Query psy3716
Match_columns 436
No_of_seqs 290 out of 675
Neff 6.3
Searched_HMMs 46136
Date Fri Aug 16 23:42:08 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3716.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3716hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2908|consensus 100.0 8.9E-92 1.9E-96 687.5 34.5 351 5-362 2-355 (380)
2 KOG2753|consensus 100.0 9.5E-41 2.1E-45 326.5 22.7 302 42-362 47-355 (378)
3 KOG2908|consensus 99.9 2.2E-23 4.7E-28 205.8 18.2 76 350-425 277-352 (380)
4 KOG3250|consensus 99.8 6.4E-21 1.4E-25 177.5 7.4 168 208-391 26-194 (258)
5 PF01399 PCI: PCI domain; Int 99.6 8.4E-15 1.8E-19 122.4 11.0 100 243-346 2-105 (105)
6 KOG1464|consensus 99.4 3.5E-11 7.6E-16 117.2 17.3 273 60-346 82-409 (440)
7 smart00753 PAM PCI/PINT associ 99.3 1.2E-11 2.6E-16 101.3 6.8 81 275-361 2-82 (88)
8 smart00088 PINT motif in prote 99.3 1.2E-11 2.6E-16 101.3 6.8 81 275-361 2-82 (88)
9 KOG2753|consensus 99.1 6E-11 1.3E-15 117.7 3.7 78 350-432 281-358 (378)
10 smart00088 PINT motif in prote 98.8 1.5E-08 3.2E-13 82.9 6.2 64 365-431 22-85 (88)
11 smart00753 PAM PCI/PINT associ 98.8 1.5E-08 3.2E-13 82.9 6.2 64 365-431 22-85 (88)
12 KOG2581|consensus 98.5 4.8E-05 1E-09 78.1 24.2 166 161-342 244-419 (493)
13 PF01399 PCI: PCI domain; Int 98.5 1.5E-07 3.2E-12 78.4 5.1 48 365-412 58-105 (105)
14 KOG0687|consensus 98.0 0.0034 7.3E-08 63.3 23.3 284 37-346 62-362 (393)
15 KOG1463|consensus 97.8 0.0011 2.3E-08 67.2 16.1 243 94-349 142-393 (411)
16 KOG0686|consensus 97.7 0.0012 2.6E-08 68.2 16.2 165 205-393 269-441 (466)
17 COG5187 RPN7 26S proteasome re 97.6 0.044 9.5E-07 54.9 23.7 234 95-347 130-377 (412)
18 KOG1497|consensus 97.4 0.015 3.3E-07 58.6 18.9 86 250-346 271-362 (399)
19 KOG2688|consensus 97.3 0.0057 1.2E-07 63.4 14.1 215 116-349 161-387 (394)
20 KOG2758|consensus 97.2 0.13 2.8E-06 52.1 22.7 187 137-348 181-396 (432)
21 KOG2581|consensus 96.9 0.052 1.1E-06 56.4 17.2 258 117-407 125-418 (493)
22 COG5600 Transcription-associat 96.9 0.21 4.5E-06 51.6 20.6 204 124-349 183-406 (413)
23 COG5159 RPN6 26S proteasome re 96.8 0.31 6.8E-06 48.9 21.1 164 178-346 220-388 (421)
24 KOG3250|consensus 96.2 0.0087 1.9E-07 57.1 5.8 129 288-427 29-170 (258)
25 KOG1498|consensus 96.2 0.37 8E-06 50.1 17.9 249 80-349 131-401 (439)
26 KOG1076|consensus 95.5 5.4 0.00012 44.4 24.6 128 223-350 633-767 (843)
27 PF14938 SNAP: Soluble NSF att 95.3 0.81 1.8E-05 45.3 16.1 172 95-272 89-266 (282)
28 KOG2582|consensus 95.1 1.7 3.7E-05 44.9 17.4 302 22-346 22-360 (422)
29 PF10075 PCI_Csn8: COP9 signal 93.1 0.48 1E-05 42.2 8.2 107 213-325 12-121 (143)
30 KOG1497|consensus 92.3 0.13 2.8E-06 52.1 3.5 49 367-415 317-365 (399)
31 KOG2072|consensus 90.7 35 0.00077 38.9 20.7 204 136-346 245-493 (988)
32 PF09976 TPR_21: Tetratricopep 90.0 11 0.00024 33.1 13.5 128 23-183 10-137 (145)
33 PF09012 FeoC: FeoC like trans 88.4 0.66 1.4E-05 36.2 3.9 45 286-334 3-47 (69)
34 PF03399 SAC3_GANP: SAC3/GANP/ 85.4 11 0.00024 34.9 11.1 100 206-312 101-203 (204)
35 KOG1464|consensus 85.0 0.64 1.4E-05 46.5 2.5 51 360-412 359-409 (440)
36 PF09756 DDRGK: DDRGK domain; 84.4 1.9 4.1E-05 40.8 5.3 85 284-378 100-184 (188)
37 PF09339 HTH_IclR: IclR helix- 84.3 2.2 4.7E-05 31.3 4.6 46 284-332 4-49 (52)
38 PF09743 DUF2042: Uncharacteri 83.1 3 6.5E-05 41.6 6.4 115 300-425 129-243 (272)
39 PF02082 Rrf2: Transcriptional 82.5 4.1 9E-05 32.8 6.0 60 283-345 9-68 (83)
40 COG1595 RpoE DNA-directed RNA 81.5 11 0.00024 34.4 9.3 27 301-327 143-169 (182)
41 TIGR02010 IscR iron-sulfur clu 81.5 4.3 9.3E-05 35.8 6.2 51 281-333 7-57 (135)
42 PF10602 RPN7: 26S proteasome 79.6 52 0.0011 30.5 14.4 117 93-218 49-168 (177)
43 PRK10857 DNA-binding transcrip 78.4 6 0.00013 36.4 6.3 52 280-333 6-57 (164)
44 PF09012 FeoC: FeoC like trans 77.9 3 6.4E-05 32.5 3.5 38 365-402 12-49 (69)
45 PF13412 HTH_24: Winged helix- 77.2 7.4 0.00016 27.7 5.2 39 290-332 10-48 (48)
46 PRK12529 RNA polymerase sigma 74.7 40 0.00087 30.6 10.8 27 301-327 143-169 (178)
47 smart00346 HTH_ICLR helix_turn 72.3 11 0.00024 30.2 5.7 48 284-334 6-53 (91)
48 PF13424 TPR_12: Tetratricopep 71.3 44 0.00095 25.6 9.2 64 120-188 7-70 (78)
49 PF08281 Sigma70_r4_2: Sigma-7 70.5 5.4 0.00012 29.1 3.2 27 301-327 26-52 (54)
50 PRK07670 RNA polymerase sigma 70.2 11 0.00025 36.5 6.4 91 300-393 124-243 (251)
51 TIGR02944 suf_reg_Xantho FeS a 69.5 10 0.00022 32.9 5.3 47 285-334 12-58 (130)
52 TIGR00738 rrf2_super rrf2 fami 68.8 15 0.00033 31.7 6.3 50 282-333 8-57 (132)
53 PRK11179 DNA-binding transcrip 67.6 11 0.00025 33.8 5.3 34 300-333 22-55 (153)
54 PRK09651 RNA polymerase sigma 66.4 97 0.0021 27.9 11.3 28 300-327 134-161 (172)
55 PF09295 ChAPs: ChAPs (Chs5p-A 66.2 1.6E+02 0.0035 31.1 14.2 128 42-197 170-297 (395)
56 smart00344 HTH_ASNC helix_turn 65.9 14 0.0003 30.7 5.2 34 300-333 16-49 (108)
57 PRK12525 RNA polymerase sigma 65.3 83 0.0018 28.2 10.6 27 301-327 134-160 (168)
58 PRK11920 rirA iron-responsive 64.7 14 0.0003 33.5 5.3 49 284-335 10-58 (153)
59 PF04545 Sigma70_r4: Sigma-70, 64.1 16 0.00036 26.2 4.6 28 300-327 19-46 (50)
60 COG1522 Lrp Transcriptional re 61.3 11 0.00024 33.3 4.0 34 301-334 22-55 (154)
61 PF02284 COX5A: Cytochrome c o 61.0 1.1E+02 0.0024 26.4 9.7 68 44-115 12-80 (108)
62 PF02082 Rrf2: Transcriptional 60.7 16 0.00035 29.3 4.5 57 366-424 24-80 (83)
63 PF04967 HTH_10: HTH DNA bindi 60.5 14 0.00031 27.7 3.8 32 293-327 18-49 (53)
64 KOG0686|consensus 60.3 12 0.00027 39.3 4.6 53 367-419 365-417 (466)
65 PF13730 HTH_36: Helix-turn-he 59.1 43 0.00094 24.2 6.2 50 280-331 6-55 (55)
66 smart00550 Zalpha Z-DNA-bindin 58.9 24 0.00051 27.5 5.0 33 301-333 22-54 (68)
67 PF09756 DDRGK: DDRGK domain; 58.7 13 0.00029 35.1 4.2 47 365-411 111-157 (188)
68 PF01978 TrmB: Sugar-specific 58.6 11 0.00023 29.0 2.9 36 300-335 21-56 (68)
69 COG1191 FliA DNA-directed RNA 58.5 21 0.00046 35.2 5.7 94 299-393 124-238 (247)
70 PF01022 HTH_5: Bacterial regu 58.5 31 0.00067 24.6 5.2 33 300-332 14-46 (47)
71 PF08784 RPA_C: Replication pr 58.4 18 0.0004 30.1 4.6 39 299-337 63-101 (102)
72 PF08281 Sigma70_r4_2: Sigma-7 58.2 13 0.00029 26.9 3.3 27 367-393 26-52 (54)
73 PF09743 DUF2042: Uncharacteri 57.7 40 0.00086 33.7 7.5 93 300-404 69-167 (272)
74 TIGR02997 Sig70-cyanoRpoD RNA 57.5 18 0.00039 36.2 5.2 90 300-393 176-295 (298)
75 COG1959 Predicted transcriptio 56.6 30 0.00064 31.3 5.9 51 282-334 8-58 (150)
76 cd00092 HTH_CRP helix_turn_hel 56.5 34 0.00073 25.5 5.4 35 299-333 23-57 (67)
77 PF12840 HTH_20: Helix-turn-he 56.3 31 0.00067 25.9 5.2 35 300-334 23-57 (61)
78 PRK07122 RNA polymerase sigma 56.1 39 0.00086 33.2 7.2 92 300-393 142-257 (264)
79 PF08784 RPA_C: Replication pr 55.9 17 0.00036 30.3 3.9 40 364-403 62-101 (102)
80 PF13412 HTH_24: Winged helix- 55.3 21 0.00046 25.3 3.9 32 367-398 17-48 (48)
81 PF09339 HTH_IclR: IclR helix- 54.2 23 0.00049 25.8 4.0 34 365-398 16-49 (52)
82 TIGR02479 FliA_WhiG RNA polyme 52.8 21 0.00046 33.8 4.6 27 367-393 191-217 (224)
83 PF09202 Rio2_N: Rio2, N-termi 52.5 33 0.00072 28.0 5.0 66 282-351 8-73 (82)
84 PF13404 HTH_AsnC-type: AsnC-t 52.3 21 0.00045 25.3 3.3 21 300-320 16-36 (42)
85 PF01978 TrmB: Sugar-specific 52.1 20 0.00044 27.4 3.6 37 365-401 20-56 (68)
86 smart00653 eIF2B_5 domain pres 51.5 46 0.00099 28.8 6.0 61 367-435 21-81 (110)
87 PRK00135 scpB segregation and 51.4 71 0.0015 30.2 7.8 110 283-398 3-132 (188)
88 TIGR02941 Sigma_B RNA polymera 51.3 20 0.00043 34.8 4.2 27 367-393 221-247 (255)
89 PF12802 MarR_2: MarR family; 51.3 52 0.0011 24.2 5.7 40 300-339 20-59 (62)
90 TIGR02850 spore_sigG RNA polym 51.1 32 0.0007 33.4 5.7 27 367-393 222-248 (254)
91 PRK11169 leucine-responsive tr 51.1 21 0.00046 32.5 4.1 35 299-333 26-60 (164)
92 PRK05949 RNA polymerase sigma 51.0 38 0.00083 34.6 6.4 28 366-393 285-312 (327)
93 PF09940 DUF2172: Domain of un 50.5 22 0.00047 37.2 4.4 48 279-332 339-386 (386)
94 smart00550 Zalpha Z-DNA-bindin 50.5 24 0.00051 27.5 3.7 41 359-399 14-54 (68)
95 PF10668 Phage_terminase: Phag 49.7 17 0.00037 28.0 2.7 23 299-321 20-42 (60)
96 PRK06986 fliA flagellar biosyn 49.6 28 0.00061 33.3 4.9 27 367-393 200-226 (236)
97 PF13601 HTH_34: Winged helix 49.6 61 0.0013 26.0 6.1 52 284-340 2-53 (80)
98 PRK09210 RNA polymerase sigma 49.6 34 0.00075 35.4 5.9 90 300-393 231-351 (367)
99 KOG3054|consensus 49.3 24 0.00051 34.8 4.2 72 299-378 212-285 (299)
100 PF11817 Foie-gras_1: Foie gra 49.1 2.1E+02 0.0045 27.8 10.9 92 93-192 151-246 (247)
101 PF04545 Sigma70_r4: Sigma-70, 49.1 24 0.00052 25.3 3.4 28 366-393 19-46 (50)
102 smart00422 HTH_MERR helix_turn 48.9 38 0.00083 25.6 4.7 66 302-387 1-66 (70)
103 PRK09191 two-component respons 48.1 1.2E+02 0.0027 28.5 9.2 27 301-327 104-130 (261)
104 PF13463 HTH_27: Winged helix 47.9 24 0.00053 26.5 3.4 44 364-407 15-58 (68)
105 PF12802 MarR_2: MarR family; 47.7 32 0.00068 25.4 4.0 41 366-406 20-60 (62)
106 PRK06288 RNA polymerase sigma 47.7 19 0.00042 35.3 3.5 27 367-393 228-254 (268)
107 PF10007 DUF2250: Uncharacteri 47.7 21 0.00046 29.9 3.2 29 370-398 24-52 (92)
108 PRK07408 RNA polymerase sigma 47.4 54 0.0012 32.0 6.6 27 367-393 219-245 (256)
109 PF10007 DUF2250: Uncharacteri 47.4 21 0.00047 29.8 3.2 28 305-332 25-52 (92)
110 TIGR02431 pcaR_pcaU beta-ketoa 47.3 40 0.00086 32.6 5.6 46 284-332 10-55 (248)
111 TIGR02885 spore_sigF RNA polym 47.3 37 0.00079 32.3 5.3 27 367-393 199-225 (231)
112 PF12895 Apc3: Anaphase-promot 47.1 1.4E+02 0.0029 23.3 8.2 79 94-187 3-81 (84)
113 PRK07598 RNA polymerase sigma 46.7 46 0.001 35.3 6.3 90 300-393 277-396 (415)
114 PF14559 TPR_19: Tetratricopep 46.5 42 0.00091 24.8 4.5 50 94-152 5-54 (68)
115 PF08280 HTH_Mga: M protein tr 46.2 60 0.0013 24.4 5.3 38 278-322 3-40 (59)
116 PRK14165 winged helix-turn-hel 46.2 53 0.0012 31.8 6.2 47 300-346 20-66 (217)
117 PRK05911 RNA polymerase sigma 46.1 47 0.001 32.5 6.0 27 367-393 221-247 (257)
118 smart00344 HTH_ASNC helix_turn 46.0 29 0.00062 28.8 3.9 39 367-405 17-55 (108)
119 COG1414 IclR Transcriptional r 45.8 45 0.00097 32.5 5.7 46 284-332 5-50 (246)
120 KOG1126|consensus 44.9 1.2E+02 0.0026 33.8 9.2 160 9-186 407-613 (638)
121 COG5071 RPN5 26S proteasome re 44.9 3.7E+02 0.0081 27.8 17.3 48 300-347 352-399 (439)
122 TIGR02980 SigBFG RNA polymeras 44.9 25 0.00054 33.3 3.7 27 367-393 194-220 (227)
123 PRK12537 RNA polymerase sigma 44.4 24 0.00053 32.1 3.5 27 301-327 149-175 (182)
124 PF03979 Sigma70_r1_1: Sigma-7 44.4 48 0.001 26.7 4.8 42 285-330 9-53 (82)
125 PF12840 HTH_20: Helix-turn-he 44.2 41 0.00089 25.2 4.1 36 365-400 22-57 (61)
126 PRK07405 RNA polymerase sigma 44.1 48 0.001 33.7 5.8 90 300-393 183-302 (317)
127 PF04539 Sigma70_r3: Sigma-70 44.1 22 0.00049 27.7 2.8 26 299-324 18-43 (78)
128 smart00347 HTH_MARR helix_turn 43.7 96 0.0021 24.5 6.6 42 301-342 24-65 (101)
129 smart00418 HTH_ARSR helix_turn 43.5 62 0.0014 23.1 5.0 35 300-334 9-43 (66)
130 PF10975 DUF2802: Protein of u 43.2 25 0.00054 27.9 2.8 23 367-389 44-66 (70)
131 PRK11179 DNA-binding transcrip 43.2 31 0.00067 31.0 3.9 34 367-400 23-56 (153)
132 cd00592 HTH_MerR-like Helix-Tu 42.4 75 0.0016 26.0 5.8 66 302-388 1-66 (100)
133 PF09202 Rio2_N: Rio2, N-termi 42.3 27 0.00059 28.5 3.0 48 358-405 15-62 (82)
134 PF12569 NARP1: NMDA receptor- 42.2 5E+02 0.011 28.4 13.7 19 274-292 344-362 (517)
135 PRK11014 transcriptional repre 42.0 53 0.0012 29.0 5.2 48 285-334 11-58 (141)
136 PRK09047 RNA polymerase factor 41.7 51 0.0011 28.9 5.1 27 301-327 122-148 (161)
137 PHA02943 hypothetical protein; 41.7 71 0.0015 29.4 5.8 34 300-333 23-56 (165)
138 PRK08215 sporulation sigma fac 41.6 52 0.0011 32.0 5.5 27 367-393 225-251 (258)
139 TIGR02393 RpoD_Cterm RNA polym 41.6 53 0.0012 31.5 5.5 28 366-393 195-222 (238)
140 PRK05657 RNA polymerase sigma 41.4 54 0.0012 33.4 5.7 28 366-393 281-308 (325)
141 PRK11569 transcriptional repre 41.3 55 0.0012 32.2 5.7 47 283-332 28-74 (274)
142 cd00090 HTH_ARSR Arsenical Res 41.2 57 0.0012 24.0 4.6 36 302-337 21-56 (78)
143 TIGR02944 suf_reg_Xantho FeS a 41.2 43 0.00094 29.0 4.4 63 365-429 23-85 (130)
144 COG1522 Lrp Transcriptional re 41.1 34 0.00075 30.1 3.8 38 368-405 23-60 (154)
145 COG2524 Predicted transcriptio 41.0 65 0.0014 32.2 5.8 52 280-334 7-58 (294)
146 PF05331 DUF742: Protein of un 40.9 42 0.00092 29.2 4.1 41 287-333 47-87 (114)
147 PF05158 RNA_pol_Rpc34: RNA po 40.7 1.2E+02 0.0026 31.1 8.1 110 299-410 24-145 (327)
148 PF01022 HTH_5: Bacterial regu 40.7 46 0.001 23.6 3.7 33 366-398 14-46 (47)
149 PF08220 HTH_DeoR: DeoR-like h 40.5 65 0.0014 24.0 4.6 42 286-331 3-44 (57)
150 COG5631 Predicted transcriptio 40.4 50 0.0011 30.7 4.6 102 301-417 37-149 (199)
151 PRK10163 DNA-binding transcrip 40.4 59 0.0013 32.0 5.7 47 283-332 25-71 (271)
152 KOG0687|consensus 40.3 28 0.00061 35.8 3.4 46 366-411 316-361 (393)
153 TIGR02959 SigZ RNA polymerase 40.3 1.5E+02 0.0034 26.5 8.1 28 300-327 115-142 (170)
154 cd01104 HTH_MlrA-CarA Helix-Tu 40.3 84 0.0018 23.6 5.4 66 303-388 2-67 (68)
155 PF01325 Fe_dep_repress: Iron 40.1 86 0.0019 23.8 5.3 45 284-332 9-53 (60)
156 smart00419 HTH_CRP helix_turn_ 40.1 49 0.0011 22.8 3.8 33 301-333 8-40 (48)
157 PF04539 Sigma70_r3: Sigma-70 39.6 28 0.00061 27.2 2.7 28 363-390 16-43 (78)
158 PRK06811 RNA polymerase factor 39.5 1.9E+02 0.0042 26.3 8.7 27 301-327 147-173 (189)
159 PF00325 Crp: Bacterial regula 39.4 51 0.0011 22.2 3.4 30 368-397 3-32 (32)
160 PF14947 HTH_45: Winged helix- 39.2 80 0.0017 25.0 5.3 42 300-345 18-59 (77)
161 PF00046 Homeobox: Homeobox do 39.2 31 0.00068 25.2 2.7 24 300-323 26-49 (57)
162 TIGR00311 aIF-2beta translatio 38.9 85 0.0018 28.0 5.9 60 367-435 39-98 (133)
163 PF00403 HMA: Heavy-metal-asso 38.7 63 0.0014 23.9 4.4 45 385-430 13-59 (62)
164 PRK12427 flagellar biosynthesi 38.5 76 0.0017 30.5 6.0 90 300-393 116-225 (231)
165 PRK04214 rbn ribonuclease BN/u 38.0 1.8E+02 0.0038 30.7 9.1 34 299-332 308-341 (412)
166 PRK06759 RNA polymerase factor 37.8 38 0.00082 29.6 3.5 27 301-327 122-148 (154)
167 KOG1498|consensus 37.8 83 0.0018 33.2 6.3 50 366-415 352-401 (439)
168 PF04297 UPF0122: Putative hel 37.7 26 0.00056 29.9 2.3 42 351-392 17-58 (101)
169 PF12569 NARP1: NMDA receptor- 37.6 5.3E+02 0.011 28.2 12.8 114 57-187 121-251 (517)
170 KOG2047|consensus 37.5 2.5E+02 0.0054 31.8 10.1 102 29-155 174-280 (835)
171 PRK09954 putative kinase; Prov 37.3 1E+02 0.0022 31.4 7.0 45 300-344 16-63 (362)
172 TIGR02337 HpaR homoprotocatech 37.1 1.2E+02 0.0026 25.6 6.4 50 300-349 41-90 (118)
173 smart00421 HTH_LUXR helix_turn 37.0 50 0.0011 23.1 3.5 27 301-327 18-44 (58)
174 TIGR03826 YvyF flagellar opero 36.5 30 0.00066 31.1 2.6 31 359-389 38-68 (137)
175 PF00382 TFIIB: Transcription 36.5 54 0.0012 25.3 3.8 67 305-384 2-71 (71)
176 KOG3151|consensus 36.4 4.4E+02 0.0095 26.1 13.5 179 138-323 17-215 (260)
177 PRK09642 RNA polymerase sigma 36.4 41 0.00088 29.7 3.5 27 301-327 122-148 (160)
178 TIGR02999 Sig-70_X6 RNA polyme 36.3 40 0.00087 30.4 3.5 27 301-327 150-176 (183)
179 PF11972 HTH_13: HTH DNA bindi 36.3 77 0.0017 24.0 4.3 37 287-328 3-39 (54)
180 KOG2688|consensus 36.3 32 0.0007 36.2 3.2 49 366-414 332-386 (394)
181 PF10255 Paf67: RNA polymerase 36.0 5.6E+02 0.012 27.2 13.6 187 118-323 122-343 (404)
182 cd04766 HTH_HspR Helix-Turn-He 35.7 1.1E+02 0.0024 24.9 5.7 68 302-389 2-69 (91)
183 PF13411 MerR_1: MerR HTH fami 35.7 78 0.0017 23.9 4.6 64 303-387 2-65 (69)
184 KOG2235|consensus 35.6 45 0.00097 37.0 4.2 99 300-403 132-231 (776)
185 TIGR02983 SigE-fam_strep RNA p 35.6 42 0.00092 29.6 3.5 27 301-327 126-152 (162)
186 PF04703 FaeA: FaeA-like prote 35.5 53 0.0011 25.4 3.5 33 300-332 14-46 (62)
187 PRK12523 RNA polymerase sigma 35.4 42 0.00092 30.1 3.5 27 301-327 135-161 (172)
188 PF12085 DUF3562: Protein of u 35.4 45 0.00098 26.3 3.1 26 367-392 7-32 (66)
189 cd06170 LuxR_C_like C-terminal 35.3 56 0.0012 23.1 3.5 27 301-327 15-41 (57)
190 PF03444 HrcA_DNA-bdg: Winged 35.1 1.7E+02 0.0036 23.9 6.4 52 280-334 5-56 (78)
191 PF13463 HTH_27: Winged helix 35.0 94 0.002 23.2 4.9 42 299-340 16-57 (68)
192 PF08279 HTH_11: HTH domain; 34.8 1.1E+02 0.0024 22.0 5.1 42 285-329 2-43 (55)
193 cd00923 Cyt_c_Oxidase_Va Cytoc 34.6 3E+02 0.0064 23.6 9.4 67 43-113 8-75 (103)
194 PRK12537 RNA polymerase sigma 34.6 41 0.00088 30.6 3.3 27 367-393 149-175 (182)
195 PRK15090 DNA-binding transcrip 34.6 79 0.0017 30.7 5.5 46 283-332 14-59 (257)
196 PF14394 DUF4423: Domain of un 34.0 80 0.0017 29.2 5.1 35 302-336 40-76 (171)
197 PF01873 eIF-5_eIF-2B: Domain 33.6 1.2E+02 0.0027 26.7 6.0 60 368-435 35-94 (125)
198 COG5117 NOC3 Protein involved 33.4 5.9E+02 0.013 27.7 11.7 37 74-113 130-168 (657)
199 PF10771 DUF2582: Protein of u 33.4 83 0.0018 24.7 4.3 44 299-344 20-63 (65)
200 PF13518 HTH_28: Helix-turn-he 32.9 1.3E+02 0.0028 21.1 5.2 33 303-336 14-46 (52)
201 PF13429 TPR_15: Tetratricopep 32.9 4.5E+02 0.0098 25.2 12.1 87 91-193 157-243 (280)
202 PRK07037 extracytoplasmic-func 32.6 51 0.0011 29.1 3.5 27 301-327 125-151 (163)
203 KOG2004|consensus 32.6 8.4E+02 0.018 28.3 13.7 39 64-104 232-273 (906)
204 cd01279 HTH_HspR-like Helix-Tu 32.5 1.3E+02 0.0028 25.0 5.8 67 302-388 2-68 (98)
205 KOG1861|consensus 32.4 3.9E+02 0.0085 29.0 10.3 140 164-315 348-492 (540)
206 PRK03988 translation initiatio 32.3 1.2E+02 0.0027 27.2 5.9 59 368-435 45-103 (138)
207 TIGR02947 SigH_actino RNA poly 32.2 50 0.0011 30.3 3.5 27 301-327 147-173 (193)
208 PF01047 MarR: MarR family; I 32.2 1E+02 0.0022 22.4 4.6 40 301-340 17-56 (59)
209 PF11242 DUF2774: Protein of u 32.1 49 0.0011 25.7 2.7 37 354-393 3-39 (63)
210 smart00418 HTH_ARSR helix_turn 31.9 1.2E+02 0.0026 21.5 4.9 36 366-401 9-44 (66)
211 PRK12514 RNA polymerase sigma 31.8 52 0.0011 29.7 3.5 27 301-327 145-171 (179)
212 TIGR02010 IscR iron-sulfur clu 31.6 67 0.0014 28.2 4.0 62 365-429 23-85 (135)
213 cd08327 CARD_RAIDD Caspase act 31.5 87 0.0019 26.3 4.4 59 210-272 24-82 (94)
214 smart00342 HTH_ARAC helix_turn 31.4 1.1E+02 0.0023 23.1 4.8 73 302-391 2-75 (84)
215 cd00092 HTH_CRP helix_turn_hel 31.4 83 0.0018 23.3 4.1 35 365-399 23-57 (67)
216 PF08221 HTH_9: RNA polymerase 31.1 65 0.0014 24.6 3.4 33 300-332 26-58 (62)
217 PRK12527 RNA polymerase sigma 31.1 56 0.0012 28.8 3.5 27 301-327 121-147 (159)
218 PRK10747 putative protoheme IX 31.0 4.4E+02 0.0095 27.3 10.6 133 37-189 249-389 (398)
219 PF07381 DUF1495: Winged helix 30.9 2.2E+02 0.0048 23.7 6.7 49 280-331 7-65 (90)
220 PRK12520 RNA polymerase sigma 30.5 56 0.0012 29.9 3.5 27 301-327 147-173 (191)
221 smart00421 HTH_LUXR helix_turn 30.5 53 0.0011 23.0 2.7 28 366-393 17-44 (58)
222 TIGR03879 near_KaiC_dom probab 30.4 78 0.0017 25.4 3.8 30 300-329 31-60 (73)
223 smart00345 HTH_GNTR helix_turn 30.4 1.4E+02 0.0031 21.1 5.1 33 300-332 18-51 (60)
224 PRK12528 RNA polymerase sigma 30.2 59 0.0013 28.7 3.5 27 301-327 129-155 (161)
225 PRK12543 RNA polymerase sigma 30.2 56 0.0012 29.6 3.4 27 301-327 133-159 (179)
226 PRK12529 RNA polymerase sigma 30.1 56 0.0012 29.7 3.4 27 367-393 143-169 (178)
227 smart00420 HTH_DEOR helix_turn 30.1 1.5E+02 0.0032 20.5 5.0 33 301-333 14-46 (53)
228 smart00419 HTH_CRP helix_turn_ 30.0 88 0.0019 21.4 3.7 33 367-399 8-40 (48)
229 PF07389 DUF1500: Protein of u 30.0 81 0.0018 26.3 3.8 29 301-330 48-76 (100)
230 TIGR00738 rrf2_super rrf2 fami 30.0 77 0.0017 27.2 4.1 62 366-429 24-85 (132)
231 PRK12522 RNA polymerase sigma 29.8 60 0.0013 29.1 3.5 27 301-327 135-161 (173)
232 COG1497 Predicted transcriptio 29.7 1.2E+02 0.0025 30.1 5.5 56 283-345 11-66 (260)
233 COG2390 DeoR Transcriptional r 29.7 1E+02 0.0022 31.6 5.5 54 367-432 26-79 (321)
234 KOG1586|consensus 29.7 5.8E+02 0.013 25.5 10.7 34 240-273 233-266 (288)
235 PF06056 Terminase_5: Putative 29.4 54 0.0012 24.9 2.7 24 301-324 13-36 (58)
236 PRK12511 RNA polymerase sigma 29.4 60 0.0013 29.8 3.5 35 301-337 127-161 (182)
237 TIGR01764 excise DNA binding d 29.1 1.2E+02 0.0026 20.6 4.3 30 302-335 2-31 (49)
238 PF13424 TPR_12: Tetratricopep 29.1 2.3E+02 0.0049 21.4 6.3 58 91-153 16-76 (78)
239 PRK08301 sporulation sigma fac 29.0 59 0.0013 30.9 3.5 28 300-327 197-224 (234)
240 cd04787 HTH_HMRTR_unk Helix-Tu 29.0 1.8E+02 0.0038 25.5 6.3 67 302-388 1-67 (133)
241 PRK12530 RNA polymerase sigma 28.9 62 0.0013 29.7 3.5 27 301-327 150-176 (189)
242 PF13542 HTH_Tnp_ISL3: Helix-t 28.9 71 0.0015 22.8 3.1 24 302-325 28-51 (52)
243 cd00086 homeodomain Homeodomai 28.8 82 0.0018 22.7 3.5 25 300-324 26-50 (59)
244 cd00090 HTH_ARSR Arsenical Res 28.6 1.3E+02 0.0028 21.9 4.8 36 368-403 21-56 (78)
245 PRK09645 RNA polymerase sigma 28.6 64 0.0014 28.8 3.5 27 301-327 134-160 (173)
246 PF07163 Pex26: Pex26 protein; 28.4 6.5E+02 0.014 25.7 15.1 93 28-146 87-181 (309)
247 PRK15431 ferrous iron transpor 28.2 1.7E+02 0.0036 23.9 5.4 35 299-333 14-48 (78)
248 cd04774 HTH_YfmP Helix-Turn-He 28.1 1.8E+02 0.0038 24.1 5.8 66 303-388 2-67 (96)
249 PF13413 HTH_25: Helix-turn-he 28.1 55 0.0012 25.1 2.5 23 365-387 8-30 (62)
250 TIGR03643 conserved hypothetic 28.1 93 0.002 24.9 3.8 33 287-324 4-36 (72)
251 PRK12513 RNA polymerase sigma 27.9 66 0.0014 29.4 3.5 28 300-327 154-181 (194)
252 TIGR02479 FliA_WhiG RNA polyme 27.9 1.6E+02 0.0034 27.8 6.2 27 301-327 191-217 (224)
253 PRK09651 RNA polymerase sigma 27.8 66 0.0014 29.0 3.4 27 367-393 135-161 (172)
254 PRK06759 RNA polymerase factor 27.8 67 0.0015 28.0 3.4 27 367-393 122-148 (154)
255 PRK12547 RNA polymerase sigma 27.7 69 0.0015 28.5 3.5 27 301-327 128-154 (164)
256 PF10985 DUF2805: Protein of u 27.6 94 0.002 25.0 3.7 31 288-323 4-34 (73)
257 cd04773 HTH_TioE_rpt2 Second H 27.6 1.9E+02 0.0041 24.4 6.0 68 302-389 1-68 (108)
258 PF08221 HTH_9: RNA polymerase 27.6 81 0.0018 24.1 3.4 32 367-398 27-58 (62)
259 PRK07406 RNA polymerase sigma 27.5 1.3E+02 0.0029 31.4 6.0 28 366-393 330-357 (373)
260 PRK03573 transcriptional regul 27.3 2E+02 0.0043 25.0 6.4 80 301-388 46-127 (144)
261 COG5187 RPN7 26S proteasome re 27.2 53 0.0012 33.5 2.8 47 366-412 330-376 (412)
262 PF10975 DUF2802: Protein of u 27.0 61 0.0013 25.7 2.6 21 302-322 45-65 (70)
263 PRK12533 RNA polymerase sigma 26.6 70 0.0015 30.5 3.5 27 301-327 150-176 (216)
264 PF14947 HTH_45: Winged helix- 26.6 1E+02 0.0022 24.4 3.9 42 366-411 18-59 (77)
265 PRK12512 RNA polymerase sigma 26.5 73 0.0016 28.8 3.5 27 301-327 147-173 (184)
266 PF02002 TFIIE_alpha: TFIIE al 26.4 1E+02 0.0023 25.6 4.2 47 366-412 26-74 (105)
267 KOG1840|consensus 26.4 8.8E+02 0.019 26.5 16.7 95 94-194 255-358 (508)
268 TIGR02952 Sig70_famx2 RNA poly 26.3 75 0.0016 28.0 3.5 27 301-327 138-164 (170)
269 PRK05901 RNA polymerase sigma 26.3 1.2E+02 0.0025 33.2 5.5 90 300-393 373-493 (509)
270 PRK09646 RNA polymerase sigma 26.3 72 0.0016 29.3 3.5 27 301-327 158-184 (194)
271 PRK09642 RNA polymerase sigma 26.2 74 0.0016 28.0 3.4 27 367-393 122-148 (160)
272 PRK09047 RNA polymerase factor 26.0 75 0.0016 27.8 3.4 27 367-393 122-148 (161)
273 TIGR02999 Sig-70_X6 RNA polyme 25.9 74 0.0016 28.7 3.4 27 367-393 150-176 (183)
274 PRK12545 RNA polymerase sigma 25.9 74 0.0016 29.6 3.5 27 301-327 155-181 (201)
275 PRK07921 RNA polymerase sigma 25.7 1.4E+02 0.0031 30.4 5.8 28 366-393 281-308 (324)
276 PRK12523 RNA polymerase sigma 25.7 75 0.0016 28.5 3.4 27 367-393 135-161 (172)
277 PF04218 CENP-B_N: CENP-B N-te 25.6 1.6E+02 0.0034 21.8 4.5 35 279-322 9-43 (53)
278 PRK09649 RNA polymerase sigma 25.6 78 0.0017 29.0 3.5 27 301-327 146-172 (185)
279 smart00346 HTH_ICLR helix_turn 25.5 1.1E+02 0.0023 24.2 4.0 35 366-400 19-53 (91)
280 PRK12516 RNA polymerase sigma 25.5 77 0.0017 29.2 3.5 27 301-327 132-158 (187)
281 COG3413 Predicted DNA binding 25.5 82 0.0018 29.9 3.8 40 293-336 173-212 (215)
282 TIGR02983 SigE-fam_strep RNA p 25.4 78 0.0017 27.9 3.4 27 367-393 126-152 (162)
283 TIGR02989 Sig-70_gvs1 RNA poly 25.2 82 0.0018 27.5 3.5 27 301-327 127-153 (159)
284 PRK12517 RNA polymerase sigma 25.1 80 0.0017 29.1 3.5 27 301-327 144-170 (188)
285 PRK11169 leucine-responsive tr 25.1 99 0.0022 28.0 4.1 40 365-404 26-65 (164)
286 TIGR03001 Sig-70_gmx1 RNA poly 25.1 76 0.0016 30.9 3.5 27 301-327 177-203 (244)
287 PF02002 TFIIE_alpha: TFIIE al 25.0 59 0.0013 27.2 2.4 35 300-334 26-60 (105)
288 cd04761 HTH_MerR-SF Helix-Turn 25.0 1.6E+02 0.0034 20.4 4.3 28 302-333 1-28 (49)
289 TIGR02943 Sig70_famx1 RNA poly 24.8 82 0.0018 29.0 3.5 27 301-327 147-173 (188)
290 PF02796 HTH_7: Helix-turn-hel 24.6 45 0.00099 23.6 1.4 35 349-386 3-40 (45)
291 PF04703 FaeA: FaeA-like prote 24.6 1.1E+02 0.0023 23.8 3.5 33 366-398 14-46 (62)
292 cd04782 HTH_BltR Helix-Turn-He 24.5 2.4E+02 0.0053 23.2 6.0 67 303-389 2-68 (97)
293 TIGR02954 Sig70_famx3 RNA poly 24.4 86 0.0019 27.9 3.5 27 301-327 135-161 (169)
294 COG1601 GCD7 Translation initi 24.4 2.3E+02 0.0049 26.0 6.1 58 370-435 49-106 (151)
295 TIGR02985 Sig70_bacteroi1 RNA 24.3 85 0.0018 27.1 3.4 27 367-393 129-155 (161)
296 PRK12519 RNA polymerase sigma 24.3 85 0.0018 28.7 3.5 27 301-327 157-183 (194)
297 PF13384 HTH_23: Homeodomain-l 24.2 63 0.0014 22.8 2.1 29 301-329 17-45 (50)
298 cd04788 HTH_NolA-AlbR Helix-Tu 24.2 2.5E+02 0.0054 23.1 6.0 67 302-388 1-67 (96)
299 PRK12522 RNA polymerase sigma 24.2 83 0.0018 28.2 3.4 27 367-393 135-161 (173)
300 TIGR02787 codY_Gpos GTP-sensin 24.0 2.6E+02 0.0057 27.7 6.9 37 299-335 196-232 (251)
301 PRK09647 RNA polymerase sigma 23.7 86 0.0019 29.4 3.5 27 301-327 154-180 (203)
302 PRK12527 RNA polymerase sigma 23.7 88 0.0019 27.5 3.4 27 367-393 121-147 (159)
303 cd06171 Sigma70_r4 Sigma70, re 23.7 1.2E+02 0.0026 20.6 3.5 26 301-326 26-51 (55)
304 TIGR02835 spore_sigmaE RNA pol 23.7 89 0.0019 29.9 3.7 28 300-327 197-224 (234)
305 smart00653 eIF2B_5 domain pres 23.7 1.2E+02 0.0025 26.2 4.0 45 302-349 22-66 (110)
306 PF00325 Crp: Bacterial regula 23.6 1.5E+02 0.0032 20.0 3.6 30 302-331 3-32 (32)
307 PRK13919 putative RNA polymera 23.6 89 0.0019 28.3 3.5 27 301-327 151-177 (186)
308 PRK09834 DNA-binding transcrip 23.4 1.7E+02 0.0038 28.5 5.7 46 284-332 12-57 (263)
309 TIGR02846 spore_sigmaK RNA pol 23.4 92 0.002 29.6 3.7 28 300-327 193-220 (227)
310 PRK10870 transcriptional repre 23.4 2.7E+02 0.0059 25.5 6.7 51 300-350 70-120 (176)
311 PRK11920 rirA iron-responsive 23.4 1.1E+02 0.0023 27.7 3.9 63 365-429 22-84 (153)
312 PRK12540 RNA polymerase sigma 23.3 92 0.002 28.5 3.5 27 301-327 127-153 (182)
313 TIGR02947 SigH_actino RNA poly 23.2 86 0.0019 28.7 3.4 27 367-393 147-173 (193)
314 smart00345 HTH_GNTR helix_turn 23.2 1.7E+02 0.0036 20.8 4.3 32 367-398 19-51 (60)
315 TIGR02950 SigM_subfam RNA poly 23.1 95 0.0021 26.9 3.5 27 301-327 121-147 (154)
316 TIGR02939 RpoE_Sigma70 RNA pol 23.1 92 0.002 28.1 3.5 27 301-327 154-180 (190)
317 PRK09652 RNA polymerase sigma 23.0 95 0.002 27.5 3.5 27 301-327 144-170 (182)
318 TIGR02985 Sig70_bacteroi1 RNA 22.9 97 0.0021 26.7 3.5 27 301-327 129-155 (161)
319 PRK12536 RNA polymerase sigma 22.8 95 0.0021 28.1 3.5 27 301-327 145-171 (181)
320 PRK12532 RNA polymerase sigma 22.7 95 0.002 28.5 3.5 27 301-327 152-178 (195)
321 PRK12535 RNA polymerase sigma 22.7 94 0.002 28.9 3.5 27 301-327 149-175 (196)
322 cd05804 StaR_like StaR_like; a 22.6 6.1E+02 0.013 24.9 9.6 53 92-149 160-212 (355)
323 PRK12511 RNA polymerase sigma 22.5 93 0.002 28.5 3.4 27 367-393 127-153 (182)
324 PF05920 Homeobox_KN: Homeobox 22.4 1E+02 0.0022 21.6 2.8 22 304-325 16-37 (40)
325 COG2178 Predicted RNA-binding 22.4 5.6E+02 0.012 24.6 8.5 45 117-168 30-74 (204)
326 PF12895 Apc3: Anaphase-promot 22.4 3.7E+02 0.008 20.7 6.8 76 62-148 8-83 (84)
327 PRK12539 RNA polymerase sigma 22.4 93 0.002 28.3 3.4 27 301-327 147-173 (184)
328 PRK12520 RNA polymerase sigma 22.3 94 0.002 28.4 3.4 27 367-393 147-173 (191)
329 PRK09648 RNA polymerase sigma 22.3 99 0.0021 28.1 3.5 27 301-327 155-181 (189)
330 PRK12518 RNA polymerase sigma 22.3 99 0.0021 27.6 3.5 27 301-327 136-162 (175)
331 PRK12528 RNA polymerase sigma 22.2 98 0.0021 27.3 3.4 27 367-393 129-155 (161)
332 PF14394 DUF4423: Domain of un 22.2 72 0.0016 29.5 2.6 34 369-402 41-76 (171)
333 cd07377 WHTH_GntR Winged helix 22.1 2.6E+02 0.0057 20.2 5.3 32 301-332 24-56 (66)
334 COG3355 Predicted transcriptio 22.1 1.2E+02 0.0026 26.9 3.8 34 300-333 41-74 (126)
335 COG5600 Transcription-associat 22.0 1.2E+02 0.0025 32.0 4.2 99 316-415 288-406 (413)
336 KOG2235|consensus 22.0 1.3E+02 0.0028 33.6 4.7 92 300-403 72-169 (776)
337 PRK12525 RNA polymerase sigma 22.0 99 0.0021 27.6 3.4 27 367-393 134-160 (168)
338 PRK12542 RNA polymerase sigma 21.7 1E+02 0.0022 28.0 3.5 27 301-327 138-164 (185)
339 smart00389 HOX Homeodomain. DN 21.6 1.5E+02 0.0033 21.1 3.8 24 301-324 27-50 (56)
340 TIGR02846 spore_sigmaK RNA pol 21.6 96 0.0021 29.5 3.4 28 366-393 193-220 (227)
341 TIGR03504 FimV_Cterm FimV C-te 21.5 1.2E+02 0.0025 21.8 3.0 25 122-151 3-27 (44)
342 PF07079 DUF1347: Protein of u 21.4 1.1E+03 0.024 25.8 12.9 185 17-215 186-386 (549)
343 PRK00118 putative DNA-binding 21.4 1.2E+02 0.0026 26.0 3.5 27 301-327 33-59 (104)
344 PRK07037 extracytoplasmic-func 21.3 1E+02 0.0023 27.1 3.4 27 367-393 125-151 (163)
345 PRK15418 transcriptional regul 21.3 2E+02 0.0042 29.3 5.7 37 367-403 29-65 (318)
346 smart00347 HTH_MARR helix_turn 21.3 2.2E+02 0.0047 22.4 5.0 49 367-415 24-72 (101)
347 TIGR00373 conserved hypothetic 21.2 3.8E+02 0.0083 24.3 7.1 60 366-429 27-88 (158)
348 PRK12512 RNA polymerase sigma 21.2 1E+02 0.0022 27.8 3.4 27 367-393 147-173 (184)
349 PRK09645 RNA polymerase sigma 21.1 1E+02 0.0022 27.5 3.4 27 367-393 134-160 (173)
350 PRK06704 RNA polymerase factor 21.1 1E+02 0.0022 29.8 3.5 27 301-327 132-158 (228)
351 COG1595 RpoE DNA-directed RNA 21.0 1E+02 0.0023 27.9 3.4 27 367-393 143-169 (182)
352 TIGR03643 conserved hypothetic 21.0 1E+02 0.0022 24.7 2.8 29 367-395 13-41 (72)
353 PF01726 LexA_DNA_bind: LexA D 20.7 3.9E+02 0.0085 20.6 6.1 33 300-332 24-57 (65)
354 PF06163 DUF977: Bacterial pro 20.7 2E+02 0.0042 25.7 4.8 42 287-332 16-57 (127)
355 PRK11512 DNA-binding transcrip 20.7 1.7E+02 0.0036 25.7 4.6 70 347-416 33-103 (144)
356 TIGR02943 Sig70_famx1 RNA poly 20.6 1.1E+02 0.0023 28.2 3.4 27 367-393 147-173 (188)
357 PRK12336 translation initiatio 20.6 2.3E+02 0.005 26.9 5.8 60 367-435 40-99 (201)
358 PF13730 HTH_36: Helix-turn-he 20.6 1.5E+02 0.0032 21.3 3.5 29 369-397 27-55 (55)
359 PRK09638 RNA polymerase sigma 20.6 1.1E+02 0.0024 27.2 3.5 27 301-327 142-168 (176)
360 PF04297 UPF0122: Putative hel 20.5 1E+02 0.0022 26.3 2.9 27 300-326 32-58 (101)
361 PRK09649 RNA polymerase sigma 20.4 1.1E+02 0.0024 28.0 3.4 27 367-393 146-172 (185)
362 PRK08301 sporulation sigma fac 20.4 1E+02 0.0023 29.2 3.4 28 366-393 197-224 (234)
363 PRK12543 RNA polymerase sigma 20.4 1.1E+02 0.0023 27.8 3.3 27 367-393 133-159 (179)
364 PRK11924 RNA polymerase sigma 20.3 1.2E+02 0.0025 26.8 3.5 27 301-327 141-167 (179)
365 PRK12533 RNA polymerase sigma 20.2 1.1E+02 0.0023 29.2 3.4 27 367-393 150-176 (216)
366 PRK12514 RNA polymerase sigma 20.2 1.1E+02 0.0024 27.5 3.3 27 367-393 145-171 (179)
367 PF12085 DUF3562: Protein of u 20.2 1.4E+02 0.003 23.6 3.3 25 303-327 9-33 (66)
368 PRK12530 RNA polymerase sigma 20.2 1.1E+02 0.0024 28.0 3.4 27 367-393 150-176 (189)
369 PRK12524 RNA polymerase sigma 20.2 1.1E+02 0.0024 28.1 3.5 27 301-327 152-178 (196)
370 PRK09640 RNA polymerase sigma 20.1 1.2E+02 0.0025 27.7 3.5 27 301-327 150-176 (188)
No 1
>KOG2908|consensus
Probab=100.00 E-value=8.9e-92 Score=687.49 Aligned_cols=351 Identities=46% Similarity=0.783 Sum_probs=343.5
Q ss_pred CChhHHHhHHHHhhcCCchHHHHHHHHHHHHHhhhHHHHHHHHHHHhcCcccccchhHHHHHHHHHHHHhhccCchhHHH
Q psy3716 5 VDPTVYLTAKQEAYSKNPEISAQWLNLEELYNKKLWHQLTLAVLAFVQNPAIQKEGELRDLYHKFVISFETKINPVSLME 84 (436)
Q Consensus 5 ~~~~~~l~~~~~~~~~~~~~~~~~~~l~~l~~~KLWhQLT~~l~~~~~~p~~~~~~~~~~ly~~fI~~f~~kin~l~l~~ 84 (436)
.++++||+ ++ ..+++|++++.|.+++++|++|||||||.++.+||.+|+|+.++.++++|.|||+.|+.||||+++|+
T Consensus 2 ~~~~~~L~-~~-~~~a~~~l~~ew~~leeLy~eKLW~QLt~~l~~fvd~~~f~~~~~~l~lY~NFvsefe~kINplslve 79 (380)
T KOG2908|consen 2 MNAPDYLQ-TQ-LKSANPSLAAEWDRLEELYEEKLWHQLTLALVDFVDDPPFQAGDLLLQLYLNFVSEFETKINPLSLVE 79 (380)
T ss_pred CcHHHHHH-HH-HhhcCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHhccccccchHHHHHHHHHHHHHhhccChHHHHH
Confidence 46889998 67 78899999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhccCCCHHHHHHHHHHHHHhhcCCcc--hhHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHHHHHhcccChhH-
Q psy3716 85 IMEVITNHLSDQEEALVLLQSFEDKVKNNLE--AKSLCKILQAQMIMNKDADKPGSLDEVEKLIDEIELLVNDIEGVTA- 161 (436)
Q Consensus 85 i~~~v~~~~~d~~~aL~~L~~l~~~l~~~~e--a~~~~~~~i~~~~l~~~~~~~~~l~~~~~~L~~~~~~L~~~~~~~~- 161 (436)
|++.++++++|+++||+||+++.++++..++ +.+|+.+++|+.+|. .||+.++|+.|++.++.+++.+++++
T Consensus 80 i~l~~~~~~~D~~~al~~Le~i~~~~~~~~e~~av~~~~t~~~r~~L~-----i~DLk~~kk~ldd~~~~ld~~~~v~~~ 154 (380)
T KOG2908|consen 80 ILLVVSEQISDKDEALEFLEKIIEKLKEYKEPDAVIYILTEIARLKLE-----INDLKEIKKLLDDLKSMLDSLDGVTSN 154 (380)
T ss_pred HHHHHHHHhccHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHHh-----cccHHHHHHHHHHHHHHHhcccCCChh
Confidence 9999999999999999999999999988766 999999999999999 99999999999999999999999975
Q ss_pred HHHHHHHHHHHHHHHhhcHHHHHHHHHHHhccCCCCCCChhHHHHHHHHHHHHHhcCCCCCCCchhccCcccccccCCCc
Q psy3716 162 IHSRFYLVASTLYRKQAKLSLYYRTALRYLGCVDLNDLTASDQVQHAFLIGLAALLADSVYNIGELLAHPILDSLQQTPN 241 (436)
Q Consensus 162 v~~~~y~~~a~~~k~~~~~~~~Y~~~L~yL~~~~~~~l~~~e~~~~A~~l~iaALl~~~iynFgeLl~~p~v~~L~~t~~ 241 (436)
||+.||++++.|||..|++++||+++|+||+|.+.+++|.++++++|++|++|||+|++||||||||+||++.+|.||++
T Consensus 155 Vh~~fY~lssqYyk~~~d~a~yYr~~L~YL~~~d~~~l~~se~~~lA~~L~~aALLGe~iyNfGELL~HPilesL~gT~~ 234 (380)
T KOG2908|consen 155 VHSSFYSLSSQYYKKIGDFASYYRHALLYLGCSDIDDLSESEKQDLAFDLSLAALLGENIYNFGELLAHPILESLKGTNR 234 (380)
T ss_pred hhhhHHHHHHHHHHHHHhHHHHHHHHHHHhccccccccCHHHHHHHHHHHHHHHHhccccccHHHHHhhHHHHHhcCCcH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHHhcCChhHHHhhhhhhhcCchhhhhHHHHHHHHHHHHHHHHHhhcCCCCcccCHHHHHHHhCCChhhHHHH
Q psy3716 242 AWLVELLRAFNAGDIEKFELMRPQWSAMNDIKANENKLSQKIALLCLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFL 321 (436)
Q Consensus 242 ~wl~~LL~~f~~Gdl~~f~~~~~~~~~~~~L~~~~~~l~~KirLlaL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~l 321 (436)
.||+++|.+||.||+..|++.+..|.++|+|+.++.++++||||||||++||.+|++.|++||++||++|+||.+|||++
T Consensus 235 eWL~dll~Afn~Gdl~~f~~l~~~~~~~p~L~~~e~~L~qKI~LmaLiEi~F~rpa~~R~lsf~~Ia~~tkip~~eVE~L 314 (380)
T KOG2908|consen 235 EWLKDLLIAFNSGDLKRFESLKGVWGKQPDLASNEDFLLQKIRLLALIEITFSRPANERTLSFKEIAEATKIPNKEVELL 314 (380)
T ss_pred HHHHHHHHHhccCCHHHHHHHHHHhccCchHHHHHHHHHHHHHHHHHHHHHhcCcchhccccHHHHHHHhCCCHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhCCcccccccCCccEEEEEeccccccccchhhcccc
Q psy3716 322 IIKALALGLVKGHIDQVDESFNVTWVQPRVLSKDQLAFKKI 362 (436)
Q Consensus 322 vikAi~~gLI~G~IDQv~~~v~vtwv~pRvL~l~Qi~~lr~ 362 (436)
||||+|.|||+|+|||++|+|+++|||||+++..|+..|+.
