Query 046187
Match_columns 510
No_of_seqs 246 out of 1067
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 09:31:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046187.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046187hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1597 Transcription initiati 100.0 9.4E-76 2E-80 581.3 28.4 307 1-337 1-308 (308)
2 PRK00423 tfb transcription ini 100.0 4.3E-64 9.3E-69 513.7 31.6 294 1-320 12-308 (310)
3 COG1405 SUA7 Transcription ini 100.0 4.8E-57 1E-61 455.5 28.5 281 1-320 2-283 (285)
4 KOG1598 Transcription initiati 100.0 4.2E-40 9.1E-45 348.8 16.8 252 1-321 1-259 (521)
5 PF00382 TFIIB: Transcription 99.7 3.7E-17 8.1E-22 132.8 9.9 71 139-209 1-71 (71)
6 KOG0835 Cyclin L [General func 99.7 2.7E-15 5.8E-20 152.2 17.5 182 135-318 26-231 (367)
7 PF00382 TFIIB: Transcription 99.6 6.5E-16 1.4E-20 125.6 9.7 71 235-305 1-71 (71)
8 KOG0834 CDK9 kinase-activating 99.6 6.6E-15 1.4E-19 151.5 17.7 184 133-318 40-247 (323)
9 TIGR00569 ccl1 cyclin ccl1. Un 99.6 9.5E-14 2.1E-18 142.5 19.9 168 130-300 52-234 (305)
10 COG5333 CCL1 Cdk activating ki 99.4 2.4E-12 5.2E-17 130.4 13.2 154 135-290 48-211 (297)
11 PRK00423 tfb transcription ini 99.4 1.5E-12 3.2E-17 134.0 11.8 88 137-224 221-308 (310)
12 PF08271 TF_Zn_Ribbon: TFIIB z 99.4 1.4E-13 3E-18 102.1 0.6 43 1-46 1-43 (43)
13 KOG0794 CDK8 kinase-activating 99.2 2.9E-10 6.2E-15 111.3 13.8 175 137-314 46-236 (264)
14 cd00043 CYCLIN Cyclin box fold 99.0 2.2E-09 4.8E-14 86.7 10.3 84 230-313 4-88 (88)
15 smart00385 CYCLIN domain prese 99.0 2.1E-09 4.5E-14 86.1 9.5 81 233-313 1-82 (83)
16 cd00043 CYCLIN Cyclin box fold 99.0 4.2E-09 9.1E-14 85.1 11.2 82 135-216 5-87 (88)
17 smart00385 CYCLIN domain prese 99.0 3.5E-09 7.6E-14 84.8 9.3 79 139-217 3-82 (83)
18 COG1405 SUA7 Transcription ini 98.9 6.1E-09 1.3E-13 106.3 11.4 92 231-322 100-191 (285)
19 KOG1597 Transcription initiati 98.8 2.5E-08 5.5E-13 100.8 9.3 85 138-222 206-290 (308)
20 KOG0656 G1/S-specific cyclin D 98.5 5.3E-06 1.2E-10 86.3 18.7 176 133-310 79-268 (335)
21 KOG2496 Cdk activating kinase 98.1 3.6E-05 7.7E-10 78.7 13.6 145 138-282 62-219 (325)
22 PF00134 Cyclin_N: Cyclin, N-t 98.0 0.0001 2.2E-09 64.8 11.5 89 135-223 34-125 (127)
23 KOG0653 Cyclin B and related k 97.9 8E-05 1.7E-09 79.5 12.2 149 138-288 164-316 (391)
24 PF02984 Cyclin_C: Cyclin, C-t 97.9 7.3E-05 1.6E-09 64.5 8.7 90 230-319 2-92 (118)
25 KOG1598 Transcription initiati 97.8 2.5E-05 5.3E-10 84.9 5.2 79 147-225 179-259 (521)
26 PF01857 RB_B: Retinoblastoma- 97.7 0.00018 3.9E-09 66.3 9.1 70 135-204 14-85 (135)
27 COG5024 Cyclin [Cell division 97.7 0.00035 7.5E-09 75.4 11.6 176 141-319 222-402 (440)
28 KOG4557 Origin recognition com 97.6 0.0032 6.9E-08 61.9 16.2 171 139-317 3-182 (262)
29 KOG0655 G1/S-specific cyclin E 96.3 0.079 1.7E-06 55.4 13.4 170 139-318 152-337 (408)
30 KOG0835 Cyclin L [General func 96.2 0.03 6.4E-07 58.4 9.7 102 136-242 142-246 (367)
31 PF00134 Cyclin_N: Cyclin, N-t 95.7 0.096 2.1E-06 45.9 9.8 86 231-316 34-122 (127)
32 TIGR02393 RpoD_Cterm RNA polym 95.6 2 4.4E-05 42.4 19.8 125 189-320 100-228 (238)
33 TIGR00569 ccl1 cyclin ccl1. Un 95.2 0.11 2.3E-06 54.2 9.4 70 232-301 60-131 (305)
34 PF02984 Cyclin_C: Cyclin, C-t 94.7 0.16 3.4E-06 43.6 7.8 73 149-221 17-90 (118)
35 PF01857 RB_B: Retinoblastoma- 94.3 0.17 3.8E-06 46.7 7.5 69 232-300 15-85 (135)
36 TIGR01206 lysW lysine biosynth 94.2 0.025 5.5E-07 44.3 1.6 30 2-33 4-33 (54)
37 PRK05657 RNA polymerase sigma 94.0 5.9 0.00013 41.5 19.3 189 124-320 83-314 (325)
38 PRK07405 RNA polymerase sigma 93.8 6.4 0.00014 41.1 18.9 181 128-316 82-304 (317)
39 PRK09210 RNA polymerase sigma 93.7 6 0.00013 42.1 18.9 186 125-318 127-355 (367)
40 KOG0834 CDK9 kinase-activating 93.4 0.2 4.4E-06 52.6 7.1 85 232-316 43-131 (323)
41 PF11781 RRN7: RNA polymerase 93.3 0.046 1E-06 39.4 1.5 28 1-33 9-36 (36)
42 PRK05911 RNA polymerase sigma 93.1 11 0.00023 38.0 20.9 32 287-318 220-251 (257)
43 TIGR02394 rpoS_proteo RNA poly 93.1 7.7 0.00017 39.5 17.9 35 287-321 241-275 (285)
44 PRK05901 RNA polymerase sigma 92.7 8.2 0.00018 43.1 18.5 181 128-318 272-497 (509)
45 TIGR02997 Sig70-cyanoRpoD RNA 92.4 10 0.00022 38.9 17.9 180 128-315 75-296 (298)
46 PRK05949 RNA polymerase sigma 92.1 13 0.00028 39.0 18.4 180 129-316 93-314 (327)
47 PHA00626 hypothetical protein 91.8 0.1 2.2E-06 41.2 1.7 30 1-32 1-33 (59)
48 PF08613 Cyclin: Cyclin; Inte 91.7 2.7 5.9E-05 38.9 11.4 89 229-317 52-146 (149)
49 PRK07921 RNA polymerase sigma 91.4 15 0.00032 38.6 17.9 183 128-317 87-311 (324)
50 TIGR02392 rpoH_proteo alternat 91.4 17 0.00038 36.7 19.3 186 125-318 33-266 (270)
51 PRK00464 nrdR transcriptional 91.4 0.11 2.4E-06 49.0 1.9 32 1-32 1-38 (154)
52 PRK07406 RNA polymerase sigma 91.2 22 0.00047 38.2 19.2 183 128-318 137-361 (373)
53 PRK00415 rps27e 30S ribosomal 91.0 0.089 1.9E-06 42.0 0.7 30 2-34 13-42 (59)
54 COG2051 RPS27A Ribosomal prote 90.9 0.09 2E-06 42.8 0.7 30 2-34 21-50 (67)
55 PF13248 zf-ribbon_3: zinc-rib 90.9 0.13 2.8E-06 34.2 1.3 22 1-30 3-24 (26)
56 COG5333 CCL1 Cdk activating ki 90.7 0.54 1.2E-05 48.8 6.2 87 232-318 49-143 (297)
57 PRK07408 RNA polymerase sigma 90.4 21 0.00046 35.9 17.3 186 124-320 22-251 (256)
58 KOG1010 Rb (Retinoblastoma tum 90.2 0.52 1.1E-05 54.6 6.2 69 135-203 680-750 (920)
59 PRK07598 RNA polymerase sigma 90.1 25 0.00053 38.5 18.5 180 128-316 176-398 (415)
60 PF08613 Cyclin: Cyclin; Inte 89.9 4.3 9.4E-05 37.6 11.1 85 139-223 58-148 (149)
61 TIGR00244 transcriptional regu 89.8 0.2 4.4E-06 46.9 2.1 32 1-32 1-38 (147)
62 COG1191 FliA DNA-directed RNA 89.2 28 0.00061 35.5 18.6 70 131-200 27-110 (247)
63 PTZ00083 40S ribosomal protein 89.0 0.2 4.4E-06 42.7 1.4 30 2-34 37-66 (85)
64 PF01667 Ribosomal_S27e: Ribos 88.8 0.15 3.2E-06 40.2 0.4 30 2-34 9-38 (55)
65 PF13240 zinc_ribbon_2: zinc-r 88.5 0.25 5.5E-06 32.1 1.3 22 2-31 1-22 (23)
66 KOG4164 Cyclin ik3-1/CABLES [C 88.5 1.1 2.4E-05 48.0 6.6 85 138-222 388-477 (497)
67 PF05460 ORC6: Origin recognit 88.0 0.15 3.4E-06 54.0 0.0 78 147-224 11-89 (353)
68 TIGR02098 MJ0042_CXXC MJ0042 f 87.8 0.21 4.5E-06 35.7 0.6 30 2-33 4-36 (38)
69 PLN00209 ribosomal protein S27 87.6 0.22 4.8E-06 42.5 0.7 30 2-34 38-67 (86)
70 PRK00420 hypothetical protein; 87.1 0.36 7.8E-06 43.4 1.8 26 2-32 25-50 (112)
71 PF13613 HTH_Tnp_4: Helix-turn 86.8 1.1 2.4E-05 34.4 4.2 43 279-321 10-52 (53)
72 PRK07500 rpoH2 RNA polymerase 86.8 40 0.00088 34.6 18.8 191 125-320 38-277 (289)
73 TIGR02885 spore_sigF RNA polym 86.6 33 0.00072 33.5 18.7 31 287-317 198-228 (231)
74 PRK07670 RNA polymerase sigma 86.6 36 0.00078 33.9 21.4 32 287-318 216-247 (251)
75 PF10571 UPF0547: Uncharacteri 86.6 0.38 8.3E-06 32.3 1.3 24 2-33 2-25 (26)
76 KOG4557 Origin recognition com 86.5 2 4.4E-05 42.7 6.8 82 138-220 95-181 (262)
77 PRK06288 RNA polymerase sigma 86.2 40 0.00087 34.0 19.8 29 287-315 227-255 (268)
78 PF14803 Nudix_N_2: Nudix N-te 86.1 0.36 7.9E-06 34.4 1.0 29 2-32 2-32 (34)
79 PF04545 Sigma70_r4: Sigma-70, 86.0 2.2 4.7E-05 32.0 5.4 32 285-316 17-48 (50)
80 PRK00432 30S ribosomal protein 85.3 0.55 1.2E-05 36.2 1.8 26 2-32 22-47 (50)
81 PRK08215 sporulation sigma fac 85.2 43 0.00094 33.5 20.3 31 287-317 224-254 (258)
82 COG1998 RPS31 Ribosomal protei 84.8 0.53 1.2E-05 36.3 1.5 26 2-31 21-46 (51)
83 KOG0654 G2/Mitotic-specific cy 84.6 6.1 0.00013 42.2 9.8 135 177-313 182-320 (359)
84 PF13730 HTH_36: Helix-turn-he 84.5 2.4 5.2E-05 32.1 5.1 26 290-315 27-52 (55)
85 PF09538 FYDLN_acid: Protein o 84.3 0.56 1.2E-05 41.9 1.6 29 2-35 11-39 (108)
86 COG1645 Uncharacterized Zn-fin 84.0 0.57 1.2E-05 43.2 1.6 25 2-32 30-55 (131)
87 PF03966 Trm112p: Trm112p-like 84.0 0.59 1.3E-05 37.9 1.5 17 14-32 47-63 (68)
88 PF08792 A2L_zn_ribbon: A2L zi 83.6 0.65 1.4E-05 32.9 1.4 27 2-32 5-31 (33)
89 smart00342 HTH_ARAC helix_turn 83.6 12 0.00026 29.4 9.1 26 288-313 50-76 (84)
90 PF13404 HTH_AsnC-type: AsnC-t 83.5 2.8 6.1E-05 31.0 4.8 28 286-313 15-42 (42)
91 smart00661 RPOL9 RNA polymeras 83.5 0.77 1.7E-05 34.7 1.9 29 2-33 2-31 (52)
92 PF01325 Fe_dep_repress: Iron 83.3 3 6.6E-05 33.1 5.3 38 277-315 12-49 (60)
93 PRK11827 hypothetical protein; 83.1 0.75 1.6E-05 36.9 1.7 28 1-32 9-36 (60)
94 PRK05658 RNA polymerase sigma 83.0 68 0.0015 36.6 18.0 178 130-318 383-606 (619)
95 PF13412 HTH_24: Winged helix- 82.8 3.1 6.8E-05 30.8 5.0 30 286-315 15-44 (48)
96 PF08279 HTH_11: HTH domain; 82.7 3 6.4E-05 31.6 4.9 31 286-316 13-43 (55)
97 KOG2496 Cdk activating kinase 82.6 6.6 0.00014 41.0 8.7 69 231-299 59-129 (325)
98 TIGR02479 FliA_WhiG RNA polyme 82.2 51 0.0011 32.0 16.8 31 287-317 190-220 (224)
99 TIGR02850 spore_sigG RNA polym 81.7 59 0.0013 32.4 19.8 31 287-317 221-251 (254)
100 PRK00135 scpB segregation and 81.5 36 0.00079 33.2 13.0 110 174-302 5-118 (188)
101 PF13384 HTH_23: Homeodomain-l 81.0 2.5 5.4E-05 31.4 3.9 27 288-314 17-43 (50)
102 smart00342 HTH_ARAC helix_turn 80.6 8 0.00017 30.4 7.0 71 139-216 4-75 (84)
103 COG1327 Predicted transcriptio 80.6 1 2.2E-05 42.5 1.9 31 1-31 1-37 (156)
104 PF13936 HTH_38: Helix-turn-he 80.3 2.8 6.2E-05 31.1 3.9 29 282-310 14-42 (44)
105 PF13542 HTH_Tnp_ISL3: Helix-t 80.3 5.1 0.00011 30.0 5.4 30 283-312 22-51 (52)
106 KOG0794 CDK8 kinase-activating 80.0 2.8 6E-05 42.3 4.8 57 232-288 45-101 (264)
107 KOG1010 Rb (Retinoblastoma tum 79.9 9 0.0002 44.9 9.4 121 138-261 37-166 (920)
108 cd00092 HTH_CRP helix_turn_hel 79.7 6.3 0.00014 30.5 6.0 30 286-315 23-52 (67)
109 TIGR02300 FYDLN_acid conserved 79.5 1.1 2.4E-05 41.1 1.7 29 2-35 11-39 (129)
110 TIGR02395 rpoN_sigma RNA polym 79.5 15 0.00033 40.1 10.8 75 139-218 116-208 (429)
111 smart00421 HTH_LUXR helix_turn 79.1 4.1 8.9E-05 29.9 4.5 30 288-317 18-47 (58)
112 PF10668 Phage_terminase: Phag 79.0 4.3 9.3E-05 32.6 4.8 38 268-308 5-42 (60)
113 PF13545 HTH_Crp_2: Crp-like h 78.3 5.1 0.00011 32.0 5.2 30 287-316 27-56 (76)
114 PF00356 LacI: Bacterial regul 77.9 2.6 5.7E-05 31.8 3.1 21 290-310 1-21 (46)
115 PRK00398 rpoP DNA-directed RNA 77.4 1.3 2.7E-05 33.2 1.2 26 2-31 5-30 (46)
116 TIGR03697 NtcA_cyano global ni 77.3 13 0.00027 34.6 8.3 29 287-315 142-170 (193)
117 PRK07122 RNA polymerase sigma 76.4 91 0.002 31.5 18.0 33 286-318 229-261 (264)
118 smart00345 HTH_GNTR helix_turn 76.4 4.8 0.0001 30.1 4.3 29 287-315 18-47 (60)
119 PF00196 GerE: Bacterial regul 76.2 3.8 8.3E-05 31.6 3.7 33 286-318 16-48 (58)
120 PF02150 RNA_POL_M_15KD: RNA p 75.0 1.3 2.8E-05 31.6 0.7 29 2-33 3-31 (35)
121 PRK06596 RNA polymerase factor 74.7 1.1E+02 0.0023 31.5 20.2 187 124-318 45-278 (284)
122 PF02796 HTH_7: Helix-turn-hel 74.7 2.2 4.7E-05 31.7 1.9 29 281-309 14-42 (45)
123 PF04967 HTH_10: HTH DNA bindi 74.5 10 0.00022 29.6 5.7 28 288-315 23-50 (53)
124 PF08220 HTH_DeoR: DeoR-like h 74.2 4.1 8.9E-05 31.8 3.4 29 287-315 13-41 (57)
125 TIGR03879 near_KaiC_dom probab 73.7 4.2 9E-05 33.9 3.5 27 287-313 31-57 (73)
126 smart00778 Prim_Zn_Ribbon Zinc 73.2 2.8 6E-05 30.5 2.0 27 2-30 5-33 (37)
127 cd06170 LuxR_C_like C-terminal 73.1 8.8 0.00019 28.3 5.0 32 287-318 14-45 (57)
128 PRK14892 putative transcriptio 73.0 1.8 3.9E-05 38.1 1.2 31 2-34 23-54 (99)
129 TIGR02010 IscR iron-sulfur clu 72.9 8 0.00017 35.1 5.5 46 174-219 7-52 (135)
130 PRK12286 rpmF 50S ribosomal pr 72.3 2.3 4.9E-05 33.8 1.6 26 2-36 29-54 (57)
131 PF08281 Sigma70_r4_2: Sigma-7 72.0 6 0.00013 29.8 3.8 30 286-315 24-53 (54)
132 smart00419 HTH_CRP helix_turn_ 71.9 6.5 0.00014 28.3 3.9 30 286-315 6-35 (48)
133 PF00392 GntR: Bacterial regul 71.8 5.8 0.00013 31.2 3.8 30 286-315 21-51 (64)
134 PRK11169 leucine-responsive tr 71.6 6.2 0.00014 37.0 4.7 32 286-317 26-57 (164)
135 PF08274 PhnA_Zn_Ribbon: PhnA 71.5 2.1 4.6E-05 29.7 1.1 25 2-31 4-28 (30)
136 PF00325 Crp: Bacterial regula 71.4 6.4 0.00014 27.8 3.5 28 288-315 2-29 (32)
137 PF05129 Elf1: Transcription e 71.4 1.9 4.1E-05 36.5 1.0 34 2-35 24-59 (81)
138 COG1326 Uncharacterized archae 71.1 1.8 3.9E-05 42.3 0.9 33 1-34 7-42 (201)
139 TIGR02443 conserved hypothetic 71.1 2.1 4.5E-05 34.3 1.1 30 2-31 11-40 (59)
140 PF08279 HTH_11: HTH domain; 71.0 9.4 0.0002 28.8 4.7 35 186-220 9-43 (55)
141 TIGR01384 TFS_arch transcripti 71.0 2.4 5.2E-05 36.8 1.6 28 1-34 1-28 (104)
142 PF01022 HTH_5: Bacterial regu 70.4 10 0.00023 28.1 4.7 33 283-315 10-42 (47)
143 PRK11179 DNA-binding transcrip 70.2 8.4 0.00018 35.7 5.1 32 286-317 21-52 (153)
144 PF01371 Trp_repressor: Trp re 69.7 11 0.00024 32.4 5.3 31 284-314 45-75 (87)
145 PRK05932 RNA polymerase factor 69.6 58 0.0013 36.0 12.2 76 138-218 140-234 (455)
146 TIGR03697 NtcA_cyano global ni 69.6 18 0.0004 33.6 7.3 29 191-219 142-170 (193)
147 PF12802 MarR_2: MarR family; 69.4 10 0.00022 29.1 4.6 28 288-315 21-48 (62)
148 PF09526 DUF2387: Probable met 69.2 2.3 5.1E-05 35.2 1.1 30 2-31 10-39 (71)
149 PF02082 Rrf2: Transcriptional 69.2 7.7 0.00017 32.2 4.2 45 175-219 8-52 (83)
150 PF09297 zf-NADH-PPase: NADH p 69.0 2.3 5.1E-05 29.4 0.9 26 2-31 5-30 (32)
151 PRK12520 RNA polymerase sigma 68.9 4 8.8E-05 38.5 2.8 38 287-324 146-183 (191)
152 COG2835 Uncharacterized conser 68.8 2.7 5.8E-05 33.8 1.2 28 1-32 9-36 (60)
153 COG5216 Uncharacterized conser 68.5 2.2 4.7E-05 34.2 0.7 29 3-32 25-54 (67)
154 PRK04217 hypothetical protein; 68.2 6.2 0.00013 35.4 3.6 34 287-320 57-90 (110)
155 PF07282 OrfB_Zn_ribbon: Putat 68.1 3.2 6.9E-05 33.2 1.6 27 2-32 30-56 (69)
156 TIGR01610 phage_O_Nterm phage 67.5 37 0.0008 29.1 8.2 31 286-316 45-75 (95)
157 PRK14088 dnaA chromosomal repl 67.3 50 0.0011 36.1 11.1 51 264-316 362-415 (440)
158 PF01783 Ribosomal_L32p: Ribos 67.1 2.2 4.8E-05 33.5 0.5 22 2-32 28-49 (56)
159 TIGR00122 birA_repr_reg BirA b 66.7 13 0.00029 29.5 5.0 32 284-315 9-40 (69)
160 smart00834 CxxC_CXXC_SSSS Puta 66.5 2.7 5.9E-05 30.0 0.9 30 2-32 7-36 (41)
161 PF02082 Rrf2: Transcriptional 66.4 7.5 0.00016 32.3 3.6 38 278-315 15-52 (83)
162 COG1997 RPL43A Ribosomal prote 65.7 3.7 8E-05 35.4 1.6 27 2-32 37-63 (89)
163 PF00325 Crp: Bacterial regula 65.7 7.6 0.00016 27.4 2.9 28 192-219 2-29 (32)
164 PRK05572 sporulation sigma fac 65.2 1.5E+02 0.0033 29.5 20.0 33 287-319 217-249 (252)
165 TIGR02147 Fsuc_second hypothet 65.0 1.6E+02 0.0034 30.5 13.5 123 183-315 17-166 (271)
166 PRK10857 DNA-binding transcrip 64.5 15 0.00032 35.0 5.6 47 173-219 6-52 (164)
167 TIGR02980 SigBFG RNA polymeras 64.3 1.4E+02 0.0031 28.9 18.8 32 287-318 193-224 (227)
168 TIGR02943 Sig70_famx1 RNA poly 64.3 5.4 0.00012 37.9 2.6 40 287-326 146-185 (188)
169 PF13717 zinc_ribbon_4: zinc-r 64.3 3.6 7.7E-05 29.5 1.1 29 2-32 4-35 (36)
170 PRK12529 RNA polymerase sigma 64.0 10 0.00022 35.5 4.5 35 287-321 142-176 (178)
171 PRK10840 transcriptional regul 63.6 11 0.00024 35.8 4.7 33 286-318 163-195 (216)
172 TIGR02985 Sig70_bacteroi1 RNA 63.5 10 0.00022 33.8 4.2 32 287-318 128-159 (161)
173 PRK11014 transcriptional repre 63.4 10 0.00022 34.6 4.2 39 277-315 14-52 (141)
174 PF05344 DUF746: Domain of Unk 63.4 16 0.00035 29.9 4.7 41 283-323 8-48 (65)
175 PRK12427 flagellar biosynthesi 63.2 1.6E+02 0.0035 29.1 20.2 33 286-318 197-229 (231)
176 COG2888 Predicted Zn-ribbon RN 63.0 3.5 7.7E-05 33.1 0.9 8 23-30 51-58 (61)
177 TIGR01321 TrpR trp operon repr 63.0 9.1 0.0002 33.5 3.5 31 283-313 50-80 (94)
178 TIGR03655 anti_R_Lar restricti 63.0 4.4 9.5E-05 31.3 1.4 32 2-33 3-37 (53)
179 PF13545 HTH_Crp_2: Crp-like h 62.7 18 0.00039 28.8 5.1 29 191-219 27-55 (76)
180 TIGR01031 rpmF_bact ribosomal 62.6 4.6 0.0001 31.8 1.5 24 2-34 28-51 (55)
181 cd06171 Sigma70_r4 Sigma70, re 62.6 20 0.00043 25.5 4.9 30 287-316 25-54 (55)
182 PF04079 DUF387: Putative tran 62.5 82 0.0018 29.9 10.2 97 177-303 2-111 (159)
183 PRK11161 fumarate/nitrate redu 62.4 38 0.00082 32.8 8.2 32 287-318 183-214 (235)
184 PF14255 Cys_rich_CPXG: Cystei 62.2 3.9 8.4E-05 32.0 1.0 32 1-32 1-34 (52)
185 PRK12532 RNA polymerase sigma 62.1 6.9 0.00015 37.0 3.0 40 287-326 151-190 (195)
186 PRK12516 RNA polymerase sigma 61.9 7 0.00015 37.2 2.9 37 287-323 131-167 (187)
187 COG1510 Predicted transcriptio 61.9 26 0.00057 33.9 6.7 63 245-314 5-67 (177)
188 PRK12540 RNA polymerase sigma 61.5 12 0.00026 35.4 4.5 37 287-323 126-162 (182)
189 PRK13918 CRP/FNR family transc 61.3 40 0.00088 31.6 8.0 29 287-315 148-176 (202)
190 KOG2923 Uncharacterized conser 61.1 3.7 8E-05 33.4 0.7 29 3-32 25-54 (67)
191 KOG1779 40s ribosomal protein 61.1 2.8 6.1E-05 35.4 0.1 28 2-32 36-63 (84)
192 PF05225 HTH_psq: helix-turn-h 61.1 26 0.00057 26.2 5.3 27 285-312 14-40 (45)
193 PRK09047 RNA polymerase factor 60.9 8.5 0.00018 34.9 3.2 35 287-321 121-155 (161)
194 PF06044 DRP: Dam-replacing fa 60.7 3.5 7.6E-05 41.8 0.7 31 1-33 32-64 (254)
195 TIGR02937 sigma70-ECF RNA poly 60.6 16 0.00035 31.6 4.8 32 287-318 125-156 (158)
196 smart00344 HTH_ASNC helix_turn 60.6 18 0.00038 31.0 5.0 29 287-315 16-44 (108)
197 PF11023 DUF2614: Protein of u 60.2 2.9 6.3E-05 37.6 -0.0 37 2-47 71-107 (114)
198 cd07377 WHTH_GntR Winged helix 60.2 14 0.0003 28.1 3.9 26 290-315 27-52 (66)
199 cd00092 HTH_CRP helix_turn_hel 60.1 34 0.00074 26.3 6.1 31 189-219 22-52 (67)
200 COG2197 CitB Response regulato 60.1 13 0.00029 36.3 4.6 36 283-318 158-193 (211)
201 TIGR02859 spore_sigH RNA polym 59.9 12 0.00027 35.1 4.2 34 287-320 164-197 (198)
202 PRK12531 RNA polymerase sigma 59.9 9.8 0.00021 36.1 3.6 36 287-322 156-191 (194)
203 PRK15411 rcsA colanic acid cap 59.7 14 0.0003 35.9 4.6 32 287-318 151-182 (207)
204 PF06677 Auto_anti-p27: Sjogre 59.7 5.8 0.00013 29.5 1.5 23 2-29 19-41 (41)
205 cd06571 Bac_DnaA_C C-terminal 59.6 22 0.00048 30.1 5.3 41 276-318 34-75 (90)
206 PRK09642 RNA polymerase sigma 59.3 10 0.00022 34.6 3.4 34 287-320 121-154 (160)
207 smart00418 HTH_ARSR helix_turn 58.4 24 0.00051 26.1 4.8 30 286-315 8-37 (66)
208 PRK02935 hypothetical protein; 58.3 5.8 0.00013 35.4 1.5 36 2-46 72-107 (110)
209 cd06571 Bac_DnaA_C C-terminal 58.3 25 0.00054 29.8 5.4 43 179-223 33-76 (90)
210 PF08280 HTH_Mga: M protein tr 58.3 12 0.00027 29.2 3.3 31 287-317 18-48 (59)
211 PF08273 Prim_Zn_Ribbon: Zinc- 58.2 6.4 0.00014 29.1 1.5 28 2-31 5-35 (40)
212 TIGR00686 phnA alkylphosphonat 58.1 7.9 0.00017 34.6 2.4 25 2-31 4-28 (109)
213 PF12116 SpoIIID: Stage III sp 58.1 10 0.00023 32.2 2.9 30 280-309 11-40 (82)
214 PF05732 RepL: Firmicute plasm 58.0 22 0.00049 33.8 5.6 28 289-316 76-103 (165)
215 PF04161 Arv1: Arv1-like famil 57.7 5 0.00011 39.4 1.2 36 1-37 1-38 (208)
216 PRK06266 transcription initiat 57.5 3.6 7.8E-05 39.7 0.1 30 2-34 119-148 (178)
217 TIGR00738 rrf2_super rrf2 fami 57.5 24 0.00051 31.4 5.4 44 175-218 8-51 (132)
218 COG1594 RPB9 DNA-directed RNA 57.4 5 0.00011 36.0 1.0 33 1-35 3-35 (113)
219 PHA02591 hypothetical protein; 57.3 17 0.00038 30.8 4.1 29 282-310 53-81 (83)
220 PF01978 TrmB: Sugar-specific 57.1 15 0.00032 29.1 3.7 37 278-315 13-49 (68)
221 PRK11920 rirA iron-responsive 57.1 25 0.00055 32.8 5.7 45 174-219 7-51 (153)
222 PRK12547 RNA polymerase sigma 57.0 13 0.00028 34.2 3.8 34 287-320 127-160 (164)
223 PF13518 HTH_28: Helix-turn-he 56.7 23 0.00051 26.0 4.5 27 289-315 13-39 (52)
224 COG1522 Lrp Transcriptional re 56.7 20 0.00043 32.5 4.9 31 286-316 20-50 (154)
225 TIGR02999 Sig-70_X6 RNA polyme 56.7 13 0.00028 34.5 3.8 32 287-318 149-180 (183)
226 PRK09645 RNA polymerase sigma 56.6 15 0.00033 33.8 4.1 34 287-320 133-166 (173)
227 TIGR00281 segregation and cond 56.6 1.7E+02 0.0037 28.5 11.5 108 175-302 3-115 (186)
228 smart00420 HTH_DEOR helix_turn 56.5 31 0.00068 24.9 5.1 29 287-315 13-41 (53)
229 PRK13719 conjugal transfer tra 56.2 18 0.0004 36.2 4.8 33 286-318 156-188 (217)
230 TIGR00721 tfx DNA-binding prot 56.0 18 0.00039 33.7 4.4 33 286-318 19-51 (137)
231 PF10058 DUF2296: Predicted in 55.8 4.8 0.0001 31.6 0.5 28 1-30 23-52 (54)
232 PRK06759 RNA polymerase factor 55.7 18 0.00039 32.5 4.4 31 287-317 121-151 (154)
233 PF01325 Fe_dep_repress: Iron 55.6 32 0.0007 27.2 5.3 37 181-218 12-48 (60)
234 PRK12469 RNA polymerase factor 55.6 78 0.0017 35.4 10.0 80 138-218 162-261 (481)
235 PRK13870 transcriptional regul 55.6 19 0.00042 35.8 5.0 32 287-318 187-218 (234)
236 COG1318 Predicted transcriptio 55.3 25 0.00054 34.1 5.3 61 240-310 23-83 (182)
237 PRK05654 acetyl-CoA carboxylas 55.0 4.3 9.4E-05 42.2 0.3 43 1-48 28-78 (292)
238 PF05876 Terminase_GpA: Phage 55.0 6.1 0.00013 44.5 1.4 43 1-45 201-255 (557)
239 PRK10870 transcriptional repre 54.7 70 0.0015 30.4 8.4 29 286-314 69-97 (176)
240 TIGR02952 Sig70_famx2 RNA poly 54.5 17 0.00038 33.0 4.2 32 287-318 137-168 (170)
241 PRK11753 DNA-binding transcrip 54.4 65 0.0014 30.3 8.2 30 287-316 167-196 (211)
242 PF02042 RWP-RK: RWP-RK domain 54.4 17 0.00036 28.5 3.3 26 287-312 14-39 (52)
243 PRK09863 putative frv operon r 54.3 67 0.0015 36.2 9.5 104 191-317 16-121 (584)
244 PF13412 HTH_24: Winged helix- 54.0 38 0.00083 24.8 5.2 35 183-218 9-43 (48)
245 PF13413 HTH_25: Helix-turn-he 53.7 28 0.00062 27.7 4.7 56 187-247 5-60 (62)
246 PF14502 HTH_41: Helix-turn-he 53.5 20 0.00043 27.7 3.5 30 289-318 7-36 (48)
247 PRK01381 Trp operon repressor; 53.5 12 0.00026 33.0 2.7 34 280-313 47-80 (99)
248 TIGR02983 SigE-fam_strep RNA p 53.4 17 0.00036 33.1 3.8 33 288-320 126-158 (162)
249 PRK00118 putative DNA-binding 53.3 25 0.00055 31.2 4.8 32 287-318 32-63 (104)
250 PF01096 TFIIS_C: Transcriptio 53.3 6.4 0.00014 28.6 0.8 31 1-31 1-37 (39)
251 PRK06704 RNA polymerase factor 53.2 20 0.00043 35.8 4.6 35 288-322 132-166 (228)
252 PF00165 HTH_AraC: Bacterial r 53.1 20 0.00044 25.7 3.5 27 286-312 6-32 (42)
253 PF13453 zf-TFIIB: Transcripti 53.1 7.5 0.00016 28.4 1.2 29 2-32 1-29 (41)
254 PF03444 HrcA_DNA-bdg: Winged 53.1 23 0.00049 30.1 4.1 30 285-314 20-49 (78)
255 smart00550 Zalpha Z-DNA-bindin 52.9 38 0.00082 27.3 5.4 33 284-316 17-50 (68)
256 PF00440 TetR_N: Bacterial reg 52.8 23 0.00049 26.2 3.8 38 276-313 4-41 (47)
257 PF13719 zinc_ribbon_5: zinc-r 52.7 7.1 0.00015 28.0 1.0 29 2-32 4-35 (37)
258 COG4888 Uncharacterized Zn rib 52.7 6.2 0.00014 34.9 0.8 29 2-32 24-56 (104)
259 smart00550 Zalpha Z-DNA-bindin 52.6 36 0.00078 27.4 5.2 38 182-219 11-49 (68)
260 TIGR02950 SigM_subfam RNA poly 52.5 17 0.00037 32.6 3.7 32 287-318 120-151 (154)
261 TIGR02944 suf_reg_Xantho FeS a 52.4 36 0.00078 30.4 5.7 45 173-218 7-51 (130)
262 TIGR03020 EpsA transcriptional 52.2 22 0.00047 36.1 4.7 32 287-318 204-235 (247)
263 PRK05978 hypothetical protein; 52.2 9 0.0002 36.1 1.9 28 1-32 34-62 (148)
264 PRK09639 RNA polymerase sigma 52.1 20 0.00043 32.7 4.1 34 287-320 126-159 (166)
265 PRK10188 DNA-binding transcrip 51.6 22 0.00048 35.5 4.7 32 287-318 193-224 (240)
266 cd04762 HTH_MerR-trunc Helix-T 51.6 19 0.0004 25.6 3.1 22 290-311 2-23 (49)
267 PRK08301 sporulation sigma fac 51.6 15 0.00032 36.0 3.4 30 287-316 197-226 (234)
268 PRK14890 putative Zn-ribbon RN 51.6 7.1 0.00015 31.3 0.9 8 23-30 49-56 (59)
269 PRK09649 RNA polymerase sigma 51.5 22 0.00048 33.6 4.4 32 287-318 145-176 (185)
270 PRK12542 RNA polymerase sigma 51.4 17 0.00038 34.0 3.7 33 287-319 137-169 (185)
271 PRK12528 RNA polymerase sigma 51.4 22 0.00048 32.3 4.3 30 287-316 128-157 (161)
272 PRK09415 RNA polymerase factor 51.3 17 0.00037 34.0 3.6 34 287-320 142-175 (179)
273 PF09723 Zn-ribbon_8: Zinc rib 51.2 6.4 0.00014 29.0 0.6 35 2-37 7-41 (42)
274 PRK12546 RNA polymerase sigma 51.1 24 0.00051 33.7 4.6 38 287-324 128-165 (188)
275 smart00419 HTH_CRP helix_turn_ 50.8 25 0.00054 25.2 3.7 30 190-219 6-35 (48)
276 PRK09391 fixK transcriptional 50.8 85 0.0018 30.6 8.6 29 287-315 178-206 (230)
277 PF05043 Mga: Mga helix-turn-h 50.7 24 0.00052 29.2 4.1 34 285-318 27-60 (87)
278 PRK12536 RNA polymerase sigma 50.6 20 0.00043 33.5 4.0 34 287-320 144-177 (181)
279 PRK11922 RNA polymerase sigma 50.5 15 0.00032 36.1 3.2 38 287-324 164-201 (231)
280 COG1725 Predicted transcriptio 50.5 20 0.00043 32.9 3.8 30 286-315 32-62 (125)
281 PRK11161 fumarate/nitrate redu 50.4 58 0.0013 31.5 7.3 29 191-219 183-211 (235)
282 PRK12527 RNA polymerase sigma 50.4 17 0.00036 33.1 3.3 34 287-320 120-153 (159)
283 KOG3134 Predicted membrane pro 50.3 4.9 0.00011 40.1 -0.2 32 1-32 1-34 (225)
284 PRK15201 fimbriae regulatory p 50.1 27 0.00059 34.2 4.7 33 286-318 146-178 (198)
285 PRK12543 RNA polymerase sigma 49.9 17 0.00036 34.0 3.3 32 287-318 132-163 (179)
286 PF13542 HTH_Tnp_ISL3: Helix-t 49.8 65 0.0014 23.8 6.0 23 193-215 28-50 (52)
287 PRK12535 RNA polymerase sigma 49.8 20 0.00043 34.4 3.8 40 287-326 148-187 (196)
288 PRK11337 DNA-binding transcrip 49.7 48 0.001 33.6 6.9 56 231-310 12-68 (292)
289 PF12773 DZR: Double zinc ribb 49.7 11 0.00025 28.1 1.7 28 2-34 14-41 (50)
290 PRK15320 transcriptional activ 49.7 24 0.00052 35.2 4.4 35 284-318 175-209 (251)
291 PF12802 MarR_2: MarR family; 49.6 36 0.00077 25.9 4.6 39 180-218 9-47 (62)
292 PRK12533 RNA polymerase sigma 49.6 24 0.00052 34.7 4.5 35 287-321 149-183 (216)
293 TIGR02947 SigH_actino RNA poly 49.5 17 0.00036 34.3 3.3 34 287-320 146-179 (193)
294 TIGR02954 Sig70_famx3 RNA poly 49.5 21 0.00046 32.8 3.9 32 288-319 135-166 (169)
295 PRK13130 H/ACA RNA-protein com 49.4 7.4 0.00016 30.9 0.7 21 2-32 7-27 (56)
296 TIGR01764 excise DNA binding d 49.4 21 0.00045 25.5 3.1 22 289-310 2-23 (49)
297 PRK11753 DNA-binding transcrip 49.3 69 0.0015 30.2 7.5 29 191-219 167-195 (211)
298 PF07900 DUF1670: Protein of u 49.3 67 0.0014 32.3 7.5 132 135-307 71-216 (220)
299 PF03604 DNA_RNApol_7kD: DNA d 49.2 11 0.00024 26.6 1.5 24 2-30 2-25 (32)
300 TIGR02944 suf_reg_Xantho FeS a 49.1 39 0.00084 30.2 5.4 38 277-315 15-52 (130)
301 PRK12537 RNA polymerase sigma 49.1 20 0.00044 33.5 3.8 32 287-318 148-179 (182)
302 PF15616 TerY-C: TerY-C metal 48.9 8.4 0.00018 35.6 1.1 20 2-32 79-98 (131)
303 PRK09483 response regulator; P 48.8 27 0.00057 32.4 4.5 32 287-318 162-193 (217)
304 TIGR02939 RpoE_Sigma70 RNA pol 48.8 20 0.00043 33.4 3.6 34 287-320 153-186 (190)
305 smart00440 ZnF_C2C2 C2C2 Zinc 48.8 7.8 0.00017 28.4 0.7 28 2-31 2-37 (40)
306 PF00356 LacI: Bacterial regul 48.6 21 0.00045 27.0 3.0 20 194-213 1-20 (46)
307 PF02591 DUF164: Putative zinc 48.4 4.9 0.00011 31.2 -0.5 31 2-32 24-56 (56)
308 cd00090 HTH_ARSR Arsenical Res 48.3 46 0.001 25.2 5.1 27 289-315 21-47 (78)
309 cd04761 HTH_MerR-SF Helix-Turn 48.3 20 0.00043 26.1 2.8 19 290-308 2-20 (49)
310 PF09339 HTH_IclR: IclR helix- 48.3 28 0.00061 26.2 3.7 37 182-218 8-44 (52)
311 PRK09710 lar restriction allev 48.2 9.9 0.00022 31.0 1.3 28 3-31 9-36 (64)
312 COG2771 CsgD DNA-binding HTH d 48.2 46 0.001 25.2 5.1 33 286-318 17-49 (65)
313 PF07638 Sigma70_ECF: ECF sigm 48.1 30 0.00066 32.9 4.8 30 288-317 151-180 (185)
314 PRK12518 RNA polymerase sigma 47.7 19 0.0004 33.2 3.2 35 287-321 135-169 (175)
315 PF05191 ADK_lid: Adenylate ki 47.7 6.2 0.00013 28.5 0.0 29 2-32 3-31 (36)
316 PRK11475 DNA-binding transcrip 47.6 29 0.00063 33.9 4.7 32 287-318 148-179 (207)
317 TIGR02989 Sig-70_gvs1 RNA poly 47.6 29 0.00062 31.3 4.4 31 287-317 126-156 (159)
318 TIGR02844 spore_III_D sporulat 47.3 21 0.00045 30.2 3.1 23 287-309 18-40 (80)
319 smart00659 RPOLCX RNA polymera 47.0 11 0.00023 28.4 1.2 25 2-31 4-28 (44)
320 PF13463 HTH_27: Winged helix 46.9 37 0.0008 26.3 4.4 31 285-315 15-45 (68)
321 PF14446 Prok-RING_1: Prokaryo 46.9 11 0.00024 29.8 1.3 25 2-32 7-31 (54)
322 TIGR02405 trehalos_R_Ecol treh 46.5 18 0.00039 36.4 3.2 23 288-310 1-23 (311)
323 PRK12530 RNA polymerase sigma 46.4 15 0.00031 34.9 2.3 33 288-320 150-182 (189)
324 PRK09652 RNA polymerase sigma 46.4 21 0.00045 32.6 3.3 34 287-320 143-176 (182)
325 PF13613 HTH_Tnp_4: Helix-turn 46.2 37 0.00079 25.9 4.1 36 187-222 14-49 (53)
326 PRK12526 RNA polymerase sigma 46.2 22 0.00049 34.2 3.6 34 287-320 168-201 (206)
327 COG1656 Uncharacterized conser 46.2 8.5 0.00018 36.9 0.7 10 23-32 131-140 (165)
328 PRK12525 RNA polymerase sigma 46.1 29 0.00064 32.0 4.3 31 287-317 133-163 (168)
329 PRK08295 RNA polymerase factor 46.1 22 0.00047 33.7 3.5 34 287-320 169-202 (208)
330 PF04218 CENP-B_N: CENP-B N-te 46.0 14 0.0003 28.5 1.8 26 286-311 20-45 (53)
331 PRK09644 RNA polymerase sigma 46.0 19 0.00042 33.0 3.1 35 287-321 123-157 (165)
332 PRK12495 hypothetical protein; 45.7 12 0.00025 37.6 1.6 28 2-35 44-71 (226)
333 PF01710 HTH_Tnp_IS630: Transp 45.5 1.3E+02 0.0029 26.7 8.3 80 137-223 19-102 (119)
334 PF05460 ORC6: Origin recognit 45.5 7 0.00015 41.7 0.0 75 244-318 12-87 (353)
335 TIGR02984 Sig-70_plancto1 RNA 45.3 27 0.00058 32.4 3.9 33 287-319 155-187 (189)
336 PRK10434 srlR DNA-bindng trans 45.3 21 0.00046 36.0 3.5 29 287-315 18-46 (256)
337 PF04703 FaeA: FaeA-like prote 45.3 34 0.00075 27.6 4.0 35 188-222 11-45 (62)
338 COG2260 Predicted Zn-ribbon RN 45.3 10 0.00022 30.4 0.9 21 2-32 7-27 (59)
339 TIGR02366 DHAK_reg probable di 45.3 22 0.00047 32.8 3.3 50 272-321 7-56 (176)
340 PF01047 MarR: MarR family; I 45.1 55 0.0012 24.7 5.0 28 288-315 17-44 (59)
341 KOG3507 DNA-directed RNA polym 44.9 10 0.00022 30.5 0.8 24 2-30 22-45 (62)
342 PRK10219 DNA-binding transcrip 44.8 86 0.0019 26.7 6.8 39 273-312 7-45 (107)
343 PF14354 Lar_restr_allev: Rest 44.6 14 0.0003 28.8 1.6 28 2-30 5-37 (61)
344 PRK10100 DNA-binding transcrip 44.6 34 0.00074 33.6 4.7 32 287-318 169-200 (216)
345 PRK13919 putative RNA polymera 44.4 27 0.00059 32.5 3.9 32 287-318 150-181 (186)
346 PF09862 DUF2089: Protein of u 44.4 42 0.00091 30.4 4.8 31 288-318 49-79 (113)
347 PTZ00255 60S ribosomal protein 44.4 12 0.00026 32.5 1.2 28 1-32 37-64 (90)
348 PF12840 HTH_20: Helix-turn-he 44.2 46 0.00099 25.8 4.5 31 285-315 21-51 (61)
349 PRK12519 RNA polymerase sigma 44.2 32 0.0007 32.3 4.3 32 287-318 156-187 (194)
350 TIGR02835 spore_sigmaE RNA pol 44.1 26 0.00055 34.6 3.7 30 287-316 197-226 (234)
351 TIGR00515 accD acetyl-CoA carb 43.9 7.4 0.00016 40.4 -0.1 41 2-47 28-76 (285)
352 PRK09643 RNA polymerase sigma 43.9 24 0.00053 33.4 3.5 33 287-319 149-181 (192)
353 COG1309 AcrR Transcriptional r 43.9 21 0.00046 31.1 2.9 44 273-317 17-61 (201)
354 PF01418 HTH_6: Helix-turn-hel 43.8 21 0.00045 29.4 2.6 26 287-312 33-58 (77)
355 PF13022 HTH_Tnp_1_2: Helix-tu 43.8 63 0.0014 30.4 5.9 54 268-321 11-70 (142)
356 PF01780 Ribosomal_L37ae: Ribo 43.7 9.9 0.00021 33.0 0.7 27 2-32 37-63 (90)
357 PF07900 DUF1670: Protein of u 43.7 31 0.00067 34.6 4.2 36 288-323 105-140 (220)
358 COG5349 Uncharacterized protei 43.5 13 0.00028 34.0 1.4 26 2-32 23-50 (126)
359 PRK09526 lacI lac repressor; R 43.4 21 0.00046 36.1 3.2 23 288-310 5-27 (342)
360 cd01104 HTH_MlrA-CarA Helix-Tu 43.4 28 0.00062 27.1 3.3 22 290-311 2-23 (68)
361 PF12728 HTH_17: Helix-turn-he 43.4 27 0.0006 25.9 3.0 22 289-310 2-23 (51)
362 PRK12541 RNA polymerase sigma 43.3 33 0.00072 31.2 4.2 32 287-318 127-158 (161)
363 COG3809 Uncharacterized protei 43.3 14 0.00031 31.4 1.5 32 1-34 2-33 (88)
364 PRK03975 tfx putative transcri 43.3 40 0.00087 31.5 4.7 31 287-317 20-50 (141)
365 PRK12523 RNA polymerase sigma 43.3 35 0.00075 31.6 4.3 30 287-316 134-163 (172)
366 PRK05602 RNA polymerase sigma 43.2 28 0.00061 32.5 3.8 34 287-320 143-176 (186)
367 COG0333 RpmF Ribosomal protein 43.1 14 0.00031 29.4 1.4 24 2-34 29-52 (57)
368 cd00569 HTH_Hin_like Helix-tur 43.1 38 0.00082 21.4 3.4 22 287-308 20-41 (42)
369 PRK13918 CRP/FNR family transc 43.1 1.3E+02 0.0028 28.1 8.3 30 190-219 147-176 (202)
370 PRK12522 RNA polymerase sigma 43.0 21 0.00046 33.0 2.8 32 287-318 134-165 (173)
371 PF13463 HTH_27: Winged helix 43.0 46 0.00099 25.8 4.4 31 188-218 14-44 (68)
372 smart00346 HTH_ICLR helix_turn 42.7 77 0.0017 25.9 5.9 29 287-315 19-47 (91)
373 PRK11924 RNA polymerase sigma 42.7 19 0.00042 32.8 2.5 34 287-320 140-173 (179)
374 PRK10402 DNA-binding transcrip 42.7 75 0.0016 30.8 6.8 29 288-316 169-197 (226)
375 PRK12514 RNA polymerase sigma 42.6 28 0.0006 32.3 3.6 32 287-318 144-175 (179)
376 PRK09648 RNA polymerase sigma 42.5 29 0.00064 32.5 3.8 31 288-318 155-185 (189)
377 PRK10220 hypothetical protein; 42.4 14 0.00031 33.2 1.4 24 2-30 5-28 (111)
378 cd00202 ZnF_GATA Zinc finger D 42.4 12 0.00026 29.3 0.9 29 2-32 1-31 (54)
379 PRK13509 transcriptional repre 42.3 30 0.00066 34.8 4.0 28 287-314 18-45 (251)
380 TIGR02010 IscR iron-sulfur clu 42.3 42 0.00091 30.4 4.6 40 276-315 13-52 (135)
381 COG0177 Nth Predicted EndoIII- 42.2 1.6E+02 0.0035 29.4 8.9 75 165-246 78-152 (211)
382 PF00165 HTH_AraC: Bacterial r 42.2 35 0.00076 24.5 3.3 27 190-216 6-32 (42)
383 PF01726 LexA_DNA_bind: LexA D 42.1 46 0.00099 26.9 4.2 31 284-314 21-52 (65)
384 PRK11923 algU RNA polymerase s 42.0 36 0.00078 32.0 4.3 32 287-318 153-184 (193)
385 PRK10703 DNA-binding transcrip 42.0 21 0.00045 36.2 2.9 23 289-311 2-24 (341)
386 PRK12517 RNA polymerase sigma 42.0 26 0.00056 33.3 3.3 34 287-320 143-176 (188)
387 TIGR02959 SigZ RNA polymerase 41.9 27 0.00059 32.4 3.4 34 287-320 115-148 (170)
388 COG1321 TroR Mn-dependent tran 41.9 46 0.001 31.3 4.9 38 277-315 14-51 (154)
389 PRK12545 RNA polymerase sigma 41.8 35 0.00077 32.6 4.3 34 287-320 154-187 (201)
390 PRK07037 extracytoplasmic-func 41.8 30 0.00066 31.4 3.6 32 287-318 124-155 (163)
391 COG5024 Cyclin [Cell division 41.8 75 0.0016 35.1 7.1 85 234-318 219-306 (440)
392 PRK10014 DNA-binding transcrip 41.7 24 0.00051 35.8 3.2 25 287-311 5-29 (342)
393 PRK12511 RNA polymerase sigma 41.7 26 0.00057 33.1 3.3 34 287-320 126-159 (182)
394 PRK09492 treR trehalose repres 41.5 24 0.00053 35.2 3.2 23 288-310 4-26 (315)
395 TIGR02531 yecD_yerC TrpR-relat 41.5 39 0.00084 29.1 4.0 23 287-310 49-71 (88)
396 smart00354 HTH_LACI helix_turn 41.3 30 0.00065 27.8 3.1 20 290-309 2-21 (70)
397 COG1595 RpoE DNA-directed RNA 41.3 30 0.00065 32.4 3.6 34 287-320 142-175 (182)
398 PRK12512 RNA polymerase sigma 41.2 32 0.0007 32.0 3.8 34 288-321 147-180 (184)
399 PRK15481 transcriptional regul 41.2 60 0.0013 34.7 6.3 31 286-316 26-57 (431)
400 PRK09391 fixK transcriptional 41.2 1.1E+02 0.0023 29.9 7.6 30 190-219 177-206 (230)
401 PF00376 MerR: MerR family reg 41.1 21 0.00047 25.8 2.0 17 290-306 1-17 (38)
402 TIGR02960 SigX5 RNA polymerase 41.1 33 0.00072 35.1 4.2 35 287-321 157-191 (324)
403 TIGR00738 rrf2_super rrf2 fami 41.0 66 0.0014 28.5 5.6 44 272-315 8-52 (132)
404 PRK12534 RNA polymerase sigma 40.9 29 0.00063 32.4 3.5 33 287-319 152-184 (187)
405 KOG1921 Endonuclease III [Repl 40.7 74 0.0016 32.7 6.3 109 128-245 92-202 (286)
406 PRK12539 RNA polymerase sigma 40.6 31 0.00068 32.3 3.6 34 287-320 146-179 (184)
407 PRK09651 RNA polymerase sigma 40.6 40 0.00088 31.2 4.3 30 287-316 134-163 (172)
408 TIGR03541 reg_near_HchA LuxR f 40.5 43 0.00093 33.1 4.7 32 287-318 185-216 (232)
409 TIGR02948 SigW_bacill RNA poly 40.4 31 0.00068 31.9 3.6 32 287-318 151-182 (187)
410 PRK12544 RNA polymerase sigma 40.4 20 0.00044 34.7 2.4 37 287-323 163-199 (206)
411 PRK09678 DNA-binding transcrip 40.3 15 0.00032 30.6 1.2 31 1-32 2-39 (72)
412 TIGR01610 phage_O_Nterm phage 40.3 82 0.0018 27.0 5.8 30 189-218 44-73 (95)
413 PRK11511 DNA-binding transcrip 40.3 91 0.002 27.9 6.4 43 269-312 7-49 (127)
414 PF09339 HTH_IclR: IclR helix- 40.1 44 0.00096 25.1 3.7 30 286-315 16-45 (52)
415 CHL00174 accD acetyl-CoA carbo 39.9 9 0.00019 40.0 -0.2 43 1-48 39-89 (296)
416 PF13551 HTH_29: Winged helix- 39.8 45 0.00098 28.1 4.2 30 287-316 10-40 (112)
417 smart00421 HTH_LUXR helix_turn 39.8 57 0.0012 23.6 4.3 31 193-223 19-49 (58)
418 PRK15418 transcriptional regul 39.8 50 0.0011 34.6 5.3 36 279-314 20-55 (318)
419 TIGR03338 phnR_burk phosphonat 39.4 35 0.00076 32.7 3.8 30 286-315 32-61 (212)
420 smart00401 ZnF_GATA zinc finge 39.4 23 0.00049 27.4 2.0 31 1-32 4-35 (52)
421 PRK04841 transcriptional regul 39.3 38 0.00083 39.4 4.8 32 287-318 852-883 (903)
422 PF11672 DUF3268: Protein of u 38.9 19 0.0004 32.0 1.7 30 2-32 4-41 (102)
423 PRK04984 fatty acid metabolism 38.9 41 0.00088 32.9 4.3 30 286-315 28-58 (239)
424 KOG0656 G1/S-specific cyclin D 38.7 95 0.002 33.1 7.1 87 231-317 81-174 (335)
425 COG4565 CitB Response regulato 38.7 2.2E+02 0.0048 28.8 9.2 86 132-219 113-200 (224)
426 PRK10402 DNA-binding transcrip 38.7 86 0.0019 30.4 6.5 30 190-219 167-196 (226)
427 PRK12524 RNA polymerase sigma 38.7 33 0.00072 32.5 3.5 34 287-320 151-184 (196)
428 PRK06930 positive control sigm 38.5 44 0.00096 31.9 4.3 35 286-320 128-162 (170)
429 PRK09480 slmA division inhibit 38.4 32 0.0007 31.9 3.3 41 271-311 13-53 (194)
430 COG1959 Predicted transcriptio 38.3 71 0.0015 29.8 5.5 44 176-219 9-52 (150)
431 PRK12513 RNA polymerase sigma 38.3 33 0.00071 32.3 3.4 32 287-318 154-185 (194)
432 COG2973 TrpR Trp operon repres 38.3 42 0.00091 29.7 3.7 35 274-308 46-80 (103)
433 PRK11920 rirA iron-responsive 38.3 57 0.0012 30.5 4.9 39 276-315 13-51 (153)
434 PRK14087 dnaA chromosomal repl 38.2 3.7E+02 0.0081 29.6 11.9 39 277-317 392-431 (450)
435 PF14353 CpXC: CpXC protein 38.2 15 0.00033 32.9 1.1 10 23-32 39-48 (128)
436 PRK09646 RNA polymerase sigma 38.1 36 0.00077 32.3 3.6 33 287-319 157-189 (194)
437 cd04764 HTH_MlrA-like_sg1 Heli 38.1 39 0.00084 26.5 3.3 22 290-311 2-23 (67)
438 PF01726 LexA_DNA_bind: LexA D 38.1 73 0.0016 25.7 4.9 32 187-218 20-52 (65)
439 TIGR01481 ccpA catabolite cont 38.1 28 0.0006 35.1 3.0 22 289-310 2-23 (329)
440 PF04703 FaeA: FaeA-like prote 38.0 65 0.0014 26.0 4.5 30 286-315 13-42 (62)
441 PRK09647 RNA polymerase sigma 38.0 32 0.0007 33.2 3.3 34 287-320 153-186 (203)
442 PF13404 HTH_AsnC-type: AsnC-t 38.0 80 0.0017 23.3 4.7 30 188-217 13-42 (42)
443 PRK01110 rpmF 50S ribosomal pr 37.9 18 0.00039 29.0 1.3 27 2-38 29-55 (60)
444 PF14952 zf-tcix: Putative tre 37.8 18 0.00039 27.4 1.1 25 2-34 13-39 (44)
445 PRK09392 ftrB transcriptional 37.7 1.2E+02 0.0025 29.4 7.2 30 287-316 172-201 (236)
446 TIGR03209 P21_Cbot clostridium 37.7 21 0.00045 31.9 1.8 21 287-307 122-142 (142)
447 PRK10411 DNA-binding transcrip 37.6 40 0.00086 33.8 4.0 29 287-315 17-45 (240)
448 PRK04023 DNA polymerase II lar 37.5 21 0.00046 42.9 2.2 30 292-322 1080-1109(1121)
449 PRK14088 dnaA chromosomal repl 37.4 44 0.00095 36.5 4.6 67 150-220 345-415 (440)
450 cd06170 LuxR_C_like C-terminal 37.4 65 0.0014 23.5 4.3 32 192-223 15-46 (57)
451 smart00347 HTH_MARR helix_turn 37.1 91 0.002 25.4 5.5 28 288-315 24-51 (101)
452 PRK14999 histidine utilization 37.1 46 0.00099 32.8 4.3 30 286-315 33-63 (241)
453 PRK06986 fliA flagellar biosyn 37.1 4.1E+02 0.0089 26.0 18.2 33 287-319 199-231 (236)
454 TIGR02417 fruct_sucro_rep D-fr 37.0 29 0.00063 35.0 3.0 21 290-310 1-21 (327)
455 PRK09641 RNA polymerase sigma 37.0 39 0.00084 31.3 3.6 32 287-318 151-182 (187)
456 PF04545 Sigma70_r4: Sigma-70, 36.9 67 0.0015 23.8 4.2 31 190-220 18-48 (50)
457 PRK10430 DNA-binding transcrip 36.9 54 0.0012 31.8 4.8 34 283-316 173-206 (239)
458 PRK12538 RNA polymerase sigma 36.9 33 0.00072 34.0 3.3 34 287-320 186-219 (233)
459 PRK11303 DNA-binding transcrip 36.7 30 0.00065 34.8 3.0 21 290-310 2-22 (328)
460 smart00351 PAX Paired Box doma 36.7 57 0.0012 29.4 4.5 29 287-315 32-60 (125)
461 PRK09685 DNA-binding transcrip 36.3 1.9E+02 0.004 29.1 8.7 42 270-311 196-237 (302)
462 PRK14987 gluconate operon tran 36.2 28 0.00062 35.2 2.8 22 288-309 5-26 (331)
463 PRK08558 adenine phosphoribosy 36.2 53 0.0011 33.1 4.6 56 185-247 16-71 (238)
464 PRK15369 two component system 36.2 56 0.0012 29.4 4.4 32 287-318 163-194 (211)
465 PRK03837 transcriptional regul 36.1 49 0.0011 32.3 4.3 30 286-315 34-64 (241)
466 PRK06030 hypothetical protein; 36.1 81 0.0018 28.9 5.4 70 149-220 25-97 (124)
467 TIGR03001 Sig-70_gmx1 RNA poly 36.1 48 0.001 33.2 4.3 34 287-320 176-209 (244)
468 TIGR00280 L37a ribosomal prote 36.0 17 0.00038 31.6 1.0 27 2-32 37-63 (91)
469 PF13309 HTH_22: HTH domain 35.9 83 0.0018 25.2 4.8 55 232-306 4-60 (64)
470 TIGR02605 CxxC_CxxC_SSSS putat 35.8 19 0.00042 27.1 1.1 35 2-37 7-41 (52)
471 cd04763 HTH_MlrA-like Helix-Tu 35.8 43 0.00094 26.4 3.2 22 290-311 2-23 (68)
472 COG0777 AccD Acetyl-CoA carbox 35.8 12 0.00026 38.7 -0.0 28 2-32 30-57 (294)
473 TIGR02404 trehalos_R_Bsub treh 35.8 43 0.00094 32.7 3.9 30 286-315 21-51 (233)
474 PRK07218 replication factor A; 35.7 18 0.00039 39.6 1.3 20 2-31 299-318 (423)
475 PRK00135 scpB segregation and 35.6 92 0.002 30.4 6.0 44 270-317 5-49 (188)
476 PRK09636 RNA polymerase sigma 35.5 50 0.0011 33.6 4.4 35 287-321 130-164 (293)
477 PF13744 HTH_37: Helix-turn-he 35.4 75 0.0016 26.2 4.7 30 280-309 23-52 (80)
478 PF07754 DUF1610: Domain of un 35.4 26 0.00057 23.3 1.5 24 3-30 1-24 (24)
479 PRK11302 DNA-binding transcrip 35.4 1.1E+02 0.0023 30.7 6.7 53 234-310 3-56 (284)
480 PF13011 LZ_Tnp_IS481: leucine 35.3 83 0.0018 27.1 5.0 37 279-315 16-52 (85)
481 PF09241 Herp-Cyclin: Herpesvi 35.3 3E+02 0.0064 23.8 10.1 86 232-318 5-100 (106)
482 PRK09638 RNA polymerase sigma 35.2 43 0.00094 30.8 3.6 32 287-318 141-172 (176)
483 PRK14086 dnaA chromosomal repl 35.2 3.4E+02 0.0073 31.4 11.2 40 276-317 559-598 (617)
484 PRK10339 DNA-binding transcrip 35.2 28 0.00061 35.2 2.5 22 289-310 2-23 (327)
485 PRK09637 RNA polymerase sigma 35.0 54 0.0012 30.9 4.3 35 287-321 121-155 (181)
486 PRK10079 phosphonate metabolis 35.0 45 0.00097 32.9 3.9 30 286-315 32-62 (241)
487 smart00345 HTH_GNTR helix_turn 34.9 59 0.0013 24.0 3.7 26 194-219 22-47 (60)
488 COG4530 Uncharacterized protei 34.8 21 0.00045 32.3 1.3 27 2-33 11-37 (129)
489 PRK03976 rpl37ae 50S ribosomal 34.7 18 0.0004 31.4 0.9 27 2-32 38-64 (90)
490 TIGR02325 C_P_lyase_phnF phosp 34.6 46 0.001 32.4 3.9 30 286-315 29-59 (238)
491 PRK15482 transcriptional regul 34.6 1.1E+02 0.0025 30.8 6.8 53 234-310 3-56 (285)
492 PRK10401 DNA-binding transcrip 34.5 35 0.00076 34.8 3.1 22 289-310 2-23 (346)
493 PRK08402 replication factor A; 34.3 23 0.00051 37.8 1.8 26 2-31 214-239 (355)
494 PF13730 HTH_36: Helix-turn-he 34.3 88 0.0019 23.4 4.6 25 194-218 27-51 (55)
495 PRK10219 DNA-binding transcrip 34.2 1.4E+02 0.0031 25.4 6.4 39 177-216 7-45 (107)
496 PF01381 HTH_3: Helix-turn-hel 34.2 47 0.001 24.7 3.1 25 286-310 7-31 (55)
497 PRK10651 transcriptional regul 34.2 64 0.0014 29.4 4.6 32 287-318 169-200 (216)
498 PHA00542 putative Cro-like pro 33.8 51 0.0011 27.6 3.4 27 284-310 27-53 (82)
499 PRK10727 DNA-binding transcrip 33.7 35 0.00076 34.7 3.0 21 289-309 2-22 (343)
500 PRK11014 transcriptional repre 33.7 82 0.0018 28.7 5.1 44 176-219 9-52 (141)
No 1
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=100.00 E-value=9.4e-76 Score=581.28 Aligned_cols=307 Identities=38% Similarity=0.520 Sum_probs=286.1
Q ss_pred CCCCCCCCCCC-cccccCCCCccccccccceecccceeecccccccccCCCCcccccCCCCCCCCCCCCCCCCCCCCCCC
Q 046187 1 MKCPYCSAAQG-RCATTSTGRSITECGSCGRVIAERQCQNHHLFHIRAQDTPLCLVTSDLPSIPQPQQNDGVDEDPFQPT 79 (510)
Q Consensus 1 m~Cp~C~~~~~-~i~D~~~Gd~~~VC~~CG~Vleer~Id~~~EwR~fs~d~~~~~~~~d~p~~~~d~sRvg~~~dP~l~~ 79 (510)
|.|++|++.+. .++||++|| +||.+||+||++|+||+++|||+|+||+ .+.||||||++.|||+.+
T Consensus 1 ~~c~~C~~~~~~~V~d~~~gd--tvC~~CGlVl~~r~Id~~sEwrtfsnd~-----------~~~DPsrvG~~sNPlL~~ 67 (308)
T KOG1597|consen 1 MTCPDCKRHPENLVEDHSAGD--TVCSECGLVLEDRIIDEGSEWRTFSNDD-----------SDADPSRVGASSNPLLDG 67 (308)
T ss_pred CCCCCCCCCCCCeeeeccCCc--eecccCCeeeccccccccccccccccCC-----------CCCCccccCCCCCCCCCC
Confidence 78999999888 668999999 9999999999999999999999999996 255679999999999999
Q ss_pred CccceeecccCCCCcccccccccccchhhHHHHHHHhhcCCCCCCCchhhHHHHHHHHHHHHHHHHhCCCHHHHHHHHHH
Q 046187 80 GFITAFSAWSLVPSPLFLRSSHSFSGQLAELERTFELLSSSTTSTSSSVMMDNLRAYLQIIDVASILGLDYDICDHAFQL 159 (510)
Q Consensus 80 ~~~tt~i~~~~~~npl~~~T~i~f~~~~~eL~R~~~~s~~~~~~~~~~~~er~L~a~~~I~~ic~~L~LP~~VidtA~~L 159 (510)
++++|||+|+.+.++.+ .++|.|+|++.++.+ +++. ...+|+.|..||+.|+||..+.|+|.++
T Consensus 68 g~L~T~I~~g~g~~s~~----------~s~l~~~Q~~~sm~~--~d~~----~~~a~~~I~~m~d~~~Lp~~I~d~A~~i 131 (308)
T KOG1597|consen 68 GDLSTFISKGTGTSSSF----------ASSLGKAQNRNSMSN--SDRV----LKAAFKEITAMCDRLSLPATIKDRANEI 131 (308)
T ss_pred CCcceeeecCCCCCHHH----------HHHHHHHhcccccCC--ccHH----HHHHHHHHHHHHHHhCCchHHHHHHHHH
Confidence 99999999997766543 245789998777755 5554 5669999999999999999999999999
Q ss_pred HHHHHhCCccCCccHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhcccCCCCCcchhhhHHHHH
Q 046187 160 FRDCCSATCLRNRSVEALATAALVQAIREAQEPRTLQEISIAANVPQKEIGKYIKILGEALQLSQPINSNSIAVHMPRFC 239 (510)
Q Consensus 160 yK~a~e~~~lrGRs~eaVaAACLYIACR~~~~PrTLkEIa~vt~VskkeIgr~yk~L~k~L~i~~pv~~~~p~~~I~Rfc 239 (510)
||++++.+.+|||+.++++|||||+|||++++|||||||+.+++|++|||||++|.|.+.|+...+....+..+||+|||
T Consensus 132 fk~v~~~k~lrGks~eai~AAclyiACRq~~~pRT~kEI~~~anv~kKEIgr~~K~i~~~l~~s~~~~s~~t~~~m~RFC 211 (308)
T KOG1597|consen 132 FKLVEDSKLLRGKSVEALAAACLYIACRQEDVPRTFKEISAVANVSKKEIGRCVKLIGEALETSVDLISISTGDFMPRFC 211 (308)
T ss_pred HHHHHHhhhhcCccHHHHHHHHHHHHHHhcCCCchHHHHHHHHcCCHHHHHHHHHHHHHHHhccchhhhhhHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999887766666899999999
Q ss_pred hhcCCCHHHHHHHHHHHHHHHhccccCCCChHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhccc
Q 046187 240 TLLQLNKSAQVLATHIGEVVINKCFCTRRNPISISAAAIYLACQLEDKRKTQAEICKVTGLTEVTLRKVYKELLENWDDL 319 (510)
Q Consensus 240 s~L~L~~~V~~~A~~Ia~~a~~~~l~~GRsP~sIAAAaIYlAarl~g~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~L 319 (510)
+.|+|+..++++|.++++++.+..++.||+|.+||||+|||+++++.++++++||.+++||+|+|||+.||+||+++.+|
T Consensus 212 s~L~L~~~~q~aA~e~a~ka~~~~~~~gRsPiSIAAa~IYmisqls~~kkt~keI~~vtgVaE~TIr~sYK~Lyp~~~~l 291 (308)
T KOG1597|consen 212 SNLGLPKSAQEAATEIAEKAEEMDIRAGRSPISIAAAAIYMISQLSDEKKTQKEIGEVTGVAEVTIRNSYKDLYPHADKL 291 (308)
T ss_pred HhcCCCHHHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHhccCcccHHHHHHHhhhhHHHHHHHHHHHhhchhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCCCCCccCCCc
Q 046187 320 LPSNYTPAVPPEKAFPTT 337 (510)
Q Consensus 320 ip~~~~~~~~i~~~~p~~ 337 (510)
+|.||.++++ +++||++
T Consensus 292 iP~~~a~~~~-lk~Lp~~ 308 (308)
T KOG1597|consen 292 IPSWYANAVP-LKNLPGP 308 (308)
T ss_pred Chhhhccccc-hhhcCCC
Confidence 9999999999 9999974
No 2
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=100.00 E-value=4.3e-64 Score=513.67 Aligned_cols=294 Identities=30% Similarity=0.390 Sum_probs=257.2
Q ss_pred CCCCCCCCCCCcccccCCCCccccccccceecccceeecccccccccCCCCcccccCCCCCCCCCCCCCCCCCCCCCCCC
Q 046187 1 MKCPYCSAAQGRCATTSTGRSITECGSCGRVIAERQCQNHHLFHIRAQDTPLCLVTSDLPSIPQPQQNDGVDEDPFQPTG 80 (510)
Q Consensus 1 m~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vleer~Id~~~EwR~fs~d~~~~~~~~d~p~~~~d~sRvg~~~dP~l~~~ 80 (510)
++||+||+ +.+++|+++|+ +||++||+||+|++||+++|||+|++|+ ..|++|||++.+|++.+.
