat 76.0 3.7 8E-05 36.5 3.9 30 2-33 3-32 (109)
120 PF10668 Phage_terminase: Phag 76.0 6.3 0.00014 31.5 4.9 38 214-254 5-42 (60)
121 PF00165 HTH_AraC: Bacterial r 75.8 5.5 0.00012 28.7 4.3 36 232-272 6-41 (42)
122 TIGR03697 NtcA_cyano global ni 75.8 11 0.00023 35.8 7.5 30 233-262 142-171 (193)
123 KOG2906 RNA polymerase III sub 75.8 1.7 3.7E-05 37.8 1.7 31 1-31 1-32 (105)
124 PF00356 LacI: Bacterial regul 75.7 2.6 5.6E-05 31.7 2.5 21 236-256 1-21 (46)
125 PRK13130 H/ACA RNA-protein com 74.9 1.3 2.9E-05 34.8 0.8 34 1-44 5-38 (56)
126 PTZ00255 60S ribosomal protein 74.6 2 4.3E-05 37.0 1.9 32 3-35 38-69 (90)
127 PF02796 HTH_7: Helix-turn-hel 74.6 1.8 3.9E-05 32.1 1.4 28 229-256 16-43 (45)
128 COG2888 Predicted Zn-ribbon RN 74.5 1.8 3.9E-05 34.3 1.4 25 3-28 11-35 (61)
129 cd00092 HTH_CRP helix_turn_hel 74.4 8.5 0.00018 30.0 5.4 30 232-261 23-52 (67)
130 PF15616 TerY-C: TerY-C metal 74.3 1.8 3.9E-05 39.9 1.6 20 3-30 79-98 (131)
131 PF09986 DUF2225: Uncharacteri 74.0 10 0.00022 37.9 7.0 51 75-126 75-125 (214)
132 PF05876 Terminase_GpA: Phage 74.0 1.6 3.5E-05 49.7 1.5 45 1-45 200-257 (557)
133 PF00325 Crp: Bacterial regula 73.3 4.7 0.0001 28.1 3.1 27 133-159 2-28 (32)
134 PF04545 Sigma70_r4: Sigma-70, 72.7 6.3 0.00014 29.5 4.1 28 232-259 18-45 (50)
135 TIGR02010 IscR iron-sulfur clu 72.7 6.8 0.00015 35.9 5.1 47 114-160 6-52 (135)
136 PF00325 Crp: Bacterial regula 72.6 3.7 7.9E-05 28.6 2.4 28 234-261 2-29 (32)
137 PRK05932 RNA polymerase factor 72.5 31 0.00066 38.4 11.0 185 77-274 140-384 (455)
138 KOG0794 CDK8 kinase-activating 72.2 6.5 0.00014 39.6 5.0 57 176-234 45-101 (264)
139 COG5333 CCL1 Cdk activating ki 72.0 3.1 6.7E-05 43.4 2.9 55 176-232 49-103 (297)
140 smart00419 HTH_CRP helix_turn_ 71.7 5.1 0.00011 29.1 3.3 30 232-261 6-35 (48)
141 COG1326 Uncharacterized archae 71.1 2 4.3E-05 41.9 1.2 30 3-32 8-42 (201)
142 PRK00135 scpB segregation and 70.7 19 0.00042 35.2 8.0 116 115-252 5-122 (188)
143 COG3809 Uncharacterized protei 70.3 2.9 6.4E-05 34.9 1.8 30 1-30 1-31 (88)
144 TIGR00280 L37a ribosomal prote 70.0 2.8 6.1E-05 36.2 1.7 32 3-35 37-68 (91)
145 PF02082 Rrf2: Transcriptional 69.9 6.4 0.00014 32.9 3.9 46 115-160 7-52 (83)
146 PF08220 HTH_DeoR: DeoR-like h 69.7 4.6 0.0001 31.5 2.8 30 232-261 12-41 (57)
147 COG1522 Lrp Transcriptional re 69.7 6.4 0.00014 36.3 4.3 33 230-262 18-50 (154)
148 TIGR01384 TFS_arch transcripti 69.3 3 6.5E-05 36.5 1.8 27 3-32 2-28 (104)
149 COG2824 PhnA Uncharacterized Z 68.7 3.4 7.3E-05 36.6 1.9 32 1-34 3-34 (112)
150 smart00344 HTH_ASNC helix_turn 68.6 7.5 0.00016 33.7 4.3 30 232-261 15-44 (108)
151 COG3478 Predicted nucleic-acid 68.6 3 6.6E-05 33.5 1.5 27 2-28 5-48 (68)
152 PRK05949 RNA polymerase sigma 68.2 1.7E+02 0.0036 31.1 17.8 24 233-256 285-308 (327)
153 PF01096 TFIIS_C: Transcriptio 68.2 2.6 5.5E-05 30.5 1.0 27 3-29 2-37 (39)
154 TIGR03879 near_KaiC_dom probab 68.1 13 0.00028 30.9 5.2 27 233-259 31-57 (73)
155 PRK07406 RNA polymerase sigma 67.7 70 0.0015 34.7 12.2 89 66-155 162-261 (373)
156 PRK12286 rpmF 50S ribosomal pr 67.7 3.3 7.1E-05 32.7 1.6 26 2-33 28-53 (57)
157 PRK03976 rpl37ae 50S ribosomal 67.4 3.3 7.1E-05 35.7 1.6 32 3-35 38-69 (90)
158 PRK10572 DNA-binding transcrip 67.3 1.5E+02 0.0032 30.1 17.8 100 118-275 185-285 (290)
159 PF01783 Ribosomal_L32p: Ribos 66.5 2.5 5.5E-05 33.1 0.7 24 2-31 27-50 (56)
160 COG1656 Uncharacterized conser 66.5 2.5 5.5E-05 40.3 0.9 29 1-29 97-139 (165)
161 smart00834 CxxC_CXXC_SSSS Puta 66.4 3.2 7E-05 29.6 1.2 28 3-30 7-36 (41)
162 TIGR02395 rpoN_sigma RNA polym 66.3 23 0.0005 39.1 8.4 182 77-273 115-358 (429)
163 PF11672 DUF3268: Protein of u 66.1 4.5 9.8E-05 35.7 2.3 30 2-31 3-42 (102)
164 TIGR00122 birA_repr_reg BirA b 65.9 10 0.00022 30.3 4.2 30 231-260 10-39 (69)
165 smart00345 HTH_GNTR helix_turn 65.8 8.8 0.00019 29.0 3.7 30 232-261 17-47 (60)
166 TIGR03697 NtcA_cyano global ni 65.3 23 0.00049 33.5 7.3 29 132-160 142-170 (193)
167 COG1327 Predicted transcriptio 65.2 3.8 8.3E-05 38.5 1.7 28 2-29 1-37 (156)
168 PRK07122 RNA polymerase sigma 64.8 72 0.0016 32.6 11.2 28 232-259 229-256 (264)
169 smart00421 HTH_LUXR helix_turn 64.7 8.4 0.00018 28.5 3.3 26 234-259 18-43 (58)
170 PF05225 HTH_psq: helix-turn-h 64.7 11 0.00025 28.0 3.9 28 231-259 14-41 (45)
171 COG1318 Predicted transcriptio 64.6 9.9 0.00021 36.6 4.4 73 190-274 27-99 (182)
172 PRK11511 DNA-binding transcrip 64.6 29 0.00062 31.4 7.4 54 215-274 7-60 (127)
173 PF05129 Elf1: Transcription e 64.4 3.8 8.2E-05 34.6 1.4 31 3-33 24-59 (81)
174 TIGR01031 rpmF_bact ribosomal 64.3 4.5 9.8E-05 31.6 1.7 25 2-32 27-51 (55)
175 TIGR02885 spore_sigF RNA polym 64.2 1.5E+02 0.0033 29.2 16.8 28 232-259 197-224 (231)
176 PF12773 DZR: Double zinc ribb 64.1 4.7 0.0001 30.3 1.8 30 2-33 13-42 (50)
177 PRK10857 DNA-binding transcrip 64.0 13 0.00028 35.6 5.1 47 114-160 6-52 (164)
178 COG0333 RpmF Ribosomal protein 64.0 3.8 8.3E-05 32.3 1.3 26 1-32 27-52 (57)
179 PRK14890 putative Zn-ribbon RN 63.9 4.6 0.0001 32.0 1.7 26 3-29 9-34 (59)
180 COG3877 Uncharacterized protei 63.4 33 0.00072 30.5 7.0 67 123-202 52-120 (122)
181 PF13545 HTH_Crp_2: Crp-like h 63.0 16 0.00035 29.4 4.9 44 118-161 3-56 (76)
182 PF13613 HTH_Tnp_4: Helix-turn 62.8 9.2 0.0002 29.3 3.2 37 225-261 10-46 (53)
183 TIGR02394 rpoS_proteo RNA poly 62.7 1.9E+02 0.0041 29.7 18.1 26 233-258 241-266 (285)
184 COG2207 AraC AraC-type DNA-bin 62.5 1E+02 0.0022 26.4 10.7 37 120-157 24-60 (127)
185 PF13613 HTH_Tnp_4: Helix-turn 61.9 14 0.00031 28.2 4.2 35 130-164 16-50 (53)
186 smart00659 RPOLCX RNA polymera 61.6 4.9 0.00011 30.0 1.4 25 3-29 4-28 (44)
187 PF01325 Fe_dep_repress: Iron 61.4 22 0.00048 28.1 5.2 37 122-159 12-48 (60)
188 PF14446 Prok-RING_1: Prokaryo 61.3 5.3 0.00012 31.2 1.6 25 3-30 7-31 (54)
189 PRK14088 dnaA chromosomal repl 61.3 67 0.0015 35.5 10.9 52 207-260 359-413 (440)
190 PF02082 Rrf2: Transcriptional 61.1 10 0.00022 31.7 3.4 39 223-261 14-52 (83)
191 TIGR02997 Sig70-cyanoRpoD RNA 61.0 2.1E+02 0.0046 29.7 18.0 26 232-257 267-292 (298)
192 PRK11920 rirA iron-responsive 61.0 17 0.00037 34.2 5.3 46 114-160 6-51 (153)
193 PRK07598 RNA polymerase sigma 61.0 2.6E+02 0.0057 30.8 18.8 99 65-163 175-308 (415)
194 PF12802 MarR_2: MarR family; 60.8 18 0.00039 27.8 4.7 28 234-261 21-48 (62)
195 PF11023 DUF2614: Protein of u 60.5 3.3 7.1E-05 37.0 0.4 40 1-43 69-108 (114)
196 PF01022 HTH_5: Bacterial regu 60.5 16 0.00035 27.0 4.1 32 230-261 11-42 (47)
197 PF10122 Mu-like_Com: Mu-like 60.2 2.7 6E-05 32.3 -0.1 29 2-30 5-34 (51)
198 PF09855 DUF2082: Nucleic-acid 59.7 6.2 0.00013 31.9 1.8 27 3-29 2-45 (64)
199 PF14353 CpXC: CpXC protein 59.6 5.5 0.00012 36.1 1.7 29 2-30 2-48 (128)
200 PRK09393 ftrA transcriptional 59.5 1.1E+02 0.0024 31.8 11.8 104 114-274 215-319 (322)
201 smart00420 HTH_DEOR helix_turn 59.5 23 0.00049 25.8 4.9 27 234-260 14-40 (53)
202 PRK13502 transcriptional activ 59.4 1.1E+02 0.0023 31.1 11.3 104 112-273 172-276 (282)
203 PRK11161 fumarate/nitrate redu 59.0 34 0.00073 33.6 7.4 31 233-263 183-213 (235)
204 PRK13500 transcriptional activ 58.9 2.3E+02 0.005 29.4 14.5 87 131-274 220-307 (312)
205 PF01371 Trp_repressor: Trp re 58.8 14 0.00031 31.6 4.0 32 230-261 45-76 (87)
206 PF03604 DNA_RNApol_7kD: DNA d 58.8 6.3 0.00014 27.5 1.5 24 3-28 2-25 (32)
207 PF07754 DUF1610: Domain of un 58.4 7.3 0.00016 25.4 1.6 24 4-28 1-24 (24)
208 PF14122 YokU: YokU-like prote 58.1 5.3 0.00012 34.0 1.2 22 19-40 34-55 (87)
209 cd06170 LuxR_C_like C-terminal 58.1 14 0.00029 27.5 3.4 27 234-260 15-41 (57)
210 PRK13918 CRP/FNR family transc 58.0 36 0.00078 32.5 7.3 30 233-262 148-177 (202)
211 PRK10219 DNA-binding transcrip 57.8 53 0.0011 28.3 7.6 50 219-274 7-56 (107)
212 TIGR00515 accD acetyl-CoA carb 57.8 3 6.5E-05 43.5 -0.4 29 2-30 27-55 (285)
213 PRK05654 acetyl-CoA carboxylas 57.0 3.2 6.8E-05 43.5 -0.4 29 2-30 28-56 (292)
214 PF04079 DUF387: Putative tran 56.8 94 0.002 29.6 9.6 108 118-258 2-120 (159)
215 PRK05901 RNA polymerase sigma 56.5 3.5E+02 0.0075 30.8 17.2 25 232-256 465-489 (509)
216 cd06571 Bac_DnaA_C C-terminal 56.4 32 0.00069 29.2 5.8 41 121-163 34-75 (90)
217 TIGR01610 phage_O_Nterm phage 56.1 31 0.00068 29.7 5.8 31 231-261 44-74 (95)
218 COG0777 AccD Acetyl-CoA carbox 56.0 3.4 7.5E-05 42.5 -0.3 30 1-30 28-57 (294)
219 PRK05978 hypothetical protein; 56.0 8.3 0.00018 36.4 2.3 30 2-31 34-63 (148)
220 PF02042 RWP-RK: RWP-RK domain 55.9 14 0.0003 28.7 3.1 28 232-259 13-40 (52)
221 PRK02935 hypothetical protein; 55.9 7.4 0.00016 34.4 1.8 39 2-43 71-109 (110)
222 PF08280 HTH_Mga: M protein tr 55.8 16 0.00035 28.6 3.6 30 232-261 17-46 (59)
223 PF08281 Sigma70_r4_2: Sigma-7 55.8 15 0.00033 27.7 3.4 27 232-258 24-50 (54)
224 COG4068 Uncharacterized protei 55.7 2.9 6.3E-05 33.0 -0.7 24 3-31 10-34 (64)
225 CHL00174 accD acetyl-CoA carbo 55.6 3.3 7.2E-05 43.3 -0.5 29 2-30 39-67 (296)
226 PF01978 TrmB: Sugar-specific 55.6 12 0.00026 29.8 2.9 38 223-261 12-49 (68)
227 TIGR02980 SigBFG RNA polymeras 55.0 2.2E+02 0.0047 28.0 16.3 27 233-259 193-219 (227)
228 PF01726 LexA_DNA_bind: LexA D 54.7 14 0.00031 29.7 3.2 32 229-260 20-52 (65)
229 PF02954 HTH_8: Bacterial regu 54.6 15 0.00033 26.6 3.1 26 233-258 17-42 (42)
230 PRK05911 RNA polymerase sigma 54.1 2.5E+02 0.0054 28.5 18.4 28 232-259 219-246 (257)
231 PRK09391 fixK transcriptional 53.6 53 0.0011 32.5 7.8 30 233-262 178-207 (230)
232 PF06044 DRP: Dam-replacing fa 53.5 5.7 0.00012 40.2 0.8 29 2-30 32-63 (254)
233 PRK07500 rpoH2 RNA polymerase 53.3 2.8E+02 0.0061 28.7 16.3 28 232-259 243-270 (289)
234 cd00092 HTH_CRP helix_turn_hel 53.3 43 0.00094 25.9 5.8 30 131-160 23-52 (67)
235 PF08279 HTH_11: HTH domain; 53.2 32 0.0007 25.9 4.9 34 128-161 10-43 (55)
236 PHA02591 hypothetical protein; 53.0 17 0.00036 30.6 3.3 32 225-256 50-81 (83)
237 smart00418 HTH_ARSR helix_turn 53.0 26 0.00056 26.3 4.4 29 232-260 8-36 (66)
238 PF07638 Sigma70_ECF: ECF sigm 53.0 22 0.00047 34.2 4.8 25 235-259 152-176 (185)
239 TIGR02605 CxxC_CxxC_SSSS putat 52.8 7.4 0.00016 29.5 1.2 26 3-28 7-34 (52)
240 TIGR00738 rrf2_super rrf2 fami 52.5 26 0.00057 31.4 5.0 45 115-159 7-51 (132)
241 PRK08215 sporulation sigma fac 52.0 2.7E+02 0.0058 28.1 17.8 26 233-258 224-249 (258)
242 TIGR02479 FliA_WhiG RNA polyme 51.9 2.4E+02 0.0053 27.6 16.7 26 233-258 190-215 (224)
243 PRK10434 srlR DNA-bindng trans 51.7 16 0.00035 37.2 3.9 30 232-261 17-46 (256)
244 PRK13501 transcriptional activ 51.7 2.8E+02 0.006 28.2 13.9 124 93-273 152-276 (290)
245 cd00350 rubredoxin_like Rubred 51.6 9.2 0.0002 26.5 1.4 23 3-28 3-25 (33)
246 KOG3915 Transcription regulato 51.5 53 0.0012 36.3 7.6 19 437-459 530-548 (641)
247 cd00090 HTH_ARSR Arsenical Res 51.5 31 0.00068 26.6 4.7 26 235-260 21-46 (78)
248 PRK11014 transcriptional repre 51.2 21 0.00046 32.8 4.2 40 222-261 13-52 (141)
249 TIGR02944 suf_reg_Xantho FeS a 51.2 33 0.00071 30.9 5.4 38 223-261 15-52 (130)
250 TIGR02443 conserved hypothetic 51.1 11 0.00024 30.0 1.9 28 2-29 10-40 (59)
251 PF00392 GntR: Bacterial regul 51.0 18 0.00038 28.5 3.2 30 231-260 20-50 (64)
252 PF00165 HTH_AraC: Bacterial r 51.0 20 0.00043 25.7 3.2 27 131-157 6-32 (42)
253 PRK11161 fumarate/nitrate redu 50.8 59 0.0013 31.9 7.6 32 132-163 183-214 (235)
254 PF13518 HTH_28: Helix-turn-he 50.4 33 0.00072 25.3 4.5 26 236-261 14-39 (52)
255 TIGR02944 suf_reg_Xantho FeS a 50.4 34 0.00074 30.8 5.3 45 114-159 7-51 (130)
256 TIGR02844 spore_III_D sporulat 50.4 24 0.00053 29.8 4.0 23 233-255 18-40 (80)
257 KOG1088 Uncharacterized conser 50.3 7.2 0.00016 35.1 0.8 18 14-31 92-109 (124)
258 PRK08402 replication factor A; 50.1 9.5 0.00021 41.0 1.9 26 3-29 214-239 (355)
259 PF03119 DNA_ligase_ZBD: NAD-d 50.0 11 0.00023 25.4 1.5 22 3-25 1-22 (28)
260 PF14255 Cys_rich_CPXG: Cystei 49.9 9.9 0.00021 29.5 1.4 29 3-31 2-35 (52)
261 PRK04217 hypothetical protein; 49.9 21 0.00046 31.9 3.8 27 233-259 57-83 (110)
262 PRK00241 nudC NADH pyrophospha 49.9 12 0.00026 38.4 2.5 29 2-31 100-128 (256)
263 PF00440 TetR_N: Bacterial reg 49.8 34 0.00074 25.2 4.3 35 222-256 4-38 (47)
264 PF09526 DUF2387: Probable met 49.7 11 0.00024 31.1 1.8 30 2-31 9-41 (71)
265 KOG2593 Transcription initiati 49.7 7.7 0.00017 42.3 1.1 30 3-32 130-165 (436)
266 PF00356 LacI: Bacterial regul 49.5 17 0.00037 27.3 2.7 20 135-154 1-20 (46)
267 PRK07408 RNA polymerase sigma 49.3 3E+02 0.0064 27.9 16.5 27 233-259 218-244 (256)
268 COG3877 Uncharacterized protei 49.0 13 0.00029 32.9 2.2 26 3-33 8-33 (122)
269 smart00550 Zalpha Z-DNA-bindin 48.8 37 0.0008 27.4 4.8 38 224-261 11-49 (68)
270 PRK12380 hydrogenase nickel in 48.8 9.7 0.00021 34.1 1.5 35 2-41 71-105 (113)
271 KOG0654 G2/Mitotic-specific cy 48.7 1.9E+02 0.0041 31.3 11.3 136 121-263 185-323 (359)
272 COG5349 Uncharacterized protei 48.6 9.9 0.00021 34.5 1.4 29 3-31 23-51 (126)
273 PRK10402 DNA-binding transcrip 48.5 44 0.00096 32.9 6.3 30 233-262 168-197 (226)
274 cd06171 Sigma70_r4 Sigma70, re 48.4 33 0.0007 24.6 4.1 27 233-259 25-51 (55)
275 TIGR01321 TrpR trp operon repr 48.3 20 0.00044 31.2 3.3 30 230-259 51-80 (94)
276 cd07377 WHTH_GntR Winged helix 48.3 22 0.00047 27.3 3.2 26 236-261 27-52 (66)
277 cd04762 HTH_MerR-trunc Helix-T 48.2 20 0.00042 25.6 2.8 22 236-257 2-23 (49)
278 PF00196 GerE: Bacterial regul 48.1 18 0.0004 27.8 2.8 27 233-259 17-43 (58)
279 TIGR01764 excise DNA binding d 48.1 19 0.00042 25.9 2.8 23 235-257 2-24 (49)
280 smart00647 IBR In Between Ring 48.1 14 0.0003 28.7 2.1 29 2-30 19-50 (64)
281 PF05460 ORC6: Origin recognit 47.5 6.2 0.00013 42.4 0.0 80 182-261 4-84 (353)
282 PRK12336 translation initiatio 47.5 9.1 0.0002 37.8 1.2 29 2-30 99-129 (201)
283 PRK11511 DNA-binding transcrip 47.1 55 0.0012 29.5 6.1 103 115-275 8-111 (127)
284 cd00202 ZnF_GATA Zinc finger D 46.9 7.7 0.00017 30.2 0.4 29 3-31 1-32 (54)
285 PF12802 MarR_2: MarR family; 46.7 47 0.001 25.4 4.9 41 120-160 8-48 (62)
286 PRK13413 mpi multiple promoter 46.7 52 0.0011 32.0 6.4 25 234-258 172-196 (200)
287 PRK06288 RNA polymerase sigma 46.6 3.3E+02 0.0072 27.6 17.5 25 233-257 227-251 (268)
288 PRK13509 transcriptional repre 46.5 19 0.00042 36.6 3.4 29 232-260 17-45 (251)
289 COG1779 C4-type Zn-finger prot 46.5 8.6 0.00019 37.8 0.8 34 2-35 15-58 (201)
290 PF13551 HTH_29: Winged helix- 46.5 41 0.0009 28.7 5.1 27 236-262 14-40 (112)
291 cd00569 HTH_Hin_like Helix-tur 46.5 20 0.00043 23.1 2.4 21 234-254 21-41 (42)
292 PF05344 DUF746: Domain of Unk 45.7 32 0.00068 28.0 3.7 31 229-259 8-38 (65)
293 PF12833 HTH_18: Helix-turn-he 45.7 66 0.0014 26.0 6.0 67 81-157 1-70 (81)
294 PF04552 Sigma54_DBD: Sigma-54 45.3 14 0.00029 35.4 1.9 24 132-155 48-71 (160)
295 COG1102 Cmk Cytidylate kinase 45.2 64 0.0014 31.2 6.4 119 136-268 17-147 (179)
296 KOG0402 60S ribosomal protein 45.1 8.4 0.00018 32.6 0.4 31 3-34 38-68 (92)
297 PF12116 SpoIIID: Stage III sp 45.0 15 0.00031 31.1 1.8 34 224-257 9-42 (82)
298 PF09723 Zn-ribbon_8: Zinc rib 44.9 12 0.00025 27.5 1.1 26 3-28 7-34 (42)
299 PF09862 DUF2089: Protein of u 44.7 22 0.00047 32.1 3.0 27 235-261 50-76 (113)
300 COG4977 Transcriptional regula 44.4 1.8E+02 0.0038 31.1 10.2 84 133-273 236-320 (328)
301 PF00301 Rubredoxin: Rubredoxi 44.1 13 0.00028 28.2 1.3 14 21-34 2-15 (47)
302 COG3677 Transposase and inacti 44.1 14 0.00031 33.9 1.8 31 1-31 30-64 (129)
303 PF13542 HTH_Tnp_ISL3: Helix-t 44.0 64 0.0014 23.9 5.2 24 134-157 28-51 (52)
304 PRK11753 DNA-binding transcrip 44.0 87 0.0019 30.0 7.5 30 233-262 167-196 (211)
305 COG2260 Predicted Zn-ribbon RN 43.9 11 0.00024 29.9 0.9 33 1-43 5-37 (59)
306 TIGR03830 CxxCG_CxxCG_HTH puta 43.7 17 0.00036 32.5 2.2 27 4-30 1-41 (127)
307 PRK00118 putative DNA-binding 43.5 31 0.00068 30.6 3.8 28 233-260 32-59 (104)
308 COG1510 Predicted transcriptio 43.4 63 0.0014 31.3 6.0 56 199-261 13-68 (177)
309 PF04216 FdhE: Protein involve 43.4 11 0.00024 39.1 1.1 29 3-31 174-208 (290)
310 COG1996 RPC10 DNA-directed RNA 43.3 12 0.00025 28.7 0.9 25 3-28 8-32 (49)
311 PF01396 zf-C4_Topoisom: Topoi 43.2 25 0.00053 25.4 2.6 30 2-31 2-35 (39)
312 PF13022 HTH_Tnp_1_2: Helix-tu 43.2 39 0.00084 31.6 4.5 41 215-255 12-55 (142)
313 PRK15418 transcriptional regul 43.1 18 0.0004 38.2 2.7 45 225-269 20-64 (318)
314 PRK10572 DNA-binding transcrip 43.1 82 0.0018 32.1 7.5 14 17-30 72-85 (290)
315 PF09339 HTH_IclR: IclR helix- 43.0 33 0.00071 25.9 3.4 32 230-261 14-45 (52)
316 smart00346 HTH_ICLR helix_turn 42.8 63 0.0014 26.7 5.5 28 233-260 19-46 (91)
317 smart00419 HTH_CRP helix_turn_ 42.8 34 0.00074 24.6 3.4 30 131-160 6-35 (48)
318 PRK06030 hypothetical protein; 42.7 70 0.0015 29.3 6.1 39 121-161 59-97 (124)
319 COG1959 Predicted transcriptio 42.6 47 0.001 31.1 5.1 46 115-160 7-52 (150)
320 PRK09526 lacI lac repressor; R 42.6 20 0.00043 37.1 2.8 43 233-277 4-46 (342)
321 PF12840 HTH_20: Helix-turn-he 42.5 40 0.00086 26.3 3.9 32 230-261 20-51 (61)
322 PF10080 DUF2318: Predicted me 42.3 15 0.00032 32.5 1.5 31 3-35 37-67 (102)
323 TIGR00281 segregation and cond 42.1 1E+02 0.0022 30.2 7.5 119 116-257 3-124 (186)
324 PRK10870 transcriptional repre 42.1 1.1E+02 0.0024 29.3 7.8 31 231-261 68-98 (176)
325 PRK14962 DNA polymerase III su 42.1 5.4E+02 0.012 28.8 14.8 82 133-222 229-327 (472)
326 PRK10402 DNA-binding transcrip 41.9 68 0.0015 31.5 6.5 46 115-160 151-196 (226)
327 COG1725 Predicted transcriptio 41.9 27 0.00058 32.1 3.2 30 231-260 31-61 (125)
328 PF04545 Sigma70_r4: Sigma-70, 41.8 45 0.00098 24.8 4.0 31 131-161 18-48 (50)
329 PF04703 FaeA: FaeA-like prote 41.8 54 0.0012 26.3 4.6 34 131-164 13-46 (62)
330 COG1386 scpB Chromosome segreg 41.6 1.5E+02 0.0033 28.9 8.6 120 116-259 10-131 (184)
331 PF04703 FaeA: FaeA-like prote 41.4 41 0.00089 27.0 3.8 30 232-261 13-42 (62)
332 PF04606 Ogr_Delta: Ogr/Delta- 41.3 15 0.00033 27.6 1.3 28 3-30 1-37 (47)
333 TIGR02405 trehalos_R_Ecol treh 41.3 20 0.00043 36.8 2.6 24 234-257 1-24 (311)
334 TIGR00100 hypA hydrogenase nic 41.2 13 0.00029 33.3 1.2 34 3-41 72-105 (115)
335 cd04761 HTH_MerR-SF Helix-Turn 41.1 26 0.00056 25.5 2.5 23 236-258 2-24 (49)
336 COG1191 FliA DNA-directed RNA 41.0 4.1E+02 0.009 27.2 16.6 72 69-140 27-109 (247)
337 PRK09642 RNA polymerase sigma 40.8 14 0.0003 34.1 1.3 27 233-259 121-147 (160)
338 PF14502 HTH_41: Helix-turn-he 40.7 30 0.00064 26.5 2.7 31 235-265 7-37 (48)
339 TIGR02985 Sig70_bacteroi1 RNA 40.7 27 0.00058 31.7 3.1 27 233-259 128-154 (161)
340 COG1508 RpoN DNA-directed RNA 40.5 4.5E+02 0.0098 29.3 12.8 43 234-276 330-373 (444)
341 PF01485 IBR: IBR domain; Int 40.4 17 0.00037 28.0 1.6 28 2-30 19-50 (64)
342 TIGR03831 YgiT_finger YgiT-typ 40.4 19 0.00041 26.1 1.7 10 21-30 33-42 (46)
343 PRK10014 DNA-binding transcrip 40.4 22 0.00048 36.8 2.8 24 233-256 5-28 (342)
344 cd00730 rubredoxin Rubredoxin; 40.2 21 0.00046 27.4 1.9 13 21-33 2-14 (50)
345 PF10083 DUF2321: Uncharacteri 40.2 12 0.00026 35.4 0.7 29 3-39 30-58 (158)
346 PRK11753 DNA-binding transcrip 40.1 1.2E+02 0.0025 29.1 7.7 29 132-160 167-195 (211)
347 PF00376 MerR: MerR family reg 40.1 21 0.00046 25.6 1.8 19 236-254 1-19 (38)
348 smart00401 ZnF_GATA zinc finge 39.4 20 0.00043 27.6 1.7 28 3-30 5-35 (52)
349 PF06397 Desulfoferrod_N: Desu 39.3 12 0.00027 26.7 0.5 21 3-23 8-28 (36)
350 PF13556 HTH_30: PucR C-termin 39.3 37 0.00081 26.4 3.3 34 233-266 11-44 (59)
351 PRK03824 hypA hydrogenase nick 39.3 17 0.00036 33.7 1.5 11 19-29 106-116 (135)
352 PRK08329 threonine synthase; V 39.2 19 0.00041 38.4 2.1 26 1-31 1-26 (347)
353 PRK01110 rpmF 50S ribosomal pr 39.2 13 0.00029 29.6 0.7 27 2-35 28-54 (60)
354 TIGR02010 IscR iron-sulfur clu 39.2 50 0.0011 30.1 4.7 40 222-261 13-52 (135)
355 TIGR02392 rpoH_proteo alternat 39.0 4.4E+02 0.0095 26.8 16.5 27 232-258 234-260 (270)
356 PRK12529 RNA polymerase sigma 38.8 29 0.00063 32.9 3.1 25 233-257 142-166 (178)
357 PRK09956 hypothetical protein; 38.7 94 0.002 32.7 7.2 79 174-253 224-305 (308)
358 PF00196 GerE: Bacterial regul 38.7 41 0.00089 25.8 3.4 34 132-165 17-50 (58)
359 PF12728 HTH_17: Helix-turn-he 38.7 35 0.00076 25.4 3.0 22 235-256 2-23 (51)
360 TIGR02850 spore_sigG RNA polym 38.6 4.2E+02 0.0092 26.6 17.6 26 233-258 221-246 (254)
361 PF05732 RepL: Firmicute plasm 38.5 44 0.00096 32.0 4.3 27 235-261 76-102 (165)
362 PF13824 zf-Mss51: Zinc-finger 38.3 21 0.00046 28.0 1.7 24 3-30 1-24 (55)
363 PRK03681 hypA hydrogenase nick 38.3 18 0.00038 32.5 1.5 35 3-41 72-106 (114)
364 PF13412 HTH_24: Winged helix- 38.1 85 0.0018 23.0 4.9 29 131-159 15-43 (48)
365 PF04810 zf-Sec23_Sec24: Sec23 38.0 26 0.00056 25.4 2.0 28 2-29 3-33 (40)
366 PF13011 LZ_Tnp_IS481: leucine 37.7 65 0.0014 27.6 4.7 37 225-261 16-52 (85)
367 PRK09492 treR trehalose repres 37.7 23 0.00049 36.2 2.4 23 234-256 4-26 (315)
368 PF04161 Arv1: Arv1-like famil 37.7 16 0.00035 36.1 1.2 31 2-32 1-36 (208)
369 TIGR00595 priA primosomal prot 37.7 22 0.00047 40.1 2.4 28 3-31 224-251 (505)
370 cd01104 HTH_MlrA-CarA Helix-Tu 37.6 32 0.0007 27.0 2.8 23 236-258 2-24 (68)
371 PRK01381 Trp operon repressor; 37.6 25 0.00055 30.9 2.3 37 226-262 47-83 (99)
372 PRK14086 dnaA chromosomal repl 37.5 76 0.0016 36.8 6.6 71 91-163 527-599 (617)
373 KOG1010 Rb (Retinoblastoma tum 37.4 2.6E+02 0.0057 33.5 10.8 55 76-133 36-90 (920)
374 PF13453 zf-TFIIB: Transcripti 37.3 24 0.00052 25.6 1.7 27 3-29 1-28 (41)
375 smart00354 HTH_LACI helix_turn 37.1 30 0.00065 27.9 2.5 22 235-256 1-22 (70)
376 TIGR00155 pqiA_fam integral me 37.1 21 0.00045 39.1 2.0 29 3-31 15-44 (403)
377 TIGR02999 Sig-70_X6 RNA polyme 37.0 32 0.0007 32.4 3.1 26 233-258 149-174 (183)
378 PF07278 DUF1441: Protein of u 36.6 28 0.00061 33.0 2.6 41 234-274 1-43 (152)
379 PRK13918 CRP/FNR family transc 36.6 1.3E+02 0.0029 28.5 7.5 29 132-160 148-176 (202)
380 PRK10411 DNA-binding transcrip 36.3 35 0.00076 34.5 3.4 28 233-260 17-44 (240)
381 smart00550 Zalpha Z-DNA-bindin 36.1 84 0.0018 25.3 5.0 38 123-160 11-49 (68)
382 PF14471 DUF4428: Domain of un 36.1 14 0.00029 28.5 0.3 27 3-30 1-30 (51)
383 PRK09392 ftrB transcriptional 35.9 1E+02 0.0022 30.3 6.6 30 233-262 172-201 (236)
384 PRK09391 fixK transcriptional 35.8 1.5E+02 0.0033 29.2 7.9 47 114-160 154-206 (230)
385 TIGR02147 Fsuc_second hypothet 35.7 5.2E+02 0.011 26.8 12.8 40 223-262 126-167 (271)
386 PF01155 HypA: Hydrogenase exp 35.6 8.7 0.00019 34.4 -1.0 34 3-41 72-105 (113)
387 PF01381 HTH_3: Helix-turn-hel 35.4 36 0.00078 25.5 2.6 39 232-275 7-45 (55)
388 PF08646 Rep_fac-A_C: Replicat 35.4 26 0.00056 32.4 2.1 28 3-32 20-49 (146)
389 PRK14559 putative protein seri 35.3 20 0.00043 41.6 1.6 25 3-32 29-53 (645)
390 PF13744 HTH_37: Helix-turn-he 35.3 63 0.0014 26.8 4.2 46 226-275 23-68 (80)
391 TIGR02702 SufR_cyano iron-sulf 35.3 62 0.0013 31.6 4.9 28 234-261 15-42 (203)
392 COG3413 Predicted DNA binding 35.1 53 0.0012 32.4 4.5 26 234-259 178-203 (215)
393 PF05043 Mga: Mga helix-turn-h 35.0 42 0.00091 27.9 3.2 30 230-259 26-55 (87)
394 PRK09685 DNA-binding transcrip 34.9 1.5E+02 0.0033 30.2 7.9 54 215-274 195-248 (302)
395 PRK09645 RNA polymerase sigma 34.7 36 0.00079 31.7 3.1 26 233-258 133-158 (173)
396 PF14206 Cys_rich_CPCC: Cystei 34.7 28 0.00061 29.3 2.0 27 3-29 3-29 (78)
397 PF08299 Bac_DnaA_C: Bacterial 34.5 93 0.002 25.2 5.0 45 111-157 23-70 (70)
398 cd00131 PAX Paired Box domain 34.5 52 0.0011 30.0 3.9 31 233-263 32-62 (128)
399 TIGR02297 HpaA 4-hydroxyphenyl 34.4 1.8E+02 0.0039 29.3 8.4 38 119-157 189-226 (287)
400 PF01418 HTH_6: Helix-turn-hel 34.3 35 0.00075 28.1 2.5 27 233-259 33-59 (77)
401 PHA00542 putative Cro-like pro 34.3 34 0.00074 28.6 2.5 29 230-258 27-55 (82)
402 PF13443 HTH_26: Cro/C1-type H 34.3 61 0.0013 25.0 3.8 40 233-276 9-48 (63)
403 PRK06759 RNA polymerase factor 34.3 39 0.00084 30.8 3.1 26 233-258 121-146 (154)
404 PRK09047 RNA polymerase factor 34.2 39 0.00084 31.0 3.1 27 233-259 121-147 (161)
405 COG1309 AcrR Transcriptional r 34.1 42 0.00092 29.9 3.4 39 219-258 17-56 (201)
406 smart00421 HTH_LUXR helix_turn 34.1 69 0.0015 23.4 4.0 31 134-164 19-49 (58)
407 PF01047 MarR: MarR family; I 34.1 74 0.0016 24.1 4.2 27 234-260 17-43 (59)
408 PRK14873 primosome assembly pr 34.0 25 0.00053 41.1 2.1 27 2-29 393-419 (665)
409 PRK12543 RNA polymerase sigma 34.0 55 0.0012 30.9 4.2 27 233-259 132-158 (179)
410 PRK07921 RNA polymerase sigma 33.9 6E+02 0.013 26.9 17.4 90 66-155 87-211 (324)
411 PRK03564 formate dehydrogenase 33.9 27 0.00058 36.9 2.2 27 3-29 189-221 (309)
412 PF01807 zf-CHC2: CHC2 zinc fi 33.9 21 0.00045 31.0 1.1 27 2-28 34-62 (97)
413 PRK09954 putative kinase; Prov 33.8 54 0.0012 34.8 4.5 30 231-260 14-43 (362)
414 PF09339 HTH_IclR: IclR helix- 33.7 74 0.0016 23.9 4.1 35 125-159 10-44 (52)
415 TIGR00310 ZPR1_znf ZPR1 zinc f 33.7 25 0.00053 34.6 1.7 30 3-32 2-42 (192)
416 PRK05580 primosome assembly pr 33.6 27 0.00058 40.8 2.4 28 3-31 392-419 (679)
417 smart00351 PAX Paired Box doma 33.6 56 0.0012 29.6 4.0 30 234-263 33-62 (125)
418 PRK14987 gluconate operon tran 33.5 29 0.00062 35.8 2.4 24 234-257 5-28 (331)
419 TIGR02937 sigma70-ECF RNA poly 33.4 54 0.0012 28.8 3.9 27 233-259 125-151 (158)
420 PF14369 zf-RING_3: zinc-finge 33.1 25 0.00054 24.9 1.2 26 3-28 4-29 (35)
421 smart00347 HTH_MARR helix_turn 33.1 99 0.0021 25.5 5.3 28 234-261 24-51 (101)
422 PRK12523 RNA polymerase sigma 33.1 41 0.00088 31.5 3.1 25 233-257 134-158 (172)
423 COG3415 Transposase and inacti 33.1 64 0.0014 30.1 4.3 34 231-264 18-51 (138)
424 COG3355 Predicted transcriptio 32.8 76 0.0017 29.2 4.6 39 224-262 32-70 (126)
425 TIGR01481 ccpA catabolite cont 32.8 31 0.00066 35.5 2.4 23 235-257 2-24 (329)
426 COG0664 Crp cAMP-binding prote 32.8 1.7E+02 0.0036 27.4 7.4 30 233-262 170-199 (214)
427 TIGR03070 couple_hipB transcri 32.7 50 0.0011 24.5 3.0 39 232-275 13-51 (58)
428 PRK12525 RNA polymerase sigma 32.6 42 0.00092 31.3 3.1 26 233-258 133-158 (168)
429 PF01710 HTH_Tnp_IS630: Transp 32.5 2.4E+02 0.0053 25.1 7.9 75 77-161 20-99 (119)
430 PF14768 RPA_interact_C: Repli 32.5 34 0.00075 28.8 2.2 26 3-31 1-26 (82)
431 PRK14088 dnaA chromosomal repl 32.4 74 0.0016 35.2 5.4 68 91-161 345-415 (440)
432 PRK10703 DNA-binding transcrip 32.4 33 0.00071 35.5 2.6 22 235-256 2-23 (341)
433 COG1321 TroR Mn-dependent tran 32.4 67 0.0015 30.4 4.4 38 223-261 14-51 (154)
434 TIGR02947 SigH_actino RNA poly 32.4 41 0.00089 32.1 3.1 27 233-259 146-172 (193)
435 PRK11303 DNA-binding transcrip 32.3 34 0.00073 35.2 2.6 22 236-257 2-23 (328)
436 PF05344 DUF746: Domain of Unk 32.0 1.1E+02 0.0024 24.9 4.8 46 127-181 7-52 (65)
437 PF13790 DUF4182: Domain of un 32.0 23 0.0005 25.7 0.9 13 19-31 2-14 (38)
438 TIGR02531 yecD_yerC TrpR-relat 32.0 57 0.0012 28.0 3.5 23 233-256 49-71 (88)
439 cd06170 LuxR_C_like C-terminal 32.0 77 0.0017 23.2 4.0 32 133-164 15-46 (57)
440 PF13463 HTH_27: Winged helix 32.0 64 0.0014 25.1 3.6 31 231-261 15-45 (68)
441 PF13463 HTH_27: Winged helix 31.9 89 0.0019 24.2 4.5 32 129-160 14-45 (68)
442 PRK12528 RNA polymerase sigma 31.9 45 0.00097 30.8 3.1 26 233-258 128-153 (161)
443 PRK15103 paraquat-inducible me 31.8 26 0.00057 38.5 1.8 30 3-32 12-42 (419)
444 PRK15121 right oriC-binding tr 31.8 88 0.0019 32.1 5.6 54 115-182 4-57 (289)
445 PRK12531 RNA polymerase sigma 31.7 43 0.00093 32.1 3.1 27 233-259 156-182 (194)
446 PRK10130 transcriptional regul 31.6 93 0.002 33.3 5.9 54 115-182 239-292 (350)
447 PF10058 DUF2296: Predicted in 31.5 25 0.00054 27.4 1.1 26 3-28 24-52 (54)
448 PRK00564 hypA hydrogenase nick 31.5 23 0.00049 32.0 1.0 35 3-41 73-107 (117)
449 TIGR01562 FdhE formate dehydro 31.4 29 0.00064 36.6 2.0 9 20-28 224-232 (305)
450 PF04967 HTH_10: HTH DNA bindi 31.3 1.8E+02 0.0039 22.6 5.8 26 134-159 24-49 (53)
451 PF04218 CENP-B_N: CENP-B N-te 31.1 31 0.00066 26.5 1.6 22 235-256 23-44 (53)
452 PF03444 HrcA_DNA-bdg: Winged 31.1 66 0.0014 27.1 3.6 31 230-260 19-49 (78)
453 cd04476 RPA1_DBD_C RPA1_DBD_C: 31.1 31 0.00067 32.6 1.9 27 3-31 36-62 (166)
454 PF07900 DUF1670: Protein of u 31.0 47 0.001 33.3 3.2 28 234-261 105-132 (220)
455 TIGR02417 fruct_sucro_rep D-fr 31.0 34 0.00074 35.1 2.4 22 236-257 1-22 (327)
456 cd04764 HTH_MlrA-like_sg1 Heli 30.9 50 0.0011 26.0 2.8 23 236-258 2-24 (67)
457 PF10668 Phage_terminase: Phag 30.7 1.1E+02 0.0024 24.5 4.6 23 130-152 19-41 (60)
458 PRK11014 transcriptional repre 30.6 85 0.0018 28.8 4.7 46 115-160 7-52 (141)
459 PRK12527 RNA polymerase sigma 30.6 48 0.0011 30.5 3.1 26 233-258 120-145 (159)
460 PRK03564 formate dehydrogenase 30.6 33 0.00071 36.3 2.2 9 22-30 254-262 (309)
461 PF01726 LexA_DNA_bind: LexA D 30.5 76 0.0016 25.5 3.8 32 128-159 20-52 (65)
462 COG2093 DNA-directed RNA polym 30.5 29 0.00062 27.9 1.3 22 3-29 6-27 (64)
463 TIGR00498 lexA SOS regulatory 30.3 81 0.0018 30.5 4.8 33 229-261 20-53 (199)
464 PF03428 RP-C: Replication pro 30.2 1.7E+02 0.0038 28.4 6.9 58 190-262 41-99 (177)
465 PRK09649 RNA polymerase sigma 30.2 48 0.001 31.6 3.1 27 233-259 145-171 (185)
466 PF01047 MarR: MarR family; I 30.2 1.4E+02 0.003 22.6 5.2 37 122-160 8-44 (59)
467 COG1476 Predicted transcriptio 30.1 40 0.00087 27.6 2.1 26 232-257 12-37 (68)
468 PRK00430 fis global DNA-bindin 29.9 1.2E+02 0.0026 26.3 5.2 26 234-259 68-93 (95)
469 PRK07218 replication factor A; 29.8 26 0.00056 38.6 1.3 31 3-42 299-329 (423)
470 TIGR02952 Sig70_famx2 RNA poly 29.7 56 0.0012 30.1 3.4 27 233-259 137-163 (170)
471 PRK12542 RNA polymerase sigma 29.7 47 0.001 31.5 3.0 42 233-274 137-181 (185)
472 cd04763 HTH_MlrA-like Helix-Tu 29.6 53 0.0011 26.0 2.8 23 236-258 2-24 (68)
473 PRK11512 DNA-binding transcrip 29.6 94 0.002 28.4 4.8 29 232-260 52-80 (144)
474 TIGR00319 desulf_FeS4 desulfof 29.5 29 0.00062 24.1 1.0 11 20-30 7-17 (34)
475 PRK10130 transcriptional regul 29.5 1.5E+02 0.0032 31.9 6.9 52 217-274 240-291 (350)
476 PF01498 HTH_Tnp_Tc3_2: Transp 29.3 54 0.0012 26.2 2.8 27 233-259 12-43 (72)
477 smart00422 HTH_MERR helix_turn 29.3 49 0.0011 26.0 2.5 22 236-257 2-23 (70)
478 PRK10906 DNA-binding transcrip 29.3 45 0.00098 33.9 2.9 28 233-260 18-45 (252)
479 TIGR02366 DHAK_reg probable di 29.2 72 0.0016 29.7 4.1 42 218-259 7-48 (176)
480 COG3620 Predicted transcriptio 29.2 56 0.0012 31.4 3.2 44 231-274 15-73 (187)
481 PRK12520 RNA polymerase sigma 29.2 48 0.001 31.6 3.0 27 233-259 146-172 (191)
482 PRK12545 RNA polymerase sigma 29.2 48 0.001 32.2 2.9 27 233-259 154-180 (201)
483 PRK10727 DNA-binding transcrip 29.2 38 0.00082 35.2 2.4 22 235-256 2-23 (343)
484 PRK09685 DNA-binding transcrip 29.1 2.5E+02 0.0053 28.6 8.4 42 115-156 196-237 (302)
485 PRK10401 DNA-binding transcrip 29.1 40 0.00086 35.1 2.5 22 235-256 2-23 (346)
486 smart00345 HTH_GNTR helix_turn 29.1 86 0.0019 23.3 3.8 26 135-160 22-47 (60)
487 TIGR02950 SigM_subfam RNA poly 28.9 50 0.0011 30.0 2.9 26 233-258 120-145 (154)
488 PRK00149 dnaA chromosomal repl 28.9 1E+02 0.0022 34.0 5.8 71 91-163 360-433 (450)
489 PRK09978 DNA-binding transcrip 28.9 3.2E+02 0.0068 28.4 9.0 52 216-274 141-192 (274)
490 PRK09480 slmA division inhibit 28.9 66 0.0014 30.2 3.8 44 214-257 10-53 (194)
491 PF05930 Phage_AlpA: Prophage 28.9 57 0.0012 24.6 2.7 22 235-256 4-25 (51)
492 PRK11920 rirA iron-responsive 28.9 91 0.002 29.3 4.7 39 222-261 13-51 (153)
493 PRK14165 winged helix-turn-hel 28.8 63 0.0014 32.4 3.8 31 231-261 18-48 (217)
494 PRK12366 replication factor A; 28.8 27 0.00059 40.5 1.3 24 3-29 534-557 (637)
495 PRK08301 sporulation sigma fac 28.7 51 0.0011 32.7 3.1 26 233-258 197-222 (234)
496 PRK09413 IS2 repressor TnpA; R 28.7 1E+02 0.0022 27.6 4.8 32 230-261 25-56 (121)
497 PRK10339 DNA-binding transcrip 28.7 35 0.00076 35.2 2.0 22 235-256 2-23 (327)
498 TIGR00738 rrf2_super rrf2 fami 28.4 1.5E+02 0.0032 26.5 5.9 42 220-261 10-52 (132)
499 cd00974 DSRD Desulforedoxin (D 28.4 31 0.00068 23.9 1.1 22 3-24 6-27 (34)
500 PF13411 MerR_1: MerR HTH fami 28.3 43 0.00094 26.3 2.1 24 236-259 2-25 (69)
No 1
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=100.00 E-value=1.3e-82 Score=674.82 Aligned_cols=482 Identities=32% Similarity=0.444 Sum_probs=392.2
Q ss_pred CCCCCCCCCCceeccCCCceecCcccceeccccccccccccccCCCCccccCccceeecccc---cchHHHHHHHHHHHH
Q 008455 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATFVKNAAGQSQLSGNFVRTIQSEY---GASRERLMEKAFDDM 78 (565)
Q Consensus 2 ~~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vlee~~id~~~ef~e~~~G~s~v~G~~v~~~~~~~---~~srer~l~~a~~~I 78 (565)
++|++||++++..|.++|.++|+.||+|+|+++|+++++|.+. ++|+||+..|.+. .++|+++++++++.|
T Consensus 1 ~~C~~C~~s~fe~d~a~g~~~C~~CG~v~E~~~ivsev~F~e~------~~G~~v~~~~~g~~~s~e~r~~t~~n~r~~i 74 (521)
T KOG1598|consen 1 MVCKNCGGSNFERDEATGNLYCTACGTVLEYNNIVAEVTFVEG------AQGQFVRVGQSGAGSSLESREKTIYNARRLI 74 (521)
T ss_pred CcCCCCCCCCcccccccCCceeccccceeeccceeEEeeeecc------cceeEEeccccCCccchHHHHHHHHHHHhHH
Confidence 5799999999999999999999999999999999999999987 6899998777653 489999999999999
Q ss_pred HHHHHHcCCCChhHHHHHHHHHHHHHHhCccccCCchhHHHHHHHHHHHHhcCCCccHHHHHhhhccChHHHHHHHHHHH
Q 008455 79 RQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLC 158 (565)
Q Consensus 79 ~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~p~tL~DIa~~~~vsv~~Lgr~~~~L~ 158 (565)
..++.+|+|+ + +++.|.+||++|.++||++||+...|+|+|+|++||+++++|+|+||+++++|++|.||++|++|+
T Consensus 75 ~~~~~~l~l~--~-~~~~a~~~~k~a~~~nftkGr~~~~vvasClY~vcR~e~t~hlliDfS~~Lqv~Vy~LG~~~l~l~ 151 (521)
T KOG1598|consen 75 EELTERLNLG--N-KTEVAFNFFKLAPDRNFTKGRRSTEVVAACLYLVCRLEKTDHLLIDFSSYLQVSVYDLGSNFLEVT 151 (521)
T ss_pred HHHHHhcCcc--h-HHHHHHHHHHHHhhCCCCCCcchHHHHHHHHHHHHHhhCCceEEEEeccceEEehhhhhHHHHHHH
Confidence 9999999999 7 999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhccccccccccCCchhhHHHHHHhh-CCCCCHHHHHHHHHHHHHhhhccccCCCChhHHHHHHHHHHHHhcCCCCCH
Q 008455 159 QVLYIADESNVLKQVDPSIFLHKFTDRL-LPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSK 237 (565)
Q Consensus 159 ~~L~i~~~~~~~~~vdP~~~I~Rf~~~L-~~~l~~~V~~~A~~Lv~~m~~~~l~~GR~P~~IaaAALylAar~~g~~~t~ 237 (565)
+.|.+.. |+.+++||+.||+||+.+| +++.+++|+.+|++|+++|++|||++||+|+||||||||+|||+||+++|+
T Consensus 152 ~~L~i~e--n~~plvDpsL~i~Rfa~~L~~g~~~~~Vv~~a~~L~~rMkrdwm~tGRRPsglcGAaLliAar~h~~~rsi 229 (521)
T KOG1598|consen 152 DSLSIGE--NVSPLVDPSLYIVRFSCRLLFGDKTEDVAKTATRLAQRMKRDWMQTGRRPSGLCGAALLIAARMHGFRRTI 229 (521)
T ss_pred HHhcccc--ccccccCcceeeechhHhhhcCCchHHHHHHHHHHHHHHHHHHHHhCCCccchhHHHHHHHHHHcCccccH
Confidence 9999974 2566899999999999999 677889999999999999999999999999999999999999999999999
Q ss_pred hHHHHHhccCHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhhhccCCCCCCCCCC------CCCchhhhhhccccCCCcc
Q 008455 238 SDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARKKELHEGVAANLPNNGPK------VSGMNEVLCKHKDTGKPFA 311 (565)
Q Consensus 238 ~eIa~v~~Vse~TIrkR~kE~~~t~s~~Lt~~~f~~~~~~~e~e~~~~~~~~~~~------~~~~~~~~~~~k~~~~~~~ 311 (565)
.||++++|||+.||++||+||.+|+++.||+++|+.+|+ +.+++||.+...+. .++.+.+.+.|.+. .++.
T Consensus 230 ~dIv~vvhV~e~Tl~kRl~Ef~~T~s~~Lti~ef~~~d~--e~~~~ppsft~~~~~~~k~~~~~k~~l~~~~~~~-e~~~ 306 (521)
T KOG1598|consen 230 GDIAKVVHVCESTLSKRLKEFSDTLSGDLTIDELAEIDL--EYESDPPSFTASPSKEAKYVEDKKKMLSRTMQLV-ELAN 306 (521)
T ss_pred HHHHHHHHHhHHHHHHHHHHHhccccccccHHHHHhhhh--hhccCcchhhcccchhhhhhhhhhhhhhhhhhhh-hccc
Confidence 999999999999999999999999999999999999998 66666665554332 13334444444442 3688
Q ss_pred cCchhhhhhhhhhcccCCCCCCCCchhhHHHHHHHHHHhhhhccchhcccCCccccccCcCCCCCCC-CCCCCCCccccc
Q 008455 312 CGLCRSCYEEFMTISEGLEGGADPPAFQVAERERMVKASAEENSSFERESDSPFMSRVDKVQSPEPE-RVPKNCTTQTAS 390 (565)
Q Consensus 312 ~g~~~~~~~~~~~~~~~~~~~~dppaf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~ 390 (565)
.++|..|+..+..+++++.+..++|.|+..+.++-..... ++ . +.+....-+... ..+....+..+.
T Consensus 307 ~~~~~~~~~~~~~~~~~l~~~~q~~~~~~~~~e~~~~~~~-e~-----~------~ssE~~dk~~~g~~~~~~~~~sd~~ 374 (521)
T KOG1598|consen 307 ETWLVTLRHSLPVITGGLFLAWQDLQPRDRLVESYDDLAS-EC-----P------LSSEDEDKPASGRLAELLAVLSDMA 374 (521)
T ss_pred chhhhccccCCcccchhhhcccccchhhhhhhhhhhhhhh-cC-----c------ccccccCCcCccccchhhhcccccc
Confidence 8899999999999999999999999998876664111100 00 0 000000000000 000000000000
Q ss_pred cCCCCCCCCCCCCCCCccCCCCCCCCCCCChHHHhhcCCChHHHHHHHHHhhhcCHHHHHHHHHHHHHHHHHHHHHHhhh
Q 008455 391 NEGEGDHTKTPGVDATTEASDGSDNFSDIDDFEVDGYLHNEEEKHYKKIIWEEMNREYLEEQAAKEAAAAAAKAALEASY 470 (565)
Q Consensus 391 ~~~~~~~~~~~~~~~~~~~~~~~~~lsdiDD~Eid~~il~eeE~~~K~~iW~~~N~eyl~eq~~K~~~~~~~k~~~~~~~ 470 (565)
.+-...|. .....+....++++||.+++.++|++++.+.++.+ | +|++||.|+..+.++++++++.
T Consensus 375 ~~~~~~~~-------~~~~~d~~~~~~~~~~~~l~r~~l~~~a~~~a~~~-~-~n~e~l~E~~~~~~~~ak~~~~----- 440 (521)
T KOG1598|consen 375 EQLASVWL-------RVLTLDKRSGVKHIDDLLLERQLLEESAGRDATEP-M-ENAETLVEERPGKAKAAKEREE----- 440 (521)
T ss_pred hhhhhcch-------hhhhccccccccccCHHHHHHHHhhhHHhhhcchh-h-hhHHHHHhhchhhhhhhHhhhh-----
Confidence 00000000 12234667889999999999999999999999999 7 9999999999998887653321
Q ss_pred cCCCcchHHHHHHHHHHHHHHhhhhhHHHhhhHhhhcCCCCCCCHHHHHHHHHHhcccccccCHHHHhhhhCCCCcc
Q 008455 471 KNCPEGLQAAQELAAAAAAAVAKSRKEKQQKRAAEAKNSGPAQTALEATRRMLTKKRLSSKINYDVLEKLFDDSVCL 547 (565)
Q Consensus 471 ~~~~~~~~~~~~~~~~~~~~~~~~~k~k~~k~~~~~~~~~~a~ta~EA~~~ml~~k~~S~kINYd~l~~L~~~~~~~ 547 (565)
++. . ++++..+.++.+++.||.||+++|++++.+|++|||++|++||+.....
T Consensus 441 -------------------g~~-~----~~~k~~~r~~s~~~~t~~eavk~~~~i~~~s~~in~~~L~~i~d~~~e~ 493 (521)
T KOG1598|consen 441 -------------------GIN-S----LSKKVGERRNSPELLTAPEAVKSMKEIKPVSSVINYSVLENISDAEIEQ 493 (521)
T ss_pred -------------------ccc-c----cccccccccCCCcccccHHHHHHHHhccccccchHHHHHHHHhhhhccc
Confidence 210 1 1133334568999999999999999999999999999999999876543
No 2
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=100.00 E-value=4e-53 Score=439.42 Aligned_cols=250 Identities=23% Similarity=0.391 Sum_probs=227.7
Q ss_pred CCCCCCCCCCceeccCCCceecCcccceeccccccccccccccCC----CCccccC------------------------
Q 008455 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATFVKNAA----GQSQLSG------------------------ 53 (565)
Q Consensus 2 ~~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vlee~~id~~~ef~e~~~----G~s~v~G------------------------ 53 (565)
..||+||+..+++|+.+|++||++||+||+|++||.+++|+.++. .++++++
T Consensus 12 ~~Cp~Cg~~~iv~d~~~Ge~vC~~CG~Vl~e~~iD~g~EWR~f~~~~~~~~~RvG~~~~~~~~~~gl~T~I~~~~~~~~g 91 (310)
T PRK00423 12 LVCPECGSDKLIYDYERGEIVCADCGLVIEENIIDQGPEWRAFDPEQREKRSRVGAPMTYTIHDKGLSTDIDWRNKDSYG 91 (310)
T ss_pred CcCcCCCCCCeeEECCCCeEeecccCCcccccccccCCCccCCCccccCCccccCCCCCccccCCCCceEeecCCccccc
Confidence 369999998899999999999999999999999999999986542 1222221
Q ss_pred ccce-----------eeccc--ccchHHHHHHHHHHHHHHHHHHcCCCChhHHHHHHHHHHHHHHhCccccCCchhHHHH
Q 008455 54 NFVR-----------TIQSE--YGASRERLMEKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQA 120 (565)
Q Consensus 54 ~~v~-----------~~~~~--~~~srer~l~~a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaA 120 (565)
..++ .||.+ ..++.|++|..|+..|+++|+.|+|| +.++++|..+|++++++++++||+.+.++|
T Consensus 92 ~~l~~~~~~~~~rl~~~~~~~~~~~~~er~l~~a~~~I~~~~~~L~Lp--~~v~e~A~~iyk~~~~~~~~rgrs~~~i~A 169 (310)
T PRK00423 92 KSISGKNRAQLYRLRKWQRRIRVSNAAERNLAFALSELDRIASQLGLP--RSVREEAAVIYRKAVEKGLIRGRSIEGVVA 169 (310)
T ss_pred ccccHHHHHHHHHHHHHhhhcccCChHhHHHHHHHHHHHHHHHHcCCC--HHHHHHHHHHHHHHHhcCcccCCCHHHHHH
Confidence 1111 12222 23678999999999999999999999 999999999999999999999999999999
Q ss_pred HHHHHHHHhcCCCccHHHHHhhhccChHHHHHHHHHHHHHhhccccccccccCCchhhHHHHHHhhCCCCCHHHHHHHHH
Q 008455 121 SCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARD 200 (565)
Q Consensus 121 ACLYiACR~e~~p~tL~DIa~~~~vsv~~Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~~~l~~~V~~~A~~ 200 (565)
||||+|||++++|+||+||+.++++++++|+++|+.|.+.|+++.++ ++|+.||+|||+.|+ ++..|.+.|.+
T Consensus 170 AclYiACR~~~~prtl~eI~~~~~v~~k~i~~~~~~l~k~L~~~~~~-----~~p~~~i~r~~~~L~--L~~~v~~~A~~ 242 (310)
T PRK00423 170 AALYAACRRCKVPRTLDEIAEVSRVSRKEIGRCYRFLLRELNLKLPP-----TDPIDYVPRFASELG--LSGEVQKKAIE 242 (310)
T ss_pred HHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCCC-----CCHHHHHHHHHHHcC--CCHHHHHHHHH
Confidence 99999999999999999999999999999999999999999998765 899999999999998 89999999999
Q ss_pred HHHHhhhccccCCCChhHHHHHHHHHHHHhcCCCCCHhHHHHHhccCHHHHHHHHHHHHc
Q 008455 201 ILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (565)
Q Consensus 201 Lv~~m~~~~l~~GR~P~~IaaAALylAar~~g~~~t~~eIa~v~~Vse~TIrkR~kE~~~ 260 (565)
|++.+.+.|++.||+|.+|||||||+||+++|.++|+++|+.+++|++.||++||+||..
T Consensus 243 i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g~~~t~keIa~v~~Vs~~tI~~~ykel~~ 302 (310)
T PRK00423 243 ILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERRTQREVAEVAGVTEVTVRNRYKELAE 302 (310)
T ss_pred HHHHHHhcCcccCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999999985
No 3
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=100.00 E-value=8.8e-53 Score=428.33 Aligned_cols=253 Identities=27% Similarity=0.471 Sum_probs=230.4
Q ss_pred CCCCCCCCCCCceeccCCCceecCcccceecccccccccccccc---CC---C-C----------ccccCc-------cc
Q 008455 1 MVWCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATFVKN---AA---G-Q----------SQLSGN-------FV 56 (565)
Q Consensus 1 M~~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vlee~~id~~~ef~e~---~~---G-~----------s~v~G~-------~v 56 (565)
|..||+||+..++.|+..|++||.+||.|++|..||.+|+|+.+ .. | + ++..|. -+
T Consensus 1 ~~~CpeCg~~~~~~d~~~ge~VC~~CG~Vi~~~~id~gpewr~f~e~~~~r~g~P~t~~~~d~~l~t~i~~~~~~~~~rl 80 (285)
T COG1405 1 VMSCPECGSTNIITDYERGEIVCADCGLVLEDSLIDPGPEWRAFDERHERRVGAPLTPSIHDKGLSTIIGWGDKDKMYRL 80 (285)
T ss_pred CCCCCCCCCccceeeccCCeEEeccCCEEeccccccCCCCcccccccccccccCCCccccCccchhhhcccchhHHHHHH
Confidence 56899999999999999999999999999999999999999942 21 1 1 111111 01
Q ss_pred eeeccc--ccchHHHHHHHHHHHHHHHHHHcCCCChhHHHHHHHHHHHHHHhCccccCCchhHHHHHHHHHHHHhcCCCc
Q 008455 57 RTIQSE--YGASRERLMEKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPF 134 (565)
Q Consensus 57 ~~~~~~--~~~srer~l~~a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~p~ 134 (565)
+.||.+ .+++.|+++..++.+|..++.+|+|| .++.++|..||++++++++++||+.+.++|||||+|||+++.|+
T Consensus 81 r~~~~~~~v~~~~ernl~~a~~~l~~~~~~l~LP--~~v~e~A~~iyr~a~~~~l~rGRsie~v~AA~iY~acR~~~~pr 158 (285)
T COG1405 81 RKWQIRIRVSSAKERNLITALEELERIASALGLP--ESVRETAARIYRKAVDKGLLRGRSIESVAAACIYAACRINGVPR 158 (285)
T ss_pred HHHHhccccccchhhHHHHHHHHHHHHHHHhCCC--chHHHHHHHHHHHHhhcCCCcCCcHHHHHHHHHHHHHHHcCCCc
Confidence 234433 35679999999999999999999999 99999999999999999999999999999999999999999999
Q ss_pred cHHHHHhhhccChHHHHHHHHHHHHHhhccccccccccCCchhhHHHHHHhhCCCCCHHHHHHHHHHHHHhhhccccCCC
Q 008455 135 LLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGR 214 (565)
Q Consensus 135 tL~DIa~~~~vsv~~Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~~~l~~~V~~~A~~Lv~~m~~~~l~~GR 214 (565)
||.||+++++|+.++|+++|+.+.+.|++..+| ++|.+||+|||+.|+ ++++|...|.+|++.+.+.++..||
T Consensus 159 tl~eIa~a~~V~~kei~rtyr~~~~~L~l~~~~-----~~p~~yi~rf~s~L~--l~~~v~~~a~ei~~~~~~~g~~~Gk 231 (285)
T COG1405 159 TLDEIAKALGVSKKEIGRTYRLLVRELKLKIPP-----VDPSDYIPRFASKLG--LSDEVRRKAIEIVKKAKRAGLTAGK 231 (285)
T ss_pred cHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCCC-----CCHHHHHHHHHHHcC--CCHHHHHHHHHHHHHHHHhCcccCC
Confidence 999999999999999999999999999998877 999999999999999 9999999999999999999999999
Q ss_pred ChhHHHHHHHHHHHHhcCCCCCHhHHHHHhccCHHHHHHHHHHHHccC
Q 008455 215 KPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTD 262 (565)
Q Consensus 215 ~P~~IaaAALylAar~~g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t~ 262 (565)
+|.||||||||+|++++|+++||++|+.++||+|+|||+||+|+.+.-
T Consensus 232 ~P~glAaaaiy~as~l~~~~~tq~eva~v~~vtevTIrnrykel~~~~ 279 (285)
T COG1405 232 SPAGLAAAAIYLASLLLGERRTQKEVAKVAGVTEVTIRNRYKELADAL 279 (285)
T ss_pred CchhHHHHHHHHHHHHhCCchHHHHHHHHhCCeeeHHHHHHHHHHHhh
Confidence 999999999999999999999999999999999999999999997543
No 4
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=100.00 E-value=4e-47 Score=377.56 Aligned_cols=265 Identities=20% Similarity=0.351 Sum_probs=234.8
Q ss_pred CCCCCCCCC--CceeccCCCceecCcccceeccccccccccccccCC-----CCccccC--------ccce---------
Q 008455 2 VWCSSCARH--VTGHRPYDSQLCCDRCGKVLEDHNFSTEATFVKNAA-----GQSQLSG--------NFVR--------- 57 (565)
Q Consensus 2 ~~Cp~Cgs~--~i~~D~~~G~~VCt~CG~Vlee~~id~~~ef~e~~~-----G~s~v~G--------~~v~--------- 57 (565)
++|+.|... .+++|+..|+.||..||.|+++++||.+.+|+.+++ .+++|++ ..++
T Consensus 1 ~~c~~C~~~~~~~V~d~~~gdtvC~~CGlVl~~r~Id~~sEwrtfsnd~~~~DPsrvG~~sNPlL~~g~L~T~I~~g~g~ 80 (308)
T KOG1597|consen 1 MTCPDCKRHPENLVEDHSAGDTVCSECGLVLEDRIIDEGSEWRTFSNDDSDADPSRVGASSNPLLDGGDLSTFISKGTGT 80 (308)
T ss_pred CCCCCCCCCCCCeeeeccCCceecccCCeeeccccccccccccccccCCCCCCccccCCCCCCCCCCCCcceeeecCCCC
Confidence 379999876 489999999999999999999999997777765432 2455432 1111
Q ss_pred ---------eeccc-ccchHHHHHHHHHHHHHHHHHHcCCCChhHHHHHHHHHHHHHHhCccccCCchhHHHHHHHHHHH
Q 008455 58 ---------TIQSE-YGASRERLMEKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLAC 127 (565)
Q Consensus 58 ---------~~~~~-~~~srer~l~~a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiAC 127 (565)
.+|++ .+++.++.+..++..|..|+++|+|| ..|.+.|.++|+++.+.+.+|||+.++++|||||+||
T Consensus 81 ~s~~~s~l~~~Q~~~sm~~~d~~~~~a~~~I~~m~d~~~Lp--~~I~d~A~~ifk~v~~~k~lrGks~eai~AAclyiAC 158 (308)
T KOG1597|consen 81 SSSFASSLGKAQNRNSMSNSDRVLKAAFKEITAMCDRLSLP--ATIKDRANEIFKLVEDSKLLRGKSVEALAAACLYIAC 158 (308)
T ss_pred CHHHHHHHHHHhcccccCCccHHHHHHHHHHHHHHHHhCCc--hHHHHHHHHHHHHHHHhhhhcCccHHHHHHHHHHHHH
Confidence 23432 24567889999999999999999999 9999999999999999999999999999999999999
Q ss_pred HhcCCCccHHHHHhhhccChHHHHHHHHHHHHHhhccccccccccCCchhhHHHHHHhhCCCCCHHHHHHHHHHHHHhhh
Q 008455 128 RQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKR 207 (565)
Q Consensus 128 R~e~~p~tL~DIa~~~~vsv~~Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~~~l~~~V~~~A~~Lv~~m~~ 207 (565)
|+++.|||++||+.+.+|+.++||+.++.|.+.|++..+.+ .+...+||+|||+.|. ++..+++.|.++++....