T Consensus 315 VMKAlslgLikG~Idqv~~~v~~swvqPRvl~~~qI~~Mk~ 355 (380)
T KOG2908|consen 315 VMKALSLGLIKGSIDQVEGVVYMSWVQPRVLDRSQIVKMKD 355 (380)
T ss_pred HHHHHhccceeeeecccccEEEEecccccccCHHHHHhHHH
Confidence 99999999999999999999999999999999999999973
No 2
>KOG2753|consensus
Probab=100.00 E-value=9.5e-41 Score=326.52 Aligned_cols=302 Identities=18% Similarity=0.230 Sum_probs=261.9
Q ss_pred HHHHHHHHHhcCcccccchhHHHHHHHHHHHHhhccCchhHH----HHHHHHhccCCC--HHHHHHHHHHHHHhhcCCcc
Q psy3716 42 QLTLAVLAFVQNPAIQKEGELRDLYHKFVISFETKINPVSLM----EIMEVITNHLSD--QEEALVLLQSFEDKVKNNLE 115 (436)
Q Consensus 42 QLT~~l~~~~~~p~~~~~~~~~~ly~~fI~~f~~kin~l~l~----~i~~~v~~~~~d--~~~aL~~L~~l~~~l~~~~e 115 (436)
+.+..+......| ++++..+|+.|++.+..-- |-+-. .||-.++.+..+ |..+|..|.+++|.+.+..+
T Consensus 47 ~ii~~c~v~~k~~----ekdle~vlnsi~sLi~~~~-~e~~e~~v~a~~ekva~q~n~~~~~l~L~vLsnLfn~~d~~~~ 121 (378)
T KOG2753|consen 47 MIIEACDVLAKIP----EKDLECVLNSIVSLIKNAP-PEKVEEMVKAICEKVAKQPNDKTASLRLQVLSNLFNGVDKPTP 121 (378)
T ss_pred HHHHHhHHhhcCC----cchHHHHHHHHHHHHHhCC-HHHhHHHHHHHHHHHhcCccCCCcccHHHHHHHHHhccCCCch
Confidence 3344444455555 4668999999998875444 76644 455555555443 56899999999999988777
Q ss_pred hhHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHHHHHhcccChhHHHHHHHHHHHHHHHHhhcHHHHHHHHHHHhccCC
Q psy3716 116 AKSLCKILQAQMIMNKDADKPGSLDEVEKLIDEIELLVNDIEGVTAIHSRFYLVASTLYRKQAKLSLYYRTALRYLGCVD 195 (436)
Q Consensus 116 a~~~~~~~i~~~~l~~~~~~~~~l~~~~~~L~~~~~~L~~~~~~~~v~~~~y~~~a~~~k~~~~~~~~Y~~~L~yL~~~~ 195 (436)
++.-+.+....+... .+.+...-+-++.+++|+.+|+...+.++.+|++.++..+..+..++.-+.+..||++++
T Consensus 122 aR~~Vy~~lv~la~~-----~~~~~~i~~~lk~~~~~lkew~~~vedqrel~r~v~~al~~~k~~~~s~kvmt~lLgtyt 196 (378)
T KOG2753|consen 122 ARYQVYMSLVTLAAS-----CKLIEYIVPNLKQLDDWLKEWNISVEDQRELLRAVHKALKDNKSVDESSKVMTELLGTYT 196 (378)
T ss_pred HHHHHHHHHHHHHhh-----cceeeeecccHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHhcchhhhHHHHHHHHHHHhc
Confidence 887777666555555 667788888999999999999999999999999999999988888899999999999998
Q ss_pred CCCCChhHHHHHHHHHHHHHhcCCCCCCCchhccCcccccccCCCchhHHHHHHHHhcCChhHHHhhhhhhhcC-chhhh
Q psy3716 196 LNDLTASDQVQHAFLIGLAALLADSVYNIGELLAHPILDSLQQTPNAWLVELLRAFNAGDIEKFELMRPQWSAM-NDIKA 274 (436)
Q Consensus 196 ~~~l~~~e~~~~A~~l~iaALl~~~iynFgeLl~~p~v~~L~~t~~~wl~~LL~~f~~Gdl~~f~~~~~~~~~~-~~L~~ 274 (436)
.++ .+++++.|.++++.|+.+|++|.|++|+.+|+|+.|+++. +|+||.+|.+|.+++|.+|.+.++++ ...+.
T Consensus 197 ~dn--as~AredA~rcV~~av~dP~~F~fD~Ll~L~pV~qLE~d~---i~qLL~IF~s~~L~aYveF~~~N~~Fvqs~gl 271 (378)
T KOG2753|consen 197 EDN--ASEAREDAMRCVVEAVKDPKIFLFDHLLTLPPVKQLEGDL---IHQLLKIFVSGKLDAYVEFVAANSGFVQSQGL 271 (378)
T ss_pred ccc--hhHHHHHHHHHHHHHHcCCceeccchhccCchHHHhccch---HHHHHHHHHhcchHHHHHHHHhChHHHHHhcc
Confidence 877 7789999999999999999999999999999999999877 89999999999999999999887775 55677
Q ss_pred hHHHHHHHHHHHHHHHHHhhcCCCCcccCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCCccEEEEEecccccccc
Q psy3716 275 NENKLSQKIALLCLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPRVLSK 354 (436)
Q Consensus 275 ~~~~l~~KirLlaL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv~~~v~vtwv~pRvL~l 354 (436)
.++.+.+||||||||+||.. +.+|||++|+++|+|.+||||.|||+||+.|+|+|+|||.+++|+|+.+++|.|+.
T Consensus 272 ~~E~~~~KMRLLTlm~LA~e----s~eisy~~l~k~LqI~edeVE~fVIdaI~aklV~~kidq~~~~viVs~~~hR~FG~ 347 (378)
T KOG2753|consen 272 VHEQNMAKMRLLTLMSLAEE----SNEISYDTLAKELQINEDEVELFVIDAIRAKLVEGKIDQMNRTVIVSSSTHRTFGK 347 (378)
T ss_pred cHHHHHHHHHHHHHHHHhcc----CCCCCHHHHHHHhccCHHHHHHHHHHHHHHHHHHhhHHhhcceEEeehhhhhhccc
Confidence 88899999999999999983 36999999999999999999999999999999999999999999999999999999
Q ss_pred chhhcccc
Q psy3716 355 DQLAFKKI 362 (436)
Q Consensus 355 ~Qi~~lr~ 362 (436)
.||+.++.
T Consensus 348 ~qW~~L~~ 355 (378)
T KOG2753|consen 348 QQWQQLRD 355 (378)
T ss_pred HHHHHHHH
Confidence 99999975
No 3
>KOG2908|consensus
Probab=99.91 E-value=2.2e-23 Score=205.83 Aligned_cols=76 Identities=46% Similarity=0.781 Sum_probs=74.5
Q ss_pred cccccchhhccccCCcccccHHHHHHHcCCChhhHHHHHHHHHhcccceeecccccceEEEeeecccccchhhhhH
Q psy3716 350 RVLSKDQLAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPRVLSKDQVFW 425 (436)
Q Consensus 350 RvL~l~Qi~~lr~~~~r~~sf~~i~~~~~~~~~~ve~lvmka~s~~li~g~idqv~~~v~~~wv~pr~l~~~q~~~ 425 (436)
|.|+++++.|.+|+++|++||++||+.|++|.++||+|||||+|+|||+|+||||+|.|+++|||||||+++||.-
T Consensus 277 ~LmaLiEi~F~rpa~~R~lsf~~Ia~~tkip~~eVE~LVMKAlslgLikG~Idqv~~~v~~swvqPRvl~~~qI~~ 352 (380)
T KOG2908|consen 277 RLLALIEITFSRPANERTLSFKEIAEATKIPNKEVELLVMKALSLGLIKGSIDQVEGVVYMSWVQPRVLDRSQIVK 352 (380)
T ss_pred HHHHHHHHHhcCcchhccccHHHHHHHhCCCHHHHHHHHHHHHhccceeeeecccccEEEEecccccccCHHHHHh
Confidence 6999999999999999999999999999999999999999999999999999999999999999999999999964
No 4
>KOG3250|consensus
Probab=99.83 E-value=6.4e-21 Score=177.54 Aligned_cols=168 Identities=22% Similarity=0.273 Sum_probs=147.9
Q ss_pred HHHHHHHHhcCCCCCCCchhccCcccccccCCCchhHHHHHHHHhcCChhHHHhhhhhhhcCchhhhhHHHHHHHHHHHH
Q psy3716 208 AFLIGLAALLADSVYNIGELLAHPILDSLQQTPNAWLVELLRAFNAGDIEKFELMRPQWSAMNDIKANENKLSQKIALLC 287 (436)
Q Consensus 208 A~~l~iaALl~~~iynFgeLl~~p~v~~L~~t~~~wl~~LL~~f~~Gdl~~f~~~~~~~~~~~~L~~~~~~l~~KirLla 287 (436)
.-.++..|+-+|++|.|||||..|.+..|.++..+..++||++|++|++.+|.. ++...|.|... -..|++-++
T Consensus 26 l~~lIsqale~P~vf~F~ELl~l~nv~qlae~~dsa~lrlL~lFa~Gt~~Dy~a---ea~rlp~Ls~~---q~~kLk~lt 99 (258)
T KOG3250|consen 26 LEELISQALEAPGVFVFGELLILPNVVQLAEPIDSAYLRLLELFAYGTYRDYSA---EALRLPKLSLA---QLNKLKHLT 99 (258)
T ss_pred HHHHHHHHhcCCCeeeHHHHHhhhhHHHHcccccHHHHHHHHHHhcCchhhhhh---hhhcCCCCCHH---HHHhhhcce
Confidence 566788999999999999999999999999988888999999999999999987 34455666544 478999999
Q ss_pred HHHHHhhcCCCCcccCHHHHHHHhCC-ChhhHHHHHHHHHhCCcccccccCCccEEEEEeccccccccchhhccccCCcc
Q psy3716 288 LMELAFKKIPGSHQLSFAEISEAAQL-PLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPRVLSKDQLAFKKIPGSH 366 (436)
Q Consensus 288 L~~L~~~~p~~~r~isf~~Ia~~l~i-~~~eVE~lvikAi~~gLI~G~IDQv~~~v~vtwv~pRvL~l~Qi~~lr~~~~r 366 (436)
..++|.. ++.|+|..+-+.+.. +..++|++||.|+++++++|||||.+|+++|.|+..|.+...++..|.
T Consensus 100 V~slas~----~k~lpy~~Ll~~l~~~nvrelEd~iieamya~IlrGkldqr~q~leV~faigRdlr~k~i~nm~----- 170 (258)
T KOG3250|consen 100 VVSLASF----EKCLPYLVLLRLLPSRNVRELEDLIIEAMYADILRGKLDQRNQTLEVDFAIGRDLRSKDIDNMK----- 170 (258)
T ss_pred ehhhhhh----chhhhHHHHHhhccCCchhHHHHHHHHHHHHHHHHhhHHhhcceEeechhhcccccHhHHHHHH-----
Confidence 9999975 479999999999999 689999999999999999999999999999999999999999999995
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHH
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKA 391 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka 391 (436)
-|+++|++.|..-+-.+|.-|-+|
T Consensus 171 -~TL~~w~~~cenvL~~ie~qv~~a 194 (258)
T KOG3250|consen 171 -YTLDEWCEGCENVLFGIEAQVPRA 194 (258)
T ss_pred -HHHHHHHHHHHHHHHHHHhccchh
Confidence 688999998876666666555444
No 5
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=99.59 E-value=8.4e-15 Score=122.42 Aligned_cols=100 Identities=32% Similarity=0.366 Sum_probs=89.6
Q ss_pred hHHHHHHHHhcCChhHHHhhhhhh----hcCchhhhhHHHHHHHHHHHHHHHHHhhcCCCCcccCHHHHHHHhCCChhhH
Q psy3716 243 WLVELLRAFNAGDIEKFELMRPQW----SAMNDIKANENKLSQKIALLCLMELAFKKIPGSHQLSFAEISEAAQLPLIEV 318 (436)
Q Consensus 243 wl~~LL~~f~~Gdl~~f~~~~~~~----~~~~~L~~~~~~l~~KirLlaL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eV 318 (436)
|+++|+++|..||+..|.++...+ ..++.+....+.++++++..+|..++. + .+++++++||+.++++.++|
T Consensus 2 ~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~l~~~i~~~~l~~l~~--~--y~~i~~~~ia~~l~~~~~~v 77 (105)
T PF01399_consen 2 PYSELLRAFRSGDLQEFEEFLEKHSESLFKDPFLAEYVEQLKEKIRRRNLRQLSK--P--YSSISISEIAKALQLSEEEV 77 (105)
T ss_dssp HHHHHHHHHHCT-HHHHHHHHHHTCHHHHHCTTHHHHHHHHHHHHHHHHHHHHHH--C---SEEEHHHHHHHHTCCHHHH
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHHHHHH--H--hcccchHHHHHHhccchHHH
Confidence 789999999999999999886654 345778888999999999999999997 3 47999999999999999999
Q ss_pred HHHHHHHHhCCcccccccCCccEEEEEe
Q psy3716 319 EFLIIKALALGLVKGHIDQVDESFNVTW 346 (436)
Q Consensus 319 E~lvikAi~~gLI~G~IDQv~~~v~vtw 346 (436)
|.+++++|..|+|+|+|||.+|+|+++|
T Consensus 78 E~~l~~~I~~~~i~~~ID~~~~~v~~~k 105 (105)
T PF01399_consen 78 ESILIDLISNGLIKAKIDQVNGVVVFSK 105 (105)
T ss_dssp HHHHHHHHHTTSSEEEEETTTTEEEE-S
T ss_pred HHHHHHHHHCCCEEEEEECCCCEEEecC
Confidence 9999999999999999999999999987
No 6
>KOG1464|consensus
Probab=99.35 E-value=3.5e-11 Score=117.19 Aligned_cols=273 Identities=16% Similarity=0.272 Sum_probs=185.3
Q ss_pred hhHHHHHHHHHHHHhh----ccCchhHHHHHHHHhccCCCHHHHHHHHHHHHHhhcCCcchhH--HHHHHHHHHhhccCC
Q psy3716 60 GELRDLYHKFVISFET----KINPVSLMEIMEVITNHLSDQEEALVLLQSFEDKVKNNLEAKS--LCKILQAQMIMNKDA 133 (436)
Q Consensus 60 ~~~~~ly~~fI~~f~~----kin~l~l~~i~~~v~~~~~d~~~aL~~L~~l~~~l~~~~ea~~--~~~~~i~~~~l~~~~ 133 (436)
++..+-|...+.-+.+ .-..-+.-.|+-.++.. .....--+|-++....++....-++ -..+..|.+++.
T Consensus 82 ~eMm~~Y~qlLTYIkSAVTrNySEKsIN~IlDyiStS-~~m~LLQ~FYeTTL~ALkdAKNeRLWFKTNtKLgkl~fd--- 157 (440)
T KOG1464|consen 82 KEMMERYKQLLTYIKSAVTRNYSEKSINSILDYISTS-KNMDLLQEFYETTLDALKDAKNERLWFKTNTKLGKLYFD--- 157 (440)
T ss_pred HHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHhhh-hhhHHHHHHHHHHHHHHHhhhcceeeeeccchHhhhhee---
Confidence 4566666665443322 22233344455555421 1122222455555555554333232 234556677777
Q ss_pred CCCCChHHHHHHHHHHHHHHhcccChh-----HHHHHHHHHHHHHHHH---hhcHHHHHHHHHHHhc-------------
Q psy3716 134 DKPGSLDEVEKLIDEIELLVNDIEGVT-----AIHSRFYLVASTLYRK---QAKLSLYYRTALRYLG------------- 192 (436)
Q Consensus 134 ~~~~~l~~~~~~L~~~~~~L~~~~~~~-----~v~~~~y~~~a~~~k~---~~~~~~~Y~~~L~yL~------------- 192 (436)
.+++....++++++......-+|.+ ...-..|-+-.+.|-. .+.....|..+|..-+
T Consensus 158 --~~e~~kl~KIlkqLh~SCq~edGedD~kKGtQLLEiYAlEIQmYT~qKnNKkLK~lYeqalhiKSAIPHPlImGvIRE 235 (440)
T KOG1464|consen 158 --RGEYTKLQKILKQLHQSCQTEDGEDDQKKGTQLLEIYALEIQMYTEQKNNKKLKALYEQALHIKSAIPHPLIMGVIRE 235 (440)
T ss_pred --HHHHHHHHHHHHHHHHHhccccCchhhhccchhhhhHhhHhhhhhhhcccHHHHHHHHHHHHhhccCCchHHHhHHHH
Confidence 7888888899999888876555531 1111223222222211 2333445555554433
Q ss_pred ---------------------cC-CCCCCChhHHHHHHHHHHHHHhcC-CCCCCCchhccCcccccccC-CCchhHHHHH
Q psy3716 193 ---------------------CV-DLNDLTASDQVQHAFLIGLAALLA-DSVYNIGELLAHPILDSLQQ-TPNAWLVELL 248 (436)
Q Consensus 193 ---------------------~~-~~~~l~~~e~~~~A~~l~iaALl~-~~iynFgeLl~~p~v~~L~~-t~~~wl~~LL 248 (436)
.| +.|+.+++.+..+.+++++|.++- .+|..|+.--+.|. ++ ++.-.+.+|+
T Consensus 236 CGGKMHlreg~fe~AhTDFFEAFKNYDEsGspRRttCLKYLVLANMLmkS~iNPFDsQEAKPy----KNdPEIlAMTnlv 311 (440)
T KOG1464|consen 236 CGGKMHLREGEFEKAHTDFFEAFKNYDESGSPRRTTCLKYLVLANMLMKSGINPFDSQEAKPY----KNDPEILAMTNLV 311 (440)
T ss_pred cCCccccccchHHHHHhHHHHHHhcccccCCcchhHHHHHHHHHHHHHHcCCCCCcccccCCC----CCCHHHHHHHHHH
Confidence 12 446777888999999999999886 67888988777775 44 5667789999
Q ss_pred HHHhcCChhHHHhhhhh----hhcCchhhhhHHHHHHHHHHHHHHHHHhhcCCCCcccCHHHHHHHhCCChhhHHHHHHH
Q psy3716 249 RAFNAGDIEKFELMRPQ----WSAMNDIKANENKLSQKIALLCLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIK 324 (436)
Q Consensus 249 ~~f~~Gdl~~f~~~~~~----~~~~~~L~~~~~~l~~KirLlaL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lvik 324 (436)
.++...|+.+|+.+... +..+|.+..+.+.+.++||-..|+.|+ +|+.+-.||| |+++|+||+.|||.|++.
T Consensus 312 ~aYQ~NdI~eFE~Il~~~~~~IM~DpFIReh~EdLl~niRTQVLlkLI--kPYt~i~Ipf--is~~Lnv~~~dV~~LLV~ 387 (440)
T KOG1464|consen 312 AAYQNNDIIEFERILKSNRSNIMDDPFIREHIEDLLRNIRTQVLLKLI--KPYTNIGIPF--ISKELNVPEADVESLLVS 387 (440)
T ss_pred HHHhcccHHHHHHHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHh--ccccccCchh--hHhhcCCCHHHHHHHHHH
Confidence 99999999999997543 556799999999999999999999999 6865444555 999999999999999999
Q ss_pred HHhCCcccccccCCccEEEEEe
Q psy3716 325 ALALGLVKGHIDQVDESFNVTW 346 (436)
Q Consensus 325 Ai~~gLI~G~IDQv~~~v~vtw 346 (436)
||-..-|+|+|||+++.+....
T Consensus 388 ~ILD~~i~g~Ide~n~~l~~~~ 409 (440)
T KOG1464|consen 388 CILDDTIDGRIDEVNQYLELDK 409 (440)
T ss_pred HHhccccccchHHhhhHhccCc
Confidence 9999999999999998876543
No 7
>smart00753 PAM PCI/PINT associated module.
Probab=99.25 E-value=1.2e-11 Score=101.29 Aligned_cols=81 Identities=30% Similarity=0.364 Sum_probs=73.0
Q ss_pred hHHHHHHHHHHHHHHHHHhhcCCCCcccCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCCccEEEEEecccccccc
Q psy3716 275 NENKLSQKIALLCLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPRVLSK 354 (436)
Q Consensus 275 ~~~~l~~KirLlaL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv~~~v~vtwv~pRvL~l 354 (436)
+.+.+.+|+|..++..++.. +++|+|++|++.+++|.++||.+|+++|..|.|.|+|||.+++|.++|..||. .
T Consensus 2 ~~~~l~~~~~~~~l~~l~~~----y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~~r~--~ 75 (88)
T smart00753 2 LVERLQRKIRLTNLLQLSEP----YSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVDPRR--S 75 (88)
T ss_pred hHHHHHHHHHHHHHHHHhHH----hceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCchhh--h
Confidence 35678999999999999963 47999999999999999999999999999999999999999999999999997 5
Q ss_pred chhhccc
Q psy3716 355 DQLAFKK 361 (436)
Q Consensus 355 ~Qi~~lr 361 (436)
.+|..+.
T Consensus 76 ~~~~~~~ 82 (88)
T smart00753 76 EPLAQFA 82 (88)
T ss_pred hHHHHHH
Confidence 5666553
No 8
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=99.25 E-value=1.2e-11 Score=101.29 Aligned_cols=81 Identities=30% Similarity=0.364 Sum_probs=73.0
Q ss_pred hHHHHHHHHHHHHHHHHHhhcCCCCcccCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCCccEEEEEecccccccc
Q psy3716 275 NENKLSQKIALLCLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPRVLSK 354 (436)
Q Consensus 275 ~~~~l~~KirLlaL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv~~~v~vtwv~pRvL~l 354 (436)
+.+.+.+|+|..++..++.. +++|+|++|++.+++|.++||.+|+++|..|.|.|+|||.+++|.++|..||. .
T Consensus 2 ~~~~l~~~~~~~~l~~l~~~----y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~~r~--~ 75 (88)
T smart00088 2 LVERLQRKIRLTNLLQLSEP----YSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVDPRR--S 75 (88)
T ss_pred hHHHHHHHHHHHHHHHHhHH----hceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCchhh--h
Confidence 35678999999999999963 47999999999999999999999999999999999999999999999999997 5
Q ss_pred chhhccc
Q psy3716 355 DQLAFKK 361 (436)
Q Consensus 355 ~Qi~~lr 361 (436)
.+|..+.
T Consensus 76 ~~~~~~~ 82 (88)
T smart00088 76 EPLAQFA 82 (88)
T ss_pred hHHHHHH
Confidence 5666553
No 9
>KOG2753|consensus
Probab=99.08 E-value=6e-11 Score=117.66 Aligned_cols=78 Identities=31% Similarity=0.428 Sum_probs=70.5
Q ss_pred cccccchhhccccCCcccccHHHHHHHcCCChhhHHHHHHHHHhcccceeecccccceEEEeeecccccchhhhhHHHHH
Q psy3716 350 RVLSKDQLAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPRVLSKDQVFWSLEE 429 (436)
Q Consensus 350 RvL~l~Qi~~lr~~~~r~~sf~~i~~~~~~~~~~ve~lvmka~s~~li~g~idqv~~~v~~~wv~pr~l~~~q~~~~~~~ 429 (436)
|+|+.+++.. ...++||++|++++++..||||.+|++|+..|||+|+|||.+++|+|+.+++|++++.||+ +||+
T Consensus 281 RLLTlm~LA~----es~eisy~~l~k~LqI~edeVE~fVIdaI~aklV~~kidq~~~~viVs~~~hR~FG~~qW~-~L~~ 355 (378)
T KOG2753|consen 281 RLLTLMSLAE----ESNEISYDTLAKELQINEDEVELFVIDAIRAKLVEGKIDQMNRTVIVSSSTHRTFGKQQWQ-QLRD 355 (378)
T ss_pred HHHHHHHHhc----cCCCCCHHHHHHHhccCHHHHHHHHHHHHHHHHHHhhHHhhcceEEeehhhhhhcccHHHH-HHHH
Confidence 6777777777 2458999999999999999999999999999999999999999999999999999999997 5776
Q ss_pred HHh
Q psy3716 430 TVA 432 (436)
Q Consensus 430 ~~~ 432 (436)
..|
T Consensus 356 kL~ 358 (378)
T KOG2753|consen 356 KLA 358 (378)
T ss_pred HHH
Confidence 554
No 10
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=98.76 E-value=1.5e-08 Score=82.91 Aligned_cols=64 Identities=28% Similarity=0.400 Sum_probs=56.7
Q ss_pred cccccHHHHHHHcCCChhhHHHHHHHHHhcccceeecccccceEEEeeecccccchhhhhHHHHHHH
Q psy3716 365 SHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPRVLSKDQVFWSLEETV 431 (436)
Q Consensus 365 ~r~~sf~~i~~~~~~~~~~ve~lvmka~s~~li~g~idqv~~~v~~~wv~pr~l~~~q~~~~~~~~~ 431 (436)
.++++|++||+.+++|.++||.+|++++..|.+.|+|||.+++|+++|.+||. .+||. .+.+++
T Consensus 22 y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~~r~--~~~~~-~~~~~l 85 (88)
T smart00088 22 YSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVDPRR--SEPLA-QFAETL 85 (88)
T ss_pred hceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCchhh--hhHHH-HHHHHh
Confidence 46899999999999999999999999999999999999999999999999998 55554 444443
No 11
>smart00753 PAM PCI/PINT associated module.
Probab=98.76 E-value=1.5e-08 Score=82.91 Aligned_cols=64 Identities=28% Similarity=0.400 Sum_probs=56.7
Q ss_pred cccccHHHHHHHcCCChhhHHHHHHHHHhcccceeecccccceEEEeeecccccchhhhhHHHHHHH
Q psy3716 365 SHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPRVLSKDQVFWSLEETV 431 (436)
Q Consensus 365 ~r~~sf~~i~~~~~~~~~~ve~lvmka~s~~li~g~idqv~~~v~~~wv~pr~l~~~q~~~~~~~~~ 431 (436)
.++++|++||+.+++|.++||.+|++++..|.+.|+|||.+++|+++|.+||. .+||. .+.+++
T Consensus 22 y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~~r~--~~~~~-~~~~~l 85 (88)
T smart00753 22 YSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVDPRR--SEPLA-QFAETL 85 (88)
T ss_pred hceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCchhh--hhHHH-HHHHHh
Confidence 46899999999999999999999999999999999999999999999999998 55554 444443
No 12
>KOG2581|consensus
Probab=98.51 E-value=4.8e-05 Score=78.15 Aligned_cols=166 Identities=20% Similarity=0.253 Sum_probs=109.9
Q ss_pred HHHHHHHHHHHHHHHHhhcHHHHHHHHHHHhccCCCCCCChhHHHHHHHHHHHHHhcCCCCCCCchhccCcccc-cccCC
Q psy3716 161 AIHSRFYLVASTLYRKQAKLSLYYRTALRYLGCVDLNDLTASDQVQHAFLIGLAALLADSVYNIGELLAHPILD-SLQQT 239 (436)
Q Consensus 161 ~v~~~~y~~~a~~~k~~~~~~~~Y~~~L~yL~~~~~~~l~~~e~~~~A~~l~iaALl~~~iynFgeLl~~p~v~-~L~~t 239 (436)
...++|..-.....-..++|++.-++.+..+.-.|. +....-+++.-+-+++..|+.-+|-.- .....|+++ +|
T Consensus 244 ne~ARY~yY~GrIkaiqldYssA~~~~~qa~rkapq-~~alGf~q~v~k~~ivv~ll~geiPer-s~F~Qp~~~ksL--- 318 (493)
T KOG2581|consen 244 NEWARYLYYLGRIKAIQLDYSSALEYFLQALRKAPQ-HAALGFRQQVNKLMIVVELLLGEIPER-SVFRQPGMRKSL--- 318 (493)
T ss_pred HHHHHHHHHHhhHHHhhcchhHHHHHHHHHHHhCcc-hhhhhHHHHHHHHHHHHHHHcCCCcch-hhhcCccHHHHH---
Confidence 355554444444444578888888877777766554 334444555555555555554223211 122346554 24
Q ss_pred CchhHHHHHHHHhcCChhHHHhhhhh----hhcCch----hhhhHHHHHHHHHHHHHHHHHhhcCCCCcccCHHHHHHHh
Q psy3716 240 PNAWLVELLRAFNAGDIEKFELMRPQ----WSAMND----IKANENKLSQKIALLCLMELAFKKIPGSHQLSFAEISEAA 311 (436)
Q Consensus 240 ~~~wl~~LL~~f~~Gdl~~f~~~~~~----~~~~~~----L~~~~~~l~~KirLlaL~~L~~~~p~~~r~isf~~Ia~~l 311 (436)
...++|-.+.-.||++.|+....+ +..+.- ....++.++.=||.++|. . ..||+.+||+.|
T Consensus 319 --~~Yf~Lt~AVr~gdlkkF~~~leq~k~~f~~D~ty~LivRLR~NVIkTgIR~ISls---Y------SRISl~DIA~kL 387 (493)
T KOG2581|consen 319 --RPYFKLTQAVRLGDLKKFNETLEQFKDKFQADGTYTLIVRLRHNVIKTGIRKISLS---Y------SRISLQDIAKKL 387 (493)
T ss_pred --HHHHHHHHHHHHhhHHHHHHHHHHHHHHHhhCCcchHHHHHHHHHHHHhhhheeee---e------eeccHHHHHHHh
Confidence 237999999999999999986443 333311 123466777777776553 3 479999999999
Q ss_pred CC-ChhhHHHHHHHHHhCCcccccccCCccEE
Q psy3716 312 QL-PLIEVEFLIIKALALGLVKGHIDQVDESF 342 (436)
Q Consensus 312 ~i-~~~eVE~lvikAi~~gLI~G~IDQv~~~v 342 (436)
++ ++++||.+|=|||+.|+|+|+||--+|.+
T Consensus 388 ~l~Seed~EyiVakAIRDGvIea~Id~~~g~m 419 (493)
T KOG2581|consen 388 GLNSEEDAEYIVAKAIRDGVIEAKIDHEDGFM 419 (493)
T ss_pred cCCCchhHHHHHHHHHHhccceeeeccccCce
Confidence 99 56679999999999999999999998843
No 13
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=98.50 E-value=1.5e-07 Score=78.45 Aligned_cols=48 Identities=35% Similarity=0.450 Sum_probs=45.1
Q ss_pred cccccHHHHHHHcCCChhhHHHHHHHHHhcccceeecccccceEEEee
Q psy3716 365 SHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTW 412 (436)
Q Consensus 365 ~r~~sf~~i~~~~~~~~~~ve~lvmka~s~~li~g~idqv~~~v~~~w 412 (436)
-+++++++||+.++++.++||.+|+++++.|+|+|+|||++|+|+++|
T Consensus 58 y~~i~~~~ia~~l~~~~~~vE~~l~~~I~~~~i~~~ID~~~~~v~~~k 105 (105)
T PF01399_consen 58 YSSISISEIAKALQLSEEEVESILIDLISNGLIKAKIDQVNGVVVFSK 105 (105)
T ss_dssp -SEEEHHHHHHHHTCCHHHHHHHHHHHHHTTSSEEEEETTTTEEEE-S
T ss_pred hcccchHHHHHHhccchHHHHHHHHHHHHCCCEEEEEECCCCEEEecC
Confidence 468999999999999999999999999999999999999999999998
No 14
>KOG0687|consensus
Probab=97.97 E-value=0.0034 Score=63.34 Aligned_cols=284 Identities=14% Similarity=0.122 Sum_probs=187.6
Q ss_pred hhhHHHHHHHHHHHhcCcccccchhHHHHHHHHHHHHhhccCchhHHHHHHHHhc---cCCCHHHHHHHHHHHHHhhcC-
Q psy3716 37 KKLWHQLTLAVLAFVQNPAIQKEGELRDLYHKFVISFETKINPVSLMEIMEVITN---HLSDQEEALVLLQSFEDKVKN- 112 (436)
Q Consensus 37 ~KLWhQLT~~l~~~~~~p~~~~~~~~~~ly~~fI~~f~~kin~l~l~~i~~~v~~---~~~d~~~aL~~L~~l~~~l~~- 112 (436)
.++|-++-..++.-+... +.+.++=.+.-|.+-+.........++-...++ ++.|.+.|++.+....++--.
T Consensus 62 e~~~i~~D~~~l~~m~~~----neeki~eld~~iedaeenlGE~ev~ea~~~kaeYycqigDkena~~~~~~t~~ktvs~ 137 (393)
T KOG0687|consen 62 ESLVIKLDQDLLNSMKKA----NEEKIKELDEKIEDAEENLGESEVREAMLRKAEYYCQIGDKENALEALRKTYEKTVSL 137 (393)
T ss_pred hhcceeccHHHHHHHHHh----hHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHhhc
Confidence 367766666655544332 233455557777777777767767776666654 356999999999888876322
Q ss_pred C-cchhHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHHHHHhc---ccCh--hHHHHHHHHHHHHHHHHhhcHHHHHHH
Q psy3716 113 N-LEAKSLCKILQAQMIMNKDADKPGSLDEVEKLIDEIELLVND---IEGV--TAIHSRFYLVASTLYRKQAKLSLYYRT 186 (436)
Q Consensus 113 ~-~ea~~~~~~~i~~~~l~~~~~~~~~l~~~~~~L~~~~~~L~~---~~~~--~~v~~~~y~~~a~~~k~~~~~~~~Y~~ 186 (436)
. .=-.+++.+-+|.++. |.+-+.+-|+.+++.+++ |+-- -.++..+|.++..-+| +.-..
T Consensus 138 g~kiDVvf~~iRlglfy~--------D~~lV~~~iekak~liE~GgDWeRrNRlKvY~Gly~msvR~Fk------~Aa~L 203 (393)
T KOG0687|consen 138 GHKIDVVFYKIRLGLFYL--------DHDLVTESIEKAKSLIEEGGDWERRNRLKVYQGLYCMSVRNFK------EAADL 203 (393)
T ss_pred ccchhhHHHHHHHHHhhc--------cHHHHHHHHHHHHHHHHhCCChhhhhhHHHHHHHHHHHHHhHH------HHHHH
Confidence 1 1124666666666654 678888888999888864 5543 2677777777765444 44445
Q ss_pred HHHHhccCCCCCC-ChhHHHHHHHHHHHHHhcCCCCCCC-chhccCcccccccCCCchhHHHHHHHHhcCChhHHHhh--
Q psy3716 187 ALRYLGCVDLNDL-TASDQVQHAFLIGLAALLADSVYNI-GELLAHPILDSLQQTPNAWLVELLRAFNAGDIEKFELM-- 262 (436)
Q Consensus 187 ~L~yL~~~~~~~l-~~~e~~~~A~~l~iaALl~~~iynF-geLl~~p~v~~L~~t~~~wl~~LL~~f~~Gdl~~f~~~-- 262 (436)
.+..+++|..-++ |-+.. +.+.++.++.+=+--.. .-.+..|.+...-.+ -..+.+++..+-.-+++.|-.-
T Consensus 204 fld~vsTFtS~El~~Y~~~---v~Ytv~~g~i~leR~dlktKVi~~~Evl~vl~~-l~~~~q~l~SLY~C~Y~~Ff~~L~ 279 (393)
T KOG0687|consen 204 FLDSVSTFTSYELMSYETF---VRYTVITGLIALERVDLKTKVIKCPEVLEVLHK-LPSVSQLLNSLYECDYSDFFNDLA 279 (393)
T ss_pred HHHHcccccceecccHHHH---HHHHHHHhhheeccchHHhhhcCcHHHHHHhhc-CchHHHHHHHHHhccHHHHHHHHH
Confidence 5667778765444 44444 44555555444111111 123444555442222 1126677777777777776542
Q ss_pred ---hhhhhcCchhhhhHHHHHHHHHHHHHHHHHhhcCCCCcccCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCCc
Q psy3716 263 ---RPQWSAMNDIKANENKLSQKIALLCLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVD 339 (436)
Q Consensus 263 ---~~~~~~~~~L~~~~~~l~~KirLlaL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv~ 339 (436)
..++..+-.++.+...--+-||..+-..+-.+ .|+++.+..|++.|++++=++.=+=+-|..|-+.++||-|+
T Consensus 280 ~~~~~~lk~D~~l~~h~~yyvREMR~rvY~QlLES----Yrsl~l~~MA~aFgVSVefiDreL~rFI~~grL~ckIDrVn 355 (393)
T KOG0687|consen 280 AVEAKQLKDDRYLGPHYRYYVREMRRRVYAQLLES----YRSLTLESMAKAFGVSVEFIDRELGRFIAAGRLHCKIDRVN 355 (393)
T ss_pred HHHHHhhccchhcchHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHhCchHHHHHhHHHHhhccCceeeeeeccc
Confidence 22333345567777777888999998887753 58999999999999999999999999999999999999999
Q ss_pred cEEEEEe
Q psy3716 340 ESFNVTW 346 (436)
Q Consensus 340 ~~v~vtw 346 (436)
|+|.+++
T Consensus 356 GVVEtNr 362 (393)
T KOG0687|consen 356 GVVETNR 362 (393)
T ss_pred ceeecCC
Confidence 9999875
No 15
>KOG1463|consensus
Probab=97.77 E-value=0.0011 Score=67.19 Aligned_cols=243 Identities=13% Similarity=0.114 Sum_probs=159.0
Q ss_pred CCHHHHHHHHHHHHHhhcCCcch----hHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHHHHHhcccChhHHHHHHHHH
Q psy3716 94 SDQEEALVLLQSFEDKVKNNLEA----KSLCKILQAQMIMNKDADKPGSLDEVEKLIDEIELLVNDIEGVTAIHSRFYLV 169 (436)
Q Consensus 94 ~d~~~aL~~L~~l~~~l~~~~ea----~~~~~~~i~~~~l~~~~~~~~~l~~~~~~L~~~~~~L~~~~~~~~v~~~~y~~ 169 (436)
....+||.....+...++.=++- .+++.-..+.+.+ .++..+|.-|......-...-..+...+.+=..
T Consensus 142 ~~YteAlaL~~~L~rElKKlDDK~lLvev~llESK~y~~l-------~Nl~KakasLTsART~AnaiYcpPqlQa~lDLq 214 (411)
T KOG1463|consen 142 KRYTEALALINDLLRELKKLDDKILLVEVHLLESKAYHAL-------RNLPKAKASLTSARTTANAIYCPPQLQATLDLQ 214 (411)
T ss_pred HHHHHHHHHHHHHHHHHHhcccccceeeehhhhhHHHHHH-------hcchhHHHHHHHHHHhhcccccCHHHHHHHHHh
Confidence 35667777777777766652222 2333334444444 366666666665554433333334455555554
Q ss_pred HHHHHHHhhcHHHHHHHHHHHhccCCCCCCCh-hHHHHHHHHHHHHHhcCCCCCCCchhccCcccccccCCCchhHHHHH
Q psy3716 170 ASTLYRKQAKLSLYYRTALRYLGCVDLNDLTA-SDQVQHAFLIGLAALLADSVYNIGELLAHPILDSLQQTPNAWLVELL 248 (436)
Q Consensus 170 ~a~~~k~~~~~~~~Y~~~L~yL~~~~~~~l~~-~e~~~~A~~l~iaALl~~~iynFgeLl~~p~v~~L~~t~~~wl~~LL 248 (436)
+.=+|-.-.+|.-.|.+-......|+. +.. ..+..-.+++.++-+--+..=.-+.|+.....-...+++...+...-
T Consensus 215 SGIlha~ekDykTafSYFyEAfEgf~s--~~~~v~A~~sLKYMlLcKIMln~~ddv~~lls~K~~l~y~g~~i~AmkavA 292 (411)
T KOG1463|consen 215 SGILHAAEKDYKTAFSYFYEAFEGFDS--LDDDVKALTSLKYMLLCKIMLNLPDDVAALLSAKLALKYAGRDIDAMKAVA 292 (411)
T ss_pred ccceeecccccchHHHHHHHHHccccc--cCCcHHHHHHHHHHHHHHHHhcCHHHHHHHHhhHHHHhccCcchHHHHHHH
Confidence 444444445666666665555555533 222 45566666666665554444444556665443346677877789999
Q ss_pred HHHhcCChhHHHhh----hhhhhcCchhhhhHHHHHHHHHHHHHHHHHhhcCCCCcccCHHHHHHHhCCChhhHHHHHHH
Q psy3716 249 RAFNAGDIEKFELM----RPQWSAMNDIKANENKLSQKIALLCLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIK 324 (436)
Q Consensus 249 ~~f~~Gdl~~f~~~----~~~~~~~~~L~~~~~~l~~KirLlaL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lvik 324 (436)
++|...++.+|+.- .+++..+|....+-..|...|-=--|+.++ .|+ ..+..+.||+-.|++...||.-+=+
T Consensus 293 eA~~nRSLkdF~~AL~~yk~eL~~D~ivr~Hl~~Lyd~lLEknl~riI--EPy--S~Vei~hIA~~IGl~~~~VEkKLsq 368 (411)
T KOG1463|consen 293 EAFGNRSLKDFEKALADYKKELAEDPIVRSHLQSLYDNLLEKNLCRII--EPY--SRVEISHIAEVIGLDVPQVEKKLSQ 368 (411)
T ss_pred HHhcCCcHHHHHHHHHHhHHHHhcChHHHHHHHHHHHHHHHHhHHHHc--Cch--hhhhHHHHHHHHCCCcHHHHHHHHH
Confidence 99999999999974 445666787777766666666555566666 364 5788888999999999999999999
Q ss_pred HHhCCcccccccCCccEEEEEeccc
Q psy3716 325 ALALGLVKGHIDQVDESFNVTWVQP 349 (436)
Q Consensus 325 Ai~~gLI~G~IDQv~~~v~vtwv~p 349 (436)
.|-.+...|.+||-++++.|.=-.|
T Consensus 369 MILDKkf~G~LDQg~g~Liv~~e~~ 393 (411)
T KOG1463|consen 369 MILDKKFYGTLDQGEGCLIVFEEPP 393 (411)
T ss_pred HHHHHHhhcccccCCCeEEEeCCCC
Confidence 9999999999999999998864433
No 16
>KOG0686|consensus
Probab=97.73 E-value=0.0012 Score=68.16 Aligned_cols=165 Identities=15% Similarity=0.182 Sum_probs=119.4
Q ss_pred HHHHHHHHHHHhcCCCCCCCchhc----cCcccccccCCCchhHHHHHHHHhcCChhHHHhhhhhhhc----CchhhhhH
Q psy3716 205 VQHAFLIGLAALLADSVYNIGELL----AHPILDSLQQTPNAWLVELLRAFNAGDIEKFELMRPQWSA----MNDIKANE 276 (436)
Q Consensus 205 ~~~A~~l~iaALl~~~iynFgeLl----~~p~v~~L~~t~~~wl~~LL~~f~~Gdl~~f~~~~~~~~~----~~~L~~~~ 276 (436)
..++.+-++.||.. |.-.+|. ..-.++.+-+.++. |.++|..|.++.++.--++..++.. ++-|..+.
T Consensus 269 sdv~iYggLcALAt---fdr~~Lk~~vi~n~~Fk~flel~Pq-lr~il~~fy~sky~~cl~~L~~~k~~llLD~yLaphV 344 (466)
T KOG0686|consen 269 SDVAIYGGLCALAT---FDRQDLKLNVIKNESFKLFLELEPQ-LREILFKFYSSKYASCLELLREIKPRLLLDMYLAPHV 344 (466)
T ss_pred hhhHHHHhhHhhcc---CCHHHHHHHHHcchhhhhHHhcChH-HHHHHHHHhhhhHHHHHHHHHHhccceeechhcchhH
Confidence 35578888888765 2222332 22222222233344 8899999999988877776555433 46678889
Q ss_pred HHHHHHHHHHHHHHHHhhcCCCCcccCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCCccEEEEEeccccccccch
Q psy3716 277 NKLSQKIALLCLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPRVLSKDQ 356 (436)
Q Consensus 277 ~~l~~KirLlaL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv~~~v~vtwv~pRvL~l~Q 356 (436)
+.|..+||=-+|+.-- .| .-+++++.+|.+.+.++...|.=+++.|-.|.|.|+||+-++.+.+.
T Consensus 345 d~Ly~~IR~r~llqy~--~p--y~s~~m~~mA~af~~sv~~le~~l~~LI~~~~i~~rIDs~~ki~~~~----------- 409 (466)
T KOG0686|consen 345 DNLYSLIRNRALLQYL--SP--YSSADMSKMAEAFNTSVAILESELLELILEGKISGRIDSHNKILYAR----------- 409 (466)
T ss_pred HHHHHHHHHhhHHHhc--Cc--cccchHHHHHHHhcccHHHHHHHHHHHHHccchheeeccccceeeec-----------
Confidence 9999999999999855 46 36899999999999999999999999999999999999999887654
Q ss_pred hhccccCCcccccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 357 LAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 357 i~~lr~~~~r~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
++.+|.-+|+++-.-++-..-+.-.++.||.-
T Consensus 410 -----~~~~en~~fe~~~~~~~~~~~~~kal~lr~~~ 441 (466)
T KOG0686|consen 410 -----DADSENATFERVLPMGKRSQLEAKALLLRAAL 441 (466)
T ss_pred -----ccccccchhhhcchhhHHHHHHHHHHHHHHHH
Confidence 44455566666555555555566677777655
No 17
>COG5187 RPN7 26S proteasome regulatory complex component, contains PCI domain [Posttranslational modification, protein turnover, chaperones]
Probab=97.56 E-value=0.044 Score=54.86 Aligned_cols=234 Identities=11% Similarity=0.060 Sum_probs=147.6
Q ss_pred CHHHHHHHHHHHHHhhcCCcchhHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHHHHHhc---ccChh--HHHHHHHHH
Q psy3716 95 DQEEALVLLQSFEDKVKNNLEAKSLCKILQAQMIMNKDADKPGSLDEVEKLIDEIELLVND---IEGVT--AIHSRFYLV 169 (436)
Q Consensus 95 d~~~aL~~L~~l~~~l~~~~ea~~~~~~~i~~~~l~~~~~~~~~l~~~~~~L~~~~~~L~~---~~~~~--~v~~~~y~~ 169 (436)
|.+.+.+.+..++.+-- +..+.+-+...++++-+. -|+...+++.|+.+++.++. |+--. .++-..|..
T Consensus 130 D~~ng~~~~~~~~~~a~-stg~KiDv~l~kiRlg~~-----y~d~~vV~e~lE~~~~~iEkGgDWeRrNRyK~Y~Gi~~m 203 (412)
T COG5187 130 DIQNGFEWMRRLMRDAM-STGLKIDVFLCKIRLGLI-----YGDRKVVEESLEVADDIIEKGGDWERRNRYKVYKGIFKM 203 (412)
T ss_pred hhhhHHHHHHHHHHHHH-hcccchhhHHHHHHHHHh-----hccHHHHHHHHHHHHHHHHhCCCHHhhhhHHHHHHHHHH
Confidence 55666666655554421 123445555556666666 78889999999999999974 44211 233333333
Q ss_pred HHHHHHHhhcHHHHHHHHHHHhccCCCCCCCh-hHHHHHHHHHHHHHhcCCCCC-CCchhccCcccccccCC-C-chhHH
Q psy3716 170 ASTLYRKQAKLSLYYRTALRYLGCVDLNDLTA-SDQVQHAFLIGLAALLADSVY-NIGELLAHPILDSLQQT-P-NAWLV 245 (436)
Q Consensus 170 ~a~~~k~~~~~~~~Y~~~L~yL~~~~~~~l~~-~e~~~~A~~l~iaALl~~~iy-nFgeLl~~p~v~~L~~t-~-~~wl~ 245 (436)
. ..++.+.-.-.+..|++|...++.+ +.. +.+.++..++.=+-- -=.-++..|.+-++-++ + -.-+.
T Consensus 204 ~------~RnFkeAa~Ll~d~l~tF~S~El~sY~~~---vrYa~~~Gl~~leR~diktki~dspevl~vi~~~e~l~sl~ 274 (412)
T COG5187 204 M------RRNFKEAAILLSDILPTFESSELISYSRA---VRYAIFCGLLRLERRDIKTKILDSPEVLDVIGSSEKLGSLV 274 (412)
T ss_pred H------HHhhHHHHHHHHHHhccccccccccHHHH---HHHHHHhhhheeehhhhhhhhcCCHHHHHhccchhhhhhHH
Confidence 3 3456666677778888987766533 333 556666666541111 11123444433332221 1 11133
Q ss_pred HHHHHHhcCChh-HHHh----hhhhhhcCchhhhhHHHHHHHHHHHHHHHHHhhcCCCCcccCHHHHHHHhCCChhhHHH
Q psy3716 246 ELLRAFNAGDIE-KFEL----MRPQWSAMNDIKANENKLSQKIALLCLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEF 320 (436)
Q Consensus 246 ~LL~~f~~Gdl~-~f~~----~~~~~~~~~~L~~~~~~l~~KirLlaL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~ 320 (436)
+|...+-.-|+. .|.. +++++..+-.++.+.+.--+-||.-+-..+--+ .|.++.+..|+..|++++=|+.
T Consensus 275 ~l~~SLy~cdY~~~F~~ll~~~~n~L~~d~fl~rh~d~fvREMRrrvYaQlLES----Yr~lsl~sMA~tFgVSV~yvdr 350 (412)
T COG5187 275 QLATSLYECDYGGDFMNLLYLFCNSLQDDVFLGRHVDLFVREMRRRVYAQLLES----YRLLSLESMAQTFGVSVEYVDR 350 (412)
T ss_pred HHHHHHHHhccchhhHHHHHHHHhhccchHHHHHHHHHHHHHHHHHHHHHHHHH----HHHhhHHHHHHHhCccHHHHhh
Confidence 333333333433 2332 344555556788888888888999988888764 5899999999999999999998
Q ss_pred HHHHHHhCCcccccccCCccEEEEEec
Q psy3716 321 LIIKALALGLVKGHIDQVDESFNVTWV 347 (436)
Q Consensus 321 lvikAi~~gLI~G~IDQv~~~v~vtwv 347 (436)
=+=+-|-.|-+.+.||-++|+|..++-
T Consensus 351 DLg~FIp~~~LncvIDRvnGvVetnrp 377 (412)
T COG5187 351 DLGEFIPEGRLNCVIDRVNGVVETNRP 377 (412)
T ss_pred hHHhhCCCCceeeeeecccceEeccCc
Confidence 888889999999999999999998753
No 18
>KOG1497|consensus
Probab=97.45 E-value=0.015 Score=58.63 Aligned_cols=86 Identities=15% Similarity=0.243 Sum_probs=62.1
Q ss_pred HHhcCChhHHHhhhhhhhc------CchhhhhHHHHHHHHHHHHHHHHHhhcCCCCcccCHHHHHHHhCCChhhHHHHHH
Q psy3716 250 AFNAGDIEKFELMRPQWSA------MNDIKANENKLSQKIALLCLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLII 323 (436)
Q Consensus 250 ~f~~Gdl~~f~~~~~~~~~------~~~L~~~~~~l~~KirLlaL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lvi 323 (436)
+....+++.|..+..-+.+ ...+. ...+. =-++++-+|- ..|||+++++.++||.+.+|..+=
T Consensus 271 iI~k~el~ef~~~L~pHQka~~~dgssil~--ra~~E--hNlls~Skly-------~nisf~~Lg~ll~i~~ekaekiaa 339 (399)
T KOG1497|consen 271 IIRKEELQEFEAFLQPHQKAHTMDGSSILD--RAVIE--HNLLSASKLY-------NNISFEELGALLKIDAEKAEKIAA 339 (399)
T ss_pred HhcchhHHHHHHHhcchhhhcccCcchhhh--hHHHH--HhHHHHHHHH-------HhccHHHHHHHhCCCHHHHHHHHH
Confidence 4445568888886432211 12222 11222 2355655554 369999999999999999999999
Q ss_pred HHHhCCcccccccCCccEEEEEe
Q psy3716 324 KALALGLVKGHIDQVDESFNVTW 346 (436)
Q Consensus 324 kAi~~gLI~G~IDQv~~~v~vtw 346 (436)
..|..|-+.|.|||.++.+|.--
T Consensus 340 ~MI~qeRmng~IDQ~egiihFe~ 362 (399)
T KOG1497|consen 340 QMITQERMNGSIDQIEGIIHFED 362 (399)
T ss_pred HHHhHHHhccchHhhcceEeecc
Confidence 99999999999999999999865
No 19
>KOG2688|consensus
Probab=97.26 E-value=0.0057 Score=63.42 Aligned_cols=215 Identities=17% Similarity=0.129 Sum_probs=132.4
Q ss_pred hhHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHHHHHh---cccChhHHHHHHHHHHHHHHHHhhcHHHHHHHHHHHhc
Q psy3716 116 AKSLCKILQAQMIMNKDADKPGSLDEVEKLIDEIELLVN---DIEGVTAIHSRFYLVASTLYRKQAKLSLYYRTALRYLG 192 (436)
Q Consensus 116 a~~~~~~~i~~~~l~~~~~~~~~l~~~~~~L~~~~~~L~---~~~~~~~v~~~~y~~~a~~~k~~~~~~~~Y~~~L~yL~ 192 (436)
+.+++--+.-+++.+ .+.+.-|++.+...++... .+...+-+.-.||.- .++--..++...+..+.....
T Consensus 161 ~~~~i~n~lf~Iyfr-----i~~~~L~k~l~ra~~~~~~~~~~~~l~~~v~y~YylG--r~a~~~~d~~~A~~~L~~af~ 233 (394)
T KOG2688|consen 161 AMLYIVNQLFQIYFR-----IEKLLLCKNLIRAFDQSGSDISDFPLAQLVVYHYYLG--RYAMFESDFLNAFLQLNEAFR 233 (394)
T ss_pred HHHHHHHHHHHHHHH-----HhhHHHhHHHHHHhhccccchhhcccccceeeeeeee--eehhhhhhHHHHHHHHHHHHH
Confidence 456666667778888 8899999998887776642 222222222233322 111112333444444444333
Q ss_pred cCCCCCCChhHHHHHHHHHHHHHhcCCCCCCCchhccCcccccccCCCchhHHHHHHHHhcCChhHHHhhhhhhhcCchh
Q psy3716 193 CVDLNDLTASDQVQHAFLIGLAALLADSVYNIGELLAHPILDSLQQTPNAWLVELLRAFNAGDIEKFELMRPQWSAMNDI 272 (436)
Q Consensus 193 ~~~~~~l~~~e~~~~A~~l~iaALl~~~iynFgeLl~~p~v~~L~~t~~~wl~~LL~~f~~Gdl~~f~~~~~~~~~~~~L 272 (436)
.++. ........+..+++...++-.. +|-..-|..-+-..+-.|+.+...||+..|....+.++.. ..
T Consensus 234 ~cp~--~~~~n~~~iliylip~~~llg~---------~Pt~~lL~~~~~~~~~~lv~aVr~Gnl~~f~~al~~~E~~-f~ 301 (394)
T KOG2688|consen 234 LCPD--LLLKNKRLILIYLIPTGLLLGR---------IPTKELLDFYTLDKYSPLVQAVRSGNLRLFDLALADNERF-FI 301 (394)
T ss_pred hCcH--HHHhhhhhHHHHHhHHHHHhcc---------CcchhhHhHhhHHhHHHHHHHHHhccHHHHHHHHhhhHHH-HH
Confidence 3332 2233455566666655444322 4554444432233467899999999999999876654432 11
Q ss_pred hhhHHHHHHHHHHHHHHHHHhhc---CCCCcccCHHHHHHHhCC-C-----hhhHHHHHHHHHhCCcccccccCCccEEE
Q psy3716 273 KANENKLSQKIALLCLMELAFKK---IPGSHQLSFAEISEAAQL-P-----LIEVEFLIIKALALGLVKGHIDQVDESFN 343 (436)
Q Consensus 273 ~~~~~~l~~KirLlaL~~L~~~~---p~~~r~isf~~Ia~~l~i-~-----~~eVE~lvikAi~~gLI~G~IDQv~~~v~ 343 (436)
....=-...|.++++.-+|..+. -.....+|++.+..+++. + .+|||-.+..+|+.|.|+|.|+...+++.
T Consensus 302 ~~gi~l~l~~l~lv~yrnL~kkv~~~~~~~~~lpls~~~~al~~~~~~~~~~deveciLa~lI~~G~ikgYish~~~~~V 381 (394)
T KOG2688|consen 302 RSGIYLTLEKLPLVVYRNLFKKVIQLWGKTSQLPLSRFLTALQFSGVTDVDLDEVECILANLIDLGRIKGYISHQLQTLV 381 (394)
T ss_pred HhccHHHhhhhhHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHhhcCCCCCchhhHHHHHHhhhhhccccchhchhhheEE
Confidence 22222345557777777766421 012358999999999986 3 68999999999999999999999999999
Q ss_pred EEeccc
Q psy3716 344 VTWVQP 349 (436)
Q Consensus 344 vtwv~p 349 (436)
++.--|
T Consensus 382 ~sK~~p 387 (394)
T KOG2688|consen 382 FSKKDP 387 (394)
T ss_pred EecCCC
Confidence 876544
No 20
>KOG2758|consensus
Probab=97.23 E-value=0.13 Score=52.13 Aligned_cols=187 Identities=11% Similarity=0.087 Sum_probs=122.4
Q ss_pred CChHHHHHHHHHHHHHHhcccChh---HHH-H--HHHHHHHHHHH-HhhcH--------H--------HHHHHHHHHhcc
Q psy3716 137 GSLDEVEKLIDEIELLVNDIEGVT---AIH-S--RFYLVASTLYR-KQAKL--------S--------LYYRTALRYLGC 193 (436)
Q Consensus 137 ~~l~~~~~~L~~~~~~L~~~~~~~---~v~-~--~~y~~~a~~~k-~~~~~--------~--------~~Y~~~L~yL~~ 193 (436)
.+.+.+.+.|..+++.+++-+-.+ .+. | -+++..--++. .+|.- . -.--+.|+||++
T Consensus 181 qnWd~A~edL~rLre~IDs~~f~~~~~~l~qRtWLiHWslfv~fnhpkgrd~iid~fly~p~YLNaIQt~cPhllRYLat 260 (432)
T KOG2758|consen 181 QNWDGALEDLTRLREYIDSKSFSTSAQQLQQRTWLIHWSLFVFFNHPKGRDTIIDMFLYQPPYLNAIQTSCPHLLRYLAT 260 (432)
T ss_pred hhHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHhhccCCChhhHHHHHHccCHHHHHHHHhhCHHHHHHHHH
Confidence 467888888888888887644432 221 1 22222222232 12211 1 122356788887
Q ss_pred CCCCCCCh-hHHHHHHHHHHHHHhcCCCCCCCchhccCcccccccCCCchhHHHHHH-HHhcCChhHHHhhh---h-hhh
Q psy3716 194 VDLNDLTA-SDQVQHAFLIGLAALLADSVYNIGELLAHPILDSLQQTPNAWLVELLR-AFNAGDIEKFELMR---P-QWS 267 (436)
Q Consensus 194 ~~~~~l~~-~e~~~~A~~l~iaALl~~~iynFgeLl~~p~v~~L~~t~~~wl~~LL~-~f~~Gdl~~f~~~~---~-~~~ 267 (436)
. -++. ..++...++++. +.....|.+.| |+. +.|. .|..-|+++-.... . -+.