T Consensus 12 ~~Cp~Cg~-~~iv~d~~~Ge--~vC~~CG~Vl~e~~iD~g~EWR~f~~~~------------~~~~~RvG~~~~~~~~~~ 76 (310)
T PRK00423 12 LVCPECGS-DKLIYDYERGE--IVCADCGLVIEENIIDQGPEWRAFDPEQ------------REKRSRVGAPMTYTIHDK 76 (310)
T ss_pred CcCcCCCC-CCeeEECCCCe--EeecccCCcccccccccCCCccCCCccc------------cCCccccCCCCCccccCC
Confidence 47999998 56779999999 9999999999999999999999999985 237799999999999998
Q ss_pred ccceeecccCCCCcccccccccccc--hhhHHHHHHHhhcCCCCCCCchhhHHHHH-HHHHHHHHHHHhCCCHHHHHHHH
Q 046187 81 FITAFSAWSLVPSPLFLRSSHSFSG--QLAELERTFELLSSSTTSTSSSVMMDNLR-AYLQIIDVASILGLDYDICDHAF 157 (510)
Q Consensus 81 ~~tt~i~~~~~~npl~~~T~i~f~~--~~~eL~R~~~~s~~~~~~~~~~~~er~L~-a~~~I~~ic~~L~LP~~VidtA~ 157 (510)
+++|.|+|..... .+..++... ....|.|||.+..... ..+|+|. +|..|.++|+.|+||+.|+|+|+
T Consensus 77 gl~T~I~~~~~~~---~g~~l~~~~~~~~~rl~~~~~~~~~~~------~~er~l~~a~~~I~~~~~~L~Lp~~v~e~A~ 147 (310)
T PRK00423 77 GLSTDIDWRNKDS---YGKSISGKNRAQLYRLRKWQRRIRVSN------AAERNLAFALSELDRIASQLGLPRSVREEAA 147 (310)
T ss_pred CCceEeecCCccc---ccccccHHHHHHHHHHHHHhhhcccCC------hHhHHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 8999988753211 001111110 1234667776654311 2344555 77888899999999999999999
Q ss_pred HHHHHHHhCCccCCccHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhcccCCCCCcchhhhHHH
Q 046187 158 QLFRDCCSATCLRNRSVEALATAALVQAIREAQEPRTLQEISIAANVPQKEIGKYIKILGEALQLSQPINSNSIAVHMPR 237 (510)
Q Consensus 158 ~LyK~a~e~~~lrGRs~eaVaAACLYIACR~~~~PrTLkEIa~vt~VskkeIgr~yk~L~k~L~i~~pv~~~~p~~~I~R 237 (510)
+||+++++.++++||+.++++|||||+|||++++||||+||+.++++++++|+++|+.|.+.|++..++. +|++||.|
T Consensus 148 ~iyk~~~~~~~~rgrs~~~i~AAclYiACR~~~~prtl~eI~~~~~v~~k~i~~~~~~l~k~L~~~~~~~--~p~~~i~r 225 (310)
T PRK00423 148 VIYRKAVEKGLIRGRSIEGVVAAALYAACRRCKVPRTLDEIAEVSRVSRKEIGRCYRFLLRELNLKLPPT--DPIDYVPR 225 (310)
T ss_pred HHHHHHHhcCcccCCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCCCC--CHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999999999876653 59999999
Q ss_pred HHhhcCCCHHHHHHHHHHHHHHHhccccCCCChHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhc
Q 046187 238 FCTLLQLNKSAQVLATHIGEVVINKCFCTRRNPISISAAAIYLACQLEDKRKTQAEICKVTGLTEVTLRKVYKELLENWD 317 (510)
Q Consensus 238 fcs~L~L~~~V~~~A~~Ia~~a~~~~l~~GRsP~sIAAAaIYlAarl~g~~~t~keIa~vagVSe~TIRkrYKEL~e~l~ 317 (510)
||++|+|++++.+.|++|++++.+.+++.||+|.+||||||||||+++|.++|++||++++||++.||+++||+|+++++
T Consensus 226 ~~~~L~L~~~v~~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g~~~t~keIa~v~~Vs~~tI~~~ykel~~~l~ 305 (310)
T PRK00423 226 FASELGLSGEVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERRTQREVAEVAGVTEVTVRNRYKELAEKLD 305 (310)
T ss_pred HHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHHHHHhC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred ccC
Q 046187 318 DLL 320 (510)
Q Consensus 318 ~Li 320 (510)
..+
T Consensus 306 ~~~ 308 (310)
T PRK00423 306 IKI 308 (310)
T ss_pred ccc
Confidence 765
No 3
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=100.00 E-value=4.8e-57 Score=455.52 Aligned_cols=281 Identities=30% Similarity=0.423 Sum_probs=251.0
Q ss_pred CCCCCCCCCCCcccccCCCCccccccccceecccceeecccccccccCCCCcccccCCCCCCCCCCCCCCCCCCCCCCCC
Q 046187 1 MKCPYCSAAQGRCATTSTGRSITECGSCGRVIAERQCQNHHLFHIRAQDTPLCLVTSDLPSIPQPQQNDGVDEDPFQPTG 80 (510)
Q Consensus 1 m~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vleer~Id~~~EwR~fs~d~~~~~~~~d~p~~~~d~sRvg~~~dP~l~~~ 80 (510)
|.||+|++. .++.|+..|+ .||.+||+|++|++||.++|||.| |. ...+ |+|.+..+...+.
T Consensus 2 ~~CpeCg~~-~~~~d~~~ge--~VC~~CG~Vi~~~~id~gpewr~f--~e------------~~~~-r~g~P~t~~~~d~ 63 (285)
T COG1405 2 MSCPECGST-NIITDYERGE--IVCADCGLVLEDSLIDPGPEWRAF--DE------------RHER-RVGAPLTPSIHDK 63 (285)
T ss_pred CCCCCCCCc-cceeeccCCe--EEeccCCEEeccccccCCCCcccc--cc------------cccc-cccCCCccccCcc
Confidence 689999996 5558899998 999999999999999999999999 32 1123 9999999999988
Q ss_pred ccceeecccCCCCcccccccccccchhhHHHHHHHhhcCCCCCCCchhhHHHHH-HHHHHHHHHHHhCCCHHHHHHHHHH
Q 046187 81 FITAFSAWSLVPSPLFLRSSHSFSGQLAELERTFELLSSSTTSTSSSVMMDNLR-AYLQIIDVASILGLDYDICDHAFQL 159 (510)
Q Consensus 81 ~~tt~i~~~~~~npl~~~T~i~f~~~~~eL~R~~~~s~~~~~~~~~~~~er~L~-a~~~I~~ic~~L~LP~~VidtA~~L 159 (510)
+++|+++|.... ..++|.|||.+....+ ..++++. ++..|..+|+.|+||..+.|+|..|
T Consensus 64 ~l~t~i~~~~~~-------------~~~rlr~~~~~~~v~~------~~ernl~~a~~~l~~~~~~l~LP~~v~e~A~~i 124 (285)
T COG1405 64 GLSTIIGWGDKD-------------KMYRLRKWQIRIRVSS------AKERNLITALEELERIASALGLPESVRETAARI 124 (285)
T ss_pred chhhhcccchhH-------------HHHHHHHHHhcccccc------chhhHHHHHHHHHHHHHHHhCCCchHHHHHHHH
Confidence 887777766221 2367888886554421 2345566 6677778999999999999999999
Q ss_pred HHHHHhCCccCCccHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhcccCCCCCcchhhhHHHHH
Q 046187 160 FRDCCSATCLRNRSVEALATAALVQAIREAQEPRTLQEISIAANVPQKEIGKYIKILGEALQLSQPINSNSIAVHMPRFC 239 (510)
Q Consensus 160 yK~a~e~~~lrGRs~eaVaAACLYIACR~~~~PrTLkEIa~vt~VskkeIgr~yk~L~k~L~i~~pv~~~~p~~~I~Rfc 239 (510)
|+++++.++++||+.+.++|||||+|||++++||||+||+.+++|++++|+|+|+.+.+.|++..+. .+|.+||+|||
T Consensus 125 yr~a~~~~l~rGRsie~v~AA~iY~acR~~~~prtl~eIa~a~~V~~kei~rtyr~~~~~L~l~~~~--~~p~~yi~rf~ 202 (285)
T COG1405 125 YRKAVDKGLLRGRSIESVAAACIYAACRINGVPRTLDEIAKALGVSKKEIGRTYRLLVRELKLKIPP--VDPSDYIPRFA 202 (285)
T ss_pred HHHHhhcCCCcCCcHHHHHHHHHHHHHHHcCCCccHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCCC--CCHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999999987665 45999999999
Q ss_pred hhcCCCHHHHHHHHHHHHHHHhccccCCCChHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhccc
Q 046187 240 TLLQLNKSAQVLATHIGEVVINKCFCTRRNPISISAAAIYLACQLEDKRKTQAEICKVTGLTEVTLRKVYKELLENWDDL 319 (510)
Q Consensus 240 s~L~L~~~V~~~A~~Ia~~a~~~~l~~GRsP~sIAAAaIYlAarl~g~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~L 319 (510)
++|+|+++|...|.+|++++.+.++..||+|.+|||||||||+.++|+++||++|+.++||+++|||++||+|.++++..
T Consensus 203 s~L~l~~~v~~~a~ei~~~~~~~g~~~Gk~P~glAaaaiy~as~l~~~~~tq~eva~v~~vtevTIrnrykel~~~~~i~ 282 (285)
T COG1405 203 SKLGLSDEVRRKAIEIVKKAKRAGLTAGKSPAGLAAAAIYLASLLLGERRTQKEVAKVAGVTEVTIRNRYKELADALDIE 282 (285)
T ss_pred HHcCCCHHHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhCCchHHHHHHHHhCCeeeHHHHHHHHHHHhhccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999998875
Q ss_pred C
Q 046187 320 L 320 (510)
Q Consensus 320 i 320 (510)
+
T Consensus 283 ~ 283 (285)
T COG1405 283 V 283 (285)
T ss_pred c
Confidence 4
No 4
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=100.00 E-value=4.2e-40 Score=348.78 Aligned_cols=252 Identities=22% Similarity=0.295 Sum_probs=217.5
Q ss_pred CCCCCCCCCCCcccccCCCCccccccccceecccceeecccccccccCCCCcccccCCCCCCCCCCCCCCCCCCCCCCCC
Q 046187 1 MKCPYCSAAQGRCATTSTGRSITECGSCGRVIAERQCQNHHLFHIRAQDTPLCLVTSDLPSIPQPQQNDGVDEDPFQPTG 80 (510)
Q Consensus 1 m~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vleer~Id~~~EwR~fs~d~~~~~~~~d~p~~~~d~sRvg~~~dP~l~~~ 80 (510)
|.|++|++..+. .|.++|+ ++|+.||+|+|++.|+++..|.+.++|.
T Consensus 1 ~~C~~C~~s~fe-~d~a~g~--~~C~~CG~v~E~~~ivsev~F~e~~~G~------------------------------ 47 (521)
T KOG1598|consen 1 MVCKNCGGSNFE-RDEATGN--LYCTACGTVLEYNNIVAEVTFVEGAQGQ------------------------------ 47 (521)
T ss_pred CcCCCCCCCCcc-cccccCC--ceeccccceeeccceeEEeeeeccccee------------------------------
Confidence 789999995444 7999999 9999999999999999999988754332
Q ss_pred ccceeecccCCCCcccccccccccchhhHHHHHHHhhcCCCCCCCchhhHHHHH-HHHHHHHHHHHhCCCHHHHHHHHHH
Q 046187 81 FITAFSAWSLVPSPLFLRSSHSFSGQLAELERTFELLSSSTTSTSSSVMMDNLR-AYLQIIDVASILGLDYDICDHAFQL 159 (510)
Q Consensus 81 ~~tt~i~~~~~~npl~~~T~i~f~~~~~eL~R~~~~s~~~~~~~~~~~~er~L~-a~~~I~~ic~~L~LP~~VidtA~~L 159 (510)
+ |.....+ +++ +.+ +|. +++. +.+.|.+++.+|+|++ +++.|+.+
T Consensus 48 ~----v~~~~~g--------~~~---s~e-~r~-----------------~t~~n~r~~i~~~~~~l~l~~-~~~~a~~~ 93 (521)
T KOG1598|consen 48 F----VRVGQSG--------AGS---SLE-SRE-----------------KTIYNARRLIEELTERLNLGN-KTEVAFNF 93 (521)
T ss_pred E----EeccccC--------Ccc---chH-HHH-----------------HHHHHHHhHHHHHHHhcCcch-HHHHHHHH
Confidence 1 1111000 000 011 122 2334 6677888999999999 99999999
Q ss_pred HHHHHhCCccCCccHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhccc---CCCCCcchhhhHH
Q 046187 160 FRDCCSATCLRNRSVEALATAALVQAIREAQEPRTLQEISIAANVPQKEIGKYIKILGEALQLS---QPINSNSIAVHMP 236 (510)
Q Consensus 160 yK~a~e~~~lrGRs~eaVaAACLYIACR~~~~PrTLkEIa~vt~VskkeIgr~yk~L~k~L~i~---~pv~~~~p~~~I~ 236 (510)
|+++.++++.+||+...++|||+|++||++++++++.|++++++|++++||+.|++|.+.|.+. .|.. +|..||+
T Consensus 94 ~k~a~~~nftkGr~~~~vvasClY~vcR~e~t~hlliDfS~~Lqv~Vy~LG~~~l~l~~~L~i~en~~plv--DpsL~i~ 171 (521)
T KOG1598|consen 94 FKLAPDRNFTKGRRSTEVVAACLYLVCRLEKTDHLLIDFSSYLQVSVYDLGSNFLEVTDSLSIGENVSPLV--DPSLYIV 171 (521)
T ss_pred HHHHhhCCCCCCcchHHHHHHHHHHHHHhhCCceEEEEeccceEEehhhhhHHHHHHHHHhcccccccccc--Ccceeee
Confidence 9999999999999999999999999999999999999999999999999999999999999998 5544 5899999
Q ss_pred HHHhhcCCC---HHHHHHHHHHHHHHHhccccCCCChHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046187 237 RFCTLLQLN---KSAQVLATHIGEVVINKCFCTRRNPISISAAAIYLACQLEDKRKTQAEICKVTGLTEVTLRKVYKELL 313 (510)
Q Consensus 237 Rfcs~L~L~---~~V~~~A~~Ia~~a~~~~l~~GRsP~sIAAAaIYlAarl~g~~~t~keIa~vagVSe~TIRkrYKEL~ 313 (510)
||+..|.+. ++|...|.+|+++|.++|+.+||+|.+||+||||+||+++|++++..||+.+++|++.||++||+||.
T Consensus 172 Rfa~~L~~g~~~~~Vv~~a~~L~~rMkrdwm~tGRRPsglcGAaLliAar~h~~~rsi~dIv~vvhV~e~Tl~kRl~Ef~ 251 (521)
T KOG1598|consen 172 RFSCRLLFGDKTEDVAKTATRLAQRMKRDWMQTGRRPSGLCGAALLIAARMHGFRRTIGDIAKVVHVCESTLSKRLKEFS 251 (521)
T ss_pred chhHhhhcCCchHHHHHHHHHHHHHHHHHHHHhCCCccchhHHHHHHHHHHcCccccHHHHHHHHHHhHHHHHHHHHHHh
Confidence 999999875 46999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhcccCC
Q 046187 314 ENWDDLLP 321 (510)
Q Consensus 314 e~l~~Lip 321 (510)
+.+..-++
T Consensus 252 ~T~s~~Lt 259 (521)
T KOG1598|consen 252 DTLSGDLT 259 (521)
T ss_pred cccccccc
Confidence 98776554
No 5
>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=99.71 E-value=3.7e-17 Score=132.84 Aligned_cols=71 Identities=37% Similarity=0.478 Sum_probs=65.8
Q ss_pred HHHHHHHhCCCHHHHHHHHHHHHHHHhCCccCCccHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHH
Q 046187 139 IIDVASILGLDYDICDHAFQLFRDCCSATCLRNRSVEALATAALVQAIREAQEPRTLQEISIAANVPQKEI 209 (510)
Q Consensus 139 I~~ic~~L~LP~~VidtA~~LyK~a~e~~~lrGRs~eaVaAACLYIACR~~~~PrTLkEIa~vt~VskkeI 209 (510)
|.++|+.|+||..+.++|++||+++.+.++++||++..++|||||+|||+++.|+|++||+++++|++++|
T Consensus 1 I~r~~~~L~L~~~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~~~~t~~eIa~~~~Vs~~tI 71 (71)
T PF00382_consen 1 IPRICSKLGLPEDVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNGVPRTLKEIAEAAGVSEKTI 71 (71)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTTSSSSHHHHHHHCTSSHHHH
T ss_pred ChHHHhHcCCCHHHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHhCCCCCcC
Confidence 45799999999999999999999999999999999999999999999999999999999999999999886
No 6
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=99.66 E-value=2.7e-15 Score=152.16 Aligned_cols=182 Identities=16% Similarity=0.172 Sum_probs=157.3
Q ss_pred HHHHHHHHHHHhCCCHHHHHHHHHHHHHHHhCCccCCccHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCC----------
Q 046187 135 AYLQIIDVASILGLDYDICDHAFQLFRDCCSATCLRNRSVEALATAALVQAIREAQEPRTLQEISIAANV---------- 204 (510)
Q Consensus 135 a~~~I~~ic~~L~LP~~VidtA~~LyK~a~e~~~lrGRs~eaVaAACLYIACR~~~~PrTLkEIa~vt~V---------- 204 (510)
+..-|++-|-.|+||+...-++..||++++..+.+.+...+++++|||.+|.+.++.|++++||+.+++-
T Consensus 26 G~e~Iqea~ILL~L~q~a~atgqVLFqRf~~~ks~v~~~~e~vv~ACv~LASKiEE~Prr~rdVinVFh~L~~r~~~~~~ 105 (367)
T KOG0835|consen 26 GCELIQEAGILLNLPQVAMATGQVLFQRFCYSKSFVRHDFEIVVMACVLLASKIEEEPRRIRDVINVFHYLEQRRESEAA 105 (367)
T ss_pred hHHHHHhhhHhhcCcHHHHHHHHHHHHHHHhccccccccHHHHHHHHHHHHhhhccccccHhHHHHHHHHHHHHHhccCc
Confidence 5577888999999999999999999999999999999999999999999999999999999999998731
Q ss_pred -----------CHHHHHHHHHHHHHHhcccCCCCCcchhhhHHHHHhhcCCCHH--HHHHHHHHHHHHHhccccCCCChH
Q 046187 205 -----------PQKEIGKYIKILGEALQLSQPINSNSIAVHMPRFCTLLQLNKS--AQVLATHIGEVVINKCFCTRRNPI 271 (510)
Q Consensus 205 -----------skkeIgr~yk~L~k~L~i~~pv~~~~p~~~I~Rfcs~L~L~~~--V~~~A~~Ia~~a~~~~l~~GRsP~ 271 (510)
-+-.+.++...|.++||+...+.+ |+.+|.-|..-|++++. +.+++|.+.++..+..++...+|.
T Consensus 106 ~~~~~~~~~~~lk~~~ir~e~~ILr~LGF~~Hv~h--Phklii~YLqtL~~~~~~~l~Q~~wNfmNDslRT~v~vry~pe 183 (367)
T KOG0835|consen 106 EHLILARLYINLKMQVIRAERRILRELGFDVHVEH--PHKLIIMYLQTLQLPPNLKLLQAAWNFMNDSLRTDVFVRYSPE 183 (367)
T ss_pred chhhhhhHHhhhhhHHHHHHHHHHHHhCCeeeeec--cHHHHHHHHHHhcCCCchhHHHHHHHhhhhccccceeeecCHH
Confidence 123456777788999999877654 89999999999999853 689999999999999999999999
Q ss_pred HHHHHHHHHHHHHcCCCCC-HHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 272 SISAAAIYLACQLEDKRKT-QAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 272 sIAAAaIYlAarl~g~~~t-~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
+||+||||||++.++++++ +..+..++++++.-|-.....+.+....
T Consensus 184 ~iACaciyLaAR~~eIpLp~~P~Wf~~Fd~~k~eid~ic~~l~~lY~~ 231 (367)
T KOG0835|consen 184 SIACACIYLAARNLEIPLPFQPHWFKAFDTTKREIDEICYRLIPLYKR 231 (367)
T ss_pred HHHHHHHHHHHhhhcCCCCCCccHHHHcCCcHHHHHHHHHHHHHHHHh
Confidence 9999999999999997765 3489999999998887665555444433
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=99.65 E-value=6.5e-16 Score=125.55 Aligned_cols=71 Identities=35% Similarity=0.568 Sum_probs=66.7
Q ss_pred HHHHHhhcCCCHHHHHHHHHHHHHHHhccccCCCChHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHH
Q 046187 235 MPRFCTLLQLNKSAQVLATHIGEVVINKCFCTRRNPISISAAAIYLACQLEDKRKTQAEICKVTGLTEVTL 305 (510)
Q Consensus 235 I~Rfcs~L~L~~~V~~~A~~Ia~~a~~~~l~~GRsP~sIAAAaIYlAarl~g~~~t~keIa~vagVSe~TI 305 (510)
|+|||+.|+|++.|.+.|.+|++.+.+.++..||+|.+|||||||+||++++.++|++||+++++|++.||
T Consensus 1 I~r~~~~L~L~~~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~~~~t~~eIa~~~~Vs~~tI 71 (71)
T PF00382_consen 1 IPRICSKLGLPEDVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNGVPRTLKEIAEAAGVSEKTI 71 (71)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTTSSSSHHHHHHHCTSSHHHH
T ss_pred ChHHHhHcCCCHHHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHhCCCCCcC
Confidence 68999999999999999999999999999999999999999999999999999999999999999999997
No 8
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=99.64 E-value=6.6e-15 Score=151.51 Aligned_cols=184 Identities=16% Similarity=0.190 Sum_probs=156.4
Q ss_pred HHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHhCCccCCccHHHHHHHHHHHHHHhcCCCCCHHHHHHHhC--CCH----
Q 046187 133 LRAYLQIIDVASILGLDYDICDHAFQLFRDCCSATCLRNRSVEALATAALVQAIREAQEPRTLQEISIAAN--VPQ---- 206 (510)
Q Consensus 133 L~a~~~I~~ic~~L~LP~~VidtA~~LyK~a~e~~~lrGRs~eaVaAACLYIACR~~~~PrTLkEIa~vt~--Vsk---- 206 (510)
.++..-|.+++.+|++|+..+.+|+.||++++-...++.-....+|++|||+||+.++.|+.++||..+.. ..+
T Consensus 40 ~~~~~fI~elg~~L~~~~~ti~tA~~~~hRFy~~~s~~~~~~~~vA~sclfLAgKvEetp~kl~dIi~~s~~~~~~~~~~ 119 (323)
T KOG0834|consen 40 QEGAKFIQELGVRLKMPQKTIATAIVIFHRFYMFHSFKKFDPYTVAASCLFLAGKVEETPRKLEDIIKVSYRYLNPKDLE 119 (323)
T ss_pred HHHHHHHHHHHHHcCCCccchhhhhhhhhhhhhhcccccCcHHHHHHHHHHHHhhcccCcccHHHHHHHHHHHcCccccc
Confidence 34778899999999999999999999999999999999999999999999999999999999999988742 222
Q ss_pred ---------HHHHHHHHHHHHHhcccCCCCCcchhhhHHHHHhhcCCCHH----HHHHHHHHHHHHHhccccCCCChHHH
Q 046187 207 ---------KEIGKYIKILGEALQLSQPINSNSIAVHMPRFCTLLQLNKS----AQVLATHIGEVVINKCFCTRRNPISI 273 (510)
Q Consensus 207 ---------keIgr~yk~L~k~L~i~~pv~~~~p~~~I~Rfcs~L~L~~~----V~~~A~~Ia~~a~~~~l~~GRsP~sI 273 (510)
++|--.-+.|.+.|+++..+.. |+.||.+|+..|+.... ++..||.++++.....++....|..|
T Consensus 120 ~~~~~~~~~~~Iv~~E~~lL~tl~Fdl~v~h--Py~~ll~~~k~l~~~~~~~~~~a~~Aw~~~nD~~~t~~cL~y~p~~I 197 (323)
T KOG0834|consen 120 LEEVYWELKERIVQLELLLLETLGFDLNVEH--PYKYLLKYLKKLKADENLKQPLAQAAWNFVNDSLRTTLCLQYSPHSI 197 (323)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHccCceeccC--chHHHHHHHHHhhhhhhccccHHHHHHHHhchhheeeeeEeecCcEE
Confidence 2233334445667777776654 89999999999988764 89999999999999888999999999
Q ss_pred HHHHHHHHHHHcCCCCCH---HHHHHHhC--CCHHHHHHHHHHHHHhhcc
Q 046187 274 SAAAIYLACQLEDKRKTQ---AEICKVTG--LTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 274 AAAaIYlAarl~g~~~t~---keIa~vag--VSe~TIRkrYKEL~e~l~~ 318 (510)
|+||||+|+++.|...+. +.+.+.++ |+..-|+....++......
T Consensus 198 Ava~i~lA~~~~~~~~~~~~~~~w~~~~d~~vt~e~l~~i~~~~l~~y~~ 247 (323)
T KOG0834|consen 198 AVACIHLAAKLLGVELPSDTDKRWWREFDETVTNELLDDICHEFLDLYEQ 247 (323)
T ss_pred EeehhhHHHHHcCCCCCCCcccchhhhhcccCCHHHHHHHHHHHHHHHhh
Confidence 999999999999986543 25788888 9999999998888887754
No 9
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=99.58 E-value=9.5e-14 Score=142.55 Aligned_cols=168 Identities=11% Similarity=0.070 Sum_probs=139.2
Q ss_pred HHHHH-HH-HHHHHHHHHhC--CCHHHHHHHHHHHHHHHhCCccCCccHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCC
Q 046187 130 MDNLR-AY-LQIIDVASILG--LDYDICDHAFQLFRDCCSATCLRNRSVEALATAALVQAIREAQEPRTLQEISIAANVP 205 (510)
Q Consensus 130 er~L~-a~-~~I~~ic~~L~--LP~~VidtA~~LyK~a~e~~~lrGRs~eaVaAACLYIACR~~~~PrTLkEIa~vt~Vs 205 (510)
|..+. .| ..|.++|.+|+ ||+.|+-+|..||++++-.+.+.-..+..|+++|||+||+.++.|+++.+++..+.-.
T Consensus 52 E~~l~~~y~~~i~~~~~~lkp~Lpq~viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE~~~si~~fv~~~~~~ 131 (305)
T TIGR00569 52 ELDLVKYYEKRLLDFCSAFKPTMPTSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFVGNLKET 131 (305)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccccCcCHHHHHhhccCC
Confidence 34455 33 56778999999 9999999999999999999988888999999999999999999999999999866533
Q ss_pred ----HHHHHHHHHHHHHHhcccCCCCCcchhhhHHHHHhhcC-----C--CHHHHHHHHHHHHHHHhccccCCCChHHHH
Q 046187 206 ----QKEIGKYIKILGEALQLSQPINSNSIAVHMPRFCTLLQ-----L--NKSAQVLATHIGEVVINKCFCTRRNPISIS 274 (510)
Q Consensus 206 ----kkeIgr~yk~L~k~L~i~~pv~~~~p~~~I~Rfcs~L~-----L--~~~V~~~A~~Ia~~a~~~~l~~GRsP~sIA 274 (510)
..+|...-..|.+.|+++..+.. |..++..|...|+ + .+.+.+.|+.+++++....++.-..|..||
T Consensus 132 ~~~~~~~Il~~E~~lL~~L~F~L~V~h--Pyr~L~~~l~dl~~~l~~~~~~~~l~q~a~~~lndsl~Td~~L~y~Ps~IA 209 (305)
T TIGR00569 132 PLKALEQVLEYELLLIQQLNFHLIVHN--PYRPLEGFLIDIKTRLPGLENPEYLRKHADKFLNRTLLTDAYLLYTPSQIA 209 (305)
T ss_pred chhhHHHHHHHHHHHHHHCCCcEEeeC--ccHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHHHcCCceecCCHHHHH
Confidence 36788888889999998876643 7887777775442 2 246888999999999888888889999999
Q ss_pred HHHHHHHHHHcCCCCCHHHHHHHhCC
Q 046187 275 AAAIYLACQLEDKRKTQAEICKVTGL 300 (510)
Q Consensus 275 AAaIYlAarl~g~~~t~keIa~vagV 300 (510)
+||||+|++.++.+.+-.+. ++..+
T Consensus 210 lAAI~lA~~~~~~~l~~~~~-e~~~~ 234 (305)
T TIGR00569 210 LAAILHTASRAGLNMESYLT-EQLSV 234 (305)
T ss_pred HHHHHHHHHHhCCCCcccch-hhhcc
Confidence 99999999999987765443 55666
No 10
>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=99.40 E-value=2.4e-12 Score=130.42 Aligned_cols=154 Identities=20% Similarity=0.205 Sum_probs=132.3
Q ss_pred HHHHHHHHHHHhCCCHHHHHHHHHHHHHHHhCCccCCccHHHHHHHHHHHHHHhcCCCCCHHHHHHHhC--------CCH
Q 046187 135 AYLQIIDVASILGLDYDICDHAFQLFRDCCSATCLRNRSVEALATAALVQAIREAQEPRTLQEISIAAN--------VPQ 206 (510)
Q Consensus 135 a~~~I~~ic~~L~LP~~VidtA~~LyK~a~e~~~lrGRs~eaVaAACLYIACR~~~~PrTLkEIa~vt~--------Vsk 206 (510)
.++.|.++|.+|+||..+.++|..+|++++-....++.+...++++|||+|||.++.|+-+.=.+...+ -+.
T Consensus 48 ~~k~i~~l~~~L~lp~~~laTAi~~f~Rf~Lk~sv~e~~~~~vv~tcv~LA~K~ed~~~~I~i~~~~~~~~~se~~~~sr 127 (297)
T COG5333 48 YLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPRDISIESFEARDLWSEEPKSSR 127 (297)
T ss_pred HHHHHHHHHHhcCCCcchHHHHHHHHHHHHhhcccccccHHHHHHhheeeeeecccccchhhHHHHHhhccccccccccH
Confidence 558888999999999999999999999999999999999999999999999999998765554444433 256
Q ss_pred HHHHHHHHHHHHHhcccCCCCCcchhhhHHHHHhhcCCCH--HHHHHHHHHHHHHHhccccCCCChHHHHHHHHHHHHHH
Q 046187 207 KEIGKYIKILGEALQLSQPINSNSIAVHMPRFCTLLQLNK--SAQVLATHIGEVVINKCFCTRRNPISISAAAIYLACQL 284 (510)
Q Consensus 207 keIgr~yk~L~k~L~i~~pv~~~~p~~~I~Rfcs~L~L~~--~V~~~A~~Ia~~a~~~~l~~GRsP~sIAAAaIYlAarl 284 (510)
+.|-..-..+.+.|+++..+.. |..++..|...+.+.. +..+.||.++.++-+..++.=..|..||.|||++||..
T Consensus 128 ~~Il~~E~~lLEaL~fd~~V~h--Py~~l~~f~~~~q~~~~~~~~~~aw~~inDa~~t~~~llypphiIA~a~l~ia~~~ 205 (297)
T COG5333 128 ERILEYEFELLEALDFDLHVHH--PYKYLEGFLKDLQEKDKYKLLQIAWKIINDALRTDLCLLYPPHIIALAALLIACEV 205 (297)
T ss_pred HHHHHHHHHHHHHcccceEecc--ccHHHHHHHHHHHhccHHHHHHHHHHHHHhhhhceeeeecChHHHHHHHHHHHHHh
Confidence 7777777788899988876654 8889999998887654 59999999999999988888899999999999999999
Q ss_pred cCCCCC
Q 046187 285 EDKRKT 290 (510)
Q Consensus 285 ~g~~~t 290 (510)
.|.+..
T Consensus 206 ~~~~~~ 211 (297)
T COG5333 206 LGMPII 211 (297)
T ss_pred cCCccc
Confidence 987653
No 11
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=99.40 E-value=1.5e-12 Score=134.04 Aligned_cols=88 Identities=24% Similarity=0.230 Sum_probs=83.0
Q ss_pred HHHHHHHHHhCCCHHHHHHHHHHHHHHHhCCccCCccHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046187 137 LQIIDVASILGLDYDICDHAFQLFRDCCSATCLRNRSVEALATAALVQAIREAQEPRTLQEISIAANVPQKEIGKYIKIL 216 (510)
Q Consensus 137 ~~I~~ic~~L~LP~~VidtA~~LyK~a~e~~~lrGRs~eaVaAACLYIACR~~~~PrTLkEIa~vt~VskkeIgr~yk~L 216 (510)
.-|.++|+.|+||..+.++|.+|++++.+.+++.||++..+||||||+|||.++.|+|++||+.+++|+..+|++.|+.|
T Consensus 221 ~~i~r~~~~L~L~~~v~~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g~~~t~keIa~v~~Vs~~tI~~~ykel 300 (310)
T PRK00423 221 DYVPRFASELGLSGEVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERRTQREVAEVAGVTEVTVRNRYKEL 300 (310)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHH
Confidence 34557999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhcccC
Q 046187 217 GEALQLSQ 224 (510)
Q Consensus 217 ~k~L~i~~ 224 (510)
.+.|++..
T Consensus 301 ~~~l~~~~ 308 (310)
T PRK00423 301 AEKLDIKI 308 (310)
T ss_pred HHHhCccc
Confidence 99988643
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=99.35 E-value=1.4e-13 Score=102.11 Aligned_cols=43 Identities=26% Similarity=0.522 Sum_probs=38.2
Q ss_pred CCCCCCCCCCCcccccCCCCccccccccceecccceeecccccccc
Q 046187 1 MKCPYCSAAQGRCATTSTGRSITECGSCGRVIAERQCQNHHLFHIR 46 (510)
Q Consensus 1 m~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vleer~Id~~~EwR~f 46 (510)
|+||+|++.. ++.|+.+|+ .||++||.||+|++||+++|||+|
T Consensus 1 m~Cp~Cg~~~-~~~D~~~g~--~vC~~CG~Vl~e~~i~~~~e~r~f 43 (43)
T PF08271_consen 1 MKCPNCGSKE-IVFDPERGE--LVCPNCGLVLEENIIDEGPEWREF 43 (43)
T ss_dssp ESBTTTSSSE-EEEETTTTE--EEETTT-BBEE-TTBSCCCSCCHC
T ss_pred CCCcCCcCCc-eEEcCCCCe--EECCCCCCEeecccccCCcccccC
Confidence 8999999955 668999998 999999999999999999999987
No 13
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=99.19 E-value=2.9e-10 Score=111.29 Aligned_cols=175 Identities=19% Similarity=0.207 Sum_probs=131.1
Q ss_pred HHHHHHHHHhCCCHHHHHHHHHHHHHHHhCCccCCccHHHHHHHHHHHHHHhcCCC-CCHHHHHHHhC------------
Q 046187 137 LQIIDVASILGLDYDICDHAFQLFRDCCSATCLRNRSVEALATAALVQAIREAQEP-RTLQEISIAAN------------ 203 (510)
Q Consensus 137 ~~I~~ic~~L~LP~~VidtA~~LyK~a~e~~~lrGRs~eaVaAACLYIACR~~~~P-rTLkEIa~vt~------------ 203 (510)
.-|..+++.|+|-+.|+.+|..+|||++-++.+++-....+|+.|||+||+.++.| .-.+-|+..+.
T Consensus 46 n~I~~lg~~lklRQ~ViATAivY~rRfy~r~S~k~~~p~lla~TClyLAcKvEE~~i~~~r~l~~~a~~L~~~f~~~~e~ 125 (264)
T KOG0794|consen 46 NVIQKLGQHLKLRQRVIATAIVYFRRFYLRKSLKEIEPRLLAPTCLYLACKVEECPIVHIRLLVNEAKVLKTRFSYWPEK 125 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCHHHHHHHHHHHHhhhhhcchHHHHHHHHHHHHHhhhcccchhh
Confidence 56778999999999999999999999999999999999999999999999999998 22223332211
Q ss_pred --CCHHHHHHHHHHHHHHhcccCCCCCcchhhhHHHHHhhcCCC-HHHHHHHHHHHHHHHhccccCCCChHHHHHHHHHH
Q 046187 204 --VPQKEIGKYIKILGEALQLSQPINSNSIAVHMPRFCTLLQLN-KSAQVLATHIGEVVINKCFCTRRNPISISAAAIYL 280 (510)
Q Consensus 204 --VskkeIgr~yk~L~k~L~i~~pv~~~~p~~~I~Rfcs~L~L~-~~V~~~A~~Ia~~a~~~~l~~GRsP~sIAAAaIYl 280 (510)
...+.|-..--.|.+.|+--.-+. +|..-+..+...+|+. ....+.+|.|+++.-+..++.=..|.-||.||||+
T Consensus 126 ~~~~~~~I~e~Ef~llE~Ld~~LIVh--HPYrsL~q~~qd~gi~d~~~l~~~W~ivNDSyr~Dl~Ll~PPh~IalAcl~I 203 (264)
T KOG0794|consen 126 FPYERKDILEMEFYLLEALDCYLIVH--HPYRSLLQFVQDMGINDQKLLQLAWSIVNDSYRMDLCLLYPPHQIALACLYI 203 (264)
T ss_pred cCCCcCcchhhhhhHHhhhceeEEEe--cCCccHHHHHHHhcccchhhhhhhHhhhcchhhcceeeecCHHHHHHHHHHH
Confidence 122334334344555555333222 3666788999999984 55889999999999999999899999999999999
Q ss_pred HHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046187 281 ACQLEDKRKTQAEICKVTGLTEVTLRKVYKELLE 314 (510)
Q Consensus 281 Aarl~g~~~t~keIa~vagVSe~TIRkrYKEL~e 314 (510)
||...+...+ +.+-....|.-.-+.+...+++.
T Consensus 204 a~~~~~k~~~-~~w~~el~vD~ekV~~~v~~I~~ 236 (264)
T KOG0794|consen 204 ACVIDEKDIP-KAWFAELSVDMEKVKDIVQEILK 236 (264)
T ss_pred HHhhcCCChH-HHHHHHHhccHHHHHHHHHHHHH
Confidence 9998876554 44544555555555555555444
No 14
>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=99.03 E-value=2.2e-09 Score=86.75 Aligned_cols=84 Identities=26% Similarity=0.322 Sum_probs=79.4
Q ss_pred chhhhHHHHHhhcCCCHHHHHHHHHHHHHHHhccccCCCChHHHHHHHHHHHHHHcCCCCCHHHHHHHhCC-CHHHHHHH
Q 046187 230 SIAVHMPRFCTLLQLNKSAQVLATHIGEVVINKCFCTRRNPISISAAAIYLACQLEDKRKTQAEICKVTGL-TEVTLRKV 308 (510)
Q Consensus 230 ~p~~~I~Rfcs~L~L~~~V~~~A~~Ia~~a~~~~l~~GRsP~sIAAAaIYlAarl~g~~~t~keIa~vagV-Se~TIRkr 308 (510)
.+.++|.++++.++++.++...|..++++........+++|..||+||||+|+++.+...+.+++...++. +..+|++.
T Consensus 4 ~~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~~~~~i~~~ 83 (88)
T cd00043 4 TPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEIPPWLKDLVHVTGYATEEEILRM 83 (88)
T ss_pred hHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCCCCCHHHHhHHhCCCCHHHHHHH
Confidence 46889999999999999999999999999988888889999999999999999999999999999999999 99999999
Q ss_pred HHHHH
Q 046187 309 YKELL 313 (510)
Q Consensus 309 YKEL~ 313 (510)
+++|+
T Consensus 84 e~~il 88 (88)
T cd00043 84 EKLLL 88 (88)
T ss_pred HHHhC
Confidence 98873
No 15
>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=99.01 E-value=2.1e-09 Score=86.13 Aligned_cols=81 Identities=28% Similarity=0.374 Sum_probs=74.7
Q ss_pred hhHHHHHhhcCCCHHHHHHHHHHHHHHHhccccCCCChHHHHHHHHHHHHHHcCCCCCHHHHHHHhCC-CHHHHHHHHHH
Q 046187 233 VHMPRFCTLLQLNKSAQVLATHIGEVVINKCFCTRRNPISISAAAIYLACQLEDKRKTQAEICKVTGL-TEVTLRKVYKE 311 (510)
Q Consensus 233 ~~I~Rfcs~L~L~~~V~~~A~~Ia~~a~~~~l~~GRsP~sIAAAaIYlAarl~g~~~t~keIa~vagV-Se~TIRkrYKE 311 (510)
+||.++++.++++.++...|..+++++....-+.+++|..||+||||+|+++.+...+.+++...+++ ++.+|++.+++
T Consensus 1 ~~l~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~~~~~i~~~~~~ 80 (83)
T smart00385 1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLAAKTEEIPPWTKELVHYTGYFTEEEILRMEKL 80 (83)
T ss_pred CHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHhcCCCCchhHhHhhCCCCHHHHHHHHHH
Confidence 48999999999999999999999999987544556999999999999999999998999999999999 99999999998
Q ss_pred HH
Q 046187 312 LL 313 (510)
Q Consensus 312 L~ 313 (510)
|.
T Consensus 81 il 82 (83)
T smart00385 81 LL 82 (83)
T ss_pred Hh
Confidence 86
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=99.01 E-value=4.2e-09 Score=85.08 Aligned_cols=82 Identities=24% Similarity=0.226 Sum_probs=76.7
Q ss_pred HHHHHHHHHHHhCCCHHHHHHHHHHHHHHHhCCccCCccHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCC-CHHHHHHHH
Q 046187 135 AYLQIIDVASILGLDYDICDHAFQLFRDCCSATCLRNRSVEALATAALVQAIREAQEPRTLQEISIAANV-PQKEIGKYI 213 (510)
Q Consensus 135 a~~~I~~ic~~L~LP~~VidtA~~LyK~a~e~~~lrGRs~eaVaAACLYIACR~~~~PrTLkEIa~vt~V-skkeIgr~y 213 (510)
.+.-|.++|..++++..+...|..+++++...+.+.+++...+++||||+|||.++.+.+++|+...++. +..+|.+.+
T Consensus 5 ~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~~~~~i~~~e 84 (88)
T cd00043 5 PLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEIPPWLKDLVHVTGYATEEEILRME 84 (88)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCCCCCHHHHhHHhCCCCHHHHHHHH
Confidence 4566778999999999999999999999999999999999999999999999999999999999999999 999999888
Q ss_pred HHH
Q 046187 214 KIL 216 (510)
Q Consensus 214 k~L 216 (510)
+.|
T Consensus 85 ~~i 87 (88)
T cd00043 85 KLL 87 (88)
T ss_pred HHh
Confidence 765
No 17
>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=98.97 E-value=3.5e-09 Score=84.81 Aligned_cols=79 Identities=24% Similarity=0.200 Sum_probs=71.5
Q ss_pred HHHHHHHhCCCHHHHHHHHHHHHHHHhCCccCCccHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCC-CHHHHHHHHHHHH
Q 046187 139 IIDVASILGLDYDICDHAFQLFRDCCSATCLRNRSVEALATAALVQAIREAQEPRTLQEISIAANV-PQKEIGKYIKILG 217 (510)
Q Consensus 139 I~~ic~~L~LP~~VidtA~~LyK~a~e~~~lrGRs~eaVaAACLYIACR~~~~PrTLkEIa~vt~V-skkeIgr~yk~L~ 217 (510)
|.+++..+++|..+...|..+++++.....+.+++...++|||||+|||.++.+++.+++...+++ +.++|.+.++.|.
T Consensus 3 l~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~~~~~i~~~~~~il 82 (83)
T smart00385 3 LRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLAAKTEEIPPWTKELVHYTGYFTEEEILRMEKLLL 82 (83)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHhcCCCCchhHhHhhCCCCHHHHHHHHHHHh
Confidence 567999999999999999999999998544445999999999999999999999999999999999 9999999888764
No 18
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=98.93 E-value=6.1e-09 Score=106.32 Aligned_cols=92 Identities=25% Similarity=0.389 Sum_probs=87.3
Q ss_pred hhhhHHHHHhhcCCCHHHHHHHHHHHHHHHhccccCCCChHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHH
Q 046187 231 IAVHMPRFCTLLQLNKSAQVLATHIGEVVINKCFCTRRNPISISAAAIYLACQLEDKRKTQAEICKVTGLTEVTLRKVYK 310 (510)
Q Consensus 231 p~~~I~Rfcs~L~L~~~V~~~A~~Ia~~a~~~~l~~GRsP~sIAAAaIYlAarl~g~~~t~keIa~vagVSe~TIRkrYK 310 (510)
.-.++.++|+.|+|+..|...|..|.+.+.+.+++.||+..+++|||||+||+..+.++++.||+.+++|+..-|.++|+
T Consensus 100 a~~~l~~~~~~l~LP~~v~e~A~~iyr~a~~~~l~rGRsie~v~AA~iY~acR~~~~prtl~eIa~a~~V~~kei~rtyr 179 (285)
T COG1405 100 ALEELERIASALGLPESVRETAARIYRKAVDKGLLRGRSIESVAAACIYAACRINGVPRTLDEIAKALGVSKKEIGRTYR 179 (285)
T ss_pred HHHHHHHHHHHhCCCchHHHHHHHHHHHHhhcCCCcCCcHHHHHHHHHHHHHHHcCCCccHHHHHHHHCCCHHHHHHHHH
Confidence 34688899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhcccCCC
Q 046187 311 ELLENWDDLLPS 322 (510)
Q Consensus 311 EL~e~l~~Lip~ 322 (510)
.+.+.+..-+++
T Consensus 180 ~~~~~L~l~~~~ 191 (285)
T COG1405 180 LLVRELKLKIPP 191 (285)
T ss_pred HHHHhcCCCCCC
Confidence 999999987654
No 19
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=98.77 E-value=2.5e-08 Score=100.81 Aligned_cols=85 Identities=21% Similarity=0.130 Sum_probs=80.0
Q ss_pred HHHHHHHHhCCCHHHHHHHHHHHHHHHhCCccCCccHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046187 138 QIIDVASILGLDYDICDHAFQLFRDCCSATCLRNRSVEALATAALVQAIREAQEPRTLQEISIAANVPQKEIGKYIKILG 217 (510)
Q Consensus 138 ~I~~ic~~L~LP~~VidtA~~LyK~a~e~~~lrGRs~eaVaAACLYIACR~~~~PrTLkEIa~vt~VskkeIgr~yk~L~ 217 (510)
-|.++|..|+||..+.+.|.++.+++.+.....||++-.||||+|||+|+....+++++||.+++||..-.|+..||.|-
T Consensus 206 ~m~RFCs~L~L~~~~q~aA~e~a~ka~~~~~~~gRsPiSIAAa~IYmisqls~~kkt~keI~~vtgVaE~TIr~sYK~Ly 285 (308)
T KOG1597|consen 206 FMPRFCSNLGLPKSAQEAATEIAEKAEEMDIRAGRSPISIAAAAIYMISQLSDEKKTQKEIGEVTGVAEVTIRNSYKDLY 285 (308)
T ss_pred HHHHHHHhcCCCHHHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHhccCcccHHHHHHHhhhhHHHHHHHHHHHh
Confidence 44579999999999999999999999999999999999999999999999999999999999999999999999999987
Q ss_pred HHhcc
Q 046187 218 EALQL 222 (510)
Q Consensus 218 k~L~i 222 (510)
..+..
T Consensus 286 p~~~~ 290 (308)
T KOG1597|consen 286 PHADK 290 (308)
T ss_pred hchhh
Confidence 76643
No 20
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning]
Probab=98.53 E-value=5.3e-06 Score=86.34 Aligned_cols=176 Identities=15% Similarity=0.073 Sum_probs=135.5
Q ss_pred HHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHhCCccCCcc---HHHHHHHHHHHHHHhcCC--CCCHHHHHHHh--CCC
Q 046187 133 LRAYLQIIDVASILGLDYDICDHAFQLFRDCCSATCLRNRS---VEALATAALVQAIREAQE--PRTLQEISIAA--NVP 205 (510)
Q Consensus 133 L~a~~~I~~ic~~L~LP~~VidtA~~LyK~a~e~~~lrGRs---~eaVaAACLYIACR~~~~--PrTLkEIa~vt--~Vs 205 (510)
..|+.=|.++|...+....+.=-|+.|+.|+.....+..-+ ...+|+|||.+|.|.+++ |.++.-.+..+ -..
T Consensus 79 ~~A~~WIl~V~~~~~~~~~~~~LA~NYlDRFls~~~l~k~k~W~lQLlAvaCLsLAsKmeE~~vPll~dl~v~~~~~~fe 158 (335)
T KOG0656|consen 79 KQALDWILKVCEEYNFEPLVFLLAMNYLDRFLSSQKLPKDKPWMLQLLAVACLSLASKMEETDVPLLADLQVEYTDNVFE 158 (335)
T ss_pred HHHHHHHHHHHHHhCCchHHHHHHHHHHHHhhcccccCCCchHHHHHHHHHHHHHHHhhcCcCCchhhhhhhcccccccc
Confidence 34777888999999999999999999999999875555444 788999999999999887 66555555543 367
Q ss_pred HHHHHHHHHHHHHHhcccCCCCCcchhhhHHHHHhhcCCC----HHHHHHHHHHHHHHHhccccCCCChHHHHHHHHHHH
Q 046187 206 QKEIGKYIKILGEALQLSQPINSNSIAVHMPRFCTLLQLN----KSAQVLATHIGEVVINKCFCTRRNPISISAAAIYLA 281 (510)
Q Consensus 206 kkeIgr~yk~L~k~L~i~~pv~~~~p~~~I~Rfcs~L~L~----~~V~~~A~~Ia~~a~~~~l~~GRsP~sIAAAaIYlA 281 (510)
.+.|.|.-..|...|+=..... .|.+|+.-|+++++.. ..+...+..++-....+.-..+..|..||||++..+
T Consensus 159 aktI~rmELLVLstL~Wrl~aV--TP~sF~~~fl~ki~~~~~~~~~~~~~~s~~ll~~~~d~~Fl~y~pSviAaa~~~~v 236 (335)
T KOG0656|consen 159 AKTIQRMELLVLSTLKWRLRAV--TPFSFIDHFLSKISQKDHNKHLFLKHASLFLLSVITDIKFLEYPPSVIAAAAILSV 236 (335)
T ss_pred HHHHHHHHHHHHhhccccccCC--CchHHHHHHHHHcCcccchHHHHHHHHHHHHHHHhhhhhhhcCChHHHHHHHHHHH
Confidence 8999999999999998655432 3899999999999985 345666665554444455567899999999999777
Q ss_pred HHHc-CCCC--CHHHHHHHhCCCHHHHHHHHH
Q 046187 282 CQLE-DKRK--TQAEICKVTGLTEVTLRKVYK 310 (510)
Q Consensus 282 arl~-g~~~--t~keIa~vagVSe~TIRkrYK 310 (510)
+... +... ....+.....|+...+++.|.
T Consensus 237 ~~~~~~l~~~~~~~~~~~~~~l~~e~~~~~~~ 268 (335)
T KOG0656|consen 237 SASVDGLDFREYENNLLSLLSLSKEKVNRCYD 268 (335)
T ss_pred HHhhcchhhhhhhHHHHHHHHhhHHhhhcchh
Confidence 7543 3322 235577778899999998888
No 21
>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=98.14 E-value=3.6e-05 Score=78.66 Aligned_cols=145 Identities=14% Similarity=0.144 Sum_probs=100.8
Q ss_pred HHHHHHHHh--CCCHHHHHHHHHHHHHHHhCCccCCccHHHHHHHHHHHHHHhcCCCCCHHHHHHHhC----CCHHHHHH
Q 046187 138 QIIDVASIL--GLDYDICDHAFQLFRDCCSATCLRNRSVEALATAALVQAIREAQEPRTLQEISIAAN----VPQKEIGK 211 (510)
Q Consensus 138 ~I~~ic~~L--~LP~~VidtA~~LyK~a~e~~~lrGRs~eaVaAACLYIACR~~~~PrTLkEIa~vt~----VskkeIgr 211 (510)
...++|+++ +||..|+-+|..+||+++-.+..-.-++..|+++|+|+||+.++.-+++.+|+.-.+ -....|-+
T Consensus 62 ~l~~f~~k~~p~lp~~Vv~TA~~fFkRffL~nsvme~~pk~I~~tc~flA~Kieef~ISieqFvkn~~~~~~k~~e~vLk 141 (325)
T KOG2496|consen 62 SLVNFYSKFKPNLPTSVVSTAIEFFKRFFLENSVMEYSPKIIMATCFFLACKIEEFYISIEQFVKNMNGRKWKTHEIVLK 141 (325)
T ss_pred HHHHHHHHhcCCCchHHHHHHHHHHHHHHHhcchhhcChHHHHHHHHHHHhhhHhheecHHHHHhhccCcccccHHHHHh
Confidence 344677777 599999999999999999999888889999999999999999999999999998766 23344444
Q ss_pred HHHHHHHHhcccCCCCC--cchhhhHHHHHhhcC-C--CHHHHH--HHHHHHHHHHhccccCCCChHHHHHHHHHHHH
Q 046187 212 YIKILGEALQLSQPINS--NSIAVHMPRFCTLLQ-L--NKSAQV--LATHIGEVVINKCFCTRRNPISISAAAIYLAC 282 (510)
Q Consensus 212 ~yk~L~k~L~i~~pv~~--~~p~~~I~Rfcs~L~-L--~~~V~~--~A~~Ia~~a~~~~l~~GRsP~sIAAAaIYlAa 282 (510)
.-..+.+.|++...+.. -..+-|+..+-..|. + ++.... ....+++++.-.....=..|.-||.|||..++
T Consensus 142 ~E~~llqsL~f~L~vh~PyRPleGFl~D~kt~l~~~~n~d~~~~~~d~~~fl~~~lltDa~lLytPsQIALaAil~a~ 219 (325)
T KOG2496|consen 142 YEFLLLQSLKFSLTVHNPYRPLEGFLLDMKTRLPALENPDILRKHDDSKKFLDRALLTDAYLLYTPSQIALAAILHAA 219 (325)
T ss_pred chHHHHHhhhhhheecCCCCchHHHHHHHHHHHHhccCHHHHhhhhhHHHHHHHHHHhccceecChHHHHHHHHHHHh
Confidence 44556777776644321 012344444333321 1 121111 22356666655566666899999999995554
No 22
>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=97.97 E-value=0.0001 Score=64.84 Aligned_cols=89 Identities=19% Similarity=0.236 Sum_probs=74.6
Q ss_pred HHHHHHHHHHHhCCCHHHHHHHHHHHHHHHhCCccCCccHHHHHHHHHHHHHHhcCC-CCCHHHHHHHhC--CCHHHHHH
Q 046187 135 AYLQIIDVASILGLDYDICDHAFQLFRDCCSATCLRNRSVEALATAALVQAIREAQE-PRTLQEISIAAN--VPQKEIGK 211 (510)
Q Consensus 135 a~~~I~~ic~~L~LP~~VidtA~~LyK~a~e~~~lrGRs~eaVaAACLYIACR~~~~-PrTLkEIa~vt~--VskkeIgr 211 (510)
...-|.+++..++++..+.-.|..+|.++.........+...+++||+|+|||.++. +.++.++....+ .++++|.+
T Consensus 34 ~~~~i~~~~~~~~l~~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~e~~~~~~~~~~~~~~~~~~~~~i~~ 113 (127)
T PF00134_consen 34 IIDWIIELCQRLKLSPETLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKMEEDNPPSISDLIRISDNTFTKKDILE 113 (127)
T ss_dssp HHHHHHHHHHHTT-BHHHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHHTSS--HHHHHHHHTTTSSHHHHHHH
T ss_pred HHHHHHHHHHhcccchhHHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhhccccchHHHHHHHHcCCCCHHHHHH
Confidence 445677899999999999999999999999988888888899999999999999887 888999988773 67889999
Q ss_pred HHHHHHHHhccc
Q 046187 212 YIKILGEALQLS 223 (510)
Q Consensus 212 ~yk~L~k~L~i~ 223 (510)
.-+.|.+.|+.+
T Consensus 114 ~E~~iL~~L~f~ 125 (127)
T PF00134_consen 114 MEREILSALNFD 125 (127)
T ss_dssp HHHHHHHHTTT-
T ss_pred HHHHHHHHCCCC
Confidence 988888888764
No 23
>KOG0653 consensus Cyclin B and related kinase-activating proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=97.93 E-value=8e-05 Score=79.47 Aligned_cols=149 Identities=16% Similarity=0.193 Sum_probs=120.8
Q ss_pred HHHHHHHHhCCCHHHHHHHHHHHHHHHhCCccCCccHHHHHHHHHH-HHHHhcCC-CCCHHHHHHHhC--CCHHHHHHHH
Q 046187 138 QIIDVASILGLDYDICDHAFQLFRDCCSATCLRNRSVEALATAALV-QAIREAQE-PRTLQEISIAAN--VPQKEIGKYI 213 (510)
Q Consensus 138 ~I~~ic~~L~LP~~VidtA~~LyK~a~e~~~lrGRs~eaVaAACLY-IACR~~~~-PrTLkEIa~vt~--VskkeIgr~y 213 (510)
-+.++-.+++|...+.--|..|++++.....+..++...+..+|++ ||||.+.. +-++.|+.-+++ .+..+|.+.-
T Consensus 164 wlvevh~~F~L~~ETL~LaVnliDRfL~~~~v~~~~lqLvgvsalf~IA~K~EE~~~P~v~dlv~isd~~~s~~~il~mE 243 (391)
T KOG0653|consen 164 WLVEVHEKFGLSPETLYLAVNLIDRFLSKVKVPLKKLQLVGVSALLSIACKYEEISLPSVEDLVLITDGAYSREEILRME 243 (391)
T ss_pred HHHHhhhhcCcCHHHHHHHHHHHHHHHHHhcccHHHhhHHhHHHHHHHHHhhhhccCCccceeEeeeCCccchHHHHHHH
Confidence 3557889999999999999999999999877777888888888866 99996444 344777766654 7899999999
Q ss_pred HHHHHHhcccCCCCCcchhhhHHHHHhhcCCCHHHHHHHHHHHHHHHhccccCCCChHHHHHHHHHHHHHHcCCC
Q 046187 214 KILGEALQLSQPINSNSIAVHMPRFCTLLQLNKSAQVLATHIGEVVINKCFCTRRNPISISAAAIYLACQLEDKR 288 (510)
Q Consensus 214 k~L~k~L~i~~pv~~~~p~~~I~Rfcs~L~L~~~V~~~A~~Ia~~a~~~~l~~GRsP~sIAAAaIYlAarl~g~~ 288 (510)
+.+...|+...... .|..|+.||.+...........+..+++...-..-.....|..+|||+.+++.++...+
T Consensus 244 ~~il~~L~f~l~~p--~~~~FLrr~~ka~~~d~~~~~~~k~~~El~l~d~~~~~~~~s~~aaa~~~~~~~~~~~~ 316 (391)
T KOG0653|consen 244 KYILNVLEFDLSVP--TPLSFLRRFLKAADYDIKTRTLVKYLLELSLCDYSMLSIPPSSSAAASFTLALRMLSKG 316 (391)
T ss_pred HHHHhccCeeecCC--chHHHHHHHHHhhhcchhHHHHHHHHHHHHHhhhHHhccCcHHHHHHHHHHHHHHhccC
Confidence 99999998776554 37899999999999777777777777776665555567889999999999999988655
No 24
>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=97.87 E-value=7.3e-05 Score=64.54 Aligned_cols=90 Identities=21% Similarity=0.200 Sum_probs=74.9
Q ss_pred chhhhHHHHHhhcCCCHHHHHHHHHHHHHHHhccccCCCChHHHHHHHHHHHHHHcCC-CCCHHHHHHHhCCCHHHHHHH
Q 046187 230 SIAVHMPRFCTLLQLNKSAQVLATHIGEVVINKCFCTRRNPISISAAAIYLACQLEDK-RKTQAEICKVTGLTEVTLRKV 308 (510)
Q Consensus 230 ~p~~~I~Rfcs~L~L~~~V~~~A~~Ia~~a~~~~l~~GRsP~sIAAAaIYlAarl~g~-~~t~keIa~vagVSe~TIRkr 308 (510)
.|..|+.+|....+.+.++...|+.|++.+.-..-..+.+|..|||||||+|...++. +.....+...+|+....|+..
T Consensus 2 Tp~~Fl~~~~~~~~~~~~~~~~a~~l~el~l~~~~fl~~~PS~iAaAai~lA~~~~~~~~~~~~~l~~~t~~~~~~l~~c 81 (118)
T PF02984_consen 2 TPYDFLRRFLKISNADQEVRNLARYLLELSLLDYEFLQYPPSVIAAAAILLARKILGKEPPWPESLEKLTGYDKEDLKEC 81 (118)
T ss_dssp -HHHHHHHHHTSSSHHHHHHHHHHHHHHHHHHSHHHTTS-HHHHHHHHHHHHHHHHHSSTCSHHHHHHHHTS-HHHHHHH
T ss_pred cHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhCccccCCccchhhcCCCHHHHHHH
Confidence 4789999997666667789999999999887777788899999999999999999875 455677888999999999999
Q ss_pred HHHHHHhhccc
Q 046187 309 YKELLENWDDL 319 (510)
Q Consensus 309 YKEL~e~l~~L 319 (510)
++.|.+.....