T Consensus 159 Rq~~~pRT~kEI~~~anv~kKEIgr~~K~i~~~l~~s~~~~---s~~t~~~m~RFCs~L~--L~~~~q~aA~e~a~ka~~ 233 (308)
T KOG1597|consen 159 RQEDVPRTFKEISAVANVSKKEIGRCVKLIGEALETSVDLI---SISTGDFMPRFCSNLG--LPKSAQEAATEIAEKAEE 233 (308)
T ss_pred HhcCCCchHHHHHHHHcCCHHHHHHHHHHHHHHHhccchhh---hhhHHHHHHHHHHhcC--CCHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999876542 4568899999999999 999999999999999999
Q ss_pred ccccCCCChhHHHHHHHHHHHHhcCCCCCHhHHHHHhccCHHHHHHHHHHHHccCCCCCCHHHHHHH
Q 008455 208 DWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMAR 274 (565)
Q Consensus 208 ~~l~~GR~P~~IaaAALylAar~~g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t~s~~Lt~~~f~~~ 274 (565)
..+..||.|.+||||+|||++++...++|+++|..++||+|+|||+.||+|+ ++...|.+.+|...
T Consensus 234 ~~~~~gRsPiSIAAa~IYmisqls~~kkt~keI~~vtgVaE~TIr~sYK~Ly-p~~~~liP~~~a~~ 299 (308)
T KOG1597|consen 234 MDIRAGRSPISIAAAAIYMISQLSDEKKTQKEIGEVTGVAEVTIRNSYKDLY-PHADKLIPSWYANA 299 (308)
T ss_pred hccccCCCchhHHHHHHHHHHHhccCcccHHHHHHHhhhhHHHHHHHHHHHh-hchhhhChhhhccc
Confidence 9999999999999999999999999999999999999999999999999999 56668889998654
No 5
>PF07741 BRF1: Brf1-like TBP-binding domain; InterPro: IPR011665 The Vaccinia virus has an infection-induced host cell cycle control mechanism. p53 and Rb, which are associated with the is inactivated Rb, which are associated with the RNA polymerase III transcription factor B (TFIIIB) subunits, TBP and Brf1, are inactivated [, ]. TFIIB, Brf1, and Brf2 share related N-terminal zinc ribbon and core domains. TFIIB bridges RNA polymerase II (Pol II) with the promoter-bound pre-initiation complex, whereas Brf1 and Brf2 are involved in the recruitment of Pol III. Brf1 and Brf2 both have a C-terminal extension absent in TFIIB, but their C-terminal extensions are unrelated. In yeast Brf1, the C-terminal extension interacts with the TBP/TATA box complex and contributes to the recruitment of Bdp1 []. It is suggested that the structure of the TBP-DNA complex may be altered upon entry of Brf1 and Bdp1 into the complex. Entry of Brf1 and Bdp1 into the complex imposes a strict sequence preference for the downstream half of the TATA box []. This region covers both the Brf homology II and III regions []. ; GO: 0008270 zinc ion binding, 0045893 positive regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1NGM_J.
Probab=99.95 E-value=6.6e-30 Score=221.89 Aligned_cols=96 Identities=53% Similarity=0.784 Sum_probs=34.6
Q ss_pred hHHHhhcCCChHHHHHHHHHhhhcCHHHHHHHHHHHHHHHHHHHHHHhhhcCCCcchHHHHHHHHHHHHHHhhhhhHHHh
Q 008455 421 DFEVDGYLHNEEEKHYKKIIWEEMNREYLEEQAAKEAAAAAAKAALEASYKNCPEGLQAAQELAAAAAAAVAKSRKEKQQ 500 (565)
Q Consensus 421 D~Eid~~il~eeE~~~K~~iW~~~N~eyl~eq~~K~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~k~~ 500 (565)
|+|||.|||||+|+++|++||+++|+|||++|++|+++++++.+ .+++ ++|++++
T Consensus 1 DdEid~~il~eeE~~~K~~iW~~~NkdyL~~~~~K~~~~~~~~~----------------------~~~~---~~k~k~~ 55 (97)
T PF07741_consen 1 DDEIDNYILSEEEVKIKERIWMEMNKDYLEEQEEKELKAKAEEE----------------------AGAK---SRKKKKK 55 (97)
T ss_dssp -HHHHTTC--HHHHHHHHHHHHHHTHHHHHHHHHCCCCT-----------------------------------------
T ss_pred ChHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh----------------------hccC---CCccccc
Confidence 56999999999999999999999999999999999987654221 1112 2222222
Q ss_pred hhHhhhcC-CCCCCCHHHHHHHHHHhcccccccCHHHHhhhh
Q 008455 501 KRAAEAKN-SGPAQTALEATRRMLTKKRLSSKINYDVLEKLF 541 (565)
Q Consensus 501 k~~~~~~~-~~~a~ta~EA~~~ml~~k~~S~kINYd~l~~L~ 541 (565)
+++...++ .+||.||+||+++||++|+||+|||||+|++||
T Consensus 56 rk~~~~~~~~~~a~ta~EA~~~ml~~k~~S~KINYd~L~~LF 97 (97)
T PF07741_consen 56 RKRRKKKNQAPPAETAAEAARKMLKKKKFSKKINYDALESLF 97 (97)
T ss_dssp ------------------------------------------
T ss_pred cccccccCCCCCCCCHHHHHHHHHHhcCcccccCHHHHHhhC
Confidence 33333344 899999999999999999999999999999998
No 6
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.
Probab=99.67 E-value=2.5e-16 Score=129.12 Aligned_cols=71 Identities=27% Similarity=0.516 Sum_probs=66.2
Q ss_pred HHHHHHHcCCCChhHHHHHHHHHHHHHHhCccccCCchhHHHHHHHHHHHHhcCCCccHHHHHhhhccChHHH
Q 008455 78 MRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYEL 150 (565)
Q Consensus 78 I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~p~tL~DIa~~~~vsv~~L 150 (565)
|+++|+.|+|| .++.+.|..+|+.+.+.++++||++..++|||||+|||+++.|+|++||+++++|+.++|
T Consensus 1 I~r~~~~L~L~--~~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~~~~t~~eIa~~~~Vs~~tI 71 (71)
T PF00382_consen 1 IPRICSKLGLP--EDVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNGVPRTLKEIAEAAGVSEKTI 71 (71)
T ss_dssp HHHHHHHTT----HHHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTTSSSSHHHHHHHCTSSHHHH
T ss_pred ChHHHhHcCCC--HHHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHhCCCCCcC
Confidence 68899999999 999999999999999999999999999999999999999999999999999999999875
No 7
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.
Probab=99.60 E-value=3.3e-15 Score=122.42 Aligned_cols=71 Identities=18% Similarity=0.365 Sum_probs=66.7
Q ss_pred HHHHHHhhCCCCCHHHHHHHHHHHHHhhhccccCCCChhHHHHHHHHHHHHhcCCCCCHhHHHHHhccCHHHH
Q 008455 179 LHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATL 251 (565)
Q Consensus 179 I~Rf~~~L~~~l~~~V~~~A~~Lv~~m~~~~l~~GR~P~~IaaAALylAar~~g~~~t~~eIa~v~~Vse~TI 251 (565)
|+|||+.|+ +++.|.+.|.+|++.+.+.|+..||+|.+|||||||+|||.+|.++|++||+.+++|++.||
T Consensus 1 I~r~~~~L~--L~~~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~~~~t~~eIa~~~~Vs~~tI 71 (71)
T PF00382_consen 1 IPRICSKLG--LPEDVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNGVPRTLKEIAEAAGVSEKTI 71 (71)
T ss_dssp HHHHHHHTT----HHHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTTSSSSHHHHHHHCTSSHHHH
T ss_pred ChHHHhHcC--CCHHHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHhCCCCCcC
Confidence 689999999 99999999999999999999999999999999999999999999999999999999999997
No 8
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=99.36 E-value=3.6e-11 Score=124.85 Aligned_cols=164 Identities=16% Similarity=0.114 Sum_probs=135.8
Q ss_pred HHHHHH-HHHHHHHHHHHHcC--CCChhHHHHHHHHHHHHHHhCccccCCchhHHHHHHHHHHHHhcCCCccHHHHHhhh
Q 008455 67 RERLME-KAFDDMRQMKNALN--IGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYL 143 (565)
Q Consensus 67 rer~l~-~a~~~I~~ia~~L~--Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~p~tL~DIa~~~ 143 (565)
.|..+. .+...|..+|..|+ || +.++-+|..||++.+-.+.+.--.+..|+++|||+||+.+..|+++.+|+..+
T Consensus 51 eE~~l~~~y~~~i~~~~~~lkp~Lp--q~viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE~~~si~~fv~~~ 128 (305)
T TIGR00569 51 EELDLVKYYEKRLLDFCSAFKPTMP--TSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFVGNL 128 (305)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCCC--chHHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccccCcCHHHHHhhc
Confidence 355554 45699999999999 99 99999999999999988877777899999999999999999999999999876
Q ss_pred ccC----hHHHHHHHHHHHHHhhccccccccccCCchhhHHHHHHhhC-----CCCCHHHHHHHHHHHHHhhhccccCCC
Q 008455 144 NIN----VYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLL-----PGGNKKVCDTARDILASMKRDWITTGR 214 (565)
Q Consensus 144 ~vs----v~~Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~-----~~l~~~V~~~A~~Lv~~m~~~~l~~GR 214 (565)
.-+ ...|...-..|++.|++.... ..|..++..|...|. ......+...|+.+++.+....+.-=-
T Consensus 129 ~~~~~~~~~~Il~~E~~lL~~L~F~L~V-----~hPyr~L~~~l~dl~~~l~~~~~~~~l~q~a~~~lndsl~Td~~L~y 203 (305)
T TIGR00569 129 KETPLKALEQVLEYELLLIQQLNFHLIV-----HNPYRPLEGFLIDIKTRLPGLENPEYLRKHADKFLNRTLLTDAYLLY 203 (305)
T ss_pred cCCchhhHHHHHHHHHHHHHHCCCcEEe-----eCccHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHHHcCCceecC
Confidence 543 377888899999999988764 679998888876542 113456788999999877665555559
Q ss_pred ChhHHHHHHHHHHHHhcCCCCCH
Q 008455 215 KPSGLCGAALYVSALTHGLKFSK 237 (565)
Q Consensus 215 ~P~~IaaAALylAar~~g~~~t~ 237 (565)
.|+-||.||||+|++.+|.+..-
T Consensus 204 ~Ps~IAlAAI~lA~~~~~~~l~~ 226 (305)
T TIGR00569 204 TPSQIALAAILHTASRAGLNMES 226 (305)
T ss_pred CHHHHHHHHHHHHHHHhCCCCcc
Confidence 99999999999999999987654
No 9
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=99.34 E-value=5.3e-11 Score=121.20 Aligned_cols=189 Identities=14% Similarity=0.153 Sum_probs=157.5
Q ss_pred hHHHHHHHHHHHHHHHHHHcCCCChhHHHHHHHHHHHHHHhCccccCCchhHHHHHHHHHHHHhcCCCccHHHHHhhhcc
Q 008455 66 SRERLMEKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNI 145 (565)
Q Consensus 66 srer~l~~a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~p~tL~DIa~~~~v 145 (565)
..+....=|...|++-|-.|+|| +..+-++..+|+...-..-+.+-..++++.|||.+|.+.+..|++++||..+++-
T Consensus 18 ~e~el~~LG~e~Iqea~ILL~L~--q~a~atgqVLFqRf~~~ks~v~~~~e~vv~ACv~LASKiEE~Prr~rdVinVFh~ 95 (367)
T KOG0835|consen 18 TEEELRILGCELIQEAGILLNLP--QVAMATGQVLFQRFCYSKSFVRHDFEIVVMACVLLASKIEEEPRRIRDVINVFHY 95 (367)
T ss_pred hHHHHHHHhHHHHHhhhHhhcCc--HHHHHHHHHHHHHHHhccccccccHHHHHHHHHHHHhhhccccccHhHHHHHHHH
Confidence 33444456889999999999999 9999999999999988888888899999999999999999999999999988752
Q ss_pred ----------C-----------hHHHHHHHHHHHHHhhccccccccccCCchhhHHHHHHhhCCCCCHHHHHHHHHHHHH
Q 008455 146 ----------N-----------VYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILAS 204 (565)
Q Consensus 146 ----------s-----------v~~Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~~~l~~~V~~~A~~Lv~~ 204 (565)
. .-.+-++..+|++.||+..+. .+|..+|-.|..-|+..-+.++.+.+|.+++.
T Consensus 96 L~~r~~~~~~~~~~~~~~~~~lk~~~ir~e~~ILr~LGF~~Hv-----~hPhklii~YLqtL~~~~~~~l~Q~~wNfmND 170 (367)
T KOG0835|consen 96 LEQRRESEAAEHLILARLYINLKMQVIRAERRILRELGFDVHV-----EHPHKLIIMYLQTLQLPPNLKLLQAAWNFMND 170 (367)
T ss_pred HHHHHhccCcchhhhhhHHhhhhhHHHHHHHHHHHHhCCeeee-----eccHHHHHHHHHHhcCCCchhHHHHHHHhhhh
Confidence 0 112456778999999999886 89999999999999733345679999999999
Q ss_pred hhhccccCCCChhHHHHHHHHHHHHhcCCCCC-HhHHHHHhccCHHHHH---HHHHHHHcc
Q 008455 205 MKRDWITTGRKPSGLCGAALYVSALTHGLKFS-KSDIVKIVHICEATLM---KRLIEFENT 261 (565)
Q Consensus 205 m~~~~l~~GR~P~~IaaAALylAar~~g~~~t-~~eIa~v~~Vse~TIr---kR~kE~~~t 261 (565)
..+..+..--.|.+||+||||||||..+++++ +...-.+++++...|. -++-.|+..
T Consensus 171 slRT~v~vry~pe~iACaciyLaAR~~eIpLp~~P~Wf~~Fd~~k~eid~ic~~l~~lY~~ 231 (367)
T KOG0835|consen 171 SLRTDVFVRYSPESIACACIYLAARNLEIPLPFQPHWFKAFDTTKREIDEICYRLIPLYKR 231 (367)
T ss_pred ccccceeeecCHHHHHHHHHHHHHhhhcCCCCCCccHHHHcCCcHHHHHHHHHHHHHHHHh
Confidence 99999999999999999999999999997753 5588888888876544 455555544
No 10
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=99.31 E-value=1e-11 Score=129.69 Aligned_cols=89 Identities=16% Similarity=0.227 Sum_probs=85.8
Q ss_pred HHHHHHHHHHHcCCCChhHHHHHHHHHHHHHHhCccccCCchhHHHHHHHHHHHHhcCCCccHHHHHhhhccChHHHHHH
Q 008455 74 AFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAV 153 (565)
Q Consensus 74 a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~p~tL~DIa~~~~vsv~~Lgr~ 153 (565)
...+|.++|+.|+|| ..+.+.|..+++.+.+.+++.||++..++|||||+|||.+|.|+|++||+++++|+..+|++.
T Consensus 219 p~~~i~r~~~~L~L~--~~v~~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g~~~t~keIa~v~~Vs~~tI~~~ 296 (310)
T PRK00423 219 PIDYVPRFASELGLS--GEVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERRTQREVAEVAGVTEVTVRNR 296 (310)
T ss_pred HHHHHHHHHHHcCCC--HHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHH
Confidence 468999999999999 999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhcc
Q 008455 154 YLQLCQVLYIA 164 (565)
Q Consensus 154 ~~~L~~~L~i~ 164 (565)
|+.|.+.|++.
T Consensus 297 ykel~~~l~~~ 307 (310)
T PRK00423 297 YKELAEKLDIK 307 (310)
T ss_pred HHHHHHHhCcc
Confidence 99999999864
No 11
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=99.24 E-value=3.5e-11 Score=125.00 Aligned_cols=158 Identities=20% Similarity=0.226 Sum_probs=130.0
Q ss_pred HHHHHHHHHHHHHcCCCChhHHHHHHHHHHHHHHhCccccCCchhHHHHHHHHHHHHhcCCCccHHHHHhhhc--cCh--
Q 008455 72 EKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLN--INV-- 147 (565)
Q Consensus 72 ~~a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~p~tL~DIa~~~~--vsv-- 147 (565)
..+...|.+++.+|++| ...+.+|+.||.+.+-...++.-.+..+|++|||+|++.++.|+.+.||..+.. .++
T Consensus 40 ~~~~~fI~elg~~L~~~--~~ti~tA~~~~hRFy~~~s~~~~~~~~vA~sclfLAgKvEetp~kl~dIi~~s~~~~~~~~ 117 (323)
T KOG0834|consen 40 QEGAKFIQELGVRLKMP--QKTIATAIVIFHRFYMFHSFKKFDPYTVAASCLFLAGKVEETPRKLEDIIKVSYRYLNPKD 117 (323)
T ss_pred HHHHHHHHHHHHHcCCC--ccchhhhhhhhhhhhhhcccccCcHHHHHHHHHHHHhhcccCcccHHHHHHHHHHHcCccc
Confidence 57899999999999999 899999999999999888888877889999999999999999999999988753 333
Q ss_pred HHHHHH-----------HHHHHHHhhccccccccccCCchhhHHHHHHhhCCCCC--HHHHHHHHHHHHHhhhccccCCC
Q 008455 148 YELGAV-----------YLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGN--KKVCDTARDILASMKRDWITTGR 214 (565)
Q Consensus 148 ~~Lgr~-----------~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~~~l~--~~V~~~A~~Lv~~m~~~~l~~GR 214 (565)
.++... -+.|+++|+++... -.|..|+.+++..|..+.+ ..++..|+.+++.....-+.---
T Consensus 118 ~~~~~~~~~~~~~Iv~~E~~lL~tl~Fdl~v-----~hPy~~ll~~~k~l~~~~~~~~~~a~~Aw~~~nD~~~t~~cL~y 192 (323)
T KOG0834|consen 118 LELEEVYWELKERIVQLELLLLETLGFDLNV-----EHPYKYLLKYLKKLKADENLKQPLAQAAWNFVNDSLRTTLCLQY 192 (323)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHccCceec-----cCchHHHHHHHHHhhhhhhccccHHHHHHHHhchhheeeeeEee
Confidence 233333 44556667766543 6799999999999964433 35899999999887776666668
Q ss_pred ChhHHHHHHHHHHHHhcCCCCC
Q 008455 215 KPSGLCGAALYVSALTHGLKFS 236 (565)
Q Consensus 215 ~P~~IaaAALylAar~~g~~~t 236 (565)
.|..||.||||||+.+.|+..+
T Consensus 193 ~p~~IAva~i~lA~~~~~~~~~ 214 (323)
T KOG0834|consen 193 SPHSIAVACIHLAAKLLGVELP 214 (323)
T ss_pred cCcEEEeehhhHHHHHcCCCCC
Confidence 9999999999999999998544
No 12
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=99.18 E-value=9.2e-12 Score=92.29 Aligned_cols=43 Identities=23% Similarity=0.524 Sum_probs=38.2
Q ss_pred CCCCCCCCCCceeccCCCceecCcccceecccccccccccccc
Q 008455 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATFVKN 44 (565)
Q Consensus 2 ~~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vlee~~id~~~ef~e~ 44 (565)
+.||+||+..+++|+.+|++||+.||.||+++.|+++++|+++
T Consensus 1 m~Cp~Cg~~~~~~D~~~g~~vC~~CG~Vl~e~~i~~~~e~r~f 43 (43)
T PF08271_consen 1 MKCPNCGSKEIVFDPERGELVCPNCGLVLEENIIDEGPEWREF 43 (43)
T ss_dssp ESBTTTSSSEEEEETTTTEEEETTT-BBEE-TTBSCCCSCCHC
T ss_pred CCCcCCcCCceEEcCCCCeEECCCCCCEeecccccCCcccccC
Confidence 4699999998999999999999999999999999999999863
No 13
>COG5333 CCL1 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]
Probab=99.06 E-value=1.5e-09 Score=110.62 Aligned_cols=158 Identities=18% Similarity=0.163 Sum_probs=133.2
Q ss_pred HHHHHHHHHHHHHcCCCChhHHHHHHHHHHHHHHhCccccCCchhHHHHHHHHHHHHhcCCCccHHHHHhhh--------
Q 008455 72 EKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYL-------- 143 (565)
Q Consensus 72 ~~a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~p~tL~DIa~~~-------- 143 (565)
..++..|..+|.+|+|| ..+..+|..+|++.+-++...+-....|+++|||+||+.+.+|+-+.-.+-..
T Consensus 46 i~~~k~i~~l~~~L~lp--~~~laTAi~~f~Rf~Lk~sv~e~~~~~vv~tcv~LA~K~ed~~~~I~i~~~~~~~~~se~~ 123 (297)
T COG5333 46 IYYLKLIMDLCTRLNLP--QTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPRDISIESFEARDLWSEEP 123 (297)
T ss_pred HHHHHHHHHHHHhcCCC--cchHHHHHHHHHHHHhhcccccccHHHHHHhheeeeeecccccchhhHHHHHhhccccccc
Confidence 45779999999999999 99999999999999999999999999999999999999999765443333322
Q ss_pred ccChHHHHHHHHHHHHHhhccccccccccCCchhhHHHHHHhhCCCCCHHHHHHHHHHHHHhhhccccCCCChhHHHHHH
Q 008455 144 NINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAA 223 (565)
Q Consensus 144 ~vsv~~Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~~~l~~~V~~~A~~Lv~~m~~~~l~~GR~P~~IaaAA 223 (565)
--+...|-..-..+++.|+.+... ..|..++..|...+......++.+.|+.++...-+..++-=-.|..||.||
T Consensus 124 ~~sr~~Il~~E~~lLEaL~fd~~V-----~hPy~~l~~f~~~~q~~~~~~~~~~aw~~inDa~~t~~~llypphiIA~a~ 198 (297)
T COG5333 124 KSSRERILEYEFELLEALDFDLHV-----HHPYKYLEGFLKDLQEKDKYKLLQIAWKIINDALRTDLCLLYPPHIIALAA 198 (297)
T ss_pred cccHHHHHHHHHHHHHHcccceEe-----ccccHHHHHHHHHHHhccHHHHHHHHHHHHHhhhhceeeeecChHHHHHHH
Confidence 246677888888899999988765 779999999998884222347999999999998888777778999999999
Q ss_pred HHHHHHhcCCCCC
Q 008455 224 LYVSALTHGLKFS 236 (565)
Q Consensus 224 LylAar~~g~~~t 236 (565)
|++|+...|.+.-
T Consensus 199 l~ia~~~~~~~~~ 211 (297)
T COG5333 199 LLIACEVLGMPII 211 (297)
T ss_pred HHHHHHhcCCccc
Confidence 9999999887653
No 14
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=98.98 E-value=1.9e-09 Score=110.81 Aligned_cols=91 Identities=18% Similarity=0.212 Sum_probs=87.1
Q ss_pred HHHHHHHHHHHHcCCCChhHHHHHHHHHHHHHHhCccccCCchhHHHHHHHHHHHHhcCCCccHHHHHhhhccChHHHHH
Q 008455 73 KAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGA 152 (565)
Q Consensus 73 ~a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~p~tL~DIa~~~~vsv~~Lgr 152 (565)
+...+|.++|+.|+|| +.+...|.++.+++...|.+-||++..++|||||+|++.+|.++|.++|+.+++|...+|..
T Consensus 193 ~p~~yi~rf~s~L~l~--~~v~~~a~ei~~~~~~~g~~~Gk~P~glAaaaiy~as~l~~~~~tq~eva~v~~vtevTIrn 270 (285)
T COG1405 193 DPSDYIPRFASKLGLS--DEVRRKAIEIVKKAKRAGLTAGKSPAGLAAAAIYLASLLLGERRTQKEVAKVAGVTEVTIRN 270 (285)
T ss_pred CHHHHHHHHHHHcCCC--HHHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhCCchHHHHHHHHhCCeeeHHHH
Confidence 3568999999999999 99999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhhccc
Q 008455 153 VYLQLCQVLYIAD 165 (565)
Q Consensus 153 ~~~~L~~~L~i~~ 165 (565)
.|+.|...+++..
T Consensus 271 rykel~~~~~i~~ 283 (285)
T COG1405 271 RYKELADALDIEV 283 (285)
T ss_pred HHHHHHHhhcccc
Confidence 9999999998753
No 15
>cd00043 CYCLIN Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain.
Probab=98.83 E-value=3.4e-08 Score=81.56 Aligned_cols=83 Identities=23% Similarity=0.257 Sum_probs=77.8
Q ss_pred HHHHHHHHHHHHcCCCChhHHHHHHHHHHHHHHhCccccCCchhHHHHHHHHHHHHhcCCCccHHHHHhhhcc-ChHHHH
Q 008455 73 KAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNI-NVYELG 151 (565)
Q Consensus 73 ~a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~p~tL~DIa~~~~v-sv~~Lg 151 (565)
.+...|.+++..++++ ..+...|..+++++...+...++++..+++||||+||+.++.|.++.+|..+++. +..+|.
T Consensus 4 ~~~~~l~~~~~~~~~~--~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~~~~~i~ 81 (88)
T cd00043 4 TPLDFLRRVAKALGLS--PETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEIPPWLKDLVHVTGYATEEEIL 81 (88)
T ss_pred hHHHHHHHHHHHcCCC--HHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCCCCCHHHHhHHhCCCCHHHHH
Confidence 4678899999999999 9999999999999999988899999999999999999999999999999999999 999998
Q ss_pred HHHHHH
Q 008455 152 AVYLQL 157 (565)
Q Consensus 152 r~~~~L 157 (565)
+.++.|
T Consensus 82 ~~e~~i 87 (88)
T cd00043 82 RMEKLL 87 (88)
T ss_pred HHHHHh
Confidence 887765
No 16
>cd00043 CYCLIN Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain.
Probab=98.82 E-value=2.9e-08 Score=81.95 Aligned_cols=84 Identities=23% Similarity=0.276 Sum_probs=79.3
Q ss_pred CCchhhHHHHHHhhCCCCCHHHHHHHHHHHHHhhhccccCCCChhHHHHHHHHHHHHhcCCCCCHhHHHHHhcc-CHHHH
Q 008455 173 VDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHI-CEATL 251 (565)
Q Consensus 173 vdP~~~I~Rf~~~L~~~l~~~V~~~A~~Lv~~m~~~~l~~GR~P~~IaaAALylAar~~g~~~t~~eIa~v~~V-se~TI 251 (565)
..|..||.+++..++ ++..+...|..+++++...+...|++|..||+||||+|+++.+...+.++++.+++. +..+|
T Consensus 3 ~~~~~~l~~~~~~~~--~~~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~~~~~i 80 (88)
T cd00043 3 PTPLDFLRRVAKALG--LSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEIPPWLKDLVHVTGYATEEEI 80 (88)
T ss_pred chHHHHHHHHHHHcC--CCHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCCCCCHHHHhHHhCCCCHHHH
Confidence 457889999999998 899999999999999988888899999999999999999999999999999999999 99999
Q ss_pred HHHHHHH
Q 008455 252 MKRLIEF 258 (565)
Q Consensus 252 rkR~kE~ 258 (565)
.+.+++|
T Consensus 81 ~~~e~~i 87 (88)
T cd00043 81 LRMEKLL 87 (88)
T ss_pred HHHHHHh
Confidence 9999876
No 17
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=98.80 E-value=2.1e-08 Score=101.39 Aligned_cols=88 Identities=13% Similarity=0.127 Sum_probs=84.0
Q ss_pred HHHHHHHHHHHHcCCCChhHHHHHHHHHHHHHHhCccccCCchhHHHHHHHHHHHHhcCCCccHHHHHhhhccChHHHHH
Q 008455 73 KAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGA 152 (565)
Q Consensus 73 ~a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~p~tL~DIa~~~~vsv~~Lgr 152 (565)
..-..|.++|+.|+|| .+++..|.++.+.+.+..+..||++..|+||.+||+|+....+++++||.+++||...+|..
T Consensus 202 ~t~~~m~RFCs~L~L~--~~~q~aA~e~a~ka~~~~~~~gRsPiSIAAa~IYmisqls~~kkt~keI~~vtgVaE~TIr~ 279 (308)
T KOG1597|consen 202 STGDFMPRFCSNLGLP--KSAQEAATEIAEKAEEMDIRAGRSPISIAAAAIYMISQLSDEKKTQKEIGEVTGVAEVTIRN 279 (308)
T ss_pred hHHHHHHHHHHhcCCC--HHHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHhccCcccHHHHHHHhhhhHHHHHH
Confidence 3568899999999999 99999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhh
Q 008455 153 VYLQLCQVLY 162 (565)
Q Consensus 153 ~~~~L~~~L~ 162 (565)
+|+.|...+.
T Consensus 280 sYK~Lyp~~~ 289 (308)
T KOG1597|consen 280 SYKDLYPHAD 289 (308)
T ss_pred HHHHHhhchh
Confidence 9999987765
No 18
>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma. A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.
Probab=98.79 E-value=3.7e-08 Score=80.55 Aligned_cols=81 Identities=20% Similarity=0.214 Sum_probs=74.4
Q ss_pred hhHHHHHHhhCCCCCHHHHHHHHHHHHHhhhccccCCCChhHHHHHHHHHHHHhcCCCCCHhHHHHHhcc-CHHHHHHHH
Q 008455 177 IFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHI-CEATLMKRL 255 (565)
Q Consensus 177 ~~I~Rf~~~L~~~l~~~V~~~A~~Lv~~m~~~~l~~GR~P~~IaaAALylAar~~g~~~t~~eIa~v~~V-se~TIrkR~ 255 (565)
.||.+++..++ +++++...|..+++++....-..+++|..||+||||+|+++.+.+++.++++..+++ ++.+|.+.+
T Consensus 1 ~~l~~~~~~~~--~~~~~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~~~~~i~~~~ 78 (83)
T smart00385 1 DFLRRVCKALN--LDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLAAKTEEIPPWTKELVHYTGYFTEEEILRME 78 (83)
T ss_pred CHHHHHHHHcC--CCHHHHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHhcCCCCchhHhHhhCCCCHHHHHHHH
Confidence 47899999998 899999999999999987544556999999999999999999999999999999999 999999999
Q ss_pred HHHH
Q 008455 256 IEFE 259 (565)
Q Consensus 256 kE~~ 259 (565)
++|.
T Consensus 79 ~~il 82 (83)
T smart00385 79 KLLL 82 (83)
T ss_pred HHHh
Confidence 9885
No 19
>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma. A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.
Probab=98.72 E-value=6.1e-08 Score=79.22 Aligned_cols=79 Identities=22% Similarity=0.270 Sum_probs=71.9
Q ss_pred HHHHHHHHcCCCChhHHHHHHHHHHHHHHh-CccccCCchhHHHHHHHHHHHHhcCCCccHHHHHhhhcc-ChHHHHHHH
Q 008455 77 DMRQMKNALNIGESDEIVHVAKRFYGIAVA-RNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNI-NVYELGAVY 154 (565)
Q Consensus 77 ~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~-~~~~rGR~~~~vaAACLYiACR~e~~p~tL~DIa~~~~v-sv~~Lgr~~ 154 (565)
.|.+++..++++ ..+...|..+++++.. .++.+ +++..++|||||+||+.++.+.+..++...+++ +..+|.+.+
T Consensus 2 ~l~~~~~~~~~~--~~~~~~a~~~~~~~l~~~~~~~-~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~~~~~i~~~~ 78 (83)
T smart00385 2 FLRRVCKALNLD--PETLNLAVNLLDRFLSDYKFLK-YSPSLIAAAALYLAAKTEEIPPWTKELVHYTGYFTEEEILRME 78 (83)
T ss_pred HHHHHHHHcCCC--HHHHHHHHHHHHHHHHHhhccc-CCHHHHHHHHHHHHHHHhcCCCCchhHhHhhCCCCHHHHHHHH
Confidence 578899999999 9999999999999988 45554 999999999999999999999999999999999 999999888
Q ss_pred HHHH
Q 008455 155 LQLC 158 (565)
Q Consensus 155 ~~L~ 158 (565)
+.|.
T Consensus 79 ~~il 82 (83)
T smart00385 79 KLLL 82 (83)
T ss_pred HHHh
Confidence 8764
No 20
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=98.71 E-value=2.2e-07 Score=91.14 Aligned_cols=176 Identities=15% Similarity=0.175 Sum_probs=126.2
Q ss_pred HHHHHHHHHHHcCCCChhHHHHHHHHHHHHHHhCccccCCchhHHHHHHHHHHHHhcCCCccH-HHH---Hhhh------
Q 008455 74 AFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLL-IDF---SNYL------ 143 (565)
Q Consensus 74 a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~p~tL-~DI---a~~~------ 143 (565)
..+.|+.++..|+|- +.++.+|..+|++.+-++..++-.+..+|+.|||+||+.+..|+.- +-+ +..+
T Consensus 44 ~~n~I~~lg~~lklR--Q~ViATAivY~rRfy~r~S~k~~~p~lla~TClyLAcKvEE~~i~~~r~l~~~a~~L~~~f~~ 121 (264)
T KOG0794|consen 44 MANVIQKLGQHLKLR--QRVIATAIVYFRRFYLRKSLKEIEPRLLAPTCLYLACKVEECPIVHIRLLVNEAKVLKTRFSY 121 (264)
T ss_pred HHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHhhhccCHHHHHHHHHHHHhhhhhcchHHHHHHHHHHHHHhhhccc
Confidence 458899999999999 9999999999999999988999999999999999999999998221 122 2222
Q ss_pred -----ccChHHHHHHHHHHHHHhhccccccccccCCchhhHHHHHHhhCCCCCHHHHHHHHHHHHHhhhccccCCCChhH
Q 008455 144 -----NINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSG 218 (565)
Q Consensus 144 -----~vsv~~Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~~~l~~~V~~~A~~Lv~~m~~~~l~~GR~P~~ 218 (565)
......|-..-..|...|+-=.- .-.|..-+..|...++- .+.+....++.|++..-+..++-=-.|.-
T Consensus 122 ~~e~~~~~~~~I~e~Ef~llE~Ld~~LI-----VhHPYrsL~q~~qd~gi-~d~~~l~~~W~ivNDSyr~Dl~Ll~PPh~ 195 (264)
T KOG0794|consen 122 WPEKFPYERKDILEMEFYLLEALDCYLI-----VHHPYRSLLQFVQDMGI-NDQKLLQLAWSIVNDSYRMDLCLLYPPHQ 195 (264)
T ss_pred chhhcCCCcCcchhhhhhHHhhhceeEE-----EecCCccHHHHHHHhcc-cchhhhhhhHhhhcchhhcceeeecCHHH
Confidence 11222333334445555552211 24566668888888751 36778899999999888877787899999
Q ss_pred HHHHHHHHHHHhcCCCCCHhHHHHHhccCHHHHHHHHHHH
Q 008455 219 LCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEF 258 (565)
Q Consensus 219 IaaAALylAar~~g~~~t~~eIa~v~~Vse~TIrkR~kE~ 258 (565)
||-||||+|+-..+...+ +..-..+.|--.-+.....+|
T Consensus 196 IalAcl~Ia~~~~~k~~~-~~w~~el~vD~ekV~~~v~~I 234 (264)
T KOG0794|consen 196 IALACLYIACVIDEKDIP-KAWFAELSVDMEKVKDIVQEI 234 (264)
T ss_pred HHHHHHHHHHhhcCCChH-HHHHHHHhccHHHHHHHHHHH
Confidence 999999999998887664 333333444444444444443
No 21
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning]
Probab=98.52 E-value=3.5e-06 Score=88.13 Aligned_cols=178 Identities=16% Similarity=0.209 Sum_probs=141.3
Q ss_pred HHHHHHHHHHHHHcCCCChhHHHHHHHHHHHHHHhC-ccccCC--chhHHHHHHHHHHHHhcCC--CccHHHHHhh--hc
Q 008455 72 EKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVAR-NFTKGR--RTEQVQASCLYLACRQKSK--PFLLIDFSNY--LN 144 (565)
Q Consensus 72 ~~a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~-~~~rGR--~~~~vaAACLYiACR~e~~--p~tL~DIa~~--~~ 144 (565)
..|...|-++|...+.. ..+.=-|++|+.+.+.- .+-+++ -.+.+++|||.+|.+.+.+ |.++--.... .-
T Consensus 79 ~~A~~WIl~V~~~~~~~--~~~~~LA~NYlDRFls~~~l~k~k~W~lQLlAvaCLsLAsKmeE~~vPll~dl~v~~~~~~ 156 (335)
T KOG0656|consen 79 KQALDWILKVCEEYNFE--PLVFLLAMNYLDRFLSSQKLPKDKPWMLQLLAVACLSLASKMEETDVPLLADLQVEYTDNV 156 (335)
T ss_pred HHHHHHHHHHHHHhCCc--hHHHHHHHHHHHHhhcccccCCCchHHHHHHHHHHHHHHHhhcCcCCchhhhhhhcccccc
Confidence 35889999999999999 89999999999998764 444443 2688999999999999876 6555444444 23
Q ss_pred cChHHHHHHHHHHHHHhhccccccccccCCchhhHHHHHHhhCC--CCCHHHHHHHHHHHHHhhhccccCCCChhHHHHH
Q 008455 145 INVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLP--GGNKKVCDTARDILASMKRDWITTGRKPSGLCGA 222 (565)
Q Consensus 145 vsv~~Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~~--~l~~~V~~~A~~Lv~~m~~~~l~~GR~P~~IaaA 222 (565)
+..++|.+.-+.++..|+-...+ +.|..||..|+.+++. ...+.+...+..++-....+.-..+-.|+.||||
T Consensus 157 feaktI~rmELLVLstL~Wrl~a-----VTP~sF~~~fl~ki~~~~~~~~~~~~~~s~~ll~~~~d~~Fl~y~pSviAaa 231 (335)
T KOG0656|consen 157 FEAKTIQRMELLVLSTLKWRLRA-----VTPFSFIDHFLSKISQKDHNKHLFLKHASLFLLSVITDIKFLEYPPSVIAAA 231 (335)
T ss_pred ccHHHHHHHHHHHHhhccccccC-----CCchHHHHHHHHHcCcccchHHHHHHHHHHHHHHHhhhhhhhcCChHHHHHH
Confidence 68899999999999999988876 9999999999999952 2356778888887777777777789999999999
Q ss_pred HHHHHHHh-cCCC--CCHhHHHHHhccCHHHHHHHHH
Q 008455 223 ALYVSALT-HGLK--FSKSDIVKIVHICEATLMKRLI 256 (565)
Q Consensus 223 ALylAar~-~g~~--~t~~eIa~v~~Vse~TIrkR~k 256 (565)
++..++.. .+.. .....+.....|+.-.+++.|.
T Consensus 232 ~~~~v~~~~~~l~~~~~~~~~~~~~~l~~e~~~~~~~ 268 (335)
T KOG0656|consen 232 AILSVSASVDGLDFREYENNLLSLLSLSKEKVNRCYD 268 (335)
T ss_pred HHHHHHHhhcchhhhhhhHHHHHHHHhhHHhhhcchh
Confidence 88766653 3433 2246667778888888888887
No 22
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=98.31 E-value=5.5e-07 Score=97.87 Aligned_cols=159 Identities=14% Similarity=0.173 Sum_probs=106.6
Q ss_pred HHHHHHHHcCCCC-hhHHHHHHHHHHHHHHhCccccCCchhHHHHHHHHHHHHhcCCCccHHHHHhhhccChHHHHHHHH
Q 008455 77 DMRQMKNALNIGE-SDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYL 155 (565)
Q Consensus 77 ~I~~ia~~L~Lp~-~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~p~tL~DIa~~~~vsv~~Lgr~~~ 155 (565)
+|.+++..|-..+ ...|+.+|.++...+..-....||++..++.||||||||.||+++++.||+.+.+|+..+|.+.|+
T Consensus 169 ~i~Rfa~~L~~g~~~~~Vv~~a~~L~~rMkrdwm~tGRRPsglcGAaLliAar~h~~~rsi~dIv~vvhV~e~Tl~kRl~ 248 (521)
T KOG1598|consen 169 YIVRFSCRLLFGDKTEDVAKTATRLAQRMKRDWMQTGRRPSGLCGAALLIAARMHGFRRTIGDIAKVVHVCESTLSKRLK 248 (521)
T ss_pred eeechhHhhhcCCchHHHHHHHHHHHHHHHHHHHHhCCCccchhHHHHHHHHHHcCccccHHHHHHHHHHhHHHHHHHHH
Confidence 4555666654432 134666666666665555677899999999999999999999999999999999999999999999
Q ss_pred HHHHHhhcccccc------ccccCCchhhHHHHH-HhhCCCCCHHHHHHHHHHHHHhhhccccCCCChhHHHHHHHHHHH
Q 008455 156 QLCQVLYIADESN------VLKQVDPSIFLHKFT-DRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSA 228 (565)
Q Consensus 156 ~L~~~L~i~~~~~------~~~~vdP~~~I~Rf~-~~L~~~l~~~V~~~A~~Lv~~m~~~~l~~GR~P~~IaaAALylAa 228 (565)
.+.+++..+.+.. ...-.||-.|-..=- .+-..+...+....-...+.-+...|..+++.+...+-++++.++
T Consensus 249 Ef~~T~s~~Lti~ef~~~d~e~~~~ppsft~~~~~~~k~~~~~k~~l~~~~~~~e~~~~~~~~~~~~~~~~~~~~l~~~~ 328 (521)
T KOG1598|consen 249 EFSDTLSGDLTIDELAEIDLEYESDPPSFTASPSKEAKYVEDKKKMLSRTMQLVELANETWLVTLRHSLPVITGGLFLAW 328 (521)
T ss_pred HHhccccccccHHHHHhhhhhhccCcchhhcccchhhhhhhhhhhhhhhhhhhhhcccchhhhccccCCcccchhhhccc
Confidence 9999876544320 111233333322110 000000122223333344555667899999999999999999888
Q ss_pred HhcCCCC
Q 008455 229 LTHGLKF 235 (565)
Q Consensus 229 r~~g~~~ 235 (565)
+-.....
T Consensus 329 q~~~~~~ 335 (521)
T KOG1598|consen 329 QDLQPRD 335 (521)
T ss_pred ccchhhh
Confidence 7554443
No 23
>KOG4557 consensus Origin recognition complex, subunit 6 [Replication, recombination and repair]
Probab=97.55 E-value=0.0026 Score=62.21 Aligned_cols=159 Identities=14% Similarity=0.162 Sum_probs=120.2
Q ss_pred HHHHHHHHcCCCChhHHHHHHHHHHHHHHhC--ccccCCchhHHHHHHHHHHHHhcCCCccHHHHHhhhccChHHHHHHH
Q 008455 77 DMRQMKNALNIGESDEIVHVAKRFYGIAVAR--NFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVY 154 (565)
Q Consensus 77 ~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~--~~~rGR~~~~vaAACLYiACR~e~~p~tL~DIa~~~~vsv~~Lgr~~ 154 (565)
.|.+++.+|||.....+++.|.+|.++..-+ +..-|-.-..-+.-|+=+|.-.-++|+--...-...|.+...-.+.|
T Consensus 2 lI~~l~~klgL~~ep~~lrKa~E~~RL~~~~~~~~~~~v~E~~kaV~CldlAa~~l~i~fDr~~avKLSGl~k~~Y~~~~ 81 (262)
T KOG4557|consen 2 LISDLGRKLGLDNEPLLLRKAAEIRRLCDAQFDSSIIGVGEICKAVICLDLAATRLQIIFDRQAAVKLSGLSKKAYSRSF 81 (262)
T ss_pred cHHHHHHhcCCccChHHHHHHHHHHHHHHhhccCccccccchhHHHHhHHHHHHHhcccccHHHHHHhccccHHHHHHHH
Confidence 4788999999955578999999999886433 33334444556668999998888999887777788899999999999
Q ss_pred HHHHHHhhccccccccccCCchhhHHHHHHhhCCCCCHHHHHHHHHHHHHhhhcc-----ccCC-CChhHHHHHHHHHHH
Q 008455 155 LQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDW-----ITTG-RKPSGLCGAALYVSA 228 (565)
Q Consensus 155 ~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~~~l~~~V~~~A~~Lv~~m~~~~-----l~~G-R~P~~IaaAALylAa 228 (565)
+.+-..||++... -|..+|-+|+ -.+|++.|..|+...+..- +-+. -+| -.++||+|+||
T Consensus 82 ~sfe~llgln~~~----------~VrdlaVQfg---c~evi~~a~~vl~syk~~lpaT~~~~~D~SrP-~ft~aA~~~ac 147 (262)
T KOG4557|consen 82 NSFENLLGLNIKL----------NVRDLAVQFG---CVEVIKSAQNVLSSYKERLPATRRANADFSRP-VFTAAAFYLAC 147 (262)
T ss_pred HHHHHHhcchhhc----------CHHHHHHHHh---HHHHHHHHHHHHHHHHhcCchhhhcCCcccch-HHHHHHHHHHH
Confidence 9999999987543 2556777775 4578888888888766421 1122 233 46789999999
Q ss_pred HhcCCCCCHhHHHHHhccCHH
Q 008455 229 LTHGLKFSKSDIVKIVHICEA 249 (565)
Q Consensus 229 r~~g~~~t~~eIa~v~~Vse~ 249 (565)
+....+++......+.|++++
T Consensus 148 k~lKlKVdK~kli~~sg~~~s 168 (262)
T KOG4557|consen 148 KKLKLKVDKLKLIEVSGTSES 168 (262)
T ss_pred HHHHHhhhHhhcccccCCCHH
Confidence 999999888888777777764
No 24
>PF00134 Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR006671 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. Cyclins contain two domains of similar all-alpha fold, of which this entry is associated with the N-terminal domain.; PDB: 2W2H_B 3RGF_B 1KXU_A 1JKW_A 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D ....
Probab=97.55 E-value=0.00095 Score=59.73 Aligned_cols=92 Identities=13% Similarity=0.243 Sum_probs=76.1
Q ss_pred HHHHHHHHHHHHHHcCCCChhHHHHHHHHHHHHHHhCccccCCchhHHHHHHHHHHHHhcCC-CccHHHHHhhhc--cCh
Q 008455 71 MEKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSK-PFLLIDFSNYLN--INV 147 (565)
Q Consensus 71 l~~a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~-p~tL~DIa~~~~--vsv 147 (565)
.......|..++..++++ ..+.-.|..+|.+..............++++|+|+||+.+.. +.++.++....+ .+.
T Consensus 31 r~~~~~~i~~~~~~~~l~--~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~e~~~~~~~~~~~~~~~~~~~ 108 (127)
T PF00134_consen 31 RQIIIDWIIELCQRLKLS--PETLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKMEEDNPPSISDLIRISDNTFTK 108 (127)
T ss_dssp HHHHHHHHHHHHHHTT-B--HHHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHHTSS--HHHHHHHHTTTSSHH
T ss_pred HHHHHHHHHHHHHhcccc--hhHHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhhccccchHHHHHHHHcCCCCH
Confidence 356778999999999999 999999999999999888777788889999999999999877 788888888773 678
Q ss_pred HHHHHHHHHHHHHhhcc
Q 008455 148 YELGAVYLQLCQVLYIA 164 (565)
Q Consensus 148 ~~Lgr~~~~L~~~L~i~ 164 (565)
.+|-..-..+...|+.+
T Consensus 109 ~~i~~~E~~iL~~L~f~ 125 (127)
T PF00134_consen 109 KDILEMEREILSALNFD 125 (127)
T ss_dssp HHHHHHHHHHHHHTTT-
T ss_pred HHHHHHHHHHHHHCCCC
Confidence 88888888888888764
No 25
>KOG2496 consensus Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell cycle control, cell division, chromosome partitioning; Transcription; Replication, recombination and repair]
Probab=97.47 E-value=0.0021 Score=65.98 Aligned_cols=147 Identities=18% Similarity=0.179 Sum_probs=96.6
Q ss_pred HHHHHHHc--CCCChhHHHHHHHHHHHHHHhCccccCCchhHHHHHHHHHHHHhcCCCccHHHHHhhhc----cChHHHH
Q 008455 78 MRQMKNAL--NIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLN----INVYELG 151 (565)
Q Consensus 78 I~~ia~~L--~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~p~tL~DIa~~~~----vsv~~Lg 151 (565)
+-++++.+ +|| .+|+-+|..+|++++=.+...--.+..+.++|+|+||+.+...+++-+|+.-.. -+...|-
T Consensus 63 l~~f~~k~~p~lp--~~Vv~TA~~fFkRffL~nsvme~~pk~I~~tc~flA~Kieef~ISieqFvkn~~~~~~k~~e~vL 140 (325)
T KOG2496|consen 63 LVNFYSKFKPNLP--TSVVSTAIEFFKRFFLENSVMEYSPKIIMATCFFLACKIEEFYISIEQFVKNMNGRKWKTHEIVL 140 (325)
T ss_pred HHHHHHHhcCCCc--hHHHHHHHHHHHHHHHhcchhhcChHHHHHHHHHHHhhhHhheecHHHHHhhccCcccccHHHHH
Confidence 33344444 789 999999999999999888888888999999999999999999999999998776 4555566
Q ss_pred HHHHHHHHHhhccccccccccCCc-hhhHHHHHHhhCCCCCHHHH-HHH--HHHHHHhhhccccCCCChhHHHHHHHHHH
Q 008455 152 AVYLQLCQVLYIADESNVLKQVDP-SIFLHKFTDRLLPGGNKKVC-DTA--RDILASMKRDWITTGRKPSGLCGAALYVS 227 (565)
Q Consensus 152 r~~~~L~~~L~i~~~~~~~~~vdP-~~~I~Rf~~~L~~~l~~~V~-~~A--~~Lv~~m~~~~l~~GR~P~~IaaAALylA 227 (565)
+--..|++.|...... ..+-.| +-|+..+-..|.+-.++... ... .+.++++.-....-=-.|+-||-|||+.|
T Consensus 141 k~E~~llqsL~f~L~v--h~PyRPleGFl~D~kt~l~~~~n~d~~~~~~d~~~fl~~~lltDa~lLytPsQIALaAil~a 218 (325)
T KOG2496|consen 141 KYEFLLLQSLKFSLTV--HNPYRPLEGFLLDMKTRLPALENPDILRKHDDSKKFLDRALLTDAYLLYTPSQIALAAILHA 218 (325)
T ss_pred hchHHHHHhhhhhhee--cCCCCchHHHHHHHHHHHHhccCHHHHhhhhhHHHHHHHHHHhccceecChHHHHHHHHHHH
Confidence 6666777777765432 011222 34444444444211233221 111 23344333222333478999999999544
Q ss_pred H
Q 008455 228 A 228 (565)
Q Consensus 228 a 228 (565)
+
T Consensus 219 ~ 219 (325)
T KOG2496|consen 219 A 219 (325)
T ss_pred h
Confidence 4
No 26
>KOG0653 consensus Cyclin B and related kinase-activating proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=97.33 E-value=0.0027 Score=68.84 Aligned_cols=153 Identities=14% Similarity=0.091 Sum_probs=121.1
Q ss_pred HHHHHHHHHHHcCCCChhHHHHHHHHHHHHHHhCccccCCchhHHHHHHHH-HHHHhcCC-CccHHHHHhhhc--cChHH
Q 008455 74 AFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLY-LACRQKSK-PFLLIDFSNYLN--INVYE 149 (565)
Q Consensus 74 a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLY-iACR~e~~-p~tL~DIa~~~~--vsv~~ 149 (565)
-.+.+-.+-..++|. ....-.|..++.+.+....+..++...|..+||+ |||+.+.. +-++.|+.-+.+ .+...
T Consensus 161 Lvdwlvevh~~F~L~--~ETL~LaVnliDRfL~~~~v~~~~lqLvgvsalf~IA~K~EE~~~P~v~dlv~isd~~~s~~~ 238 (391)
T KOG0653|consen 161 LVDWLVEVHEKFGLS--PETLYLAVNLIDRFLSKVKVPLKKLQLVGVSALLSIACKYEEISLPSVEDLVLITDGAYSREE 238 (391)
T ss_pred HHHHHHHhhhhcCcC--HHHHHHHHHHHHHHHHHhcccHHHhhHHhHHHHHHHHHhhhhccCCccceeEeeeCCccchHH
Confidence 347777888999999 8999999999999988766777888888888855 99996443 333667766654 68889
Q ss_pred HHHHHHHHHHHhhccccccccccCCchhhHHHHHHhhCCCCCHHHHHHHHHHHHHhhhccccCCCChhHHHHHHHHHHHH
Q 008455 150 LGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSAL 229 (565)
Q Consensus 150 Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~~~l~~~V~~~A~~Lv~~m~~~~l~~GR~P~~IaaAALylAar 229 (565)
|.+.-+.+...|+..... ..|..|+.||..... ........+..++....-+.-.....|+.++||+.+++.+
T Consensus 239 il~mE~~il~~L~f~l~~-----p~~~~FLrr~~ka~~--~d~~~~~~~k~~~El~l~d~~~~~~~~s~~aaa~~~~~~~ 311 (391)
T KOG0653|consen 239 ILRMEKYILNVLEFDLSV-----PTPLSFLRRFLKAAD--YDIKTRTLVKYLLELSLCDYSMLSIPPSSSAAASFTLALR 311 (391)
T ss_pred HHHHHHHHHhccCeeecC-----CchHHHHHHHHHhhh--cchhHHHHHHHHHHHHHhhhHHhccCcHHHHHHHHHHHHH
Confidence 999999999998876543 679999999998886 5556666666677766666656778999999999999999
Q ss_pred hcCCCC
Q 008455 230 THGLKF 235 (565)
Q Consensus 230 ~~g~~~ 235 (565)
+.+.+.
T Consensus 312 ~~~~~~ 317 (391)
T KOG0653|consen 312 MLSKGD 317 (391)
T ss_pred HhccCC
Confidence 987664
No 27
>PF01857 RB_B: Retinoblastoma-associated protein B domain; InterPro: IPR002719 Retinoblastoma-like and retinoblastoma-associated proteins may have a function in cell cycle regulation. They form a complex with adenovirus E1A and SV40 large T antigen, and may bind and modulate the function of certain cellular proteins with which T and E1A compete for pocket binding. The proteins may act as tumor suppressors, and are potent inhibitors of E2F-mediated trans-activation. This domain has the cyclin fold []. The crystal structure of the Rb pocket bound to a nine-residue E7 peptide containing the LxCxE motif, shared by other Rb-binding viral and cellular proteins, shows that the LxCxE peptide binds a highly conserved groove on the B-box portion of the pocket; the A-box portion (see IPR002720 from INTERPRO) appears to be required for the stable folding of the B box. Also highly conserved is the extensive A-B interface, suggesting that it may be an additional protein-binding site. The A and B boxes each contain the cyclin-fold structural motif, with the LxCxE-binding site on the B-box cyclin fold being similar to a Cdk2-binding site of cyclin A and to a TBP-binding site of TFIIB []. The A and B boxes are found at the C-terminal end of the protein; the B-box is on C-terminal side of the A-box.; GO: 0051726 regulation of cell cycle, 0005634 nucleus; PDB: 1GUX_B 3POM_A 1GH6_B 1N4M_A 1O9K_H 4ELL_B 2R7G_C 4ELJ_A.
Probab=97.29 E-value=0.0017 Score=60.05 Aligned_cols=84 Identities=12% Similarity=0.220 Sum_probs=65.4
Q ss_pred HHHHHHHHHHHHHHHcCCCChhHHHHHHHHHHHHHHhC--ccccCCchhHHHHHHHHHHHHhcCCCccHHHHHhhhccCh
Q 008455 70 LMEKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVAR--NFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINV 147 (565)
Q Consensus 70 ~l~~a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~--~~~rGR~~~~vaAACLYiACR~e~~p~tL~DIa~~~~vsv 147 (565)
.+.-|..+|+.+|+.|+|+ +.+.+....+|..++.. .++++|...+++-+|+|+.||..+.+++++||-....--+
T Consensus 10 vy~la~~Rl~~LC~~L~l~--~~~~~~iwt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~~~sF~~Ii~~Yr~qp 87 (135)
T PF01857_consen 10 VYKLAAVRLQDLCERLDLS--SDLREKIWTCFEHSLTHHTELMKDRHLDQIILCAIYGICKVSKEELSFKDIIKAYRKQP 87 (135)
T ss_dssp HHHHHHHHHHHHHHHHTTS--TTHHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHHHHHHHHTT-S--HHHHHHHHTTST
T ss_pred HHHHHHHHHHHHHHHcCCc--HHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhhcCCCCHHHHHHHHHhcc
Confidence 3445788999999999999 89999999999988753 5789999999999999999999999999999988776544
Q ss_pred HHHHHHHH
Q 008455 148 YELGAVYL 155 (565)
Q Consensus 148 ~~Lgr~~~ 155 (565)
..-..+|+
T Consensus 88 q~~~~Vyr 95 (135)
T PF01857_consen 88 QASSHVYR 95 (135)
T ss_dssp T--THHHH
T ss_pred cccccceE
Confidence 44444444
No 28
>PF02984 Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR004367 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This is the C-terminal domain of cyclins.; GO: 0005634 nucleus; PDB: 3QHR_D 3QHW_B 1W98_B 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D 2IW9_D ....
Probab=97.09 E-value=0.0014 Score=57.50 Aligned_cols=86 Identities=19% Similarity=0.162 Sum_probs=68.0
Q ss_pred CchhhHHHHHHhhCCCCCHHHHHHHHHHHHHhhhccccCCCChhHHHHHHHHHHHHhcCC-CCCHhHHHHHhccCHHHHH
Q 008455 174 DPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGL-KFSKSDIVKIVHICEATLM 252 (565)
Q Consensus 174 dP~~~I~Rf~~~L~~~l~~~V~~~A~~Lv~~m~~~~l~~GR~P~~IaaAALylAar~~g~-~~t~~eIa~v~~Vse~TIr 252 (565)
.|..||.+|....+ .+..+...|..|++.+..+.-..+-+|+.||+||+|+|....+. ..-...+...+|+....|+
T Consensus 2 Tp~~Fl~~~~~~~~--~~~~~~~~a~~l~el~l~~~~fl~~~PS~iAaAai~lA~~~~~~~~~~~~~l~~~t~~~~~~l~ 79 (118)
T PF02984_consen 2 TPYDFLRRFLKISN--ADQEVRNLARYLLELSLLDYEFLQYPPSVIAAAAILLARKILGKEPPWPESLEKLTGYDKEDLK 79 (118)
T ss_dssp -HHHHHHHHHTSSS--HHHHHHHHHHHHHHHHHHSHHHTTS-HHHHHHHHHHHHHHHHHSSTCSHHHHHHHHTS-HHHHH
T ss_pred cHHHHHHHHHHHcC--CcHHHHHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhCccccCCccchhhcCCCHHHHH
Confidence 37889999944333 46789999999999888787788999999999999999999875 3445668888899999999
Q ss_pred HHHHHHHcc
Q 008455 253 KRLIEFENT 261 (565)
Q Consensus 253 kR~kE~~~t 261 (565)
..++.|.+.
T Consensus 80 ~c~~~i~~~ 88 (118)
T PF02984_consen 80 ECIELIQEL 88 (118)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHH
Confidence 988888743
No 29
>COG5024 Cyclin [Cell division and chromosome partitioning]
Probab=96.64 E-value=0.012 Score=64.33 Aligned_cols=148 Identities=14% Similarity=0.054 Sum_probs=110.8
Q ss_pred HHHHHHHHHcCCCChhHHHHHHHHHHHHHHhCccccCCchhHHHHHHHHHHHHhcCC-CccHHHHHhhhc--cChHHHHH
Q 008455 76 DDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSK-PFLLIDFSNYLN--INVYELGA 152 (565)
Q Consensus 76 ~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~-p~tL~DIa~~~~--vsv~~Lgr 152 (565)
+.|.++=..+++- ......|..|..+.+..+.+.=-+...|.+.||+|||+.+.+ +-++.++.-++. .+...|.+
T Consensus 218 ~wlvevH~~F~ll--peTL~lainiiDrfLs~~~v~l~k~QLvg~s~LfIa~K~EE~~~p~i~~l~~~t~g~~t~~~i~~ 295 (440)
T COG5024 218 DWLVEVHGKFGLL--PETLFLAINIIDRFLSSRVVSLEKYQLVGISALFIASKYEEVNCPSIKDLVYATDGAFTRDDIIR 295 (440)
T ss_pred HHHHHhccccccc--chHHHHHHHHHHHHhccCcccHHHHHHHHHHHHHHHHhHhHhcCHHHHHHHHHHcccccHHHHHH
Confidence 5566677788888 788999999999999888777777889999999999998865 445788888774 78999999
Q ss_pred HHHHHHHHhhccccccccccCCchhhHHHHHHhhCCCCCHHHHHHHHHHHHHhhhc-cccCCCChhHHHHHHHHHHHHhc
Q 008455 153 VYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRD-WITTGRKPSGLCGAALYVSALTH 231 (565)
Q Consensus 153 ~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~~~l~~~V~~~A~~Lv~~m~~~-~l~~GR~P~~IaaAALylAar~~ 231 (565)
+.+.+...|+.++-. ..|..|+.|+..... ........+..++....-+ .+...+ |+.+++||-|++-.+.
T Consensus 296 aE~~ml~~l~f~is~-----P~P~sFLRriSka~d--yd~~srt~~k~~~e~s~~~~~f~~~~-~S~~~aaa~~~s~~~~ 367 (440)
T COG5024 296 AERYMLEVLDFNISW-----PSPMSFLRRISKASD--YDIFSRTPAKFSSEISPVDYKFIQIS-PSWCAAAAMYLSRKIL 367 (440)
T ss_pred HHHHHhhhcccccCC-----CChHHHHHHHHhhcc--cchhhhhhHhhhCCchHhhhhhccCC-chHHHHHHHHHHHhhh
Confidence 999999999987543 679999888876654 3333333344433332222 233445 9999999999998887
Q ss_pred CC
Q 008455 232 GL 233 (565)
Q Consensus 232 g~ 233 (565)
+-
T Consensus 368 ~~ 369 (440)
T COG5024 368 SQ 369 (440)
T ss_pred cc
Confidence 54
No 30
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=96.26 E-value=0.0025 Score=45.47 Aligned_cols=27 Identities=33% Similarity=0.637 Sum_probs=23.3
Q ss_pred CCCCCCCCCceeccCCCceecCcccceec
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vle 31 (565)
.|+.||+. .+...+|..+|..||+|++
T Consensus 10 ~C~~C~~~--~~~~~dG~~yC~~cG~~~E 36 (36)
T PF11781_consen 10 PCPVCGSR--WFYSDDGFYYCDRCGHQSE 36 (36)
T ss_pred cCCCCCCe--EeEccCCEEEhhhCceEcC
Confidence 49999998 5667799999999999975
No 31
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=96.21 E-value=0.07 Score=47.81 Aligned_cols=55 Identities=11% Similarity=0.037 Sum_probs=44.0
Q ss_pred cHHHHHhhhccChHHHHHHHHHHHHHhhccccccccccCCchhhHHHHHHhh-CCCCCHH
Q 008455 135 LLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRL-LPGGNKK 193 (565)
Q Consensus 135 tL~DIa~~~~vsv~~Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L-~~~l~~~ 193 (565)
+|++++..+||+.-+++..+..|.+.|+....+ ..........+.++| .|+++.+
T Consensus 51 nlKe~e~~lgiSYPTvR~rLd~ii~~lg~~~~~----~~~~~~~~~~IL~~L~~GeIs~e 106 (113)
T PF09862_consen 51 NLKEMEKELGISYPTVRNRLDKIIEKLGYEEDE----EEEEEDERKEILDKLEKGEISVE 106 (113)
T ss_pred CHHHHHHHHCCCcHHHHHHHHHHHHHhCCCCCc----ccccchhHHHHHHHHHcCCCCHH
Confidence 689999999999999999999999999983322 144567788888888 5667765
No 32
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=95.80 E-value=0.056 Score=56.29 Aligned_cols=105 Identities=16% Similarity=0.284 Sum_probs=77.9
Q ss_pred HHHHHHHHHHHcCCCChhHHHHHHHHHHHHHHhCccccCCchhHHHHHHHHHHHHhcCCCccHH-HHHhhhccChHHHHH
Q 008455 74 AFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLI-DFSNYLNINVYELGA 152 (565)
Q Consensus 74 a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~p~tL~-DIa~~~~vsv~~Lgr 152 (565)
-.+.|-.+.+-|++|++..+...+.+|....+.-.+..--+++.||+||+|+|.|..++|++.. .--.+++++..+|-.