T Consensus 261 A---vvtnk~~rr~~lkdlvk--VIqqE~ysYkD----Pit------------eFl~clyvn~DFdgAq~kl~eCeeVl~ 319 (432)
T KOG2758|consen 261 A---VVTNKRRRRNRLKDLVK--VIQQESYSYKD----PIT------------EFLECLYVNYDFDGAQKKLRECEEVLV 319 (432)
T ss_pred H---hhcchHhhHHHHHHHHH--HHHHhccccCC----cHH------------HHHHHHhhccchHHHHHHHHHHHHHHh
Confidence 3 1222 556667777764 45556777754 443 2332 34445555555432 2 245
Q ss_pred cCchhhhhHHHHHHHHHHHHHHHHHhhcCCCCcccCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCCccEEEEEec
Q psy3716 268 AMNDIKANENKLSQKIALLCLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWV 347 (436)
Q Consensus 268 ~~~~L~~~~~~l~~KirLlaL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv~~~v~vtwv 347 (436)
+++.|..--+.-++-.|++-.-..|-- +.+|+.+-+|+.|+.+.+|.|.|++..|+...++++||.--|.|.+.--
T Consensus 320 nDfFLva~l~~F~E~ARl~ifEtfCRI----HqcIti~mLA~kLnm~~eeaErwivnlIr~~rl~AkidSklg~Vvmg~~ 395 (432)
T KOG2758|consen 320 NDFFLVALLDEFLENARLLIFETFCRI----HQCITIDMLADKLNMDPEEAERWIVNLIRTARLDAKIDSKLGHVVMGHP 395 (432)
T ss_pred cchhHHHHHHHHHHHHHHHHHHHHHHH----HHheeHHHHHHHhcCCHHHHHHHHHHHHHHhhhhhhhccccCceeecCC
Confidence 567777777777889999988887754 3699999999999999999999999999999999999999999877643
Q ss_pred c
Q psy3716 348 Q 348 (436)
Q Consensus 348 ~ 348 (436)
+
T Consensus 396 ~ 396 (432)
T KOG2758|consen 396 T 396 (432)
T ss_pred C
Confidence 3
No 21
>KOG2581|consensus
Probab=96.93 E-value=0.052 Score=56.38 Aligned_cols=258 Identities=17% Similarity=0.221 Sum_probs=134.8
Q ss_pred hHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHHHHHhcccC--hhHHHHHHHHHHHHHHHHhhcHHH--HHHHHHHHhc
Q psy3716 117 KSLCKILQAQMIMNKDADKPGSLDEVEKLIDEIELLVNDIEG--VTAIHSRFYLVASTLYRKQAKLSL--YYRTALRYLG 192 (436)
Q Consensus 117 ~~~~~~~i~~~~l~~~~~~~~~l~~~~~~L~~~~~~L~~~~~--~~~v~~~~y~~~a~~~k~~~~~~~--~Y~~~L~yL~ 192 (436)
.+|+.+....+... ..++.++.+.-++.=..+...+- .+-+.++.|.-.+-.|+..|+... .+-+++.--+
T Consensus 125 ~aY~~lLv~Lfl~d-----~K~~kea~~~~~~~l~~i~~~nrRtlD~i~ak~~fy~~l~~E~~~~l~~~rs~l~~~lrtA 199 (493)
T KOG2581|consen 125 EAYLYLLVLLFLID-----QKEYKEADKISDALLASISIQNRRTLDLIAAKLYFYLYLSYELEGRLADIRSFLHALLRTA 199 (493)
T ss_pred HHHHHHHHHHHHHh-----hHHHHHHHHHHHHHHHHHHhcchhhHHHHHHHHHHHHHHHHHhhcchHHHHHHHHHHHHHh
Confidence 34554444444444 45566666555544333332222 245566666666666777777433 3333333333
Q ss_pred cCCCCCCChhHHHHHHHHHHHHHhcCCCCCCCchhccCcccccccCCCchhHH---HHHHHHh-cCChhHHHh-hhhhhh
Q psy3716 193 CVDLNDLTASDQVQHAFLIGLAALLADSVYNIGELLAHPILDSLQQTPNAWLV---ELLRAFN-AGDIEKFEL-MRPQWS 267 (436)
Q Consensus 193 ~~~~~~l~~~e~~~~A~~l~iaALl~~~iynFgeLl~~p~v~~L~~t~~~wl~---~LL~~f~-~Gdl~~f~~-~~~~~~ 267 (436)
+..- .++-+.....+.+...++.+.|.=.+=+-...+-.=..+...|-. =+=.|+. .+|+.+-.+ |.+..-
T Consensus 200 tLrh----d~e~qavLiN~LLr~yL~n~lydqa~~lvsK~~~pe~~snne~ARY~yY~GrIkaiqldYssA~~~~~qa~r 275 (493)
T KOG2581|consen 200 TLRH----DEEGQAVLINLLLRNYLHNKLYDQADKLVSKSVYPEAASNNEWARYLYYLGRIKAIQLDYSSALEYFLQALR 275 (493)
T ss_pred hhcC----cchhHHHHHHHHHHHHhhhHHHHHHHHHhhcccCccccccHHHHHHHHHHhhHHHhhcchhHHHHHHHHHHH
Confidence 3321 345667777888888888888865542221111000112224422 1212221 344433333 222222
Q ss_pred cCchhhhhHHHHHHHHHHHHHHHHH---------hhcCCCCcc-cCHHHHHHHhCCC-hh----hHHHH-----------
Q psy3716 268 AMNDIKANENKLSQKIALLCLMELA---------FKKIPGSHQ-LSFAEISEAAQLP-LI----EVEFL----------- 321 (436)
Q Consensus 268 ~~~~L~~~~~~l~~KirLlaL~~L~---------~~~p~~~r~-isf~~Ia~~l~i~-~~----eVE~l----------- 321 (436)
+-|. ...-.+..+-..++++++|- |..|+-.+. .+|=.++++.++. .. -+|.+
T Consensus 276 kapq-~~alGf~q~v~k~~ivv~ll~geiPers~F~Qp~~~ksL~~Yf~Lt~AVr~gdlkkF~~~leq~k~~f~~D~ty~ 354 (493)
T KOG2581|consen 276 KAPQ-HAALGFRQQVNKLMIVVELLLGEIPERSVFRQPGMRKSLRPYFKLTQAVRLGDLKKFNETLEQFKDKFQADGTYT 354 (493)
T ss_pred hCcc-hhhhhHHHHHHHHHHHHHHHcCCCcchhhhcCccHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHhhCCcch
Confidence 3343 23344556666777777764 344422222 3677777777663 21 22222
Q ss_pred HHHHHhCCcccccccCCccEEEEEeccccccccchhhccccCCcccccHHHHHHHcCC-ChhhHHHHHHHHHhcccceee
Q psy3716 322 IIKALALGLVKGHIDQVDESFNVTWVQPRVLSKDQLAFKKIPGSHQLSFAEISEAAQL-PLIEVEFLIIKALALGLVKGH 400 (436)
Q Consensus 322 vikAi~~gLI~G~IDQv~~~v~vtwv~pRvL~l~Qi~~lr~~~~r~~sf~~i~~~~~~-~~~~ve~lvmka~s~~li~g~ 400 (436)
++.-++.+.|+--|-++ .++ =..+|.++||..+++ +.+|||++|-||++-|+|+|+
T Consensus 355 LivRLR~NVIkTgIR~I----Sls-------------------YSRISl~DIA~kL~l~Seed~EyiVakAIRDGvIea~ 411 (493)
T KOG2581|consen 355 LIVRLRHNVIKTGIRKI----SLS-------------------YSRISLQDIAKKLGLNSEEDAEYIVAKAIRDGVIEAK 411 (493)
T ss_pred HHHHHHHHHHHHhhhhe----eee-------------------eeeccHHHHHHHhcCCCchhHHHHHHHHHHhccceee
Confidence 22233333333222111 011 135999999999999 455699999999999999999
Q ss_pred cccccce
Q psy3716 401 IDQVDES 407 (436)
Q Consensus 401 idqv~~~ 407 (436)
||.-+|.
T Consensus 412 Id~~~g~ 418 (493)
T KOG2581|consen 412 IDHEDGF 418 (493)
T ss_pred eccccCc
Confidence 9998873
No 22
>COG5600 Transcription-associated recombination protein [DNA replication, recombination, and repair]
Probab=96.85 E-value=0.21 Score=51.56 Aligned_cols=204 Identities=19% Similarity=0.261 Sum_probs=113.6
Q ss_pred HHHHhhccCCCCCCChHHHHHHHHHHHHHHhcccChh------HHHHHHHHHHHHHHHHhhcHHHHHHHHHH-HhccCCC
Q psy3716 124 QAQMIMNKDADKPGSLDEVEKLIDEIELLVNDIEGVT------AIHSRFYLVASTLYRKQAKLSLYYRTALR-YLGCVDL 196 (436)
Q Consensus 124 i~~~~l~~~~~~~~~l~~~~~~L~~~~~~L~~~~~~~------~v~~~~y~~~a~~~k~~~~~~~~Y~~~L~-yL~~~~~ 196 (436)
...++++ .+.++-|+..++..+. .+..... .|-=.||.- .||--..++.+.|-+... ++.|-..
T Consensus 183 L~~iY~R-----l~~~~l~~n~lka~~~--vs~~Di~~~~~sq~v~f~YYLG--~~~l~~en~heA~~~L~~aFl~c~~l 253 (413)
T COG5600 183 LFQIYLR-----LGRFKLCENFLKASKE--VSMPDISEYQKSQVVVFHYYLG--IYYLLNENFHEAFLHLNEAFLQCPWL 253 (413)
T ss_pred HHHHHHH-----hccHHHHHHHHHhccc--ccccccchhhhcceeehhhHHH--HHHHHHHhHHHHHHHHHHHHHhChhh
Confidence 3466777 8999999888876655 2222211 111122222 222222233333333333 4555332
Q ss_pred CCCChhHHHHHHHHHHHHHhcCCCCCCCchhccCcccccccCCC-chhHHHHHHHHhcCChhHHHhhhhhhhcCchhhh-
Q psy3716 197 NDLTASDQVQHAFLIGLAALLADSVYNIGELLAHPILDSLQQTP-NAWLVELLRAFNAGDIEKFELMRPQWSAMNDIKA- 274 (436)
Q Consensus 197 ~~l~~~e~~~~A~~l~iaALl~~~iynFgeLl~~p~v~~L~~t~-~~wl~~LL~~f~~Gdl~~f~~~~~~~~~~~~L~~- 274 (436)
-.-.+..++-..+..+|+-.+.+ |--.-|.... -+..--|..+.-+||+++|....+.++.. +..
T Consensus 254 ---~~~n~~rIl~~~ipt~Llv~~~~--------Ptk~~L~r~~~~s~~~~LvkavrsGni~~~~~~l~~ner~--~~~~ 320 (413)
T COG5600 254 ---ITRNRKRILPYYIPTSLLVNKFP--------PTKDLLERFKRCSVYSPLVKAVRSGNIEDFDLALSRNERK--FAKR 320 (413)
T ss_pred ---hhcchheehhHHhhHHHHhCCCC--------CchHHHHhccccchhHHHHHHHHcCCHHHHHHHHHHhHHH--HHHc
Confidence 12234556667777777766555 2222233222 23345688999999999999876654331 211
Q ss_pred -hHHHHHHHHHHHHHHHHHhh---cCCCCcccCHHHHHHHhCC---C----hhhHHHHHHHHHhCCcccccccCCccEEE
Q psy3716 275 -NENKLSQKIALLCLMELAFK---KIPGSHQLSFAEISEAAQL---P----LIEVEFLIIKALALGLVKGHIDQVDESFN 343 (436)
Q Consensus 275 -~~~~l~~KirLlaL~~L~~~---~p~~~r~isf~~Ia~~l~i---~----~~eVE~lvikAi~~gLI~G~IDQv~~~v~ 343 (436)
-.-.+..+-.+++.-+|.-+ .-..+..+|++-+...+++ + .++||-.+..+|+.|+++|.|.--.++|.
T Consensus 321 ~l~ltl~~~~~~V~~RNL~rk~w~~~~~qsrlp~sil~~~~qls~~dn~~~~~~VEciL~tlI~~G~lrgYis~s~~~vV 400 (413)
T COG5600 321 GLYLTLLAHYPLVCFRNLFRKIWRLHGKQSRLPLSILLIVLQLSAIDNFHSFKEVECILVTLIGLGLLRGYISHSRRTVV 400 (413)
T ss_pred chHHHHHhhccHHHHHHHHHHHHhhccccccCcHHHHHHHHHccCCCcccChHHHHHHHHHHHhhhhhhheecccceEEE
Confidence 12223333444444443321 0111223555555555444 2 56899999999999999999999999999
Q ss_pred EEeccc
Q psy3716 344 VTWVQP 349 (436)
Q Consensus 344 vtwv~p 349 (436)
++.-.|
T Consensus 401 ~sk~~p 406 (413)
T COG5600 401 FSKKDP 406 (413)
T ss_pred EecCCC
Confidence 887655
No 23
>COG5159 RPN6 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=96.84 E-value=0.31 Score=48.91 Aligned_cols=164 Identities=12% Similarity=0.076 Sum_probs=108.7
Q ss_pred hcHHHHHHHHHHHhccCCCCCCChhHHHHHHHHHHHHHhcCCCCCCCchhccCcc-cccccCCCchhHHHHHHHHhcCCh
Q psy3716 178 AKLSLYYRTALRYLGCVDLNDLTASDQVQHAFLIGLAALLADSVYNIGELLAHPI-LDSLQQTPNAWLVELLRAFNAGDI 256 (436)
Q Consensus 178 ~~~~~~Y~~~L~yL~~~~~~~l~~~e~~~~A~~l~iaALl~~~iynFgeLl~~p~-v~~L~~t~~~wl~~LL~~f~~Gdl 256 (436)
.+|.-.|.+-...+..|..-+. ..++..-..++.++-+-...+=.-+.++.... +.+.++.....+...-++|+..++
T Consensus 220 ~dyktA~SYF~Ea~Egft~l~~-d~kAc~sLkYmlLSkIMlN~~~evk~vl~~K~t~~~y~~r~I~am~avaea~~NRsL 298 (421)
T COG5159 220 RDYKTASSYFIEALEGFTLLKM-DVKACVSLKYMLLSKIMLNRREEVKAVLRNKNTLKHYDDRMIRAMLAVAEAFGNRSL 298 (421)
T ss_pred ccchhHHHHHHHHHhccccccc-hHHHHHHHHHHHHHHHHHhhHHHHHHHHccchhHhhhhhhhHHHHHHHHHHhCCCcH
Confidence 3444444444444444432111 24555566666666655544444555555433 334666666778888899999999
Q ss_pred hHHHhhh----hhhhcCchhhhhHHHHHHHHHHHHHHHHHhhcCCCCcccCHHHHHHHhCCChhhHHHHHHHHHhCCccc
Q psy3716 257 EKFELMR----PQWSAMNDIKANENKLSQKIALLCLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVK 332 (436)
Q Consensus 257 ~~f~~~~----~~~~~~~~L~~~~~~l~~KirLlaL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~ 332 (436)
.+|+... +++.++|....+-..+..-+-=--|+..+ .|. ..+..+-||+-.|++..+||.-+-+.|-.++.-
T Consensus 299 ~df~~aL~qY~~el~~D~~iRsHl~~LYD~LLe~Nl~kii--EPf--s~VeishIa~viGldt~qvEgKLsqMILDKify 374 (421)
T COG5159 299 KDFSDALAQYSDELHQDSFIRSHLQYLYDVLLEKNLVKII--EPF--SVVEISHIADVIGLDTNQVEGKLSQMILDKIFY 374 (421)
T ss_pred hhHHHHHHHhhHHhccCHHHHHHHHHHHHHHHHhhhhhhc--Ccc--eeeehhHHHHHhcccHHHHHHHHHHHHHHHHHH
Confidence 9999753 34555666665544444433333444444 353 467777899999999999999999999999999
Q ss_pred ccccCCccEEEEEe
Q psy3716 333 GHIDQVDESFNVTW 346 (436)
Q Consensus 333 G~IDQv~~~v~vtw 346 (436)
|.+||.++.+.|.-
T Consensus 375 G~LDqg~gcLivy~ 388 (421)
T COG5159 375 GTLDQGDGCLIVYG 388 (421)
T ss_pred hhhccCCceEEEeC
Confidence 99999999998864
No 24
>KOG3250|consensus
Probab=96.23 E-value=0.0087 Score=57.08 Aligned_cols=129 Identities=19% Similarity=0.226 Sum_probs=90.6
Q ss_pred HHHHHhhcCCCCcccCHHHHHHHhCC-----ChhhHHHHHHHHHhCCcccccccCCccEEEEEeccccccccchhhcccc
Q psy3716 288 LMELAFKKIPGSHQLSFAEISEAAQL-----PLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPRVLSKDQLAFKKI 362 (436)
Q Consensus 288 L~~L~~~~p~~~r~isf~~Ia~~l~i-----~~~eVE~lvikAi~~gLI~G~IDQv~~~v~vtwv~pRvL~l~Qi~~lr~ 362 (436)
|++=|-..| ...-|.+|-...++ |.+-+-.=+++.+.-|=+.-.+-.- ..---|++.|+..++.
T Consensus 29 lIsqale~P---~vf~F~ELl~l~nv~qlae~~dsa~lrlL~lFa~Gt~~Dy~aea--------~rlp~Ls~~q~~kLk~ 97 (258)
T KOG3250|consen 29 LISQALEAP---GVFVFGELLILPNVVQLAEPIDSAYLRLLELFAYGTYRDYSAEA--------LRLPKLSLAQLNKLKH 97 (258)
T ss_pred HHHHHhcCC---CeeeHHHHHhhhhHHHHcccccHHHHHHHHHHhcCchhhhhhhh--------hcCCCCCHHHHHhhhc
Confidence 344455566 47788888877765 4556666667777777665544432 1112344445444432
Q ss_pred -------CCcccccHHHHHHHcCC-ChhhHHHHHHHHHhcccceeecccccceEEEeeecccccchhhhhHHH
Q psy3716 363 -------PGSHQLSFAEISEAAQL-PLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPRVLSKDQVFWSL 427 (436)
Q Consensus 363 -------~~~r~~sf~~i~~~~~~-~~~~ve~lvmka~s~~li~g~idqv~~~v~~~wv~pr~l~~~q~~~~~ 427 (436)
+-.+.+++...-+.... +.-++|.+||.|+=.+.++|+|||-+++++|+|.--|-|...+|.+-.
T Consensus 98 ltV~slas~~k~lpy~~Ll~~l~~~nvrelEd~iieamya~IlrGkldqr~q~leV~faigRdlr~k~i~nm~ 170 (258)
T KOG3250|consen 98 LTVVSLASFEKCLPYLVLLRLLPSRNVRELEDLIIEAMYADILRGKLDQRNQTLEVDFAIGRDLRSKDIDNMK 170 (258)
T ss_pred ceehhhhhhchhhhHHHHHhhccCCchhHHHHHHHHHHHHHHHHhhHHhhcceEeechhhcccccHhHHHHHH
Confidence 12346666666666655 677999999999999999999999999999999999999999887643
No 25
>KOG1498|consensus
Probab=96.23 E-value=0.37 Score=50.06 Aligned_cols=249 Identities=15% Similarity=0.195 Sum_probs=153.8
Q ss_pred hhHHHHHHHHhccCCCHHHHHHHHHHH----HHhhcCCcchhHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHHHHHhc
Q psy3716 80 VSLMEIMEVITNHLSDQEEALVLLQSF----EDKVKNNLEAKSLCKILQAQMIMNKDADKPGSLDEVEKLIDEIELLVND 155 (436)
Q Consensus 80 l~l~~i~~~v~~~~~d~~~aL~~L~~l----~~~l~~~~ea~~~~~~~i~~~~l~~~~~~~~~l~~~~~~L~~~~~~L~~ 155 (436)
-++.+.+..+-+...|-.+|..+|..+ +..+..+ +-.-| .++.-++-+. .+|+-.+..+-+.+....-+
T Consensus 131 arlTk~L~~ike~~Gdi~~Aa~il~el~VETygsm~~~-ekV~f-iLEQmrKOG~-----~~D~vra~i~skKI~~K~F~ 203 (439)
T KOG1498|consen 131 ARLTKMLAKIKEEQGDIAEAADILCELQVETYGSMEKS-EKVAF-ILEQMRLCLL-----RLDYVRAQIISKKINKKFFE 203 (439)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHhcchhhhhhhHHH-HHHHH-HHHHHHHHHH-----hhhHHHHHHHHHHhhHHhcC
Confidence 446666666666667777888777654 2222211 22222 2344455555 68898888888899888877
Q ss_pred ccChhHHHHHHHHHHHHHHHHhhcHHHHHHHHHHHhccCCCCCCCh-hHH-HHHHHHHHHHHhcCCCCCCCchhccCccc
Q psy3716 156 IEGVTAIHSRFYLVASTLYRKQAKLSLYYRTALRYLGCVDLNDLTA-SDQ-VQHAFLIGLAALLADSVYNIGELLAHPIL 233 (436)
Q Consensus 156 ~~~~~~v~~~~y~~~a~~~k~~~~~~~~Y~~~L~yL~~~~~~~l~~-~e~-~~~A~~l~iaALl~~~iynFgeLl~~p~v 233 (436)
-+.+.+....||.+.-.++-..+.| +.-+=.|=+.++...... +++ .......+..++++|..--=.+|+++-.-
T Consensus 204 ~~~~~~lKlkyY~lmI~l~lh~~~Y---l~v~~~Yraiy~t~~vk~d~~kw~~vL~~iv~f~~LAp~dneQsdll~~is~ 280 (439)
T KOG1498|consen 204 KPDVQELKLKYYELMIRLGLHDRAY---LNVCRSYRAIYDTGNVKEDPEKWIEVLRSIVSFCVLAPHDNEQSDLLARISN 280 (439)
T ss_pred CccHHHHHHHHHHHHHHhcccccch---hhHHHHHHHHhcccccccChhhhhhhhhhheeEEeecCCCcHHHHHHHHHhc
Confidence 6667788899999877754333332 222222333444333322 222 34444444566777766555566665332
Q ss_pred c-cccCCCchhHHHHHHHHhcCChhHHHhhhh----hhhcC-----chhh------hhHHHHHHHHHHHHHHHHHhhcCC
Q psy3716 234 D-SLQQTPNAWLVELLRAFNAGDIEKFELMRP----QWSAM-----NDIK------ANENKLSQKIALLCLMELAFKKIP 297 (436)
Q Consensus 234 ~-~L~~t~~~wl~~LL~~f~~Gdl~~f~~~~~----~~~~~-----~~L~------~~~~~l~~KirLlaL~~L~~~~p~ 297 (436)
+ .|.+-+ -.-++|..|.+|.+-.|..+.. .+... ...+ .......+.||+++=-
T Consensus 281 dKkL~e~p--~~k~lLklfv~~EL~rw~s~~~~yg~~l~~~~~~~~~~~gek~~~dL~~RIiEHNiRiiA~y-------- 350 (439)
T KOG1498|consen 281 DKKLSELP--DYKELLKLFVTMELIRWVSLVESYGDELRTNDFFDGGEEGEKRWSDLKLRIIEHNIRIIAKY-------- 350 (439)
T ss_pred ccccccCc--cHHHHHHHHHhcceeeehhHhhhhHHHHhhcccccccchhhhHHHHHHHHHHHHHHHHHHHH--------
Confidence 2 243322 1458899999998766653311 11111 1111 1123344556665422
Q ss_pred CCcccCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCCccEEEEEeccc
Q psy3716 298 GSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQP 349 (436)
Q Consensus 298 ~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv~~~v~vtwv~p 349 (436)
+..||+.++++-++.|.++.|.++=..+..|-+.+|||+..+.+...-++.
T Consensus 351 -YSrIt~~rl~eLLdl~~ee~E~~LS~lv~t~ti~aKidrpsgII~F~k~K~ 401 (439)
T KOG1498|consen 351 -YSRITLKRLAELLDLPVEEMEKFLSDLVVTGTIYAKIDRPSGIINFQKVKD 401 (439)
T ss_pred -HhhccHHHHHHHhCCCHHHHHHHHHHHHhccceEEEecCCCceEEEEeccc
Confidence 247999999999999999999999999999999999999999988876653
No 26
>KOG1076|consensus
Probab=95.49 E-value=5.4 Score=44.44 Aligned_cols=128 Identities=19% Similarity=0.257 Sum_probs=99.1
Q ss_pred CCchhccCcccccccCCC---chhHHHHHHHHhcCChhHHHhhhhh----hhcCchhhhhHHHHHHHHHHHHHHHHHhhc
Q psy3716 223 NIGELLAHPILDSLQQTP---NAWLVELLRAFNAGDIEKFELMRPQ----WSAMNDIKANENKLSQKIALLCLMELAFKK 295 (436)
Q Consensus 223 nFgeLl~~p~v~~L~~t~---~~wl~~LL~~f~~Gdl~~f~~~~~~----~~~~~~L~~~~~~l~~KirLlaL~~L~~~~ 295 (436)
+|--+|.+-.=+++.|+| -..+..--.++..||+.+-.+|.-. |.=+|.--.-.+.+.+||+--+|-..-|.=
T Consensus 633 ~frr~Le~serqsf~gPPEn~RehVvaAsKAm~~Gnw~~c~~fi~nn~KvW~Lfpn~d~V~~Ml~~rIqEEsLRTYLftY 712 (843)
T KOG1076|consen 633 SFRRQLEHSERQSFTGPPENTREHVVAASKAMQKGNWQKCFEFIVNNIKVWDLFPNADTVLDMLTERIQEESLRTYLFTY 712 (843)
T ss_pred HHHHHHHHHhhccccCCchhHHHHHHHHHHHHhcCCHHHHHHHHHhhhhHHHhcccHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 344455555556666654 2334555678889999988886433 322333334467789999999999877755
Q ss_pred CCCCcccCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCCccEEEEEecccc
Q psy3716 296 IPGSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPR 350 (436)
Q Consensus 296 p~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv~~~v~vtwv~pR 350 (436)
++-+.++|.+.+|+-..+|+..|--.|=+.|...=|.+++||..++|.+++|+|.
T Consensus 713 ss~Y~SvSl~~LA~mFdLp~~~VhsIiSkmiineEl~AslDqpt~~iv~hrvE~s 767 (843)
T KOG1076|consen 713 SSVYDSVSLAKLADMFDLPEPKVHSIISKMIINEELHASLDQPTQCIVMHRVEPS 767 (843)
T ss_pred hhhhhhccHHHHHHHhCCCchhHHHHHHHHHHHHHhhhccCCCcceEEEeeccch
Confidence 5557799999999999999999999999999999999999999999999999986
No 27
>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A.
Probab=95.33 E-value=0.81 Score=45.30 Aligned_cols=172 Identities=15% Similarity=0.146 Sum_probs=103.5
Q ss_pred CHHHHHHHHHHHHHhhcCCc--chhHHHHHHHHHHhhccCCCCC-CChHHHHHHHHHHHHHHhcccChhHHHHHHHHHHH
Q psy3716 95 DQEEALVLLQSFEDKVKNNL--EAKSLCKILQAQMIMNKDADKP-GSLDEVEKLIDEIELLVNDIEGVTAIHSRFYLVAS 171 (436)
Q Consensus 95 d~~~aL~~L~~l~~~l~~~~--ea~~~~~~~i~~~~l~~~~~~~-~~l~~~~~~L~~~~~~L~~~~~~~~v~~~~y~~~a 171 (436)
+|++|++.+++..+-..... .....+...+|.++-. . |+++.+-....+.-.+...-+ .+......+.-.+
T Consensus 89 ~~~~Ai~~~~~A~~~y~~~G~~~~aA~~~~~lA~~ye~-----~~~d~e~Ai~~Y~~A~~~y~~e~-~~~~a~~~~~~~A 162 (282)
T PF14938_consen 89 DPDEAIECYEKAIEIYREAGRFSQAAKCLKELAEIYEE-----QLGDYEKAIEYYQKAAELYEQEG-SPHSAAECLLKAA 162 (282)
T ss_dssp THHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHCC-----TT--HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHH-----HcCCHHHHHHHHHHHHHHHHHCC-ChhhHHHHHHHHH
Confidence 78888888888777654322 2334555677778776 6 899999888888888876644 3444556666677
Q ss_pred HHHHHhhcHHHHHHHHHHHhccCCCCCCChhHHHHHHHHHHHHHhcCCCCCCCchhccC-ccc-ccccCC-CchhHHHHH
Q psy3716 172 TLYRKQAKLSLYYRTALRYLGCVDLNDLTASDQVQHAFLIGLAALLADSVYNIGELLAH-PIL-DSLQQT-PNAWLVELL 248 (436)
Q Consensus 172 ~~~k~~~~~~~~Y~~~L~yL~~~~~~~l~~~e~~~~A~~l~iaALl~~~iynFgeLl~~-p~v-~~L~~t-~~~wl~~LL 248 (436)
..+-..|+|.+.....-+.....-...+..-...+.....++.-|..++...-...+.- -.. -...+| ++.-+.+|+
T Consensus 163 ~l~~~l~~y~~A~~~~e~~~~~~l~~~l~~~~~~~~~l~a~l~~L~~~D~v~A~~~~~~~~~~~~~F~~s~E~~~~~~l~ 242 (282)
T PF14938_consen 163 DLYARLGRYEEAIEIYEEVAKKCLENNLLKYSAKEYFLKAILCHLAMGDYVAARKALERYCSQDPSFASSREYKFLEDLL 242 (282)
T ss_dssp HHHHHTT-HHHHHHHHHHHHHTCCCHCTTGHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHGTTSTTSTTSHHHHHHHHHH
T ss_pred HHHHHhCCHHHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCCCcHHHHHHHHHH
Confidence 77777788777666655544433222344445566666677767766543322222210 000 012333 578899999
Q ss_pred HHHhcCChhHHHhhhhhhhcCchh
Q psy3716 249 RAFNAGDIEKFELMRPQWSAMNDI 272 (436)
Q Consensus 249 ~~f~~Gdl~~f~~~~~~~~~~~~L 272 (436)
++|..||.+.|.+......+...|
T Consensus 243 ~A~~~~D~e~f~~av~~~d~~~~l 266 (282)
T PF14938_consen 243 EAYEEGDVEAFTEAVAEYDSISRL 266 (282)
T ss_dssp HHHHTT-CCCHHHHCHHHTTSS--
T ss_pred HHHHhCCHHHHHHHHHHHcccCcc
Confidence 999999999999876655444333
No 28
>KOG2582|consensus
Probab=95.07 E-value=1.7 Score=44.90 Aligned_cols=302 Identities=14% Similarity=0.144 Sum_probs=153.3
Q ss_pred chHHHHHHHHHHHHHhhhHHHHHHHHHH----------------HhcCcccc-cchhHHHHHHHHHHHHh-hccCc--hh
Q psy3716 22 PEISAQWLNLEELYNKKLWHQLTLAVLA----------------FVQNPAIQ-KEGELRDLYHKFVISFE-TKINP--VS 81 (436)
Q Consensus 22 ~~~~~~~~~l~~l~~~KLWhQLT~~l~~----------------~~~~p~~~-~~~~~~~ly~~fI~~f~-~kin~--l~ 81 (436)
.++++...+-.++.+++.=| +-..|.. -+..|... ....++.+++.||+..- ..++. -.
T Consensus 22 ~eL~~~i~~~~ell~k~~~~-~~~~L~~ld~~~hSlgml~~l~~~f~~~~~~~~~~~li~~~~~FV~~~n~eqlr~as~~ 100 (422)
T KOG2582|consen 22 GELAELIVKSKELLAKNSSD-LDAVLLHLDPQVHSLGMLAVLKVKFHTPSANPDPETLIELLNDFVDENNGEQLRLASEI 100 (422)
T ss_pred HHHHHHHHhhHHHHHhCcch-HHHHHHhcCccccchhhhhhhhccccCcccCCCHHHHHHHHHHHHHhcChHHHhhHHHH
Confidence 47788888888888877443 3222222 11122211 12467889999998762 33332 22
Q ss_pred HHHHHHHHhc---cCCCHHHHHHHHHHHHHhhcCCcchhHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHHHHHhcccC
Q psy3716 82 LMEIMEVITN---HLSDQEEALVLLQSFEDKVKNNLEAKSLCKILQAQMIMNKDADKPGSLDEVEKLIDEIELLVNDIEG 158 (436)
Q Consensus 82 l~~i~~~v~~---~~~d~~~aL~~L~~l~~~l~~~~ea~~~~~~~i~~~~l~~~~~~~~~l~~~~~~L~~~~~~L~~~~~ 158 (436)
+...|..+.. +-..|.-.++.+.+...++.+.....--+..-+....|+ .+++....+.++.----+..-+.
T Consensus 101 f~~lc~~l~~~~~~~~~p~~gi~ii~~av~k~~~~~~qlT~~H~~l~~~~L~-----ak~y~~~~p~ld~divei~~~n~ 175 (422)
T KOG2582|consen 101 FFPLCHDLTEAVVKKNKPLRGIRIIMQAVDKMQPSNGQLTSIHADLLQLCLE-----AKDYASVLPYLDDDIVEICKANP 175 (422)
T ss_pred HHHHHHHHHHHHHhcCCccccchHHHHHHHHhccCccchhhhHHHHHHHHHH-----hhcccccCCccchhHHHHhccCC
Confidence 3333433332 223666667788887777765443211111222233444 44554444433311111111111
Q ss_pred hhHHHHHHHHHHHHHHH-----HhhcHHHHHHHHHHHhccCCCCCCChhHHHHHHH-H-HHHHHhcCCCCCCCchhccCc
Q psy3716 159 VTAIHSRFYLVASTLYR-----KQAKLSLYYRTALRYLGCVDLNDLTASDQVQHAF-L-IGLAALLADSVYNIGELLAHP 231 (436)
Q Consensus 159 ~~~v~~~~y~~~a~~~k-----~~~~~~~~Y~~~L~yL~~~~~~~l~~~e~~~~A~-~-l~iaALl~~~iynFgeLl~~p 231 (436)
-.+.+++.. ..||- ..++++. ....|=.|+.....+....-.-|| . +.++-++.-.++...+=-..-
T Consensus 176 --h~~~k~fL~-Y~yYgg~iciglk~fe~---Al~~~e~~v~~Pa~~vs~~hlEaYkkylLvsLI~~GK~~ql~k~ts~~ 249 (422)
T KOG2582|consen 176 --HLDPKYFLL-YLYYGGMICIGLKRFER---ALYLLEICVTTPAMAVSHIHLEAYKKYLLVSLILTGKVFQLPKNTSQN 249 (422)
T ss_pred --CCCHHHHHH-HHHhcceeeeccccHHH---HHHHHHHHHhcchhHHHHHHHHHHHHHHHHHhhhcCceeeccccchhh
Confidence 122222221 11221 1223222 222232333222222222222222 2 333333334454443322222
Q ss_pred ccccccCCCchhHHHHHHHHhcCChhHHHhhhhh-hhc-----CchhhhhHHHHHHHHHHHHHHHHHhhcCCCCcccCHH
Q psy3716 232 ILDSLQQTPNAWLVELLRAFNAGDIEKFELMRPQ-WSA-----MNDIKANENKLSQKIALLCLMELAFKKIPGSHQLSFA 305 (436)
Q Consensus 232 ~v~~L~~t~~~wl~~LL~~f~~Gdl~~f~~~~~~-~~~-----~~~L~~~~~~l~~KirLlaL~~L~~~~p~~~r~isf~ 305 (436)
+....+. --....+++++++.+...+.+.+..+ |+. +..|....-.-.-|=+++.|.... -+++.+
T Consensus 250 ~~r~~K~-ms~pY~ef~~~Y~~~~~~eLr~lVk~~~~rF~kDnnt~l~k~av~sl~k~nI~rltktF-------~sLsL~ 321 (422)
T KOG2582|consen 250 AGRFFKP-MSNPYHEFLNVYLKDSSTELRTLVKKHSERFTKDNNTGLAKQAVSSLYKKNIQRLTKTF-------LSLSLS 321 (422)
T ss_pred hHHhccc-CCchHHHHHHHHhcCCcHHHHHHHHHHHHHHhhcCcHHHHHHHHHHHHHHHHHHHHHHH-------HHhhHH
Confidence 2222222 11137899999999998887776433 222 233444444445666777777754 269999
Q ss_pred HHHHHhCC-ChhhHHHHHHHHHhCCcccccccCCccEEEEEe
Q psy3716 306 EISEAAQL-PLIEVEFLIIKALALGLVKGHIDQVDESFNVTW 346 (436)
Q Consensus 306 ~Ia~~l~i-~~~eVE~lvikAi~~gLI~G~IDQv~~~v~vtw 346 (436)
+||+..++ +.+|||..|+.-|..|-|-..|| |-|..+.
T Consensus 322 dIA~~vQLa~~qevek~Ilqmie~~~i~a~iN---G~v~f~~ 360 (422)
T KOG2582|consen 322 DIASRVQLASAQEVEKYILQMIEDGEIFASIN---GMVFFTD 360 (422)
T ss_pred HHHHHHHhcchHHHHHHHHHHhccCceEEEec---ceEEEec
Confidence 99998888 56899999999999999999999 5555543
No 29
>PF10075 PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro: IPR019280 The photomorphogenic 9 (COP9) signalosome or CSN complex is composed of eight subunits: Cops1/GPS1, Cops2, Cops3, Cops4, Cops5, Cop6, Cops7 (Cops7A or Cops7B) and Cops8. In the complex, Cops8, which is the smallest subunit, probably interacts directly with Cops3, Cops4 and Cops7 (Cops7A or Cops7B). This signalosome is homologous to the lid subcomplex of the 26S proteasome and regulates the ubiquitin-proteasome pathway. It functions as a structural scaffold for subunit-subunit interactions within the complex and is a key regulator of photomorphogenic development [].; PDB: 1RZ4_A.
Probab=93.14 E-value=0.48 Score=42.19 Aligned_cols=107 Identities=20% Similarity=0.134 Sum_probs=61.7
Q ss_pred HHHhcCCCCCCCchhccCccccccc-CCCchhHHHHHHHHhcCChhHHHhhhhhhhcCchhhhhHHHHHHHHHH--HHHH
Q psy3716 213 LAALLADSVYNIGELLAHPILDSLQ-QTPNAWLVELLRAFNAGDIEKFELMRPQWSAMNDIKANENKLSQKIAL--LCLM 289 (436)
Q Consensus 213 iaALl~~~iynFgeLl~~p~v~~L~-~t~~~wl~~LL~~f~~Gdl~~f~~~~~~~~~~~~L~~~~~~l~~KirL--laL~ 289 (436)
+.+|...++.+|.-++..-.-...+ +++..-+..|.+.+-.|++.+|-......+-.|.+......+..+||- ..++
T Consensus 12 l~~L~~~~~~df~~~~~rip~~~~~~~~~i~~i~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~iR~~i~~~i 91 (143)
T PF10075_consen 12 LKYLMQNDLSDFRLLWKRIPEELKQSDPEIKAIWSLGQALWEGDYSKFWQALRSNPWSPDYKPFVPGFEDTIRERIAHLI 91 (143)
T ss_dssp HHHHHTTTSTHHHHHHHTS-HHHHTS-TTHHHHHHHHHHHHTT-HHHHHHHS-TT----HHHHTSTTHHHHHHHHHHHHH
T ss_pred HHHHHcCCchHHHHHHHcCCHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHhccchHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344444555554444322112222 245556889999999999999887544321123444444444555554 4445
Q ss_pred HHHhhcCCCCcccCHHHHHHHhCCChhhHHHHHHHH
Q psy3716 290 ELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKA 325 (436)
Q Consensus 290 ~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lvikA 325 (436)
+.++ .+|+.+.+++-||++.+|++.++.+-
T Consensus 92 ~~aY------~sIs~~~la~~Lg~~~~el~~~~~~~ 121 (143)
T PF10075_consen 92 SKAY------SSISLSDLAEMLGLSEEELEKFIKSR 121 (143)
T ss_dssp HHH-------SEE-HHHHHHHTTS-HHHHHHHHHHH
T ss_pred HHHH------hHcCHHHHHHHhCCCHHHHHHHHHHc
Confidence 5554 58999999999999999999998774
No 30
>KOG1497|consensus
Probab=92.25 E-value=0.13 Score=52.10 Aligned_cols=49 Identities=16% Similarity=0.266 Sum_probs=45.4
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHhcccceeecccccceEEEeeecc
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQP 415 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s~~li~g~idqv~~~v~~~wv~p 415 (436)
.+||++.++..++|.+.+|..+-..++.|=+.|+|||.+|.+|+--+.|
T Consensus 317 nisf~~Lg~ll~i~~ekaekiaa~MI~qeRmng~IDQ~egiihFe~~e~ 365 (399)
T KOG1497|consen 317 NISFEELGALLKIDAEKAEKIAAQMITQERMNGSIDQIEGIIHFEDREE 365 (399)
T ss_pred hccHHHHHHHhCCCHHHHHHHHHHHHhHHHhccchHhhcceEeecchhh
Confidence 4999999999999999999999999999999999999999999875433
No 31
>KOG2072|consensus
Probab=90.72 E-value=35 Score=38.95 Aligned_cols=204 Identities=18% Similarity=0.167 Sum_probs=120.5
Q ss_pred CCChHHHHHHHHHHHHHHhc--ccChhHHHHHHHHHHHHHHHHhhcHHHHHHHHHHHhccC-CC-CCCChhHHHHHHHHH
Q psy3716 136 PGSLDEVEKLIDEIELLVND--IEGVTAIHSRFYLVASTLYRKQAKLSLYYRTALRYLGCV-DL-NDLTASDQVQHAFLI 211 (436)
Q Consensus 136 ~~~l~~~~~~L~~~~~~L~~--~~~~~~v~~~~y~~~a~~~k~~~~~~~~Y~~~L~yL~~~-~~-~~l~~~e~~~~A~~l 211 (436)
++-..++..-++.+..++.- -...++..+.||.=.+..+=..|++----..+++|-..+ +. ..++.++.+..|-..
T Consensus 245 lELWQEAyrSiEDIhgLm~lSKrtPkp~~laNYY~KL~~VF~~sgn~LfHAaAw~k~f~l~k~~~K~~Tqde~q~~as~V 324 (988)
T KOG2072|consen 245 LELWQEAYRSIEDIHGLMKLSKRTPKPSTLANYYEKLAKVFWKSGNPLFHAAAWLKLFKLYKNMNKNLTQDELQRMASRV 324 (988)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHH
Confidence 45567888888888877752 222357889999988888887887532222233333333 22 357899999999999
Q ss_pred HHHHhcCCCCCC---CchhccCcccccccCCCchhHHH------------HHHHHh-cCC-------hhHHHh-------
Q psy3716 212 GLAALLADSVYN---IGELLAHPILDSLQQTPNAWLVE------------LLRAFN-AGD-------IEKFEL------- 261 (436)
Q Consensus 212 ~iaALl~~~iyn---FgeLl~~p~v~~L~~t~~~wl~~------------LL~~f~-~Gd-------l~~f~~------- 261 (436)
.+|||.-|-... ++-++..+..- -..+.-|.. ||.-.. .|- +.+.-+
T Consensus 325 lLaaLSIP~~~~~~~~~r~~e~e~~~---~ek~~rla~LL~L~~~PTR~~ll~e~v~~gV~~~v~qe~kdLY~iLEveF~ 401 (988)
T KOG2072|consen 325 LLAALSIPIPDARSDSARLIEIEDIG---KEKNLRLANLLGLPAPPTRKGLLKEAVREGVLSKVDQEVKDLYNILEVEFH 401 (988)
T ss_pred HHHHhcCCCCCcccccccccccccch---hhHHHHHHHHhCCCCCccHHHHHHHHHHhccHhhhhHHHHHHHHHHHhcCC
Confidence 999999873332 22233332220 001111111 111111 111 111111
Q ss_pred ----------hhhhhhcCchhhhhHHHHHHHHHHHHHHHHHhhcCCCCcccCHHHHHHHhC-CChhhHHHHHHHHHhCCc
Q psy3716 262 ----------MRPQWSAMNDIKANENKLSQKIALLCLMELAFKKIPGSHQLSFAEISEAAQ-LPLIEVEFLIIKALALGL 330 (436)
Q Consensus 262 ----------~~~~~~~~~~L~~~~~~l~~KirLlaL~~L~~~~p~~~r~isf~~Ia~~l~-i~~~eVE~lvikAi~~gL 330 (436)
+...+.+.|....+.+.| +++.++-|+.-++.. ..+|+|+.+.+-.- .+.-++|.++|.|-..+.
T Consensus 402 PL~l~k~lq~ll~~ls~~~~~~QYI~sL-q~v~~~RllqQvSqi---Y~sIs~~~l~~La~F~~~~~lEk~~v~a~k~~~ 477 (988)
T KOG2072|consen 402 PLKLCKKLQPLLDKLSESPDKSQYIPSL-QDVIILRLLQQVSQI---YESISFERLYKLAPFFSAFELEKLLVEAAKHND 477 (988)
T ss_pred HHHHHHHHHHHHHHHHcCCCccccchhH-HHHHHHHHHHHHHHH---HHHHhHHHHHHHHhhcCHHHHHHHHHHHHhccc
Confidence 111223334444444444 334444444434332 35799988887654 488899999999999999
Q ss_pred ccccccCCccEEEEEe
Q psy3716 331 VKGHIDQVDESFNVTW 346 (436)
Q Consensus 331 I~G~IDQv~~~v~vtw 346 (436)
+.-+||-..++|.+..
T Consensus 478 v~iriDH~~~~v~Fgs 493 (988)
T KOG2072|consen 478 VSIRIDHESNSVSFGS 493 (988)
T ss_pred eeEEeccccceeeecc
Confidence 9999999999998875
No 32
>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=90.01 E-value=11 Score=33.10 Aligned_cols=128 Identities=16% Similarity=0.145 Sum_probs=79.8
Q ss_pred hHHHHHHHHHHHHHhhhHHHHHHHHHHHhcCcccccchhHHHHHHHHHHHHhhccCchhHHHHHHHHhccCCCHHHHHHH
Q psy3716 23 EISAQWLNLEELYNKKLWHQLTLAVLAFVQNPAIQKEGELRDLYHKFVISFETKINPVSLMEIMEVITNHLSDQEEALVL 102 (436)
Q Consensus 23 ~~~~~~~~l~~l~~~KLWhQLT~~l~~~~~~p~~~~~~~~~~ly~~fI~~f~~kin~l~l~~i~~~v~~~~~d~~~aL~~ 102 (436)
+-+..|..+...+..+=|..+...+..|+.+..- .. |..+. .+.++.+.. .-.+.++|.+.
T Consensus 10 ~a~~~y~~~~~~~~~~~~~~~~~~~~~l~~~~~~---s~----ya~~A--------~l~lA~~~~----~~g~~~~A~~~ 70 (145)
T PF09976_consen 10 QASALYEQALQALQAGDPAKAEAAAEQLAKDYPS---SP----YAALA--------ALQLAKAAY----EQGDYDEAKAA 70 (145)
T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCC---Ch----HHHHH--------HHHHHHHHH----HCCCHHHHHHH
Confidence 4555666666666666666666666666655311 10 11110 112233332 23589999999
Q ss_pred HHHHHHhhcCCcchhHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHHHHHhcccChhHHHHHHHHHHHHHHHHhhcHHH
Q psy3716 103 LQSFEDKVKNNLEAKSLCKILQAQMIMNKDADKPGSLDEVEKLIDEIELLVNDIEGVTAIHSRFYLVASTLYRKQAKLSL 182 (436)
Q Consensus 103 L~~l~~~l~~~~ea~~~~~~~i~~~~l~~~~~~~~~l~~~~~~L~~~~~~L~~~~~~~~v~~~~y~~~a~~~k~~~~~~~ 182 (436)
|+.+.+.- ++++..-.+.+.+|.+.+. .|+++++...|+.+.. ......++.+..+.|...|++.+
T Consensus 71 l~~~~~~~-~d~~l~~~a~l~LA~~~~~-----~~~~d~Al~~L~~~~~--------~~~~~~~~~~~Gdi~~~~g~~~~ 136 (145)
T PF09976_consen 71 LEKALANA-PDPELKPLARLRLARILLQ-----QGQYDEALATLQQIPD--------EAFKALAAELLGDIYLAQGDYDE 136 (145)
T ss_pred HHHHHhhC-CCHHHHHHHHHHHHHHHHH-----cCCHHHHHHHHHhccC--------cchHHHHHHHHHHHHHHCCCHHH
Confidence 99988865 4444455667778889998 9999999888865221 23445567778888888888766
Q ss_pred H
Q psy3716 183 Y 183 (436)
Q Consensus 183 ~ 183 (436)
.
T Consensus 137 A 137 (145)
T PF09976_consen 137 A 137 (145)
T ss_pred H
Confidence 3
No 33
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=88.40 E-value=0.66 Score=36.22 Aligned_cols=45 Identities=13% Similarity=0.204 Sum_probs=34.3
Q ss_pred HHHHHHHhhcCCCCcccCHHHHHHHhCCChhhHHHHHHHHHhCCccccc
Q psy3716 286 LCLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGH 334 (436)
Q Consensus 286 laL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~ 334 (436)
..|.+....+ +.+|+++||.++++|++.||.++=.-+..|.|+-.
T Consensus 3 ~~i~~~l~~~----~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~ 47 (69)
T PF09012_consen 3 QEIRDYLRER----GRVSLAELAREFGISPEAVEAMLEQLIRKGYIRKV 47 (69)
T ss_dssp HHHHHHHHHS-----SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEEE
T ss_pred HHHHHHHHHc----CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEe
Confidence 3445544443 68999999999999999999999999999998843
No 34
>PF03399 SAC3_GANP: SAC3/GANP/Nin1/mts3/eIF-3 p25 family; InterPro: IPR005062 This large family includes diverse proteins involved in large complexes [, , ]. The alignment contains one highly conserved negatively charged residue and one highly conserved positively charged residue that are probably important for the function of these proteins. The family includes the yeast nuclear export factor Sac3 [], and mammalian GANP/MCM3-associated proteins, which facilitate the nuclear localisation of MCM3, a protein that associates with chromatin in the G1 phase of the cell-cycle. The 26S protease (or 26S proteasome) is responsible for degrading ubiquitin conjugates. It consists of 19S regulatory complexes associated with the ends of 20S proteasomes. The 19S regulatory complex is composed of about 20 different polypeptides and confers ATP-dependence and substrate specificity to the 26S enzyme. The conserved region occurs at the C-terminal of the Nin1-like regulatory subunit [, , ]. This family includes several eukaryotic translation initiation factor 3 subunit 11 (eIF-3 p25) proteins. Eukaryotic initiation factor 3 (eIF3) is a multisubunit complex that is required for binding of mRNA to 40 S ribosomal subunits, stabilisation of ternary complex binding to 40 S subunits, and dissociation of 40 and 60 S subunits [].; PDB: 3T5V_D.
Probab=85.43 E-value=11 Score=34.93 Aligned_cols=100 Identities=17% Similarity=0.196 Sum_probs=55.2
Q ss_pred HHHHHHHHHHhcCCCCCCCchhcc-CcccccccCCCchhHHHHHHHHhcCChhHHHhhhhhhhcCchhhhh-HHHHHHHH
Q psy3716 206 QHAFLIGLAALLADSVYNIGELLA-HPILDSLQQTPNAWLVELLRAFNAGDIEKFELMRPQWSAMNDIKAN-ENKLSQKI 283 (436)
Q Consensus 206 ~~A~~l~iaALl~~~iynFgeLl~-~p~v~~L~~t~~~wl~~LL~~f~~Gdl~~f~~~~~~~~~~~~L~~~-~~~l~~Ki 283 (436)
=.++.+ +..+...+.-.|...+. .|. .-+.++...-..++..++..||+..|-+...+ .+.|.+... .+....+|
T Consensus 101 f~~y~l-L~~l~~~~~~~~~~~l~~l~~-~~~~~~~i~~al~l~~a~~~gny~~ff~l~~~-~~~~~l~~~l~~~~~~~i 177 (204)
T PF03399_consen 101 FIAYYL-LYLLCQNNIPDFHMELELLPS-EILSSPYIQFALELCRALMEGNYVRFFRLYRS-KSAPYLFACLMERFFNRI 177 (204)
T ss_dssp HHHHHH-HHTT-T---THHHHHHTTS-H-HHHTSHHHHHHHHHHHHH--TTHHHHHHHHT--TTS-HHHHHHHGGGHHHH
T ss_pred HHHHHH-HHHHHcccchHHHHHHHHCch-hhhcCHHHHHHHHHHHHHHcCCHHHHHHHHhc-cCCChHHHHHHHHHHHHH
Confidence 334444 44554443444443322 221 11233344556789999999999999887622 233444322 33467899
Q ss_pred HHHHHHHHHhhcCCCCcc-cCHHHHHHHhC
Q psy3716 284 ALLCLMELAFKKIPGSHQ-LSFAEISEAAQ 312 (436)
Q Consensus 284 rLlaL~~L~~~~p~~~r~-isf~~Ia~~l~ 312 (436)
|..+|-.++.+- +. +|.+.+++-|+
T Consensus 178 R~~al~~i~~ay----~~~i~l~~l~~~L~ 203 (204)
T PF03399_consen 178 RLRALQSISKAY----RSSIPLSFLAELLG 203 (204)
T ss_dssp HHHHHHHHHHHS-----T-EEHHHHHHHTT
T ss_pred HHHHHHHHHHHc----CCCCCHHHHHHHcC
Confidence 999999988653 45 88888887765
No 35
>KOG1464|consensus
Probab=85.02 E-value=0.64 Score=46.48 Aligned_cols=51 Identities=24% Similarity=0.371 Sum_probs=41.1
Q ss_pred cccCCcccccHHHHHHHcCCChhhHHHHHHHHHhcccceeecccccceEEEee
Q psy3716 360 KKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTW 412 (436)
Q Consensus 360 lr~~~~r~~sf~~i~~~~~~~~~~ve~lvmka~s~~li~g~idqv~~~v~~~w 412 (436)
++|-..-.++| |++++++|..|||+|+..|+=-.=|.|+||||++.+...-
T Consensus 359 IkPYt~i~Ipf--is~~Lnv~~~dV~~LLV~~ILD~~i~g~Ide~n~~l~~~~ 409 (440)
T KOG1464|consen 359 IKPYTNIGIPF--ISKELNVPEADVESLLVSCILDDTIDGRIDEVNQYLELDK 409 (440)
T ss_pred hccccccCchh--hHhhcCCCHHHHHHHHHHHHhccccccchHHhhhHhccCc
Confidence 44443334555 9999999999999999999999999999999998765443
No 36
>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues. They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.
Probab=84.43 E-value=1.9 Score=40.76 Aligned_cols=85 Identities=15% Similarity=0.182 Sum_probs=43.0
Q ss_pred HHHHHHHHHhhcCCCCcccCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCCccEEEEEeccccccccchhhccccC
Q psy3716 284 ALLCLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPRVLSKDQLAFKKIP 363 (436)
Q Consensus 284 rLlaL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv~~~v~vtwv~pRvL~l~Qi~~lr~~ 363 (436)
-|-.+++.+..+ +.+...++|.+.+++..+|-.-|-.....|.|.|-||.-.+.++||----.-++ .|++..