T Consensus 82 ~~~i~~~~~~~ 92 (118)
T PF02984_consen 82 IELIQELLSKA 92 (118)
T ss_dssp HHHHHHHHHHC
T ss_pred HHHHHHHHHhc
Confidence 99999887643
No 25
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=97.78 E-value=2.5e-05 Score=84.93 Aligned_cols=79 Identities=22% Similarity=0.150 Sum_probs=62.7
Q ss_pred CCCHH--HHHHHHHHHHHHHhCCccCCccHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhcccC
Q 046187 147 GLDYD--ICDHAFQLFRDCCSATCLRNRSVEALATAALVQAIREAQEPRTLQEISIAANVPQKEIGKYIKILGEALQLSQ 224 (510)
Q Consensus 147 ~LP~~--VidtA~~LyK~a~e~~~lrGRs~eaVaAACLYIACR~~~~PrTLkEIa~vt~VskkeIgr~yk~L~k~L~i~~ 224 (510)
..+.+ |+.+|..|..+...-=...||++..++.||||||||.+|+++|..||+.+.+|+...|.+.|+.|...+....
T Consensus 179 ~g~~~~~Vv~~a~~L~~rMkrdwm~tGRRPsglcGAaLliAar~h~~~rsi~dIv~vvhV~e~Tl~kRl~Ef~~T~s~~L 258 (521)
T KOG1598|consen 179 FGDKTEDVAKTATRLAQRMKRDWMQTGRRPSGLCGAALLIAARMHGFRRTIGDIAKVVHVCESTLSKRLKEFSDTLSGDL 258 (521)
T ss_pred cCCchHHHHHHHHHHHHHHHHHHHHhCCCccchhHHHHHHHHHHcCccccHHHHHHHHHHhHHHHHHHHHHHhccccccc
Confidence 34444 4444544444444434678999999999999999999999999999999999999999999999988776544
Q ss_pred C
Q 046187 225 P 225 (510)
Q Consensus 225 p 225 (510)
+
T Consensus 259 t 259 (521)
T KOG1598|consen 259 T 259 (521)
T ss_pred c
Confidence 3
No 26
>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=97.72 E-value=0.00018 Score=66.27 Aligned_cols=70 Identities=16% Similarity=0.292 Sum_probs=60.3
Q ss_pred HHHHHHHHHHHhCCCHHHHHHHHHHHHHHHhC--CccCCccHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCC
Q 046187 135 AYLQIIDVASILGLDYDICDHAFQLFRDCCSA--TCLRNRSVEALATAALVQAIREAQEPRTLQEISIAANV 204 (510)
Q Consensus 135 a~~~I~~ic~~L~LP~~VidtA~~LyK~a~e~--~~lrGRs~eaVaAACLYIACR~~~~PrTLkEIa~vt~V 204 (510)
|+.+|.++|++|+|++.+.+....+|+.+... .++++|..+.++..|+|+.||..+..+||+||.....-
T Consensus 14 a~~Rl~~LC~~L~l~~~~~~~iwt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~~~sF~~Ii~~Yr~ 85 (135)
T PF01857_consen 14 AAVRLQDLCERLDLSSDLREKIWTCFEHSLTHHTELMKDRHLDQIILCAIYGICKVSKEELSFKDIIKAYRK 85 (135)
T ss_dssp HHHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHHHHHHHHTT-S--HHHHHHHHTT
T ss_pred HHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhhcCCCCHHHHHHHHHh
Confidence 77899999999999999999999999888754 78999999999999999999999999999999887653
No 27
>COG5024 Cyclin [Cell division and chromosome partitioning]
Probab=97.66 E-value=0.00035 Score=75.45 Aligned_cols=176 Identities=16% Similarity=0.169 Sum_probs=130.6
Q ss_pred HHHHHhCCCHHHHHHHHHHHHHHHhCCccCCccHHHHHHHHHHHHHHhcCC-CCCHHHHHHHhC--CCHHHHHHHHHHHH
Q 046187 141 DVASILGLDYDICDHAFQLFRDCCSATCLRNRSVEALATAALVQAIREAQE-PRTLQEISIAAN--VPQKEIGKYIKILG 217 (510)
Q Consensus 141 ~ic~~L~LP~~VidtA~~LyK~a~e~~~lrGRs~eaVaAACLYIACR~~~~-PrTLkEIa~vt~--VskkeIgr~yk~L~ 217 (510)
++-..|+|-..+...|..|..+++..+...=.+...+++.|+||||+-+++ +.+++++.-++. .+.++|.++.+.+.
T Consensus 222 evH~~F~llpeTL~lainiiDrfLs~~~v~l~k~QLvg~s~LfIa~K~EE~~~p~i~~l~~~t~g~~t~~~i~~aE~~ml 301 (440)
T COG5024 222 EVHGKFGLLPETLFLAINIIDRFLSSRVVSLEKYQLVGISALFIASKYEEVNCPSIKDLVYATDGAFTRDDIIRAERYML 301 (440)
T ss_pred HhcccccccchHHHHHHHHHHHHhccCcccHHHHHHHHHHHHHHHHhHhHhcCHHHHHHHHHHcccccHHHHHHHHHHHh
Confidence 466778888889999999999999987777677788999999999998776 456888888763 78999999999999
Q ss_pred HHhcccCCCCCcchhhhHHHHHhhcCCCHHHHHHHHHHHHHHHhc-cccCCCChHHHHHHHHHHHHHHcCCCCCHHHHHH
Q 046187 218 EALQLSQPINSNSIAVHMPRFCTLLQLNKSAQVLATHIGEVVINK-CFCTRRNPISISAAAIYLACQLEDKRKTQAEICK 296 (510)
Q Consensus 218 k~L~i~~pv~~~~p~~~I~Rfcs~L~L~~~V~~~A~~Ia~~a~~~-~l~~GRsP~sIAAAaIYlAarl~g~~~t~keIa~ 296 (510)
..|+.+.-.+ .|..|++|+....+.+......+..+..-..-. .+.... |..+||||-|++-.+++..-.-....-
T Consensus 302 ~~l~f~is~P--~P~sFLRriSka~dyd~~srt~~k~~~e~s~~~~~f~~~~-~S~~~aaa~~~s~~~~~~~~w~~~l~~ 378 (440)
T COG5024 302 EVLDFNISWP--SPMSFLRRISKASDYDIFSRTPAKFSSEISPVDYKFIQIS-PSWCAAAAMYLSRKILSQNQWDRTLIH 378 (440)
T ss_pred hhcccccCCC--ChHHHHHHHHhhcccchhhhhhHhhhCCchHhhhhhccCC-chHHHHHHHHHHHhhhccCCCCccccc
Confidence 9998876543 478899999888888877776777665443322 344445 999999999999988864321111122
Q ss_pred HhC-CCHHHHHHHHHHHHHhhccc
Q 046187 297 VTG-LTEVTLRKVYKELLENWDDL 319 (510)
Q Consensus 297 vag-VSe~TIRkrYKEL~e~l~~L 319 (510)
..| -+..-++.....+.+.+...
T Consensus 379 ySg~y~~~~l~~~~~~~~~~l~~~ 402 (440)
T COG5024 379 YSGNYTNPDLKPLNESNKENLQNP 402 (440)
T ss_pred cCCCCCchhHHHHHHHHHHHhccc
Confidence 223 45556676777777766553
No 28
>KOG4557 consensus Origin recognition complex, subunit 6 [Replication, recombination and repair]
Probab=97.60 E-value=0.0032 Score=61.93 Aligned_cols=171 Identities=18% Similarity=0.163 Sum_probs=124.9
Q ss_pred HHHHHHHhCC--CHHHHHHHHHHHHHHHhC--CccCCccHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHH
Q 046187 139 IIDVASILGL--DYDICDHAFQLFRDCCSA--TCLRNRSVEALATAALVQAIREAQEPRTLQEISIAANVPQKEIGKYIK 214 (510)
Q Consensus 139 I~~ic~~L~L--P~~VidtA~~LyK~a~e~--~~lrGRs~eaVaAACLYIACR~~~~PrTLkEIa~vt~VskkeIgr~yk 214 (510)
|.+++.+||| ...+++.|.+|.+.+.-. +..-|-.-..-|.-|+=+|.-..+++..-.-...+.|++++...+.++
T Consensus 3 I~~l~~klgL~~ep~~lrKa~E~~RL~~~~~~~~~~~v~E~~kaV~CldlAa~~l~i~fDr~~avKLSGl~k~~Y~~~~~ 82 (262)
T KOG4557|consen 3 ISDLGRKLGLDNEPLLLRKAAEIRRLCDAQFDSSIIGVGEICKAVICLDLAATRLQIIFDRQAAVKLSGLSKKAYSRSFN 82 (262)
T ss_pred HHHHHHhcCCccChHHHHHHHHHHHHHHhhccCccccccchhHHHHhHHHHHHHhcccccHHHHHHhccccHHHHHHHHH
Confidence 6679999999 358999999998887654 444444444556778888888888888777777788999999999999
Q ss_pred HHHHHhcccCCCCCcchhhhHHHHHhhcCCCHHHHHHHHHHHHHHHhc-----cccCCCChHHHHHHHHHHHHHHcCCCC
Q 046187 215 ILGEALQLSQPINSNSIAVHMPRFCTLLQLNKSAQVLATHIGEVVINK-----CFCTRRNPISISAAAIYLACQLEDKRK 289 (510)
Q Consensus 215 ~L~k~L~i~~pv~~~~p~~~I~Rfcs~L~L~~~V~~~A~~Ia~~a~~~-----~l~~GRsP~sIAAAaIYlAarl~g~~~ 289 (510)
.+...|+++... -|..+|=+||+. +|.+-|..|+...... ..-.-.+-...++||+|.||+++..++
T Consensus 83 sfe~llgln~~~-------~VrdlaVQfgc~-evi~~a~~vl~syk~~lpaT~~~~~D~SrP~ft~aA~~~ack~lKlKV 154 (262)
T KOG4557|consen 83 SFENLLGLNIKL-------NVRDLAVQFGCV-EVIKSAQNVLSSYKERLPATRRANADFSRPVFTAAAFYLACKKLKLKV 154 (262)
T ss_pred HHHHHhcchhhc-------CHHHHHHHHhHH-HHHHHHHHHHHHHHhcCchhhhcCCcccchHHHHHHHHHHHHHHHHhh
Confidence 999999987654 345666667665 4666677666555431 111223344678999999999999998
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHhhc
Q 046187 290 TQAEICKVTGLTEVTLRKVYKELLENWD 317 (510)
Q Consensus 290 t~keIa~vagVSe~TIRkrYKEL~e~l~ 317 (510)
.....-.+.|++++-..--.|.+.....
T Consensus 155 dK~kli~~sg~~~s~F~~l~kqler~~~ 182 (262)
T KOG4557|consen 155 DKLKLIEVSGTSESEFSCLSKQLERNYK 182 (262)
T ss_pred hHhhcccccCCCHHHHHHHHHHHHHHHH
Confidence 8888888999999876655555544443
No 29
>KOG0655 consensus G1/S-specific cyclin E [Cell cycle control, cell division, chromosome partitioning]
Probab=96.27 E-value=0.079 Score=55.38 Aligned_cols=170 Identities=14% Similarity=0.131 Sum_probs=115.9
Q ss_pred HHHHHHHhCCCHHHHHHHHHHHHHHHhCCc-cCCccHHHHHHHHHHHHHHhcCC-CCCHHHHHHHhC--CCHHHHHHHHH
Q 046187 139 IIDVASILGLDYDICDHAFQLFRDCCSATC-LRNRSVEALATAALVQAIREAQE-PRTLQEISIAAN--VPQKEIGKYIK 214 (510)
Q Consensus 139 I~~ic~~L~LP~~VidtA~~LyK~a~e~~~-lrGRs~eaVaAACLYIACR~~~~-PrTLkEIa~vt~--VskkeIgr~yk 214 (510)
+.++|+-..|-+.+---|..+|.++++-.. ...-....|-.+|||||.+.+++ |-.+.|+|-++. ++..+|...-+
T Consensus 152 lmEVCEvykLHRETFyLAvDy~DRyl~t~~~v~kt~lQLIGitsLFIAAK~EEIYpPKl~eFAyvTDgAcs~ddIltmE~ 231 (408)
T KOG0655|consen 152 LMEVCEVYKLHRETFYLAVDYFDRYLETQVEVSKTNLQLIGITSLFIAAKLEEIYPPKLIEFAYVTDGACSEDDILTMEL 231 (408)
T ss_pred HHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHhhccCccccceeeeccCccchHHHHHHHH
Confidence 447999999999999999999999987431 22223456778999999998876 778999999874 78899999999
Q ss_pred HHHHHhcccCCCCCcchhhhHHHHHhhcCCCH------------HHHHHHHHHHHHHHhccccCCCChHHHHHHHHHHHH
Q 046187 215 ILGEALQLSQPINSNSIAVHMPRFCTLLQLNK------------SAQVLATHIGEVVINKCFCTRRNPISISAAAIYLAC 282 (510)
Q Consensus 215 ~L~k~L~i~~pv~~~~p~~~I~Rfcs~L~L~~------------~V~~~A~~Ia~~a~~~~l~~GRsP~sIAAAaIYlAa 282 (510)
.|.+.|+-...+. .+-.++.-|.+-++++. ...+.|. |+..+.=.--..-.+-..|||||||.-.
T Consensus 232 iilkal~W~l~Pi--Tii~WL~vylQv~~~n~~~k~l~Pq~~~~efiqiaq-lLDlc~ldids~~fsYrilaAAal~h~~ 308 (408)
T KOG0655|consen 232 IILKALKWELSPI--TIISWLNVYLQVDALNDAPKVLLPQYSQEEFIQIAQ-LLDLCILDIDSLEFSYRILAAAALCHFT 308 (408)
T ss_pred HHHHHhcccccce--ehHHHHHHHHHHHhcCCCCceeccccchHHHHHHHH-HHHHHHhccccccchHHHHHHHHHHHHh
Confidence 9999998764322 24567777777665542 1223332 2233322222345778889999997543
Q ss_pred HHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 283 QLEDKRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 283 rl~g~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
. ..-+-++.|.--..|.++.+-+.++...
T Consensus 309 s-------~e~v~kaSG~~w~~ie~cv~wm~Pf~rv 337 (408)
T KOG0655|consen 309 S-------IEVVKKASGLEWDSIEECVDWMVPFVRV 337 (408)
T ss_pred H-------HHHHHHcccccHHHHHHHHHHHHHHHHH
Confidence 2 2234455676667777777766665544
No 30
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=96.16 E-value=0.03 Score=58.36 Aligned_cols=102 Identities=21% Similarity=0.205 Sum_probs=74.2
Q ss_pred HHHHHHHHHHhCCCHHH--HHHHHHHHHHHHhCCccCCccHHHHHHHHHHHHHHhcCCCCCHHH-HHHHhCCCHHHHHHH
Q 046187 136 YLQIIDVASILGLDYDI--CDHAFQLFRDCCSATCLRNRSVEALATAALVQAIREAQEPRTLQE-ISIAANVPQKEIGKY 212 (510)
Q Consensus 136 ~~~I~~ic~~L~LP~~V--idtA~~LyK~a~e~~~lrGRs~eaVaAACLYIACR~~~~PrTLkE-Ia~vt~VskkeIgr~ 212 (510)
++.|+.+-..|+||++. ...+..|.....--.++.--+++.||+||+|+|.|..++|.+..- ...+++.++.+|-..
T Consensus 142 hklii~YLqtL~~~~~~~l~Q~~wNfmNDslRT~v~vry~pe~iACaciyLaAR~~eIpLp~~P~Wf~~Fd~~k~eid~i 221 (367)
T KOG0835|consen 142 HKLIIMYLQTLQLPPNLKLLQAAWNFMNDSLRTDVFVRYSPESIACACIYLAARNLEIPLPFQPHWFKAFDTTKREIDEI 221 (367)
T ss_pred HHHHHHHHHHhcCCCchhHHHHHHHhhhhccccceeeecCHHHHHHHHHHHHHhhhcCCCCCCccHHHHcCCcHHHHHHH
Confidence 45677788889999755 666677667776667777788999999999999999999887764 455788999888776
Q ss_pred HHHHHHHhcccCCCCCcchhhhHHHHHhhc
Q 046187 213 IKILGEALQLSQPINSNSIAVHMPRFCTLL 242 (510)
Q Consensus 213 yk~L~k~L~i~~pv~~~~p~~~I~Rfcs~L 242 (510)
...+........+ + ..+|.-|+..+
T Consensus 222 c~~l~~lY~~~~p--~---~~li~~~vd~~ 246 (367)
T KOG0835|consen 222 CYRLIPLYKRAKP--D---ETLIEAFVDRL 246 (367)
T ss_pred HHHHHHHHHhccc--C---HHHHHHHHHHh
Confidence 6666555443211 1 45666666554
No 31
>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=95.70 E-value=0.096 Score=45.88 Aligned_cols=86 Identities=19% Similarity=0.315 Sum_probs=63.8
Q ss_pred hhhhHHHHHhhcCCCHHHHHHHHHHHHHHHhccccCCCChHHHHHHHHHHHHHHcCC-CCCHHHHHHHhC--CCHHHHHH
Q 046187 231 IAVHMPRFCTLLQLNKSAQVLATHIGEVVINKCFCTRRNPISISAAAIYLACQLEDK-RKTQAEICKVTG--LTEVTLRK 307 (510)
Q Consensus 231 p~~~I~Rfcs~L~L~~~V~~~A~~Ia~~a~~~~l~~GRsP~sIAAAaIYlAarl~g~-~~t~keIa~vag--VSe~TIRk 307 (510)
..++|...+.+++++..+...|..++++...........+.-|++||+++|+++... ..+..++....+ .+..-|..
T Consensus 34 ~~~~i~~~~~~~~l~~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~e~~~~~~~~~~~~~~~~~~~~~i~~ 113 (127)
T PF00134_consen 34 IIDWIIELCQRLKLSPETLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKMEEDNPPSISDLIRISDNTFTKKDILE 113 (127)
T ss_dssp HHHHHHHHHHHTT-BHHHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHHTSS--HHHHHHHHTTTSSHHHHHHH
T ss_pred HHHHHHHHHHhcccchhHHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhhccccchHHHHHHHHcCCCCHHHHHH
Confidence 357889999999999999999999999887776778889999999999999999976 455777777763 34444444
Q ss_pred HHHHHHHhh
Q 046187 308 VYKELLENW 316 (510)
Q Consensus 308 rYKEL~e~l 316 (510)
.=..|+..+
T Consensus 114 ~E~~iL~~L 122 (127)
T PF00134_consen 114 MEREILSAL 122 (127)
T ss_dssp HHHHHHHHT
T ss_pred HHHHHHHHC
Confidence 444444443
No 32
>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=95.60 E-value=2 Score=42.45 Aligned_cols=125 Identities=15% Similarity=0.114 Sum_probs=66.5
Q ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhcccCCCCCcchhhhHHHHHhhcCCCHH--HH-HHHHHHHHHHHhcccc
Q 046187 189 AQEPRTLQEISIAANVPQKEIGKYIKILGEALQLSQPINSNSIAVHMPRFCTLLQLNKS--AQ-VLATHIGEVVINKCFC 265 (510)
Q Consensus 189 ~~~PrTLkEIa~vt~VskkeIgr~yk~L~k~L~i~~pv~~~~p~~~I~Rfcs~L~L~~~--V~-~~A~~Ia~~a~~~~l~ 265 (510)
.+.+-|..|||..++++.+++.+..+.....+-++.++.......+...+.+.-.-.++ +. ......+..+..
T Consensus 100 ~g~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~~~~p~~~~~~~~~~~~l~~~l~---- 175 (238)
T TIGR02393 100 LGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDTSIESPDDYAAKELLREQLDEVLE---- 175 (238)
T ss_pred hCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCCcCCCCCCCCcccHHHHhcCCCCCChHHHHHHHHHHHHHHHHHH----
Confidence 46667889999999999999988765443333344433211111233333332111221 11 111111222211
Q ss_pred CCCChHHHHHHHHHHHHHHc-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccC
Q 046187 266 TRRNPISISAAAIYLACQLE-DKRKTQAEICKVTGLTEVTLRKVYKELLENWDDLL 320 (510)
Q Consensus 266 ~GRsP~sIAAAaIYlAarl~-g~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Li 320 (510)
.-+|.--. +|.+---+. ..+.|++|||+.+|||..+|++.++.....+...+
T Consensus 176 -~L~~~er~--vl~l~ygl~~~~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~~ 228 (238)
T TIGR02393 176 -TLTERERK--VLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHPS 228 (238)
T ss_pred -hCCHHHHH--HHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhhH
Confidence 11222111 111111112 35799999999999999999999887777766544
No 33
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=95.16 E-value=0.11 Score=54.22 Aligned_cols=70 Identities=16% Similarity=0.185 Sum_probs=58.7
Q ss_pred hhhHHHHHhhcC--CCHHHHHHHHHHHHHHHhccccCCCChHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCC
Q 046187 232 AVHMPRFCTLLQ--LNKSAQVLATHIGEVVINKCFCTRRNPISISAAAIYLACQLEDKRKTQAEICKVTGLT 301 (510)
Q Consensus 232 ~~~I~Rfcs~L~--L~~~V~~~A~~Ia~~a~~~~l~~GRsP~sIAAAaIYlAarl~g~~~t~keIa~vagVS 301 (510)
..+|.++|.+|+ |+..|.-.|..+.++.--.+-+.-.+|.-|+++|||+||......+++.+++..+.-.
T Consensus 60 ~~~i~~~~~~lkp~Lpq~viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE~~~si~~fv~~~~~~ 131 (305)
T TIGR00569 60 EKRLLDFCSAFKPTMPTSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFVGNLKET 131 (305)
T ss_pred HHHHHHHHHHhcCCCCchHHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccccCcCHHHHHhhccCC
Confidence 457889999999 9999999999888766544445568999999999999999999999999988766544
No 34
>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=94.66 E-value=0.16 Score=43.63 Aligned_cols=73 Identities=15% Similarity=0.158 Sum_probs=56.1
Q ss_pred CHHHHHHHHHHHHHHHhCCccCCccHHHHHHHHHHHHHHhcCC-CCCHHHHHHHhCCCHHHHHHHHHHHHHHhc
Q 046187 149 DYDICDHAFQLFRDCCSATCLRNRSVEALATAALVQAIREAQE-PRTLQEISIAANVPQKEIGKYIKILGEALQ 221 (510)
Q Consensus 149 P~~VidtA~~LyK~a~e~~~lrGRs~eaVaAACLYIACR~~~~-PrTLkEIa~vt~VskkeIgr~yk~L~k~L~ 221 (510)
...+...|..|.....-...+-+-+...+||||+|+|.+..+. +.--..+...++++..+|..+++.|.+.+.
T Consensus 17 ~~~~~~~a~~l~el~l~~~~fl~~~PS~iAaAai~lA~~~~~~~~~~~~~l~~~t~~~~~~l~~c~~~i~~~~~ 90 (118)
T PF02984_consen 17 DQEVRNLARYLLELSLLDYEFLQYPPSVIAAAAILLARKILGKEPPWPESLEKLTGYDKEDLKECIELIQELLS 90 (118)
T ss_dssp HHHHHHHHHHHHHHHHHSHHHTTS-HHHHHHHHHHHHHHHHHSSTCSHHHHHHHHTS-HHHHHHHHHHHHHHHH
T ss_pred cHHHHHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhCccccCCccchhhcCCCHHHHHHHHHHHHHHHH
Confidence 4457777777777766655566788899999999999999775 444455777889999999999999988775
No 35
>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=94.25 E-value=0.17 Score=46.67 Aligned_cols=69 Identities=20% Similarity=0.225 Sum_probs=55.1
Q ss_pred hhhHHHHHhhcCCCHHHHHHHHHHHHHHH--hccccCCCChHHHHHHHHHHHHHHcCCCCCHHHHHHHhCC
Q 046187 232 AVHMPRFCTLLQLNKSAQVLATHIGEVVI--NKCFCTRRNPISISAAAIYLACQLEDKRKTQAEICKVTGL 300 (510)
Q Consensus 232 ~~~I~Rfcs~L~L~~~V~~~A~~Ia~~a~--~~~l~~GRsP~sIAAAaIYlAarl~g~~~t~keIa~vagV 300 (510)
..-|..+|++|+|++++.+..|.+.+.+. +..++.+|.-.-|...|||..|++.+..++.++|-+.-.-
T Consensus 15 ~~Rl~~LC~~L~l~~~~~~~iwt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~~~sF~~Ii~~Yr~ 85 (135)
T PF01857_consen 15 AVRLQDLCERLDLSSDLREKIWTCFEHSLTHHTELMKDRHLDQIILCAIYGICKVSKEELSFKDIIKAYRK 85 (135)
T ss_dssp HHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHHHHHHHHTT-S--HHHHHHHHTT
T ss_pred HHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhhcCCCCHHHHHHHHHh
Confidence 45677899999999988888888887776 4578999999999999999999999988888888765543
No 36
>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=94.20 E-value=0.025 Score=44.34 Aligned_cols=30 Identities=27% Similarity=0.719 Sum_probs=23.3
Q ss_pred CCCCCCCCCCcccccCCCCccccccccceecc
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRVIA 33 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vle 33 (510)
+||.|+. ...+-|...|. +..|..||.-|+
T Consensus 4 ~CP~CG~-~iev~~~~~Ge-iV~Cp~CGaele 33 (54)
T TIGR01206 4 ECPDCGA-EIELENPELGE-LVICDECGAELE 33 (54)
T ss_pred CCCCCCC-EEecCCCccCC-EEeCCCCCCEEE
Confidence 7999998 34444555686 889999999884
No 37
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=94.04 E-value=5.9 Score=41.54 Aligned_cols=189 Identities=14% Similarity=0.102 Sum_probs=92.8
Q ss_pred CCchhhHHHHHHHHH-HHHHHHHhC-----CCHHHHHHHHHHHHHHHhCCccCCccHHHHHHHHHHHHH-----------
Q 046187 124 TSSSVMMDNLRAYLQ-IIDVASILG-----LDYDICDHAFQLFRDCCSATCLRNRSVEALATAALVQAI----------- 186 (510)
Q Consensus 124 ~~~~~~er~L~a~~~-I~~ic~~L~-----LP~~VidtA~~LyK~a~e~~~lrGRs~eaVaAACLYIAC----------- 186 (510)
++....+.++..|.. |..+|..+- .-+-+.+.-..+|+.+.....-+|-+..+.++-.+.++.
T Consensus 83 Gd~~A~~~Li~~y~~~V~~~a~~~~~~~~~aeDLvQE~fi~l~~ai~~fd~~rg~~Fstyatw~iR~ai~~~i~~~~r~i 162 (325)
T PRK05657 83 GDFAARQRMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTI 162 (325)
T ss_pred CCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHHHHHHHHHHcCCcc
Confidence 344455556666644 445776663 223445566667777766555555544443332222211
Q ss_pred --------------Hh-------cCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhcccCCCCCcchh-hhHHHHHhhcCC
Q 046187 187 --------------RE-------AQEPRTLQEISIAANVPQKEIGKYIKILGEALQLSQPINSNSIA-VHMPRFCTLLQL 244 (510)
Q Consensus 187 --------------R~-------~~~PrTLkEIa~vt~VskkeIgr~yk~L~k~L~i~~pv~~~~p~-~~I~Rfcs~L~L 244 (510)
|. .+...++.|||..++++.+++.+....-...+.+..+... +.. .+..-+...-.-
T Consensus 163 r~p~~~~~~l~~~~R~~~~l~~~l~r~~t~~eiA~~l~~~~~~v~~~l~~~~~~~sld~~~~~-~~~~~l~d~l~d~~~~ 241 (325)
T PRK05657 163 RLPVHVVKELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLGG-DPEKSLLDILADEQEN 241 (325)
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhccCCcccCCCCCC-CCCcchhhhccCCCCC
Confidence 11 1345578899999999998887765422222222222211 111 122222221111
Q ss_pred CHH-HH--HHHHHHHHHHHhccccCCCChHHHHHHHHHHHHHHc-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccC
Q 046187 245 NKS-AQ--VLATHIGEVVINKCFCTRRNPISISAAAIYLACQLE-DKRKTQAEICKVTGLTEVTLRKVYKELLENWDDLL 320 (510)
Q Consensus 245 ~~~-V~--~~A~~Ia~~a~~~~l~~GRsP~sIAAAaIYlAarl~-g~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Li 320 (510)
+++ .. ......+..+.. .-+|.--. +|.+---+. -..+|.++||+.+||+..||+.++..-+..+...+
T Consensus 242 ~pe~~~~~~e~~~~L~~aL~-----~L~~~~R~--vl~lrygL~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l 314 (325)
T PRK05657 242 GPEDTTQDDDMKQSIVKWLF-----ELNDKQRE--VLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREIL 314 (325)
T ss_pred CHHHHHHHHHHHHHHHHHHH-----cCCHHHHH--HHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 111 11 111122222221 11222211 111100022 35799999999999999999999877777666544
No 38
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=93.79 E-value=6.4 Score=41.08 Aligned_cols=181 Identities=17% Similarity=0.112 Sum_probs=90.0
Q ss_pred hhHHHHHHHH-HHHHHHHHhC-----CCHHHHHHHHHHHHHHHhCCccCCccHHHHHHHHHHHHH---------------
Q 046187 128 VMMDNLRAYL-QIIDVASILG-----LDYDICDHAFQLFRDCCSATCLRNRSVEALATAALVQAI--------------- 186 (510)
Q Consensus 128 ~~er~L~a~~-~I~~ic~~L~-----LP~~VidtA~~LyK~a~e~~~lrGRs~eaVaAACLYIAC--------------- 186 (510)
..+++...|. .+..+|.++- ..+-+.|.-..+++.+.....-+|-+..+.+.-.|=.+.
T Consensus 82 A~~~L~~~~~~~V~~~a~~~~~~~~~~eDLvQEg~i~L~~a~~~fd~~~g~rf~tYa~~wIR~~I~~~i~~~~~~ir~p~ 161 (317)
T PRK07405 82 AKRKMVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPI 161 (317)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcCCCCChHHHHHHHHHHHHHHHHHhcCCCccCCh
Confidence 3444555554 4445776663 223445555556666655554455555554442111111
Q ss_pred -----------------HhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhcccCCCCCcchhhhHHHHHhhcCCCH-HH
Q 046187 187 -----------------REAQEPRTLQEISIAANVPQKEIGKYIKILGEALQLSQPINSNSIAVHMPRFCTLLQLNK-SA 248 (510)
Q Consensus 187 -----------------R~~~~PrTLkEIa~vt~VskkeIgr~yk~L~k~L~i~~pv~~~~p~~~I~Rfcs~L~L~~-~V 248 (510)
...|..-|..|||..++++..++..+++...+.+.++.++.......+..-+... ...+ +.
T Consensus 162 ~~~~~~~~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~~~d~-~~~pe~~ 240 (317)
T PRK07405 162 HITEKLNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDT-GASPEDF 240 (317)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCeeecCCCCCCCCccHHHhhcCC-CCCHHHH
Confidence 1234455788999999999999888876655444444443221111222222221 1222 21
Q ss_pred HH--HHHHHHHHHHhccccCCCChHHHHHHHHHHHHHHc-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q 046187 249 QV--LATHIGEVVINKCFCTRRNPISISAAAIYLACQLE-DKRKTQAEICKVTGLTEVTLRKVYKELLENW 316 (510)
Q Consensus 249 ~~--~A~~Ia~~a~~~~l~~GRsP~sIAAAaIYlAarl~-g~~~t~keIa~vagVSe~TIRkrYKEL~e~l 316 (510)
.. .-...+..+.+ .-+|.- --+|.+---+. +.+.|++||++.+|||..+||...+.-...+
T Consensus 241 ~~~~~~~~~l~~al~-----~L~~re--r~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVRqi~~rAl~kL 304 (317)
T PRK07405 241 ATQSSLQLDLERLME-----DLTPQQ--KEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKL 304 (317)
T ss_pred HHHHHHHHHHHHHHH-----cCCHHH--HHHHHHHhhcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 11 11111222221 112211 11111111112 3679999999999999999998765544443
No 39
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=93.73 E-value=6 Score=42.11 Aligned_cols=186 Identities=19% Similarity=0.196 Sum_probs=96.1
Q ss_pred CchhhHHHHHHHHH-HHHHHHHhC-----CCHHHHHHHHHHHHHHHhCCccCCccHHHHHHHHHHHHHHh----------
Q 046187 125 SSSVMMDNLRAYLQ-IIDVASILG-----LDYDICDHAFQLFRDCCSATCLRNRSVEALATAALVQAIRE---------- 188 (510)
Q Consensus 125 ~~~~~er~L~a~~~-I~~ic~~L~-----LP~~VidtA~~LyK~a~e~~~lrGRs~eaVaAACLYIACR~---------- 188 (510)
+....++++..|.. +..+|.++. +-+-+.+.-..+++.+.....-+|.+..+.|.-.|+-+.+.
T Consensus 127 d~~A~~~Li~~~~~lV~~iA~~~~~~~~~~eDLiQEg~igL~~a~~~fd~~~g~~FsTyA~~wIr~aI~~~i~~~~r~ir 206 (367)
T PRK09210 127 DEEAKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIR 206 (367)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHcCCcee
Confidence 33344555665544 445777763 22344555566777777766667888888777777755421
Q ss_pred ----------------------cCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhcccCCCCCcchhhhHHHHH-hhcCCC
Q 046187 189 ----------------------AQEPRTLQEISIAANVPQKEIGKYIKILGEALQLSQPINSNSIAVHMPRFC-TLLQLN 245 (510)
Q Consensus 189 ----------------------~~~PrTLkEIa~vt~VskkeIgr~yk~L~k~L~i~~pv~~~~p~~~I~Rfc-s~L~L~ 245 (510)
.+..-|..|||..++++..++....+.-...+-++.++... ....+..+. +.-..+
T Consensus 207 ip~~~~~~~~~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~-~~~~l~d~i~d~~~~~ 285 (367)
T PRK09210 207 IPVHMVETINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEE-DDSHLGDFIEDQDATS 285 (367)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCCcCCCCCCC-CcchhhhhccCCCCCC
Confidence 12333567788888888888877655433333333333211 111122221 111112
Q ss_pred HH--HH-HHHHHHHHHHHhccccCCCChHHHHHHHHHHHHHHc-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 246 KS--AQ-VLATHIGEVVINKCFCTRRNPISISAAAIYLACQLE-DKRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 246 ~~--V~-~~A~~Ia~~a~~~~l~~GRsP~sIAAAaIYlAarl~-g~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
+. +. ..-...++.+. ..-+|.---.-.+|+. +. |...|++||++.+|||...||...+.-...|..
T Consensus 286 p~~~~~~~~~~~~l~~~l-----~~L~~rEr~Vl~lryg--l~~~~~~tl~EIa~~lgvs~erVrQi~~~Al~kLr~ 355 (367)
T PRK09210 286 PADHAAYELLKEQLEDVL-----DTLTDREENVLRLRFG--LDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRH 355 (367)
T ss_pred HHHHHHHHHHHHHHHHHH-----HhCCHHHHHHHHHHhc--cCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhC
Confidence 21 11 01111122211 1122222211111111 11 367999999999999999999988766655544
No 40
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=93.43 E-value=0.2 Score=52.57 Aligned_cols=85 Identities=21% Similarity=0.282 Sum_probs=66.6
Q ss_pred hhhHHHHHhhcCCCHHHHHHHHHHHHHHHhccccCCCChHHHHHHHHHHHHHHcCCCCCHHHHHHHh----CCCHHHHHH
Q 046187 232 AVHMPRFCTLLQLNKSAQVLATHIGEVVINKCFCTRRNPISISAAAIYLACQLEDKRKTQAEICKVT----GLTEVTLRK 307 (510)
Q Consensus 232 ~~~I~Rfcs~L~L~~~V~~~A~~Ia~~a~~~~l~~GRsP~sIAAAaIYlAarl~g~~~t~keIa~va----gVSe~TIRk 307 (510)
..||...+.+|+++......|.-+..+.--..-+....|..||++|||+|++..+.++..++|..+. +..+.+...
T Consensus 43 ~~fI~elg~~L~~~~~ti~tA~~~~hRFy~~~s~~~~~~~~vA~sclfLAgKvEetp~kl~dIi~~s~~~~~~~~~~~~~ 122 (323)
T KOG0834|consen 43 AKFIQELGVRLKMPQKTIATAIVIFHRFYMFHSFKKFDPYTVAASCLFLAGKVEETPRKLEDIIKVSYRYLNPKDLELEE 122 (323)
T ss_pred HHHHHHHHHHcCCCccchhhhhhhhhhhhhhcccccCcHHHHHHHHHHHHhhcccCcccHHHHHHHHHHHcCcccccHHH
Confidence 5789999999999987777777777666555567788899999999999999999999999987664 333346667
Q ss_pred HHHHHHHhh
Q 046187 308 VYKELLENW 316 (510)
Q Consensus 308 rYKEL~e~l 316 (510)
+|-++++.+
T Consensus 123 ~~~~~~~~I 131 (323)
T KOG0834|consen 123 VYWELKERI 131 (323)
T ss_pred HHHHHHHHH
Confidence 777666643
No 41
>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=93.29 E-value=0.046 Score=39.37 Aligned_cols=28 Identities=25% Similarity=0.598 Sum_probs=22.8
Q ss_pred CCCCCCCCCCCcccccCCCCccccccccceecc
Q 046187 1 MKCPYCSAAQGRCATTSTGRSITECGSCGRVIA 33 (510)
Q Consensus 1 m~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vle 33 (510)
|.|+.|++. ......|. .+|..||.|.+
T Consensus 9 ~~C~~C~~~---~~~~~dG~--~yC~~cG~~~E 36 (36)
T PF11781_consen 9 EPCPVCGSR---WFYSDDGF--YYCDRCGHQSE 36 (36)
T ss_pred CcCCCCCCe---EeEccCCE--EEhhhCceEcC
Confidence 469999984 35567898 99999999874
No 42
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=93.11 E-value=11 Score=38.03 Aligned_cols=32 Identities=19% Similarity=0.264 Sum_probs=27.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
..++.+|||+.+|+|..||+..++.....+..
T Consensus 220 e~~t~~EIA~~lgis~~~V~~~~~ral~kLr~ 251 (257)
T PRK05911 220 EELVLKEIGKILGVSESRVSQIHSKALLKLRA 251 (257)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 57899999999999999999988776665544
No 43
>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=93.08 E-value=7.7 Score=39.53 Aligned_cols=35 Identities=26% Similarity=0.365 Sum_probs=28.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccCC
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDLLP 321 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Lip 321 (510)
...|++|||+.+|+|+.||+.+.+.-.+.+...+.
T Consensus 241 e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l~ 275 (285)
T TIGR02394 241 EPATLEEVAAEVGLTRERVRQIQVEALKKLRRILE 275 (285)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 57899999999999999999888766666555443
No 44
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=92.68 E-value=8.2 Score=43.15 Aligned_cols=181 Identities=17% Similarity=0.121 Sum_probs=94.9
Q ss_pred hhHHHHHHHHHHH-HHHHHh---CC--CHHHHHHHHHHHHHHHhCCccCCccHHHHHHHHHHHHHH--------------
Q 046187 128 VMMDNLRAYLQII-DVASIL---GL--DYDICDHAFQLFRDCCSATCLRNRSVEALATAALVQAIR-------------- 187 (510)
Q Consensus 128 ~~er~L~a~~~I~-~ic~~L---~L--P~~VidtA~~LyK~a~e~~~lrGRs~eaVaAACLYIACR-------------- 187 (510)
.+++++.++..+. .+|.++ |+ -+-|.+--.-|.+-+.....-+|-+....|.=+|--+..
T Consensus 272 Ar~~LI~sNLrLVvsIAkrY~~~Gl~~eDLIQEGnIGLikAvekFDp~rG~rFSTYA~wWIRqaI~raI~d~~r~IRvP~ 351 (509)
T PRK05901 272 AKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPV 351 (509)
T ss_pred HHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCchhhhHHHHHHHHHHHHHHcCCceecCH
Confidence 4455666665555 477776 33 345555666688877777778887777766655544331
Q ss_pred ------------------hcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhcccCCCCCcchhhhHHHHHhhcCCCH-H-
Q 046187 188 ------------------EAQEPRTLQEISIAANVPQKEIGKYIKILGEALQLSQPINSNSIAVHMPRFCTLLQLNK-S- 247 (510)
Q Consensus 188 ------------------~~~~PrTLkEIa~vt~VskkeIgr~yk~L~k~L~i~~pv~~~~p~~~I~Rfcs~L~L~~-~- 247 (510)
..|..-|..|||..++++..++....+.....+-++.++....-..+...+...-...+ +
T Consensus 352 ~~~e~i~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~~p~~~ 431 (509)
T PRK05901 352 HMVETINKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTIGKEGDSQFGDFIEDSEAVSPVDA 431 (509)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccccccccCCcccHHHhccCCCCCCHHHH
Confidence 12334456778888888887777664433222333333221111112222222111111 1
Q ss_pred HHH-HHHHHHHHHHhccccCCCChHHHHHHHHHHHHHHc----CCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 248 AQV-LATHIGEVVINKCFCTRRNPISISAAAIYLACQLE----DKRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 248 V~~-~A~~Ia~~a~~~~l~~GRsP~sIAAAaIYlAarl~----g~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
+.. .-...+..+.. -+ ++.--- +....+ +.+.|+++|++.+|||...||+..+.....|..
T Consensus 432 ~~~~~l~~~L~~aL~--~L---~eREr~-----VI~lRyGL~~~e~~TL~EIa~~lGVSrERVRQIe~kAL~KLR~ 497 (509)
T PRK05901 432 VSFTLLQDQLQEVLE--TL---SEREAG-----VIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLRH 497 (509)
T ss_pred HHHHHHHHHHHHHHh--hC---CHHHHH-----HHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 111 11111222211 11 122111 111223 357999999999999999999887766665544
No 45
>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=92.43 E-value=10 Score=38.93 Aligned_cols=180 Identities=15% Similarity=0.119 Sum_probs=92.8
Q ss_pred hhHHHHHHHHH-HHHHHHHhC-----CCHHHHHHHHHHHHHHHhCCccCCccHHHHHH-----HHH--------------
Q 046187 128 VMMDNLRAYLQ-IIDVASILG-----LDYDICDHAFQLFRDCCSATCLRNRSVEALAT-----AAL-------------- 182 (510)
Q Consensus 128 ~~er~L~a~~~-I~~ic~~L~-----LP~~VidtA~~LyK~a~e~~~lrGRs~eaVaA-----ACL-------------- 182 (510)
..+++...+.. +..+|.++. +-+-+.|.-.-+++.+.....-+|-+..+.+. +..
T Consensus 75 A~~~Lv~~~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~~a~~kfd~~~g~rFsTya~~wIr~~I~r~i~~~~r~vr~p~ 154 (298)
T TIGR02997 75 AKEKMIKANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPI 154 (298)
T ss_pred HHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCccCCCChHHHHHHHHHHHHHHHHHhcCCCeeCcH
Confidence 33445555543 335666652 33556667777787777766666755555544 111
Q ss_pred -----HHHH--------HhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhcccCCCCCcchhhhHHHHHhhcCCCHH--
Q 046187 183 -----VQAI--------REAQEPRTLQEISIAANVPQKEIGKYIKILGEALQLSQPINSNSIAVHMPRFCTLLQLNKS-- 247 (510)
Q Consensus 183 -----YIAC--------R~~~~PrTLkEIa~vt~VskkeIgr~yk~L~k~L~i~~pv~~~~p~~~I~Rfcs~L~L~~~-- 247 (510)
+-.. ...|..-|..||+..++++..++..........+-++.++....-..+...+.+. ..+++
T Consensus 155 ~~~~~~~~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~~~~~~~~~-~~~pe~~ 233 (298)
T TIGR02997 155 HITEKLNKIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLEDD-GESPEEQ 233 (298)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHcccCcccCCCcCCCCcchHHHhccCC-CCCHHHH
Confidence 1111 1234556789999999999999988766554444444443211111122222221 12221
Q ss_pred HHH-HHHHHHHHHHhccccCCCChHHHHHHHHHHHHHHc-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 248 AQV-LATHIGEVVINKCFCTRRNPISISAAAIYLACQLE-DKRKTQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 248 V~~-~A~~Ia~~a~~~~l~~GRsP~sIAAAaIYlAarl~-g~~~t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
+.. .....+..+.+ .-+|.-= -+|.+---+. ..+.|++|||+.+|||..|||...+.-...
T Consensus 234 ~~~~~~~~~L~~~L~-----~L~~rer--~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVrq~~~rAl~k 296 (298)
T TIGR02997 234 VERESLRQDLESLLA-----ELTPRER--QVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRK 296 (298)
T ss_pred HHHHHHHHHHHHHHH-----cCCHHHH--HHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 111 11112222221 1122211 1111111112 357999999999999999999887655443
No 46
>PRK05949 RNA polymerase sigma factor; Validated
Probab=92.08 E-value=13 Score=39.04 Aligned_cols=180 Identities=14% Similarity=0.097 Sum_probs=90.9
Q ss_pred hHHHHHHHH-HHHHHHHHhC-----CCHHHHHHHHHHHHHHHhCCccCCccHHHHHHHHHH-------------------
Q 046187 129 MMDNLRAYL-QIIDVASILG-----LDYDICDHAFQLFRDCCSATCLRNRSVEALATAALV------------------- 183 (510)
Q Consensus 129 ~er~L~a~~-~I~~ic~~L~-----LP~~VidtA~~LyK~a~e~~~lrGRs~eaVaAACLY------------------- 183 (510)
.+++...|. .+..+|.++- +-+-|.|.-..+++.+.....-+|.+..+.|.-+|-
T Consensus 93 ~~~Li~~~~~~V~~iA~~y~~~~~~~eDLvQEg~igL~~a~~kfd~~~G~rFsTYa~wwIrq~I~r~i~~~~r~iRlP~~ 172 (327)
T PRK05949 93 KQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIH 172 (327)
T ss_pred HHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHhcCCcCCCChhhhhHHHHHHHHHHHHHHcCCceeCCHH
Confidence 344555554 4446777762 234556666668887777666677655554442111
Q ss_pred ------HHH-------HhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhcccCCCCCcchhhhHHHHHhhcCCCHH-HH
Q 046187 184 ------QAI-------REAQEPRTLQEISIAANVPQKEIGKYIKILGEALQLSQPINSNSIAVHMPRFCTLLQLNKS-AQ 249 (510)
Q Consensus 184 ------IAC-------R~~~~PrTLkEIa~vt~VskkeIgr~yk~L~k~L~i~~pv~~~~p~~~I~Rfcs~L~L~~~-V~ 249 (510)
..- ...+..-+..|||..+++++.++......-...+-++.++.......+..-+... ..+++ ..
T Consensus 173 ~~~~~~~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~l~d~-~~~pe~~~ 251 (327)
T PRK05949 173 ITEKLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDTELSELLEDE-GPSPDQYI 251 (327)
T ss_pred HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccccccCCCcCCCCCccHHhhcCCC-CCCHHHHH
Confidence 111 1234556788999999999988877655433333344443211111122211111 12222 11
Q ss_pred H--HHHHHHHHHHhccccCCCChHHHHHHHHHHHHHHc-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q 046187 250 V--LATHIGEVVINKCFCTRRNPISISAAAIYLACQLE-DKRKTQAEICKVTGLTEVTLRKVYKELLENW 316 (510)
Q Consensus 250 ~--~A~~Ia~~a~~~~l~~GRsP~sIAAAaIYlAarl~-g~~~t~keIa~vagVSe~TIRkrYKEL~e~l 316 (510)
. .-...+..+.. .-+|.- -.+|.+---+. +.+.|.+|||+.+|||..+||.....-...+
T Consensus 252 ~~~~~~~~L~~~L~-----~L~~re--r~Vi~lr~gl~~~e~~Tl~EIa~~lgiS~erVrq~~~rAl~kL 314 (327)
T PRK05949 252 TQELLRQDLNNLLA-----ELTPQQ--REVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHL 314 (327)
T ss_pred HHHHHHHHHHHHHH-----hCCHHH--HHHHHHHhccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 1 11112222221 112221 11222211122 2579999999999999999997765444433
No 47
>PHA00626 hypothetical protein
Probab=91.76 E-value=0.1 Score=41.22 Aligned_cols=30 Identities=23% Similarity=0.448 Sum_probs=20.7
Q ss_pred CCCCCCCCCCCcc---cccCCCCccccccccceec
Q 046187 1 MKCPYCSAAQGRC---ATTSTGRSITECGSCGRVI 32 (510)
Q Consensus 1 m~Cp~C~~~~~~i---~D~~~Gd~~~VC~~CG~Vl 32 (510)
|.||+||+...+- +--.+.+ .+|..||+-.
T Consensus 1 m~CP~CGS~~Ivrcg~cr~~snr--YkCkdCGY~f 33 (59)
T PHA00626 1 MSCPKCGSGNIAKEKTMRGWSDD--YVCCDCGYND 33 (59)
T ss_pred CCCCCCCCceeeeeceecccCcc--eEcCCCCCee
Confidence 8999999954321 1122566 9999999954
No 48
>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=91.65 E-value=2.7 Score=38.94 Aligned_cols=89 Identities=21% Similarity=0.189 Sum_probs=65.7
Q ss_pred cchhhhHHHHHhhcCCCHHHHHHHHHHHHHHHh---c--cccCCCChHHHHHHHHHHHHHHcC-CCCCHHHHHHHhCCCH
Q 046187 229 NSIAVHMPRFCTLLQLNKSAQVLATHIGEVVIN---K--CFCTRRNPISISAAAIYLACQLED-KRKTQAEICKVTGLTE 302 (510)
Q Consensus 229 ~~p~~~I~Rfcs~L~L~~~V~~~A~~Ia~~a~~---~--~l~~GRsP~sIAAAaIYlAarl~g-~~~t~keIa~vagVSe 302 (510)
.+..+|+.|+.....++..+.-.|...++++.. . ..+...+..-+-.+||.+|++++. ...+.+.+|++.|++.
T Consensus 52 i~i~~fl~ri~~~~~~s~~~~i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v~gis~ 131 (149)
T PF08613_consen 52 ISIRDFLSRILKYTQCSPECLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNTYSNKSWAKVGGISL 131 (149)
T ss_dssp S-HHHHHHHHHHHTT--HHHHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS---HHHHHHHHTS-H
T ss_pred CcHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhcccccccHHHHHhhcCCCH
Confidence 457899999999999999998888888887776 1 224567788899999999999875 4677899999999998
Q ss_pred HHHHHHHHHHHHhhc
Q 046187 303 VTLRKVYKELLENWD 317 (510)
Q Consensus 303 ~TIRkrYKEL~e~l~ 317 (510)
.-+.+-=.+++..++
T Consensus 132 ~eln~lE~~fL~~l~ 146 (149)
T PF08613_consen 132 KELNELEREFLKLLD 146 (149)
T ss_dssp HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHHCC
Confidence 888877777776654
No 49
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=91.44 E-value=15 Score=38.64 Aligned_cols=183 Identities=18% Similarity=0.183 Sum_probs=93.8
Q ss_pred hhHHHHHHHHHH-HHHHHHhC-----CCHHHHHHHHHHHHHHHhCCccCCccHHHHHHHHHHHHHH----h---------
Q 046187 128 VMMDNLRAYLQI-IDVASILG-----LDYDICDHAFQLFRDCCSATCLRNRSVEALATAALVQAIR----E--------- 188 (510)
Q Consensus 128 ~~er~L~a~~~I-~~ic~~L~-----LP~~VidtA~~LyK~a~e~~~lrGRs~eaVaAACLYIACR----~--------- 188 (510)
..++++..|... ..+|.++. +-+-+.+....+++.+....--+|-+..+.|.-.|.-+.. .
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 344555555443 45777763 2234555666688877777777888877776655544321 1
Q ss_pred -------------------cCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhcccCCCCCcchhhhHHHHHhhcCCCHH--
Q 046187 189 -------------------AQEPRTLQEISIAANVPQKEIGKYIKILGEALQLSQPINSNSIAVHMPRFCTLLQLNKS-- 247 (510)
Q Consensus 189 -------------------~~~PrTLkEIa~vt~VskkeIgr~yk~L~k~L~i~~pv~~~~p~~~I~Rfcs~L~L~~~-- 247 (510)
.+.+-|..|||..++++..++..........+-++.++....-..+..-+.+.-..+++
T Consensus 167 ~~~~~~~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~~~~pe~~ 246 (324)
T PRK07921 167 HLVEQVNKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSEATSAENA 246 (324)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCceecCCCCCCCCchHHHHhcCCCCCCHHHH
Confidence 13334567888888888888877654333333344333211111122222221111221
Q ss_pred HHH-HHHHHHHHHHhccccCCCChHHHHHHHHHHHHHHc-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhc
Q 046187 248 AQV-LATHIGEVVINKCFCTRRNPISISAAAIYLACQLE-DKRKTQAEICKVTGLTEVTLRKVYKELLENWD 317 (510)
Q Consensus 248 V~~-~A~~Ia~~a~~~~l~~GRsP~sIAAAaIYlAarl~-g~~~t~keIa~vagVSe~TIRkrYKEL~e~l~ 317 (510)
+.. ....-+..+.. .+.-|--..| ..|+. +. +.+.|++||++.+|||...||...+.-...+.
T Consensus 247 ~~~~~~~~~l~~~L~--~L~eREr~Vl---~~ryg--l~~~~~~Tl~eIa~~lgvS~eRVrQIe~~Al~KLr 311 (324)
T PRK07921 247 VIAGLLHTDIRSVLA--TLDEREQQVI---RLRFG--LDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLR 311 (324)
T ss_pred HHHHHHHHHHHHHHH--hCCHHHHHHH---HHHHh--cCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 111 11111222211 1221211111 11110 11 35799999999999999999987765555443
No 50
>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=91.44 E-value=17 Score=36.69 Aligned_cols=186 Identities=12% Similarity=0.116 Sum_probs=90.9
Q ss_pred CchhhHHHHHHHHHHH-HHHHHhC-----CCHHHHHHHHHHHHHHHhCCccCCccHHHHHHHHHHHHHHh----------
Q 046187 125 SSSVMMDNLRAYLQII-DVASILG-----LDYDICDHAFQLFRDCCSATCLRNRSVEALATAALVQAIRE---------- 188 (510)
Q Consensus 125 ~~~~~er~L~a~~~I~-~ic~~L~-----LP~~VidtA~~LyK~a~e~~~lrGRs~eaVaAACLYIACR~---------- 188 (510)
+....++++..|..+. .+|.++- +-+-+.+.-.-+++.+....--+|.+..+.|.-+|--+...
T Consensus 33 d~~a~~~Lv~~~~~lV~~~a~~~~~~~~~~eDLvQeg~igl~~a~~~fd~~~~~~FsTYA~~~Ir~~i~~~l~~~~~~ir 112 (270)
T TIGR02392 33 DLDAAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYILRNWRLVK 112 (270)
T ss_pred CHHHHHHHHHHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCChHHhhHHHHHHHHHHHHHHcCCcee
Confidence 4444455555554444 4666662 12333445555777777666566666665555444433220
Q ss_pred ----------------------c-CCCCCHHHHHHHhCCCHHHHHHHHHHHHH-HhcccCCCCCcch--hhhHHHHHhhc
Q 046187 189 ----------------------A-QEPRTLQEISIAANVPQKEIGKYIKILGE-ALQLSQPINSNSI--AVHMPRFCTLL 242 (510)
Q Consensus 189 ----------------------~-~~PrTLkEIa~vt~VskkeIgr~yk~L~k-~L~i~~pv~~~~p--~~~I~Rfcs~L 242 (510)
. ..|-+..|||..++++..++......+.. .+-++.++.+.+. ..++..+.+..
T Consensus 113 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eiA~~l~~~~~~v~~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~l~d~~ 192 (270)
T TIGR02392 113 VATTKAQRKLFFNLRKMKKRLQGWLNPEEVEAIAEELGVSEREVREMESRLSGQDMSLNASIDDDEDDGGAPIAYLVDKT 192 (270)
T ss_pred cCchHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHHHHccCCCccCCCCCCCCCCccccHHHHhcCCC
Confidence 0 12335778888888888887664332221 1222233221101 12333333332
Q ss_pred CCCHH-HHHH-----HHHHHHHHHhccccCCCChHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q 046187 243 QLNKS-AQVL-----ATHIGEVVINKCFCTRRNPISISAAAIYLACQLEDKRKTQAEICKVTGLTEVTLRKVYKELLENW 316 (510)
Q Consensus 243 ~L~~~-V~~~-----A~~Ia~~a~~~~l~~GRsP~sIAAAaIYlAarl~g~~~t~keIa~vagVSe~TIRkrYKEL~e~l 316 (510)
.-+.+ +... ....++.+.. -+ ++.-=-.-.++ ...+..+|++|||+.+|||..+|++..+.....+
T Consensus 193 ~~pe~~~~~~~~~~~~~~~L~~al~--~L---~~rer~vl~l~---y~~~~~~t~~eIA~~lgvS~~~V~q~~~~Al~kL 264 (270)
T TIGR02392 193 SDPEDTLEEEQWEELQRQALANALG--SL---DARSRRIIEAR---WLDDDKLTLQELAAEYGVSAERIRQIEKNAMKKL 264 (270)
T ss_pred CChHHHHHHHHHHHHHHHHHHHHHH--cC---CHHHHHHHHHH---hcCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 22222 1111 1111222221 11 11111111111 1124579999999999999999997777666655
Q ss_pred cc
Q 046187 317 DD 318 (510)
Q Consensus 317 ~~ 318 (510)
..
T Consensus 265 r~ 266 (270)
T TIGR02392 265 KA 266 (270)
T ss_pred HH
Confidence 43
No 51
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=91.36 E-value=0.11 Score=49.00 Aligned_cols=32 Identities=34% Similarity=0.947 Sum_probs=21.7
Q ss_pred CCCCCCCCCCCcccccC---CCCcc---ccccccceec
Q 046187 1 MKCPYCSAAQGRCATTS---TGRSI---TECGSCGRVI 32 (510)
Q Consensus 1 m~Cp~C~~~~~~i~D~~---~Gd~~---~VC~~CG~Vl 32 (510)
|+||+||..-..+.|.. .|... .-|.+||.-.
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f 38 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRF 38 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcc
Confidence 89999998554555533 56412 4599999843
No 52
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=91.19 E-value=22 Score=38.24 Aligned_cols=183 Identities=16% Similarity=0.106 Sum_probs=93.1
Q ss_pred hhHHHHHHHHH-HHHHHHHhC-----CCHHHHHHHHHHHHHHHhCCccCCccHHHHHHHHHHHHH----Hhc--------
Q 046187 128 VMMDNLRAYLQ-IIDVASILG-----LDYDICDHAFQLFRDCCSATCLRNRSVEALATAALVQAI----REA-------- 189 (510)
Q Consensus 128 ~~er~L~a~~~-I~~ic~~L~-----LP~~VidtA~~LyK~a~e~~~lrGRs~eaVaAACLYIAC----R~~-------- 189 (510)
..++++..|.. +..+|.++. +-+-+.+.-.-+++.+.....-+|.+..+.|.=.|--+. +..
T Consensus 137 A~~~Li~~~l~lV~~iA~ry~~~~~~~eDLiQEG~igL~~Ai~kFd~~kg~~FsTYA~wWIRqaI~~~I~~~~r~IRlP~ 216 (373)
T PRK07406 137 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV 216 (373)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcCCceeCCH
Confidence 34455555544 445777763 334566677778888887777778777666543333222 111
Q ss_pred --------------------CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhcccCCCCCcchhhhHHHHHhhcCCCHH--
Q 046187 190 --------------------QEPRTLQEISIAANVPQKEIGKYIKILGEALQLSQPINSNSIAVHMPRFCTLLQLNKS-- 247 (510)
Q Consensus 190 --------------------~~PrTLkEIa~vt~VskkeIgr~yk~L~k~L~i~~pv~~~~p~~~I~Rfcs~L~L~~~-- 247 (510)
|..-|..|||..++++..++..........+-++.++....-..++.-+.+. .-+++
T Consensus 217 ~~~~~~~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~~~~~~~~~SLd~~i~~~~~~~l~d~l~d~-~~~pee~ 295 (373)
T PRK07406 217 HLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEAD-GETPEDD 295 (373)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCcccHHHhcCCC-CCCHHHH
Confidence 2223567788888888888766544322223333333211111122222121 11221
Q ss_pred HHHH-HHHHHHHHHhccccCCCChHHHHHHHHHHHHHHc-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 248 AQVL-ATHIGEVVINKCFCTRRNPISISAAAIYLACQLE-DKRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 248 V~~~-A~~Ia~~a~~~~l~~GRsP~sIAAAaIYlAarl~-g~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
+... -...+..+.. .-+|.--- +|.+---+. +...|+++||+.+|||..+||...+.-...|..
T Consensus 296 ~~~~~~~~~L~~aL~-----~L~~rEr~--IL~lrygl~~~~~~Tl~EIA~~lgiS~eRVRQie~rAL~KLR~ 361 (373)
T PRK07406 296 VAKNLLREDLEGVLA-----TLSPRERD--VLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRH 361 (373)
T ss_pred HHHHHHHHHHHHHHH-----cCCHHHHH--HHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 1110 0111111111 11222211 111111111 247899999999999999999998877776654
No 53
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=90.95 E-value=0.089 Score=42.00 Aligned_cols=30 Identities=33% Similarity=0.737 Sum_probs=25.0
Q ss_pred CCCCCCCCCCcccccCCCCccccccccceeccc
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRVIAE 34 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vlee 34 (510)
+||+|+..+ ++.+|++-. ..|..||.+|.+
T Consensus 13 kCp~C~n~q-~vFsha~t~--V~C~~Cg~~L~~ 42 (59)
T PRK00415 13 KCPDCGNEQ-VVFSHASTV--VRCLVCGKTLAE 42 (59)
T ss_pred ECCCCCCeE-EEEecCCcE--EECcccCCCccc
Confidence 699998754 558888887 999999999954
No 54
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=90.92 E-value=0.09 Score=42.81 Aligned_cols=30 Identities=33% Similarity=0.690 Sum_probs=24.8
Q ss_pred CCCCCCCCCCcccccCCCCccccccccceeccc
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRVIAE 34 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vlee 34 (510)
+||+|+-.+ ++.+|++-. .-|..||.+|-+
T Consensus 21 kCpdC~N~q-~vFshast~--V~C~~CG~~l~~ 50 (67)
T COG2051 21 KCPDCGNEQ-VVFSHASTV--VTCLICGTTLAE 50 (67)
T ss_pred ECCCCCCEE-EEeccCceE--EEecccccEEEe
Confidence 699998754 557888777 999999999855
No 55
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=90.86 E-value=0.13 Score=34.25 Aligned_cols=22 Identities=36% Similarity=0.862 Sum_probs=17.0
Q ss_pred CCCCCCCCCCCcccccCCCCccccccccce
Q 046187 1 MKCPYCSAAQGRCATTSTGRSITECGSCGR 30 (510)
Q Consensus 1 m~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~ 30 (510)
|+||+||. . + ..++ .+|.+||.
T Consensus 3 ~~Cp~Cg~-~-~----~~~~--~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGA-E-I----DPDA--KFCPNCGA 24 (26)
T ss_pred CCCcccCC-c-C----Cccc--ccChhhCC
Confidence 57999988 2 2 3556 99999996
No 56
>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=90.68 E-value=0.54 Score=48.76 Aligned_cols=87 Identities=21% Similarity=0.187 Sum_probs=63.6
Q ss_pred hhhHHHHHhhcCCCHHHHHHHHHHHHHHHhccccCCCChHHHHHHHHHHHHHHcC--CCCCHH-HHHH-----HhCCCHH
Q 046187 232 AVHMPRFCTLLQLNKSAQVLATHIGEVVINKCFCTRRNPISISAAAIYLACQLED--KRKTQA-EICK-----VTGLTEV 303 (510)
Q Consensus 232 ~~~I~Rfcs~L~L~~~V~~~A~~Ia~~a~~~~l~~GRsP~sIAAAaIYlAarl~g--~~~t~k-eIa~-----vagVSe~ 303 (510)
..+|.++|.+|+|+..+..+|..+.++..-..-..+.++..||++|||+||+..+ ..+... -+++ ...-+..
T Consensus 49 ~k~i~~l~~~L~lp~~~laTAi~~f~Rf~Lk~sv~e~~~~~vv~tcv~LA~K~ed~~~~I~i~~~~~~~~~se~~~~sr~ 128 (297)
T COG5333 49 LKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPRDISIESFEARDLWSEEPKSSRE 128 (297)
T ss_pred HHHHHHHHHhcCCCcchHHHHHHHHHHHHhhcccccccHHHHHHhheeeeeecccccchhhHHHHHhhccccccccccHH
Confidence 4689999999999999999999888777655568899999999999999999877 333222 1222 4445555
Q ss_pred HHHHHHHHHHHhhcc
Q 046187 304 TLRKVYKELLENWDD 318 (510)
Q Consensus 304 TIRkrYKEL~e~l~~ 318 (510)
-|-+.=.++.+.++-
T Consensus 129 ~Il~~E~~lLEaL~f 143 (297)
T COG5333 129 RILEYEFELLEALDF 143 (297)
T ss_pred HHHHHHHHHHHHccc
Confidence 565555566665553
No 57
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=90.39 E-value=21 Score=35.85 Aligned_cols=186 Identities=16% Similarity=0.100 Sum_probs=92.6
Q ss_pred CCchhhHHHHHHHHHHH-HHHHHh-C---CC-HHHH-HHHHHHHHHHHhCCccCCccHHHHHHHHHHHHHHh----c---
Q 046187 124 TSSSVMMDNLRAYLQII-DVASIL-G---LD-YDIC-DHAFQLFRDCCSATCLRNRSVEALATAALVQAIRE----A--- 189 (510)
Q Consensus 124 ~~~~~~er~L~a~~~I~-~ic~~L-~---LP-~~Vi-dtA~~LyK~a~e~~~lrGRs~eaVaAACLYIACR~----~--- 189 (510)
++....+++...|..+. .+|.++ + .+ ++++ +.-.-|++.+.....-+|-+..+.+.-+|.-+|.. .
T Consensus 22 gd~~a~~~Lv~~~~~lV~~ia~~~~~~~~~~~eDL~Qeg~igL~~a~~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~~~~ 101 (256)
T PRK07408 22 PSIALRNQLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSPT 101 (256)
T ss_pred CCHHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHHcCCe
Confidence 34445556666665544 577776 2 22 3343 33444777777767667777766665554444332 1
Q ss_pred -------------------------CCCCCHHHHHHHhCCCHHHHHHHHHHHHH--HhcccCCCCCc-c-hhhhHHHHHh
Q 046187 190 -------------------------QEPRTLQEISIAANVPQKEIGKYIKILGE--ALQLSQPINSN-S-IAVHMPRFCT 240 (510)
Q Consensus 190 -------------------------~~PrTLkEIa~vt~VskkeIgr~yk~L~k--~L~i~~pv~~~-~-p~~~I~Rfcs 240 (510)
|.+-|..|||..++++.+++......... .+-++.+.... + ...+......