T Consensus 141 Phklii~YLqtL~~~~~~~l~Q~~wNfmNDslRT~v~vry~pe~iACaciyLaAR~~eIpLp~~P~Wf~~Fd~~k~eid~ 220 (367)
T KOG0835|consen 141 PHKLIIMYLQTLQLPPNLKLLQAAWNFMNDSLRTDVFVRYSPESIACACIYLAARNLEIPLPFQPHWFKAFDTTKREIDE 220 (367)
T ss_pred cHHHHHHHHHHhcCCCchhHHHHHHHhhhhccccceeeecCHHHHHHHHHHHHHhhhcCCCCCCccHHHHcCCcHHHHHH
Confidence 3456777888999996566788888888888777766667899999999999999999887654 555667788888877
Q ss_pred HHHHHHHHhhccccccccccCCchhhHHHHHHhh
Q 008455 153 VYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRL 186 (565)
Q Consensus 153 ~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L 186 (565)
...++........ | -..+|.-|++.+
T Consensus 221 ic~~l~~lY~~~~-p-------~~~li~~~vd~~ 246 (367)
T KOG0835|consen 221 ICYRLIPLYKRAK-P-------DETLIEAFVDRL 246 (367)
T ss_pred HHHHHHHHHHhcc-c-------CHHHHHHHHHHh
Confidence 7777666554421 1 245677777666
No 33
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=94.77 E-value=0.015 Score=45.95 Aligned_cols=31 Identities=26% Similarity=0.541 Sum_probs=28.6
Q ss_pred CCCCCCCCCCceeccCCCceecCcccceecc
Q 008455 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (565)
Q Consensus 2 ~~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vlee 32 (565)
++||.|+...+++++++-.+.|..||.+|-+
T Consensus 12 VkCp~C~n~q~vFsha~t~V~C~~Cg~~L~~ 42 (59)
T PRK00415 12 VKCPDCGNEQVVFSHASTVVRCLVCGKTLAE 42 (59)
T ss_pred EECCCCCCeEEEEecCCcEEECcccCCCccc
Confidence 3799999999999999999999999999864
No 34
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=94.73 E-value=0.016 Score=46.56 Aligned_cols=31 Identities=23% Similarity=0.521 Sum_probs=28.6
Q ss_pred CCCCCCCCCCceeccCCCceecCcccceecc
Q 008455 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (565)
Q Consensus 2 ~~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vlee 32 (565)
+.||.||...+++++..-.+.|..||.+|-+
T Consensus 20 VkCpdC~N~q~vFshast~V~C~~CG~~l~~ 50 (67)
T COG2051 20 VKCPDCGNEQVVFSHASTVVTCLICGTTLAE 50 (67)
T ss_pred EECCCCCCEEEEeccCceEEEecccccEEEe
Confidence 4799999999999999999999999999874
No 35
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 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 [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=94.61 E-value=0.016 Score=45.21 Aligned_cols=31 Identities=29% Similarity=0.503 Sum_probs=23.7
Q ss_pred CCCCCCCCCCceeccCCCceecCcccceecc
Q 008455 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (565)
Q Consensus 2 ~~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vlee 32 (565)
+.||.|+...++++++.-.+.|..||+||-+
T Consensus 8 VkCp~C~~~q~vFSha~t~V~C~~Cg~~L~~ 38 (55)
T PF01667_consen 8 VKCPGCYNIQTVFSHAQTVVKCVVCGTVLAQ 38 (55)
T ss_dssp EE-TTT-SEEEEETT-SS-EE-SSSTSEEEE
T ss_pred EECCCCCCeeEEEecCCeEEEcccCCCEecC
Confidence 4799999999999999999999999999964
No 36
>KOG0655 consensus G1/S-specific cyclin E [Cell cycle control, cell division, chromosome partitioning]
Probab=94.19 E-value=0.61 Score=48.91 Aligned_cols=170 Identities=12% Similarity=0.085 Sum_probs=108.8
Q ss_pred HHHHHHHHHHHcCCCChhHHHHHHHHHHHHHHhCcc-ccCCchhHHHHHHHHHHHHhcCC-CccHHHHHhhhc--cChHH
Q 008455 74 AFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNF-TKGRRTEQVQASCLYLACRQKSK-PFLLIDFSNYLN--INVYE 149 (565)
Q Consensus 74 a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~-~rGR~~~~vaAACLYiACR~e~~-p~tL~DIa~~~~--vsv~~ 149 (565)
-.+.+-.+|.--.|. ....-.|..||.+.+.-.. ...-....+--+|||||.+.+.+ |--++|||-++. ++...
T Consensus 148 LlDWlmEVCEvykLH--RETFyLAvDy~DRyl~t~~~v~kt~lQLIGitsLFIAAK~EEIYpPKl~eFAyvTDgAcs~dd 225 (408)
T KOG0655|consen 148 LLDWLMEVCEVYKLH--RETFYLAVDYFDRYLETQVEVSKTNLQLIGITSLFIAAKLEEIYPPKLIEFAYVTDGACSEDD 225 (408)
T ss_pred HHHHHHHHHHHHHHh--hhHHHHHHHHHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHhhccCccccceeeeccCccchHH
Confidence 357888899999999 8888999999988764321 12223345556999999998765 888999999985 78899
Q ss_pred HHHHHHHHHHHhhccccccccccCCchhhHHHHHHhhC-CCC--------CH-HHHHHHHHHHHHhhhccccCCCChhHH
Q 008455 150 LGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLL-PGG--------NK-KVCDTARDILASMKRDWITTGRKPSGL 219 (565)
Q Consensus 150 Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~-~~l--------~~-~V~~~A~~Lv~~m~~~~l~~GR~P~~I 219 (565)
|...-+.|++.|+...-| +..-.++.-|..-+. ++. +. ..++.| .|+....-+.=.---.-..|
T Consensus 226 IltmE~iilkal~W~l~P-----iTii~WL~vylQv~~~n~~~k~l~Pq~~~~efiqia-qlLDlc~ldids~~fsYril 299 (408)
T KOG0655|consen 226 ILTMELIILKALKWELSP-----ITIISWLNVYLQVDALNDAPKVLLPQYSQEEFIQIA-QLLDLCILDIDSLEFSYRIL 299 (408)
T ss_pred HHHHHHHHHHHhcccccc-----eehHHHHHHHHHHHhcCCCCceeccccchHHHHHHH-HHHHHHHhccccccchHHHH
Confidence 999999999999987766 444555555554442 221 11 222222 23333221111122556677
Q ss_pred HHHHHHHHHHhcCCCCCHhHHHHHhccCHHHHHHHHHHH
Q 008455 220 CGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEF 258 (565)
Q Consensus 220 aaAALylAar~~g~~~t~~eIa~v~~Vse~TIrkR~kE~ 258 (565)
||||||.-. +..-+-++.|.--..|.++.+=+
T Consensus 300 aAAal~h~~-------s~e~v~kaSG~~w~~ie~cv~wm 331 (408)
T KOG0655|consen 300 AAAALCHFT-------SIEVVKKASGLEWDSIEECVDWM 331 (408)
T ss_pred HHHHHHHHh-------HHHHHHHcccccHHHHHHHHHHH
Confidence 888877422 12223355667677777765533
No 37
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=94.16 E-value=0.029 Score=43.68 Aligned_cols=31 Identities=29% Similarity=0.632 Sum_probs=23.1
Q ss_pred CCCCCCCCCCCceeccCCC-ceecCcccceec
Q 008455 1 MVWCSSCARHVTGHRPYDS-QLCCDRCGKVLE 31 (565)
Q Consensus 1 M~~Cp~Cgs~~i~~D~~~G-~~VCt~CG~Vle 31 (565)
|..||.||...-+.+...| .+.|..||.-++
T Consensus 2 ~~~CP~CG~~iev~~~~~GeiV~Cp~CGaele 33 (54)
T TIGR01206 2 QFECPDCGAEIELENPELGELVICDECGAELE 33 (54)
T ss_pred ccCCCCCCCEEecCCCccCCEEeCCCCCCEEE
Confidence 4589999997444444445 677999999987
No 38
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 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. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=94.03 E-value=0.03 Score=39.70 Aligned_cols=31 Identities=19% Similarity=0.574 Sum_probs=20.4
Q ss_pred CCCCCCCCCCCceeccCCCceecCcccceec
Q 008455 1 MVWCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (565)
Q Consensus 1 M~~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vle 31 (565)
|..||.||.-........+..+|..||++.+
T Consensus 1 m~FCp~C~nlL~p~~~~~~~~~C~~C~Y~~~ 31 (35)
T PF02150_consen 1 MRFCPECGNLLYPKEDKEKRVACRTCGYEEP 31 (35)
T ss_dssp --BETTTTSBEEEEEETTTTEEESSSS-EEE
T ss_pred CeeCCCCCccceEcCCCccCcCCCCCCCccC
Confidence 7789999987544444455558999999854
No 39
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=94.02 E-value=0.028 Score=37.08 Aligned_cols=24 Identities=21% Similarity=0.670 Sum_probs=18.6
Q ss_pred CCCCCCCCCCCceeccCCCceecCcccce
Q 008455 1 MVWCSSCARHVTGHRPYDSQLCCDRCGKV 29 (565)
Q Consensus 1 M~~Cp~Cgs~~i~~D~~~G~~VCt~CG~V 29 (565)
++.||+||.. + ..+..+|..||.=
T Consensus 2 ~~~Cp~Cg~~-~----~~~~~fC~~CG~~ 25 (26)
T PF13248_consen 2 EMFCPNCGAE-I----DPDAKFCPNCGAK 25 (26)
T ss_pred cCCCcccCCc-C----CcccccChhhCCC
Confidence 4589999984 2 3578899999973
No 40
>PLN00209 ribosomal protein S27; Provisional
Probab=93.82 E-value=0.034 Score=47.04 Aligned_cols=31 Identities=26% Similarity=0.487 Sum_probs=28.7
Q ss_pred CCCCCCCCCCceeccCCCceecCcccceecc
Q 008455 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (565)
Q Consensus 2 ~~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vlee 32 (565)
+.||.|+...+++.++.-.+.|..||++|-+
T Consensus 37 VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~ 67 (86)
T PLN00209 37 VKCQGCFNITTVFSHSQTVVVCGSCQTVLCQ 67 (86)
T ss_pred EECCCCCCeeEEEecCceEEEccccCCEeec
Confidence 4799999999999999999999999999964
No 41
>PF02984 Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR004367 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This is the C-terminal domain of cyclins.; GO: 0005634 nucleus; PDB: 3QHR_D 3QHW_B 1W98_B 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D 2IW9_D ....
Probab=93.78 E-value=0.32 Score=42.46 Aligned_cols=86 Identities=14% Similarity=0.150 Sum_probs=62.6
Q ss_pred HHHHHHHHHHcCCCChhHHHHHHHHHHHHHHhCccccCCchhHHHHHHHHHHHHhcCC-CccHHHHHhhhccChHHHHHH
Q 008455 75 FDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSK-PFLLIDFSNYLNINVYELGAV 153 (565)
Q Consensus 75 ~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~-p~tL~DIa~~~~vsv~~Lgr~ 153 (565)
+..|+.+....+.. ..+...|.-+...+.-...+-+-++..+||||+|+|.+..+. +.--..+...++++...|...
T Consensus 4 ~~Fl~~~~~~~~~~--~~~~~~a~~l~el~l~~~~fl~~~PS~iAaAai~lA~~~~~~~~~~~~~l~~~t~~~~~~l~~c 81 (118)
T PF02984_consen 4 YDFLRRFLKISNAD--QEVRNLARYLLELSLLDYEFLQYPPSVIAAAAILLARKILGKEPPWPESLEKLTGYDKEDLKEC 81 (118)
T ss_dssp HHHHHHHHTSSSHH--HHHHHHHHHHHHHHHHSHHHTTS-HHHHHHHHHHHHHHHHHSSTCSHHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHHHHcCCc--HHHHHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhCccccCCccchhhcCCCHHHHHHH
Confidence 45566664434444 678888888888866544455577889999999999998765 444566777889999999999
Q ss_pred HHHHHHHhh
Q 008455 154 YLQLCQVLY 162 (565)
Q Consensus 154 ~~~L~~~L~ 162 (565)
+..|...+.
T Consensus 82 ~~~i~~~~~ 90 (118)
T PF02984_consen 82 IELIQELLS 90 (118)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHH
Confidence 999888775
No 42
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=93.76 E-value=0.033 Score=35.76 Aligned_cols=22 Identities=27% Similarity=0.889 Sum_probs=17.6
Q ss_pred CCCCCCCCCceeccCCCceecCcccce
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGKV 29 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~V 29 (565)
+||+||... ..+..+|..||+-
T Consensus 1 ~Cp~CG~~~-----~~~~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAEI-----EDDAKFCPNCGTP 22 (23)
T ss_pred CCcccCCCC-----CCcCcchhhhCCc
Confidence 599999873 2577799999974
No 43
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=93.75 E-value=0.028 Score=39.60 Aligned_cols=28 Identities=21% Similarity=0.634 Sum_probs=15.8
Q ss_pred CCCCCCCCCc---eeccCCCceecCccccee
Q 008455 3 WCSSCARHVT---GHRPYDSQLCCDRCGKVL 30 (565)
Q Consensus 3 ~Cp~Cgs~~i---~~D~~~G~~VCt~CG~Vl 30 (565)
.||.||+... ......--.||+.||.|-
T Consensus 2 fC~~CG~~l~~~ip~gd~r~R~vC~~Cg~Ih 32 (34)
T PF14803_consen 2 FCPQCGGPLERRIPEGDDRERLVCPACGFIH 32 (34)
T ss_dssp B-TTT--B-EEE--TT-SS-EEEETTTTEEE
T ss_pred ccccccChhhhhcCCCCCccceECCCCCCEE
Confidence 6999999822 122345678999999983
No 44
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=93.65 E-value=0.039 Score=46.57 Aligned_cols=31 Identities=23% Similarity=0.473 Sum_probs=28.8
Q ss_pred CCCCCCCCCCceeccCCCceecCcccceecc
Q 008455 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (565)
Q Consensus 2 ~~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vlee 32 (565)
+.||.|+...+++.++.-.+.|..||++|-+
T Consensus 36 VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~ 66 (85)
T PTZ00083 36 VKCPGCSQITTVFSHAQTVVLCGGCSSQLCQ 66 (85)
T ss_pred EECCCCCCeeEEEecCceEEEccccCCEeec
Confidence 4799999999999999999999999999964
No 45
>PRK00420 hypothetical protein; Validated
Probab=93.63 E-value=0.047 Score=48.86 Aligned_cols=27 Identities=26% Similarity=0.492 Sum_probs=22.0
Q ss_pred CCCCCCCCCceeccCCCceecCcccceec
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vle 31 (565)
.||.||...+. ..+|..+|..||.++.
T Consensus 25 ~CP~Cg~pLf~--lk~g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 25 HCPVCGLPLFE--LKDGEVVCPVHGKVYI 51 (112)
T ss_pred CCCCCCCccee--cCCCceECCCCCCeee
Confidence 69999977443 2689999999999865
No 46
>PF00134 Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR006671 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. Cyclins contain two domains of similar all-alpha fold, of which this entry is associated with the N-terminal domain.; PDB: 2W2H_B 3RGF_B 1KXU_A 1JKW_A 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D ....
Probab=93.37 E-value=0.27 Score=43.72 Aligned_cols=67 Identities=15% Similarity=0.095 Sum_probs=51.5
Q ss_pred hhhHHHHHHhhCCCCCHHHHHHHHHHHHHhhhccccCCCChhHHHHHHHHHHHHhcCC-CCCHhHHHHHh
Q 008455 176 SIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGL-KFSKSDIVKIV 244 (565)
Q Consensus 176 ~~~I~Rf~~~L~~~l~~~V~~~A~~Lv~~m~~~~l~~GR~P~~IaaAALylAar~~g~-~~t~~eIa~v~ 244 (565)
..||...+..+. +++.+.-.|..+++++..........+.-|++||+++|+++.+. ..+..+++...
T Consensus 35 ~~~i~~~~~~~~--l~~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~e~~~~~~~~~~~~~ 102 (127)
T PF00134_consen 35 IDWIIELCQRLK--LSPETLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKMEEDNPPSISDLIRIS 102 (127)
T ss_dssp HHHHHHHHHHTT---BHHHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHHTSS--HHHHHHHHT
T ss_pred HHHHHHHHHhcc--cchhHHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhhccccchHHHHHHHH
Confidence 456777788887 89999999999999987666677899999999999999998877 34455555443
No 47
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=93.35 E-value=0.06 Score=37.68 Aligned_cols=27 Identities=26% Similarity=0.465 Sum_probs=22.6
Q ss_pred CCCCCCCCCceeccCCCceecCccccee
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vl 30 (565)
.|+.||+..++. ..++..+|..||.+-
T Consensus 5 ~C~~C~~~~i~~-~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 5 KCSKCGGNGIVN-KEDDYEVCIFCGSSF 31 (33)
T ss_pred EcCCCCCCeEEE-ecCCeEEcccCCcEe
Confidence 699999987653 568999999999874
No 48
>PHA00626 hypothetical protein
Probab=93.31 E-value=0.061 Score=41.82 Aligned_cols=30 Identities=17% Similarity=0.465 Sum_probs=22.5
Q ss_pred CCCCCCCCCCceec----cCCCceecCcccceec
Q 008455 2 VWCSSCARHVTGHR----PYDSQLCCDRCGKVLE 31 (565)
Q Consensus 2 ~~Cp~Cgs~~i~~D----~~~G~~VCt~CG~Vle 31 (565)
+.||.||+..++.. --+..++|.+||.-..
T Consensus 1 m~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft 34 (59)
T PHA00626 1 MSCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDS 34 (59)
T ss_pred CCCCCCCCceeeeeceecccCcceEcCCCCCeec
Confidence 46999999766542 2268999999998644
No 49
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=92.75 E-value=0.061 Score=38.41 Aligned_cols=30 Identities=20% Similarity=0.576 Sum_probs=21.0
Q ss_pred CCCCCCCCCCcee-c---cCCCceecCcccceec
Q 008455 2 VWCSSCARHVTGH-R---PYDSQLCCDRCGKVLE 31 (565)
Q Consensus 2 ~~Cp~Cgs~~i~~-D---~~~G~~VCt~CG~Vle 31 (565)
..||+||...-+. + ...+.+.|..||.++.
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEE
Confidence 4799999862222 2 2345799999999875
No 50
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=92.52 E-value=0.52 Score=49.50 Aligned_cols=69 Identities=13% Similarity=0.089 Sum_probs=54.7
Q ss_pred hhHHHHHHhhCCCCCHHHHHHHHHHHHHhhhccccCCCChhHHHHHHHHHHHHhcCCCCCHhHHHHHhc
Q 008455 177 IFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVH 245 (565)
Q Consensus 177 ~~I~Rf~~~L~~~l~~~V~~~A~~Lv~~m~~~~l~~GR~P~~IaaAALylAar~~g~~~t~~eIa~v~~ 245 (565)
.+|..++..|..-+++.|+-+|.-+.+++--.+-+.--.|.-|+++||||||..-.+.+++.+++..+.
T Consensus 61 ~~i~~~~~~lkp~Lpq~viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE~~~si~~fv~~~~ 129 (305)
T TIGR00569 61 KRLLDFCSAFKPTMPTSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFVGNLK 129 (305)
T ss_pred HHHHHHHHHhcCCCCchHHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccccCcCHHHHHhhcc
Confidence 345566666643378999999999998875555455689999999999999999999999988887543
No 51
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=92.26 E-value=0.11 Score=35.64 Aligned_cols=28 Identities=25% Similarity=0.531 Sum_probs=15.1
Q ss_pred CCCCCCCCCCCceeccCCCceecCccccee
Q 008455 1 MVWCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (565)
Q Consensus 1 M~~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vl 30 (565)
+..||.|++...-. +...+||..||.-.
T Consensus 2 ~p~Cp~C~se~~y~--D~~~~vCp~C~~ew 29 (30)
T PF08274_consen 2 LPKCPLCGSEYTYE--DGELLVCPECGHEW 29 (30)
T ss_dssp S---TTT-----EE---SSSEEETTTTEEE
T ss_pred CCCCCCCCCcceec--cCCEEeCCcccccC
Confidence 45899999985544 46799999999753
No 52
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=92.14 E-value=0.085 Score=48.31 Aligned_cols=23 Identities=26% Similarity=0.739 Sum_probs=19.9
Q ss_pred CCCCCCCCCceeccCCCceecCcccc
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGK 28 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~ 28 (565)
.||.||...+. .+|.++|..||+
T Consensus 30 hCp~Cg~PLF~---KdG~v~CPvC~~ 52 (131)
T COG1645 30 HCPKCGTPLFR---KDGEVFCPVCGY 52 (131)
T ss_pred hCcccCCccee---eCCeEECCCCCc
Confidence 69999998654 689999999994
No 53
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=91.24 E-value=1.7 Score=34.88 Aligned_cols=75 Identities=16% Similarity=0.207 Sum_probs=50.7
Q ss_pred CccHHHHHhhhccChHHHHHHHHHHHHHhhccccccccccCCchhhHHHHHHhhCCCCCHHHHHHHHHHHHHhhhccccC
Q 008455 133 PFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITT 212 (565)
Q Consensus 133 p~tL~DIa~~~~vsv~~Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~~~l~~~V~~~A~~Lv~~m~~~~l~~ 212 (565)
|.++.+||..++++...|.+.|+.. .+ ..|..|+... +
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~~~---~~----------~s~~~~~~~~---------------------r-------- 38 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFKKE---TG----------TTPKQYLRDR---------------------R-------- 38 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHH---hC----------cCHHHHHHHH---------------------H--------
Confidence 4688999999999988888776644 22 2233332210 0
Q ss_pred CCChhHHHHHHHHHHHHhcCCCCCHhHHHHHhcc-CHHHHHHHHHHHH
Q 008455 213 GRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHI-CEATLMKRLIEFE 259 (565)
Q Consensus 213 GR~P~~IaaAALylAar~~g~~~t~~eIa~v~~V-se~TIrkR~kE~~ 259 (565)
+.-|.-||... +.++.+||..+|+ +..++.+.++...
T Consensus 39 ------~~~a~~~l~~~----~~~~~~ia~~~g~~s~~~f~r~Fk~~~ 76 (84)
T smart00342 39 ------LERARRLLRDT----DLSVTEIALRVGFSSQSYFSRAFKKLF 76 (84)
T ss_pred ------HHHHHHHHHcC----CCCHHHHHHHhCCCChHHHHHHHHHHH
Confidence 12233344321 8999999999999 9999999998876
No 54
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=90.74 E-value=0.49 Score=49.99 Aligned_cols=82 Identities=17% Similarity=0.137 Sum_probs=63.3
Q ss_pred hhhHHHHHHhhCCCCCHHHHHHHHHHHHHhhhccccCCCChhHHHHHHHHHHHHhcCCCCCHhHHHHHhc----cCHHHH
Q 008455 176 SIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVH----ICEATL 251 (565)
Q Consensus 176 ~~~I~Rf~~~L~~~l~~~V~~~A~~Lv~~m~~~~l~~GR~P~~IaaAALylAar~~g~~~t~~eIa~v~~----Vse~TI 251 (565)
..||..++.+|+ .+.....+|.-+..++---.-+..-.|..||++|||||+...+..+..++|..+.. ....+.
T Consensus 43 ~~fI~elg~~L~--~~~~ti~tA~~~~hRFy~~~s~~~~~~~~vA~sclfLAgKvEetp~kl~dIi~~s~~~~~~~~~~~ 120 (323)
T KOG0834|consen 43 AKFIQELGVRLK--MPQKTIATAIVIFHRFYMFHSFKKFDPYTVAASCLFLAGKVEETPRKLEDIIKVSYRYLNPKDLEL 120 (323)
T ss_pred HHHHHHHHHHcC--CCccchhhhhhhhhhhhhhcccccCcHHHHHHHHHHHHhhcccCcccHHHHHHHHHHHcCcccccH
Confidence 457777788886 55566777777888776656667788899999999999999999999999998743 222467
Q ss_pred HHHHHHHH
Q 008455 252 MKRLIEFE 259 (565)
Q Consensus 252 rkR~kE~~ 259 (565)
..+|-+++
T Consensus 121 ~~~~~~~~ 128 (323)
T KOG0834|consen 121 EEVYWELK 128 (323)
T ss_pred HHHHHHHH
Confidence 77777766
No 55
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=90.68 E-value=0.19 Score=40.77 Aligned_cols=17 Identities=24% Similarity=0.638 Sum_probs=14.8
Q ss_pred eccCCCceecCccccee
Q 008455 14 HRPYDSQLCCDRCGKVL 30 (565)
Q Consensus 14 ~D~~~G~~VCt~CG~Vl 30 (565)
++..+|.++|.+||++.
T Consensus 47 ~~i~eg~L~Cp~c~r~Y 63 (68)
T PF03966_consen 47 VEIVEGELICPECGREY 63 (68)
T ss_dssp EETTTTEEEETTTTEEE
T ss_pred ccccCCEEEcCCCCCEE
Confidence 46789999999999974
No 56
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=90.24 E-value=0.2 Score=42.62 Aligned_cols=30 Identities=27% Similarity=0.536 Sum_probs=25.6
Q ss_pred CCCCCCCCCceeccCCCceecCcccceeccc
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDH 33 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vlee~ 33 (565)
.||.||+. .+.....|-..|..||.+..-.
T Consensus 37 ~Cp~C~~~-~VkR~a~GIW~C~kCg~~fAGg 66 (89)
T COG1997 37 VCPFCGRT-TVKRIATGIWKCRKCGAKFAGG 66 (89)
T ss_pred cCCCCCCc-ceeeeccCeEEcCCCCCeeccc
Confidence 59999998 6677889999999999987543
No 57
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=90.03 E-value=0.59 Score=34.42 Aligned_cols=32 Identities=19% Similarity=0.294 Sum_probs=24.6
Q ss_pred HHhcCCCCCHhHHHHHhccCHHHHHHHHHHHH
Q 008455 228 ALTHGLKFSKSDIVKIVHICEATLMKRLIEFE 259 (565)
Q Consensus 228 ar~~g~~~t~~eIa~v~~Vse~TIrkR~kE~~ 259 (565)
....+-+.|..+||..+|+|+.|+.+|++.+.
T Consensus 11 ~Lq~d~r~s~~~la~~lglS~~~v~~Ri~rL~ 42 (42)
T PF13404_consen 11 LLQEDGRRSYAELAEELGLSESTVRRRIRRLE 42 (42)
T ss_dssp HHHH-TTS-HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHcCCccHHHHHHHHCcCHHHHHHHHHHhC
Confidence 33455788999999999999999999998763
No 58
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=89.94 E-value=0.23 Score=35.68 Aligned_cols=27 Identities=19% Similarity=0.388 Sum_probs=20.1
Q ss_pred CCCCCCCCC-Cceecc--CCCceecCcccc
Q 008455 2 VWCSSCARH-VTGHRP--YDSQLCCDRCGK 28 (565)
Q Consensus 2 ~~Cp~Cgs~-~i~~D~--~~G~~VCt~CG~ 28 (565)
..||.||+. -+-+|. .+|..+|..||.
T Consensus 4 ~pCP~CGG~DrFr~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 4 GPCPNCGGSDRFRFDDKDGRGTWFCSVCGA 33 (37)
T ss_pred cCCCCCCCccccccccCCCCcCEEeCCCCC
Confidence 369999987 333443 459999999985
No 59
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=89.89 E-value=0.23 Score=37.67 Aligned_cols=29 Identities=17% Similarity=0.623 Sum_probs=20.4
Q ss_pred CCCCCCCCCceeccCC-CceecCcccceec
Q 008455 3 WCSSCARHVTGHRPYD-SQLCCDRCGKVLE 31 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~-G~~VCt~CG~Vle 31 (565)
.||.||.-....+... ..++|..||.+..
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~~ 31 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCGYEEP 31 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCCCeEE
Confidence 6999998643332222 3899999998754
No 60
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=89.81 E-value=0.27 Score=38.72 Aligned_cols=27 Identities=22% Similarity=0.429 Sum_probs=20.2
Q ss_pred CCCCCCCCCCceeccCCC-------ceecCcccc
Q 008455 2 VWCSSCARHVTGHRPYDS-------QLCCDRCGK 28 (565)
Q Consensus 2 ~~Cp~Cgs~~i~~D~~~G-------~~VCt~CG~ 28 (565)
..||.||+..+.+....+ .+.|++||.
T Consensus 4 kPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 4 KPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred cCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 469999988776665443 366999999
No 61
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=89.78 E-value=0.23 Score=38.12 Aligned_cols=26 Identities=19% Similarity=0.539 Sum_probs=20.6
Q ss_pred CCCCCCCCCceeccCCCceecCccccee
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vl 30 (565)
.||.||+. +..++ .+...|..||...
T Consensus 22 fCP~Cg~~-~m~~~-~~r~~C~~Cgyt~ 47 (50)
T PRK00432 22 FCPRCGSG-FMAEH-LDRWHCGKCGYTE 47 (50)
T ss_pred cCcCCCcc-hhecc-CCcEECCCcCCEE
Confidence 69999997 54443 5899999999863
No 62
>PF08613 Cyclin: Cyclin; InterPro: IPR013922 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This entry includes cyclin PHO80 and other cyclins that partner with the cyclin-dependent kinase (CDK) PHO85. The PHO80/PHO85 cyclin-cdk complex is used for a regulatory process other than cell-cycle control []. This entry also includes other PHO80-like cyclins that are involved in the cell-cycle control. They belong to the P/U family and interact preferentially with CDKA1 [].; GO: 0019901 protein kinase binding, 0000079 regulation of cyclin-dependent protein kinase activity; PDB: 2PK9_D 2PMI_D.
Probab=89.09 E-value=5.6 Score=37.16 Aligned_cols=89 Identities=11% Similarity=0.091 Sum_probs=66.5
Q ss_pred HHHHHHHHHHHcCCCChhHHHHHHHHHHHHHHh---Cc--cccCCchhHHHHHHHHHHHHh-cCCCccHHHHHhhhccCh
Q 008455 74 AFDDMRQMKNALNIGESDEIVHVAKRFYGIAVA---RN--FTKGRRTEQVQASCLYLACRQ-KSKPFLLIDFSNYLNINV 147 (565)
Q Consensus 74 a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~---~~--~~rGR~~~~vaAACLYiACR~-e~~p~tL~DIa~~~~vsv 147 (565)
..++|.++....+++ ..+.-.|.-|..+... .. .+.......+..+||-+|.+. .....+.+.+|.+.|+++
T Consensus 54 i~~fl~ri~~~~~~s--~~~~i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v~gis~ 131 (149)
T PF08613_consen 54 IRDFLSRILKYTQCS--PECLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNTYSNKSWAKVGGISL 131 (149)
T ss_dssp HHHHHHHHHHHTT----HHHHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS---HHHHHHHHTS-H
T ss_pred HHHHHHHHHHHcCCC--hHHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhcccccccHHHHHhhcCCCH
Confidence 467888899999999 8999999999888877 22 233455667888999999995 678899999999999999
Q ss_pred HHHHHHHHHHHHHhhcc
Q 008455 148 YELGAVYLQLCQVLYIA 164 (565)
Q Consensus 148 ~~Lgr~~~~L~~~L~i~ 164 (565)
.+|.+.-..++..|+.+
T Consensus 132 ~eln~lE~~fL~~l~~~ 148 (149)
T PF08613_consen 132 KELNELEREFLKLLDYN 148 (149)
T ss_dssp HHHHHHHHHHHHHTTT-
T ss_pred HHHHHHHHHHHHHCCCc
Confidence 99999999998887753
No 63
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=88.69 E-value=0.25 Score=35.37 Aligned_cols=28 Identities=21% Similarity=0.624 Sum_probs=20.9
Q ss_pred CCCCCCCC-Cceec---cCCCceecCccccee
Q 008455 3 WCSSCARH-VTGHR---PYDSQLCCDRCGKVL 30 (565)
Q Consensus 3 ~Cp~Cgs~-~i~~D---~~~G~~VCt~CG~Vl 30 (565)
.||+|+.. .+..+ ...+.+-|+.||.|.
T Consensus 4 ~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred ECCCCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 69999987 33222 346799999999985
No 64
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=88.33 E-value=0.36 Score=36.08 Aligned_cols=27 Identities=26% Similarity=0.695 Sum_probs=21.2
Q ss_pred CCCCCCCCCceeccCCCceecCccccee
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vl 30 (565)
.|++||.. +.+|+..+.+.|..||.-+
T Consensus 5 ~C~~CG~~-~~~~~~~~~~~Cp~CG~~~ 31 (46)
T PRK00398 5 KCARCGRE-VELDEYGTGVRCPYCGYRI 31 (46)
T ss_pred ECCCCCCE-EEECCCCCceECCCCCCeE
Confidence 69999986 4556666689999999743
No 65
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=87.98 E-value=0.33 Score=45.94 Aligned_cols=29 Identities=24% Similarity=0.462 Sum_probs=19.9
Q ss_pred CCCCCCCCCC-ceeccC---CCce-----ecCccccee
Q 008455 2 VWCSSCARHV-TGHRPY---DSQL-----CCDRCGKVL 30 (565)
Q Consensus 2 ~~Cp~Cgs~~-i~~D~~---~G~~-----VCt~CG~Vl 30 (565)
+.||+||+.. .+.+.. .|.. -|.+||.-.
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f 38 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRF 38 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcc
Confidence 5799999875 455543 4544 499999853
No 66
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=87.20 E-value=2 Score=34.50 Aligned_cols=71 Identities=7% Similarity=0.136 Sum_probs=45.6
Q ss_pred HHHHHHHcCCCChhHHHHHHHHHHHHHHhCccccCCchhHHHHHHHHHHHHhcCCCccHHHHHhhhcc-ChHHHHHHHHH
Q 008455 78 MRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNI-NVYELGAVYLQ 156 (565)
Q Consensus 78 I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~p~tL~DIa~~~~v-sv~~Lgr~~~~ 156 (565)
|..+|..+|++ ...... +|+......+..-.....+.-|+-|+.- + +.++.+||..+|+ +...+.+.|++
T Consensus 4 ~~~la~~~~~s--~~~l~~---~f~~~~~~s~~~~~~~~r~~~a~~~l~~---~-~~~~~~ia~~~g~~s~~~f~r~Fk~ 74 (84)
T smart00342 4 LEDLAEALGMS--PRHLQR---LFKKETGTTPKQYLRDRRLERARRLLRD---T-DLSVTEIALRVGFSSQSYFSRAFKK 74 (84)
T ss_pred HHHHHHHhCCC--HHHHHH---HHHHHhCcCHHHHHHHHHHHHHHHHHHc---C-CCCHHHHHHHhCCCChHHHHHHHHH
Confidence 67899999999 544333 4444332222221122234445555532 2 8999999999999 99999998876
Q ss_pred H
Q 008455 157 L 157 (565)
Q Consensus 157 L 157 (565)
.
T Consensus 75 ~ 75 (84)
T smart00342 75 L 75 (84)
T ss_pred H
Confidence 6
No 67
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=87.08 E-value=0.34 Score=43.23 Aligned_cols=29 Identities=21% Similarity=0.527 Sum_probs=24.0
Q ss_pred CCCCCCCCCceeccCCCceecCcccceeccc
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDH 33 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vlee~ 33 (565)
.||+||.. .||-...-+||..||++..-.
T Consensus 11 ~Cp~CG~k--FYDLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 11 TCPSCGAK--FYDLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred cCCCCcch--hccCCCCCccCCCCCCccCcc
Confidence 69999987 467667788999999998754
No 68
>KOG2496 consensus Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell cycle control, cell division, chromosome partitioning; Transcription; Replication, recombination and repair]
Probab=86.92 E-value=1.6 Score=45.43 Aligned_cols=71 Identities=14% Similarity=0.186 Sum_probs=63.1
Q ss_pred chhhHHHHHHhhCCCCCHHHHHHHHHHHHHhhhccccCCCChhHHHHHHHHHHHHhcCCCCCHhHHHHHhc
Q 008455 175 PSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVH 245 (565)
Q Consensus 175 P~~~I~Rf~~~L~~~l~~~V~~~A~~Lv~~m~~~~l~~GR~P~~IaaAALylAar~~g~~~t~~eIa~v~~ 245 (565)
-+..+-.|++++...++..|+.+|.....++--.|-++--.|..|.++|+|+||....+.+|..++++-..
T Consensus 59 ~E~~l~~f~~k~~p~lp~~Vv~TA~~fFkRffL~nsvme~~pk~I~~tc~flA~Kieef~ISieqFvkn~~ 129 (325)
T KOG2496|consen 59 EELSLVNFYSKFKPNLPTSVVSTAIEFFKRFFLENSVMEYSPKIIMATCFFLACKIEEFYISIEQFVKNMN 129 (325)
T ss_pred HHHHHHHHHHHhcCCCchHHHHHHHHHHHHHHHhcchhhcChHHHHHHHHHHHhhhHhheecHHHHHhhcc
Confidence 45667788888855589999999999999998888899999999999999999999999999999998665
No 69
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=86.64 E-value=35 Score=36.16 Aligned_cols=27 Identities=7% Similarity=0.069 Sum_probs=23.6
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHHH
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEFE 259 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~~ 259 (565)
...|.++||..+||+..||++++..-.
T Consensus 281 e~~s~~EIA~~Lgis~~tV~~~~~rAl 307 (325)
T PRK05657 281 EAATLEDVAREIGLTRERVRQIQVEAL 307 (325)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 468999999999999999999976544
No 70
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=86.60 E-value=0.49 Score=36.52 Aligned_cols=31 Identities=19% Similarity=0.340 Sum_probs=21.4
Q ss_pred CCCCCCCCCCc-ee---cc--CCCceecCcccceecc
Q 008455 2 VWCSSCARHVT-GH---RP--YDSQLCCDRCGKVLED 32 (565)
Q Consensus 2 ~~Cp~Cgs~~i-~~---D~--~~G~~VCt~CG~Vlee 32 (565)
..||.||+... +. +. ..|...|..||.....
T Consensus 2 kPCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~~~ 38 (53)
T TIGR03655 2 KPCPFCGGADVYLRRGFDPLDLSHYFECSTCGASGPV 38 (53)
T ss_pred CCCCCCCCcceeeEeccCCCCCEEEEECCCCCCCccc
Confidence 46999999855 22 22 2455679999997653
No 71
>PRK11827 hypothetical protein; Provisional
Probab=86.49 E-value=0.54 Score=37.46 Aligned_cols=27 Identities=15% Similarity=0.252 Sum_probs=22.4
Q ss_pred CCCCCCCCCceeccCCCceecCccccee
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vl 30 (565)
.||.|++. +.+|.....+||..||.+.
T Consensus 10 aCP~ckg~-L~~~~~~~~Lic~~~~laY 36 (60)
T PRK11827 10 ACPVCNGK-LWYNQEKQELICKLDNLAF 36 (60)
T ss_pred ECCCCCCc-CeEcCCCCeEECCccCeec
Confidence 69999886 4577667889999999875
No 72
>PF05460 ORC6: Origin recognition complex subunit 6 (ORC6); InterPro: IPR008721 The Origin Recognition Complex (ORC) is a six-subunit ATP-dependent DNA-binding complex encoded in yeast by ORC1-6 []. ORC is a central component for eukaryotic DNA replication, and binds chromatin at replication origins throughout the cell cycle []. ORC directs DNA replication throughout the genome and is required for its initiation [, , ]. ORC bound at replication origins serves as the foundation for assembly of the pre-replicative complex (pre-RC), which includes Cdc6, Tah11 (aka Cdt1), and the Mcm2-7 complex [, , ]. Pre-RC assembly during G1 is required for replication licensing of chromosomes prior to DNA synthesis during S phase [, , ]. Cell cycle-regulated phosphorylation of Orc2, Orc6, Cdc6, and MCM by the cyclin-dependent protein kinase Cdc28 regulates initiation of DNA replication, including blocking reinitiation in G2/M phase [, , , ]. In yeast, ORC also plays a role in the establishment of silencing at the mating-type loci Hidden MAT Left (HML) and Hidden MAT Right (HMR) [, , ]. ORC participates in the assembly of transcriptionally silent chromatin at HML and HMR by recruiting the Sir1 silencing protein to the HML and HMR silencers [, , ]. Both Orc1 and Orc5 bind ATP, though only Orc1 has ATPase activity []. The binding of ATP by Orc1 is required for ORC binding to DNA and is essential for cell viability []. The ATPase activity of Orc1 is involved in formation of the pre-RC [, , ]. ATP binding by Orc5 is crucial for the stability of ORC as a whole. Only the Orc1-5 subunits are required for origin binding; Orc6 is essential for maintenance of pre-RCs once formed []. Interactions within ORC suggest that Orc2-3-6 may form a core complex []. ORC homologues have been found in various eukaryotes, including fission yeast, insects, amphibians, and humans []. This entry represents subunit 6, which directs DNA replication by binding to replication origins and is also involved in transcriptional silencing; interacts with Spp1 and with trimethylated histone H3; phosphorylated by Cdc28 [, ]. In Saccharomyces cerevisiae (Baker's yeast), both ends of the Orc6 interact with Cdt1 [] and the N terminus mediates an interaction with the S-phase cyclin Clb5 []. ; GO: 0003677 DNA binding, 0006260 DNA replication, 0005664 nuclear origin of replication recognition complex; PDB: 3M03_B.
Probab=86.27 E-value=0.22 Score=53.38 Aligned_cols=86 Identities=13% Similarity=0.092 Sum_probs=0.0
Q ss_pred HHHHHcCCCChhHHHHHHHHHHHHHH-hCccccCCchhHHHHHHHHHHHHhcCCCccHHHHHhhhccChHHHHHHHHHHH
Q 008455 80 QMKNALNIGESDEIVHVAKRFYGIAV-ARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLC 158 (565)
Q Consensus 80 ~ia~~L~Lp~~~~i~e~A~~iyk~a~-~~~~~rGR~~~~vaAACLYiACR~e~~p~tL~DIa~~~~vsv~~Lgr~~~~L~ 158 (565)
.|+..++++.+..++..|..||++.. ....+++..-.+-+.+|+||||...+.++-+..+....++++....+.|..|.
T Consensus 3 ~l~p~~~~~~~~~ll~~a~~L~~ls~~~~~~l~~~~EiaR~~iCa~lA~~~l~~~~dl~~~~~~~pl~pk~y~~l~~~~~ 82 (353)
T PF05460_consen 3 DLIPKLGGGLPPKLLSKASELYRLSRQKKSSLKPEEEIARAHICAELACERLKEKLDLPYAIKRSPLPPKVYKKLLNTFE 82 (353)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred hhhhccCCCCCHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhCCccCchhhcCCCCCCHHHHHHHHHHHH
Confidence 34445554423899999999999987 44556666666778899999999999999888888888999888888888888
Q ss_pred HHhhccc
Q 008455 159 QVLYIAD 165 (565)
Q Consensus 159 ~~L~i~~ 165 (565)
+.|+...
T Consensus 83 ~~L~~~s 89 (353)
T PF05460_consen 83 NLLGNSS 89 (353)
T ss_dssp -------
T ss_pred HHHhCCC
Confidence 7777643
No 73
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=86.00 E-value=0.44 Score=31.56 Aligned_cols=24 Identities=33% Similarity=0.731 Sum_probs=18.7
Q ss_pred CCCCCCCCCceeccCCCceecCcccceec
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vle 31 (565)
.||.|+... ......|..||.+..
T Consensus 2 ~CP~C~~~V-----~~~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 2 TCPECGAEV-----PESAKFCPHCGYDFE 25 (26)
T ss_pred cCCCCcCCc-----hhhcCcCCCCCCCCc
Confidence 699999874 246679999998753
No 74
>KOG4164 consensus Cyclin ik3-1/CABLES [Cell cycle control, cell division, chromosome partitioning]
Probab=85.88 E-value=2.5 Score=45.41 Aligned_cols=91 Identities=18% Similarity=0.234 Sum_probs=65.1
Q ss_pred HHHHHHHHHHHcCCCChhHHHHHHHHHHHHHHhCccccCCchhHHHHHHHHHHHHhcCCC----ccHHH-HHhhhccChH
Q 008455 74 AFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKP----FLLID-FSNYLNINVY 148 (565)
Q Consensus 74 a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~p----~tL~D-Ia~~~~vsv~ 148 (565)
..++|++++.--+|. ...+.+|..||.++.=+|++...++..+|.|||.+|.+.+..- .+|+| .-+.++.+..
T Consensus 385 lKREMr~l~~d~~id--~~TVa~AyVYFEKliLkglisK~NRKlcAGAclLlaaKmnD~Kks~vKslIek~Ee~fR~nrr 462 (497)
T KOG4164|consen 385 LKREMRELGEDCGID--VVTVAMAYVYFEKLILKGLISKQNRKLCAGACLLLAAKMNDLKKSTVKSLIEKLEEQFRLNRR 462 (497)
T ss_pred HHHHHHHhhhccCcc--ceeehhHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHhcccHH
Confidence 356777788777888 7899999999999888888887788899999999999987552 22332 2344666666
Q ss_pred HHHHHHHHHHHHhhcccc
Q 008455 149 ELGAVYLQLCQVLYIADE 166 (565)
Q Consensus 149 ~Lgr~~~~L~~~L~i~~~ 166 (565)
+|-.--.-++-.|.+..+
T Consensus 463 dLia~Ef~VlvaLefaL~ 480 (497)
T KOG4164|consen 463 DLIAFEFPVLVALEFALH 480 (497)
T ss_pred hhhhhhhhHHHhhhhhcc
Confidence 665554455555554433
No 75
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=85.86 E-value=40 Score=33.68 Aligned_cols=27 Identities=4% Similarity=-0.053 Sum_probs=23.3
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHHH
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEFE 259 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~~ 259 (565)
...|+++||..+|||..+|+++++.-.
T Consensus 195 ~~~t~~EIA~~lgis~~~V~q~~~~al 221 (238)
T TIGR02393 195 RPHTLEEVGKEFNVTRERIRQIESKAL 221 (238)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHHHH
Confidence 568999999999999999998865443
No 76
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=85.43 E-value=0.52 Score=42.36 Aligned_cols=33 Identities=24% Similarity=0.584 Sum_probs=25.5
Q ss_pred CCCCCCCCCCCc-eeccCCCceecCcccceeccc
Q 008455 1 MVWCSSCARHVT-GHRPYDSQLCCDRCGKVLEDH 33 (565)
Q Consensus 1 M~~Cp~Cgs~~i-~~D~~~G~~VCt~CG~Vlee~ 33 (565)
|..||.||+-.+ ..|..++.++|..||...+-.
T Consensus 2 m~FCp~Cgsll~p~~~~~~~~l~C~kCgye~~~~ 35 (113)
T COG1594 2 MRFCPKCGSLLYPKKDDEGGKLVCRKCGYEEEAS 35 (113)
T ss_pred ccccCCccCeeEEeEcCCCcEEECCCCCcchhcc
Confidence 678999998743 334467899999999987654
No 77
>PF01857 RB_B: Retinoblastoma-associated protein B domain; InterPro: IPR002719 Retinoblastoma-like and retinoblastoma-associated proteins may have a function in cell cycle regulation. They form a complex with adenovirus E1A and SV40 large T antigen, and may bind and modulate the function of certain cellular proteins with which T and E1A compete for pocket binding. The proteins may act as tumor suppressors, and are potent inhibitors of E2F-mediated trans-activation. This domain has the cyclin fold []. The crystal structure of the Rb pocket bound to a nine-residue E7 peptide containing the LxCxE motif, shared by other Rb-binding viral and cellular proteins, shows that the LxCxE peptide binds a highly conserved groove on the B-box portion of the pocket; the A-box portion (see IPR002720 from INTERPRO) appears to be required for the stable folding of the B box. Also highly conserved is the extensive A-B interface, suggesting that it may be an additional protein-binding site. The A and B boxes each contain the cyclin-fold structural motif, with the LxCxE-binding site on the B-box cyclin fold being similar to a Cdk2-binding site of cyclin A and to a TBP-binding site of TFIIB []. The A and B boxes are found at the C-terminal end of the protein; the B-box is on C-terminal side of the A-box.; GO: 0051726 regulation of cell cycle, 0005634 nucleus; PDB: 1GUX_B 3POM_A 1GH6_B 1N4M_A 1O9K_H 4ELL_B 2R7G_C 4ELJ_A.
Probab=85.18 E-value=3.2 Score=38.48 Aligned_cols=64 Identities=16% Similarity=0.134 Sum_probs=49.6
Q ss_pred HHHHHHhhCCCCCHHHHHHHHHHHHHhh--hccccCCCChhHHHHHHHHHHHHhcCCCCCHhHHHHHh
Q 008455 179 LHKFTDRLLPGGNKKVCDTARDILASMK--RDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIV 244 (565)
Q Consensus 179 I~Rf~~~L~~~l~~~V~~~A~~Lv~~m~--~~~l~~GR~P~~IaaAALylAar~~g~~~t~~eIa~v~ 244 (565)
|..+|++|. +++++....+.+++.+. ...|..+|+-.-|.-.|+|+.|++++..+|.++|...-
T Consensus 18 l~~LC~~L~--l~~~~~~~iwt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~~~sF~~Ii~~Y 83 (135)
T PF01857_consen 18 LQDLCERLD--LSSDLREKIWTCFEHSLTHHTELMKDRHLDQIILCAIYGICKVSKEELSFKDIIKAY 83 (135)
T ss_dssp HHHHHHHHT--TSTTHHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHHHHHHHHTT-S--HHHHHHHH
T ss_pred HHHHHHHcC--CcHHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhhcCCCCHHHHHHHH
Confidence 566788887 77778888888888765 46789999999999999999999999888888887643
No 78
>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=85.00 E-value=1.7 Score=32.31 Aligned_cols=29 Identities=14% Similarity=0.326 Sum_probs=24.5
Q ss_pred CCCCCHhHHHHHhccCHHHHHHHHHHHHc
Q 008455 232 GLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (565)
Q Consensus 232 g~~~t~~eIa~v~~Vse~TIrkR~kE~~~ 260 (565)
+-..|+++||+.+|+|..|+++++++|.+
T Consensus 15 ~~~~t~~ela~~~~is~~tv~~~l~~L~~ 43 (48)
T PF13412_consen 15 NPRITQKELAEKLGISRSTVNRYLKKLEE 43 (48)
T ss_dssp CTTS-HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred cCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 45599999999999999999999999875
No 79
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=84.41 E-value=0.61 Score=35.52 Aligned_cols=26 Identities=27% Similarity=0.701 Sum_probs=21.3
Q ss_pred CCCCCCCCCceeccCCCceecCcccce
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGKV 29 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~V 29 (565)
.||.||...+--|+.+ -+.|..||..
T Consensus 21 ~CPrCG~gvfmA~H~d-R~~CGkCgyT 46 (51)
T COG1998 21 FCPRCGPGVFMADHKD-RWACGKCGYT 46 (51)
T ss_pred cCCCCCCcchhhhcCc-eeEeccccce
Confidence 6999998766666654 8999999986
No 80
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=84.25 E-value=57 Score=35.17 Aligned_cols=92 Identities=9% Similarity=0.030 Sum_probs=52.5
Q ss_pred chHHHHHHHHHHHHHHHHHHcC---CCChhHHHHHHHHHHHHHHhCccccCCchhHHHHHHHHHHHH-------------
Q 008455 65 ASRERLMEKAFDDMRQMKNALN---IGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACR------------- 128 (565)
Q Consensus 65 ~srer~l~~a~~~I~~ia~~L~---Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR------------- 128 (565)
..+++.+..-...+..+|.++. +.-.+-+.+.-..+++-+..-...+|-+....|.-.|+-+-+
T Consensus 129 ~A~~~Li~~~~~lV~~iA~~~~~~~~~~eDLiQEg~igL~~a~~~fd~~~g~~FsTyA~~wIr~aI~~~i~~~~r~irip 208 (367)
T PRK09210 129 EAKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIP 208 (367)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHcCCceecc
Confidence 3344444555566777777662 211133444444455555444444677777766666664431
Q ss_pred -------------------hcCCCccHHHHHhhhccChHHHHHHHHH
Q 008455 129 -------------------QKSKPFLLIDFSNYLNINVYELGAVYLQ 156 (565)
Q Consensus 129 -------------------~e~~p~tL~DIa~~~~vsv~~Lgr~~~~ 156 (565)
..|.+-|..+||..+++++..+......
T Consensus 209 ~~~~~~~~~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~ 255 (367)
T PRK09210 209 VHMVETINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKI 255 (367)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHH
Confidence 1233446778888899988888776543
No 81
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=84.15 E-value=0.54 Score=41.01 Aligned_cols=29 Identities=21% Similarity=0.535 Sum_probs=23.0
Q ss_pred CCCCCCCCCce---ecc--CCCceecCcccceec
Q 008455 3 WCSSCARHVTG---HRP--YDSQLCCDRCGKVLE 31 (565)
Q Consensus 3 ~Cp~Cgs~~i~---~D~--~~G~~VCt~CG~Vle 31 (565)
.||.||+..++ ++- .-|.++|..||.-.+
T Consensus 24 tCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e 57 (104)
T COG4888 24 TCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFE 57 (104)
T ss_pred ecCccCCeeeeEEEEEecCceeEEEcccCcceEE
Confidence 59999998665 553 468999999998655
No 82
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=84.03 E-value=0.71 Score=36.67 Aligned_cols=28 Identities=21% Similarity=0.442 Sum_probs=24.8
Q ss_pred CCCCCCCCCCceeccCCCceecCccccee
Q 008455 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (565)
Q Consensus 2 ~~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vl 30 (565)
..||.|.+. +.+|...+.+||..||...
T Consensus 9 LaCP~~kg~-L~~~~~~~~L~c~~~~~aY 36 (60)
T COG2835 9 LACPVCKGP-LVYDEEKQELICPRCKLAY 36 (60)
T ss_pred eeccCcCCc-ceEeccCCEEEecccCcee
Confidence 479999988 7788889999999999874
No 83
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=83.85 E-value=0.7 Score=40.58 Aligned_cols=30 Identities=20% Similarity=0.426 Sum_probs=22.8
Q ss_pred CCCCCCCCCc--eeccCCCceecCcccceecc
Q 008455 3 WCSSCARHVT--GHRPYDSQLCCDRCGKVLED 32 (565)
Q Consensus 3 ~Cp~Cgs~~i--~~D~~~G~~VCt~CG~Vlee 32 (565)
.||+||...+ ..|...+.++|..||+.-+-
T Consensus 23 ~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 23 ECPRCGKVSISVKIKKNIAIITCGNCGLYTEF 54 (99)
T ss_pred ECCCCCCeEeeeecCCCcceEECCCCCCccCE
Confidence 6999996533 34556789999999998653
No 84
>COG4640 Predicted membrane protein [Function unknown]
Probab=83.09 E-value=0.62 Score=49.81 Aligned_cols=26 Identities=23% Similarity=0.804 Sum_probs=20.5
Q ss_pred CCCCCCCCCCCceeccCCCceecCcccceec
Q 008455 1 MVWCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (565)
Q Consensus 1 M~~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vle 31 (565)
|..||.||+.. .+|..-|+.||.-+.
T Consensus 1 M~fC~kcG~qk-----~Ed~~qC~qCG~~~t 26 (465)
T COG4640 1 MKFCPKCGSQK-----AEDDVQCTQCGHKFT 26 (465)
T ss_pred CCccccccccc-----ccccccccccCCcCC
Confidence 88999999864 356667999998544
No 85
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=82.93 E-value=0.93 Score=37.49 Aligned_cols=31 Identities=16% Similarity=0.469 Sum_probs=23.0
Q ss_pred CCCCCCCCCCCceecc-------CCCceecC--cccceec
Q 008455 1 MVWCSSCARHVTGHRP-------YDSQLCCD--RCGKVLE 31 (565)
Q Consensus 1 M~~Cp~Cgs~~i~~D~-------~~G~~VCt--~CG~Vle 31 (565)
|+.||.||....+.+. .+-...|+ +||...-
T Consensus 1 mm~CP~Cg~~a~irtSr~~s~~~~~~Y~qC~N~eCg~tF~ 40 (72)
T PRK09678 1 MFHCPLCQHAAHARTSRYITDTTKERYHQCQNVNCSATFI 40 (72)
T ss_pred CccCCCCCCccEEEEChhcChhhheeeeecCCCCCCCEEE
Confidence 8999999998766553 23456799 8998643
No 86
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=82.90 E-value=0.72 Score=42.06 Aligned_cols=29 Identities=7% Similarity=0.033 Sum_probs=23.8
Q ss_pred CCCCCCCCCceeccCCCceecCcccceeccc
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDH 33 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vlee~ 33 (565)
.||+||.. .||-..--+||..||.+....
T Consensus 11 ~Cp~cg~k--FYDLnk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 11 ICPNTGSK--FYDLNRRPAVSPYTGEQFPPE 39 (129)
T ss_pred cCCCcCcc--ccccCCCCccCCCcCCccCcc
Confidence 69999987 467667889999999997654
No 87
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=82.43 E-value=0.92 Score=36.56 Aligned_cols=28 Identities=21% Similarity=0.590 Sum_probs=20.8
Q ss_pred CCCCCCCCCceeccCCCceecCcccceec
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vle 31 (565)
.||.||..... .......+|..||.+.+
T Consensus 30 ~C~~CG~~~~~-~~~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 30 TCPRCGHRNKK-RRSGRVFTCPNCGFEMD 57 (69)
T ss_pred CccCccccccc-ccccceEEcCCCCCEEC
Confidence 69999987433 34567889999998865
No 88
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=82.42 E-value=1.1 Score=30.86 Aligned_cols=26 Identities=23% Similarity=0.599 Sum_probs=15.1
Q ss_pred CCCCCCCCCceeccCCCceecCcccce
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGKV 29 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~V 29 (565)
.|+.||+.... ....-..+|..||..
T Consensus 5 fC~~CG~~t~~-~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 5 FCGRCGAPTKP-APGGWARRCPSCGHE 30 (32)
T ss_dssp B-TTT--BEEE--SSSS-EEESSSS-E
T ss_pred ccCcCCccccC-CCCcCEeECCCCcCE
Confidence 69999988543 344568899999985
No 89
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=82.33 E-value=0.62 Score=38.78 Aligned_cols=30 Identities=23% Similarity=0.551 Sum_probs=26.8
Q ss_pred CCCCCCCCCCceeccCCCceecCcccceec
Q 008455 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (565)
Q Consensus 2 ~~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vle 31 (565)
++||.|-....++.++...+||.+|++|+=
T Consensus 35 VkC~gc~~iT~vfSHaqtvVvc~~c~~il~ 64 (84)
T KOG1779|consen 35 VKCPGCFKITTVFSHAQTVVVCEGCSTILC 64 (84)
T ss_pred EEcCCceEEEEEeecCceEEEcCCCceEEE
Confidence 479999888888999999999999999974
No 90
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=82.24 E-value=1.9 Score=41.00 Aligned_cols=38 Identities=16% Similarity=0.259 Sum_probs=32.4
Q ss_pred HHHHhcCCCCCHhHHHHHhccCHHHHHHHHHHHHccCC
Q 008455 226 VSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDS 263 (565)
Q Consensus 226 lAar~~g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t~s 263 (565)
|.+...+-+.|..+||+.+|+|++|+++|++.|.+..-
T Consensus 20 L~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~Gv 57 (164)
T PRK11169 20 LNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQGF 57 (164)
T ss_pred HHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCC
Confidence 44455677899999999999999999999999987654
No 91
>PF13730 HTH_36: Helix-turn-helix domain
Probab=82.13 E-value=2.9 Score=31.86 Aligned_cols=26 Identities=19% Similarity=0.333 Sum_probs=24.3
Q ss_pred CHhHHHHHhccCHHHHHHHHHHHHcc
Q 008455 236 SKSDIVKIVHICEATLMKRLIEFENT 261 (565)
Q Consensus 236 t~~eIa~v~~Vse~TIrkR~kE~~~t 261 (565)
|++.|++.+|++..||++.++++.+.
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~~ 52 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEEK 52 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 89999999999999999999999754
No 92
>PRK12495 hypothetical protein; Provisional
Probab=81.73 E-value=0.9 Score=45.14 Aligned_cols=27 Identities=22% Similarity=0.608 Sum_probs=23.0
Q ss_pred CCCCCCCCCceeccCCCceecCcccceecc
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vlee 32 (565)
.|+.||...+ ...|.++|..|+.++.+
T Consensus 44 hC~~CG~PIp---a~pG~~~Cp~CQ~~~~~ 70 (226)
T PRK12495 44 HCDECGDPIF---RHDGQEFCPTCQQPVTE 70 (226)
T ss_pred hcccccCccc---CCCCeeECCCCCCcccc
Confidence 6999999865 34799999999999765
No 93
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=81.15 E-value=1.3 Score=32.45 Aligned_cols=27 Identities=19% Similarity=0.379 Sum_probs=15.0
Q ss_pred CCCCCCCCC-ce-ecc--CCCceecCcccce
Q 008455 3 WCSSCARHV-TG-HRP--YDSQLCCDRCGKV 29 (565)
Q Consensus 3 ~Cp~Cgs~~-i~-~D~--~~G~~VCt~CG~V 29 (565)
.||.||+.. +- ++. .+|..+|..||.+
T Consensus 5 pCP~CGG~DrFri~~d~~~~G~~~C~~C~~~ 35 (40)
T PF08273_consen 5 PCPICGGKDRFRIFDDKDGRGTWICRQCGGD 35 (40)
T ss_dssp --TTTT-TTTEEEETT----S-EEETTTTBE
T ss_pred CCCCCcCccccccCcCcccCCCEECCCCCCc
Confidence 599999873 22 442 3699999999434
No 94
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=80.91 E-value=3.3 Score=32.21 Aligned_cols=35 Identities=17% Similarity=0.274 Sum_probs=27.1
Q ss_pred HHHHHhcCC-----CCCHhHHHHHhccCHHHHHHHHHHHH
Q 008455 225 YVSALTHGL-----KFSKSDIVKIVHICEATLMKRLIEFE 259 (565)
Q Consensus 225 ylAar~~g~-----~~t~~eIa~v~~Vse~TIrkR~kE~~ 259 (565)
+.+|.-.|+ .+|..|||+.+|||.+|+..+++.-.
T Consensus 9 L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~LRrae 48 (53)
T PF04967_consen 9 LKAAYELGYFDVPRRITLEELAEELGISKSTVSEHLRRAE 48 (53)
T ss_pred HHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 344445554 47899999999999999999997543
No 95
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=80.90 E-value=36 Score=29.40 Aligned_cols=39 Identities=8% Similarity=0.135 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHhcCCCccHHHHHhhhccChHHHHHHHHHH
Q 008455 118 VQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQL 157 (565)
Q Consensus 118 vaAACLYiACR~e~~p~tL~DIa~~~~vsv~~Lgr~~~~L 157 (565)
+..++-|+... ...|.++.++|+.++++...|.+.|++.
T Consensus 7 ~~~~~~~i~~~-~~~~~~~~~lA~~~~~S~~~l~r~f~~~ 45 (107)
T PRK10219 7 IQTLIAWIDEH-IDQPLNIDVVAKKSGYSKWYLQRMFRTV 45 (107)
T ss_pred HHHHHHHHHHh-cCCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 34445555554 3457999999999999999999888765
No 96
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=80.65 E-value=1.4 Score=32.91 Aligned_cols=26 Identities=19% Similarity=0.450 Sum_probs=19.7
Q ss_pred CCCCCCCCCceeccCCCceecCcccc
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGK 28 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~ 28 (565)
.||.||+.....-...+..-|..|+.
T Consensus 20 ~CP~Cg~~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 20 VCPHCGSTKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCeeeEEeCCCCeEECCCCCC
Confidence 69999997544434469999999984
No 97
>KOG1010 consensus Rb (Retinoblastoma tumor suppressor)-related protein [Cell cycle control, cell division, chromosome partitioning]
Probab=80.05 E-value=4.2 Score=47.66 Aligned_cols=85 Identities=12% Similarity=0.212 Sum_probs=69.6
Q ss_pred HHHHHHHHHHHHHHcCCCChhHHHHHHHHHHHHHHhC--ccccCCchhHHHHHHHHHHHHhcCCCccHHHHHhhhccChH
Q 008455 71 MEKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVAR--NFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVY 148 (565)
Q Consensus 71 l~~a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~--~~~rGR~~~~vaAACLYiACR~e~~p~tL~DIa~~~~vsv~ 148 (565)
+.-|..+|+.+|.+|.|. +.+......+|.-.+.+ .+++.|...++.-+|+|+.||..+...++.+|-...+--+.
T Consensus 677 Y~LAavRL~~Lc~rL~l~--~e~r~~IWtlFehsl~~et~Lm~dRHLDQillCaiy~i~KV~~~~ltF~eIm~~YR~QPq 754 (920)
T KOG1010|consen 677 YHLAAVRLNDLCERLSLS--DELREQIWTLFEHSLTNETELMRDRHLDQILLCAIYGIAKVKKEDLTFSEIMRAYRRQPQ 754 (920)
T ss_pred HHHHHHHHHHHHHHhhhh--hHHHHHHHHHHHHHHhccHHHHHhhhHHHHHHHHHHhheehhcccchHHHHHHHHhcCch
Confidence 344778999999999999 88888888888776544 57889999999999999999999999999999887765555
Q ss_pred HHHHHHHHH
Q 008455 149 ELGAVYLQL 157 (565)
Q Consensus 149 ~Lgr~~~~L 157 (565)
-...+|+.+
T Consensus 755 a~~~vyRsV 763 (920)
T KOG1010|consen 755 AVSLVYRSV 763 (920)
T ss_pred hhhhhhhhe
Confidence 555555543
No 98
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=80.02 E-value=2.4 Score=31.34 Aligned_cols=30 Identities=17% Similarity=0.079 Sum_probs=20.6
Q ss_pred HHHhcCCCCCHhHHHHHhccCHHHHHHHHH
Q 008455 227 SALTHGLKFSKSDIVKIVHICEATLMKRLI 256 (565)
Q Consensus 227 Aar~~g~~~t~~eIa~v~~Vse~TIrkR~k 256 (565)
...++....|+++||+.+|++.+||.+-++
T Consensus 13 I~~l~~~G~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 13 IEALLEQGMSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp HHHHHCS---HHHHHHHTT--HHHHHHHHH
T ss_pred HHHHHHcCCCHHHHHHHHCcCcHHHHHHHh
Confidence 344566789999999999999999998765
No 99
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=79.89 E-value=1.3 Score=35.64 Aligned_cols=28 Identities=14% Similarity=0.354 Sum_probs=21.5
Q ss_pred CCCCCCCCCceeccCCC--ceecCccccee
Q 008455 3 WCSSCARHVTGHRPYDS--QLCCDRCGKVL 30 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G--~~VCt~CG~Vl 30 (565)
.||.||...+.+-..+| ..+|..||...
T Consensus 8 PCPFCG~~~~~v~~~~g~~~v~C~~CgA~~ 37 (64)
T PRK09710 8 PCPFCGCPSVTVKAISGYYRAKCNGCESRT 37 (64)
T ss_pred CCCCCCCceeEEEecCceEEEEcCCCCcCc
Confidence 59999998665555555 57999999963
No 100
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=79.83 E-value=1.1 Score=31.98 Aligned_cols=28 Identities=25% Similarity=0.718 Sum_probs=19.8
Q ss_pred CCCCCCCCCceec----cCCCceecCccccee
Q 008455 3 WCSSCARHVTGHR----PYDSQLCCDRCGKVL 30 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D----~~~G~~VCt~CG~Vl 30 (565)
.||+|+..--+.| .....+-|+.||.+.
T Consensus 4 ~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 4 TCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred ECCCCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 6999998722223 234578999999874
No 101
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=79.58 E-value=1.2 Score=32.41 Aligned_cols=27 Identities=22% Similarity=0.604 Sum_probs=19.6
Q ss_pred CCCCCCCCCceec---------cCCCceecCcccce
Q 008455 3 WCSSCARHVTGHR---------PYDSQLCCDRCGKV 29 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D---------~~~G~~VCt~CG~V 29 (565)
.||.||....++= +.+-.++|.+||..
T Consensus 2 ~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~ 37 (40)
T smart00440 2 PCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGHR 37 (40)
T ss_pred cCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCCE
Confidence 6999998855431 22448999999964
No 102
>PF08613 Cyclin: Cyclin; InterPro: IPR013922 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This entry includes cyclin PHO80 and other cyclins that partner with the cyclin-dependent kinase (CDK) PHO85. The PHO80/PHO85 cyclin-cdk complex is used for a regulatory process other than cell-cycle control []. This entry also includes other PHO80-like cyclins that are involved in the cell-cycle control. They belong to the P/U family and interact preferentially with CDKA1 [].; GO: 0019901 protein kinase binding, 0000079 regulation of cyclin-dependent protein kinase activity; PDB: 2PK9_D 2PMI_D.
Probab=79.07 E-value=13 Score=34.77 Aligned_cols=79 Identities=14% Similarity=0.045 Sum_probs=55.2
Q ss_pred CCchhhHHHHHHhhCCCCCHHHHHHHHHHHHHhhh---c--cccCCCChhHHHHHHHHHHHHhcC-CCCCHhHHHHHhcc
Q 008455 173 VDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKR---D--WITTGRKPSGLCGAALYVSALTHG-LKFSKSDIVKIVHI 246 (565)
Q Consensus 173 vdP~~~I~Rf~~~L~~~l~~~V~~~A~~Lv~~m~~---~--~l~~GR~P~~IaaAALylAar~~g-~~~t~~eIa~v~~V 246 (565)
++-..|+.|+..... .++.+.-.|+-++.++.. . .......+.-+-.+||.+|+.+.+ ...+.+..+++.||
T Consensus 52 i~i~~fl~ri~~~~~--~s~~~~i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v~gi 129 (149)
T PF08613_consen 52 ISIRDFLSRILKYTQ--CSPECLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNTYSNKSWAKVGGI 129 (149)
T ss_dssp S-HHHHHHHHHHHTT----HHHHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS---HHHHHHHHTS
T ss_pred CcHHHHHHHHHHHcC--CChHHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhcccccccHHHHHhhcCC
Confidence 667788888888777 889999999999999887 1 223456677788999999998774 45789999999998
Q ss_pred CHHHHHH
Q 008455 247 CEATLMK 253 (565)
Q Consensus 247 se~TIrk 253 (565)
+..-|.+
T Consensus 130 s~~eln~ 136 (149)
T PF08613_consen 130 SLKELNE 136 (149)
T ss_dssp -HHHHHH
T ss_pred CHHHHHH
Confidence 7655443
No 103
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=79.06 E-value=2.7 Score=31.30 Aligned_cols=29 Identities=14% Similarity=0.321 Sum_probs=19.3
Q ss_pred CCCHhHHHHHhccCHHHHHHHHHHHHccC
Q 008455 234 KFSKSDIVKIVHICEATLMKRLIEFENTD 262 (565)
Q Consensus 234 ~~t~~eIa~v~~Vse~TIrkR~kE~~~t~ 262 (565)
..|.++||+.+|||..||.+-++.|.+..