T Consensus 100 lL~~Fi~yIK~~----Kvv~ledla~~f~l~t~~~i~ri~~L~~~g~ltGv~DdrGkfIyIs~eE~~~va----~fi~~r 171 (188)
T PF09756_consen 100 LLQEFINYIKEH----KVVNLEDLAAEFGLRTQDVINRIQELEAEGRLTGVIDDRGKFIYISEEEMEAVA----KFIKQR 171 (188)
T ss_dssp HHHHHHHHHHH-----SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE--------------------
T ss_pred HHHHHHHHHHHc----ceeeHHHHHHHcCCCHHHHHHHHHHHHHCCCceeeEcCCCCeEEecHHHHHHHH----HHHHHc
Confidence 566677777654 799999999999999999999999999999999999998877777633222211 122221
Q ss_pred CcccccHHHHHHHcC
Q psy3716 364 GSHQLSFAEISEAAQ 378 (436)
Q Consensus 364 ~~r~~sf~~i~~~~~ 378 (436)
.| +|..++++.|+
T Consensus 172 -GR-vsi~el~~~~N 184 (188)
T PF09756_consen 172 -GR-VSISELAQESN 184 (188)
T ss_dssp ---------------
T ss_pred -CC-ccHHHHHHHHH
Confidence 23 48888888775
No 37
>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=84.25 E-value=2.2 Score=31.30 Aligned_cols=46 Identities=26% Similarity=0.290 Sum_probs=37.0
Q ss_pred HHHHHHHHHhhcCCCCcccCHHHHHHHhCCChhhHHHHHHHHHhCCccc
Q psy3716 284 ALLCLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVK 332 (436)
Q Consensus 284 rLlaL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~ 332 (436)
|-+.+++.....+ +.++..+||+++++|..-|-.++-.-...|+|+
T Consensus 4 ral~iL~~l~~~~---~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~ 49 (52)
T PF09339_consen 4 RALRILEALAESG---GPLTLSEIARALGLPKSTVHRLLQTLVEEGYVE 49 (52)
T ss_dssp HHHHHHHCHHCTB---SCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHcCC---CCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCee
Confidence 5567777665543 568999999999999999999999988888875
No 38
>PF09743 DUF2042: Uncharacterized conserved protein (DUF2042); InterPro: IPR018611 The ubiquitin fold modifier 1 (Ufm1) is the most recently discovered ubiquitin-like modifier whose conjugation (ufmylation) system is conserved in multicellular organisms. Ufm1 is known to covalently attach with cellular protein(s) via a specific E1-activating enzyme (Uba5), an E2-conjugating enzyme (Ufc1), and a E3-ligating enzyme []. This entry represents E3 UFM1-protein ligase 1.
Probab=83.08 E-value=3 Score=41.64 Aligned_cols=115 Identities=16% Similarity=0.179 Sum_probs=83.9
Q ss_pred cccCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCCccEEEEEeccccccccchhhccccCCcccccHHHHHHHcCC
Q psy3716 300 HQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPRVLSKDQLAFKKIPGSHQLSFAEISEAAQL 379 (436)
Q Consensus 300 r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv~~~v~vtwv~pRvL~l~Qi~~lr~~~~r~~sf~~i~~~~~~ 379 (436)
+.++.+++|+..++|.+=+-..++.+..-++|+|++|+. ...+-+|+.. -...+...-.+-.|..++..+..++++
T Consensus 129 G~vsi~eLa~~~~Lp~efl~~~li~~~lg~~I~g~~d~~-~lyT~ayv~r---~ka~iRG~l~a~T~Pt~l~~l~~~~~~ 204 (272)
T PF09743_consen 129 GQVSISELAKQYDLPSEFLKEELISKRLGKIIKGRLDGD-VLYTEAYVAR---QKARIRGALSAITRPTPLSSLLKRYGF 204 (272)
T ss_pred CeEeHHHHHHhcCCcHHHHHHHHhhhhcCcceeEEEeCC-EEecHHHHHH---HHHHHHHHHhcCccceEHHHHHHHhCC
Confidence 689999999999999988887889998899999999998 1112122221 122333333445688999999999999
Q ss_pred ChhhHHHHHHHHHhcccceeecccccceEEEeeecccccchhhhhH
Q psy3716 380 PLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPRVLSKDQVFW 425 (436)
Q Consensus 380 ~~~~ve~lvmka~s~~li~g~idqv~~~v~~~wv~pr~l~~~q~~~ 425 (436)
+..=+-.++=.-...|=+.|+|-. .-..|-+..+.|-.+
T Consensus 205 ~~~l~~~il~~Li~~~~l~G~i~G-------~~yvP~iy~~~q~~~ 243 (272)
T PF09743_consen 205 EEKLFQSILEELIKSGELPGSIVG-------ASYVPDIYSQAQQEW 243 (272)
T ss_pred cHHHHHHHHHHHHhcCcceEEEEC-------CEEechHHHHHHHHH
Confidence 977666666666677888888877 444577777776443
No 39
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=82.55 E-value=4.1 Score=32.77 Aligned_cols=60 Identities=20% Similarity=0.189 Sum_probs=43.2
Q ss_pred HHHHHHHHHHhhcCCCCcccCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCCccEEEEE
Q psy3716 283 IALLCLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVT 345 (436)
Q Consensus 283 irLlaL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv~~~v~vt 345 (436)
..+-.|+-|+.... .+.++.++||+.+++|..-|+..+=+.-..|+|+.+ -..++-+...
T Consensus 9 ~Al~~l~~la~~~~--~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~-~G~~GGy~L~ 68 (83)
T PF02082_consen 9 YALRILLYLARHPD--GKPVSSKEIAERLGISPSYLRKILQKLKKAGLIESS-RGRGGGYRLA 68 (83)
T ss_dssp HHHHHHHHHHCTTT--SC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE-TSTTSEEEES
T ss_pred HHHHHHHHHHhCCC--CCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEec-CCCCCceeec
Confidence 44556666665432 345999999999999999999999999999999764 2444444443
No 40
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=81.55 E-value=11 Score=34.42 Aligned_cols=27 Identities=26% Similarity=0.282 Sum_probs=25.1
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
.+||++||+.+++|..-|...+-+|..
T Consensus 143 gls~~EIA~~l~i~~~tVks~l~ra~~ 169 (182)
T COG1595 143 GLSYEEIAEILGISVGTVKSRLHRARK 169 (182)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 589999999999999999999998865
No 41
>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=81.51 E-value=4.3 Score=35.83 Aligned_cols=51 Identities=29% Similarity=0.410 Sum_probs=43.3
Q ss_pred HHHHHHHHHHHHhhcCCCCcccCHHHHHHHhCCChhhHHHHHHHHHhCCcccc
Q psy3716 281 QKIALLCLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKG 333 (436)
Q Consensus 281 ~KirLlaL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G 333 (436)
.+..+.+++.||+... .+.++-++||+.+++|..-|+..+=+.-..|+|..
T Consensus 7 ~~YAl~~l~~La~~~~--~~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s 57 (135)
T TIGR02010 7 GRYAVTAMLDLALNAE--TGPVTLADISERQGISLSYLEQLFAKLRKAGLVKS 57 (135)
T ss_pred HHHHHHHHHHHHhCCC--CCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEE
Confidence 4556788888887532 35799999999999999999999999999999974
No 42
>PF10602 RPN7: 26S proteasome subunit RPN7; InterPro: IPR019585 This entry represents the regulatory subunit RPN7 (known as the non-ATPase regulatory subunit 6 in higher eukaryotes) of the 26S proteasome. This entry also matches the evolutionarily related subunit 1 of the COP9 signalosome complex (CSN) from Arabidopsis []. The 26S proteasome plays a major role in ATP-dependent degradation of ubiquitinated proteins. Substrate specificity is conferred by the regulatory particle (RP), which can dissociate into stable lid and base subcomplexes. The regulatory subunit RPN7 is one of the lid subunits of the 26S proteasome and has been shown in Saccharomyces cerevisiae (Baker's yeast) to be required for structural integrity []. The COP9 signalosome is a conserved protein complex composed of eight subunits, where Individual subunits of the complex have been linked to various signal transduction pathways leading to gene expression and cell cycle control []. The overall organisation and the amino acid sequences of the COP9 signalosome subunits resemble the lid subcomplex of the 19 S regulatory particle for the 26 S proteasome []. COP9 subunit 1 (CSN1 or GPS1) of the COP9 complex is an essential subunit of the complex with regard to both structural integrity and functionality. The N-terminal region of subunit 1 (CSN1-N) can inhibit c-fos expression from either a transfected template or a chromosomal transgene (fos-lacZ), and may contain the activity domain that confers most of the repression functions of CSN1. The C-terminal region of subunit 1 (CSN1-C) allows integration of the protein into the COP9 signalosome.
Probab=79.60 E-value=52 Score=30.46 Aligned_cols=117 Identities=20% Similarity=0.106 Sum_probs=72.3
Q ss_pred CCCHHHHHHHHHHHHHhhcCCcchhHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHHHHHhcccChhHHHHHHHHHHHH
Q psy3716 93 LSDQEEALVLLQSFEDKVKNNLEAKSLCKILQAQMIMNKDADKPGSLDEVEKLIDEIELLVNDIEGVTAIHSRFYLVAST 172 (436)
Q Consensus 93 ~~d~~~aL~~L~~l~~~l~~~~ea~~~~~~~i~~~~l~~~~~~~~~l~~~~~~L~~~~~~L~~~~~~~~v~~~~y~~~a~ 172 (436)
+.|.+.|++......+.-.. ....+-+-+.+.++.+. .|++..+.+.++.++..++.-+ ..+.+.++--..+-
T Consensus 49 ~Gd~~~A~k~y~~~~~~~~~-~~~~id~~l~~irv~i~-----~~d~~~v~~~i~ka~~~~~~~~-d~~~~nrlk~~~gL 121 (177)
T PF10602_consen 49 IGDLEEALKAYSRARDYCTS-PGHKIDMCLNVIRVAIF-----FGDWSHVEKYIEKAESLIEKGG-DWERRNRLKVYEGL 121 (177)
T ss_pred hhhHHHHHHHHHHHhhhcCC-HHHHHHHHHHHHHHHHH-----hCCHHHHHHHHHHHHHHHhccc-hHHHHHHHHHHHHH
Confidence 45888999988887765422 33445555566677777 8999999999999999998722 22222222222222
Q ss_pred HHHHhhcHHHHHHHHHHHhccCCC---CCCChhHHHHHHHHHHHHHhcC
Q psy3716 173 LYRKQAKLSLYYRTALRYLGCVDL---NDLTASDQVQHAFLIGLAALLA 218 (436)
Q Consensus 173 ~~k~~~~~~~~Y~~~L~yL~~~~~---~~l~~~e~~~~A~~l~iaALl~ 218 (436)
++=..++|...-+..+.-+.++.. .+ .-.-.++|++.++.||.+
T Consensus 122 ~~l~~r~f~~AA~~fl~~~~t~~~~~~~e--l~s~~d~a~Y~~l~aLat 168 (177)
T PF10602_consen 122 ANLAQRDFKEAAELFLDSLSTFTSLQYTE--LISYNDFAIYGGLCALAT 168 (177)
T ss_pred HHHHhchHHHHHHHHHccCcCCCCCchhh--hcCHHHHHHHHHHHHHHh
Confidence 222346655555555555555543 22 223456788888888876
No 43
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=78.42 E-value=6 Score=36.41 Aligned_cols=52 Identities=23% Similarity=0.342 Sum_probs=44.7
Q ss_pred HHHHHHHHHHHHHhhcCCCCcccCHHHHHHHhCCChhhHHHHHHHHHhCCcccc
Q psy3716 280 SQKIALLCLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKG 333 (436)
Q Consensus 280 ~~KirLlaL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G 333 (436)
+....|.+++.||+... .+.+|-++||+++++|..-|+..+-+.-..|||..
T Consensus 6 ~~~yAl~~l~~lA~~~~--~~~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s 57 (164)
T PRK10857 6 KGRYAVTAMLDVALNSE--AGPVPLADISERQGISLSYLEQLFSRLRKNGLVSS 57 (164)
T ss_pred HHHHHHHHHHHHHhCCC--CCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe
Confidence 34567888888887643 35799999999999999999999999999999996
No 44
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=77.87 E-value=3 Score=32.51 Aligned_cols=38 Identities=16% Similarity=0.191 Sum_probs=30.5
Q ss_pred cccccHHHHHHHcCCChhhHHHHHHHHHhcccceeecc
Q psy3716 365 SHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHID 402 (436)
Q Consensus 365 ~r~~sf~~i~~~~~~~~~~ve~lvmka~s~~li~g~id 402 (436)
.+.+|+++||.+++++.+.||.++-.-...|-|+-.-+
T Consensus 12 ~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~~~ 49 (69)
T PF09012_consen 12 RGRVSLAELAREFGISPEAVEAMLEQLIRKGYIRKVDM 49 (69)
T ss_dssp S-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEEEEE
T ss_pred cCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEecC
Confidence 46799999999999999999999999999888874443
No 45
>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=77.15 E-value=7.4 Score=27.72 Aligned_cols=39 Identities=15% Similarity=0.174 Sum_probs=31.2
Q ss_pred HHHhhcCCCCcccCHHHHHHHhCCChhhHHHHHHHHHhCCccc
Q psy3716 290 ELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVK 332 (436)
Q Consensus 290 ~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~ 332 (436)
......| .+|..+||+.++++..-|-..+=+....|+|+
T Consensus 10 ~~l~~~~----~~t~~ela~~~~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 10 NYLRENP----RITQKELAEKLGISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHCT----TS-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHcC----CCCHHHHHHHhCCCHHHHHHHHHHHHHCcCcC
Confidence 3344454 69999999999999999999999999999885
No 46
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=74.70 E-value=40 Score=30.63 Aligned_cols=27 Identities=22% Similarity=0.273 Sum_probs=25.0
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
..||++||+.+|+|+.-|...+-+|+.
T Consensus 143 g~s~~EIA~~lgis~~tVk~~l~rAl~ 169 (178)
T PRK12529 143 GMKQKDIAQALDIALPTVKKYIHQAYV 169 (178)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 589999999999999999999988875
No 47
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=72.32 E-value=11 Score=30.15 Aligned_cols=48 Identities=21% Similarity=0.203 Sum_probs=39.0
Q ss_pred HHHHHHHHHhhcCCCCcccCHHHHHHHhCCChhhHHHHHHHHHhCCccccc
Q psy3716 284 ALLCLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGH 334 (436)
Q Consensus 284 rLlaL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~ 334 (436)
|.+.++++....+ +.++..+||+.+++|..-|-..+-.....|+|...
T Consensus 6 r~~~Il~~l~~~~---~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~ 53 (91)
T smart00346 6 RGLAVLRALAEEP---GGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQD 53 (91)
T ss_pred HHHHHHHHHHhCC---CCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeec
Confidence 4455666555442 47999999999999999999999999999999763
No 48
>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H ....
Probab=71.26 E-value=44 Score=25.55 Aligned_cols=64 Identities=8% Similarity=-0.059 Sum_probs=45.3
Q ss_pred HHHHHHHHhhccCCCCCCChHHHHHHHHHHHHHHhcccChhHHHHHHHHHHHHHHHHhhcHHHHHHHHH
Q psy3716 120 CKILQAQMIMNKDADKPGSLDEVEKLIDEIELLVNDIEGVTAIHSRFYLVASTLYRKQAKLSLYYRTAL 188 (436)
Q Consensus 120 ~~~~i~~~~l~~~~~~~~~l~~~~~~L~~~~~~L~~~~~~~~v~~~~y~~~a~~~k~~~~~~~~Y~~~L 188 (436)
+...+|.++.. .|+++.+.+..+++-+..+..+......+..|.-.+..+...|++++.-...-
T Consensus 7 ~~~~la~~~~~-----~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~ 70 (78)
T PF13424_consen 7 AYNNLARVYRE-----LGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQ 70 (78)
T ss_dssp HHHHHHHHHHH-----TT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHH
T ss_pred HHHHHHHHHHH-----cCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence 34567778888 99999999999998888555554444556667777777777888776554433
No 49
>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=70.49 E-value=5.4 Score=29.06 Aligned_cols=27 Identities=26% Similarity=0.266 Sum_probs=21.5
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
..||++||+.+++|.+.|..++-+|..
T Consensus 26 g~s~~eIa~~l~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 26 GMSYAEIAEILGISESTVKRRLRRARK 52 (54)
T ss_dssp ---HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence 689999999999999999999998864
No 50
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=70.23 E-value=11 Score=36.47 Aligned_cols=91 Identities=21% Similarity=0.266 Sum_probs=53.8
Q ss_pred cccCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCC-----cc-EEEEEecc---cc----cccc------ch-hhc
Q psy3716 300 HQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQV-----DE-SFNVTWVQ---PR----VLSK------DQ-LAF 359 (436)
Q Consensus 300 r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv-----~~-~v~vtwv~---pR----vL~l------~Q-i~~ 359 (436)
|..+..+||++++++.++|+..+..+.....+ .+|.. ++ .+..++.. +. .... .+ +..
T Consensus 124 ~~~~~~eia~~l~~~~~~v~~~~~~~~~~~~~--sld~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~ 201 (251)
T PRK07670 124 RNVTPKEVAAELGMTEEEVEATMNEGFFANLL--SIDEKTHDQDDGENVSVTIRDDKTPTPEEKLLKEELIEELAEKIKQ 201 (251)
T ss_pred CCCCHHHHHHHhCcCHHHHHHHHHHHhccCcc--ccCccccCCCCcchhhhhhcCcCCCCHHHHHHHHHHHHHHHHHHhc
Confidence 67889999999999999999977655432221 22211 10 01011110 00 0000 00 111
Q ss_pred cccCC---------cccccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 360 KKIPG---------SHQLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 360 lr~~~---------~r~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
+ |+. ....|++|||+.+++|..-|...+-+|+.
T Consensus 202 L-~~~~r~vl~l~~~~~~s~~EIA~~lgis~~tV~~~~~ra~~ 243 (251)
T PRK07670 202 L-SEKEQLVISLFYKEELTLTEIGQVLNLSTSRISQIHSKALF 243 (251)
T ss_pred C-CHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 1 111 23789999999999999999999988765
No 51
>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=69.55 E-value=10 Score=32.92 Aligned_cols=47 Identities=30% Similarity=0.262 Sum_probs=38.0
Q ss_pred HHHHHHHHhhcCCCCcccCHHHHHHHhCCChhhHHHHHHHHHhCCccccc
Q psy3716 285 LLCLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGH 334 (436)
Q Consensus 285 LlaL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~ 334 (436)
+.+|+.|+.. + ++.++..+||+.+++|..-|...+=+.-..|+|.+.
T Consensus 12 l~~l~~la~~-~--~~~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~~ 58 (130)
T TIGR02944 12 TLVLTTLAQN-D--SQPYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTSK 58 (130)
T ss_pred HHHHHHHHhC-C--CCCccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEec
Confidence 3445555543 2 357999999999999999999999999999999774
No 52
>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=68.84 E-value=15 Score=31.65 Aligned_cols=50 Identities=26% Similarity=0.311 Sum_probs=39.5
Q ss_pred HHHHHHHHHHHhhcCCCCcccCHHHHHHHhCCChhhHHHHHHHHHhCCcccc
Q psy3716 282 KIALLCLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKG 333 (436)
Q Consensus 282 KirLlaL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G 333 (436)
...+.+++.++.. + +...++.++||+.+++|...|...+-+....|+|..
T Consensus 8 ~~al~~l~~la~~-~-~~~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~ 57 (132)
T TIGR00738 8 EYALRALLDLALN-P-DEGPVSVKEIAERQGISRSYLEKILRTLRRAGLVES 57 (132)
T ss_pred HHHHHHHHHHHhC-C-CCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEe
Confidence 3455556666643 2 224799999999999999999999999999999975
No 53
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=67.58 E-value=11 Score=33.81 Aligned_cols=34 Identities=15% Similarity=0.274 Sum_probs=32.6
Q ss_pred cccCHHHHHHHhCCChhhHHHHHHHHHhCCcccc
Q psy3716 300 HQLSFAEISEAAQLPLIEVEFLIIKALALGLVKG 333 (436)
Q Consensus 300 r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G 333 (436)
..+||++||+.+|++...|-.=+=+....|.|+|
T Consensus 22 ~R~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI~~ 55 (153)
T PRK11179 22 ARTPYAELAKQFGVSPGTIHVRVEKMKQAGIITG 55 (153)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeee
Confidence 4799999999999999999999999999999996
No 54
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=66.40 E-value=97 Score=27.87 Aligned_cols=28 Identities=21% Similarity=0.334 Sum_probs=25.4
Q ss_pred cccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 300 HQLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 300 r~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
...||++||+.+|+|+.-|...+-+|+.
T Consensus 134 ~g~s~~EIA~~lgis~~tV~~~l~Ra~~ 161 (172)
T PRK09651 134 DGLTYSEIAHKLGVSVSSVKKYVAKATE 161 (172)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3589999999999999999999988875
No 55
>PF09295 ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); InterPro: IPR015374 ChAPs (Chs5p-Arf1p-binding proteins) are required for the export of specialised cargo from the Golgi. They physically interact with Chs3, Chs5 and the small GTPase Arf1, and they also form interactions with each other [].
Probab=66.20 E-value=1.6e+02 Score=31.08 Aligned_cols=128 Identities=16% Similarity=0.204 Sum_probs=73.9
Q ss_pred HHHHHHHHHhcCcccccchhHHHHHHHHHHHHhhccCchhHHHHHHHHhccCCCHHHHHHHHHHHHHhhcCCcchhHHHH
Q psy3716 42 QLTLAVLAFVQNPAIQKEGELRDLYHKFVISFETKINPVSLMEIMEVITNHLSDQEEALVLLQSFEDKVKNNLEAKSLCK 121 (436)
Q Consensus 42 QLT~~l~~~~~~p~~~~~~~~~~ly~~fI~~f~~kin~l~l~~i~~~v~~~~~d~~~aL~~L~~l~~~l~~~~ea~~~~~ 121 (436)
-|+..|..+++.-. .....+++++.+.... |- .+-++..+.-.+....+|++++++....-+.+ +. +.
T Consensus 170 yLv~~Ll~~l~~t~--~~~~ai~lle~L~~~~-----pe-v~~~LA~v~l~~~~E~~AI~ll~~aL~~~p~d--~~--LL 237 (395)
T PF09295_consen 170 YLVDTLLKYLSLTQ--RYDEAIELLEKLRERD-----PE-VAVLLARVYLLMNEEVEAIRLLNEALKENPQD--SE--LL 237 (395)
T ss_pred HHHHHHHHHHhhcc--cHHHHHHHHHHHHhcC-----Cc-HHHHHHHHHHhcCcHHHHHHHHHHHHHhCCCC--HH--HH
Confidence 57778888876642 2344455555554332 32 22233333334557788888888776444333 22 23
Q ss_pred HHHHHHhhccCCCCCCChHHHHHHHHHHHHHHhcccChhHHHHHHHHHHHHHHHHhhcHHHHHHHHHHHhccCCCC
Q psy3716 122 ILQAQMIMNKDADKPGSLDEVEKLIDEIELLVNDIEGVTAIHSRFYLVASTLYRKQAKLSLYYRTALRYLGCVDLN 197 (436)
Q Consensus 122 ~~i~~~~l~~~~~~~~~l~~~~~~L~~~~~~L~~~~~~~~v~~~~y~~~a~~~k~~~~~~~~Y~~~L~yL~~~~~~ 197 (436)
...|.+.+. .++++.|.+..+..-.. .+......|.++.- |-..|+ |++||..|.++|.-
T Consensus 238 ~~Qa~fLl~-----k~~~~lAL~iAk~av~l------sP~~f~~W~~La~~-Yi~~~d----~e~ALlaLNs~Pm~ 297 (395)
T PF09295_consen 238 NLQAEFLLS-----KKKYELALEIAKKAVEL------SPSEFETWYQLAEC-YIQLGD----FENALLALNSCPML 297 (395)
T ss_pred HHHHHHHHh-----cCCHHHHHHHHHHHHHh------CchhHHHHHHHHHH-HHhcCC----HHHHHHHHhcCcCC
Confidence 456788887 78887666655443322 23455556665444 444666 56789999988753
No 56
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=65.91 E-value=14 Score=30.74 Aligned_cols=34 Identities=24% Similarity=0.339 Sum_probs=32.0
Q ss_pred cccCHHHHHHHhCCChhhHHHHHHHHHhCCcccc
Q psy3716 300 HQLSFAEISEAAQLPLIEVEFLIIKALALGLVKG 333 (436)
Q Consensus 300 r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G 333 (436)
..+|+.+||+.++++...|-..+-+....|+|+|
T Consensus 16 ~~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~~ 49 (108)
T smart00344 16 ARISLAELAKKVGLSPSTVHNRVKRLEEEGVIKG 49 (108)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeec
Confidence 3699999999999999999999999999999995
No 57
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=65.29 E-value=83 Score=28.16 Aligned_cols=27 Identities=22% Similarity=0.433 Sum_probs=24.7
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
..|+++||+.+++|..-|...+-+|+.
T Consensus 134 g~s~~EIA~~l~is~~tV~~~l~ra~~ 160 (168)
T PRK12525 134 GLTYVEIGERLGVSLSRIHQYMVEAFK 160 (168)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 689999999999999999999888875
No 58
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=64.72 E-value=14 Score=33.49 Aligned_cols=49 Identities=20% Similarity=0.105 Sum_probs=40.8
Q ss_pred HHHHHHHHHhhcCCCCcccCHHHHHHHhCCChhhHHHHHHHHHhCCcccccc
Q psy3716 284 ALLCLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHI 335 (436)
Q Consensus 284 rLlaL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~I 335 (436)
-+.+|+.||.. + .+.++-++||+..+||..=++..+-+.-..|+|+..=
T Consensus 10 Alr~L~~LA~~-~--~~~~s~~eIA~~~~is~~~L~kIl~~L~~aGlv~S~r 58 (153)
T PRK11920 10 AIRMLMYCAAN-D--GKLSRIPEIARAYGVSELFLFKILQPLVEAGLVETVR 58 (153)
T ss_pred HHHHHHHHHhC-C--CCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeec
Confidence 45677777754 3 3568999999999999999999999999999998643
No 59
>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=64.12 E-value=16 Score=26.17 Aligned_cols=28 Identities=25% Similarity=0.338 Sum_probs=24.2
Q ss_pred cccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 300 HQLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 300 r~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
...|+++||+.+|+|...|-.+.-+|+.
T Consensus 19 ~~~t~~eIa~~lg~s~~~V~~~~~~al~ 46 (50)
T PF04545_consen 19 EGLTLEEIAERLGISRSTVRRILKRALK 46 (50)
T ss_dssp ST-SHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHCCcHHHHHHHHHHHHH
Confidence 4699999999999999999998888874
No 60
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=61.28 E-value=11 Score=33.31 Aligned_cols=34 Identities=29% Similarity=0.273 Sum_probs=32.5
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHhCCccccc
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALALGLVKGH 334 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~ 334 (436)
.+||.+||+.+++|...|=.-|=+....|+|+|.
T Consensus 22 r~~~~eia~~lglS~~~v~~Ri~~L~~~GiI~~~ 55 (154)
T COG1522 22 RISNAELAERVGLSPSTVLRRIKRLEEEGVIKGY 55 (154)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHCCceeeE
Confidence 4999999999999999999999999999999994
No 61
>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits is known as Va.; GO: 0004129 cytochrome-c oxidase activity; PDB: 2DYR_R 3AG1_E 3ABL_E 1V54_R 2EIJ_R 1OCR_E 2DYS_E 2EIM_E 2OCC_E 3ASN_R ....
Probab=61.03 E-value=1.1e+02 Score=26.42 Aligned_cols=68 Identities=18% Similarity=0.198 Sum_probs=41.6
Q ss_pred HHHHHHHhcCcccccchhHHHHHHHHHHHHh-hccCchhHHHHHHHHhccCCCHHHHHHHHHHHHHhhcCCcc
Q psy3716 44 TLAVLAFVQNPAIQKEGELRDLYHKFVISFE-TKINPVSLMEIMEVITNHLSDQEEALVLLQSFEDKVKNNLE 115 (436)
Q Consensus 44 T~~l~~~~~~p~~~~~~~~~~ly~~fI~~f~-~kin~l~l~~i~~~v~~~~~d~~~aL~~L~~l~~~l~~~~e 115 (436)
+..-..||++|... .-++=..+=..|. +=+...+.++-++..|+..+|...|++||+.++.|..+..+
T Consensus 12 ~ary~~~F~~~~iD----~we~rrglN~l~~~DlVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~K~~~~~~ 80 (108)
T PF02284_consen 12 DARYEKYFNRPDID----GWELRRGLNNLFGYDLVPEPKIIEAALRACRRVNDFALAVRILEGIKDKCGNKKE 80 (108)
T ss_dssp HHHHHHHHH-TT------HHHHHHHHHHHTTSSB---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHTTT-TT
T ss_pred HHHHHHHhCCcccc----HHHHHHHHHHHhccccCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHHHccChHH
Confidence 33345677766432 1233233333453 45556678888999999999999999999999999876543
No 62
>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=60.66 E-value=16 Score=29.30 Aligned_cols=57 Identities=14% Similarity=0.200 Sum_probs=39.7
Q ss_pred ccccHHHHHHHcCCChhhHHHHHHHHHhcccceeecccccceEEEeeecccccchhhhh
Q psy3716 366 HQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPRVLSKDQVF 424 (436)
Q Consensus 366 r~~sf~~i~~~~~~~~~~ve~lvmka~s~~li~g~idqv~~~v~~~wv~pr~l~~~q~~ 424 (436)
+.+|.++||+++++|..-|+.++=+--..|+|+.. -+.++....+- .|.-.+.-+|.
T Consensus 24 ~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~-~G~~GGy~L~~-~~~~Itl~dI~ 80 (83)
T PF02082_consen 24 KPVSSKEIAERLGISPSYLRKILQKLKKAGLIESS-RGRGGGYRLAR-PPEEITLLDIV 80 (83)
T ss_dssp C-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE-TSTTSEEEESS--CCGSBHHHHH
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEec-CCCCCceeecC-CHHHCCHHHHH
Confidence 34999999999999999999999999999998754 24455554443 44444444443
No 63
>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=60.51 E-value=14 Score=27.67 Aligned_cols=32 Identities=16% Similarity=0.206 Sum_probs=26.7
Q ss_pred hhcCCCCcccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 293 FKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 293 ~~~p~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
|..| |.++.++||+.++|+..-|..-+=+|.+
T Consensus 18 fd~P---R~~tl~elA~~lgis~st~~~~LRrae~ 49 (53)
T PF04967_consen 18 FDVP---RRITLEELAEELGISKSTVSEHLRRAER 49 (53)
T ss_pred CCCC---CcCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4556 8999999999999999888877766654
No 64
>KOG0686|consensus
Probab=60.28 E-value=12 Score=39.34 Aligned_cols=53 Identities=13% Similarity=0.201 Sum_probs=47.5
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHhcccceeecccccceEEEeeecccccc
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPRVLS 419 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s~~li~g~idqv~~~v~~~wv~pr~l~ 419 (436)
++.+..+|...+.+....|.-|+.-+-.|.|+|+||+-++++.+.-.--|.=+
T Consensus 365 s~~m~~mA~af~~sv~~le~~l~~LI~~~~i~~rIDs~~ki~~~~~~~~en~~ 417 (466)
T KOG0686|consen 365 SADMSKMAEAFNTSVAILESELLELILEGKISGRIDSHNKILYARDADSENAT 417 (466)
T ss_pred cchHHHHHHHhcccHHHHHHHHHHHHHccchheeeccccceeeecccccccch
Confidence 68899999999999999999999999999999999999999988777544433
No 65
>PF13730 HTH_36: Helix-turn-helix domain
Probab=59.11 E-value=43 Score=24.24 Aligned_cols=50 Identities=22% Similarity=0.199 Sum_probs=38.0
Q ss_pred HHHHHHHHHHHHHhhcCCCCcccCHHHHHHHhCCChhhHHHHHHHHHhCCcc
Q psy3716 280 SQKIALLCLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALALGLV 331 (436)
Q Consensus 280 ~~KirLlaL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI 331 (436)
.+|+-++.|...+... +.---|.+.||+.++++.+.|...+=+....|+|
T Consensus 6 ~~~~v~~~l~~~~~~~--~~~~pS~~~la~~~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 6 TAKLVYLYLASYANKN--GGCFPSQETLAKDLGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred HHHHHHHHHHHhcCCC--CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCcCC
Confidence 3566777777776322 1223489999999999999999999888888875
No 66
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=58.86 E-value=24 Score=27.47 Aligned_cols=33 Identities=18% Similarity=0.141 Sum_probs=31.1
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHhCCcccc
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALALGLVKG 333 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G 333 (436)
.++-.+||++++++...|...+-+....|+|.-
T Consensus 22 ~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~ 54 (68)
T smart00550 22 TSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCK 54 (68)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence 499999999999999999999999999999965
No 67
>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues. They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.
Probab=58.74 E-value=13 Score=35.10 Aligned_cols=47 Identities=17% Similarity=0.179 Sum_probs=34.7
Q ss_pred cccccHHHHHHHcCCChhhHHHHHHHHHhcccceeecccccceEEEe
Q psy3716 365 SHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVT 411 (436)
Q Consensus 365 ~r~~sf~~i~~~~~~~~~~ve~lvmka~s~~li~g~idqv~~~v~~~ 411 (436)
.+.+.++++|.+.++...||..-|-.-.+.|.+.|.||.-..-++||
T Consensus 111 ~Kvv~ledla~~f~l~t~~~i~ri~~L~~~g~ltGv~DdrGkfIyIs 157 (188)
T PF09756_consen 111 HKVVNLEDLAAEFGLRTQDVINRIQELEAEGRLTGVIDDRGKFIYIS 157 (188)
T ss_dssp -SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE--
T ss_pred cceeeHHHHHHHcCCCHHHHHHHHHHHHHCCCceeeEcCCCCeEEec
Confidence 47899999999999999999999999999999999999976666666
No 68
>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=58.60 E-value=11 Score=28.99 Aligned_cols=36 Identities=19% Similarity=0.081 Sum_probs=33.1
Q ss_pred cccCHHHHHHHhCCChhhHHHHHHHHHhCCcccccc
Q psy3716 300 HQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHI 335 (436)
Q Consensus 300 r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~I 335 (436)
+..+-.+||+.+++|...|-..+=+....|+|+-.-
T Consensus 21 ~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~~ 56 (68)
T PF01978_consen 21 GPATAEEIAEELGISRSTVYRALKSLEEKGLVEREE 56 (68)
T ss_dssp CHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEc
Confidence 479999999999999999999999999999997644
No 69
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=58.47 E-value=21 Score=35.17 Aligned_cols=94 Identities=17% Similarity=0.094 Sum_probs=58.1
Q ss_pred CcccCHHHHHHHhCCChhhHHHHHHHHHhCCc---ccccccCCccEEEEEecccc--ccccchh-----hccccCCc---
Q psy3716 299 SHQLSFAEISEAAQLPLIEVEFLIIKALALGL---VKGHIDQVDESFNVTWVQPR--VLSKDQL-----AFKKIPGS--- 365 (436)
Q Consensus 299 ~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gL---I~G~IDQv~~~v~vtwv~pR--vL~l~Qi-----~~lr~~~~--- 365 (436)
.|.-+-.+||+.++++.+||-.+....-+.++ ......+.++. ......+. .+...+. ..+.+=.+
T Consensus 124 ~r~pt~~EIA~~L~i~~ee~~~~~~~~~~~~~~sld~~~~~~~d~~-~~~~~~~~~~~~~~~~~~~~l~~ai~~L~EREk 202 (247)
T COG1191 124 GREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDVLKDDDDD-VDDQIENPDDGVEKEELLEILKEAIEPLPEREK 202 (247)
T ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHHhccccccchhhhhccccccc-hhhccccchhHHHHHHHHHHHHHHHHccCHHHH
Confidence 47899999999999999999888877743333 33333344443 11111111 0111111 11111112
Q ss_pred --------ccccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 366 --------HQLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 366 --------r~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
..+|..|||+.++++.-.|=.+.=||+.
T Consensus 203 ~Vl~l~y~eelt~kEI~~~LgISes~VSql~kkai~ 238 (247)
T COG1191 203 LVLVLRYKEELTQKEIAEVLGISESRVSRLHKKAIK 238 (247)
T ss_pred HHHHHHHHhccCHHHHHHHhCccHHHHHHHHHHHHH
Confidence 2689999999999999999998888764
No 70
>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=58.47 E-value=31 Score=24.56 Aligned_cols=33 Identities=27% Similarity=0.315 Sum_probs=29.0
Q ss_pred cccCHHHHHHHhCCChhhHHHHHHHHHhCCccc
Q psy3716 300 HQLSFAEISEAAQLPLIEVEFLIIKALALGLVK 332 (436)
Q Consensus 300 r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~ 332 (436)
+..++.+|++.++++...|-+-+=.....|+|+
T Consensus 14 ~~~~~~el~~~l~~s~~~vs~hL~~L~~~glV~ 46 (47)
T PF01022_consen 14 GPLTVSELAEELGLSQSTVSHHLKKLREAGLVE 46 (47)
T ss_dssp SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred CCCchhhHHHhccccchHHHHHHHHHHHCcCee
Confidence 469999999999999999999998888899875
No 71
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=58.36 E-value=18 Score=30.06 Aligned_cols=39 Identities=18% Similarity=0.124 Sum_probs=34.7
Q ss_pred CcccCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccC
Q psy3716 299 SHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQ 337 (436)
Q Consensus 299 ~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQ 337 (436)
+.=++.++|++.|+++.++|+.-|=..+..|.|=-.||.
T Consensus 63 ~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd 101 (102)
T PF08784_consen 63 EEGVHVDEIAQQLGMSENEVRKALDFLSNEGHIYSTIDD 101 (102)
T ss_dssp TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTTSEEESSST
T ss_pred CCcccHHHHHHHhCcCHHHHHHHHHHHHhCCeEecccCC
Confidence 456999999999999999999999999999999888775
No 72
>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=58.24 E-value=13 Score=26.92 Aligned_cols=27 Identities=26% Similarity=0.266 Sum_probs=21.5
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
-.|++|||+.++++...|...+-+|..
T Consensus 26 g~s~~eIa~~l~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 26 GMSYAEIAEILGISESTVKRRLRRARK 52 (54)
T ss_dssp ---HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence 579999999999999999999998864
No 73
>PF09743 DUF2042: Uncharacterized conserved protein (DUF2042); InterPro: IPR018611 The ubiquitin fold modifier 1 (Ufm1) is the most recently discovered ubiquitin-like modifier whose conjugation (ufmylation) system is conserved in multicellular organisms. Ufm1 is known to covalently attach with cellular protein(s) via a specific E1-activating enzyme (Uba5), an E2-conjugating enzyme (Ufc1), and a E3-ligating enzyme []. This entry represents E3 UFM1-protein ligase 1.
Probab=57.68 E-value=40 Score=33.72 Aligned_cols=93 Identities=17% Similarity=0.194 Sum_probs=69.4
Q ss_pred cccCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCCccEEEEEeccccccccchhhcccc------CCcccccHHHH
Q psy3716 300 HQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPRVLSKDQLAFKKI------PGSHQLSFAEI 373 (436)
Q Consensus 300 r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv~~~v~vtwv~pRvL~l~Qi~~lr~------~~~r~~sf~~i 373 (436)
+.++.-++++.++|+.+.||.-+=+.+...- .+..+..-+++..=+..+.. .....++..+.
T Consensus 69 GRv~~~dL~~~LnVd~~~ie~~~~~i~~~~~------------~~~l~~gelit~~Yld~l~~Eine~Lqe~G~vsi~eL 136 (272)
T PF09743_consen 69 GRVNLVDLAQALNVDLDHIERRAQEIVKSDK------------SLQLVQGELITDSYLDSLAEEINEKLQESGQVSISEL 136 (272)
T ss_pred CceEHHHHHHhcCcCHHHHHHHHHHHHhCCC------------cEEEECCEEccHHHHHHHHHHHHHHHHHcCeEeHHHH
Confidence 5799999999999999999998877666432 13344444555443333322 12368999999
Q ss_pred HHHcCCChhhHHHHHHHHHhcccceeecccc
Q psy3716 374 SEAAQLPLIEVEFLIIKALALGLVKGHIDQV 404 (436)
Q Consensus 374 ~~~~~~~~~~ve~lvmka~s~~li~g~idqv 404 (436)
|+..++|.|=+-..++.+---+.|+|.+|+.
T Consensus 137 a~~~~Lp~efl~~~li~~~lg~~I~g~~d~~ 167 (272)
T PF09743_consen 137 AKQYDLPSEFLKEELISKRLGKIIKGRLDGD 167 (272)
T ss_pred HHhcCCcHHHHHHHHhhhhcCcceeEEEeCC
Confidence 9999999998887788877778999999996
No 74
>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=57.53 E-value=18 Score=36.20 Aligned_cols=90 Identities=27% Similarity=0.235 Sum_probs=54.0
Q ss_pred cccCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCCc---c--E----EEEEecccc-----------------ccc
Q psy3716 300 HQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVD---E--S----FNVTWVQPR-----------------VLS 353 (436)
Q Consensus 300 r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv~---~--~----v~vtwv~pR-----------------vL~ 353 (436)
|.-+..+||+.++++.++|+.+...+ . . ..++|..- . . +.-....|- .|+
T Consensus 176 ~~pt~~eia~~l~~~~~~v~~~~~~~-~-~--~~SLd~~~~~~~~~~~~~~~~~~~~~pe~~~~~~~~~~~L~~~L~~L~ 251 (298)
T TIGR02997 176 RTPSEAEIAEALELEPEQVRELLQRA-R-Q--PVSLDAPVGDEEDTELGDLLEDDGESPEEQVERESLRQDLESLLAELT 251 (298)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHc-c-c--CcccCCCcCCCCcchHHHhccCCCCCHHHHHHHHHHHHHHHHHHHcCC
Confidence 56789999999999999999985432 1 1 11233220 0 0 000111110 122
Q ss_pred cch--hhccccC--CcccccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 354 KDQ--LAFKKIP--GSHQLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 354 l~Q--i~~lr~~--~~r~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
..+ +..++-- .....|++|||+.++++.+-|..+.-+|+.
T Consensus 252 ~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVrq~~~rAl~ 295 (298)
T TIGR02997 252 PRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALR 295 (298)
T ss_pred HHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 222 2222211 134689999999999999999999999875
No 75
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=56.60 E-value=30 Score=31.33 Aligned_cols=51 Identities=31% Similarity=0.260 Sum_probs=42.6
Q ss_pred HHHHHHHHHHHhhcCCCCcccCHHHHHHHhCCChhhHHHHHHHHHhCCccccc
Q psy3716 282 KIALLCLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGH 334 (436)
Q Consensus 282 KirLlaL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~ 334 (436)
..-+-+|+.||...+ ++.+|-++||+..+||+.=++.++-+.-.+|||+..
T Consensus 8 ~yal~~L~~LA~~~~--~~~~s~~~IA~~~~is~~~L~kil~~L~kaGlV~S~ 58 (150)
T COG1959 8 EYALRALLYLALLPG--GGPVSSAEIAERQGISPSYLEKILSKLRKAGLVKSV 58 (150)
T ss_pred hHHHHHHHHHHhCCC--CCcccHHHHHHHhCcCHHHHHHHHHHHHHcCCEEee
Confidence 355778888886543 247889999999999999999999999999999853
No 76
>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=56.47 E-value=34 Score=25.48 Aligned_cols=35 Identities=20% Similarity=0.129 Sum_probs=31.7
Q ss_pred CcccCHHHHHHHhCCChhhHHHHHHHHHhCCcccc
Q psy3716 299 SHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKG 333 (436)
Q Consensus 299 ~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G 333 (436)
+..++..+||+.++++...|...+-+....|+|.-
T Consensus 23 ~~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~ 57 (67)
T cd00092 23 QLPLTRQEIADYLGLTRETVSRTLKELEEEGLISR 57 (67)
T ss_pred cCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence 35799999999999999999999999999999874
No 77
>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=56.29 E-value=31 Score=25.86 Aligned_cols=35 Identities=17% Similarity=0.287 Sum_probs=31.1
Q ss_pred cccCHHHHHHHhCCChhhHHHHHHHHHhCCccccc
Q psy3716 300 HQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGH 334 (436)
Q Consensus 300 r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~ 334 (436)
+..++.+||+.+++|...|-+-+=+.-..|||+..
T Consensus 23 ~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli~~~ 57 (61)
T PF12840_consen 23 GPMTVSELAEELGISQSTVSYHLKKLEEAGLIEVE 57 (61)
T ss_dssp STBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEe
Confidence 57999999999999999999999999999999863
No 78
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=56.06 E-value=39 Score=33.22 Aligned_cols=92 Identities=16% Similarity=0.121 Sum_probs=53.4
Q ss_pred cccCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCC-----ccEEEEEecccc-------------------ccccc
Q psy3716 300 HQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQV-----DESFNVTWVQPR-------------------VLSKD 355 (436)
Q Consensus 300 r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv-----~~~v~vtwv~pR-------------------vL~l~ 355 (436)
|.-+-++||+.++++.++|....-....... .++|.. ++...+....+. .|+..
T Consensus 142 ~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~--~SLd~~~~~~~~~~~~~~d~~~~~~~~~e~~~~~~~l~~~l~~L~~r 219 (264)
T PRK07122 142 RAPTASELAAELGMDREEVVEGLVAGSAYNT--LSIDSGGGSGDDDARAIADTLGDVDAGLDQIENREALRPLLAALPER 219 (264)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHhhcCCC--CcccccccCCCCCcccchhccCCcHHHHHHHHHHHHHHHHHHcCCHH
Confidence 5678999999999999999886543322111 123322 111111111111 01111
Q ss_pred hhhccccCCcccccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 356 QLAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 356 Qi~~lr~~~~r~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
+-.-+.-.-....|+++||+.++++..-|-..+-+|+.
T Consensus 220 er~vl~l~y~~~~t~~EIA~~lgis~~~V~~~~~ral~ 257 (264)
T PRK07122 220 ERTVLVLRFFESMTQTQIAERVGISQMHVSRLLAKTLA 257 (264)
T ss_pred HHHHHHHHhcCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 11111111123789999999999999999999888875
No 79
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=55.91 E-value=17 Score=30.32 Aligned_cols=40 Identities=18% Similarity=0.124 Sum_probs=35.2
Q ss_pred CcccccHHHHHHHcCCChhhHHHHHHHHHhcccceeeccc
Q psy3716 364 GSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQ 403 (436)
Q Consensus 364 ~~r~~sf~~i~~~~~~~~~~ve~lvmka~s~~li~g~idq 403 (436)
.+.=+++++|++.+++|.++|+.-|=.-...|.|.=.||+
T Consensus 62 ~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd 101 (102)
T PF08784_consen 62 SEEGVHVDEIAQQLGMSENEVRKALDFLSNEGHIYSTIDD 101 (102)
T ss_dssp -TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTTSEEESSST
T ss_pred CCCcccHHHHHHHhCcCHHHHHHHHHHHHhCCeEecccCC
Confidence 3456999999999999999999999999999999999986
No 80
>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=55.28 E-value=21 Score=25.30 Aligned_cols=32 Identities=19% Similarity=0.254 Sum_probs=27.8
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHhcccce
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALALGLVK 398 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s~~li~ 398 (436)
.+|..+||+.++++..-|-..+=+-...|+|+
T Consensus 17 ~~t~~ela~~~~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 17 RITQKELAEKLGISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp TS-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHCcCcC
Confidence 49999999999999999999999999999885
No 81
>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=54.24 E-value=23 Score=25.79 Aligned_cols=34 Identities=29% Similarity=0.383 Sum_probs=28.1
Q ss_pred cccccHHHHHHHcCCChhhHHHHHHHHHhcccce
Q psy3716 365 SHQLSFAEISEAAQLPLIEVEFLIIKALALGLVK 398 (436)
Q Consensus 365 ~r~~sf~~i~~~~~~~~~~ve~lvmka~s~~li~ 398 (436)
.+.+++.+||+++++|..-|-.++---...|+++
T Consensus 16 ~~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~ 49 (52)
T PF09339_consen 16 GGPLTLSEIARALGLPKSTVHRLLQTLVEEGYVE 49 (52)
T ss_dssp BSCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCee
Confidence 3458999999999999999999888777777764
No 82
>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=52.79 E-value=21 Score=33.83 Aligned_cols=27 Identities=30% Similarity=0.309 Sum_probs=24.4
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
..|++|||+.++++..-|...+-+|+.
T Consensus 191 ~~s~~eIA~~lgis~~tV~~~~~ra~~ 217 (224)
T TIGR02479 191 ELNLKEIGEVLGLTESRVSQIHSQALK 217 (224)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 689999999999999999998888764
No 83
>PF09202 Rio2_N: Rio2, N-terminal; InterPro: IPR015285 This N-terminal domain is found in RIO2 kinases, and is structurally homologous to the winged helix (wHTH) domain. It adopts a structure consisting of four alpha helices followed by two beta strands and a fifth alpha helix. The domain confers DNA binding properties to the protein, as per other winged helix domains []. ; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1TQP_A 1ZAR_A 1TQI_A 1ZAO_A 1TQM_A.
Probab=52.54 E-value=33 Score=27.98 Aligned_cols=66 Identities=20% Similarity=0.240 Sum_probs=47.1
Q ss_pred HHHHHHHHHHHhhcCCCCcccCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCCccEEEEEeccccc
Q psy3716 282 KIALLCLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPRV 351 (436)
Q Consensus 282 KirLlaL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv~~~v~vtwv~pRv 351 (436)
-.|+|.-+++.-+ ++.-+|.+.|++..+++..+|+.-+-+....|||.-+.-..+| ..+|+.-.-.
T Consensus 8 d~rvL~aiE~gmk---~hE~VP~~~I~~~s~l~~~~~~~~L~~L~~~kLv~~~~~~Y~G-YrLT~~GYD~ 73 (82)
T PF09202_consen 8 DFRVLRAIEMGMK---NHEWVPLELIEKISGLSEGEVEKRLKRLVKLKLVSRRNKPYDG-YRLTFLGYDY 73 (82)
T ss_dssp HHHHHHHHHTTTT---T-SSEEHHHHHHHHT--HHHHHHHHHHHHHTTSEEEE-SSS-E-EEE-HHHHHH
T ss_pred HHHHHHHHHHccc---CCccCCHHHHHHHhCcCHHHHHHHHHHHHhcCCccccCCCcce-EEEeecchhH
Confidence 3688888888754 4689999999999999999999999999999999985544433 3555444333
No 84
>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=52.32 E-value=21 Score=25.29 Aligned_cols=21 Identities=29% Similarity=0.268 Sum_probs=16.4
Q ss_pred cccCHHHHHHHhCCChhhHHH
Q psy3716 300 HQLSFAEISEAAQLPLIEVEF 320 (436)
Q Consensus 300 r~isf~~Ia~~l~i~~~eVE~ 320 (436)
...||.+||+.+|++...|-.
T Consensus 16 ~r~s~~~la~~lglS~~~v~~ 36 (42)
T PF13404_consen 16 GRRSYAELAEELGLSESTVRR 36 (42)
T ss_dssp TTS-HHHHHHHHTS-HHHHHH
T ss_pred CCccHHHHHHHHCcCHHHHHH
Confidence 479999999999999988754
No 85
>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=52.08 E-value=20 Score=27.39 Aligned_cols=37 Identities=19% Similarity=0.087 Sum_probs=33.1
Q ss_pred cccccHHHHHHHcCCChhhHHHHHHHHHhcccceeec
Q psy3716 365 SHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHI 401 (436)
Q Consensus 365 ~r~~sf~~i~~~~~~~~~~ve~lvmka~s~~li~g~i 401 (436)
....|-++||+.+++|...|-..+-+-...|||+-.-
T Consensus 20 ~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~~ 56 (68)
T PF01978_consen 20 NGPATAEEIAEELGISRSTVYRALKSLEEKGLVEREE 56 (68)
T ss_dssp HCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE
T ss_pred cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEc
Confidence 3468999999999999999999999999999997654
No 86
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=51.54 E-value=46 Score=28.76 Aligned_cols=61 Identities=21% Similarity=0.252 Sum_probs=48.5
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHhcccceeecccccceEEEeeecccccchhhhhHHHHHHHhhcc
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPRVLSKDQVFWSLEETVATEV 435 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s~~li~g~idqv~~~v~~~wv~pr~l~~~q~~~~~~~~~~~~~ 435 (436)
..-|.+||+..+=+.+.|-.++++-|+ ..|+||.- +.+.++ --++.++++..|+.-+.+=|
T Consensus 21 i~Nf~~I~~~L~R~p~hv~kyl~~ELg---t~g~id~~-~rlii~----G~~~~~~i~~~l~~yI~~yV 81 (110)
T smart00653 21 IVNFADIAKALNRPPDHVLKFLLAELG---TQGSIDGK-GRLIVN----GRFTPKKLQDLLRRYIKEYV 81 (110)
T ss_pred EEcHHHHHHHHCCCHHHHHHHHHHHhC---CceeECCC-CeEEEE----EeeCHHHHHHHHHHHHHhcE
Confidence 356999999999999999999999999 89999975 444443 45677888888887665543
No 87
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=51.43 E-value=71 Score=30.18 Aligned_cols=110 Identities=23% Similarity=0.334 Sum_probs=65.0
Q ss_pred HHHHHHHH-HHhhcCCCCcc-cCHHHHHHHhCCChhhHHHHHHHHHhC--Ccccc-cccCCccEEEEE-------ecc--
Q psy3716 283 IALLCLME-LAFKKIPGSHQ-LSFAEISEAAQLPLIEVEFLIIKALAL--GLVKG-HIDQVDESFNVT-------WVQ-- 348 (436)
Q Consensus 283 irLlaL~~-L~~~~p~~~r~-isf~~Ia~~l~i~~~eVE~lvikAi~~--gLI~G-~IDQv~~~v~vt-------wv~-- 348 (436)
+++.+.++ +-|.. .+. +|.++|++.++++.++|+..+-+.... +-=+| .|=++.+...+. |+.
T Consensus 3 ~~~~~~iEA~LF~s---g~pgls~~~La~~l~~~~~~v~~~l~~L~~~y~~~~~gi~i~~~~~~y~l~tk~e~~~~v~~~ 79 (188)
T PRK00135 3 MNYKSIIEALLFVS---GEEGLSLEQLAEILELEPTEVQQLLEELQEKYEGDDRGLKLIEFNDVYKLVTKEENADYLQKL 79 (188)
T ss_pred ccHHHHHHHHHHHc---CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhhCCCCEEEEEECCEEEEEEcHHHHHHHHHH
Confidence 44455555 33443 245 999999999999999998877654332 11223 344444444332 221
Q ss_pred -----ccccccchhhcccc-CCcccccHHHHHHHcCCChhhHHHHHHHHHhcccce
Q psy3716 349 -----PRVLSKDQLAFKKI-PGSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVK 398 (436)
Q Consensus 349 -----pRvL~l~Qi~~lr~-~~~r~~sf~~i~~~~~~~~~~ve~lvmka~s~~li~ 398 (436)
++.|+...+..+.- +....+|-.+|++..|++.+.+ |-+-+..|||+
T Consensus 80 ~~~~~~~~LS~aaLEtLaiIay~qPiTr~eI~~irGv~~~~i---i~~L~~~gLI~ 132 (188)
T PRK00135 80 VKTPIKQSLSQAALEVLAIIAYKQPITRIEIDEIRGVNSDGA---LQTLLAKGLIK 132 (188)
T ss_pred hcccccCCCCHHHHHHHHHHHHcCCcCHHHHHHHHCCCHHHH---HHHHHHCCCeE
Confidence 12344444433322 1234789999999999987544 55555689985
No 88
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=51.34 E-value=20 Score=34.77 Aligned_cols=27 Identities=26% Similarity=0.255 Sum_probs=24.5
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
..|+++||+.++++..-|...+-+|+.
T Consensus 221 g~s~~eIA~~lgis~~~V~~~~~ra~~ 247 (255)
T TIGR02941 221 NLSQKETGERLGISQMHVSRLQRQAIS 247 (255)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 689999999999999999999888865
No 89
>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=51.33 E-value=52 Score=24.17 Aligned_cols=40 Identities=23% Similarity=0.269 Sum_probs=33.9
Q ss_pred cccCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCCc
Q psy3716 300 HQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVD 339 (436)
Q Consensus 300 r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv~ 339 (436)
..++..+|++.++++..-|-..|=+....|+|+-.-|.-+
T Consensus 20 ~~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~~~~~D 59 (62)
T PF12802_consen 20 EELTQSELAERLGISKSTVSRIVKRLEKKGLVERERDPGD 59 (62)
T ss_dssp SGEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE-SSS
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCCCC
Confidence 3599999999999999999999999999999987766544
No 90
>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=51.07 E-value=32 Score=33.42 Aligned_cols=27 Identities=22% Similarity=0.155 Sum_probs=24.8
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
..|+++||+.++++..-|.....+|+.
T Consensus 222 ~~t~~eIA~~lgis~~~V~~~~~ral~ 248 (254)
T TIGR02850 222 GKTQMEVAEEIGISQAQVSRLEKAALK 248 (254)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 679999999999999999999888875
No 91
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=51.05 E-value=21 Score=32.47 Aligned_cols=35 Identities=17% Similarity=0.192 Sum_probs=33.0
Q ss_pred CcccCHHHHHHHhCCChhhHHHHHHHHHhCCcccc
Q psy3716 299 SHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKG 333 (436)
Q Consensus 299 ~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G 333 (436)
+..+|+.+||+++|++..-|-.=+=+....|.|+|
T Consensus 26 d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~GvI~~ 60 (164)
T PRK11169 26 DGRISNVELSKRVGLSPTPCLERVRRLERQGFIQG 60 (164)
T ss_pred CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEE
Confidence 35899999999999999999999999999999997
No 92
>PRK05949 RNA polymerase sigma factor; Validated
Probab=51.01 E-value=38 Score=34.60 Aligned_cols=28 Identities=36% Similarity=0.366 Sum_probs=25.3
Q ss_pred ccccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 366 HQLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 366 r~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
...|++|||+.++++.+-|....-+|+.