T Consensus 102 vr~pr~~~~~~~~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d~~~d 181 (256)
T PRK07408 102 VRIPRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRTPLSLDAPVNQDEDGSTSLGDLLPD 181 (256)
T ss_pred eeeCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHhhccCCccccccCCCCCCCccccccccCC
Confidence 23335678888889998888765432211 11222221100 0 0001111110
Q ss_pred hcCCCHHH-HHHHHHHHHHHHhccccCCCChHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhccc
Q 046187 241 LLQLNKSA-QVLATHIGEVVINKCFCTRRNPISISAAAIYLACQLEDKRKTQAEICKVTGLTEVTLRKVYKELLENWDDL 319 (510)
Q Consensus 241 ~L~L~~~V-~~~A~~Ia~~a~~~~l~~GRsP~sIAAAaIYlAarl~g~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~L 319 (510)
.-.-.... ......|.+.+.. -+|.-=..-.++ +....++++||+.+|+|..||+.+++.....+...
T Consensus 182 ~~~~~~~~~~~~~~~l~~~l~~------L~~~~r~vl~l~-----y~~~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~ 250 (256)
T PRK07408 182 PRYRSFQLAQEDRIRLQQALAQ------LEERTREVLEFV-----FLHDLTQKEAAERLGISPVTVSRRVKKGLDQLKKL 250 (256)
T ss_pred cccchhhhhHHHHHHHHHHHHc------CCHHHHHHHHHH-----HHCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 00000001 1111122222211 122211111111 13578999999999999999999988777776654
Q ss_pred C
Q 046187 320 L 320 (510)
Q Consensus 320 i 320 (510)
+
T Consensus 251 l 251 (256)
T PRK07408 251 L 251 (256)
T ss_pred h
Confidence 4
No 58
>KOG1010 consensus Rb (Retinoblastoma tumor suppressor)-related protein [Cell cycle control, cell division, chromosome partitioning]
Probab=90.20 E-value=0.52 Score=54.57 Aligned_cols=69 Identities=20% Similarity=0.324 Sum_probs=62.1
Q ss_pred HHHHHHHHHHHhCCCHHHHHHHHHHHHHHHhC--CccCCccHHHHHHHHHHHHHHhcCCCCCHHHHHHHhC
Q 046187 135 AYLQIIDVASILGLDYDICDHAFQLFRDCCSA--TCLRNRSVEALATAALVQAIREAQEPRTLQEISIAAN 203 (510)
Q Consensus 135 a~~~I~~ic~~L~LP~~VidtA~~LyK~a~e~--~~lrGRs~eaVaAACLYIACR~~~~PrTLkEIa~vt~ 203 (510)
|+.+|.++|++|.|.+...+.-..+|.-.... .+++.|..+.+.-.|+|+.||..+..+||+||.....
T Consensus 680 AavRL~~Lc~rL~l~~e~r~~IWtlFehsl~~et~Lm~dRHLDQillCaiy~i~KV~~~~ltF~eIm~~YR 750 (920)
T KOG1010|consen 680 AAVRLNDLCERLSLSDELREQIWTLFEHSLTNETELMRDRHLDQILLCAIYGIAKVKKEDLTFSEIMRAYR 750 (920)
T ss_pred HHHHHHHHHHHhhhhhHHHHHHHHHHHHHHhccHHHHHhhhHHHHHHHHHHhheehhcccchHHHHHHHHh
Confidence 77899999999999999999999999877654 6889999999999999999999999999999977543
No 59
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=90.09 E-value=25 Score=38.48 Aligned_cols=180 Identities=12% Similarity=0.114 Sum_probs=97.4
Q ss_pred hhHHHHHHHHHHH-HHHHHhC-----CCHHHHHHHHHHHHHHHhCCccCCccHHHHHH------HHHHHH----------
Q 046187 128 VMMDNLRAYLQII-DVASILG-----LDYDICDHAFQLFRDCCSATCLRNRSVEALAT------AALVQA---------- 185 (510)
Q Consensus 128 ~~er~L~a~~~I~-~ic~~L~-----LP~~VidtA~~LyK~a~e~~~lrGRs~eaVaA------ACLYIA---------- 185 (510)
..++++.++..+. .+|.++. +-+-|.+...-+++.+....-.+|.+..+.+- -.-+++
T Consensus 176 A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQEG~iGL~ravekFDp~rG~rFSTYa~wwIRqaI~r~i~~~srtIrlP~ 255 (415)
T PRK07598 176 AKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPV 255 (415)
T ss_pred HHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHHcCCceehhH
Confidence 4455666665444 5777762 33566677777888888777777877666553 112221
Q ss_pred ---------H-------HhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhcccCCCCCcchhhhHHHHHhhcCCCHH--
Q 046187 186 ---------I-------REAQEPRTLQEISIAANVPQKEIGKYIKILGEALQLSQPINSNSIAVHMPRFCTLLQLNKS-- 247 (510)
Q Consensus 186 ---------C-------R~~~~PrTLkEIa~vt~VskkeIgr~yk~L~k~L~i~~pv~~~~p~~~I~Rfcs~L~L~~~-- 247 (510)
- ...|..-+..|||..++++.+++..+.......+-++.++....-..+.. +...=..+++
T Consensus 256 ~i~e~l~~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~~l~~~~~~~SLd~~vg~~~d~~l~d-~l~~~~~~pee~ 334 (415)
T PRK07598 256 HITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLLRVPRSVSLETKVGKDKDTELGD-LLETDDISPEEM 334 (415)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHccCCcccccccCCCccccHHH-hccCCCCCHHHH
Confidence 0 12345677889999999999999888766554444444432211111211 1111111221
Q ss_pred HH--HHHHHHHHHHHhccccCCCChHHHHHHHHHHHHHHc-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q 046187 248 AQ--VLATHIGEVVINKCFCTRRNPISISAAAIYLACQLE-DKRKTQAEICKVTGLTEVTLRKVYKELLENW 316 (510)
Q Consensus 248 V~--~~A~~Ia~~a~~~~l~~GRsP~sIAAAaIYlAarl~-g~~~t~keIa~vagVSe~TIRkrYKEL~e~l 316 (510)
+. .....|...+. .-+|.--- +|.+--.+. +.+.|++||++.+|||..+||...+.-...|
T Consensus 335 ~~~~~l~~~L~~~L~------~L~~reR~--VI~LRygl~d~~~~Tl~EIA~~LGvS~erVRqie~rAl~KL 398 (415)
T PRK07598 335 LMRESLQRDLQHLLA------DLTSRERD--VIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQKL 398 (415)
T ss_pred HHHHHHHHHHHHHHH------hCCHHHHH--HHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 11 11112222221 12222211 111111122 3679999999999999999998876544444
No 60
>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=89.94 E-value=4.3 Score=37.58 Aligned_cols=85 Identities=11% Similarity=0.063 Sum_probs=62.7
Q ss_pred HHHHHHHhCCCHHHHHHHHHHHHHHHh---C--CccCCccHHHHHHHHHHHHHHh-cCCCCCHHHHHHHhCCCHHHHHHH
Q 046187 139 IIDVASILGLDYDICDHAFQLFRDCCS---A--TCLRNRSVEALATAALVQAIRE-AQEPRTLQEISIAANVPQKEIGKY 212 (510)
Q Consensus 139 I~~ic~~L~LP~~VidtA~~LyK~a~e---~--~~lrGRs~eaVaAACLYIACR~-~~~PrTLkEIa~vt~VskkeIgr~ 212 (510)
+.++....+++..+.-.|..|.+++.. . ..+.......+..+||.+|.|- .+...+.+..+.+.|++.++|.+.
T Consensus 58 l~ri~~~~~~s~~~~i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v~gis~~eln~l 137 (149)
T PF08613_consen 58 LSRILKYTQCSPECLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNTYSNKSWAKVGGISLKELNEL 137 (149)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS---HHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHcCCChHHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhcccccccHHHHHhhcCCCHHHHHHH
Confidence 556778889999999999999999888 2 2244566778899999999995 577889999999999999999999
Q ss_pred HHHHHHHhccc
Q 046187 213 IKILGEALQLS 223 (510)
Q Consensus 213 yk~L~k~L~i~ 223 (510)
-..+...|+.+
T Consensus 138 E~~fL~~l~~~ 148 (149)
T PF08613_consen 138 EREFLKLLDYN 148 (149)
T ss_dssp HHHHHHHTTT-
T ss_pred HHHHHHHCCCc
Confidence 88888887653
No 61
>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=89.81 E-value=0.2 Score=46.88 Aligned_cols=32 Identities=34% Similarity=0.817 Sum_probs=23.6
Q ss_pred CCCCCCCCCCCccccc---CCCCcc---ccccccceec
Q 046187 1 MKCPYCSAAQGRCATT---STGRSI---TECGSCGRVI 32 (510)
Q Consensus 1 m~Cp~C~~~~~~i~D~---~~Gd~~---~VC~~CG~Vl 32 (510)
|+||.|+.....++|+ ..|..+ -.|.+||.=.
T Consensus 1 M~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RF 38 (147)
T TIGR00244 1 MHCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERF 38 (147)
T ss_pred CCCCCCCCCCCEeeeccccCCCCeeeecccCCccCCcc
Confidence 9999999988888884 345411 3599999743
No 62
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=89.15 E-value=28 Score=35.45 Aligned_cols=70 Identities=16% Similarity=0.196 Sum_probs=45.6
Q ss_pred HHHHHHHHHHH-HHHHhC--CC----HHHHHHHHHHHHHHHhCCccCCccHHHHHHHH----HHHHHHhcC---CCCCHH
Q 046187 131 DNLRAYLQIID-VASILG--LD----YDICDHAFQLFRDCCSATCLRNRSVEALATAA----LVQAIREAQ---EPRTLQ 196 (510)
Q Consensus 131 r~L~a~~~I~~-ic~~L~--LP----~~VidtA~~LyK~a~e~~~lrGRs~eaVaAAC----LYIACR~~~---~PrTLk 196 (510)
++...|.-+.. ++.++. +| +-+.--..-|.+-+.....-+|.+..+.|.=| ++--+|..+ +||+++
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 46667766664 777773 55 23334555666777767888898888766544 555667655 688887
Q ss_pred HHHH
Q 046187 197 EISI 200 (510)
Q Consensus 197 EIa~ 200 (510)
+...
T Consensus 107 ~~~~ 110 (247)
T COG1191 107 ELGR 110 (247)
T ss_pred HHHH
Confidence 7743
No 63
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=89.01 E-value=0.2 Score=42.66 Aligned_cols=30 Identities=27% Similarity=0.651 Sum_probs=25.0
Q ss_pred CCCCCCCCCCcccccCCCCccccccccceeccc
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRVIAE 34 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vlee 34 (510)
+||+|+..+ +|..|+.-. ..|..||.+|.+
T Consensus 37 kCp~C~n~q-~VFShA~t~--V~C~~Cg~~L~~ 66 (85)
T PTZ00083 37 KCPGCSQIT-TVFSHAQTV--VLCGGCSSQLCQ 66 (85)
T ss_pred ECCCCCCee-EEEecCceE--EEccccCCEeec
Confidence 699998854 558888887 999999999954
No 64
>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=88.83 E-value=0.15 Score=40.25 Aligned_cols=30 Identities=33% Similarity=0.698 Sum_probs=20.5
Q ss_pred CCCCCCCCCCcccccCCCCccccccccceeccc
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRVIAE 34 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vlee 34 (510)
+||+|+..+ +|.+|+.-. ..|..||.+|-+
T Consensus 9 kCp~C~~~q-~vFSha~t~--V~C~~Cg~~L~~ 38 (55)
T PF01667_consen 9 KCPGCYNIQ-TVFSHAQTV--VKCVVCGTVLAQ 38 (55)
T ss_dssp E-TTT-SEE-EEETT-SS---EE-SSSTSEEEE
T ss_pred ECCCCCCee-EEEecCCeE--EEcccCCCEecC
Confidence 799998854 558888887 999999999954
No 65
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=88.54 E-value=0.25 Score=32.12 Aligned_cols=22 Identities=32% Similarity=0.762 Sum_probs=16.1
Q ss_pred CCCCCCCCCCcccccCCCCcccccccccee
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRV 31 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~V 31 (510)
+||+||.. + ..+. .+|.+||.-
T Consensus 1 ~Cp~CG~~--~----~~~~--~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAE--I----EDDA--KFCPNCGTP 22 (23)
T ss_pred CCcccCCC--C----CCcC--cchhhhCCc
Confidence 69999982 2 2344 899999974
No 66
>KOG4164 consensus Cyclin ik3-1/CABLES [Cell cycle control, cell division, chromosome partitioning]
Probab=88.49 E-value=1.1 Score=48.05 Aligned_cols=85 Identities=13% Similarity=0.142 Sum_probs=59.3
Q ss_pred HHHHHHHHhCCCHHHHHHHHHHHHHHHhCCccCCccHHHHHHHHHHHHHHhcCCC-CCHHHHHH----HhCCCHHHHHHH
Q 046187 138 QIIDVASILGLDYDICDHAFQLFRDCCSATCLRNRSVEALATAALVQAIREAQEP-RTLQEISI----AANVPQKEIGKY 212 (510)
Q Consensus 138 ~I~~ic~~L~LP~~VidtA~~LyK~a~e~~~lrGRs~eaVaAACLYIACR~~~~P-rTLkEIa~----vt~VskkeIgr~ 212 (510)
++.++...-+|...++.+|..||.++.-.+++..-++..+|.|||.+|.+.+..- .++|.+.+ .+..++++|-..
T Consensus 388 EMr~l~~d~~id~~TVa~AyVYFEKliLkglisK~NRKlcAGAclLlaaKmnD~Kks~vKslIek~Ee~fR~nrrdLia~ 467 (497)
T KOG4164|consen 388 EMRELGEDCGIDVVTVAMAYVYFEKLILKGLISKQNRKLCAGACLLLAAKMNDLKKSTVKSLIEKLEEQFRLNRRDLIAF 467 (497)
T ss_pred HHHHhhhccCccceeehhHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHhcccHHhhhhh
Confidence 4445666667888899999999999988888888888899999999999988664 23333332 355666665444
Q ss_pred HHHHHHHhcc
Q 046187 213 IKILGEALQL 222 (510)
Q Consensus 213 yk~L~k~L~i 222 (510)
---++-.|.+
T Consensus 468 Ef~VlvaLef 477 (497)
T KOG4164|consen 468 EFPVLVALEF 477 (497)
T ss_pred hhhHHHhhhh
Confidence 3334444443
No 67
>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=87.95 E-value=0.15 Score=54.01 Aligned_cols=78 Identities=21% Similarity=0.158 Sum_probs=0.0
Q ss_pred CCCHHHHHHHHHHHHHHH-hCCccCCccHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhcccC
Q 046187 147 GLDYDICDHAFQLFRDCC-SATCLRNRSVEALATAALVQAIREAQEPRTLQEISIAANVPQKEIGKYIKILGEALQLSQ 224 (510)
Q Consensus 147 ~LP~~VidtA~~LyK~a~-e~~~lrGRs~eaVaAACLYIACR~~~~PrTLkEIa~vt~VskkeIgr~yk~L~k~L~i~~ 224 (510)
.+|..++..|.+||+... ....+++..--+-+.+|+||||...+.+..+..+....+++++...+.|..|.+.|+...
T Consensus 11 ~~~~~ll~~a~~L~~ls~~~~~~l~~~~EiaR~~iCa~lA~~~l~~~~dl~~~~~~~pl~pk~y~~l~~~~~~~L~~~s 89 (353)
T PF05460_consen 11 GLPPKLLSKASELYRLSRQKKSSLKPEEEIARAHICAELACERLKEKLDLPYAIKRSPLPPKVYKKLLNTFENLLGNSS 89 (353)
T ss_dssp -------------------------------------------------------------------------------
T ss_pred CCCHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhCCccCchhhcCCCCCCHHHHHHHHHHHHHHHhCCC
Confidence 467899999999999998 445666665566789999999999999998888888889999999999999999887654
No 68
>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=87.84 E-value=0.21 Score=35.70 Aligned_cols=30 Identities=33% Similarity=0.825 Sum_probs=19.4
Q ss_pred CCCCCCCCCCccc-c--cCCCCccccccccceecc
Q 046187 2 KCPYCSAAQGRCA-T--TSTGRSITECGSCGRVIA 33 (510)
Q Consensus 2 ~Cp~C~~~~~~i~-D--~~~Gd~~~VC~~CG~Vle 33 (510)
.||+|+.. ..+- | ...|. ...|.+||.++.
T Consensus 4 ~CP~C~~~-~~v~~~~~~~~~~-~v~C~~C~~~~~ 36 (38)
T TIGR02098 4 QCPNCKTS-FRVVDSQLGANGG-KVRCGKCGHVWY 36 (38)
T ss_pred ECCCCCCE-EEeCHHHcCCCCC-EEECCCCCCEEE
Confidence 59999883 2332 2 12332 489999999874
No 69
>PLN00209 ribosomal protein S27; Provisional
Probab=87.58 E-value=0.22 Score=42.52 Aligned_cols=30 Identities=30% Similarity=0.589 Sum_probs=25.1
Q ss_pred CCCCCCCCCCcccccCCCCccccccccceeccc
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRVIAE 34 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vlee 34 (510)
+||+|+..+ +|..|+.-. ..|..||.+|.+
T Consensus 38 kCp~C~n~q-~VFShA~t~--V~C~~Cg~~L~~ 67 (86)
T PLN00209 38 KCQGCFNIT-TVFSHSQTV--VVCGSCQTVLCQ 67 (86)
T ss_pred ECCCCCCee-EEEecCceE--EEccccCCEeec
Confidence 699998854 558888887 999999999954
No 70
>PRK00420 hypothetical protein; Validated
Probab=87.14 E-value=0.36 Score=43.36 Aligned_cols=26 Identities=27% Similarity=0.598 Sum_probs=20.5
Q ss_pred CCCCCCCCCCcccccCCCCccccccccceec
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRVI 32 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vl 32 (510)
.||.||. +. .....|. .+|..||.++
T Consensus 25 ~CP~Cg~--pL-f~lk~g~--~~Cp~Cg~~~ 50 (112)
T PRK00420 25 HCPVCGL--PL-FELKDGE--VVCPVHGKVY 50 (112)
T ss_pred CCCCCCC--cc-eecCCCc--eECCCCCCee
Confidence 5999986 23 3337888 9999999987
No 71
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=86.80 E-value=1.1 Score=34.43 Aligned_cols=43 Identities=14% Similarity=0.207 Sum_probs=35.8
Q ss_pred HHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccCC
Q 046187 279 YLACQLEDKRKTQAEICKVTGLTEVTLRKVYKELLENWDDLLP 321 (510)
Q Consensus 279 YlAarl~g~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Lip 321 (510)
+++-..+....+..++|..+|||++|+.+.++++.+.+....+
T Consensus 10 ll~L~~LR~~~~~~~La~~FgIs~stvsri~~~~~~~L~~~l~ 52 (53)
T PF13613_consen 10 LLTLMYLRLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQVLK 52 (53)
T ss_pred HHHHHHHHcCCcHhHHhhheeecHHHHHHHHHHHHHHHHHhcC
Confidence 3444455678999999999999999999999999998877654
No 72
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=86.79 E-value=40 Score=34.61 Aligned_cols=191 Identities=14% Similarity=0.109 Sum_probs=93.5
Q ss_pred CchhhHHHHHHHHHHH-HHHHHhCC-----CHHHHHHHHHHHHHHHhCCccCCccHHHHHHHHHHHHHH-----------
Q 046187 125 SSSVMMDNLRAYLQII-DVASILGL-----DYDICDHAFQLFRDCCSATCLRNRSVEALATAALVQAIR----------- 187 (510)
Q Consensus 125 ~~~~~er~L~a~~~I~-~ic~~L~L-----P~~VidtA~~LyK~a~e~~~lrGRs~eaVaAACLYIACR----------- 187 (510)
+....+++...|.... .+|.++-- -+-+.+.-..+++.+.....-+|.+..+.|.-+|--+.+
T Consensus 38 d~~A~~~Lv~~~~~lV~~~a~~~~~~~~~~eDLvQeg~i~L~~a~~~fd~~~~~~f~tya~~~Ir~~I~~~lr~~~~~iR 117 (289)
T PRK07500 38 DEDALHRIISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSIVR 117 (289)
T ss_pred CHHHHHHHHHHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHCCCcee
Confidence 4444455666665444 57777632 234455556677777665555565556555554422211
Q ss_pred --------------------------hcCCCCCHHHHHHHhCCCHHHHHHHHHHHH-HHhcccCCCCCcch--hhhHHHH
Q 046187 188 --------------------------EAQEPRTLQEISIAANVPQKEIGKYIKILG-EALQLSQPINSNSI--AVHMPRF 238 (510)
Q Consensus 188 --------------------------~~~~PrTLkEIa~vt~VskkeIgr~yk~L~-k~L~i~~pv~~~~p--~~~I~Rf 238 (510)
..+..-|..||+..++++..++........ +.+-++.++..... ..++..+
T Consensus 118 ~p~~~~~~~~~~~~~~~~~~~~~~~~~l~~~pt~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d~i 197 (289)
T PRK07500 118 GGTSSAQKALFFNLRRLRARLAQADEELTKQEIHREIATALGVSLSDVEMMDARLSGPDASLNAPQSEEDEGRSERMDFL 197 (289)
T ss_pred cCccHHHHHHHHHHHHHHHHHHhhhcccCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCccccCCCCCCCCCcccHHHhc
Confidence 122333578899999999988754322111 22223333221001 1233333
Q ss_pred HhhcCCCHHH-HHH--HHHHHHHHHhccccCCCChHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 239 CTLLQLNKSA-QVL--ATHIGEVVINKCFCTRRNPISISAAAIYLACQLEDKRKTQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 239 cs~L~L~~~V-~~~--A~~Ia~~a~~~~l~~GRsP~sIAAAaIYlAarl~g~~~t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
...-.-+.+. ... ...+...+.+ .+..-+|.---.--++ ......+|++|||+.+|||..||++..+.-...
T Consensus 198 ~d~~~~pe~~~~~~~~~~~~~~~l~~--al~~L~~rer~vl~lr---~~~~~~~t~~EIa~~lgvs~~~V~q~~~~Al~k 272 (289)
T PRK07500 198 VDDSPLPDEQVESSIDGERRRRWLTQ--ALQTLNERELRIIRER---RLREDGATLEALGEELGISKERVRQIEARALEK 272 (289)
T ss_pred cCCCCCchHHHHHHHHHHHHHHHHHH--HHhcCCHHHHHHHHHH---hcCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 3221112222 111 1111111111 1112223222111111 123468999999999999999999877666665
Q ss_pred hcccC
Q 046187 316 WDDLL 320 (510)
Q Consensus 316 l~~Li 320 (510)
+...+
T Consensus 273 Lr~~l 277 (289)
T PRK07500 273 LRRAL 277 (289)
T ss_pred HHHHH
Confidence 55433
No 73
>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=86.64 E-value=33 Score=33.47 Aligned_cols=31 Identities=29% Similarity=0.552 Sum_probs=26.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWD 317 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~ 317 (510)
...|+++||+.+|||..+|++..+.....+.
T Consensus 198 ~~~t~~eIA~~lgis~~~V~~~~~~al~~Lr 228 (231)
T TIGR02885 198 KDKTQTEVANMLGISQVQVSRLEKKVLKKMK 228 (231)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 5789999999999999999988877766554
No 74
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=86.63 E-value=36 Score=33.88 Aligned_cols=32 Identities=19% Similarity=0.222 Sum_probs=27.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
...+.+|||+.+|+|+.||+.+++.....+..
T Consensus 216 ~~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 247 (251)
T PRK07670 216 EELTLTEIGQVLNLSTSRISQIHSKALFKLKK 247 (251)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 57899999999999999999998776666544
No 75
>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=86.57 E-value=0.38 Score=32.27 Aligned_cols=24 Identities=29% Similarity=0.684 Sum_probs=17.6
Q ss_pred CCCCCCCCCCcccccCCCCccccccccceecc
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRVIA 33 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vle 33 (510)
.||+|+.. + .... .+|..||.+..
T Consensus 2 ~CP~C~~~--V----~~~~--~~Cp~CG~~F~ 25 (26)
T PF10571_consen 2 TCPECGAE--V----PESA--KFCPHCGYDFE 25 (26)
T ss_pred cCCCCcCC--c----hhhc--CcCCCCCCCCc
Confidence 69999872 2 2344 79999999763
No 76
>KOG4557 consensus Origin recognition complex, subunit 6 [Replication, recombination and repair]
Probab=86.53 E-value=2 Score=42.73 Aligned_cols=82 Identities=13% Similarity=0.082 Sum_probs=60.2
Q ss_pred HHHHHHHHhCCCHHHHHHHHHHHHHHHhC-----CccCCccHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHH
Q 046187 138 QIIDVASILGLDYDICDHAFQLFRDCCSA-----TCLRNRSVEALATAALVQAIREAQEPRTLQEISIAANVPQKEIGKY 212 (510)
Q Consensus 138 ~I~~ic~~L~LP~~VidtA~~LyK~a~e~-----~~lrGRs~eaVaAACLYIACR~~~~PrTLkEIa~vt~VskkeIgr~ 212 (510)
.|.++|-+||+.+ ++..|.++++.+.++ ..--.-++-..++|++|.|||..+.-..-..+..+.|+++.++.+.
T Consensus 95 ~VrdlaVQfgc~e-vi~~a~~vl~syk~~lpaT~~~~~D~SrP~ft~aA~~~ack~lKlKVdK~kli~~sg~~~s~F~~l 173 (262)
T KOG4557|consen 95 NVRDLAVQFGCVE-VIKSAQNVLSSYKERLPATRRANADFSRPVFTAAAFYLACKKLKLKVDKLKLIEVSGTSESEFSCL 173 (262)
T ss_pred CHHHHHHHHhHHH-HHHHHHHHHHHHHhcCchhhhcCCcccchHHHHHHHHHHHHHHHHhhhHhhcccccCCCHHHHHHH
Confidence 4557999999875 777888888777663 1111234456789999999999988877777888889998777777
Q ss_pred HHHHHHHh
Q 046187 213 IKILGEAL 220 (510)
Q Consensus 213 yk~L~k~L 220 (510)
.+.+.+..
T Consensus 174 ~kqler~~ 181 (262)
T KOG4557|consen 174 SKQLERNY 181 (262)
T ss_pred HHHHHHHH
Confidence 66666544
No 77
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=86.18 E-value=40 Score=33.95 Aligned_cols=29 Identities=28% Similarity=0.312 Sum_probs=23.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
...+.+|||+.+|+|..||+.+++.....
T Consensus 227 ~~~s~~eIA~~lgis~~tV~~~~~ra~~~ 255 (268)
T PRK06288 227 EDLTLKEIGKVLGVTESRISQLHTKAVLQ 255 (268)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 47899999999999999999666543333
No 78
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=86.05 E-value=0.36 Score=34.41 Aligned_cols=29 Identities=28% Similarity=0.633 Sum_probs=14.2
Q ss_pred CCCCCCCCCCc-cc-ccCCCCccccccccceec
Q 046187 2 KCPYCSAAQGR-CA-TTSTGRSITECGSCGRVI 32 (510)
Q Consensus 2 ~Cp~C~~~~~~-i~-D~~~Gd~~~VC~~CG~Vl 32 (510)
.||.||..... +. +-..=+ .||..||.|-
T Consensus 2 fC~~CG~~l~~~ip~gd~r~R--~vC~~Cg~Ih 32 (34)
T PF14803_consen 2 FCPQCGGPLERRIPEGDDRER--LVCPACGFIH 32 (34)
T ss_dssp B-TTT--B-EEE--TT-SS-E--EEETTTTEEE
T ss_pred ccccccChhhhhcCCCCCccc--eECCCCCCEE
Confidence 59999983211 12 122333 8999999973
No 79
>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=86.00 E-value=2.2 Score=31.95 Aligned_cols=32 Identities=25% Similarity=0.320 Sum_probs=27.0
Q ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q 046187 285 EDKRKTQAEICKVTGLTEVTLRKVYKELLENW 316 (510)
Q Consensus 285 ~g~~~t~keIa~vagVSe~TIRkrYKEL~e~l 316 (510)
+....|++|||+.+|+|..||++.++...+.+
T Consensus 17 y~~~~t~~eIa~~lg~s~~~V~~~~~~al~kL 48 (50)
T PF04545_consen 17 YFEGLTLEEIAERLGISRSTVRRILKRALKKL 48 (50)
T ss_dssp HTST-SHHHHHHHHTSCHHHHHHHHHHHHHHH
T ss_pred hcCCCCHHHHHHHHCCcHHHHHHHHHHHHHHh
Confidence 36789999999999999999999998776654
No 80
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=85.31 E-value=0.55 Score=36.22 Aligned_cols=26 Identities=35% Similarity=0.728 Sum_probs=19.4
Q ss_pred CCCCCCCCCCcccccCCCCccccccccceec
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRVI 32 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vl 32 (510)
.||.||.. .+.++. +. ..|..||+..
T Consensus 22 fCP~Cg~~--~m~~~~-~r--~~C~~Cgyt~ 47 (50)
T PRK00432 22 FCPRCGSG--FMAEHL-DR--WHCGKCGYTE 47 (50)
T ss_pred cCcCCCcc--hheccC-Cc--EECCCcCCEE
Confidence 69999883 434443 66 9999999864
No 81
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=85.21 E-value=43 Score=33.47 Aligned_cols=31 Identities=23% Similarity=0.402 Sum_probs=26.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWD 317 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~ 317 (510)
...+++|||+.+|+|..||+...+.....+.
T Consensus 224 ~~~t~~eIA~~lgis~~~V~~~~~~al~kLr 254 (258)
T PRK08215 224 QGKTQMEVAEEIGISQAQVSRLEKAALKHMR 254 (258)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 4689999999999999999988776665554
No 82
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=84.80 E-value=0.53 Score=36.34 Aligned_cols=26 Identities=35% Similarity=0.714 Sum_probs=20.1
Q ss_pred CCCCCCCCCCcccccCCCCcccccccccee
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRV 31 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~V 31 (510)
.||.||. ...+.||.. + ..|+.||+.
T Consensus 21 ~CPrCG~-gvfmA~H~d-R--~~CGkCgyT 46 (51)
T COG1998 21 FCPRCGP-GVFMADHKD-R--WACGKCGYT 46 (51)
T ss_pred cCCCCCC-cchhhhcCc-e--eEeccccce
Confidence 5999986 234477776 5 999999986
No 83
>KOG0654 consensus G2/Mitotic-specific cyclin A [Cell cycle control, cell division, chromosome partitioning]
Probab=84.65 E-value=6.1 Score=42.25 Aligned_cols=135 Identities=16% Similarity=0.134 Sum_probs=87.9
Q ss_pred HHHHHHHHHHHhc-CCCCCHHHHHHHhCCC--HHHHHHHHHHHHHHhcccCCCCCcchhhhHHHHHhhc-CCCHHHHHHH
Q 046187 177 LATAALVQAIREA-QEPRTLQEISIAANVP--QKEIGKYIKILGEALQLSQPINSNSIAVHMPRFCTLL-QLNKSAQVLA 252 (510)
Q Consensus 177 VaAACLYIACR~~-~~PrTLkEIa~vt~Vs--kkeIgr~yk~L~k~L~i~~pv~~~~p~~~I~Rfcs~L-~L~~~V~~~A 252 (510)
+--+|-+|+.+-+ ..+..+.|++..+... ..++-+....++..|.+..... ....|+.||...- +..-++...+
T Consensus 182 ~g~s~m~I~sk~ee~~~~~~~ef~~itd~ty~~~qv~~~~~~il~~l~~~~~~p--t~~~~l~~~~~~~~~~~~~~e~~~ 259 (359)
T KOG0654|consen 182 VGISAMLIASKYEEIKEPRVEEFCYITDNTYTYWQVLRMEIDILNALTFELVRP--TSKTFLRRFLRVAQTPELQVEPLA 259 (359)
T ss_pred hCcccceeeccchhhcchHHHHHHhhhhhhhHHHHHHHHHHHHHHHhHHHHhCc--hHHHHHHHHHHhhcchhHHHHHHH
Confidence 4456777777754 4456677787766432 3344444444555555543322 2567888886443 2344566677
Q ss_pred HHHHHHHHhccccCCCChHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046187 253 THIGEVVINKCFCTRRNPISISAAAIYLACQLEDKRKTQAEICKVTGLTEVTLRKVYKELL 313 (510)
Q Consensus 253 ~~Ia~~a~~~~l~~GRsP~sIAAAaIYlAarl~g~~~t~keIa~vagVSe~TIRkrYKEL~ 313 (510)
..+.+...=.-......|.-|||||+++|=..++..-....+..-++++-.+++.....|.
T Consensus 260 ~yl~elsll~~~~l~y~PSliAasAv~lA~~~~~~~pW~~~L~~~T~y~~edl~~~v~~L~ 320 (359)
T KOG0654|consen 260 NYLTELSLLDYIFLKYLPSLIAASAVFLARLTLDFHPWNQTLEDYTGYKAEDLKPCVLDLH 320 (359)
T ss_pred HHHHHhhhhhHHHhccChHHHHHHHHHHHHhhccCCCCchhhHHhhcccHHHHHHHHHHHh
Confidence 7666544333335567899999999999987777444445577788999999998888887
No 84
>PF13730 HTH_36: Helix-turn-helix domain
Probab=84.52 E-value=2.4 Score=32.14 Aligned_cols=26 Identities=31% Similarity=0.450 Sum_probs=24.0
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 290 TQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 290 t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
+++.||+.+|+++.||+++.++|.+.
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~~ 52 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEEK 52 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 78999999999999999999999764
No 85
>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=84.26 E-value=0.56 Score=41.86 Aligned_cols=29 Identities=24% Similarity=0.631 Sum_probs=23.0
Q ss_pred CCCCCCCCCCcccccCCCCccccccccceecccc
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRVIAER 35 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vleer 35 (510)
.||+||. ..+|-..-= .||..||.++.-.
T Consensus 11 ~Cp~CG~---kFYDLnk~P--ivCP~CG~~~~~~ 39 (108)
T PF09538_consen 11 TCPSCGA---KFYDLNKDP--IVCPKCGTEFPPE 39 (108)
T ss_pred cCCCCcc---hhccCCCCC--ccCCCCCCccCcc
Confidence 5999987 668866644 8899999988554
No 86
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=84.04 E-value=0.57 Score=43.17 Aligned_cols=25 Identities=32% Similarity=0.798 Sum_probs=19.2
Q ss_pred CCCCCCCCCCcccccCCCCccccccccc-eec
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCG-RVI 32 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG-~Vl 32 (510)
.||.||. +. .. .+|+ ++|..|| +|+
T Consensus 30 hCp~Cg~--PL-F~-KdG~--v~CPvC~~~~~ 55 (131)
T COG1645 30 HCPKCGT--PL-FR-KDGE--VFCPVCGYREV 55 (131)
T ss_pred hCcccCC--cc-ee-eCCe--EECCCCCceEE
Confidence 4999998 33 33 8998 9999999 443
No 87
>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=83.99 E-value=0.59 Score=37.86 Aligned_cols=17 Identities=29% Similarity=0.620 Sum_probs=14.2
Q ss_pred cccCCCCccccccccceec
Q 046187 14 ATTSTGRSITECGSCGRVI 32 (510)
Q Consensus 14 ~D~~~Gd~~~VC~~CG~Vl 32 (510)
++--+|. ++|.+||+++
T Consensus 47 ~~i~eg~--L~Cp~c~r~Y 63 (68)
T PF03966_consen 47 VEIVEGE--LICPECGREY 63 (68)
T ss_dssp EETTTTE--EEETTTTEEE
T ss_pred ccccCCE--EEcCCCCCEE
Confidence 3566887 9999999987
No 88
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=83.57 E-value=0.65 Score=32.88 Aligned_cols=27 Identities=22% Similarity=0.523 Sum_probs=20.0
Q ss_pred CCCCCCCCCCcccccCCCCccccccccceec
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRVI 32 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vl 32 (510)
+|+.|+.. .++-...+. .+|..||.+.
T Consensus 5 ~C~~C~~~--~i~~~~~~~--~~C~~Cg~~~ 31 (33)
T PF08792_consen 5 KCSKCGGN--GIVNKEDDY--EVCIFCGSSF 31 (33)
T ss_pred EcCCCCCC--eEEEecCCe--EEcccCCcEe
Confidence 59999983 344345565 9999999874
No 89
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=83.57 E-value=12 Score=29.36 Aligned_cols=26 Identities=19% Similarity=0.401 Sum_probs=23.2
Q ss_pred CCCHHHHHHHhCC-CHHHHHHHHHHHH
Q 046187 288 RKTQAEICKVTGL-TEVTLRKVYKELL 313 (510)
Q Consensus 288 ~~t~keIa~vagV-Se~TIRkrYKEL~ 313 (510)
+.++.+||..+|. +...+.+.+|+..
T Consensus 50 ~~~~~~ia~~~g~~s~~~f~r~Fk~~~ 76 (84)
T smart00342 50 DLSVTEIALRVGFSSQSYFSRAFKKLF 76 (84)
T ss_pred CCCHHHHHHHhCCCChHHHHHHHHHHH
Confidence 7899999999999 9999998888764
No 90
>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=83.52 E-value=2.8 Score=30.99 Aligned_cols=28 Identities=36% Similarity=0.549 Sum_probs=22.8
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046187 286 DKRKTQAEICKVTGLTEVTLRKVYKELL 313 (510)
Q Consensus 286 g~~~t~keIa~vagVSe~TIRkrYKEL~ 313 (510)
+-+.+..+||+.+|+|+.|+..|++.|.
T Consensus 15 d~r~s~~~la~~lglS~~~v~~Ri~rL~ 42 (42)
T PF13404_consen 15 DGRRSYAELAEELGLSESTVRRRIRRLE 42 (42)
T ss_dssp -TTS-HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred cCCccHHHHHHHHCcCHHHHHHHHHHhC
Confidence 4678999999999999999999999873
No 91
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=83.47 E-value=0.77 Score=34.68 Aligned_cols=29 Identities=24% Similarity=0.440 Sum_probs=18.2
Q ss_pred CCCCCCCCCCcccccCC-CCccccccccceecc
Q 046187 2 KCPYCSAAQGRCATTST-GRSITECGSCGRVIA 33 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~-Gd~~~VC~~CG~Vle 33 (510)
.||+||.--.. .+... -. .+|..||.+..
T Consensus 2 FCp~Cg~~l~~-~~~~~~~~--~vC~~Cg~~~~ 31 (52)
T smart00661 2 FCPKCGNMLIP-KEGKEKRR--FVCRKCGYEEP 31 (52)
T ss_pred CCCCCCCcccc-ccCCCCCE--EECCcCCCeEE
Confidence 69999882211 11111 24 99999998753
No 92
>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=83.31 E-value=3 Score=33.05 Aligned_cols=38 Identities=26% Similarity=0.368 Sum_probs=31.2
Q ss_pred HHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 277 AIYLACQLEDKRKTQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 277 aIYlAarl~g~~~t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
+||.... .+..++.++||+.++|+..|+.+..+.|.+.
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 4666655 5678999999999999999999999998763
No 93
>PRK11827 hypothetical protein; Provisional
Probab=83.12 E-value=0.75 Score=36.94 Aligned_cols=28 Identities=14% Similarity=0.295 Sum_probs=20.0
Q ss_pred CCCCCCCCCCCcccccCCCCccccccccceec
Q 046187 1 MKCPYCSAAQGRCATTSTGRSITECGSCGRVI 32 (510)
Q Consensus 1 m~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vl 32 (510)
+.||-|++. ...|.... ++||..||+++
T Consensus 9 LaCP~ckg~--L~~~~~~~--~Lic~~~~laY 36 (60)
T PRK11827 9 IACPVCNGK--LWYNQEKQ--ELICKLDNLAF 36 (60)
T ss_pred eECCCCCCc--CeEcCCCC--eEECCccCeec
Confidence 469999882 22443333 49999999987
No 94
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=83.00 E-value=68 Score=36.63 Aligned_cols=178 Identities=20% Similarity=0.220 Sum_probs=90.1
Q ss_pred HHHHHHHHHHH-HHHHHh---CCC--HHHHHHHHHHHHHHHhCCccCCccHHHHHHHHHHHHHH----hc----CCCC--
Q 046187 130 MDNLRAYLQII-DVASIL---GLD--YDICDHAFQLFRDCCSATCLRNRSVEALATAALVQAIR----EA----QEPR-- 193 (510)
Q Consensus 130 er~L~a~~~I~-~ic~~L---~LP--~~VidtA~~LyK~a~e~~~lrGRs~eaVaAACLYIACR----~~----~~Pr-- 193 (510)
.++..++..+. .+|.++ ||+ +-|.+--.-|.+-+.....-+|-+..+.|.-+|--|.. .. .+|+
T Consensus 383 ~~Li~~nlrlV~~iA~ky~~~gl~~~DLiQeG~iGL~~Av~kfd~~~G~~FstYA~~wIr~aI~~~i~~~~r~irip~~~ 462 (619)
T PRK05658 383 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 462 (619)
T ss_pred HHHHHHHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHHHhcCccCCCchHHHhHHHHHHHHHHHHHHcCCceecCHHH
Confidence 44555655444 477775 344 45555556677877777778898888877766654432 11 2333
Q ss_pred ----------------------CHHHHHHHhCCCHHHHHHHHHHHHHHhcccCCCCCcchhhhHHHHHhhcCC-CH-HHH
Q 046187 194 ----------------------TLQEISIAANVPQKEIGKYIKILGEALQLSQPINSNSIAVHMPRFCTLLQL-NK-SAQ 249 (510)
Q Consensus 194 ----------------------TLkEIa~vt~VskkeIgr~yk~L~k~L~i~~pv~~~~p~~~I~Rfcs~L~L-~~-~V~ 249 (510)
|..|||..++++..++.+..+.....+-++.|+.... ...+..|...=+. .+ +..
T Consensus 463 ~~~~~k~~~~~~~~~~~~gr~pt~~eiA~~l~~~~~~v~~~~~~~~~~~Sld~~i~~~~-~~~l~d~i~d~~~~~p~~~~ 541 (619)
T PRK05658 463 IETINKLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGDDE-DSHLGDFIEDKNAELPIDAA 541 (619)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCCcCCCCCCCCC-CCchhhhcCCCCCCChHHHH
Confidence 4566777777777777666443322222333322110 1111111111011 11 111
Q ss_pred -H-HHHHHHHHHHhccccCCCChHHHHHHHHHHHHHHcC----CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 250 -V-LATHIGEVVINKCFCTRRNPISISAAAIYLACQLED----KRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 250 -~-~A~~Ia~~a~~~~l~~GRsP~sIAAAaIYlAarl~g----~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
. .-...+..+. ..-+|.--- +.-..+| .+.|+++|++.+|||...||...+.-...|..
T Consensus 542 ~~~~~~~~l~~~l-----~~L~~rE~~-----Vl~~r~g~~~~~~~tl~ei~~~lgvs~eRVrQie~~al~kLr~ 606 (619)
T PRK05658 542 IQESLREATTDVL-----ASLTPREAK-----VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 606 (619)
T ss_pred HHHHHHHHHHHHH-----HcCCHHHHH-----HHHHhcCCCCCCCccHHHHHHHhCCCHHHHHHHHHHHHHHHhc
Confidence 0 0011111111 111222111 1111232 57999999999999999999877766555543
No 95
>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=82.78 E-value=3.1 Score=30.75 Aligned_cols=30 Identities=30% Similarity=0.452 Sum_probs=25.0
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 286 DKRKTQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 286 g~~~t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
+-..++++||+.+|+|..|++..+++|.+.
T Consensus 15 ~~~~t~~ela~~~~is~~tv~~~l~~L~~~ 44 (48)
T PF13412_consen 15 NPRITQKELAEKLGISRSTVNRYLKKLEEK 44 (48)
T ss_dssp CTTS-HHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred cCCCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 446999999999999999999999999764
No 96
>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=82.74 E-value=3 Score=31.64 Aligned_cols=31 Identities=29% Similarity=0.297 Sum_probs=27.0
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q 046187 286 DKRKTQAEICKVTGLTEVTLRKVYKELLENW 316 (510)
Q Consensus 286 g~~~t~keIa~vagVSe~TIRkrYKEL~e~l 316 (510)
+..+|.+++|+.++||..||++-.++|.+..
T Consensus 13 ~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 13 KEPITAKELAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp TTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred CCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 4459999999999999999999999998776
No 97
>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=82.60 E-value=6.6 Score=41.03 Aligned_cols=69 Identities=17% Similarity=0.203 Sum_probs=58.7
Q ss_pred hhhhHHHHHhhc--CCCHHHHHHHHHHHHHHHhccccCCCChHHHHHHHHHHHHHHcCCCCCHHHHHHHhC
Q 046187 231 IAVHMPRFCTLL--QLNKSAQVLATHIGEVVINKCFCTRRNPISISAAAIYLACQLEDKRKTQAEICKVTG 299 (510)
Q Consensus 231 p~~~I~Rfcs~L--~L~~~V~~~A~~Ia~~a~~~~l~~GRsP~sIAAAaIYlAarl~g~~~t~keIa~vag 299 (510)
-+..+..||+++ .|+..|+.+|....++.-=.+-..-.+|..|.++|+|+||....+.++..++++-..
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 345666777776 578899999999888877677788899999999999999999999999999988766
No 98
>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=82.18 E-value=51 Score=32.03 Aligned_cols=31 Identities=26% Similarity=0.346 Sum_probs=26.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWD 317 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~ 317 (510)
...+.+|||+.+|+|..||+++++.-.+.+.
T Consensus 190 ~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr 220 (224)
T TIGR02479 190 EELNLKEIGEVLGLTESRVSQIHSQALKKLR 220 (224)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 5789999999999999999998776665554
No 99
>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=81.71 E-value=59 Score=32.44 Aligned_cols=31 Identities=23% Similarity=0.399 Sum_probs=26.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWD 317 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~ 317 (510)
...|+++||+.+|+|..+|+...+.....+.
T Consensus 221 ~~~t~~eIA~~lgis~~~V~~~~~ral~kLr 251 (254)
T TIGR02850 221 EGKTQMEVAEEIGISQAQVSRLEKAALKHMR 251 (254)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 5789999999999999999988877666554
No 100
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=81.48 E-value=36 Score=33.19 Aligned_cols=110 Identities=17% Similarity=0.176 Sum_probs=64.1
Q ss_pred HHHHHHHHHHHHHHhcCCC-CCHHHHHHHhCCCHHHHHHHHHHHHHHhcccCCCCCcchhhhHHHHHh--hcCCCHHHHH
Q 046187 174 VEALATAALVQAIREAQEP-RTLQEISIAANVPQKEIGKYIKILGEALQLSQPINSNSIAVHMPRFCT--LLQLNKSAQV 250 (510)
Q Consensus 174 ~eaVaAACLYIACR~~~~P-rTLkEIa~vt~VskkeIgr~yk~L~k~L~i~~pv~~~~p~~~I~Rfcs--~L~L~~~V~~ 250 (510)
...++=|+||.+ +-| .++++|+.+++++..++..++..|.+.+...... --|..+.. +|...++...
T Consensus 5 ~~~~iEA~LF~s----g~pgls~~~La~~l~~~~~~v~~~l~~L~~~y~~~~~g------i~i~~~~~~y~l~tk~e~~~ 74 (188)
T PRK00135 5 YKSIIEALLFVS----GEEGLSLEQLAEILELEPTEVQQLLEELQEKYEGDDRG------LKLIEFNDVYKLVTKEENAD 74 (188)
T ss_pred HHHHHHHHHHHc----CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhhCCCC------EEEEEECCEEEEEEcHHHHH
Confidence 456777888884 667 9999999999999999999999998877532110 00001111 1222333333
Q ss_pred HHHHHHHHHHhccccCCCChHHHHHHHHH-HHHHHcCCCCCHHHHHHHhCCCH
Q 046187 251 LATHIGEVVINKCFCTRRNPISISAAAIY-LACQLEDKRKTQAEICKVTGLTE 302 (510)
Q Consensus 251 ~A~~Ia~~a~~~~l~~GRsP~sIAAAaIY-lAarl~g~~~t~keIa~vagVSe 302 (510)
...+++.. +.+.-+.-|++= +|...+..++|..+|+++.||+.
T Consensus 75 ~v~~~~~~---------~~~~~LS~aaLEtLaiIay~qPiTr~eI~~irGv~~ 118 (188)
T PRK00135 75 YLQKLVKT---------PIKQSLSQAALEVLAIIAYKQPITRIEIDEIRGVNS 118 (188)
T ss_pred HHHHHhcc---------cccCCCCHHHHHHHHHHHHcCCcCHHHHHHHHCCCH
Confidence 33333211 111122222221 22233467999999999999996
No 101
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=80.98 E-value=2.5 Score=31.40 Aligned_cols=27 Identities=26% Similarity=0.233 Sum_probs=18.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046187 288 RKTQAEICKVTGLTEVTLRKVYKELLE 314 (510)
Q Consensus 288 ~~t~keIa~vagVSe~TIRkrYKEL~e 314 (510)
..+.++||+.+|||..||.+..+.+.+
T Consensus 17 G~s~~~ia~~lgvs~~Tv~~w~kr~~~ 43 (50)
T PF13384_consen 17 GWSIREIAKRLGVSRSTVYRWIKRYRE 43 (50)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHT----
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHccc
Confidence 789999999999999999988777653
No 102
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=80.65 E-value=8 Score=30.39 Aligned_cols=71 Identities=18% Similarity=0.165 Sum_probs=42.9
Q ss_pred HHHHHHHhCCCHHHHHHHHHHHHHHHhCCccCCccHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCC-CHHHHHHHHHHH
Q 046187 139 IIDVASILGLDYDICDHAFQLFRDCCSATCLRNRSVEALATAALVQAIREAQEPRTLQEISIAANV-PQKEIGKYIKIL 216 (510)
Q Consensus 139 I~~ic~~L~LP~~VidtA~~LyK~a~e~~~lrGRs~eaVaAACLYIACR~~~~PrTLkEIa~vt~V-skkeIgr~yk~L 216 (510)
|.++|..++++.....+. |+.........-.....+.-|+-|+.- + +.++.||+..+|+ +...+.+.|++.
T Consensus 4 ~~~la~~~~~s~~~l~~~---f~~~~~~s~~~~~~~~r~~~a~~~l~~---~-~~~~~~ia~~~g~~s~~~f~r~Fk~~ 75 (84)
T smart00342 4 LEDLAEALGMSPRHLQRL---FKKETGTTPKQYLRDRRLERARRLLRD---T-DLSVTEIALRVGFSSQSYFSRAFKKL 75 (84)
T ss_pred HHHHHHHhCCCHHHHHHH---HHHHhCcCHHHHHHHHHHHHHHHHHHc---C-CCCHHHHHHHhCCCChHHHHHHHHHH
Confidence 456888888886554433 333322111111112234445555532 2 8999999999999 999998888754
No 103
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=80.64 E-value=1 Score=42.51 Aligned_cols=31 Identities=32% Similarity=0.844 Sum_probs=22.6
Q ss_pred CCCCCCCCCCCcccccC---CCCc---ccccccccee
Q 046187 1 MKCPYCSAAQGRCATTS---TGRS---ITECGSCGRV 31 (510)
Q Consensus 1 m~Cp~C~~~~~~i~D~~---~Gd~---~~VC~~CG~V 31 (510)
|+||.|+...+.++|+. .|.. --.|.+||.=
T Consensus 1 M~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~R 37 (156)
T COG1327 1 MKCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGER 37 (156)
T ss_pred CCCCCCCCCCCeeeecccccccchhhhhhcccccccc
Confidence 99999999888888843 3420 0369999963
No 104
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=80.30 E-value=2.8 Score=31.05 Aligned_cols=29 Identities=24% Similarity=0.234 Sum_probs=19.7
Q ss_pred HHHcCCCCCHHHHHHHhCCCHHHHHHHHH
Q 046187 282 CQLEDKRKTQAEICKVTGLTEVTLRKVYK 310 (510)
Q Consensus 282 arl~g~~~t~keIa~vagVSe~TIRkrYK 310 (510)
..++....++++||+.+|++..||.+..|
T Consensus 14 ~~l~~~G~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 14 EALLEQGMSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp HHHHCS---HHHHHHHTT--HHHHHHHHH
T ss_pred HHHHHcCCCHHHHHHHHCcCcHHHHHHHh
Confidence 34567789999999999999999987654
No 105
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=80.27 E-value=5.1 Score=29.98 Aligned_cols=30 Identities=13% Similarity=0.399 Sum_probs=24.5
Q ss_pred HHcCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046187 283 QLEDKRKTQAEICKVTGLTEVTLRKVYKEL 312 (510)
Q Consensus 283 rl~g~~~t~keIa~vagVSe~TIRkrYKEL 312 (510)
.++....++++||+.+|||..||+..+++.
T Consensus 22 ~~~~~~~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 22 KLLRESRSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred HHHhhcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 334444899999999999999999988753
No 106
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=80.05 E-value=2.8 Score=42.30 Aligned_cols=57 Identities=18% Similarity=0.209 Sum_probs=44.8
Q ss_pred hhhHHHHHhhcCCCHHHHHHHHHHHHHHHhccccCCCChHHHHHHHHHHHHHHcCCC
Q 046187 232 AVHMPRFCTLLQLNKSAQVLATHIGEVVINKCFCTRRNPISISAAAIYLACQLEDKR 288 (510)
Q Consensus 232 ~~~I~Rfcs~L~L~~~V~~~A~~Ia~~a~~~~l~~GRsP~sIAAAaIYlAarl~g~~ 288 (510)
..+|..++.+|.|..+|..+|.-..++.--..-+.+-.|.-+|..|||+||.....+
T Consensus 45 ~n~I~~lg~~lklRQ~ViATAivY~rRfy~r~S~k~~~p~lla~TClyLAcKvEE~~ 101 (264)
T KOG0794|consen 45 ANVIQKLGQHLKLRQRVIATAIVYFRRFYLRKSLKEIEPRLLAPTCLYLACKVEECP 101 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCHHHHHHHHHHHHhhhhhcc
Confidence 468889999999999998888766544432223778999999999999999876554
No 107
>KOG1010 consensus Rb (Retinoblastoma tumor suppressor)-related protein [Cell cycle control, cell division, chromosome partitioning]
Probab=79.91 E-value=9 Score=44.90 Aligned_cols=121 Identities=13% Similarity=0.106 Sum_probs=78.3
Q ss_pred HHHHHHHHhCCCHHHHHHHHHHHHHHHhCCccCCccHHHHHHHHHHHHHHhcCCCCCHHHHHHH-hCCCHHHHHHHHHHH
Q 046187 138 QIIDVASILGLDYDICDHAFQLFRDCCSATCLRNRSVEALATAALVQAIREAQEPRTLQEISIA-ANVPQKEIGKYIKIL 216 (510)
Q Consensus 138 ~I~~ic~~L~LP~~VidtA~~LyK~a~e~~~lrGRs~eaVaAACLYIACR~~~~PrTLkEIa~v-t~VskkeIgr~yk~L 216 (510)
.....|..|+|++.....|-+.|..+...-.+.| +-.++.|.+||.+||...+|.-.+-|... ..|+--.|-|+++..
T Consensus 37 ~~~~~c~~lnld~~~~~ea~d~yta~~q~~sleg-s~~hW~~cAlY~~~r~S~~~~v~~~~~~~~n~vsL~~Ilrs~k~s 115 (920)
T KOG1010|consen 37 DSDELCRPLNLDEQTETEAWDTYTAVSQRLSLEG-SESHWLACALYTACRRSSVPTVGGGIVEGKNEVSLTRILRSFKMS 115 (920)
T ss_pred hhhhhhhhhcccchhhhhhHHHHHHHHhHhCCCc-cHHHHHHHHHHHHHHhccCCccCcceeeecceehHHHHHHHHHHH
Confidence 4456899999999999999999999887766666 46789999999999999888655555444 445555565655542
Q ss_pred --------HHHhcccCCCCCcchhhhHHHHHhhcCCCHHHHHHHHHHHHHHHh
Q 046187 217 --------GEALQLSQPINSNSIAVHMPRFCTLLQLNKSAQVLATHIGEVVIN 261 (510)
Q Consensus 217 --------~k~L~i~~pv~~~~p~~~I~Rfcs~L~L~~~V~~~A~~Ia~~a~~ 261 (510)
.+...+..-+ ..-..+|.|+=..+.++.-+.+.-..|.+.+..
T Consensus 116 v~eff~km~~w~~ma~s~--~~f~~~ieel~~~f~vssvl~KkY~~iF~~iF~ 166 (920)
T KOG1010|consen 116 VIEFFTKMKQWVDMANSP--QEFREEIEELQRNFKVSSVLFKKYKRIFRDIFK 166 (920)
T ss_pred HHHHHHHHHHHHHHhcCH--HHHHHHHHHHHhccceehhHHHHHHHHHHHHHh
Confidence 2222211110 012345666666666665555555555555543
No 108
>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=79.72 E-value=6.3 Score=30.47 Aligned_cols=30 Identities=37% Similarity=0.409 Sum_probs=26.9
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 286 DKRKTQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 286 g~~~t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
...+++++||+.+|++..|+.+.++.|.+.
T Consensus 23 ~~~~s~~ela~~~g~s~~tv~r~l~~L~~~ 52 (67)
T cd00092 23 QLPLTRQEIADYLGLTRETVSRTLKELEEE 52 (67)
T ss_pred cCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 356899999999999999999999999874
No 109
>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=79.51 E-value=1.1 Score=41.10 Aligned_cols=29 Identities=10% Similarity=0.178 Sum_probs=22.8
Q ss_pred CCCCCCCCCCcccccCCCCccccccccceecccc
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRVIAER 35 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vleer 35 (510)
.||+||. ..+|-..-- .||..||.++...
T Consensus 11 ~Cp~cg~---kFYDLnk~p--~vcP~cg~~~~~~ 39 (129)
T TIGR02300 11 ICPNTGS---KFYDLNRRP--AVSPYTGEQFPPE 39 (129)
T ss_pred cCCCcCc---cccccCCCC--ccCCCcCCccCcc
Confidence 5999987 567755554 9999999998554
No 110
>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=79.49 E-value=15 Score=40.14 Aligned_cols=75 Identities=9% Similarity=0.213 Sum_probs=51.1
Q ss_pred HHHHHHHhCCCHHHHHHHHHHHHHHHhCCccCCccHHHHHHHHHHHHHHhcCC------------------CCCHHHHHH
Q 046187 139 IIDVASILGLDYDICDHAFQLFRDCCSATCLRNRSVEALATAALVQAIREAQE------------------PRTLQEISI 200 (510)
Q Consensus 139 I~~ic~~L~LP~~VidtA~~LyK~a~e~~~lrGRs~eaVaAACLYIACR~~~~------------------PrTLkEIa~ 200 (510)
+.++|+.|+++...++.|..+++.+.=.|..- |+ ..=||.+=.+..+. -..++.|+.
T Consensus 116 ~~eia~~l~~~~~~ve~~l~~iq~leP~GIgA-r~----L~EcLllQl~~~~~~~~~~a~~il~~~le~l~~~~~~~i~~ 190 (429)
T TIGR02395 116 LEEIADELEVSEEEVEKVLELIQRLDPAGVGA-RD----LQECLLLQLERLDIDDPELAYNILLEHLELLAEKDFRRLAK 190 (429)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHhcCCCCccCc-CC----HHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHhccHHHHHH
Confidence 56799999999999999999999876665332 22 11233333332211 134677888
Q ss_pred HhCCCHHHHHHHHHHHHH
Q 046187 201 AANVPQKEIGKYIKILGE 218 (510)
Q Consensus 201 vt~VskkeIgr~yk~L~k 218 (510)
.++++..++..++..|+.
T Consensus 191 ~l~is~~~v~~~~~~I~~ 208 (429)
T TIGR02395 191 KLGLSEEELKEALDLIKS 208 (429)
T ss_pred HHCcCHHHHHHHHHHHhC
Confidence 899999999888877654
No 111
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=79.06 E-value=4.1 Score=29.89 Aligned_cols=30 Identities=20% Similarity=0.344 Sum_probs=26.8
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHhhc
Q 046187 288 RKTQAEICKVTGLTEVTLRKVYKELLENWD 317 (510)
Q Consensus 288 ~~t~keIa~vagVSe~TIRkrYKEL~e~l~ 317 (510)
..+.++||+.+++|..||+.+.+.+...+.
T Consensus 18 g~s~~eia~~l~is~~tv~~~~~~~~~kl~ 47 (58)
T smart00421 18 GLTNKEIAERLGISEKTVKTHLSNIMRKLG 47 (58)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence 569999999999999999999998877665
No 112
>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=79.03 E-value=4.3 Score=32.64 Aligned_cols=38 Identities=29% Similarity=0.394 Sum_probs=30.0
Q ss_pred CChHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHH
Q 046187 268 RNPISISAAAIYLACQLEDKRKTQAEICKVTGLTEVTLRKV 308 (510)
Q Consensus 268 RsP~sIAAAaIYlAarl~g~~~t~keIa~vagVSe~TIRkr 308 (510)
|+|.-=-|=-||+. ++-.++.+|||+.+||++.|||+.
T Consensus 5 Rsp~rdkA~e~y~~---~~g~i~lkdIA~~Lgvs~~tIr~W 42 (60)
T PF10668_consen 5 RSPNRDKAFEIYKE---SNGKIKLKDIAEKLGVSESTIRKW 42 (60)
T ss_pred CCcCHHHHHHHHHH---hCCCccHHHHHHHHCCCHHHHHHH
Confidence 56666666667754 466899999999999999999954
No 113
>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=78.32 E-value=5.1 Score=32.03 Aligned_cols=30 Identities=27% Similarity=0.361 Sum_probs=26.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENW 316 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l 316 (510)
.+.++.+||+.+|+|..|+.+.+++|.+.=
T Consensus 27 ~~lt~~~iA~~~g~sr~tv~r~l~~l~~~g 56 (76)
T PF13545_consen 27 LPLTQEEIADMLGVSRETVSRILKRLKDEG 56 (76)
T ss_dssp EESSHHHHHHHHTSCHHHHHHHHHHHHHTT
T ss_pred ecCCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 467899999999999999999999998753
No 114
>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=77.94 E-value=2.6 Score=31.85 Aligned_cols=21 Identities=24% Similarity=0.476 Sum_probs=18.5
Q ss_pred CHHHHHHHhCCCHHHHHHHHH
Q 046187 290 TQAEICKVTGLTEVTLRKVYK 310 (510)
Q Consensus 290 t~keIa~vagVSe~TIRkrYK 310 (510)
|++|||+.+|||..|+.+++.
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 689999999999999987653
No 115
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=77.39 E-value=1.3 Score=33.19 Aligned_cols=26 Identities=23% Similarity=0.450 Sum_probs=18.5
Q ss_pred CCCCCCCCCCcccccCCCCcccccccccee
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRV 31 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~V 31 (510)
+|++||. ....|...+. ..|..||.-
T Consensus 5 ~C~~CG~--~~~~~~~~~~--~~Cp~CG~~ 30 (46)
T PRK00398 5 KCARCGR--EVELDEYGTG--VRCPYCGYR 30 (46)
T ss_pred ECCCCCC--EEEECCCCCc--eECCCCCCe
Confidence 6999998 2334544445 899999963
No 116
>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=77.35 E-value=13 Score=34.63 Aligned_cols=29 Identities=24% Similarity=0.392 Sum_probs=27.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
.++|+.|||+.+|++..|+.+..++|.+.
T Consensus 142 ~~~t~~~iA~~lG~tretvsR~l~~l~~~ 170 (193)
T TIGR03697 142 LRLSHQAIAEAIGSTRVTITRLLGDLRKK 170 (193)
T ss_pred CCCCHHHHHHHhCCcHHHHHHHHHHHHHC
Confidence 57899999999999999999999999875
No 117
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=76.39 E-value=91 Score=31.55 Aligned_cols=33 Identities=18% Similarity=0.343 Sum_probs=27.1
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 286 DKRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 286 g~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
....+++|||+.+|+|..||++.++.....+..
T Consensus 229 ~~~~t~~EIA~~lgis~~~V~~~~~ral~kLr~ 261 (264)
T PRK07122 229 FESMTQTQIAERVGISQMHVSRLLAKTLARLRD 261 (264)
T ss_pred cCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 357899999999999999999987766665543
No 118
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=76.37 E-value=4.8 Score=30.14 Aligned_cols=29 Identities=17% Similarity=0.353 Sum_probs=25.8
Q ss_pred CCC-CHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 287 KRK-TQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 287 ~~~-t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
..+ +.+++++.++||..||+++++.|.+.
T Consensus 18 ~~l~s~~~la~~~~vs~~tv~~~l~~L~~~ 47 (60)
T smart00345 18 DKLPSERELAAQLGVSRTTVREALSRLEAE 47 (60)
T ss_pred CcCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 345 79999999999999999999999874
No 119
>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=76.19 E-value=3.8 Score=31.61 Aligned_cols=33 Identities=15% Similarity=0.305 Sum_probs=27.9
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 286 DKRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 286 g~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
-...+.++||+..+|++.||+...+.++..++.
T Consensus 16 ~~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~ 48 (58)
T PF00196_consen 16 AQGMSNKEIAEELGISEKTVKSHRRRIMKKLGV 48 (58)
T ss_dssp HTTS-HHHHHHHHTSHHHHHHHHHHHHHHHHT-
T ss_pred HhcCCcchhHHhcCcchhhHHHHHHHHHHHhCC
Confidence 357889999999999999999999999988764
No 120
>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=74.96 E-value=1.3 Score=31.65 Aligned_cols=29 Identities=24% Similarity=0.508 Sum_probs=17.2
Q ss_pred CCCCCCCCCCcccccCCCCccccccccceecc
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRVIA 33 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vle 33 (510)
.||+|+.-- ...+...+. ..|..||++.+
T Consensus 3 FCp~C~nlL-~p~~~~~~~--~~C~~C~Y~~~ 31 (35)
T PF02150_consen 3 FCPECGNLL-YPKEDKEKR--VACRTCGYEEP 31 (35)
T ss_dssp BETTTTSBE-EEEEETTTT--EEESSSS-EEE
T ss_pred eCCCCCccc-eEcCCCccC--cCCCCCCCccC
Confidence 699998721 112234444 36999999853
No 121
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=74.72 E-value=1.1e+02 Score=31.45 Aligned_cols=187 Identities=11% Similarity=0.063 Sum_probs=95.6
Q ss_pred CCchhhHHHHHHHHHHH-HHHHHhCCC-----HHHHHHHHHHHHHHHhCCccCCccHHHHHHHHHHHHHH----hc----
Q 046187 124 TSSSVMMDNLRAYLQII-DVASILGLD-----YDICDHAFQLFRDCCSATCLRNRSVEALATAALVQAIR----EA---- 189 (510)
Q Consensus 124 ~~~~~~er~L~a~~~I~-~ic~~L~LP-----~~VidtA~~LyK~a~e~~~lrGRs~eaVaAACLYIACR----~~---- 189 (510)
++....+.++..|.... .+|.++.-. +-+.+.-.-+++.+....--+|-+..+.|.-+|--+.. ..