T Consensus 17 G~s~~~ia~~lgvs~~Tv~~w~kr~~~~G 45 (50)
T PF13384_consen 17 GWSIREIAKRLGVSRSTVYRWIKRYREEG 45 (50)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHT------
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHccccc
Confidence 78999999999999999999998887543
No 104
>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=78.93 E-value=3.6 Score=31.29 Aligned_cols=31 Identities=6% Similarity=0.164 Sum_probs=26.2
Q ss_pred cCCCCCHhHHHHHhccCHHHHHHHHHHHHcc
Q 008455 231 HGLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (565)
Q Consensus 231 ~g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t 261 (565)
++-.+|..++|+.++||..||++-++++.+.
T Consensus 12 ~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~ 42 (55)
T PF08279_consen 12 SKEPITAKELAEELGVSRRTIRRDIKELREW 42 (55)
T ss_dssp TTTSBEHHHHHHHCTS-HHHHHHHHHHHHHT
T ss_pred cCCCcCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 4445999999999999999999999999743
No 105
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=78.93 E-value=0.62 Score=45.17 Aligned_cols=30 Identities=27% Similarity=0.741 Sum_probs=23.9
Q ss_pred CCCCCCCCCceeccCCCceecCcccceecc
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vlee 32 (565)
.||.|+..-...|..+....|..||.+|.+
T Consensus 119 ~Cp~C~~rytf~eA~~~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 119 FCPNCHIRFTFDEAMEYGFRCPQCGEMLEE 148 (178)
T ss_pred ECCCCCcEEeHHHHhhcCCcCCCCCCCCee
Confidence 599999774444555778999999999985
No 106
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 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 ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=78.91 E-value=0.99 Score=38.86 Aligned_cols=32 Identities=22% Similarity=0.540 Sum_probs=25.5
Q ss_pred CCCCCCCCCceeccCCCceecCcccceeccccc
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNF 35 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vlee~~i 35 (565)
.||.||... +.....|-..|..||.++....+
T Consensus 37 ~Cp~Cgk~~-vkR~a~GIW~C~~C~~~~AGGAy 68 (90)
T PF01780_consen 37 TCPFCGKTS-VKRVATGIWKCKKCGKKFAGGAY 68 (90)
T ss_dssp EESSSSSSE-EEEEETTEEEETTTTEEEE-BSS
T ss_pred cCCCCCCce-eEEeeeEEeecCCCCCEEeCCCc
Confidence 599999986 45567899999999998875443
No 107
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=78.69 E-value=7.4 Score=29.16 Aligned_cols=25 Identities=12% Similarity=0.146 Sum_probs=22.8
Q ss_pred CCCHhHHHHHhccCHHHHHHHHHHH
Q 008455 234 KFSKSDIVKIVHICEATLMKRLIEF 258 (565)
Q Consensus 234 ~~t~~eIa~v~~Vse~TIrkR~kE~ 258 (565)
..|+++||+..|||..||++.++.+
T Consensus 27 ~~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 27 SRSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 3899999999999999999998765
No 108
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=78.62 E-value=93 Score=32.81 Aligned_cols=25 Identities=12% Similarity=0.111 Sum_probs=22.1
Q ss_pred CCCCCHhHHHHHhccCHHHHHHHHH
Q 008455 232 GLKFSKSDIVKIVHICEATLMKRLI 256 (565)
Q Consensus 232 g~~~t~~eIa~v~~Vse~TIrkR~k 256 (565)
+...|+++|+..+|||..|||++..
T Consensus 274 ~~~~Tl~EIa~~lgiS~erVRqi~~ 298 (317)
T PRK07405 274 GQPLTLAKIGERLNISRERVRQIER 298 (317)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 3679999999999999999998754
No 109
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=78.53 E-value=2.9 Score=39.13 Aligned_cols=38 Identities=13% Similarity=0.228 Sum_probs=32.2
Q ss_pred HHHHhcCCCCCHhHHHHHhccCHHHHHHHHHHHHccCC
Q 008455 226 VSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDS 263 (565)
Q Consensus 226 lAar~~g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t~s 263 (565)
|.+...+-+.|..+||+.+|+|+.|+++|++.+.+...
T Consensus 15 l~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~Gv 52 (153)
T PRK11179 15 LEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQAGI 52 (153)
T ss_pred HHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCC
Confidence 44455667899999999999999999999999987654
No 110
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=78.43 E-value=1.7 Score=32.02 Aligned_cols=23 Identities=30% Similarity=0.871 Sum_probs=18.2
Q ss_pred CCCCCCCCCceeccCCCceecCccc
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCG 27 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG 27 (565)
.||.||... ....+|.++|..||
T Consensus 19 ~Cp~C~~PL--~~~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 19 HCPDCGTPL--MRDKDGKIYCVSCG 41 (41)
T ss_pred ccCCCCCee--EEecCCCEECCCCC
Confidence 699997653 33468999999997
No 111
>KOG4557 consensus Origin recognition complex, subunit 6 [Replication, recombination and repair]
Probab=78.23 E-value=6.9 Score=38.93 Aligned_cols=83 Identities=14% Similarity=0.162 Sum_probs=54.5
Q ss_pred HHHHHHHHHcCCCChhHHHHHHHHHHHHHHhC-----ccccCCchhHHHHHHHHHHHHhcCCCccHHHHHhhhccChHHH
Q 008455 76 DDMRQMKNALNIGESDEIVHVAKRFYGIAVAR-----NFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYEL 150 (565)
Q Consensus 76 ~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~-----~~~rGR~~~~vaAACLYiACR~e~~p~tL~DIa~~~~vsv~~L 150 (565)
-.|+.+|=+||+. .++..|.++.+..-++ ..----+.....+|.+|.|||..+.-+.-.-+-.+.|++...+
T Consensus 94 ~~VrdlaVQfgc~---evi~~a~~vl~syk~~lpaT~~~~~D~SrP~ft~aA~~~ack~lKlKVdK~kli~~sg~~~s~F 170 (262)
T KOG4557|consen 94 LNVRDLAVQFGCV---EVIKSAQNVLSSYKERLPATRRANADFSRPVFTAAAFYLACKKLKLKVDKLKLIEVSGTSESEF 170 (262)
T ss_pred cCHHHHHHHHhHH---HHHHHHHHHHHHHHhcCchhhhcCCcccchHHHHHHHHHHHHHHHHhhhHhhcccccCCCHHHH
Confidence 3466677777776 5777777777665432 1111234467889999999999887666656666677877776
Q ss_pred HHHHHHHHHHh
Q 008455 151 GAVYLQLCQVL 161 (565)
Q Consensus 151 gr~~~~L~~~L 161 (565)
....++|-+..
T Consensus 171 ~~l~kqler~~ 181 (262)
T KOG4557|consen 171 SCLSKQLERNY 181 (262)
T ss_pred HHHHHHHHHHH
Confidence 66666555543
No 112
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=78.10 E-value=1.7 Score=40.72 Aligned_cols=29 Identities=24% Similarity=0.502 Sum_probs=21.5
Q ss_pred CCCCCCCCC-Cceecc---CCCcee-----cCccccee
Q 008455 2 VWCSSCARH-VTGHRP---YDSQLC-----CDRCGKVL 30 (565)
Q Consensus 2 ~~Cp~Cgs~-~i~~D~---~~G~~V-----Ct~CG~Vl 30 (565)
|.||.||.. .-++|+ .+|..| |..||.=.
T Consensus 1 M~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RF 38 (147)
T TIGR00244 1 MHCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERF 38 (147)
T ss_pred CCCCCCCCCCCEeeeccccCCCCeeeecccCCccCCcc
Confidence 579999986 446674 467666 99999743
No 113
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=77.89 E-value=0.61 Score=33.30 Aligned_cols=28 Identities=32% Similarity=0.695 Sum_probs=20.0
Q ss_pred CCCCCCCC-CceeccCCCceecCccccee
Q 008455 3 WCSSCARH-VTGHRPYDSQLCCDRCGKVL 30 (565)
Q Consensus 3 ~Cp~Cgs~-~i~~D~~~G~~VCt~CG~Vl 30 (565)
.|+.||.. ++.+++-.-.-+|..||.-|
T Consensus 3 ~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~~L 31 (36)
T PF05191_consen 3 ICPKCGRIYHIEFNPPKVEGVCDNCGGEL 31 (36)
T ss_dssp EETTTTEEEETTTB--SSTTBCTTTTEBE
T ss_pred CcCCCCCccccccCCCCCCCccCCCCCee
Confidence 59999986 66677655566999999744
No 114
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=77.01 E-value=1.3 Score=51.13 Aligned_cols=25 Identities=28% Similarity=0.756 Sum_probs=14.6
Q ss_pred CCCCCCCCCCCceeccCCCceecCccccee
Q 008455 1 MVWCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (565)
Q Consensus 1 M~~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vl 30 (565)
|..||.||..+ ..|..+|..||+-+
T Consensus 1 M~~Cp~Cg~~n-----~~~akFC~~CG~~l 25 (645)
T PRK14559 1 MLICPQCQFEN-----PNNNRFCQKCGTSL 25 (645)
T ss_pred CCcCCCCCCcC-----CCCCccccccCCCC
Confidence 77777777653 23444555555554
No 115
>PRK10220 hypothetical protein; Provisional
Probab=76.96 E-value=1.8 Score=38.42 Aligned_cols=28 Identities=21% Similarity=0.565 Sum_probs=21.3
Q ss_pred CCCCCCCCCceeccCCCceecCcccceecc
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vlee 32 (565)
.||.|++.-.-.| ...+||.+||.--..
T Consensus 5 ~CP~C~seytY~d--~~~~vCpeC~hEW~~ 32 (111)
T PRK10220 5 HCPKCNSEYTYED--NGMYICPECAHEWND 32 (111)
T ss_pred cCCCCCCcceEcC--CCeEECCcccCcCCc
Confidence 7999999855443 568999999985543
No 116
>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=76.68 E-value=4.3 Score=32.77 Aligned_cols=29 Identities=14% Similarity=0.383 Sum_probs=26.7
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHHHcc
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEFENT 261 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~~~t 261 (565)
++.|+.+||..+|+|..|+.+-+++|.+-
T Consensus 27 ~~lt~~~iA~~~g~sr~tv~r~l~~l~~~ 55 (76)
T PF13545_consen 27 LPLTQEEIADMLGVSRETVSRILKRLKDE 55 (76)
T ss_dssp EESSHHHHHHHHTSCHHHHHHHHHHHHHT
T ss_pred ecCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 56899999999999999999999999854
No 117
>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=76.56 E-value=5.6 Score=31.51 Aligned_cols=38 Identities=18% Similarity=0.255 Sum_probs=31.0
Q ss_pred HHHHHHHhcCCCCCHhHHHHHhccCHHHHHHHHHHHHcc
Q 008455 223 ALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (565)
Q Consensus 223 ALylAar~~g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t 261 (565)
+||.... .+..++..+||+.++|+.+|+..-++.|.+-
T Consensus 12 ~Iy~l~~-~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~ 49 (60)
T PF01325_consen 12 AIYELSE-EGGPVRTKDIAERLGVSPPTVTEMLKRLAEK 49 (60)
T ss_dssp HHHHHHH-CTSSBBHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHc-CCCCccHHHHHHHHCCChHHHHHHHHHHHHC
Confidence 4565555 6788999999999999999999999988753
No 118
>PF12773 DZR: Double zinc ribbon
Probab=76.10 E-value=1.5 Score=32.97 Aligned_cols=12 Identities=33% Similarity=0.783 Sum_probs=5.5
Q ss_pred ceecCcccceec
Q 008455 20 QLCCDRCGKVLE 31 (565)
Q Consensus 20 ~~VCt~CG~Vle 31 (565)
..+|..||+.|.
T Consensus 12 ~~fC~~CG~~l~ 23 (50)
T PF12773_consen 12 AKFCPHCGTPLP 23 (50)
T ss_pred ccCChhhcCChh
Confidence 444444444444
No 119
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=76.02 E-value=3.7 Score=36.46 Aligned_cols=30 Identities=27% Similarity=0.498 Sum_probs=22.8
Q ss_pred CCCCCCCCCCceeccCCCceecCcccceeccc
Q 008455 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLEDH 33 (565)
Q Consensus 2 ~~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vlee~ 33 (565)
..||.|++.-.-.| ...+||.+||.--...
T Consensus 3 p~CP~C~seytY~d--g~~~iCpeC~~EW~~~ 32 (109)
T TIGR00686 3 PPCPKCNSEYTYHD--GTQLICPSCLYEWNEN 32 (109)
T ss_pred CcCCcCCCcceEec--CCeeECcccccccccc
Confidence 47999999855444 4689999999876543
No 120
>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=75.96 E-value=6.3 Score=31.46 Aligned_cols=38 Identities=24% Similarity=0.282 Sum_probs=30.7
Q ss_pred CChhHHHHHHHHHHHHhcCCCCCHhHHHHHhccCHHHHHHH
Q 008455 214 RKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKR 254 (565)
Q Consensus 214 R~P~~IaaAALylAar~~g~~~t~~eIa~v~~Vse~TIrkR 254 (565)
|.|.-=-|=-||+ -++-.++.++||..+||++.|||+-
T Consensus 5 Rsp~rdkA~e~y~---~~~g~i~lkdIA~~Lgvs~~tIr~W 42 (60)
T PF10668_consen 5 RSPNRDKAFEIYK---ESNGKIKLKDIAEKLGVSESTIRKW 42 (60)
T ss_pred CCcCHHHHHHHHH---HhCCCccHHHHHHHHCCCHHHHHHH
Confidence 5665555666775 4678999999999999999999964
No 121
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=75.78 E-value=5.5 Score=28.72 Aligned_cols=36 Identities=11% Similarity=0.146 Sum_probs=26.1
Q ss_pred CCCCCHhHHHHHhccCHHHHHHHHHHHHccCCCCCCHHHHH
Q 008455 232 GLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFM 272 (565)
Q Consensus 232 g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t~s~~Lt~~~f~ 272 (565)
..+.++.+||..+|+|+..+++.+++.. -+|+-+|+
T Consensus 6 ~~~~~l~~iA~~~g~S~~~f~r~Fk~~~-----g~tp~~y~ 41 (42)
T PF00165_consen 6 QQKLTLEDIAEQAGFSPSYFSRLFKKET-----GMTPKQYR 41 (42)
T ss_dssp -SS--HHHHHHHHTS-HHHHHHHHHHHT-----SS-HHHHH
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHH-----CcCHHHHh
Confidence 3568999999999999999999998875 45666664
No 122
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=75.77 E-value=11 Score=35.80 Aligned_cols=30 Identities=17% Similarity=0.301 Sum_probs=27.5
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHHHccC
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEFENTD 262 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~~~t~ 262 (565)
++.|+.+||..+|++..|+.+-+++|.+-.
T Consensus 142 ~~~t~~~iA~~lG~tretvsR~l~~l~~~g 171 (193)
T TIGR03697 142 LRLSHQAIAEAIGSTRVTITRLLGDLRKKK 171 (193)
T ss_pred CCCCHHHHHHHhCCcHHHHHHHHHHHHHCC
Confidence 678999999999999999999999998654
No 123
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=75.76 E-value=1.7 Score=37.82 Aligned_cols=31 Identities=19% Similarity=0.569 Sum_probs=23.1
Q ss_pred CCCCCCCCCCCceeccC-CCceecCcccceec
Q 008455 1 MVWCSSCARHVTGHRPY-DSQLCCDRCGKVLE 31 (565)
Q Consensus 1 M~~Cp~Cgs~~i~~D~~-~G~~VCt~CG~Vle 31 (565)
|..||.||.-.++.-.. -....|..|++|..
T Consensus 1 m~FCP~Cgn~Live~g~~~~rf~C~tCpY~~~ 32 (105)
T KOG2906|consen 1 MLFCPTCGNMLIVESGESCNRFSCRTCPYVFP 32 (105)
T ss_pred CcccCCCCCEEEEecCCeEeeEEcCCCCceee
Confidence 78999999875544322 35678999999954
No 124
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 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. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=75.67 E-value=2.6 Score=31.72 Aligned_cols=21 Identities=19% Similarity=0.276 Sum_probs=19.5
Q ss_pred CHhHHHHHhccCHHHHHHHHH
Q 008455 236 SKSDIVKIVHICEATLMKRLI 256 (565)
Q Consensus 236 t~~eIa~v~~Vse~TIrkR~k 256 (565)
|++|||+.+|||..|+.+.|.
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln 21 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLN 21 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHT
T ss_pred CHHHHHHHHCcCHHHHHHHHh
Confidence 689999999999999999876
No 125
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=74.94 E-value=1.3 Score=34.80 Aligned_cols=34 Identities=18% Similarity=0.393 Sum_probs=23.1
Q ss_pred CCCCCCCCCCCceeccCCCceecCcccceecccccccccccccc
Q 008455 1 MVWCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATFVKN 44 (565)
Q Consensus 1 M~~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vlee~~id~~~ef~e~ 44 (565)
|..|+.||...+ ..+|..||.... +.+-+-|+-+
T Consensus 5 mr~C~~CgvYTL-------k~~CP~CG~~t~---~~~P~rfSp~ 38 (56)
T PRK13130 5 IRKCPKCGVYTL-------KEICPVCGGKTK---NPHPPRFSPE 38 (56)
T ss_pred ceECCCCCCEEc-------cccCcCCCCCCC---CCCCCCCCCC
Confidence 668999998754 459999998743 2334445543
No 126
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=74.58 E-value=2 Score=37.02 Aligned_cols=32 Identities=22% Similarity=0.600 Sum_probs=25.6
Q ss_pred CCCCCCCCCceeccCCCceecCcccceeccccc
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNF 35 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vlee~~i 35 (565)
.||.||...+ .....|-..|..||.++.-..+
T Consensus 38 ~CpfCgk~~v-kR~a~GIW~C~~C~~~~AGGAy 69 (90)
T PTZ00255 38 FCPFCGKHAV-KRQAVGIWRCKGCKKTVAGGAW 69 (90)
T ss_pred cCCCCCCCce-eeeeeEEEEcCCCCCEEeCCcc
Confidence 5999998764 4456899999999999875544
No 127
>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=74.55 E-value=1.8 Score=32.11 Aligned_cols=28 Identities=18% Similarity=0.131 Sum_probs=20.3
Q ss_pred HhcCCCCCHhHHHHHhccCHHHHHHHHH
Q 008455 229 LTHGLKFSKSDIVKIVHICEATLMKRLI 256 (565)
Q Consensus 229 r~~g~~~t~~eIa~v~~Vse~TIrkR~k 256 (565)
+|+.-..|+.+||+.+|||..||.+.++
T Consensus 16 ~l~~~G~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 16 ELYAEGMSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp HHHHTT--HHHHHHHTTS-HHHHHHHHC
T ss_pred HHHHCCCCHHHHHHHHCcCHHHHHHHHh
Confidence 3444459999999999999999998764
No 128
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=74.47 E-value=1.8 Score=34.32 Aligned_cols=25 Identities=28% Similarity=0.777 Sum_probs=12.0
Q ss_pred CCCCCCCCCceeccCCCceecCcccc
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGK 28 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~ 28 (565)
.|.+||... ..+..--...|.+||-
T Consensus 11 ~CtSCg~~i-~p~e~~v~F~CPnCGe 35 (61)
T COG2888 11 VCTSCGREI-APGETAVKFPCPNCGE 35 (61)
T ss_pred eeccCCCEe-ccCCceeEeeCCCCCc
Confidence 466666542 1222223455666663
No 129
>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=74.45 E-value=8.5 Score=30.01 Aligned_cols=30 Identities=20% Similarity=0.399 Sum_probs=26.9
Q ss_pred CCCCCHhHHHHHhccCHHHHHHHHHHHHcc
Q 008455 232 GLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (565)
Q Consensus 232 g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t 261 (565)
...+|+.+||+.+|++..|+++.++.|.+-
T Consensus 23 ~~~~s~~ela~~~g~s~~tv~r~l~~L~~~ 52 (67)
T cd00092 23 QLPLTRQEIADYLGLTRETVSRTLKELEEE 52 (67)
T ss_pred cCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 467899999999999999999999998753
No 130
>PF15616 TerY-C: TerY-C metal binding domain
Probab=74.35 E-value=1.8 Score=39.90 Aligned_cols=20 Identities=30% Similarity=0.855 Sum_probs=12.8
Q ss_pred CCCCCCCCCceeccCCCceecCccccee
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vl 30 (565)
-||+||.. .+.++| .||.|.
T Consensus 79 gCP~CGn~-------~~fa~C-~CGkl~ 98 (131)
T PF15616_consen 79 GCPHCGNQ-------YAFAVC-GCGKLF 98 (131)
T ss_pred CCCCCcCh-------hcEEEe-cCCCEE
Confidence 59999975 345555 455553
No 131
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=74.01 E-value=10 Score=37.85 Aligned_cols=51 Identities=16% Similarity=0.209 Sum_probs=32.0
Q ss_pred HHHHHHHHHHcCCCChhHHHHHHHHHHHHHHhCccccCCchhHHHHHHHHHH
Q 008455 75 FDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLA 126 (565)
Q Consensus 75 ~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiA 126 (565)
...|...-.....+. ....+.|...|++|+-....++-+...+|-.||=+|
T Consensus 75 ~~~i~~~~~~~~~~~-~Rt~~~ai~~YkLAll~~~~~~~~~s~~A~l~LrlA 125 (214)
T PF09986_consen 75 KENISSRWKPRDFSG-ERTLEEAIESYKLALLCAQIKKEKPSKKAGLCLRLA 125 (214)
T ss_pred HHHHHhhcccCCCCC-CCCHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHH
Confidence 333333333345553 557788888888887665556655666666777666
No 132
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=73.95 E-value=1.6 Score=49.68 Aligned_cols=45 Identities=22% Similarity=0.531 Sum_probs=29.5
Q ss_pred CCCCCCCCCCCc------eec----cCCCceecCcccceeccccc---cccccccccC
Q 008455 1 MVWCSSCARHVT------GHR----PYDSQLCCDRCGKVLEDHNF---STEATFVKNA 45 (565)
Q Consensus 1 M~~Cp~Cgs~~i------~~D----~~~G~~VCt~CG~Vlee~~i---d~~~ef~e~~ 45 (565)
++.||+||.... .++ +..-.++|..||..++|..- +..-.|....
T Consensus 200 ~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~e~~k~~m~~~G~Wv~~~ 257 (557)
T PF05876_consen 200 YVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIEEHDKRRMVRRGRWVATN 257 (557)
T ss_pred EccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCCHHHHhhccCCeEEEecc
Confidence 357999998633 222 34578999999999998542 2233455443
No 133
>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=73.33 E-value=4.7 Score=28.07 Aligned_cols=27 Identities=19% Similarity=0.373 Sum_probs=22.2
Q ss_pred CccHHHHHhhhccChHHHHHHHHHHHH
Q 008455 133 PFLLIDFSNYLNINVYELGAVYLQLCQ 159 (565)
Q Consensus 133 p~tL~DIa~~~~vsv~~Lgr~~~~L~~ 159 (565)
|.+-.|||+.+|+...++.|++++|.+
T Consensus 2 ~mtr~diA~~lG~t~ETVSR~l~~l~~ 28 (32)
T PF00325_consen 2 PMTRQDIADYLGLTRETVSRILKKLER 28 (32)
T ss_dssp E--HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CcCHHHHHHHhCCcHHHHHHHHHHHHH
Confidence 677899999999999999999999876
No 134
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=72.68 E-value=6.3 Score=29.46 Aligned_cols=28 Identities=14% Similarity=0.052 Sum_probs=23.9
Q ss_pred CCCCCHhHHHHHhccCHHHHHHHHHHHH
Q 008455 232 GLKFSKSDIVKIVHICEATLMKRLIEFE 259 (565)
Q Consensus 232 g~~~t~~eIa~v~~Vse~TIrkR~kE~~ 259 (565)
....|+.+||...|+|..||+++++.-.
T Consensus 18 ~~~~t~~eIa~~lg~s~~~V~~~~~~al 45 (50)
T PF04545_consen 18 FEGLTLEEIAERLGISRSTVRRILKRAL 45 (50)
T ss_dssp TST-SHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHCCcHHHHHHHHHHHH
Confidence 6789999999999999999999987643
No 135
>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=72.67 E-value=6.8 Score=35.88 Aligned_cols=47 Identities=21% Similarity=0.275 Sum_probs=40.1
Q ss_pred chhHHHHHHHHHHHHhcCCCccHHHHHhhhccChHHHHHHHHHHHHH
Q 008455 114 RTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (565)
Q Consensus 114 ~~~~vaAACLYiACR~e~~p~tL~DIa~~~~vsv~~Lgr~~~~L~~~ 160 (565)
+..+-+.+++|+|-+..+.|++..+||..++++...|.+...+|.+.
T Consensus 6 ~~~YAl~~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~ 52 (135)
T TIGR02010 6 KGRYAVTAMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKA 52 (135)
T ss_pred HHHHHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 45566778999998766779999999999999999999988888773
No 136
>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=72.63 E-value=3.7 Score=28.62 Aligned_cols=28 Identities=18% Similarity=0.350 Sum_probs=22.6
Q ss_pred CCCHhHHHHHhccCHHHHHHHHHHHHcc
Q 008455 234 KFSKSDIVKIVHICEATLMKRLIEFENT 261 (565)
Q Consensus 234 ~~t~~eIa~v~~Vse~TIrkR~kE~~~t 261 (565)
+.|..|||+.+|++..|+.+-++.|.+.
T Consensus 2 ~mtr~diA~~lG~t~ETVSR~l~~l~~~ 29 (32)
T PF00325_consen 2 PMTRQDIADYLGLTRETVSRILKKLERQ 29 (32)
T ss_dssp E--HHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred CcCHHHHHHHhCCcHHHHHHHHHHHHHc
Confidence 5788999999999999999999998753
No 137
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=72.47 E-value=31 Score=38.45 Aligned_cols=185 Identities=15% Similarity=0.218 Sum_probs=102.6
Q ss_pred HHHHHHHHcCCCChhHHHHHHHHHHHHHHhCccccCCchhHHHHHHHHHHHHhcC-C------------------CccHH
Q 008455 77 DMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKS-K------------------PFLLI 137 (565)
Q Consensus 77 ~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~-~------------------p~tL~ 137 (565)
-+..++..|+++ ...++.|..+...+.-.|+.. |+ ..=||.+=.+..+ . ..-+.
T Consensus 140 ~~~eia~~l~~~--~~~v~~~l~~lQ~leP~GigA-r~----L~ECLllQl~~~~~~~~~~~~~~il~~~le~la~~~~~ 212 (455)
T PRK05932 140 DLEEIAESLGVE--LDEVEAVLKRIQSFDPAGVGA-RD----LQECLLLQLEQLDDTPRLDEAMEIISDHLDLLARRDFR 212 (455)
T ss_pred CHHHHHHHcCCC--HHHHHHHHHHHhcCCCCccCc-CC----HHHHHHHHHhccCCCchHHHHHHHHHHHHHHHHcCCHH
Confidence 467789999999 888999888887765555421 11 1123333322211 0 12356
Q ss_pred HHHhhhccChHHHHHHHHHHHHHhhcccccc--c----cccCCchhhHHHH----------------------HHhhCCC
Q 008455 138 DFSNYLNINVYELGAVYLQLCQVLYIADESN--V----LKQVDPSIFLHKF----------------------TDRLLPG 189 (565)
Q Consensus 138 DIa~~~~vsv~~Lgr~~~~L~~~L~i~~~~~--~----~~~vdP~~~I~Rf----------------------~~~L~~~ 189 (565)
.|+..++++..+|..+...| +.|+- .|. + ...+-|..+|.+. ...+...
T Consensus 213 ~ia~~l~is~~~v~~~~~~I-r~L~P--~Pg~~~~~~~~~yi~PDv~V~~~~~~~~v~ln~~~~P~l~in~~Y~~~~~~~ 289 (455)
T PRK05932 213 TLAKKLGVKEEDLQEALDLI-RSLDP--KPGAGFGTEEPEYVVPDVFVRKINGGWLVELNPDSLPRLRINQEYAALVSRS 289 (455)
T ss_pred HHHHHHCcCHHHHHHHHHHH-hCCCC--CCccccCCCCCCccCCCEEEEEeCCEEEEEECCCCCceEEECHHHHHHHHhc
Confidence 78889999999999887655 44541 221 1 1123344444322 1111100
Q ss_pred CCHHHHHHHHHHHHHhhh-ccccC--CCChhHHHHHHHHHHHHh-----cC----CCCCHhHHHHHhccCHHHHHHHHH-
Q 008455 190 GNKKVCDTARDILASMKR-DWITT--GRKPSGLCGAALYVSALT-----HG----LKFSKSDIVKIVHICEATLMKRLI- 256 (565)
Q Consensus 190 l~~~V~~~A~~Lv~~m~~-~~l~~--GR~P~~IaaAALylAar~-----~g----~~~t~~eIa~v~~Vse~TIrkR~k- 256 (565)
.+.++.. .|-+.+.+ .|+.. .+|-.+|.-.+-.|+-+- .| .+.|+++||..+|++++||++..+
T Consensus 290 ~~~e~~~---ylk~k~~~A~~li~~i~~R~~TL~~v~~~Iv~~Q~~Ff~~G~~~LkPLtlkdvAe~lglheSTVSRav~~ 366 (455)
T PRK05932 290 ARDEDKQ---FLREKLQEAKWLIKSLEQRKETLLKVARCIVEQQRDFFEHGEEALKPLVLKDIAEELGMHESTISRATTN 366 (455)
T ss_pred cchHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccCcCccHHHHHHHhCCCccchhhhhcC
Confidence 0011111 11111111 24332 244556655555555542 34 258999999999999999999884
Q ss_pred HHHccCCCCCCHHHHHHH
Q 008455 257 EFENTDSGSLTIEDFMAR 274 (565)
Q Consensus 257 E~~~t~s~~Lt~~~f~~~ 274 (565)
-+..||-|-+-+..|-+.
T Consensus 367 Kyv~tp~Gi~~lk~FFs~ 384 (455)
T PRK05932 367 KYMATPRGIFELKYFFSS 384 (455)
T ss_pred ceeecCCceEEHHHhccc
Confidence 456677777767666543
No 138
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=72.18 E-value=6.5 Score=39.61 Aligned_cols=57 Identities=16% Similarity=0.109 Sum_probs=45.6
Q ss_pred hhhHHHHHHhhCCCCCHHHHHHHHHHHHHhhhccccCCCChhHHHHHHHHHHHHhcCCC
Q 008455 176 SIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLK 234 (565)
Q Consensus 176 ~~~I~Rf~~~L~~~l~~~V~~~A~~Lv~~m~~~~l~~GR~P~~IaaAALylAar~~g~~ 234 (565)
..+|..++.+|. +.+.|+.+|.-..++.--..-..+-.|.-+|..||||||..-..+
T Consensus 45 ~n~I~~lg~~lk--lRQ~ViATAivY~rRfy~r~S~k~~~p~lla~TClyLAcKvEE~~ 101 (264)
T KOG0794|consen 45 ANVIQKLGQHLK--LRQRVIATAIVYFRRFYLRKSLKEIEPRLLAPTCLYLACKVEECP 101 (264)
T ss_pred HHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHhhhccCHHHHHHHHHHHHhhhhhcc
Confidence 456777788887 789999999988887543333788999999999999999866554
No 139
>COG5333 CCL1 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]
Probab=72.01 E-value=3.1 Score=43.37 Aligned_cols=55 Identities=11% Similarity=0.038 Sum_probs=48.9
Q ss_pred hhhHHHHHHhhCCCCCHHHHHHHHHHHHHhhhccccCCCChhHHHHHHHHHHHHhcC
Q 008455 176 SIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHG 232 (565)
Q Consensus 176 ~~~I~Rf~~~L~~~l~~~V~~~A~~Lv~~m~~~~l~~GR~P~~IaaAALylAar~~g 232 (565)
..+|.++|.+|. ++..+..+|.-+.++.--..-+++-.|..||.+|||||++..+
T Consensus 49 ~k~i~~l~~~L~--lp~~~laTAi~~f~Rf~Lk~sv~e~~~~~vv~tcv~LA~K~ed 103 (297)
T COG5333 49 LKLIMDLCTRLN--LPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVED 103 (297)
T ss_pred HHHHHHHHHhcC--CCcchHHHHHHHHHHHHhhcccccccHHHHHHhheeeeeeccc
Confidence 467889999998 8999999999999987666668999999999999999999776
No 140
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=71.68 E-value=5.1 Score=29.10 Aligned_cols=30 Identities=17% Similarity=0.409 Sum_probs=27.1
Q ss_pred CCCCCHhHHHHHhccCHHHHHHHHHHHHcc
Q 008455 232 GLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (565)
Q Consensus 232 g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t 261 (565)
.++.++.+||+.++++..|+++.++.|.+.
T Consensus 6 ~~~~s~~~la~~l~~s~~tv~~~l~~L~~~ 35 (48)
T smart00419 6 RLPLTRQEIAELLGLTRETVSRTLKRLEKE 35 (48)
T ss_pred EeccCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 467899999999999999999999999864
No 141
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=71.05 E-value=2 Score=41.94 Aligned_cols=30 Identities=27% Similarity=0.614 Sum_probs=20.0
Q ss_pred CCCCCCCCCceec--cCCC---ceecCcccceecc
Q 008455 3 WCSSCARHVTGHR--PYDS---QLCCDRCGKVLED 32 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D--~~~G---~~VCt~CG~Vlee 32 (565)
.||.||+..+... -..| .+-|.+||+|-.+
T Consensus 8 ~Cp~Cg~eev~hEVik~~g~~~lvrC~eCG~V~~~ 42 (201)
T COG1326 8 ECPSCGSEEVSHEVIKERGREPLVRCEECGTVHPA 42 (201)
T ss_pred ECCCCCcchhhHHHHHhcCCceEEEccCCCcEeec
Confidence 6999995544111 1223 5789999999855
No 142
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=70.70 E-value=19 Score=35.24 Aligned_cols=116 Identities=14% Similarity=0.153 Sum_probs=66.8
Q ss_pred hhHHHHHHHHHHHHhcCCC-ccHHHHHhhhccChHHHHHHHHHHHHHhhccccccccccCCchhhHHHHHHhhCCCCCHH
Q 008455 115 TEQVQASCLYLACRQKSKP-FLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKK 193 (565)
Q Consensus 115 ~~~vaAACLYiACR~e~~p-~tL~DIa~~~~vsv~~Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~~~l~~~ 193 (565)
...++=|+||+ .+-| +++.+|+.+++++...+..+...|...+.-..... -|..+.+.......++
T Consensus 5 ~~~~iEA~LF~----sg~pgls~~~La~~l~~~~~~v~~~l~~L~~~y~~~~~gi---------~i~~~~~~y~l~tk~e 71 (188)
T PRK00135 5 YKSIIEALLFV----SGEEGLSLEQLAEILELEPTEVQQLLEELQEKYEGDDRGL---------KLIEFNDVYKLVTKEE 71 (188)
T ss_pred HHHHHHHHHHH----cCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhhCCCCE---------EEEEECCEEEEEEcHH
Confidence 45567788887 4777 99999999999999889998888888765322110 0111111110002222
Q ss_pred HHHHHHHHHHHhhhccccCCCChhHHHHHHH-HHHHHhcCCCCCHhHHHHHhccCHHHHH
Q 008455 194 VCDTARDILASMKRDWITTGRKPSGLCGAAL-YVSALTHGLKFSKSDIVKIVHICEATLM 252 (565)
Q Consensus 194 V~~~A~~Lv~~m~~~~l~~GR~P~~IaaAAL-ylAar~~g~~~t~~eIa~v~~Vse~TIr 252 (565)
......+++ ...+|.-+--|++ -||...+.-++|..+|+++.||+..-+-
T Consensus 72 ~~~~v~~~~---------~~~~~~~LS~aaLEtLaiIay~qPiTr~eI~~irGv~~~~ii 122 (188)
T PRK00135 72 NADYLQKLV---------KTPIKQSLSQAALEVLAIIAYKQPITRIEIDEIRGVNSDGAL 122 (188)
T ss_pred HHHHHHHHh---------cccccCCCCHHHHHHHHHHHHcCCcCHHHHHHHHCCCHHHHH
Confidence 222222111 1112222333333 2444456689999999999999964333
No 143
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=70.30 E-value=2.9 Score=34.93 Aligned_cols=30 Identities=23% Similarity=0.411 Sum_probs=20.2
Q ss_pred CCCCCCCCCCCceec-cCCCceecCccccee
Q 008455 1 MVWCSSCARHVTGHR-PYDSQLCCDRCGKVL 30 (565)
Q Consensus 1 M~~Cp~Cgs~~i~~D-~~~G~~VCt~CG~Vl 30 (565)
|+.||.|+...+-.+ ..--.-.|..|+-|-
T Consensus 1 ~llCP~C~v~l~~~~rs~vEiD~CPrCrGVW 31 (88)
T COG3809 1 MLLCPICGVELVMSVRSGVEIDYCPRCRGVW 31 (88)
T ss_pred CcccCcCCceeeeeeecCceeeeCCccccEe
Confidence 788999998733222 222345799998874
No 144
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=70.01 E-value=2.8 Score=36.18 Aligned_cols=32 Identities=19% Similarity=0.587 Sum_probs=25.8
Q ss_pred CCCCCCCCCceeccCCCceecCcccceeccccc
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNF 35 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vlee~~i 35 (565)
.||.||...+ .....|-..|..||.++.-..+
T Consensus 37 ~CpfCgk~~v-kR~a~GIW~C~~C~~~~AGGAy 68 (91)
T TIGR00280 37 VCPFCGKKTV-KRGSTGIWTCRKCGAKFAGGAY 68 (91)
T ss_pred cCCCCCCCce-EEEeeEEEEcCCCCCEEeCCcc
Confidence 6999998764 5567899999999999875544
No 145
>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=69.90 E-value=6.4 Score=32.86 Aligned_cols=46 Identities=24% Similarity=0.257 Sum_probs=37.1
Q ss_pred hhHHHHHHHHHHHHhcCCCccHHHHHhhhccChHHHHHHHHHHHHH
Q 008455 115 TEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (565)
Q Consensus 115 ~~~vaAACLYiACR~e~~p~tL~DIa~~~~vsv~~Lgr~~~~L~~~ 160 (565)
....+-+.+|+|-...+.|.+..+||+.++++...|.+.+..|.+.
T Consensus 7 ~~~Al~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~ 52 (83)
T PF02082_consen 7 TDYALRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKA 52 (83)
T ss_dssp HHHHHHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhC
Confidence 3445557788887777778999999999999999999999999884
No 146
>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=69.73 E-value=4.6 Score=31.48 Aligned_cols=30 Identities=20% Similarity=0.247 Sum_probs=26.4
Q ss_pred CCCCCHhHHHHHhccCHHHHHHHHHHHHcc
Q 008455 232 GLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (565)
Q Consensus 232 g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t 261 (565)
.-.++.++++..++||+.|||+=+.+|.+.
T Consensus 12 ~~~~s~~ela~~~~VS~~TiRRDl~~L~~~ 41 (57)
T PF08220_consen 12 KGKVSVKELAEEFGVSEMTIRRDLNKLEKQ 41 (57)
T ss_pred cCCEEHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 357899999999999999999999988754
No 147
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=69.73 E-value=6.4 Score=36.27 Aligned_cols=33 Identities=15% Similarity=0.396 Sum_probs=29.0
Q ss_pred hcCCCCCHhHHHHHhccCHHHHHHHHHHHHccC
Q 008455 230 THGLKFSKSDIVKIVHICEATLMKRLIEFENTD 262 (565)
Q Consensus 230 ~~g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t~ 262 (565)
..+.++|+.+||+.+|+|+.|+++|++.+.+..
T Consensus 18 ~~d~r~~~~eia~~lglS~~~v~~Ri~~L~~~G 50 (154)
T COG1522 18 QEDARISNAELAERVGLSPSTVLRRIKRLEEEG 50 (154)
T ss_pred HHhCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 445679999999999999999999999998654
No 148
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=69.25 E-value=3 Score=36.45 Aligned_cols=27 Identities=30% Similarity=0.776 Sum_probs=21.3
Q ss_pred CCCCCCCCCceeccCCCceecCcccceecc
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vlee 32 (565)
.||.||+-.. +..|.++|..||.+.+.
T Consensus 2 fC~~Cg~~l~---~~~~~~~C~~C~~~~~~ 28 (104)
T TIGR01384 2 FCPKCGSLMT---PKNGVYVCPSCGYEKEK 28 (104)
T ss_pred CCcccCcccc---cCCCeEECcCCCCcccc
Confidence 6999998642 34689999999998653
No 149
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=68.66 E-value=3.4 Score=36.56 Aligned_cols=32 Identities=22% Similarity=0.513 Sum_probs=23.0
Q ss_pred CCCCCCCCCCCceeccCCCceecCcccceecccc
Q 008455 1 MVWCSSCARHVTGHRPYDSQLCCDRCGKVLEDHN 34 (565)
Q Consensus 1 M~~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vlee~~ 34 (565)
|..||.|++.-. ++ ..+.++|..|+.--.++-
T Consensus 3 lp~cp~c~sEyt-Ye-d~~~~~cpec~~ew~~~~ 34 (112)
T COG2824 3 LPPCPKCNSEYT-YE-DGGQLICPECAHEWNENE 34 (112)
T ss_pred CCCCCccCCceE-Ee-cCceEeCchhcccccccc
Confidence 357999998743 43 356999999998766433
No 150
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=68.63 E-value=7.5 Score=33.71 Aligned_cols=30 Identities=20% Similarity=0.346 Sum_probs=27.2
Q ss_pred CCCCCHhHHHHHhccCHHHHHHHHHHHHcc
Q 008455 232 GLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (565)
Q Consensus 232 g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t 261 (565)
+-+.|..+|++.+|+++.|+++|++.|.+.
T Consensus 15 ~~~~~~~~la~~l~~s~~tv~~~l~~L~~~ 44 (108)
T smart00344 15 DARISLAELAKKVGLSPSTVHNRVKRLEEE 44 (108)
T ss_pred hCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 357899999999999999999999999864
No 151
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=68.56 E-value=3 Score=33.54 Aligned_cols=27 Identities=19% Similarity=0.582 Sum_probs=18.2
Q ss_pred CCCCCCCCCCceeccC--CC---------------ceecCcccc
Q 008455 2 VWCSSCARHVTGHRPY--DS---------------QLCCDRCGK 28 (565)
Q Consensus 2 ~~Cp~Cgs~~i~~D~~--~G---------------~~VCt~CG~ 28 (565)
..||.||......+.. +| .+.|.+||+
T Consensus 5 ~kCpKCgn~~~~ekei~~tg~~lskifdvq~n~f~~itCk~CgY 48 (68)
T COG3478 5 FKCPKCGNTNYEEKEIAATGGGLSKIFDVQNNKFIVITCKNCGY 48 (68)
T ss_pred ccCCCcCCcchhhceeeccCCCcceeEEecccEEEEEEeccCCc
Confidence 4699999886655431 22 256889987
No 152
>PRK05949 RNA polymerase sigma factor; Validated
Probab=68.21 E-value=1.7e+02 Score=31.09 Aligned_cols=24 Identities=4% Similarity=0.029 Sum_probs=21.7
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHH
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLI 256 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~k 256 (565)
...|.++|+..+|||..||+++..
T Consensus 285 e~~Tl~EIa~~lgiS~erVrq~~~ 308 (327)
T PRK05949 285 KELSLAKVGERLNLSRERVRQLEH 308 (327)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHH
Confidence 579999999999999999998754
No 153
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=68.16 E-value=2.6 Score=30.55 Aligned_cols=27 Identities=22% Similarity=0.524 Sum_probs=16.4
Q ss_pred CCCCCCCCCceec---------cCCCceecCcccce
Q 008455 3 WCSSCARHVTGHR---------PYDSQLCCDRCGKV 29 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D---------~~~G~~VCt~CG~V 29 (565)
.||.||+...++- +.+-.++|.+||..
T Consensus 2 ~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~ 37 (39)
T PF01096_consen 2 KCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHR 37 (39)
T ss_dssp --SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEE
T ss_pred CCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCe
Confidence 6999999854332 12447899999964
No 154
>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=68.12 E-value=13 Score=30.89 Aligned_cols=27 Identities=19% Similarity=0.064 Sum_probs=23.7
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHHH
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEFE 259 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~~ 259 (565)
...|+++||..+|||+.||++++....
T Consensus 31 eGlS~kEIAe~LGIS~~TVk~~l~~~~ 57 (73)
T TIGR03879 31 AGKTASEIAEELGRTEQTVRNHLKGET 57 (73)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhcCc
Confidence 457999999999999999999998543
No 155
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=67.72 E-value=70 Score=34.71 Aligned_cols=89 Identities=9% Similarity=0.101 Sum_probs=49.1
Q ss_pred hHHHHHHHHHHHHHHHHHHcCCCChhHHHHHHHHHHHHHHhCcccc-C---CchhHHH-------HHHHHHHHHhcCCCc
Q 008455 66 SRERLMEKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTK-G---RRTEQVQ-------ASCLYLACRQKSKPF 134 (565)
Q Consensus 66 srer~l~~a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~r-G---R~~~~va-------AACLYiACR~e~~p~ 134 (565)
..+-.++.|+-.+-+-..++.-.-+.....-|..+.+.+..+-+.. + |-+.++. -+.--+. ...|..-
T Consensus 162 ~~eDLiQEG~igL~~Ai~kFd~~kg~~FsTYA~wWIRqaI~~~I~~~~r~IRlP~~~~~~~~~i~~a~~~l~-~~lgr~P 240 (373)
T PRK07406 162 SFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLS-QEFGRKP 240 (373)
T ss_pred CHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcCCceeCCHHHHHHHHHHHHHHHHHH-HHhCCCC
Confidence 3455667777666666666654422356677777766665433221 1 1112221 1111111 2234444
Q ss_pred cHHHHHhhhccChHHHHHHHH
Q 008455 135 LLIDFSNYLNINVYELGAVYL 155 (565)
Q Consensus 135 tL~DIa~~~~vsv~~Lgr~~~ 155 (565)
+..+||..+++++..|.....
T Consensus 241 t~~EIA~~lg~~~e~v~~~~~ 261 (373)
T PRK07406 241 TEEEIAESMEMTIEKLRFIAK 261 (373)
T ss_pred CHHHHHHHhCCCHHHHHHHHH
Confidence 799999999999999876533
No 156
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=67.69 E-value=3.3 Score=32.68 Aligned_cols=26 Identities=23% Similarity=0.543 Sum_probs=19.1
Q ss_pred CCCCCCCCCCceeccCCCceecCcccceeccc
Q 008455 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLEDH 33 (565)
Q Consensus 2 ~~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vlee~ 33 (565)
+.||.||.... -..||..||+--+..
T Consensus 28 ~~C~~CG~~~~------~H~vC~~CG~Y~gr~ 53 (57)
T PRK12286 28 VECPNCGEPKL------PHRVCPSCGYYKGRE 53 (57)
T ss_pred eECCCCCCccC------CeEECCCCCcCCCEE
Confidence 46999998643 466999999865543
No 157
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=67.35 E-value=3.3 Score=35.72 Aligned_cols=32 Identities=22% Similarity=0.541 Sum_probs=25.7
Q ss_pred CCCCCCCCCceeccCCCceecCcccceeccccc
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNF 35 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vlee~~i 35 (565)
.||.||...+ .....|-..|..||.++.....
T Consensus 38 ~CpfCgk~~v-kR~a~GIW~C~~C~~~~AGGAy 69 (90)
T PRK03976 38 VCPVCGRPKV-KRVGTGIWECRKCGAKFAGGAY 69 (90)
T ss_pred cCCCCCCCce-EEEEEEEEEcCCCCCEEeCCcc
Confidence 5999987754 4567899999999999876544
No 158
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=67.28 E-value=1.5e+02 Score=30.15 Aligned_cols=100 Identities=14% Similarity=0.167 Sum_probs=62.8
Q ss_pred HHHHHHHHHHHhcCCCccHHHHHhhhccChHHHHHHHHHHHHHhhccccccccccCCchhhHHHHHHhhCCCCCHHHHHH
Q 008455 118 VQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDT 197 (565)
Q Consensus 118 vaAACLYiACR~e~~p~tL~DIa~~~~vsv~~Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~~~l~~~V~~~ 197 (565)
+..++-||.-. ...++++.++|+.++++...|.+.|++. +| ..|..||.+. -...
T Consensus 185 i~~~~~~i~~~-~~~~isl~~lA~~~~lS~~~l~r~Fk~~---~G----------~tp~~~l~~~-----------Rl~~ 239 (290)
T PRK10572 185 VREACQYISDH-LASEFDIESVAQHVCLSPSRLAHLFRQQ---LG----------ISVLRWREDQ-----------RISR 239 (290)
T ss_pred HHHHHHHHHhc-ccCCCCHHHHHHHHCCCHHHHHHHHHHH---HC----------cCHHHHHHHH-----------HHHH
Confidence 44555566433 3368888999999999888888877754 33 2344444422 1112
Q ss_pred HHHHHHHhhhccccCCCChhHHHHHHHHHHHHhcCCCCCHhHHHHHhccC-HHHHHHHHHHHHccCCCCCCHHHHHHHH
Q 008455 198 ARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHIC-EATLMKRLIEFENTDSGSLTIEDFMARK 275 (565)
Q Consensus 198 A~~Lv~~m~~~~l~~GR~P~~IaaAALylAar~~g~~~t~~eIa~v~~Vs-e~TIrkR~kE~~~t~s~~Lt~~~f~~~~ 275 (565)
|..++. .-+.++.+||..+|-+ .+...+.+|... .+|+.+|++.-
T Consensus 240 A~~lL~----------------------------~t~~sI~eIA~~~GF~d~s~Fsr~FKk~~-----G~SP~~yR~~~ 285 (290)
T PRK10572 240 AKLLLQ----------------------------TTRMPIATIGRNVGYDDQLYFSRVFKKCT-----GASPSEFRARC 285 (290)
T ss_pred HHHHHH----------------------------cCCCCHHHHHHHhCCCCHHHHHHHHHHHH-----CcCHHHHHHHh
Confidence 222221 2357788888888876 577778777776 67778887653
No 159
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 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 [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=66.52 E-value=2.5 Score=33.08 Aligned_cols=24 Identities=25% Similarity=0.560 Sum_probs=17.4
Q ss_pred CCCCCCCCCCceeccCCCceecCcccceec
Q 008455 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (565)
Q Consensus 2 ~~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vle 31 (565)
+.||.||... -...||..||+.=.
T Consensus 27 ~~c~~cg~~~------~~H~vc~~cG~y~~ 50 (56)
T PF01783_consen 27 VKCPNCGEPK------LPHRVCPSCGYYKG 50 (56)
T ss_dssp EESSSSSSEE------STTSBCTTTBBSSS
T ss_pred eeeccCCCEe------cccEeeCCCCeECC
Confidence 4699999642 35679999997544
No 160
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=66.50 E-value=2.5 Score=40.29 Aligned_cols=29 Identities=28% Similarity=0.780 Sum_probs=18.9
Q ss_pred CCCCCCCCCCCcee--------------ccCCCceecCcccce
Q 008455 1 MVWCSSCARHVTGH--------------RPYDSQLCCDRCGKV 29 (565)
Q Consensus 1 M~~Cp~Cgs~~i~~--------------D~~~G~~VCt~CG~V 29 (565)
++.||.|++....+ -..+-..+|+.||.|
T Consensus 97 ~~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~Cgki 139 (165)
T COG1656 97 FSRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKI 139 (165)
T ss_pred cccCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCccc
Confidence 35799999863322 122346779999987
No 161
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=66.41 E-value=3.2 Score=29.63 Aligned_cols=28 Identities=21% Similarity=0.535 Sum_probs=18.8
Q ss_pred CCCCCCCC-CceeccC-CCceecCccccee
Q 008455 3 WCSSCARH-VTGHRPY-DSQLCCDRCGKVL 30 (565)
Q Consensus 3 ~Cp~Cgs~-~i~~D~~-~G~~VCt~CG~Vl 30 (565)
.|+.||.. .+..... .....|..||.-+
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~ 36 (41)
T smart00834 7 RCEDCGHTFEVLQKISDDPLATCPECGGDV 36 (41)
T ss_pred EcCCCCCEEEEEEecCCCCCCCCCCCCCcc
Confidence 69999985 2222222 4578899999843
No 162
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=66.34 E-value=23 Score=39.10 Aligned_cols=182 Identities=14% Similarity=0.185 Sum_probs=100.8
Q ss_pred HHHHHHHHcCCCChhHHHHHHHHHHHHHHhCccccCCchhHHHHHHHHHHHHhcCC------------------CccHHH
Q 008455 77 DMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSK------------------PFLLID 138 (565)
Q Consensus 77 ~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~------------------p~tL~D 138 (565)
-+..+|..|+++ ...++.|..++..+.-.|+.. |+ ..=||.+=.+..+. ..-+..
T Consensus 115 ~~~eia~~l~~~--~~~ve~~l~~iq~leP~GIgA-r~----L~EcLllQl~~~~~~~~~~a~~il~~~le~l~~~~~~~ 187 (429)
T TIGR02395 115 DLEEIADELEVS--EEEVEKVLELIQRLDPAGVGA-RD----LQECLLLQLERLDIDDPELAYNILLEHLELLAEKDFRR 187 (429)
T ss_pred CHHHHHHHcCCC--HHHHHHHHHHHhcCCCCccCc-CC----HHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHhccHHH
Confidence 367789999999 899999988887755445421 11 11233333332211 123567
Q ss_pred HHhhhccChHHHHHHHHHHHHHhhccccccc-----cccCCchhhHHHHHHhh----CCC------CCHH----------
Q 008455 139 FSNYLNINVYELGAVYLQLCQVLYIADESNV-----LKQVDPSIFLHKFTDRL----LPG------GNKK---------- 193 (565)
Q Consensus 139 Ia~~~~vsv~~Lgr~~~~L~~~L~i~~~~~~-----~~~vdP~~~I~Rf~~~L----~~~------l~~~---------- 193 (565)
|+..++++..++..+...|.. |+-.....+ ...+-|..+|.+.-..+ ... +++.
T Consensus 188 i~~~l~is~~~v~~~~~~I~~-L~P~Pg~~~~~~~~~~yi~PDv~V~~~~~~~~v~ln~~~~P~l~i~~~y~~~~~~~~~ 266 (429)
T TIGR02395 188 LAKKLGLSEEELKEALDLIKS-LSPKPGKEFADPEEVEYVIPDVIVTKKNGEWVVELNGRSLPELRINEEYFKLLKDAEK 266 (429)
T ss_pred HHHHHCcCHHHHHHHHHHHhC-CCCCCcccccCCCCCCccCCCEEEEEECCEEEEEEcCCCCceEEECHHHHHHHHhccc
Confidence 888999999999887765544 541100000 11234544443322211 000 1111
Q ss_pred --H-------HHHHHHHHHHhhhccccCCCChhHHHHHHHHHHHH-----hcC----CCCCHhHHHHHhccCHHHHHHHH
Q 008455 194 --V-------CDTARDILASMKRDWITTGRKPSGLCGAALYVSAL-----THG----LKFSKSDIVKIVHICEATLMKRL 255 (565)
Q Consensus 194 --V-------~~~A~~Lv~~m~~~~l~~GR~P~~IaaAALylAar-----~~g----~~~t~~eIa~v~~Vse~TIrkR~ 255 (565)
+ .+.|..|++.+ -+|-.+|.-.+-.|+-+ ..| .+.|+++||..+|++++||++..
T Consensus 267 ~~~~~ylk~k~~~A~~li~~i-------~~R~~TL~~v~~~Iv~~Q~~Ff~~G~~~LkPLtlkdiA~~lglheSTVSRav 339 (429)
T TIGR02395 267 EAAAQYLKQKLKEARWLIKAL-------EQREETLLKVAEAIVEHQKDFFLGGPAALKPLTLREVAEELGLHESTISRAI 339 (429)
T ss_pred hHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHhcCcccCcCCcHHHHHHHhCCCccchhhhh
Confidence 1 12223333222 24445555555555543 234 36899999999999999999988
Q ss_pred H-HHHccCCCCCCHHHHHH
Q 008455 256 I-EFENTDSGSLTIEDFMA 273 (565)
Q Consensus 256 k-E~~~t~s~~Lt~~~f~~ 273 (565)
+ -+..||-|-+-+..|-+
T Consensus 340 ~~Kyi~tp~Gi~~lk~FFs 358 (429)
T TIGR02395 340 NNKYLQTPRGVFELKYFFS 358 (429)
T ss_pred cCceEecCCceEEHHHhcC
Confidence 4 45567777666666654
No 163
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=66.10 E-value=4.5 Score=35.73 Aligned_cols=30 Identities=17% Similarity=0.392 Sum_probs=21.6
Q ss_pred CCCCCCCCCCceecc--------CC-Cc-eecCcccceec
Q 008455 2 VWCSSCARHVTGHRP--------YD-SQ-LCCDRCGKVLE 31 (565)
Q Consensus 2 ~~Cp~Cgs~~i~~D~--------~~-G~-~VCt~CG~Vle 31 (565)
..||+||+.....+. .. +. ++|+.|+.-+.
T Consensus 3 ~~CpYCg~~~~l~~~~~iYg~~~~~~~~~y~C~~C~AyVG 42 (102)
T PF11672_consen 3 IICPYCGGPAELVDGSEIYGHRYDDGPYLYVCTPCDAYVG 42 (102)
T ss_pred cccCCCCCeeEEcccchhcCccCCCCceeEECCCCCceee
Confidence 479999998554441 12 33 89999999876
No 164
>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=65.86 E-value=10 Score=30.34 Aligned_cols=30 Identities=10% Similarity=0.185 Sum_probs=26.4
Q ss_pred cCCCCCHhHHHHHhccCHHHHHHHHHHHHc
Q 008455 231 HGLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (565)
Q Consensus 231 ~g~~~t~~eIa~v~~Vse~TIrkR~kE~~~ 260 (565)
.+-..+..+|+..++||..||+++++.+.+
T Consensus 10 ~~~~~~~~eLa~~l~vS~~tv~~~l~~L~~ 39 (69)
T TIGR00122 10 ADNPFSGEKLGEALGMSRTAVNKHIQTLRE 39 (69)
T ss_pred HcCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 344578999999999999999999999975
No 165
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=65.75 E-value=8.8 Score=28.96 Aligned_cols=30 Identities=20% Similarity=0.334 Sum_probs=26.0
Q ss_pred CCCC-CHhHHHHHhccCHHHHHHHHHHHHcc
Q 008455 232 GLKF-SKSDIVKIVHICEATLMKRLIEFENT 261 (565)
Q Consensus 232 g~~~-t~~eIa~v~~Vse~TIrkR~kE~~~t 261 (565)
|..+ |.++++..++||..||++.++.|.+.
T Consensus 17 ~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~ 47 (60)
T smart00345 17 GDKLPSERELAAQLGVSRTTVREALSRLEAE 47 (60)
T ss_pred CCcCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 3345 89999999999999999999999854
No 166
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=65.30 E-value=23 Score=33.48 Aligned_cols=29 Identities=3% Similarity=-0.074 Sum_probs=27.0
Q ss_pred CCccHHHHHhhhccChHHHHHHHHHHHHH
Q 008455 132 KPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (565)
Q Consensus 132 ~p~tL~DIa~~~~vsv~~Lgr~~~~L~~~ 160 (565)
.|.|..|||+.+|++..+|.|++++|.+.
T Consensus 142 ~~~t~~~iA~~lG~tretvsR~l~~l~~~ 170 (193)
T TIGR03697 142 LRLSHQAIAEAIGSTRVTITRLLGDLRKK 170 (193)
T ss_pred CCCCHHHHHHHhCCcHHHHHHHHHHHHHC
Confidence 68899999999999999999999999885
No 167
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=65.20 E-value=3.8 Score=38.51 Aligned_cols=28 Identities=21% Similarity=0.436 Sum_probs=19.9
Q ss_pred CCCCCCCCCCc-eecc---CCCce-----ecCcccce
Q 008455 2 VWCSSCARHVT-GHRP---YDSQL-----CCDRCGKV 29 (565)
Q Consensus 2 ~~Cp~Cgs~~i-~~D~---~~G~~-----VCt~CG~V 29 (565)
|.||.|++... +.|+ .+|.. .|.+||.=
T Consensus 1 M~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~R 37 (156)
T COG1327 1 MKCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGER 37 (156)
T ss_pred CCCCCCCCCCCeeeecccccccchhhhhhcccccccc
Confidence 57999998833 5664 35654 59999974
No 168
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=64.79 E-value=72 Score=32.61 Aligned_cols=28 Identities=14% Similarity=0.110 Sum_probs=23.8
Q ss_pred CCCCCHhHHHHHhccCHHHHHHHHHHHH
Q 008455 232 GLKFSKSDIVKIVHICEATLMKRLIEFE 259 (565)
Q Consensus 232 g~~~t~~eIa~v~~Vse~TIrkR~kE~~ 259 (565)
....|+++||..+|||..||+++++...
T Consensus 229 ~~~~t~~EIA~~lgis~~~V~~~~~ral 256 (264)
T PRK07122 229 FESMTQTQIAERVGISQMHVSRLLAKTL 256 (264)
T ss_pred cCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 3578999999999999999999876543
No 169
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=64.70 E-value=8.4 Score=28.51 Aligned_cols=26 Identities=19% Similarity=0.287 Sum_probs=23.6
Q ss_pred CCCHhHHHHHhccCHHHHHHHHHHHH
Q 008455 234 KFSKSDIVKIVHICEATLMKRLIEFE 259 (565)
Q Consensus 234 ~~t~~eIa~v~~Vse~TIrkR~kE~~ 259 (565)
..+.++||..++||..||++++..+.
T Consensus 18 g~s~~eia~~l~is~~tv~~~~~~~~ 43 (58)
T smart00421 18 GLTNKEIAERLGISEKTVKTHLSNIM 43 (58)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 36999999999999999999998875
No 170
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=64.70 E-value=11 Score=28.01 Aligned_cols=28 Identities=25% Similarity=0.196 Sum_probs=21.3
Q ss_pred cCCCCCHhHHHHHhccCHHHHHHHHHHHH
Q 008455 231 HGLKFSKSDIVKIVHICEATLMKRLIEFE 259 (565)
Q Consensus 231 ~g~~~t~~eIa~v~~Vse~TIrkR~kE~~ 259 (565)
+|. .|++..|+..||..+||+.|++.-.
T Consensus 14 ~g~-~S~r~AA~~ygVp~sTL~~r~~g~~ 41 (45)
T PF05225_consen 14 NGK-MSIRKAAKKYGVPRSTLRRRLRGKP 41 (45)
T ss_dssp TTS-S-HHHHHHHHT--HHHHHHHHHHTT
T ss_pred hCC-CCHHHHHHHHCcCHHHHHHHHcCCC
Confidence 555 9999999999999999999887543
No 171
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=64.59 E-value=9.9 Score=36.62 Aligned_cols=73 Identities=22% Similarity=0.236 Sum_probs=47.3
Q ss_pred CCHHHHHHHHHHHHHhhhccccCCCChhHHHHHHHHHHHHhcCCCCCHhHHHHHhccCHHHHHHHHHHHHccCCCCCCHH
Q 008455 190 GNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIE 269 (565)
Q Consensus 190 l~~~V~~~A~~Lv~~m~~~~l~~GR~P~~IaaAALylAar~~g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t~s~~Lt~~ 269 (565)
..+.|.........+. .|+.+ +|-|| ++.+| ...-.|..+||.-+|.|+.|||+.++. +|..++|--+
T Consensus 27 ~~~evlkli~~~~~~l--TWvdS------LavAA-ga~ar-ekag~Ti~EIAeelG~TeqTir~hlkg--etkAG~lv~e 94 (182)
T COG1318 27 FRPEVLKLIKDPYERL--TWVDS------LAVAA-GALAR-EKAGMTISEIAEELGRTEQTVRNHLKG--ETKAGQLVRE 94 (182)
T ss_pred ccHHHHHHHhCccccc--chhhH------HHHHH-HHHHH-HHccCcHHHHHHHhCCCHHHHHHHHhc--chhhhhHHHH
Confidence 3455555544444333 46533 34333 33344 567799999999999999999999984 5667766555
Q ss_pred HHHHH
Q 008455 270 DFMAR 274 (565)
Q Consensus 270 ~f~~~ 274 (565)
-|..+
T Consensus 95 tY~~l 99 (182)
T COG1318 95 TYEKL 99 (182)
T ss_pred HHHHH
Confidence 55444
No 172
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=64.55 E-value=29 Score=31.38 Aligned_cols=54 Identities=4% Similarity=0.022 Sum_probs=42.5
Q ss_pred ChhHHHHHHHHHHHHhcCCCCCHhHHHHHhccCHHHHHHHHHHHHccCCCCCCHHHHHHH
Q 008455 215 KPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMAR 274 (565)
Q Consensus 215 ~P~~IaaAALylAar~~g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t~s~~Lt~~~f~~~ 274 (565)
....|..+.-||-.... .+.++.+||+.+|+|+.++.+.+++.. .+|+.+|...
T Consensus 7 ~~~~i~~~~~~I~~~~~-~~~sl~~lA~~~g~S~~~l~r~Fk~~~-----G~s~~~~l~~ 60 (127)
T PRK11511 7 DAITIHSILDWIEDNLE-SPLSLEKVSERSGYSKWHLQRMFKKET-----GHSLGQYIRS 60 (127)
T ss_pred cHHHHHHHHHHHHHhcC-CCCCHHHHHHHHCcCHHHHHHHHHHHH-----CcCHHHHHHH
Confidence 34455666667766654 479999999999999999999999887 5778888654
No 173
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=64.44 E-value=3.8 Score=34.64 Aligned_cols=31 Identities=19% Similarity=0.404 Sum_probs=17.2
Q ss_pred CCCCCCCC-Cc--eecc--CCCceecCcccceeccc
Q 008455 3 WCSSCARH-VT--GHRP--YDSQLCCDRCGKVLEDH 33 (565)
Q Consensus 3 ~Cp~Cgs~-~i--~~D~--~~G~~VCt~CG~Vlee~ 33 (565)
.||.||.. .+ .+|. ..|.+.|..||...+-.
T Consensus 24 ~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~~ 59 (81)
T PF05129_consen 24 DCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQTK 59 (81)
T ss_dssp --TTT--SS-EEEEEETTTTEEEEEESSS--EEEEE
T ss_pred cCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEEEc
Confidence 59999944 33 3443 46899999999987643
No 174
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=64.32 E-value=4.5 Score=31.64 Aligned_cols=25 Identities=24% Similarity=0.559 Sum_probs=18.1
Q ss_pred CCCCCCCCCCceeccCCCceecCcccceecc
Q 008455 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (565)
Q Consensus 2 ~~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vlee 32 (565)
+.||+||... --.-||..||+--+-
T Consensus 27 ~~C~~cG~~~------~~H~vc~~cG~Y~gr 51 (55)
T TIGR01031 27 VVCPNCGEFK------LPHRVCPSCGYYKGR 51 (55)
T ss_pred eECCCCCCcc------cCeeECCccCeECCE
Confidence 4699999863 345699999976543
No 175
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=64.18 E-value=1.5e+02 Score=29.17 Aligned_cols=28 Identities=4% Similarity=0.055 Sum_probs=23.7
Q ss_pred CCCCCHhHHHHHhccCHHHHHHHHHHHH
Q 008455 232 GLKFSKSDIVKIVHICEATLMKRLIEFE 259 (565)
Q Consensus 232 g~~~t~~eIa~v~~Vse~TIrkR~kE~~ 259 (565)
....|+++||..+|||..||++..+...
T Consensus 197 ~~~~t~~eIA~~lgis~~~V~~~~~~al 224 (231)
T TIGR02885 197 FKDKTQTEVANMLGISQVQVSRLEKKVL 224 (231)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 3568999999999999999998876543
No 176
>PF12773 DZR: Double zinc ribbon
Probab=64.14 E-value=4.7 Score=30.25 Aligned_cols=30 Identities=23% Similarity=0.616 Sum_probs=21.3
Q ss_pred CCCCCCCCCCceeccCCCceecCcccceeccc
Q 008455 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLEDH 33 (565)
Q Consensus 2 ~~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vlee~ 33 (565)
..|++||.... .......+|..||..+..+
T Consensus 13 ~fC~~CG~~l~--~~~~~~~~C~~Cg~~~~~~ 42 (50)
T PF12773_consen 13 KFCPHCGTPLP--PPDQSKKICPNCGAENPPN 42 (50)
T ss_pred cCChhhcCChh--hccCCCCCCcCCcCCCcCC
Confidence 47999998744 2234577999999976643
No 177
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=64.02 E-value=13 Score=35.58 Aligned_cols=47 Identities=19% Similarity=0.230 Sum_probs=39.4
Q ss_pred chhHHHHHHHHHHHHhcCCCccHHHHHhhhccChHHHHHHHHHHHHH
Q 008455 114 RTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (565)
Q Consensus 114 ~~~~vaAACLYiACR~e~~p~tL~DIa~~~~vsv~~Lgr~~~~L~~~ 160 (565)
+.++-+.+++|+|....+-|.++.+||+.++++..-|.+.+..|.+.