T Consensus 285 e~~Tl~EIa~~lgiS~erVrq~~~rAl~ 312 (327)
T PRK05949 285 KELSLAKVGERLNLSRERVRQLEHQALA 312 (327)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4689999999999999999999888876
No 93
>PF09940 DUF2172: Domain of unknown function (DUF2172); InterPro: IPR012353 The proteins in this entry are encoded by genes located in polysaccharide biosynthesis gene clusters, and are therefore believed to be involved in polysaccharide biosynthesis. The ste gene cluster (for Streptomyces eps) is involved in exopolysaccharide EPS 139A biosynthesis in Streptomyces sp. 139 []. Members of this group exhibit distant sequence similarity to aminopeptidases (IPR007484 from INTERPRO, MEROPS peptidase family M28).; PDB: 3K9T_A.
Probab=50.53 E-value=22 Score=37.21 Aligned_cols=48 Identities=29% Similarity=0.396 Sum_probs=36.4
Q ss_pred HHHHHHHHHHHHHHhhcCCCCcccCHHHHHHHhCCChhhHHHHHHHHHhCCccc
Q psy3716 279 LSQKIALLCLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVK 332 (436)
Q Consensus 279 l~~KirLlaL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~ 332 (436)
-.+.+-+|-+++++ +..-++-+||+.+++|.++|...+-+.+..|||+
T Consensus 339 ~~~~~~~l~~L~~~------DG~~slldIA~~~~~~~~~~~~~~~~l~~~~Llk 386 (386)
T PF09940_consen 339 KAQQMAMLWVLNYS------DGKNSLLDIAERIGLPFDELADAARKLLEAGLLK 386 (386)
T ss_dssp ---HHHHHHHHHH-------EEEEEHHHHHHHHT--HHHHHHHHHHHHHTT-EE
T ss_pred HHHHHHHHHHHHhc------cCCCcHHHHHHHHCcCHHHHHHHHHHHHHcCCCC
Confidence 34556677777777 4689999999999999999999999999999986
No 94
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=50.51 E-value=24 Score=27.47 Aligned_cols=41 Identities=20% Similarity=0.205 Sum_probs=33.6
Q ss_pred ccccCCcccccHHHHHHHcCCChhhHHHHHHHHHhccccee
Q psy3716 359 FKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKG 399 (436)
Q Consensus 359 ~lr~~~~r~~sf~~i~~~~~~~~~~ve~lvmka~s~~li~g 399 (436)
.++......++-.+||+.++++...|...+.+-.+.|+|.-
T Consensus 14 ~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~ 54 (68)
T smart00550 14 FLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCK 54 (68)
T ss_pred HHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence 34333333599999999999999999999999999999864
No 95
>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=49.73 E-value=17 Score=28.04 Aligned_cols=23 Identities=9% Similarity=0.166 Sum_probs=20.8
Q ss_pred CcccCHHHHHHHhCCChhhHHHH
Q psy3716 299 SHQLSFAEISEAAQLPLIEVEFL 321 (436)
Q Consensus 299 ~r~isf~~Ia~~l~i~~~eVE~l 321 (436)
...+++.+||+.|+|+...|-.|
T Consensus 20 ~g~i~lkdIA~~Lgvs~~tIr~W 42 (60)
T PF10668_consen 20 NGKIKLKDIAEKLGVSESTIRKW 42 (60)
T ss_pred CCCccHHHHHHHHCCCHHHHHHH
Confidence 46899999999999999998776
No 96
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=49.64 E-value=28 Score=33.30 Aligned_cols=27 Identities=19% Similarity=0.227 Sum_probs=24.8
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
..|++|||+.++++..-|...+-+|+.
T Consensus 200 g~s~~EIA~~lgis~~tV~~~~~ra~~ 226 (236)
T PRK06986 200 ELNLKEIGAVLGVSESRVSQIHSQAIK 226 (236)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 689999999999999999999888875
No 97
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=49.58 E-value=61 Score=26.04 Aligned_cols=52 Identities=19% Similarity=0.112 Sum_probs=37.9
Q ss_pred HHHHHHHHHhhcCCCCcccCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCCcc
Q psy3716 284 ALLCLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDE 340 (436)
Q Consensus 284 rLlaL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv~~ 340 (436)
|+-.|.-|... +.++|++|.+.++++...+-.-+=+.-..|+|+-+-.-.++
T Consensus 2 Rl~Il~~L~~~-----~~~~f~~L~~~l~lt~g~Ls~hL~~Le~~GyV~~~k~~~~~ 53 (80)
T PF13601_consen 2 RLAILALLYAN-----EEATFSELKEELGLTDGNLSKHLKKLEEAGYVEVEKEFEGR 53 (80)
T ss_dssp HHHHHHHHHHH-----SEEEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEE-SSS
T ss_pred HHHHHHHHhhc-----CCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEEEeccCC
Confidence 44444444442 58999999999999999999999999999999986554433
No 98
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=49.57 E-value=34 Score=35.43 Aligned_cols=90 Identities=16% Similarity=0.183 Sum_probs=52.9
Q ss_pred cccCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCC----ccEEEEEe------cccc-----------------cc
Q psy3716 300 HQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQV----DESFNVTW------VQPR-----------------VL 352 (436)
Q Consensus 300 r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv----~~~v~vtw------v~pR-----------------vL 352 (436)
|.-|.++||+.++++.++|+.+.-.+ ... .++|.. ...-.... ..|- .|
T Consensus 231 r~pt~~EiA~~l~~~~~~v~~~~~~~--~~~--~SLd~~~~~~~~~~l~d~i~d~~~~~p~~~~~~~~~~~~l~~~l~~L 306 (367)
T PRK09210 231 REPTPEEIAEEMDMPPEKVREILKIA--QEP--VSLETPIGEEDDSHLGDFIEDQDATSPADHAAYELLKEQLEDVLDTL 306 (367)
T ss_pred CCCCHHHHHHHhCcCHHHHHHHHHHh--cCC--CCcCCCCCCCCcchhhhhccCCCCCCHHHHHHHHHHHHHHHHHHHhC
Confidence 67889999999999999999975432 111 122221 11100000 1110 12
Q ss_pred ccch--hhccccC--CcccccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 353 SKDQ--LAFKKIP--GSHQLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 353 ~l~Q--i~~lr~~--~~r~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
+..| +..++-- ..+..|+++||+.++++.+-|-.+--+|+.
T Consensus 307 ~~rEr~Vl~lrygl~~~~~~tl~EIa~~lgvs~erVrQi~~~Al~ 351 (367)
T PRK09210 307 TDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALR 351 (367)
T ss_pred CHHHHHHHHHHhccCCCCCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 2221 2222221 225689999999999999988888777765
No 99
>KOG3054|consensus
Probab=49.31 E-value=24 Score=34.77 Aligned_cols=72 Identities=19% Similarity=0.252 Sum_probs=53.1
Q ss_pred CcccCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCCccEEEEEeccccccccchhhcccc--CCcccccHHHHHHH
Q psy3716 299 SHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPRVLSKDQLAFKKI--PGSHQLSFAEISEA 376 (436)
Q Consensus 299 ~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv~~~v~vtwv~pRvL~l~Qi~~lr~--~~~r~~sf~~i~~~ 376 (436)
++.++.+++|.+.++-..++=.=+-.-+..|++.|.||--.+.++|+ ..++..... +..-.+|..+||+.
T Consensus 212 nKvV~ledLas~f~Lrtqd~inriq~~l~eg~ltGVmDDRGKfIYIS--------~eEl~AVAkfIkqrGRVSIaelAe~ 283 (299)
T KOG3054|consen 212 NKVVPLEDLASEFGLRTQDSINRIQELLAEGLLTGVMDDRGKFIYIS--------MEELAAVAKFIKQRGRVSIAELAEK 283 (299)
T ss_pred cCeeeHHHHHHHhCccHHHHHHHHHHHHHhhhheeeecCCCceEEec--------HHHHHHHHHHHHHcCceeHHHHHHh
Confidence 47999999999999977777777778888999999999999988876 333322211 11235788888876
Q ss_pred cC
Q psy3716 377 AQ 378 (436)
Q Consensus 377 ~~ 378 (436)
.+
T Consensus 284 SN 285 (299)
T KOG3054|consen 284 SN 285 (299)
T ss_pred hc
Confidence 43
No 100
>PF11817 Foie-gras_1: Foie gras liver health family 1; InterPro: IPR021773 Mutating the gene foie gras in zebrafish has been shown to affect development; the mutants develop large, lipid-filled hepatocytes in the liver, resembling those in individuals with fatty liver disease []. Foie-gras protein is long and has several well-defined domains though none of them has a known function. We have annotated this one as the first []. THe C terminus of this region contains TPR repeats.
Probab=49.10 E-value=2.1e+02 Score=27.78 Aligned_cols=92 Identities=14% Similarity=0.135 Sum_probs=64.1
Q ss_pred CCCHHHHHHHHHHHHHhhcCCcc--hhHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHHHHH--hcccChhHHHHHHHH
Q psy3716 93 LSDQEEALVLLQSFEDKVKNNLE--AKSLCKILQAQMIMNKDADKPGSLDEVEKLIDEIELLV--NDIEGVTAIHSRFYL 168 (436)
Q Consensus 93 ~~d~~~aL~~L~~l~~~l~~~~e--a~~~~~~~i~~~~l~~~~~~~~~l~~~~~~L~~~~~~L--~~~~~~~~v~~~~y~ 168 (436)
.......++.|++..+.++.... ..-++...+|..+.. .|+++.+.+.++.+-... ++|... ...+..
T Consensus 151 ~~hs~~iI~lL~~A~~~f~~~~~~R~~~~l~~~~A~ey~~-----~g~~~~A~~~l~~~~~~yr~egW~~l---~~~~l~ 222 (247)
T PF11817_consen 151 VDHSKLIIELLEKAYEQFKKYGQNRMASYLSLEMAEEYFR-----LGDYDKALKLLEPAASSYRREGWWSL---LTEVLW 222 (247)
T ss_pred cchHHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHH-----CCCHHHHHHHHHHHHHHHHhCCcHHH---HHHHHH
Confidence 44566778888888887766443 346677889999998 999999999999994444 356643 223333
Q ss_pred HHHHHHHHhhcHHHHHHHHHHHhc
Q psy3716 169 VASTLYRKQAKLSLYYRTALRYLG 192 (436)
Q Consensus 169 ~~a~~~k~~~~~~~~Y~~~L~yL~ 192 (436)
...+.++..|+...|-..+++-++
T Consensus 223 ~l~~Ca~~~~~~~~~l~~~leLls 246 (247)
T PF11817_consen 223 RLLECAKRLGDVEDYLTTSLELLS 246 (247)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHhc
Confidence 333344458898999888887654
No 101
>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=49.07 E-value=24 Score=25.27 Aligned_cols=28 Identities=25% Similarity=0.338 Sum_probs=24.3
Q ss_pred ccccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 366 HQLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 366 r~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
...|+++||+.++++..-|-...-+|+.
T Consensus 19 ~~~t~~eIa~~lg~s~~~V~~~~~~al~ 46 (50)
T PF04545_consen 19 EGLTLEEIAERLGISRSTVRRILKRALK 46 (50)
T ss_dssp ST-SHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHCCcHHHHHHHHHHHHH
Confidence 4689999999999999999999888875
No 102
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=48.93 E-value=38 Score=25.58 Aligned_cols=66 Identities=17% Similarity=0.261 Sum_probs=41.2
Q ss_pred cCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCCccEEEEEeccccccccchhhccccCCcccccHHHHHHHcCCCh
Q psy3716 302 LSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPRVLSKDQLAFKKIPGSHQLSFAEISEAAQLPL 381 (436)
Q Consensus 302 isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv~~~v~vtwv~pRvL~l~Qi~~lr~~~~r~~sf~~i~~~~~~~~ 381 (436)
++..++|+.+|++...+-.|. ..|++...-...++ .|.++..++..++. ...+ ...++|+
T Consensus 1 ~s~~eva~~~gvs~~tlr~~~----~~gli~~~~~~~~g--------~r~y~~~dl~~l~~----i~~l----r~~g~~~ 60 (70)
T smart00422 1 YTIGEVAKLAGVSVRTLRYYE----RIGLLPPPIRTEGG--------YRLYSDEDLERLRF----IKRL----KELGFSL 60 (70)
T ss_pred CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCccCCCC--------CEecCHHHHHHHHH----HHHH----HHcCCCH
Confidence 357899999999999999994 58887764222222 35566666655431 1111 3467777
Q ss_pred hhHHHH
Q psy3716 382 IEVEFL 387 (436)
Q Consensus 382 ~~ve~l 387 (436)
++|...
T Consensus 61 ~~i~~~ 66 (70)
T smart00422 61 EEIKEL 66 (70)
T ss_pred HHHHHH
Confidence 776554
No 103
>PRK09191 two-component response regulator; Provisional
Probab=48.06 E-value=1.2e+02 Score=28.49 Aligned_cols=27 Identities=30% Similarity=0.210 Sum_probs=24.8
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
.+||++||+.+++|++-|...+-+|+.
T Consensus 104 ~~s~~eIA~~l~~s~~tV~~~l~ra~~ 130 (261)
T PRK09191 104 GFSVEEAAEILGVDPAEAEALLDDARA 130 (261)
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 689999999999999999999988775
No 104
>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=47.95 E-value=24 Score=26.47 Aligned_cols=44 Identities=20% Similarity=0.238 Sum_probs=35.2
Q ss_pred CcccccHHHHHHHcCCChhhHHHHHHHHHhcccceeecccccce
Q psy3716 364 GSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDES 407 (436)
Q Consensus 364 ~~r~~sf~~i~~~~~~~~~~ve~lvmka~s~~li~g~idqv~~~ 407 (436)
.++.++..+||+.++++...|-..|=+....|||.=.-|..++.
T Consensus 15 ~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~~~~~d~R 58 (68)
T PF13463_consen 15 SDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLVEKERDPHDKR 58 (68)
T ss_dssp -TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEESSCTT
T ss_pred cCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecCCCCcCC
Confidence 36789999999999999999999999999999997776766654
No 105
>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=47.71 E-value=32 Score=25.36 Aligned_cols=41 Identities=22% Similarity=0.266 Sum_probs=34.6
Q ss_pred ccccHHHHHHHcCCChhhHHHHHHHHHhcccceeecccccc
Q psy3716 366 HQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDE 406 (436)
Q Consensus 366 r~~sf~~i~~~~~~~~~~ve~lvmka~s~~li~g~idqv~~ 406 (436)
..++..+||+.++++.--|-..|=+-...|||+-.-|.-++
T Consensus 20 ~~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~~~~~D~ 60 (62)
T PF12802_consen 20 EELTQSELAERLGISKSTVSRIVKRLEKKGLVERERDPGDR 60 (62)
T ss_dssp SGEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE-SSST
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCCCCC
Confidence 35899999999999999999999999999999887776553
No 106
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=47.71 E-value=19 Score=35.27 Aligned_cols=27 Identities=22% Similarity=0.260 Sum_probs=24.4
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
..|+++||+.++++..-|...+.+|+.
T Consensus 228 ~~s~~eIA~~lgis~~tV~~~~~ra~~ 254 (268)
T PRK06288 228 DLTLKEIGKVLGVTESRISQLHTKAVL 254 (268)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 689999999999999999988887765
No 107
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=47.68 E-value=21 Score=29.87 Aligned_cols=29 Identities=28% Similarity=0.374 Sum_probs=26.1
Q ss_pred HHHHHHHcCCChhhHHHHHHHHHhcccce
Q psy3716 370 FAEISEAAQLPLIEVEFLIIKALALGLVK 398 (436)
Q Consensus 370 f~~i~~~~~~~~~~ve~lvmka~s~~li~ 398 (436)
-.-||..+++|.++|+..+-+-...|||+
T Consensus 24 ~k~ia~~l~~~~~~v~~~l~~Le~~GLle 52 (92)
T PF10007_consen 24 AKSIARRLKIPLEEVREALEKLEEMGLLE 52 (92)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHCCCeE
Confidence 35699999999999999999999999875
No 108
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=47.41 E-value=54 Score=32.00 Aligned_cols=27 Identities=22% Similarity=0.231 Sum_probs=25.2
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
..|+++||+.++++..-|...+-+|+.
T Consensus 219 ~~s~~eIA~~lgvs~~~V~~~~~ra~~ 245 (256)
T PRK07408 219 DLTQKEAAERLGISPVTVSRRVKKGLD 245 (256)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 689999999999999999999999876
No 109
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=47.38 E-value=21 Score=29.85 Aligned_cols=28 Identities=29% Similarity=0.414 Sum_probs=26.0
Q ss_pred HHHHHHhCCChhhHHHHHHHHHhCCccc
Q psy3716 305 AEISEAAQLPLIEVEFLIIKALALGLVK 332 (436)
Q Consensus 305 ~~Ia~~l~i~~~eVE~lvikAi~~gLI~ 332 (436)
..||..+++|.++|+..+-+....|||+
T Consensus 25 k~ia~~l~~~~~~v~~~l~~Le~~GLle 52 (92)
T PF10007_consen 25 KSIARRLKIPLEEVREALEKLEEMGLLE 52 (92)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCeE
Confidence 4599999999999999999999999986
No 110
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=47.29 E-value=40 Score=32.58 Aligned_cols=46 Identities=20% Similarity=0.299 Sum_probs=38.3
Q ss_pred HHHHHHHHHhhcCCCCcccCHHHHHHHhCCChhhHHHHHHHHHhCCccc
Q psy3716 284 ALLCLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVK 332 (436)
Q Consensus 284 rLlaL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~ 332 (436)
|-+.++++.... .+.++..+||+++++|..-|-.++-.....|+++
T Consensus 10 ral~IL~~l~~~---~~~~~l~eia~~lglpksT~~RlL~tL~~~G~l~ 55 (248)
T TIGR02431 10 RGLAVIEAFGAE---RPRLTLTDVAEATGLTRAAARRFLLTLVELGYVT 55 (248)
T ss_pred HHHHHHHHHhcC---CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 556666655433 2579999999999999999999999999999997
No 111
>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=47.29 E-value=37 Score=32.32 Aligned_cols=27 Identities=19% Similarity=0.212 Sum_probs=23.2
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
..|+++||+.++++..-|-.+.-+|+.
T Consensus 199 ~~t~~eIA~~lgis~~~V~~~~~~al~ 225 (231)
T TIGR02885 199 DKTQTEVANMLGISQVQVSRLEKKVLK 225 (231)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 579999999999999999888777764
No 112
>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A.
Probab=47.07 E-value=1.4e+02 Score=23.30 Aligned_cols=79 Identities=16% Similarity=0.190 Sum_probs=45.4
Q ss_pred CCHHHHHHHHHHHHHhhcCCcchhHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHHHHHhcccChhHHHHHHHHHHHHH
Q psy3716 94 SDQEEALVLLQSFEDKVKNNLEAKSLCKILQAQMIMNKDADKPGSLDEVEKLIDEIELLVNDIEGVTAIHSRFYLVASTL 173 (436)
Q Consensus 94 ~d~~~aL~~L~~l~~~l~~~~ea~~~~~~~i~~~~l~~~~~~~~~l~~~~~~L~~~~~~L~~~~~~~~v~~~~y~~~a~~ 173 (436)
.+.+.|+.+.+++...-+.+.+..++. .+|..+.. .|+++.|-..++. ..++ +......|.. +..
T Consensus 3 ~~y~~Ai~~~~k~~~~~~~~~~~~~~~--~la~~~~~-----~~~y~~A~~~~~~-----~~~~--~~~~~~~~l~-a~~ 67 (84)
T PF12895_consen 3 GNYENAIKYYEKLLELDPTNPNSAYLY--NLAQCYFQ-----QGKYEEAIELLQK-----LKLD--PSNPDIHYLL-ARC 67 (84)
T ss_dssp T-HHHHHHHHHHHHHHHCGTHHHHHHH--HHHHHHHH-----TTHHHHHHHHHHC-----HTHH--HCHHHHHHHH-HHH
T ss_pred ccHHHHHHHHHHHHHHCCCChhHHHHH--HHHHHHHH-----CCCHHHHHHHHHH-----hCCC--CCCHHHHHHH-HHH
Confidence 367889999999988876542333332 25667777 8899988777766 1111 1111222333 444
Q ss_pred HHHhhcHHHHHHHH
Q psy3716 174 YRKQAKLSLYYRTA 187 (436)
Q Consensus 174 ~k~~~~~~~~Y~~~ 187 (436)
+-..|++++.-+..
T Consensus 68 ~~~l~~y~eAi~~l 81 (84)
T PF12895_consen 68 LLKLGKYEEAIKAL 81 (84)
T ss_dssp HHHTT-HHHHHHHH
T ss_pred HHHhCCHHHHHHHH
Confidence 44578877765544
No 113
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=46.72 E-value=46 Score=35.32 Aligned_cols=90 Identities=18% Similarity=0.233 Sum_probs=54.5
Q ss_pred cccCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCCcc---------EEEEEecccc-----------------ccc
Q psy3716 300 HQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDE---------SFNVTWVQPR-----------------VLS 353 (436)
Q Consensus 300 r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv~~---------~v~vtwv~pR-----------------vL~ 353 (436)
|.-+..+||+++++++++|..+...+- +-+ ++|+.-+ .+.-.-..|- .|+
T Consensus 277 R~pt~~EiA~~l~is~~~vr~~l~~~~--~~~--SLd~~vg~~~d~~l~d~l~~~~~~pee~~~~~~l~~~L~~~L~~L~ 352 (415)
T PRK07598 277 RTPTIEDIAQELEMTPTQVREVLLRVP--RSV--SLETKVGKDKDTELGDLLETDDISPEEMLMRESLQRDLQHLLADLT 352 (415)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHcc--CCc--ccccccCCCccccHHHhccCCCCCHHHHHHHHHHHHHHHHHHHhCC
Confidence 667899999999999999999876542 111 2222110 1110001110 111
Q ss_pred cch--hhccccC--CcccccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 354 KDQ--LAFKKIP--GSHQLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 354 l~Q--i~~lr~~--~~r~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
..| +..++-- ..+..|++|||+.+++|.+-|....-+|+.
T Consensus 353 ~reR~VI~LRygl~d~~~~Tl~EIA~~LGvS~erVRqie~rAl~ 396 (415)
T PRK07598 353 SRERDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQ 396 (415)
T ss_pred HHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 111 2222211 235689999999999999999999888876
No 114
>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A ....
Probab=46.48 E-value=42 Score=24.77 Aligned_cols=50 Identities=32% Similarity=0.430 Sum_probs=36.7
Q ss_pred CCHHHHHHHHHHHHHhhcCCcchhHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHHHH
Q psy3716 94 SDQEEALVLLQSFEDKVKNNLEAKSLCKILQAQMIMNKDADKPGSLDEVEKLIDEIELL 152 (436)
Q Consensus 94 ~d~~~aL~~L~~l~~~l~~~~ea~~~~~~~i~~~~l~~~~~~~~~l~~~~~~L~~~~~~ 152 (436)
.+.++|++.++++...-+.+.++.+ ..|..++. .|++++++..++.+...
T Consensus 5 ~~~~~A~~~~~~~l~~~p~~~~~~~----~la~~~~~-----~g~~~~A~~~l~~~~~~ 54 (68)
T PF14559_consen 5 GDYDEAIELLEKALQRNPDNPEARL----LLAQCYLK-----QGQYDEAEELLERLLKQ 54 (68)
T ss_dssp THHHHHHHHHHHHHHHTTTSHHHHH----HHHHHHHH-----TT-HHHHHHHHHCCHGG
T ss_pred cCHHHHHHHHHHHHHHCCCCHHHHH----HHHHHHHH-----cCCHHHHHHHHHHHHHH
Confidence 3688999999999888777655433 46778888 89999988877665443
No 115
>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=46.19 E-value=60 Score=24.36 Aligned_cols=38 Identities=16% Similarity=0.287 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHHHHHhhcCCCCcccCHHHHHHHhCCChhhHHHHH
Q psy3716 278 KLSQKIALLCLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLI 322 (436)
Q Consensus 278 ~l~~KirLlaL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lv 322 (436)
...++++|+.++- .. +.+++++||+.++++...+-.-+
T Consensus 3 ~i~rq~~Ll~~L~---~~----~~~~~~ela~~l~~S~rti~~~i 40 (59)
T PF08280_consen 3 DIKRQLKLLELLL---KN----KWITLKELAKKLNISERTIKNDI 40 (59)
T ss_dssp HHHHHHHHHHHHH---HH----TSBBHHHHHHHCTS-HHHHHHHH
T ss_pred hHHHHHHHHHHHH---cC----CCCcHHHHHHHHCCCHHHHHHHH
Confidence 3567777777764 32 58999999999999987655443
No 116
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=46.17 E-value=53 Score=31.75 Aligned_cols=47 Identities=11% Similarity=0.057 Sum_probs=41.2
Q ss_pred cccCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCCccEEEEEe
Q psy3716 300 HQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTW 346 (436)
Q Consensus 300 r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv~~~v~vtw 346 (436)
..+|.++||+.++++..-|=..+-+.-..|+|+-..+.-++.+.+|-
T Consensus 20 ~~IS~~eLA~~L~iS~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~LTe 66 (217)
T PRK14165 20 VKISSSEFANHTGTSSKTAARILKQLEDEGYITRTIVPRGQLITITE 66 (217)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEEcCCceEEEECH
Confidence 47999999999999999999999999999999998887666666654
No 117
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=46.11 E-value=47 Score=32.48 Aligned_cols=27 Identities=26% Similarity=0.233 Sum_probs=24.8
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
..|++|||+.++++..-|.....+|+.
T Consensus 221 ~~t~~EIA~~lgis~~~V~~~~~ral~ 247 (257)
T PRK05911 221 ELVLKEIGKILGVSESRVSQIHSKALL 247 (257)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 789999999999999999999888875
No 118
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=45.98 E-value=29 Score=28.81 Aligned_cols=39 Identities=21% Similarity=0.308 Sum_probs=34.3
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHhcccceeeccccc
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVD 405 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s~~li~g~idqv~ 405 (436)
.+|+.+||+.++++...|-..+.+-...|+|+|.--.++
T Consensus 17 ~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~~~~~~~~ 55 (108)
T smart00344 17 RISLAELAKKVGLSPSTVHNRVKRLEEEGVIKGYTAVIN 55 (108)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeceEEEeC
Confidence 589999999999999999999999999999996544443
No 119
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=45.79 E-value=45 Score=32.55 Aligned_cols=46 Identities=30% Similarity=0.396 Sum_probs=38.5
Q ss_pred HHHHHHHHHhhcCCCCcccCHHHHHHHhCCChhhHHHHHHHHHhCCccc
Q psy3716 284 ALLCLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVK 332 (436)
Q Consensus 284 rLlaL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~ 332 (436)
|-+.++++....| +.+++.+||+.+++|...|-.++......|+++
T Consensus 5 ral~iL~~l~~~~---~~l~l~ela~~~glpksT~~RlL~tL~~~G~v~ 50 (246)
T COG1414 5 RALAILDLLAEGP---GGLSLAELAERLGLPKSTVHRLLQTLVELGYVE 50 (246)
T ss_pred HHHHHHHHHHhCC---CCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEE
Confidence 4456666665555 458999999999999999999999999999986
No 120
>KOG1126|consensus
Probab=44.94 E-value=1.2e+02 Score=33.84 Aligned_cols=160 Identities=18% Similarity=0.307 Sum_probs=96.6
Q ss_pred HHHhHHHHhhcCCchHHHHHHHHHHHHHhhhHHHHHHHHHH-Hhc-Ccccc-----cc----------------------
Q psy3716 9 VYLTAKQEAYSKNPEISAQWLNLEELYNKKLWHQLTLAVLA-FVQ-NPAIQ-----KE---------------------- 59 (436)
Q Consensus 9 ~~l~~~~~~~~~~~~~~~~~~~l~~l~~~KLWhQLT~~l~~-~~~-~p~~~-----~~---------------------- 59 (436)
.||+|.. ...+|.--+-|--+-++|.=..||+=..+..+ .++ ||.|. .|
T Consensus 407 s~Laq~L--i~~~~~sPesWca~GNcfSLQkdh~~Aik~f~RAiQldp~faYayTLlGhE~~~~ee~d~a~~~fr~Al~~ 484 (638)
T KOG1126|consen 407 SYLAQDL--IDTDPNSPESWCALGNCFSLQKDHDTAIKCFKRAIQLDPRFAYAYTLLGHESIATEEFDKAMKSFRKALGV 484 (638)
T ss_pred HHHHHHH--HhhCCCCcHHHHHhcchhhhhhHHHHHHHHHHHhhccCCccchhhhhcCChhhhhHHHHhHHHHHHhhhcC
Confidence 4676333 44556666678888888888888887766544 222 23221 00
Q ss_pred -hhHHHH-------------HHHHHHHH--hhccCchhHHHHHHHHh--ccCCCHHHHHHHHHHHHHhhcCCcchhHHHH
Q psy3716 60 -GELRDL-------------YHKFVISF--ETKINPVSLMEIMEVIT--NHLSDQEEALVLLQSFEDKVKNNLEAKSLCK 121 (436)
Q Consensus 60 -~~~~~l-------------y~~fI~~f--~~kin~l~l~~i~~~v~--~~~~d~~~aL~~L~~l~~~l~~~~ea~~~~~ 121 (436)
+.-++. |+.--..| .-.|||-..|-+|..-. .+....++||.++++.+-. .+ .-.+|+
T Consensus 485 ~~rhYnAwYGlG~vy~Kqek~e~Ae~~fqkA~~INP~nsvi~~~~g~~~~~~k~~d~AL~~~~~A~~l-d~---kn~l~~ 560 (638)
T KOG1126|consen 485 DPRHYNAWYGLGTVYLKQEKLEFAEFHFQKAVEINPSNSVILCHIGRIQHQLKRKDKALQLYEKAIHL-DP---KNPLCK 560 (638)
T ss_pred CchhhHHHHhhhhheeccchhhHHHHHHHhhhcCCccchhHHhhhhHHHHHhhhhhHHHHHHHHHHhc-CC---CCchhH
Confidence 000111 11111223 35799999887776443 3456888999998876532 22 223455
Q ss_pred HHHHHHhhccCCCCCCChHHHHHHHHHHHHHHhcccChhHHHHHHHHHHHHHHHHhhcHHHHHHH
Q psy3716 122 ILQAQMIMNKDADKPGSLDEVEKLIDEIELLVNDIEGVTAIHSRFYLVASTLYRKQAKLSLYYRT 186 (436)
Q Consensus 122 ~~i~~~~l~~~~~~~~~l~~~~~~L~~~~~~L~~~~~~~~v~~~~y~~~a~~~k~~~~~~~~Y~~ 186 (436)
...|.+..- .+++++|-..||++++.. +.-+..|.+....||..|+...+-++
T Consensus 561 ~~~~~il~~-----~~~~~eal~~LEeLk~~v-------P~es~v~~llgki~k~~~~~~~Al~~ 613 (638)
T KOG1126|consen 561 YHRASILFS-----LGRYVEALQELEELKELV-------PQESSVFALLGKIYKRLGNTDLALLH 613 (638)
T ss_pred HHHHHHHHh-----hcchHHHHHHHHHHHHhC-------cchHHHHHHHHHHHHHHccchHHHHh
Confidence 566777776 899999999999998873 22334455566677777775554333
No 121
>COG5071 RPN5 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=44.90 E-value=3.7e+02 Score=27.76 Aligned_cols=48 Identities=10% Similarity=0.125 Sum_probs=44.2
Q ss_pred cccCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCCccEEEEEec
Q psy3716 300 HQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWV 347 (436)
Q Consensus 300 r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv~~~v~vtwv 347 (436)
..|+..+|..-++.|++|.|..|-.....|.+-+||+|..+.+....-
T Consensus 352 SrI~~~rl~~lld~~~s~te~~ISdlVN~G~~yaKiNrpa~Ii~FEK~ 399 (439)
T COG5071 352 SRIHCSRLGVLLDMSPSETEQFISDLVNKGHFYAKINRPAQIISFEKS 399 (439)
T ss_pred hhhhHHHHHHHHcCCHHHHHHHHHHHHhcCcEEEEecCccceEEeecc
Confidence 369999999999999999999999999999999999999998876543
No 122
>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=44.86 E-value=25 Score=33.31 Aligned_cols=27 Identities=26% Similarity=0.326 Sum_probs=24.2
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
..|+++||+.++++..-|...+-+|+.
T Consensus 194 ~~s~~eIA~~lgis~~~v~~~~~ra~~ 220 (227)
T TIGR02980 194 DKTQSEIAERLGISQMHVSRLLRRALK 220 (227)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 689999999999999999998877765
No 123
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=44.45 E-value=24 Score=32.09 Aligned_cols=27 Identities=33% Similarity=0.326 Sum_probs=25.4
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
.+||++||+.+|+|++-|...+.+|..
T Consensus 149 ~~s~~eIA~~lgis~~tV~~~l~ra~~ 175 (182)
T PRK12537 149 GCSHAEIAQRLGAPLGTVKAWIKRSLK 175 (182)
T ss_pred CCCHHHHHHHHCCChhhHHHHHHHHHH
Confidence 699999999999999999999999874
No 124
>PF03979 Sigma70_r1_1: Sigma-70 factor, region 1.1; InterPro: IPR007127 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 [, ]. This entry represents Region 1.1 which modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase [, ]. Region 1.1 is also involved in promoter binding.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2K6X_A.
Probab=44.37 E-value=48 Score=26.73 Aligned_cols=42 Identities=24% Similarity=0.252 Sum_probs=27.4
Q ss_pred HHHHHHHHhhcCCCCcccCHHHHHHHhC---CChhhHHHHHHHHHhCCc
Q psy3716 285 LLCLMELAFKKIPGSHQLSFAEISEAAQ---LPLIEVEFLIIKALALGL 330 (436)
Q Consensus 285 LlaL~~L~~~~p~~~r~isf~~Ia~~l~---i~~~eVE~lvikAi~~gL 330 (436)
+-.|+..+.++ +.|||++|.+++. ++.++++.++...-..|+
T Consensus 9 i~~Li~~gK~~----G~lT~~eI~~~L~~~~~~~e~id~i~~~L~~~gI 53 (82)
T PF03979_consen 9 IKKLIEKGKKK----GYLTYDEINDALPEDDLDPEQIDEIYDTLEDEGI 53 (82)
T ss_dssp HHHHHHHHHHH----SS-BHHHHHHH-S-S---HHHHHHHHHHHHTT--
T ss_pred HHHHHHHHhhc----CcCCHHHHHHHcCccCCCHHHHHHHHHHHHHCCC
Confidence 34577777654 6899999999998 577888888776666654
No 125
>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=44.19 E-value=41 Score=25.17 Aligned_cols=36 Identities=17% Similarity=0.288 Sum_probs=31.2
Q ss_pred cccccHHHHHHHcCCChhhHHHHHHHHHhcccceee
Q psy3716 365 SHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGH 400 (436)
Q Consensus 365 ~r~~sf~~i~~~~~~~~~~ve~lvmka~s~~li~g~ 400 (436)
....|+.+||+.+++|...|-+=+=+--..|||+..
T Consensus 22 ~~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli~~~ 57 (61)
T PF12840_consen 22 NGPMTVSELAEELGISQSTVSYHLKKLEEAGLIEVE 57 (61)
T ss_dssp CSTBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEe
Confidence 467999999999999999999998888899999864
No 126
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=44.09 E-value=48 Score=33.66 Aligned_cols=90 Identities=18% Similarity=0.203 Sum_probs=53.5
Q ss_pred cccCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCC----cc-----EEEEEecccc-----------------ccc
Q psy3716 300 HQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQV----DE-----SFNVTWVQPR-----------------VLS 353 (436)
Q Consensus 300 r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv----~~-----~v~vtwv~pR-----------------vL~ 353 (436)
|.-+.++||+.++++.++|+...-.+ .. ..++|.. .. .+.-.-..|- .|+
T Consensus 183 r~pt~~eiA~~~~~~~~~v~~~~~~~-~~---~~SLd~~~~~~~~~~l~~~~~d~~~~pe~~~~~~~~~~~l~~al~~L~ 258 (317)
T PRK07405 183 RAATIGELAEELELTPKQVREYLERA-RQ---PLSLDLRVGDNQDTELGELLEDTGASPEDFATQSSLQLDLERLMEDLT 258 (317)
T ss_pred CCCCHHHHHHHhCcCHHHHHHHHHHc-CC---CeeecCCCCCCCCccHHHhhcCCCCCHHHHHHHHHHHHHHHHHHHcCC
Confidence 56678999999999999999885432 21 1133321 00 0000001110 122
Q ss_pred cc--hhhccccC--CcccccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 354 KD--QLAFKKIP--GSHQLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 354 l~--Qi~~lr~~--~~r~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
.. ++..++-- .....|++|||+.+++|.+-|..+.-+|+.
T Consensus 259 ~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVRqi~~rAl~ 302 (317)
T PRK07405 259 PQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALS 302 (317)
T ss_pred HHHHHHHHHHhhcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 21 12233321 135689999999999999999998888875
No 127
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 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 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; 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: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=44.09 E-value=22 Score=27.74 Aligned_cols=26 Identities=23% Similarity=0.230 Sum_probs=20.0
Q ss_pred CcccCHHHHHHHhCCChhhHHHHHHH
Q psy3716 299 SHQLSFAEISEAAQLPLIEVEFLIIK 324 (436)
Q Consensus 299 ~r~isf~~Ia~~l~i~~~eVE~lvik 324 (436)
.|.-+-++||+.++++.++|..++-.
T Consensus 18 gr~Pt~eEiA~~lgis~~~v~~~l~~ 43 (78)
T PF04539_consen 18 GREPTDEEIAEELGISVEEVRELLQA 43 (78)
T ss_dssp SS--BHHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCCCHHHHHHHHcccHHHHHHHHHh
Confidence 37889999999999999999977643
No 128
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=43.72 E-value=96 Score=24.51 Aligned_cols=42 Identities=17% Similarity=0.158 Sum_probs=36.2
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCCccEE
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESF 342 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv~~~v 342 (436)
.++..+|++.++++...|-..+=+....|+|.-.-++.++..
T Consensus 24 ~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~~~~~~~r~ 65 (101)
T smart00347 24 PLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRLPSPEDRRS 65 (101)
T ss_pred CcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEecCCCCCCCe
Confidence 599999999999999999999999999999987666544433
No 129
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=43.46 E-value=62 Score=23.06 Aligned_cols=35 Identities=26% Similarity=0.298 Sum_probs=30.9
Q ss_pred cccCHHHHHHHhCCChhhHHHHHHHHHhCCccccc
Q psy3716 300 HQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGH 334 (436)
Q Consensus 300 r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~ 334 (436)
+.+++.+|++.++++...|-..+=+....|+|.-.
T Consensus 9 ~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~~ 43 (66)
T smart00418 9 GELCVCELAEILGLSQSTVSHHLKKLREAGLVESR 43 (66)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeeee
Confidence 46899999999999999999999888889999744
No 130
>PF10975 DUF2802: Protein of unknown function (DUF2802); InterPro: IPR021244 This bacterial family of proteins has no known function.
Probab=43.19 E-value=25 Score=27.85 Aligned_cols=23 Identities=30% Similarity=0.348 Sum_probs=20.3
Q ss_pred cccHHHHHHHcCCChhhHHHHHH
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLII 389 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvm 389 (436)
-.+.+||+++|++|..|.|.++.
T Consensus 44 Ga~~~el~~~CgL~~aEAeLl~~ 66 (70)
T PF10975_consen 44 GASVEELMEECGLSRAEAELLLS 66 (70)
T ss_pred CCCHHHHHHHcCCCHHHHHHHHH
Confidence 47889999999999999998763
No 131
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=43.17 E-value=31 Score=30.95 Aligned_cols=34 Identities=15% Similarity=0.279 Sum_probs=32.3
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHhcccceee
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALALGLVKGH 400 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s~~li~g~ 400 (436)
..||.+||+.++++...|-.=+-|-.+.|.|+|.
T Consensus 23 R~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI~~~ 56 (153)
T PRK11179 23 RTPYAELAKQFGVSPGTIHVRVEKMKQAGIITGT 56 (153)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeE
Confidence 5899999999999999999999999999999975
No 132
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, 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=42.42 E-value=75 Score=26.03 Aligned_cols=66 Identities=15% Similarity=0.267 Sum_probs=43.1
Q ss_pred cCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCCccEEEEEeccccccccchhhccccCCcccccHHHHHHHcCCCh
Q psy3716 302 LSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPRVLSKDQLAFKKIPGSHQLSFAEISEAAQLPL 381 (436)
Q Consensus 302 isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv~~~v~vtwv~pRvL~l~Qi~~lr~~~~r~~sf~~i~~~~~~~~ 381 (436)
++..++|+.+||+.+.+-+|. ..|++...-+.- ..|.++..++..++. .... ...++|+
T Consensus 1 ~~~~eva~~~gi~~~tlr~~~----~~Gll~~~~~~~---------g~r~y~~~dv~~l~~-------i~~l-~~~g~~~ 59 (100)
T cd00592 1 YTIGEVAKLLGVSVRTLRYYE----EKGLLPPERSEN---------GYRLYSEEDLERLRL-------IRRL-RELGLSL 59 (100)
T ss_pred CCHHHHHHHHCcCHHHHHHHH----HCCCcCCCcCCC---------CCcccCHHHHHHHHH-------HHHH-HHcCCCH
Confidence 367899999999999999993 578887544332 246677766655531 1111 2367777
Q ss_pred hhHHHHH
Q psy3716 382 IEVEFLI 388 (436)
Q Consensus 382 ~~ve~lv 388 (436)
++|..++
T Consensus 60 ~~i~~~l 66 (100)
T cd00592 60 KEIRELL 66 (100)
T ss_pred HHHHHHH
Confidence 7777555
No 133
>PF09202 Rio2_N: Rio2, N-terminal; InterPro: IPR015285 This N-terminal domain is found in RIO2 kinases, and is structurally homologous to the winged helix (wHTH) domain. It adopts a structure consisting of four alpha helices followed by two beta strands and a fifth alpha helix. The domain confers DNA binding properties to the protein, as per other winged helix domains []. ; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1TQP_A 1ZAR_A 1TQI_A 1ZAO_A 1TQM_A.
Probab=42.27 E-value=27 Score=28.49 Aligned_cols=48 Identities=19% Similarity=0.110 Sum_probs=36.5
Q ss_pred hccccCCcccccHHHHHHHcCCChhhHHHHHHHHHhcccceeeccccc
Q psy3716 358 AFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVD 405 (436)
Q Consensus 358 ~~lr~~~~r~~sf~~i~~~~~~~~~~ve~lvmka~s~~li~g~idqv~ 405 (436)
.++..++..-++++.|++.++++..+|+.-+-+-...|||.-..-..+
T Consensus 15 iE~gmk~hE~VP~~~I~~~s~l~~~~~~~~L~~L~~~kLv~~~~~~Y~ 62 (82)
T PF09202_consen 15 IEMGMKNHEWVPLELIEKISGLSEGEVEKRLKRLVKLKLVSRRNKPYD 62 (82)
T ss_dssp HHTTTTT-SSEEHHHHHHHHT--HHHHHHHHHHHHHTTSEEEE-SSS-
T ss_pred HHHcccCCccCCHHHHHHHhCcCHHHHHHHHHHHHhcCCccccCCCcc
Confidence 344456677999999999999999999999999999999998554443
No 134
>PF12569 NARP1: NMDA receptor-regulated protein 1 ; InterPro: IPR021183 This group represents N-terminal acetyltransferase A (NatA) auxiliary subunit and represents a non-catalytic component of the NatA N-terminal acetyltransferase, which catalyzes acetylation of proteins beginning with Met-Ser, Met-Gly and Met-Ala. N-terminal acetylation plays a role in normal eukaryotic translation and processing, protect against proteolytic degradation and protein turnover. NAT1 anchors ARD1 and NAT5 to the ribosome and may present the N- terminal of nascent polypeptides for acetylation [], [].
Probab=42.17 E-value=5e+02 Score=28.43 Aligned_cols=19 Identities=11% Similarity=0.146 Sum_probs=12.5
Q ss_pred hhHHHHHHHHHHHHHHHHH
Q psy3716 274 ANENKLSQKIALLCLMELA 292 (436)
Q Consensus 274 ~~~~~l~~KirLlaL~~L~ 292 (436)
..+.-|.+|+.+-+-++|.
T Consensus 344 DFH~Yc~RK~t~r~Y~~~L 362 (517)
T PF12569_consen 344 DFHSYCLRKMTLRAYVDML 362 (517)
T ss_pred cHHHHHHhhccHHHHHHHH
Confidence 4466677777776666665
No 135
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=42.02 E-value=53 Score=28.99 Aligned_cols=48 Identities=19% Similarity=0.126 Sum_probs=38.1
Q ss_pred HHHHHHHHhhcCCCCcccCHHHHHHHhCCChhhHHHHHHHHHhCCccccc
Q psy3716 285 LLCLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGH 334 (436)
Q Consensus 285 LlaL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~ 334 (436)
+.+++-++...| ...++-++||+.+++|..=|+..+-+.-..|||+.+
T Consensus 11 l~~~i~la~~~~--g~~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~ 58 (141)
T PRK11014 11 LRALIYMASLPE--GRMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAV 58 (141)
T ss_pred HHHHHHHhcCCC--CCccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEe
Confidence 344445554444 257899999999999999999999999999999764
No 136
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=41.74 E-value=51 Score=28.91 Aligned_cols=27 Identities=19% Similarity=0.051 Sum_probs=24.8
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
.+|+++||+.+|+|+.-|...+-+|+.
T Consensus 122 g~s~~EIA~~lgis~~tV~~~l~ra~~ 148 (161)
T PRK09047 122 DMDVAETAAAMGCSEGSVKTHCSRATH 148 (161)
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 689999999999999999999888764
No 137
>PHA02943 hypothetical protein; Provisional
Probab=41.66 E-value=71 Score=29.42 Aligned_cols=34 Identities=9% Similarity=-0.011 Sum_probs=30.4
Q ss_pred cccCHHHHHHHhCCChhhHHHHHHHHHhCCcccc
Q psy3716 300 HQLSFAEISEAAQLPLIEVEFLIIKALALGLVKG 333 (436)
Q Consensus 300 r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G 333 (436)
..-|-++||++||+|-.+|+..+.-.-+.|.|+-
T Consensus 23 G~~TtseIAkaLGlS~~qa~~~LyvLErEG~Vkr 56 (165)
T PHA02943 23 GCKTTSRIANKLGVSHSMARNALYQLAKEGMVLK 56 (165)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHHHHHcCceEE
Confidence 4788999999999999999999998888888774
No 138
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=41.62 E-value=52 Score=31.99 Aligned_cols=27 Identities=22% Similarity=0.155 Sum_probs=24.2
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
..|..+||+.++++..-|-....+|+.
T Consensus 225 ~~t~~eIA~~lgis~~~V~~~~~~al~ 251 (258)
T PRK08215 225 GKTQMEVAEEIGISQAQVSRLEKAALK 251 (258)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 579999999999999999998888775
No 139
>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=41.57 E-value=53 Score=31.50 Aligned_cols=28 Identities=14% Similarity=0.172 Sum_probs=24.7
Q ss_pred ccccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 366 HQLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 366 r~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
...|+++||+.++++.+-|..+.-+|+.
T Consensus 195 ~~~t~~EIA~~lgis~~~V~q~~~~al~ 222 (238)
T TIGR02393 195 RPHTLEEVGKEFNVTRERIRQIESKALR 222 (238)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4689999999999999999998877765
No 140
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=41.38 E-value=54 Score=33.39 Aligned_cols=28 Identities=14% Similarity=0.237 Sum_probs=24.7
Q ss_pred ccccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 366 HQLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 366 r~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
...|+++||+.++++.+-|...+.+|+.
T Consensus 281 e~~s~~EIA~~Lgis~~tV~~~~~rAl~ 308 (325)
T PRK05657 281 EAATLEDVAREIGLTRERVRQIQVEALR 308 (325)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3579999999999999999999888765
No 141
>PRK11569 transcriptional repressor IclR; Provisional
Probab=41.27 E-value=55 Score=32.23 Aligned_cols=47 Identities=21% Similarity=0.285 Sum_probs=38.4
Q ss_pred HHHHHHHHHHhhcCCCCcccCHHHHHHHhCCChhhHHHHHHHHHhCCccc
Q psy3716 283 IALLCLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVK 332 (436)
Q Consensus 283 irLlaL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~ 332 (436)
-|-+.++++.... .+.++..+||+++++|...|-.++-.....|+++
T Consensus 28 ~ral~IL~~l~~~---~~~~~lseia~~lglpksTv~RlL~tL~~~G~l~ 74 (274)
T PRK11569 28 TRGLKLLEWIAES---NGSVALTELAQQAGLPNSTTHRLLTTMQQQGFVR 74 (274)
T ss_pred HHHHHHHHHHHhC---CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 3555666655443 3579999999999999999999999999999995
No 142
>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=41.20 E-value=57 Score=24.01 Aligned_cols=36 Identities=25% Similarity=0.266 Sum_probs=32.3
Q ss_pred cCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccC
Q psy3716 302 LSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQ 337 (436)
Q Consensus 302 isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQ 337 (436)
+++.+|++.++++...+-..+=.....|+|...-+.
T Consensus 21 ~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~~~~ 56 (78)
T cd00090 21 LTVSELAERLGLSQSTVSRHLKKLEEAGLVESRREG 56 (78)
T ss_pred cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEEEec
Confidence 999999999999999999998888899999876554
No 143
>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=41.15 E-value=43 Score=28.96 Aligned_cols=63 Identities=22% Similarity=0.300 Sum_probs=45.7
Q ss_pred cccccHHHHHHHcCCChhhHHHHHHHHHhcccceeecccccceEEEeeecccccchhhhhHHHHH
Q psy3716 365 SHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPRVLSKDQVFWSLEE 429 (436)
Q Consensus 365 ~r~~sf~~i~~~~~~~~~~ve~lvmka~s~~li~g~idqv~~~v~~~wv~pr~l~~~q~~~~~~~ 429 (436)
+..+|.++||++.++|..-|...+-+--+.|+|++.- ..++...+.- .|.-.+..++...+++
T Consensus 23 ~~~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~~~-g~~ggy~l~~-~~~~it~~~v~~~l~~ 85 (130)
T TIGR02944 23 SQPYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTSKR-GVEGGYTLAR-APRDITVADIVKAVEG 85 (130)
T ss_pred CCCccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEecC-CCCCChhhcC-CccccCHHHHHHHHcC
Confidence 4579999999999999999999999999999997753 2333333321 4445556666666654
No 144
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=41.12 E-value=34 Score=30.08 Aligned_cols=38 Identities=29% Similarity=0.267 Sum_probs=34.9
Q ss_pred ccHHHHHHHcCCChhhHHHHHHHHHhcccceeeccccc
Q psy3716 368 LSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVD 405 (436)
Q Consensus 368 ~sf~~i~~~~~~~~~~ve~lvmka~s~~li~g~idqv~ 405 (436)
.|+.+||++.++|...|-.-|-|-...|+|+|.-=.++
T Consensus 23 ~~~~eia~~lglS~~~v~~Ri~~L~~~GiI~~~~~~v~ 60 (154)
T COG1522 23 ISNAELAERVGLSPSTVLRRIKRLEEEGVIKGYTAVLD 60 (154)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCceeeEEEEEC
Confidence 99999999999999999999999999999999755554
No 145
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=40.95 E-value=65 Score=32.23 Aligned_cols=52 Identities=33% Similarity=0.272 Sum_probs=46.2
Q ss_pred HHHHHHHHHHHHHhhcCCCCcccCHHHHHHHhCCChhhHHHHHHHHHhCCccccc
Q psy3716 280 SQKIALLCLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGH 334 (436)
Q Consensus 280 ~~KirLlaL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~ 334 (436)
.||=-|.||++|-.++ +|.+.=++||+.++-++.-|-.-++-.=++||++|+
T Consensus 7 ~QkeIL~aLi~LY~~~---~r~IKgeeIA~~l~rnpGTVRNqmq~LkaLgLVegv 58 (294)
T COG2524 7 SQKEILQALINLYRRK---KRPIKGEEIAEVLNRNPGTVRNQMQSLKALGLVEGV 58 (294)
T ss_pred HHHHHHHHHHHHHHhc---CCCcchHHHHHHHccCcchHHHHHHHHHhcCccccc
Confidence 4667789999998765 589999999999999999999999888899999987
No 146
>PF05331 DUF742: Protein of unknown function (DUF742); InterPro: IPR007995 This family consists of several uncharacterised Streptomyces proteins as well as one from Mycobacterium tuberculosis. The function of these proteins is unknown.
Probab=40.94 E-value=42 Score=29.20 Aligned_cols=41 Identities=37% Similarity=0.460 Sum_probs=34.9
Q ss_pred HHHHHHhhcCCCCcccCHHHHHHHhCCChhhHHHHHHHHHhCCcccc
Q psy3716 287 CLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKG 333 (436)
Q Consensus 287 aL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G 333 (436)
.+++||.. .+|..|||..+++|..=|--|+=+.+..|+|.-
T Consensus 47 ~Il~lC~~------~~SVAEiAA~L~lPlgVvrVLvsDL~~~G~v~v 87 (114)
T PF05331_consen 47 AILELCRR------PLSVAEIAARLGLPLGVVRVLVSDLADAGLVRV 87 (114)
T ss_pred HHHHHHCC------CccHHHHHHhhCCCchhhhhhHHHHHhCCCEEE
Confidence 35567743 599999999999999999999999999998864
No 147
>PF05158 RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; InterPro: IPR007832 The family comprises a subunit specific to RNA Pol III, the tRNA specific polymerase. The C34 subunit of Saccharomyces cerevisiae RNA Pol III is part of a subcomplex of three subunits which have no counterpart in the other two nuclear RNA polymerases. This subunit interacts with TFIIIB70 and therefore participates in Pol III recruitment [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2DK8_A 2DK5_A 2YU3_A.