T Consensus 45 Gd~~a~~~Lv~~~~~lV~~ia~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~~~FstYA~~~Ir~~i~~~l~~~~~~v 124 (284)
T PRK06596 45 GDLEAAKQLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIV 124 (284)
T ss_pred CCHHHHHHHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHcCCee
Confidence 44455556666665444 577766322 33445555588877777767777777666666544432 11
Q ss_pred ------------------------CCCCCHHHHHHHhCCCHHHHHHHHHHHHH-HhcccCCCCCc-c-hhhhHHHHHhhc
Q 046187 190 ------------------------QEPRTLQEISIAANVPQKEIGKYIKILGE-ALQLSQPINSN-S-IAVHMPRFCTLL 242 (510)
Q Consensus 190 ------------------------~~PrTLkEIa~vt~VskkeIgr~yk~L~k-~L~i~~pv~~~-~-p~~~I~Rfcs~L 242 (510)
+.+-+..|||..++++.+++......+.. .+-++.++.+. + -..++..+.+.-
T Consensus 125 r~p~~~~~~~~~~~~~~~~~~l~~~~~~t~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~~~l~d~~ 204 (284)
T PRK06596 125 KVATTKAQRKLFFNLRKAKKRLGWLNPEEVEMVAEELGVSEEEVREMESRLSGQDASLDAPIDDDDEESGAPQDYLEDKS 204 (284)
T ss_pred eccchHHHHHHHHHHHHHHHHhccCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCcCcCCCCCCCCCCcchHHHHcCCCC
Confidence 13445677888888888888765433221 22222222110 0 012333333331
Q ss_pred CCCHHHHHH------HHHHHHHHHhccccCCCChHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q 046187 243 QLNKSAQVL------ATHIGEVVINKCFCTRRNPISISAAAIYLACQLEDKRKTQAEICKVTGLTEVTLRKVYKELLENW 316 (510)
Q Consensus 243 ~L~~~V~~~------A~~Ia~~a~~~~l~~GRsP~sIAAAaIYlAarl~g~~~t~keIa~vagVSe~TIRkrYKEL~e~l 316 (510)
.-+.+.... ....+..+.. .+. +.---.-..|+ ..+...|++|||+.+|||..+|+...+.-...|
T Consensus 205 ~~p~~~~~~~~~~~~~~~~L~~al~--~L~---~rEr~VL~lry---~~~~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kL 276 (284)
T PRK06596 205 SDPADVLEEDNWEDQRRALLADALE--GLD---ERSRDIIEARW---LDDDKSTLQELAAEYGVSAERVRQIEKNAMKKL 276 (284)
T ss_pred CCchHHHHHHHHHHHHHHHHHHHHh--cCC---HHHHHHHHHHh---cCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 112221111 1111222221 121 21111111111 113579999999999999999998877665555
Q ss_pred cc
Q 046187 317 DD 318 (510)
Q Consensus 317 ~~ 318 (510)
..
T Consensus 277 R~ 278 (284)
T PRK06596 277 KA 278 (284)
T ss_pred HH
Confidence 43
No 122
>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=74.68 E-value=2.2 Score=31.72 Aligned_cols=29 Identities=24% Similarity=0.242 Sum_probs=20.4
Q ss_pred HHHHcCCCCCHHHHHHHhCCCHHHHHHHH
Q 046187 281 ACQLEDKRKTQAEICKVTGLTEVTLRKVY 309 (510)
Q Consensus 281 Aarl~g~~~t~keIa~vagVSe~TIRkrY 309 (510)
+-+|+....+..+||+.+|||..||.+..
T Consensus 14 i~~l~~~G~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 14 IKELYAEGMSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp HHHHHHTT--HHHHHHHTTS-HHHHHHHH
T ss_pred HHHHHHCCCCHHHHHHHHCcCHHHHHHHH
Confidence 34455556999999999999999998654
No 123
>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=74.53 E-value=10 Score=29.65 Aligned_cols=28 Identities=18% Similarity=0.277 Sum_probs=23.4
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 288 RKTQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 288 ~~t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
..++.|||+.+|||..|+..+.+.-...
T Consensus 23 ~~tl~elA~~lgis~st~~~~LRrae~k 50 (53)
T PF04967_consen 23 RITLEELAEELGISKSTVSEHLRRAERK 50 (53)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 4789999999999999998887765443
No 124
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=74.20 E-value=4.1 Score=31.77 Aligned_cols=29 Identities=21% Similarity=0.386 Sum_probs=25.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
-.++.+++++.++||+.|||+-+.+|.+.
T Consensus 13 ~~~s~~ela~~~~VS~~TiRRDl~~L~~~ 41 (57)
T PF08220_consen 13 GKVSVKELAEEFGVSEMTIRRDLNKLEKQ 41 (57)
T ss_pred CCEEHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 46889999999999999999988888764
No 125
>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=73.66 E-value=4.2 Score=33.94 Aligned_cols=27 Identities=37% Similarity=0.327 Sum_probs=23.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELL 313 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~ 313 (510)
...|.+|||+.+|+|+.||++.++.+.
T Consensus 31 eGlS~kEIAe~LGIS~~TVk~~l~~~~ 57 (73)
T TIGR03879 31 AGKTASEIAEELGRTEQTVRNHLKGET 57 (73)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhcCc
Confidence 578999999999999999999887543
No 126
>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=73.24 E-value=2.8 Score=30.54 Aligned_cols=27 Identities=26% Similarity=0.623 Sum_probs=17.9
Q ss_pred CCCCCCCCCCccccc--CCCCccccccccce
Q 046187 2 KCPYCSAAQGRCATT--STGRSITECGSCGR 30 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~--~~Gd~~~VC~~CG~ 30 (510)
-||.|+...-.=.|. .+|. .+|..||.
T Consensus 5 pCP~CGG~DrFr~~d~~g~G~--~~C~~Cg~ 33 (37)
T smart00778 5 PCPNCGGSDRFRFDDKDGRGT--WFCSVCGA 33 (37)
T ss_pred CCCCCCCccccccccCCCCcC--EEeCCCCC
Confidence 599999832221443 3465 99999984
No 127
>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=73.12 E-value=8.8 Score=28.26 Aligned_cols=32 Identities=22% Similarity=0.432 Sum_probs=27.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
...+.++||+.++++..||+.+.+.+.+.+..
T Consensus 14 ~~~s~~eia~~l~~s~~tv~~~~~~~~~~l~~ 45 (57)
T cd06170 14 EGKTNKEIADILGISEKTVKTHLRNIMRKLGV 45 (57)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence 35799999999999999999999988776553
No 128
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=72.96 E-value=1.8 Score=38.12 Aligned_cols=31 Identities=26% Similarity=0.610 Sum_probs=20.9
Q ss_pred CCCCCCCCCCcc-cccCCCCccccccccceeccc
Q 046187 2 KCPYCSAAQGRC-ATTSTGRSITECGSCGRVIAE 34 (510)
Q Consensus 2 ~Cp~C~~~~~~i-~D~~~Gd~~~VC~~CG~Vlee 34 (510)
.||+|++....+ .|. |....+|..||...+-
T Consensus 23 ~CP~Cge~~v~v~~~k--~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 23 ECPRCGKVSISVKIKK--NIAIITCGNCGLYTEF 54 (99)
T ss_pred ECCCCCCeEeeeecCC--CcceEECCCCCCccCE
Confidence 599999632222 344 4445999999997643
No 129
>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=72.91 E-value=8 Score=35.13 Aligned_cols=46 Identities=24% Similarity=0.203 Sum_probs=38.6
Q ss_pred HHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 046187 174 VEALATAALVQAIREAQEPRTLQEISIAANVPQKEIGKYIKILGEA 219 (510)
Q Consensus 174 ~eaVaAACLYIACR~~~~PrTLkEIa~vt~VskkeIgr~yk~L~k~ 219 (510)
.+.-+.+++|+|-+..+.|.+..||++..+++...+.+.+..|.+.
T Consensus 7 ~~YAl~~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~ 52 (135)
T TIGR02010 7 GRYAVTAMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKA 52 (135)
T ss_pred HHHHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 4445678899997766778999999999999999999998888773
No 130
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=72.30 E-value=2.3 Score=33.79 Aligned_cols=26 Identities=27% Similarity=0.639 Sum_probs=17.9
Q ss_pred CCCCCCCCCCcccccCCCCccccccccceecccce
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRVIAERQ 36 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vleer~ 36 (510)
.||+||+... .- .||.+||+--+..+
T Consensus 29 ~C~~CG~~~~------~H---~vC~~CG~Y~gr~v 54 (57)
T PRK12286 29 ECPNCGEPKL------PH---RVCPSCGYYKGREV 54 (57)
T ss_pred ECCCCCCccC------Ce---EECCCCCcCCCEEe
Confidence 5999998432 22 79999997554433
No 131
>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=72.01 E-value=6 Score=29.82 Aligned_cols=30 Identities=20% Similarity=0.344 Sum_probs=22.0
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 286 DKRKTQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 286 g~~~t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
-...+.+|||+.+|+|+.||+..+..-...
T Consensus 24 ~~g~s~~eIa~~l~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 24 FQGMSYAEIAEILGISESTVKRRLRRARKK 53 (54)
T ss_dssp TS---HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred HHCcCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence 357899999999999999999998766543
No 132
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=71.86 E-value=6.5 Score=28.34 Aligned_cols=30 Identities=30% Similarity=0.374 Sum_probs=26.7
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 286 DKRKTQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 286 g~~~t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
.++.++++||+.++++..|+.+.++.|.+.
T Consensus 6 ~~~~s~~~la~~l~~s~~tv~~~l~~L~~~ 35 (48)
T smart00419 6 RLPLTRQEIAELLGLTRETVSRTLKRLEKE 35 (48)
T ss_pred EeccCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 357889999999999999999999998874
No 133
>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=71.79 E-value=5.8 Score=31.23 Aligned_cols=30 Identities=20% Similarity=0.399 Sum_probs=25.0
Q ss_pred CCCC-CHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 286 DKRK-TQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 286 g~~~-t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
|..+ +..++++.++||..|++++++.|.+.
T Consensus 21 g~~lps~~~la~~~~vsr~tvr~al~~L~~~ 51 (64)
T PF00392_consen 21 GDRLPSERELAERYGVSRTTVREALRRLEAE 51 (64)
T ss_dssp TSBE--HHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred CCEeCCHHHHHHHhccCCcHHHHHHHHHHHC
Confidence 4677 88999999999999999999998764
No 134
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=71.65 E-value=6.2 Score=37.03 Aligned_cols=32 Identities=22% Similarity=0.202 Sum_probs=28.5
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhc
Q 046187 286 DKRKTQAEICKVTGLTEVTLRKVYKELLENWD 317 (510)
Q Consensus 286 g~~~t~keIa~vagVSe~TIRkrYKEL~e~l~ 317 (510)
+-+.+.++||+.+|+|+.|+++|++.|.+.--
T Consensus 26 d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~Gv 57 (164)
T PRK11169 26 DGRISNVELSKRVGLSPTPCLERVRRLERQGF 57 (164)
T ss_pred CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCC
Confidence 45789999999999999999999999988543
No 135
>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=71.54 E-value=2.1 Score=29.73 Aligned_cols=25 Identities=32% Similarity=0.885 Sum_probs=12.7
Q ss_pred CCCCCCCCCCcccccCCCCcccccccccee
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRV 31 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~V 31 (510)
+||.|++.. ... .|. ..||..||.-
T Consensus 4 ~Cp~C~se~-~y~---D~~-~~vCp~C~~e 28 (30)
T PF08274_consen 4 KCPLCGSEY-TYE---DGE-LLVCPECGHE 28 (30)
T ss_dssp --TTT------EE----SS-SEEETTTTEE
T ss_pred CCCCCCCcc-eec---cCC-EEeCCccccc
Confidence 699998843 323 333 5999999974
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=71.44 E-value=6.4 Score=27.76 Aligned_cols=28 Identities=29% Similarity=0.418 Sum_probs=22.5
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 288 RKTQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 288 ~~t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
+.+..|||+.+|++..|+...++.|.+.
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 4678999999999999999999998763
No 137
>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=71.44 E-value=1.9 Score=36.51 Aligned_cols=34 Identities=24% Similarity=0.721 Sum_probs=20.3
Q ss_pred CCCCCCCCCCcc--cccCCCCccccccccceecccc
Q 046187 2 KCPYCSAAQGRC--ATTSTGRSITECGSCGRVIAER 35 (510)
Q Consensus 2 ~Cp~C~~~~~~i--~D~~~Gd~~~VC~~CG~Vleer 35 (510)
.||.|+....+. .|..+|.+.+.|..||...+-.
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 599999544444 5677777789999999877443
No 138
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=71.12 E-value=1.8 Score=42.33 Aligned_cols=33 Identities=27% Similarity=0.778 Sum_probs=19.9
Q ss_pred CCCCCCCCCCC--cccccCCCCc-cccccccceeccc
Q 046187 1 MKCPYCSAAQG--RCATTSTGRS-ITECGSCGRVIAE 34 (510)
Q Consensus 1 m~Cp~C~~~~~--~i~D~~~Gd~-~~VC~~CG~Vlee 34 (510)
|.||.|+.-.. .++- ..|++ -+-|.+||.|--+
T Consensus 7 ~~Cp~Cg~eev~hEVik-~~g~~~lvrC~eCG~V~~~ 42 (201)
T COG1326 7 IECPSCGSEEVSHEVIK-ERGREPLVRCEECGTVHPA 42 (201)
T ss_pred EECCCCCcchhhHHHHH-hcCCceEEEccCCCcEeec
Confidence 57999994222 1222 23432 2679999999844
No 139
>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=71.11 E-value=2.1 Score=34.33 Aligned_cols=30 Identities=30% Similarity=0.596 Sum_probs=20.9
Q ss_pred CCCCCCCCCCcccccCCCCcccccccccee
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRV 31 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~V 31 (510)
.||.|++--.+..=...|.....|.+||+-
T Consensus 11 ~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~ 40 (59)
T TIGR02443 11 VCPACSAQDTLAMWKENNIELVECVECGYQ 40 (59)
T ss_pred cCCCCcCccEEEEEEeCCceEEEeccCCCc
Confidence 599999844443323456556899999984
No 140
>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=71.02 E-value=9.4 Score=28.83 Aligned_cols=35 Identities=31% Similarity=0.347 Sum_probs=29.2
Q ss_pred HHhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Q 046187 186 IREAQEPRTLQEISIAANVPQKEIGKYIKILGEAL 220 (510)
Q Consensus 186 CR~~~~PrTLkEIa~vt~VskkeIgr~yk~L~k~L 220 (510)
...++-+.|..|||+.++|+...|.+.++.|...+
T Consensus 9 L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 9 LLESKEPITAKELAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp HHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred HHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 33566679999999999999999999999997766
No 141
>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=71.01 E-value=2.4 Score=36.81 Aligned_cols=28 Identities=32% Similarity=0.631 Sum_probs=20.7
Q ss_pred CCCCCCCCCCCcccccCCCCccccccccceeccc
Q 046187 1 MKCPYCSAAQGRCATTSTGRSITECGSCGRVIAE 34 (510)
Q Consensus 1 m~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vlee 34 (510)
+.||+||.. .....+. .+|..||.+.+.
T Consensus 1 ~fC~~Cg~~----l~~~~~~--~~C~~C~~~~~~ 28 (104)
T TIGR01384 1 KFCPKCGSL----MTPKNGV--YVCPSCGYEKEK 28 (104)
T ss_pred CCCcccCcc----cccCCCe--EECcCCCCcccc
Confidence 579999872 2234566 999999998654
No 142
>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=70.43 E-value=10 Score=28.10 Aligned_cols=33 Identities=27% Similarity=0.337 Sum_probs=27.6
Q ss_pred HHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 283 QLEDKRKTQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 283 rl~g~~~t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
.+...+.+..||++.++++..||....+.|.+.
T Consensus 10 ~L~~~~~~~~el~~~l~~s~~~vs~hL~~L~~~ 42 (47)
T PF01022_consen 10 LLSEGPLTVSELAEELGLSQSTVSHHLKKLREA 42 (47)
T ss_dssp HHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHhCCCchhhHHHhccccchHHHHHHHHHHHC
Confidence 345578899999999999999999999988764
No 143
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=70.16 E-value=8.4 Score=35.68 Aligned_cols=32 Identities=19% Similarity=0.186 Sum_probs=28.6
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhc
Q 046187 286 DKRKTQAEICKVTGLTEVTLRKVYKELLENWD 317 (510)
Q Consensus 286 g~~~t~keIa~vagVSe~TIRkrYKEL~e~l~ 317 (510)
+-+.+..+||+.+|+|+.|++.|++.|.+.--
T Consensus 21 d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~Gv 52 (153)
T PRK11179 21 NARTPYAELAKQFGVSPGTIHVRVEKMKQAGI 52 (153)
T ss_pred cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCC
Confidence 45789999999999999999999999988543
No 144
>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=69.66 E-value=11 Score=32.37 Aligned_cols=31 Identities=32% Similarity=0.366 Sum_probs=26.7
Q ss_pred HcCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046187 284 LEDKRKTQAEICKVTGLTEVTLRKVYKELLE 314 (510)
Q Consensus 284 l~g~~~t~keIa~vagVSe~TIRkrYKEL~e 314 (510)
++...+|+++|++.+|||..||...-+.|..
T Consensus 45 lL~~g~syreIa~~tgvS~aTItRvsr~Lk~ 75 (87)
T PF01371_consen 45 LLDEGKSYREIAEETGVSIATITRVSRCLKY 75 (87)
T ss_dssp HHHTTSSHHHHHHHHTSTHHHHHHHHHHHHH
T ss_pred HHHCCCCHHHHHHHhCCCHHHHHHHHHHHHc
Confidence 6667899999999999999999977776654
No 145
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=69.61 E-value=58 Score=35.96 Aligned_cols=76 Identities=12% Similarity=0.250 Sum_probs=51.0
Q ss_pred HHHHHHHHhCCCHHHHHHHHHHHHHHHhCCccCCccHHHHHHHHHHHHHHhc------------------CC-CCCHHHH
Q 046187 138 QIIDVASILGLDYDICDHAFQLFRDCCSATCLRNRSVEALATAALVQAIREA------------------QE-PRTLQEI 198 (510)
Q Consensus 138 ~I~~ic~~L~LP~~VidtA~~LyK~a~e~~~lrGRs~eaVaAACLYIACR~~------------------~~-PrTLkEI 198 (510)
.+.++|..|+++...++.|..+++.+.=.|..- |+ ..=||.+=.+.. .. -..++.|
T Consensus 140 ~~~eia~~l~~~~~~v~~~l~~lQ~leP~GigA-r~----L~ECLllQl~~~~~~~~~~~~~~il~~~le~la~~~~~~i 214 (455)
T PRK05932 140 DLEEIAESLGVELDEVEAVLKRIQSFDPAGVGA-RD----LQECLLLQLEQLDDTPRLDEAMEIISDHLDLLARRDFRTL 214 (455)
T ss_pred CHHHHHHHcCCCHHHHHHHHHHHhcCCCCccCc-CC----HHHHHHHHHhccCCCchHHHHHHHHHHHHHHHHcCCHHHH
Confidence 455799999999999999999999876665432 11 112232222221 11 2347778
Q ss_pred HHHhCCCHHHHHHHHHHHHH
Q 046187 199 SIAANVPQKEIGKYIKILGE 218 (510)
Q Consensus 199 a~vt~VskkeIgr~yk~L~k 218 (510)
+..++++..++.+++..|+.
T Consensus 215 a~~l~is~~~v~~~~~~Ir~ 234 (455)
T PRK05932 215 AKKLGVKEEDLQEALDLIRS 234 (455)
T ss_pred HHHHCcCHHHHHHHHHHHhC
Confidence 88899999999999877654
No 146
>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=69.55 E-value=18 Score=33.56 Aligned_cols=29 Identities=17% Similarity=0.082 Sum_probs=27.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 046187 191 EPRTLQEISIAANVPQKEIGKYIKILGEA 219 (510)
Q Consensus 191 ~PrTLkEIa~vt~VskkeIgr~yk~L~k~ 219 (510)
.|.|-.|||+.+|++...+.|.+++|++.
T Consensus 142 ~~~t~~~iA~~lG~tretvsR~l~~l~~~ 170 (193)
T TIGR03697 142 LRLSHQAIAEAIGSTRVTITRLLGDLRKK 170 (193)
T ss_pred CCCCHHHHHHHhCCcHHHHHHHHHHHHHC
Confidence 68899999999999999999999999875
No 147
>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=69.37 E-value=10 Score=29.07 Aligned_cols=28 Identities=25% Similarity=0.431 Sum_probs=24.5
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 288 RKTQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 288 ~~t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
..++.+|++.++++..|+....+.|.+.
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 4899999999999999999999988764
No 148
>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=69.23 E-value=2.3 Score=35.19 Aligned_cols=30 Identities=30% Similarity=0.599 Sum_probs=21.4
Q ss_pred CCCCCCCCCCcccccCCCCcccccccccee
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRV 31 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~V 31 (510)
.||.|++.-.+..=...|.....|.+||+.
T Consensus 10 ~CP~C~~~D~i~~~~e~~ve~vECV~CGy~ 39 (71)
T PF09526_consen 10 VCPKCQAMDTIMMWRENGVEYVECVECGYT 39 (71)
T ss_pred cCCCCcCccEEEEEEeCCceEEEecCCCCe
Confidence 599999854443223355667999999996
No 149
>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=69.15 E-value=7.7 Score=32.20 Aligned_cols=45 Identities=18% Similarity=0.165 Sum_probs=35.6
Q ss_pred HHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 046187 175 EALATAALVQAIREAQEPRTLQEISIAANVPQKEIGKYIKILGEA 219 (510)
Q Consensus 175 eaVaAACLYIACR~~~~PrTLkEIa~vt~VskkeIgr~yk~L~k~ 219 (510)
+.-.-+.+|+|-...+.|.+.+|||+.++++...+.+.+..|.+.
T Consensus 8 ~~Al~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~ 52 (83)
T PF02082_consen 8 DYALRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKA 52 (83)
T ss_dssp HHHHHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhC
Confidence 334556778887777778999999999999999999999998773
No 150
>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=69.02 E-value=2.3 Score=29.41 Aligned_cols=26 Identities=35% Similarity=0.646 Sum_probs=13.3
Q ss_pred CCCCCCCCCCcccccCCCCcccccccccee
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRV 31 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~V 31 (510)
.|+.||..+.. .+ .| ...+|.+||..
T Consensus 5 fC~~CG~~t~~-~~--~g-~~r~C~~Cg~~ 30 (32)
T PF09297_consen 5 FCGRCGAPTKP-AP--GG-WARRCPSCGHE 30 (32)
T ss_dssp B-TTT--BEEE--S--SS-S-EEESSSS-E
T ss_pred ccCcCCccccC-CC--Cc-CEeECCCCcCE
Confidence 59999984322 22 23 25899999985
No 151
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=68.92 E-value=4 Score=38.51 Aligned_cols=38 Identities=13% Similarity=0.138 Sum_probs=32.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccCCCCC
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDLLPSNY 324 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Lip~~~ 324 (510)
...+.+|||+.+|+|+.||+.++......+...+...|
T Consensus 146 ~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~ 183 (191)
T PRK12520 146 LELETEEICQELQITATNAWVLLYRARMRLRECLDLHW 183 (191)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 36889999999999999999998887777777665555
No 152
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=68.76 E-value=2.7 Score=33.82 Aligned_cols=28 Identities=18% Similarity=0.492 Sum_probs=22.3
Q ss_pred CCCCCCCCCCCcccccCCCCccccccccceec
Q 046187 1 MKCPYCSAAQGRCATTSTGRSITECGSCGRVI 32 (510)
Q Consensus 1 m~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vl 32 (510)
+.||.|+.. ..+|...+. +||..||+..
T Consensus 9 LaCP~~kg~--L~~~~~~~~--L~c~~~~~aY 36 (60)
T COG2835 9 LACPVCKGP--LVYDEEKQE--LICPRCKLAY 36 (60)
T ss_pred eeccCcCCc--ceEeccCCE--EEecccCcee
Confidence 359999983 447767776 9999999986
No 153
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=68.48 E-value=2.2 Score=34.24 Aligned_cols=29 Identities=24% Similarity=0.701 Sum_probs=23.3
Q ss_pred CCCCCC-CCCcccccCCCCccccccccceec
Q 046187 3 CPYCSA-AQGRCATTSTGRSITECGSCGRVI 32 (510)
Q Consensus 3 Cp~C~~-~~~~i~D~~~Gd~~~VC~~CG~Vl 32 (510)
|| ||. .+.-++|-..|.-..+|.+|.+++
T Consensus 25 CP-CGDRFeIsLeDl~~GE~VArCPSCSLiv 54 (67)
T COG5216 25 CP-CGDRFEISLEDLRNGEVVARCPSCSLIV 54 (67)
T ss_pred CC-CCCEeEEEHHHhhCCceEEEcCCceEEE
Confidence 88 877 444457888998888999999987
No 154
>PRK04217 hypothetical protein; Provisional
Probab=68.17 E-value=6.2 Score=35.36 Aligned_cols=34 Identities=21% Similarity=0.207 Sum_probs=28.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccC
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDLL 320 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Li 320 (510)
...+++|||+.+|||..||+++++...+.+...+
T Consensus 57 eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre~L 90 (110)
T PRK04217 57 EGLTQEEAGKRMGVSRGTVWRALTSARKKVAQML 90 (110)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4679999999999999999999887777776544
No 155
>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=68.14 E-value=3.2 Score=33.23 Aligned_cols=27 Identities=30% Similarity=0.837 Sum_probs=17.6
Q ss_pred CCCCCCCCCCcccccCCCCccccccccceec
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRVI 32 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vl 32 (510)
.||.||... .+...+. ..+|.+||.+.
T Consensus 30 ~C~~CG~~~---~~~~~~r-~~~C~~Cg~~~ 56 (69)
T PF07282_consen 30 TCPRCGHRN---KKRRSGR-VFTCPNCGFEM 56 (69)
T ss_pred CccCccccc---ccccccc-eEEcCCCCCEE
Confidence 589998733 2222333 58899999875
No 156
>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=67.48 E-value=37 Score=29.10 Aligned_cols=31 Identities=26% Similarity=0.371 Sum_probs=27.3
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q 046187 286 DKRKTQAEICKVTGLTEVTLRKVYKELLENW 316 (510)
Q Consensus 286 g~~~t~keIa~vagVSe~TIRkrYKEL~e~l 316 (510)
...+++.|||+.+|++..|+.+..++|.+.-
T Consensus 45 ~~~is~~eLa~~~g~sr~tVsr~L~~Le~~G 75 (95)
T TIGR01610 45 QDRVTATVIAELTGLSRTHVSDAIKSLARRR 75 (95)
T ss_pred CCccCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 4678999999999999999999999987643
No 157
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=67.33 E-value=50 Score=36.10 Aligned_cols=51 Identities=10% Similarity=0.112 Sum_probs=41.5
Q ss_pred ccCCCChHHHHHH---HHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q 046187 264 FCTRRNPISISAA---AIYLACQLEDKRKTQAEICKVTGLTEVTLRKVYKELLENW 316 (510)
Q Consensus 264 l~~GRsP~sIAAA---aIYlAarl~g~~~t~keIa~vagVSe~TIRkrYKEL~e~l 316 (510)
+...++-..|+-| |+|++-++.+ .+..+|++.+|.+.+||..+++.+.+.+
T Consensus 362 l~s~~R~~~i~~aR~iamyl~r~~~~--~s~~~Ig~~fgr~hstV~~a~~~i~~~~ 415 (440)
T PRK14088 362 ILSNSRNVKALLARRIGMYVAKNYLG--SSLRTIAEKFNRSHPVVVDSVKKVKDSL 415 (440)
T ss_pred HhCCCCCccccHHHHHHHHHHHHHhC--CCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 4455555677777 9999977654 5899999999999999999999988854
No 158
>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=67.15 E-value=2.2 Score=33.53 Aligned_cols=22 Identities=36% Similarity=0.857 Sum_probs=15.7
Q ss_pred CCCCCCCCCCcccccCCCCccccccccceec
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRVI 32 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vl 32 (510)
.||+||+. . -.- .||.+||+.=
T Consensus 28 ~c~~cg~~--~-----~~H--~vc~~cG~y~ 49 (56)
T PF01783_consen 28 KCPNCGEP--K-----LPH--RVCPSCGYYK 49 (56)
T ss_dssp ESSSSSSE--E-----STT--SBCTTTBBSS
T ss_pred eeccCCCE--e-----ccc--EeeCCCCeEC
Confidence 59999973 2 222 7999999654
No 159
>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=66.66 E-value=13 Score=29.55 Aligned_cols=32 Identities=19% Similarity=0.267 Sum_probs=27.5
Q ss_pred HcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 284 LEDKRKTQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 284 l~g~~~t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
+.+...+.++||+.++||..||+++.+.|.+.
T Consensus 9 L~~~~~~~~eLa~~l~vS~~tv~~~l~~L~~~ 40 (69)
T TIGR00122 9 LADNPFSGEKLGEALGMSRTAVNKHIQTLREW 40 (69)
T ss_pred HHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 44556789999999999999999999999764
No 160
>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=66.54 E-value=2.7 Score=30.01 Aligned_cols=30 Identities=20% Similarity=0.539 Sum_probs=18.5
Q ss_pred CCCCCCCCCCcccccCCCCccccccccceec
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRVI 32 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vl 32 (510)
+|++||..-........+ ....|..||.-+
T Consensus 7 ~C~~Cg~~fe~~~~~~~~-~~~~CP~Cg~~~ 36 (41)
T smart00834 7 RCEDCGHTFEVLQKISDD-PLATCPECGGDV 36 (41)
T ss_pred EcCCCCCEEEEEEecCCC-CCCCCCCCCCcc
Confidence 699998832222222223 358899999844
No 161
>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=66.40 E-value=7.5 Score=32.26 Aligned_cols=38 Identities=29% Similarity=0.461 Sum_probs=28.0
Q ss_pred HHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 278 IYLACQLEDKRKTQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 278 IYlAarl~g~~~t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
+|+|.+-.+.+.+.++||+.+++++..+++..+.|.+.
T Consensus 15 ~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~ 52 (83)
T PF02082_consen 15 LYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKA 52 (83)
T ss_dssp HHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhC
Confidence 34443322334899999999999999999999999874
No 162
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=65.74 E-value=3.7 Score=35.40 Aligned_cols=27 Identities=30% Similarity=0.813 Sum_probs=21.0
Q ss_pred CCCCCCCCCCcccccCCCCccccccccceec
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRVI 32 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vl 32 (510)
.||.|+.. .+.--++|- -.|..||.++
T Consensus 37 ~Cp~C~~~--~VkR~a~GI--W~C~kCg~~f 63 (89)
T COG1997 37 VCPFCGRT--TVKRIATGI--WKCRKCGAKF 63 (89)
T ss_pred cCCCCCCc--ceeeeccCe--EEcCCCCCee
Confidence 59999984 334467776 9999999975
No 163
>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=65.73 E-value=7.6 Score=27.40 Aligned_cols=28 Identities=21% Similarity=0.325 Sum_probs=22.5
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 046187 192 PRTLQEISIAANVPQKEIGKYIKILGEA 219 (510)
Q Consensus 192 PrTLkEIa~vt~VskkeIgr~yk~L~k~ 219 (510)
|.|-.||++.++++...+.|.+++|.+.
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 5678899999999999999999998763
No 164
>PRK05572 sporulation sigma factor SigF; Validated
Probab=65.20 E-value=1.5e+02 Score=29.45 Aligned_cols=33 Identities=30% Similarity=0.527 Sum_probs=28.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhccc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDL 319 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~L 319 (510)
...|+++||+.+|+|..||+.+.+...+.+...
T Consensus 217 ~~~s~~eIA~~lgis~~~V~~~~~ral~kLr~~ 249 (252)
T PRK05572 217 KDKTQSEVAKRLGISQVQVSRLEKKILKQMKEK 249 (252)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 579999999999999999999888777766543
No 165
>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=65.01 E-value=1.6e+02 Score=30.47 Aligned_cols=123 Identities=10% Similarity=0.039 Sum_probs=71.0
Q ss_pred HHHHHhcCC-CCCHHHHHHHhCCCHHHHHHHHHHHHHHhcccCCCCCcchhhhHHHHHhhcCCCHHHHHHH---------
Q 046187 183 VQAIREAQE-PRTLQEISIAANVPQKEIGKYIKILGEALQLSQPINSNSIAVHMPRFCTLLQLNKSAQVLA--------- 252 (510)
Q Consensus 183 YIACR~~~~-PrTLkEIa~vt~VskkeIgr~yk~L~k~L~i~~pv~~~~p~~~I~Rfcs~L~L~~~V~~~A--------- 252 (510)
|+..|+... -.|++++|..+|++... .|...++=.-++ +...+.+++..|+|+..-...-
T Consensus 17 ~ye~rk~~~p~fS~R~fa~~~G~ss~s------~L~~v~~Gkr~L----s~~~~~k~a~~l~L~~~E~~yF~~lV~f~~a 86 (271)
T TIGR02147 17 YYEERKKTDPAFSWRFFAEKAGFSSTS------YLNDIIKGKKNL----TKRMIPKFAEALGLDEKEAAYFEAMVNFGQA 86 (271)
T ss_pred HHHHHhccCcCcCHHHHHHHhCCCCHH------HHHHHHcCCCCC----CHHHHHHHHHHcCCCHHHHHHHHHHHHHhcc
Confidence 556666655 58999999999987632 122222212222 2578999999999985321110
Q ss_pred ------HHHHHHHHh------ccccCCCCh---HHHHHHHHHHHHHHcCCCCCHHHHHHHhC--CCHHHHHHHHHHHHHh
Q 046187 253 ------THIGEVVIN------KCFCTRRNP---ISISAAAIYLACQLEDKRKTQAEICKVTG--LTEVTLRKVYKELLEN 315 (510)
Q Consensus 253 ------~~Ia~~a~~------~~l~~GRsP---~sIAAAaIYlAarl~g~~~t~keIa~vag--VSe~TIRkrYKEL~e~ 315 (510)
..+.+++.+ ..++.+..- .+.--.+|.-...+.+...+..+||+.++ ||..-+++....|.+.
T Consensus 87 k~~~~k~~~~~~~~~~~~~~~~~~L~~~~~~y~~~W~~~virel~~~~~~~~~~~~ia~~l~p~is~~ev~~sL~~L~~~ 166 (271)
T TIGR02147 87 KTDTEKQQFFEEMQALKPRPRLRVLAADQFEYYRHWYNSVIRELLGVMPFADDPEELAKRCFPKISAEQVKESLDLLERL 166 (271)
T ss_pred CCHHHHHHHHHHHHHHhhhchheeccHHHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHhCCCCCHHHHHHHHHHHHHC
Confidence 111122221 111221111 13344445444455556667889999999 9999999998877653
No 166
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=64.52 E-value=15 Score=34.98 Aligned_cols=47 Identities=19% Similarity=0.166 Sum_probs=38.3
Q ss_pred cHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 046187 173 SVEALATAALVQAIREAQEPRTLQEISIAANVPQKEIGKYIKILGEA 219 (510)
Q Consensus 173 s~eaVaAACLYIACR~~~~PrTLkEIa~vt~VskkeIgr~yk~L~k~ 219 (510)
+.+.-..+++|+|-...+-|.+.+||++..+++..-+.+.+..|.+.
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 34555677888885555679999999999999999999998888773
No 167
>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=64.31 E-value=1.4e+02 Score=28.87 Aligned_cols=32 Identities=22% Similarity=0.480 Sum_probs=27.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
...+++|||+.+|+|..||+.+.+.....+..
T Consensus 193 ~~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~ 224 (227)
T TIGR02980 193 EDKTQSEIAERLGISQMHVSRLLRRALKKLRE 224 (227)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 47899999999999999999988777666543
No 168
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=64.28 E-value=5.4 Score=37.90 Aligned_cols=40 Identities=13% Similarity=0.084 Sum_probs=33.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccCCCCCCC
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDLLPSNYTP 326 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Lip~~~~~ 326 (510)
...+.+|||+.+|+|..||+.++......+...+...|..
T Consensus 146 ~g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~~~~~~ 185 (188)
T TIGR02943 146 LGFESDEICQELEISTSNCHVLLYRARLSLRACLSINWFG 185 (188)
T ss_pred hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 4789999999999999999999888888777766655543
No 169
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=64.25 E-value=3.6 Score=29.53 Aligned_cols=29 Identities=34% Similarity=0.847 Sum_probs=20.6
Q ss_pred CCCCCCCCCCcccc---cCCCCccccccccceec
Q 046187 2 KCPYCSAAQGRCAT---TSTGRSITECGSCGRVI 32 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D---~~~Gd~~~VC~~CG~Vl 32 (510)
.||+|+. ...|-| +..|. .+-|+.||.+.
T Consensus 4 ~Cp~C~~-~y~i~d~~ip~~g~-~v~C~~C~~~f 35 (36)
T PF13717_consen 4 TCPNCQA-KYEIDDEKIPPKGR-KVRCSKCGHVF 35 (36)
T ss_pred ECCCCCC-EEeCCHHHCCCCCc-EEECCCCCCEe
Confidence 5999987 345444 45665 58899999874
No 170
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=64.03 E-value=10 Score=35.49 Aligned_cols=35 Identities=17% Similarity=0.239 Sum_probs=27.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccCC
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDLLP 321 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Lip 321 (510)
...+.+|||+.+|+|++||+.++..-+.++-..++
T Consensus 142 ~g~s~~EIA~~lgis~~tVk~~l~rAl~~~~~~~~ 176 (178)
T PRK12529 142 DGMKQKDIAQALDIALPTVKKYIHQAYVTCLSLMP 176 (178)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhCC
Confidence 47899999999999999999988765555544333
No 171
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=63.63 E-value=11 Score=35.81 Aligned_cols=33 Identities=15% Similarity=0.002 Sum_probs=29.9
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 286 DKRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 286 g~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
....+.++||+.+++|+.||++..+.|+..++.
T Consensus 163 ~~G~s~~eIA~~l~iS~~TV~~h~~~i~~Kl~v 195 (216)
T PRK10840 163 AEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGV 195 (216)
T ss_pred HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence 357899999999999999999999999998874
No 172
>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=63.51 E-value=10 Score=33.84 Aligned_cols=32 Identities=19% Similarity=0.229 Sum_probs=27.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
...+.+|||+.+|+|+.||+.++......+..
T Consensus 128 ~~~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 128 EGKSYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 47899999999999999999999887776643
No 173
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=63.40 E-value=10 Score=34.61 Aligned_cols=39 Identities=23% Similarity=0.387 Sum_probs=30.9
Q ss_pred HHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 277 AIYLACQLEDKRKTQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 277 aIYlAarl~g~~~t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
.||++..--|...+.++||+..+|+..+|++.++.|...
T Consensus 14 ~i~la~~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~ 52 (141)
T PRK11014 14 LIYMASLPEGRMTSISEVTEVYGVSRNHMVKIINQLSRA 52 (141)
T ss_pred HHHHhcCCCCCccCHHHHHHHHCcCHHHHHHHHHHHHhC
Confidence 345554334556788999999999999999999999874
No 174
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=63.38 E-value=16 Score=29.93 Aligned_cols=41 Identities=20% Similarity=0.161 Sum_probs=38.1
Q ss_pred HHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccCCCC
Q 046187 283 QLEDKRKTQAEICKVTGLTEVTLRKVYKELLENWDDLLPSN 323 (510)
Q Consensus 283 rl~g~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Lip~~ 323 (510)
++++..++..+.|+.+|+.+.+|++..+.+...+..|-|..
T Consensus 8 rlLs~~~s~~~Aa~~lG~~~~~v~~wv~~fR~wll~LDPSG 48 (65)
T PF05344_consen 8 RLLSQQISVAQAADRLGTDPGTVRRWVRMFRQWLLQLDPSG 48 (65)
T ss_pred HHhcccccHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCCC
Confidence 57788999999999999999999999999999999998765
No 175
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=63.19 E-value=1.6e+02 Score=29.10 Aligned_cols=33 Identities=21% Similarity=0.288 Sum_probs=28.7
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 286 DKRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 286 g~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
....|++|||+.+|||..+|+..-+.+...+..
T Consensus 197 ~~~~t~~EIA~~lgis~~~V~q~~~~~~~kLr~ 229 (231)
T PRK12427 197 QHEMSLKEIALVLDLTEARICQLNKKIAQKIKS 229 (231)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHh
Confidence 357899999999999999999999888877653
No 176
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=63.00 E-value=3.5 Score=33.11 Aligned_cols=8 Identities=38% Similarity=0.974 Sum_probs=4.9
Q ss_pred ccccccce
Q 046187 23 TECGSCGR 30 (510)
Q Consensus 23 ~VC~~CG~ 30 (510)
++|.+||.
T Consensus 51 Y~Cp~CGF 58 (61)
T COG2888 51 YRCPKCGF 58 (61)
T ss_pred eECCCcCc
Confidence 56666664
No 177
>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=62.99 E-value=9.1 Score=33.49 Aligned_cols=31 Identities=23% Similarity=0.273 Sum_probs=25.2
Q ss_pred HHcCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046187 283 QLEDKRKTQAEICKVTGLTEVTLRKVYKELL 313 (510)
Q Consensus 283 rl~g~~~t~keIa~vagVSe~TIRkrYKEL~ 313 (510)
.+....+||+||++.+|||..||.+.-+.+.
T Consensus 50 ~Ll~~~~tQrEIa~~lGiS~atIsR~sn~lk 80 (94)
T TIGR01321 50 ELLNGNMSQREIASKLGVSIATITRGSNNLK 80 (94)
T ss_pred HHHhCCCCHHHHHHHhCCChhhhhHHHhhcc
Confidence 3445689999999999999999987665554
No 178
>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=62.95 E-value=4.4 Score=31.25 Aligned_cols=32 Identities=25% Similarity=0.539 Sum_probs=19.6
Q ss_pred CCCCCCCCCCccc---ccCCCCccccccccceecc
Q 046187 2 KCPYCSAAQGRCA---TTSTGRSITECGSCGRVIA 33 (510)
Q Consensus 2 ~Cp~C~~~~~~i~---D~~~Gd~~~VC~~CG~Vle 33 (510)
-||-||+....+. +...+.+..+|..||....
T Consensus 3 PCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~~ 37 (53)
T TIGR03655 3 PCPFCGGADVYLRRGFDPLDLSHYFECSTCGASGP 37 (53)
T ss_pred CCCCCCCcceeeEeccCCCCCEEEEECCCCCCCcc
Confidence 4999999554232 2222222257999998754
No 179
>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=62.74 E-value=18 Score=28.80 Aligned_cols=29 Identities=24% Similarity=0.343 Sum_probs=26.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 046187 191 EPRTLQEISIAANVPQKEIGKYIKILGEA 219 (510)
Q Consensus 191 ~PrTLkEIa~vt~VskkeIgr~yk~L~k~ 219 (510)
.|.|..|||+.+|++...+.+.++.|.+.
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 57899999999999999999999999874
No 180
>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=62.65 E-value=4.6 Score=31.78 Aligned_cols=24 Identities=29% Similarity=0.671 Sum_probs=16.6
Q ss_pred CCCCCCCCCCcccccCCCCccccccccceeccc
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRVIAE 34 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vlee 34 (510)
.||+||+.. + .- -||..||.--+.
T Consensus 28 ~C~~cG~~~--~----~H---~vc~~cG~Y~gr 51 (55)
T TIGR01031 28 VCPNCGEFK--L----PH---RVCPSCGYYKGR 51 (55)
T ss_pred ECCCCCCcc--c----Ce---eECCccCeECCE
Confidence 599999832 1 23 799999975433
No 181
>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=62.58 E-value=20 Score=25.46 Aligned_cols=30 Identities=20% Similarity=0.367 Sum_probs=25.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENW 316 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l 316 (510)
...+.++||+.+|++..||+...+.....+
T Consensus 25 ~~~~~~~ia~~~~~s~~~i~~~~~~~~~~l 54 (55)
T cd06171 25 EGLSYEEIAEILGISRSTVRQRLHRALKKL 54 (55)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHc
Confidence 567999999999999999998887766543
No 182
>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=62.53 E-value=82 Score=29.92 Aligned_cols=97 Identities=16% Similarity=0.165 Sum_probs=56.2
Q ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhcccCC------CC-------CcchhhhHHHHHhhcC
Q 046187 177 LATAALVQAIREAQEPRTLQEISIAANVPQKEIGKYIKILGEALQLSQP------IN-------SNSIAVHMPRFCTLLQ 243 (510)
Q Consensus 177 VaAACLYIACR~~~~PrTLkEIa~vt~VskkeIgr~yk~L~k~L~i~~p------v~-------~~~p~~~I~Rfcs~L~ 243 (510)
++=|.||.+ +-|.++++|+.+++ +..++.+.+..|.+.+.-... +. ...-..|+.++... .
T Consensus 2 ~iEAlLF~s----~~pvs~~~La~~l~-~~~~v~~~l~~L~~~y~~~~~gl~l~~~~~~y~l~tk~~~~~~v~~~~~~-~ 75 (159)
T PF04079_consen 2 IIEALLFAS----GEPVSIEELAEILG-SEDEVEEALEELQEEYNEEDRGLELVEVGGGYRLQTKPEYAEYVEKLFKK-P 75 (159)
T ss_dssp HHHHHHHH-----SS-B-HHHHHHHCT--HHHHHHHHHHHHHHHHHCT-SEEEEEETTEEEEEE-GGGHHHHHHHHCT-C
T ss_pred hhHhhHHHc----CCCCCHHHHHHHhC-CHHHHHHHHHHHHHHhccCCCCEEEEEECCEEEEEEhHHHHHHHHHHhcc-C
Confidence 455777775 56899999999999 999999999999998832210 00 11223444444443 1
Q ss_pred CCHHHHHHHHHHHHHHHhccccCCCChHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHH
Q 046187 244 LNKSAQVLATHIGEVVINKCFCTRRNPISISAAAIYLACQLEDKRKTQAEICKVTGLTEV 303 (510)
Q Consensus 244 L~~~V~~~A~~Ia~~a~~~~l~~GRsP~sIAAAaIYlAarl~g~~~t~keIa~vagVSe~ 303 (510)
-.....+.|.+.+ |...+..++|..||-++=||.-.
T Consensus 76 ~~~~LS~aalEtL------------------------AiIAY~QPiTr~eIe~IRGv~s~ 111 (159)
T PF04079_consen 76 KPPKLSQAALETL------------------------AIIAYKQPITRAEIEEIRGVNSD 111 (159)
T ss_dssp CCHHHHHHHHHHH------------------------HHHHHH-SEEHHHHHHHHTS--H
T ss_pred ccCCCCHHHHHHH------------------------HHHHhcCCcCHHHHHHHcCCChH
Confidence 1233333333322 22234579999999999998743
No 183
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=62.36 E-value=38 Score=32.75 Aligned_cols=32 Identities=19% Similarity=0.144 Sum_probs=27.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
.++|+++||+.+|++..|+.+..++|.+.--.
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 57899999999999999999999998875443
No 184
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=62.17 E-value=3.9 Score=31.96 Aligned_cols=32 Identities=31% Similarity=0.664 Sum_probs=23.9
Q ss_pred CCCCCCCCCCCcccccCCCCcccc--ccccceec
Q 046187 1 MKCPYCSAAQGRCATTSTGRSITE--CGSCGRVI 32 (510)
Q Consensus 1 m~Cp~C~~~~~~i~D~~~Gd~~~V--C~~CG~Vl 32 (510)
..||+||......+|.+.|+.+.+ |.-|-.=+
T Consensus 1 i~CPyCge~~~~~iD~s~~~Q~yiEDC~vCC~PI 34 (52)
T PF14255_consen 1 IQCPYCGEPIEILIDPSAGDQEYIEDCQVCCRPI 34 (52)
T ss_pred CCCCCCCCeeEEEEecCCCCeeEEeehhhcCCcc
Confidence 369999997666799999964443 77777644
No 185
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=62.10 E-value=6.9 Score=37.04 Aligned_cols=40 Identities=13% Similarity=0.177 Sum_probs=32.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccCCCCCCC
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDLLPSNYTP 326 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Lip~~~~~ 326 (510)
...+.+|||+.+|+|..||+.++..-...+...+...|+.
T Consensus 151 ~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~~~ 190 (195)
T PRK12532 151 LGFSSDEIQQMCGISTSNYHTIMHRARESLRQCLQIKWFN 190 (195)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 4688999999999999999999887777777665545433
No 186
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=61.94 E-value=7 Score=37.20 Aligned_cols=37 Identities=11% Similarity=0.144 Sum_probs=30.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccCCCC
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDLLPSN 323 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Lip~~ 323 (510)
...+.+|||+.+|+|+.||+.++..-...+...+...
T Consensus 131 ~g~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~~~ 167 (187)
T PRK12516 131 SGFAYEEAAEICGCAVGTIKSRVNRARQRLQEILQIE 167 (187)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 5789999999999999999998877777776655443
No 187
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=61.85 E-value=26 Score=33.92 Aligned_cols=63 Identities=17% Similarity=0.278 Sum_probs=46.2
Q ss_pred CHHHHHHHHHHHHHHHhccccCCCChHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046187 245 NKSAQVLATHIGEVVINKCFCTRRNPISISAAAIYLACQLEDKRKTQAEICKVTGLTEVTLRKVYKELLE 314 (510)
Q Consensus 245 ~~~V~~~A~~Ia~~a~~~~l~~GRsP~sIAAAaIYlAarl~g~~~t~keIa~vagVSe~TIRkrYKEL~e 314 (510)
.+........|++.+.+.++- +-.|..-|++| ++..+.|+.||++++|+|.+.+....|+|..
T Consensus 5 eqak~~~Ie~fae~m~r~G~n---rtVG~iYgily----ls~~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~ 67 (177)
T COG1510 5 EQAKDIFIEHFAETMSRWGIN---RTVGQIYGILY----LSRKPLTLDEIAEALGMSKSNVSMGLKKLQD 67 (177)
T ss_pred HHHHHHHHHHHHHHHHHhCCc---chHHHHhhhhe----ecCCCccHHHHHHHHCCCcchHHHHHHHHHh
Confidence 344555667777777765543 22344444444 5678999999999999999999999999987
No 188
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=61.49 E-value=12 Score=35.39 Aligned_cols=37 Identities=11% Similarity=0.093 Sum_probs=29.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccCCCC
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDLLPSN 323 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Lip~~ 323 (510)
...+.+|||+.+|+|+.||+.++..-.+.+...+...
T Consensus 126 ~g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~~~ 162 (182)
T PRK12540 126 SGFSYEDAAAICGCAVGTIKSRVNRARSKLSALLYVD 162 (182)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence 5788999999999999999988877666666655443
No 189
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=61.26 E-value=40 Score=31.60 Aligned_cols=29 Identities=28% Similarity=0.282 Sum_probs=26.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
.++|+++||+.+|++..|+.+..++|.+.
T Consensus 148 ~~~t~~~iA~~lG~tretvsR~l~~l~~~ 176 (202)
T PRK13918 148 IYATHDELAAAVGSVRETVTKVIGELSRE 176 (202)
T ss_pred ecCCHHHHHHHhCccHHHHHHHHHHHHHC
Confidence 57899999999999999999999999864
No 190
>KOG2923 consensus Uncharacterized conserved protein [Function unknown]
Probab=61.15 E-value=3.7 Score=33.42 Aligned_cols=29 Identities=31% Similarity=0.764 Sum_probs=22.1
Q ss_pred CCCCCCC-CCcccccCCCCccccccccceec
Q 046187 3 CPYCSAA-QGRCATTSTGRSITECGSCGRVI 32 (510)
Q Consensus 3 Cp~C~~~-~~~i~D~~~Gd~~~VC~~CG~Vl 32 (510)
|| ||.. +.-..|-..|.....|.+|.+++
T Consensus 25 Cp-CGDrf~It~edL~~ge~Va~CpsCSL~I 54 (67)
T KOG2923|consen 25 CP-CGDRFQITLEDLENGEDVARCPSCSLII 54 (67)
T ss_pred CC-CCCeeeecHHHHhCCCeeecCCCceEEE
Confidence 77 8873 22226778898889999999987
No 191
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=61.15 E-value=2.8 Score=35.39 Aligned_cols=28 Identities=21% Similarity=0.577 Sum_probs=22.4
Q ss_pred CCCCCCCCCCcccccCCCCccccccccceec
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRVI 32 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vl 32 (510)
+||.|-.-+. +.-|+... .+|.+|+.|+
T Consensus 36 kC~gc~~iT~-vfSHaqtv--Vvc~~c~~il 63 (84)
T KOG1779|consen 36 KCPGCFKITT-VFSHAQTV--VVCEGCSTIL 63 (84)
T ss_pred EcCCceEEEE-EeecCceE--EEcCCCceEE
Confidence 6999976443 36678777 9999999998
No 192
>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=61.08 E-value=26 Score=26.16 Aligned_cols=27 Identities=22% Similarity=0.272 Sum_probs=20.2
Q ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046187 285 EDKRKTQAEICKVTGLTEVTLRKVYKEL 312 (510)
Q Consensus 285 ~g~~~t~keIa~vagVSe~TIRkrYKEL 312 (510)
.|. +++++.|+..||...||+.+++..
T Consensus 14 ~g~-~S~r~AA~~ygVp~sTL~~r~~g~ 40 (45)
T PF05225_consen 14 NGK-MSIRKAAKKYGVPRSTLRRRLRGK 40 (45)
T ss_dssp TTS-S-HHHHHHHHT--HHHHHHHHHHT
T ss_pred hCC-CCHHHHHHHHCcCHHHHHHHHcCC
Confidence 444 999999999999999999887753
No 193
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=60.87 E-value=8.5 Score=34.86 Aligned_cols=35 Identities=14% Similarity=0.130 Sum_probs=28.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccCC
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDLLP 321 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Lip 321 (510)
...+.+|||+.+|+|+.||+.++..-...+...+.
T Consensus 121 ~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 155 (161)
T PRK09047 121 EDMDVAETAAAMGCSEGSVKTHCSRATHALAKALE 155 (161)
T ss_pred hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 47889999999999999999888776666655443
No 194
>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=60.75 E-value=3.5 Score=41.78 Aligned_cols=31 Identities=19% Similarity=0.446 Sum_probs=11.2
Q ss_pred CCCCCCCCCCCcc-cc-cCCCCccccccccceecc
Q 046187 1 MKCPYCSAAQGRC-AT-TSTGRSITECGSCGRVIA 33 (510)
Q Consensus 1 m~Cp~C~~~~~~i-~D-~~~Gd~~~VC~~CG~Vle 33 (510)
|.||+||..+..- .+ .-..| ..|.+|+--.|
T Consensus 32 ~yCP~Cg~~~L~~f~NN~PVaD--F~C~~C~eeyE 64 (254)
T PF06044_consen 32 MYCPNCGSKPLSKFENNRPVAD--FYCPNCNEEYE 64 (254)
T ss_dssp ---TTT--SS-EE--------E--EE-TTT--EEE
T ss_pred CcCCCCCChhHhhccCCCccce--eECCCCchHHh
Confidence 6899999953222 22 33455 99999986543
No 195
>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=60.59 E-value=16 Score=31.60 Aligned_cols=32 Identities=16% Similarity=0.271 Sum_probs=28.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
...+..+||+.+|+|+.||+++++...+.+..
T Consensus 125 ~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 125 EGLSYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 36799999999999999999999988876654
No 196
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=60.55 E-value=18 Score=31.00 Aligned_cols=29 Identities=34% Similarity=0.408 Sum_probs=26.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
-+.+.++|++.+|+++.|++++++.|.+.
T Consensus 16 ~~~~~~~la~~l~~s~~tv~~~l~~L~~~ 44 (108)
T smart00344 16 ARISLAELAKKVGLSPSTVHNRVKRLEEE 44 (108)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 47899999999999999999999999884
No 197
>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=60.24 E-value=2.9 Score=37.61 Aligned_cols=37 Identities=19% Similarity=0.388 Sum_probs=26.0
Q ss_pred CCCCCCCCCCcccccCCCCccccccccceecccceeeccccccccc
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRVIAERQCQNHHLFHIRA 47 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vleer~Id~~~EwR~fs 47 (510)
.||+|+..+-. -|+ +.-|..|+.-| .+|.+.|=.+|.
T Consensus 71 ~CP~C~K~TKm-----LGr-~D~CM~C~~pL---TLd~~legkef~ 107 (114)
T PF11023_consen 71 ECPNCGKQTKM-----LGR-VDACMHCKEPL---TLDPSLEGKEFD 107 (114)
T ss_pred ECCCCCChHhh-----hch-hhccCcCCCcC---ccCchhhcchhh
Confidence 69999985544 466 34899999977 577655555543
No 198
>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=60.20 E-value=14 Score=28.14 Aligned_cols=26 Identities=23% Similarity=0.469 Sum_probs=23.9
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 290 TQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 290 t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
+.++||+.+++|..||++.++.|.+.
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L~~~ 52 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELEAE 52 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 48999999999999999999999874
No 199
>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=60.09 E-value=34 Score=26.26 Aligned_cols=31 Identities=29% Similarity=0.316 Sum_probs=27.0
Q ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 046187 189 AQEPRTLQEISIAANVPQKEIGKYIKILGEA 219 (510)
Q Consensus 189 ~~~PrTLkEIa~vt~VskkeIgr~yk~L~k~ 219 (510)
...+.+..||++.++++...+.+.++.|.+.
T Consensus 22 ~~~~~s~~ela~~~g~s~~tv~r~l~~L~~~ 52 (67)
T cd00092 22 VQLPLTRQEIADYLGLTRETVSRTLKELEEE 52 (67)
T ss_pred ccCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 3467899999999999999999999988773
No 200
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=60.06 E-value=13 Score=36.30 Aligned_cols=36 Identities=19% Similarity=0.240 Sum_probs=31.1
Q ss_pred HHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 283 QLEDKRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 283 rl~g~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
++.....+.+|||+.+++|+.|||.....|+..++.
T Consensus 158 ~lla~G~snkeIA~~L~iS~~TVk~h~~~i~~KL~v 193 (211)
T COG2197 158 RLLAEGLSNKEIAEELNLSEKTVKTHVSNILRKLGV 193 (211)
T ss_pred HHHHCCCCHHHHHHHHCCCHhHHHHHHHHHHHHcCC
Confidence 344568899999999999999999999999988764
No 201
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=59.89 E-value=12 Score=35.09 Aligned_cols=34 Identities=12% Similarity=0.119 Sum_probs=30.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccC
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDLL 320 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Li 320 (510)
...+.+|||+.+|++..||+.++......+...+
T Consensus 164 ~~~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~~l 197 (198)
T TIGR02859 164 DGKSYQEIACDLNRHVKSIDNALQRVKRKLEKYL 197 (198)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhc
Confidence 4899999999999999999999998888776543
No 202
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=59.89 E-value=9.8 Score=36.10 Aligned_cols=36 Identities=6% Similarity=0.131 Sum_probs=30.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccCCC
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDLLPS 322 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Lip~ 322 (510)
..++.+|||+.+|+|..||+++++.....+...+..
T Consensus 156 eg~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l~~ 191 (194)
T PRK12531 156 EELPHQQVAEMFDIPLGTVKSRLRLAVEKLRHSMDA 191 (194)
T ss_pred cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHhhh
Confidence 478999999999999999999988777777665543
No 203
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=59.73 E-value=14 Score=35.95 Aligned_cols=32 Identities=6% Similarity=0.049 Sum_probs=29.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
...+.+|||+.+++|+.||++..+.|+..++.
T Consensus 151 ~G~snkeIA~~L~iS~~TVk~h~~~I~~KL~v 182 (207)
T PRK15411 151 AGQGTIQISDQMNIKAKTVSSHKGNIKRKIKT 182 (207)
T ss_pred cCCCHHHHHHHcCCCHHHHHHHHHHHHHHhCC
Confidence 47889999999999999999999999998874
No 204
>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=59.67 E-value=5.8 Score=29.50 Aligned_cols=23 Identities=35% Similarity=0.859 Sum_probs=16.9
Q ss_pred CCCCCCCCCCcccccCCCCccccccccc
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCG 29 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG 29 (510)
.||.|+. +. .....|. .+|..|+
T Consensus 19 ~Cp~C~~--PL-~~~k~g~--~~Cv~C~ 41 (41)
T PF06677_consen 19 HCPDCGT--PL-MRDKDGK--IYCVSCG 41 (41)
T ss_pred ccCCCCC--ee-EEecCCC--EECCCCC
Confidence 4999964 33 3346787 9999996
No 205
>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=59.63 E-value=22 Score=30.11 Aligned_cols=41 Identities=24% Similarity=0.324 Sum_probs=33.6
Q ss_pred HHHHHHHHHcCCCCCHHHHHHHhC-CCHHHHHHHHHHHHHhhcc
Q 046187 276 AAIYLACQLEDKRKTQAEICKVTG-LTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 276 AaIYlAarl~g~~~t~keIa~vag-VSe~TIRkrYKEL~e~l~~ 318 (510)
-++|++-+.. ..+..+|++.+| .+.+||...++.+.+.+..
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 3567776655 678999999999 9999999999988886653
No 206
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=59.33 E-value=10 Score=34.57 Aligned_cols=34 Identities=12% Similarity=-0.022 Sum_probs=27.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccC
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDLL 320 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Li 320 (510)
...+.+|||+.+|+|+.||+.++......+...+
T Consensus 121 ~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (160)
T PRK09642 121 EEKSYQEIALQEKIEVKTVEMKLYRARKWIKKHW 154 (160)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4789999999999999999988876666665543
No 207
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=58.43 E-value=24 Score=26.14 Aligned_cols=30 Identities=23% Similarity=0.371 Sum_probs=26.8
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 286 DKRKTQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 286 g~~~t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
....+..+|++.++++..|+++..+.|.+.
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~~ 37 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLREA 37 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 567899999999999999999999998863
No 208
>PRK02935 hypothetical protein; Provisional
Probab=58.35 E-value=5.8 Score=35.35 Aligned_cols=36 Identities=19% Similarity=0.404 Sum_probs=25.2
Q ss_pred CCCCCCCCCCcccccCCCCccccccccceecccceeecccccccc
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRVIAERQCQNHHLFHIR 46 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vleer~Id~~~EwR~f 46 (510)
.||+|+..+.. -|+ +..|..|+.-| .+|.+.|=.+|
T Consensus 72 ~CP~C~K~TKm-----LGr-vD~CM~C~~PL---TLd~~legkef 107 (110)
T PRK02935 72 ICPSCEKPTKM-----LGR-VDACMHCNQPL---TLDRSLEGKEF 107 (110)
T ss_pred ECCCCCchhhh-----ccc-eeecCcCCCcC---CcCccccccCc
Confidence 59999886655 465 56899999877 45655554443
No 209
>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=58.33 E-value=25 Score=29.77 Aligned_cols=43 Identities=19% Similarity=0.120 Sum_probs=35.8
Q ss_pred HHHHHHHHHhcCCCCCHHHHHHHhC-CCHHHHHHHHHHHHHHhccc
Q 046187 179 TAALVQAIREAQEPRTLQEISIAAN-VPQKEIGKYIKILGEALQLS 223 (510)
Q Consensus 179 AACLYIACR~~~~PrTLkEIa~vt~-VskkeIgr~yk~L~k~L~i~ 223 (510)
.-|+|++-+..+ .++.||+..++ .+-..+..+++++.+.+..+
T Consensus 33 ~ia~yl~~~~~~--~s~~~Ig~~fg~r~hStV~~a~~ri~~~~~~d 76 (90)
T cd06571 33 QIAMYLARELTG--LSLPEIGRAFGGRDHSTVLHAVRKIEELLEED 76 (90)
T ss_pred HHHHHHHHHHhC--CCHHHHHHHhCCCCHhHHHHHHHHHHHHHHhC
Confidence 467888866654 58999999999 99999999999999988643
No 210
>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=58.32 E-value=12 Score=29.23 Aligned_cols=31 Identities=29% Similarity=0.296 Sum_probs=25.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWD 317 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~ 317 (510)
...+.+++|+.+++|+.||++...+|.+.+.
T Consensus 18 ~~~~~~ela~~l~~S~rti~~~i~~L~~~f~ 48 (59)
T PF08280_consen 18 KWITLKELAKKLNISERTIKNDINELNEFFP 48 (59)
T ss_dssp TSBBHHHHHHHCTS-HHHHHHHHHHHHTT--
T ss_pred CCCcHHHHHHHHCCCHHHHHHHHHHHHHHhh
Confidence 4678999999999999999999888876654
No 211
>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=58.22 E-value=6.4 Score=29.14 Aligned_cols=28 Identities=25% Similarity=0.577 Sum_probs=14.3
Q ss_pred CCCCCCCCCCc-cccc--CCCCcccccccccee
Q 046187 2 KCPYCSAAQGR-CATT--STGRSITECGSCGRV 31 (510)
Q Consensus 2 ~Cp~C~~~~~~-i~D~--~~Gd~~~VC~~CG~V 31 (510)
-||.|+...-. +.+. .+|. .+|..|+-+
T Consensus 5 pCP~CGG~DrFri~~d~~~~G~--~~C~~C~~~ 35 (40)
T PF08273_consen 5 PCPICGGKDRFRIFDDKDGRGT--WICRQCGGD 35 (40)
T ss_dssp --TTTT-TTTEEEETT----S---EEETTTTBE
T ss_pred CCCCCcCccccccCcCcccCCC--EECCCCCCc
Confidence 49999984322 2343 3465 999999434
No 212
>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=58.09 E-value=7.9 Score=34.64 Aligned_cols=25 Identities=32% Similarity=0.588 Sum_probs=17.6
Q ss_pred CCCCCCCCCCcccccCCCCcccccccccee
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRV 31 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~V 31 (510)
.||.|.+. +.+..|. ..||.+||.-
T Consensus 4 ~CP~C~se----ytY~dg~-~~iCpeC~~E 28 (109)
T TIGR00686 4 PCPKCNSE----YTYHDGT-QLICPSCLYE 28 (109)
T ss_pred cCCcCCCc----ceEecCC-eeECcccccc
Confidence 59999872 2234454 5999999973
No 213
>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=58.07 E-value=10 Score=32.24 Aligned_cols=30 Identities=23% Similarity=0.305 Sum_probs=19.4
Q ss_pred HHHHHcCCCCCHHHHHHHhCCCHHHHHHHH
Q 046187 280 LACQLEDKRKTQAEICKVTGLTEVTLRKVY 309 (510)
Q Consensus 280 lAarl~g~~~t~keIa~vagVSe~TIRkrY 309 (510)
++-.+...+-|+++.|.++|||.+||-+-.