T Consensus 6 ~~~yAl~~l~~lA~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~a 52 (164)
T PRK10857 6 KGRYAVTAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLRKN 52 (164)
T ss_pred HHHHHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 45667778999995555679999999999999999999988888773
No 178
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=63.98 E-value=3.8 Score=32.33 Aligned_cols=26 Identities=19% Similarity=0.520 Sum_probs=18.7
Q ss_pred CCCCCCCCCCCceeccCCCceecCcccceecc
Q 008455 1 MVWCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (565)
Q Consensus 1 M~~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vlee 32 (565)
|+.|++||...+ -.-||..||+--+.
T Consensus 27 ~~~c~~cG~~~l------~Hrvc~~cg~Y~g~ 52 (57)
T COG0333 27 LSVCPNCGEYKL------PHRVCLKCGYYKGR 52 (57)
T ss_pred ceeccCCCCccc------CceEcCCCCCccCe
Confidence 457999998744 34599999975443
No 179
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=63.93 E-value=4.6 Score=32.04 Aligned_cols=26 Identities=27% Similarity=0.733 Sum_probs=14.6
Q ss_pred CCCCCCCCCceeccCCCceecCcccce
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGKV 29 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~V 29 (565)
.|.+||......+ ..-...|.+||.+
T Consensus 9 ~CtSCg~~i~~~~-~~~~F~CPnCG~~ 34 (59)
T PRK14890 9 KCTSCGIEIAPRE-KAVKFLCPNCGEV 34 (59)
T ss_pred cccCCCCcccCCC-ccCEeeCCCCCCe
Confidence 4777776532221 1235667777765
No 180
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=63.44 E-value=33 Score=30.48 Aligned_cols=67 Identities=19% Similarity=0.216 Sum_probs=47.8
Q ss_pred HHHHHHhcCCCccHHHHHhhhccChHHHHHHHHHHHHHhhccccccccccCCchhh-HHHHHHhh-CCCCCHHHHHHHHH
Q 008455 123 LYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIF-LHKFTDRL-LPGGNKKVCDTARD 200 (565)
Q Consensus 123 LYiACR~e~~p~tL~DIa~~~~vsv~~Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~-I~Rf~~~L-~~~l~~~V~~~A~~ 200 (565)
||+-||= .|++|-..+|++..+++.-+-.+.+.++.+... -+|... =..+.++| .|+++++ .|.+
T Consensus 52 lf~r~RG-----nlKEvEr~lg~sYptvR~kld~vlramgy~p~~-----e~~~~i~~~~i~~qle~Gei~pe---eA~~ 118 (122)
T COG3877 52 LFLRCRG-----NLKEVERELGISYPTVRTKLDEVLRAMGYNPDS-----ENSVNIGKKKIIDQLEKGEISPE---EAIK 118 (122)
T ss_pred HHHHHcc-----CHHHHHHHHCCccHHHHHHHHHHHHHcCCCCCC-----CChhhhhHHHHHHHHHcCCCCHH---HHHH
Confidence 5555552 589999999999999999999999999987543 344332 23466777 4667765 4555
Q ss_pred HH
Q 008455 201 IL 202 (565)
Q Consensus 201 Lv 202 (565)
++
T Consensus 119 ~L 120 (122)
T COG3877 119 ML 120 (122)
T ss_pred Hh
Confidence 44
No 181
>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=62.97 E-value=16 Score=29.35 Aligned_cols=44 Identities=16% Similarity=0.111 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHhcC----------CCccHHHHHhhhccChHHHHHHHHHHHHHh
Q 008455 118 VQASCLYLACRQKS----------KPFLLIDFSNYLNINVYELGAVYLQLCQVL 161 (565)
Q Consensus 118 vaAACLYiACR~e~----------~p~tL~DIa~~~~vsv~~Lgr~~~~L~~~L 161 (565)
++...++++.+... .|.+..+||+.+|++..++.++++.|.+.=
T Consensus 3 la~~Ll~l~~~~~~~~~~~~~~~~~~lt~~~iA~~~g~sr~tv~r~l~~l~~~g 56 (76)
T PF13545_consen 3 LARFLLELAERFGRRQDGDGIRIPLPLTQEEIADMLGVSRETVSRILKRLKDEG 56 (76)
T ss_dssp HHHHHHHHHHHHEEEEETTEEEEEEESSHHHHHHHHTSCHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHCCCCCCCCceEEecCCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 44555555555432 478899999999999999999999998853
No 182
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=62.79 E-value=9.2 Score=29.28 Aligned_cols=37 Identities=14% Similarity=0.176 Sum_probs=30.0
Q ss_pred HHHHHhcCCCCCHhHHHHHhccCHHHHHHHHHHHHcc
Q 008455 225 YVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (565)
Q Consensus 225 ylAar~~g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t 261 (565)
+++-.......+..++|..+|||++|+.+...++.+.
T Consensus 10 ll~L~~LR~~~~~~~La~~FgIs~stvsri~~~~~~~ 46 (53)
T PF13613_consen 10 LLTLMYLRLNLTFQDLAYRFGISQSTVSRIFHEWIPL 46 (53)
T ss_pred HHHHHHHHcCCcHhHHhhheeecHHHHHHHHHHHHHH
Confidence 3444445678999999999999999999999988654
No 183
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=62.73 E-value=1.9e+02 Score=29.74 Aligned_cols=26 Identities=8% Similarity=0.043 Sum_probs=22.8
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHH
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~ 258 (565)
...|+++||..+||+..||++++..-
T Consensus 241 e~~s~~EIA~~Lgis~~tVk~~l~rA 266 (285)
T TIGR02394 241 EPATLEEVAAEVGLTRERVRQIQVEA 266 (285)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHHH
Confidence 46899999999999999999987643
No 184
>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]
Probab=62.50 E-value=1e+02 Score=26.44 Aligned_cols=37 Identities=16% Similarity=0.277 Sum_probs=28.6
Q ss_pred HHHHHHHHHhcCCCccHHHHHhhhccChHHHHHHHHHH
Q 008455 120 ASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQL 157 (565)
Q Consensus 120 AACLYiACR~e~~p~tL~DIa~~~~vsv~~Lgr~~~~L 157 (565)
-++-||.- ....+.++.++|..++++...|.+.|+..
T Consensus 24 ~~~~~i~~-~~~~~~~l~~la~~~g~S~~~l~r~f~~~ 60 (127)
T COG2207 24 RALDYIEE-NLAEPLTLEDLARRLGMSRRTLSRLFKKE 60 (127)
T ss_pred HHHHHHHH-HhcCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 44455555 56667999999999999999998877744
No 185
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=61.86 E-value=14 Score=28.19 Aligned_cols=35 Identities=11% Similarity=0.224 Sum_probs=30.4
Q ss_pred cCCCccHHHHHhhhccChHHHHHHHHHHHHHhhcc
Q 008455 130 KSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIA 164 (565)
Q Consensus 130 e~~p~tL~DIa~~~~vsv~~Lgr~~~~L~~~L~i~ 164 (565)
.+...+..++|..+||+..++.+.+..+...|...
T Consensus 16 LR~~~~~~~La~~FgIs~stvsri~~~~~~~L~~~ 50 (53)
T PF13613_consen 16 LRLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQV 50 (53)
T ss_pred HHcCCcHhHHhhheeecHHHHHHHHHHHHHHHHHh
Confidence 34567899999999999999999999999988754
No 186
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=61.62 E-value=4.9 Score=29.98 Aligned_cols=25 Identities=24% Similarity=0.646 Sum_probs=18.7
Q ss_pred CCCCCCCCCceeccCCCceecCcccce
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGKV 29 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~V 29 (565)
.|..||.... .+ ..+.+-|..||.=
T Consensus 4 ~C~~Cg~~~~-~~-~~~~irC~~CG~r 28 (44)
T smart00659 4 ICGECGRENE-IK-SKDVVRCRECGYR 28 (44)
T ss_pred ECCCCCCEee-cC-CCCceECCCCCce
Confidence 5999998632 33 4678999999973
No 187
>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=61.41 E-value=22 Score=28.08 Aligned_cols=37 Identities=14% Similarity=0.248 Sum_probs=30.6
Q ss_pred HHHHHHHhcCCCccHHHHHhhhccChHHHHHHHHHHHH
Q 008455 122 CLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQ 159 (565)
Q Consensus 122 CLYiACR~e~~p~tL~DIa~~~~vsv~~Lgr~~~~L~~ 159 (565)
+||.... .+.+.+..|||..++|+.-++..++++|.+
T Consensus 12 ~Iy~l~~-~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~ 48 (60)
T PF01325_consen 12 AIYELSE-EGGPVRTKDIAERLGVSPPTVTEMLKRLAE 48 (60)
T ss_dssp HHHHHHH-CTSSBBHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHc-CCCCccHHHHHHHHCCChHHHHHHHHHHHH
Confidence 3555555 788999999999999999999999999876
No 188
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=61.32 E-value=5.3 Score=31.19 Aligned_cols=25 Identities=24% Similarity=0.672 Sum_probs=19.0
Q ss_pred CCCCCCCCCceeccCCCceecCccccee
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vl 30 (565)
.|+.||.... +.+--+||..||++.
T Consensus 7 ~C~~Cg~~~~---~~dDiVvCp~Cgapy 31 (54)
T PF14446_consen 7 KCPVCGKKFK---DGDDIVVCPECGAPY 31 (54)
T ss_pred cChhhCCccc---CCCCEEECCCCCCcc
Confidence 6999998732 234578999999975
No 189
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=61.32 E-value=67 Score=35.51 Aligned_cols=52 Identities=15% Similarity=0.166 Sum_probs=42.3
Q ss_pred hccccCCCChhHHHHH---HHHHHHHhcCCCCCHhHHHHHhccCHHHHHHHHHHHHc
Q 008455 207 RDWITTGRKPSGLCGA---ALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (565)
Q Consensus 207 ~~~l~~GR~P~~IaaA---ALylAar~~g~~~t~~eIa~v~~Vse~TIrkR~kE~~~ 260 (565)
...|..++|-..|+-| |.|++-++.+ .|..+|+..+|.+.+||...++.+.+
T Consensus 359 ~~~l~s~~R~~~i~~aR~iamyl~r~~~~--~s~~~Ig~~fgr~hstV~~a~~~i~~ 413 (440)
T PRK14088 359 REEILSNSRNVKALLARRIGMYVAKNYLG--SSLRTIAEKFNRSHPVVVDSVKKVKD 413 (440)
T ss_pred HHHHhCCCCCccccHHHHHHHHHHHHHhC--CCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3456666666778878 9999977555 49999999999999999999988875
No 190
>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=61.08 E-value=10 Score=31.67 Aligned_cols=39 Identities=23% Similarity=0.324 Sum_probs=29.4
Q ss_pred HHHHHHHhcCCCCCHhHHHHHhccCHHHHHHHHHHHHcc
Q 008455 223 ALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (565)
Q Consensus 223 ALylAar~~g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t 261 (565)
.+|+|..-.+.+.|.++||+.+++++..+++-+..|.+.
T Consensus 14 l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~ 52 (83)
T PF02082_consen 14 LLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKA 52 (83)
T ss_dssp HHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhC
Confidence 345555444445999999999999999999999998753
No 191
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=61.00 E-value=2.1e+02 Score=29.69 Aligned_cols=26 Identities=8% Similarity=0.160 Sum_probs=22.9
Q ss_pred CCCCCHhHHHHHhccCHHHHHHHHHH
Q 008455 232 GLKFSKSDIVKIVHICEATLMKRLIE 257 (565)
Q Consensus 232 g~~~t~~eIa~v~~Vse~TIrkR~kE 257 (565)
+...|+++||..+|||..|||++...
T Consensus 267 ~~~~Tl~EIa~~lgiS~erVrq~~~r 292 (298)
T TIGR02997 267 GEPLTLAEIGRRLNLSRERVRQIEAK 292 (298)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 35799999999999999999998754
No 192
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=60.99 E-value=17 Score=34.24 Aligned_cols=46 Identities=13% Similarity=0.108 Sum_probs=38.0
Q ss_pred chhHHHHHHHHHHHHhcCCCccHHHHHhhhccChHHHHHHHHHHHHH
Q 008455 114 RTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (565)
Q Consensus 114 ~~~~vaAACLYiACR~e~~p~tL~DIa~~~~vsv~~Lgr~~~~L~~~ 160 (565)
+.++-+-+++|+|- ..+.+++..+||+..+++..-|.+.+..|.+.
T Consensus 6 ~~~YAlr~L~~LA~-~~~~~~s~~eIA~~~~is~~~L~kIl~~L~~a 51 (153)
T PRK11920 6 QTNYAIRMLMYCAA-NDGKLSRIPEIARAYGVSELFLFKILQPLVEA 51 (153)
T ss_pred HHhHHHHHHHHHHh-CCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 34556668899994 45668899999999999999999999888873
No 193
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=60.98 E-value=2.6e+02 Score=30.83 Aligned_cols=99 Identities=12% Similarity=0.116 Sum_probs=57.9
Q ss_pred chHHHHHHHHHHHHHHHHHHcC---CCChhHHHHHHHHHHHHHHhCccccCCchhHHHH------HHHHHH---------
Q 008455 65 ASRERLMEKAFDDMRQMKNALN---IGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQA------SCLYLA--------- 126 (565)
Q Consensus 65 ~srer~l~~a~~~I~~ia~~L~---Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaA------ACLYiA--------- 126 (565)
..+++-+..-...+-.+|.++. +.-.+-|.+...-+++-+..-.-.+|-+....+- -.-+++
T Consensus 175 ~A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQEG~iGL~ravekFDp~rG~rFSTYa~wwIRqaI~r~i~~~srtIrlP 254 (415)
T PRK07598 175 RAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLP 254 (415)
T ss_pred HHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHHcCCceehh
Confidence 3455555556667777777752 2211455555555666665544556665544442 222221
Q ss_pred -----------------HHhcCCCccHHHHHhhhccChHHHHHHHHHHHHHhhc
Q 008455 127 -----------------CRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYI 163 (565)
Q Consensus 127 -----------------CR~e~~p~tL~DIa~~~~vsv~~Lgr~~~~L~~~L~i 163 (565)
....|.+-+..+||..+++++..|..+.......+.+
T Consensus 255 ~~i~e~l~~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~~l~~~~~~~SL 308 (415)
T PRK07598 255 VHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLLRVPRSVSL 308 (415)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHccCCccc
Confidence 0123556678999999999999999876665444444
No 194
>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=60.80 E-value=18 Score=27.77 Aligned_cols=28 Identities=14% Similarity=0.351 Sum_probs=24.4
Q ss_pred CCCHhHHHHHhccCHHHHHHHHHHHHcc
Q 008455 234 KFSKSDIVKIVHICEATLMKRLIEFENT 261 (565)
Q Consensus 234 ~~t~~eIa~v~~Vse~TIrkR~kE~~~t 261 (565)
.+|+.+|++.++++..|+.+.++.|.+-
T Consensus 21 ~~t~~~la~~l~~~~~~vs~~v~~L~~~ 48 (62)
T PF12802_consen 21 ELTQSELAERLGISKSTVSRIVKRLEKK 48 (62)
T ss_dssp GEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 4899999999999999999999988743
No 195
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=60.48 E-value=3.3 Score=37.03 Aligned_cols=40 Identities=18% Similarity=0.273 Sum_probs=24.1
Q ss_pred CCCCCCCCCCCceeccCCCceecCcccceeccccccccccccc
Q 008455 1 MVWCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATFVK 43 (565)
Q Consensus 1 M~~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vlee~~id~~~ef~e 43 (565)
++.||+|+...-..- -..-|..||.-|.=..--++-+|.+
T Consensus 69 ~V~CP~C~K~TKmLG---r~D~CM~C~~pLTLd~~legkef~~ 108 (114)
T PF11023_consen 69 QVECPNCGKQTKMLG---RVDACMHCKEPLTLDPSLEGKEFDE 108 (114)
T ss_pred eeECCCCCChHhhhc---hhhccCcCCCcCccCchhhcchhhH
Confidence 357999998732221 1238999999875322224445654
No 196
>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=60.48 E-value=16 Score=27.04 Aligned_cols=32 Identities=9% Similarity=0.189 Sum_probs=26.8
Q ss_pred hcCCCCCHhHHHHHhccCHHHHHHHHHHHHcc
Q 008455 230 THGLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (565)
Q Consensus 230 ~~g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t 261 (565)
+..-+.+..+|++.++++.+||+..++.+.+.
T Consensus 11 L~~~~~~~~el~~~l~~s~~~vs~hL~~L~~~ 42 (47)
T PF01022_consen 11 LSEGPLTVSELAEELGLSQSTVSHHLKKLREA 42 (47)
T ss_dssp HTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHhCCCchhhHHHhccccchHHHHHHHHHHHC
Confidence 34467899999999999999999999998754
No 197
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=60.20 E-value=2.7 Score=32.29 Aligned_cols=29 Identities=17% Similarity=0.591 Sum_probs=21.9
Q ss_pred CCCCCCCCCCce-eccCCCceecCccccee
Q 008455 2 VWCSSCARHVTG-HRPYDSQLCCDRCGKVL 30 (565)
Q Consensus 2 ~~Cp~Cgs~~i~-~D~~~G~~VCt~CG~Vl 30 (565)
.+|++|+.-... -+....++-|..||+|-
T Consensus 5 iRC~~CnklLa~~g~~~~leIKCpRC~tiN 34 (51)
T PF10122_consen 5 IRCGHCNKLLAKAGEVIELEIKCPRCKTIN 34 (51)
T ss_pred eeccchhHHHhhhcCccEEEEECCCCCccc
Confidence 379999976433 24556899999999983
No 198
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=59.70 E-value=6.2 Score=31.92 Aligned_cols=27 Identities=19% Similarity=0.534 Sum_probs=18.1
Q ss_pred CCCCCCCCCceecc---CCC--------------ceecCcccce
Q 008455 3 WCSSCARHVTGHRP---YDS--------------QLCCDRCGKV 29 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~---~~G--------------~~VCt~CG~V 29 (565)
.||.||+.....+. ..| .++|++||..
T Consensus 2 ~C~KCg~~~~e~~~v~~tgg~~skiFdvq~~~f~~v~C~~CGYT 45 (64)
T PF09855_consen 2 KCPKCGNEEYESGEVRATGGGLSKIFDVQNKKFTTVSCTNCGYT 45 (64)
T ss_pred CCCCCCCcceecceEEccCCeeEEEEEecCcEEEEEECCCCCCE
Confidence 59999987554432 111 3589999986
No 199
>PF14353 CpXC: CpXC protein
Probab=59.56 E-value=5.5 Score=36.11 Aligned_cols=29 Identities=21% Similarity=0.645 Sum_probs=18.9
Q ss_pred CCCCCCCCC--CceeccC-------------CC---ceecCccccee
Q 008455 2 VWCSSCARH--VTGHRPY-------------DS---QLCCDRCGKVL 30 (565)
Q Consensus 2 ~~Cp~Cgs~--~i~~D~~-------------~G---~~VCt~CG~Vl 30 (565)
..||+||.. .-+++.. +| ..+|..||...
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~ 48 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKF 48 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCce
Confidence 479999986 1122211 22 67999999865
No 200
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=59.52 E-value=1.1e+02 Score=31.80 Aligned_cols=104 Identities=13% Similarity=0.132 Sum_probs=0.0
Q ss_pred chhHHHHHHHHHHHHhcCCCccHHHHHhhhccChHHHHHHHHHHHHHhhccccccccccCCchhhHHHHHHhhCCCCCHH
Q 008455 114 RTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKK 193 (565)
Q Consensus 114 ~~~~vaAACLYiACR~e~~p~tL~DIa~~~~vsv~~Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~~~l~~~ 193 (565)
.....+..++-+.-..-..++++.++|..++++...|.+.|++... ..|..|+.++
T Consensus 215 ~~~~~~~~~~~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~~~g-------------~s~~~~~~~~----------- 270 (322)
T PRK09393 215 RESDRLGPLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAATG-------------MTPAEWLLRE----------- 270 (322)
T ss_pred cchHHHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHC-------------cCHHHHHHHH-----------
Q ss_pred HHHHHHHHHHHhhhccccCCCChhHHHHHHHHHHHHhcCCCCCHhHHHHHhcc-CHHHHHHHHHHHHccCCCCCCHHHHH
Q 008455 194 VCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHI-CEATLMKRLIEFENTDSGSLTIEDFM 272 (565)
Q Consensus 194 V~~~A~~Lv~~m~~~~l~~GR~P~~IaaAALylAar~~g~~~t~~eIa~v~~V-se~TIrkR~kE~~~t~s~~Lt~~~f~ 272 (565)
-...|..++..-.. ++.+||..+|- +.+...+.++.+. .+|+.+|+
T Consensus 271 Rl~~A~~lL~~~~~----------------------------~i~~IA~~~Gf~~~s~F~r~Fk~~~-----G~tP~~yr 317 (322)
T PRK09393 271 RLARARDLLESSAL----------------------------SIDQIAERAGFGSEESLRHHFRRRA-----ATSPAAYR 317 (322)
T ss_pred HHHHHHHHHHcCCC----------------------------CHHHHHHHhCCCCHHHHHHHHHHHH-----CcCHHHHH
Q ss_pred HH
Q 008455 273 AR 274 (565)
Q Consensus 273 ~~ 274 (565)
+.
T Consensus 318 ~~ 319 (322)
T PRK09393 318 KR 319 (322)
T ss_pred HH
No 201
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=59.50 E-value=23 Score=25.84 Aligned_cols=27 Identities=22% Similarity=0.433 Sum_probs=25.0
Q ss_pred CCCHhHHHHHhccCHHHHHHHHHHHHc
Q 008455 234 KFSKSDIVKIVHICEATLMKRLIEFEN 260 (565)
Q Consensus 234 ~~t~~eIa~v~~Vse~TIrkR~kE~~~ 260 (565)
..++.+|+..++++..|+++.++.|.+
T Consensus 14 ~~s~~~l~~~l~~s~~tv~~~l~~L~~ 40 (53)
T smart00420 14 KVSVEELAELLGVSEMTIRRDLNKLEE 40 (53)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 489999999999999999999999875
No 202
>PRK13502 transcriptional activator RhaR; Provisional
Probab=59.44 E-value=1.1e+02 Score=31.08 Aligned_cols=104 Identities=13% Similarity=0.073 Sum_probs=0.0
Q ss_pred CCchhHHHHHHHHHHHHhcCCCccHHHHHhhhccChHHHHHHHHHHHHHhhccccccccccCCchhhHHHHHHhhCCCCC
Q 008455 112 GRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGN 191 (565)
Q Consensus 112 GR~~~~vaAACLYiACR~e~~p~tL~DIa~~~~vsv~~Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~~~l~ 191 (565)
......+..++-||.-.... +.++.++|..+++++..|.+.|++... ..|..||.+.
T Consensus 172 ~~~~~~~~~~~~~I~~~~~~-~~~~~~lA~~~~iS~~~L~r~fk~~~G-------------~t~~~yi~~~--------- 228 (282)
T PRK13502 172 TSRETLLDKLITALANSLEC-PFALDAFCQQEQCSERVLRQQFRAQTG-------------MTINQYLRQV--------- 228 (282)
T ss_pred cchHHHHHHHHHHHHhcccC-CCCHHHHHHHHCcCHHHHHHHHHHHHC-------------cCHHHHHHHH---------
Q ss_pred HHHHHHHHHHHHHhhhccccCCCChhHHHHHHHHHHHHhcCCCCCHhHHHHHhccCH-HHHHHHHHHHHccCCCCCCHHH
Q 008455 192 KKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICE-ATLMKRLIEFENTDSGSLTIED 270 (565)
Q Consensus 192 ~~V~~~A~~Lv~~m~~~~l~~GR~P~~IaaAALylAar~~g~~~t~~eIa~v~~Vse-~TIrkR~kE~~~t~s~~Lt~~~ 270 (565)
-...|.+++..- +.|+.+||..+|.+. +...+.+|... .+||.+
T Consensus 229 --Rl~~A~~lL~~t----------------------------~~sI~eIA~~~GF~d~s~F~r~FKk~~-----G~tP~~ 273 (282)
T PRK13502 229 --RICHAQYLLQHS----------------------------PLMISEISMQCGFEDSNYFSVVFTRET-----GMTPSQ 273 (282)
T ss_pred --HHHHHHHHHHcC----------------------------CCCHHHHHHHcCCCCHHHHHHHHHHHH-----CcCHHH
Q ss_pred HHH
Q 008455 271 FMA 273 (565)
Q Consensus 271 f~~ 273 (565)
|++
T Consensus 274 yRk 276 (282)
T PRK13502 274 WRH 276 (282)
T ss_pred HHH
No 203
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=59.02 E-value=34 Score=33.64 Aligned_cols=31 Identities=19% Similarity=0.330 Sum_probs=27.7
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHHHccCC
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEFENTDS 263 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~~~t~s 263 (565)
+++|+++||..+|++..|+.+-+++|.+..-
T Consensus 183 ~~lt~~~iA~~lG~sr~tvsR~l~~l~~~g~ 213 (235)
T PRK11161 183 LTMTRGDIGNYLGLTVETISRLLGRFQKSGM 213 (235)
T ss_pred ccccHHHHHHHhCCcHHHHHHHHHHHHHCCC
Confidence 5789999999999999999999999986543
No 204
>PRK13500 transcriptional activator RhaR; Provisional
Probab=58.87 E-value=2.3e+02 Score=29.44 Aligned_cols=87 Identities=14% Similarity=0.090 Sum_probs=56.4
Q ss_pred CCCccHHHHHhhhccChHHHHHHHHHHHHHhhccccccccccCCchhhHHHHHHhhCCCCCHHHHHHHHHHHHHhhhccc
Q 008455 131 SKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWI 210 (565)
Q Consensus 131 ~~p~tL~DIa~~~~vsv~~Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~~~l~~~V~~~A~~Lv~~m~~~~l 210 (565)
..++++.++|+.+++++..|.+.|++. .| ..|..||.++ ....|
T Consensus 220 ~e~isl~~lA~~~~iS~~~L~r~FK~~---tG----------~T~~~yi~~~-----------RL~~A------------ 263 (312)
T PRK13500 220 KSPFALDKFCDEASCSERVLRQQFRQQ---TG----------MTINQYLRQV-----------RVCHA------------ 263 (312)
T ss_pred cCCCCHHHHHHHHCcCHHHHHHHHHHH---HC----------cCHHHHHHHH-----------HHHHH------------
Confidence 446888888888888888888777654 23 2344555432 01111
Q ss_pred cCCCChhHHHHHHHHHHHHhcCCCCCHhHHHHHhccCH-HHHHHHHHHHHccCCCCCCHHHHHHH
Q 008455 211 TTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICE-ATLMKRLIEFENTDSGSLTIEDFMAR 274 (565)
Q Consensus 211 ~~GR~P~~IaaAALylAar~~g~~~t~~eIa~v~~Vse-~TIrkR~kE~~~t~s~~Lt~~~f~~~ 274 (565)
.-+| ..-+.++.+||..+|-.. +...+.+|... .+||.+|++.
T Consensus 264 ------------~~LL----~~t~~sI~eIA~~~GF~d~s~Fsr~FKk~~-----G~TP~~yRk~ 307 (312)
T PRK13500 264 ------------QYLL----QHSRLLISDISTECGFEDSNYFSVVFTRET-----GMTPSQWRHL 307 (312)
T ss_pred ------------HHHH----HcCCCCHHHHHHHhCCCCHHHHHHHHHHHH-----CcCHHHHHHH
Confidence 1111 123678999999999866 57777777776 5788899865
No 205
>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression. The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan []. The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....
Probab=58.84 E-value=14 Score=31.62 Aligned_cols=32 Identities=13% Similarity=-0.049 Sum_probs=28.2
Q ss_pred hcCCCCCHhHHHHHhccCHHHHHHHHHHHHcc
Q 008455 230 THGLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (565)
Q Consensus 230 ~~g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t 261 (565)
+..-..|+++|++.+|||-.||.+-=+.+..-
T Consensus 45 lL~~g~syreIa~~tgvS~aTItRvsr~Lk~~ 76 (87)
T PF01371_consen 45 LLDEGKSYREIAEETGVSIATITRVSRCLKYG 76 (87)
T ss_dssp HHHTTSSHHHHHHHHTSTHHHHHHHHHHHHHS
T ss_pred HHHCCCCHHHHHHHhCCCHHHHHHHHHHHHcC
Confidence 66678999999999999999999988888743
No 206
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=58.79 E-value=6.3 Score=27.45 Aligned_cols=24 Identities=25% Similarity=0.700 Sum_probs=16.4
Q ss_pred CCCCCCCCCceeccCCCceecCcccc
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGK 28 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~ 28 (565)
.|..||.... ......+-|..||.
T Consensus 2 ~C~~Cg~~~~--~~~~~~irC~~CG~ 25 (32)
T PF03604_consen 2 ICGECGAEVE--LKPGDPIRCPECGH 25 (32)
T ss_dssp BESSSSSSE---BSTSSTSSBSSSS-
T ss_pred CCCcCCCeeE--cCCCCcEECCcCCC
Confidence 4889998733 33456788999996
No 207
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=58.36 E-value=7.3 Score=25.39 Aligned_cols=24 Identities=33% Similarity=0.822 Sum_probs=15.0
Q ss_pred CCCCCCCCceeccCCCceecCcccc
Q 008455 4 CSSCARHVTGHRPYDSQLCCDRCGK 28 (565)
Q Consensus 4 Cp~Cgs~~i~~D~~~G~~VCt~CG~ 28 (565)
|..||.... .....-...|.+||.
T Consensus 1 C~sC~~~i~-~r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGRPIA-PREQAVPFPCPNCGF 24 (24)
T ss_pred CccCCCccc-CcccCceEeCCCCCC
Confidence 778887632 111234778999983
No 208
>PF14122 YokU: YokU-like protein
Probab=58.12 E-value=5.3 Score=34.02 Aligned_cols=22 Identities=27% Similarity=0.653 Sum_probs=16.8
Q ss_pred CceecCcccceecccccccccc
Q 008455 19 SQLCCDRCGKVLEDHNFSTEAT 40 (565)
Q Consensus 19 G~~VCt~CG~Vlee~~id~~~e 40 (565)
-.++|++||.|--+..+..+.+
T Consensus 34 P~i~C~~CgmvYq~d~vi~EIE 55 (87)
T PF14122_consen 34 PAIICSNCGMVYQDDEVIKEIE 55 (87)
T ss_pred ceeeecCCCcEEehhHHHHHHh
Confidence 3489999999987776665553
No 209
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=58.10 E-value=14 Score=27.48 Aligned_cols=27 Identities=22% Similarity=0.278 Sum_probs=24.1
Q ss_pred CCCHhHHHHHhccCHHHHHHHHHHHHc
Q 008455 234 KFSKSDIVKIVHICEATLMKRLIEFEN 260 (565)
Q Consensus 234 ~~t~~eIa~v~~Vse~TIrkR~kE~~~ 260 (565)
..+.++||+.++++..||+++++.+..
T Consensus 15 ~~s~~eia~~l~~s~~tv~~~~~~~~~ 41 (57)
T cd06170 15 GKTNKEIADILGISEKTVKTHLRNIMR 41 (57)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 469999999999999999999988754
No 210
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=58.02 E-value=36 Score=32.48 Aligned_cols=30 Identities=13% Similarity=0.172 Sum_probs=27.6
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHHHccC
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEFENTD 262 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~~~t~ 262 (565)
+++|+.+||..+|++..|+.+-+++|.+..
T Consensus 148 ~~~t~~~iA~~lG~tretvsR~l~~l~~~g 177 (202)
T PRK13918 148 IYATHDELAAAVGSVRETVTKVIGELSREG 177 (202)
T ss_pred ecCCHHHHHHHhCccHHHHHHHHHHHHHCC
Confidence 578999999999999999999999998653
No 211
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=57.82 E-value=53 Score=28.34 Aligned_cols=50 Identities=8% Similarity=0.096 Sum_probs=38.4
Q ss_pred HHHHHHHHHHHhcCCCCCHhHHHHHhccCHHHHHHHHHHHHccCCCCCCHHHHHHH
Q 008455 219 LCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMAR 274 (565)
Q Consensus 219 IaaAALylAar~~g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t~s~~Lt~~~f~~~ 274 (565)
|.-+.-|+.... ..++++.+||+.+|+|..++.+++++.. .+|+.+|...
T Consensus 7 ~~~~~~~i~~~~-~~~~~~~~lA~~~~~S~~~l~r~f~~~~-----g~s~~~~i~~ 56 (107)
T PRK10219 7 IQTLIAWIDEHI-DQPLNIDVVAKKSGYSKWYLQRMFRTVT-----HQTLGDYIRQ 56 (107)
T ss_pred HHHHHHHHHHhc-CCCCCHHHHHHHHCCCHHHHHHHHHHHH-----CcCHHHHHHH
Confidence 333444555543 4579999999999999999999999975 6777887654
No 212
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=57.79 E-value=3 Score=43.48 Aligned_cols=29 Identities=14% Similarity=0.432 Sum_probs=22.3
Q ss_pred CCCCCCCCCCceeccCCCceecCccccee
Q 008455 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (565)
Q Consensus 2 ~~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vl 30 (565)
..||.|+......|-.....||..||.-.
T Consensus 27 ~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 55 (285)
T TIGR00515 27 TKCPKCGQVLYTKELERNLEVCPKCDHHM 55 (285)
T ss_pred eECCCCcchhhHHHHHhhCCCCCCCCCcC
Confidence 47999998755555556778999999864
No 213
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=56.99 E-value=3.2 Score=43.46 Aligned_cols=29 Identities=21% Similarity=0.530 Sum_probs=22.0
Q ss_pred CCCCCCCCCCceeccCCCceecCccccee
Q 008455 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (565)
Q Consensus 2 ~~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vl 30 (565)
..||.|+......|-.....||..||.-.
T Consensus 28 ~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 56 (292)
T PRK05654 28 TKCPSCGQVLYRKELEANLNVCPKCGHHM 56 (292)
T ss_pred eECCCccchhhHHHHHhcCCCCCCCCCCe
Confidence 47999998755455555677999999865
No 214
>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=56.82 E-value=94 Score=29.58 Aligned_cols=108 Identities=18% Similarity=0.273 Sum_probs=59.9
Q ss_pred HHHHHHHHHHHhcCCCccHHHHHhhhccChHHHHHHHHHHHHHhhccccc--------cccccC--CchhhHHHHHHhhC
Q 008455 118 VQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADES--------NVLKQV--DPSIFLHKFTDRLL 187 (565)
Q Consensus 118 vaAACLYiACR~e~~p~tL~DIa~~~~vsv~~Lgr~~~~L~~~L~i~~~~--------~~~~~v--dP~~~I~Rf~~~L~ 187 (565)
++=|.||.+ +-|+++.+++++++ +...+......|.+.+.-.... .|.-.+ +-..||.++...
T Consensus 2 ~iEAlLF~s----~~pvs~~~La~~l~-~~~~v~~~l~~L~~~y~~~~~gl~l~~~~~~y~l~tk~~~~~~v~~~~~~-- 74 (159)
T PF04079_consen 2 IIEALLFAS----GEPVSIEELAEILG-SEDEVEEALEELQEEYNEEDRGLELVEVGGGYRLQTKPEYAEYVEKLFKK-- 74 (159)
T ss_dssp HHHHHHHH-----SS-B-HHHHHHHCT--HHHHHHHHHHHHHHHHHCT-SEEEEEETTEEEEEE-GGGHHHHHHHHCT--
T ss_pred hhHhhHHHc----CCCCCHHHHHHHhC-CHHHHHHHHHHHHHHhccCCCCEEEEEECCEEEEEEhHHHHHHHHHHhcc--
Confidence 345777775 67999999999999 9999999999999988422211 011111 112222222221
Q ss_pred CCCCHHHHHHHHHHHHHhhhccccCCCChhHHHHHHHH-HHHHhcCCCCCHhHHHHHhccCHHHHHHHHHHH
Q 008455 188 PGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALY-VSALTHGLKFSKSDIVKIVHICEATLMKRLIEF 258 (565)
Q Consensus 188 ~~l~~~V~~~A~~Lv~~m~~~~l~~GR~P~~IaaAALy-lAar~~g~~~t~~eIa~v~~Vse~TIrkR~kE~ 258 (565)
++|..+--|++= ||.-.+..++|..+|.++-||.-..+-+.|.+.
T Consensus 75 --------------------------~~~~~LS~aalEtLAiIAY~QPiTr~eIe~IRGv~s~~~i~~L~e~ 120 (159)
T PF04079_consen 75 --------------------------PKPPKLSQAALETLAIIAYKQPITRAEIEEIRGVNSDSVIKTLLER 120 (159)
T ss_dssp --------------------------CCCHHHHHHHHHHHHHHHHH-SEEHHHHHHHHTS--HCHHHHHHHT
T ss_pred --------------------------CccCCCCHHHHHHHHHHHhcCCcCHHHHHHHcCCChHHHHHHHHHC
Confidence 223333333332 333445689999999999999755444444443
No 215
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=56.50 E-value=3.5e+02 Score=30.77 Aligned_cols=25 Identities=8% Similarity=0.068 Sum_probs=21.4
Q ss_pred CCCCCHhHHHHHhccCHHHHHHHHH
Q 008455 232 GLKFSKSDIVKIVHICEATLMKRLI 256 (565)
Q Consensus 232 g~~~t~~eIa~v~~Vse~TIrkR~k 256 (565)
+...|+.+|+..+|||...||+.-+
T Consensus 465 ~e~~TL~EIa~~lGVSrERVRQIe~ 489 (509)
T PRK05901 465 GQPKTLDEIGQVYGVTRERIRQIES 489 (509)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3579999999999999999996543
No 216
>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins. The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple copies of DnaA, which is an ATPase, bind to 9-mers at the origin and form an initial complex in which the DNA strands are being separated in an ATP-dependent step.
Probab=56.44 E-value=32 Score=29.22 Aligned_cols=41 Identities=12% Similarity=0.078 Sum_probs=34.9
Q ss_pred HHHHHHHHhcCCCccHHHHHhhhc-cChHHHHHHHHHHHHHhhc
Q 008455 121 SCLYLACRQKSKPFLLIDFSNYLN-INVYELGAVYLQLCQVLYI 163 (565)
Q Consensus 121 ACLYiACR~e~~p~tL~DIa~~~~-vsv~~Lgr~~~~L~~~L~i 163 (565)
.|.|++-+.. ..++.+|+..+| .+..++..+++++.+.+..
T Consensus 34 ia~yl~~~~~--~~s~~~Ig~~fg~r~hStV~~a~~ri~~~~~~ 75 (90)
T cd06571 34 IAMYLARELT--GLSLPEIGRAFGGRDHSTVLHAVRKIEELLEE 75 (90)
T ss_pred HHHHHHHHHh--CCCHHHHHHHhCCCCHhHHHHHHHHHHHHHHh
Confidence 6778776665 467899999999 9999999999999998764
No 217
>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=56.12 E-value=31 Score=29.66 Aligned_cols=31 Identities=3% Similarity=0.128 Sum_probs=27.6
Q ss_pred cCCCCCHhHHHHHhccCHHHHHHHHHHHHcc
Q 008455 231 HGLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (565)
Q Consensus 231 ~g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t 261 (565)
....+|+.+||+.+|++..|+++.+++|.+-
T Consensus 44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~ 74 (95)
T TIGR01610 44 KQDRVTATVIAELTGLSRTHVSDAIKSLARR 74 (95)
T ss_pred cCCccCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 4567999999999999999999999998753
No 218
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=56.04 E-value=3.4 Score=42.51 Aligned_cols=30 Identities=20% Similarity=0.515 Sum_probs=22.9
Q ss_pred CCCCCCCCCCCceeccCCCceecCccccee
Q 008455 1 MVWCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (565)
Q Consensus 1 M~~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vl 30 (565)
+.+||.||.-...-|-.....||..||.-.
T Consensus 28 w~KCp~c~~~~y~~eL~~n~~vcp~c~~h~ 57 (294)
T COG0777 28 WTKCPSCGEMLYRKELESNLKVCPKCGHHM 57 (294)
T ss_pred eeECCCccceeeHHHHHhhhhcccccCccc
Confidence 357999998654445567889999999854
No 219
>PRK05978 hypothetical protein; Provisional
Probab=55.96 E-value=8.3 Score=36.36 Aligned_cols=30 Identities=17% Similarity=0.336 Sum_probs=20.7
Q ss_pred CCCCCCCCCCceeccCCCceecCcccceec
Q 008455 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (565)
Q Consensus 2 ~~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vle 31 (565)
.+||+||...+-.-.-.=.--|..||.-++
T Consensus 34 grCP~CG~G~LF~g~Lkv~~~C~~CG~~~~ 63 (148)
T PRK05978 34 GRCPACGEGKLFRAFLKPVDHCAACGEDFT 63 (148)
T ss_pred CcCCCCCCCcccccccccCCCccccCCccc
Confidence 379999988663222233447999999766
No 220
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=55.94 E-value=14 Score=28.67 Aligned_cols=28 Identities=14% Similarity=0.169 Sum_probs=25.4
Q ss_pred CCCCCHhHHHHHhccCHHHHHHHHHHHH
Q 008455 232 GLKFSKSDIVKIVHICEATLMKRLIEFE 259 (565)
Q Consensus 232 g~~~t~~eIa~v~~Vse~TIrkR~kE~~ 259 (565)
-|..++.+.|+.+|||..+++++.+++.
T Consensus 13 ~fhlp~~eAA~~Lgv~~T~LKr~CR~~G 40 (52)
T PF02042_consen 13 YFHLPIKEAAKELGVSVTTLKRRCRRLG 40 (52)
T ss_pred HhCCCHHHHHHHhCCCHHHHHHHHHHcC
Confidence 3789999999999999999999999875
No 221
>PRK02935 hypothetical protein; Provisional
Probab=55.93 E-value=7.4 Score=34.40 Aligned_cols=39 Identities=21% Similarity=0.332 Sum_probs=23.5
Q ss_pred CCCCCCCCCCceeccCCCceecCcccceeccccccccccccc
Q 008455 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATFVK 43 (565)
Q Consensus 2 ~~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vlee~~id~~~ef~e 43 (565)
+.||+|+...-.. .-...|..|+.-|.=..--++.+|.+
T Consensus 71 V~CP~C~K~TKmL---GrvD~CM~C~~PLTLd~~legkefde 109 (110)
T PRK02935 71 VICPSCEKPTKML---GRVDACMHCNQPLTLDRSLEGKEFDE 109 (110)
T ss_pred eECCCCCchhhhc---cceeecCcCCCcCCcCccccccCcCc
Confidence 4799999862211 12348999999875322234445543
No 222
>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=55.85 E-value=16 Score=28.56 Aligned_cols=30 Identities=17% Similarity=0.243 Sum_probs=25.7
Q ss_pred CCCCCHhHHHHHhccCHHHHHHHHHHHHcc
Q 008455 232 GLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (565)
Q Consensus 232 g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t 261 (565)
+-.++.+++|...++|+.||++-+.+|.+.
T Consensus 17 ~~~~~~~ela~~l~~S~rti~~~i~~L~~~ 46 (59)
T PF08280_consen 17 NKWITLKELAKKLNISERTIKNDINELNEF 46 (59)
T ss_dssp HTSBBHHHHHHHCTS-HHHHHHHHHHHHTT
T ss_pred CCCCcHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 456799999999999999999999999854
No 223
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=55.77 E-value=15 Score=27.66 Aligned_cols=27 Identities=30% Similarity=0.324 Sum_probs=20.2
Q ss_pred CCCCCHhHHHHHhccCHHHHHHHHHHH
Q 008455 232 GLKFSKSDIVKIVHICEATLMKRLIEF 258 (565)
Q Consensus 232 g~~~t~~eIa~v~~Vse~TIrkR~kE~ 258 (565)
-...|.++||...|+|+.||++++..-
T Consensus 24 ~~g~s~~eIa~~l~~s~~~v~~~l~ra 50 (54)
T PF08281_consen 24 FQGMSYAEIAEILGISESTVKRRLRRA 50 (54)
T ss_dssp TS---HHHHHHHCTS-HHHHHHHHHHH
T ss_pred HHCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 467899999999999999999998653
No 224
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=55.68 E-value=2.9 Score=33.01 Aligned_cols=24 Identities=25% Similarity=0.908 Sum_probs=17.6
Q ss_pred CCCCCCCCCceeccCCCceecCc-ccceec
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDR-CGKVLE 31 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~-CG~Vle 31 (565)
.|+.||.... -|+.+|++ ||-+++
T Consensus 10 HC~VCg~aIp-----~de~~CSe~C~eil~ 34 (64)
T COG4068 10 HCVVCGKAIP-----PDEQVCSEECGEILN 34 (64)
T ss_pred cccccCCcCC-----CccchHHHHHHHHHH
Confidence 6999987632 46778886 887765
No 225
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=55.63 E-value=3.3 Score=43.31 Aligned_cols=29 Identities=24% Similarity=0.423 Sum_probs=22.7
Q ss_pred CCCCCCCCCCceeccCCCceecCccccee
Q 008455 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (565)
Q Consensus 2 ~~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vl 30 (565)
.+||.|+......+-.....||..||.-.
T Consensus 39 ~kc~~C~~~~~~~~l~~~~~vcp~c~~h~ 67 (296)
T CHL00174 39 VQCENCYGLNYKKFLKSKMNICEQCGYHL 67 (296)
T ss_pred eECCCccchhhHHHHHHcCCCCCCCCCCc
Confidence 47999998755555567788999999854
No 226
>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=55.57 E-value=12 Score=29.77 Aligned_cols=38 Identities=18% Similarity=0.318 Sum_probs=30.6
Q ss_pred HHHHHHHhcCCCCCHhHHHHHhccCHHHHHHHHHHHHcc
Q 008455 223 ALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (565)
Q Consensus 223 ALylAar~~g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t 261 (565)
.+|++-. ..-..|..+|++.++++..|+.+.++.|.+.
T Consensus 12 ~vy~~Ll-~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~ 49 (68)
T PF01978_consen 12 KVYLALL-KNGPATAEEIAEELGISRSTVYRALKSLEEK 49 (68)
T ss_dssp HHHHHHH-HHCHEEHHHHHHHHTSSHHHHHHHHHHHHHT
T ss_pred HHHHHHH-HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 4455443 4467899999999999999999999998753
No 227
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=54.98 E-value=2.2e+02 Score=27.96 Aligned_cols=27 Identities=15% Similarity=0.103 Sum_probs=23.5
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHHH
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEFE 259 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~~ 259 (565)
...|+++||...|++..||+++++...
T Consensus 193 ~~~s~~eIA~~lgis~~~v~~~~~ra~ 219 (227)
T TIGR02980 193 EDKTQSEIAERLGISQMHVSRLLRRAL 219 (227)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 467999999999999999999986543
No 228
>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=54.74 E-value=14 Score=29.74 Aligned_cols=32 Identities=16% Similarity=0.242 Sum_probs=25.5
Q ss_pred HhcCCCCCHhHHHHHhccC-HHHHHHHHHHHHc
Q 008455 229 LTHGLKFSKSDIVKIVHIC-EATLMKRLIEFEN 260 (565)
Q Consensus 229 r~~g~~~t~~eIa~v~~Vs-e~TIrkR~kE~~~ 260 (565)
.-+|++.|++||++.+|++ .+|+...|+-|.+
T Consensus 20 ~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~ 52 (65)
T PF01726_consen 20 EENGYPPTVREIAEALGLKSTSTVQRHLKALER 52 (65)
T ss_dssp HHHSS---HHHHHHHHTSSSHHHHHHHHHHHHH
T ss_pred HHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 3579999999999999996 9999999998864
No 229
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=54.58 E-value=15 Score=26.64 Aligned_cols=26 Identities=19% Similarity=0.298 Sum_probs=19.8
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHH
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~ 258 (565)
..=++...|..+||+..|+.++++.+
T Consensus 17 ~~gn~~~aA~~Lgisr~tL~~klkk~ 42 (42)
T PF02954_consen 17 CGGNVSKAARLLGISRRTLYRKLKKY 42 (42)
T ss_dssp TTT-HHHHHHHHTS-HHHHHHHHHHC
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHhC
Confidence 33456789999999999999999863
No 230
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=54.13 E-value=2.5e+02 Score=28.45 Aligned_cols=28 Identities=14% Similarity=0.050 Sum_probs=24.1
Q ss_pred CCCCCHhHHHHHhccCHHHHHHHHHHHH
Q 008455 232 GLKFSKSDIVKIVHICEATLMKRLIEFE 259 (565)
Q Consensus 232 g~~~t~~eIa~v~~Vse~TIrkR~kE~~ 259 (565)
....|.++||..+|||..||++++....
T Consensus 219 ~e~~t~~EIA~~lgis~~~V~~~~~ral 246 (257)
T PRK05911 219 YEELVLKEIGKILGVSESRVSQIHSKAL 246 (257)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 3578999999999999999999876543
No 231
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=53.61 E-value=53 Score=32.53 Aligned_cols=30 Identities=20% Similarity=0.368 Sum_probs=27.4
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHHHccC
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEFENTD 262 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~~~t~ 262 (565)
++.|+++||..+|++..|+.+.+++|.+..
T Consensus 178 i~lt~~~IA~~lGisretlsR~L~~L~~~G 207 (230)
T PRK09391 178 LPMSRRDIADYLGLTIETVSRALSQLQDRG 207 (230)
T ss_pred ecCCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 578999999999999999999999998663
No 232
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=53.55 E-value=5.7 Score=40.24 Aligned_cols=29 Identities=14% Similarity=0.552 Sum_probs=11.4
Q ss_pred CCCCCCCCCCcee---ccCCCceecCccccee
Q 008455 2 VWCSSCARHVTGH---RPYDSQLCCDRCGKVL 30 (565)
Q Consensus 2 ~~Cp~Cgs~~i~~---D~~~G~~VCt~CG~Vl 30 (565)
+.||+||+..+.. +.--.+..|.+|+--.
T Consensus 32 ~yCP~Cg~~~L~~f~NN~PVaDF~C~~C~eey 63 (254)
T PF06044_consen 32 MYCPNCGSKPLSKFENNRPVADFYCPNCNEEY 63 (254)
T ss_dssp ---TTT--SS-EE--------EEE-TTT--EE
T ss_pred CcCCCCCChhHhhccCCCccceeECCCCchHH
Confidence 4799999984422 1224789999998643
No 233
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=53.29 E-value=2.8e+02 Score=28.74 Aligned_cols=28 Identities=4% Similarity=-0.169 Sum_probs=24.2
Q ss_pred CCCCCHhHHHHHhccCHHHHHHHHHHHH
Q 008455 232 GLKFSKSDIVKIVHICEATLMKRLIEFE 259 (565)
Q Consensus 232 g~~~t~~eIa~v~~Vse~TIrkR~kE~~ 259 (565)
....|+++||..+|||..||+++...-.
T Consensus 243 ~~~~t~~EIa~~lgvs~~~V~q~~~~Al 270 (289)
T PRK07500 243 EDGATLEALGEELGISKERVRQIEARAL 270 (289)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3679999999999999999998876554
No 234
>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=53.28 E-value=43 Score=25.88 Aligned_cols=30 Identities=13% Similarity=0.246 Sum_probs=26.7
Q ss_pred CCCccHHHHHhhhccChHHHHHHHHHHHHH
Q 008455 131 SKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (565)
Q Consensus 131 ~~p~tL~DIa~~~~vsv~~Lgr~~~~L~~~ 160 (565)
..+.+..+||+.++++..++.+.+..|.+.
T Consensus 23 ~~~~s~~ela~~~g~s~~tv~r~l~~L~~~ 52 (67)
T cd00092 23 QLPLTRQEIADYLGLTRETVSRTLKELEEE 52 (67)
T ss_pred cCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 457899999999999999999999888774
No 235
>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=53.16 E-value=32 Score=25.92 Aligned_cols=34 Identities=9% Similarity=0.072 Sum_probs=28.1
Q ss_pred HhcCCCccHHHHHhhhccChHHHHHHHHHHHHHh
Q 008455 128 RQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVL 161 (565)
Q Consensus 128 R~e~~p~tL~DIa~~~~vsv~~Lgr~~~~L~~~L 161 (565)
..++-|++..++|+.++|+..+|.+....|...+
T Consensus 10 ~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 10 LESKEPITAKELAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp HHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred HHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 3456679999999999999999999999886655
No 236
>PHA02591 hypothetical protein; Provisional
Probab=52.99 E-value=17 Score=30.60 Aligned_cols=32 Identities=13% Similarity=0.118 Sum_probs=26.6
Q ss_pred HHHHHhcCCCCCHhHHHHHhccCHHHHHHHHH
Q 008455 225 YVSALTHGLKFSKSDIVKIVHICEATLMKRLI 256 (565)
Q Consensus 225 ylAar~~g~~~t~~eIa~v~~Vse~TIrkR~k 256 (565)
-+|..+.....|+.+||..+||+..|+++-++
T Consensus 50 ~vA~eL~eqGlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 50 SVTHELARKGFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHh
Confidence 35556666778999999999999999998765
No 237
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=52.98 E-value=26 Score=26.25 Aligned_cols=29 Identities=10% Similarity=0.276 Sum_probs=26.5
Q ss_pred CCCCCHhHHHHHhccCHHHHHHHHHHHHc
Q 008455 232 GLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (565)
Q Consensus 232 g~~~t~~eIa~v~~Vse~TIrkR~kE~~~ 260 (565)
+-..|..+|+..++++..|+++.++.|.+
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~ 36 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLRE 36 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 56789999999999999999999999875
No 238
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=52.97 E-value=22 Score=34.22 Aligned_cols=25 Identities=28% Similarity=0.347 Sum_probs=23.3
Q ss_pred CCHhHHHHHhccCHHHHHHHHHHHH
Q 008455 235 FSKSDIVKIVHICEATLMKRLIEFE 259 (565)
Q Consensus 235 ~t~~eIa~v~~Vse~TIrkR~kE~~ 259 (565)
.|..|||..+|||+.||++++.-+.
T Consensus 152 ls~~EIA~~lgiS~~tV~r~l~~aR 176 (185)
T PF07638_consen 152 LSVEEIAERLGISERTVRRRLRRAR 176 (185)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4999999999999999999998776
No 239
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=52.75 E-value=7.4 Score=29.48 Aligned_cols=26 Identities=23% Similarity=0.653 Sum_probs=17.7
Q ss_pred CCCCCCCC-Cceec-cCCCceecCcccc
Q 008455 3 WCSSCARH-VTGHR-PYDSQLCCDRCGK 28 (565)
Q Consensus 3 ~Cp~Cgs~-~i~~D-~~~G~~VCt~CG~ 28 (565)
.|+.||.. .+..- .+.+.+.|..||.
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 7 RCTACGHRFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EeCCCCCEeEEEEecCCCCCCCCCCCCC
Confidence 69999984 32221 2246788999998
No 240
>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=52.50 E-value=26 Score=31.40 Aligned_cols=45 Identities=20% Similarity=0.158 Sum_probs=35.4
Q ss_pred hhHHHHHHHHHHHHhcCCCccHHHHHhhhccChHHHHHHHHHHHH
Q 008455 115 TEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQ 159 (565)
Q Consensus 115 ~~~vaAACLYiACR~e~~p~tL~DIa~~~~vsv~~Lgr~~~~L~~ 159 (565)
....+.+.+|++-...+.|.+..+||+.++++...+.+....|.+
T Consensus 7 ~~~al~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~~ 51 (132)
T TIGR00738 7 TEYALRALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRR 51 (132)
T ss_pred HHHHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 345566777777332345999999999999999999998888877
No 241
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=51.98 E-value=2.7e+02 Score=28.11 Aligned_cols=26 Identities=8% Similarity=0.049 Sum_probs=22.6
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHH
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~ 258 (565)
...|+++||..+|||..||+++.+..
T Consensus 224 ~~~t~~eIA~~lgis~~~V~~~~~~a 249 (258)
T PRK08215 224 QGKTQMEVAEEIGISQAQVSRLEKAA 249 (258)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 46899999999999999999887643
No 242
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=51.88 E-value=2.4e+02 Score=27.62 Aligned_cols=26 Identities=8% Similarity=0.123 Sum_probs=22.6
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHH
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~ 258 (565)
...|.++||..+|++..||++++..-
T Consensus 190 ~~~s~~eIA~~lgis~~tV~~~~~ra 215 (224)
T TIGR02479 190 EELNLKEIGEVLGLTESRVSQIHSQA 215 (224)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 56799999999999999999987543
No 243
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=51.75 E-value=16 Score=37.20 Aligned_cols=30 Identities=20% Similarity=0.226 Sum_probs=26.4
Q ss_pred CCCCCHhHHHHHhccCHHHHHHHHHHHHcc
Q 008455 232 GLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (565)
Q Consensus 232 g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t 261 (565)
.-.++.+|+++.++||+.|||+.+++|.+.
T Consensus 17 ~~~v~v~eLa~~l~VS~~TIRRDL~~Le~~ 46 (256)
T PRK10434 17 QGKTSVEELAQYFDTTGTTIRKDLVILEHA 46 (256)
T ss_pred cCCEEHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 346899999999999999999999998744
No 244
>PRK13501 transcriptional activator RhaR; Provisional
Probab=51.70 E-value=2.8e+02 Score=28.24 Aligned_cols=124 Identities=12% Similarity=0.046 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHhCccccCCchhHHHHHHHHHHHHhcCCCccHHHHHhhhccChHHHHHHHHHHHHHhhcccccccccc
Q 008455 93 IVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQ 172 (565)
Q Consensus 93 i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~p~tL~DIa~~~~vsv~~Lgr~~~~L~~~L~i~~~~~~~~~ 172 (565)
+..-...+.+.........+..........+-..-.....++++.++|..++++...|.+.|++..-
T Consensus 152 l~~l~~~l~~~~~~~~~~~~~~~~~~~~~i~~~I~~~~~e~~sl~~lA~~~~lS~~~l~r~Fk~~~G------------- 218 (290)
T PRK13501 152 LLQLAIVLKRHRYRAEQAHLLPDGEQLDLIMSALQQSLGAYFDMADFCHKNQLVERSLKQLFRQQTG------------- 218 (290)
T ss_pred HHHHHHHHHhhccCccccccCCchHHHHHHHHHHHHhhccCCCHHHHHHHHCcCHHHHHHHHHHHHC-------------
Q ss_pred CCchhhHHHHHHhhCCCCCHHHHHHHHHHHHHhhhccccCCCChhHHHHHHHHHHHHhcCCCCCHhHHHHHhcc-CHHHH
Q 008455 173 VDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHI-CEATL 251 (565)
Q Consensus 173 vdP~~~I~Rf~~~L~~~l~~~V~~~A~~Lv~~m~~~~l~~GR~P~~IaaAALylAar~~g~~~t~~eIa~v~~V-se~TI 251 (565)
..|..||.+. .+..|.+++.. -..++.+||..+|- +.+..
T Consensus 219 ~T~~qyi~~~-----------Ri~~A~~LL~~----------------------------t~~sI~eIA~~~GF~~~s~F 259 (290)
T PRK13501 219 MSISHYLRQI-----------RLCHAKCLLRG----------------------------SEHRISDIAARCGFEDSNYF 259 (290)
T ss_pred cCHHHHHHHH-----------HHHHHHHHHHc----------------------------CCCCHHHHHHHhCCCCHHHH
Q ss_pred HHHHHHHHccCCCCCCHHHHHH
Q 008455 252 MKRLIEFENTDSGSLTIEDFMA 273 (565)
Q Consensus 252 rkR~kE~~~t~s~~Lt~~~f~~ 273 (565)
.+.+|... .+|+.+|++
T Consensus 260 ~r~FKk~~-----G~TP~~yR~ 276 (290)
T PRK13501 260 SAVFTREA-----GMTPRDYRQ 276 (290)
T ss_pred HHHHHHHH-----CcCHHHHHH
No 245
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=51.65 E-value=9.2 Score=26.53 Aligned_cols=23 Identities=22% Similarity=0.531 Sum_probs=16.3
Q ss_pred CCCCCCCCCceeccCCCceecCcccc
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGK 28 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~ 28 (565)
.|+.||- ++|......+|..||.
T Consensus 3 ~C~~CGy---~y~~~~~~~~CP~Cg~ 25 (33)
T cd00350 3 VCPVCGY---IYDGEEAPWVCPVCGA 25 (33)
T ss_pred ECCCCCC---EECCCcCCCcCcCCCC
Confidence 5888884 3555556778888886
No 246
>KOG3915 consensus Transcription regulator dachshund, contains SKI/SNO domain [Transcription]
Probab=51.47 E-value=53 Score=36.29 Aligned_cols=19 Identities=21% Similarity=0.356 Sum_probs=14.9
Q ss_pred HHHHhhhcCHHHHHHHHHHHHHH
Q 008455 437 KKIIWEEMNREYLEEQAAKEAAA 459 (565)
Q Consensus 437 K~~iW~~~N~eyl~eq~~K~~~~ 459 (565)
|+.||| |+|+|++-||-..
T Consensus 530 k~ELkm----d~lrerelresle 548 (641)
T KOG3915|consen 530 KTELKM----DFLRERELRESLE 548 (641)
T ss_pred HHHHHH----HHHHHHHHHHHHH
Confidence 788998 7888888877543
No 247
>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=51.46 E-value=31 Score=26.58 Aligned_cols=26 Identities=15% Similarity=0.390 Sum_probs=24.5
Q ss_pred CCHhHHHHHhccCHHHHHHHHHHHHc
Q 008455 235 FSKSDIVKIVHICEATLMKRLIEFEN 260 (565)
Q Consensus 235 ~t~~eIa~v~~Vse~TIrkR~kE~~~ 260 (565)
++..+|++.++++..||++.++.|..
T Consensus 21 ~~~~ei~~~~~i~~~~i~~~l~~L~~ 46 (78)
T cd00090 21 LTVSELAERLGLSQSTVSRHLKKLEE 46 (78)
T ss_pred cCHHHHHHHHCcCHhHHHHHHHHHHH
Confidence 99999999999999999999999874
No 248
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=51.22 E-value=21 Score=32.83 Aligned_cols=40 Identities=18% Similarity=0.366 Sum_probs=32.6
Q ss_pred HHHHHHHHhcCCCCCHhHHHHHhccCHHHHHHHHHHHHcc
Q 008455 222 AALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (565)
Q Consensus 222 AALylAar~~g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t 261 (565)
+.||++..-.|...+.++||+..+|+..+|++-+..+...
T Consensus 13 ~~i~la~~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~ 52 (141)
T PRK11014 13 ALIYMASLPEGRMTSISEVTEVYGVSRNHMVKIINQLSRA 52 (141)
T ss_pred HHHHHhcCCCCCccCHHHHHHHHCcCHHHHHHHHHHHHhC
Confidence 4456665555667899999999999999999999999753
No 249
>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=51.16 E-value=33 Score=30.92 Aligned_cols=38 Identities=13% Similarity=0.164 Sum_probs=31.2
Q ss_pred HHHHHHHhcCCCCCHhHHHHHhccCHHHHHHHHHHHHcc
Q 008455 223 ALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (565)
Q Consensus 223 ALylAar~~g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t 261 (565)
.+|||. ..+-+.|..+|+..++++..+++++++.+.+.
T Consensus 15 l~~la~-~~~~~~s~~eia~~l~is~~~v~~~l~~L~~~ 52 (130)
T TIGR02944 15 LTTLAQ-NDSQPYSAAEIAEQTGLNAPTVSKILKQLSLA 52 (130)
T ss_pred HHHHHh-CCCCCccHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 445553 34567899999999999999999999999864
No 250
>TIGR02443 conserved hypothetical metal-binding protein. Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria.
Probab=51.11 E-value=11 Score=29.98 Aligned_cols=28 Identities=21% Similarity=0.408 Sum_probs=18.7
Q ss_pred CCCCCCCCCCc--ee-ccCCCceecCcccce
Q 008455 2 VWCSSCARHVT--GH-RPYDSQLCCDRCGKV 29 (565)
Q Consensus 2 ~~Cp~Cgs~~i--~~-D~~~G~~VCt~CG~V 29 (565)
..||.|+.-+. .+ +...-.+-|..||.-
T Consensus 10 A~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~ 40 (59)
T TIGR02443 10 AVCPACSAQDTLAMWKENNIELVECVECGYQ 40 (59)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEeccCCCc
Confidence 37999998632 22 222335789999985
No 251
>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=51.01 E-value=18 Score=28.53 Aligned_cols=30 Identities=17% Similarity=0.290 Sum_probs=24.9
Q ss_pred cCCCC-CHhHHHHHhccCHHHHHHHHHHHHc
Q 008455 231 HGLKF-SKSDIVKIVHICEATLMKRLIEFEN 260 (565)
Q Consensus 231 ~g~~~-t~~eIa~v~~Vse~TIrkR~kE~~~ 260 (565)
.|..+ |..+|++..+||..|+++.|..|..
T Consensus 20 ~g~~lps~~~la~~~~vsr~tvr~al~~L~~ 50 (64)
T PF00392_consen 20 PGDRLPSERELAERYGVSRTTVREALRRLEA 50 (64)
T ss_dssp TTSBE--HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCCEeCCHHHHHHHhccCCcHHHHHHHHHHH
Confidence 35678 9999999999999999999999874
No 252
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=50.98 E-value=20 Score=25.72 Aligned_cols=27 Identities=7% Similarity=0.114 Sum_probs=20.4
Q ss_pred CCCccHHHHHhhhccChHHHHHHHHHH
Q 008455 131 SKPFLLIDFSNYLNINVYELGAVYLQL 157 (565)
Q Consensus 131 ~~p~tL~DIa~~~~vsv~~Lgr~~~~L 157 (565)
..+.++.|||..+|++...+.+.|++.
T Consensus 6 ~~~~~l~~iA~~~g~S~~~f~r~Fk~~ 32 (42)
T PF00165_consen 6 QQKLTLEDIAEQAGFSPSYFSRLFKKE 32 (42)
T ss_dssp -SS--HHHHHHHHTS-HHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 457899999999999999999988754
No 253
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=50.85 E-value=59 Score=31.93 Aligned_cols=32 Identities=16% Similarity=0.183 Sum_probs=27.7
Q ss_pred CCccHHHHHhhhccChHHHHHHHHHHHHHhhc
Q 008455 132 KPFLLIDFSNYLNINVYELGAVYLQLCQVLYI 163 (565)
Q Consensus 132 ~p~tL~DIa~~~~vsv~~Lgr~~~~L~~~L~i 163 (565)
.|+|..+||+.+|++..+|.|..++|.+.=-|
T Consensus 183 ~~lt~~~iA~~lG~sr~tvsR~l~~l~~~g~I 214 (235)
T PRK11161 183 LTMTRGDIGNYLGLTVETISRLLGRFQKSGML 214 (235)
T ss_pred ccccHHHHHHHhCCcHHHHHHHHHHHHHCCCE
Confidence 57899999999999999999999988875333
No 254
>PF13518 HTH_28: Helix-turn-helix domain
Probab=50.45 E-value=33 Score=25.27 Aligned_cols=26 Identities=15% Similarity=0.296 Sum_probs=23.8
Q ss_pred CHhHHHHHhccCHHHHHHHHHHHHcc
Q 008455 236 SKSDIVKIVHICEATLMKRLIEFENT 261 (565)
Q Consensus 236 t~~eIa~v~~Vse~TIrkR~kE~~~t 261 (565)
|+.+||..+|||..||.+-++.|.+.
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~~~ 39 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYREG 39 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHHhc
Confidence 99999999999999999998888753
No 255
>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=50.39 E-value=34 Score=30.83 Aligned_cols=45 Identities=18% Similarity=0.199 Sum_probs=36.9
Q ss_pred chhHHHHHHHHHHHHhcCCCccHHHHHhhhccChHHHHHHHHHHHH
Q 008455 114 RTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQ 159 (565)
Q Consensus 114 ~~~~vaAACLYiACR~e~~p~tL~DIa~~~~vsv~~Lgr~~~~L~~ 159 (565)
..+..+.+++|++- ..+.+.+..+||+.++++...+.+....|.+
T Consensus 7 ~~~yal~~l~~la~-~~~~~~s~~eia~~l~is~~~v~~~l~~L~~ 51 (130)
T TIGR02944 7 LTDYATLVLTTLAQ-NDSQPYSAAEIAEQTGLNAPTVSKILKQLSL 51 (130)
T ss_pred HHhHHHHHHHHHHh-CCCCCccHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 34566777888874 3456899999999999999999998888877
No 256
>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=50.36 E-value=24 Score=29.75 Aligned_cols=23 Identities=17% Similarity=0.286 Sum_probs=21.0
Q ss_pred CCCCHhHHHHHhccCHHHHHHHH
Q 008455 233 LKFSKSDIVKIVHICEATLMKRL 255 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~ 255 (565)
-..|+.+||+.+|||..||++.+
T Consensus 18 ~~~ti~dvA~~~gvS~~TVsr~L 40 (80)
T TIGR02844 18 TKATVRETAKVFGVSKSTVHKDV 40 (80)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHh
Confidence 56799999999999999999966
No 257
>KOG1088 consensus Uncharacterized conserved protein [Function unknown]
Probab=50.33 E-value=7.2 Score=35.13 Aligned_cols=18 Identities=22% Similarity=0.532 Sum_probs=14.9
Q ss_pred eccCCCceecCcccceec
Q 008455 14 HRPYDSQLCCDRCGKVLE 31 (565)
Q Consensus 14 ~D~~~G~~VCt~CG~Vle 31 (565)
.|-.+|.++|.+||+|..