Probab=40.73 E-value=1.2e+02 Score=31.12 Aligned_cols=110 Identities=15% Similarity=0.173 Sum_probs=72.5
Q ss_pred CcccCHHHHHHH-hCCChhhHHHHHHHHHhCCcccccccCCccEEEEEeccc------cccccchh---hccccCCcccc
Q psy3716 299 SHQLSFAEISEA-AQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQP------RVLSKDQL---AFKKIPGSHQL 368 (436)
Q Consensus 299 ~r~isf~~Ia~~-l~i~~~eVE~lvikAi~~gLI~G~IDQv~~~v~vtwv~p------RvL~l~Qi---~~lr~~~~r~~ 368 (436)
.+.++.++|.+. .+.+..++...+=..++.|+++..= .++.+...++.+ +-|+..|- .-+..+.+.-+
T Consensus 24 ~~~~~~~~L~~~~~~~~~~~~~~~in~Ll~~~~~~~~~--~~~~l~~~~~~~~~a~k~~~l~~~e~lvy~~I~~ag~~GI 101 (327)
T PF05158_consen 24 PKGFSQEDLQQLIPGLDLQELVKAINELLSSGLLKLLK--KGGGLSYKAVSEEEAKKLKGLSDEERLVYQLIEEAGNKGI 101 (327)
T ss_dssp SS-EEHHHHHHH-TTS-HHHHHHHHHHHHHHTSEEEEE---SSSEEEEE--SSS-----SSSCCHHHHHHHHHHHTTT-E
T ss_pred CCCcCHHHHHhhcCCCCHHHHHHHHHHHHhCCCEEEEE--cCCEEEEEEeCHHHHhhhcCCCHHHHHHHHHHHHhCCCCC
Confidence 378999999999 5678888888888999999998754 444455555432 34444442 23444567789
Q ss_pred cHHHHHHHcCCChhhHHHHHHHHHhccccee--ecccccceEEE
Q psy3716 369 SFAEISEAAQLPLIEVEFLIIKALALGLVKG--HIDQVDESFNV 410 (436)
Q Consensus 369 sf~~i~~~~~~~~~~ve~lvmka~s~~li~g--~idqv~~~v~~ 410 (436)
.-.+|..+|+++...|...+-.--+.||||- .+..-.++++|
T Consensus 102 w~~~i~~~t~l~~~~~~k~lk~Le~k~lIK~vksv~~~~rK~Ym 145 (327)
T PF05158_consen 102 WTKDIKKKTNLHQTQLTKILKSLESKKLIKSVKSVKNPNRKVYM 145 (327)
T ss_dssp EHHHHHHHCT--HHHHHHHHHHHHHTTSEEEE--SS-SS--EEE
T ss_pred cHHHHHHHcCCCHHHHHHHHHHHHhCCCEEEecCcCCCCeEEEE
Confidence 9999999999999999998877778899985 44454556655
No 148
>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=40.67 E-value=46 Score=23.65 Aligned_cols=33 Identities=27% Similarity=0.315 Sum_probs=29.1
Q ss_pred ccccHHHHHHHcCCChhhHHHHHHHHHhcccce
Q psy3716 366 HQLSFAEISEAAQLPLIEVEFLIIKALALGLVK 398 (436)
Q Consensus 366 r~~sf~~i~~~~~~~~~~ve~lvmka~s~~li~ 398 (436)
+..++.+|++.++++..-|-+=+=+-...|+|+
T Consensus 14 ~~~~~~el~~~l~~s~~~vs~hL~~L~~~glV~ 46 (47)
T PF01022_consen 14 GPLTVSELAEELGLSQSTVSHHLKKLREAGLVE 46 (47)
T ss_dssp SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred CCCchhhHHHhccccchHHHHHHHHHHHCcCee
Confidence 568999999999999999999998888888885
No 149
>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=40.46 E-value=65 Score=24.04 Aligned_cols=42 Identities=21% Similarity=0.237 Sum_probs=33.0
Q ss_pred HHHHHHHhhcCCCCcccCHHHHHHHhCCChhhHHHHHHHHHhCCcc
Q psy3716 286 LCLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALALGLV 331 (436)
Q Consensus 286 laL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI 331 (436)
-.++++...+ +.++.+++|+.++++..-+-.=+.+.-..|+|
T Consensus 3 ~~Il~~l~~~----~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~i 44 (57)
T PF08220_consen 3 QQILELLKEK----GKVSVKELAEEFGVSEMTIRRDLNKLEKQGLI 44 (57)
T ss_pred HHHHHHHHHc----CCEEHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence 3455555544 58999999999999999888888877777774
No 150
>COG5631 Predicted transcription regulator, contains HTH domain (MarR family) [Transcription]
Probab=40.41 E-value=50 Score=30.69 Aligned_cols=102 Identities=20% Similarity=0.188 Sum_probs=69.6
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCCccEEEEEecccc--------ccccchhhcc--ccCCcccccH
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPR--------VLSKDQLAFK--KIPGSHQLSF 370 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv~~~v~vtwv~pR--------vL~l~Qi~~l--r~~~~r~~sf 370 (436)
.++=.-+++.+.....|||+-+|.|-.+ .++++-| .++..++.-+ -...+|.-++
T Consensus 37 ivssaHLa~~~sp~~sEvEyaL~~ay~A---------------f~rW~vrCmAaag~~~ls~~e~l~lH~irhrdR~K~l 101 (199)
T COG5631 37 IVSSAHLARTLSPDVSEVEYALMRAYEA---------------FGRWQVRCMAAAGEFSLSGPENLLLHIIRHRDRPKSL 101 (199)
T ss_pred hhhHHHHHhcCCccHHHHHHHHHHHHHH---------------HHHHHHHHHHHhcCCCCcchHHHHHHHHhhcCchhhH
Confidence 3455667777777788999888766432 1122222 3333332222 2245799999
Q ss_pred HHHHHHcCC-ChhhHHHHHHHHHhcccceeecccccceEEEeeecccc
Q psy3716 371 AEISEAAQL-PLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPRV 417 (436)
Q Consensus 371 ~~i~~~~~~-~~~~ve~lvmka~s~~li~g~idqv~~~v~~~wv~pr~ 417 (436)
.+||+.+++ +.--|-+-+-|-+..|||.|.=..-+.++.+|-.-.|+
T Consensus 102 aDic~~ln~eDth~itYslrKL~k~gLit~t~~gkevTy~vTa~G~~a 149 (199)
T COG5631 102 ADICQMLNREDTHNITYSLRKLLKGGLITRTGSGKEVTYEVTALGHRA 149 (199)
T ss_pred HHHHHHhccccchhHHHHHHHHHhccceecCCCCceEEEEEecchHHH
Confidence 999999988 44567888999999999999988888788887655544
No 151
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=40.36 E-value=59 Score=32.00 Aligned_cols=47 Identities=21% Similarity=0.133 Sum_probs=38.0
Q ss_pred HHHHHHHHHHhhcCCCCcccCHHHHHHHhCCChhhHHHHHHHHHhCCccc
Q psy3716 283 IALLCLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVK 332 (436)
Q Consensus 283 irLlaL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~ 332 (436)
-|-+.++++.... .+.+++.+||+++++|..-|-.++-.....|++.
T Consensus 25 ~r~l~IL~~~~~~---~~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~ 71 (271)
T PRK10163 25 ERGIAILQYLEKS---GGSSSVSDISLNLDLPLSTTFRLLKVLQAADFVY 71 (271)
T ss_pred HHHHHHHHHHHhC---CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 3556666655433 2579999999999999999999999999999984
No 152
>KOG0687|consensus
Probab=40.33 E-value=28 Score=35.84 Aligned_cols=46 Identities=15% Similarity=0.242 Sum_probs=44.2
Q ss_pred ccccHHHHHHHcCCChhhHHHHHHHHHhcccceeecccccceEEEe
Q psy3716 366 HQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVT 411 (436)
Q Consensus 366 r~~sf~~i~~~~~~~~~~ve~lvmka~s~~li~g~idqv~~~v~~~ 411 (436)
|++|.+-.|+..|++.+=|+.=+-+-+..|=.-|+||-|+|.|..+
T Consensus 316 rsl~l~~MA~aFgVSVefiDreL~rFI~~grL~ckIDrVnGVVEtN 361 (393)
T KOG0687|consen 316 RSLTLESMAKAFGVSVEFIDRELGRFIAAGRLHCKIDRVNGVVETN 361 (393)
T ss_pred HHHHHHHHHHHhCchHHHHHhHHHHhhccCceeeeeecccceeecC
Confidence 7899999999999999999999999999999999999999999876
No 153
>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=40.33 E-value=1.5e+02 Score=26.51 Aligned_cols=28 Identities=25% Similarity=0.197 Sum_probs=24.3
Q ss_pred cccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 300 HQLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 300 r~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
...|+++||+.+++|+.-|...+-+|..
T Consensus 115 ~g~s~~eIA~~lgis~~tV~~~l~Rar~ 142 (170)
T TIGR02959 115 EGLSQQEIAEKLGLSLSGAKSRVQRGRK 142 (170)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3699999999999999999999877653
No 154
>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=40.30 E-value=84 Score=23.59 Aligned_cols=66 Identities=9% Similarity=0.102 Sum_probs=39.9
Q ss_pred CHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCCccEEEEEeccccccccchhhccccCCcccccHHHHHHHcCCChh
Q psy3716 303 SFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPRVLSKDQLAFKKIPGSHQLSFAEISEAAQLPLI 382 (436)
Q Consensus 303 sf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv~~~v~vtwv~pRvL~l~Qi~~lr~~~~r~~sf~~i~~~~~~~~~ 382 (436)
+..++|+.++|+...+-.|.-+ .|++...-+. -.+|.++..++..++ .....- ..|+|++
T Consensus 2 s~~eva~~~gvs~~tlr~w~~~---~g~~~~~r~~---------~~~r~yt~~~v~~l~-------~i~~l~-~~g~~l~ 61 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAWERR---YGLPAPQRTD---------GGHRLYSEADVARLR-------LIRRLT-SEGVRIS 61 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHh---CCCCCCCcCC---------CCCeecCHHHHHHHH-------HHHHHH-HCCCCHH
Confidence 6789999999999999999732 2444332111 134666666655542 111112 3677777
Q ss_pred hHHHHH
Q psy3716 383 EVEFLI 388 (436)
Q Consensus 383 ~ve~lv 388 (436)
++..++
T Consensus 62 ~i~~~~ 67 (68)
T cd01104 62 QAAALA 67 (68)
T ss_pred HHHHHh
Confidence 776554
No 155
>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=40.14 E-value=86 Score=23.79 Aligned_cols=45 Identities=20% Similarity=0.214 Sum_probs=35.8
Q ss_pred HHHHHHHHHhhcCCCCcccCHHHHHHHhCCChhhHHHHHHHHHhCCccc
Q psy3716 284 ALLCLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVK 332 (436)
Q Consensus 284 rLlaL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~ 332 (436)
.|.++.+|... ...++-.+||+.++++..-|=..+=+.-..|+|+
T Consensus 9 YL~~Iy~l~~~----~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV~ 53 (60)
T PF01325_consen 9 YLKAIYELSEE----GGPVRTKDIAERLGVSPPTVTEMLKRLAEKGLVE 53 (60)
T ss_dssp HHHHHHHHHHC----TSSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHcC----CCCccHHHHHHHHCCChHHHHHHHHHHHHCCCEE
Confidence 45566666653 3689999999999999999999999998999885
No 156
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=40.13 E-value=49 Score=22.76 Aligned_cols=33 Identities=24% Similarity=0.184 Sum_probs=29.9
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHhCCcccc
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALALGLVKG 333 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G 333 (436)
.++..+||+.++++...|-..+-+....|+|+-
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~~ 40 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLEKEGLISR 40 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 478999999999999999999999999999863
No 157
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 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 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; 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: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=39.61 E-value=28 Score=27.16 Aligned_cols=28 Identities=21% Similarity=0.156 Sum_probs=21.3
Q ss_pred CCcccccHHHHHHHcCCChhhHHHHHHH
Q psy3716 363 PGSHQLSFAEISEAAQLPLIEVEFLIIK 390 (436)
Q Consensus 363 ~~~r~~sf~~i~~~~~~~~~~ve~lvmk 390 (436)
...|.-|-+|||+.++++.++|..++-.
T Consensus 16 ~lgr~Pt~eEiA~~lgis~~~v~~~l~~ 43 (78)
T PF04539_consen 16 ELGREPTDEEIAEELGISVEEVRELLQA 43 (78)
T ss_dssp HHSS--BHHHHHHHHTS-HHHHHHHHHH
T ss_pred HhCCCCCHHHHHHHHcccHHHHHHHHHh
Confidence 3468899999999999999999977654
No 158
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=39.50 E-value=1.9e+02 Score=26.30 Aligned_cols=27 Identities=11% Similarity=0.086 Sum_probs=23.8
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
.+|+++||+.+|+|..-|...+=+|..
T Consensus 147 g~s~~EIAe~lgis~~~V~~~l~Ra~~ 173 (189)
T PRK06811 147 GEKIEEIAKKLGLTRSAIDNRLSRGRK 173 (189)
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 589999999999999999998876653
No 159
>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=39.35 E-value=51 Score=22.19 Aligned_cols=30 Identities=20% Similarity=0.232 Sum_probs=24.5
Q ss_pred ccHHHHHHHcCCChhhHHHHHHHHHhcccc
Q psy3716 368 LSFAEISEAAQLPLIEVEFLIIKALALGLV 397 (436)
Q Consensus 368 ~sf~~i~~~~~~~~~~ve~lvmka~s~~li 397 (436)
+|-++||+.++++.+-|-..+-|--..|||
T Consensus 3 mtr~diA~~lG~t~ETVSR~l~~l~~~glI 32 (32)
T PF00325_consen 3 MTRQDIADYLGLTRETVSRILKKLERQGLI 32 (32)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred cCHHHHHHHhCCcHHHHHHHHHHHHHcCCC
Confidence 678999999999999999999888887775
No 160
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=39.23 E-value=80 Score=25.02 Aligned_cols=42 Identities=21% Similarity=0.196 Sum_probs=31.6
Q ss_pred cccCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCCccEEEEE
Q psy3716 300 HQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVT 345 (436)
Q Consensus 300 r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv~~~v~vt 345 (436)
...++.+|+..+++|...+...+=.....|||++ .++.+.+|
T Consensus 18 ~~~~~t~i~~~~~L~~~~~~~yL~~L~~~gLI~~----~~~~Y~lT 59 (77)
T PF14947_consen 18 GGAKKTEIMYKANLNYSTLKKYLKELEEKGLIKK----KDGKYRLT 59 (77)
T ss_dssp T-B-HHHHHTTST--HHHHHHHHHHHHHTTSEEE----ETTEEEE-
T ss_pred CCCCHHHHHHHhCcCHHHHHHHHHHHHHCcCeeC----CCCEEEEC
Confidence 4688999999999999999999999999999954 45555554
No 161
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=39.20 E-value=31 Score=25.16 Aligned_cols=24 Identities=13% Similarity=0.037 Sum_probs=20.7
Q ss_pred cccCHHHHHHHhCCChhhHHHHHH
Q psy3716 300 HQLSFAEISEAAQLPLIEVEFLII 323 (436)
Q Consensus 300 r~isf~~Ia~~l~i~~~eVE~lvi 323 (436)
..-...+||..++++...|..|.-
T Consensus 26 ~~~~~~~la~~l~l~~~~V~~WF~ 49 (57)
T PF00046_consen 26 SKEEREELAKELGLTERQVKNWFQ 49 (57)
T ss_dssp HHHHHHHHHHHHTSSHHHHHHHHH
T ss_pred cccccccccccccccccccccCHH
Confidence 356688999999999999999974
No 162
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=38.94 E-value=85 Score=28.03 Aligned_cols=60 Identities=15% Similarity=0.161 Sum_probs=47.8
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHhcccceeecccccceEEEeeecccccchhhhhHHHHHHHhhcc
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPRVLSKDQVFWSLEETVATEV 435 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s~~li~g~idqv~~~v~~~wv~pr~l~~~q~~~~~~~~~~~~~ 435 (436)
..-|.+||+..+=+.+.|=.++++-|+ ..|+||. +.+.|+ --++.++++..|+.-+.+=|
T Consensus 39 i~Nf~~Ia~~L~R~~~~v~ky~~~ELg---t~g~i~~--~rlii~----G~~~~~~i~~~L~~yI~~yV 98 (133)
T TIGR00311 39 IQNFREVAKALNRDEQHLLKYLLKELG---TAGNLEG--GRLILQ----GKFTHFLLNERIEDYVRKYV 98 (133)
T ss_pred EecHHHHHHHHCCCHHHHHHHHHHHhC---CCceecC--CEEEEE----eecCHHHHHHHHHHHHhheE
Confidence 346999999999999999999999999 8899984 444333 45788888888887766544
No 163
>PF00403 HMA: Heavy-metal-associated domain; InterPro: IPR006121 Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures. These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases []. A conserved domain has been found in a number of these heavy metal transport or detoxification proteins []. The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding. Structure solution of the fourth HMA domain of the Menke's copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel beta-sheet and two alpha helices packed in an alpha-beta sandwich fold []. This fold is common to other domains and is classified as "ferredoxin-like".; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2VOY_A 1P6T_A 1KQK_A 2RML_A 1JWW_A 3K7R_F 1FES_A 1CC8_A 1FD8_A 2GGP_A ....
Probab=38.75 E-value=63 Score=23.86 Aligned_cols=45 Identities=20% Similarity=0.271 Sum_probs=36.4
Q ss_pred HHHHHHHHhc--ccceeecccccceEEEeeecccccchhhhhHHHHHH
Q psy3716 385 EFLIIKALAL--GLVKGHIDQVDESFNVTWVQPRVLSKDQVFWSLEET 430 (436)
Q Consensus 385 e~lvmka~s~--~li~g~idqv~~~v~~~wv~pr~l~~~q~~~~~~~~ 430 (436)
..-|.+|++. |.-.-.+|-.+++|.|+|-.|+ .+.++|...++++
T Consensus 13 ~~~v~~~l~~~~GV~~v~vd~~~~~v~v~~~~~~-~~~~~i~~~i~~~ 59 (62)
T PF00403_consen 13 AKKVEKALSKLPGVKSVKVDLETKTVTVTYDPDK-TSIEKIIEAIEKA 59 (62)
T ss_dssp HHHHHHHHHTSTTEEEEEEETTTTEEEEEESTTT-SCHHHHHHHHHHT
T ss_pred HHHHHHHHhcCCCCcEEEEECCCCEEEEEEecCC-CCHHHHHHHHHHh
Confidence 3445566665 7778899999999999999888 8889999888763
No 164
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=38.54 E-value=76 Score=30.50 Aligned_cols=90 Identities=23% Similarity=0.246 Sum_probs=49.0
Q ss_pred cccCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCC---ccEEEEEecccc-----ccc---cch-hhccccC----
Q psy3716 300 HQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQV---DESFNVTWVQPR-----VLS---KDQ-LAFKKIP---- 363 (436)
Q Consensus 300 r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv---~~~v~vtwv~pR-----vL~---l~Q-i~~lr~~---- 363 (436)
|.-+.++||+.+|++.++|..+...+..... .++|.. ++...+ ..+. ... ..+ +..+.++
T Consensus 116 ~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~--~SLd~~~~~~~~~~~--~~~~~~~~~~~~~~~l~~~l~~L~~~er~v 191 (231)
T PRK12427 116 HEPNFEEISAELNLTAEEYQEYLLLENAGTL--ESLDELLALEAHNDI--LQSRDLEENIIIEDNLKQALSQLDEREQLI 191 (231)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHhccCCc--eeccCcccCCCcccc--cCCCCHHHHHHHHHHHHHHHHcCCHHHHHH
Confidence 5678999999999999999887543222111 123322 000000 0000 000 001 1111111
Q ss_pred ----CcccccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 364 ----GSHQLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 364 ----~~r~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
-....|+++||+.++++..-|-.+.-+|+.
T Consensus 192 i~l~~~~~~t~~EIA~~lgis~~~V~q~~~~~~~ 225 (231)
T PRK12427 192 LHLYYQHEMSLKEIALVLDLTEARICQLNKKIAQ 225 (231)
T ss_pred HHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 012688999999999999988766666553
No 165
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=38.01 E-value=1.8e+02 Score=30.67 Aligned_cols=34 Identities=21% Similarity=0.309 Sum_probs=31.7
Q ss_pred CcccCHHHHHHHhCCChhhHHHHHHHHHhCCccc
Q psy3716 299 SHQLSFAEISEAAQLPLIEVEFLIIKALALGLVK 332 (436)
Q Consensus 299 ~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~ 332 (436)
.+.+|.++|++++++|.++|+.++=+-...|+|.
T Consensus 308 g~~~t~~~La~~l~~~~~~v~~iL~~L~~agLI~ 341 (412)
T PRK04214 308 GKALDVDEIRRLEPMGYDELGELLCELARIGLLR 341 (412)
T ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCeE
Confidence 3688999999999999999999999999999996
No 166
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=37.83 E-value=38 Score=29.59 Aligned_cols=27 Identities=19% Similarity=0.342 Sum_probs=24.9
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
..|+++||+.+|+|..-|...+-+|+.
T Consensus 122 ~~s~~EIA~~l~is~~tV~~~~~ra~~ 148 (154)
T PRK06759 122 GKTMGEIALETEMTYYQVRWIYRQALE 148 (154)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 689999999999999999999988864
No 167
>KOG1498|consensus
Probab=37.78 E-value=83 Score=33.24 Aligned_cols=50 Identities=20% Similarity=0.348 Sum_probs=46.1
Q ss_pred ccccHHHHHHHcCCChhhHHHHHHHHHhcccceeecccccceEEEeeecc
Q psy3716 366 HQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQP 415 (436)
Q Consensus 366 r~~sf~~i~~~~~~~~~~ve~lvmka~s~~li~g~idqv~~~v~~~wv~p 415 (436)
..+||.++++-.++|.++.|-++-.-.-.|-+.++||+-.+++++.-++-
T Consensus 352 SrIt~~rl~eLLdl~~ee~E~~LS~lv~t~ti~aKidrpsgII~F~k~K~ 401 (439)
T KOG1498|consen 352 SRITLKRLAELLDLPVEEMEKFLSDLVVTGTIYAKIDRPSGIINFQKVKD 401 (439)
T ss_pred hhccHHHHHHHhCCCHHHHHHHHHHHHhccceEEEecCCCceEEEEeccc
Confidence 46999999999999999999999999999999999999999998876653
No 168
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=37.73 E-value=26 Score=29.92 Aligned_cols=42 Identities=24% Similarity=0.189 Sum_probs=28.8
Q ss_pred ccccchhhccccCCcccccHHHHHHHcCCChhhHHHHHHHHH
Q psy3716 351 VLSKDQLAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKAL 392 (436)
Q Consensus 351 vL~l~Qi~~lr~~~~r~~sf~~i~~~~~~~~~~ve~lvmka~ 392 (436)
.|+..|..-+.-.-...+|++|||+.++++-.-|--.+-||-
T Consensus 17 LLT~kQ~~~l~lyy~eDlSlsEIAe~~~iSRqaV~d~ikr~~ 58 (101)
T PF04297_consen 17 LLTEKQREILELYYEEDLSLSEIAEELGISRQAVYDSIKRAE 58 (101)
T ss_dssp GS-HHHHHHHHHHCTS---HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred HCCHHHHHHHHHHHccCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 455666666655556789999999999999999988887765
No 169
>PF12569 NARP1: NMDA receptor-regulated protein 1 ; InterPro: IPR021183 This group represents N-terminal acetyltransferase A (NatA) auxiliary subunit and represents a non-catalytic component of the NatA N-terminal acetyltransferase, which catalyzes acetylation of proteins beginning with Met-Ser, Met-Gly and Met-Ala. N-terminal acetylation plays a role in normal eukaryotic translation and processing, protect against proteolytic degradation and protein turnover. NAT1 anchors ARD1 and NAT5 to the ribosome and may present the N- terminal of nascent polypeptides for acetylation [], [].
Probab=37.63 E-value=5.3e+02 Score=28.25 Aligned_cols=114 Identities=11% Similarity=0.161 Sum_probs=69.9
Q ss_pred ccchhHHHHHHHHHHHHhhccCchhHHHHHHHHhccCCCHHHHHHHHHHHHH----hhcC-------------CcchhHH
Q psy3716 57 QKEGELRDLYHKFVISFETKINPVSLMEIMEVITNHLSDQEEALVLLQSFED----KVKN-------------NLEAKSL 119 (436)
Q Consensus 57 ~~~~~~~~ly~~fI~~f~~kin~l~l~~i~~~v~~~~~d~~~aL~~L~~l~~----~l~~-------------~~ea~~~ 119 (436)
.+|+++....+.||...-.|==|.-++.+--. +.|+.. ...+..+.. .+.. .+.+.+.
T Consensus 121 ~~g~~F~~~~~~yl~~~l~KgvPslF~~lk~L----y~d~~K-~~~i~~l~~~~~~~l~~~~~~~~~~~~~~~~p~~~lw 195 (517)
T PF12569_consen 121 LEGDEFKERLDEYLRPQLRKGVPSLFSNLKPL----YKDPEK-AAIIESLVEEYVNSLESNGSFSNGDDEEKEPPSTLLW 195 (517)
T ss_pred CCHHHHHHHHHHHHHHHHhcCCchHHHHHHHH----HcChhH-HHHHHHHHHHHHHhhcccCCCCCccccccCCchHHHH
Confidence 34677778888888888777555556555332 224432 334444333 3311 1122455
Q ss_pred HHHHHHHHhhccCCCCCCChHHHHHHHHHHHHHHhcccChhHHHHHHHHHHHHHHHHhhcHHHHHHHH
Q psy3716 120 CKILQAQMIMNKDADKPGSLDEVEKLIDEIELLVNDIEGVTAIHSRFYLVASTLYRKQAKLSLYYRTA 187 (436)
Q Consensus 120 ~~~~i~~~~l~~~~~~~~~l~~~~~~L~~~~~~L~~~~~~~~v~~~~y~~~a~~~k~~~~~~~~Y~~~ 187 (436)
+..-+|+++-. .|+++.+- +.+++-|+.. +....+|.+-+..+|..|++.+....+
T Consensus 196 ~~~~lAqhyd~-----~g~~~~Al---~~Id~aI~ht----Pt~~ely~~KarilKh~G~~~~Aa~~~ 251 (517)
T PF12569_consen 196 TLYFLAQHYDY-----LGDYEKAL---EYIDKAIEHT----PTLVELYMTKARILKHAGDLKEAAEAM 251 (517)
T ss_pred HHHHHHHHHHH-----hCCHHHHH---HHHHHHHhcC----CCcHHHHHHHHHHHHHCCCHHHHHHHH
Confidence 66667788777 88988554 4455555543 334568999999999999988877653
No 170
>KOG2047|consensus
Probab=37.48 E-value=2.5e+02 Score=31.78 Aligned_cols=102 Identities=11% Similarity=0.118 Sum_probs=64.4
Q ss_pred HHHHHHHHhhhHHHHHHHHHHHhcCccccc--chhHHHHHHHH---HHHHhhccCchhHHHHHHHHhccCCCHHHHHHHH
Q psy3716 29 LNLEELYNKKLWHQLTLAVLAFVQNPAIQK--EGELRDLYHKF---VISFETKINPVSLMEIMEVITNHLSDQEEALVLL 103 (436)
Q Consensus 29 ~~l~~l~~~KLWhQLT~~l~~~~~~p~~~~--~~~~~~ly~~f---I~~f~~kin~l~l~~i~~~v~~~~~d~~~aL~~L 103 (436)
+-++-|.+..+|-+-...+...++++.|.+ |+.-..+|..+ |+...+++-.+.+-.|+..-.+.++|.
T Consensus 174 eyie~L~~~d~~~eaa~~la~vln~d~f~sk~gkSn~qlw~elcdlis~~p~~~~slnvdaiiR~gi~rftDq------- 246 (835)
T KOG2047|consen 174 EYIEYLAKSDRLDEAAQRLATVLNQDEFVSKKGKSNHQLWLELCDLISQNPDKVQSLNVDAIIRGGIRRFTDQ------- 246 (835)
T ss_pred HHHHHHHhccchHHHHHHHHHhcCchhhhhhcccchhhHHHHHHHHHHhCcchhcccCHHHHHHhhcccCcHH-------
Confidence 346667888999999999999999998875 33333444433 222234444444444444443333222
Q ss_pred HHHHHhhcCCcchhHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHHHHHhc
Q psy3716 104 QSFEDKVKNNLEAKSLCKILQAQMIMNKDADKPGSLDEVEKLIDEIELLVND 155 (436)
Q Consensus 104 ~~l~~~l~~~~ea~~~~~~~i~~~~l~~~~~~~~~l~~~~~~L~~~~~~L~~ 155 (436)
.-.+-+..|.++++ .|.++.|+.+.++.-...-.
T Consensus 247 -------------~g~Lw~SLAdYYIr-----~g~~ekarDvyeeai~~v~t 280 (835)
T KOG2047|consen 247 -------------LGFLWCSLADYYIR-----SGLFEKARDVYEEAIQTVMT 280 (835)
T ss_pred -------------HHHHHHHHHHHHHH-----hhhhHHHHHHHHHHHHhhee
Confidence 22333567889998 99999999998876555433
No 171
>PRK09954 putative kinase; Provisional
Probab=37.32 E-value=1e+02 Score=31.41 Aligned_cols=45 Identities=20% Similarity=0.272 Sum_probs=37.8
Q ss_pred cccCHHHHHHHhCCChhhHHHHHHHHHhCCccccc---ccCCccEEEE
Q psy3716 300 HQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGH---IDQVDESFNV 344 (436)
Q Consensus 300 r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~---IDQv~~~v~v 344 (436)
..+|.++||+.++++...|...+-+....|.|+|+ +|.....+.|
T Consensus 16 ~~~s~~~la~~l~~s~~~v~~~i~~L~~~g~i~~~~~~l~~~~~v~vi 63 (362)
T PRK09954 16 PLIQQNEIADILQISRSRVAAHIMDLMRKGRIKGKGYILTEQEYCVVV 63 (362)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCcCCcEEEEcCCccEEEE
Confidence 37999999999999999999999999999999884 5555544433
No 172
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=37.15 E-value=1.2e+02 Score=25.61 Aligned_cols=50 Identities=14% Similarity=0.129 Sum_probs=41.7
Q ss_pred cccCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCCccEEEEEeccc
Q psy3716 300 HQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQP 349 (436)
Q Consensus 300 r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv~~~v~vtwv~p 349 (436)
..++..+||+.++++..-|=..|=+....|+|...-|..++....-..+|
T Consensus 41 ~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~LT~ 90 (118)
T TIGR02337 41 GSMEFTQLANQACILRPSLTGILARLERDGLVTRLKASNDQRRVYISLTP 90 (118)
T ss_pred CCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeccCCCCCCeeEEEECH
Confidence 36899999999999999999999999999999999888776554444444
No 173
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=37.01 E-value=50 Score=23.13 Aligned_cols=27 Identities=19% Similarity=0.155 Sum_probs=23.5
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
..++.+||+.++++...|...+-++..
T Consensus 18 g~s~~eia~~l~is~~tv~~~~~~~~~ 44 (58)
T smart00421 18 GLTNKEIAERLGISEKTVKTHLSNIMR 44 (58)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 479999999999999999998877643
No 174
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=36.51 E-value=30 Score=31.08 Aligned_cols=31 Identities=19% Similarity=0.155 Sum_probs=26.1
Q ss_pred ccccCCcccccHHHHHHHcCCChhhHHHHHH
Q psy3716 359 FKKIPGSHQLSFAEISEAAQLPLIEVEFLII 389 (436)
Q Consensus 359 ~lr~~~~r~~sf~~i~~~~~~~~~~ve~lvm 389 (436)
+++....|..|..+|+++|+++.+.|..||=
T Consensus 38 yLr~~p~~~ati~eV~e~tgVs~~~I~~~Ir 68 (137)
T TIGR03826 38 FLRKHENRQATVSEIVEETGVSEKLILKFIR 68 (137)
T ss_pred HHHHCCCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 4555566789999999999999999988874
No 175
>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=36.49 E-value=54 Score=25.30 Aligned_cols=67 Identities=22% Similarity=0.238 Sum_probs=40.8
Q ss_pred HHHHHHhCCCh---hhHHHHHHHHHhCCcccccccCCccEEEEEeccccccccchhhccccCCcccccHHHHHHHcCCCh
Q psy3716 305 AEISEAAQLPL---IEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPRVLSKDQLAFKKIPGSHQLSFAEISEAAQLPL 381 (436)
Q Consensus 305 ~~Ia~~l~i~~---~eVE~lvikAi~~gLI~G~IDQv~~~v~vtwv~pRvL~l~Qi~~lr~~~~r~~sf~~i~~~~~~~~ 381 (436)
..|+..|++|. +.-..+.-++...|+.+|+= |..+.-.=+-.-..-.+-..|+.+|++.++++.
T Consensus 2 ~r~~~~L~L~~~v~~~A~~i~~~~~~~~~~~Gr~-------------~~~iaAA~iY~acr~~~~~~t~~eIa~~~~Vs~ 68 (71)
T PF00382_consen 2 PRICSKLGLPEDVRERAKEIYKKAQERGLLKGRS-------------PESIAAACIYLACRLNGVPRTLKEIAEAAGVSE 68 (71)
T ss_dssp HHHHHHTT--HHHHHHHHHHHHHHHHTTTSTTS--------------HHHHHHHHHHHHHHHTTSSSSHHHHHHHCTSSH
T ss_pred hHHHhHcCCCHHHHHHHHHHHHHHHHcCCcccCC-------------HHHHHHHHHHHHHHHcCCCcCHHHHHHHhCCCC
Confidence 56899999986 35667788889999999962 222211111111111223579999999999887
Q ss_pred hhH
Q psy3716 382 IEV 384 (436)
Q Consensus 382 ~~v 384 (436)
.++
T Consensus 69 ~tI 71 (71)
T PF00382_consen 69 KTI 71 (71)
T ss_dssp HHH
T ss_pred CcC
Confidence 654
No 176
>KOG3151|consensus
Probab=36.45 E-value=4.4e+02 Score=26.13 Aligned_cols=179 Identities=16% Similarity=0.137 Sum_probs=106.2
Q ss_pred ChHHHHHHHHHHHHHHhcccCh-------------hHHHHHHHHHHHHHHHHhhcHHHHHHHHHHHhccC-CCC-CCChh
Q psy3716 138 SLDEVEKLIDEIELLVNDIEGV-------------TAIHSRFYLVASTLYRKQAKLSLYYRTALRYLGCV-DLN-DLTAS 202 (436)
Q Consensus 138 ~l~~~~~~L~~~~~~L~~~~~~-------------~~v~~~~y~~~a~~~k~~~~~~~~Y~~~L~yL~~~-~~~-~l~~~ 202 (436)
|+..|.+.|+.++=-|-..+.. -...|..|.++...-=...|+..|-+++-.---|+ +.. -++++
T Consensus 17 d~~aC~klL~~lKveL~K~n~l~~~~~~~~~~k~~l~~aR~ilEi~vl~SI~t~D~~sFerY~~Qlk~YY~d~~~~l~~S 96 (260)
T KOG3151|consen 17 DLVACEKLLDQLKVELTKNNLLPPDLNISDIDKQQLIIARDILEIGVLLSILTKDFESFERYMNQLKPYYFDYNEKLSES 96 (260)
T ss_pred cHHHHHHHHhHHHHHHHHHhcCCCCcccchhhHHHHHHHHHHHHHHHHHHHHhccHHHHHHHHHHhcchhcccccccCcc
Confidence 8999999999776555332210 13456788887776666788888877766644443 443 36777
Q ss_pred HHHHHHHHHHHHHhcC-CCCCCCchhccCcccccccC-CCchhHHHHHHHHhcCChhHHHhhhhhhhcCchhhhhHHHHH
Q psy3716 203 DQVQHAFLIGLAALLA-DSVYNIGELLAHPILDSLQQ-TPNAWLVELLRAFNAGDIEKFELMRPQWSAMNDIKANENKLS 280 (436)
Q Consensus 203 e~~~~A~~l~iaALl~-~~iynFgeLl~~p~v~~L~~-t~~~wl~~LL~~f~~Gdl~~f~~~~~~~~~~~~L~~~~~~l~ 280 (436)
++.-...-|=+--|++ ..+-.|.-.|..=..+.+.. +=..|...|=+-+-+|.++.--......+ .|...-..+-+.
T Consensus 97 ~~~~~l~GLnLL~LLsqNRiaeFHteLe~lp~~~l~~~~~I~~~v~LEq~~MEGaYnKv~~a~~s~p-~~~y~~FmdIl~ 175 (260)
T KOG3151|consen 97 EKKHKLLGLNLLYLLSQNRIAEFHTELELLPKKILQHNPYISHPVSLEQSLMEGAYNKVLSAKQSIP-SEEYTYFMDILL 175 (260)
T ss_pred hhhhHHHHHHHHHHHHhccHHHHHHHHHhccHHHhhccchhhhHHHHHHHHHhhHHHHHHHHHhcCC-cHHHHHHHHHHH
Confidence 7776666665566666 55666753333222233433 33567778888888887665554433332 244444444444
Q ss_pred HHHH--HHHHHHHHhhcCCCCcccCHHHHHHHhCCC-hhhHHHHHH
Q psy3716 281 QKIA--LLCLMELAFKKIPGSHQLSFAEISEAAQLP-LIEVEFLII 323 (436)
Q Consensus 281 ~Kir--LlaL~~L~~~~p~~~r~isf~~Ia~~l~i~-~~eVE~lvi 323 (436)
.-|| +-+=++.++ ..||++++++.|..+ .++.+.+.-
T Consensus 176 ~tiRdEIA~c~EKsY------d~l~~s~a~~~L~f~~~~e~~~~~~ 215 (260)
T KOG3151|consen 176 DTIRDEIAGCIEKSY------DKLSASDATQMLLFNNDKELKKFAT 215 (260)
T ss_pred HHHHHHHHHHHHHHH------hhcCHHHHHHHHhcCChHHHHHHHH
Confidence 4444 222333333 479999999999996 445554443
No 177
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=36.43 E-value=41 Score=29.70 Aligned_cols=27 Identities=22% Similarity=0.333 Sum_probs=24.9
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
.+|+++||+.+|+|+.-|...+-+|..
T Consensus 122 g~s~~EIA~~lgis~~tV~~~l~Rar~ 148 (160)
T PRK09642 122 EKSYQEIALQEKIEVKTVEMKLYRARK 148 (160)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 699999999999999999999988865
No 178
>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=36.28 E-value=40 Score=30.43 Aligned_cols=27 Identities=30% Similarity=0.124 Sum_probs=24.8
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
.+||++||+.+|+|+.-|...+-+|..
T Consensus 150 g~s~~EIA~~lgis~~tVk~~l~Rar~ 176 (183)
T TIGR02999 150 GLTVEEIAELLGVSVRTVERDWRFARA 176 (183)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 699999999999999999999988764
No 179
>PF11972 HTH_13: HTH DNA binding domain; InterPro: IPR021068 The proteins in this entry have not been characterised. They contain a C-terminal helix-turn-helix DNA binding domain.
Probab=36.27 E-value=77 Score=24.00 Aligned_cols=37 Identities=19% Similarity=0.236 Sum_probs=31.1
Q ss_pred HHHHHHhhcCCCCcccCHHHHHHHhCCChhhHHHHHHHHHhC
Q psy3716 287 CLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALAL 328 (436)
Q Consensus 287 aL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~ 328 (436)
.|++++.++| -+|-.-++++++++..-+..+| +-+..
T Consensus 3 ~Lidll~~~P----~Vsa~mva~~L~vT~~~A~~li-~eLg~ 39 (54)
T PF11972_consen 3 RLIDLLLSRP----LVSAPMVAKELGVTPQAAQRLI-AELGL 39 (54)
T ss_pred HHHHHHHhCc----cccHHHHHHHhCCCHHHHHHHH-HHhhc
Confidence 4788999998 8999999999999999888875 44444
No 180
>KOG2688|consensus
Probab=36.25 E-value=32 Score=36.16 Aligned_cols=49 Identities=24% Similarity=0.334 Sum_probs=40.4
Q ss_pred ccccHHHHHHHc------CCChhhHHHHHHHHHhcccceeecccccceEEEeeec
Q psy3716 366 HQLSFAEISEAA------QLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQ 414 (436)
Q Consensus 366 r~~sf~~i~~~~------~~~~~~ve~lvmka~s~~li~g~idqv~~~v~~~wv~ 414 (436)
..++.+.+.... ..+.|+||-.+--++..|.|||.|+.+.+++-++---
T Consensus 332 ~~lpls~~~~al~~~~~~~~~~deveciLa~lI~~G~ikgYish~~~~~V~sK~~ 386 (394)
T KOG2688|consen 332 SQLPLSRFLTALQFSGVTDVDLDEVECILANLIDLGRIKGYISHQLQTLVFSKKD 386 (394)
T ss_pred CCCCHHHHHHHHhhcCCCCCchhhHHHHHHhhhhhccccchhchhhheEEEecCC
Confidence 457777777754 4467999999999999999999999999998776443
No 181
>PF10255 Paf67: RNA polymerase I-associated factor PAF67; InterPro: IPR019382 RNA polymerase I is a multi-subunit enzyme and its transcription competence is dependent on the presence of PAF67 [].
Probab=36.01 E-value=5.6e+02 Score=27.22 Aligned_cols=187 Identities=16% Similarity=0.152 Sum_probs=99.5
Q ss_pred HHHHHHHHHHhhccCCCCCCChHHHHHHHHHHHHHHhc-ccChhHHH-HHHHHHHHHHHH--HhhcHHHHHHHHHHHhcc
Q psy3716 118 SLCKILQAQMIMNKDADKPGSLDEVEKLIDEIELLVND-IEGVTAIH-SRFYLVASTLYR--KQAKLSLYYRTALRYLGC 193 (436)
Q Consensus 118 ~~~~~~i~~~~l~~~~~~~~~l~~~~~~L~~~~~~L~~-~~~~~~v~-~~~y~~~a~~~k--~~~~~~~~Y~~~L~yL~~ 193 (436)
++..+...+++.. +||+..+-+.|+.++---.. ...|+.+| +-||.+.-.|.= .-.|...-+...|.|+.-
T Consensus 122 YFSligLlRvh~L-----LGDY~~Alk~l~~idl~~~~l~~~V~~~~is~~YyvGFaylMlrRY~DAir~f~~iL~yi~r 196 (404)
T PF10255_consen 122 YFSLIGLLRVHCL-----LGDYYQALKVLENIDLNKKGLYTKVPACHISTYYYVGFAYLMLRRYADAIRTFSQILLYIQR 196 (404)
T ss_pred HHHHHHHHHHHHh-----ccCHHHHHHHhhccCcccchhhccCcchheehHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455666777777 99999999998877542222 22345555 456666554442 223444456677777765
Q ss_pred CC-C--CCCCh-----hHHHHHHHHHHHHHhcCCCCCCCchhccCcccccccCCCchhHHHHHHHHhcCChhHHHhhhh-
Q psy3716 194 VD-L--NDLTA-----SDQVQHAFLIGLAALLADSVYNIGELLAHPILDSLQQTPNAWLVELLRAFNAGDIEKFELMRP- 264 (436)
Q Consensus 194 ~~-~--~~l~~-----~e~~~~A~~l~iaALl~~~iynFgeLl~~p~v~~L~~t~~~wl~~LL~~f~~Gdl~~f~~~~~- 264 (436)
.. . ...+. ...-+.-..++++-.+.|.- . .-.+.+.+++. + -+=+.....||++.|+++-.
T Consensus 197 ~k~~~~~~~~q~d~i~K~~eqMyaLlAic~~l~p~~--l----de~i~~~lkek-y---~ek~~kmq~gd~~~f~elF~~ 266 (404)
T PF10255_consen 197 TKNQYHQRSYQYDQINKKNEQMYALLAICLSLCPQR--L----DESISSQLKEK-Y---GEKMEKMQRGDEEAFEELFSF 266 (404)
T ss_pred hhhhhccccchhhHHHhHHHHHHHHHHHHHHhCCCC--C----CHHHHHHHHHH-H---HHHHHHHHccCHHHHHHHHHh
Confidence 54 1 11111 11112222344444455644 2 23455556654 2 25556678899999998621
Q ss_pred hhhcC--ch---h------h-----------hhHHHHHHHHHHHHHHHHHhhcCCCCcccCHHHHHHHhCCChhhHHHHH
Q psy3716 265 QWSAM--ND---I------K-----------ANENKLSQKIALLCLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLI 322 (436)
Q Consensus 265 ~~~~~--~~---L------~-----------~~~~~l~~KirLlaL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lv 322 (436)
.-|++ |. . . ..-+.+++-..+-+|-+... = ..+|+.+.+|.-++++++++-..+
T Consensus 267 acPKFIsp~~pp~~~~~~~~~~~e~~~~Ql~~Fl~eV~~q~~l~~lRSyLK--L--Ytti~l~KLA~fl~vd~~~lr~~L 342 (404)
T PF10255_consen 267 ACPKFISPVSPPDYDGPSQNKNKEPYRRQLKLFLDEVKQQQKLPTLRSYLK--L--YTTIPLEKLASFLDVDEEELRSQL 342 (404)
T ss_pred hCCCccCCCCCCCcccccchhhhhHHHHHHHHHHHHHHHhhhhhHHHHHHH--h--hcCCCHHHHHHHcCCCHHHHHHHH
Confidence 11111 11 1 0 11122223333333333221 1 358999999999999988665555
Q ss_pred H
Q psy3716 323 I 323 (436)
Q Consensus 323 i 323 (436)
|
T Consensus 343 l 343 (404)
T PF10255_consen 343 L 343 (404)
T ss_pred H
Confidence 4
No 182
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=35.74 E-value=1.1e+02 Score=24.86 Aligned_cols=68 Identities=12% Similarity=0.142 Sum_probs=46.5
Q ss_pred cCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCCccEEEEEeccccccccchhhccccCCcccccHHHHHHHcCCCh
Q psy3716 302 LSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPRVLSKDQLAFKKIPGSHQLSFAEISEAAQLPL 381 (436)
Q Consensus 302 isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv~~~v~vtwv~pRvL~l~Qi~~lr~~~~r~~sf~~i~~~~~~~~ 381 (436)
.+..++|+.+||+...+-.|. ..|+|...=+. -.+|.++..++..++ ......+..++|+
T Consensus 2 ~~i~e~A~~~gvs~~tLr~ye----~~Gli~p~r~~---------~g~R~y~~~dv~~l~-------~i~~L~~d~g~~l 61 (91)
T cd04766 2 YVISVAAELSGMHPQTLRLYE----RLGLLSPSRTD---------GGTRRYSERDIERLR-------RIQRLTQELGVNL 61 (91)
T ss_pred cCHHHHHHHHCcCHHHHHHHH----HCCCcCCCcCC---------CCCeeECHHHHHHHH-------HHHHHHHHcCCCH
Confidence 478999999999999999994 57888752121 145777777776653 2223334477888
Q ss_pred hhHHHHHH
Q psy3716 382 IEVEFLII 389 (436)
Q Consensus 382 ~~ve~lvm 389 (436)
+++-.++.
T Consensus 62 ~~i~~~l~ 69 (91)
T cd04766 62 AGVKRILE 69 (91)
T ss_pred HHHHHHHH
Confidence 87766553
No 183
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=35.66 E-value=78 Score=23.85 Aligned_cols=64 Identities=16% Similarity=0.234 Sum_probs=38.9
Q ss_pred CHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCCccEEEEEeccccccccchhhccccCCcccccHHHHHHHcCCChh
Q psy3716 303 SFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPRVLSKDQLAFKKIPGSHQLSFAEISEAAQLPLI 382 (436)
Q Consensus 303 sf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv~~~v~vtwv~pRvL~l~Qi~~lr~~~~r~~sf~~i~~~~~~~~~ 382 (436)
+..++|+.+|+|.+.+-.| ...|++...-+.-+ .|.++..++..++ .....-+ .|+|++
T Consensus 2 ti~eva~~~gvs~~tlr~y----~~~gll~~~~~~~g---------~r~y~~~dv~~l~-------~i~~l~~-~G~sl~ 60 (69)
T PF13411_consen 2 TIKEVAKLLGVSPSTLRYY----EREGLLPPPRDENG---------YRYYSEEDVERLR-------EIKELRK-QGMSLE 60 (69)
T ss_dssp EHHHHHHHTTTTHHHHHHH----HHTTSSTTBESTTS---------SEEE-HHHHHHHH-------HHHHHHH-TTTHHH
T ss_pred cHHHHHHHHCcCHHHHHHH----HHhcCcccccccCc---------eeeccHHHHHHHH-------HHHHHHH-CcCCHH
Confidence 5689999999999999999 45677666553322 3555655554442 1222222 566666
Q ss_pred hHHHH
Q psy3716 383 EVEFL 387 (436)
Q Consensus 383 ~ve~l 387 (436)
+|..+
T Consensus 61 ~I~~~ 65 (69)
T PF13411_consen 61 EIKKL 65 (69)
T ss_dssp HHHHH
T ss_pred HHHHH
Confidence 66544
No 184
>KOG2235|consensus
Probab=35.62 E-value=45 Score=36.99 Aligned_cols=99 Identities=18% Similarity=0.245 Sum_probs=70.1
Q ss_pred cccCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCCccEEEEEeccccccccchhhccccCCcccccHHHHHHHcCC
Q psy3716 300 HQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPRVLSKDQLAFKKIPGSHQLSFAEISEAAQL 379 (436)
Q Consensus 300 r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv~~~v~vtwv~pRvL~l~Qi~~lr~~~~r~~sf~~i~~~~~~ 379 (436)
..++.+++|+.+++|-+=+..+++.-+.-.+|+|++|. ...++=.+|..|- + -+...-.+-.|......|.+..|+
T Consensus 132 gqvtiaeLakq~dl~sellqs~l~ek~lg~iikgr~dg-gviyT~Ayv~r~k-a--~iRga~~aItrptnvs~i~~k~gv 207 (776)
T KOG2235|consen 132 GQVTIAELAKQWDLPSELLQSLLIEKLLGSIIKGRVDG-GVIYTSAYVNRRK-A--VIRGALIAITRPTNVSTIQKKVGV 207 (776)
T ss_pred cchHHHHHHHhcCCcHHHHHHHHHHHhhccceeeeecC-CEEeeHHHHHHHH-H--HHHHHHHHhhcCCcHHHHHHHhcc
Confidence 58999999999999999999999999888999999999 3333333444331 1 111222223467788999999997
Q ss_pred ChhhHHHHHHHH-Hhcccceeeccc
Q psy3716 380 PLIEVEFLIIKA-LALGLVKGHIDQ 403 (436)
Q Consensus 380 ~~~~ve~lvmka-~s~~li~g~idq 403 (436)
.+. +++-+..- ..+|.++|.+=.
T Consensus 208 qek-~~~s~feei~n~g~~~gt~ig 231 (776)
T KOG2235|consen 208 QEK-RFYSAFEEIQNLGEIPGTLIG 231 (776)
T ss_pred cHH-HHHHHHHHHHhcccCcccccc
Confidence 655 66666654 467888887533
No 185
>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=35.58 E-value=42 Score=29.59 Aligned_cols=27 Identities=33% Similarity=0.345 Sum_probs=25.1
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
.+|+++||+.+|+|.+.|...+-+|..
T Consensus 126 g~s~~eIA~~lgis~~tV~~~l~ra~~ 152 (162)
T TIGR02983 126 DLSEAQVAEALGISVGTVKSRLSRALA 152 (162)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 589999999999999999999998865
No 186
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=35.53 E-value=53 Score=25.43 Aligned_cols=33 Identities=24% Similarity=0.308 Sum_probs=28.9
Q ss_pred cccCHHHHHHHhCCChhhHHHHHHHHHhCCccc
Q psy3716 300 HQLSFAEISEAAQLPLIEVEFLIIKALALGLVK 332 (436)
Q Consensus 300 r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~ 332 (436)
..++=.+||++++++.-.|-+++...-..|.|+
T Consensus 14 ~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~ 46 (62)
T PF04703_consen 14 GPLKTREIADALGLSIYQARYYLEKLEKEGKVE 46 (62)
T ss_dssp S-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEE
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence 358999999999999999999999999999886
No 187
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=35.45 E-value=42 Score=30.15 Aligned_cols=27 Identities=22% Similarity=0.313 Sum_probs=25.1
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
.+||++||+.+++|+.-|...+-+|+.
T Consensus 135 g~s~~EIA~~lgis~~tV~~~l~ra~~ 161 (172)
T PRK12523 135 GMGHAEIAERLGVSVSRVRQYLAQGLR 161 (172)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 699999999999999999999988875
No 188
>PF12085 DUF3562: Protein of unknown function (DUF3562); InterPro: IPR021945 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 62 to 84 amino acids in length. This protein has two completely conserved residues (A and Y) that may be functionally important.
Probab=35.41 E-value=45 Score=26.28 Aligned_cols=26 Identities=15% Similarity=0.144 Sum_probs=21.4
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHH
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKAL 392 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~ 392 (436)
.-....||++|++|.+.|..+..+.+
T Consensus 7 ~e~i~~iA~~t~~P~e~V~~my~dt~ 32 (66)
T PF12085_consen 7 DEVIRSIAEETGTPAETVRRMYDDTM 32 (66)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence 34678999999999999999876544
No 189
>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=35.34 E-value=56 Score=23.06 Aligned_cols=27 Identities=11% Similarity=0.059 Sum_probs=23.4
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
..++.+||+.++++...|+.++-++..
T Consensus 15 ~~s~~eia~~l~~s~~tv~~~~~~~~~ 41 (57)
T cd06170 15 GKTNKEIADILGISEKTVKTHLRNIMR 41 (57)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 479999999999999999999776543
No 190
>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=35.13 E-value=1.7e+02 Score=23.86 Aligned_cols=52 Identities=21% Similarity=0.226 Sum_probs=42.7
Q ss_pred HHHHHHHHHHHHHhhcCCCCcccCHHHHHHHhCCChhhHHHHHHHHHhCCccccc
Q psy3716 280 SQKIALLCLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGH 334 (436)
Q Consensus 280 ~~KirLlaL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~ 334 (436)
+++--|.+|+++--+. .+-+.-++||+.++++..-|-.-..+.-..|||++.
T Consensus 5 rq~~IL~alV~~Y~~~---~~PVgSk~ia~~l~~s~aTIRN~M~~Le~lGlve~~ 56 (78)
T PF03444_consen 5 RQREILKALVELYIET---GEPVGSKTIAEELGRSPATIRNEMADLEELGLVESQ 56 (78)
T ss_pred HHHHHHHHHHHHHHhc---CCCcCHHHHHHHHCCChHHHHHHHHHHHHCCCccCC
Confidence 5677788999976654 478999999999999988888777777789999763
No 191
>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=35.00 E-value=94 Score=23.15 Aligned_cols=42 Identities=21% Similarity=0.248 Sum_probs=32.6
Q ss_pred CcccCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCCcc
Q psy3716 299 SHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDE 340 (436)
Q Consensus 299 ~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv~~ 340 (436)
++.++..+|++.++++...|-..|=+....|+|+=.=|..++
T Consensus 16 ~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~~~~~d~ 57 (68)
T PF13463_consen 16 DGPMTQSDLAERLGISKSTVSRIIKKLEEKGLVEKERDPHDK 57 (68)
T ss_dssp TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEESSCT
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecCCCCcC
Confidence 367999999999999999999999999999999655444443
No 192
>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=34.85 E-value=1.1e+02 Score=21.98 Aligned_cols=42 Identities=12% Similarity=0.120 Sum_probs=27.3
Q ss_pred HHHHHHHHhhcCCCCcccCHHHHHHHhCCChhhHHHHHHHHHhCC
Q psy3716 285 LLCLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALALG 329 (436)
Q Consensus 285 LlaL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~g 329 (436)
...++.+....+ ..+|-++||+.++++..-|..-+=..-..|
T Consensus 2 ~~~il~~L~~~~---~~it~~eLa~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 2 QKQILKLLLESK---EPITAKELAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp HHHHHHHHHHTT---TSBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHcC---CCcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 334444443332 349999999999999988877665554444
No 193
>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Va is one of three mammalian subunits that lacks a transmembrane region. Subunit Va is located on the matrix side of the membrane and binds thyroid hormone T2, releasing allosteric inhibition caused by the binding of ATP to subunit IV and allowing high turnover at elevated intramitochondrial ATP/ADP ratios.
Probab=34.64 E-value=3e+02 Score=23.63 Aligned_cols=67 Identities=15% Similarity=0.207 Sum_probs=44.8
Q ss_pred HHHHHHHHhcCcccccchhHHHHHHHHHHHHh-hccCchhHHHHHHHHhccCCCHHHHHHHHHHHHHhhcCC
Q psy3716 43 LTLAVLAFVQNPAIQKEGELRDLYHKFVISFE-TKINPVSLMEIMEVITNHLSDQEEALVLLQSFEDKVKNN 113 (436)
Q Consensus 43 LT~~l~~~~~~p~~~~~~~~~~ly~~fI~~f~-~kin~l~l~~i~~~v~~~~~d~~~aL~~L~~l~~~l~~~ 113 (436)
++..-..||+.|... + -++=..+=..|. +=+...+...-++..|+..+|...|++||+.++.|...+
T Consensus 8 F~aRye~~F~~~~iD-~---we~rr~mN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~vK~K~~~~ 75 (103)
T cd00923 8 FDARYETYFNRPDID-G---WELRRGLNNLFGYDLVPEPKVIEAALRACRRVNDFALAVRILEAIKDKCGAH 75 (103)
T ss_pred HHHHHHHHhCCcCcc-H---HHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHccCc
Confidence 334445677777432 1 222222223343 455666788889999999999999999999998888653
No 194
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=34.63 E-value=41 Score=30.61 Aligned_cols=27 Identities=33% Similarity=0.326 Sum_probs=25.4
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
.+|+++||+.+++|..-|.-.+.+|+.