T Consensus 11 i~~yIi~~~aTVR~~Ak~FGvSKSTVHkDv 40 (82)
T PF12116_consen 11 IANYIIETKATVRQAAKVFGVSKSTVHKDV 40 (82)
T ss_dssp HHHHHHHH---HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHcccHHHHHHHHHCCcHHHHHHHH
Confidence 344445567899999999999999986443
No 214
>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=58.02 E-value=22 Score=33.83 Aligned_cols=28 Identities=36% Similarity=0.430 Sum_probs=25.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q 046187 289 KTQAEICKVTGLTEVTLRKVYKELLENW 316 (510)
Q Consensus 289 ~t~keIa~vagVSe~TIRkrYKEL~e~l 316 (510)
.++++||+.+++|..||.+.+|+|.+.-
T Consensus 76 ~t~~~ia~~l~iS~~Tv~r~ik~L~e~~ 103 (165)
T PF05732_consen 76 ATQKEIAEKLGISKPTVSRAIKELEEKN 103 (165)
T ss_pred eeHHHHHHHhCCCHHHHHHHHHHHHhCC
Confidence 6899999999999999999999998754
No 215
>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=57.74 E-value=5 Score=39.42 Aligned_cols=36 Identities=28% Similarity=0.580 Sum_probs=24.6
Q ss_pred CCCCCCCCCCCcc-cccCCC-Cccccccccceeccccee
Q 046187 1 MKCPYCSAAQGRC-ATTSTG-RSITECGSCGRVIAERQC 37 (510)
Q Consensus 1 m~Cp~C~~~~~~i-~D~~~G-d~~~VC~~CG~Vleer~I 37 (510)
|+|=+||..-..+ .+++.| ---+.|.+||.|. |..|
T Consensus 1 miCIeCg~~v~~Ly~~Ys~~~irLt~C~~C~~va-DkYi 38 (208)
T PF04161_consen 1 MICIECGHPVKSLYRQYSPGNIRLTKCPNCGKVA-DKYI 38 (208)
T ss_pred CEeccCCCcchhhhhccCCCcEEEeeccccCCcc-ccee
Confidence 8999999843333 456665 2236899999987 4444
No 216
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=57.55 E-value=3.6 Score=39.70 Aligned_cols=30 Identities=23% Similarity=0.542 Sum_probs=0.0
Q ss_pred CCCCCCCCCCcccccCCCCccccccccceeccc
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRVIAE 34 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vlee 34 (510)
.||+|+. .....|--+.. -.|..||-+|++
T Consensus 119 ~Cp~C~~-rytf~eA~~~~--F~Cp~Cg~~L~~ 148 (178)
T PRK06266 119 FCPNCHI-RFTFDEAMEYG--FRCPQCGEMLEE 148 (178)
T ss_pred ECCCCCc-EEeHHHHhhcC--CcCCCCCCCCee
No 217
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=57.51 E-value=24 Score=31.37 Aligned_cols=44 Identities=20% Similarity=0.277 Sum_probs=34.3
Q ss_pred HHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046187 175 EALATAALVQAIREAQEPRTLQEISIAANVPQKEIGKYIKILGE 218 (510)
Q Consensus 175 eaVaAACLYIACR~~~~PrTLkEIa~vt~VskkeIgr~yk~L~k 218 (510)
+....+.+|++-...+.|.+..||++.++++...+.+.+..|.+
T Consensus 8 ~~al~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~~ 51 (132)
T TIGR00738 8 EYALRALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRR 51 (132)
T ss_pred HHHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 34456667777332345999999999999999999999988876
No 218
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=57.35 E-value=5 Score=35.99 Aligned_cols=33 Identities=21% Similarity=0.371 Sum_probs=21.0
Q ss_pred CCCCCCCCCCCcccccCCCCccccccccceecccc
Q 046187 1 MKCPYCSAAQGRCATTSTGRSITECGSCGRVIAER 35 (510)
Q Consensus 1 m~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vleer 35 (510)
+.||+|++--..-.|-..+ .++|.+||...+-+
T Consensus 3 ~FCp~Cgsll~p~~~~~~~--~l~C~kCgye~~~~ 35 (113)
T COG1594 3 RFCPKCGSLLYPKKDDEGG--KLVCRKCGYEEEAS 35 (113)
T ss_pred cccCCccCeeEEeEcCCCc--EEECCCCCcchhcc
Confidence 4699999822111222334 49999999976554
No 219
>PHA02591 hypothetical protein; Provisional
Probab=57.31 E-value=17 Score=30.81 Aligned_cols=29 Identities=21% Similarity=0.297 Sum_probs=23.4
Q ss_pred HHHcCCCCCHHHHHHHhCCCHHHHHHHHH
Q 046187 282 CQLEDKRKTQAEICKVTGLTEVTLRKVYK 310 (510)
Q Consensus 282 arl~g~~~t~keIa~vagVSe~TIRkrYK 310 (510)
-+|.....|+.+||+.+||+..++++..+
T Consensus 53 ~eL~eqGlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 53 HELARKGFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHHHh
Confidence 33444578999999999999999997654
No 220
>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=57.11 E-value=15 Score=29.10 Aligned_cols=37 Identities=30% Similarity=0.435 Sum_probs=29.4
Q ss_pred HHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 278 IYLACQLEDKRKTQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 278 IYlAarl~g~~~t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
||.+-. ..-+.|..||++.+|++..|+.+..+.|.+.
T Consensus 13 vy~~Ll-~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~ 49 (68)
T PF01978_consen 13 VYLALL-KNGPATAEEIAEELGISRSTVYRALKSLEEK 49 (68)
T ss_dssp HHHHHH-HHCHEEHHHHHHHHTSSHHHHHHHHHHHHHT
T ss_pred HHHHHH-HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 444432 3457899999999999999999999998764
No 221
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=57.08 E-value=25 Score=32.84 Aligned_cols=45 Identities=20% Similarity=0.086 Sum_probs=36.7
Q ss_pred HHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 046187 174 VEALATAALVQAIREAQEPRTLQEISIAANVPQKEIGKYIKILGEA 219 (510)
Q Consensus 174 ~eaVaAACLYIACR~~~~PrTLkEIa~vt~VskkeIgr~yk~L~k~ 219 (510)
.+.-+-+.+|+| ...+.+.+.+|||+..+++..-|.+.+..|++.
T Consensus 7 ~~YAlr~L~~LA-~~~~~~~s~~eIA~~~~is~~~L~kIl~~L~~a 51 (153)
T PRK11920 7 TNYAIRMLMYCA-ANDGKLSRIPEIARAYGVSELFLFKILQPLVEA 51 (153)
T ss_pred HhHHHHHHHHHH-hCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 344566788999 445668899999999999999999999888774
No 222
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=57.04 E-value=13 Score=34.23 Aligned_cols=34 Identities=12% Similarity=0.148 Sum_probs=29.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccC
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDLL 320 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Li 320 (510)
...+.+|||+.+|+|+.||+.++......+...+
T Consensus 127 ~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 160 (164)
T PRK12547 127 SGFSYEDAAAICGCAVGTIKSRVSRARNRLQELL 160 (164)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 4788999999999999999999988777776544
No 223
>PF13518 HTH_28: Helix-turn-helix domain
Probab=56.70 E-value=23 Score=25.99 Aligned_cols=27 Identities=22% Similarity=0.309 Sum_probs=23.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 289 KTQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 289 ~t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
.+..+||..+|||..||....+.+.+.
T Consensus 13 ~s~~~~a~~~gis~~tv~~w~~~y~~~ 39 (52)
T PF13518_consen 13 ESVREIAREFGISRSTVYRWIKRYREG 39 (52)
T ss_pred CCHHHHHHHHCCCHhHHHHHHHHHHhc
Confidence 399999999999999999888877763
No 224
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=56.69 E-value=20 Score=32.52 Aligned_cols=31 Identities=32% Similarity=0.384 Sum_probs=27.7
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q 046187 286 DKRKTQAEICKVTGLTEVTLRKVYKELLENW 316 (510)
Q Consensus 286 g~~~t~keIa~vagVSe~TIRkrYKEL~e~l 316 (510)
+.++++++||+.+|+|..|+++|.+.|.+.=
T Consensus 20 d~r~~~~eia~~lglS~~~v~~Ri~~L~~~G 50 (154)
T COG1522 20 DARISNAELAERVGLSPSTVLRRIKRLEEEG 50 (154)
T ss_pred hCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 4568999999999999999999999998753
No 225
>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=56.66 E-value=13 Score=34.50 Aligned_cols=32 Identities=19% Similarity=0.183 Sum_probs=26.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
...+.+|||+.+|+|+.||+.++..-...+..
T Consensus 149 ~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 149 AGLTVEEIAELLGVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 47899999999999999999988766665543
No 226
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=56.61 E-value=15 Score=33.85 Aligned_cols=34 Identities=21% Similarity=0.171 Sum_probs=27.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccC
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDLL 320 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Li 320 (510)
...+.+|||+.+|+++.||+.++..-...+...+
T Consensus 133 ~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 166 (173)
T PRK09645 133 RGWSTAQIAADLGIPEGTVKSRLHYALRALRLAL 166 (173)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 4789999999999999999988776666665544
No 227
>TIGR00281 segregation and condensation protein B. Shown to be required for chromosome segregation and condensation in B. subtilis.
Probab=56.59 E-value=1.7e+02 Score=28.51 Aligned_cols=108 Identities=18% Similarity=0.204 Sum_probs=59.1
Q ss_pred HHHHHHHHHHHHHhcCCC-CCHHHHHHHhCCCH-HHHHHHHHHHHHHhcccCCCCCcchhhhHHHHHhh--cCCCHHHHH
Q 046187 175 EALATAALVQAIREAQEP-RTLQEISIAANVPQ-KEIGKYIKILGEALQLSQPINSNSIAVHMPRFCTL--LQLNKSAQV 250 (510)
Q Consensus 175 eaVaAACLYIACR~~~~P-rTLkEIa~vt~Vsk-keIgr~yk~L~k~L~i~~pv~~~~p~~~I~Rfcs~--L~L~~~V~~ 250 (510)
.+++=|.||++ +-| .++++|+.+++++. .++......|.....-.... --|..+... |...++...
T Consensus 3 ~~~iEAlLF~s----g~pgls~~~La~il~~~~~~~~~~~l~~l~~~~~~~~~g------l~l~~~~~~y~l~tk~e~~~ 72 (186)
T TIGR00281 3 KAIIEALLFVS----GEPGVTLAELVRILGKEKAEKLNAIMELLEDYLSRDTAG------IEIIKFGQSYSLVTKPAFAD 72 (186)
T ss_pred HHHHHHHHHHc----CCCCCCHHHHHHHhCCCchHHHHHHHHHHHHHHhcCCCC------EEEEEECCEEEEEEhHHHHH
Confidence 45677888887 778 99999999999984 46666666666654322110 001111111 222233333
Q ss_pred HHHHHHHHHHhccccCCCChHHHHHHHH-HHHHHHcCCCCCHHHHHHHhCCCH
Q 046187 251 LATHIGEVVINKCFCTRRNPISISAAAI-YLACQLEDKRKTQAEICKVTGLTE 302 (510)
Q Consensus 251 ~A~~Ia~~a~~~~l~~GRsP~sIAAAaI-YlAarl~g~~~t~keIa~vagVSe 302 (510)
...++... . ++. +.-|++ -+|...+..++|..+|-++=||.-
T Consensus 73 ~i~~~~~~----~----~~~--LS~aaLEtLAIIAY~QPITr~eIe~IRGv~s 115 (186)
T TIGR00281 73 YIHRFLPA----K----LKN--LNSASLEVLAIIAYKQPITRARINEIRGVKS 115 (186)
T ss_pred HHHHHhcc----c----ccc--CCHHHHHHHHHHHHcCCcCHHHHHHHcCCCH
Confidence 33333221 0 111 111222 123334578999999999999974
No 228
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=56.52 E-value=31 Score=24.86 Aligned_cols=29 Identities=24% Similarity=0.471 Sum_probs=26.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
...+..+|++.++++..|+++..+.|.+.
T Consensus 13 ~~~s~~~l~~~l~~s~~tv~~~l~~L~~~ 41 (53)
T smart00420 13 GKVSVEELAELLGVSEMTIRRDLNKLEEQ 41 (53)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 35899999999999999999999998775
No 229
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=56.23 E-value=18 Score=36.16 Aligned_cols=33 Identities=12% Similarity=0.092 Sum_probs=30.2
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 286 DKRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 286 g~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
....+.+|||+.+++|+.||++..+.|++.++.
T Consensus 156 a~G~SnkEIA~~L~IS~~TVk~hvs~I~~KLgv 188 (217)
T PRK13719 156 SFGFSHEYIAQLLNITVGSSKNKISEILKFFGI 188 (217)
T ss_pred HCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 457899999999999999999999999998875
No 230
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=56.02 E-value=18 Score=33.68 Aligned_cols=33 Identities=27% Similarity=0.319 Sum_probs=28.4
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 286 DKRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 286 g~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
....|++|||+.+|+|..||+...+...+.+..
T Consensus 19 ~~GlTq~EIAe~LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 19 EKGLSQKEIAKELKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence 357899999999999999999888887777764
No 231
>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=55.80 E-value=4.8 Score=31.60 Aligned_cols=28 Identities=21% Similarity=0.523 Sum_probs=19.9
Q ss_pred CCCCCCCCCCCcc--cccCCCCccccccccce
Q 046187 1 MKCPYCSAAQGRC--ATTSTGRSITECGSCGR 30 (510)
Q Consensus 1 m~Cp~C~~~~~~i--~D~~~Gd~~~VC~~CG~ 30 (510)
|+|+.|....... +++..=. .+|..||.
T Consensus 23 LIC~~C~~hNGla~~~~~~~i~--y~C~~Cg~ 52 (54)
T PF10058_consen 23 LICSKCFSHNGLAPKEEFEEIQ--YRCPYCGA 52 (54)
T ss_pred EECcccchhhcccccccCCceE--EEcCCCCC
Confidence 5799998855444 4555556 89999985
No 232
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=55.67 E-value=18 Score=32.47 Aligned_cols=31 Identities=32% Similarity=0.367 Sum_probs=26.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWD 317 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~ 317 (510)
...+.+|||+.+|+|+.||+++.......+.
T Consensus 121 ~~~s~~EIA~~l~is~~tV~~~~~ra~~~Lr 151 (154)
T PRK06759 121 VGKTMGEIALETEMTYYQVRWIYRQALEKMR 151 (154)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence 4788999999999999999999877666554
No 233
>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=55.64 E-value=32 Score=27.20 Aligned_cols=37 Identities=19% Similarity=0.257 Sum_probs=31.0
Q ss_pred HHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046187 181 ALVQAIREAQEPRTLQEISIAANVPQKEIGKYIKILGE 218 (510)
Q Consensus 181 CLYIACR~~~~PrTLkEIa~vt~VskkeIgr~yk~L~k 218 (510)
+||.... .+.+.+.+|||..++|++-.+...+++|.+
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 4666655 888999999999999999999999998876
No 234
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=55.59 E-value=78 Score=35.35 Aligned_cols=80 Identities=18% Similarity=0.158 Sum_probs=49.6
Q ss_pred HHHHHHHH----hCCCHHHHHHHHHHHHHHHhCCccCCccH-H-------------HHHHHHHHHHH-HhcCC-CCCHHH
Q 046187 138 QIIDVASI----LGLDYDICDHAFQLFRDCCSATCLRNRSV-E-------------ALATAALVQAI-REAQE-PRTLQE 197 (510)
Q Consensus 138 ~I~~ic~~----L~LP~~VidtA~~LyK~a~e~~~lrGRs~-e-------------aVaAACLYIAC-R~~~~-PrTLkE 197 (510)
.+.++|+. |+++...++.|..+++.+.=.|..- |+. + ....-+..+.. ..+.. -+.++.
T Consensus 162 ~~~eia~~~~~~l~~~~~~ve~vL~~iQ~leP~GVgA-RdL~ECL~lQL~~~~~~~~~~~~a~~il~~~le~La~~~~~~ 240 (481)
T PRK12469 162 DLSELAEAADPELGLSEQELEVALRLVQSLDPPGVAA-RDLSECLLLQLDALPADTPALEEAKEIARHHLERLARRETAE 240 (481)
T ss_pred CHHHHHhccccccCCCHHHHHHHHHHHhcCCCCccCc-CCHHHHHHHHHHhccCCCchHHHHHHHHHHHHHHHHccCHHH
Confidence 34568888 9999999999999999876555322 111 0 00000111111 11222 256778
Q ss_pred HHHHhCCCHHHHHHHHHHHHH
Q 046187 198 ISIAANVPQKEIGKYIKILGE 218 (510)
Q Consensus 198 Ia~vt~VskkeIgr~yk~L~k 218 (510)
|+..++++..+|..++..|+.
T Consensus 241 i~~~l~~~~~~l~~a~~~Ir~ 261 (481)
T PRK12469 241 IQRRIGCDQETLREACALVRR 261 (481)
T ss_pred HHHHhCcCHHHHHHHHHHHhC
Confidence 888899999999998876654
No 235
>PRK13870 transcriptional regulator TraR; Provisional
Probab=55.57 E-value=19 Score=35.85 Aligned_cols=32 Identities=28% Similarity=0.386 Sum_probs=28.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
..+|..|||.++|||+.|++...+.....|+.
T Consensus 187 ~GKT~~EIa~ILgISe~TV~~Hl~na~~KLga 218 (234)
T PRK13870 187 VGKTMEEIADVEGVKYNSVRVKLREAMKRFDV 218 (234)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence 47899999999999999999999998888764
No 236
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=55.30 E-value=25 Score=34.12 Aligned_cols=61 Identities=23% Similarity=0.195 Sum_probs=41.8
Q ss_pred hhcCCCHHHHHHHHHHHHHHHhccccCCCChHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHH
Q 046187 240 TLLQLNKSAQVLATHIGEVVINKCFCTRRNPISISAAAIYLACQLEDKRKTQAEICKVTGLTEVTLRKVYK 310 (510)
Q Consensus 240 s~L~L~~~V~~~A~~Ia~~a~~~~l~~GRsP~sIAAAaIYlAarl~g~~~t~keIa~vagVSe~TIRkrYK 310 (510)
-...+...+.+......+.+. |+. -..+||+++- + .....|..+||.-+|.|+.|||+..+
T Consensus 23 ~atl~~~evlkli~~~~~~lT--Wvd----SLavAAga~a---r-ekag~Ti~EIAeelG~TeqTir~hlk 83 (182)
T COG1318 23 VATLFRPEVLKLIKDPYERLT--WVD----SLAVAAGALA---R-EKAGMTISEIAEELGRTEQTVRNHLK 83 (182)
T ss_pred HHHhccHHHHHHHhCcccccc--hhh----HHHHHHHHHH---H-HHccCcHHHHHHHhCCCHHHHHHHHh
Confidence 334566777777776665543 433 2355555543 2 55678999999999999999998765
No 237
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=55.00 E-value=4.3 Score=42.16 Aligned_cols=43 Identities=19% Similarity=0.351 Sum_probs=28.6
Q ss_pred CCCCCCCCCCCcc-cccCCCCccccccccceeccc-------ceeecccccccccC
Q 046187 1 MKCPYCSAAQGRC-ATTSTGRSITECGSCGRVIAE-------RQCQNHHLFHIRAQ 48 (510)
Q Consensus 1 m~Cp~C~~~~~~i-~D~~~Gd~~~VC~~CG~Vlee-------r~Id~~~EwR~fs~ 48 (510)
.+||.|+.. +. .|..... .||..||.-+.= .++|+++ |+++..
T Consensus 28 ~~c~~c~~~--~~~~~l~~~~--~vc~~c~~h~rl~areRi~~L~D~gs-F~E~~~ 78 (292)
T PRK05654 28 TKCPSCGQV--LYRKELEANL--NVCPKCGHHMRISARERLDLLLDEGS-FVELDA 78 (292)
T ss_pred eECCCccch--hhHHHHHhcC--CCCCCCCCCeeCCHHHHHHHHccCCc-cEEecC
Confidence 379999882 22 3444444 799999987642 2567776 777654
No 238
>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=54.97 E-value=6.1 Score=44.53 Aligned_cols=43 Identities=26% Similarity=0.417 Sum_probs=28.6
Q ss_pred CCCCCCCCCCCcc-----c----ccCCCCccccccccceecccce---eeccccccc
Q 046187 1 MKCPYCSAAQGRC-----A----TTSTGRSITECGSCGRVIAERQ---CQNHHLFHI 45 (510)
Q Consensus 1 m~Cp~C~~~~~~i-----~----D~~~Gd~~~VC~~CG~Vleer~---Id~~~EwR~ 45 (510)
..||+||..+... . +..+-. .+|..||..++|.. +...-+|+-
T Consensus 201 vpCPhCg~~~~l~~~~l~w~~~~~~~~a~--y~C~~Cg~~i~e~~k~~m~~~G~Wv~ 255 (557)
T PF05876_consen 201 VPCPHCGEEQVLEWENLKWDKGEAPETAR--YVCPHCGCEIEEHDKRRMVRRGRWVA 255 (557)
T ss_pred ccCCCCCCCccccccceeecCCCCccceE--EECCCCcCCCCHHHHhhccCCeEEEe
Confidence 3699999965432 1 122334 99999999998853 334566775
No 239
>PRK10870 transcriptional repressor MprA; Provisional
Probab=54.65 E-value=70 Score=30.44 Aligned_cols=29 Identities=14% Similarity=0.226 Sum_probs=25.5
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046187 286 DKRKTQAEICKVTGLTEVTLRKVYKELLE 314 (510)
Q Consensus 286 g~~~t~keIa~vagVSe~TIRkrYKEL~e 314 (510)
+..+++++||+.++++..|+....+.|.+
T Consensus 69 ~~~it~~eLa~~l~l~~~tvsr~v~rLe~ 97 (176)
T PRK10870 69 NHSIQPSELSCALGSSRTNATRIADELEK 97 (176)
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 45689999999999999999988888765
No 240
>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=54.55 E-value=17 Score=33.04 Aligned_cols=32 Identities=16% Similarity=0.229 Sum_probs=27.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
...+.+|||+.+|+|+.||++++....+.+..
T Consensus 137 ~g~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 137 QNLPIAEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46899999999999999999999877776654
No 241
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=54.45 E-value=65 Score=30.34 Aligned_cols=30 Identities=23% Similarity=0.300 Sum_probs=27.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENW 316 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l 316 (510)
.++++++||+.+|++..|+.+.+++|.+.=
T Consensus 167 ~~~t~~~lA~~lG~tr~tvsR~l~~l~~~g 196 (211)
T PRK11753 167 IKITRQEIGRIVGCSREMVGRVLKMLEDQG 196 (211)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 478999999999999999999999988753
No 242
>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=54.41 E-value=17 Score=28.48 Aligned_cols=26 Identities=23% Similarity=0.268 Sum_probs=23.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKEL 312 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL 312 (510)
+..+++|.|+.+||+..+++++++++
T Consensus 14 fhlp~~eAA~~Lgv~~T~LKr~CR~~ 39 (52)
T PF02042_consen 14 FHLPIKEAAKELGVSVTTLKRRCRRL 39 (52)
T ss_pred hCCCHHHHHHHhCCCHHHHHHHHHHc
Confidence 57899999999999999999998864
No 243
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=54.34 E-value=67 Score=36.16 Aligned_cols=104 Identities=12% Similarity=0.064 Sum_probs=63.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhcccCCCCCcchhhhHHH-HHhhcCCCHHHHHHHHHHHHHHHhccccCCCC
Q 046187 191 EPRTLQEISIAANVPQKEIGKYIKILGEALQLSQPINSNSIAVHMPR-FCTLLQLNKSAQVLATHIGEVVINKCFCTRRN 269 (510)
Q Consensus 191 ~PrTLkEIa~vt~VskkeIgr~yk~L~k~L~i~~pv~~~~p~~~I~R-fcs~L~L~~~V~~~A~~Ia~~a~~~~l~~GRs 269 (510)
.+.|..++|..++|+.++|.+-++.|.+.|.-.... .+.+ -.-.|...+. ..-..+.. . ..
T Consensus 16 ~~~t~~~LA~~l~VS~RTIr~dI~~in~~l~~~~~~-------~i~~~~Gy~l~~~~~--~~~~~~~~---~------~~ 77 (584)
T PRK09863 16 QDRSGGELAQQLGVSRRTIVRDIAYINFTLNGKAIG-------SISGSAKYHLEILNR--RSLFQLLQ---K------SD 77 (584)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhcchh-------heecCCceEEEeCCH--HHHHHHHh---c------CC
Confidence 489999999999999999999999998877532110 0000 0111221111 00011111 0 12
Q ss_pred hHHHHHHHHHHHH-HHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhc
Q 046187 270 PISISAAAIYLAC-QLEDKRKTQAEICKVTGLTEVTLRKVYKELLENWD 317 (510)
Q Consensus 270 P~sIAAAaIYlAa-rl~g~~~t~keIa~vagVSe~TIRkrYKEL~e~l~ 317 (510)
+.-. ++.. .+....++..++|+.+.||+.||.+-.+++.+.+.
T Consensus 78 ~e~~-----~il~~Ll~~~~~~~~~La~~l~vS~sTi~~dl~~v~~~l~ 121 (584)
T PRK09863 78 NEDR-----LLLLRLLLNTFTPMAQLASALNLSRTWVAERLPRLNQRYE 121 (584)
T ss_pred HHHH-----HHHHHHHHcCCccHHHHHHHhCCCHHHHHHHHHHHHHhhh
Confidence 2222 1222 22245688999999999999999999999998665
No 244
>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=54.01 E-value=38 Score=24.84 Aligned_cols=35 Identities=23% Similarity=0.420 Sum_probs=25.9
Q ss_pred HHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046187 183 VQAIREAQEPRTLQEISIAANVPQKEIGKYIKILGE 218 (510)
Q Consensus 183 YIACR~~~~PrTLkEIa~vt~VskkeIgr~yk~L~k 218 (510)
+...+. +-..|.+||+..++++...+.+.++.|.+
T Consensus 9 l~~l~~-~~~~t~~ela~~~~is~~tv~~~l~~L~~ 43 (48)
T PF13412_consen 9 LNYLRE-NPRITQKELAEKLGISRSTVNRYLKKLEE 43 (48)
T ss_dssp HHHHHH-CTTS-HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHH-cCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 334444 33499999999999999999999988865
No 245
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=53.74 E-value=28 Score=27.73 Aligned_cols=56 Identities=5% Similarity=0.147 Sum_probs=30.7
Q ss_pred HhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhcccCCCCCcchhhhHHHHHhhcCCCHH
Q 046187 187 REAQEPRTLQEISIAANVPQKEIGKYIKILGEALQLSQPINSNSIAVHMPRFCTLLQLNKS 247 (510)
Q Consensus 187 R~~~~PrTLkEIa~vt~VskkeIgr~yk~L~k~L~i~~pv~~~~p~~~I~Rfcs~L~L~~~ 247 (510)
..+..-.|+.||+..++++...|.. |... ++..-....-..-||..||..|||+.+
T Consensus 5 ~R~~~glsl~~va~~t~I~~~~l~a----iE~~-~~~~lp~~~y~rg~lr~Ya~~Lgld~~ 60 (62)
T PF13413_consen 5 AREAKGLSLEDVAEETKISVSYLEA----IENG-DFDSLPSPVYARGYLRKYARFLGLDPD 60 (62)
T ss_dssp HHHCTT--HHHHHHHCS--HHHHHH----HHCT--GCCSSSHHHHHHHHHHHHHHTT--HH
T ss_pred HHHHcCCCHHHHHHHhCCCHHHHHH----HHCc-ChhhCCcHHHHHHHHHHHHHHhCcCcc
Confidence 4566678999999999999876632 2111 111111111246799999999999864
No 246
>PF14502 HTH_41: Helix-turn-helix domain
Probab=53.50 E-value=20 Score=27.71 Aligned_cols=30 Identities=27% Similarity=0.179 Sum_probs=26.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 289 KTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 289 ~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
.++.|.++.++||.+||.++++.|.+.-..
T Consensus 7 ~tI~e~~~~~~vs~GtiQ~Alk~Le~~gaI 36 (48)
T PF14502_consen 7 PTISEYSEKFGVSRGTIQNALKFLEENGAI 36 (48)
T ss_pred CCHHHHHHHhCcchhHHHHHHHHHHHCCcE
Confidence 468899999999999999999999886443
No 247
>PRK01381 Trp operon repressor; Provisional
Probab=53.49 E-value=12 Score=33.05 Aligned_cols=34 Identities=21% Similarity=0.165 Sum_probs=26.9
Q ss_pred HHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046187 280 LACQLEDKRKTQAEICKVTGLTEVTLRKVYKELL 313 (510)
Q Consensus 280 lAarl~g~~~t~keIa~vagVSe~TIRkrYKEL~ 313 (510)
++..++.-.+|++||++.+|||..||...-+.|.
T Consensus 47 I~~~L~~g~~sQREIa~~lGvSiaTITRgsn~Lk 80 (99)
T PRK01381 47 IVEELLRGELSQREIKQELGVGIATITRGSNSLK 80 (99)
T ss_pred HHHHHHcCCcCHHHHHHHhCCceeeehhhHHHhc
Confidence 4445666689999999999999999986655554
No 248
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=53.36 E-value=17 Score=33.12 Aligned_cols=33 Identities=18% Similarity=0.331 Sum_probs=28.7
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccC
Q 046187 288 RKTQAEICKVTGLTEVTLRKVYKELLENWDDLL 320 (510)
Q Consensus 288 ~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Li 320 (510)
..+.+|||+.+|+|+.||++++....+.+...+
T Consensus 126 g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 158 (162)
T TIGR02983 126 DLSEAQVAEALGISVGTVKSRLSRALARLRELL 158 (162)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 789999999999999999999888877776544
No 249
>PRK00118 putative DNA-binding protein; Validated
Probab=53.33 E-value=25 Score=31.18 Aligned_cols=32 Identities=13% Similarity=0.095 Sum_probs=26.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
...+.++||+.+|+|..||+++++.....+..
T Consensus 32 eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~ 63 (104)
T PRK00118 32 DDYSLGEIAEEFNVSRQAVYDNIKRTEKLLED 63 (104)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 47899999999999999999887765555443
No 250
>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=53.26 E-value=6.4 Score=28.64 Aligned_cols=31 Identities=26% Similarity=0.636 Sum_probs=16.6
Q ss_pred CCCCCCCCCCCcccc--cCCCCc----ccccccccee
Q 046187 1 MKCPYCSAAQGRCAT--TSTGRS----ITECGSCGRV 31 (510)
Q Consensus 1 m~Cp~C~~~~~~i~D--~~~Gd~----~~VC~~CG~V 31 (510)
..||.||........ ..++|+ -.+|.+||..
T Consensus 1 ~~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~ 37 (39)
T PF01096_consen 1 IKCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHR 37 (39)
T ss_dssp S--SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEE
T ss_pred CCCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCe
Confidence 369999986544432 223331 1689999964
No 251
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=53.16 E-value=20 Score=35.80 Aligned_cols=35 Identities=14% Similarity=0.151 Sum_probs=29.7
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccCCC
Q 046187 288 RKTQAEICKVTGLTEVTLRKVYKELLENWDDLLPS 322 (510)
Q Consensus 288 ~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Lip~ 322 (510)
..+.+|||+.+|+|++||+.+...-.+.+...+..
T Consensus 132 g~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l~~ 166 (228)
T PRK06704 132 QYSIADIAKVCSVSEGAVKASLFRSRNRLKTVSEE 166 (228)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHh
Confidence 68999999999999999999987777777666544
No 252
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=53.11 E-value=20 Score=25.71 Aligned_cols=27 Identities=15% Similarity=0.385 Sum_probs=20.7
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046187 286 DKRKTQAEICKVTGLTEVTLRKVYKEL 312 (510)
Q Consensus 286 g~~~t~keIa~vagVSe~TIRkrYKEL 312 (510)
..++++.+||..+|+|+..+++.+|+.
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 356899999999999999999998875
No 253
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=53.09 E-value=7.5 Score=28.36 Aligned_cols=29 Identities=31% Similarity=0.644 Sum_probs=18.9
Q ss_pred CCCCCCCCCCcccccCCCCccccccccceec
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRVI 32 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vl 32 (510)
+||.|+. ....... .+-...+|.+||=+-
T Consensus 1 ~CP~C~~-~l~~~~~-~~~~id~C~~C~G~W 29 (41)
T PF13453_consen 1 KCPRCGT-ELEPVRL-GDVEIDVCPSCGGIW 29 (41)
T ss_pred CcCCCCc-ccceEEE-CCEEEEECCCCCeEE
Confidence 6999987 2222233 444567899999764
No 254
>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=53.06 E-value=23 Score=30.06 Aligned_cols=30 Identities=20% Similarity=0.235 Sum_probs=26.8
Q ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046187 285 EDKRKTQAEICKVTGLTEVTLRKVYKELLE 314 (510)
Q Consensus 285 ~g~~~t~keIa~vagVSe~TIRkrYKEL~e 314 (510)
.+.++.-++|++.+++|..|||+-...|.+
T Consensus 20 ~~~PVgSk~ia~~l~~s~aTIRN~M~~Le~ 49 (78)
T PF03444_consen 20 TGEPVGSKTIAEELGRSPATIRNEMADLEE 49 (78)
T ss_pred cCCCcCHHHHHHHHCCChHHHHHHHHHHHH
Confidence 367888999999999999999999998865
No 255
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=52.90 E-value=38 Score=27.28 Aligned_cols=33 Identities=18% Similarity=0.195 Sum_probs=27.5
Q ss_pred HcCC-CCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q 046187 284 LEDK-RKTQAEICKVTGLTEVTLRKVYKELLENW 316 (510)
Q Consensus 284 l~g~-~~t~keIa~vagVSe~TIRkrYKEL~e~l 316 (510)
..|. .++.+|||+.+|++..++++.+..|.+.=
T Consensus 17 ~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G 50 (68)
T smart00550 17 NSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKG 50 (68)
T ss_pred HCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 3444 49999999999999999999988887753
No 256
>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=52.78 E-value=23 Score=26.16 Aligned_cols=38 Identities=13% Similarity=0.170 Sum_probs=27.0
Q ss_pred HHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046187 276 AAIYLACQLEDKRKTQAEICKVTGLTEVTLRKVYKELL 313 (510)
Q Consensus 276 AaIYlAarl~g~~~t~keIa~vagVSe~TIRkrYKEL~ 313 (510)
|++-+..+.-=...+.++|++.+||+..+|-..|....
T Consensus 4 aa~~l~~~~G~~~~s~~~Ia~~~gvs~~~~y~~f~~k~ 41 (47)
T PF00440_consen 4 AALELFAEKGYEAVSIRDIARRAGVSKGSFYRYFPSKD 41 (47)
T ss_dssp HHHHHHHHHHTTTSSHHHHHHHHTSCHHHHHHHCSSHH
T ss_pred HHHHHHHHhCHHhCCHHHHHHHHccchhhHHHHcCCHH
Confidence 44444443222468999999999999999987775433
No 257
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=52.75 E-value=7.1 Score=28.05 Aligned_cols=29 Identities=34% Similarity=0.851 Sum_probs=19.9
Q ss_pred CCCCCCCCCCccccc---CCCCccccccccceec
Q 046187 2 KCPYCSAAQGRCATT---STGRSITECGSCGRVI 32 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~---~~Gd~~~VC~~CG~Vl 32 (510)
.||+|+. ...|-|. ..|. .+-|..||.|.
T Consensus 4 ~CP~C~~-~f~v~~~~l~~~~~-~vrC~~C~~~f 35 (37)
T PF13719_consen 4 TCPNCQT-RFRVPDDKLPAGGR-KVRCPKCGHVF 35 (37)
T ss_pred ECCCCCc-eEEcCHHHcccCCc-EEECCCCCcEe
Confidence 5999987 3454442 3343 58999999875
No 258
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=52.70 E-value=6.2 Score=34.88 Aligned_cols=29 Identities=28% Similarity=0.771 Sum_probs=20.7
Q ss_pred CCCCCCCCCCcc--cc--cCCCCccccccccceec
Q 046187 2 KCPYCSAAQGRC--AT--TSTGRSITECGSCGRVI 32 (510)
Q Consensus 2 ~Cp~C~~~~~~i--~D--~~~Gd~~~VC~~CG~Vl 32 (510)
.||.|+...... ++ ..-|. ++|.+||+-.
T Consensus 24 tCp~Cghe~vs~ctvkk~~~~g~--~~Cg~CGls~ 56 (104)
T COG4888 24 TCPRCGHEKVSSCTVKKTVNIGT--AVCGNCGLSF 56 (104)
T ss_pred ecCccCCeeeeEEEEEecCceeE--EEcccCcceE
Confidence 599999854332 55 34555 9999999865
No 259
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=52.58 E-value=36 Score=27.42 Aligned_cols=38 Identities=13% Similarity=0.340 Sum_probs=30.5
Q ss_pred HHHHHHhcCC-CCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 046187 182 LVQAIREAQE-PRTLQEISIAANVPQKEIGKYIKILGEA 219 (510)
Q Consensus 182 LYIACR~~~~-PrTLkEIa~vt~VskkeIgr~yk~L~k~ 219 (510)
|+..-+..+- ..+..||+..+++++..+.+.+..|.+.
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 4445556665 4999999999999999999998888664
No 260
>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=52.48 E-value=17 Score=32.59 Aligned_cols=32 Identities=13% Similarity=0.120 Sum_probs=27.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
...+.+|||+.+|+++.||++++......+..
T Consensus 120 ~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 120 KEFSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred ccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 47899999999999999999998777666554
No 261
>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=52.39 E-value=36 Score=30.39 Aligned_cols=45 Identities=16% Similarity=0.149 Sum_probs=36.2
Q ss_pred cHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046187 173 SVEALATAALVQAIREAQEPRTLQEISIAANVPQKEIGKYIKILGE 218 (510)
Q Consensus 173 s~eaVaAACLYIACR~~~~PrTLkEIa~vt~VskkeIgr~yk~L~k 218 (510)
..+....+.+|+|- ..+-+.+..||++.++++...+.+.++.|.+
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 34455667788873 4466899999999999999999999988877
No 262
>TIGR03020 EpsA transcriptional regulator EpsA. Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.
Probab=52.22 E-value=22 Score=36.12 Aligned_cols=32 Identities=22% Similarity=0.458 Sum_probs=29.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
..++.+|||+.++||+.||+..++.++..++.
T Consensus 204 ~G~s~~eIA~~L~IS~~TVk~hl~~i~~KL~v 235 (247)
T TIGR03020 204 DGKTNEEIAAILGISSLTVKNHLQHIFKKLDV 235 (247)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCC
Confidence 46899999999999999999999999988764
No 263
>PRK05978 hypothetical protein; Provisional
Probab=52.20 E-value=9 Score=36.12 Aligned_cols=28 Identities=25% Similarity=0.662 Sum_probs=18.3
Q ss_pred CCCCCCCCCCCcccc-cCCCCccccccccceec
Q 046187 1 MKCPYCSAAQGRCAT-TSTGRSITECGSCGRVI 32 (510)
Q Consensus 1 m~Cp~C~~~~~~i~D-~~~Gd~~~VC~~CG~Vl 32 (510)
++||.||+ ..+.+ +-.=. .-|..||.-+
T Consensus 34 grCP~CG~--G~LF~g~Lkv~--~~C~~CG~~~ 62 (148)
T PRK05978 34 GRCPACGE--GKLFRAFLKPV--DHCAACGEDF 62 (148)
T ss_pred CcCCCCCC--CcccccccccC--CCccccCCcc
Confidence 47999998 33333 11222 5799999976
No 264
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=52.07 E-value=20 Score=32.67 Aligned_cols=34 Identities=12% Similarity=0.240 Sum_probs=29.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccC
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDLL 320 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Li 320 (510)
...+.++||+.+|+++.||++++......+...+
T Consensus 126 ~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l 159 (166)
T PRK09639 126 SGYSYKEIAEALGIKESSVGTTLARAKKKFRKIY 159 (166)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 6889999999999999999999887777766554
No 265
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=51.64 E-value=22 Score=35.49 Aligned_cols=32 Identities=25% Similarity=0.350 Sum_probs=29.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
..+|.+|||+.++||+.||+...+.+++.++.
T Consensus 193 ~G~t~~eIa~~l~is~~TV~~h~~~~~~KL~~ 224 (240)
T PRK10188 193 EGKTSAEIAMILSISENTVNFHQKNMQKKFNA 224 (240)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 57899999999999999999999999998874
No 266
>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=51.61 E-value=19 Score=25.57 Aligned_cols=22 Identities=36% Similarity=0.493 Sum_probs=19.3
Q ss_pred CHHHHHHHhCCCHHHHHHHHHH
Q 046187 290 TQAEICKVTGLTEVTLRKVYKE 311 (510)
Q Consensus 290 t~keIa~vagVSe~TIRkrYKE 311 (510)
+..|+|+.+||+..||++..++
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~~ 23 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHHc
Confidence 6789999999999999977664
No 267
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=51.60 E-value=15 Score=36.03 Aligned_cols=30 Identities=20% Similarity=0.464 Sum_probs=24.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENW 316 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l 316 (510)
...+.+|||+.+|||+.||++++......+
T Consensus 197 eg~s~~EIA~~lgis~~tVk~~~~rA~~~L 226 (234)
T PRK08301 197 EEKTQKEVADMLGISQSYISRLEKRIIKRL 226 (234)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 579999999999999999988865444443
No 268
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=51.58 E-value=7.1 Score=31.33 Aligned_cols=8 Identities=38% Similarity=0.953 Sum_probs=4.3
Q ss_pred ccccccce
Q 046187 23 TECGSCGR 30 (510)
Q Consensus 23 ~VC~~CG~ 30 (510)
++|.+||.
T Consensus 49 Y~CP~CGF 56 (59)
T PRK14890 49 YTCPKCGF 56 (59)
T ss_pred eECCCCCC
Confidence 45555554
No 269
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=51.49 E-value=22 Score=33.55 Aligned_cols=32 Identities=16% Similarity=0.033 Sum_probs=27.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
...+.+|||+.+|+|+.||+.++..-...+..
T Consensus 145 ~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 145 LGLSYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 47889999999999999999998877776665
No 270
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=51.43 E-value=17 Score=34.01 Aligned_cols=33 Identities=27% Similarity=0.402 Sum_probs=26.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhccc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDL 319 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~L 319 (510)
...+.+|||+.+|+|+.||++++..-...+...
T Consensus 137 ~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 169 (185)
T PRK12542 137 YNLTYQEISSVMGITEANVRKQFERARKRVQNM 169 (185)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 468999999999999999998876555554443
No 271
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=51.42 E-value=22 Score=32.35 Aligned_cols=30 Identities=13% Similarity=0.155 Sum_probs=26.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENW 316 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l 316 (510)
...+.+|||+.+|+|..||+.++..-.+.+
T Consensus 128 ~g~s~~EIA~~l~is~~tV~~~l~ra~~~~ 157 (161)
T PRK12528 128 DGLGYGEIATELGISLATVKRYLNKAAMRC 157 (161)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 478999999999999999999988776654
No 272
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=51.29 E-value=17 Score=34.01 Aligned_cols=34 Identities=29% Similarity=0.304 Sum_probs=28.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccC
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDLL 320 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Li 320 (510)
...+.+|||+.+|+|..||+.++..-++.+...+
T Consensus 142 ~g~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l 175 (179)
T PRK09415 142 EELSIKEIAEVTGVNENTVKTRLKKAKELLKKGL 175 (179)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4789999999999999999999887777666544
No 273
>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=51.17 E-value=6.4 Score=29.00 Aligned_cols=35 Identities=20% Similarity=0.411 Sum_probs=21.2
Q ss_pred CCCCCCCCCCcccccCCCCccccccccceeccccee
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRVIAERQC 37 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vleer~I 37 (510)
+|++||..-.++.-.+. +....|..||-.--.|+|
T Consensus 7 ~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~~~~~r~~ 41 (42)
T PF09723_consen 7 RCEECGHEFEVLQSISE-DDPVPCPECGSTEVRRVI 41 (42)
T ss_pred EeCCCCCEEEEEEEcCC-CCCCcCCCCCCCceEEec
Confidence 59999863333333333 335899999984335544
No 274
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=51.05 E-value=24 Score=33.69 Aligned_cols=38 Identities=13% Similarity=0.104 Sum_probs=31.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccCCCCC
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDLLPSNY 324 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Lip~~~ 324 (510)
...+.+|||+.+|+|..||+.++......+...+....
T Consensus 128 ~g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~~~~ 165 (188)
T PRK12546 128 SGFSYEEAAEMCGVAVGTVKSRANRARARLAELLQLEE 165 (188)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhccc
Confidence 57899999999999999999999888887777665443
No 275
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=50.84 E-value=25 Score=25.19 Aligned_cols=30 Identities=23% Similarity=0.312 Sum_probs=26.3
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 046187 190 QEPRTLQEISIAANVPQKEIGKYIKILGEA 219 (510)
Q Consensus 190 ~~PrTLkEIa~vt~VskkeIgr~yk~L~k~ 219 (510)
..|.+..||++.++++...+.+.++.|.+.
T Consensus 6 ~~~~s~~~la~~l~~s~~tv~~~l~~L~~~ 35 (48)
T smart00419 6 RLPLTRQEIAELLGLTRETVSRTLKRLEKE 35 (48)
T ss_pred EeccCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 457899999999999999999999888763
No 276
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=50.75 E-value=85 Score=30.64 Aligned_cols=29 Identities=21% Similarity=0.299 Sum_probs=26.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
.++++++||+.+|++..|+.+..++|.+.
T Consensus 178 i~lt~~~IA~~lGisretlsR~L~~L~~~ 206 (230)
T PRK09391 178 LPMSRRDIADYLGLTIETVSRALSQLQDR 206 (230)
T ss_pred ecCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 57899999999999999999999999875
No 277
>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=50.72 E-value=24 Score=29.20 Aligned_cols=34 Identities=9% Similarity=0.110 Sum_probs=28.2
Q ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 285 EDKRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 285 ~g~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
.+...++.++|+...||+.||++..+++.+.+..
T Consensus 27 ~~~~~s~~~la~~~~iS~sti~~~i~~l~~~l~~ 60 (87)
T PF05043_consen 27 NNEYVSIEDLAEELFISRSTIYRDIKKLNKYLKK 60 (87)
T ss_dssp H-SEEEHHHHHHHHT--HHHHHHHHHHHHHHHHC
T ss_pred cCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4678899999999999999999999999998874
No 278
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=50.57 E-value=20 Score=33.53 Aligned_cols=34 Identities=21% Similarity=0.245 Sum_probs=28.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccC
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDLL 320 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Li 320 (510)
...+.+|||+.+|+|+.||++++..-...+...+
T Consensus 144 ~g~s~~EIA~~l~is~~tV~~~l~rar~~Lr~~l 177 (181)
T PRK12536 144 EGLSVAETAQLTGLSESAVKVGIHRGLKALAAKI 177 (181)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 4789999999999999999999877777665543
No 279
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=50.51 E-value=15 Score=36.11 Aligned_cols=38 Identities=16% Similarity=0.175 Sum_probs=31.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccCCCCC
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDLLPSNY 324 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Lip~~~ 324 (510)
...+.+|||+.+|+|..||+.++......+...+...+
T Consensus 164 ~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l~~~~ 201 (231)
T PRK11922 164 EELSVEETAQALGLPEETVKTRLHRARRLLRESLAREI 201 (231)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHhc
Confidence 47899999999999999999998887777777665444
No 280
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=50.45 E-value=20 Score=32.91 Aligned_cols=30 Identities=23% Similarity=0.409 Sum_probs=26.4
Q ss_pred CCCC-CHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 286 DKRK-TQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 286 g~~~-t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
|.++ |.++.|..++|...|++++|++|.+.
T Consensus 32 GdkLPSvRelA~~~~VNpnTv~raY~eLE~e 62 (125)
T COG1725 32 GDKLPSVRELAKDLGVNPNTVQRAYQELERE 62 (125)
T ss_pred CCCCCcHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 5565 48999999999999999999999874
No 281
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=50.44 E-value=58 Score=31.47 Aligned_cols=29 Identities=10% Similarity=0.087 Sum_probs=26.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 046187 191 EPRTLQEISIAANVPQKEIGKYIKILGEA 219 (510)
Q Consensus 191 ~PrTLkEIa~vt~VskkeIgr~yk~L~k~ 219 (510)
.|.|.+|||+.+|++...+.|.+++|.+.
T Consensus 183 ~~lt~~~iA~~lG~sr~tvsR~l~~l~~~ 211 (235)
T PRK11161 183 LTMTRGDIGNYLGLTVETISRLLGRFQKS 211 (235)
T ss_pred ccccHHHHHHHhCCcHHHHHHHHHHHHHC
Confidence 68899999999999999999999988775
No 282
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=50.38 E-value=17 Score=33.13 Aligned_cols=34 Identities=9% Similarity=0.159 Sum_probs=28.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccC
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDLL 320 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Li 320 (510)
...+.+|||+.+|+|++||+.++..-...+...+
T Consensus 120 ~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l 153 (159)
T PRK12527 120 EGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRM 153 (159)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 5789999999999999999998876666665543
No 283
>KOG3134 consensus Predicted membrane protein [Function unknown]
Probab=50.27 E-value=4.9 Score=40.11 Aligned_cols=32 Identities=25% Similarity=0.604 Sum_probs=25.1
Q ss_pred CCCCCCCCCCCcc-cccCCC-Cccccccccceec
Q 046187 1 MKCPYCSAAQGRC-ATTSTG-RSITECGSCGRVI 32 (510)
Q Consensus 1 m~Cp~C~~~~~~i-~D~~~G-d~~~VC~~CG~Vl 32 (510)
|+|-+||+....+ .+++.| ---+.|.+|+.|+
T Consensus 1 ~~CVeCg~~vksLy~~Ys~g~irlt~C~nC~e~v 34 (225)
T KOG3134|consen 1 YRCVECGSEVKSLYTQYSPGNIRLTKCPNCQEVV 34 (225)
T ss_pred CcccccCchHHHHHHhcCCCcEEEeeCCchhhHH
Confidence 7899999954444 568889 3347899999998
No 284
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=50.12 E-value=27 Score=34.24 Aligned_cols=33 Identities=9% Similarity=0.155 Sum_probs=29.5
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 286 DKRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 286 g~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
....+.+|||+.+++|+.||++..+.+++.++.
T Consensus 146 AqGkTnKEIAe~L~IS~rTVkth~srImkKLgV 178 (198)
T PRK15201 146 ASGYHLSETAALLSLSEEQTKSLRRSIMRKLHV 178 (198)
T ss_pred HCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 347889999999999999999999999988775
No 285
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=49.86 E-value=17 Score=34.02 Aligned_cols=32 Identities=16% Similarity=0.190 Sum_probs=26.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
...+.+|||+.+|+|+.||+.++......+..
T Consensus 132 e~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 163 (179)
T PRK12543 132 HDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQ 163 (179)
T ss_pred ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 36799999999999999999887766665554
No 286
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=49.79 E-value=65 Score=23.83 Aligned_cols=23 Identities=9% Similarity=0.258 Sum_probs=21.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 046187 193 RTLQEISIAANVPQKEIGKYIKI 215 (510)
Q Consensus 193 rTLkEIa~vt~VskkeIgr~yk~ 215 (510)
.|+++||..++|+...+.+.++.
T Consensus 28 ~s~~~vA~~~~vs~~TV~ri~~~ 50 (52)
T PF13542_consen 28 RSFKDVARELGVSWSTVRRIFDR 50 (52)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHh
Confidence 89999999999999999998865
No 287
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=49.77 E-value=20 Score=34.43 Aligned_cols=40 Identities=13% Similarity=0.022 Sum_probs=32.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccCCCCCCC
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDLLPSNYTP 326 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Lip~~~~~ 326 (510)
...+.+|||+.+|++..||+.++..-...+..++++....
T Consensus 148 ~g~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~~~~~ 187 (196)
T PRK12535 148 LGYTYEEAAKIADVRVGTIRSRVARARADLIAATATGQAS 187 (196)
T ss_pred hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhccccch
Confidence 4678999999999999999999887777777776666533
No 288
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=49.74 E-value=48 Score=33.57 Aligned_cols=56 Identities=13% Similarity=-0.002 Sum_probs=42.9
Q ss_pred hhhhHHHHHhhcC-CCHHHHHHHHHHHHHHHhccccCCCChHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHH
Q 046187 231 IAVHMPRFCTLLQ-LNKSAQVLATHIGEVVINKCFCTRRNPISISAAAIYLACQLEDKRKTQAEICKVTGLTEVTLRKVY 309 (510)
Q Consensus 231 p~~~I~Rfcs~L~-L~~~V~~~A~~Ia~~a~~~~l~~GRsP~sIAAAaIYlAarl~g~~~t~keIa~vagVSe~TIRkrY 309 (510)
|..++.++-+.+. |++.-.++|..|++. |.-+ ...+.++||+.++||+.||-+..
T Consensus 12 ~~~i~~~i~~~~~~Lt~~e~~Ia~yil~~-----------~~~v-------------~~~si~~lA~~~~vS~aTi~Rf~ 67 (292)
T PRK11337 12 GIGLGPYIRMKQEGLTPLESRVVEWLLKP-----------GDLS-------------EATALKDIAEALAVSEAMIVKVA 67 (292)
T ss_pred chhHHHHHHHHHhhcCHHHHHHHHHHHhC-----------HHHH-------------HhcCHHHHHHHhCCChHHHHHHH
Confidence 6778888888886 888888888888753 3332 24578999999999999997554
Q ss_pred H
Q 046187 310 K 310 (510)
Q Consensus 310 K 310 (510)
|
T Consensus 68 k 68 (292)
T PRK11337 68 K 68 (292)
T ss_pred H
Confidence 3
No 289
>PF12773 DZR: Double zinc ribbon
Probab=49.71 E-value=11 Score=28.13 Aligned_cols=28 Identities=21% Similarity=0.570 Sum_probs=16.5
Q ss_pred CCCCCCCCCCcccccCCCCccccccccceeccc
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRVIAE 34 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vlee 34 (510)
+|++||.... ...... .+|..||..+..
T Consensus 14 fC~~CG~~l~---~~~~~~--~~C~~Cg~~~~~ 41 (50)
T PF12773_consen 14 FCPHCGTPLP---PPDQSK--KICPNCGAENPP 41 (50)
T ss_pred CChhhcCChh---hccCCC--CCCcCCcCCCcC
Confidence 5788877332 111222 689999987644
No 290
>PRK15320 transcriptional activator SprB; Provisional
Probab=49.66 E-value=24 Score=35.23 Aligned_cols=35 Identities=20% Similarity=0.159 Sum_probs=31.2
Q ss_pred HcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 284 LEDKRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 284 l~g~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
++....+++|||+.+++|+.||+++...|.+.++.
T Consensus 175 LLAkG~SNKEIAekL~LS~KTVSTYKnRLLeKLgA 209 (251)
T PRK15320 175 LLSSGHPAIELAKKFGLGTKTVSIYRKKVMYRLGM 209 (251)
T ss_pred HHHcCCCHHHHHHHhccchhhHHHHHHHHHHHcCC
Confidence 34467899999999999999999999999998885
No 291
>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=49.59 E-value=36 Score=25.92 Aligned_cols=39 Identities=18% Similarity=0.271 Sum_probs=29.1
Q ss_pred HHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046187 180 AALVQAIREAQEPRTLQEISIAANVPQKEIGKYIKILGE 218 (510)
Q Consensus 180 ACLYIACR~~~~PrTLkEIa~vt~VskkeIgr~yk~L~k 218 (510)
.+|++.....+...++.||++.+++++-.+.+.++.|.+
T Consensus 9 ~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~ 47 (62)
T PF12802_consen 9 RVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEK 47 (62)
T ss_dssp HHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 344444444444479999999999999999999998866
No 292
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=49.58 E-value=24 Score=34.67 Aligned_cols=35 Identities=14% Similarity=0.097 Sum_probs=30.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccCC
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDLLP 321 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Lip 321 (510)
...+.+|||+.+|+|+.||++++......+...+.
T Consensus 149 eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l~ 183 (216)
T PRK12533 149 EDMSYREIAAIADVPVGTVMSRLARARRRLAALLG 183 (216)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHc
Confidence 47899999999999999999998887777777653
No 293
>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=49.55 E-value=17 Score=34.35 Aligned_cols=34 Identities=15% Similarity=0.056 Sum_probs=27.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccC
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDLL 320 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Li 320 (510)
...+.+|||+.+|+|+.||+.++..-...+...+
T Consensus 146 ~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 179 (193)
T TIGR02947 146 EGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQL 179 (193)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4689999999999999999988776666555433
No 294
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=49.47 E-value=21 Score=32.80 Aligned_cols=32 Identities=22% Similarity=0.195 Sum_probs=27.2
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHhhccc
Q 046187 288 RKTQAEICKVTGLTEVTLRKVYKELLENWDDL 319 (510)
Q Consensus 288 ~~t~keIa~vagVSe~TIRkrYKEL~e~l~~L 319 (510)
..+.+|||+.+|+|+.||+.+.......+...
T Consensus 135 g~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~ 166 (169)
T TIGR02954 135 DLTIKEIAEVMNKPEGTVKTYLHRALKKLKKR 166 (169)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 68999999999999999999887777666543
No 295
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=49.39 E-value=7.4 Score=30.91 Aligned_cols=21 Identities=33% Similarity=0.781 Sum_probs=16.0
Q ss_pred CCCCCCCCCCcccccCCCCccccccccceec
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRVI 32 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vl 32 (510)
+|+.||.++. . .+|..||...
T Consensus 7 ~C~~CgvYTL--------k--~~CP~CG~~t 27 (56)
T PRK13130 7 KCPKCGVYTL--------K--EICPVCGGKT 27 (56)
T ss_pred ECCCCCCEEc--------c--ccCcCCCCCC
Confidence 5999988553 2 7899999764
No 296
>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=49.39 E-value=21 Score=25.53 Aligned_cols=22 Identities=18% Similarity=0.246 Sum_probs=19.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHH
Q 046187 289 KTQAEICKVTGLTEVTLRKVYK 310 (510)
Q Consensus 289 ~t~keIa~vagVSe~TIRkrYK 310 (510)
.+.+|+|+.+||+..||.+..+
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~ 23 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIH 23 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
Confidence 4789999999999999997764
No 297
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=49.35 E-value=69 Score=30.18 Aligned_cols=29 Identities=24% Similarity=0.337 Sum_probs=26.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 046187 191 EPRTLQEISIAANVPQKEIGKYIKILGEA 219 (510)
Q Consensus 191 ~PrTLkEIa~vt~VskkeIgr~yk~L~k~ 219 (510)
.|.|.+|||+.+|++...+.|.+++|++.
T Consensus 167 ~~~t~~~lA~~lG~tr~tvsR~l~~l~~~ 195 (211)
T PRK11753 167 IKITRQEIGRIVGCSREMVGRVLKMLEDQ 195 (211)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 58899999999999999999999998774
No 298
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=49.34 E-value=67 Score=32.31 Aligned_cols=132 Identities=15% Similarity=0.146 Sum_probs=79.4
Q ss_pred HHHHHHHHHHHhCCCHHHHHHHHHHHHHHHhCCccCCccHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHH
Q 046187 135 AYLQIIDVASILGLDYDICDHAFQLFRDCCSATCLRNRSVEALATAALVQAIREAQEPRTLQEISIAANVPQKEIGKYIK 214 (510)
Q Consensus 135 a~~~I~~ic~~L~LP~~VidtA~~LyK~a~e~~~lrGRs~eaVaAACLYIACR~~~~PrTLkEIa~vt~VskkeIgr~yk 214 (510)
....|....++.++..--..+..++++.+++.+. -.|..|++-+++++...|++-++
T Consensus 71 ~~ED~e~~~~~~~~~elr~~rIvRl~~EAy~Qgg-----------------------lLT~~Dla~LL~~S~~TI~~~i~ 127 (220)
T PF07900_consen 71 DPEDIEMRNEKYGLSELRKHRIVRLTNEAYDQGG-----------------------LLTQEDLAMLLGISPRTISKDIK 127 (220)
T ss_pred CHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHcCC-----------------------cccHHHHHHHHCCCHHHHHHHHH
Confidence 3345555556566666666777788888887542 25788999999999999999999
Q ss_pred HHHHHhcccCCCC----Ccch-----hhhHHHHHhhcCCCHHHHHHHHHHHHHHHhccccCCCChHHHHHHHHHHH----
Q 046187 215 ILGEALQLSQPIN----SNSI-----AVHMPRFCTLLQLNKSAQVLATHIGEVVINKCFCTRRNPISISAAAIYLA---- 281 (510)
Q Consensus 215 ~L~k~L~i~~pv~----~~~p-----~~~I~Rfcs~L~L~~~V~~~A~~Ia~~a~~~~l~~GRsP~sIAAAaIYlA---- 281 (510)
.+.++.+.-.|.- +..| ...|..|...... .++.+...+ +|.+| ==|+-
T Consensus 128 ~yq~e~g~vvPtrG~i~DiGp~~tHK~~ii~~~l~g~~~-~eiar~t~H--------------S~~av---~rYi~~F~r 189 (220)
T PF07900_consen 128 EYQKEHGVVVPTRGTIHDIGPGVTHKKIIIRLYLKGKPT-PEIARRTNH--------------SPEAV---DRYIKDFKR 189 (220)
T ss_pred HHHHHcCceeccCCcccccCCcchHHHHHHHHHHcCCCH-HHHHHHhcc--------------CHHHH---HHHHHhhHH
Confidence 9999977654421 1111 1223333332111 122222211 11111 11111
Q ss_pred -HHHcCCCCCHHHHHHHhCCCHHHHHH
Q 046187 282 -CQLEDKRKTQAEICKVTGLTEVTLRK 307 (510)
Q Consensus 282 -arl~g~~~t~keIa~vagVSe~TIRk 307 (510)
..+.+...+..+|+.++|.|+..|..
T Consensus 190 V~~l~~~~~~~~eia~~tg~S~~Lv~e 216 (220)
T PF07900_consen 190 VLMLYEKGMSPEEIAFITGMSERLVKE 216 (220)
T ss_pred hHHHHHcCCCHHHHHHHHCCCHHHHHH
Confidence 12345678899999999999998875
No 299
>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=49.19 E-value=11 Score=26.56 Aligned_cols=24 Identities=29% Similarity=0.671 Sum_probs=15.3
Q ss_pred CCCCCCCCCCcccccCCCCccccccccce
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGR 30 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~ 30 (510)
+|.+||.... ...++ ..-|.+||.
T Consensus 2 ~C~~Cg~~~~----~~~~~-~irC~~CG~ 25 (32)
T PF03604_consen 2 ICGECGAEVE----LKPGD-PIRCPECGH 25 (32)
T ss_dssp BESSSSSSE-----BSTSS-TSSBSSSS-
T ss_pred CCCcCCCeeE----cCCCC-cEECCcCCC
Confidence 5899988322 23444 378999996
No 300
>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=49.15 E-value=39 Score=30.18 Aligned_cols=38 Identities=32% Similarity=0.321 Sum_probs=30.6
Q ss_pred HHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 277 AIYLACQLEDKRKTQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 277 aIYlAarl~g~~~t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
.+|++. ..+...+..+|++.++++..+++++.+.|.+.
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 23456899999999999999999999999873
No 301
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=49.08 E-value=20 Score=33.50 Aligned_cols=32 Identities=22% Similarity=0.199 Sum_probs=27.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
...+.+|||+.+|+|++|+++++....+.+..
T Consensus 148 ~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 179 (182)
T PRK12537 148 DGCSHAEIAQRLGAPLGTVKAWIKRSLKALRE 179 (182)
T ss_pred cCCCHHHHHHHHCCChhhHHHHHHHHHHHHHH
Confidence 47899999999999999999998777666544
No 302
>PF15616 TerY-C: TerY-C metal binding domain
Probab=48.92 E-value=8.4 Score=35.63 Aligned_cols=20 Identities=30% Similarity=0.946 Sum_probs=12.7
Q ss_pred CCCCCCCCCCcccccCCCCccccccccceec
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRVI 32 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vl 32 (510)
-||+||.. .|. .+| +||.|+
T Consensus 79 gCP~CGn~--------~~f--a~C-~CGkl~ 98 (131)
T PF15616_consen 79 GCPHCGNQ--------YAF--AVC-GCGKLF 98 (131)
T ss_pred CCCCCcCh--------hcE--EEe-cCCCEE
Confidence 39999883 344 555 566655
No 303
>PRK09483 response regulator; Provisional
Probab=48.82 E-value=27 Score=32.44 Aligned_cols=32 Identities=16% Similarity=0.162 Sum_probs=28.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
...+.++||+.+++|+.||++..+.|+..++.
T Consensus 162 ~G~~~~~Ia~~l~is~~TV~~~~~~i~~Kl~v 193 (217)
T PRK09483 162 KGQKVNEISEQLNLSPKTVNSYRYRMFSKLNI 193 (217)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCC
Confidence 56789999999999999999999999998874
No 304
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=48.80 E-value=20 Score=33.39 Aligned_cols=34 Identities=15% Similarity=0.033 Sum_probs=28.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccC
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDLL 320 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Li 320 (510)
...+.+|||+.+|+++.||++++......+...+
T Consensus 153 ~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 153 EGLSYEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 5789999999999999999999877777665543
No 305
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=48.80 E-value=7.8 Score=28.40 Aligned_cols=28 Identities=25% Similarity=0.529 Sum_probs=18.2
Q ss_pred CCCCCCCCCCcccc--------cCCCCcccccccccee
Q 046187 2 KCPYCSAAQGRCAT--------TSTGRSITECGSCGRV 31 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D--------~~~Gd~~~VC~~CG~V 31 (510)
.||.|+........ ..+=. .+|.+||..
T Consensus 2 ~Cp~C~~~~a~~~q~Q~RsaDE~mT~f--y~C~~C~~~ 37 (40)
T smart00440 2 PCPKCGNREATFFQLQTRSADEPMTVF--YVCTKCGHR 37 (40)
T ss_pred cCCCCCCCeEEEEEEcccCCCCCCeEE--EEeCCCCCE
Confidence 69999985544321 22334 789999964
No 306
>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=48.56 E-value=21 Score=27.02 Aligned_cols=20 Identities=20% Similarity=0.471 Sum_probs=18.0
Q ss_pred CHHHHHHHhCCCHHHHHHHH
Q 046187 194 TLQEISIAANVPQKEIGKYI 213 (510)
Q Consensus 194 TLkEIa~vt~VskkeIgr~y 213 (510)
|++|||..+||+...+.|++
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 78999999999999988774
No 307
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=48.39 E-value=4.9 Score=31.24 Aligned_cols=31 Identities=26% Similarity=0.644 Sum_probs=16.9
Q ss_pred CCCCCCCCC--CcccccCCCCccccccccceec
Q 046187 2 KCPYCSAAQ--GRCATTSTGRSITECGSCGRVI 32 (510)
Q Consensus 2 ~Cp~C~~~~--~~i~D~~~Gd~~~VC~~CG~Vl 32 (510)
.|..|+-.- ..+.+-..|++...|.+||++|
T Consensus 24 ~C~gC~~~l~~~~~~~i~~~~~i~~Cp~CgRiL 56 (56)
T PF02591_consen 24 TCSGCHMELPPQELNEIRKGDEIVFCPNCGRIL 56 (56)
T ss_pred ccCCCCEEcCHHHHHHHHcCCCeEECcCCCccC
Confidence 366665411 1112334555567888888764
No 308
>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=48.35 E-value=46 Score=25.20 Aligned_cols=27 Identities=30% Similarity=0.388 Sum_probs=24.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 289 KTQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 289 ~t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
.+..+|++.++++..||++..+.|...