T Consensus 92 ~~v~EG~l~CpetG~vfp 109 (124)
T KOG1088|consen 92 IDVIEGELVCPETGRVFP 109 (124)
T ss_pred hhhccceEecCCCCcEee
Confidence 455789999999999953
No 258
>PRK08402 replication factor A; Reviewed
Probab=50.11 E-value=9.5 Score=41.04 Aligned_cols=26 Identities=27% Similarity=0.609 Sum_probs=21.0
Q ss_pred CCCCCCCCCceeccCCCceecCcccce
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGKV 29 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~V 29 (565)
.||.|+.. +..|..+|...|..||.|
T Consensus 214 aCp~CnKk-v~~~~~~~~~~Ce~~~~v 239 (355)
T PRK08402 214 ACPECRRK-VDYDPATDTWICPEHGEV 239 (355)
T ss_pred cCCCCCeE-EEEecCCCCEeCCCCCCc
Confidence 69999875 344677899999999975
No 259
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=50.03 E-value=11 Score=25.37 Aligned_cols=22 Identities=14% Similarity=0.492 Sum_probs=10.1
Q ss_pred CCCCCCCCCceeccCCCceecCc
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDR 25 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~ 25 (565)
.||.||+..+ ....+-.+.|++
T Consensus 1 ~CP~C~s~l~-~~~~ev~~~C~N 22 (28)
T PF03119_consen 1 TCPVCGSKLV-REEGEVDIRCPN 22 (28)
T ss_dssp B-TTT--BEE-E-CCTTCEEE--
T ss_pred CcCCCCCEeE-cCCCCEeEECCC
Confidence 5999998744 333444667764
No 260
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=49.90 E-value=9.9 Score=29.48 Aligned_cols=29 Identities=21% Similarity=0.460 Sum_probs=20.6
Q ss_pred CCCCCCCC-CceeccCCCc--e--ecCcccceec
Q 008455 3 WCSSCARH-VTGHRPYDSQ--L--CCDRCGKVLE 31 (565)
Q Consensus 3 ~Cp~Cgs~-~i~~D~~~G~--~--VCt~CG~Vle 31 (565)
.||+||.. .+.+|...|. + =|.-|..=+.
T Consensus 2 ~CPyCge~~~~~iD~s~~~Q~yiEDC~vCC~PI~ 35 (52)
T PF14255_consen 2 QCPYCGEPIEILIDPSAGDQEYIEDCQVCCRPIE 35 (52)
T ss_pred CCCCCCCeeEEEEecCCCCeeEEeehhhcCCccE
Confidence 69999987 7788887773 1 3777766443
No 261
>PRK04217 hypothetical protein; Provisional
Probab=49.88 E-value=21 Score=31.93 Aligned_cols=27 Identities=11% Similarity=0.151 Sum_probs=23.8
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHHH
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEFE 259 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~~ 259 (565)
...|+++||+.+|||..||.+++....
T Consensus 57 eGlS~~EIAk~LGIS~sTV~r~L~RAr 83 (110)
T PRK04217 57 EGLTQEEAGKRMGVSRGTVWRALTSAR 83 (110)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 345999999999999999999998755
No 262
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=49.86 E-value=12 Score=38.39 Aligned_cols=29 Identities=14% Similarity=0.449 Sum_probs=21.1
Q ss_pred CCCCCCCCCCceeccCCCceecCcccceec
Q 008455 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (565)
Q Consensus 2 ~~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vle 31 (565)
..||.||+.... ....-..+|..||.+.=
T Consensus 100 ~fC~~CG~~~~~-~~~~~~~~C~~c~~~~y 128 (256)
T PRK00241 100 RFCGYCGHPMHP-SKTEWAMLCPHCRERYY 128 (256)
T ss_pred ccccccCCCCee-cCCceeEECCCCCCEEC
Confidence 479999997443 33445689999998753
No 263
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=49.75 E-value=34 Score=25.20 Aligned_cols=35 Identities=20% Similarity=0.121 Sum_probs=26.0
Q ss_pred HHHHHHHHhcCCCCCHhHHHHHhccCHHHHHHHHH
Q 008455 222 AALYVSALTHGLKFSKSDIVKIVHICEATLMKRLI 256 (565)
Q Consensus 222 AALylAar~~g~~~t~~eIa~v~~Vse~TIrkR~k 256 (565)
||+-+..+.-=...|+++|++.+||+..+|-+.+.
T Consensus 4 aa~~l~~~~G~~~~s~~~Ia~~~gvs~~~~y~~f~ 38 (47)
T PF00440_consen 4 AALELFAEKGYEAVSIRDIARRAGVSKGSFYRYFP 38 (47)
T ss_dssp HHHHHHHHHHTTTSSHHHHHHHHTSCHHHHHHHCS
T ss_pred HHHHHHHHhCHHhCCHHHHHHHHccchhhHHHHcC
Confidence 45555553333468999999999999999987654
No 264
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=49.74 E-value=11 Score=31.06 Aligned_cols=30 Identities=20% Similarity=0.303 Sum_probs=20.8
Q ss_pred CCCCCCCCCCce---eccCCCceecCcccceec
Q 008455 2 VWCSSCARHVTG---HRPYDSQLCCDRCGKVLE 31 (565)
Q Consensus 2 ~~Cp~Cgs~~i~---~D~~~G~~VCt~CG~Vle 31 (565)
..||.|+..+.+ .+...-.+-|..||..-.
T Consensus 9 a~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e~ 41 (71)
T PF09526_consen 9 AVCPKCQAMDTIMMWRENGVEYVECVECGYTER 41 (71)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEecCCCCeec
Confidence 379999987332 233455778999999743
No 265
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=49.65 E-value=7.7 Score=42.32 Aligned_cols=30 Identities=20% Similarity=0.565 Sum_probs=23.3
Q ss_pred CCCCCCCC--C----ceeccCCCceecCcccceecc
Q 008455 3 WCSSCARH--V----TGHRPYDSQLCCDRCGKVLED 32 (565)
Q Consensus 3 ~Cp~Cgs~--~----i~~D~~~G~~VCt~CG~Vlee 32 (565)
.||.|++. . -.+|..+|...|+.||.=|.+
T Consensus 130 ~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~gelve 165 (436)
T KOG2593|consen 130 VCPNCQKKYTSLEALQLLDNETGEFHCENCGGELVE 165 (436)
T ss_pred cCCccccchhhhHHHHhhcccCceEEEecCCCchhc
Confidence 59999987 1 145677899999999986543
No 266
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 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. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=49.53 E-value=17 Score=27.26 Aligned_cols=20 Identities=10% Similarity=0.140 Sum_probs=17.6
Q ss_pred cHHHHHhhhccChHHHHHHH
Q 008455 135 LLIDFSNYLNINVYELGAVY 154 (565)
Q Consensus 135 tL~DIa~~~~vsv~~Lgr~~ 154 (565)
||+|||..+||+..++.+++
T Consensus 1 Ti~dIA~~agvS~~TVSr~l 20 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVL 20 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHH
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 68999999999999988754
No 267
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=49.26 E-value=3e+02 Score=27.87 Aligned_cols=27 Identities=11% Similarity=0.148 Sum_probs=24.0
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHHH
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEFE 259 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~~ 259 (565)
...|+++||..+|||..||++++....
T Consensus 218 ~~~s~~eIA~~lgvs~~~V~~~~~ra~ 244 (256)
T PRK07408 218 HDLTQKEAAERLGISPVTVSRRVKKGL 244 (256)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 578999999999999999999987654
No 268
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=48.95 E-value=13 Score=32.89 Aligned_cols=26 Identities=23% Similarity=0.689 Sum_probs=21.6
Q ss_pred CCCCCCCCCceeccCCCceecCcccceeccc
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDH 33 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vlee~ 33 (565)
.||.||...|+. .+-|.+||+-+..+
T Consensus 8 ~cPvcg~~~iVT-----eL~c~~~etTVrg~ 33 (122)
T COG3877 8 RCPVCGRKLIVT-----ELKCSNCETTVRGN 33 (122)
T ss_pred CCCcccccceeE-----EEecCCCCceEecc
Confidence 699999987764 57899999988754
No 269
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=48.78 E-value=37 Score=27.36 Aligned_cols=38 Identities=11% Similarity=0.078 Sum_probs=29.8
Q ss_pred HHHHHHhcCC-CCCHhHHHHHhccCHHHHHHHHHHHHcc
Q 008455 224 LYVSALTHGL-KFSKSDIVKIVHICEATLMKRLIEFENT 261 (565)
Q Consensus 224 LylAar~~g~-~~t~~eIa~v~~Vse~TIrkR~kE~~~t 261 (565)
|+..-..+|- .++..+||+.+|++..|+++.|..|.+-
T Consensus 11 IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~ 49 (68)
T smart00550 11 ILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKK 49 (68)
T ss_pred HHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 3333344555 4999999999999999999999988743
No 270
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=48.77 E-value=9.7 Score=34.11 Aligned_cols=35 Identities=20% Similarity=0.517 Sum_probs=20.7
Q ss_pred CCCCCCCCCCceeccCCCceecCcccceeccccccccccc
Q 008455 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATF 41 (565)
Q Consensus 2 ~~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vlee~~id~~~ef 41 (565)
.+|+.||... ....-...|..||.. +..+..|.++
T Consensus 71 ~~C~~Cg~~~---~~~~~~~~CP~Cgs~--~~~i~~G~El 105 (113)
T PRK12380 71 AWCWDCSQVV---EIHQHDAQCPHCHGE--RLRVDTGDSL 105 (113)
T ss_pred EEcccCCCEE---ecCCcCccCcCCCCC--CcEEccCCeE
Confidence 3799999542 222344569999964 3345555554
No 271
>KOG0654 consensus G2/Mitotic-specific cyclin A [Cell cycle control, cell division, chromosome partitioning]
Probab=48.74 E-value=1.9e+02 Score=31.28 Aligned_cols=136 Identities=16% Similarity=0.134 Sum_probs=84.0
Q ss_pred HHHHHHHHhc-CCCccHHHHHhhhccChHHHHHHHHHHHHHhhccccccccccCC--chhhHHHHHHhhCCCCCHHHHHH
Q 008455 121 SCLYLACRQK-SKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVD--PSIFLHKFTDRLLPGGNKKVCDT 197 (565)
Q Consensus 121 ACLYiACR~e-~~p~tL~DIa~~~~vsv~~Lgr~~~~L~~~L~i~~~~~~~~~vd--P~~~I~Rf~~~L~~~l~~~V~~~ 197 (565)
+|-+|+.+-+ ..+..+.+|.-.+. +.+....++......|..-.-. ++. ...|+.||...-.+ -.-++...
T Consensus 185 s~m~I~sk~ee~~~~~~~ef~~itd-~ty~~~qv~~~~~~il~~l~~~----~~~pt~~~~l~~~~~~~~~-~~~~~e~~ 258 (359)
T KOG0654|consen 185 SAMLIASKYEEIKEPRVEEFCYITD-NTYTYWQVLRMEIDILNALTFE----LVRPTSKTFLRRFLRVAQT-PELQVEPL 258 (359)
T ss_pred ccceeeccchhhcchHHHHHHhhhh-hhhHHHHHHHHHHHHHHHhHHH----HhCchHHHHHHHHHHhhcc-hhHHHHHH
Confidence 4555666643 44556667766554 4555566665555554321111 122 45788888544321 23344555
Q ss_pred HHHHHHHhhhccccCCCChhHHHHHHHHHHHHhcCCCCCHhHHHHHhccCHHHHHHHHHHHHccCC
Q 008455 198 ARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDS 263 (565)
Q Consensus 198 A~~Lv~~m~~~~l~~GR~P~~IaaAALylAar~~g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t~s 263 (565)
+..|...-.-+....--.|+-|||||+++|-..++..-=-.-+..-++++-.++.-.+..|. .++
T Consensus 259 ~~yl~elsll~~~~l~y~PSliAasAv~lA~~~~~~~pW~~~L~~~T~y~~edl~~~v~~L~-~~l 323 (359)
T KOG0654|consen 259 ANYLTELSLLDYIFLKYLPSLIAASAVFLARLTLDFHPWNQTLEDYTGYKAEDLKPCVLDLH-LYL 323 (359)
T ss_pred HHHHHHhhhhhHHHhccChHHHHHHHHHHHHhhccCCCCchhhHHhhcccHHHHHHHHHHHh-ccc
Confidence 55555543334445568999999999999988887444355677889999999999988887 443
No 272
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=48.62 E-value=9.9 Score=34.52 Aligned_cols=29 Identities=17% Similarity=0.352 Sum_probs=18.9
Q ss_pred CCCCCCCCCceeccCCCceecCcccceec
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vle 31 (565)
.||+||...+.--.-.=.-.|..||.=+.
T Consensus 23 rCP~CGeGrLF~gFLK~~p~C~aCG~dyg 51 (126)
T COG5349 23 RCPRCGEGRLFRGFLKVVPACEACGLDYG 51 (126)
T ss_pred CCCCCCCchhhhhhcccCchhhhcccccc
Confidence 69999987542212223447999997554
No 273
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=48.48 E-value=44 Score=32.90 Aligned_cols=30 Identities=10% Similarity=0.139 Sum_probs=26.7
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHHHccC
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEFENTD 262 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~~~t~ 262 (565)
++.|+.+||..+|+|..|+.+.+++|.+-.
T Consensus 168 ~~~t~~~lA~~lG~sretvsR~L~~L~~~G 197 (226)
T PRK10402 168 YHEKHTQAAEYLGVSYRHLLYVLAQFIQDG 197 (226)
T ss_pred ccchHHHHHHHHCCcHHHHHHHHHHHHHCC
Confidence 346899999999999999999999998654
No 274
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=48.42 E-value=33 Score=24.60 Aligned_cols=27 Identities=26% Similarity=0.277 Sum_probs=23.9
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHHH
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEFE 259 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~~ 259 (565)
...+..+||...|++..||.+++....
T Consensus 25 ~~~~~~~ia~~~~~s~~~i~~~~~~~~ 51 (55)
T cd06171 25 EGLSYEEIAEILGISRSTVRQRLHRAL 51 (55)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 557999999999999999999987765
No 275
>TIGR01321 TrpR trp operon repressor, proteobacterial. This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.
Probab=48.33 E-value=20 Score=31.21 Aligned_cols=30 Identities=13% Similarity=0.140 Sum_probs=25.4
Q ss_pred hcCCCCCHhHHHHHhccCHHHHHHHHHHHH
Q 008455 230 THGLKFSKSDIVKIVHICEATLMKRLIEFE 259 (565)
Q Consensus 230 ~~g~~~t~~eIa~v~~Vse~TIrkR~kE~~ 259 (565)
+..-.+|+++|++.+|||.+||.+-=+.+.
T Consensus 51 Ll~~~~tQrEIa~~lGiS~atIsR~sn~lk 80 (94)
T TIGR01321 51 LLNGNMSQREIASKLGVSIATITRGSNNLK 80 (94)
T ss_pred HHhCCCCHHHHHHHhCCChhhhhHHHhhcc
Confidence 334679999999999999999998777665
No 276
>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=48.29 E-value=22 Score=27.32 Aligned_cols=26 Identities=19% Similarity=0.328 Sum_probs=23.8
Q ss_pred CHhHHHHHhccCHHHHHHHHHHHHcc
Q 008455 236 SKSDIVKIVHICEATLMKRLIEFENT 261 (565)
Q Consensus 236 t~~eIa~v~~Vse~TIrkR~kE~~~t 261 (565)
+..+|+..++|+..||++.++.|.+-
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L~~~ 52 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELEAE 52 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 59999999999999999999999753
No 277
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=48.19 E-value=20 Score=25.65 Aligned_cols=22 Identities=14% Similarity=0.321 Sum_probs=19.9
Q ss_pred CHhHHHHHhccCHHHHHHHHHH
Q 008455 236 SKSDIVKIVHICEATLMKRLIE 257 (565)
Q Consensus 236 t~~eIa~v~~Vse~TIrkR~kE 257 (565)
|..++|+.+||+..||++..+.
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~~ 23 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHHc
Confidence 6789999999999999988775
No 278
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=48.11 E-value=18 Score=27.82 Aligned_cols=27 Identities=19% Similarity=0.167 Sum_probs=23.4
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHHH
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEFE 259 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~~ 259 (565)
...+.++||...+|++.||+.+.+.+.
T Consensus 17 ~G~~~~eIA~~l~is~~tV~~~~~~i~ 43 (58)
T PF00196_consen 17 QGMSNKEIAEELGISEKTVKSHRRRIM 43 (58)
T ss_dssp TTS-HHHHHHHHTSHHHHHHHHHHHHH
T ss_pred hcCCcchhHHhcCcchhhHHHHHHHHH
Confidence 457899999999999999999998876
No 279
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=48.10 E-value=19 Score=25.87 Aligned_cols=23 Identities=9% Similarity=0.260 Sum_probs=20.5
Q ss_pred CCHhHHHHHhccCHHHHHHHHHH
Q 008455 235 FSKSDIVKIVHICEATLMKRLIE 257 (565)
Q Consensus 235 ~t~~eIa~v~~Vse~TIrkR~kE 257 (565)
.|.+++|+.+||+..||.+.+++
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~ 24 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHE 24 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHc
Confidence 47899999999999999998864
No 280
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=48.05 E-value=14 Score=28.65 Aligned_cols=29 Identities=21% Similarity=0.698 Sum_probs=20.2
Q ss_pred CCCC--CCCCCCcee-ccCCCceecCccccee
Q 008455 2 VWCS--SCARHVTGH-RPYDSQLCCDRCGKVL 30 (565)
Q Consensus 2 ~~Cp--~Cgs~~i~~-D~~~G~~VCt~CG~Vl 30 (565)
.+|| .|+...... +.....+.|..||...
T Consensus 19 ~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~f 50 (64)
T smart00647 19 KWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSF 50 (64)
T ss_pred cCCCCCCCcceEEecCCCCCCeeECCCCCCeE
Confidence 4799 897764443 3356788998898653
No 281
>PF05460 ORC6: Origin recognition complex subunit 6 (ORC6); InterPro: IPR008721 The Origin Recognition Complex (ORC) is a six-subunit ATP-dependent DNA-binding complex encoded in yeast by ORC1-6 []. ORC is a central component for eukaryotic DNA replication, and binds chromatin at replication origins throughout the cell cycle []. ORC directs DNA replication throughout the genome and is required for its initiation [, , ]. ORC bound at replication origins serves as the foundation for assembly of the pre-replicative complex (pre-RC), which includes Cdc6, Tah11 (aka Cdt1), and the Mcm2-7 complex [, , ]. Pre-RC assembly during G1 is required for replication licensing of chromosomes prior to DNA synthesis during S phase [, , ]. Cell cycle-regulated phosphorylation of Orc2, Orc6, Cdc6, and MCM by the cyclin-dependent protein kinase Cdc28 regulates initiation of DNA replication, including blocking reinitiation in G2/M phase [, , , ]. In yeast, ORC also plays a role in the establishment of silencing at the mating-type loci Hidden MAT Left (HML) and Hidden MAT Right (HMR) [, , ]. ORC participates in the assembly of transcriptionally silent chromatin at HML and HMR by recruiting the Sir1 silencing protein to the HML and HMR silencers [, , ]. Both Orc1 and Orc5 bind ATP, though only Orc1 has ATPase activity []. The binding of ATP by Orc1 is required for ORC binding to DNA and is essential for cell viability []. The ATPase activity of Orc1 is involved in formation of the pre-RC [, , ]. ATP binding by Orc5 is crucial for the stability of ORC as a whole. Only the Orc1-5 subunits are required for origin binding; Orc6 is essential for maintenance of pre-RCs once formed []. Interactions within ORC suggest that Orc2-3-6 may form a core complex []. ORC homologues have been found in various eukaryotes, including fission yeast, insects, amphibians, and humans []. This entry represents subunit 6, which directs DNA replication by binding to replication origins and is also involved in transcriptional silencing; interacts with Spp1 and with trimethylated histone H3; phosphorylated by Cdc28 [, ]. In Saccharomyces cerevisiae (Baker's yeast), both ends of the Orc6 interact with Cdt1 [] and the N terminus mediates an interaction with the S-phase cyclin Clb5 []. ; GO: 0003677 DNA binding, 0006260 DNA replication, 0005664 nuclear origin of replication recognition complex; PDB: 3M03_B.
Probab=47.49 E-value=6.2 Score=42.39 Aligned_cols=80 Identities=14% Similarity=0.043 Sum_probs=0.0
Q ss_pred HHHhhCCCCCHHHHHHHHHHHHHhh-hccccCCCChhHHHHHHHHHHHHhcCCCCCHhHHHHHhccCHHHHHHHHHHHHc
Q 008455 182 FTDRLLPGGNKKVCDTARDILASMK-RDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (565)
Q Consensus 182 f~~~L~~~l~~~V~~~A~~Lv~~m~-~~~l~~GR~P~~IaaAALylAar~~g~~~t~~eIa~v~~Vse~TIrkR~kE~~~ 260 (565)
++..++++.+++++..|..|++... ...+..+-.=.+=+.+|+||||..++....+.......++......+-|+.|..
T Consensus 4 l~p~~~~~~~~~ll~~a~~L~~ls~~~~~~l~~~~EiaR~~iCa~lA~~~l~~~~dl~~~~~~~pl~pk~y~~l~~~~~~ 83 (353)
T PF05460_consen 4 LIPKLGGGLPPKLLSKASELYRLSRQKKSSLKPEEEIARAHICAELACERLKEKLDLPYAIKRSPLPPKVYKKLLNTFEN 83 (353)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred hhhccCCCCCHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhCCccCchhhcCCCCCCHHHHHHHHHHHHH
Confidence 3445544467788888888887776 455666666677788999999999999988888889999999999999988876
Q ss_pred c
Q 008455 261 T 261 (565)
Q Consensus 261 t 261 (565)
.
T Consensus 84 ~ 84 (353)
T PF05460_consen 84 L 84 (353)
T ss_dssp -
T ss_pred H
Confidence 3
No 282
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=47.48 E-value=9.1 Score=37.83 Aligned_cols=29 Identities=34% Similarity=0.503 Sum_probs=20.4
Q ss_pred CCCCCCCCCCcee--ccCCCceecCccccee
Q 008455 2 VWCSSCARHVTGH--RPYDSQLCCDRCGKVL 30 (565)
Q Consensus 2 ~~Cp~Cgs~~i~~--D~~~G~~VCt~CG~Vl 30 (565)
+.|+.|++.+..+ +...=.+.|..||..-
T Consensus 99 V~C~~C~~pdT~l~k~~~~~~l~C~aCGa~~ 129 (201)
T PRK12336 99 VICSECGLPDTRLVKEDRVLMLRCDACGAHR 129 (201)
T ss_pred EECCCCCCCCcEEEEcCCeEEEEcccCCCCc
Confidence 4699999985533 3223366899999863
No 283
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=47.09 E-value=55 Score=29.54 Aligned_cols=103 Identities=7% Similarity=0.031 Sum_probs=63.7
Q ss_pred hhHHHHHHHHHHHHhcCCCccHHHHHhhhccChHHHHHHHHHHHHHhhccccccccccCCchhhHHHHHHhhCCCCCHHH
Q 008455 115 TEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKV 194 (565)
Q Consensus 115 ~~~vaAACLYiACR~e~~p~tL~DIa~~~~vsv~~Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~~~l~~~V 194 (565)
...+..+.-||--... .+.++.++|+.+++++..|.+.|++. +| ..|..||.+.--
T Consensus 8 ~~~i~~~~~~I~~~~~-~~~sl~~lA~~~g~S~~~l~r~Fk~~---~G----------~s~~~~l~~~Rl---------- 63 (127)
T PRK11511 8 AITIHSILDWIEDNLE-SPLSLEKVSERSGYSKWHLQRMFKKE---TG----------HSLGQYIRSRKM---------- 63 (127)
T ss_pred HHHHHHHHHHHHHhcC-CCCCHHHHHHHHCcCHHHHHHHHHHH---HC----------cCHHHHHHHHHH----------
Confidence 3445555556665544 47999999999999999999887755 33 335566553311
Q ss_pred HHHHHHHHHHhhhccccCCCChhHHHHHHHHHHHHhcCCCCCHhHHHHHhccC-HHHHHHHHHHHHccCCCCCCHHHHHH
Q 008455 195 CDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHIC-EATLMKRLIEFENTDSGSLTIEDFMA 273 (565)
Q Consensus 195 ~~~A~~Lv~~m~~~~l~~GR~P~~IaaAALylAar~~g~~~t~~eIa~v~~Vs-e~TIrkR~kE~~~t~s~~Lt~~~f~~ 273 (565)
-.|+.+| ..-..++.+||..+|.+ .....+.++... .+||.+|++
T Consensus 64 -------------------------~~A~~~L----~~t~~~i~eIA~~~Gf~s~s~F~r~Fkk~~-----G~tP~~yR~ 109 (127)
T PRK11511 64 -------------------------TEIAQKL----KESNEPILYLAERYGFESQQTLTRTFKNYF-----DVPPHKYRM 109 (127)
T ss_pred -------------------------HHHHHHH----HcCCCCHHHHHHHhCCCCHHHHHHHHHHHH-----CcCHHHHHH
Confidence 0011111 11235677777777754 467777776666 466777765
Q ss_pred HH
Q 008455 274 RK 275 (565)
Q Consensus 274 ~~ 275 (565)
..
T Consensus 110 ~~ 111 (127)
T PRK11511 110 TN 111 (127)
T ss_pred hc
Confidence 43
No 284
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=46.94 E-value=7.7 Score=30.20 Aligned_cols=29 Identities=28% Similarity=0.623 Sum_probs=19.8
Q ss_pred CCCCCCCC-Cceec--cCCCceecCcccceec
Q 008455 3 WCSSCARH-VTGHR--PYDSQLCCDRCGKVLE 31 (565)
Q Consensus 3 ~Cp~Cgs~-~i~~D--~~~G~~VCt~CG~Vle 31 (565)
.|.+||.. ...+. +..+..+|..||.-.-
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~ 32 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWK 32 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHH
Confidence 48888876 33443 3367888999987654
No 285
>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=46.69 E-value=47 Score=25.41 Aligned_cols=41 Identities=12% Similarity=0.143 Sum_probs=31.3
Q ss_pred HHHHHHHHHhcCCCccHHHHHhhhccChHHHHHHHHHHHHH
Q 008455 120 ASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (565)
Q Consensus 120 AACLYiACR~e~~p~tL~DIa~~~~vsv~~Lgr~~~~L~~~ 160 (565)
..+|++..+..+...++.+|++.++++...+.+....|.+.
T Consensus 8 ~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~ 48 (62)
T PF12802_consen 8 FRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKK 48 (62)
T ss_dssp HHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 34555555555556899999999999999999999888773
No 286
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=46.68 E-value=52 Score=31.97 Aligned_cols=25 Identities=28% Similarity=0.271 Sum_probs=22.4
Q ss_pred CCCHhHHHHHhccCHHHHHHHHHHH
Q 008455 234 KFSKSDIVKIVHICEATLMKRLIEF 258 (565)
Q Consensus 234 ~~t~~eIa~v~~Vse~TIrkR~kE~ 258 (565)
..|..+||+.+|||.+|+.+.+++.
T Consensus 172 g~s~~~iak~lgis~~Tv~r~~k~~ 196 (200)
T PRK13413 172 GTSKSEIARKLGVSRTTLARFLKTR 196 (200)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHhc
Confidence 4699999999999999999998853
No 287
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=46.63 E-value=3.3e+02 Score=27.64 Aligned_cols=25 Identities=12% Similarity=0.213 Sum_probs=22.1
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHH
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIE 257 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE 257 (565)
...|.++||..+|++..||++++..
T Consensus 227 ~~~s~~eIA~~lgis~~tV~~~~~r 251 (268)
T PRK06288 227 EDLTLKEIGKVLGVTESRISQLHTK 251 (268)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 4689999999999999999987754
No 288
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=46.51 E-value=19 Score=36.58 Aligned_cols=29 Identities=10% Similarity=0.102 Sum_probs=26.2
Q ss_pred CCCCCHhHHHHHhccCHHHHHHHHHHHHc
Q 008455 232 GLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (565)
Q Consensus 232 g~~~t~~eIa~v~~Vse~TIrkR~kE~~~ 260 (565)
+-.++++++++.++||+.|||+.|++|.+
T Consensus 17 ~~~~~~~ela~~l~vS~~TirRdL~~Le~ 45 (251)
T PRK13509 17 LGFVTVEKVIERLGISPATARRDINKLDE 45 (251)
T ss_pred cCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 45689999999999999999999999864
No 289
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=46.51 E-value=8.6 Score=37.81 Aligned_cols=34 Identities=26% Similarity=0.572 Sum_probs=22.4
Q ss_pred CCCCCCCCCCce----ec-cCCC-----ceecCcccceeccccc
Q 008455 2 VWCSSCARHVTG----HR-PYDS-----QLCCDRCGKVLEDHNF 35 (565)
Q Consensus 2 ~~Cp~Cgs~~i~----~D-~~~G-----~~VCt~CG~Vlee~~i 35 (565)
+.||.||+.... +| |.-| ..+|..||+=..|-..
T Consensus 15 ~~CPvCg~~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~~DV~~ 58 (201)
T COG1779 15 IDCPVCGGTLKAHMYLYDIPYFGEVLISTGVCERCGYRSTDVKT 58 (201)
T ss_pred ecCCcccceeeEEEeeecCCccceEEEEEEEccccCCcccceee
Confidence 479999996221 12 2344 4589999997776444
No 290
>PF13551 HTH_29: Winged helix-turn helix
Probab=46.50 E-value=41 Score=28.74 Aligned_cols=27 Identities=15% Similarity=0.308 Sum_probs=24.9
Q ss_pred CHhHHHHHhccCHHHHHHHHHHHHccC
Q 008455 236 SKSDIVKIVHICEATLMKRLIEFENTD 262 (565)
Q Consensus 236 t~~eIa~v~~Vse~TIrkR~kE~~~t~ 262 (565)
|+.+||+.+|||..||.+-++.|.+..
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~~~G 40 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYREGG 40 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHccc
Confidence 799999999999999999999998655
No 291
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=46.47 E-value=20 Score=23.10 Aligned_cols=21 Identities=19% Similarity=0.256 Sum_probs=18.5
Q ss_pred CCCHhHHHHHhccCHHHHHHH
Q 008455 234 KFSKSDIVKIVHICEATLMKR 254 (565)
Q Consensus 234 ~~t~~eIa~v~~Vse~TIrkR 254 (565)
..+..+|+..++++..||.+.
T Consensus 21 ~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 21 GESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCCHHHHHHHHCCCHHHHHHh
Confidence 459999999999999999875
No 292
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=45.75 E-value=32 Score=27.98 Aligned_cols=31 Identities=10% Similarity=0.012 Sum_probs=29.3
Q ss_pred HhcCCCCCHhHHHHHhccCHHHHHHHHHHHH
Q 008455 229 LTHGLKFSKSDIVKIVHICEATLMKRLIEFE 259 (565)
Q Consensus 229 r~~g~~~t~~eIa~v~~Vse~TIrkR~kE~~ 259 (565)
++.+..+|..+.|+.+|+.+.||++.+..|.
T Consensus 8 rlLs~~~s~~~Aa~~lG~~~~~v~~wv~~fR 38 (65)
T PF05344_consen 8 RLLSQQISVAQAADRLGTDPGTVRRWVRMFR 38 (65)
T ss_pred HHhcccccHHHHHHHHCcCHHHHHHHHHHHH
Confidence 6889999999999999999999999999887
No 293
>PF12833 HTH_18: Helix-turn-helix domain; PDB: 2K9S_A 3LSG_C 3OIO_A 1D5Y_B 3GBG_A 3OOU_A 1BL0_A 1XS9_A 3MN2_B 3MKL_B ....
Probab=45.73 E-value=66 Score=26.02 Aligned_cols=67 Identities=7% Similarity=0.163 Sum_probs=36.2
Q ss_pred HHHHcCCCChhHHHHHHHHHHHHHHhCccccCCchhHHHHHHHHHHHHhc--CCCccHHHHHhhhcc-ChHHHHHHHHHH
Q 008455 81 MKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQK--SKPFLLIDFSNYLNI-NVYELGAVYLQL 157 (565)
Q Consensus 81 ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e--~~p~tL~DIa~~~~v-sv~~Lgr~~~~L 157 (565)
+|+.|+++ ... -..+|+......+. ..+...=+-.|++.- +...++.|||..+|. +...+.+.|++.
T Consensus 1 lA~~~~~s--~~~---l~~~f~~~~g~s~~-----~~~~~~R~~~a~~~L~~~~~~~i~~ia~~~Gf~~~~~f~~~fk~~ 70 (81)
T PF12833_consen 1 LADELGMS--ERY---LSRIFKKETGMSFK-----QYLRELRLQRAKELLRQNTDLSIAEIAEECGFSSQSHFSRAFKRY 70 (81)
T ss_dssp HHHHCTS---HHH---HHHHHHHHHSS-HH-----HHHHHHHHHHHHHHHHHHTT--HHHHHHHTT-SSHHHHHHHHHHH
T ss_pred ChHHhCcC--HHH---HHHHHHHHHCcCHH-----HHHHHHHHHHHHHHHHHhhcccHHHHHHHcCCCCHHHHHHHHHHH
Confidence 57788888 433 33456554444332 223333344444432 467899999999985 466677766655
No 294
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.
Probab=45.31 E-value=14 Score=35.35 Aligned_cols=24 Identities=17% Similarity=0.300 Sum_probs=0.0
Q ss_pred CCccHHHHHhhhccChHHHHHHHH
Q 008455 132 KPFLLIDFSNYLNINVYELGAVYL 155 (565)
Q Consensus 132 ~p~tL~DIa~~~~vsv~~Lgr~~~ 155 (565)
.|.++.|||+.+|+++.+|.|+..
T Consensus 48 ~PLt~~~iA~~lgl~~STVSRav~ 71 (160)
T PF04552_consen 48 KPLTMKDIADELGLHESTVSRAVK 71 (160)
T ss_dssp ------------------------
T ss_pred cCCCHHHHHHHhCCCHhHHHHHHc
Confidence 489999999999999999998765
No 295
>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]
Probab=45.18 E-value=64 Score=31.22 Aligned_cols=119 Identities=13% Similarity=0.211 Sum_probs=71.1
Q ss_pred HHHHHhhhccChHHHHHHHHHHHHHhhccccccccccCCchhhHHHHHHhhCCCCCHHHHHHHHHHHHHhhhccccCCCC
Q 008455 136 LIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRK 215 (565)
Q Consensus 136 L~DIa~~~~vsv~~Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~~~l~~~V~~~A~~Lv~~m~~~~l~~GR~ 215 (565)
-+.+|+.+|.....-|..|+.+.+..|++... +.+++..= .+....+=+....+++ ..+-++.||-
T Consensus 17 a~~lAe~~gl~~vsaG~iFR~~A~e~gmsl~e-----------f~~~AE~~-p~iD~~iD~rq~e~a~--~~nvVlegrL 82 (179)
T COG1102 17 ARELAEHLGLKLVSAGTIFREMARERGMSLEE-----------FSRYAEED-PEIDKEIDRRQKELAK--EGNVVLEGRL 82 (179)
T ss_pred HHHHHHHhCCceeeccHHHHHHHHHcCCCHHH-----------HHHHHhcC-chhhHHHHHHHHHHHH--cCCeEEhhhh
Confidence 36889999999999999999999999875422 23344332 1234444445555554 4455666664
Q ss_pred hhHHHH--H--HHHHHH-------Hhc-CCCCCHhHHHHHhccCHHHHHHHHHHHHccCCCCCCH
Q 008455 216 PSGLCG--A--ALYVSA-------LTH-GLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTI 268 (565)
Q Consensus 216 P~~Iaa--A--ALylAa-------r~~-g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t~s~~Lt~ 268 (565)
-.=++. | .|||-| |.. -..+++.++...+-.-|..=++||++|+...-..||+
T Consensus 83 A~Wi~k~~adlkI~L~Apl~vRa~Ria~REgi~~~~a~~~~~~RE~se~kRY~~~YgIDidDlSi 147 (179)
T COG1102 83 AGWIVREYADLKIWLKAPLEVRAERIAKREGIDVDEALAETVEREESEKKRYKKIYGIDIDDLSI 147 (179)
T ss_pred HHHHhccccceEEEEeCcHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHhCCCCcccee
Confidence 333333 1 122211 111 1245566666666666677789999999776666654
No 296
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=45.14 E-value=8.4 Score=32.63 Aligned_cols=31 Identities=26% Similarity=0.494 Sum_probs=24.7
Q ss_pred CCCCCCCCCceeccCCCceecCcccceecccc
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDHN 34 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vlee~~ 34 (565)
.|+.||...+ -..+-|-..|..|..|+.-..
T Consensus 38 ~CsfCGK~~v-KR~AvGiW~C~~C~kv~agga 68 (92)
T KOG0402|consen 38 TCSFCGKKTV-KRKAVGIWKCGSCKKVVAGGA 68 (92)
T ss_pred hhhhcchhhh-hhhceeEEecCCccceeccce
Confidence 5999998754 445789999999999987543
No 297
>PF12116 SpoIIID: Stage III sporulation protein D; InterPro: IPR014208 Members of this entry represent 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. In Bacillus subtilis SpoIIID is a DNA binding protein that is involved in gene repression as well as activation [].; PDB: 2L0K_A.
Probab=45.05 E-value=15 Score=31.10 Aligned_cols=34 Identities=15% Similarity=0.208 Sum_probs=22.1
Q ss_pred HHHHHHhcCCCCCHhHHHHHhccCHHHHHHHHHH
Q 008455 224 LYVSALTHGLKFSKSDIVKIVHICEATLMKRLIE 257 (565)
Q Consensus 224 LylAar~~g~~~t~~eIa~v~~Vse~TIrkR~kE 257 (565)
|-++..+...+-|++..|+++|||.+||-+=+.|
T Consensus 9 i~i~~yIi~~~aTVR~~Ak~FGvSKSTVHkDvte 42 (82)
T PF12116_consen 9 IEIANYIIETKATVRQAAKVFGVSKSTVHKDVTE 42 (82)
T ss_dssp HHHHHHHHHH---HHHHHHHHTS-HHHHHHHHTT
T ss_pred HHHHHHHHHcccHHHHHHHHHCCcHHHHHHHHHH
Confidence 3444445556889999999999999999765543
No 298
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=44.91 E-value=12 Score=27.50 Aligned_cols=26 Identities=23% Similarity=0.626 Sum_probs=17.1
Q ss_pred CCCCCCCC-Cceec-cCCCceecCcccc
Q 008455 3 WCSSCARH-VTGHR-PYDSQLCCDRCGK 28 (565)
Q Consensus 3 ~Cp~Cgs~-~i~~D-~~~G~~VCt~CG~ 28 (565)
.|+.||.. .+..- .+.....|..||.
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 7 RCEECGHEFEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EeCCCCCEEEEEEEcCCCCCCcCCCCCC
Confidence 59999965 22221 1246889999998
No 299
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=44.66 E-value=22 Score=32.06 Aligned_cols=27 Identities=19% Similarity=0.106 Sum_probs=24.0
Q ss_pred CCHhHHHHHhccCHHHHHHHHHHHHcc
Q 008455 235 FSKSDIVKIVHICEATLMKRLIEFENT 261 (565)
Q Consensus 235 ~t~~eIa~v~~Vse~TIrkR~kE~~~t 261 (565)
=+++++++..|||=.|+|+||.++...
T Consensus 50 GnlKe~e~~lgiSYPTvR~rLd~ii~~ 76 (113)
T PF09862_consen 50 GNLKEMEKELGISYPTVRNRLDKIIEK 76 (113)
T ss_pred CCHHHHHHHHCCCcHHHHHHHHHHHHH
Confidence 478999999999999999999998744
No 300
>COG4977 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]
Probab=44.36 E-value=1.8e+02 Score=31.12 Aligned_cols=84 Identities=13% Similarity=0.241 Sum_probs=0.0
Q ss_pred CccHHHHHhhhccChHHHHHHHHHHHHHhhccccccccccCCchhhHHHHHHhhCCCCCHHHHHHHHHHHHHhhhccccC
Q 008455 133 PFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITT 212 (565)
Q Consensus 133 p~tL~DIa~~~~vsv~~Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~~~l~~~V~~~A~~Lv~~m~~~~l~~ 212 (565)
|+++.++|+.++++..+|-|.|++-.. ..|..|..++ =.+.|.+|+..
T Consensus 236 plsl~~LA~~~~~S~R~leRlF~~~lG-------------~sP~~yy~~l-----------RL~~Ar~LL~~-------- 283 (328)
T COG4977 236 PLSLEELADRAGLSRRQLERLFRAELG-------------VSPARYYLRL-----------RLERARRLLEQ-------- 283 (328)
T ss_pred CcCHHHHHHHhCCCHHHHHHHHHHHhC-------------CCHHHHHHHH-----------HHHHHHHHHHh--------
Q ss_pred CCChhHHHHHHHHHHHHhcCCCCCHhHHHHHhc-cCHHHHHHHHHHHHccCCCCCCHHHHHH
Q 008455 213 GRKPSGLCGAALYVSALTHGLKFSKSDIVKIVH-ICEATLMKRLIEFENTDSGSLTIEDFMA 273 (565)
Q Consensus 213 GR~P~~IaaAALylAar~~g~~~t~~eIa~v~~-Vse~TIrkR~kE~~~t~s~~Lt~~~f~~ 273 (565)
-+.++.+||-.+| .+.+..++.|++.. .+++.+++.
T Consensus 284 --------------------t~~si~~IA~~~GF~sa~~fsr~fr~~f-----g~~P~~~R~ 320 (328)
T COG4977 284 --------------------TRLSIAEIAVACGFSSASHFSRAFRRQF-----GLSPSEYRR 320 (328)
T ss_pred --------------------CCCcHHHHHHHhCCCCHHHHHHHHHHHh-----CCChHHHHH
No 301
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=44.09 E-value=13 Score=28.20 Aligned_cols=14 Identities=29% Similarity=0.691 Sum_probs=8.8
Q ss_pred eecCcccceecccc
Q 008455 21 LCCDRCGKVLEDHN 34 (565)
Q Consensus 21 ~VCt~CG~Vlee~~ 34 (565)
.+|+.||.|.++..
T Consensus 2 y~C~~CgyvYd~~~ 15 (47)
T PF00301_consen 2 YQCPVCGYVYDPEK 15 (47)
T ss_dssp EEETTTSBEEETTT
T ss_pred cCCCCCCEEEcCCc
Confidence 46777777766543
No 302
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=44.06 E-value=14 Score=33.94 Aligned_cols=31 Identities=19% Similarity=0.445 Sum_probs=20.6
Q ss_pred CCCCCCCCCCCceec-c-C--CCceecCcccceec
Q 008455 1 MVWCSSCARHVTGHR-P-Y--DSQLCCDRCGKVLE 31 (565)
Q Consensus 1 M~~Cp~Cgs~~i~~D-~-~--~G~~VCt~CG~Vle 31 (565)
|..||.|++..+..- . . .--..|..||.-..
T Consensus 30 ~~~cP~C~s~~~~k~g~~~~~~qRyrC~~C~~tf~ 64 (129)
T COG3677 30 KVNCPRCKSSNVVKIGGIRRGHQRYKCKSCGSTFT 64 (129)
T ss_pred cCcCCCCCccceeeECCccccccccccCCcCccee
Confidence 568999999872221 1 1 23578999998643
No 303
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=44.04 E-value=64 Score=23.95 Aligned_cols=24 Identities=8% Similarity=0.110 Sum_probs=21.8
Q ss_pred ccHHHHHhhhccChHHHHHHHHHH
Q 008455 134 FLLIDFSNYLNINVYELGAVYLQL 157 (565)
Q Consensus 134 ~tL~DIa~~~~vsv~~Lgr~~~~L 157 (565)
.++.+||..+|++..+|.+.|...
T Consensus 28 ~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 28 RSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHhh
Confidence 799999999999999999988753
No 304
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=44.03 E-value=87 Score=29.95 Aligned_cols=30 Identities=20% Similarity=0.325 Sum_probs=27.1
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHHHccC
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEFENTD 262 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~~~t~ 262 (565)
+++|+++||..+|++..|+.+-+++|.+-.
T Consensus 167 ~~~t~~~lA~~lG~tr~tvsR~l~~l~~~g 196 (211)
T PRK11753 167 IKITRQEIGRIVGCSREMVGRVLKMLEDQG 196 (211)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 579999999999999999999999998543
No 305
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=43.89 E-value=11 Score=29.87 Aligned_cols=33 Identities=21% Similarity=0.440 Sum_probs=22.2
Q ss_pred CCCCCCCCCCCceeccCCCceecCcccceeccccccccccccc
Q 008455 1 MVWCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATFVK 43 (565)
Q Consensus 1 M~~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vlee~~id~~~ef~e 43 (565)
|..|+.||...+. -.|..||-+.- +.+-+-|+-
T Consensus 5 ~rkC~~cg~YTLk-------e~Cp~CG~~t~---~~~PprFSP 37 (59)
T COG2260 5 IRKCPKCGRYTLK-------EKCPVCGGDTK---VPHPPRFSP 37 (59)
T ss_pred hhcCcCCCceeec-------ccCCCCCCccc---cCCCCCCCc
Confidence 4579999987542 38999998643 444455653
No 306
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=43.72 E-value=17 Score=32.47 Aligned_cols=27 Identities=26% Similarity=0.555 Sum_probs=0.0
Q ss_pred CCCCCCCCceeccCC--------------CceecCccccee
Q 008455 4 CSSCARHVTGHRPYD--------------SQLCCDRCGKVL 30 (565)
Q Consensus 4 Cp~Cgs~~i~~D~~~--------------G~~VCt~CG~Vl 30 (565)
||.||+..+..+... .-.+|..||-++
T Consensus 1 C~~C~~~~~~~~~~~~~~~~~G~~~~v~~~~~~C~~CGe~~ 41 (127)
T TIGR03830 1 CPICGSGELVRDVKDEPYTYKGESITIGVPGWYCPACGEEL 41 (127)
T ss_pred CCCCCCccceeeeecceEEEcCEEEEEeeeeeECCCCCCEE
No 307
>PRK00118 putative DNA-binding protein; Validated
Probab=43.53 E-value=31 Score=30.57 Aligned_cols=28 Identities=11% Similarity=0.221 Sum_probs=24.7
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHHHc
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEFEN 260 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~~~ 260 (565)
...|.++||..+|||+.||.+++.....
T Consensus 32 eg~S~~EIAe~lGIS~~TV~r~L~RArk 59 (104)
T PRK00118 32 DDYSLGEIAEEFNVSRQAVYDNIKRTEK 59 (104)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4789999999999999999999886653
No 308
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=43.38 E-value=63 Score=31.30 Aligned_cols=56 Identities=11% Similarity=0.157 Sum_probs=39.8
Q ss_pred HHHHHHhhhccccCCCChhHHHHHHHHHHHHhcCCCCCHhHHHHHhccCHHHHHHHHHHHHcc
Q 008455 199 RDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (565)
Q Consensus 199 ~~Lv~~m~~~~l~~GR~P~~IaaAALylAar~~g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t 261 (565)
..+.+.|.+.++. +-- +.||-+--+++-+.|..||+.++|+|.+.++.-++++...
T Consensus 13 e~fae~m~r~G~n---rtV----G~iYgilyls~~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~~ 68 (177)
T COG1510 13 EHFAETMSRWGIN---RTV----GQIYGILYLSRKPLTLDEIAEALGMSKSNVSMGLKKLQDW 68 (177)
T ss_pred HHHHHHHHHhCCc---chH----HHHhhhheecCCCccHHHHHHHHCCCcchHHHHHHHHHhc
Confidence 3445555555432 122 3444444467899999999999999999999999999843
No 309
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=43.36 E-value=11 Score=39.13 Aligned_cols=29 Identities=28% Similarity=0.594 Sum_probs=12.8
Q ss_pred CCCCCCCC-Cc-eeccCC--C--ceecCcccceec
Q 008455 3 WCSSCARH-VT-GHRPYD--S--QLCCDRCGKVLE 31 (565)
Q Consensus 3 ~Cp~Cgs~-~i-~~D~~~--G--~~VCt~CG~Vle 31 (565)
.||.||+. .+ ++.... | .+.|+-||+-=.
T Consensus 174 ~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~ 208 (290)
T PF04216_consen 174 YCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWR 208 (290)
T ss_dssp S-TTT---EEEEEEE------EEEEEETTT--EEE
T ss_pred cCCCCCCcCceEEEecCCCCccEEEEcCCCCCeee
Confidence 79999997 22 223222 5 789999998644
No 310
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=43.26 E-value=12 Score=28.74 Aligned_cols=25 Identities=28% Similarity=0.668 Sum_probs=19.3
Q ss_pred CCCCCCCCCceeccCCCceecCcccc
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGK 28 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~ 28 (565)
.|-.||... ..|.....+.|..||.
T Consensus 8 ~C~~Cg~~~-~~~~~~~~irCp~Cg~ 32 (49)
T COG1996 8 KCARCGREV-ELDQETRGIRCPYCGS 32 (49)
T ss_pred EhhhcCCee-ehhhccCceeCCCCCc
Confidence 588998863 4456678899999996
No 311
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=43.19 E-value=25 Score=25.44 Aligned_cols=30 Identities=20% Similarity=0.369 Sum_probs=20.6
Q ss_pred CCCCCCCCCCceeccCCC-ceecCc---ccceec
Q 008455 2 VWCSSCARHVTGHRPYDS-QLCCDR---CGKVLE 31 (565)
Q Consensus 2 ~~Cp~Cgs~~i~~D~~~G-~~VCt~---CG~Vle 31 (565)
..||.||+..+......| ++.|++ |.....
T Consensus 2 ~~CP~Cg~~lv~r~~k~g~F~~Cs~yP~C~~~~~ 35 (39)
T PF01396_consen 2 EKCPKCGGPLVLRRGKKGKFLGCSNYPECKYTEP 35 (39)
T ss_pred cCCCCCCceeEEEECCCCCEEECCCCCCcCCeEe
Confidence 469999976555444444 678887 877654
No 312
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=43.16 E-value=39 Score=31.62 Aligned_cols=41 Identities=20% Similarity=0.115 Sum_probs=27.0
Q ss_pred ChhHHHHHHHHHHHHhcC---CCCCHhHHHHHhccCHHHHHHHH
Q 008455 215 KPSGLCGAALYVSALTHG---LKFSKSDIVKIVHICEATLMKRL 255 (565)
Q Consensus 215 ~P~~IaaAALylAar~~g---~~~t~~eIa~v~~Vse~TIrkR~ 255 (565)
.|.-+=||.|+.+-.++. -++|+.+||+.+||+++|+=+.-
T Consensus 12 ~~~Q~kAa~ll~~ne~~~~~~~r~T~~eiAee~Gis~~tLYrWr 55 (142)
T PF13022_consen 12 TLQQRKAAQLLVENELMPENGERRTQAEIAEEVGISRSTLYRWR 55 (142)
T ss_dssp -HHHHHHHHHHHHHHHS------S-HHHHHHHHTS-HHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHhhhccccchHHHHHHHhCCCHHHHHHHH
Confidence 344455666666666664 46999999999999999997665
No 313
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=43.14 E-value=18 Score=38.15 Aligned_cols=45 Identities=9% Similarity=0.022 Sum_probs=37.4
Q ss_pred HHHHHhcCCCCCHhHHHHHhccCHHHHHHHHHHHHccCCCCCCHH
Q 008455 225 YVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIE 269 (565)
Q Consensus 225 ylAar~~g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t~s~~Lt~~ 269 (565)
-+|...+-...||.|||+.+|||..||.+-|++=++..-=+++|.
T Consensus 20 ~vA~lYY~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~GiV~I~I~ 64 (318)
T PRK15418 20 RIAWFYYHDGLTQSEIGERLGLTRLKVSRLLEKGRQSGIIRVQIN 64 (318)
T ss_pred HHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHcCcEEEEEe
Confidence 455566678899999999999999999999999887766666554
No 314
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=43.09 E-value=82 Score=32.07 Aligned_cols=14 Identities=14% Similarity=0.009 Sum_probs=9.7
Q ss_pred CCCceecCccccee
Q 008455 17 YDSQLCCDRCGKVL 30 (565)
Q Consensus 17 ~~G~~VCt~CG~Vl 30 (565)
..|++++-..|.+.
T Consensus 72 ~~g~~i~i~p~~~h 85 (290)
T PRK10572 72 RPGDLLLFPPGEIH 85 (290)
T ss_pred CCCCEEEECCCCce
Confidence 45777777777764
No 315
>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=42.98 E-value=33 Score=25.87 Aligned_cols=32 Identities=16% Similarity=0.235 Sum_probs=26.0
Q ss_pred hcCCCCCHhHHHHHhccCHHHHHHHHHHHHcc
Q 008455 230 THGLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (565)
Q Consensus 230 ~~g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t 261 (565)
.++-..|+.+|++.+|++.+|+.+-+..|.+.
T Consensus 14 ~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~ 45 (52)
T PF09339_consen 14 ESGGPLTLSEIARALGLPKSTVHRLLQTLVEE 45 (52)
T ss_dssp CTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred cCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 34455799999999999999999999988753
No 316
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=42.84 E-value=63 Score=26.69 Aligned_cols=28 Identities=7% Similarity=0.159 Sum_probs=25.8
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHHHc
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEFEN 260 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~~~ 260 (565)
-..|..+|++.++++.+|+++.++.|.+
T Consensus 19 ~~~t~~~ia~~l~i~~~tv~r~l~~L~~ 46 (91)
T smart00346 19 GGLTLAELAERLGLSKSTAHRLLNTLQE 46 (91)
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4799999999999999999999999964
No 317
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=42.83 E-value=34 Score=24.56 Aligned_cols=30 Identities=10% Similarity=0.136 Sum_probs=26.2
Q ss_pred CCCccHHHHHhhhccChHHHHHHHHHHHHH
Q 008455 131 SKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (565)
Q Consensus 131 ~~p~tL~DIa~~~~vsv~~Lgr~~~~L~~~ 160 (565)
..|.+..|+|+.++++...+.+.+..|.+.
T Consensus 6 ~~~~s~~~la~~l~~s~~tv~~~l~~L~~~ 35 (48)
T smart00419 6 RLPLTRQEIAELLGLTRETVSRTLKRLEKE 35 (48)
T ss_pred EeccCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 357899999999999999999988888773
No 318
>PRK06030 hypothetical protein; Provisional
Probab=42.74 E-value=70 Score=29.27 Aligned_cols=39 Identities=8% Similarity=0.100 Sum_probs=32.5
Q ss_pred HHHHHHHHhcCCCccHHHHHhhhccChHHHHHHHHHHHHHh
Q 008455 121 SCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVL 161 (565)
Q Consensus 121 ACLYiACR~e~~p~tL~DIa~~~~vsv~~Lgr~~~~L~~~L 161 (565)
.+.|++-...+ .++.+|+..+|-+..++..+++++.+.+
T Consensus 59 IAMYL~r~~~~--~sl~~IG~~FGRDHSTV~haikkIe~~~ 97 (124)
T PRK06030 59 IAMYVAHVSLG--WPMNEVALAFGRDRTTVGHACHTVEDLR 97 (124)
T ss_pred HHHHHHHHHcC--CCHHHHHHHHCCChhHHHHHHHHHHHHh
Confidence 67888766654 5899999999999999999999887754
No 319
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=42.61 E-value=47 Score=31.15 Aligned_cols=46 Identities=20% Similarity=0.171 Sum_probs=39.5
Q ss_pred hhHHHHHHHHHHHHhcCCCccHHHHHhhhccChHHHHHHHHHHHHH
Q 008455 115 TEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (565)
Q Consensus 115 ~~~vaAACLYiACR~e~~p~tL~DIa~~~~vsv~~Lgr~~~~L~~~ 160 (565)
..+.+=|.+|+|....+.|.++.+||...+|+..-|.+.+..|.+.
T Consensus 7 ~~yal~~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~ka 52 (150)
T COG1959 7 GEYALRALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLRKA 52 (150)
T ss_pred HhHHHHHHHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHHc
Confidence 3455668899998877779999999999999999999999998874
No 320
>PRK09526 lacI lac repressor; Reviewed
Probab=42.57 E-value=20 Score=37.13 Aligned_cols=43 Identities=16% Similarity=0.112 Sum_probs=29.3
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHHHccCCCCCCHHHHHHHHHH
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARKKE 277 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~~~t~s~~Lt~~~f~~~~~~ 277 (565)
.+.|++|||+.+|||.+|+++.|+.- ..-+.-|-+..+....+
T Consensus 4 ~~~ti~dIA~~aGVS~~TVSrvLn~~--~~vs~~tr~rV~~~a~e 46 (342)
T PRK09526 4 KPVTLYDVARYAGVSYQTVSRVLNQA--SHVSAKTREKVEAAMAE 46 (342)
T ss_pred CCCcHHHHHHHhCCCHHHHHHHhcCC--CCCCHHHHHHHHHHHHH
Confidence 35799999999999999999999742 11223344444544443
No 321
>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=42.53 E-value=40 Score=26.25 Aligned_cols=32 Identities=16% Similarity=0.235 Sum_probs=27.8
Q ss_pred hcCCCCCHhHHHHHhccCHHHHHHHHHHHHcc
Q 008455 230 THGLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (565)
Q Consensus 230 ~~g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t 261 (565)
..+-+.|..+|++.++++.+|+...++.+.+.
T Consensus 20 ~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~a 51 (61)
T PF12840_consen 20 ASNGPMTVSELAEELGISQSTVSYHLKKLEEA 51 (61)
T ss_dssp HHCSTBEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred hcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 35788999999999999999999999999864
No 322
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=42.34 E-value=15 Score=32.52 Aligned_cols=31 Identities=23% Similarity=0.423 Sum_probs=23.1
Q ss_pred CCCCCCCCCceeccCCCceecCcccceeccccc
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNF 35 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vlee~~i 35 (565)
.|--|+..-.. ...+.+||..||++..-..|
T Consensus 37 aCeiC~~~GY~--q~g~~lvC~~C~~~~~~~~i 67 (102)
T PF10080_consen 37 ACEICGPKGYY--QEGDQLVCKNCGVRFNLPTI 67 (102)
T ss_pred eccccCCCceE--EECCEEEEecCCCEEehhhc
Confidence 58899776433 45789999999999864433
No 323
>TIGR00281 segregation and condensation protein B. Shown to be required for chromosome segregation and condensation in B. subtilis.
Probab=42.13 E-value=1e+02 Score=30.16 Aligned_cols=119 Identities=18% Similarity=0.214 Sum_probs=62.5
Q ss_pred hHHHHHHHHHHHHhcCCC-ccHHHHHhhhccCh-HHHHHHHHHHHHHhhccccccccccCCchhhHHHHHHhhCCCCCHH
Q 008455 116 EQVQASCLYLACRQKSKP-FLLIDFSNYLNINV-YELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKK 193 (565)
Q Consensus 116 ~~vaAACLYiACR~e~~p-~tL~DIa~~~~vsv-~~Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~~~l~~~ 193 (565)
..++=|.||++ |-| +++.+|+.+++++. ..+..+...|.....-...+ .-|..+.+.......++
T Consensus 3 ~~~iEAlLF~s----g~pgls~~~La~il~~~~~~~~~~~l~~l~~~~~~~~~g---------l~l~~~~~~y~l~tk~e 69 (186)
T TIGR00281 3 KAIIEALLFVS----GEPGVTLAELVRILGKEKAEKLNAIMELLEDYLSRDTAG---------IEIIKFGQSYSLVTKPA 69 (186)
T ss_pred HHHHHHHHHHc----CCCCCCHHHHHHHhCCCchHHHHHHHHHHHHHHhcCCCC---------EEEEEECCEEEEEEhHH
Confidence 45667888887 788 99999999999984 45555555554443321111 00111111110002222
Q ss_pred HHHHHHHHHHHhhhccccCCCChhHHHHHHH-HHHHHhcCCCCCHhHHHHHhccCHHHHHHHHHH
Q 008455 194 VCDTARDILASMKRDWITTGRKPSGLCGAAL-YVSALTHGLKFSKSDIVKIVHICEATLMKRLIE 257 (565)
Q Consensus 194 V~~~A~~Lv~~m~~~~l~~GR~P~~IaaAAL-ylAar~~g~~~t~~eIa~v~~Vse~TIrkR~kE 257 (565)
......+++. ..+++ +--|++ -||.-.+..++|..+|..+-||.-..+-+.|.+
T Consensus 70 ~~~~i~~~~~--------~~~~~--LS~aaLEtLAIIAY~QPITr~eIe~IRGv~s~~~l~~L~e 124 (186)
T TIGR00281 70 FADYIHRFLP--------AKLKN--LNSASLEVLAIIAYKQPITRARINEIRGVKSYQIVDDLVE 124 (186)
T ss_pred HHHHHHHHhc--------ccccc--CCHHHHHHHHHHHHcCCcCHHHHHHHcCCCHHHHHHHHHH
Confidence 2222222111 11111 222333 344456678999999999999976555554444
No 324
>PRK10870 transcriptional repressor MprA; Provisional
Probab=42.08 E-value=1.1e+02 Score=29.26 Aligned_cols=31 Identities=10% Similarity=0.069 Sum_probs=26.9
Q ss_pred cCCCCCHhHHHHHhccCHHHHHHHHHHHHcc
Q 008455 231 HGLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (565)
Q Consensus 231 ~g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t 261 (565)
.+..+++.+|+..++++.+|+.+.++.+..-
T Consensus 68 ~~~~it~~eLa~~l~l~~~tvsr~v~rLe~k 98 (176)
T PRK10870 68 ENHSIQPSELSCALGSSRTNATRIADELEKR 98 (176)
T ss_pred CCCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 3567899999999999999999999988743
No 325
>PRK14962 DNA polymerase III subunits gamma and tau; Provisional
Probab=42.05 E-value=5.4e+02 Score=28.82 Aligned_cols=82 Identities=13% Similarity=0.186 Sum_probs=45.9
Q ss_pred CccHHHHHhhhccChHHHHH-------------HHHHHHHHhhccccccccccCCchhhHHHHHHhhC---CCCC-HHHH
Q 008455 133 PFLLIDFSNYLNINVYELGA-------------VYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLL---PGGN-KKVC 195 (565)
Q Consensus 133 p~tL~DIa~~~~vsv~~Lgr-------------~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~---~~l~-~~V~ 195 (565)
.++..++..+++......-. ++..+.+.+ ....||..++.|+...+. +.-+ +...
T Consensus 229 ~It~e~V~~~l~~~~~~~i~~li~si~~~d~~~Al~~l~~ll--------~~Gedp~~i~r~l~~~~~edi~~a~~~~~~ 300 (472)
T PRK14962 229 KITLETVHEALGLIPIEVVRDYINAIFNGDVKRVFTVLDDVY--------YSGKDYEVLIQQAIEDLVEDLERERANDII 300 (472)
T ss_pred CCCHHHHHHHHcCCCHHHHHHHHHHHHcCCHHHHHHHHHHHH--------HcCCCHHHHHHHHHHHHHHHccCCCchHHH
Confidence 48888888888765432221 111122211 123677888888766551 2223 5555
Q ss_pred HHHHHHHHHhhhccccCCCChhHHHHH
Q 008455 196 DTARDILASMKRDWITTGRKPSGLCGA 222 (565)
Q Consensus 196 ~~A~~Lv~~m~~~~l~~GR~P~~IaaA 222 (565)
..+..+++....-++-.|+.|.+=.+-
T Consensus 301 ~~~~~~~~~~~~i~~~e~~~~l~~~~~ 327 (472)
T PRK14962 301 QVSRQLLNILREIKFAEEKRLVCKLGS 327 (472)
T ss_pred HHHHHHHHHHHHhCCcchHHHHHHHHH
Confidence 566666666666667777777555533
No 326
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=41.93 E-value=68 Score=31.53 Aligned_cols=46 Identities=20% Similarity=0.078 Sum_probs=33.4
Q ss_pred hhHHHHHHHHHHHHhcCCCccHHHHHhhhccChHHHHHHHHHHHHH
Q 008455 115 TEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (565)
Q Consensus 115 ~~~vaAACLYiACR~e~~p~tL~DIa~~~~vsv~~Lgr~~~~L~~~ 160 (565)
...-+|..|+........|.+..|||+.+|++..+|.|++++|.+.
T Consensus 151 ~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvsR~L~~L~~~ 196 (226)
T PRK10402 151 LENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLLYVLAQFIQD 196 (226)
T ss_pred HHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHHHHHHHHHHC
Confidence 3444444444333223456788999999999999999999999885
No 327
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=41.87 E-value=27 Score=32.07 Aligned_cols=30 Identities=23% Similarity=0.289 Sum_probs=26.3
Q ss_pred cCCCC-CHhHHHHHhccCHHHHHHHHHHHHc
Q 008455 231 HGLKF-SKSDIVKIVHICEATLMKRLIEFEN 260 (565)
Q Consensus 231 ~g~~~-t~~eIa~v~~Vse~TIrkR~kE~~~ 260 (565)
-|.++ |+++.|..++|...|+++.|+||..
T Consensus 31 pGdkLPSvRelA~~~~VNpnTv~raY~eLE~ 61 (125)
T COG1725 31 PGDKLPSVRELAKDLGVNPNTVQRAYQELER 61 (125)
T ss_pred CCCCCCcHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 35664 7999999999999999999999974
No 328
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=41.84 E-value=45 Score=24.75 Aligned_cols=31 Identities=13% Similarity=0.129 Sum_probs=25.6
Q ss_pred CCCccHHHHHhhhccChHHHHHHHHHHHHHh
Q 008455 131 SKPFLLIDFSNYLNINVYELGAVYLQLCQVL 161 (565)
Q Consensus 131 ~~p~tL~DIa~~~~vsv~~Lgr~~~~L~~~L 161 (565)
..+.|+.|||..+|++...+.+...+..+.|
T Consensus 18 ~~~~t~~eIa~~lg~s~~~V~~~~~~al~kL 48 (50)
T PF04545_consen 18 FEGLTLEEIAERLGISRSTVRRILKRALKKL 48 (50)
T ss_dssp TST-SHHHHHHHHTSCHHHHHHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHCCcHHHHHHHHHHHHHHh
Confidence 5578999999999999999998887776655
No 329
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=41.84 E-value=54 Score=26.32 Aligned_cols=34 Identities=12% Similarity=0.193 Sum_probs=26.9
Q ss_pred CCCccHHHHHhhhccChHHHHHHHHHHHHHhhcc
Q 008455 131 SKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIA 164 (565)
Q Consensus 131 ~~p~tL~DIa~~~~vsv~~Lgr~~~~L~~~L~i~ 164 (565)
+.|.+-.|||+.++++.+.+.+....|.+.=.+.
T Consensus 13 ~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~ 46 (62)
T PF04703_consen 13 NGPLKTREIADALGLSIYQARYYLEKLEKEGKVE 46 (62)
T ss_dssp TS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEE
T ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence 7899999999999999999998777777754443
No 330
>COG1386 scpB Chromosome segregation and condensation protein B [DNA replication, recombination and repair]
Probab=41.64 E-value=1.5e+02 Score=28.93 Aligned_cols=120 Identities=16% Similarity=0.218 Sum_probs=67.9
Q ss_pred hHHHHHHHHHHHHhcCCCccHHHHHhhhcc-ChHHHHHHHHHHHHHhhccccccccccCCchhhHHHHHHhhCCCCCHHH
Q 008455 116 EQVQASCLYLACRQKSKPFLLIDFSNYLNI-NVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKV 194 (565)
Q Consensus 116 ~~vaAACLYiACR~e~~p~tL~DIa~~~~v-sv~~Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~~~l~~~V 194 (565)
..++.|.||.+ +.|+++++++.++++ +...+......+.....-.. +. |..+...... .+...