T Consensus 149 ~~s~~eIA~~lgis~~tV~~~l~ra~~ 175 (182)
T PRK12537 149 GCSHAEIAQRLGAPLGTVKAWIKRSLK 175 (182)
T ss_pred CCCHHHHHHHHCCChhhHHHHHHHHHH
Confidence 589999999999999999999999975
No 195
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=34.59 E-value=79 Score=30.71 Aligned_cols=46 Identities=13% Similarity=0.243 Sum_probs=37.7
Q ss_pred HHHHHHHHHHhhcCCCCcccCHHHHHHHhCCChhhHHHHHHHHHhCCccc
Q psy3716 283 IALLCLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVK 332 (436)
Q Consensus 283 irLlaL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~ 332 (436)
-|-+.++++.... +.++.++||+++++|..-|-.++-.....|+++
T Consensus 14 ~r~l~IL~~l~~~----~~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~ 59 (257)
T PRK15090 14 LKVFGILQALGEE----REIGITELSQRVMMSKSTVYRFLQTMKTLGYVA 59 (257)
T ss_pred HHHHHHHHHhhcC----CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 3566666655432 469999999999999999999999999999985
No 196
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=34.01 E-value=80 Score=29.21 Aligned_cols=35 Identities=23% Similarity=0.088 Sum_probs=31.3
Q ss_pred cCHHHHHHHh--CCChhhHHHHHHHHHhCCccccccc
Q psy3716 302 LSFAEISEAA--QLPLIEVEFLIIKALALGLVKGHID 336 (436)
Q Consensus 302 isf~~Ia~~l--~i~~~eVE~lvikAi~~gLI~G~ID 336 (436)
-....||+.| +||.+||+.-+=-....|+|+=.=|
T Consensus 40 ~d~~~iak~l~p~is~~ev~~sL~~L~~~gli~k~~~ 76 (171)
T PF14394_consen 40 PDPEWIAKRLRPKISAEEVRDSLEFLEKLGLIKKDGD 76 (171)
T ss_pred CCHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEECCC
Confidence 3899999999 9999999999999999999985444
No 197
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=33.56 E-value=1.2e+02 Score=26.66 Aligned_cols=60 Identities=22% Similarity=0.202 Sum_probs=48.6
Q ss_pred ccHHHHHHHcCCChhhHHHHHHHHHhcccceeecccccceEEEeeecccccchhhhhHHHHHHHhhcc
Q psy3716 368 LSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPRVLSKDQVFWSLEETVATEV 435 (436)
Q Consensus 368 ~sf~~i~~~~~~~~~~ve~lvmka~s~~li~g~idqv~~~v~~~wv~pr~l~~~q~~~~~~~~~~~~~ 435 (436)
.-|.+||+..+-+.+.|-.++++-|+ ..|+||.- +.+.|+ --++.++++.-|+.-+.+=|
T Consensus 35 ~Nf~dI~~~L~R~p~~~~ky~~~ELg---t~~~id~~-~~lii~----G~~~~~~i~~~L~~fI~~yV 94 (125)
T PF01873_consen 35 VNFVDICKALNRDPEHVLKYFGKELG---TQGSIDGK-GRLIIN----GRFSSKQIQDLLDKFIKEYV 94 (125)
T ss_dssp TTHHHHHHHHTSSHHHHHHHHHHHSS---SEEEEETT-TEEEEE----SSSSCCHHHHHHHHHHCHHS
T ss_pred ecHHHHHHHHCCCHHHHHHHHHHHHC---CceEECCC-CEEEEE----EecCHHHHHHHHHHHHHHEE
Confidence 46999999999999999999999998 78999986 444443 46777888888887665544
No 198
>COG5117 NOC3 Protein involved in the nuclear export of pre-ribosomes [Translation, ribosomal structure and biogenesis / Intracellular trafficking and secretion]
Probab=33.42 E-value=5.9e+02 Score=27.73 Aligned_cols=37 Identities=16% Similarity=0.274 Sum_probs=28.0
Q ss_pred hhccCchh--HHHHHHHHhccCCCHHHHHHHHHHHHHhhcCC
Q psy3716 74 ETKINPVS--LMEIMEVITNHLSDQEEALVLLQSFEDKVKNN 113 (436)
Q Consensus 74 ~~kin~l~--l~~i~~~v~~~~~d~~~aL~~L~~l~~~l~~~ 113 (436)
+++|...+ ++.+|..+.+ .|++.+..+..+|..+.+.
T Consensus 130 kqqi~~~Ke~ia~~~tki~E---ePeeNl~~~~~vf~mi~S~ 168 (657)
T COG5117 130 KQQIDSEKERIASICTKIIE---EPEENLGMMEEVFSMITSM 168 (657)
T ss_pred HHHHHhHHHHHHHHHHHHHh---ChHHHHHHHHHHHHHhccc
Confidence 45555554 6777777755 6999999999999998653
No 199
>PF10771 DUF2582: Protein of unknown function (DUF2582); InterPro: IPR019707 This entry represents conserved proteins found in bacteria and archaea. The function is not known. ; PDB: 2L02_B 2L01_A.
Probab=33.36 E-value=83 Score=24.65 Aligned_cols=44 Identities=18% Similarity=0.147 Sum_probs=30.0
Q ss_pred CcccCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCCccEEEE
Q psy3716 299 SHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNV 344 (436)
Q Consensus 299 ~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv~~~v~v 344 (436)
++.+|+++|++.++++.++|-.-+=-..+.|-|. +++.++.+.|
T Consensus 20 ~~~~s~~el~k~~~l~~~~~~~AiGWLarE~KI~--~~~~~~~~~v 63 (65)
T PF10771_consen 20 NGEWSVSELKKATGLSDKEVYLAIGWLARENKIE--FEEKNGELYV 63 (65)
T ss_dssp SSSEEHHHHHHHCT-SCHHHHHHHHHHHCTTSEE--EEEETTEEEE
T ss_pred CCCcCHHHHHHHhCcCHHHHHHHHHHHhccCcee--EEeeCCEEEE
Confidence 4789999999999999988876555555555553 3455555544
No 200
>PF13518 HTH_28: Helix-turn-helix domain
Probab=32.92 E-value=1.3e+02 Score=21.08 Aligned_cols=33 Identities=21% Similarity=0.123 Sum_probs=27.8
Q ss_pred CHHHHHHHhCCChhhHHHHHHHHHhCCccccccc
Q psy3716 303 SFAEISEAAQLPLIEVEFLIIKALALGLVKGHID 336 (436)
Q Consensus 303 sf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~ID 336 (436)
|+.+||+.++|+...|..|+=+--..| +.|-.+
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~~~G-~~~l~~ 46 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYREGG-IEGLKP 46 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHHhcC-HHHhcc
Confidence 999999999999999999998877767 455444
No 201
>PF13429 TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2_B.
Probab=32.90 E-value=4.5e+02 Score=25.24 Aligned_cols=87 Identities=14% Similarity=0.148 Sum_probs=51.1
Q ss_pred ccCCCHHHHHHHHHHHHHhhcCCcchhHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHHHHHhcccChhHHHHHHHHHH
Q psy3716 91 NHLSDQEEALVLLQSFEDKVKNNLEAKSLCKILQAQMIMNKDADKPGSLDEVEKLIDEIELLVNDIEGVTAIHSRFYLVA 170 (436)
Q Consensus 91 ~~~~d~~~aL~~L~~l~~~l~~~~ea~~~~~~~i~~~~l~~~~~~~~~l~~~~~~L~~~~~~L~~~~~~~~v~~~~y~~~ 170 (436)
.+..++++|++.+++..+.-+.+.++. ...+.+.+. .|+.++++..++...+-...-+ . ++...
T Consensus 157 ~~~G~~~~A~~~~~~al~~~P~~~~~~----~~l~~~li~-----~~~~~~~~~~l~~~~~~~~~~~---~----~~~~l 220 (280)
T PF13429_consen 157 EQLGDPDKALRDYRKALELDPDDPDAR----NALAWLLID-----MGDYDEAREALKRLLKAAPDDP---D----LWDAL 220 (280)
T ss_dssp HHCCHHHHHHHHHHHHHHH-TT-HHHH----HHHHHHHCT-----TCHHHHHHHHHHHHHHH-HTSC---C----HCHHH
T ss_pred HHcCCHHHHHHHHHHHHHcCCCCHHHH----HHHHHHHHH-----CCChHHHHHHHHHHHHHCcCHH---H----HHHHH
Confidence 456789999999999988877765543 234456666 7888888888877666642211 1 22222
Q ss_pred HHHHHHhhcHHHHHHHHHHHhcc
Q psy3716 171 STLYRKQAKLSLYYRTALRYLGC 193 (436)
Q Consensus 171 a~~~k~~~~~~~~Y~~~L~yL~~ 193 (436)
+..|...|++.+.....-+.+..
T Consensus 221 a~~~~~lg~~~~Al~~~~~~~~~ 243 (280)
T PF13429_consen 221 AAAYLQLGRYEEALEYLEKALKL 243 (280)
T ss_dssp HHHHHHHT-HHHHHHHHHHHHHH
T ss_pred HHHhccccccccccccccccccc
Confidence 33333456666655555555553
No 202
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=32.62 E-value=51 Score=29.12 Aligned_cols=27 Identities=22% Similarity=0.247 Sum_probs=24.5
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
..|+++||+.+|+|..-|...+-+|+.
T Consensus 125 ~~s~~EIA~~lgis~~tV~~~l~ra~~ 151 (163)
T PRK07037 125 GETQKDIARELGVSPTLVNFMIRDALV 151 (163)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 689999999999999999999887764
No 203
>KOG2004|consensus
Probab=32.56 E-value=8.4e+02 Score=28.27 Aligned_cols=39 Identities=21% Similarity=0.342 Sum_probs=25.5
Q ss_pred HHHHHHHHHH---hhccCchhHHHHHHHHhccCCCHHHHHHHHH
Q psy3716 64 DLYHKFVISF---ETKINPVSLMEIMEVITNHLSDQEEALVLLQ 104 (436)
Q Consensus 64 ~ly~~fI~~f---~~kin~l~l~~i~~~v~~~~~d~~~aL~~L~ 104 (436)
.+|..+|..+ ..-.||.+|++|+..++.- +..+.+++|+
T Consensus 232 ~l~r~~v~~~~~~~~~~~~~~LaD~~aai~~~--~~~elq~vL~ 273 (906)
T KOG2004|consen 232 SLFREQVATLSQLIVEDNPIKLADFGAAISGA--EFHELQEVLE 273 (906)
T ss_pred HHHHHHHHHHHHHhcccChhHHHHHHHHHhcc--CHHHHHHHHH
Confidence 4555555555 3456899999999999863 4555555553
No 204
>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator HspR and related proteins, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription 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 conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=32.52 E-value=1.3e+02 Score=24.96 Aligned_cols=67 Identities=16% Similarity=0.176 Sum_probs=44.1
Q ss_pred cCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCCccEEEEEeccccccccchhhccccCCcccccHHHHHHHcCCCh
Q psy3716 302 LSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPRVLSKDQLAFKKIPGSHQLSFAEISEAAQLPL 381 (436)
Q Consensus 302 isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv~~~v~vtwv~pRvL~l~Qi~~lr~~~~r~~sf~~i~~~~~~~~ 381 (436)
.+..++|+.+||+..-+-+| ...|++...-+. ...|.++..++..++. .....+..++|+
T Consensus 2 ~~i~eva~~~gVs~~tLR~y----e~~Gli~p~r~~---------~g~R~Ys~~dv~~l~~-------I~~L~~~~G~~l 61 (98)
T cd01279 2 YPISVAAELLGIHPQTLRVY----DRLGLVSPARTN---------GGGRRYSNNDLELLRQ-------VQRLSQDEGFNL 61 (98)
T ss_pred cCHHHHHHHHCcCHHHHHHH----HHCCCCCCCcCC---------CCCeeECHHHHHHHHH-------HHHHHHHCCCCH
Confidence 57889999999999999999 468888652221 2446777777766632 222223366666
Q ss_pred hhHHHHH
Q psy3716 382 IEVEFLI 388 (436)
Q Consensus 382 ~~ve~lv 388 (436)
++|..++
T Consensus 62 ~~i~~~l 68 (98)
T cd01279 62 AGIKRII 68 (98)
T ss_pred HHHHHHH
Confidence 6665554
No 205
>KOG1861|consensus
Probab=32.35 E-value=3.9e+02 Score=29.05 Aligned_cols=140 Identities=9% Similarity=0.067 Sum_probs=77.0
Q ss_pred HHHHHHHHHHHHHhhcHHHHHHHHHHHhccCCCCCCChhHHHHHHHHHHHHHhcCCCCCCCchhccC-cccc-cccC-CC
Q psy3716 164 SRFYLVASTLYRKQAKLSLYYRTALRYLGCVDLNDLTASDQVQHAFLIGLAALLADSVYNIGELLAH-PILD-SLQQ-TP 240 (436)
Q Consensus 164 ~~~y~~~a~~~k~~~~~~~~Y~~~L~yL~~~~~~~l~~~e~~~~A~~l~iaALl~~~iynFgeLl~~-p~v~-~L~~-t~ 240 (436)
...|..-|...-.+||..+|=+.--..-.-+ .+.++-. ..+.+.+=++.-+...|-- |++.. ..+. .++. .-
T Consensus 348 veVYEtHARIALEkGD~~EfNQCQtQLk~LY-~egipg~-~~EF~AYriLY~i~tkN~~---di~sll~~lt~E~ked~~ 422 (540)
T KOG1861|consen 348 VEVYETHARIALEKGDLEEFNQCQTQLKALY-SEGIPGA-YLEFTAYRILYYIFTKNYP---DILSLLRDLTEEDKEDEA 422 (540)
T ss_pred eeeehhhhHHHHhcCCHHHHHHHHHHHHHHH-ccCCCCc-hhhHHHHHHHHHHHhcCch---HHHHHHHhccHhhccCHH
Confidence 3455555555555788777655433222222 1223333 3333333344455554322 54442 1111 1222 22
Q ss_pred chhHHHHHHHHhcCChhHHHhhhhhhhcCchhhhh-HHHHHHHHHHHHHHHHHhhcCCCCc-ccCHHHHHHHhCCCh
Q psy3716 241 NAWLVELLRAFNAGDIEKFELMRPQWSAMNDIKAN-ENKLSQKIALLCLMELAFKKIPGSH-QLSFAEISEAAQLPL 315 (436)
Q Consensus 241 ~~wl~~LL~~f~~Gdl~~f~~~~~~~~~~~~L~~~-~~~l~~KirLlaL~~L~~~~p~~~r-~isf~~Ia~~l~i~~ 315 (436)
-+-.+++-.+...||+..|-.+...-+. +..+ .+.-.++.|..+|.=+|..- | +|+++-|+..+....
T Consensus 423 V~hAL~vR~A~~~GNY~kFFrLY~~AP~---M~~yLmdlF~erER~~Al~ii~Ksy----rP~i~~~fi~~~laf~~ 492 (540)
T KOG1861|consen 423 VAHALEVRSAVTLGNYHKFFRLYLTAPN---MSGYLMDLFLERERKKALTIICKSY----RPTITVDFIASELAFDS 492 (540)
T ss_pred HHHHHHHHHHHHhccHHHHHHHHhhccc---chhHHHHHHHHHHHHHHHHHHHHHc----CCCccHHHHhhhhhhch
Confidence 3335788889999999999887554322 3222 33446777777777777542 4 899999999887743
No 206
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=32.29 E-value=1.2e+02 Score=27.17 Aligned_cols=59 Identities=19% Similarity=0.226 Sum_probs=46.9
Q ss_pred ccHHHHHHHcCCChhhHHHHHHHHHhcccceeecccccceEEEeeecccccchhhhhHHHHHHHhhcc
Q psy3716 368 LSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPRVLSKDQVFWSLEETVATEV 435 (436)
Q Consensus 368 ~sf~~i~~~~~~~~~~ve~lvmka~s~~li~g~idqv~~~v~~~wv~pr~l~~~q~~~~~~~~~~~~~ 435 (436)
.-|.+||+..+=+.+.|=.++++-|+ ..|+|++ +.+.++ --++.++++.-|+.-+.+=|
T Consensus 45 ~Nf~~I~~~L~R~~~hv~ky~~~ELg---t~g~i~~--~~lii~----G~~~~~~i~~~L~~yI~~yV 103 (138)
T PRK03988 45 RNFKEIADRLNRDPKHVAKFLLKELG---TAGNIEG--GRLILQ----GKFSPRVINEKIDRYVKEYV 103 (138)
T ss_pred ecHHHHHHHHCCCHHHHHHHHHHHhC---CceeecC--CEEEEE----EeeCHHHHHHHHHHHHHhcE
Confidence 35999999999999999999999999 8899964 555444 33677888888887766544
No 207
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=32.24 E-value=50 Score=30.28 Aligned_cols=27 Identities=19% Similarity=0.233 Sum_probs=24.8
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
.+||++||+.+|+|+.-|...+-+|..
T Consensus 147 g~s~~EIA~~lgis~~tVk~~l~Rar~ 173 (193)
T TIGR02947 147 GFAYKEIAEIMGTPIGTVMSRLHRGRK 173 (193)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 699999999999999999999888765
No 208
>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=32.21 E-value=1e+02 Score=22.41 Aligned_cols=40 Identities=20% Similarity=0.243 Sum_probs=35.4
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCCcc
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDE 340 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv~~ 340 (436)
.++..+||+.++++..-|=.++=+....|+|+=.-|.-|+
T Consensus 17 ~~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~~~~~D~ 56 (59)
T PF01047_consen 17 GITQSELAEKLGISRSTVTRIIKRLEKKGLIERERDPDDR 56 (59)
T ss_dssp SEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTET
T ss_pred CCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEeccCCCCC
Confidence 5999999999999999999999999999999988777664
No 209
>PF11242 DUF2774: Protein of unknown function (DUF2774); InterPro: IPR021404 This entry is represented by Bacteriophage T4, Gp24.3; it is a family of uncharacterised viral proteins.
Probab=32.05 E-value=49 Score=25.73 Aligned_cols=37 Identities=27% Similarity=0.248 Sum_probs=29.4
Q ss_pred cchhhccccCCcccccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 354 KDQLAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 354 l~Qi~~lr~~~~r~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
..|+-||+ +--.+|-+||+..++...||-.+.-++-+
T Consensus 3 ~v~vhflh---E~g~~FveIAr~~~i~a~e~a~~w~~Ve~ 39 (63)
T PF11242_consen 3 KVQVHFLH---ESGLSFVEIARKIGITAKEVAKAWAEVET 39 (63)
T ss_pred chhhhhHH---HcCCcHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 45667774 34599999999999999999888776654
No 210
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=31.86 E-value=1.2e+02 Score=21.53 Aligned_cols=36 Identities=25% Similarity=0.267 Sum_probs=31.1
Q ss_pred ccccHHHHHHHcCCChhhHHHHHHHHHhcccceeec
Q psy3716 366 HQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHI 401 (436)
Q Consensus 366 r~~sf~~i~~~~~~~~~~ve~lvmka~s~~li~g~i 401 (436)
+..++.+|++.++++...|-..+=+-...|++.-.-
T Consensus 9 ~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~~~ 44 (66)
T smart00418 9 GELCVCELAEILGLSQSTVSHHLKKLREAGLVESRR 44 (66)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeee
Confidence 468999999999999999999998888889887443
No 211
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=31.85 E-value=52 Score=29.67 Aligned_cols=27 Identities=26% Similarity=0.459 Sum_probs=24.3
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
..||++||+.+|+|+.-|...+-+|..
T Consensus 145 g~s~~eIA~~lgis~~tV~~~l~Rar~ 171 (179)
T PRK12514 145 GLSYKELAERHDVPLNTMRTWLRRSLL 171 (179)
T ss_pred CCCHHHHHHHHCCChHHHHHHHHHHHH
Confidence 589999999999999999999888764
No 212
>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=31.58 E-value=67 Score=28.17 Aligned_cols=62 Identities=23% Similarity=0.260 Sum_probs=44.9
Q ss_pred cccccHHHHHHHcCCChhhHHHHHHHHHhcccceeecccccceEEEeee-cccccchhhhhHHHHH
Q psy3716 365 SHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWV-QPRVLSKDQVFWSLEE 429 (436)
Q Consensus 365 ~r~~sf~~i~~~~~~~~~~ve~lvmka~s~~li~g~idqv~~~v~~~wv-~pr~l~~~q~~~~~~~ 429 (436)
.+.+|.++||+++++|..-|+.++=+--..|||.. .-+..|. ..+. -|.-++..+|...+++
T Consensus 23 ~~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s-~~G~~Gg--y~l~~~~~~Itl~dv~~a~eg 85 (135)
T TIGR02010 23 TGPVTLADISERQGISLSYLEQLFAKLRKAGLVKS-VRGPGGG--YQLGRPAEDISVADIIDAVDE 85 (135)
T ss_pred CCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEE-EeCCCCC--EeccCCHHHCcHHHHHHHhCC
Confidence 45799999999999999999999988888899964 2233332 2232 3566666677666654
No 213
>cd08327 CARD_RAIDD Caspase activation and recruitment domain of RIP-associated ICH-1 homologous protein with a death domain. Caspase activation and recruitment domain (CARD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal CARD, which interacts with the caspase-2 CARD, and a C-terminal Death domain (DD), which interacts with the DD of PIDD. In general, CARDs are DDs associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodime
Probab=31.48 E-value=87 Score=26.25 Aligned_cols=59 Identities=12% Similarity=0.134 Sum_probs=43.1
Q ss_pred HHHHHHhcCCCCCCCchhccCcccccccCCCchhHHHHHHHHhcCChhHHHhhhhhhhcCchh
Q psy3716 210 LIGLAALLADSVYNIGELLAHPILDSLQQTPNAWLVELLRAFNAGDIEKFELMRPQWSAMNDI 272 (436)
Q Consensus 210 ~l~iaALl~~~iynFgeLl~~p~v~~L~~t~~~wl~~LL~~f~~Gdl~~f~~~~~~~~~~~~L 272 (436)
+.+...|.+.+|+.-++. ..+++ ++|.......||.+.-+..-..|..|++.+...|.|
T Consensus 24 ~~v~~~L~~~gIlT~~~~---e~I~a-~~T~~~k~~~LLdiLp~RG~~AF~~F~~aL~e~~~l 82 (94)
T cd08327 24 GLVIQYLYQEGILTESHV---EEIES-QTTSRRKTMKLLDILPSRGPKAFHAFLDSLEEFPWV 82 (94)
T ss_pred HHHHHHHHhCCCCCHHHH---HHHHc-cCChHHHHHHHHHHHHhhChhHHHHHHHHHHHHHHH
Confidence 356667889989888763 33333 345566689999999999999999999886544444
No 214
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=31.43 E-value=1.1e+02 Score=23.11 Aligned_cols=73 Identities=15% Similarity=0.073 Sum_probs=47.0
Q ss_pred cCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCCccEEEEEeccccccccchhhccccCCcccccHHHHHHHcCC-C
Q psy3716 302 LSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPRVLSKDQLAFKKIPGSHQLSFAEISEAAQL-P 380 (436)
Q Consensus 302 isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv~~~v~vtwv~pRvL~l~Qi~~lr~~~~r~~sf~~i~~~~~~-~ 380 (436)
++.++||+.++++...+...+-+..+...-+ .++.. | .......-..+ .++.++||+.+++ +
T Consensus 2 ~~~~~la~~~~~s~~~l~~~f~~~~~~s~~~-~~~~~-----------r---~~~a~~~l~~~--~~~~~~ia~~~g~~s 64 (84)
T smart00342 2 LTLEDLAEALGMSPRHLQRLFKKETGTTPKQ-YLRDR-----------R---LERARRLLRDT--DLSVTEIALRVGFSS 64 (84)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHhCcCHHH-HHHHH-----------H---HHHHHHHHHcC--CCCHHHHHHHhCCCC
Confidence 6889999999999999999888776544322 22211 1 11111111111 6999999999999 7
Q ss_pred hhhHHHHHHHH
Q psy3716 381 LIEVEFLIIKA 391 (436)
Q Consensus 381 ~~~ve~lvmka 391 (436)
....-...-+.
T Consensus 65 ~~~f~r~Fk~~ 75 (84)
T smart00342 65 QSYFSRAFKKL 75 (84)
T ss_pred hHHHHHHHHHH
Confidence 77766655443
No 215
>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=31.36 E-value=83 Score=23.26 Aligned_cols=35 Identities=20% Similarity=0.129 Sum_probs=30.6
Q ss_pred cccccHHHHHHHcCCChhhHHHHHHHHHhccccee
Q psy3716 365 SHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKG 399 (436)
Q Consensus 365 ~r~~sf~~i~~~~~~~~~~ve~lvmka~s~~li~g 399 (436)
+..+|..+||+.++++..-|...+-+-...|+|.-
T Consensus 23 ~~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~ 57 (67)
T cd00092 23 QLPLTRQEIADYLGLTRETVSRTLKELEEEGLISR 57 (67)
T ss_pred cCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence 34699999999999999999999988888888763
No 216
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=31.14 E-value=65 Score=24.64 Aligned_cols=33 Identities=21% Similarity=0.282 Sum_probs=28.0
Q ss_pred cccCHHHHHHHhCCChhhHHHHHHHHHhCCccc
Q psy3716 300 HQLSFAEISEAAQLPLIEVEFLIIKALALGLVK 332 (436)
Q Consensus 300 r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~ 332 (436)
...|..+|.+.+++|.++|-.-++-.|..|++.
T Consensus 26 G~ltl~~i~~~t~l~~~~Vk~~L~~LiQh~~v~ 58 (62)
T PF08221_consen 26 GRLTLREIVRRTGLSPKQVKKALVVLIQHNLVQ 58 (62)
T ss_dssp -SEEHHHHHHHHT--HHHHHHHHHHHHHTTSEE
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHHHHHcCCee
Confidence 579999999999999999999999999998875
No 217
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=31.06 E-value=56 Score=28.81 Aligned_cols=27 Identities=30% Similarity=0.288 Sum_probs=24.7
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
.+|+++||+.+|+|+.-|...+-+|+.
T Consensus 121 ~~s~~eIA~~lgis~~tv~~~l~ra~~ 147 (159)
T PRK12527 121 GLSHQQIAEHLGISRSLVEKHIVNAMK 147 (159)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 699999999999999999999888765
No 218
>PRK10747 putative protoheme IX biogenesis protein; Provisional
Probab=31.02 E-value=4.4e+02 Score=27.27 Aligned_cols=133 Identities=10% Similarity=0.068 Sum_probs=0.0
Q ss_pred hhhHHHHHHHHHH-----HhcCcccccchhHHHHHHHHHHHHhhccCchhHHHHHHHHhccCCCHHHHHHHHHHHHHhhc
Q psy3716 37 KKLWHQLTLAVLA-----FVQNPAIQKEGELRDLYHKFVISFETKINPVSLMEIMEVITNHLSDQEEALVLLQSFEDKVK 111 (436)
Q Consensus 37 ~KLWhQLT~~l~~-----~~~~p~~~~~~~~~~ly~~fI~~f~~kin~l~l~~i~~~v~~~~~d~~~aL~~L~~l~~~l~ 111 (436)
.++|+++.....+ +..-......++.-+.....-......-+| .++.+...+.. .+++.++.+++....+-+
T Consensus 249 ~~~w~~lp~~~~~~~~~~~~~A~~l~~~g~~~~A~~~L~~~l~~~~~~-~l~~l~~~l~~--~~~~~al~~~e~~lk~~P 325 (398)
T PRK10747 249 KRWWKNQSRKTRHQVALQVAMAEHLIECDDHDTAQQIILDGLKRQYDE-RLVLLIPRLKT--NNPEQLEKVLRQQIKQHG 325 (398)
T ss_pred HHHHHhCCHHHhCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCH-HHHHHHhhccC--CChHHHHHHHHHHHhhCC
Q ss_pred CCcchhHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHHHHHhcccChhHHHHHHHHHHHHHHHHhhcHHH---HHHHHH
Q psy3716 112 NNLEAKSLCKILQAQMIMNKDADKPGSLDEVEKLIDEIELLVNDIEGVTAIHSRFYLVASTLYRKQAKLSL---YYRTAL 188 (436)
Q Consensus 112 ~~~ea~~~~~~~i~~~~l~~~~~~~~~l~~~~~~L~~~~~~L~~~~~~~~v~~~~y~~~a~~~k~~~~~~~---~Y~~~L 188 (436)
++.+ ..+..|++.+. .++++.++..++..-+. .-...-|...+..+...|+.++ +|+.+|
T Consensus 326 ~~~~----l~l~lgrl~~~-----~~~~~~A~~~le~al~~--------~P~~~~~~~La~~~~~~g~~~~A~~~~~~~l 388 (398)
T PRK10747 326 DTPL----LWSTLGQLLMK-----HGEWQEASLAFRAALKQ--------RPDAYDYAWLADALDRLHKPEEAAAMRRDGL 388 (398)
T ss_pred CCHH----HHHHHHHHHHH-----CCCHHHHHHHHHHHHhc--------CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Q ss_pred H
Q psy3716 189 R 189 (436)
Q Consensus 189 ~ 189 (436)
.
T Consensus 389 ~ 389 (398)
T PRK10747 389 M 389 (398)
T ss_pred h
No 219
>PF07381 DUF1495: Winged helix DNA-binding domain (DUF1495); InterPro: IPR010863 This family consists of several hypothetical archaeal proteins of around 110 residues in length. The function of this family is unknown, although one sequence (Q8U3W1 from SWISSPROT) is described as a putative HTH transcription regulator.
Probab=30.89 E-value=2.2e+02 Score=23.72 Aligned_cols=49 Identities=20% Similarity=0.059 Sum_probs=38.4
Q ss_pred HHHHHHHHHHHHHhhcCCCCcccCHHHHHHHhCCChhhHHHHHHH----------HHhCCcc
Q psy3716 280 SQKIALLCLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIK----------ALALGLV 331 (436)
Q Consensus 280 ~~KirLlaL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lvik----------Ai~~gLI 331 (436)
+-|+|--.|.=|+..-| +.....+||+.++++...|=.-+.- .+.+||+
T Consensus 7 rS~~R~~vl~~L~~~yp---~~~~~~eIar~v~~~~snV~GaL~G~g~rY~~e~SLv~lGLV 65 (90)
T PF07381_consen 7 RSKVRKKVLEYLCSIYP---EPAYPSEIARSVGSDYSNVLGALRGDGKRYNKEDSLVGLGLV 65 (90)
T ss_pred HHHHHHHHHHHHHHcCC---CcCCHHHHHHHHCCCHHHHHHHHhcCCCCcCcchhHHHcCCe
Confidence 35666667777777656 6899999999999999988776654 5778888
No 220
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=30.50 E-value=56 Score=29.89 Aligned_cols=27 Identities=22% Similarity=0.259 Sum_probs=24.4
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
..||++||+.+|+|+.-|...+-+|..
T Consensus 147 g~s~~EIA~~lgis~~tV~~~l~Rar~ 173 (191)
T PRK12520 147 ELETEEICQELQITATNAWVLLYRARM 173 (191)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 589999999999999999999887754
No 221
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=30.50 E-value=53 Score=23.03 Aligned_cols=28 Identities=18% Similarity=0.154 Sum_probs=24.0
Q ss_pred ccccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 366 HQLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 366 r~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
.-.|..+||+.++++..-|...+-++..
T Consensus 17 ~g~s~~eia~~l~is~~tv~~~~~~~~~ 44 (58)
T smart00421 17 EGLTNKEIAERLGISEKTVKTHLSNIMR 44 (58)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3479999999999999999998877654
No 222
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=30.45 E-value=78 Score=25.41 Aligned_cols=30 Identities=17% Similarity=0.021 Sum_probs=24.6
Q ss_pred cccCHHHHHHHhCCChhhHHHHHHHHHhCC
Q psy3716 300 HQLSFAEISEAAQLPLIEVEFLIIKALALG 329 (436)
Q Consensus 300 r~isf~~Ia~~l~i~~~eVE~lvikAi~~g 329 (436)
..+|+++||+.+++|..-|..++-+-.+.|
T Consensus 31 eGlS~kEIAe~LGIS~~TVk~~l~~~~~~~ 60 (73)
T TIGR03879 31 AGKTASEIAEELGRTEQTVRNHLKGETKAG 60 (73)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhcCcccc
Confidence 479999999999999999998876544444
No 223
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=30.42 E-value=1.4e+02 Score=21.14 Aligned_cols=33 Identities=24% Similarity=0.219 Sum_probs=29.9
Q ss_pred ccc-CHHHHHHHhCCChhhHHHHHHHHHhCCccc
Q psy3716 300 HQL-SFAEISEAAQLPLIEVEFLIIKALALGLVK 332 (436)
Q Consensus 300 r~i-sf~~Ia~~l~i~~~eVE~lvikAi~~gLI~ 332 (436)
..+ |..+||+.++++..-|...+-+.-..|+|.
T Consensus 18 ~~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i~ 51 (60)
T smart00345 18 DKLPSERELAAQLGVSRTTVREALSRLEAEGLVQ 51 (60)
T ss_pred CcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 357 899999999999999999999999999885
No 224
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=30.24 E-value=59 Score=28.73 Aligned_cols=27 Identities=26% Similarity=0.332 Sum_probs=24.7
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
.+|+++||+.+|+|..-|...+-+|..
T Consensus 129 g~s~~EIA~~l~is~~tV~~~l~ra~~ 155 (161)
T PRK12528 129 GLGYGEIATELGISLATVKRYLNKAAM 155 (161)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 699999999999999999999988864
No 225
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=30.22 E-value=56 Score=29.62 Aligned_cols=27 Identities=33% Similarity=0.332 Sum_probs=24.2
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
.+||++||+.+|+|..-|...+-+|+.
T Consensus 133 ~~s~~EIA~~lgis~~tV~~~l~ra~~ 159 (179)
T PRK12543 133 DYSQEEIAQLLQIPIGTVKSRIHAALK 159 (179)
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 589999999999999999999887753
No 226
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=30.11 E-value=56 Score=29.68 Aligned_cols=27 Identities=22% Similarity=0.273 Sum_probs=25.3
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
.+|++|||+.+++|..-|.-.+-+|+.
T Consensus 143 g~s~~EIA~~lgis~~tVk~~l~rAl~ 169 (178)
T PRK12529 143 GMKQKDIAQALDIALPTVKKYIHQAYV 169 (178)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 589999999999999999999999886
No 227
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=30.09 E-value=1.5e+02 Score=20.45 Aligned_cols=33 Identities=18% Similarity=0.209 Sum_probs=28.9
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHhCCcccc
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALALGLVKG 333 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G 333 (436)
.++..+|++.++++...|...+-.....|+|.-
T Consensus 14 ~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~ 46 (53)
T smart00420 14 KVSVEELAELLGVSEMTIRRDLNKLEEQGLLTR 46 (53)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 599999999999999999998888778877753
No 228
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=30.01 E-value=88 Score=21.42 Aligned_cols=33 Identities=24% Similarity=0.184 Sum_probs=29.0
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHhccccee
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALALGLVKG 399 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s~~li~g 399 (436)
.++..+||+.++++...|-..+-+-.+.|++.-
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~~ 40 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLEKEGLISR 40 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 478899999999999999999988888888863
No 229
>PF07389 DUF1500: Protein of unknown function (DUF1500); InterPro: IPR009974 This family consists of several Orthopoxvirus specific proteins, which include Vaccinia virus, B6 protein, they are around 100 residues in length. The function of this family is unknown.
Probab=30.00 E-value=81 Score=26.29 Aligned_cols=29 Identities=17% Similarity=0.193 Sum_probs=23.4
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHhCCc
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALALGL 330 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~~gL 330 (436)
.++|..|-+.+. +++.||.|||+.+..|.
T Consensus 48 vi~Fd~iVr~mp-Nes~v~qWV~dtln~i~ 76 (100)
T PF07389_consen 48 VIPFDDIVRTMP-NESRVKQWVIDTLNDIM 76 (100)
T ss_pred cccHHHHHHhCC-CHHHHHHHHHHHHHhHh
Confidence 689999999822 46799999999887554
No 230
>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=29.99 E-value=77 Score=27.22 Aligned_cols=62 Identities=18% Similarity=0.196 Sum_probs=41.7
Q ss_pred ccccHHHHHHHcCCChhhHHHHHHHHHhcccceeecccccceEEEeeecccccchhhhhHHHHH
Q psy3716 366 HQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPRVLSKDQVFWSLEE 429 (436)
Q Consensus 366 r~~sf~~i~~~~~~~~~~ve~lvmka~s~~li~g~idqv~~~v~~~wv~pr~l~~~q~~~~~~~ 429 (436)
..+|.++||+.+++|..-|..++-+-...|+|...- ...+.... =-.|.-++...|...++.
T Consensus 24 ~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~~~-g~~ggy~l-~~~~~~itl~~I~~~~e~ 85 (132)
T TIGR00738 24 GPVSVKEIAERQGISRSYLEKILRTLRRAGLVESVR-GPGGGYRL-ARPPEEITVGDVVRAVEG 85 (132)
T ss_pred CcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEecc-CCCCCccC-CCCHHHCCHHHHHHHHcC
Confidence 479999999999999999999999988999986421 22221111 123445555555555543
No 231
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=29.76 E-value=60 Score=29.13 Aligned_cols=27 Identities=30% Similarity=0.422 Sum_probs=24.7
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
..|+++||+.+|+|++-|...+-+|..
T Consensus 135 ~~s~~EIA~~lgis~~tV~~~l~Ra~~ 161 (173)
T PRK12522 135 QYSYKEMSEILNIPIGTVKYRLNYAKK 161 (173)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 689999999999999999999988764
No 232
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=29.74 E-value=1.2e+02 Score=30.13 Aligned_cols=56 Identities=20% Similarity=0.270 Sum_probs=43.5
Q ss_pred HHHHHHHHHHhhcCCCCcccCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCCccEEEEE
Q psy3716 283 IALLCLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVT 345 (436)
Q Consensus 283 irLlaL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv~~~v~vt 345 (436)
+|-+-|.+++-+.| .+.-++||+.++|++.-|-..+=..+..|+|+- .-.+.-.||
T Consensus 11 t~fqIL~ei~~~qp----~v~q~eIA~~lgiT~QaVsehiK~Lv~eG~i~~---~gR~~Y~iT 66 (260)
T COG1497 11 TRFQILSEIAVRQP----RVKQKEIAKKLGITLQAVSEHIKELVKEGLIEK---EGRGEYEIT 66 (260)
T ss_pred hHHHHHHHHHHhCC----CCCHHHHHHHcCCCHHHHHHHHHHHHhccceee---cCCeeEEEe
Confidence 55667777887777 789999999999999999999988899888764 223344555
No 233
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=29.70 E-value=1e+02 Score=31.58 Aligned_cols=54 Identities=28% Similarity=0.231 Sum_probs=43.7
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHhcccceeecccccceEEEeeecccccchhhhhHHHHHHHh
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPRVLSKDQVFWSLEETVA 432 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s~~li~g~idqv~~~v~~~wv~pr~l~~~q~~~~~~~~~~ 432 (436)
-+|=+|||++.+++---|-.++-+|...|+|+=+|+ |++..--.+..+|+|-|.
T Consensus 26 gltQ~eIA~~LgiSR~~v~rlL~~Ar~~GiV~I~i~------------~~~~~~~~Le~~L~~~fg 79 (321)
T COG2390 26 GLTQSEIAERLGISRATVSRLLAKAREEGIVKISIN------------SPVEGCLELEQQLKERFG 79 (321)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHCCeEEEEeC------------CCCcchHHHHHHHHHhcC
Confidence 578899999999999999999999999999987666 255555556677776553
No 234
>KOG1586|consensus
Probab=29.67 E-value=5.8e+02 Score=25.50 Aligned_cols=34 Identities=26% Similarity=0.479 Sum_probs=28.2
Q ss_pred CchhHHHHHHHHhcCChhHHHhhhhhhhcCchhh
Q psy3716 240 PNAWLVELLRAFNAGDIEKFELMRPQWSAMNDIK 273 (436)
Q Consensus 240 ~~~wl~~LL~~f~~Gdl~~f~~~~~~~~~~~~L~ 273 (436)
+...|-+|+.+..++|++.|.+...++.+...|-
T Consensus 233 Eckflk~L~~aieE~d~e~fte~vkefDsisrLD 266 (288)
T KOG1586|consen 233 ECKFLKDLLDAIEEQDIEKFTEVVKEFDSISRLD 266 (288)
T ss_pred HHHHHHHHHHHHhhhhHHHHHHHHHhhhccchHH
Confidence 6788999999999999999999877766655453
No 235
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=29.43 E-value=54 Score=24.90 Aligned_cols=24 Identities=25% Similarity=0.148 Sum_probs=21.3
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHH
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIK 324 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvik 324 (436)
-.+..+||+.|++|..-|-.|+=+
T Consensus 13 G~~~~eIA~~Lg~~~~TV~~W~~r 36 (58)
T PF06056_consen 13 GWSIKEIAEELGVPRSTVYSWKDR 36 (58)
T ss_pred CCCHHHHHHHHCCChHHHHHHHHh
Confidence 478999999999999999999754
No 236
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=29.36 E-value=60 Score=29.80 Aligned_cols=35 Identities=20% Similarity=0.219 Sum_probs=28.6
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccC
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQ 337 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQ 337 (436)
..|+++||+.+++|+.-|...+-+|... ++..+++
T Consensus 127 g~s~~EIA~~lgis~~tV~~~l~Rar~~--Lr~~~~~ 161 (182)
T PRK12511 127 GLSYQEAAAVLGIPIGTLMSRIGRARAA--LRAFEEG 161 (182)
T ss_pred CCCHHHHHHHhCcCHHHHHHHHHHHHHH--HHHHHHh
Confidence 6899999999999999999999888763 4444443
No 237
>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=29.10 E-value=1.2e+02 Score=20.63 Aligned_cols=30 Identities=23% Similarity=0.088 Sum_probs=24.7
Q ss_pred cCHHHHHHHhCCChhhHHHHHHHHHhCCcccccc
Q psy3716 302 LSFAEISEAAQLPLIEVEFLIIKALALGLVKGHI 335 (436)
Q Consensus 302 isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~I 335 (436)
++.+++|+.++++..-+..|+ ..|.+.+..
T Consensus 2 lt~~e~a~~lgis~~ti~~~~----~~g~i~~~~ 31 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLI----HEGELPAYR 31 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHH----HcCCCCeEE
Confidence 688999999999999999886 567777643
No 238
>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H ....
Probab=29.07 E-value=2.3e+02 Score=21.43 Aligned_cols=58 Identities=12% Similarity=0.059 Sum_probs=40.7
Q ss_pred ccCCCHHHHHHHHHHHHHh---hcCCcchhHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHHHHH
Q psy3716 91 NHLSDQEEALVLLQSFEDK---VKNNLEAKSLCKILQAQMIMNKDADKPGSLDEVEKLIDEIELLV 153 (436)
Q Consensus 91 ~~~~d~~~aL~~L~~l~~~---l~~~~ea~~~~~~~i~~~~l~~~~~~~~~l~~~~~~L~~~~~~L 153 (436)
....+.++|++.+++..+. +.++.+-.+.+...+|.++.. .|+++.+.+.++++-+..
T Consensus 16 ~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~-----~g~~~~A~~~~~~al~i~ 76 (78)
T PF13424_consen 16 RELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYR-----LGDYEEALEYYQKALDIF 76 (78)
T ss_dssp HHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHH-----TTHHHHHHHHHHHHHHHH
T ss_pred HHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHH-----cCCHHHHHHHHHHHHhhh
Confidence 3456899999999886655 333223346666778888888 899999998888776543
No 239
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=28.99 E-value=59 Score=30.91 Aligned_cols=28 Identities=7% Similarity=0.083 Sum_probs=25.2
Q ss_pred cccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 300 HQLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 300 r~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
..+|+++||+.+|+|+.-|...+-+|+.
T Consensus 197 eg~s~~EIA~~lgis~~tVk~~~~rA~~ 224 (234)
T PRK08301 197 EEKTQKEVADMLGISQSYISRLEKRIIK 224 (234)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4799999999999999999999888864
No 240
>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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. This subgroup lacks one of the c
Probab=28.97 E-value=1.8e+02 Score=25.52 Aligned_cols=67 Identities=21% Similarity=0.333 Sum_probs=47.0
Q ss_pred cCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCCccEEEEEeccccccccchhhccccCCcccccHHHHHHHcCCCh
Q psy3716 302 LSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPRVLSKDQLAFKKIPGSHQLSFAEISEAAQLPL 381 (436)
Q Consensus 302 isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv~~~v~vtwv~pRvL~l~Qi~~lr~~~~r~~sf~~i~~~~~~~~ 381 (436)
++..++|+.+||+.+-+-++ -..|||...-+.-++ +|.++..++..++ |=.-.+.+|+|+
T Consensus 1 m~IgE~A~~~gvs~~TLRyY----E~~GLl~p~r~~~~g--------yR~Y~~~~~~~l~--------~I~~lr~~G~sL 60 (133)
T cd04787 1 MKVKELANAAGVTPDTVRFY----TRIGLLRPTRDPVNG--------YRLYSEKDLSRLR--------FILSARQLGFSL 60 (133)
T ss_pred CCHHHHHHHHCcCHHHHHHH----HHCCCCCCCcCCCCC--------eeeCCHHHHHHHH--------HHHHHHHcCCCH
Confidence 36789999999999999888 478999886554343 4778877766552 222234677777
Q ss_pred hhHHHHH
Q psy3716 382 IEVEFLI 388 (436)
Q Consensus 382 ~~ve~lv 388 (436)
+|+-.++
T Consensus 61 ~eI~~~l 67 (133)
T cd04787 61 KDIKEIL 67 (133)
T ss_pred HHHHHHH
Confidence 7766654
No 241
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=28.93 E-value=62 Score=29.74 Aligned_cols=27 Identities=19% Similarity=0.311 Sum_probs=24.3
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
..||++||+.+|+|+.-|...+-+|..
T Consensus 150 g~s~~EIA~~lgis~~tVk~~l~RAr~ 176 (189)
T PRK12530 150 ELSSEQICQECDISTSNLHVLLYRARL 176 (189)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 589999999999999999999887764
No 242
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=28.92 E-value=71 Score=22.78 Aligned_cols=24 Identities=13% Similarity=0.174 Sum_probs=21.0
Q ss_pred cCHHHHHHHhCCChhhHHHHHHHH
Q psy3716 302 LSFAEISEAAQLPLIEVEFLIIKA 325 (436)
Q Consensus 302 isf~~Ia~~l~i~~~eVE~lvikA 325 (436)
.|+.+||+.+|++.+.|...+-++
T Consensus 28 ~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 28 RSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHhh
Confidence 699999999999999998877543
No 243
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=28.79 E-value=82 Score=22.69 Aligned_cols=25 Identities=12% Similarity=0.101 Sum_probs=21.2
Q ss_pred cccCHHHHHHHhCCChhhHHHHHHH
Q psy3716 300 HQLSFAEISEAAQLPLIEVEFLIIK 324 (436)
Q Consensus 300 r~isf~~Ia~~l~i~~~eVE~lvik 324 (436)
..-..++||..++++..+|..|...
T Consensus 26 ~~~~~~~la~~~~l~~~qV~~WF~n 50 (59)
T cd00086 26 SREEREELAKELGLTERQVKIWFQN 50 (59)
T ss_pred CHHHHHHHHHHHCcCHHHHHHHHHH
Confidence 3456889999999999999999764
No 244
>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=28.64 E-value=1.3e+02 Score=21.95 Aligned_cols=36 Identities=25% Similarity=0.266 Sum_probs=31.4
Q ss_pred ccHHHHHHHcCCChhhHHHHHHHHHhcccceeeccc
Q psy3716 368 LSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQ 403 (436)
Q Consensus 368 ~sf~~i~~~~~~~~~~ve~lvmka~s~~li~g~idq 403 (436)
+++++|++.++++...|-..+=+-.+.|+|...-+.
T Consensus 21 ~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~~~~ 56 (78)
T cd00090 21 LTVSELAERLGLSQSTVSRHLKKLEEAGLVESRREG 56 (78)
T ss_pred cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEEEec
Confidence 899999999999999999888887789999876554
No 245
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=28.61 E-value=64 Score=28.83 Aligned_cols=27 Identities=26% Similarity=0.149 Sum_probs=24.6
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
..|+++||+.+|+|++-|...+-+|..
T Consensus 134 g~s~~EIA~~lgis~~tV~~~l~ra~~ 160 (173)
T PRK09645 134 GWSTAQIAADLGIPEGTVKSRLHYALR 160 (173)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 689999999999999999999888764
No 246
>PF07163 Pex26: Pex26 protein; InterPro: IPR010797 This family consists of Pex26 and related mammalian proteins. Pex26 is a type II peroxisomal membrane protein that recruits Pex6-Pex1 complexes to peroxisomes []. Mutations in Pex26 can lead to human disorders [].; GO: 0032403 protein complex binding, 0045046 protein import into peroxisome membrane, 0005779 integral to peroxisomal membrane
Probab=28.41 E-value=6.5e+02 Score=25.66 Aligned_cols=93 Identities=17% Similarity=0.358 Sum_probs=66.2
Q ss_pred HHHHHHHHHhhhHHHHHHHHHHHhcCcccccchhHHHHHHHHHHHHhhccCchhHHHHHHHHhccCCCHHHHHHHHHHHH
Q psy3716 28 WLNLEELYNKKLWHQLTLAVLAFVQNPAIQKEGELRDLYHKFVISFETKINPVSLMEIMEVITNHLSDQEEALVLLQSFE 107 (436)
Q Consensus 28 ~~~l~~l~~~KLWhQLT~~l~~~~~~p~~~~~~~~~~ly~~fI~~f~~kin~l~l~~i~~~v~~~~~d~~~aL~~L~~l~ 107 (436)
.--++-+.|-..|++---=+++++..|+ ++ |.+..++|+..-..+..|...+++-+.=.
T Consensus 87 vvGIQALAEmnrWreVLsWvlqyYq~pE--------kl-------------PpkIleLCILLysKv~Ep~amlev~~~WL 145 (309)
T PF07163_consen 87 VVGIQALAEMNRWREVLSWVLQYYQVPE--------KL-------------PPKILELCILLYSKVQEPAAMLEVASAWL 145 (309)
T ss_pred hhhHHHHHHHhhHHHHHHHHHHHhcCcc--------cC-------------CHHHHHHHHHHHHHhcCHHHHHHHHHHHH
Confidence 3467889999999999999999999983 23 66788899988888889998887766533
Q ss_pred HhhcC--CcchhHHHHHHHHHHhhccCCCCCCChHHHHHHH
Q psy3716 108 DKVKN--NLEAKSLCKILQAQMIMNKDADKPGSLDEVEKLI 146 (436)
Q Consensus 108 ~~l~~--~~ea~~~~~~~i~~~~l~~~~~~~~~l~~~~~~L 146 (436)
..=.+ -.+..-...+.+-++.+- .|-++++++.+
T Consensus 146 ~~p~Nq~lp~y~~vaELyLl~VLlP-----LG~~~eAeelv 181 (309)
T PF07163_consen 146 QDPSNQSLPEYGTVAELYLLHVLLP-----LGHFSEAEELV 181 (309)
T ss_pred hCcccCCchhhHHHHHHHHHHHHhc-----cccHHHHHHHH
Confidence 22111 123334444555566666 78888887766
No 247
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=28.25 E-value=1.7e+02 Score=23.88 Aligned_cols=35 Identities=14% Similarity=0.207 Sum_probs=31.7
Q ss_pred CcccCHHHHHHHhCCChhhHHHHHHHHHhCCcccc
Q psy3716 299 SHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKG 333 (436)
Q Consensus 299 ~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G 333 (436)
++..+-.+||.+++.|++-||..+-+-++.|.|+-
T Consensus 14 ~gr~s~~~Ls~~~~~p~~~VeaMLe~l~~kGkver 48 (78)
T PRK15431 14 RGRMEAAQISQTLNTPQPMINAMLQQLESMGKAVR 48 (78)
T ss_pred cCcccHHHHHHHHCcCHHHHHHHHHHHHHCCCeEe
Confidence 36899999999999999999999999999888764
No 248
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. 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 winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=28.11 E-value=1.8e+02 Score=24.14 Aligned_cols=66 Identities=18% Similarity=0.278 Sum_probs=44.7
Q ss_pred CHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCCccEEEEEeccccccccchhhccccCCcccccHHHHHHHcCCChh
Q psy3716 303 SFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPRVLSKDQLAFKKIPGSHQLSFAEISEAAQLPLI 382 (436)
Q Consensus 303 sf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv~~~v~vtwv~pRvL~l~Qi~~lr~~~~r~~sf~~i~~~~~~~~~ 382 (436)
+.+++|+.+|++...+-+| .+.||+...-++ -.+|.++..++..++ -....-+..++|++
T Consensus 2 ~I~e~a~~~gvs~~tLR~y----e~~Gll~p~r~~---------~g~R~Y~~~dv~~l~-------~I~~L~~~~G~~l~ 61 (96)
T cd04774 2 KVDEVAKRLGLTKRTLKYY----EEIGLVSPERSE---------GRYRLYSEEDLKRLE-------RILRLREVLGFSLQ 61 (96)
T ss_pred CHHHHHHHHCcCHHHHHHH----HHCCCCCCCcCC---------CCCEEECHHHHHHHH-------HHHHHHHHcCCCHH
Confidence 5789999999999999999 357888642221 346788877766552 11122223788888
Q ss_pred hHHHHH
Q psy3716 383 EVEFLI 388 (436)
Q Consensus 383 ~ve~lv 388 (436)
++-.++
T Consensus 62 ei~~~l 67 (96)
T cd04774 62 EVTHFL 67 (96)
T ss_pred HHHHHH
Confidence 887665
No 249
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=28.10 E-value=55 Score=25.09 Aligned_cols=23 Identities=17% Similarity=0.405 Sum_probs=15.9
Q ss_pred cccccHHHHHHHcCCChhhHHHH
Q psy3716 365 SHQLSFAEISEAAQLPLIEVEFL 387 (436)
Q Consensus 365 ~r~~sf~~i~~~~~~~~~~ve~l 387 (436)
.+.+|.+++|+.|+++.+-++.+
T Consensus 8 ~~glsl~~va~~t~I~~~~l~ai 30 (62)
T PF13413_consen 8 AKGLSLEDVAEETKISVSYLEAI 30 (62)
T ss_dssp CTT--HHHHHHHCS--HHHHHHH
T ss_pred HcCCCHHHHHHHhCCCHHHHHHH
Confidence 46799999999999999877654
No 250
>TIGR03643 conserved hypothetical protein TIGR03643. This model describes an uncharacterized bacterial protein family. Members average about 90 amino acids in length with several well-conserved uncommon amino acids (Trp, Met). The majority of species are marine bacteria. Few species have more than one copy, but Vibrio cholerae El Tor N16961 has three identical copies.
Probab=28.06 E-value=93 Score=24.94 Aligned_cols=33 Identities=24% Similarity=0.337 Sum_probs=25.8
Q ss_pred HHHHHHhhcCCCCcccCHHHHHHHhCCChhhHHHHHHH
Q psy3716 287 CLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIK 324 (436)
Q Consensus 287 aL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lvik 324 (436)
-+++||-. ...||+.|..+.|+++.||=.|.=+
T Consensus 4 riIeMAwe-----DRtpFeaI~~~fGL~E~eVi~lMR~ 36 (72)
T TIGR03643 4 RIIEMAWE-----DRTPFEAIEQQFGLSEKEVIKLMRQ 36 (72)
T ss_pred HHHHHHHc-----cCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 36778865 3689999999999999998655433
No 251
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=27.93 E-value=66 Score=29.44 Aligned_cols=28 Identities=29% Similarity=0.291 Sum_probs=24.6
Q ss_pred cccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 300 HQLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 300 r~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
...|+++||+.+|+|.+-|...+-+|..
T Consensus 154 ~g~s~~EIA~~lgis~~tV~~~l~ra~~ 181 (194)
T PRK12513 154 GDLELEEIAELTGVPEETVKSRLRYALQ 181 (194)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3689999999999999999988877764
No 252
>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=27.88 E-value=1.6e+02 Score=27.84 Aligned_cols=27 Identities=30% Similarity=0.309 Sum_probs=24.2
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
..|+++||+.+|+|..-|...+-+|+.
T Consensus 191 ~~s~~eIA~~lgis~~tV~~~~~ra~~ 217 (224)
T TIGR02479 191 ELNLKEIGEVLGLTESRVSQIHSQALK 217 (224)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 689999999999999999998877764
No 253
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=27.82 E-value=66 Score=28.98 Aligned_cols=27 Identities=22% Similarity=0.341 Sum_probs=25.1
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
..|++|||+.+++|..-|.-.+-+|+.
T Consensus 135 g~s~~EIA~~lgis~~tV~~~l~Ra~~ 161 (172)
T PRK09651 135 GLTYSEIAHKLGVSVSSVKKYVAKATE 161 (172)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 589999999999999999999999875
No 254
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=27.79 E-value=67 Score=27.98 Aligned_cols=27 Identities=19% Similarity=0.342 Sum_probs=24.9
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
..|.+|||+.+++|..-|...+.+|+.
T Consensus 122 ~~s~~EIA~~l~is~~tV~~~~~ra~~ 148 (154)
T PRK06759 122 GKTMGEIALETEMTYYQVRWIYRQALE 148 (154)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 589999999999999999999999875
No 255
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=27.69 E-value=69 Score=28.54 Aligned_cols=27 Identities=7% Similarity=0.116 Sum_probs=24.7
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
.+|+++||+.+++|..-|...+-+|..