T Consensus 21 ~~~~ei~~~~~i~~~~i~~~l~~L~~~ 47 (78)
T cd00090 21 LTVSELAERLGLSQSTVSRHLKKLEEA 47 (78)
T ss_pred cCHHHHHHHHCcCHhHHHHHHHHHHHC
Confidence 889999999999999999999988653
No 309
>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=48.30 E-value=20 Score=26.06 Aligned_cols=19 Identities=42% Similarity=0.560 Sum_probs=17.2
Q ss_pred CHHHHHHHhCCCHHHHHHH
Q 046187 290 TQAEICKVTGLTEVTLRKV 308 (510)
Q Consensus 290 t~keIa~vagVSe~TIRkr 308 (510)
+.+|+|+.+||+..||+..
T Consensus 2 ~~~e~a~~~gv~~~tlr~~ 20 (49)
T cd04761 2 TIGELAKLTGVSPSTLRYY 20 (49)
T ss_pred cHHHHHHHHCcCHHHHHHH
Confidence 6789999999999999955
No 310
>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=48.28 E-value=28 Score=26.25 Aligned_cols=37 Identities=30% Similarity=0.515 Sum_probs=28.5
Q ss_pred HHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046187 182 LVQAIREAQEPRTLQEISIAANVPQKEIGKYIKILGE 218 (510)
Q Consensus 182 LYIACR~~~~PrTLkEIa~vt~VskkeIgr~yk~L~k 218 (510)
|.-+-..++.+.++.||++.+++++..+-|....|.+
T Consensus 8 iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~ 44 (52)
T PF09339_consen 8 ILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVE 44 (52)
T ss_dssp HHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4444456677789999999999999999888877755
No 311
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=48.18 E-value=9.9 Score=31.00 Aligned_cols=28 Identities=21% Similarity=0.681 Sum_probs=20.0
Q ss_pred CCCCCCCCCcccccCCCCcccccccccee
Q 046187 3 CPYCSAAQGRCATTSTGRSITECGSCGRV 31 (510)
Q Consensus 3 Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~V 31 (510)
||-||..... +.+..|-...+|..||..
T Consensus 9 CPFCG~~~~~-v~~~~g~~~v~C~~CgA~ 36 (64)
T PRK09710 9 CPFCGCPSVT-VKAISGYYRAKCNGCESR 36 (64)
T ss_pred CCCCCCceeE-EEecCceEEEEcCCCCcC
Confidence 9999985433 444566544899999984
No 312
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=48.15 E-value=46 Score=25.21 Aligned_cols=33 Identities=18% Similarity=0.401 Sum_probs=28.7
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 286 DKRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 286 g~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
....+.++||...++|+.|++.-.+.++..++.
T Consensus 17 ~~G~s~~eia~~l~is~~tV~~h~~~i~~Kl~~ 49 (65)
T COG2771 17 AQGKSNKEIARILGISEETVKTHLRNIYRKLGV 49 (65)
T ss_pred HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Confidence 345899999999999999999998888887765
No 313
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=48.07 E-value=30 Score=32.86 Aligned_cols=30 Identities=20% Similarity=0.226 Sum_probs=26.4
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHhhc
Q 046187 288 RKTQAEICKVTGLTEVTLRKVYKELLENWD 317 (510)
Q Consensus 288 ~~t~keIa~vagVSe~TIRkrYKEL~e~l~ 317 (510)
..|.+|||+.+|||+.||+++++.+...+.
T Consensus 151 Gls~~EIA~~lgiS~~tV~r~l~~aR~~l~ 180 (185)
T PF07638_consen 151 GLSVEEIAERLGISERTVRRRLRRARAWLR 180 (185)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 569999999999999999999998876554
No 314
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=47.72 E-value=19 Score=33.22 Aligned_cols=35 Identities=14% Similarity=0.121 Sum_probs=29.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccCC
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDLLP 321 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Lip 321 (510)
...+.+|||+.+|+|+.||+.++......+...+.
T Consensus 135 ~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~ 169 (175)
T PRK12518 135 EDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQ 169 (175)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999999998887777766543
No 315
>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=47.71 E-value=6.2 Score=28.45 Aligned_cols=29 Identities=21% Similarity=0.464 Sum_probs=17.9
Q ss_pred CCCCCCCCCCcccccCCCCccccccccceec
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRVI 32 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vl 32 (510)
.||.||..=.+..++-.-+ .+|-.||--|
T Consensus 3 ~C~~Cg~~Yh~~~~pP~~~--~~Cd~cg~~L 31 (36)
T PF05191_consen 3 ICPKCGRIYHIEFNPPKVE--GVCDNCGGEL 31 (36)
T ss_dssp EETTTTEEEETTTB--SST--TBCTTTTEBE
T ss_pred CcCCCCCccccccCCCCCC--CccCCCCCee
Confidence 6999988333334432232 7999999755
No 316
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=47.64 E-value=29 Score=33.91 Aligned_cols=32 Identities=9% Similarity=0.037 Sum_probs=29.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
...+.++||+.+++|+.||++.-..|++.++.
T Consensus 148 ~G~snkeIA~~L~iS~~TV~~h~~~I~~KLgv 179 (207)
T PRK11475 148 RGYSMPQIAEQLERNIKTIRAHKFNVMSKLGV 179 (207)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence 47899999999999999999999999988774
No 317
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=47.56 E-value=29 Score=31.27 Aligned_cols=31 Identities=13% Similarity=0.095 Sum_probs=26.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWD 317 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~ 317 (510)
...+.+|||+.+|+|..||+.+.......+.
T Consensus 126 ~g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr 156 (159)
T TIGR02989 126 RGVSLTALAEQLGRTVNAVYKALSRLRVRLR 156 (159)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 4789999999999999999998877766554
No 318
>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=47.33 E-value=21 Score=30.25 Aligned_cols=23 Identities=30% Similarity=0.362 Sum_probs=20.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHH
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVY 309 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrY 309 (510)
...++++||+.+|||..||+..+
T Consensus 18 ~~~ti~dvA~~~gvS~~TVsr~L 40 (80)
T TIGR02844 18 TKATVRETAKVFGVSKSTVHKDV 40 (80)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHh
Confidence 46789999999999999999855
No 319
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=47.01 E-value=11 Score=28.39 Aligned_cols=25 Identities=24% Similarity=0.636 Sum_probs=16.6
Q ss_pred CCCCCCCCCCcccccCCCCcccccccccee
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRV 31 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~V 31 (510)
+|.+||... . .+ ..+ ...|.+||.=
T Consensus 4 ~C~~Cg~~~-~-~~-~~~--~irC~~CG~r 28 (44)
T smart00659 4 ICGECGREN-E-IK-SKD--VVRCRECGYR 28 (44)
T ss_pred ECCCCCCEe-e-cC-CCC--ceECCCCCce
Confidence 599999832 2 23 233 3899999963
No 320
>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=46.87 E-value=37 Score=26.27 Aligned_cols=31 Identities=26% Similarity=0.453 Sum_probs=24.5
Q ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 285 EDKRKTQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 285 ~g~~~t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
.+.+.++++|++.++++..++.+..+.|.+.
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 3567899999999999999999999988875
No 321
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=46.86 E-value=11 Score=29.76 Aligned_cols=25 Identities=36% Similarity=0.874 Sum_probs=18.2
Q ss_pred CCCCCCCCCCcccccCCCCccccccccceec
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRVI 32 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vl 32 (510)
+|+.||.. + ..|+..+||..||.+.
T Consensus 7 ~C~~Cg~~---~---~~~dDiVvCp~Cgapy 31 (54)
T PF14446_consen 7 KCPVCGKK---F---KDGDDIVVCPECGAPY 31 (54)
T ss_pred cChhhCCc---c---cCCCCEEECCCCCCcc
Confidence 69999872 2 2344479999999976
No 322
>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=46.47 E-value=18 Score=36.38 Aligned_cols=23 Identities=22% Similarity=0.459 Sum_probs=20.6
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHH
Q 046187 288 RKTQAEICKVTGLTEVTLRKVYK 310 (510)
Q Consensus 288 ~~t~keIa~vagVSe~TIRkrYK 310 (510)
+.|++|||+.+|||..|+++++.
T Consensus 1 ~~ti~dIA~~agVS~sTVSr~Ln 23 (311)
T TIGR02405 1 KLTIKDIARLAGVGKSTVSRVLN 23 (311)
T ss_pred CCcHHHHHHHhCCCHHHHHHHhC
Confidence 45899999999999999998884
No 323
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=46.40 E-value=15 Score=34.90 Aligned_cols=33 Identities=12% Similarity=0.204 Sum_probs=26.7
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccC
Q 046187 288 RKTQAEICKVTGLTEVTLRKVYKELLENWDDLL 320 (510)
Q Consensus 288 ~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Li 320 (510)
..+.+|||+.+|+|+.||+.++..-...+...+
T Consensus 150 g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 182 (189)
T PRK12530 150 ELSSEQICQECDISTSNLHVLLYRARLQLQACL 182 (189)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 788999999999999999988776665555433
No 324
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=46.37 E-value=21 Score=32.63 Aligned_cols=34 Identities=21% Similarity=0.129 Sum_probs=27.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccC
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDLL 320 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Li 320 (510)
...+.++||+.+|+++.||+.+.+.....+...+
T Consensus 143 ~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 176 (182)
T PRK09652 143 EGLSYEEIAEIMGCPIGTVRSRIFRAREALRAKL 176 (182)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4779999999999999999988776666665543
No 325
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=46.24 E-value=37 Score=25.95 Aligned_cols=36 Identities=11% Similarity=0.049 Sum_probs=29.8
Q ss_pred HhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhcc
Q 046187 187 REAQEPRTLQEISIAANVPQKEIGKYIKILGEALQL 222 (510)
Q Consensus 187 R~~~~PrTLkEIa~vt~VskkeIgr~yk~L~k~L~i 222 (510)
-.-..-.++.+++..++|+...+.|+++.+...|..
T Consensus 14 ~~LR~~~~~~~La~~FgIs~stvsri~~~~~~~L~~ 49 (53)
T PF13613_consen 14 MYLRLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQ 49 (53)
T ss_pred HHHHcCCcHhHHhhheeecHHHHHHHHHHHHHHHHH
Confidence 334456789999999999999999999998887753
No 326
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=46.21 E-value=22 Score=34.15 Aligned_cols=34 Identities=9% Similarity=0.106 Sum_probs=28.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccC
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDLL 320 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Li 320 (510)
...+.+|||+.+|+|+.||+.++..-...+...+
T Consensus 168 ~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 168 QELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4789999999999999999998877766665544
No 327
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=46.17 E-value=8.5 Score=36.90 Aligned_cols=10 Identities=30% Similarity=1.055 Sum_probs=8.5
Q ss_pred ccccccceec
Q 046187 23 TECGSCGRVI 32 (510)
Q Consensus 23 ~VC~~CG~Vl 32 (510)
.+|.+||.+.
T Consensus 131 ~~C~~CgkiY 140 (165)
T COG1656 131 YRCPKCGKIY 140 (165)
T ss_pred eECCCCcccc
Confidence 5699999986
No 328
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=46.09 E-value=29 Score=31.97 Aligned_cols=31 Identities=16% Similarity=0.113 Sum_probs=26.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWD 317 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~ 317 (510)
...+.+|||+.+|+++.||+.+++.-...+-
T Consensus 133 eg~s~~EIA~~l~is~~tV~~~l~ra~~~~~ 163 (168)
T PRK12525 133 EGLTYVEIGERLGVSLSRIHQYMVEAFKCCY 163 (168)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4789999999999999999988876665543
No 329
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=46.09 E-value=22 Score=33.73 Aligned_cols=34 Identities=12% Similarity=0.168 Sum_probs=29.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccC
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDLL 320 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Li 320 (510)
...+.+|||+.+|+|..||+.++......+...+
T Consensus 169 e~~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~l 202 (208)
T PRK08295 169 DGKSYQEIAEELNRHVKSIDNALQRVKRKLEKYL 202 (208)
T ss_pred ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4789999999999999999999988877776544
No 330
>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=46.03 E-value=14 Score=28.54 Aligned_cols=26 Identities=15% Similarity=0.424 Sum_probs=19.0
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046187 286 DKRKTQAEICKVTGLTEVTLRKVYKE 311 (510)
Q Consensus 286 g~~~t~keIa~vagVSe~TIRkrYKE 311 (510)
....++.+||..+||+..||++.+|.
T Consensus 20 e~g~s~~~ia~~fgv~~sTv~~I~K~ 45 (53)
T PF04218_consen 20 EEGESKRDIAREFGVSRSTVSTILKN 45 (53)
T ss_dssp HCTT-HHHHHHHHT--CCHHHHHHHC
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHHh
Confidence 33448999999999999999988764
No 331
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=46.00 E-value=19 Score=32.96 Aligned_cols=35 Identities=20% Similarity=0.065 Sum_probs=30.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccCC
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDLLP 321 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Lip 321 (510)
...+.+|||+.+|+++.||+.++....+.+...+.
T Consensus 123 ~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~ 157 (165)
T PRK09644 123 HELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLK 157 (165)
T ss_pred hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 47899999999999999999998888877776553
No 332
>PRK12495 hypothetical protein; Provisional
Probab=45.68 E-value=12 Score=37.56 Aligned_cols=28 Identities=21% Similarity=0.592 Sum_probs=21.4
Q ss_pred CCCCCCCCCCcccccCCCCccccccccceecccc
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRVIAER 35 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vleer 35 (510)
.|++||.. +. --.|. ++|..|+.++.++
T Consensus 44 hC~~CG~P--Ip--a~pG~--~~Cp~CQ~~~~~~ 71 (226)
T PRK12495 44 HCDECGDP--IF--RHDGQ--EFCPTCQQPVTED 71 (226)
T ss_pred hcccccCc--cc--CCCCe--eECCCCCCccccc
Confidence 59999983 32 23787 9999999988653
No 333
>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=45.51 E-value=1.3e+02 Score=26.67 Aligned_cols=80 Identities=19% Similarity=0.220 Sum_probs=49.0
Q ss_pred HHHHHHHHHhCCCHHHHHHHHHHHHHHHh---CCccCCc-cHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHH
Q 046187 137 LQIIDVASILGLDYDICDHAFQLFRDCCS---ATCLRNR-SVEALATAALVQAIREAQEPRTLQEISIAANVPQKEIGKY 212 (510)
Q Consensus 137 ~~I~~ic~~L~LP~~VidtA~~LyK~a~e---~~~lrGR-s~eaVaAACLYIACR~~~~PrTLkEIa~vt~VskkeIgr~ 212 (510)
..+.++|..+++....+. .++++... ....+|+ ..+ .=-+.+.=.+.--.|+.|++..++|+...|.+.
T Consensus 19 ~s~~eaa~~F~VS~~Tv~---~W~k~~~~G~~~~k~r~~~Kid----~~~L~~~v~~~pd~tl~Ela~~l~Vs~~ti~~~ 91 (119)
T PF01710_consen 19 KSIREAAKRFGVSRNTVY---RWLKRKETGDLEPKPRGRKKID----RDELKALVEENPDATLRELAERLGVSPSTIWRA 91 (119)
T ss_pred chHHHHHHHhCcHHHHHH---HHHHhccccccccccccccccc----HHHHHHHHHHCCCcCHHHHHHHcCCCHHHHHHH
Confidence 357789999998765554 44552222 1122332 111 111333334455689999999999999999988
Q ss_pred HHHHHHHhccc
Q 046187 213 IKILGEALQLS 223 (510)
Q Consensus 213 yk~L~k~L~i~ 223 (510)
++.|.-.+...
T Consensus 92 Lkrlg~t~KK~ 102 (119)
T PF01710_consen 92 LKRLGITRKKK 102 (119)
T ss_pred HHHcCchhccC
Confidence 88776555443
No 334
>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=45.49 E-value=7 Score=41.66 Aligned_cols=75 Identities=13% Similarity=0.085 Sum_probs=0.0
Q ss_pred CCHHHHHHHHHHHHHHH-hccccCCCChHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 244 LNKSAQVLATHIGEVVI-NKCFCTRRNPISISAAAIYLACQLEDKRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 244 L~~~V~~~A~~Ia~~a~-~~~l~~GRsP~sIAAAaIYlAarl~g~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
+++.+...|..|.+... ....+.+..-.+=+.+|+||||..++............++.....++.|+.|.+.|..
T Consensus 12 ~~~~ll~~a~~L~~ls~~~~~~l~~~~EiaR~~iCa~lA~~~l~~~~dl~~~~~~~pl~pk~y~~l~~~~~~~L~~ 87 (353)
T PF05460_consen 12 LPPKLLSKASELYRLSRQKKSSLKPEEEIARAHICAELACERLKEKLDLPYAIKRSPLPPKVYKKLLNTFENLLGN 87 (353)
T ss_dssp ----------------------------------------------------------------------------
T ss_pred CCHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhCCccCchhhcCCCCCCHHHHHHHHHHHHHHHhC
Confidence 34678888888887776 4556667777788899999999999888776666666777765555555555554443
No 335
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=45.34 E-value=27 Score=32.41 Aligned_cols=33 Identities=12% Similarity=0.132 Sum_probs=27.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhccc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDL 319 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~L 319 (510)
...+.++||..+|+|..||+.+.......+..+
T Consensus 155 ~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~~ 187 (189)
T TIGR02984 155 EGLSFAEVAERMDRSEGAVSMLWVRGLARLRQI 187 (189)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 577999999999999999999887776666543
No 336
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=45.33 E-value=21 Score=35.97 Aligned_cols=29 Identities=21% Similarity=0.169 Sum_probs=26.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
..++.+|+++.++||+.|||+..++|.+.
T Consensus 18 ~~v~v~eLa~~l~VS~~TIRRDL~~Le~~ 46 (256)
T PRK10434 18 GKTSVEELAQYFDTTGTTIRKDLVILEHA 46 (256)
T ss_pred CCEEHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 46889999999999999999999997765
No 337
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=45.32 E-value=34 Score=27.57 Aligned_cols=35 Identities=20% Similarity=0.235 Sum_probs=27.8
Q ss_pred hcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhcc
Q 046187 188 EAQEPRTLQEISIAANVPQKEIGKYIKILGEALQL 222 (510)
Q Consensus 188 ~~~~PrTLkEIa~vt~VskkeIgr~yk~L~k~L~i 222 (510)
+.+.|.+-+|||+.++++...+.+....|.++=.+
T Consensus 11 ~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V 45 (62)
T PF04703_consen 11 EQNGPLKTREIADALGLSIYQARYYLEKLEKEGKV 45 (62)
T ss_dssp HHTS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSE
T ss_pred HcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCE
Confidence 33789999999999999999999998888776443
No 338
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=45.31 E-value=10 Score=30.42 Aligned_cols=21 Identities=33% Similarity=0.812 Sum_probs=16.3
Q ss_pred CCCCCCCCCCcccccCCCCccccccccceec
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRVI 32 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vl 32 (510)
+|++|+.++.. ..|..||-+.
T Consensus 7 kC~~cg~YTLk----------e~Cp~CG~~t 27 (59)
T COG2260 7 KCPKCGRYTLK----------EKCPVCGGDT 27 (59)
T ss_pred cCcCCCceeec----------ccCCCCCCcc
Confidence 59999986643 4799999864
No 339
>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=45.28 E-value=22 Score=32.80 Aligned_cols=50 Identities=12% Similarity=0.064 Sum_probs=36.9
Q ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccCC
Q 046187 272 SISAAAIYLACQLEDKRKTQAEICKVTGLTEVTLRKVYKELLENWDDLLP 321 (510)
Q Consensus 272 sIAAAaIYlAarl~g~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Lip 321 (510)
-|+.|++=|..+.-=.++|++||++.+||+.+|.=..|+..++.+..++.
T Consensus 7 ~I~~a~~~Ll~~k~~~~ITV~~I~~~AgvsR~TFY~hF~dK~dLl~~~~~ 56 (176)
T TIGR02366 7 KIAKAFKDLMEVQAFSKISVSDIMSTAQIRRQTFYNHFQDKYELLTWIFE 56 (176)
T ss_pred HHHHHHHHHHHHCCCccCCHHHHHHHhCCCHHHHHHHCCCHHHHHHHHHH
Confidence 46666665554433347999999999999999998888877776665543
No 340
>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=45.09 E-value=55 Score=24.74 Aligned_cols=28 Identities=25% Similarity=0.413 Sum_probs=24.5
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 288 RKTQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 288 ~~t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
+.++.+|++.++++..|+.+..+.|.+.
T Consensus 17 ~~~~~~la~~~~~~~~~~t~~i~~L~~~ 44 (59)
T PF01047_consen 17 GITQSELAEKLGISRSTVTRIIKRLEKK 44 (59)
T ss_dssp SEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred CCCHHHHHHHHCCChhHHHHHHHHHHHC
Confidence 4899999999999999999999988764
No 341
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=44.86 E-value=10 Score=30.49 Aligned_cols=24 Identities=25% Similarity=0.697 Sum_probs=16.9
Q ss_pred CCCCCCCCCCcccccCCCCccccccccce
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGR 30 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~ 30 (510)
.|-+|+....+ +.|| ..-|.+||.
T Consensus 22 iCgdC~~en~l----k~~D-~irCReCG~ 45 (62)
T KOG3507|consen 22 ICGDCGQENTL----KRGD-VIRCRECGY 45 (62)
T ss_pred Eeccccccccc----cCCC-cEehhhcch
Confidence 48888874333 6777 566999986
No 342
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=44.81 E-value=86 Score=26.75 Aligned_cols=39 Identities=13% Similarity=0.296 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046187 273 ISAAAIYLACQLEDKRKTQAEICKVTGLTEVTLRKVYKEL 312 (510)
Q Consensus 273 IAAAaIYlAarl~g~~~t~keIa~vagVSe~TIRkrYKEL 312 (510)
|.-+.-|+... +..++++.+||+.+++|..++.+.+++.
T Consensus 7 ~~~~~~~i~~~-~~~~~~~~~lA~~~~~S~~~l~r~f~~~ 45 (107)
T PRK10219 7 IQTLIAWIDEH-IDQPLNIDVVAKKSGYSKWYLQRMFRTV 45 (107)
T ss_pred HHHHHHHHHHh-cCCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 33444455554 4457999999999999999999888875
No 343
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=44.65 E-value=14 Score=28.83 Aligned_cols=28 Identities=32% Similarity=0.816 Sum_probs=17.7
Q ss_pred CCCCCCCCCCcccccCCCC-----ccccccccce
Q 046187 2 KCPYCSAAQGRCATTSTGR-----SITECGSCGR 30 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd-----~~~VC~~CG~ 30 (510)
-||-||... +.++...+. ....|.+||.
T Consensus 5 PCPFCG~~~-~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 5 PCPFCGSAD-VLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCCCCCCcc-eEeecccCCCCCCEEEEEcCCCCC
Confidence 399997744 434444432 1256999998
No 344
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=44.64 E-value=34 Score=33.61 Aligned_cols=32 Identities=16% Similarity=0.151 Sum_probs=28.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
...+.+|||+.+++|+.|+++....++..+..
T Consensus 169 ~G~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v 200 (216)
T PRK10100 169 IGASNNEIARSLFISENTVKTHLYNLFKKIAV 200 (216)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 37899999999999999999999999887764
No 345
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=44.42 E-value=27 Score=32.51 Aligned_cols=32 Identities=22% Similarity=0.266 Sum_probs=26.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
...+.+|||+.+|+|+.||+++.....+.+..
T Consensus 150 ~~~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~ 181 (186)
T PRK13919 150 QGYTHREAAQLLGLPLGTLKTRARRALSRLKE 181 (186)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 47899999999999999999887766665543
No 346
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=44.41 E-value=42 Score=30.36 Aligned_cols=31 Identities=23% Similarity=0.299 Sum_probs=28.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 288 RKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 288 ~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
+=++|++++..|||=.|+|+++.+|.+.+..
T Consensus 49 rGnlKe~e~~lgiSYPTvR~rLd~ii~~lg~ 79 (113)
T PF09862_consen 49 RGNLKEMEKELGISYPTVRNRLDKIIEKLGY 79 (113)
T ss_pred cCCHHHHHHHHCCCcHHHHHHHHHHHHHhCC
Confidence 3479999999999999999999999999998
No 347
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=44.37 E-value=12 Score=32.54 Aligned_cols=28 Identities=21% Similarity=0.707 Sum_probs=20.9
Q ss_pred CCCCCCCCCCCcccccCCCCccccccccceec
Q 046187 1 MKCPYCSAAQGRCATTSTGRSITECGSCGRVI 32 (510)
Q Consensus 1 m~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vl 32 (510)
..||.|+.. .+--.+.|- -.|..||.++
T Consensus 37 y~CpfCgk~--~vkR~a~GI--W~C~~C~~~~ 64 (90)
T PTZ00255 37 YFCPFCGKH--AVKRQAVGI--WRCKGCKKTV 64 (90)
T ss_pred ccCCCCCCC--ceeeeeeEE--EEcCCCCCEE
Confidence 369999873 333456675 9999999986
No 348
>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=44.23 E-value=46 Score=25.84 Aligned_cols=31 Identities=23% Similarity=0.287 Sum_probs=27.0
Q ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 285 EDKRKTQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 285 ~g~~~t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
.+.+.+..+|++.+|++..|+....+.|.+.
T Consensus 21 ~~~~~t~~ela~~l~~~~~t~s~hL~~L~~a 51 (61)
T PF12840_consen 21 SNGPMTVSELAEELGISQSTVSYHLKKLEEA 51 (61)
T ss_dssp HCSTBEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred cCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 4678999999999999999999999998773
No 349
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=44.20 E-value=32 Score=32.32 Aligned_cols=32 Identities=22% Similarity=0.220 Sum_probs=25.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
...+.+|||+.+|+|+.||+.+++.-.+.+..
T Consensus 156 ~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 187 (194)
T PRK12519 156 EGLSQSEIAKRLGIPLGTVKARARQGLLKLRE 187 (194)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 37899999999999999999777655555443
No 350
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.
Probab=44.06 E-value=26 Score=34.57 Aligned_cols=30 Identities=23% Similarity=0.465 Sum_probs=24.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENW 316 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l 316 (510)
...+.+|||+.+|+|+.||++++......+
T Consensus 197 eg~s~~EIA~~Lgis~~tV~~~l~ra~~~L 226 (234)
T TIGR02835 197 TEKTQKEVADMLGISQSYISRLEKRILKRL 226 (234)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 579999999999999999998875444433
No 351
>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=43.94 E-value=7.4 Score=40.36 Aligned_cols=41 Identities=20% Similarity=0.387 Sum_probs=26.4
Q ss_pred CCCCCCCCCCcc-cccCCCCccccccccceecc-------cceeeccccccccc
Q 046187 2 KCPYCSAAQGRC-ATTSTGRSITECGSCGRVIA-------ERQCQNHHLFHIRA 47 (510)
Q Consensus 2 ~Cp~C~~~~~~i-~D~~~Gd~~~VC~~CG~Vle-------er~Id~~~EwR~fs 47 (510)
+||+|+.. +. .|-.... .||.+||.-.. +.++|.++ |+++.
T Consensus 28 ~c~~c~~~--~~~~~l~~~~--~vc~~c~~h~rl~areRi~~L~D~gs-F~E~~ 76 (285)
T TIGR00515 28 KCPKCGQV--LYTKELERNL--EVCPKCDHHMRMDARERIESLLDEGS-FEEFN 76 (285)
T ss_pred ECCCCcch--hhHHHHHhhC--CCCCCCCCcCcCCHHHHHHHceeCCe-eEEeC
Confidence 79999882 22 3444455 89999998753 23556554 66653
No 352
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=43.92 E-value=24 Score=33.44 Aligned_cols=33 Identities=15% Similarity=0.199 Sum_probs=26.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhccc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDL 319 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~L 319 (510)
...+.+|||+.+|++..||++++..-...+...
T Consensus 149 ~g~s~~EIA~~lg~s~~tV~~rl~rar~~Lr~~ 181 (192)
T PRK09643 149 QGYSVADAARMLGVAEGTVKSRCARGRARLAEL 181 (192)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 468999999999999999999876555555443
No 353
>COG1309 AcrR Transcriptional regulator [Transcription]
Probab=43.89 E-value=21 Score=31.07 Aligned_cols=44 Identities=25% Similarity=0.234 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHcCC-CCCHHHHHHHhCCCHHHHHHHHHHHHHhhc
Q 046187 273 ISAAAIYLACQLEDK-RKTQAEICKVTGLTEVTLRKVYKELLENWD 317 (510)
Q Consensus 273 IAAAaIYlAarl~g~-~~t~keIa~vagVSe~TIRkrYKEL~e~l~ 317 (510)
|..+++.+... .|+ ..|.++|++.+||+..||-..|+.-.+.+.
T Consensus 17 ii~aa~~l~~~-~G~~~~t~~~Ia~~agvs~~~~Y~~f~~K~~l~~ 61 (201)
T COG1309 17 ILDAALRLFAE-KGYAATTVDEIAKAAGVSKGTLYRHFPSKEDLLL 61 (201)
T ss_pred HHHHHHHHHHH-cCcCCCCHHHHHHHhCCCcchhHHHcCCHHHHHH
Confidence 44455544443 675 589999999999999999988875444333
No 354
>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=43.81 E-value=21 Score=29.37 Aligned_cols=26 Identities=19% Similarity=0.323 Sum_probs=19.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKEL 312 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL 312 (510)
...+..|||+.++||+.||-+..|.|
T Consensus 33 ~~~si~elA~~~~vS~sti~Rf~kkL 58 (77)
T PF01418_consen 33 AFMSISELAEKAGVSPSTIVRFCKKL 58 (77)
T ss_dssp CT--HHHHHHHCTS-HHHHHHHHHHC
T ss_pred HHccHHHHHHHcCCCHHHHHHHHHHh
Confidence 36789999999999999998776543
No 355
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=43.77 E-value=63 Score=30.38 Aligned_cols=54 Identities=26% Similarity=0.318 Sum_probs=35.6
Q ss_pred CChHHHHHHHHHHHHHHcC---CCCCHHHHHHHhCCCHHHHHHHHH---HHHHhhcccCC
Q 046187 268 RNPISISAAAIYLACQLED---KRKTQAEICKVTGLTEVTLRKVYK---ELLENWDDLLP 321 (510)
Q Consensus 268 RsP~sIAAAaIYlAarl~g---~~~t~keIa~vagVSe~TIRkrYK---EL~e~l~~Lip 321 (510)
-++.-+=||.|+..-.++. .++|+.+||+.+||++.|+=+.-+ +|.+++..+..
T Consensus 11 L~~~Q~kAa~ll~~ne~~~~~~~r~T~~eiAee~Gis~~tLYrWr~~~~~Fiey~n~la~ 70 (142)
T PF13022_consen 11 LTLQQRKAAQLLVENELMPENGERRTQAEIAEEVGISRSTLYRWRQQNKAFIEYKNELAD 70 (142)
T ss_dssp S-HHHHHHHHHHHHHHHS------S-HHHHHHHHTS-HHHHHHHHHH-HHHHHHHHHHHH
T ss_pred cCHHHHHHHHHHHHHHHhhhccccchHHHHHHHhCCCHHHHHHHHhcCHHHHHHHHHHHH
Confidence 3566677777777777765 469999999999999999965542 46666665543
No 356
>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=43.72 E-value=9.9 Score=33.02 Aligned_cols=27 Identities=30% Similarity=0.890 Sum_probs=21.5
Q ss_pred CCCCCCCCCCcccccCCCCccccccccceec
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRVI 32 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vl 32 (510)
.||.|+... +.-.+.|- -.|..||.++
T Consensus 37 ~Cp~Cgk~~--vkR~a~GI--W~C~~C~~~~ 63 (90)
T PF01780_consen 37 TCPFCGKTS--VKRVATGI--WKCKKCGKKF 63 (90)
T ss_dssp EESSSSSSE--EEEEETTE--EEETTTTEEE
T ss_pred cCCCCCCce--eEEeeeEE--eecCCCCCEE
Confidence 599999843 44467886 9999999986
No 357
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=43.71 E-value=31 Score=34.62 Aligned_cols=36 Identities=22% Similarity=0.333 Sum_probs=32.8
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccCCCC
Q 046187 288 RKTQAEICKVTGLTEVTLRKVYKELLENWDDLLPSN 323 (510)
Q Consensus 288 ~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Lip~~ 323 (510)
=+|+.|++-.+++|..||++..+++.+.-+.++|-.
T Consensus 105 lLT~~Dla~LL~~S~~TI~~~i~~yq~e~g~vvPtr 140 (220)
T PF07900_consen 105 LLTQEDLAMLLGISPRTISKDIKEYQKEHGVVVPTR 140 (220)
T ss_pred cccHHHHHHHHCCCHHHHHHHHHHHHHHcCceeccC
Confidence 478999999999999999999999999988888755
No 358
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.54 E-value=13 Score=33.99 Aligned_cols=26 Identities=31% Similarity=0.743 Sum_probs=18.9
Q ss_pred CCCCCCCCCCcccc-c-CCCCccccccccceec
Q 046187 2 KCPYCSAAQGRCAT-T-STGRSITECGSCGRVI 32 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D-~-~~Gd~~~VC~~CG~Vl 32 (510)
.||+||+ ..+.| + ... -.|..||.=+
T Consensus 23 rCP~CGe--GrLF~gFLK~~---p~C~aCG~dy 50 (126)
T COG5349 23 RCPRCGE--GRLFRGFLKVV---PACEACGLDY 50 (126)
T ss_pred CCCCCCC--chhhhhhcccC---chhhhccccc
Confidence 5999998 56655 2 333 5899999855
No 359
>PRK09526 lacI lac repressor; Reviewed
Probab=43.45 E-value=21 Score=36.10 Aligned_cols=23 Identities=17% Similarity=0.310 Sum_probs=20.0
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHH
Q 046187 288 RKTQAEICKVTGLTEVTLRKVYK 310 (510)
Q Consensus 288 ~~t~keIa~vagVSe~TIRkrYK 310 (510)
+.|++|||+.+|||..|+++++.
T Consensus 5 ~~ti~dIA~~aGVS~~TVSrvLn 27 (342)
T PRK09526 5 PVTLYDVARYAGVSYQTVSRVLN 27 (342)
T ss_pred CCcHHHHHHHhCCCHHHHHHHhc
Confidence 46899999999999999976664
No 360
>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=43.45 E-value=28 Score=27.13 Aligned_cols=22 Identities=27% Similarity=0.407 Sum_probs=19.1
Q ss_pred CHHHHHHHhCCCHHHHHHHHHH
Q 046187 290 TQAEICKVTGLTEVTLRKVYKE 311 (510)
Q Consensus 290 t~keIa~vagVSe~TIRkrYKE 311 (510)
+.+|||+.+||+..||++..++
T Consensus 2 s~~eva~~~gvs~~tlr~w~~~ 23 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAWERR 23 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHh
Confidence 6789999999999999976654
No 361
>PF12728 HTH_17: Helix-turn-helix domain
Probab=43.38 E-value=27 Score=25.91 Aligned_cols=22 Identities=18% Similarity=0.280 Sum_probs=18.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHH
Q 046187 289 KTQAEICKVTGLTEVTLRKVYK 310 (510)
Q Consensus 289 ~t~keIa~vagVSe~TIRkrYK 310 (510)
.+.+|+|+.+|||..||.+..+
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~ 23 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIR 23 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 4789999999999999986653
No 362
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=43.32 E-value=33 Score=31.18 Aligned_cols=32 Identities=16% Similarity=0.111 Sum_probs=27.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
...+.++||+.+|+|..|++.++..-...+..
T Consensus 127 ~~~s~~eIA~~lgis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 127 YGFSYKEIAEMTGLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 47899999999999999999998777666544
No 363
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.32 E-value=14 Score=31.37 Aligned_cols=32 Identities=25% Similarity=0.569 Sum_probs=22.6
Q ss_pred CCCCCCCCCCCcccccCCCCccccccccceeccc
Q 046187 1 MKCPYCSAAQGRCATTSTGRSITECGSCGRVIAE 34 (510)
Q Consensus 1 m~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vlee 34 (510)
|.||.|+.. .+.. ..+|-++..|..|+=|--+
T Consensus 2 llCP~C~v~-l~~~-~rs~vEiD~CPrCrGVWLD 33 (88)
T COG3809 2 LLCPICGVE-LVMS-VRSGVEIDYCPRCRGVWLD 33 (88)
T ss_pred cccCcCCce-eeee-eecCceeeeCCccccEeec
Confidence 679999873 2222 3577777899999988544
No 364
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=43.30 E-value=40 Score=31.52 Aligned_cols=31 Identities=26% Similarity=0.361 Sum_probs=24.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWD 317 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~ 317 (510)
...|++|||+.+|+|..||++..+...+.+.
T Consensus 20 ~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr 50 (141)
T PRK03975 20 RGLTQQEIADILGTSRANVSSIEKRARENIE 50 (141)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 5799999999999999999876665444433
No 365
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=43.27 E-value=35 Score=31.56 Aligned_cols=30 Identities=20% Similarity=0.238 Sum_probs=24.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENW 316 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l 316 (510)
...+.+|||+.+|+|++||+.++..-...+
T Consensus 134 ~g~s~~EIA~~lgis~~tV~~~l~ra~~~~ 163 (172)
T PRK12523 134 DGMGHAEIAERLGVSVSRVRQYLAQGLRQC 163 (172)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 478999999999999999998876544443
No 366
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=43.23 E-value=28 Score=32.53 Aligned_cols=34 Identities=12% Similarity=0.067 Sum_probs=27.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccC
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDLL 320 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Li 320 (510)
...+.+|||+.+|++..||+.++......+...+
T Consensus 143 ~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (186)
T PRK05602 143 QGLSNIEAAAVMDISVDALESLLARGRRALRAQL 176 (186)
T ss_pred cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 4789999999999999999988776666655543
No 367
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=43.13 E-value=14 Score=29.43 Aligned_cols=24 Identities=25% Similarity=0.605 Sum_probs=16.9
Q ss_pred CCCCCCCCCCcccccCCCCccccccccceeccc
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRVIAE 34 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vlee 34 (510)
.|++||+.- + .. -||..||+--+.
T Consensus 29 ~c~~cG~~~--l----~H---rvc~~cg~Y~g~ 52 (57)
T COG0333 29 VCPNCGEYK--L----PH---RVCLKCGYYKGR 52 (57)
T ss_pred eccCCCCcc--c----Cc---eEcCCCCCccCe
Confidence 599999843 2 44 699999975433
No 368
>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=43.10 E-value=38 Score=21.36 Aligned_cols=22 Identities=27% Similarity=0.385 Sum_probs=18.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHH
Q 046187 287 KRKTQAEICKVTGLTEVTLRKV 308 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkr 308 (510)
...+.++|++.++++..||.+.
T Consensus 20 ~~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 20 AGESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred cCCCHHHHHHHHCCCHHHHHHh
Confidence 3458999999999999999764
No 369
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=43.09 E-value=1.3e+02 Score=28.11 Aligned_cols=30 Identities=20% Similarity=0.142 Sum_probs=27.3
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 046187 190 QEPRTLQEISIAANVPQKEIGKYIKILGEA 219 (510)
Q Consensus 190 ~~PrTLkEIa~vt~VskkeIgr~yk~L~k~ 219 (510)
..|.|-.|||+.+|++...+.|.+++|++.
T Consensus 147 ~~~~t~~~iA~~lG~tretvsR~l~~l~~~ 176 (202)
T PRK13918 147 MIYATHDELAAAVGSVRETVTKVIGELSRE 176 (202)
T ss_pred EecCCHHHHHHHhCccHHHHHHHHHHHHHC
Confidence 368899999999999999999999999874
No 370
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=42.99 E-value=21 Score=32.99 Aligned_cols=32 Identities=6% Similarity=0.080 Sum_probs=26.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
..++.+|||+.+|+++.||+.++......+..
T Consensus 134 ~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 165 (173)
T PRK12522 134 EQYSYKEMSEILNIPIGTVKYRLNYAKKQMRE 165 (173)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 47899999999999999999887665555544
No 371
>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=42.96 E-value=46 Score=25.76 Aligned_cols=31 Identities=19% Similarity=0.362 Sum_probs=24.0
Q ss_pred hcCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046187 188 EAQEPRTLQEISIAANVPQKEIGKYIKILGE 218 (510)
Q Consensus 188 ~~~~PrTLkEIa~vt~VskkeIgr~yk~L~k 218 (510)
..+-+.++.+|++.+++++..+.+.++.|.+
T Consensus 14 ~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~ 44 (68)
T PF13463_consen 14 HSDGPMTQSDLAERLGISKSTVSRIIKKLEE 44 (68)
T ss_dssp --TS-BEHHHHHHHTT--HHHHHHHHHHHHH
T ss_pred ccCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 6788899999999999999999999998866
No 372
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=42.73 E-value=77 Score=25.90 Aligned_cols=29 Identities=28% Similarity=0.304 Sum_probs=25.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
.+.+..||++.++++..|+++..+.|.+.
T Consensus 19 ~~~t~~~ia~~l~i~~~tv~r~l~~L~~~ 47 (91)
T smart00346 19 GGLTLAELAERLGLSKSTAHRLLNTLQEL 47 (91)
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 47999999999999999999999888653
No 373
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=42.73 E-value=19 Score=32.76 Aligned_cols=34 Identities=15% Similarity=0.192 Sum_probs=27.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccC
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDLL 320 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Li 320 (510)
...+.+|||+.+|+|+.||+++...-...+...+
T Consensus 140 ~~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l 173 (179)
T PRK11924 140 EGLSYREIAEILGVPVGTVKSRLRRARQLLRECL 173 (179)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4789999999999999999988877666665443
No 374
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=42.72 E-value=75 Score=30.82 Aligned_cols=29 Identities=10% Similarity=0.208 Sum_probs=26.0
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q 046187 288 RKTQAEICKVTGLTEVTLRKVYKELLENW 316 (510)
Q Consensus 288 ~~t~keIa~vagVSe~TIRkrYKEL~e~l 316 (510)
..++.+||+.+|+|..|+.+.+++|.+.-
T Consensus 169 ~~t~~~lA~~lG~sretvsR~L~~L~~~G 197 (226)
T PRK10402 169 HEKHTQAAEYLGVSYRHLLYVLAQFIQDG 197 (226)
T ss_pred cchHHHHHHHHCCcHHHHHHHHHHHHHCC
Confidence 45789999999999999999999998854
No 375
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=42.64 E-value=28 Score=32.33 Aligned_cols=32 Identities=13% Similarity=0.132 Sum_probs=26.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
...+.+|||+.+|+|+.||++++..-...+..
T Consensus 144 ~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 175 (179)
T PRK12514 144 EGLSYKELAERHDVPLNTMRTWLRRSLLKLRE 175 (179)
T ss_pred cCCCHHHHHHHHCCChHHHHHHHHHHHHHHHH
Confidence 46789999999999999999988766655543
No 376
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=42.50 E-value=29 Score=32.50 Aligned_cols=31 Identities=16% Similarity=0.140 Sum_probs=26.3
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 288 RKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 288 ~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
..+.+|||+.+|++..||+.++..-...+..
T Consensus 155 g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 185 (189)
T PRK09648 155 GLSAEETAEAVGSTPGAVRVAQHRALARLRA 185 (189)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 6889999999999999999988766665544
No 377
>PRK10220 hypothetical protein; Provisional
Probab=42.44 E-value=14 Score=33.15 Aligned_cols=24 Identities=25% Similarity=0.690 Sum_probs=16.7
Q ss_pred CCCCCCCCCCcccccCCCCccccccccce
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGR 30 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~ 30 (510)
.||.|.+. +.+..|+ ..||.+||.
T Consensus 5 ~CP~C~se----ytY~d~~-~~vCpeC~h 28 (111)
T PRK10220 5 HCPKCNSE----YTYEDNG-MYICPECAH 28 (111)
T ss_pred cCCCCCCc----ceEcCCC-eEECCcccC
Confidence 49999872 2234454 499999985
No 378
>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=42.42 E-value=12 Score=29.26 Aligned_cols=29 Identities=28% Similarity=0.556 Sum_probs=19.9
Q ss_pred CCCCCCCCCCccc--ccCCCCccccccccceec
Q 046187 2 KCPYCSAAQGRCA--TTSTGRSITECGSCGRVI 32 (510)
Q Consensus 2 ~Cp~C~~~~~~i~--D~~~Gd~~~VC~~CG~Vl 32 (510)
.|.+|+...+..- ....+. .+|..||+-.
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~--~LCNaCgl~~ 31 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGS--TLCNACGLYW 31 (54)
T ss_pred CCCCCCCCCCcccccCCCCcc--hHHHHHHHHH
Confidence 5899998655542 233444 8999999865
No 379
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=42.31 E-value=30 Score=34.78 Aligned_cols=28 Identities=21% Similarity=0.208 Sum_probs=25.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLE 314 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e 314 (510)
..++++|+++.++||+.|||+-+++|.+
T Consensus 18 ~~~~~~ela~~l~vS~~TirRdL~~Le~ 45 (251)
T PRK13509 18 GFVTVEKVIERLGISPATARRDINKLDE 45 (251)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4689999999999999999999998865
No 380
>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=42.29 E-value=42 Score=30.40 Aligned_cols=40 Identities=25% Similarity=0.308 Sum_probs=32.1
Q ss_pred HHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 276 AAIYLACQLEDKRKTQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 276 AaIYlAarl~g~~~t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
+.+|||.+-.+..++.++||+..+++..-+++....|.+.
T Consensus 13 ~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~ 52 (135)
T TIGR02010 13 AMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKA 52 (135)
T ss_pred HHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 5567775533446899999999999999999999888764
No 381
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=42.24 E-value=1.6e+02 Score=29.41 Aligned_cols=75 Identities=21% Similarity=0.223 Sum_probs=48.8
Q ss_pred hCCccCCccHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhcccCCCCCcchhhhHHHHHhhcCC
Q 046187 165 SATCLRNRSVEALATAALVQAIREAQEPRTLQEISIAANVPQKEIGKYIKILGEALQLSQPINSNSIAVHMPRFCTLLQL 244 (510)
Q Consensus 165 e~~~lrGRs~eaVaAACLYIACR~~~~PrTLkEIa~vt~VskkeIgr~yk~L~k~L~i~~pv~~~~p~~~I~Rfcs~L~L 244 (510)
.-|+++.|-...+..|=+.+-=-.-++|.++.|+..+-||-.|.- .-.|...++.. .+ . .+.+|.|+++++||
T Consensus 78 ~iGlyr~KAk~I~~~~~~l~e~~~g~vP~~~~eL~~LPGVGrKTA---nvVL~~a~g~p-~i-~--VDTHV~Rvs~R~gl 150 (211)
T COG0177 78 SIGLYRNKAKNIKELARILLEKFGGEVPDTREELLSLPGVGRKTA---NVVLSFAFGIP-AI-A--VDTHVHRVSNRLGL 150 (211)
T ss_pred hcCCcHHHHHHHHHHHHHHHHHcCCCCCchHHHHHhCCCcchHHH---HHHHHhhcCCC-cc-c--ccchHHHHHHHhCC
Confidence 456666554443334334433333478999999999999998863 23444555544 22 1 36799999999999
Q ss_pred CH
Q 046187 245 NK 246 (510)
Q Consensus 245 ~~ 246 (510)
.+
T Consensus 151 ~~ 152 (211)
T COG0177 151 VP 152 (211)
T ss_pred CC
Confidence 74
No 382
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=42.21 E-value=35 Score=24.46 Aligned_cols=27 Identities=22% Similarity=0.231 Sum_probs=19.3
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046187 190 QEPRTLQEISIAANVPQKEIGKYIKIL 216 (510)
Q Consensus 190 ~~PrTLkEIa~vt~VskkeIgr~yk~L 216 (510)
..+.++.|||..++++...+.|.|++.
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 457899999999999998888877643
No 383
>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=42.05 E-value=46 Score=26.88 Aligned_cols=31 Identities=26% Similarity=0.260 Sum_probs=24.3
Q ss_pred HcCCCCCHHHHHHHhCCC-HHHHHHHHHHHHH
Q 046187 284 LEDKRKTQAEICKVTGLT-EVTLRKVYKELLE 314 (510)
Q Consensus 284 l~g~~~t~keIa~vagVS-e~TIRkrYKEL~e 314 (510)
.+|++-|.+||++.+|++ ..|+....+.|.+
T Consensus 21 ~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~ 52 (65)
T PF01726_consen 21 ENGYPPTVREIAEALGLKSTSTVQRHLKALER 52 (65)
T ss_dssp HHSS---HHHHHHHHTSSSHHHHHHHHHHHHH
T ss_pred HcCCCCCHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 458888999999999996 9999988888764
No 384
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=42.03 E-value=36 Score=31.96 Aligned_cols=32 Identities=19% Similarity=0.070 Sum_probs=26.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
...+.+|||+.+|+++.||++++......+..
T Consensus 153 ~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~ 184 (193)
T PRK11923 153 DGLSYEDIASVMQCPVGTVRSRIFRAREAIDK 184 (193)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 47899999999999999999887766655544
No 385
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=42.03 E-value=21 Score=36.24 Aligned_cols=23 Identities=22% Similarity=0.394 Sum_probs=20.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 046187 289 KTQAEICKVTGLTEVTLRKVYKE 311 (510)
Q Consensus 289 ~t~keIa~vagVSe~TIRkrYKE 311 (510)
.|++|||+.+|||..|+++++..
T Consensus 2 ~Ti~dIA~~agVS~~TVSrvLn~ 24 (341)
T PRK10703 2 ATIKDVAKRAGVSTTTVSHVINK 24 (341)
T ss_pred CCHHHHHHHhCCCHHHHHHHHcC
Confidence 48999999999999999888763
No 386
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=42.02 E-value=26 Score=33.29 Aligned_cols=34 Identities=15% Similarity=0.111 Sum_probs=28.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccC
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDLL 320 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Li 320 (510)
...+.+|||+.+|+|+.||+.++......+...+
T Consensus 143 ~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (188)
T PRK12517 143 GGFSGEEIAEILDLNKNTVMTRLFRARNQLKEAL 176 (188)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4789999999999999999999877777666544
No 387
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=41.87 E-value=27 Score=32.37 Aligned_cols=34 Identities=21% Similarity=0.217 Sum_probs=27.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccC
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDLL 320 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Li 320 (510)
...+.+|||+.+|+|+.||+.++......+...+
T Consensus 115 ~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 148 (170)
T TIGR02959 115 EGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKELL 148 (170)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4789999999999999999988776666555544
No 388
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=41.86 E-value=46 Score=31.34 Aligned_cols=38 Identities=16% Similarity=0.182 Sum_probs=30.7
Q ss_pred HHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 277 AIYLACQLEDKRKTQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 277 aIYlAarl~g~~~t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
+||...+ .+.....++||+.++|+..|+.+..+.|.+.
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 4665554 4556789999999999999999999988764
No 389
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=41.82 E-value=35 Score=32.63 Aligned_cols=34 Identities=15% Similarity=0.051 Sum_probs=27.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccC
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDLL 320 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Li 320 (510)
...+.+|||+.+|+|+.||+.++..-...+...+
T Consensus 154 eg~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 187 (201)
T PRK12545 154 LDFEIDDICTELTLTANHCSVLLYRARTRLRTCL 187 (201)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4688999999999999999988766655555443
No 390
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=41.81 E-value=30 Score=31.41 Aligned_cols=32 Identities=16% Similarity=0.281 Sum_probs=25.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
...+.+|||+.+|+|..||+.+.+.-.+.+-.
T Consensus 124 ~~~s~~EIA~~lgis~~tV~~~l~ra~~~lr~ 155 (163)
T PRK07037 124 HGETQKDIARELGVSPTLVNFMIRDALVHCRK 155 (163)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 37889999999999999999886655554444
No 391
>COG5024 Cyclin [Cell division and chromosome partitioning]
Probab=41.76 E-value=75 Score=35.11 Aligned_cols=85 Identities=14% Similarity=0.146 Sum_probs=64.4
Q ss_pred hHHHHHhhcCCCHHHHHHHHHHHHHHHhccccCCCChHHHHHHHHHHHHHHcCCCCC-HHHHHHHh--CCCHHHHHHHHH
Q 046187 234 HMPRFCTLLQLNKSAQVLATHIGEVVINKCFCTRRNPISISAAAIYLACQLEDKRKT-QAEICKVT--GLTEVTLRKVYK 310 (510)
Q Consensus 234 ~I~Rfcs~L~L~~~V~~~A~~Ia~~a~~~~l~~GRsP~sIAAAaIYlAarl~g~~~t-~keIa~va--gVSe~TIRkrYK 310 (510)
+|..+=.+++|-++..-+|..|.++......+.=..-.-+++.|+|+||+...+.++ +++.+-++ ..+..-|.++++
T Consensus 219 wlvevH~~F~llpeTL~lainiiDrfLs~~~v~l~k~QLvg~s~LfIa~K~EE~~~p~i~~l~~~t~g~~t~~~i~~aE~ 298 (440)
T COG5024 219 WLVEVHGKFGLLPETLFLAINIIDRFLSSRVVSLEKYQLVGISALFIASKYEEVNCPSIKDLVYATDGAFTRDDIIRAER 298 (440)
T ss_pred HHHHhcccccccchHHHHHHHHHHHHhccCcccHHHHHHHHHHHHHHHHhHhHhcCHHHHHHHHHHcccccHHHHHHHHH
Confidence 444444567777888888888888877665555556678899999999999887655 56655554 478888999999
Q ss_pred HHHHhhcc
Q 046187 311 ELLENWDD 318 (510)
Q Consensus 311 EL~e~l~~ 318 (510)
.+++.++-
T Consensus 299 ~ml~~l~f 306 (440)
T COG5024 299 YMLEVLDF 306 (440)
T ss_pred HHhhhccc
Confidence 99998875
No 392
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=41.72 E-value=24 Score=35.79 Aligned_cols=25 Identities=20% Similarity=0.271 Sum_probs=21.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKE 311 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKE 311 (510)
.+.|++|||+.+|||..|+++++..
T Consensus 5 ~~~Ti~dIA~~agVS~~TVSr~Ln~ 29 (342)
T PRK10014 5 KKITIHDVALAAGVSVSTVSLVLSG 29 (342)
T ss_pred CCCcHHHHHHHhCCCHHHHHHHHCC
Confidence 3679999999999999999988754
No 393
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=41.71 E-value=26 Score=33.13 Aligned_cols=34 Identities=15% Similarity=0.021 Sum_probs=27.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccC
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDLL 320 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Li 320 (510)
...+.+|||+.+|+|+.||+.++......+..++
T Consensus 126 eg~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~ 159 (182)
T PRK12511 126 EGLSYQEAAAVLGIPIGTLMSRIGRARAALRAFE 159 (182)
T ss_pred cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 4788999999999999999988766555555433
No 394
>PRK09492 treR trehalose repressor; Provisional
Probab=41.54 E-value=24 Score=35.23 Aligned_cols=23 Identities=22% Similarity=0.472 Sum_probs=20.8
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHH
Q 046187 288 RKTQAEICKVTGLTEVTLRKVYK 310 (510)
Q Consensus 288 ~~t~keIa~vagVSe~TIRkrYK 310 (510)
+.|++|||+.+|||..|+++++.
T Consensus 4 ~~ti~dIA~~agVS~~TVSrvLn 26 (315)
T PRK09492 4 KLTIKDIARLSGVGKSTVSRVLN 26 (315)
T ss_pred CCcHHHHHHHhCCCHHHHhHHhC
Confidence 56999999999999999988875
No 395
>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=41.48 E-value=39 Score=29.07 Aligned_cols=23 Identities=30% Similarity=0.382 Sum_probs=20.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYK 310 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYK 310 (510)
...+.++||+.+|||..||.+ ++
T Consensus 49 ~G~S~~eIA~~LgISrsTIyR-i~ 71 (88)
T TIGR02531 49 QGKTYSDIEAETGASTATISR-VK 71 (88)
T ss_pred CCCCHHHHHHHHCcCHHHHHH-HH
Confidence 457999999999999999987 44
No 396
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=41.33 E-value=30 Score=27.81 Aligned_cols=20 Identities=20% Similarity=0.551 Sum_probs=17.5
Q ss_pred CHHHHHHHhCCCHHHHHHHH
Q 046187 290 TQAEICKVTGLTEVTLRKVY 309 (510)
Q Consensus 290 t~keIa~vagVSe~TIRkrY 309 (510)
+++|||+.+|||..||...+
T Consensus 2 t~~~iA~~~gvS~~TVSr~l 21 (70)
T smart00354 2 TIKDVARLAGVSKATVSRVL 21 (70)
T ss_pred CHHHHHHHHCCCHHHHHHHH
Confidence 68899999999999998654
No 397
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=41.33 E-value=30 Score=32.41 Aligned_cols=34 Identities=15% Similarity=0.232 Sum_probs=28.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccC
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDLL 320 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Li 320 (510)
...+.+|||+.+||+.+||+.++..=...+...+
T Consensus 142 ~gls~~EIA~~l~i~~~tVks~l~ra~~~l~~~l 175 (182)
T COG1595 142 EGLSYEEIAEILGISVGTVKSRLHRARKKLREQL 175 (182)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4789999999999999999998877666665544
No 398
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=41.20 E-value=32 Score=32.03 Aligned_cols=34 Identities=12% Similarity=0.065 Sum_probs=28.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccCC
Q 046187 288 RKTQAEICKVTGLTEVTLRKVYKELLENWDDLLP 321 (510)
Q Consensus 288 ~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Lip 321 (510)
..+.+|||+.+|+|..||+.++......+...+.
T Consensus 147 g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l~ 180 (184)
T PRK12512 147 GASIKETAAKLSMSEGAVRVALHRGLAALAAKFR 180 (184)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Confidence 7899999999999999999998877777665543
No 399
>PRK15481 transcriptional regulatory protein PtsJ; Provisional
Probab=41.18 E-value=60 Score=34.69 Aligned_cols=31 Identities=19% Similarity=0.253 Sum_probs=27.2
Q ss_pred CCCC-CHHHHHHHhCCCHHHHHHHHHHHHHhh
Q 046187 286 DKRK-TQAEICKVTGLTEVTLRKVYKELLENW 316 (510)
Q Consensus 286 g~~~-t~keIa~vagVSe~TIRkrYKEL~e~l 316 (510)
|.++ +.+++|+.++||..||+++|.+|...=
T Consensus 26 g~~lps~r~la~~~~vsr~tv~~a~~~L~~~g 57 (431)
T PRK15481 26 GDSLPPVRELASELGVNRNTVAAAYKRLVTAG 57 (431)
T ss_pred CCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 4566 589999999999999999999998753
No 400
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=41.15 E-value=1.1e+02 Score=29.90 Aligned_cols=30 Identities=10% Similarity=0.179 Sum_probs=27.1
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 046187 190 QEPRTLQEISIAANVPQKEIGKYIKILGEA 219 (510)
Q Consensus 190 ~~PrTLkEIa~vt~VskkeIgr~yk~L~k~ 219 (510)
..|.|.+|||+.+|++...+.|.+++|++.
T Consensus 177 ~i~lt~~~IA~~lGisretlsR~L~~L~~~ 206 (230)
T PRK09391 177 ALPMSRRDIADYLGLTIETVSRALSQLQDR 206 (230)
T ss_pred EecCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 357899999999999999999999999875
No 401
>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=41.15 E-value=21 Score=25.75 Aligned_cols=17 Identities=41% Similarity=0.601 Sum_probs=14.5
Q ss_pred CHHHHHHHhCCCHHHHH
Q 046187 290 TQAEICKVTGLTEVTLR 306 (510)
Q Consensus 290 t~keIa~vagVSe~TIR 306 (510)
+..|+|+.+||+..|||
T Consensus 1 ti~e~A~~~gvs~~tlR 17 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLR 17 (38)
T ss_dssp EHHHHHHHHTS-HHHHH
T ss_pred CHHHHHHHHCCCHHHHH
Confidence 46799999999999999
No 402
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=41.06 E-value=33 Score=35.07 Aligned_cols=35 Identities=14% Similarity=0.211 Sum_probs=30.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccCC
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDLLP 321 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Lip 321 (510)
...+.+|||+.+|+|+.||++++..-.+.+...+.
T Consensus 157 ~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 191 (324)
T TIGR02960 157 LGWRAAETAELLGTSTASVNSALQRARATLDEVGP 191 (324)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhcc
Confidence 46789999999999999999998877777776654
No 403
>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=40.96 E-value=66 Score=28.48 Aligned_cols=44 Identities=18% Similarity=0.197 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHHHcC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 272 SISAAAIYLACQLED-KRKTQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 272 sIAAAaIYlAarl~g-~~~t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
..|..++++.++..+ ...+.++||+.++++..++++..+.|...
T Consensus 8 ~~al~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~~~ 52 (132)
T TIGR00738 8 EYALRALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRRA 52 (132)
T ss_pred HHHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 345555544444333 37899999999999999999999999874
No 404
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=40.92 E-value=29 Score=32.41 Aligned_cols=33 Identities=15% Similarity=0.044 Sum_probs=28.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhccc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDL 319 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~L 319 (510)
...+.+|||+.+|+|+.||+++.......+...
T Consensus 152 ~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 184 (187)
T PRK12534 152 EGITYEELAARTDTPIGTVKSWIRRGLAKLKAC 184 (187)
T ss_pred cCCCHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Confidence 578999999999999999999988777766543
No 405
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=40.69 E-value=74 Score=32.73 Aligned_cols=109 Identities=17% Similarity=0.119 Sum_probs=61.8
Q ss_pred hhHHHHHHHHHHHHHHHHhCCCH-HHHHH-HHHHHHHHHhCCccCCccHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCC
Q 046187 128 VMMDNLRAYLQIIDVASILGLDY-DICDH-AFQLFRDCCSATCLRNRSVEALATAALVQAIREAQEPRTLQEISIAANVP 205 (510)
Q Consensus 128 ~~er~L~a~~~I~~ic~~L~LP~-~Vidt-A~~LyK~a~e~~~lrGRs~eaVaAACLYIACR~~~~PrTLkEIa~vt~Vs 205 (510)
..+.+..|+.+|.+.| +|.- .|.+. -..|=..++--++.+.|-.+.--.|-|..-=-..++|.++.|+..+-||-
T Consensus 92 KDevt~~Am~rL~~~~---gLT~e~v~~~de~~l~~LI~~VgFy~rKA~ylkkta~IL~d~f~gDIP~~v~dLlsLPGVG 168 (286)
T KOG1921|consen 92 KDEVTAAAMLRLKEYG---GLTLEAVLKIDEPTLNELIYPVGFYTRKAKYLKKTAKILQDKFDGDIPDTVEDLLSLPGVG 168 (286)
T ss_pred HHHHHHHHHHHHHHhc---CCCHHHHhccChHhHHhhhhhccchHHHHHHHHHHHHHHHHHhCCCCchhHHHHhcCCCCc
Confidence 4445566777777766 4432 22111 11222333334544443333333444444434459999999999999998
Q ss_pred HHHHHHHHHHHHHHhcccCCCCCcchhhhHHHHHhhcCCC
Q 046187 206 QKEIGKYIKILGEALQLSQPINSNSIAVHMPRFCTLLQLN 245 (510)
Q Consensus 206 kkeIgr~yk~L~k~L~i~~pv~~~~p~~~I~Rfcs~L~L~ 245 (510)
.|- +|..|...-+.-.-+ ..+.++.|+|++|+.-
T Consensus 169 PKM---a~L~m~~AWn~i~GI---~VDtHVHRi~nrlgWv 202 (286)
T KOG1921|consen 169 PKM---AHLTMQVAWNKIVGI---CVDTHVHRICNRLGWV 202 (286)
T ss_pred hHH---HHHHHHHHhccceeE---EeehHHHHHHHHhccc
Confidence 873 344555555433222 2467999999999973
No 406
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=40.57 E-value=31 Score=32.31 Aligned_cols=34 Identities=18% Similarity=0.249 Sum_probs=28.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccC
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDLL 320 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Li 320 (510)
...+.+|||+.+|++..||+.+...-...+...+
T Consensus 146 ~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12539 146 EGLSVAEAATRSGMSESAVKVSVHRGLKALAALI 179 (184)
T ss_pred cCCcHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4789999999999999999998877776666544
No 407
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=40.57 E-value=40 Score=31.23 Aligned_cols=30 Identities=20% Similarity=0.236 Sum_probs=25.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENW 316 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l 316 (510)
...+.+|||+.+|++..||++++..-...+
T Consensus 134 ~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~ 163 (172)
T PRK09651 134 DGLTYSEIAHKLGVSVSSVKKYVAKATEHC 163 (172)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 578899999999999999999887655544
No 408
>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated. Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.
Probab=40.51 E-value=43 Score=33.12 Aligned_cols=32 Identities=19% Similarity=0.276 Sum_probs=29.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
..++.+|||+.+++|+.|++..++.+...+..
T Consensus 185 ~G~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~ 216 (232)
T TIGR03541 185 LGRRQADIAAILGISERTVENHLRSARRKLGV 216 (232)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCC
Confidence 57999999999999999999999999887764
No 409
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=40.40 E-value=31 Score=31.92 Aligned_cols=32 Identities=16% Similarity=0.102 Sum_probs=27.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
...+.+|||+.+|+|+.||+++.......+..
T Consensus 151 ~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T TIGR02948 151 EDLSLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 47899999999999999999988776666544
No 410
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=40.37 E-value=20 Score=34.70 Aligned_cols=37 Identities=16% Similarity=0.191 Sum_probs=29.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccCCCC
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDLLPSN 323 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Lip~~ 323 (510)
...+.+|||+.+|++..|++.++......+...+...
T Consensus 163 ~g~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~~~ 199 (206)
T PRK12544 163 IELETNEICHAVDLSVSNLNVLLYRARLRLRECLENK 199 (206)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 3788999999999999999999877777666544333
No 411
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=40.33 E-value=15 Score=30.64 Aligned_cols=31 Identities=26% Similarity=0.696 Sum_probs=19.6
Q ss_pred CCCCCCCCCCCcccccC-----CCCcccccc--ccceec
Q 046187 1 MKCPYCSAAQGRCATTS-----TGRSITECG--SCGRVI 32 (510)
Q Consensus 1 m~Cp~C~~~~~~i~D~~-----~Gd~~~VC~--~CG~Vl 32 (510)
|.||.||... .+.+.. .=+-...|. +||...