T Consensus 10 ~~~vEall~a~----~~pls~~~L~~il~~~~~~~~~~~l~~l~~~y~~rg-------~~----L~~~~~~~r~-~t~~~ 73 (184)
T COG1386 10 KALIEALLFAG----GEPLSLKELAEILGIVSADAIIDALAELKEEYEDRG-------LE----LVEVAEGWRL-QTKQE 73 (184)
T ss_pred HHHHHHHHHhc----CCCCCHHHHHHHhCCCchHHHHHHHHHHHHhhcCCC-------ee----EEEEcCceeE-EehHH
Confidence 34555655554 789999999999998 66677777766666542110 00 0111111100 11111
Q ss_pred HHHHHHHHHHhhhccccCCCChhHHHHHHH-HHHHHhcCCCCCHhHHHHHhccCHHHHHHHHHHHH
Q 008455 195 CDTARDILASMKRDWITTGRKPSGLCGAAL-YVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFE 259 (565)
Q Consensus 195 ~~~A~~Lv~~m~~~~l~~GR~P~~IaaAAL-ylAar~~g~~~t~~eIa~v~~Vse~TIrkR~kE~~ 259 (565)
. -..+..+. -. +.+..+--|++ -||.-.+..++|..+|.++-||....+-+.|.++.
T Consensus 74 ~---~~~~~~l~---~~--~~~~~LSraalEtLAiIAY~QPiTR~eI~~iRGv~~~~~i~~L~e~g 131 (184)
T COG1386 74 Y---AEYLEKLQ---EQ--RPKRELSRAALETLAIIAYKQPVTRSEIEEIRGVAVSQVISTLLERG 131 (184)
T ss_pred H---HHHHHHHh---cc--cccccccHHHHHHHHHHHHcCCccHHHHHHHhCccHHHHHHHHHHCC
Confidence 1 11111111 11 11122333333 56777788999999999999999888877777764
No 331
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=41.43 E-value=41 Score=26.98 Aligned_cols=30 Identities=10% Similarity=0.050 Sum_probs=24.9
Q ss_pred CCCCCHhHHHHHhccCHHHHHHHHHHHHcc
Q 008455 232 GLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (565)
Q Consensus 232 g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t 261 (565)
+.+++-+|||+.+++|..|+|.-|..+...
T Consensus 13 ~~p~~T~eiA~~~gls~~~aR~yL~~Le~e 42 (62)
T PF04703_consen 13 NGPLKTREIADALGLSIYQARYYLEKLEKE 42 (62)
T ss_dssp TS-EEHHHHHHHHTS-HHHHHHHHHHHHHC
T ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 567899999999999999999999988743
No 332
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=41.28 E-value=15 Score=27.55 Aligned_cols=28 Identities=18% Similarity=0.526 Sum_probs=18.9
Q ss_pred CCCCCCCCCceec-------cCCCceecCc--cccee
Q 008455 3 WCSSCARHVTGHR-------PYDSQLCCDR--CGKVL 30 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D-------~~~G~~VCt~--CG~Vl 30 (565)
.||+||+...+.- ..+-...|++ ||.-.
T Consensus 1 ~CP~Cg~~a~ir~S~~~s~~~~~~Y~qC~N~~Cg~tf 37 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQLSPLTRELYCQCTNPECGHTF 37 (47)
T ss_pred CcCCCCCeeEEEEchhhCcceEEEEEEECCCcCCCEE
Confidence 5999999754432 1235678888 99753
No 333
>TIGR02405 trehalos_R_Ecol trehalose operon repressor, proteobacterial. This family consists of repressors of the LacI family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gammaproteobacteria and does not include the GntR family TreR of Bacillus subtilis
Probab=41.28 E-value=20 Score=36.81 Aligned_cols=24 Identities=21% Similarity=0.374 Sum_probs=21.7
Q ss_pred CCCHhHHHHHhccCHHHHHHHHHH
Q 008455 234 KFSKSDIVKIVHICEATLMKRLIE 257 (565)
Q Consensus 234 ~~t~~eIa~v~~Vse~TIrkR~kE 257 (565)
+.|++|||+.+|||.+|+++.|+.
T Consensus 1 ~~ti~dIA~~agVS~sTVSr~Ln~ 24 (311)
T TIGR02405 1 KLTIKDIARLAGVGKSTVSRVLNN 24 (311)
T ss_pred CCcHHHHHHHhCCCHHHHHHHhCC
Confidence 468999999999999999999963
No 334
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=41.24 E-value=13 Score=33.31 Aligned_cols=34 Identities=15% Similarity=0.389 Sum_probs=19.5
Q ss_pred CCCCCCCCCceeccCCCceecCcccceeccccccccccc
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATF 41 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vlee~~id~~~ef 41 (565)
+|+.||.. +....-...|..||.. ...|..|.++
T Consensus 72 ~C~~Cg~~---~~~~~~~~~CP~Cgs~--~~~i~~G~El 105 (115)
T TIGR00100 72 ECEDCSEE---VSPEIDLYRCPKCHGI--MLQVRAGKEL 105 (115)
T ss_pred EcccCCCE---EecCCcCccCcCCcCC--CcEEecCCeE
Confidence 68899854 2222235679999864 2234455443
No 335
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=41.09 E-value=26 Score=25.51 Aligned_cols=23 Identities=13% Similarity=0.026 Sum_probs=19.6
Q ss_pred CHhHHHHHhccCHHHHHHHHHHH
Q 008455 236 SKSDIVKIVHICEATLMKRLIEF 258 (565)
Q Consensus 236 t~~eIa~v~~Vse~TIrkR~kE~ 258 (565)
|..++|+.+||+..||+.-.++-
T Consensus 2 ~~~e~a~~~gv~~~tlr~~~~~g 24 (49)
T cd04761 2 TIGELAKLTGVSPSTLRYYERIG 24 (49)
T ss_pred cHHHHHHHHCcCHHHHHHHHHCC
Confidence 67899999999999999765544
No 336
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=40.99 E-value=4.1e+02 Score=27.18 Aligned_cols=72 Identities=14% Similarity=0.203 Sum_probs=41.9
Q ss_pred HHHHHHHHHHHHHHHHc--CCC-ChhHHHHHHH-HHHHHHHhCccccCCchhHHHHHHH----HHHHHhcC---CCccHH
Q 008455 69 RLMEKAFDDMRQMKNAL--NIG-ESDEIVHVAK-RFYGIAVARNFTKGRRTEQVQASCL----YLACRQKS---KPFLLI 137 (565)
Q Consensus 69 r~l~~a~~~I~~ia~~L--~Lp-~~~~i~e~A~-~iyk~a~~~~~~rGR~~~~vaAACL----YiACR~e~---~p~tL~ 137 (565)
+.+.+-...+..++.++ ++| +-++.+..++ -+.+-+..-...+|.+..+.|.=|+ +--+|.++ .|++++
T Consensus 27 ~Li~~ylpLV~~ia~k~~~r~~~~~dDLiqiG~iGLi~Aieryd~~kg~kF~tyA~~~I~Gei~d~LR~~~~v~vpR~~~ 106 (247)
T COG1191 27 RLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTYAVRRIRGEILDYLRKNDSVKVPRSLR 106 (247)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHHHcCcccCcchHHHHHHHHHHHHHHHHHhCCCccCcHHHH
Confidence 45666677777787777 344 1133443333 3444443446677888877776555 44466655 466666
Q ss_pred HHH
Q 008455 138 DFS 140 (565)
Q Consensus 138 DIa 140 (565)
+..
T Consensus 107 ~~~ 109 (247)
T COG1191 107 ELG 109 (247)
T ss_pred HHH
Confidence 654
No 337
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=40.82 E-value=14 Score=34.08 Aligned_cols=27 Identities=19% Similarity=0.015 Sum_probs=23.6
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHHH
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEFE 259 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~~ 259 (565)
...|.++||..+|+++.||+.++.--.
T Consensus 121 ~g~s~~EIA~~lgis~~tV~~~l~Rar 147 (160)
T PRK09642 121 EEKSYQEIALQEKIEVKTVEMKLYRAR 147 (160)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 568999999999999999999886554
No 338
>PF14502 HTH_41: Helix-turn-helix domain
Probab=40.73 E-value=30 Score=26.45 Aligned_cols=31 Identities=13% Similarity=0.077 Sum_probs=26.8
Q ss_pred CCHhHHHHHhccCHHHHHHHHHHHHccCCCC
Q 008455 235 FSKSDIVKIVHICEATLMKRLIEFENTDSGS 265 (565)
Q Consensus 235 ~t~~eIa~v~~Vse~TIrkR~kE~~~t~s~~ 265 (565)
.|+.+.++.++||..||++.++.|.+...-.
T Consensus 7 ~tI~e~~~~~~vs~GtiQ~Alk~Le~~gaI~ 37 (48)
T PF14502_consen 7 PTISEYSEKFGVSRGTIQNALKFLEENGAIK 37 (48)
T ss_pred CCHHHHHHHhCcchhHHHHHHHHHHHCCcEE
Confidence 4789999999999999999999998765533
No 339
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=40.71 E-value=27 Score=31.69 Aligned_cols=27 Identities=15% Similarity=-0.017 Sum_probs=23.6
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHHH
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEFE 259 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~~ 259 (565)
...|.++||..+|+|+.||++++.-..
T Consensus 128 ~~~~~~eIA~~lgis~~tv~~~~~ra~ 154 (161)
T TIGR02985 128 EGKSYKEIAEELGISVKTVEYHISKAL 154 (161)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 467999999999999999999987553
No 340
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=40.51 E-value=4.5e+02 Score=29.32 Aligned_cols=43 Identities=14% Similarity=0.291 Sum_probs=36.5
Q ss_pred CCCHhHHHHHhccCHHHHHHHH-HHHHccCCCCCCHHHHHHHHH
Q 008455 234 KFSKSDIVKIVHICEATLMKRL-IEFENTDSGSLTIEDFMARKK 276 (565)
Q Consensus 234 ~~t~~eIa~v~~Vse~TIrkR~-kE~~~t~s~~Lt~~~f~~~~~ 276 (565)
+.++++||..+|++++||.+.. +.+..||.|-+-+..|-....
T Consensus 330 PL~LrdvA~~i~~HESTISRai~nKy~~tprG~feLK~FFs~~i 373 (444)
T COG1508 330 PLVLRDVADEIGMHESTISRAITNKYLATPRGLFELKYFFSSSL 373 (444)
T ss_pred cccHHHHHHHhCccHHHHHHHHhcccccCCcceeeHHHHHHHhc
Confidence 4788999999999999999988 567779998888888876643
No 341
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=40.44 E-value=17 Score=28.04 Aligned_cols=28 Identities=21% Similarity=0.705 Sum_probs=14.2
Q ss_pred CCCCC--CCCCCceeccCCCc--eecCccccee
Q 008455 2 VWCSS--CARHVTGHRPYDSQ--LCCDRCGKVL 30 (565)
Q Consensus 2 ~~Cp~--Cgs~~i~~D~~~G~--~VCt~CG~Vl 30 (565)
.+||. |+.... .+..... +.|..||+..
T Consensus 19 ~~Cp~~~C~~~~~-~~~~~~~~~~~C~~C~~~f 50 (64)
T PF01485_consen 19 RWCPNPDCEYIIE-KDDGCNSPIVTCPSCGTEF 50 (64)
T ss_dssp C--TTSST---EC-S-SSTTS--CCTTSCCSEE
T ss_pred cCCCCCCCcccEE-ecCCCCCCeeECCCCCCcC
Confidence 47988 987643 3333344 8999999763
No 342
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=40.43 E-value=19 Score=26.08 Aligned_cols=10 Identities=40% Similarity=1.122 Sum_probs=7.5
Q ss_pred eecCccccee
Q 008455 21 LCCDRCGKVL 30 (565)
Q Consensus 21 ~VCt~CG~Vl 30 (565)
.+|..||-.+
T Consensus 33 ~~C~~CGE~~ 42 (46)
T TIGR03831 33 LVCPQCGEEY 42 (46)
T ss_pred cccccCCCEe
Confidence 3699999764
No 343
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=40.41 E-value=22 Score=36.77 Aligned_cols=24 Identities=17% Similarity=0.119 Sum_probs=22.2
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHH
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLI 256 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~k 256 (565)
.+.|++|||+.+|||.+|+++.|+
T Consensus 5 ~~~Ti~dIA~~agVS~~TVSr~Ln 28 (342)
T PRK10014 5 KKITIHDVALAAGVSVSTVSLVLS 28 (342)
T ss_pred CCCcHHHHHHHhCCCHHHHHHHHC
Confidence 468999999999999999999986
No 344
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=40.23 E-value=21 Score=27.39 Aligned_cols=13 Identities=23% Similarity=0.669 Sum_probs=8.6
Q ss_pred eecCcccceeccc
Q 008455 21 LCCDRCGKVLEDH 33 (565)
Q Consensus 21 ~VCt~CG~Vlee~ 33 (565)
.+|+.||.|.++.
T Consensus 2 y~C~~CgyiYd~~ 14 (50)
T cd00730 2 YECRICGYIYDPA 14 (50)
T ss_pred cCCCCCCeEECCC
Confidence 4677777777653
No 345
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=40.21 E-value=12 Score=35.43 Aligned_cols=29 Identities=17% Similarity=0.570 Sum_probs=16.8
Q ss_pred CCCCCCCCCceeccCCCceecCcccceeccccccccc
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEA 39 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vlee~~id~~~ 39 (565)
.|..||...|. .|.+|++=|.....+.++
T Consensus 30 fC~kCG~~tI~--------~Cp~C~~~IrG~y~v~gv 58 (158)
T PF10083_consen 30 FCSKCGAKTIT--------SCPNCSTPIRGDYHVEGV 58 (158)
T ss_pred HHHHhhHHHHH--------HCcCCCCCCCCceecCCe
Confidence 46666665331 577777766655544443
No 346
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=40.14 E-value=1.2e+02 Score=29.06 Aligned_cols=29 Identities=10% Similarity=0.007 Sum_probs=26.5
Q ss_pred CCccHHHHHhhhccChHHHHHHHHHHHHH
Q 008455 132 KPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (565)
Q Consensus 132 ~p~tL~DIa~~~~vsv~~Lgr~~~~L~~~ 160 (565)
.|++..+||+.+|++..++.|.+++|.+.
T Consensus 167 ~~~t~~~lA~~lG~tr~tvsR~l~~l~~~ 195 (211)
T PRK11753 167 IKITRQEIGRIVGCSREMVGRVLKMLEDQ 195 (211)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 47889999999999999999999998874
No 347
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 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 is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=40.06 E-value=21 Score=25.59 Aligned_cols=19 Identities=16% Similarity=0.266 Sum_probs=15.3
Q ss_pred CHhHHHHHhccCHHHHHHH
Q 008455 236 SKSDIVKIVHICEATLMKR 254 (565)
Q Consensus 236 t~~eIa~v~~Vse~TIrkR 254 (565)
|..++|+.+||+..|||.-
T Consensus 1 ti~e~A~~~gvs~~tlR~y 19 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRYY 19 (38)
T ss_dssp EHHHHHHHHTS-HHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHH
Confidence 4679999999999999853
No 348
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=39.42 E-value=20 Score=27.60 Aligned_cols=28 Identities=25% Similarity=0.539 Sum_probs=17.9
Q ss_pred CCCCCCCC-Cceecc-CCCc-eecCccccee
Q 008455 3 WCSSCARH-VTGHRP-YDSQ-LCCDRCGKVL 30 (565)
Q Consensus 3 ~Cp~Cgs~-~i~~D~-~~G~-~VCt~CG~Vl 30 (565)
.|.+|+.. ...+.. ..|. ++|..||.-.
T Consensus 5 ~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~ 35 (52)
T smart00401 5 SCSNCGTTETPLWRRGPSGNKTLCNACGLYY 35 (52)
T ss_pred CcCCCCCCCCCccccCCCCCCcEeecccHHH
Confidence 58888876 334432 3454 8888888754
No 349
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=39.33 E-value=12 Score=26.75 Aligned_cols=21 Identities=24% Similarity=0.442 Sum_probs=8.4
Q ss_pred CCCCCCCCCceeccCCCceec
Q 008455 3 WCSSCARHVTGHRPYDSQLCC 23 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VC 23 (565)
+|..||.-.-+.+...|.++|
T Consensus 8 kC~~CGniVev~~~g~g~lvC 28 (36)
T PF06397_consen 8 KCEHCGNIVEVVHDGGGPLVC 28 (36)
T ss_dssp E-TTT--EEEEEE--SS-EEE
T ss_pred EccCCCCEEEEEECCCCCEEe
Confidence 466666554444555566666
No 350
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=39.32 E-value=37 Score=26.45 Aligned_cols=34 Identities=26% Similarity=0.172 Sum_probs=25.5
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHHHccCCCCC
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEFENTDSGSL 266 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~~~t~s~~L 266 (565)
...+....|+..+|...|++.|++.|.+.-.-.+
T Consensus 11 ~~~n~~~tA~~L~iHrNTl~yRl~ki~~l~g~dl 44 (59)
T PF13556_consen 11 NNGNISKTARALHIHRNTLRYRLKKIEELLGLDL 44 (59)
T ss_dssp TTT-HHHHHHHHTS-HHHHHHHHHHHHHHHS--T
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCcCC
Confidence 3567888999999999999999999987655444
No 351
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=39.31 E-value=17 Score=33.70 Aligned_cols=11 Identities=36% Similarity=0.890 Sum_probs=6.7
Q ss_pred CceecCcccce
Q 008455 19 SQLCCDRCGKV 29 (565)
Q Consensus 19 G~~VCt~CG~V 29 (565)
....|..||..
T Consensus 106 ~~~~CP~Cgs~ 116 (135)
T PRK03824 106 AFLKCPKCGSR 116 (135)
T ss_pred cCcCCcCCCCC
Confidence 44557777753
No 352
>PRK08329 threonine synthase; Validated
Probab=39.18 E-value=19 Score=38.38 Aligned_cols=26 Identities=35% Similarity=0.737 Sum_probs=18.8
Q ss_pred CCCCCCCCCCCceeccCCCceecCcccceec
Q 008455 1 MVWCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (565)
Q Consensus 1 M~~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vle 31 (565)
|..|+.||..- +.... ..| .||-.|+
T Consensus 1 ~l~C~~Cg~~~---~~~~~-~~C-~c~~~l~ 26 (347)
T PRK08329 1 MLRCTKCGRTY---EEKFK-LRC-DCGGTLL 26 (347)
T ss_pred CcCcCCCCCCc---CCCCc-eec-CCCCcEE
Confidence 78999999873 22223 789 7997765
No 353
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=39.17 E-value=13 Score=29.56 Aligned_cols=27 Identities=4% Similarity=-0.162 Sum_probs=17.8
Q ss_pred CCCCCCCCCCceeccCCCceecCcccceeccccc
Q 008455 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNF 35 (565)
Q Consensus 2 ~~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vlee~~i 35 (565)
+.|++||...+ -.-||. ||+.-+..++
T Consensus 28 ~~c~~cg~~~~------pH~vc~-cG~Y~gr~v~ 54 (60)
T PRK01110 28 SVDKTTGEYHL------PHHVSP-KGYYKGRKVL 54 (60)
T ss_pred eEcCCCCceec------cceecC-CcccCCeEee
Confidence 46899987633 344799 9976654444
No 354
>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=39.16 E-value=50 Score=30.12 Aligned_cols=40 Identities=15% Similarity=0.075 Sum_probs=33.6
Q ss_pred HHHHHHHHhcCCCCCHhHHHHHhccCHHHHHHHHHHHHcc
Q 008455 222 AALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (565)
Q Consensus 222 AALylAar~~g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t 261 (565)
+.+|||.+-.+..+|.++||...+|+...+++-+..+...
T Consensus 13 ~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~ 52 (135)
T TIGR02010 13 AMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKA 52 (135)
T ss_pred HHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 5667777644557899999999999999999999999754
No 355
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=38.97 E-value=4.4e+02 Score=26.85 Aligned_cols=27 Identities=4% Similarity=-0.025 Sum_probs=22.8
Q ss_pred CCCCCHhHHHHHhccCHHHHHHHHHHH
Q 008455 232 GLKFSKSDIVKIVHICEATLMKRLIEF 258 (565)
Q Consensus 232 g~~~t~~eIa~v~~Vse~TIrkR~kE~ 258 (565)
+...|+++||..+|||..+|+++.+.-
T Consensus 234 ~~~~t~~eIA~~lgvS~~~V~q~~~~A 260 (270)
T TIGR02392 234 DDKLTLQELAAEYGVSAERIRQIEKNA 260 (270)
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 347899999999999999999776543
No 356
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=38.76 E-value=29 Score=32.87 Aligned_cols=25 Identities=20% Similarity=0.248 Sum_probs=22.5
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHH
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIE 257 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE 257 (565)
...|.+|||..+|+|+.||+.|+.-
T Consensus 142 ~g~s~~EIA~~lgis~~tVk~~l~r 166 (178)
T PRK12529 142 DGMKQKDIAQALDIALPTVKKYIHQ 166 (178)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 5689999999999999999999863
No 357
>PRK09956 hypothetical protein; Provisional
Probab=38.75 E-value=94 Score=32.73 Aligned_cols=79 Identities=13% Similarity=0.196 Sum_probs=54.7
Q ss_pred CchhhHHHHHHhhCCCCCHHHHHHHHHHHHHhhhccccCCC---ChhHHHHHHHHHHHHhcCCCCCHhHHHHHhccCHHH
Q 008455 174 DPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGR---KPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEAT 250 (565)
Q Consensus 174 dP~~~I~Rf~~~L~~~l~~~V~~~A~~Lv~~m~~~~l~~GR---~P~~IaaAALylAar~~g~~~t~~eIa~v~~Vse~T 250 (565)
++..++..++..+.. ....+...|..+-+.....++..|| .-.|..-+++-+|-++.....+...|++++|.|...
T Consensus 224 ~~~~~i~~l~~~~~~-~~e~iMTiAe~l~qeG~e~G~q~G~~eG~qeG~~e~~~eiA~~mL~~G~~~~~i~~~tgLs~ee 302 (308)
T PRK09956 224 RFTRFIQEIAERSPL-QKERLMTIAERLRQEGHQIGWQEGKLEGLQEGMHEQAIKIALRMLEQGFDRDQVLAATQLSEAD 302 (308)
T ss_pred hHHHHHHHHHHhCcc-cchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHH
Confidence 466777777777631 2345667777776665444444554 112344456788888888889999999999999998
Q ss_pred HHH
Q 008455 251 LMK 253 (565)
Q Consensus 251 Irk 253 (565)
|.+
T Consensus 303 l~~ 305 (308)
T PRK09956 303 LAA 305 (308)
T ss_pred HHH
Confidence 876
No 358
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=38.71 E-value=41 Score=25.84 Aligned_cols=34 Identities=9% Similarity=0.065 Sum_probs=28.5
Q ss_pred CCccHHHHHhhhccChHHHHHHHHHHHHHhhccc
Q 008455 132 KPFLLIDFSNYLNINVYELGAVYLQLCQVLYIAD 165 (565)
Q Consensus 132 ~p~tL~DIa~~~~vsv~~Lgr~~~~L~~~L~i~~ 165 (565)
...+..+||..+++++.+|......+.+.|++..
T Consensus 17 ~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~~~ 50 (58)
T PF00196_consen 17 QGMSNKEIAEELGISEKTVKSHRRRIMKKLGVKN 50 (58)
T ss_dssp TTS-HHHHHHHHTSHHHHHHHHHHHHHHHHT-SS
T ss_pred hcCCcchhHHhcCcchhhHHHHHHHHHHHhCCCC
Confidence 3567899999999999999999999999999753
No 359
>PF12728 HTH_17: Helix-turn-helix domain
Probab=38.66 E-value=35 Score=25.39 Aligned_cols=22 Identities=9% Similarity=0.297 Sum_probs=19.3
Q ss_pred CCHhHHHHHhccCHHHHHHHHH
Q 008455 235 FSKSDIVKIVHICEATLMKRLI 256 (565)
Q Consensus 235 ~t~~eIa~v~~Vse~TIrkR~k 256 (565)
.|.+|+|..+|||..||.+-.+
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~ 23 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIR 23 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 4789999999999999997664
No 360
>TIGR02850 spore_sigG RNA polymerase sigma-G factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.
Probab=38.62 E-value=4.2e+02 Score=26.60 Aligned_cols=26 Identities=8% Similarity=0.033 Sum_probs=22.8
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHH
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~ 258 (565)
...|+++||..+|||..+|++..+.-
T Consensus 221 ~~~t~~eIA~~lgis~~~V~~~~~ra 246 (254)
T TIGR02850 221 EGKTQMEVAEEIGISQAQVSRLEKAA 246 (254)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 46899999999999999999887654
No 361
>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=38.48 E-value=44 Score=31.97 Aligned_cols=27 Identities=19% Similarity=0.354 Sum_probs=25.1
Q ss_pred CCHhHHHHHhccCHHHHHHHHHHHHcc
Q 008455 235 FSKSDIVKIVHICEATLMKRLIEFENT 261 (565)
Q Consensus 235 ~t~~eIa~v~~Vse~TIrkR~kE~~~t 261 (565)
.|+++||..+++|..||.+.+++|.+.
T Consensus 76 ~t~~~ia~~l~iS~~Tv~r~ik~L~e~ 102 (165)
T PF05732_consen 76 ATQKEIAEKLGISKPTVSRAIKELEEK 102 (165)
T ss_pred eeHHHHHHHhCCCHHHHHHHHHHHHhC
Confidence 689999999999999999999999854
No 362
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=38.34 E-value=21 Score=28.03 Aligned_cols=24 Identities=25% Similarity=0.751 Sum_probs=18.5
Q ss_pred CCCCCCCCCceeccCCCceecCccccee
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vl 30 (565)
.||.|++.. ...-.+.|..||...
T Consensus 1 ~Cpv~~~~~----~~~v~~~Cp~cGipt 24 (55)
T PF13824_consen 1 LCPVCKKDL----PAHVNFECPDCGIPT 24 (55)
T ss_pred CCCCCcccc----ccccCCcCCCCCCcC
Confidence 499999863 345677999999874
No 363
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=38.33 E-value=18 Score=32.51 Aligned_cols=35 Identities=20% Similarity=0.460 Sum_probs=20.0
Q ss_pred CCCCCCCCCceeccCCCceecCcccceeccccccccccc
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATF 41 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vlee~~id~~~ef 41 (565)
+|+.||...... ......|..||.. +..+..|.+|
T Consensus 72 ~C~~Cg~~~~~~--~~~~~~CP~Cgs~--~~~i~~G~El 106 (114)
T PRK03681 72 WCETCQQYVTLL--TQRVRRCPQCHGD--MLRIVADDGL 106 (114)
T ss_pred EcccCCCeeecC--CccCCcCcCcCCC--CcEEccCCeE
Confidence 799998642211 1233569999964 2345555544
No 364
>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=38.07 E-value=85 Score=22.97 Aligned_cols=29 Identities=10% Similarity=0.093 Sum_probs=23.3
Q ss_pred CCCccHHHHHhhhccChHHHHHHHHHHHH
Q 008455 131 SKPFLLIDFSNYLNINVYELGAVYLQLCQ 159 (565)
Q Consensus 131 ~~p~tL~DIa~~~~vsv~~Lgr~~~~L~~ 159 (565)
+-+.+..++|..++++...+.+.+++|.+
T Consensus 15 ~~~~t~~ela~~~~is~~tv~~~l~~L~~ 43 (48)
T PF13412_consen 15 NPRITQKELAEKLGISRSTVNRYLKKLEE 43 (48)
T ss_dssp CTTS-HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred cCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 33489999999999999999998888865
No 365
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=38.00 E-value=26 Score=25.40 Aligned_cols=28 Identities=21% Similarity=0.476 Sum_probs=16.9
Q ss_pred CCCCCCCCC---CceeccCCCceecCcccce
Q 008455 2 VWCSSCARH---VTGHRPYDSQLCCDRCGKV 29 (565)
Q Consensus 2 ~~Cp~Cgs~---~i~~D~~~G~~VCt~CG~V 29 (565)
++|..|++- -..+|......+|.-||..
T Consensus 3 ~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~ 33 (40)
T PF04810_consen 3 VRCRRCRAYLNPFCQFDDGGKTWICNFCGTK 33 (40)
T ss_dssp -B-TTT--BS-TTSEEETTTTEEEETTT--E
T ss_pred cccCCCCCEECCcceEcCCCCEEECcCCCCc
Confidence 579999875 3456666678999999985
No 366
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=37.74 E-value=65 Score=27.57 Aligned_cols=37 Identities=8% Similarity=0.037 Sum_probs=31.0
Q ss_pred HHHHHhcCCCCCHhHHHHHhccCHHHHHHHHHHHHcc
Q 008455 225 YVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (565)
Q Consensus 225 ylAar~~g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t 261 (565)
.|+-++..-..++.++|..+|||..|..|-+.-|..-
T Consensus 16 ~lv~~vv~~g~~~a~aA~~~gVS~~Ta~kW~~Ryra~ 52 (85)
T PF13011_consen 16 RLVRRVVEQGWPVAHAAAEFGVSRRTAYKWLARYRAE 52 (85)
T ss_pred HHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHHHHc
Confidence 4556666677899999999999999999999888743
No 367
>PRK09492 treR trehalose repressor; Provisional
Probab=37.67 E-value=23 Score=36.20 Aligned_cols=23 Identities=22% Similarity=0.361 Sum_probs=21.7
Q ss_pred CCCHhHHHHHhccCHHHHHHHHH
Q 008455 234 KFSKSDIVKIVHICEATLMKRLI 256 (565)
Q Consensus 234 ~~t~~eIa~v~~Vse~TIrkR~k 256 (565)
+.|++|||+.+|||.+|+++.|+
T Consensus 4 ~~ti~dIA~~agVS~~TVSrvLn 26 (315)
T PRK09492 4 KLTIKDIARLSGVGKSTVSRVLN 26 (315)
T ss_pred CCcHHHHHHHhCCCHHHHhHHhC
Confidence 57999999999999999999997
No 368
>PF04161 Arv1: Arv1-like family ; InterPro: IPR007290 Arv1 is a transmembrane protein, with potential zinc-binding motifs, that mediates sterol homeostasis. Its action is important in lipid homeostasis, which prevents free sterol toxicity []. Arv1 contains a homology domain (AHD), which consists of an N-terminal cysteine-rich subdomain with a putative zinc-binding motif, followed by a C-terminal subdomain of 33 amino acids. The C-terminal subdomain of the AHD is critical for the protein's function []. In yeast, Arv1p is important for the delivery of an early glycosylphosphatidylinositol GPI intermediate, GlcN-acylPI, to the first mannosyltransferase of GPI synthesis in the ER lumen []. It is important for the traffic of sterol in yeast and in humans. In eukaryotic cells, it may fuction in the sphingolipid metabolic pathway as a transporter of ceramides between the ER and Golgi [].
Probab=37.66 E-value=16 Score=36.14 Aligned_cols=31 Identities=26% Similarity=0.519 Sum_probs=21.8
Q ss_pred CCCCCCCCCC--ceeccCCC---ceecCcccceecc
Q 008455 2 VWCSSCARHV--TGHRPYDS---QLCCDRCGKVLED 32 (565)
Q Consensus 2 ~~Cp~Cgs~~--i~~D~~~G---~~VCt~CG~Vlee 32 (565)
+.|-+||... +-.+...| -..|.+||.|.|.
T Consensus 1 miCIeCg~~v~~Ly~~Ys~~~irLt~C~~C~~vaDk 36 (208)
T PF04161_consen 1 MICIECGHPVKSLYRQYSPGNIRLTKCPNCGKVADK 36 (208)
T ss_pred CEeccCCCcchhhhhccCCCcEEEeeccccCCcccc
Confidence 4699999883 22334334 3789999999874
No 369
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=37.65 E-value=22 Score=40.07 Aligned_cols=28 Identities=25% Similarity=0.578 Sum_probs=21.6
Q ss_pred CCCCCCCCCceeccCCCceecCcccceec
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vle 31 (565)
.||+|+.... +....+.+.|..||....
T Consensus 224 ~C~~C~~~l~-~h~~~~~l~Ch~Cg~~~~ 251 (505)
T TIGR00595 224 CCPNCDVSLT-YHKKEGKLRCHYCGYQEP 251 (505)
T ss_pred CCCCCCCceE-EecCCCeEEcCCCcCcCC
Confidence 6999988744 434678999999998754
No 370
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=37.64 E-value=32 Score=26.98 Aligned_cols=23 Identities=9% Similarity=0.180 Sum_probs=20.3
Q ss_pred CHhHHHHHhccCHHHHHHHHHHH
Q 008455 236 SKSDIVKIVHICEATLMKRLIEF 258 (565)
Q Consensus 236 t~~eIa~v~~Vse~TIrkR~kE~ 258 (565)
|..+||+.+||+..||++..+++
T Consensus 2 s~~eva~~~gvs~~tlr~w~~~~ 24 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAWERRY 24 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHhC
Confidence 67899999999999999877654
No 371
>PRK01381 Trp operon repressor; Provisional
Probab=37.61 E-value=25 Score=30.89 Aligned_cols=37 Identities=11% Similarity=0.072 Sum_probs=30.0
Q ss_pred HHHHhcCCCCCHhHHHHHhccCHHHHHHHHHHHHccC
Q 008455 226 VSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTD 262 (565)
Q Consensus 226 lAar~~g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t~ 262 (565)
|+..+..-..|+++|+..+|||.+||.+-=+.++..+
T Consensus 47 I~~~L~~g~~sQREIa~~lGvSiaTITRgsn~Lk~~~ 83 (99)
T PRK01381 47 IVEELLRGELSQREIKQELGVGIATITRGSNSLKTAP 83 (99)
T ss_pred HHHHHHcCCcCHHHHHHHhCCceeeehhhHHHhccCC
Confidence 4444555679999999999999999999988887444
No 372
>PRK14086 dnaA chromosomal replication initiation protein; Provisional
Probab=37.51 E-value=76 Score=36.76 Aligned_cols=71 Identities=13% Similarity=0.163 Sum_probs=46.0
Q ss_pred hHHHHHHHHHHHHHHhCccccCCchhHHHH--HHHHHHHHhcCCCccHHHHHhhhccChHHHHHHHHHHHHHhhc
Q 008455 91 DEIVHVAKRFYGIAVARNFTKGRRTEQVQA--SCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYI 163 (565)
Q Consensus 91 ~~i~e~A~~iyk~a~~~~~~rGR~~~~vaA--ACLYiACR~e~~p~tL~DIa~~~~vsv~~Lgr~~~~L~~~L~i 163 (565)
+.|++....+|..-.+.=..++|+...+.| .|+|++-.. +..+|.+|...||-+..+|..++++|.+.+..
T Consensus 527 d~I~~~Va~~f~v~~~dl~s~~R~~~i~~aRqiAMYL~r~l--t~~Sl~~IG~~FgRdHSTV~~A~~kI~~~~~~ 599 (617)
T PRK14086 527 AAIMAATADYFGLTVEDLCGTSRSRVLVTARQIAMYLCREL--TDLSLPKIGQQFGRDHTTVMHADRKIRALMAE 599 (617)
T ss_pred HHHHHHHHHHhCCCHHHHhCCCCCcccchHHHHHHHHHHHH--cCCCHHHHHHHhCCChhHHHHHHHHHHHHHHh
Confidence 344445555554333222223344344444 677877654 45678999999999999999999999987764
No 373
>KOG1010 consensus Rb (Retinoblastoma tumor suppressor)-related protein [Cell cycle control, cell division, chromosome partitioning]
Probab=37.40 E-value=2.6e+02 Score=33.50 Aligned_cols=55 Identities=27% Similarity=0.377 Sum_probs=44.5
Q ss_pred HHHHHHHHHcCCCChhHHHHHHHHHHHHHHhCccccCCchhHHHHHHHHHHHHhcCCC
Q 008455 76 DDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKP 133 (565)
Q Consensus 76 ~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~p 133 (565)
......|..|+++ ......|...|.-+..+--.-| +-.++.|..||.+||..++|
T Consensus 36 q~~~~~c~~lnld--~~~~~ea~d~yta~~q~~sleg-s~~hW~~cAlY~~~r~S~~~ 90 (920)
T KOG1010|consen 36 QDSDELCRPLNLD--EQTETEAWDTYTAVSQRLSLEG-SESHWLACALYTACRRSSVP 90 (920)
T ss_pred hhhhhhhhhhccc--chhhhhhHHHHHHHHhHhCCCc-cHHHHHHHHHHHHHHhccCC
Confidence 4566789999999 8999999999988766444444 46789999999999998765
No 374
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=37.28 E-value=24 Score=25.57 Aligned_cols=27 Identities=22% Similarity=0.482 Sum_probs=16.5
Q ss_pred CCCCCCCCCceeccC-CCceecCcccce
Q 008455 3 WCSSCARHVTGHRPY-DSQLCCDRCGKV 29 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~-~G~~VCt~CG~V 29 (565)
.||.|+......... --..+|..||=|
T Consensus 1 ~CP~C~~~l~~~~~~~~~id~C~~C~G~ 28 (41)
T PF13453_consen 1 KCPRCGTELEPVRLGDVEIDVCPSCGGI 28 (41)
T ss_pred CcCCCCcccceEEECCEEEEECCCCCeE
Confidence 599999863222221 124469999876
No 375
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=37.14 E-value=30 Score=27.88 Aligned_cols=22 Identities=18% Similarity=0.318 Sum_probs=19.5
Q ss_pred CCHhHHHHHhccCHHHHHHHHH
Q 008455 235 FSKSDIVKIVHICEATLMKRLI 256 (565)
Q Consensus 235 ~t~~eIa~v~~Vse~TIrkR~k 256 (565)
.|+++||+.+|||..||.+.+.
T Consensus 1 ~t~~~iA~~~gvS~~TVSr~ln 22 (70)
T smart00354 1 ATIKDVARLAGVSKATVSRVLN 22 (70)
T ss_pred CCHHHHHHHHCCCHHHHHHHHC
Confidence 3789999999999999998774
No 376
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=37.08 E-value=21 Score=39.12 Aligned_cols=29 Identities=34% Similarity=0.693 Sum_probs=19.6
Q ss_pred CCCCCCCCCceec-cCCCceecCcccceec
Q 008455 3 WCSSCARHVTGHR-PYDSQLCCDRCGKVLE 31 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D-~~~G~~VCt~CG~Vle 31 (565)
.||+|+.-.-..+ ...+...|..||.++-
T Consensus 15 ~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~ 44 (403)
T TIGR00155 15 LCSQCDMLVALPRIESGQKAACPRCGTTLT 44 (403)
T ss_pred eCCCCCCcccccCCCCCCeeECCCCCCCCc
Confidence 4999986532222 2345678999999885
No 377
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=37.01 E-value=32 Score=32.37 Aligned_cols=26 Identities=8% Similarity=0.092 Sum_probs=23.1
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHH
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~ 258 (565)
...|.+|||..+|+++.||+.|+.--
T Consensus 149 ~g~s~~EIA~~lgis~~tVk~~l~Ra 174 (183)
T TIGR02999 149 AGLTVEEIAELLGVSVRTVERDWRFA 174 (183)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 56899999999999999999998643
No 378
>PF07278 DUF1441: Protein of unknown function (DUF1441); InterPro: IPR009901 This entry is represented by Bacteriophage VT1-Sakai, H0025. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical Enterobacterial proteins of around 160 residues in length. The function of this family is unknown.
Probab=36.63 E-value=28 Score=32.96 Aligned_cols=41 Identities=15% Similarity=0.192 Sum_probs=29.6
Q ss_pred CCCHhHHHHHhccCHHHHHHHHHHHHccCC--CCCCHHHHHHH
Q 008455 234 KFSKSDIVKIVHICEATLMKRLIEFENTDS--GSLTIEDFMAR 274 (565)
Q Consensus 234 ~~t~~eIa~v~~Vse~TIrkR~kE~~~t~s--~~Lt~~~f~~~ 274 (565)
+.++..||.++|+...|+++|++++..... +.+.+=.+..+
T Consensus 1 ~~nI~qlA~~~g~~R~TV~~RL~~~~p~~g~~~~~~lY~l~dv 43 (152)
T PF07278_consen 1 KWNINQLAEAFGLHRQTVAKRLKGANPAAGSNRGLKLYALRDV 43 (152)
T ss_pred CCCHHHHHHHHcccHHHHHHHHccCCCCCCCCCCCCcchHHHH
Confidence 357788999999999999999999983322 34444444433
No 379
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=36.60 E-value=1.3e+02 Score=28.48 Aligned_cols=29 Identities=7% Similarity=-0.156 Sum_probs=26.9
Q ss_pred CCccHHHHHhhhccChHHHHHHHHHHHHH
Q 008455 132 KPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (565)
Q Consensus 132 ~p~tL~DIa~~~~vsv~~Lgr~~~~L~~~ 160 (565)
.|+|..+||+.+|++..+|.|.+++|.+.
T Consensus 148 ~~~t~~~iA~~lG~tretvsR~l~~l~~~ 176 (202)
T PRK13918 148 IYATHDELAAAVGSVRETVTKVIGELSRE 176 (202)
T ss_pred ecCCHHHHHHHhCccHHHHHHHHHHHHHC
Confidence 57899999999999999999999999874
No 380
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=36.31 E-value=35 Score=34.48 Aligned_cols=28 Identities=11% Similarity=0.322 Sum_probs=26.0
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHHHc
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEFEN 260 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~~~ 260 (565)
-.+++.++++.++||+.|||+-+++|.+
T Consensus 17 ~~~~~~eLa~~l~VS~~TiRRdL~~L~~ 44 (240)
T PRK10411 17 TSLTTEALAEQLNVSKETIRRDLNELQT 44 (240)
T ss_pred CCCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4789999999999999999999999975
No 381
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=36.14 E-value=84 Score=25.28 Aligned_cols=38 Identities=11% Similarity=0.102 Sum_probs=29.5
Q ss_pred HHHHHHhcCC-CccHHHHHhhhccChHHHHHHHHHHHHH
Q 008455 123 LYLACRQKSK-PFLLIDFSNYLNINVYELGAVYLQLCQV 160 (565)
Q Consensus 123 LYiACR~e~~-p~tL~DIa~~~~vsv~~Lgr~~~~L~~~ 160 (565)
|+...+..|- ++++.|||..+|++...+.+....|.+.
T Consensus 11 IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~ 49 (68)
T smart00550 11 ILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKK 49 (68)
T ss_pred HHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 3444455555 4999999999999999999887777664
No 382
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=36.06 E-value=14 Score=28.51 Aligned_cols=27 Identities=26% Similarity=0.573 Sum_probs=19.0
Q ss_pred CCCCCCCCCcee---ccCCCceecCccccee
Q 008455 3 WCSSCARHVTGH---RPYDSQLCCDRCGKVL 30 (565)
Q Consensus 3 ~Cp~Cgs~~i~~---D~~~G~~VCt~CG~Vl 30 (565)
.|+-||...-.+ .-.+| +||.+|--=+
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHHHHh
Confidence 499999873322 25678 7999998544
No 383
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=35.86 E-value=1e+02 Score=30.30 Aligned_cols=30 Identities=10% Similarity=0.247 Sum_probs=26.9
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHHHccC
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEFENTD 262 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~~~t~ 262 (565)
++.|+++||..+|++..|+.+-+++|.+..
T Consensus 172 i~~t~~~iA~~lG~tretvsR~l~~L~~~g 201 (236)
T PRK09392 172 LPYEKRVLASYLGMTPENLSRAFAALASHG 201 (236)
T ss_pred eeCCHHHHHHHhCCChhHHHHHHHHHHhCC
Confidence 467789999999999999999999998765
No 384
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=35.79 E-value=1.5e+02 Score=29.20 Aligned_cols=47 Identities=17% Similarity=0.178 Sum_probs=34.0
Q ss_pred chhHHHHHHHHHHHHhcC------CCccHHHHHhhhccChHHHHHHHHHHHHH
Q 008455 114 RTEQVQASCLYLACRQKS------KPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (565)
Q Consensus 114 ~~~~vaAACLYiACR~e~------~p~tL~DIa~~~~vsv~~Lgr~~~~L~~~ 160 (565)
+...-+|..|+.-.+..+ .|.+..+||+.+|++..+|.|+.++|.+.
T Consensus 154 ~~~~Rla~~Ll~l~~~~g~~~~i~i~lt~~~IA~~lGisretlsR~L~~L~~~ 206 (230)
T PRK09391 154 TAMERVAAFLLEMDERLGGAGMMALPMSRRDIADYLGLTIETVSRALSQLQDR 206 (230)
T ss_pred CHHHHHHHHHHHHHHHhCCCCEEEecCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 344444444443344332 57888999999999999999999999875
No 385
>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=35.68 E-value=5.2e+02 Score=26.78 Aligned_cols=40 Identities=10% Similarity=-0.000 Sum_probs=31.0
Q ss_pred HHHHHHHhcCCCCCHhHHHHHhc--cCHHHHHHHHHHHHccC
Q 008455 223 ALYVSALTHGLKFSKSDIVKIVH--ICEATLMKRLIEFENTD 262 (565)
Q Consensus 223 ALylAar~~g~~~t~~eIa~v~~--Vse~TIrkR~kE~~~t~ 262 (565)
+|.-.+.+.++.-+..+||+.++ ||...++..+.-+.+..
T Consensus 126 virel~~~~~~~~~~~~ia~~l~p~is~~ev~~sL~~L~~~g 167 (271)
T TIGR02147 126 VIRELLGVMPFADDPEELAKRCFPKISAEQVKESLDLLERLG 167 (271)
T ss_pred HHHHHhhcCCCCCCHHHHHHHhCCCCCHHHHHHHHHHHHHCC
Confidence 44444556677778889999998 99999999998877554
No 386
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=35.56 E-value=8.7 Score=34.37 Aligned_cols=34 Identities=21% Similarity=0.581 Sum_probs=18.2
Q ss_pred CCCCCCCCCceeccCCCceecCcccceeccccccccccc
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATF 41 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vlee~~id~~~ef 41 (565)
+|+.||.. +........|..||.-- -.|.+|.++
T Consensus 72 ~C~~Cg~~---~~~~~~~~~CP~Cgs~~--~~i~~G~el 105 (113)
T PF01155_consen 72 RCRDCGHE---FEPDEFDFSCPRCGSPD--VEIISGREL 105 (113)
T ss_dssp EETTTS-E---EECHHCCHH-SSSSSS---EEEEESS-E
T ss_pred ECCCCCCE---EecCCCCCCCcCCcCCC--cEEccCCeE
Confidence 69999876 23333447799999852 234455443
No 387
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=35.41 E-value=36 Score=25.46 Aligned_cols=39 Identities=8% Similarity=0.108 Sum_probs=28.0
Q ss_pred CCCCCHhHHHHHhccCHHHHHHHHHHHHccCCCCCCHHHHHHHH
Q 008455 232 GLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARK 275 (565)
Q Consensus 232 g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t~s~~Lt~~~f~~~~ 275 (565)
....|++++|+.+||+..||.+-.+. ....+++....+.
T Consensus 7 ~~gls~~~la~~~gis~~~i~~~~~g-----~~~~~~~~~~~ia 45 (55)
T PF01381_consen 7 EKGLSQKELAEKLGISRSTISRIENG-----KRNPSLDTLKKIA 45 (55)
T ss_dssp HTTS-HHHHHHHHTS-HHHHHHHHTT-----SSTSBHHHHHHHH
T ss_pred HcCCCHHHHHHHhCCCcchhHHHhcC-----CCCCCHHHHHHHH
Confidence 45689999999999999999987765 3355666655554
No 388
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=35.37 E-value=26 Score=32.39 Aligned_cols=28 Identities=29% Similarity=0.769 Sum_probs=19.6
Q ss_pred CCC--CCCCCCceeccCCCceecCcccceecc
Q 008455 3 WCS--SCARHVTGHRPYDSQLCCDRCGKVLED 32 (565)
Q Consensus 3 ~Cp--~Cgs~~i~~D~~~G~~VCt~CG~Vlee 32 (565)
.|| .|++.. ..+ .+|.+.|..||..++.
T Consensus 20 aC~~~~C~kKv-~~~-~~~~y~C~~C~~~~~~ 49 (146)
T PF08646_consen 20 ACPNEKCNKKV-TEN-GDGSYRCEKCNKTVEN 49 (146)
T ss_dssp E-TSTTTS-B--EEE-TTTEEEETTTTEEESS
T ss_pred CCCCccCCCEe-ecC-CCcEEECCCCCCcCCC
Confidence 599 999863 333 5699999999998753
No 389
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=35.35 E-value=20 Score=41.65 Aligned_cols=25 Identities=24% Similarity=0.550 Sum_probs=16.7
Q ss_pred CCCCCCCCCceeccCCCceecCcccceecc
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vlee 32 (565)
.||+||... ..|...|.+||+-+..
T Consensus 29 ~Cp~CG~~~-----~~~~~fC~~CG~~~~~ 53 (645)
T PRK14559 29 PCPQCGTEV-----PVDEAHCPNCGAETGT 53 (645)
T ss_pred cCCCCCCCC-----CcccccccccCCcccc
Confidence 466666542 3577789999887654
No 390
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=35.34 E-value=63 Score=26.77 Aligned_cols=46 Identities=4% Similarity=0.166 Sum_probs=29.9
Q ss_pred HHHHhcCCCCCHhHHHHHhccCHHHHHHHHHHHHccCCCCCCHHHHHHHH
Q 008455 226 VSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARK 275 (565)
Q Consensus 226 lAar~~g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t~s~~Lt~~~f~~~~ 275 (565)
|...+-....||+++|+.+||+.++|.+-.+ -.....|++.+....
T Consensus 23 i~~~~~~~~ltQ~e~A~~lgisq~~vS~l~~----g~~~~~sl~~L~~~l 68 (80)
T PF13744_consen 23 IRELREERGLTQAELAERLGISQPRVSRLEN----GKIDDFSLDTLLRYL 68 (80)
T ss_dssp HHHHHHCCT--HHHHHHHHTS-HHHHHHHHT----T-GCC--HHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHHCCChhHHHHHHc----CcccCCCHHHHHHHH
Confidence 5555667889999999999999999986443 334467788777664
No 391
>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=35.32 E-value=62 Score=31.64 Aligned_cols=28 Identities=11% Similarity=0.280 Sum_probs=25.8
Q ss_pred CCCHhHHHHHhccCHHHHHHHHHHHHcc
Q 008455 234 KFSKSDIVKIVHICEATLMKRLIEFENT 261 (565)
Q Consensus 234 ~~t~~eIa~v~~Vse~TIrkR~kE~~~t 261 (565)
..|+.+|+..++|+..|+++.|+.|.+-
T Consensus 15 ~~t~~eLA~~lgis~~tV~~~L~~Le~~ 42 (203)
T TIGR02702 15 QATAAALAEALAISPQAVRRHLKDLETE 42 (203)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 4999999999999999999999999853
No 392
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=35.10 E-value=53 Score=32.40 Aligned_cols=26 Identities=31% Similarity=0.362 Sum_probs=22.9
Q ss_pred CCCHhHHHHHhccCHHHHHHHHHHHH
Q 008455 234 KFSKSDIVKIVHICEATLMKRLIEFE 259 (565)
Q Consensus 234 ~~t~~eIa~v~~Vse~TIrkR~kE~~ 259 (565)
+++.++||+.+|||.+|+..+|+.-.
T Consensus 178 ~~~l~dLA~~lGISkst~~ehLRrAe 203 (215)
T COG3413 178 RVSLKDLAKELGISKSTLSEHLRRAE 203 (215)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 47899999999999999999997644
No 393
>PF05043 Mga: Mga helix-turn-helix domain; InterPro: IPR007737 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 []. The family also contains VirR like proteins which match only at the C terminus of the alignment.; PDB: 3SQN_A.
Probab=34.99 E-value=42 Score=27.93 Aligned_cols=30 Identities=13% Similarity=0.241 Sum_probs=24.7
Q ss_pred hcCCCCCHhHHHHHhccCHHHHHHHHHHHH
Q 008455 230 THGLKFSKSDIVKIVHICEATLMKRLIEFE 259 (565)
Q Consensus 230 ~~g~~~t~~eIa~v~~Vse~TIrkR~kE~~ 259 (565)
..+-.+++.++|....||.+||.+.++.+.
T Consensus 26 l~~~~~s~~~la~~~~iS~sti~~~i~~l~ 55 (87)
T PF05043_consen 26 LNNEYVSIEDLAEELFISRSTIYRDIKKLN 55 (87)
T ss_dssp HH-SEEEHHHHHHHHT--HHHHHHHHHHHH
T ss_pred HcCCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 357789999999999999999999999987
No 394
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=34.87 E-value=1.5e+02 Score=30.24 Aligned_cols=54 Identities=9% Similarity=0.107 Sum_probs=41.4
Q ss_pred ChhHHHHHHHHHHHHhcCCCCCHhHHHHHhccCHHHHHHHHHHHHccCCCCCCHHHHHHH
Q 008455 215 KPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMAR 274 (565)
Q Consensus 215 ~P~~IaaAALylAar~~g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t~s~~Lt~~~f~~~ 274 (565)
.+.-+.-+.-||...+..-.+|+.+||..+|||..++.+-+++. .+|+-+|...
T Consensus 195 ~~~~l~~~~~~I~~~l~~~~ls~~~lA~~~giS~r~L~r~Fk~~------G~T~~~yi~~ 248 (302)
T PRK09685 195 RERQFQKVVALIDQSIQEEILRPEWIAGELGISVRSLYRLFAEQ------GLVVAQYIRN 248 (302)
T ss_pred cHHHHHHHHHHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHHHc------CCCHHHHHHH
Confidence 34445566668888877777999999999999999999888752 3577777643
No 395
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=34.70 E-value=36 Score=31.74 Aligned_cols=26 Identities=27% Similarity=0.186 Sum_probs=22.6
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHH
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~ 258 (565)
...|.++||..+|+++.||++++.--
T Consensus 133 ~g~s~~EIA~~lgis~~tV~~~l~ra 158 (173)
T PRK09645 133 RGWSTAQIAADLGIPEGTVKSRLHYA 158 (173)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 46889999999999999999887543
No 396
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=34.67 E-value=28 Score=29.29 Aligned_cols=27 Identities=19% Similarity=0.226 Sum_probs=19.8
Q ss_pred CCCCCCCCCceeccCCCceecCcccce
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGKV 29 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~V 29 (565)
.||-||...+..+.....-||.-|+--
T Consensus 3 ~CPCCg~~Tl~~~~~~~ydIC~VC~WE 29 (78)
T PF14206_consen 3 PCPCCGYYTLEERGEGTYDICPVCFWE 29 (78)
T ss_pred cCCCCCcEEeccCCCcCceECCCCCcc
Confidence 699999876544432238899999984
No 397
>PF08299 Bac_DnaA_C: Bacterial dnaA protein helix-turn-helix; InterPro: IPR013159 This entry represents the C-terminal domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication. DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; GO: 0005524 ATP binding, 0043565 sequence-specific DNA binding, 0006270 DNA-dependent DNA replication initiation, 0006275 regulation of DNA replication; PDB: 2HCB_B 3R8F_C 1L8Q_A 3PVP_B 3PVV_A 1J1V_A.
Probab=34.51 E-value=93 Score=25.22 Aligned_cols=45 Identities=20% Similarity=0.296 Sum_probs=27.6
Q ss_pred cCCchhHHHH--HHHHHHHHhcCCCccHHHHHhhhc-cChHHHHHHHHHH
Q 008455 111 KGRRTEQVQA--SCLYLACRQKSKPFLLIDFSNYLN-INVYELGAVYLQL 157 (565)
Q Consensus 111 rGR~~~~vaA--ACLYiACR~e~~p~tL~DIa~~~~-vsv~~Lgr~~~~L 157 (565)
++|....+-| .+.|++-... ..++.+|+..+| -+..++..+++++
T Consensus 23 ~~R~~~i~~aR~va~yL~r~~~--~~sl~~Ig~~fg~rdHstV~~a~~ki 70 (70)
T PF08299_consen 23 KSRKRKIVEARQVAMYLARELT--GLSLSEIGRYFGGRDHSTVIHAIRKI 70 (70)
T ss_dssp S---HHHHHHHHHHHHHHHHHS-----HHHHHHHCTSSTHHHHHHHHHHH
T ss_pred CCCChhhcchHHHHHHHHHHHh--CCCHHHHHHHhCCCCHHHHHHHHHhC
Confidence 4444443333 4556665555 578999999999 9999988887764
No 398
>cd00131 PAX Paired Box domain
Probab=34.47 E-value=52 Score=30.00 Aligned_cols=31 Identities=19% Similarity=0.244 Sum_probs=27.2
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHHHccCC
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEFENTDS 263 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~~~t~s 263 (565)
...+..+||..++|+..||.+-++-|.++.+
T Consensus 32 ~G~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~ 62 (128)
T cd00131 32 SGIRPCDISRQLRVSHGCVSKILNRYYETGS 62 (128)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHcCC
Confidence 3479999999999999999999999987753
No 399
>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA. This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (pfam02311) and the helix-turn-helix DNA-binding domain (pfam00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway.
Probab=34.39 E-value=1.8e+02 Score=29.34 Aligned_cols=38 Identities=11% Similarity=0.184 Sum_probs=29.7
Q ss_pred HHHHHHHHHHhcCCCccHHHHHhhhccChHHHHHHHHHH
Q 008455 119 QASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQL 157 (565)
Q Consensus 119 aAACLYiACR~e~~p~tL~DIa~~~~vsv~~Lgr~~~~L 157 (565)
..++-||...- ..++++.++|+.++++...|.+.|++.
T Consensus 189 ~~~~~~I~~~~-~~~~sl~~lA~~~~~S~~~l~r~Fk~~ 226 (287)
T TIGR02297 189 NRFNFLIEENY-KQHLRLPEYADRLGISESRLNDICRRF 226 (287)
T ss_pred HHHHHHHHHhh-ccCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 34455665443 458999999999999999999988865
No 400
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=34.34 E-value=35 Score=28.10 Aligned_cols=27 Identities=11% Similarity=0.148 Sum_probs=21.2
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHHH
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEFE 259 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~~ 259 (565)
...|..+||+.++||++||.+-.+.|.
T Consensus 33 ~~~si~elA~~~~vS~sti~Rf~kkLG 59 (77)
T PF01418_consen 33 AFMSISELAEKAGVSPSTIVRFCKKLG 59 (77)
T ss_dssp CT--HHHHHHHCTS-HHHHHHHHHHCT
T ss_pred HHccHHHHHHHcCCCHHHHHHHHHHhC
Confidence 457999999999999999999888765
No 401
>PHA00542 putative Cro-like protein
Probab=34.32 E-value=34 Score=28.64 Aligned_cols=29 Identities=10% Similarity=0.116 Sum_probs=23.8
Q ss_pred hcCCCCCHhHHHHHhccCHHHHHHHHHHH
Q 008455 230 THGLKFSKSDIVKIVHICEATLMKRLIEF 258 (565)
Q Consensus 230 ~~g~~~t~~eIa~v~~Vse~TIrkR~kE~ 258 (565)
+.....|+.++|+.+||+..||.+-+..-
T Consensus 27 l~~~glTq~elA~~lgIs~~tIsr~e~g~ 55 (82)
T PHA00542 27 LIRAGWSQEQIADATDVSQPTICRIYSGR 55 (82)
T ss_pred HHHCCCCHHHHHHHHCcCHHHHHHHHcCC
Confidence 34456899999999999999999877543
No 402
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=34.29 E-value=61 Score=24.99 Aligned_cols=40 Identities=15% Similarity=0.215 Sum_probs=25.3
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHHHccCCCCCCHHHHHHHHH
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARKK 276 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~~~t~s~~Lt~~~f~~~~~ 276 (565)
..+|+.++|+.+||+..||.+-++ -....++++.+.++..
T Consensus 9 ~~it~~~La~~~gis~~tl~~~~~----~~~~~~~~~~l~~ia~ 48 (63)
T PF13443_consen 9 RGITQKDLARKTGISRSTLSRILN----GKPSNPSLDTLEKIAK 48 (63)
T ss_dssp TT--HHHHHHHHT--HHHHHHHHT----TT-----HHHHHHHHH
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHh----cccccccHHHHHHHHH
Confidence 456999999999999999998877 2235788888887764
No 403
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=34.28 E-value=39 Score=30.76 Aligned_cols=26 Identities=4% Similarity=-0.143 Sum_probs=23.0
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHH
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~ 258 (565)
...|.+|||...|+++.||++++...
T Consensus 121 ~~~s~~EIA~~l~is~~tV~~~~~ra 146 (154)
T PRK06759 121 VGKTMGEIALETEMTYYQVRWIYRQA 146 (154)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 46889999999999999999998654
No 404
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=34.17 E-value=39 Score=30.97 Aligned_cols=27 Identities=4% Similarity=0.012 Sum_probs=23.4
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHHH
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEFE 259 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~~ 259 (565)
...|.++||..+|+++.||+.++..-.
T Consensus 121 ~g~s~~EIA~~lgis~~tV~~~l~ra~ 147 (161)
T PRK09047 121 EDMDVAETAAAMGCSEGSVKTHCSRAT 147 (161)
T ss_pred hcCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 568899999999999999999886544
No 405
>COG1309 AcrR Transcriptional regulator [Transcription]
Probab=34.14 E-value=42 Score=29.92 Aligned_cols=39 Identities=23% Similarity=0.263 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHhcCCC-CCHhHHHHHhccCHHHHHHHHHHH
Q 008455 219 LCGAALYVSALTHGLK-FSKSDIVKIVHICEATLMKRLIEF 258 (565)
Q Consensus 219 IaaAALylAar~~g~~-~t~~eIa~v~~Vse~TIrkR~kE~ 258 (565)
|..+++.+... +|+. +|.++|++.+||+..||-+.+..-
T Consensus 17 ii~aa~~l~~~-~G~~~~t~~~Ia~~agvs~~~~Y~~f~~K 56 (201)
T COG1309 17 ILDAALRLFAE-KGYAATTVDEIAKAAGVSKGTLYRHFPSK 56 (201)
T ss_pred HHHHHHHHHHH-cCcCCCCHHHHHHHhCCCcchhHHHcCCH
Confidence 44455554444 8875 899999999999999999888643
No 406
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=34.12 E-value=69 Score=23.36 Aligned_cols=31 Identities=10% Similarity=0.075 Sum_probs=27.8
Q ss_pred ccHHHHHhhhccChHHHHHHHHHHHHHhhcc
Q 008455 134 FLLIDFSNYLNINVYELGAVYLQLCQVLYIA 164 (565)
Q Consensus 134 ~tL~DIa~~~~vsv~~Lgr~~~~L~~~L~i~ 164 (565)
.+..+||..++++..++.+....+.+.|+.+
T Consensus 19 ~s~~eia~~l~is~~tv~~~~~~~~~kl~~~ 49 (58)
T smart00421 19 LTNKEIAERLGISEKTVKTHLSNIMRKLGVR 49 (58)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Confidence 5889999999999999999999988888764
No 407
>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=34.08 E-value=74 Score=24.15 Aligned_cols=27 Identities=15% Similarity=0.338 Sum_probs=23.7
Q ss_pred CCCHhHHHHHhccCHHHHHHHHHHHHc
Q 008455 234 KFSKSDIVKIVHICEATLMKRLIEFEN 260 (565)
Q Consensus 234 ~~t~~eIa~v~~Vse~TIrkR~kE~~~ 260 (565)
.+++.+|++.++++.+|+.+.++.+..
T Consensus 17 ~~~~~~la~~~~~~~~~~t~~i~~L~~ 43 (59)
T PF01047_consen 17 GITQSELAEKLGISRSTVTRIIKRLEK 43 (59)
T ss_dssp SEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHCCChhHHHHHHHHHHH
Confidence 389999999999999999999998864
No 408
>PRK14873 primosome assembly protein PriA; Provisional
Probab=34.04 E-value=25 Score=41.10 Aligned_cols=27 Identities=19% Similarity=0.522 Sum_probs=20.4
Q ss_pred CCCCCCCCCCceeccCCCceecCcccce
Q 008455 2 VWCSSCARHVTGHRPYDSQLCCDRCGKV 29 (565)
Q Consensus 2 ~~Cp~Cgs~~i~~D~~~G~~VCt~CG~V 29 (565)
..||+|+.... +....+.+.|.-||..
T Consensus 393 ~~C~~C~~~L~-~h~~~~~l~Ch~CG~~ 419 (665)
T PRK14873 393 ARCRHCTGPLG-LPSAGGTPRCRWCGRA 419 (665)
T ss_pred eECCCCCCcee-EecCCCeeECCCCcCC
Confidence 46999998744 3335688999999984
No 409
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=33.99 E-value=55 Score=30.88 Aligned_cols=27 Identities=19% Similarity=0.293 Sum_probs=23.5
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHHH
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEFE 259 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~~ 259 (565)
...|.++||..+|+++.||+.++..-.
T Consensus 132 e~~s~~EIA~~lgis~~tV~~~l~ra~ 158 (179)
T PRK12543 132 HDYSQEEIAQLLQIPIGTVKSRIHAAL 158 (179)
T ss_pred ccCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 346999999999999999999987665
No 410
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=33.94 E-value=6e+02 Score=26.94 Aligned_cols=90 Identities=12% Similarity=0.037 Sum_probs=51.5
Q ss_pred hHHHHHHHHHHHHHHHHHHcCCC---ChhHHHHHHHHHHHHHHhCccccCCchhHHHHHHHHHHH---------------
Q 008455 66 SRERLMEKAFDDMRQMKNALNIG---ESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLAC--------------- 127 (565)
Q Consensus 66 srer~l~~a~~~I~~ia~~L~Lp---~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiAC--------------- 127 (565)
.+++.+..-...+..+|.++.-. -.+-+.+....+++-+..-.-.+|-+....|.-.|.-+-
T Consensus 87 A~~~Lv~~~~~lV~~iA~r~~~~~~~~eDLvQEg~igL~~a~~~fdp~~G~rFsTYA~~wIr~aI~~~i~~~~r~vrlP~ 166 (324)
T PRK07921 87 ARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPV 166 (324)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHcCCCccCCH
Confidence 44555555566677777776321 113344444456665555455667666666654443321
Q ss_pred -----------------HhcCCCccHHHHHhhhccChHHHHHHHH
Q 008455 128 -----------------RQKSKPFLLIDFSNYLNINVYELGAVYL 155 (565)
Q Consensus 128 -----------------R~e~~p~tL~DIa~~~~vsv~~Lgr~~~ 155 (565)
...|.+-+..+||..+++++..|.....
T Consensus 167 ~~~~~~~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~ 211 (324)
T PRK07921 167 HLVEQVNKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLE 211 (324)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHH
Confidence 1123344677899999999888877643
No 411
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=33.86 E-value=27 Score=36.90 Aligned_cols=27 Identities=19% Similarity=0.465 Sum_probs=16.6
Q ss_pred CCCCCCCCC---ce-eccCCC--ceecCcccce
Q 008455 3 WCSSCARHV---TG-HRPYDS--QLCCDRCGKV 29 (565)
Q Consensus 3 ~Cp~Cgs~~---i~-~D~~~G--~~VCt~CG~V 29 (565)
.||.||+.- ++ ....+| .+.|.-||+-
T Consensus 189 ~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~te 221 (309)
T PRK03564 189 FCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESE 221 (309)
T ss_pred CCCCCCCcchhheeeccCCCCceEEEcCCCCCc
Confidence 699999872 11 112344 6777777764
No 412
>PF01807 zf-CHC2: CHC2 zinc finger; InterPro: IPR002694 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents CycHisCysCys (CHC2) type zinc finger domains, which are found in bacteria and viruses. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0003896 DNA primase activity, 0008270 zinc ion binding, 0006260 DNA replication; PDB: 1D0Q_B 2AU3_A.
Probab=33.85 E-value=21 Score=30.97 Aligned_cols=27 Identities=22% Similarity=0.453 Sum_probs=16.8
Q ss_pred CCCCCCCCC--CceeccCCCceecCcccc
Q 008455 2 VWCSSCARH--VTGHRPYDSQLCCDRCGK 28 (565)
Q Consensus 2 ~~Cp~Cgs~--~i~~D~~~G~~VCt~CG~ 28 (565)
..||.|+.. .+.+++..|...|-.||.