T Consensus 2 m~CP~Cg~~a-~irtSr~~s~~~~~~Y~qC~N~eCg~tF 39 (72)
T PRK09678 2 FHCPLCQHAA-HARTSRYITDTTKERYHQCQNVNCSATF 39 (72)
T ss_pred ccCCCCCCcc-EEEEChhcChhhheeeeecCCCCCCCEE
Confidence 8899999955 444321 111125688 999865
No 412
>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=40.30 E-value=82 Score=26.96 Aligned_cols=30 Identities=20% Similarity=0.224 Sum_probs=27.1
Q ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046187 189 AQEPRTLQEISIAANVPQKEIGKYIKILGE 218 (510)
Q Consensus 189 ~~~PrTLkEIa~vt~VskkeIgr~yk~L~k 218 (510)
...+.+..||++.++++...+.|+++.|.+
T Consensus 44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le~ 73 (95)
T TIGR01610 44 KQDRVTATVIAELTGLSRTHVSDAIKSLAR 73 (95)
T ss_pred cCCccCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 567899999999999999999999988866
No 413
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=40.27 E-value=91 Score=27.89 Aligned_cols=43 Identities=16% Similarity=0.343 Sum_probs=33.1
Q ss_pred ChHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046187 269 NPISISAAAIYLACQLEDKRKTQAEICKVTGLTEVTLRKVYKEL 312 (510)
Q Consensus 269 sP~sIAAAaIYlAarl~g~~~t~keIa~vagVSe~TIRkrYKEL 312 (510)
....|..+.-||-..+. .++++.++|+.+|+|+.++...+++.
T Consensus 7 ~~~~i~~~~~~I~~~~~-~~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 7 DAITIHSILDWIEDNLE-SPLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred cHHHHHHHHHHHHHhcC-CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 34455566666666644 47999999999999999999888765
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=40.08 E-value=44 Score=25.15 Aligned_cols=30 Identities=27% Similarity=0.441 Sum_probs=24.3
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 286 DKRKTQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 286 g~~~t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
+...++.||++.+|++.+|+....+.|.+.
T Consensus 16 ~~~~t~~eia~~~gl~~stv~r~L~tL~~~ 45 (52)
T PF09339_consen 16 GGPLTLSEIARALGLPKSTVHRLLQTLVEE 45 (52)
T ss_dssp BSCEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred CCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 345789999999999999999888877653
No 415
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=39.87 E-value=9 Score=39.99 Aligned_cols=43 Identities=12% Similarity=0.309 Sum_probs=27.6
Q ss_pred CCCCCCCCCCCcc-cccCCCCccccccccceecc----c---ceeecccccccccC
Q 046187 1 MKCPYCSAAQGRC-ATTSTGRSITECGSCGRVIA----E---RQCQNHHLFHIRAQ 48 (510)
Q Consensus 1 m~Cp~C~~~~~~i-~D~~~Gd~~~VC~~CG~Vle----e---r~Id~~~EwR~fs~ 48 (510)
.+||.|+.. +. .|..... .||..||.-+. | .++|+++ |+++..
T Consensus 39 ~kc~~C~~~--~~~~~l~~~~--~vcp~c~~h~rltAreRI~~L~D~gS-F~E~~~ 89 (296)
T CHL00174 39 VQCENCYGL--NYKKFLKSKM--NICEQCGYHLKMSSSDRIELLIDPGT-WNPMDE 89 (296)
T ss_pred eECCCccch--hhHHHHHHcC--CCCCCCCCCcCCCHHHHHHHHccCCc-cEEcCC
Confidence 379999882 22 3444555 89999998664 2 2566555 666543
No 416
>PF13551 HTH_29: Winged helix-turn helix
Probab=39.80 E-value=45 Score=28.12 Aligned_cols=30 Identities=27% Similarity=0.249 Sum_probs=25.0
Q ss_pred CCC-CHHHHHHHhCCCHHHHHHHHHHHHHhh
Q 046187 287 KRK-TQAEICKVTGLTEVTLRKVYKELLENW 316 (510)
Q Consensus 287 ~~~-t~keIa~vagVSe~TIRkrYKEL~e~l 316 (510)
... +..+||+.+|+|..||.+..+.+.+.=
T Consensus 10 ~g~~~~~~ia~~lg~s~~Tv~r~~~~~~~~G 40 (112)
T PF13551_consen 10 EGVSTIAEIARRLGISRRTVYRWLKRYREGG 40 (112)
T ss_pred cCCCcHHHHHHHHCcCHHHHHHHHHHHHccc
Confidence 344 699999999999999998888877543
No 417
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=39.78 E-value=57 Score=23.59 Aligned_cols=31 Identities=16% Similarity=0.170 Sum_probs=27.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHhccc
Q 046187 193 RTLQEISIAANVPQKEIGKYIKILGEALQLS 223 (510)
Q Consensus 193 rTLkEIa~vt~VskkeIgr~yk~L~k~L~i~ 223 (510)
.+.+||+..++++...+.+..+.+.+.|+..
T Consensus 19 ~s~~eia~~l~is~~tv~~~~~~~~~kl~~~ 49 (58)
T smart00421 19 LTNKEIAERLGISEKTVKTHLSNIMRKLGVR 49 (58)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Confidence 5899999999999999999888888877643
No 418
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=39.78 E-value=50 Score=34.62 Aligned_cols=36 Identities=22% Similarity=0.221 Sum_probs=28.4
Q ss_pred HHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046187 279 YLACQLEDKRKTQAEICKVTGLTEVTLRKVYKELLE 314 (510)
Q Consensus 279 YlAarl~g~~~t~keIa~vagVSe~TIRkrYKEL~e 314 (510)
.+|...+-...||.|||+.+|||..+|.+-+++=.+
T Consensus 20 ~vA~lYY~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~ 55 (318)
T PRK15418 20 RIAWFYYHDGLTQSEIGERLGLTRLKVSRLLEKGRQ 55 (318)
T ss_pred HHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 344455678999999999999999999876665544
No 419
>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Probab=39.41 E-value=35 Score=32.66 Aligned_cols=30 Identities=17% Similarity=0.382 Sum_probs=27.1
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 286 DKRKTQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 286 g~~~t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
|..++..++|+.+|||..+||.+++.|...
T Consensus 32 G~~L~e~~La~~lgVSRtpVReAL~~L~~e 61 (212)
T TIGR03338 32 GAKLNESDIAARLGVSRGPVREAFRALEEA 61 (212)
T ss_pred CCEecHHHHHHHhCCChHHHHHHHHHHHHC
Confidence 667888999999999999999999999754
No 420
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=39.40 E-value=23 Score=27.38 Aligned_cols=31 Identities=23% Similarity=0.525 Sum_probs=18.6
Q ss_pred CCCCCCCCCCCccc-ccCCCCccccccccceec
Q 046187 1 MKCPYCSAAQGRCA-TTSTGRSITECGSCGRVI 32 (510)
Q Consensus 1 m~Cp~C~~~~~~i~-D~~~Gd~~~VC~~CG~Vl 32 (510)
..|.+|+...+..- +...|. ..+|..||+-.
T Consensus 4 ~~C~~C~~~~T~~WR~g~~g~-~~LCnaCgl~~ 35 (52)
T smart00401 4 RSCSNCGTTETPLWRRGPSGN-KTLCNACGLYY 35 (52)
T ss_pred CCcCCCCCCCCCccccCCCCC-CcEeecccHHH
Confidence 36888887554442 223332 37888888753
No 421
>PRK04841 transcriptional regulator MalT; Provisional
Probab=39.33 E-value=38 Score=39.42 Aligned_cols=32 Identities=9% Similarity=0.155 Sum_probs=29.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
..+|.+|||+..+||+.|||...+.|+..++.
T Consensus 852 ~g~~~~~ia~~l~~s~~tv~~h~~~~~~kl~v 883 (903)
T PRK04841 852 SGYSNEQIAGELDVAATTIKTHIRNLYQKLGI 883 (903)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 46788999999999999999999999998874
No 422
>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=38.92 E-value=19 Score=32.00 Aligned_cols=30 Identities=23% Similarity=0.701 Sum_probs=17.8
Q ss_pred CCCCCCCCCCcccc------cC--CCCccccccccceec
Q 046187 2 KCPYCSAAQGRCAT------TS--TGRSITECGSCGRVI 32 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D------~~--~Gd~~~VC~~CG~Vl 32 (510)
+||+||.. .++++ +. .|--..+|+.|+-=|
T Consensus 4 ~CpYCg~~-~~l~~~~~iYg~~~~~~~~~y~C~~C~AyV 41 (102)
T PF11672_consen 4 ICPYCGGP-AELVDGSEIYGHRYDDGPYLYVCTPCDAYV 41 (102)
T ss_pred ccCCCCCe-eEEcccchhcCccCCCCceeEECCCCCcee
Confidence 79999983 34444 12 122126888887755
No 423
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=38.90 E-value=41 Score=32.91 Aligned_cols=30 Identities=27% Similarity=0.453 Sum_probs=26.8
Q ss_pred CCCC-CHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 286 DKRK-TQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 286 g~~~-t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
|.++ +-.++|+.+|||..|||.+++.|...
T Consensus 28 G~~LPsE~eLae~~gVSRt~VReAL~~L~~e 58 (239)
T PRK04984 28 GSILPAERELSELIGVTRTTLREVLQRLARD 58 (239)
T ss_pred CCcCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 5678 58899999999999999999999864
No 424
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning]
Probab=38.71 E-value=95 Score=33.14 Aligned_cols=87 Identities=10% Similarity=0.131 Sum_probs=55.2
Q ss_pred hhhhHHHHHhhcCCCHHHHHHHHHHHHHHHhccccCCCC---hHHHHHHHHHHHHHHcCCCCCH--H-HHHHHhC-CCHH
Q 046187 231 IAVHMPRFCTLLQLNKSAQVLATHIGEVVINKCFCTRRN---PISISAAAIYLACQLEDKRKTQ--A-EICKVTG-LTEV 303 (510)
Q Consensus 231 p~~~I~Rfcs~L~L~~~V~~~A~~Ia~~a~~~~l~~GRs---P~sIAAAaIYlAarl~g~~~t~--k-eIa~vag-VSe~ 303 (510)
+.+.|-++|.+.++.+.+.-+|...+.+.....-+.--+ -.=||+||+.+|+++....++. . .+...-. ....
T Consensus 81 A~~WIl~V~~~~~~~~~~~~LA~NYlDRFls~~~l~k~k~W~lQLlAvaCLsLAsKmeE~~vPll~dl~v~~~~~~feak 160 (335)
T KOG0656|consen 81 ALDWILKVCEEYNFEPLVFLLAMNYLDRFLSSQKLPKDKPWMLQLLAVACLSLASKMEETDVPLLADLQVEYTDNVFEAK 160 (335)
T ss_pred HHHHHHHHHHHhCCchHHHHHHHHHHHHhhcccccCCCchHHHHHHHHHHHHHHHhhcCcCCchhhhhhhccccccccHH
Confidence 457888999999999888888887776665432232233 4578999999999988654432 2 2333222 4456
Q ss_pred HHHHHHHHHHHhhc
Q 046187 304 TLRKVYKELLENWD 317 (510)
Q Consensus 304 TIRkrYKEL~e~l~ 317 (510)
||++-=--++..|+
T Consensus 161 tI~rmELLVLstL~ 174 (335)
T KOG0656|consen 161 TIQRMELLVLSTLK 174 (335)
T ss_pred HHHHHHHHHHhhcc
Confidence 77754444444443
No 425
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=38.71 E-value=2.2e+02 Score=28.76 Aligned_cols=86 Identities=16% Similarity=0.138 Sum_probs=67.3
Q ss_pred HHHHHHHHHH-HHHHhCCCHHHHHHHHHHHHHHH-hCCccCCccHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHH
Q 046187 132 NLRAYLQIID-VASILGLDYDICDHAFQLFRDCC-SATCLRNRSVEALATAALVQAIREAQEPRTLQEISIAANVPQKEI 209 (510)
Q Consensus 132 ~L~a~~~I~~-ic~~L~LP~~VidtA~~LyK~a~-e~~~lrGRs~eaVaAACLYIACR~~~~PrTLkEIa~vt~VskkeI 209 (510)
.|..|.+-.. +...=++++.-+|.......+.. ...+.||-+...+-.-+-.+. ..+.+.|..|++..++++.-..
T Consensus 113 aL~~y~~~r~~l~~~~~~sQ~~lD~l~~~~~k~~~~~~LPkGi~~~Tl~~i~~~~~--~~~~~~Taeela~~~giSRvTa 190 (224)
T COG4565 113 ALTRYRQKRHALESHQQLSQKELDQLFNIQSKEQPPDDLPKGLDELTLQKVREALK--EPDQELTAEELAQALGISRVTA 190 (224)
T ss_pred HHHHHHHHHHHHhhhcccCHHHHHHHHhccccccCcccCCCCcCHHHHHHHHHHHh--CcCCccCHHHHHHHhCccHHHH
Confidence 3556665554 77777899999999999885532 246788888777776666555 7789999999999999999999
Q ss_pred HHHHHHHHHH
Q 046187 210 GKYIKILGEA 219 (510)
Q Consensus 210 gr~yk~L~k~ 219 (510)
+|++..|...
T Consensus 191 RRYLeyl~~~ 200 (224)
T COG4565 191 RRYLEYLVSN 200 (224)
T ss_pred HHHHHHHHhc
Confidence 9998888664
No 426
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=38.67 E-value=86 Score=30.41 Aligned_cols=30 Identities=3% Similarity=-0.116 Sum_probs=26.6
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 046187 190 QEPRTLQEISIAANVPQKEIGKYIKILGEA 219 (510)
Q Consensus 190 ~~PrTLkEIa~vt~VskkeIgr~yk~L~k~ 219 (510)
..+.+..|||+.+|++...+.|.+++|.+.
T Consensus 167 ~~~~t~~~lA~~lG~sretvsR~L~~L~~~ 196 (226)
T PRK10402 167 LYHEKHTQAAEYLGVSYRHLLYVLAQFIQD 196 (226)
T ss_pred cccchHHHHHHHHCCcHHHHHHHHHHHHHC
Confidence 346688999999999999999999999885
No 427
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=38.65 E-value=33 Score=32.55 Aligned_cols=34 Identities=15% Similarity=0.129 Sum_probs=27.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccC
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDLL 320 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Li 320 (510)
...+.+|||+.+|++..||+.++..-...+...+
T Consensus 151 ~g~s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l 184 (196)
T PRK12524 151 EGLSNPEIAEVMEIGVEAVESLTARGKRALAALL 184 (196)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4788999999999999999988877666665533
No 428
>PRK06930 positive control sigma-like factor; Validated
Probab=38.48 E-value=44 Score=31.87 Aligned_cols=35 Identities=9% Similarity=0.104 Sum_probs=29.5
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccC
Q 046187 286 DKRKTQAEICKVTGLTEVTLRKVYKELLENWDDLL 320 (510)
Q Consensus 286 g~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Li 320 (510)
....+.+|||+.+|+|..||+.+++.....+...+
T Consensus 128 ~eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l 162 (170)
T PRK06930 128 GYGLSYSEIADYLNIKKSTVQSMIERAEKKIARQI 162 (170)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 35789999999999999999999887777766544
No 429
>PRK09480 slmA division inhibitor protein; Provisional
Probab=38.42 E-value=32 Score=31.86 Aligned_cols=41 Identities=20% Similarity=0.218 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046187 271 ISISAAAIYLACQLEDKRKTQAEICKVTGLTEVTLRKVYKE 311 (510)
Q Consensus 271 ~sIAAAaIYlAarl~g~~~t~keIa~vagVSe~TIRkrYKE 311 (510)
.-|..|++-+.....|...|+++|++.+||+.+||-..|+.
T Consensus 13 ~~Il~aa~~l~~~~~G~~~ti~~Ia~~agvs~gt~Y~~F~~ 53 (194)
T PRK09480 13 EQILQALAQMLESPPGERITTAKLAARVGVSEAALYRHFPS 53 (194)
T ss_pred HHHHHHHHHHHHhcCCCccCHHHHHHHhCCCHhHHHHHCCC
Confidence 34555554444333357899999999999999999877754
No 430
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=38.35 E-value=71 Score=29.83 Aligned_cols=44 Identities=20% Similarity=0.168 Sum_probs=37.5
Q ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 046187 176 ALATAALVQAIREAQEPRTLQEISIAANVPQKEIGKYIKILGEA 219 (510)
Q Consensus 176 aVaAACLYIACR~~~~PrTLkEIa~vt~VskkeIgr~yk~L~k~ 219 (510)
...-|-+|+|....+-+.+..+||...++++.-|.+.+..|++.
T Consensus 9 yal~~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~ka 52 (150)
T COG1959 9 YALRALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLRKA 52 (150)
T ss_pred HHHHHHHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHHc
Confidence 34566789998777779999999999999999999999988774
No 431
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=38.34 E-value=33 Score=32.33 Aligned_cols=32 Identities=22% Similarity=0.321 Sum_probs=25.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
...+.+|||+.+|+|..||+++...-...+..
T Consensus 154 ~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 185 (194)
T PRK12513 154 GDLELEEIAELTGVPEETVKSRLRYALQKLRE 185 (194)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 57899999999999999999776544444433
No 432
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=38.26 E-value=42 Score=29.70 Aligned_cols=35 Identities=17% Similarity=0.206 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHH
Q 046187 274 SAAAIYLACQLEDKRKTQAEICKVTGLTEVTLRKV 308 (510)
Q Consensus 274 AAAaIYlAarl~g~~~t~keIa~vagVSe~TIRkr 308 (510)
.+.=|-++.+++.-+.+|+||++..|||..||..-
T Consensus 46 l~~Rv~Iv~eLL~ge~sQREi~~~LgvsiAtITRG 80 (103)
T COG2973 46 LGTRVRIVEELLRGELSQREIAQKLGVSIATITRG 80 (103)
T ss_pred HHHHHHHHHHHHhccccHHHHHHHhCcchhhhccc
Confidence 34455667778888999999999999999999643
No 433
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=38.25 E-value=57 Score=30.50 Aligned_cols=39 Identities=28% Similarity=0.445 Sum_probs=31.6
Q ss_pred HHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 276 AAIYLACQLEDKRKTQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 276 AaIYlAarl~g~~~t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
+.+|||.. .+..++.++||+..+|+..-+++.+..|.+.
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 4446789999999999999999999998764
No 434
>PRK14087 dnaA chromosomal replication initiation protein; Provisional
Probab=38.25 E-value=3.7e+02 Score=29.55 Aligned_cols=39 Identities=21% Similarity=0.248 Sum_probs=32.1
Q ss_pred HHHHHHHHcCCCCCHHHHHHHhC-CCHHHHHHHHHHHHHhhc
Q 046187 277 AIYLACQLEDKRKTQAEICKVTG-LTEVTLRKVYKELLENWD 317 (510)
Q Consensus 277 aIYlAarl~g~~~t~keIa~vag-VSe~TIRkrYKEL~e~l~ 317 (510)
|+|++-++. ..+..+|++.+| -...||-.+++.+.+.+.
T Consensus 392 amyL~r~~t--~~sl~~IG~~FggrdHsTV~~a~~ki~~~~~ 431 (450)
T PRK14087 392 AMYLTKEIL--NHTLAQIGEEFGGRDHTTVINAERKIEKMLK 431 (450)
T ss_pred HHHHHHHHc--CCCHHHHHHHhCCCChHHHHHHHHHHHHHHH
Confidence 677777666 458999999997 999999999998887664
No 435
>PF14353 CpXC: CpXC protein
Probab=38.19 E-value=15 Score=32.89 Aligned_cols=10 Identities=40% Similarity=0.926 Sum_probs=8.4
Q ss_pred ccccccceec
Q 046187 23 TECGSCGRVI 32 (510)
Q Consensus 23 ~VC~~CG~Vl 32 (510)
.+|.+||...
T Consensus 39 ~~CP~Cg~~~ 48 (128)
T PF14353_consen 39 FTCPSCGHKF 48 (128)
T ss_pred EECCCCCCce
Confidence 6899999865
No 436
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=38.14 E-value=36 Score=32.25 Aligned_cols=33 Identities=15% Similarity=0.074 Sum_probs=27.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhccc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDL 319 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~L 319 (510)
...+.+|||+.+|+++.||+++...-+..+...
T Consensus 157 ~~~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~ 189 (194)
T PRK09646 157 GGLTYREVAERLAVPLGTVKTRMRDGLIRLRDC 189 (194)
T ss_pred cCCCHHHHHHHhCCChHhHHHHHHHHHHHHHHH
Confidence 468999999999999999998887666655543
No 437
>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=38.14 E-value=39 Score=26.55 Aligned_cols=22 Identities=36% Similarity=0.437 Sum_probs=18.4
Q ss_pred CHHHHHHHhCCCHHHHHHHHHH
Q 046187 290 TQAEICKVTGLTEVTLRKVYKE 311 (510)
Q Consensus 290 t~keIa~vagVSe~TIRkrYKE 311 (510)
+.+|||+.+||+..|||...++
T Consensus 2 ~i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 2 TIKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred CHHHHHHHHCcCHHHHHHHHHh
Confidence 5789999999999999955443
No 438
>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=38.13 E-value=73 Score=25.69 Aligned_cols=32 Identities=25% Similarity=0.342 Sum_probs=23.7
Q ss_pred HhcCCCCCHHHHHHHhCCC-HHHHHHHHHHHHH
Q 046187 187 REAQEPRTLQEISIAANVP-QKEIGKYIKILGE 218 (510)
Q Consensus 187 R~~~~PrTLkEIa~vt~Vs-kkeIgr~yk~L~k 218 (510)
..+|.|-|++||++.+++. ...+.+.++.|.+
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 4789999999999999997 7777777777754
No 439
>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=38.09 E-value=28 Score=35.07 Aligned_cols=22 Identities=18% Similarity=0.339 Sum_probs=18.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHH
Q 046187 289 KTQAEICKVTGLTEVTLRKVYK 310 (510)
Q Consensus 289 ~t~keIa~vagVSe~TIRkrYK 310 (510)
.|++|||+.+|||..|+.+++.
T Consensus 2 ~ti~dIA~~agvS~~TVSrvLn 23 (329)
T TIGR01481 2 VTIYDVAREAGVSMATVSRVVN 23 (329)
T ss_pred CcHHHHHHHhCCCHHHHHHHhC
Confidence 4789999999999999976643
No 440
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=38.02 E-value=65 Score=25.99 Aligned_cols=30 Identities=20% Similarity=0.216 Sum_probs=23.5
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 286 DKRKTQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 286 g~~~t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
+.+++-.|||+++|+|..++|..+..|...
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 567888999999999999999777776654
No 441
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=38.02 E-value=32 Score=33.23 Aligned_cols=34 Identities=18% Similarity=0.114 Sum_probs=28.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccC
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDLL 320 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Li 320 (510)
...+.+|||+.+|+++.||+.+.......+...+
T Consensus 153 ~g~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l 186 (203)
T PRK09647 153 EGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAAL 186 (203)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4789999999999999999988877776666544
No 442
>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=37.99 E-value=80 Score=23.25 Aligned_cols=30 Identities=13% Similarity=0.283 Sum_probs=22.9
Q ss_pred hcCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046187 188 EAQEPRTLQEISIAANVPQKEIGKYIKILG 217 (510)
Q Consensus 188 ~~~~PrTLkEIa~vt~VskkeIgr~yk~L~ 217 (510)
+.+..+++.+|+..+|++..++.+.+++|.
T Consensus 13 q~d~r~s~~~la~~lglS~~~v~~Ri~rL~ 42 (42)
T PF13404_consen 13 QEDGRRSYAELAEELGLSESTVRRRIRRLE 42 (42)
T ss_dssp HH-TTS-HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHcCCccHHHHHHHHCcCHHHHHHHHHHhC
Confidence 455778999999999999999988887763
No 443
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=37.87 E-value=18 Score=28.99 Aligned_cols=27 Identities=4% Similarity=-0.207 Sum_probs=17.7
Q ss_pred CCCCCCCCCCcccccCCCCccccccccceecccceee
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRVIAERQCQ 38 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vleer~Id 38 (510)
.|++||+.-. .- .||. ||+--+..+|+
T Consensus 29 ~c~~cg~~~~------pH---~vc~-cG~Y~gr~v~~ 55 (60)
T PRK01110 29 VDKTTGEYHL------PH---HVSP-KGYYKGRKVLK 55 (60)
T ss_pred EcCCCCceec------cc---eecC-CcccCCeEeec
Confidence 5999988321 12 6899 99866555554
No 444
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=37.77 E-value=18 Score=27.42 Aligned_cols=25 Identities=36% Similarity=0.841 Sum_probs=17.6
Q ss_pred CCCCCCCCCCcccccCCCCccccc--cccceeccc
Q 046187 2 KCPYCSAAQGRCATTSTGRSITEC--GSCGRVIAE 34 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC--~~CG~Vlee 34 (510)
+||.||... -..| +.| .+|+.|+..
T Consensus 13 kCp~CGt~N-----G~R~---~~CKN~~C~~~~~~ 39 (44)
T PF14952_consen 13 KCPKCGTYN-----GTRG---LSCKNKSCPQVFNV 39 (44)
T ss_pred cCCcCcCcc-----Cccc---ccccCCccchhhhc
Confidence 699998843 2355 678 679988743
No 445
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=37.71 E-value=1.2e+02 Score=29.42 Aligned_cols=30 Identities=13% Similarity=0.183 Sum_probs=26.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENW 316 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l 316 (510)
.+.++++||+.+|++..|+.+..++|.+.-
T Consensus 172 i~~t~~~iA~~lG~tretvsR~l~~L~~~g 201 (236)
T PRK09392 172 LPYEKRVLASYLGMTPENLSRAFAALASHG 201 (236)
T ss_pred eeCCHHHHHHHhCCChhHHHHHHHHHHhCC
Confidence 466789999999999999999999988765
No 446
>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR. Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.
Probab=37.65 E-value=21 Score=31.91 Aligned_cols=21 Identities=14% Similarity=0.230 Sum_probs=19.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHH
Q 046187 287 KRKTQAEICKVTGLTEVTLRK 307 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRk 307 (510)
...+.+|||+.+|+|++||++
T Consensus 122 ~~~s~~EIA~~l~is~~tV~~ 142 (142)
T TIGR03209 122 EDMKEIDIAKKLHISRQSVYK 142 (142)
T ss_pred cCCCHHHHHHHHCcCHHhhcC
Confidence 478999999999999999974
No 447
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=37.60 E-value=40 Score=33.78 Aligned_cols=29 Identities=17% Similarity=0.257 Sum_probs=26.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
...+++|+++.++||+.|||+-+++|.+.
T Consensus 17 ~~~~~~eLa~~l~VS~~TiRRdL~~L~~~ 45 (240)
T PRK10411 17 TSLTTEALAEQLNVSKETIRRDLNELQTQ 45 (240)
T ss_pred CCCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 46889999999999999999999999873
No 448
>PRK04023 DNA polymerase II large subunit; Validated
Probab=37.54 E-value=21 Score=42.88 Aligned_cols=30 Identities=13% Similarity=0.265 Sum_probs=20.2
Q ss_pred HHHHHHhCCCHHHHHHHHHHHHHhhcccCCC
Q 046187 292 AEICKVTGLTEVTLRKVYKELLENWDDLLPS 322 (510)
Q Consensus 292 keIa~vagVSe~TIRkrYKEL~e~l~~Lip~ 322 (510)
+.+++..+|++.| |.|..-|...++.++..
T Consensus 1080 ~~la~~Y~v~~Y~-kQRi~~l~~~I~slF~~ 1109 (1121)
T PRK04023 1080 KKLAEEYGVSDYT-KQRLELLERGIKSLFEN 1109 (1121)
T ss_pred HHHHHHcCChHHH-HHHHHHHHHHHHHhhcc
Confidence 4577777777754 55777777777777654
No 449
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=37.42 E-value=44 Score=36.53 Aligned_cols=67 Identities=12% Similarity=0.037 Sum_probs=42.6
Q ss_pred HHHHHHHHHHHHHHHhCCccCCcc-HHHHHHH---HHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Q 046187 150 YDICDHAFQLFRDCCSATCLRNRS-VEALATA---ALVQAIREAQEPRTLQEISIAANVPQKEIGKYIKILGEAL 220 (510)
Q Consensus 150 ~~VidtA~~LyK~a~e~~~lrGRs-~eaVaAA---CLYIACR~~~~PrTLkEIa~vt~VskkeIgr~yk~L~k~L 220 (510)
+.+++..+.+|.--.+. ++|++ ...++-| |+|++-+ .+..++.||+..+|.+-..+.+++++|.+.+
T Consensus 345 ~~I~~~V~~~~~i~~~~--l~s~~R~~~i~~aR~iamyl~r~--~~~~s~~~Ig~~fgr~hstV~~a~~~i~~~~ 415 (440)
T PRK14088 345 DELIEIVAKVTGVSREE--ILSNSRNVKALLARRIGMYVAKN--YLGSSLRTIAEKFNRSHPVVVDSVKKVKDSL 415 (440)
T ss_pred HHHHHHHHHHcCCcHHH--HhCCCCCccccHHHHHHHHHHHH--HhCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 34455555555322221 22222 2344545 7888844 4455999999999988888999999988865
No 450
>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=37.38 E-value=65 Score=23.46 Aligned_cols=32 Identities=16% Similarity=0.215 Sum_probs=27.8
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHhccc
Q 046187 192 PRTLQEISIAANVPQKEIGKYIKILGEALQLS 223 (510)
Q Consensus 192 PrTLkEIa~vt~VskkeIgr~yk~L~k~L~i~ 223 (510)
..+.+||+..++++...+.+..+.+.+.++..
T Consensus 15 ~~s~~eia~~l~~s~~tv~~~~~~~~~~l~~~ 46 (57)
T cd06170 15 GKTNKEIADILGISEKTVKTHLRNIMRKLGVK 46 (57)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHhCCC
Confidence 46999999999999999999988888887753
No 451
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=37.12 E-value=91 Score=25.38 Aligned_cols=28 Identities=21% Similarity=0.330 Sum_probs=26.1
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 288 RKTQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 288 ~~t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
..++++|++.++++..||.+.++.|.+.
T Consensus 24 ~~~~~~la~~~~~s~~~i~~~l~~L~~~ 51 (101)
T smart00347 24 PLSVSELAKRLGVSPSTVTRVLDRLEKK 51 (101)
T ss_pred CcCHHHHHHHHCCCchhHHHHHHHHHHC
Confidence 6899999999999999999999999885
No 452
>PRK14999 histidine utilization repressor; Provisional
Probab=37.12 E-value=46 Score=32.84 Aligned_cols=30 Identities=23% Similarity=0.499 Sum_probs=26.0
Q ss_pred CCCC-CHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 286 DKRK-TQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 286 g~~~-t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
|.++ +-+++|+..|||..|||+++.+|.+.
T Consensus 33 G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~e 63 (241)
T PRK14999 33 HDRIPSEAELVAQYGFSRMTINRALRELTDE 63 (241)
T ss_pred CCcCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 4566 57899999999999999999998874
No 453
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=37.09 E-value=4.1e+02 Score=25.98 Aligned_cols=33 Identities=15% Similarity=0.234 Sum_probs=26.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhccc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDL 319 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~L 319 (510)
...+.+|||+.+|+|..||+++++.-...+...
T Consensus 199 ~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 231 (236)
T PRK06986 199 EELNLKEIGAVLGVSESRVSQIHSQAIKRLRAR 231 (236)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 568999999999999999998877665555443
No 454
>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=36.97 E-value=29 Score=34.97 Aligned_cols=21 Identities=29% Similarity=0.452 Sum_probs=18.1
Q ss_pred CHHHHHHHhCCCHHHHHHHHH
Q 046187 290 TQAEICKVTGLTEVTLRKVYK 310 (510)
Q Consensus 290 t~keIa~vagVSe~TIRkrYK 310 (510)
|++|||+.+|||..|+.+++.
T Consensus 1 ti~dIA~~aGVS~~TVSrvLn 21 (327)
T TIGR02417 1 TLSDIAKLAGVSKTTASYVIN 21 (327)
T ss_pred CHHHHHHHhCCCHHHHHHHHc
Confidence 578999999999999987763
No 455
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=36.96 E-value=39 Score=31.32 Aligned_cols=32 Identities=16% Similarity=0.102 Sum_probs=26.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
...+.+|||+.+|+|..||++++......+..
T Consensus 151 ~~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T PRK09641 151 EDLSLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 57899999999999999999887665555443
No 456
>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=36.95 E-value=67 Score=23.78 Aligned_cols=31 Identities=23% Similarity=0.237 Sum_probs=23.8
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Q 046187 190 QEPRTLQEISIAANVPQKEIGKYIKILGEAL 220 (510)
Q Consensus 190 ~~PrTLkEIa~vt~VskkeIgr~yk~L~k~L 220 (510)
....|+.||+..+|++...+.+..+...+.|
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 5578999999999999988877766654443
No 457
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=36.94 E-value=54 Score=31.79 Aligned_cols=34 Identities=18% Similarity=0.211 Sum_probs=27.8
Q ss_pred HHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q 046187 283 QLEDKRKTQAEICKVTGLTEVTLRKVYKELLENW 316 (510)
Q Consensus 283 rl~g~~~t~keIa~vagVSe~TIRkrYKEL~e~l 316 (510)
...+...+.++||+.+++|+.||++....|....
T Consensus 173 ~~~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~~~ 206 (239)
T PRK10430 173 AHQDYEFSTDELANAVNISRVSCRKYLIWLVNCH 206 (239)
T ss_pred hCCCCCcCHHHHHHHhCchHHHHHHHHHHHHhCC
Confidence 3356788999999999999999998877775543
No 458
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=36.89 E-value=33 Score=34.00 Aligned_cols=34 Identities=24% Similarity=0.298 Sum_probs=28.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccC
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDLL 320 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Li 320 (510)
...+.+|||+.+|+|+.||+.++..-+..+...+
T Consensus 186 eg~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l 219 (233)
T PRK12538 186 ENMSNGEIAEVMDTTVAAVESLLKRGRQQLRDLL 219 (233)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4789999999999999999988876666665544
No 459
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=36.71 E-value=30 Score=34.80 Aligned_cols=21 Identities=24% Similarity=0.385 Sum_probs=18.8
Q ss_pred CHHHHHHHhCCCHHHHHHHHH
Q 046187 290 TQAEICKVTGLTEVTLRKVYK 310 (510)
Q Consensus 290 t~keIa~vagVSe~TIRkrYK 310 (510)
|++|||+.+|||..|+.+++.
T Consensus 2 ti~dIA~~aGVS~~TVSrvLn 22 (328)
T PRK11303 2 KLDEIARLAGVSRTTASYVIN 22 (328)
T ss_pred CHHHHHHHhCCCHHHHHHHHc
Confidence 789999999999999987764
No 460
>smart00351 PAX Paired Box domain.
Probab=36.67 E-value=57 Score=29.41 Aligned_cols=29 Identities=10% Similarity=0.164 Sum_probs=25.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
...+.++||+.+|||..||.+..+.+.+.
T Consensus 32 ~G~s~~~iA~~~gvs~~tV~kwi~r~~~~ 60 (125)
T smart00351 32 NGVRPCDISRQLCVSHGCVSKILGRYYET 60 (125)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHc
Confidence 35689999999999999999998887664
No 461
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=36.33 E-value=1.9e+02 Score=29.09 Aligned_cols=42 Identities=10% Similarity=0.166 Sum_probs=32.9
Q ss_pred hHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046187 270 PISISAAAIYLACQLEDKRKTQAEICKVTGLTEVTLRKVYKE 311 (510)
Q Consensus 270 P~sIAAAaIYlAarl~g~~~t~keIa~vagVSe~TIRkrYKE 311 (510)
+.-+..+.-||...+....+++.+||+.+|+|+.++...+|+
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 344555666777776666699999999999999999888775
No 462
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=36.23 E-value=28 Score=35.17 Aligned_cols=22 Identities=18% Similarity=0.421 Sum_probs=19.6
Q ss_pred CCCHHHHHHHhCCCHHHHHHHH
Q 046187 288 RKTQAEICKVTGLTEVTLRKVY 309 (510)
Q Consensus 288 ~~t~keIa~vagVSe~TIRkrY 309 (510)
+.|++|||+.+|||..|+++++
T Consensus 5 ~~ti~dIA~~agVS~~TVSrvL 26 (331)
T PRK14987 5 RPVLQDVADRVGVTKMTVSRFL 26 (331)
T ss_pred CCcHHHHHHHhCCCHHHhhhhh
Confidence 4689999999999999998766
No 463
>PRK08558 adenine phosphoribosyltransferase; Provisional
Probab=36.19 E-value=53 Score=33.05 Aligned_cols=56 Identities=14% Similarity=0.306 Sum_probs=38.7
Q ss_pred HHHhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhcccCCCCCcchhhhHHHHHhhcCCCHH
Q 046187 185 AIREAQEPRTLQEISIAANVPQKEIGKYIKILGEALQLSQPINSNSIAVHMPRFCTLLQLNKS 247 (510)
Q Consensus 185 ACR~~~~PrTLkEIa~vt~VskkeIgr~yk~L~k~L~i~~pv~~~~p~~~I~Rfcs~L~L~~~ 247 (510)
.-|..+.-.|++|++.++|++...|+|+.. +-..|. .....+++..+|.++.+...
T Consensus 16 ~lr~lk~~~ty~el~~~~g~p~~~l~RYv~------g~~~P~-~~~a~~~~~~l~~~~~~~~~ 71 (238)
T PRK08558 16 VLRSLKKTYTYEELSSITGLPESVLNRYVN------GHVLPS-VERAREIVEKLGPYYNLEEE 71 (238)
T ss_pred HHHHHhcccCHHHHHHHHCCCHHHHHHHHc------CCcCCC-HHHHHHHHHHHHHhhhhHHH
Confidence 345566668999999999999999998853 111221 22466788888888876443
No 464
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=36.16 E-value=56 Score=29.36 Aligned_cols=32 Identities=13% Similarity=0.151 Sum_probs=27.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
...+.++||+.+++|+.||+...+.++..+..
T Consensus 163 ~g~~~~~Ia~~l~~s~~tv~~~~~~~~~kl~~ 194 (211)
T PRK15369 163 EGYTNRDIAEQLSISIKTVETHRLNMMRKLDV 194 (211)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 34578999999999999999999999988763
No 465
>PRK03837 transcriptional regulator NanR; Provisional
Probab=36.12 E-value=49 Score=32.27 Aligned_cols=30 Identities=13% Similarity=0.274 Sum_probs=26.8
Q ss_pred CCCC-CHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 286 DKRK-TQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 286 g~~~-t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
|..+ +..++|+.+|||..|||.+++.|...
T Consensus 34 G~~Lp~E~~Lae~~gVSRt~VREAL~~L~~e 64 (241)
T PRK03837 34 GDQLPSERELMAFFGVGRPAVREALQALKRK 64 (241)
T ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 5678 68999999999999999999999854
No 466
>PRK06030 hypothetical protein; Provisional
Probab=36.09 E-value=81 Score=28.87 Aligned_cols=70 Identities=13% Similarity=0.033 Sum_probs=0.0
Q ss_pred CHHHHHHHHHHHHHHHhCCccCCcc-HHHHHH--HHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Q 046187 149 DYDICDHAFQLFRDCCSATCLRNRS-VEALAT--AALVQAIREAQEPRTLQEISIAANVPQKEIGKYIKILGEAL 220 (510)
Q Consensus 149 P~~VidtA~~LyK~a~e~~~lrGRs-~eaVaA--ACLYIACR~~~~PrTLkEIa~vt~VskkeIgr~yk~L~k~L 220 (510)
++.|++...++|.--.+.-.-+.|. .+.+.| -|+|++-...+. ++.+|...+|-+-..+..+++++.+.+
T Consensus 25 ~d~Ii~~Va~~f~I~~~di~sk~R~rk~i~~aRqIAMYL~r~~~~~--sl~~IG~~FGRDHSTV~haikkIe~~~ 97 (124)
T PRK06030 25 CEAVIDLLALAFGVSGAEIASPLRGRREVSRIRQIAMYVAHVSLGW--PMNEVALAFGRDRTTVGHACHTVEDLR 97 (124)
T ss_pred HHHHHHHHHHHhCCCHHHHhCCCCCCcccchHHHHHHHHHHHHcCC--CHHHHHHHHCCChhHHHHHHHHHHHHh
No 467
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=36.08 E-value=48 Score=33.23 Aligned_cols=34 Identities=9% Similarity=-0.011 Sum_probs=27.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccC
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDLL 320 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Li 320 (510)
...+.+|||+.+|+++.||+.++..-...+...+
T Consensus 176 eg~S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l 209 (244)
T TIGR03001 176 DGLSMDRIGAMYQVHRSTVSRWVAQARERLLERT 209 (244)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4788999999999999999988776666555443
No 468
>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=35.99 E-value=17 Score=31.59 Aligned_cols=27 Identities=33% Similarity=0.795 Sum_probs=20.7
Q ss_pred CCCCCCCCCCcccccCCCCccccccccceec
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRVI 32 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vl 32 (510)
.||.|+.. .+--.+.|- -.|..||.++
T Consensus 37 ~CpfCgk~--~vkR~a~GI--W~C~~C~~~~ 63 (91)
T TIGR00280 37 VCPFCGKK--TVKRGSTGI--WTCRKCGAKF 63 (91)
T ss_pred cCCCCCCC--ceEEEeeEE--EEcCCCCCEE
Confidence 69999873 334456775 9999999986
No 469
>PF13309 HTH_22: HTH domain
Probab=35.89 E-value=83 Score=25.18 Aligned_cols=55 Identities=9% Similarity=0.026 Sum_probs=37.8
Q ss_pred hhhHHHHHhhcCCCHHHHHHH--HHHHHHHHhccccCCCChHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHH
Q 046187 232 AVHMPRFCTLLQLNKSAQVLA--THIGEVVINKCFCTRRNPISISAAAIYLACQLEDKRKTQAEICKVTGLTEVTLR 306 (510)
Q Consensus 232 ~~~I~Rfcs~L~L~~~V~~~A--~~Ia~~a~~~~l~~GRsP~sIAAAaIYlAarl~g~~~t~keIa~vagVSe~TIR 306 (510)
+..|..++...+.+....... ..|++.+.+.++.. .+-....||+.+|||+.||=
T Consensus 4 ~~~i~~~~~~~~~~~~~l~~~~k~~iV~~L~~~G~F~--------------------lKgav~~vA~~L~iS~~TVY 60 (64)
T PF13309_consen 4 ESIIEEVIAEVGKPPSRLSKEEKKEIVRQLYEKGIFL--------------------LKGAVEYVAEKLGISRATVY 60 (64)
T ss_pred HHHHHHHHHHhCCChhhCCHHHHHHHHHHHHHCCCcc--------------------cCcHHHHHHHHHCCCHHHHH
Confidence 467778888888776543333 45666666665443 45567789999999999974
No 470
>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=35.83 E-value=19 Score=27.12 Aligned_cols=35 Identities=20% Similarity=0.426 Sum_probs=19.2
Q ss_pred CCCCCCCCCCcccccCCCCccccccccceeccccee
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRVIAERQC 37 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vleer~I 37 (510)
+|++|+..-..+.-.+. +....|..||..--++++
T Consensus 7 ~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~~~~~r~~ 41 (52)
T TIGR02605 7 RCTACGHRFEVLQKMSD-DPLATCPECGGEKLRRLL 41 (52)
T ss_pred EeCCCCCEeEEEEecCC-CCCCCCCCCCCCceeEEe
Confidence 69999872222221122 223789999983224444
No 471
>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=35.83 E-value=43 Score=26.41 Aligned_cols=22 Identities=32% Similarity=0.407 Sum_probs=18.4
Q ss_pred CHHHHHHHhCCCHHHHHHHHHH
Q 046187 290 TQAEICKVTGLTEVTLRKVYKE 311 (510)
Q Consensus 290 t~keIa~vagVSe~TIRkrYKE 311 (510)
+..|+|+.+||+..|||...++
T Consensus 2 ~i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 2 TIGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHh
Confidence 5789999999999999955443
No 472
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=35.80 E-value=12 Score=38.74 Aligned_cols=28 Identities=29% Similarity=0.669 Sum_probs=18.5
Q ss_pred CCCCCCCCCCcccccCCCCccccccccceec
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRVI 32 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vl 32 (510)
+||.|+..-.. -|-.+-. .||.+||.-.
T Consensus 30 KCp~c~~~~y~-~eL~~n~--~vcp~c~~h~ 57 (294)
T COG0777 30 KCPSCGEMLYR-KELESNL--KVCPKCGHHM 57 (294)
T ss_pred ECCCccceeeH-HHHHhhh--hcccccCccc
Confidence 79999882111 2333444 8999999865
No 473
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR 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 Gram-positive lineages and does not include the TreR from E. coli.
Probab=35.79 E-value=43 Score=32.71 Aligned_cols=30 Identities=23% Similarity=0.246 Sum_probs=25.7
Q ss_pred CCCCC-HHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 286 DKRKT-QAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 286 g~~~t-~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
|.+++ -.++++.+|||..|||+++.+|.+.
T Consensus 21 G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~e 51 (233)
T TIGR02404 21 GDYLPSEHELMDQYGASRETVRKALNLLTEA 51 (233)
T ss_pred CCCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 45554 6799999999999999999999874
No 474
>PRK07218 replication factor A; Provisional
Probab=35.70 E-value=18 Score=39.56 Aligned_cols=20 Identities=35% Similarity=0.848 Sum_probs=14.1
Q ss_pred CCCCCCCCCCcccccCCCCcccccccccee
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRV 31 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~V 31 (510)
+||+|+.. + + . .+|..||-|
T Consensus 299 rCP~C~r~---v-~--~----~~C~~hG~v 318 (423)
T PRK07218 299 RCPECGRV---I-Q--K----GQCRSHGAV 318 (423)
T ss_pred cCcCcccc---c-c--C----CcCCCCCCc
Confidence 59999873 2 1 2 469999987
No 475
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=35.61 E-value=92 Score=30.40 Aligned_cols=44 Identities=16% Similarity=0.345 Sum_probs=36.6
Q ss_pred hHHHHHHHHHHHHHHcCCC-CCHHHHHHHhCCCHHHHHHHHHHHHHhhc
Q 046187 270 PISISAAAIYLACQLEDKR-KTQAEICKVTGLTEVTLRKVYKELLENWD 317 (510)
Q Consensus 270 P~sIAAAaIYlAarl~g~~-~t~keIa~vagVSe~TIRkrYKEL~e~l~ 317 (510)
...+.=|+||. .|.+ ++.++|+++++++...|++...+|.....
T Consensus 5 ~~~~iEA~LF~----sg~pgls~~~La~~l~~~~~~v~~~l~~L~~~y~ 49 (188)
T PRK00135 5 YKSIIEALLFV----SGEEGLSLEQLAEILELEPTEVQQLLEELQEKYE 49 (188)
T ss_pred HHHHHHHHHHH----cCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence 44666777775 4776 99999999999999999999999988765
No 476
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=35.53 E-value=50 Score=33.59 Aligned_cols=35 Identities=14% Similarity=0.088 Sum_probs=30.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccCC
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDLLP 321 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Lip 321 (510)
...+.+|||+.+|+|+.|+++++..-...+....+
T Consensus 130 ~g~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~~ 164 (293)
T PRK09636 130 FGVPFDEIASTLGRSPAACRQLASRARKHVRAARP 164 (293)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence 46899999999999999999998887777776544
No 477
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=35.43 E-value=75 Score=26.21 Aligned_cols=30 Identities=20% Similarity=0.309 Sum_probs=21.1
Q ss_pred HHHHHcCCCCCHHHHHHHhCCCHHHHHHHH
Q 046187 280 LACQLEDKRKTQAEICKVTGLTEVTLRKVY 309 (510)
Q Consensus 280 lAarl~g~~~t~keIa~vagVSe~TIRkrY 309 (510)
+...+-...+||+++|+.+|++..+|.+-.
T Consensus 23 i~~~~~~~~ltQ~e~A~~lgisq~~vS~l~ 52 (80)
T PF13744_consen 23 IRELREERGLTQAELAERLGISQPRVSRLE 52 (80)
T ss_dssp HHHHHHCCT--HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHHCCChhHHHHHH
Confidence 344455678999999999999999998654
No 478
>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=35.43 E-value=26 Score=23.27 Aligned_cols=24 Identities=25% Similarity=0.562 Sum_probs=13.3
Q ss_pred CCCCCCCCCcccccCCCCccccccccce
Q 046187 3 CPYCSAAQGRCATTSTGRSITECGSCGR 30 (510)
Q Consensus 3 Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~ 30 (510)
|..|+. .|.....|. ...|.+||.
T Consensus 1 C~sC~~---~i~~r~~~v-~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGR---PIAPREQAV-PFPCPNCGF 24 (24)
T ss_pred CccCCC---cccCcccCc-eEeCCCCCC
Confidence 566765 233333233 478888883
No 479
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=35.42 E-value=1.1e+02 Score=30.73 Aligned_cols=53 Identities=19% Similarity=0.249 Sum_probs=35.8
Q ss_pred hHHHHHhhcC-CCHHHHHHHHHHHHHHHhccccCCCChHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHH
Q 046187 234 HMPRFCTLLQ-LNKSAQVLATHIGEVVINKCFCTRRNPISISAAAIYLACQLEDKRKTQAEICKVTGLTEVTLRKVYK 310 (510)
Q Consensus 234 ~I~Rfcs~L~-L~~~V~~~A~~Ia~~a~~~~l~~GRsP~sIAAAaIYlAarl~g~~~t~keIa~vagVSe~TIRkrYK 310 (510)
++.++-.++. |++.-.++|..|++.. .-+ ...+.+++|+.++||+.||-+..|
T Consensus 3 i~~~i~~~~~~Lt~~e~~Ia~yil~n~-----------~~v-------------~~~si~~lA~~~~vS~aTv~Rf~k 56 (284)
T PRK11302 3 MLEKIQSRLEHLSKSERKVAEVILASP-----------QTA-------------IHSSIATLAKMANVSEPTVNRFCR 56 (284)
T ss_pred HHHHHHHHHhhCCHHHHHHHHHHHhCH-----------HHH-------------HhcCHHHHHHHhCCCHHHHHHHHH
Confidence 3445555554 6777777777776532 222 246899999999999999975543
No 480
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=35.34 E-value=83 Score=27.08 Aligned_cols=37 Identities=14% Similarity=0.047 Sum_probs=30.3
Q ss_pred HHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 279 YLACQLEDKRKTQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 279 YlAarl~g~~~t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
.|+-++.....++.++|+.+|||..|..+....+...
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 3455556678899999999999999999988877754
No 481
>PF09241 Herp-Cyclin: Herpesviridae viral cyclin; InterPro: IPR015322 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 represents a domain found in a family of viral cyclins that specifically activate CDK6 of host cells to a very high degree []. This domain adopts a helical structure consisting of five alpha-helices, with one helix surrounded by the others.; PDB: 1XO2_A 1JOW_A 2F2C_A 2EUF_A 1BU2_A.
Probab=35.31 E-value=3e+02 Score=23.83 Aligned_cols=86 Identities=13% Similarity=0.203 Sum_probs=57.4
Q ss_pred hhhHHHHHhhcCCCHH----HHHHH-HHHHHHHHhccccCCCChHHHHHHHHHHHHHHcCCCC-----CHHHHHHHhCCC
Q 046187 232 AVHMPRFCTLLQLNKS----AQVLA-THIGEVVINKCFCTRRNPISISAAAIYLACQLEDKRK-----TQAEICKVTGLT 301 (510)
Q Consensus 232 ~~~I~Rfcs~L~L~~~----V~~~A-~~Ia~~a~~~~l~~GRsP~sIAAAaIYlAarl~g~~~-----t~keIa~vagVS 301 (510)
.+|+--.|+.|.++++ ..+.+ ..|.+...+-.+ .=-+|--|||+-++-.-+--+.+. -+.+++.+++.|
T Consensus 5 tdflip~c~alkipe~~wpql~e~~s~tickaliqpni-all~p~licaggllttiet~ntn~~~wt~yledl~~ilnfs 83 (106)
T PF09241_consen 5 TDFLIPVCHALKIPEDFWPQLFEATSITICKALIQPNI-ALLPPCLICAGGLLTTIETDNTNCQPWTCYLEDLSCILNFS 83 (106)
T ss_dssp GGGHHHHHHHTT--GGGHHHHHHHHHHHHHHHTTSGGG-GGS-HHHHHHHHHHHHHHTS-TSSSTCHHHHHHHHHHHTCH
T ss_pred hhhHHHhhhhccCcHHHhHHHHHHHHHHHHHHHcCCCc-cccCcceeecccceEEEeccCCCCcchhhhHHhhHHHhhcc
Confidence 4788899999999864 33443 345554444333 235788999999887765444331 168999999999
Q ss_pred HHHHHHHHHHHHHhhcc
Q 046187 302 EVTLRKVYKELLENWDD 318 (510)
Q Consensus 302 e~TIRkrYKEL~e~l~~ 318 (510)
..|||.+-....+.+..
T Consensus 84 tntirt~kdqv~ea~~~ 100 (106)
T PF09241_consen 84 TNTIRTVKDQVSEAFST 100 (106)
T ss_dssp HHHHHHHHHHHHHHHHT
T ss_pred cchhhhHHHHHHHHHHh
Confidence 99999887777776543
No 482
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=35.24 E-value=43 Score=30.78 Aligned_cols=32 Identities=19% Similarity=0.165 Sum_probs=26.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
...+.++||+.+|++..|++++...-.+.+..
T Consensus 141 ~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~~ 172 (176)
T PRK09638 141 YGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRK 172 (176)
T ss_pred cCCCHHHHHHHHCCChhHHHHHHHHHHHHHHH
Confidence 47899999999999999998887766665543
No 483
>PRK14086 dnaA chromosomal replication initiation protein; Provisional
Probab=35.23 E-value=3.4e+02 Score=31.45 Aligned_cols=40 Identities=18% Similarity=0.203 Sum_probs=33.1
Q ss_pred HHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhc
Q 046187 276 AAIYLACQLEDKRKTQAEICKVTGLTEVTLRKVYKELLENWD 317 (510)
Q Consensus 276 AaIYlAarl~g~~~t~keIa~vagVSe~TIRkrYKEL~e~l~ 317 (510)
.|+||+-++. ..+..+|++.+|-...||-.+++.|.+.+.
T Consensus 559 iAMYL~r~lt--~~Sl~~IG~~FgRdHSTV~~A~~kI~~~~~ 598 (617)
T PRK14086 559 IAMYLCRELT--DLSLPKIGQQFGRDHTTVMHADRKIRALMA 598 (617)
T ss_pred HHHHHHHHHc--CCCHHHHHHHhCCChhHHHHHHHHHHHHHH
Confidence 4677776655 678999999999999999999998887654
No 484
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=35.20 E-value=28 Score=35.20 Aligned_cols=22 Identities=23% Similarity=0.336 Sum_probs=19.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHH
Q 046187 289 KTQAEICKVTGLTEVTLRKVYK 310 (510)
Q Consensus 289 ~t~keIa~vagVSe~TIRkrYK 310 (510)
.|++|||+.+|||..|+++++.
T Consensus 2 ~ti~dIA~~agVS~~TVSrvln 23 (327)
T PRK10339 2 ATLKDIAIEAGVSLATVSRVLN 23 (327)
T ss_pred CCHHHHHHHhCCCHHhhhhhhc
Confidence 4899999999999999998764
No 485
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=35.00 E-value=54 Score=30.89 Aligned_cols=35 Identities=20% Similarity=0.174 Sum_probs=28.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccCC
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDDLLP 321 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~Lip 321 (510)
...+..|||+.+|+|..||++++......+...+.
T Consensus 121 ~g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 155 (181)
T PRK09637 121 EGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLE 155 (181)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 47889999999999999999887766666655443
No 486
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=34.98 E-value=45 Score=32.88 Aligned_cols=30 Identities=17% Similarity=0.275 Sum_probs=25.3
Q ss_pred CCCCC-HHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 286 DKRKT-QAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 286 g~~~t-~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
|..++ -.++|+.+|||..|||+++.+|...
T Consensus 32 G~~LPsE~eLa~~~~VSR~TVR~Al~~L~~e 62 (241)
T PRK10079 32 GDYLPAEQQLAARYEVNRHTLRRAIDQLVEK 62 (241)
T ss_pred CCcCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 44544 6799999999999999999999874
No 487
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=34.85 E-value=59 Score=24.04 Aligned_cols=26 Identities=12% Similarity=0.207 Sum_probs=24.1
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHH
Q 046187 194 TLQEISIAANVPQKEIGKYIKILGEA 219 (510)
Q Consensus 194 TLkEIa~vt~VskkeIgr~yk~L~k~ 219 (510)
+.+||++.++++...+.+.++.|.+.
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~L~~~ 47 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSRLEAE 47 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 89999999999999999999999873
No 488
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.85 E-value=21 Score=32.26 Aligned_cols=27 Identities=7% Similarity=-0.011 Sum_probs=21.1
Q ss_pred CCCCCCCCCCcccccCCCCccccccccceecc
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRVIA 33 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vle 33 (510)
+||+|++ ..+|-.+-- .||..||.-.-
T Consensus 11 idPetg~---KFYDLNrdP--iVsPytG~s~P 37 (129)
T COG4530 11 IDPETGK---KFYDLNRDP--IVSPYTGKSYP 37 (129)
T ss_pred cCccccc---hhhccCCCc--cccCcccccch
Confidence 6999988 457766666 99999997653
No 489
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=34.67 E-value=18 Score=31.38 Aligned_cols=27 Identities=33% Similarity=0.797 Sum_probs=20.5
Q ss_pred CCCCCCCCCCcccccCCCCccccccccceec
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRVI 32 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~Vl 32 (510)
.||.|+.. .+--.+.|- -.|..||.++
T Consensus 38 ~CpfCgk~--~vkR~a~GI--W~C~~C~~~~ 64 (90)
T PRK03976 38 VCPVCGRP--KVKRVGTGI--WECRKCGAKF 64 (90)
T ss_pred cCCCCCCC--ceEEEEEEE--EEcCCCCCEE
Confidence 69999763 334456775 9999999986
No 490
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
Probab=34.65 E-value=46 Score=32.39 Aligned_cols=30 Identities=17% Similarity=0.313 Sum_probs=25.7
Q ss_pred CCCC-CHHHHHHHhCCCHHHHHHHHHHHHHh
Q 046187 286 DKRK-TQAEICKVTGLTEVTLRKVYKELLEN 315 (510)
Q Consensus 286 g~~~-t~keIa~vagVSe~TIRkrYKEL~e~ 315 (510)
|.++ +-.|+|+.+|||..|||+++++|.+.
T Consensus 29 G~~LPsE~eLa~~~~VSR~TvR~Al~~L~~e 59 (238)
T TIGR02325 29 GDYLPAEMQLAERFGVNRHTVRRAIAALVER 59 (238)
T ss_pred CCcCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 4455 46799999999999999999999874
No 491
>PRK15482 transcriptional regulator MurR; Provisional
Probab=34.64 E-value=1.1e+02 Score=30.83 Aligned_cols=53 Identities=11% Similarity=0.204 Sum_probs=35.7
Q ss_pred hHHHHHhhcC-CCHHHHHHHHHHHHHHHhccccCCCChHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHH
Q 046187 234 HMPRFCTLLQ-LNKSAQVLATHIGEVVINKCFCTRRNPISISAAAIYLACQLEDKRKTQAEICKVTGLTEVTLRKVYK 310 (510)
Q Consensus 234 ~I~Rfcs~L~-L~~~V~~~A~~Ia~~a~~~~l~~GRsP~sIAAAaIYlAarl~g~~~t~keIa~vagVSe~TIRkrYK 310 (510)
++.|+-.+.. |++.-+++|..|++. |.-+ ...+..|+|+.++||+.||-+..|
T Consensus 3 ~l~~i~~~~~~Lt~~e~~Ia~yIl~n-----------~~~v-------------~~~si~elA~~~~vS~aTv~Rf~k 56 (285)
T PRK15482 3 YLTKIRNAESEFTENEQKIADFLRAN-----------VSEL-------------KSVSSRKMAKQLGISQSSIVKFAQ 56 (285)
T ss_pred HHHHHHHHHhhcCHHHHHHHHHHHhC-----------HHHH-------------HhcCHHHHHHHhCCCHHHHHHHHH
Confidence 4455555543 677667777776653 3222 246789999999999999975543
No 492
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=34.54 E-value=35 Score=34.81 Aligned_cols=22 Identities=18% Similarity=0.382 Sum_probs=19.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHH
Q 046187 289 KTQAEICKVTGLTEVTLRKVYK 310 (510)
Q Consensus 289 ~t~keIa~vagVSe~TIRkrYK 310 (510)
.|++|||+.+|||..|+.+++.
T Consensus 2 ~ti~dIA~~aGVS~~TVSrvLn 23 (346)
T PRK10401 2 ITIRDVARQAGVSVATVSRVLN 23 (346)
T ss_pred CCHHHHHHHhCCCHHHHHHHHC
Confidence 4899999999999999987764
No 493
>PRK08402 replication factor A; Reviewed
Probab=34.32 E-value=23 Score=37.83 Aligned_cols=26 Identities=27% Similarity=0.447 Sum_probs=19.3
Q ss_pred CCCCCCCCCCcccccCCCCcccccccccee
Q 046187 2 KCPYCSAAQGRCATTSTGRSITECGSCGRV 31 (510)
Q Consensus 2 ~Cp~C~~~~~~i~D~~~Gd~~~VC~~CG~V 31 (510)
.||+|.. .+..|...|. ..|..||.|
T Consensus 214 aCp~CnK--kv~~~~~~~~--~~Ce~~~~v 239 (355)
T PRK08402 214 ACPECRR--KVDYDPATDT--WICPEHGEV 239 (355)
T ss_pred cCCCCCe--EEEEecCCCC--EeCCCCCCc
Confidence 5999987 2323666777 899999964
No 494
>PF13730 HTH_36: Helix-turn-helix domain
Probab=34.27 E-value=88 Score=23.40 Aligned_cols=25 Identities=20% Similarity=0.322 Sum_probs=22.9
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHHH
Q 046187 194 TLQEISIAANVPQKEIGKYIKILGE 218 (510)
Q Consensus 194 TLkEIa~vt~VskkeIgr~yk~L~k 218 (510)
+...|++.+++++..|.++++.|.+
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~ 51 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEE 51 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 8999999999999999999988865
No 495
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=34.23 E-value=1.4e+02 Score=25.41 Aligned_cols=39 Identities=5% Similarity=0.101 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046187 177 LATAALVQAIREAQEPRTLQEISIAANVPQKEIGKYIKIL 216 (510)
Q Consensus 177 VaAACLYIACR~~~~PrTLkEIa~vt~VskkeIgr~yk~L 216 (510)
+..+.-|+... ...+.++.|||..++++...|.|.|++.
T Consensus 7 ~~~~~~~i~~~-~~~~~~~~~lA~~~~~S~~~l~r~f~~~ 45 (107)
T PRK10219 7 IQTLIAWIDEH-IDQPLNIDVVAKKSGYSKWYLQRMFRTV 45 (107)
T ss_pred HHHHHHHHHHh-cCCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 34445555544 4567999999999999999988877653
No 496
>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=34.23 E-value=47 Score=24.69 Aligned_cols=25 Identities=20% Similarity=0.415 Sum_probs=19.0
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHH
Q 046187 286 DKRKTQAEICKVTGLTEVTLRKVYK 310 (510)
Q Consensus 286 g~~~t~keIa~vagVSe~TIRkrYK 310 (510)
...++++|+|+.+||+..||.+..+
T Consensus 7 ~~gls~~~la~~~gis~~~i~~~~~ 31 (55)
T PF01381_consen 7 EKGLSQKELAEKLGISRSTISRIEN 31 (55)
T ss_dssp HTTS-HHHHHHHHTS-HHHHHHHHT
T ss_pred HcCCCHHHHHHHhCCCcchhHHHhc
Confidence 4578999999999999999986543
No 497
>PRK10651 transcriptional regulator NarL; Provisional
Probab=34.20 E-value=64 Score=29.43 Aligned_cols=32 Identities=19% Similarity=0.198 Sum_probs=28.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q 046187 287 KRKTQAEICKVTGLTEVTLRKVYKELLENWDD 318 (510)
Q Consensus 287 ~~~t~keIa~vagVSe~TIRkrYKEL~e~l~~ 318 (510)
...+.++|++.+++|+.||+...+.|+..+..
T Consensus 169 ~g~~~~~ia~~l~is~~tV~~~~~~l~~Kl~~ 200 (216)
T PRK10651 169 QGLPNKMIARRLDITESTVKVHVKHMLKKMKL 200 (216)
T ss_pred cCCCHHHHHHHcCCCHHHHHHHHHHHHHHcCC
Confidence 45789999999999999999999999988764
No 498
>PHA00542 putative Cro-like protein
Probab=33.83 E-value=51 Score=27.55 Aligned_cols=27 Identities=22% Similarity=0.368 Sum_probs=22.3
Q ss_pred HcCCCCCHHHHHHHhCCCHHHHHHHHH
Q 046187 284 LEDKRKTQAEICKVTGLTEVTLRKVYK 310 (510)
Q Consensus 284 l~g~~~t~keIa~vagVSe~TIRkrYK 310 (510)
+....+++.++|+.+||+..||.+...
T Consensus 27 l~~~glTq~elA~~lgIs~~tIsr~e~ 53 (82)
T PHA00542 27 LIRAGWSQEQIADATDVSQPTICRIYS 53 (82)
T ss_pred HHHCCCCHHHHHHHHCcCHHHHHHHHc
Confidence 345678999999999999999986653
No 499
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=33.74 E-value=35 Score=34.75 Aligned_cols=21 Identities=19% Similarity=0.458 Sum_probs=18.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHH
Q 046187 289 KTQAEICKVTGLTEVTLRKVY 309 (510)
Q Consensus 289 ~t~keIa~vagVSe~TIRkrY 309 (510)
.|++|||+.+|||..|+.+.+
T Consensus 2 ~ti~dIA~~aGVS~~TVSrvL 22 (343)
T PRK10727 2 ATIKDVARLAGVSVATVSRVI 22 (343)
T ss_pred CCHHHHHHHhCCCHHHHHHHh
Confidence 479999999999999996554
No 500
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=33.66 E-value=82 Score=28.66 Aligned_cols=44 Identities=18% Similarity=0.117 Sum_probs=35.5
Q ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 046187 176 ALATAALVQAIREAQEPRTLQEISIAANVPQKEIGKYIKILGEA 219 (510)
Q Consensus 176 aVaAACLYIACR~~~~PrTLkEIa~vt~VskkeIgr~yk~L~k~ 219 (510)
.-+-+.+|++-...+.+.+.+|||..++|+..-|.+++..|.+.
T Consensus 9 YAl~~~i~la~~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~ 52 (141)
T PRK11014 9 YGLRALIYMASLPEGRMTSISEVTEVYGVSRNHMVKIINQLSRA 52 (141)
T ss_pred HHHHHHHHHhcCCCCCccCHHHHHHHHCcCHHHHHHHHHHHHhC
Confidence 33455667775556678899999999999999999999998774
Done!