T Consensus 34 ~~CPfH~d~~pS~~i~~~k~~~~Cf~Cg~ 62 (97)
T PF01807_consen 34 CLCPFHDDKTPSFSINPDKNRFKCFGCGK 62 (97)
T ss_dssp E--SSS--SS--EEEETTTTEEEETTT--
T ss_pred EECcCCCCCCCceEEECCCCeEEECCCCC
Confidence 369999865 557778889999999995
No 413
>PRK09954 putative kinase; Provisional
Probab=33.85 E-value=54 Score=34.80 Aligned_cols=30 Identities=10% Similarity=0.329 Sum_probs=27.2
Q ss_pred cCCCCCHhHHHHHhccCHHHHHHHHHHHHc
Q 008455 231 HGLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (565)
Q Consensus 231 ~g~~~t~~eIa~v~~Vse~TIrkR~kE~~~ 260 (565)
.+-++|+.+|++.++||..||++|++.|.+
T Consensus 14 ~~~~~s~~~la~~l~~s~~~v~~~i~~L~~ 43 (362)
T PRK09954 14 RNPLIQQNEIADILQISRSRVAAHIMDLMR 43 (362)
T ss_pred HCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 344899999999999999999999999986
No 414
>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=33.71 E-value=74 Score=23.91 Aligned_cols=35 Identities=14% Similarity=0.195 Sum_probs=26.7
Q ss_pred HHHHhcCCCccHHHHHhhhccChHHHHHHHHHHHH
Q 008455 125 LACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQ 159 (565)
Q Consensus 125 iACR~e~~p~tL~DIa~~~~vsv~~Lgr~~~~L~~ 159 (565)
-+...++.|.++.||+..++++..++.+....|.+
T Consensus 10 ~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~ 44 (52)
T PF09339_consen 10 EALAESGGPLTLSEIARALGLPKSTVHRLLQTLVE 44 (52)
T ss_dssp HCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 33445667789999999999999998887766655
No 415
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=33.66 E-value=25 Score=34.63 Aligned_cols=30 Identities=30% Similarity=0.654 Sum_probs=18.3
Q ss_pred CCCCCCCCCc----eec--cCCC-----ceecCcccceecc
Q 008455 3 WCSSCARHVT----GHR--PYDS-----QLCCDRCGKVLED 32 (565)
Q Consensus 3 ~Cp~Cgs~~i----~~D--~~~G-----~~VCt~CG~Vlee 32 (565)
.||+||.... .++ |.-| ...|..||.=-.|
T Consensus 2 ~Cp~C~~~~~~~~~~~~~IP~F~evii~sf~C~~CGyr~~e 42 (192)
T TIGR00310 2 DCPSCGGECETVMKTVNDIPYFGEVLETSTICEHCGYRSND 42 (192)
T ss_pred cCCCCCCCCEEEEEEEcCCCCcceEEEEEEECCCCCCccce
Confidence 5999996522 222 2223 4579999986443
No 416
>PRK05580 primosome assembly protein PriA; Validated
Probab=33.62 E-value=27 Score=40.84 Aligned_cols=28 Identities=21% Similarity=0.585 Sum_probs=21.4
Q ss_pred CCCCCCCCCceeccCCCceecCcccceec
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vle 31 (565)
.||+|+... .+....+.+.|..||....
T Consensus 392 ~C~~C~~~l-~~h~~~~~l~Ch~Cg~~~~ 419 (679)
T PRK05580 392 ECPHCDASL-TLHRFQRRLRCHHCGYQEP 419 (679)
T ss_pred CCCCCCCce-eEECCCCeEECCCCcCCCC
Confidence 699998863 4445678999999998754
No 417
>smart00351 PAX Paired Box domain.
Probab=33.58 E-value=56 Score=29.60 Aligned_cols=30 Identities=20% Similarity=0.225 Sum_probs=26.2
Q ss_pred CCCHhHHHHHhccCHHHHHHHHHHHHccCC
Q 008455 234 KFSKSDIVKIVHICEATLMKRLIEFENTDS 263 (565)
Q Consensus 234 ~~t~~eIa~v~~Vse~TIrkR~kE~~~t~s 263 (565)
..+..+||+.++||..||.+-++.|.++.+
T Consensus 33 G~s~~~iA~~~gvs~~tV~kwi~r~~~~G~ 62 (125)
T smart00351 33 GVRPCDISRQLCVSHGCVSKILGRYYETGS 62 (125)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHcCC
Confidence 468899999999999999999999887653
No 418
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=33.53 E-value=29 Score=35.83 Aligned_cols=24 Identities=17% Similarity=0.169 Sum_probs=21.9
Q ss_pred CCCHhHHHHHhccCHHHHHHHHHH
Q 008455 234 KFSKSDIVKIVHICEATLMKRLIE 257 (565)
Q Consensus 234 ~~t~~eIa~v~~Vse~TIrkR~kE 257 (565)
+.|++|||+.+|||.+|+++.|+.
T Consensus 5 ~~ti~dIA~~agVS~~TVSrvLn~ 28 (331)
T PRK14987 5 RPVLQDVADRVGVTKMTVSRFLRN 28 (331)
T ss_pred CCcHHHHHHHhCCCHHHhhhhhCC
Confidence 579999999999999999999963
No 419
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=33.38 E-value=54 Score=28.82 Aligned_cols=27 Identities=26% Similarity=0.299 Sum_probs=24.1
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHHH
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEFE 259 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~~ 259 (565)
...+..+||...||++.||++++....
T Consensus 125 ~g~s~~eIA~~l~~s~~~v~~~~~~~~ 151 (158)
T TIGR02937 125 EGLSYKEIAEILGISVGTVKRRLKRAR 151 (158)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 357999999999999999999998765
No 420
>PF14369 zf-RING_3: zinc-finger
Probab=33.15 E-value=25 Score=24.89 Aligned_cols=26 Identities=38% Similarity=0.902 Sum_probs=16.9
Q ss_pred CCCCCCCCCceeccCCCceecCcccc
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGK 28 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~ 28 (565)
+|-.|....-+....+..+.|..|+-
T Consensus 4 wCh~C~~~V~~~~~~~~~~~CP~C~~ 29 (35)
T PF14369_consen 4 WCHQCNRFVRIAPSPDSDVACPRCHG 29 (35)
T ss_pred eCccCCCEeEeCcCCCCCcCCcCCCC
Confidence 79999877443323344456999973
No 421
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=33.14 E-value=99 Score=25.48 Aligned_cols=28 Identities=21% Similarity=0.313 Sum_probs=26.0
Q ss_pred CCCHhHHHHHhccCHHHHHHHHHHHHcc
Q 008455 234 KFSKSDIVKIVHICEATLMKRLIEFENT 261 (565)
Q Consensus 234 ~~t~~eIa~v~~Vse~TIrkR~kE~~~t 261 (565)
..++++|+..++++..||.+.++.|.+.
T Consensus 24 ~~~~~~la~~~~~s~~~i~~~l~~L~~~ 51 (101)
T smart00347 24 PLSVSELAKRLGVSPSTVTRVLDRLEKK 51 (101)
T ss_pred CcCHHHHHHHHCCCchhHHHHHHHHHHC
Confidence 6899999999999999999999999864
No 422
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=33.12 E-value=41 Score=31.52 Aligned_cols=25 Identities=8% Similarity=0.155 Sum_probs=22.3
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHH
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIE 257 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE 257 (565)
...|.++||..+|+++.||+.++.-
T Consensus 134 ~g~s~~EIA~~lgis~~tV~~~l~r 158 (172)
T PRK12523 134 DGMGHAEIAERLGVSVSRVRQYLAQ 158 (172)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4689999999999999999999853
No 423
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=33.09 E-value=64 Score=30.10 Aligned_cols=34 Identities=15% Similarity=0.169 Sum_probs=29.4
Q ss_pred cCCCCCHhHHHHHhccCHHHHHHHHHHHHccCCC
Q 008455 231 HGLKFSKSDIVKIVHICEATLMKRLIEFENTDSG 264 (565)
Q Consensus 231 ~g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t~s~ 264 (565)
..-..|.++||+.+|||.+||.+-++.+.++.+.
T Consensus 18 ~~~G~S~re~Ak~~gvs~sTvy~wv~r~~e~G~~ 51 (138)
T COG3415 18 VGEGLSCREAAKRFGVSISTVYRWVRRYRETGLD 51 (138)
T ss_pred HHcCccHHHHHHHhCccHHHHHHHHHHhcccccc
Confidence 3466899999999999999999999999877664
No 424
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=32.82 E-value=76 Score=29.17 Aligned_cols=39 Identities=13% Similarity=0.285 Sum_probs=32.1
Q ss_pred HHHHHHhcCCCCCHhHHHHHhccCHHHHHHHHHHHHccC
Q 008455 224 LYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTD 262 (565)
Q Consensus 224 LylAar~~g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t~ 262 (565)
+|.+-.-.+-+.|+.+||..++.+.+|+.+.++-+.+..
T Consensus 32 v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~~G 70 (126)
T COG3355 32 VYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLEAG 70 (126)
T ss_pred HHHHHHhhcCCcCHHHHHHHHCccHHHHHHHHHHHHHcC
Confidence 455554356789999999999999999999999887554
No 425
>TIGR01481 ccpA catabolite control protein A. Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.
Probab=32.81 E-value=31 Score=35.47 Aligned_cols=23 Identities=13% Similarity=0.141 Sum_probs=21.0
Q ss_pred CCHhHHHHHhccCHHHHHHHHHH
Q 008455 235 FSKSDIVKIVHICEATLMKRLIE 257 (565)
Q Consensus 235 ~t~~eIa~v~~Vse~TIrkR~kE 257 (565)
.|++|||+.+|||.+|+++.|+.
T Consensus 2 ~ti~dIA~~agvS~~TVSrvLn~ 24 (329)
T TIGR01481 2 VTIYDVAREAGVSMATVSRVVNG 24 (329)
T ss_pred CcHHHHHHHhCCCHHHHHHHhCC
Confidence 58999999999999999999963
No 426
>COG0664 Crp cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
Probab=32.80 E-value=1.7e+02 Score=27.37 Aligned_cols=30 Identities=17% Similarity=0.350 Sum_probs=27.0
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHHHccC
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEFENTD 262 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~~~t~ 262 (565)
++++..+|+..+|++..|+.+.+.+|....
T Consensus 170 ~~~~~~~ia~~~g~~~~~vsr~l~~l~~~g 199 (214)
T COG0664 170 LPLTHKDLAEYLGLSRETVSRILKELRKDG 199 (214)
T ss_pred ccCCHHHHHHHhCCchhhHHHHHHHHHhCC
Confidence 679999999999999999999999998543
No 427
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=32.72 E-value=50 Score=24.53 Aligned_cols=39 Identities=5% Similarity=0.089 Sum_probs=29.1
Q ss_pred CCCCCHhHHHHHhccCHHHHHHHHHHHHccCCCCCCHHHHHHHH
Q 008455 232 GLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARK 275 (565)
Q Consensus 232 g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t~s~~Lt~~~f~~~~ 275 (565)
....|+.++|..+||+..||++-.+-- ...+++.+..+.
T Consensus 13 ~~gltq~~lA~~~gvs~~~vs~~e~g~-----~~~~~~~~~~i~ 51 (58)
T TIGR03070 13 ALGLTQADLADLAGVGLRFIRDVENGK-----PTVRLDKVLRVL 51 (58)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHCCC-----CCCCHHHHHHHH
Confidence 457899999999999999998865321 245677766654
No 428
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=32.64 E-value=42 Score=31.33 Aligned_cols=26 Identities=8% Similarity=0.115 Sum_probs=23.1
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHH
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~ 258 (565)
...|.+|||..+|+++.||+.++..-
T Consensus 133 eg~s~~EIA~~l~is~~tV~~~l~ra 158 (168)
T PRK12525 133 EGLTYVEIGERLGVSLSRIHQYMVEA 158 (168)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 56899999999999999999998653
No 429
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=32.51 E-value=2.4e+02 Score=25.10 Aligned_cols=75 Identities=11% Similarity=0.125 Sum_probs=45.4
Q ss_pred HHHHHHHHcCCCChhHHHHHHHHHHHHHHhCcc----ccCCc-hhHHHHHHHHHHHHhcCCCccHHHHHhhhccChHHHH
Q 008455 77 DMRQMKNALNIGESDEIVHVAKRFYGIAVARNF----TKGRR-TEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELG 151 (565)
Q Consensus 77 ~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~----~rGR~-~~~vaAACLYiACR~e~~p~tL~DIa~~~~vsv~~Lg 151 (565)
.+..+|..++++ ... ..++++.. +.+- .+|++ .. .=...+.=.++-..++.|+|..++|+..+|+
T Consensus 20 s~~eaa~~F~VS--~~T---v~~W~k~~-~~G~~~~k~r~~~Kid----~~~L~~~v~~~pd~tl~Ela~~l~Vs~~ti~ 89 (119)
T PF01710_consen 20 SIREAAKRFGVS--RNT---VYRWLKRK-ETGDLEPKPRGRKKID----RDELKALVEENPDATLRELAERLGVSPSTIW 89 (119)
T ss_pred hHHHHHHHhCcH--HHH---HHHHHHhc-cccccccccccccccc----HHHHHHHHHHCCCcCHHHHHHHcCCCHHHHH
Confidence 678899999998 544 44566532 2222 22332 11 1112222234556899999999999999999
Q ss_pred HHHHHHHHHh
Q 008455 152 AVYLQLCQVL 161 (565)
Q Consensus 152 r~~~~L~~~L 161 (565)
+..++|--+.
T Consensus 90 ~~Lkrlg~t~ 99 (119)
T PF01710_consen 90 RALKRLGITR 99 (119)
T ss_pred HHHHHcCchh
Confidence 8776654333
No 430
>PF14768 RPA_interact_C: Replication protein A interacting C-terminal
Probab=32.50 E-value=34 Score=28.77 Aligned_cols=26 Identities=23% Similarity=0.631 Sum_probs=20.0
Q ss_pred CCCCCCCCCceeccCCCceecCcccceec
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vle 31 (565)
+||.|....+.. ..+.+.| .||.-|.
T Consensus 1 iCPVC~~~~L~~--~~~~i~C-~Cgl~l~ 26 (82)
T PF14768_consen 1 ICPVCQKGNLRE--NSNVISC-SCGLRLN 26 (82)
T ss_pred CCCccCCCcccc--cCCeEEC-CCccEEe
Confidence 599999987655 5688888 6786655
No 431
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=32.43 E-value=74 Score=35.18 Aligned_cols=68 Identities=13% Similarity=0.160 Sum_probs=45.4
Q ss_pred hHHHHHHHHHHHHHHhCccccCCchhHHHHH---HHHHHHHhcCCCccHHHHHhhhccChHHHHHHHHHHHHHh
Q 008455 91 DEIVHVAKRFYGIAVARNFTKGRRTEQVQAS---CLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVL 161 (565)
Q Consensus 91 ~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAA---CLYiACR~e~~p~tL~DIa~~~~vsv~~Lgr~~~~L~~~L 161 (565)
+.|++....+|..-.+.=..++|+. .++-| +.|++-+ -+..++.+|+..+|.+..+|.++++++.+.+
T Consensus 345 ~~I~~~V~~~~~i~~~~l~s~~R~~-~i~~aR~iamyl~r~--~~~~s~~~Ig~~fgr~hstV~~a~~~i~~~~ 415 (440)
T PRK14088 345 DELIEIVAKVTGVSREEILSNSRNV-KALLARRIGMYVAKN--YLGSSLRTIAEKFNRSHPVVVDSVKKVKDSL 415 (440)
T ss_pred HHHHHHHHHHcCCcHHHHhCCCCCc-cccHHHHHHHHHHHH--HhCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 4555666666643322222233433 34444 7888844 5567999999999999999999999998865
No 432
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=32.38 E-value=33 Score=35.51 Aligned_cols=22 Identities=14% Similarity=0.151 Sum_probs=20.7
Q ss_pred CCHhHHHHHhccCHHHHHHHHH
Q 008455 235 FSKSDIVKIVHICEATLMKRLI 256 (565)
Q Consensus 235 ~t~~eIa~v~~Vse~TIrkR~k 256 (565)
.|++|||+.+|||.+|+++.|+
T Consensus 2 ~Ti~dIA~~agVS~~TVSrvLn 23 (341)
T PRK10703 2 ATIKDVAKRAGVSTTTVSHVIN 23 (341)
T ss_pred CCHHHHHHHhCCCHHHHHHHHc
Confidence 4899999999999999999996
No 433
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=32.36 E-value=67 Score=30.39 Aligned_cols=38 Identities=13% Similarity=0.130 Sum_probs=30.8
Q ss_pred HHHHHHHhcCCCCCHhHHHHHhccCHHHHHHHHHHHHcc
Q 008455 223 ALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (565)
Q Consensus 223 ALylAar~~g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t 261 (565)
+||.... .+-....++||...+|+.+|+.+-++.+.+-
T Consensus 14 ~Iy~l~~-~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~ 51 (154)
T COG1321 14 TIYELLE-EKGFARTKDIAERLKVSPPSVTEMLKRLERL 51 (154)
T ss_pred HHHHHHh-ccCcccHHHHHHHhCCCcHHHHHHHHHHHHC
Confidence 5665554 5667889999999999999999988888643
No 434
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=32.35 E-value=41 Score=32.14 Aligned_cols=27 Identities=26% Similarity=0.240 Sum_probs=23.8
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHHH
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEFE 259 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~~ 259 (565)
...|.++||..+|+|+.||+.|+.--.
T Consensus 146 ~g~s~~EIA~~lgis~~tVk~~l~Rar 172 (193)
T TIGR02947 146 EGFAYKEIAEIMGTPIGTVMSRLHRGR 172 (193)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 468999999999999999999987554
No 435
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=32.30 E-value=34 Score=35.16 Aligned_cols=22 Identities=9% Similarity=0.134 Sum_probs=20.4
Q ss_pred CHhHHHHHhccCHHHHHHHHHH
Q 008455 236 SKSDIVKIVHICEATLMKRLIE 257 (565)
Q Consensus 236 t~~eIa~v~~Vse~TIrkR~kE 257 (565)
|++|||+.+|||.+|+++.|+.
T Consensus 2 ti~dIA~~aGVS~~TVSrvLn~ 23 (328)
T PRK11303 2 KLDEIARLAGVSRTTASYVING 23 (328)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 7899999999999999999963
No 436
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=32.04 E-value=1.1e+02 Score=24.92 Aligned_cols=46 Identities=17% Similarity=0.073 Sum_probs=36.1
Q ss_pred HHhcCCCccHHHHHhhhccChHHHHHHHHHHHHHhhccccccccccCCchhhHHH
Q 008455 127 CRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHK 181 (565)
Q Consensus 127 CR~e~~p~tL~DIa~~~~vsv~~Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~R 181 (565)
.|..+.|+++.+.|+.+|+++..+.+....+.+-|-. .||+-...+
T Consensus 7 IrlLs~~~s~~~Aa~~lG~~~~~v~~wv~~fR~wll~---------LDPSG~~E~ 52 (65)
T PF05344_consen 7 IRLLSQQISVAQAADRLGTDPGTVRRWVRMFRQWLLQ---------LDPSGHWEA 52 (65)
T ss_pred HHHhcccccHHHHHHHHCcCHHHHHHHHHHHHHHHHH---------cCCCCChHH
Confidence 3677899999999999999999999988887775532 566655443
No 437
>PF13790 DUF4182: Domain of unknown function (DUF4182)
Probab=32.03 E-value=23 Score=25.71 Aligned_cols=13 Identities=15% Similarity=0.892 Sum_probs=12.2
Q ss_pred CceecCcccceec
Q 008455 19 SQLCCDRCGKVLE 31 (565)
Q Consensus 19 G~~VCt~CG~Vle 31 (565)
|.+||..|+.+++
T Consensus 2 GtIvCq~C~~~Id 14 (38)
T PF13790_consen 2 GTIVCQHCNETID 14 (38)
T ss_pred CEEEeccccceee
Confidence 7899999999998
No 438
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=32.01 E-value=57 Score=28.00 Aligned_cols=23 Identities=22% Similarity=0.086 Sum_probs=19.8
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHH
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLI 256 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~k 256 (565)
...|.++||..+|||..||.+ +.
T Consensus 49 ~G~S~~eIA~~LgISrsTIyR-i~ 71 (88)
T TIGR02531 49 QGKTYSDIEAETGASTATISR-VK 71 (88)
T ss_pred CCCCHHHHHHHHCcCHHHHHH-HH
Confidence 346999999999999999988 44
No 439
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=32.00 E-value=77 Score=23.22 Aligned_cols=32 Identities=9% Similarity=0.027 Sum_probs=28.5
Q ss_pred CccHHHHHhhhccChHHHHHHHHHHHHHhhcc
Q 008455 133 PFLLIDFSNYLNINVYELGAVYLQLCQVLYIA 164 (565)
Q Consensus 133 p~tL~DIa~~~~vsv~~Lgr~~~~L~~~L~i~ 164 (565)
..+..+||..+++++.++.....++.+.++..
T Consensus 15 ~~s~~eia~~l~~s~~tv~~~~~~~~~~l~~~ 46 (57)
T cd06170 15 GKTNKEIADILGISEKTVKTHLRNIMRKLGVK 46 (57)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHhCCC
Confidence 46899999999999999999999998888864
No 440
>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=31.96 E-value=64 Score=25.09 Aligned_cols=31 Identities=16% Similarity=0.288 Sum_probs=24.2
Q ss_pred cCCCCCHhHHHHHhccCHHHHHHHHHHHHcc
Q 008455 231 HGLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (565)
Q Consensus 231 ~g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t 261 (565)
.+-+.++.+|+..++++..|+.+.++.+.+-
T Consensus 15 ~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~ 45 (68)
T PF13463_consen 15 SDGPMTQSDLAERLGISKSTVSRIIKKLEEK 45 (68)
T ss_dssp -TS-BEHHHHHHHTT--HHHHHHHHHHHHHT
T ss_pred cCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 4677899999999999999999999988743
No 441
>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=31.89 E-value=89 Score=24.23 Aligned_cols=32 Identities=16% Similarity=0.232 Sum_probs=24.6
Q ss_pred hcCCCccHHHHHhhhccChHHHHHHHHHHHHH
Q 008455 129 QKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (565)
Q Consensus 129 ~e~~p~tL~DIa~~~~vsv~~Lgr~~~~L~~~ 160 (565)
..+-+.++.+|++.++++.-.+.+..++|.+.
T Consensus 14 ~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~ 45 (68)
T PF13463_consen 14 HSDGPMTQSDLAERLGISKSTVSRIIKKLEEK 45 (68)
T ss_dssp --TS-BEHHHHHHHTT--HHHHHHHHHHHHHT
T ss_pred ccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 56778899999999999999999999998874
No 442
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=31.85 E-value=45 Score=30.76 Aligned_cols=26 Identities=19% Similarity=0.102 Sum_probs=23.1
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHH
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~ 258 (565)
...|.++||..+|++..||+.|+.--
T Consensus 128 ~g~s~~EIA~~l~is~~tV~~~l~ra 153 (161)
T PRK12528 128 DGLGYGEIATELGISLATVKRYLNKA 153 (161)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 56899999999999999999998654
No 443
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=31.82 E-value=26 Score=38.52 Aligned_cols=30 Identities=30% Similarity=0.615 Sum_probs=20.4
Q ss_pred CCCCCCCCCceec-cCCCceecCcccceecc
Q 008455 3 WCSSCARHVTGHR-PYDSQLCCDRCGKVLED 32 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D-~~~G~~VCt~CG~Vlee 32 (565)
.||+|+.-.-..+ ...+...|..||.+|..
T Consensus 12 ~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~~ 42 (419)
T PRK15103 12 LCPQCDMLVALPRLEHGQKAACPRCGTTLTV 42 (419)
T ss_pred cCCCCCceeecCCCCCCCeeECCCCCCCCcC
Confidence 4999997532222 23456889999999853
No 444
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=31.80 E-value=88 Score=32.13 Aligned_cols=54 Identities=7% Similarity=0.162 Sum_probs=0.0
Q ss_pred hhHHHHHHHHHHHHhcCCCccHHHHHhhhccChHHHHHHHHHHHHHhhccccccccccCCchhhHHHH
Q 008455 115 TEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKF 182 (565)
Q Consensus 115 ~~~vaAACLYiACR~e~~p~tL~DIa~~~~vsv~~Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf 182 (565)
...+..++-||-..... +.++.++|..++++.+.|.|.|+.... ..|..||.+.
T Consensus 4 ~~~i~~~~~~i~~~~~~-~~~l~~lA~~~~~S~~~l~r~F~~~~g-------------~s~~~yi~~~ 57 (289)
T PRK15121 4 AGIIRDLLIWLEGHLDQ-PLSLDNVAAKAGYSKWHLQRMFKDVTG-------------HAIGAYIRAR 57 (289)
T ss_pred HHHHHHHHHHHHhcccC-CCCHHHHHHHHCcCHHHHHHHHHHHHC-------------cCHHHHHHHH
No 445
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=31.72 E-value=43 Score=32.14 Aligned_cols=27 Identities=15% Similarity=0.135 Sum_probs=23.6
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHHH
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEFE 259 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~~ 259 (565)
...|.++||..+|||..||+.|+.-..
T Consensus 156 eg~s~~EIA~~lgis~~tVk~rl~ra~ 182 (194)
T PRK12531 156 EELPHQQVAEMFDIPLGTVKSRLRLAV 182 (194)
T ss_pred cCCCHHHHHHHhCcCHHHHHHHHHHHH
Confidence 568999999999999999999986543
No 446
>PRK10130 transcriptional regulator EutR; Provisional
Probab=31.65 E-value=93 Score=33.35 Aligned_cols=54 Identities=19% Similarity=0.376 Sum_probs=39.7
Q ss_pred hhHHHHHHHHHHHHhcCCCccHHHHHhhhccChHHHHHHHHHHHHHhhccccccccccCCchhhHHHH
Q 008455 115 TEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKF 182 (565)
Q Consensus 115 ~~~vaAACLYiACR~e~~p~tL~DIa~~~~vsv~~Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf 182 (565)
...|..++-||--.. ..|+++.|||..++++...|.+.|++. +| ..|..||.++
T Consensus 239 ~~~v~~~~~~i~~~~-~~~ltv~~lA~~~gvS~r~L~r~Fk~~---~G----------~sp~~ylr~~ 292 (350)
T PRK10130 239 RRLLSRAREYVLENM-SEPVTVLDLCNQLHVSRRTLQNAFHAI---LG----------IGPNAWLKRI 292 (350)
T ss_pred HHHHHHHHHHHHhhh-cCCCCHHHHHHHHCCCHHHHHHHHHHH---HC----------cCHHHHHHHH
Confidence 344566666776443 458999999999999999999988865 33 4467777643
No 447
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=31.52 E-value=25 Score=27.44 Aligned_cols=26 Identities=31% Similarity=0.622 Sum_probs=18.2
Q ss_pred CCCCCCCC---CceeccCCCceecCcccc
Q 008455 3 WCSSCARH---VTGHRPYDSQLCCDRCGK 28 (565)
Q Consensus 3 ~Cp~Cgs~---~i~~D~~~G~~VCt~CG~ 28 (565)
.|++|... .+..+...-.++|..||.
T Consensus 24 IC~~C~~hNGla~~~~~~~i~y~C~~Cg~ 52 (54)
T PF10058_consen 24 ICSKCFSHNGLAPKEEFEEIQYRCPYCGA 52 (54)
T ss_pred ECcccchhhcccccccCCceEEEcCCCCC
Confidence 58888765 223455566889999986
No 448
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=31.46 E-value=23 Score=31.97 Aligned_cols=35 Identities=11% Similarity=0.309 Sum_probs=19.2
Q ss_pred CCCCCCCCCceeccCCCceecCcccceeccccccccccc
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATF 41 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vlee~~id~~~ef 41 (565)
+|+.||.... .+ ..+...|..||.- +..|..|.+|
T Consensus 73 ~C~~Cg~~~~-~~-~~~~~~CP~Cgs~--~~~i~~G~El 107 (117)
T PRK00564 73 ECKDCSHVFK-PN-ALDYGVCEKCHSK--NVIITQGNEM 107 (117)
T ss_pred EhhhCCCccc-cC-CccCCcCcCCCCC--ceEEecCCEE
Confidence 6888885421 11 1244459999864 2334555443
No 449
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=31.45 E-value=29 Score=36.57 Aligned_cols=9 Identities=22% Similarity=0.925 Sum_probs=6.5
Q ss_pred ceecCcccc
Q 008455 20 QLCCDRCGK 28 (565)
Q Consensus 20 ~~VCt~CG~ 28 (565)
-+-|+.||.
T Consensus 224 R~~C~~Cg~ 232 (305)
T TIGR01562 224 RVKCSHCEE 232 (305)
T ss_pred CccCCCCCC
Confidence 357888885
No 450
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=31.35 E-value=1.8e+02 Score=22.58 Aligned_cols=26 Identities=12% Similarity=0.097 Sum_probs=20.5
Q ss_pred ccHHHHHhhhccChHHHHHHHHHHHH
Q 008455 134 FLLIDFSNYLNINVYELGAVYLQLCQ 159 (565)
Q Consensus 134 ~tL~DIa~~~~vsv~~Lgr~~~~L~~ 159 (565)
.++.|+|+.+||+..++....++-.+
T Consensus 24 ~tl~elA~~lgis~st~~~~LRrae~ 49 (53)
T PF04967_consen 24 ITLEELAEELGISKSTVSEHLRRAER 49 (53)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 58899999999999888766555443
No 451
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=31.09 E-value=31 Score=26.55 Aligned_cols=22 Identities=27% Similarity=0.244 Sum_probs=16.8
Q ss_pred CCHhHHHHHhccCHHHHHHHHH
Q 008455 235 FSKSDIVKIVHICEATLMKRLI 256 (565)
Q Consensus 235 ~t~~eIa~v~~Vse~TIrkR~k 256 (565)
.++.+||..+||+.+||++-++
T Consensus 23 ~s~~~ia~~fgv~~sTv~~I~K 44 (53)
T PF04218_consen 23 ESKRDIAREFGVSRSTVSTILK 44 (53)
T ss_dssp T-HHHHHHHHT--CCHHHHHHH
T ss_pred CCHHHHHHHhCCCHHHHHHHHH
Confidence 3899999999999999998765
No 452
>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=31.08 E-value=66 Score=27.13 Aligned_cols=31 Identities=16% Similarity=0.239 Sum_probs=26.5
Q ss_pred hcCCCCCHhHHHHHhccCHHHHHHHHHHHHc
Q 008455 230 THGLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (565)
Q Consensus 230 ~~g~~~t~~eIa~v~~Vse~TIrkR~kE~~~ 260 (565)
..+.++.-++|++.++++..|||+-+..+.+
T Consensus 19 ~~~~PVgSk~ia~~l~~s~aTIRN~M~~Le~ 49 (78)
T PF03444_consen 19 ETGEPVGSKTIAEELGRSPATIRNEMADLEE 49 (78)
T ss_pred hcCCCcCHHHHHHHHCCChHHHHHHHHHHHH
Confidence 3477888999999999999999998887763
No 453
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=31.08 E-value=31 Score=32.57 Aligned_cols=27 Identities=22% Similarity=0.682 Sum_probs=20.6
Q ss_pred CCCCCCCCCceeccCCCceecCcccceec
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vle 31 (565)
.||.|++... +...|.+.|..|+..++
T Consensus 36 aC~~C~kkv~--~~~~~~~~C~~C~~~~~ 62 (166)
T cd04476 36 ACPGCNKKVV--EEGNGTYRCEKCNKSVP 62 (166)
T ss_pred cccccCcccE--eCCCCcEECCCCCCcCC
Confidence 5999998742 22338999999999874
No 454
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=31.01 E-value=47 Score=33.32 Aligned_cols=28 Identities=18% Similarity=0.407 Sum_probs=25.2
Q ss_pred CCCHhHHHHHhccCHHHHHHHHHHHHcc
Q 008455 234 KFSKSDIVKIVHICEATLMKRLIEFENT 261 (565)
Q Consensus 234 ~~t~~eIa~v~~Vse~TIrkR~kE~~~t 261 (565)
=.|+.|++..+++|..||++.++++.+-
T Consensus 105 lLT~~Dla~LL~~S~~TI~~~i~~yq~e 132 (220)
T PF07900_consen 105 LLTQEDLAMLLGISPRTISKDIKEYQKE 132 (220)
T ss_pred cccHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 3689999999999999999999999844
No 455
>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor. Members of this family belong the lacI helix-turn-helix family (pfam00356) of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterized members act as positive and negative transcriptional regulators of fructose and sucrose transport and metabolism. Sucrose is a disaccharide composed of fructose and glucose; D-fructose-1-phosphate rather than an intact sucrose moiety has been shown to act as the inducer.
Probab=30.99 E-value=34 Score=35.13 Aligned_cols=22 Identities=23% Similarity=0.231 Sum_probs=20.1
Q ss_pred CHhHHHHHhccCHHHHHHHHHH
Q 008455 236 SKSDIVKIVHICEATLMKRLIE 257 (565)
Q Consensus 236 t~~eIa~v~~Vse~TIrkR~kE 257 (565)
|++|||+.+|||.+|+++.|+.
T Consensus 1 ti~dIA~~aGVS~~TVSrvLn~ 22 (327)
T TIGR02417 1 TLSDIAKLAGVSKTTASYVING 22 (327)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 6899999999999999999953
No 456
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=30.93 E-value=50 Score=26.03 Aligned_cols=23 Identities=22% Similarity=0.245 Sum_probs=19.8
Q ss_pred CHhHHHHHhccCHHHHHHHHHHH
Q 008455 236 SKSDIVKIVHICEATLMKRLIEF 258 (565)
Q Consensus 236 t~~eIa~v~~Vse~TIrkR~kE~ 258 (565)
+..+||+.+||+..|||..-+++
T Consensus 2 ~i~evA~~~gvs~~tlR~~~~~g 24 (67)
T cd04764 2 TIKEVSEIIGVKPHTLRYYEKEF 24 (67)
T ss_pred CHHHHHHHHCcCHHHHHHHHHhc
Confidence 67899999999999999776653
No 457
>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=30.67 E-value=1.1e+02 Score=24.48 Aligned_cols=23 Identities=13% Similarity=0.170 Sum_probs=19.3
Q ss_pred cCCCccHHHHHhhhccChHHHHH
Q 008455 130 KSKPFLLIDFSNYLNINVYELGA 152 (565)
Q Consensus 130 e~~p~tL~DIa~~~~vsv~~Lgr 152 (565)
++-.++++|||+.++|+..+|++
T Consensus 19 ~~g~i~lkdIA~~Lgvs~~tIr~ 41 (60)
T PF10668_consen 19 SNGKIKLKDIAEKLGVSESTIRK 41 (60)
T ss_pred hCCCccHHHHHHHHCCCHHHHHH
Confidence 34457899999999999999876
No 458
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=30.59 E-value=85 Score=28.80 Aligned_cols=46 Identities=11% Similarity=0.162 Sum_probs=37.3
Q ss_pred hhHHHHHHHHHHHHhcCCCccHHHHHhhhccChHHHHHHHHHHHHH
Q 008455 115 TEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (565)
Q Consensus 115 ~~~vaAACLYiACR~e~~p~tL~DIa~~~~vsv~~Lgr~~~~L~~~ 160 (565)
.++-+-+.+|++-...|.+.+..+||..++|+..-|.+++.+|.+.
T Consensus 7 ~~YAl~~~i~la~~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~ 52 (141)
T PRK11014 7 TDYGLRALIYMASLPEGRMTSISEVTEVYGVSRNHMVKIINQLSRA 52 (141)
T ss_pred HhHHHHHHHHHhcCCCCCccCHHHHHHHHCcCHHHHHHHHHHHHhC
Confidence 3445556777776556778899999999999999999999998874
No 459
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=30.57 E-value=48 Score=30.45 Aligned_cols=26 Identities=15% Similarity=0.231 Sum_probs=22.9
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHH
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~ 258 (565)
...|.++||..+|+++.||+.|+.--
T Consensus 120 ~~~s~~eIA~~lgis~~tv~~~l~ra 145 (159)
T PRK12527 120 EGLSHQQIAEHLGISRSLVEKHIVNA 145 (159)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 56899999999999999999997643
No 460
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=30.57 E-value=33 Score=36.26 Aligned_cols=9 Identities=44% Similarity=1.202 Sum_probs=4.1
Q ss_pred ecCccccee
Q 008455 22 CCDRCGKVL 30 (565)
Q Consensus 22 VCt~CG~Vl 30 (565)
+|..||.-+
T Consensus 254 ~C~~C~~Yl 262 (309)
T PRK03564 254 SCGDCGTYL 262 (309)
T ss_pred ecccccccc
Confidence 444444443
No 461
>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=30.54 E-value=76 Score=25.53 Aligned_cols=32 Identities=9% Similarity=0.117 Sum_probs=23.6
Q ss_pred HhcCCCccHHHHHhhhccC-hHHHHHHHHHHHH
Q 008455 128 RQKSKPFLLIDFSNYLNIN-VYELGAVYLQLCQ 159 (565)
Q Consensus 128 R~e~~p~tL~DIa~~~~vs-v~~Lgr~~~~L~~ 159 (565)
..+|.|-|++||++.+|++ ...+......|.+
T Consensus 20 ~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~ 52 (65)
T PF01726_consen 20 EENGYPPTVREIAEALGLKSTSTVQRHLKALER 52 (65)
T ss_dssp HHHSS---HHHHHHHHTSSSHHHHHHHHHHHHH
T ss_pred HHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 4679999999999999997 8887776666655
No 462
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=30.52 E-value=29 Score=27.95 Aligned_cols=22 Identities=27% Similarity=0.697 Sum_probs=14.1
Q ss_pred CCCCCCCCCceeccCCCceecCcccce
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGKV 29 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~V 29 (565)
.|.+|+.-. ....-+|..||.-
T Consensus 6 AC~~Ck~l~-----~~d~e~CP~Cgs~ 27 (64)
T COG2093 6 ACKNCKRLT-----PEDTEICPVCGST 27 (64)
T ss_pred HHhhccccC-----CCCCccCCCCCCc
Confidence 588887631 1344489999863
No 463
>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=30.33 E-value=81 Score=30.51 Aligned_cols=33 Identities=18% Similarity=0.199 Sum_probs=29.1
Q ss_pred HhcCCCCCHhHHHHHhccC-HHHHHHHHHHHHcc
Q 008455 229 LTHGLKFSKSDIVKIVHIC-EATLMKRLIEFENT 261 (565)
Q Consensus 229 r~~g~~~t~~eIa~v~~Vs-e~TIrkR~kE~~~t 261 (565)
+-+++..|+++||+.++++ .+|+.++++.|.+.
T Consensus 20 ~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~ 53 (199)
T TIGR00498 20 ESTGYPPSIREIARAVGLRSPSAAEEHLKALERK 53 (199)
T ss_pred HhcCCCCcHHHHHHHhCCCChHHHHHHHHHHHHC
Confidence 3467889999999999998 99999999999754
No 464
>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=30.22 E-value=1.7e+02 Score=28.35 Aligned_cols=58 Identities=17% Similarity=0.217 Sum_probs=39.0
Q ss_pred CCHHHHHHHHHHHHHhhhccccCCCChhHHHHHHHHHHHHhcCCCCCHhHHHHHh-ccCHHHHHHHHHHHHccC
Q 008455 190 GNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIV-HICEATLMKRLIEFENTD 262 (565)
Q Consensus 190 l~~~V~~~A~~Lv~~m~~~~l~~GR~P~~IaaAALylAar~~g~~~t~~eIa~v~-~Vse~TIrkR~kE~~~t~ 262 (565)
+++.....-..|+.....+.+..|+.|. +-.|...++..+ |+++.||++.+..+.+..
T Consensus 41 l~~~~l~vL~aLls~~~~~d~~~~~~pi---------------VfpSN~~La~r~~G~s~~tlrR~l~~LveaG 99 (177)
T PF03428_consen 41 LSDRALAVLDALLSFTPPDDWEPGRRPI---------------VFPSNAQLAERLNGMSERTLRRHLARLVEAG 99 (177)
T ss_pred CChhHHHHHHHHHHhCCcccccCCCCce---------------eecCHHHHHHHHcCCCHHHHHHHHHHHHHCC
Confidence 5554444444455554444447777764 224556778888 999999999999998654
No 465
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=30.16 E-value=48 Score=31.61 Aligned_cols=27 Identities=19% Similarity=0.171 Sum_probs=23.6
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHHH
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEFE 259 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~~ 259 (565)
...|.+|||..+|+|+.||++++.--.
T Consensus 145 ~g~s~~EIA~~lgis~~tVk~~l~Rar 171 (185)
T PRK09649 145 LGLSYADAAAVCGCPVGTIRSRVARAR 171 (185)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 568899999999999999999986544
No 466
>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=30.15 E-value=1.4e+02 Score=22.58 Aligned_cols=37 Identities=11% Similarity=0.088 Sum_probs=27.9
Q ss_pred HHHHHHHhcCCCccHHHHHhhhccChHHHHHHHHHHHHH
Q 008455 122 CLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (565)
Q Consensus 122 CLYiACR~e~~p~tL~DIa~~~~vsv~~Lgr~~~~L~~~ 160 (565)
+|++..... +.++.+||+.++++...+.+...+|.+.
T Consensus 8 iL~~l~~~~--~~~~~~la~~~~~~~~~~t~~i~~L~~~ 44 (59)
T PF01047_consen 8 ILRILYENG--GITQSELAEKLGISRSTVTRIIKRLEKK 44 (59)
T ss_dssp HHHHHHHHS--SEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHcC--CCCHHHHHHHHCCChhHHHHHHHHHHHC
Confidence 344443333 3899999999999999999999988774
No 467
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=30.12 E-value=40 Score=27.64 Aligned_cols=26 Identities=15% Similarity=0.304 Sum_probs=21.3
Q ss_pred CCCCCHhHHHHHhccCHHHHHHHHHH
Q 008455 232 GLKFSKSDIVKIVHICEATLMKRLIE 257 (565)
Q Consensus 232 g~~~t~~eIa~v~~Vse~TIrkR~kE 257 (565)
....||.+.|+.+|||..||-.-=++
T Consensus 12 ~~~ltQ~elA~~vgVsRQTi~~iEkg 37 (68)
T COG1476 12 ELGLTQEELAKLVGVSRQTIIAIEKG 37 (68)
T ss_pred HhCcCHHHHHHHcCcCHHHHHHHHcC
Confidence 35689999999999999999764443
No 468
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=29.89 E-value=1.2e+02 Score=26.34 Aligned_cols=26 Identities=19% Similarity=0.289 Sum_probs=22.1
Q ss_pred CCCHhHHHHHhccCHHHHHHHHHHHH
Q 008455 234 KFSKSDIVKIVHICEATLMKRLIEFE 259 (565)
Q Consensus 234 ~~t~~eIa~v~~Vse~TIrkR~kE~~ 259 (565)
.-.+...|+.+||+..|++++++.+.
T Consensus 68 ~gn~s~AAr~LGIsRsTL~rKLkr~g 93 (95)
T PRK00430 68 RGNQTRAALMLGINRGTLRKKLKKYG 93 (95)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHhC
Confidence 34577889999999999999999863
No 469
>PRK07218 replication factor A; Provisional
Probab=29.83 E-value=26 Score=38.64 Aligned_cols=31 Identities=19% Similarity=0.433 Sum_probs=20.5
Q ss_pred CCCCCCCCCceeccCCCceecCcccceecccccccccccc
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATFV 42 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~Vlee~~id~~~ef~ 42 (565)
.||.|+... + . .+|..||.| +...+--..|.
T Consensus 299 rCP~C~r~v---~--~--~~C~~hG~v--e~~~dlrik~v 329 (423)
T PRK07218 299 RCPECGRVI---Q--K--GQCRSHGAV--EGEDDLRIKAI 329 (423)
T ss_pred cCcCccccc---c--C--CcCCCCCCc--CCeeeeEEEEE
Confidence 699999863 1 2 499999998 34444433343
No 470
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=29.74 E-value=56 Score=30.12 Aligned_cols=27 Identities=7% Similarity=0.084 Sum_probs=23.6
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHHH
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEFE 259 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~~ 259 (565)
...|.++||+.+|+++.||++++....
T Consensus 137 ~g~s~~eIA~~l~is~~tv~~~l~ra~ 163 (170)
T TIGR02952 137 QNLPIAEVARILGKTEGAVKILQFRAI 163 (170)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 468999999999999999999986544
No 471
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=29.69 E-value=47 Score=31.49 Aligned_cols=42 Identities=17% Similarity=0.295 Sum_probs=30.0
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHHHc---cCCCCCCHHHHHHH
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEFEN---TDSGSLTIEDFMAR 274 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~~~---t~s~~Lt~~~f~~~ 274 (565)
...|.++||..+|+|+.||+.++.--.. ..-...+.++|.+.
T Consensus 137 ~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~~~~~~~~ 181 (185)
T PRK12542 137 YNLTYQEISSVMGITEANVRKQFERARKRVQNMIGGIQHDEFKEL 181 (185)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHcccchHHHHHH
Confidence 4589999999999999999988754332 12245566677543
No 472
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=29.59 E-value=53 Score=26.02 Aligned_cols=23 Identities=17% Similarity=0.156 Sum_probs=20.0
Q ss_pred CHhHHHHHhccCHHHHHHHHHHH
Q 008455 236 SKSDIVKIVHICEATLMKRLIEF 258 (565)
Q Consensus 236 t~~eIa~v~~Vse~TIrkR~kE~ 258 (565)
+..++|+.+||+..|||..-+++
T Consensus 2 ~i~e~A~~~gVs~~tlr~ye~~~ 24 (68)
T cd04763 2 TIGEVALLTGIKPHVLRAWEREF 24 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHhc
Confidence 67899999999999999776664
No 473
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=29.56 E-value=94 Score=28.41 Aligned_cols=29 Identities=10% Similarity=0.124 Sum_probs=26.1
Q ss_pred CCCCCHhHHHHHhccCHHHHHHHHHHHHc
Q 008455 232 GLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (565)
Q Consensus 232 g~~~t~~eIa~v~~Vse~TIrkR~kE~~~ 260 (565)
.-.+|+.+|+..++++.+|+.+.++.+.+
T Consensus 52 ~~~~t~~eLa~~l~i~~~tvsr~l~~Le~ 80 (144)
T PRK11512 52 AACITPVELKKVLSVDLGALTRMLDRLVC 80 (144)
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 45699999999999999999999998874
No 474
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=29.48 E-value=29 Score=24.07 Aligned_cols=11 Identities=27% Similarity=0.960 Sum_probs=5.2
Q ss_pred ceecCccccee
Q 008455 20 QLCCDRCGKVL 30 (565)
Q Consensus 20 ~~VCt~CG~Vl 30 (565)
.+.|..||.|+
T Consensus 7 ~ykC~~Cgniv 17 (34)
T TIGR00319 7 VYKCEVCGNIV 17 (34)
T ss_pred EEEcCCCCcEE
Confidence 34444444444
No 475
>PRK10130 transcriptional regulator EutR; Provisional
Probab=29.47 E-value=1.5e+02 Score=31.86 Aligned_cols=52 Identities=17% Similarity=0.191 Sum_probs=40.3
Q ss_pred hHHHHHHHHHHHHhcCCCCCHhHHHHHhccCHHHHHHHHHHHHccCCCCCCHHHHHHH
Q 008455 217 SGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMAR 274 (565)
Q Consensus 217 ~~IaaAALylAar~~g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t~s~~Lt~~~f~~~ 274 (565)
.-|.-+.-||-... ..++|+.+||..+|||..|+.+.+++.. .+|+-+|...
T Consensus 240 ~~v~~~~~~i~~~~-~~~ltv~~lA~~~gvS~r~L~r~Fk~~~-----G~sp~~ylr~ 291 (350)
T PRK10130 240 RLLSRAREYVLENM-SEPVTVLDLCNQLHVSRRTLQNAFHAIL-----GIGPNAWLKR 291 (350)
T ss_pred HHHHHHHHHHHhhh-cCCCCHHHHHHHHCCCHHHHHHHHHHHH-----CcCHHHHHHH
Confidence 33445555666554 4579999999999999999999999987 6677888654
No 476
>PF01498 HTH_Tnp_Tc3_2: Transposase; InterPro: IPR002492 Transposase proteins are necessary for efficient DNA transposition. This family includes the amino-terminal region of Tc1, Tc1A, Tc1B and Tc2B transposases of Caenorhabditis elegans. The region encompasses the specific DNA binding and second DNA recognition domains as well as an amino-terminal region of the catalytic domain of Tc3 as described in []. Tc3 is a member of the Tc1/mariner family of transposable elements. This entry also includes histone-lysine N-methyltransferase SETMAR, which is a SET domain and mariner transposase fusion gene-containing protein. This histone methyltransferase has sequence-specific DNA-binding activity and recognises the 19-mer core of the 5'-terminal inverted repeats (TIRs) of the Hsmar1 element. This protein has DNA nicking activity, and has in vivo end joining activity and may mediate genomic integration of foreign DNA [, , , ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated, 0015074 DNA integration; PDB: 3K9K_B 3F2K_B 3K9J_B 1U78_A.
Probab=29.35 E-value=54 Score=26.24 Aligned_cols=27 Identities=22% Similarity=0.357 Sum_probs=18.5
Q ss_pred CCCCHhHHHHHh-----ccCHHHHHHHHHHHH
Q 008455 233 LKFSKSDIVKIV-----HICEATLMKRLIEFE 259 (565)
Q Consensus 233 ~~~t~~eIa~v~-----~Vse~TIrkR~kE~~ 259 (565)
-..|..+|+..+ .||..||+++|++..
T Consensus 12 p~~s~~~i~~~l~~~~~~vS~~TI~r~L~~~g 43 (72)
T PF01498_consen 12 PRISAREIAQELQEAGISVSKSTIRRRLREAG 43 (72)
T ss_dssp ----HHHHHHHT---T--S-HHHHHHHHHHT-
T ss_pred CCCCHHHHHHHHHHccCCcCHHHHHHHHHHcC
Confidence 347899999977 899999999999875
No 477
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=29.31 E-value=49 Score=25.99 Aligned_cols=22 Identities=14% Similarity=0.064 Sum_probs=19.0
Q ss_pred CHhHHHHHhccCHHHHHHHHHH
Q 008455 236 SKSDIVKIVHICEATLMKRLIE 257 (565)
Q Consensus 236 t~~eIa~v~~Vse~TIrkR~kE 257 (565)
|.++||+.+||+..||+...++
T Consensus 2 s~~eva~~~gvs~~tlr~~~~~ 23 (70)
T smart00422 2 TIGEVAKLAGVSVRTLRYYERI 23 (70)
T ss_pred CHHHHHHHHCcCHHHHHHHHHC
Confidence 6889999999999999976543
No 478
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=29.27 E-value=45 Score=33.94 Aligned_cols=28 Identities=14% Similarity=0.230 Sum_probs=25.5
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHHHc
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEFEN 260 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~~~ 260 (565)
-.+++.|+++.++||+.|||+-|++|.+
T Consensus 18 ~~~~~~ela~~l~vS~~TiRRdL~~Le~ 45 (252)
T PRK10906 18 GYVSTEELVEHFSVSPQTIRRDLNDLAE 45 (252)
T ss_pred CCEeHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4689999999999999999999998875
No 479
>TIGR02366 DHAK_reg probable dihydroxyacetone kinase regulator. The seed alignment for this family was built from a set of closely related uncharacterized proteins associated with operons for the type of bacterial dihydroxyacetone kinase that transfers PEP-derived phosphate from a phosphoprotein, as in phosphotransferase system transport, rather than from ATP. Members have a TetR transcriptional regulator domain (pfam00440) at the N-terminus and sequence homology throughout.
Probab=29.23 E-value=72 Score=29.72 Aligned_cols=42 Identities=19% Similarity=0.105 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHhcCCCCCHhHHHHHhccCHHHHHHHHHHHH
Q 008455 218 GLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFE 259 (565)
Q Consensus 218 ~IaaAALylAar~~g~~~t~~eIa~v~~Vse~TIrkR~kE~~ 259 (565)
-|..|++=|.....=.++|+++|++.+||+.+|.=..|+...
T Consensus 7 ~I~~a~~~Ll~~k~~~~ITV~~I~~~AgvsR~TFY~hF~dK~ 48 (176)
T TIGR02366 7 KIAKAFKDLMEVQAFSKISVSDIMSTAQIRRQTFYNHFQDKY 48 (176)
T ss_pred HHHHHHHHHHHHCCCccCCHHHHHHHhCCCHHHHHHHCCCHH
Confidence 366666656554333469999999999999999887765443
No 480
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=29.21 E-value=56 Score=31.45 Aligned_cols=44 Identities=16% Similarity=0.317 Sum_probs=33.2
Q ss_pred cCCCCCHhHHHHHhccCHH---------------HHHHHHHHHHccCCCCCCHHHHHHH
Q 008455 231 HGLKFSKSDIVKIVHICEA---------------TLMKRLIEFENTDSGSLTIEDFMAR 274 (565)
Q Consensus 231 ~g~~~t~~eIa~v~~Vse~---------------TIrkR~kE~~~t~s~~Lt~~~f~~~ 274 (565)
..+.+||+++|+.+|||.. |+++-|+-|.+....++|....|..
T Consensus 15 k~LGitQ~dLA~~aGVSQ~~IArlE~G~vdPrlSt~k~Il~aL~e~e~~~ita~~iM~s 73 (187)
T COG3620 15 KELGITQKDLARRAGVSQPYIARLEAGKVDPRLSTVKRILEALEEAEKTRITAKTIMHS 73 (187)
T ss_pred HHcCCCHHHHHHHcCccHHHHHHHhcCCCCccHHHHHHHHHHHHHhhcceEeHhhhccC
Confidence 4567899999999999874 6666777777777777777777654
No 481
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=29.20 E-value=48 Score=31.59 Aligned_cols=27 Identities=15% Similarity=0.206 Sum_probs=23.7
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHHH
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEFE 259 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~~ 259 (565)
...|.++||..+|+|+.||+.|+.--.
T Consensus 146 ~g~s~~EIA~~lgis~~tV~~~l~Rar 172 (191)
T PRK12520 146 LELETEEICQELQITATNAWVLLYRAR 172 (191)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 358999999999999999999986555
No 482
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=29.18 E-value=48 Score=32.15 Aligned_cols=27 Identities=19% Similarity=0.180 Sum_probs=23.0
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHHH
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEFE 259 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~~ 259 (565)
...|.++||..+|+++.||+.|+.--.
T Consensus 154 eg~s~~EIA~~lgis~~tVk~~l~RAr 180 (201)
T PRK12545 154 LDFEIDDICTELTLTANHCSVLLYRAR 180 (201)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 567899999999999999998876443
No 483
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=29.15 E-value=38 Score=35.17 Aligned_cols=22 Identities=14% Similarity=0.253 Sum_probs=20.6
Q ss_pred CCHhHHHHHhccCHHHHHHHHH
Q 008455 235 FSKSDIVKIVHICEATLMKRLI 256 (565)
Q Consensus 235 ~t~~eIa~v~~Vse~TIrkR~k 256 (565)
.|++|||+.+|||.+|+++.|+
T Consensus 2 ~ti~dIA~~aGVS~~TVSrvLn 23 (343)
T PRK10727 2 ATIKDVARLAGVSVATVSRVIN 23 (343)
T ss_pred CCHHHHHHHhCCCHHHHHHHhC
Confidence 4899999999999999999995
No 484
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=29.14 E-value=2.5e+02 Score=28.63 Aligned_cols=42 Identities=14% Similarity=0.072 Sum_probs=32.7
Q ss_pred hhHHHHHHHHHHHHhcCCCccHHHHHhhhccChHHHHHHHHH
Q 008455 115 TEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQ 156 (565)
Q Consensus 115 ~~~vaAACLYiACR~e~~p~tL~DIa~~~~vsv~~Lgr~~~~ 156 (565)
...+..++-||.-....-.+++.+||..+++++..|.+.|++
T Consensus 196 ~~~l~~~~~~I~~~l~~~~ls~~~lA~~~giS~r~L~r~Fk~ 237 (302)
T PRK09685 196 ERQFQKVVALIDQSIQEEILRPEWIAGELGISVRSLYRLFAE 237 (302)
T ss_pred HHHHHHHHHHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 344556677777665555589999999999999999998863
No 485
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=29.10 E-value=40 Score=35.08 Aligned_cols=22 Identities=18% Similarity=0.246 Sum_probs=20.7
Q ss_pred CCHhHHHHHhccCHHHHHHHHH
Q 008455 235 FSKSDIVKIVHICEATLMKRLI 256 (565)
Q Consensus 235 ~t~~eIa~v~~Vse~TIrkR~k 256 (565)
.|++|||+.+|||.+|+++.|+
T Consensus 2 ~ti~dIA~~aGVS~~TVSrvLn 23 (346)
T PRK10401 2 ITIRDVARQAGVSVATVSRVLN 23 (346)
T ss_pred CCHHHHHHHhCCCHHHHHHHHC
Confidence 5899999999999999999996
No 486
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=29.06 E-value=86 Score=23.30 Aligned_cols=26 Identities=8% Similarity=0.004 Sum_probs=24.1
Q ss_pred cHHHHHhhhccChHHHHHHHHHHHHH
Q 008455 135 LLIDFSNYLNINVYELGAVYLQLCQV 160 (565)
Q Consensus 135 tL~DIa~~~~vsv~~Lgr~~~~L~~~ 160 (565)
+..++|+.++++..++.+.+..|.+.
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~L~~~ 47 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSRLEAE 47 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 89999999999999999999999873
No 487
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=28.93 E-value=50 Score=29.95 Aligned_cols=26 Identities=19% Similarity=0.342 Sum_probs=23.0
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHH
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~ 258 (565)
...|.++||..+|+++.||+.++.-.
T Consensus 120 ~g~s~~eIA~~lgis~~tv~~~l~Ra 145 (154)
T TIGR02950 120 KEFSYKEIAELLNLSLAKVKSNLFRA 145 (154)
T ss_pred ccCcHHHHHHHHCCCHHHHHHHHHHH
Confidence 57899999999999999999988644
No 488
>PRK00149 dnaA chromosomal replication initiation protein; Reviewed
Probab=28.92 E-value=1e+02 Score=34.02 Aligned_cols=71 Identities=17% Similarity=0.217 Sum_probs=47.7
Q ss_pred hHHHHHHHHHHHHHHhCccccCCchhHHHH--HHHHHHHHhcCCCccHHHHHhhh-ccChHHHHHHHHHHHHHhhc
Q 008455 91 DEIVHVAKRFYGIAVARNFTKGRRTEQVQA--SCLYLACRQKSKPFLLIDFSNYL-NINVYELGAVYLQLCQVLYI 163 (565)
Q Consensus 91 ~~i~e~A~~iyk~a~~~~~~rGR~~~~vaA--ACLYiACR~e~~p~tL~DIa~~~-~vsv~~Lgr~~~~L~~~L~i 163 (565)
+.|++....+|..-.+.=..++|+...+.| .+.|++-+..+ .++.+|+..+ +-+..++.++++++.+.+..
T Consensus 360 ~~i~~~v~~~~~i~~~~l~~~~R~~~~~~aR~iamyl~~~~~~--~s~~~Ig~~fg~rdhstV~~a~~~i~~~~~~ 433 (450)
T PRK00149 360 ENIQKVVAEYYNIKVSDLKSKSRTRNIARPRQIAMYLAKELTD--LSLPEIGRAFGGRDHTTVLHAVRKIEKLLEE 433 (450)
T ss_pred HHHHHHHHHHcCCCHHHHhCCCCCcccChHHHHHHHHHHHhcC--CCHHHHHHHcCCCCHhHHHHHHHHHHHHHHh
Confidence 455555555555433322334455444444 56777766555 5899999999 59999999999999997753
No 489
>PRK09978 DNA-binding transcriptional regulator GadX; Provisional
Probab=28.89 E-value=3.2e+02 Score=28.44 Aligned_cols=52 Identities=12% Similarity=0.140 Sum_probs=40.1
Q ss_pred hhHHHHHHHHHHHHhcCCCCCHhHHHHHhccCHHHHHHHHHHHHccCCCCCCHHHHHHH
Q 008455 216 PSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMAR 274 (565)
Q Consensus 216 P~~IaaAALylAar~~g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t~s~~Lt~~~f~~~ 274 (565)
|.-+.-+.-||-.... .+.++.+||..+|+|..++.+.+++. ..|+.+|...
T Consensus 141 ~~~~~~v~~yI~~~~~-~~lsl~~lA~~~g~S~~~L~R~Fk~~------G~S~~~yl~~ 192 (274)
T PRK09978 141 PNMRTRVCTVINNNIA-HEWTLARIASELLMSPSLLKKKLREE------ETSYSQLLTE 192 (274)
T ss_pred HHHHHHHHHHHHhccc-CCCCHHHHHHHHCcCHHHHHHHHHhc------CCCHHHHHHH
Confidence 4445556667766655 48999999999999999999998752 2788888654
No 490
>PRK09480 slmA division inhibitor protein; Provisional
Probab=28.89 E-value=66 Score=30.23 Aligned_cols=44 Identities=14% Similarity=0.197 Sum_probs=31.7
Q ss_pred CChhHHHHHHHHHHHHhcCCCCCHhHHHHHhccCHHHHHHHHHH
Q 008455 214 RKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIE 257 (565)
Q Consensus 214 R~P~~IaaAALylAar~~g~~~t~~eIa~v~~Vse~TIrkR~kE 257 (565)
.+..-|.-|++-+...-.|...|+++||+.+||+..||-..++-
T Consensus 10 ~~r~~Il~aa~~l~~~~~G~~~ti~~Ia~~agvs~gt~Y~~F~~ 53 (194)
T PRK09480 10 ERREQILQALAQMLESPPGERITTAKLAARVGVSEAALYRHFPS 53 (194)
T ss_pred hHHHHHHHHHHHHHHhcCCCccCHHHHHHHhCCCHhHHHHHCCC
Confidence 33444555655554444467899999999999999999877653
No 491
>PF05930 Phage_AlpA: Prophage CP4-57 regulatory protein (AlpA); InterPro: IPR010260 This entry is represents phage P4, Orf88. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. In Escherichia coli phage P4 Orf 88 is similar to AlpA of the CP4-57 cryptic prophage []. AlpA acts as a positive transcriptional regulator of slpA, a gene linked to alpA and necessary for suppression of lon mutants [, ]. The sequence of slpA suggests that it encodes an integrase gene closely related to phage P4 int and that both alpA and slpA are part of a cryptic P4-like prophage. Increase in alpA expression increases SlpA synthesis. Increased SlpA leads, in turn, to the excision and loss of the cryptic prophage. ; PDB: 1Z4H_A.
Probab=28.88 E-value=57 Score=24.64 Aligned_cols=22 Identities=5% Similarity=0.321 Sum_probs=18.1
Q ss_pred CCHhHHHHHhccCHHHHHHHHH
Q 008455 235 FSKSDIVKIVHICEATLMKRLI 256 (565)
Q Consensus 235 ~t~~eIa~v~~Vse~TIrkR~k 256 (565)
++.++|+..+|+|..||.+..+
T Consensus 4 l~~~ev~~~~g~s~~ti~~~~k 25 (51)
T PF05930_consen 4 LRIKEVAELLGVSRSTIYRLIK 25 (51)
T ss_dssp E-HHHHHHHHSS-HHHHHHHHH
T ss_pred ccHHHHHHHHCCCHHHHHHHHh
Confidence 4688999999999999988877
No 492
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=28.86 E-value=91 Score=29.29 Aligned_cols=39 Identities=21% Similarity=0.228 Sum_probs=32.2
Q ss_pred HHHHHHHHhcCCCCCHhHHHHHhccCHHHHHHHHHHHHcc
Q 008455 222 AALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (565)
Q Consensus 222 AALylAar~~g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t 261 (565)
+.+|||.. .+..++.++||+..+|+..-++|-+..+...
T Consensus 13 ~L~~LA~~-~~~~~s~~eIA~~~~is~~~L~kIl~~L~~a 51 (153)
T PRK11920 13 MLMYCAAN-DGKLSRIPEIARAYGVSELFLFKILQPLVEA 51 (153)
T ss_pred HHHHHHhC-CCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 55677743 4556899999999999999999999998754
No 493
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=28.85 E-value=63 Score=32.40 Aligned_cols=31 Identities=19% Similarity=0.250 Sum_probs=27.4
Q ss_pred cCCCCCHhHHHHHhccCHHHHHHHHHHHHcc
Q 008455 231 HGLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (565)
Q Consensus 231 ~g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t 261 (565)
....+|+.++++.++++..|+.++++.|.+-
T Consensus 18 ~~~~IS~~eLA~~L~iS~~Tvsr~Lk~LEe~ 48 (217)
T PRK14165 18 NTVKISSSEFANHTGTSSKTAARILKQLEDE 48 (217)
T ss_pred CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 3456899999999999999999999999754
No 494
>PRK12366 replication factor A; Reviewed
Probab=28.81 E-value=27 Score=40.53 Aligned_cols=24 Identities=33% Similarity=0.948 Sum_probs=19.6
Q ss_pred CCCCCCCCCceeccCCCceecCcccce
Q 008455 3 WCSSCARHVTGHRPYDSQLCCDRCGKV 29 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt~CG~V 29 (565)
.||.|+...+ + ..|.+.|..||.+
T Consensus 534 aCp~CnkKv~--~-~~g~~~C~~c~~~ 557 (637)
T PRK12366 534 LCPNCRKRVE--E-VDGEYICEFCGEV 557 (637)
T ss_pred cccccCeEeE--c-CCCcEECCCCCCC
Confidence 5999987632 2 4799999999998
No 495
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=28.75 E-value=51 Score=32.69 Aligned_cols=26 Identities=4% Similarity=0.142 Sum_probs=22.6
Q ss_pred CCCCHhHHHHHhccCHHHHHHHHHHH
Q 008455 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (565)
Q Consensus 233 ~~~t~~eIa~v~~Vse~TIrkR~kE~ 258 (565)
...|.++||..+|||+.||++++.--
T Consensus 197 eg~s~~EIA~~lgis~~tVk~~~~rA 222 (234)
T PRK08301 197 EEKTQKEVADMLGISQSYISRLEKRI 222 (234)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 47899999999999999999887543
No 496
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=28.71 E-value=1e+02 Score=27.64 Aligned_cols=32 Identities=6% Similarity=0.086 Sum_probs=27.3
Q ss_pred hcCCCCCHhHHHHHhccCHHHHHHHHHHHHcc
Q 008455 230 THGLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (565)
Q Consensus 230 ~~g~~~t~~eIa~v~~Vse~TIrkR~kE~~~t 261 (565)
...-..|+.+||...||+..||.+-.+.|..-
T Consensus 25 ~~~~g~sv~evA~e~gIs~~tl~~W~r~y~~~ 56 (121)
T PRK09413 25 SFEPGMTVSLVARQHGVAASQLFLWRKQYQEG 56 (121)
T ss_pred HHcCCCCHHHHHHHHCcCHHHHHHHHHHHhhc
Confidence 34457899999999999999999999998753
No 497
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=28.67 E-value=35 Score=35.16 Aligned_cols=22 Identities=23% Similarity=0.116 Sum_probs=20.6
Q ss_pred CCHhHHHHHhccCHHHHHHHHH
Q 008455 235 FSKSDIVKIVHICEATLMKRLI 256 (565)
Q Consensus 235 ~t~~eIa~v~~Vse~TIrkR~k 256 (565)
.|++|||+.+|||.+|+++.|+
T Consensus 2 ~ti~dIA~~agVS~~TVSrvln 23 (327)
T PRK10339 2 ATLKDIAIEAGVSLATVSRVLN 23 (327)
T ss_pred CCHHHHHHHhCCCHHhhhhhhc
Confidence 4899999999999999999995
No 498
>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=28.44 E-value=1.5e+02 Score=26.46 Aligned_cols=42 Identities=24% Similarity=0.101 Sum_probs=31.4
Q ss_pred HHHHHHHHHHhcC-CCCCHhHHHHHhccCHHHHHHHHHHHHcc
Q 008455 220 CGAALYVSALTHG-LKFSKSDIVKIVHICEATLMKRLIEFENT 261 (565)
Q Consensus 220 aaAALylAar~~g-~~~t~~eIa~v~~Vse~TIrkR~kE~~~t 261 (565)
|-.++++-++..+ -..|..+|+..++++..++++-+..+...
T Consensus 10 al~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~~~ 52 (132)
T TIGR00738 10 ALRALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRRA 52 (132)
T ss_pred HHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 3334443344333 37899999999999999999999998753
No 499
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=28.40 E-value=31 Score=23.91 Aligned_cols=22 Identities=23% Similarity=0.333 Sum_probs=11.2
Q ss_pred CCCCCCCCCceeccCCCceecC
Q 008455 3 WCSSCARHVTGHRPYDSQLCCD 24 (565)
Q Consensus 3 ~Cp~Cgs~~i~~D~~~G~~VCt 24 (565)
+|..||.-..+.+...|.++|-
T Consensus 6 kC~~CGniv~v~~~~~~~l~Cc 27 (34)
T cd00974 6 KCEICGNIVEVLNVGGGTLVCC 27 (34)
T ss_pred EcCCCCcEEEEEECCCcceeec
Confidence 3566665444444445555553
No 500
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=28.29 E-value=43 Score=26.31 Aligned_cols=24 Identities=17% Similarity=0.098 Sum_probs=21.3
Q ss_pred CHhHHHHHhccCHHHHHHHHHHHH
Q 008455 236 SKSDIVKIVHICEATLMKRLIEFE 259 (565)
Q Consensus 236 t~~eIa~v~~Vse~TIrkR~kE~~ 259 (565)
|..|||+.+||+..|||.--+++.
T Consensus 2 ti~eva~~~gvs~~tlr~y~~~gl 25 (69)
T PF13411_consen 2 TIKEVAKLLGVSPSTLRYYEREGL 25 (69)
T ss_dssp EHHHHHHHTTTTHHHHHHHHHTTS
T ss_pred cHHHHHHHHCcCHHHHHHHHHhcC
Confidence 578999999999999998877765
Done!