T Consensus 128 g~s~~eIA~~lgis~~tV~~~l~Rar~ 154 (164)
T PRK12547 128 GFSYEDAAAICGCAVGTIKSRVSRARN 154 (164)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 689999999999999999999988764
No 256
>PF10985 DUF2805: Protein of unknown function (DUF2805); InterPro: IPR019882 This entry represents an uncharacterised bacterial protein family. Members average about 90 amino acids in length with several well-conserved uncommon amino acids (Trp, Met). The majority of species are marine bacteria. Few species have more than one copy, but Vibrio cholerae O1 biovar eltor str. N16961 has three identical copies.
Probab=27.61 E-value=94 Score=24.99 Aligned_cols=31 Identities=26% Similarity=0.352 Sum_probs=24.9
Q ss_pred HHHHHhhcCCCCcccCHHHHHHHhCCChhhHHHHHH
Q psy3716 288 LMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLII 323 (436)
Q Consensus 288 L~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lvi 323 (436)
+++||-. ...||+.|....|+++.||=.+.=
T Consensus 4 iIeMAwe-----DRtpFeaI~~qfGl~E~eVi~lMR 34 (73)
T PF10985_consen 4 IIEMAWE-----DRTPFEAIERQFGLSEKEVIKLMR 34 (73)
T ss_pred HHHHHHc-----cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 6778865 368999999999999999865543
No 257
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=27.59 E-value=1.9e+02 Score=24.43 Aligned_cols=68 Identities=10% Similarity=0.150 Sum_probs=46.0
Q ss_pred cCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCCccEEEEEeccccccccchhhccccCCcccccHHHHHHHcCCCh
Q psy3716 302 LSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPRVLSKDQLAFKKIPGSHQLSFAEISEAAQLPL 381 (436)
Q Consensus 302 isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv~~~v~vtwv~pRvL~l~Qi~~lr~~~~r~~sf~~i~~~~~~~~ 381 (436)
++..++|+.+|||..-+-+| -..|++...-+.-+ .+|.++..++..++ +=--....|+|+
T Consensus 1 ~~i~eva~~~gvs~~tlR~y----e~~Gll~p~~~~~~--------g~R~Y~~~dl~~l~--------~I~~lr~~G~~l 60 (108)
T cd04773 1 MTIGELAHLLGVPPSTLRHW----EKEGLLSPDREPET--------GYRVYDPSDVRDAR--------LIHLLRRGGYLL 60 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHH----HHCCCCCCCcCCCC--------CceeeCHHHHHHHH--------HHHHHHHCCCCH
Confidence 46789999999999999999 34688876433222 34777777766553 112234577777
Q ss_pred hhHHHHHH
Q psy3716 382 IEVEFLII 389 (436)
Q Consensus 382 ~~ve~lvm 389 (436)
+++-.++.
T Consensus 61 ~~I~~~l~ 68 (108)
T cd04773 61 EQIATVVE 68 (108)
T ss_pred HHHHHHHH
Confidence 77776654
No 258
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=27.59 E-value=81 Score=24.10 Aligned_cols=32 Identities=22% Similarity=0.306 Sum_probs=26.5
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHhcccce
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALALGLVK 398 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s~~li~ 398 (436)
.+|..+|.+.|++|.++|-.=++--+..|++.
T Consensus 27 ~ltl~~i~~~t~l~~~~Vk~~L~~LiQh~~v~ 58 (62)
T PF08221_consen 27 RLTLREIVRRTGLSPKQVKKALVVLIQHNLVQ 58 (62)
T ss_dssp SEEHHHHHHHHT--HHHHHHHHHHHHHTTSEE
T ss_pred CcCHHHHHHHhCCCHHHHHHHHHHHHHcCCee
Confidence 57899999999999999999888888888774
No 259
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=27.52 E-value=1.3e+02 Score=31.39 Aligned_cols=28 Identities=18% Similarity=0.179 Sum_probs=24.4
Q ss_pred ccccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 366 HQLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 366 r~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
+..|+++||+.++++.+-|-.+.-+|+.
T Consensus 330 ~~~Tl~EIA~~lgiS~eRVRQie~rAL~ 357 (373)
T PRK07406 330 RMKTLEEIGQIFNVTRERIRQIEAKALR 357 (373)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4579999999999999988888888775
No 260
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=27.29 E-value=2e+02 Score=25.03 Aligned_cols=80 Identities=11% Similarity=0.016 Sum_probs=57.8
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCCccEEEEEeccccccccchhhccccCCcccccHHHHHH--HcC
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPRVLSKDQLAFKKIPGSHQLSFAEISE--AAQ 378 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv~~~v~vtwv~pRvL~l~Qi~~lr~~~~r~~sf~~i~~--~~~ 378 (436)
.++-.+||+.++++..-|=..|=+....|+|+-.-|..++....-..++.--...+ .+. -.+.++.+ ..+
T Consensus 46 ~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~--~~~------~~~~~~~~~~~~~ 117 (144)
T PRK03573 46 EQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQTCASDRRAKRIKLTEKAEPLIS--EVE------AVINKTRAEILHG 117 (144)
T ss_pred CCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeecCCCCcCeeeeEEChHHHHHHH--HHH------HHHHHHHHHHHhC
Confidence 47889999999999999999999999999999999999988877777775322211 111 11122222 247
Q ss_pred CChhhHHHHH
Q psy3716 379 LPLIEVEFLI 388 (436)
Q Consensus 379 ~~~~~ve~lv 388 (436)
++.+|++.++
T Consensus 118 l~~ee~~~l~ 127 (144)
T PRK03573 118 ISAEEIEQLI 127 (144)
T ss_pred CCHHHHHHHH
Confidence 7888887764
No 261
>COG5187 RPN7 26S proteasome regulatory complex component, contains PCI domain [Posttranslational modification, protein turnover, chaperones]
Probab=27.22 E-value=53 Score=33.51 Aligned_cols=47 Identities=15% Similarity=0.157 Sum_probs=43.5
Q ss_pred ccccHHHHHHHcCCChhhHHHHHHHHHhcccceeecccccceEEEee
Q psy3716 366 HQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTW 412 (436)
Q Consensus 366 r~~sf~~i~~~~~~~~~~ve~lvmka~s~~li~g~idqv~~~v~~~w 412 (436)
|.+|.+-.|+..+++++=|+.=+-+-+-.|=..+.||-|+|.|..+.
T Consensus 330 r~lsl~sMA~tFgVSV~yvdrDLg~FIp~~~LncvIDRvnGvVetnr 376 (412)
T COG5187 330 RLLSLESMAQTFGVSVEYVDRDLGEFIPEGRLNCVIDRVNGVVETNR 376 (412)
T ss_pred HHhhHHHHHHHhCccHHHHhhhHHhhCCCCceeeeeecccceEeccC
Confidence 78999999999999999999988888889999999999999998763
No 262
>PF10975 DUF2802: Protein of unknown function (DUF2802); InterPro: IPR021244 This bacterial family of proteins has no known function.
Probab=27.04 E-value=61 Score=25.67 Aligned_cols=21 Identities=33% Similarity=0.425 Sum_probs=19.3
Q ss_pred cCHHHHHHHhCCChhhHHHHH
Q psy3716 302 LSFAEISEAAQLPLIEVEFLI 322 (436)
Q Consensus 302 isf~~Ia~~l~i~~~eVE~lv 322 (436)
.+-++|++.|++|..|.|.++
T Consensus 45 a~~~el~~~CgL~~aEAeLl~ 65 (70)
T PF10975_consen 45 ASVEELMEECGLSRAEAELLL 65 (70)
T ss_pred CCHHHHHHHcCCCHHHHHHHH
Confidence 688999999999999999875
No 263
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=26.65 E-value=70 Score=30.46 Aligned_cols=27 Identities=26% Similarity=0.358 Sum_probs=24.7
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
.+||++||+.+|||++-|...+-+|..
T Consensus 150 g~s~~EIAe~LgiS~~tVk~~L~RAr~ 176 (216)
T PRK12533 150 DMSYREIAAIADVPVGTVMSRLARARR 176 (216)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 699999999999999999999987765
No 264
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=26.65 E-value=1e+02 Score=24.41 Aligned_cols=42 Identities=21% Similarity=0.196 Sum_probs=31.2
Q ss_pred ccccHHHHHHHcCCChhhHHHHHHHHHhcccceeecccccceEEEe
Q psy3716 366 HQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVT 411 (436)
Q Consensus 366 r~~sf~~i~~~~~~~~~~ve~lvmka~s~~li~g~idqv~~~v~~~ 411 (436)
...++.+|+..++++-..+...+=.-...|||++ .++...+|
T Consensus 18 ~~~~~t~i~~~~~L~~~~~~~yL~~L~~~gLI~~----~~~~Y~lT 59 (77)
T PF14947_consen 18 GGAKKTEIMYKANLNYSTLKKYLKELEEKGLIKK----KDGKYRLT 59 (77)
T ss_dssp T-B-HHHHHTTST--HHHHHHHHHHHHHTTSEEE----ETTEEEE-
T ss_pred CCCCHHHHHHHhCcCHHHHHHHHHHHHHCcCeeC----CCCEEEEC
Confidence 4578999999999999999999999999999955 44555554
No 265
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=26.52 E-value=73 Score=28.82 Aligned_cols=27 Identities=19% Similarity=0.151 Sum_probs=24.9
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
..|+++||+.+++|..-|...+-+|..
T Consensus 147 g~s~~eIA~~l~is~~tV~~~l~ra~~ 173 (184)
T PRK12512 147 GASIKETAAKLSMSEGAVRVALHRGLA 173 (184)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 689999999999999999999988865
No 266
>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits, TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF []. This entry represents a helix-turn-helix (HTH) domain found in eukaryotic TFIIE-alpha []. It is also found in proteins from archaebacteria that are presumed to be TFIIE-alpha subunits [], the transcriptional regulator SarR, and also DNA-directed RNA polymerase III subunit Rpc3.; PDB: 1VD4_A 1Q1H_A.
Probab=26.45 E-value=1e+02 Score=25.64 Aligned_cols=47 Identities=21% Similarity=0.210 Sum_probs=29.9
Q ss_pred ccccHHHHHHHcCCChhhHHHHHHHHHhcccceeec--ccccceEEEee
Q psy3716 366 HQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHI--DQVDESFNVTW 412 (436)
Q Consensus 366 r~~sf~~i~~~~~~~~~~ve~lvmka~s~~li~g~i--dqv~~~v~~~w 412 (436)
..++.++||+.++++..+|-.++-+-...|||...- |.-.+.-...|
T Consensus 26 ~~l~de~la~~~~l~~~~vRkiL~~L~~~~lv~~~~~~d~~~~~~~~yw 74 (105)
T PF02002_consen 26 GELTDEDLAKKLGLKPKEVRKILYKLYEDGLVSYRRRKDDERGWTRYYW 74 (105)
T ss_dssp --B-HHHHHHTT-S-HHHHHHHHHHHHHHSS-EEEEE--------EEEE
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeEEEEEEcCCCcEEEEEE
Confidence 368999999999999999999999999999996653 32233334555
No 267
>KOG1840|consensus
Probab=26.41 E-value=8.8e+02 Score=26.54 Aligned_cols=95 Identities=12% Similarity=0.097 Sum_probs=59.9
Q ss_pred CCHHHHHHHHHHHHHhh----cCCcchhHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHHHHHhcccCh--hHHHHHHH
Q psy3716 94 SDQEEALVLLQSFEDKV----KNNLEAKSLCKILQAQMIMNKDADKPGSLDEVEKLIDEIELLVNDIEGV--TAIHSRFY 167 (436)
Q Consensus 94 ~d~~~aL~~L~~l~~~l----~~~~ea~~~~~~~i~~~~l~~~~~~~~~l~~~~~~L~~~~~~L~~~~~~--~~v~~~~y 167 (436)
....+|+..++....-. -.+.+++.-+...+|..+.. .|++++++...+..-+......+. +.+...+-
T Consensus 255 ~k~~eAv~ly~~AL~i~e~~~G~~h~~va~~l~nLa~ly~~-----~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~ 329 (508)
T KOG1840|consen 255 GKYDEAVNLYEEALTIREEVFGEDHPAVAATLNNLAVLYYK-----QGKFAEAEEYCERALEIYEKLLGASHPEVAAQLS 329 (508)
T ss_pred ccHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHhc-----cCChHHHHHHHHHHHHHHHHhhccChHHHHHHHH
Confidence 34566666665543332 23456666666666667777 899999999999888888775554 34444444
Q ss_pred HHHHHHHHHhhcHHH---HHHHHHHHhccC
Q psy3716 168 LVASTLYRKQAKLSL---YYRTALRYLGCV 194 (436)
Q Consensus 168 ~~~a~~~k~~~~~~~---~Y~~~L~yL~~~ 194 (436)
. .+..+..++++++ +|+.+++.+...
T Consensus 330 ~-~~~~~~~~~~~Eea~~l~q~al~i~~~~ 358 (508)
T KOG1840|consen 330 E-LAAILQSMNEYEEAKKLLQKALKIYLDA 358 (508)
T ss_pred H-HHHHHHHhcchhHHHHHHHHHHHHHHhh
Confidence 4 4444555666654 788888755543
No 268
>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=26.35 E-value=75 Score=28.04 Aligned_cols=27 Identities=22% Similarity=0.256 Sum_probs=24.7
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
..|+++||+.+++|..-|...+-+|..
T Consensus 138 g~s~~eIA~~l~is~~tv~~~l~ra~~ 164 (170)
T TIGR02952 138 NLPIAEVARILGKTEGAVKILQFRAIK 164 (170)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 599999999999999999999988864
No 269
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=26.33 E-value=1.2e+02 Score=33.23 Aligned_cols=90 Identities=14% Similarity=0.128 Sum_probs=52.6
Q ss_pred cccCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCC---cc-EEEEEe------cccc-----------------cc
Q psy3716 300 HQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQV---DE-SFNVTW------VQPR-----------------VL 352 (436)
Q Consensus 300 r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv---~~-~v~vtw------v~pR-----------------vL 352 (436)
|.-+.++||+.+++++++|..+. + +.... -++|.. ++ .-.... ..|- .|
T Consensus 373 r~PT~eELAe~Lgis~e~V~~~~-~-~~~~~--~SLD~~i~~d~~~~l~d~l~D~~~~~p~~~~~~~~l~~~L~~aL~~L 448 (509)
T PRK05901 373 REPTPEELAKEMGFTPEKVREIQ-K-YNREP--ISLDKTIGKEGDSQFGDFIEDSEAVSPVDAVSFTLLQDQLQEVLETL 448 (509)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHH-H-hcCCC--cccccccccCCcccHHHhccCCCCCCHHHHHHHHHHHHHHHHHHhhC
Confidence 67789999999999999999873 3 22222 133332 00 000000 0110 12
Q ss_pred ccch--hhccccC--CcccccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 353 SKDQ--LAFKKIP--GSHQLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 353 ~l~Q--i~~lr~~--~~r~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
+.-| +..++-. ..+..|+++||+..|++.+-|-.+--+|+.
T Consensus 449 ~eREr~VI~lRyGL~~~e~~TL~EIa~~lGVSrERVRQIe~kAL~ 493 (509)
T PRK05901 449 SEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLR 493 (509)
T ss_pred CHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 2221 2222211 245789999999999999988888777765
No 270
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=26.31 E-value=72 Score=29.33 Aligned_cols=27 Identities=26% Similarity=0.392 Sum_probs=24.5
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
..|+++||+.+|+|..-|...+-+|..
T Consensus 158 ~~s~~EIA~~Lgis~~tVk~~l~ra~~ 184 (194)
T PRK09646 158 GLTYREVAERLAVPLGTVKTRMRDGLI 184 (194)
T ss_pred CCCHHHHHHHhCCChHhHHHHHHHHHH
Confidence 699999999999999999999888764
No 271
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=26.23 E-value=74 Score=28.02 Aligned_cols=27 Identities=22% Similarity=0.333 Sum_probs=25.0
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
.+|.+|||+.+|+|..-|...+-+|..
T Consensus 122 g~s~~EIA~~lgis~~tV~~~l~Rar~ 148 (160)
T PRK09642 122 EKSYQEIALQEKIEVKTVEMKLYRARK 148 (160)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 589999999999999999999998865
No 272
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=26.04 E-value=75 Score=27.84 Aligned_cols=27 Identities=19% Similarity=0.051 Sum_probs=24.7
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
.+|++|||+.+++|..-|...+.+|+.
T Consensus 122 g~s~~EIA~~lgis~~tV~~~l~ra~~ 148 (161)
T PRK09047 122 DMDVAETAAAMGCSEGSVKTHCSRATH 148 (161)
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 589999999999999999999988865
No 273
>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=25.94 E-value=74 Score=28.65 Aligned_cols=27 Identities=30% Similarity=0.124 Sum_probs=24.8
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
.+|++|||+.+++|..-|...+-+|..
T Consensus 150 g~s~~EIA~~lgis~~tVk~~l~Rar~ 176 (183)
T TIGR02999 150 GLTVEEIAELLGVSVRTVERDWRFARA 176 (183)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 589999999999999999999988865
No 274
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=25.90 E-value=74 Score=29.57 Aligned_cols=27 Identities=15% Similarity=0.245 Sum_probs=24.5
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
..||++||+.+|+|+.-|...+-+|..
T Consensus 155 g~s~~EIA~~lgis~~tVk~~l~RAr~ 181 (201)
T PRK12545 155 DFEIDDICTELTLTANHCSVLLYRART 181 (201)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 689999999999999999998887764
No 275
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=25.73 E-value=1.4e+02 Score=30.44 Aligned_cols=28 Identities=11% Similarity=0.107 Sum_probs=24.3
Q ss_pred ccccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 366 HQLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 366 r~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
...|+++||+..+++.+-|-.+-.+|+.
T Consensus 281 ~~~Tl~eIa~~lgvS~eRVrQIe~~Al~ 308 (324)
T PRK07921 281 QPRTLDQIGKLFGLSRERVRQIEREVMS 308 (324)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4689999999999999988888877775
No 276
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=25.66 E-value=75 Score=28.49 Aligned_cols=27 Identities=22% Similarity=0.313 Sum_probs=24.9
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
.+|++|||+.+++|..-|.-.+-+|+.
T Consensus 135 g~s~~EIA~~lgis~~tV~~~l~ra~~ 161 (172)
T PRK12523 135 GMGHAEIAERLGVSVSRVRQYLAQGLR 161 (172)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 579999999999999999999998875
No 277
>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=25.58 E-value=1.6e+02 Score=21.76 Aligned_cols=35 Identities=17% Similarity=0.275 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHHHhhcCCCCcccCHHHHHHHhCCChhhHHHHH
Q psy3716 279 LSQKIALLCLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLI 322 (436)
Q Consensus 279 l~~KirLlaL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lv 322 (436)
+.+|+.++...+ . .. +..+||+.+|++...|-.++
T Consensus 9 l~eK~~iI~~~e----~----g~-s~~~ia~~fgv~~sTv~~I~ 43 (53)
T PF04218_consen 9 LEEKLEIIKRLE----E----GE-SKRDIAREFGVSRSTVSTIL 43 (53)
T ss_dssp HHHHHHHHHHHH----C----TT--HHHHHHHHT--CCHHHHHH
T ss_pred HHHHHHHHHHHH----c----CC-CHHHHHHHhCCCHHHHHHHH
Confidence 678888877764 1 23 89999999999999887765
No 278
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=25.55 E-value=78 Score=28.97 Aligned_cols=27 Identities=19% Similarity=0.273 Sum_probs=24.4
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
.+|+++||+.+++|+.-|...+-+|..
T Consensus 146 g~s~~EIA~~lgis~~tVk~~l~Rar~ 172 (185)
T PRK09649 146 GLSYADAAAVCGCPVGTIRSRVARARD 172 (185)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 689999999999999999999877764
No 279
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=25.54 E-value=1.1e+02 Score=24.23 Aligned_cols=35 Identities=26% Similarity=0.282 Sum_probs=31.7
Q ss_pred ccccHHHHHHHcCCChhhHHHHHHHHHhcccceee
Q psy3716 366 HQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGH 400 (436)
Q Consensus 366 r~~sf~~i~~~~~~~~~~ve~lvmka~s~~li~g~ 400 (436)
+.++..+||+.+++|..-|-..+-.-...|+|...
T Consensus 19 ~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~ 53 (91)
T smart00346 19 GGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQD 53 (91)
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeec
Confidence 46999999999999999999999998899999763
No 280
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=25.52 E-value=77 Score=29.16 Aligned_cols=27 Identities=11% Similarity=0.146 Sum_probs=24.5
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
.+||++||+.+++|+..|...+=+|..
T Consensus 132 g~s~~EIA~~Lgis~~tVk~~l~Rar~ 158 (187)
T PRK12516 132 GFAYEEAAEICGCAVGTIKSRVNRARQ 158 (187)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 699999999999999999999877764
No 281
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=25.47 E-value=82 Score=29.86 Aligned_cols=40 Identities=13% Similarity=0.208 Sum_probs=31.6
Q ss_pred hhcCCCCcccCHHHHHHHhCCChhhHHHHHHHHHhCCccccccc
Q psy3716 293 FKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHID 336 (436)
Q Consensus 293 ~~~p~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~ID 336 (436)
|.-| |.++..+||+.+||+..-+..-+=+|.+ +|+++.++
T Consensus 173 Fd~P---R~~~l~dLA~~lGISkst~~ehLRrAe~-Kl~~~~~~ 212 (215)
T COG3413 173 FDYP---RRVSLKDLAKELGISKSTLSEHLRRAER-KLIEAYFD 212 (215)
T ss_pred CCCC---ccCCHHHHHHHhCCCHHHHHHHHHHHHH-HHHHHhhh
Confidence 4556 9999999999999999999988888775 45544433
No 282
>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=25.38 E-value=78 Score=27.88 Aligned_cols=27 Identities=33% Similarity=0.345 Sum_probs=25.1
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
.+|.++||+.+++|.+-|.-.+.+|..
T Consensus 126 g~s~~eIA~~lgis~~tV~~~l~ra~~ 152 (162)
T TIGR02983 126 DLSEAQVAEALGISVGTVKSRLSRALA 152 (162)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 589999999999999999999999875
No 283
>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=25.23 E-value=82 Score=27.51 Aligned_cols=27 Identities=11% Similarity=0.054 Sum_probs=24.0
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
..|+++||+.+|+|...|...+-+|..
T Consensus 127 g~~~~eIA~~l~is~~tv~~~l~Rar~ 153 (159)
T TIGR02989 127 GVSLTALAEQLGRTVNAVYKALSRLRV 153 (159)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 689999999999999999998877653
No 284
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=25.15 E-value=80 Score=29.06 Aligned_cols=27 Identities=26% Similarity=0.134 Sum_probs=24.6
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
..|+++||+.||+++.-|...+-+|..
T Consensus 144 g~s~~EIA~~lgis~~tV~~~l~Rar~ 170 (188)
T PRK12517 144 GFSGEEIAEILDLNKNTVMTRLFRARN 170 (188)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 689999999999999999999888764
No 285
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=25.12 E-value=99 Score=28.03 Aligned_cols=40 Identities=15% Similarity=0.145 Sum_probs=34.6
Q ss_pred cccccHHHHHHHcCCChhhHHHHHHHHHhcccceeecccc
Q psy3716 365 SHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQV 404 (436)
Q Consensus 365 ~r~~sf~~i~~~~~~~~~~ve~lvmka~s~~li~g~idqv 404 (436)
+-.+|+.+||++++++..-|-.=+=|-...|.|+|..=.+
T Consensus 26 d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~GvI~~~~~~v 65 (164)
T PRK11169 26 DGRISNVELSKRVGLSPTPCLERVRRLERQGFIQGYTALL 65 (164)
T ss_pred CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEEEE
Confidence 3468999999999999999999999999999999844333
No 286
>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=25.10 E-value=76 Score=30.90 Aligned_cols=27 Identities=22% Similarity=0.143 Sum_probs=25.3
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
.+||++||+.+|+|+.-|+..+-+|..
T Consensus 177 g~S~~EIA~~Lgis~~TVk~rl~RAr~ 203 (244)
T TIGR03001 177 GLSMDRIGAMYQVHRSTVSRWVAQARE 203 (244)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 689999999999999999999998875
No 287
>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits, TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF []. This entry represents a helix-turn-helix (HTH) domain found in eukaryotic TFIIE-alpha []. It is also found in proteins from archaebacteria that are presumed to be TFIIE-alpha subunits [], the transcriptional regulator SarR, and also DNA-directed RNA polymerase III subunit Rpc3.; PDB: 1VD4_A 1Q1H_A.
Probab=25.00 E-value=59 Score=27.16 Aligned_cols=35 Identities=23% Similarity=0.223 Sum_probs=27.6
Q ss_pred cccCHHHHHHHhCCChhhHHHHHHHHHhCCccccc
Q psy3716 300 HQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGH 334 (436)
Q Consensus 300 r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~ 334 (436)
+.++-++||+.++++..+|-.++-+....|+|..+
T Consensus 26 ~~l~de~la~~~~l~~~~vRkiL~~L~~~~lv~~~ 60 (105)
T PF02002_consen 26 GELTDEDLAKKLGLKPKEVRKILYKLYEDGLVSYR 60 (105)
T ss_dssp --B-HHHHHHTT-S-HHHHHHHHHHHHHHSS-EEE
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeEEE
Confidence 47999999999999999999999999999999764
No 288
>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=24.96 E-value=1.6e+02 Score=20.38 Aligned_cols=28 Identities=11% Similarity=0.307 Sum_probs=23.4
Q ss_pred cCHHHHHHHhCCChhhHHHHHHHHHhCCcccc
Q psy3716 302 LSFAEISEAAQLPLIEVEFLIIKALALGLVKG 333 (436)
Q Consensus 302 isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G 333 (436)
++-+++|+.++++...|..| ...|++.+
T Consensus 1 ~~~~e~a~~~gv~~~tlr~~----~~~g~l~~ 28 (49)
T cd04761 1 YTIGELAKLTGVSPSTLRYY----ERIGLLSP 28 (49)
T ss_pred CcHHHHHHHHCcCHHHHHHH----HHCCCCCC
Confidence 35689999999999999999 46777764
No 289
>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=24.82 E-value=82 Score=28.95 Aligned_cols=27 Identities=15% Similarity=0.215 Sum_probs=24.2
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
..||++||+.+|+|..-|...+-+|..
T Consensus 147 g~s~~EIA~~lgis~~tvk~rl~Rar~ 173 (188)
T TIGR02943 147 GFESDEICQELEISTSNCHVLLYRARL 173 (188)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 699999999999999999999877743
No 290
>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=24.63 E-value=45 Score=23.60 Aligned_cols=35 Identities=26% Similarity=0.204 Sum_probs=22.0
Q ss_pred ccccccc---hhhccccCCcccccHHHHHHHcCCChhhHHH
Q psy3716 349 PRVLSKD---QLAFKKIPGSHQLSFAEISEAAQLPLIEVEF 386 (436)
Q Consensus 349 pRvL~l~---Qi~~lr~~~~r~~sf~~i~~~~~~~~~~ve~ 386 (436)
|+.++.. ++..|... -.|..+||+.++++..-|-.
T Consensus 3 p~~~~~~~~~~i~~l~~~---G~si~~IA~~~gvsr~TvyR 40 (45)
T PF02796_consen 3 PPKLSKEQIEEIKELYAE---GMSIAEIAKQFGVSRSTVYR 40 (45)
T ss_dssp SSSSSHCCHHHHHHHHHT---T--HHHHHHHTTS-HHHHHH
T ss_pred CCCCCHHHHHHHHHHHHC---CCCHHHHHHHHCcCHHHHHH
Confidence 5666664 44455433 39999999999999877654
No 291
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=24.55 E-value=1.1e+02 Score=23.77 Aligned_cols=33 Identities=24% Similarity=0.308 Sum_probs=28.1
Q ss_pred ccccHHHHHHHcCCChhhHHHHHHHHHhcccce
Q psy3716 366 HQLSFAEISEAAQLPLIEVEFLIIKALALGLVK 398 (436)
Q Consensus 366 r~~sf~~i~~~~~~~~~~ve~lvmka~s~~li~ 398 (436)
..++=.|||+.|+++...|-+.+..--..|.|+
T Consensus 14 ~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~ 46 (62)
T PF04703_consen 14 GPLKTREIADALGLSIYQARYYLEKLEKEGKVE 46 (62)
T ss_dssp S-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEE
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence 358889999999999999999999999988775
No 292
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=24.53 E-value=2.4e+02 Score=23.20 Aligned_cols=67 Identities=13% Similarity=0.115 Sum_probs=45.7
Q ss_pred CHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCCccEEEEEeccccccccchhhccccCCcccccHHHHHHHcCCChh
Q psy3716 303 SFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPRVLSKDQLAFKKIPGSHQLSFAEISEAAQLPLI 382 (436)
Q Consensus 303 sf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv~~~v~vtwv~pRvL~l~Qi~~lr~~~~r~~sf~~i~~~~~~~~~ 382 (436)
+..++|+.+||+.+-+-+| -..|||......-+ .+|.++..++..++ +=--.+.+|+|++
T Consensus 2 ~i~eva~~~gvs~~tlR~y----e~~Gll~p~~~~~~--------gyR~Y~~~~~~~l~--------~I~~lr~~G~~l~ 61 (97)
T cd04782 2 TTGEFAKLCGISKQTLFHY----DKIGLFKPEIVKEN--------GYRYYTLEQFEQLD--------IILLLKELGISLK 61 (97)
T ss_pred CHHHHHHHHCcCHHHHHHH----HHCCCCCCCccCCC--------CCccCCHHHHHHHH--------HHHHHHHcCCCHH
Confidence 6789999999999999988 34799877532222 35788777766553 1112456777888
Q ss_pred hHHHHHH
Q psy3716 383 EVEFLII 389 (436)
Q Consensus 383 ~ve~lvm 389 (436)
++..++-
T Consensus 62 eI~~~l~ 68 (97)
T cd04782 62 EIKDYLD 68 (97)
T ss_pred HHHHHHh
Confidence 7776653
No 293
>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=24.41 E-value=86 Score=27.93 Aligned_cols=27 Identities=30% Similarity=0.362 Sum_probs=24.3
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
..|+++||+.+|+|+..|...+-+|..
T Consensus 135 g~s~~eiA~~lgis~~tv~~~l~Ra~~ 161 (169)
T TIGR02954 135 DLTIKEIAEVMNKPEGTVKTYLHRALK 161 (169)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 589999999999999999998887764
No 294
>COG1601 GCD7 Translation initiation factor 2, beta subunit (eIF-2beta)/eIF-5 N-terminal domain [Translation, ribosomal structure and biogenesis]
Probab=24.39 E-value=2.3e+02 Score=25.98 Aligned_cols=58 Identities=24% Similarity=0.294 Sum_probs=46.6
Q ss_pred HHHHHHHcCCChhhHHHHHHHHHhcccceeecccccceEEEeeecccccchhhhhHHHHHHHhhcc
Q psy3716 370 FAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPRVLSKDQVFWSLEETVATEV 435 (436)
Q Consensus 370 f~~i~~~~~~~~~~ve~lvmka~s~~li~g~idqv~~~v~~~wv~pr~l~~~q~~~~~~~~~~~~~ 435 (436)
|.+||+..+=+++.+..++-|.+. --|++|.-. .+ |--+.++.++|+.-+++-+++=|
T Consensus 49 f~dia~~l~rDp~h~~k~l~kel~---t~g~~d~~~-rl----vl~g~f~~~~i~~~i~~yi~~yv 106 (151)
T COG1601 49 FGDIAEALNRDPEHLVKFLKKELG---TAGSIDGKG-RL----VLQGKFSDSEIVNEIERYIAEYV 106 (151)
T ss_pred HHHHHHHhcCCHHHHHHHHHHHhc---cccccCCcc-eE----EEEecccHHHHHHHHHHHHHhee
Confidence 779999999999999999999888 678888742 22 33488999999999998887644
No 295
>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=24.30 E-value=85 Score=27.13 Aligned_cols=27 Identities=37% Similarity=0.474 Sum_probs=24.7
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
.+|++|||+.+|+|..-|...+.+|..
T Consensus 129 ~~~~~eIA~~lgis~~tv~~~~~ra~~ 155 (161)
T TIGR02985 129 GKSYKEIAEELGISVKTVEYHISKALK 155 (161)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 589999999999999999999998864
No 296
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=24.29 E-value=85 Score=28.66 Aligned_cols=27 Identities=30% Similarity=0.277 Sum_probs=24.7
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
.+|+++||+.+|+|..-|...+-+|+.
T Consensus 157 g~s~~EIA~~lgis~~tV~~~l~Ra~~ 183 (194)
T PRK12519 157 GLSQSEIAKRLGIPLGTVKARARQGLL 183 (194)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 699999999999999999999888764
No 297
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=24.23 E-value=63 Score=22.83 Aligned_cols=29 Identities=21% Similarity=0.082 Sum_probs=18.5
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHhCC
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALALG 329 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~~g 329 (436)
-.|..+||+.+++|..-|-.|+=+--..|
T Consensus 17 G~s~~~ia~~lgvs~~Tv~~w~kr~~~~G 45 (50)
T PF13384_consen 17 GWSIREIAKRLGVSRSTVYRWIKRYREEG 45 (50)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHT------
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHccccc
Confidence 37899999999999999999986655444
No 298
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=24.22 E-value=2.5e+02 Score=23.08 Aligned_cols=67 Identities=10% Similarity=0.108 Sum_probs=42.9
Q ss_pred cCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCCccEEEEEeccccccccchhhccccCCcccccHHHHHHHcCCCh
Q psy3716 302 LSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPRVLSKDQLAFKKIPGSHQLSFAEISEAAQLPL 381 (436)
Q Consensus 302 isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv~~~v~vtwv~pRvL~l~Qi~~lr~~~~r~~sf~~i~~~~~~~~ 381 (436)
++..++|+.+|+|.+-+-+|- ..|||.......++ +|..+..++..+. +=.-...+|+|+
T Consensus 1 m~i~eva~~~gvs~~tlR~ye----~~Gll~p~~r~~~g--------yR~Y~~~~l~~l~--------~I~~lr~~G~~l 60 (96)
T cd04788 1 WKIGELARRTGLSVRTLHHYD----HIGLLSPSQRTEGG--------HRLYDRADIRRLH--------QIIALRRLGFSL 60 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCccCCCC--------ceeeCHHHHHHHH--------HHHHHHHcCCCH
Confidence 367899999999999999995 58999764433333 4777776654442 111223455566
Q ss_pred hhHHHHH
Q psy3716 382 IEVEFLI 388 (436)
Q Consensus 382 ~~ve~lv 388 (436)
+++..++
T Consensus 61 ~eI~~~l 67 (96)
T cd04788 61 REIGRAL 67 (96)
T ss_pred HHHHHHH
Confidence 5555543
No 299
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=24.16 E-value=83 Score=28.18 Aligned_cols=27 Identities=30% Similarity=0.422 Sum_probs=24.7
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
..|++|||+.+|+|.+-|...+.+|..
T Consensus 135 ~~s~~EIA~~lgis~~tV~~~l~Ra~~ 161 (173)
T PRK12522 135 QYSYKEMSEILNIPIGTVKYRLNYAKK 161 (173)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 589999999999999999999998865
No 300
>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY. This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.
Probab=23.99 E-value=2.6e+02 Score=27.66 Aligned_cols=37 Identities=11% Similarity=0.109 Sum_probs=33.2
Q ss_pred CcccCHHHHHHHhCCChhhHHHHHHHHHhCCcccccc
Q psy3716 299 SHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHI 335 (436)
Q Consensus 299 ~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~I 335 (436)
+..++..+||+.+|++..-|-.-+-+.-+.|+|+++=
T Consensus 196 egrlse~eLAerlGVSRs~ireAlrkLE~aGvIe~r~ 232 (251)
T TIGR02787 196 EGLLVASKIADRVGITRSVIVNALRKLESAGVIESRS 232 (251)
T ss_pred cccccHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecc
Confidence 4689999999999999999999999999999999863
No 301
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=23.75 E-value=86 Score=29.38 Aligned_cols=27 Identities=26% Similarity=0.241 Sum_probs=24.6
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
..||++||+.+|+|+.-|...+-+|..
T Consensus 154 g~s~~EIA~~Lgis~~tV~~~l~RArk 180 (203)
T PRK09647 154 GLSYEEIAATLGVKLGTVRSRIHRGRQ 180 (203)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 699999999999999999999988854
No 302
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=23.71 E-value=88 Score=27.53 Aligned_cols=27 Identities=30% Similarity=0.288 Sum_probs=24.8
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
.+|+++||+.+++|..-|..-+.+|+.
T Consensus 121 ~~s~~eIA~~lgis~~tv~~~l~ra~~ 147 (159)
T PRK12527 121 GLSHQQIAEHLGISRSLVEKHIVNAMK 147 (159)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 589999999999999999999988875
No 303
>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=23.70 E-value=1.2e+02 Score=20.59 Aligned_cols=26 Identities=31% Similarity=0.353 Sum_probs=22.9
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHH
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKAL 326 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi 326 (436)
..+..+||+.++++.+.|-.++-++.
T Consensus 26 ~~~~~~ia~~~~~s~~~i~~~~~~~~ 51 (55)
T cd06171 26 GLSYEEIAEILGISRSTVRQRLHRAL 51 (55)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 58999999999999999988887664
No 304
>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=23.66 E-value=89 Score=29.86 Aligned_cols=28 Identities=11% Similarity=0.089 Sum_probs=24.4
Q ss_pred cccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 300 HQLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 300 r~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
...|+++||+.+|+|++-|...+-+|+.
T Consensus 197 eg~s~~EIA~~Lgis~~tV~~~l~ra~~ 224 (234)
T TIGR02835 197 TEKTQKEVADMLGISQSYISRLEKRILK 224 (234)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3699999999999999999988876654
No 305
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=23.65 E-value=1.2e+02 Score=26.22 Aligned_cols=45 Identities=24% Similarity=0.339 Sum_probs=35.1
Q ss_pred cCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCCccEEEEEeccc
Q psy3716 302 LSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQP 349 (436)
Q Consensus 302 isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv~~~v~vtwv~p 349 (436)
..|.+||++++-+++.|=.++..-++ ..|+||.-++.+.--..++
T Consensus 22 ~Nf~~I~~~L~R~p~hv~kyl~~ELg---t~g~id~~~rlii~G~~~~ 66 (110)
T smart00653 22 VNFADIAKALNRPPDHVLKFLLAELG---TQGSIDGKGRLIVNGRFTP 66 (110)
T ss_pred EcHHHHHHHHCCCHHHHHHHHHHHhC---CceeECCCCeEEEEEeeCH
Confidence 58999999999999999999999888 6889987643333333333
No 306
>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=23.64 E-value=1.5e+02 Score=19.97 Aligned_cols=30 Identities=20% Similarity=0.232 Sum_probs=23.5
Q ss_pred cCHHHHHHHhCCChhhHHHHHHHHHhCCcc
Q psy3716 302 LSFAEISEAAQLPLIEVEFLIIKALALGLV 331 (436)
Q Consensus 302 isf~~Ia~~l~i~~~eVE~lvikAi~~gLI 331 (436)
+|=++||+.++++.+-|=..+=+.-..|+|
T Consensus 3 mtr~diA~~lG~t~ETVSR~l~~l~~~glI 32 (32)
T PF00325_consen 3 MTRQDIADYLGLTRETVSRILKKLERQGLI 32 (32)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred cCHHHHHHHhCCcHHHHHHHHHHHHHcCCC
Confidence 567899999999999998888887777775
No 307
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=23.61 E-value=89 Score=28.26 Aligned_cols=27 Identities=22% Similarity=0.231 Sum_probs=24.0
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
..|+++||+.+|+|..-|...+=+|..
T Consensus 151 ~~s~~eIA~~lgis~~~V~~~l~ra~~ 177 (186)
T PRK13919 151 GYTHREAAQLLGLPLGTLKTRARRALS 177 (186)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 699999999999999999988777654
No 308
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=23.42 E-value=1.7e+02 Score=28.48 Aligned_cols=46 Identities=15% Similarity=0.060 Sum_probs=36.8
Q ss_pred HHHHHHHHHhhcCCCCcccCHHHHHHHhCCChhhHHHHHHHHHhCCccc
Q psy3716 284 ALLCLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVK 332 (436)
Q Consensus 284 rLlaL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~ 332 (436)
|-+.+++.....+ +.++..+|++.+++|..-|-.++-.....|+|+
T Consensus 12 ral~iL~~l~~~~---~~ls~~eia~~lgl~kstv~RlL~tL~~~g~v~ 57 (263)
T PRK09834 12 RGLMVLRALNRLD---GGATVGLLAELTGLHRTTVRRLLETLQEEGYVR 57 (263)
T ss_pred HHHHHHHHHHhcC---CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 4455555443332 459999999999999999999999999999996
No 309
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.
Probab=23.38 E-value=92 Score=29.62 Aligned_cols=28 Identities=18% Similarity=0.103 Sum_probs=24.2
Q ss_pred cccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 300 HQLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 300 r~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
..+|+++||+.+++|..-|...+-+|+.
T Consensus 193 e~~S~~EIAe~lgis~~tV~~~~~rAl~ 220 (227)
T TIGR02846 193 RRKTQREIAKILGISRSYVSRIEKRALM 220 (227)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3689999999999999999988766654
No 310
>PRK10870 transcriptional repressor MprA; Provisional
Probab=23.36 E-value=2.7e+02 Score=25.54 Aligned_cols=51 Identities=12% Similarity=0.027 Sum_probs=45.8
Q ss_pred cccCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCCccEEEEEecccc
Q psy3716 300 HQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPR 350 (436)
Q Consensus 300 r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv~~~v~vtwv~pR 350 (436)
..++..+||+.++++..-|=..|=+....|+|+-.-|.-++.+..-..++.
T Consensus 70 ~~it~~eLa~~l~l~~~tvsr~v~rLe~kGlV~R~~~~~DrR~~~v~LT~~ 120 (176)
T PRK10870 70 HSIQPSELSCALGSSRTNATRIADELEKRGWIERRESDNDRRCLHLQLTEK 120 (176)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHH
Confidence 579999999999999999999999999999999999999887776666665
No 311
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=23.36 E-value=1.1e+02 Score=27.70 Aligned_cols=63 Identities=14% Similarity=0.063 Sum_probs=44.4
Q ss_pred cccccHHHHHHHcCCChhhHHHHHHHHHhcccceeecccccceEEEeeecccccchhhhhHHHHH
Q psy3716 365 SHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPRVLSKDQVFWSLEE 429 (436)
Q Consensus 365 ~r~~sf~~i~~~~~~~~~~ve~lvmka~s~~li~g~idqv~~~v~~~wv~pr~l~~~q~~~~~~~ 429 (436)
++.+|-++||+..++|..-++.++-+--..|||+..- +..|-.... -.|.-.+.-+|...++.
T Consensus 22 ~~~~s~~eIA~~~~is~~~L~kIl~~L~~aGlv~S~r-G~~GGy~La-~~p~eItl~dIi~aveg 84 (153)
T PRK11920 22 GKLSRIPEIARAYGVSELFLFKILQPLVEAGLVETVR-GRNGGVRLG-RPAADISLFDVVRVTED 84 (153)
T ss_pred CCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeec-CCCCCeeec-CCHHHCcHHHHHHHHcC
Confidence 4568999999999999999999999988889987544 344444332 23455555555555543
No 312
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=23.26 E-value=92 Score=28.54 Aligned_cols=27 Identities=7% Similarity=0.121 Sum_probs=24.5
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
..|+++||+.+++|+.-|...+-+|..
T Consensus 127 g~s~~EIA~~Lgis~~tV~~~l~RAr~ 153 (182)
T PRK12540 127 GFSYEDAAAICGCAVGTIKSRVNRARS 153 (182)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 689999999999999999999887764
No 313
>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=23.25 E-value=86 Score=28.68 Aligned_cols=27 Identities=19% Similarity=0.233 Sum_probs=24.8
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
.+|++|||+.+++|..-|...+-+|..
T Consensus 147 g~s~~EIA~~lgis~~tVk~~l~Rar~ 173 (193)
T TIGR02947 147 GFAYKEIAEIMGTPIGTVMSRLHRGRK 173 (193)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 589999999999999999999988865
No 314
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=23.16 E-value=1.7e+02 Score=20.80 Aligned_cols=32 Identities=25% Similarity=0.222 Sum_probs=28.3
Q ss_pred cc-cHHHHHHHcCCChhhHHHHHHHHHhcccce
Q psy3716 367 QL-SFAEISEAAQLPLIEVEFLIIKALALGLVK 398 (436)
Q Consensus 367 ~~-sf~~i~~~~~~~~~~ve~lvmka~s~~li~ 398 (436)
.+ |..+||+.++++..-|...+-+--+.|+|.
T Consensus 19 ~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i~ 51 (60)
T smart00345 19 KLPSERELAAQLGVSRTTVREALSRLEAEGLVQ 51 (60)
T ss_pred cCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 35 899999999999999999998888888875
No 315
>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=23.15 E-value=95 Score=26.93 Aligned_cols=27 Identities=30% Similarity=0.434 Sum_probs=23.6
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
..|+++||+.+|+|+.-|...+=+|..
T Consensus 121 g~s~~eIA~~lgis~~tv~~~l~Ra~~ 147 (154)
T TIGR02950 121 EFSYKEIAELLNLSLAKVKSNLFRARK 147 (154)
T ss_pred cCcHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 589999999999999999988877643
No 316
>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=23.12 E-value=92 Score=28.09 Aligned_cols=27 Identities=26% Similarity=0.346 Sum_probs=24.1
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
..+|++||+.+|++.+-|...+-+|..
T Consensus 154 ~~s~~EIA~~lgis~~tv~~~l~rar~ 180 (190)
T TIGR02939 154 GLSYEDIARIMDCPVGTVRSRIFRARE 180 (190)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 689999999999999999999877753
No 317
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=23.03 E-value=95 Score=27.51 Aligned_cols=27 Identities=33% Similarity=0.385 Sum_probs=24.1
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
..|+++||+.+|+|..-|...+-+|..
T Consensus 144 ~~s~~eIA~~lgis~~tV~~~l~ra~~ 170 (182)
T PRK09652 144 GLSYEEIAEIMGCPIGTVRSRIFRARE 170 (182)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 689999999999999999988877654
No 318
>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=22.94 E-value=97 Score=26.74 Aligned_cols=27 Identities=37% Similarity=0.474 Sum_probs=24.4
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
.+|+++||+.+|+|..-|...+-+|..
T Consensus 129 ~~~~~eIA~~lgis~~tv~~~~~ra~~ 155 (161)
T TIGR02985 129 GKSYKEIAEELGISVKTVEYHISKALK 155 (161)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 689999999999999999999888754
No 319
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=22.81 E-value=95 Score=28.14 Aligned_cols=27 Identities=30% Similarity=0.256 Sum_probs=24.2
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
..|+++||+.+++|+.-|...+=+|..
T Consensus 145 g~s~~EIA~~l~is~~tV~~~l~rar~ 171 (181)
T PRK12536 145 GLSVAETAQLTGLSESAVKVGIHRGLK 171 (181)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 689999999999999999999877654
No 320
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=22.71 E-value=95 Score=28.47 Aligned_cols=27 Identities=15% Similarity=0.156 Sum_probs=24.0
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
..|+++||+.+|+|..-|...+-+|..
T Consensus 152 g~s~~EIA~~lgis~~tVk~~l~Rar~ 178 (195)
T PRK12532 152 GFSSDEIQQMCGISTSNYHTIMHRARE 178 (195)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 689999999999999999988877653
No 321
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=22.67 E-value=94 Score=28.89 Aligned_cols=27 Identities=15% Similarity=0.217 Sum_probs=23.7
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
..||++||+.+++|++-|...+=+|..
T Consensus 149 g~s~~EIAe~lgis~~tV~~~l~Rar~ 175 (196)
T PRK12535 149 GYTYEEAAKIADVRVGTIRSRVARARA 175 (196)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 589999999999999999999876543
No 322
>cd05804 StaR_like StaR_like; a well-conserved protein found in bacteria, plants, and animals. A family member from Streptomyces toyocaensis, StaR is part of a gene cluster involved in the biosynthesis of glycopeptide antibiotics (GPAs), specifically A47934. It has been speculated that StaR could be a flavoprotein hydroxylating a tyrosine sidechain. Some family members have been annotated as proteins containing tetratricopeptide (TPR) repeats, which may at least indicate mostly alpha-helical secondary structure.
Probab=22.59 E-value=6.1e+02 Score=24.91 Aligned_cols=53 Identities=11% Similarity=0.117 Sum_probs=31.1
Q ss_pred cCCCHHHHHHHHHHHHHhhcCCcchhHHHHHHHHHHhhccCCCCCCChHHHHHHHHHH
Q psy3716 92 HLSDQEEALVLLQSFEDKVKNNLEAKSLCKILQAQMIMNKDADKPGSLDEVEKLIDEI 149 (436)
Q Consensus 92 ~~~d~~~aL~~L~~l~~~l~~~~ea~~~~~~~i~~~~l~~~~~~~~~l~~~~~~L~~~ 149 (436)
...+.++++.++.+.....+.+....+.+....+.+++. .|+++++...+++.
T Consensus 160 ~~g~~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~~~~~-----~G~~~~A~~~~~~~ 212 (355)
T cd05804 160 MQGRFKEGIAFMESWRDTWDCSSMLRGHNWWHLALFYLE-----RGDYEAALAIYDTH 212 (355)
T ss_pred HcCCHHHHHHHHHhhhhccCCCcchhHHHHHHHHHHHHH-----CCCHHHHHHHHHHH
Confidence 344566666666665554433333334444556666666 77777777776665
No 323
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=22.46 E-value=93 Score=28.55 Aligned_cols=27 Identities=26% Similarity=0.250 Sum_probs=25.2
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
..|++|||+.+++|..-|...+.+|..
T Consensus 127 g~s~~EIA~~lgis~~tV~~~l~Rar~ 153 (182)
T PRK12511 127 GLSYQEAAAVLGIPIGTLMSRIGRARA 153 (182)
T ss_pred CCCHHHHHHHhCcCHHHHHHHHHHHHH
Confidence 589999999999999999999998876
No 324
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=22.43 E-value=1e+02 Score=21.57 Aligned_cols=22 Identities=18% Similarity=0.219 Sum_probs=18.2
Q ss_pred HHHHHHHhCCChhhHHHHHHHH
Q psy3716 304 FAEISEAAQLPLIEVEFLIIKA 325 (436)
Q Consensus 304 f~~Ia~~l~i~~~eVE~lvikA 325 (436)
-..||+.+|++..+|..|.+.|
T Consensus 16 k~~L~~~tgls~~Qi~~WF~Na 37 (40)
T PF05920_consen 16 KEELAKQTGLSRKQISNWFINA 37 (40)
T ss_dssp HHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHHHHh
Confidence 3678999999999999999876
No 325
>COG2178 Predicted RNA-binding protein of the translin family [Translation, ribosomal structure and biogenesis]
Probab=22.41 E-value=5.6e+02 Score=24.62 Aligned_cols=45 Identities=18% Similarity=0.310 Sum_probs=28.0
Q ss_pred hHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHHHHHhcccChhHHHHHHHH
Q psy3716 117 KSLCKILQAQMIMNKDADKPGSLDEVEKLIDEIELLVNDIEGVTAIHSRFYL 168 (436)
Q Consensus 117 ~~~~~~~i~~~~l~~~~~~~~~l~~~~~~L~~~~~~L~~~~~~~~v~~~~y~ 168 (436)
..+|...| +.+. .|++++++.-++++.+.++++...-.-+..+|.
T Consensus 30 ~r~s~~aI--~~~H-----~~~~eeA~~~l~~a~~~v~~Lk~~l~~~pel~~ 74 (204)
T COG2178 30 VRLSGEAI--FLLH-----RGDFEEAEKKLKKASEAVEKLKRLLAGFPELYF 74 (204)
T ss_pred HHHHHHHH--HHHH-----hccHHHHHHHHHHHHHHHHHHHHHHhhhHHHHH
Confidence 34444333 5555 789999999888888887765533333334444
No 326
>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A.
Probab=22.40 E-value=3.7e+02 Score=20.74 Aligned_cols=76 Identities=22% Similarity=0.211 Sum_probs=43.5
Q ss_pred HHHHHHHHHHHHhhccCchhHHHHHHHHhccCCCHHHHHHHHHHHHHhhcCCcchhHHHHHHHHHHhhccCCCCCCChHH
Q psy3716 62 LRDLYHKFVISFETKINPVSLMEIMEVITNHLSDQEEALVLLQSFEDKVKNNLEAKSLCKILQAQMIMNKDADKPGSLDE 141 (436)
Q Consensus 62 ~~~ly~~fI~~f~~kin~l~l~~i~~~v~~~~~d~~~aL~~L~~l~~~l~~~~ea~~~~~~~i~~~~l~~~~~~~~~l~~ 141 (436)
-+.+|+..+..-..+-++.-+-. +..+.-+..+.+.|++++++ .++.+.. .-+...+|+..+. .|++++
T Consensus 8 Ai~~~~k~~~~~~~~~~~~~~~~-la~~~~~~~~y~~A~~~~~~--~~~~~~~---~~~~~l~a~~~~~-----l~~y~e 76 (84)
T PF12895_consen 8 AIKYYEKLLELDPTNPNSAYLYN-LAQCYFQQGKYEEAIELLQK--LKLDPSN---PDIHYLLARCLLK-----LGKYEE 76 (84)
T ss_dssp HHHHHHHHHHHHCGTHHHHHHHH-HHHHHHHTTHHHHHHHHHHC--HTHHHCH---HHHHHHHHHHHHH-----TT-HHH
T ss_pred HHHHHHHHHHHCCCChhHHHHHH-HHHHHHHCCCHHHHHHHHHH--hCCCCCC---HHHHHHHHHHHHH-----hCCHHH
Confidence 45666766665443112222222 22333345678999999988 3333321 2233345778887 899999
Q ss_pred HHHHHHH
Q psy3716 142 VEKLIDE 148 (436)
Q Consensus 142 ~~~~L~~ 148 (436)
+.+.+++
T Consensus 77 Ai~~l~~ 83 (84)
T PF12895_consen 77 AIKALEK 83 (84)
T ss_dssp HHHHHHH
T ss_pred HHHHHhc
Confidence 9988875
No 327
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=22.39 E-value=93 Score=28.29 Aligned_cols=27 Identities=22% Similarity=0.247 Sum_probs=24.4
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
..|+++||+.+|+|.+-|...+=+|..
T Consensus 147 g~s~~eIA~~lgis~~tV~~~l~ra~~ 173 (184)
T PRK12539 147 GLSVAEAATRSGMSESAVKVSVHRGLK 173 (184)
T ss_pred CCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 689999999999999999999877764
No 328
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=22.32 E-value=94 Score=28.39 Aligned_cols=27 Identities=22% Similarity=0.259 Sum_probs=24.3
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
..|++|||+.+++|..-|.-.+-+|..
T Consensus 147 g~s~~EIA~~lgis~~tV~~~l~Rar~ 173 (191)
T PRK12520 147 ELETEEICQELQITATNAWVLLYRARM 173 (191)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 479999999999999999999888754
No 329
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=22.30 E-value=99 Score=28.14 Aligned_cols=27 Identities=33% Similarity=0.167 Sum_probs=24.5
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
..|+++||+.+|+|..-|...+-+|+.
T Consensus 155 g~s~~EIA~~lgis~~tV~~~l~Ra~~ 181 (189)
T PRK09648 155 GLSAEETAEAVGSTPGAVRVAQHRALA 181 (189)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 589999999999999999999888764
No 330
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=22.29 E-value=99 Score=27.58 Aligned_cols=27 Identities=26% Similarity=0.271 Sum_probs=24.0
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
..|+++||+.+|+|..-|...+-+|..
T Consensus 136 g~s~~eIA~~lg~s~~tv~~~l~Rar~ 162 (175)
T PRK12518 136 DLPQKEIAEILNIPVGTVKSRLFYARR 162 (175)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 589999999999999999998887754
No 331
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=22.22 E-value=98 Score=27.30 Aligned_cols=27 Identities=26% Similarity=0.332 Sum_probs=24.8
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
.+|++|||+.+++|..-|..-+-+|..
T Consensus 129 g~s~~EIA~~l~is~~tV~~~l~ra~~ 155 (161)
T PRK12528 129 GLGYGEIATELGISLATVKRYLNKAAM 155 (161)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 579999999999999999999998864
No 332
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=22.16 E-value=72 Score=29.51 Aligned_cols=34 Identities=24% Similarity=0.113 Sum_probs=30.8
Q ss_pred cHHHHHHHc--CCChhhHHHHHHHHHhcccceeecc
Q psy3716 369 SFAEISEAA--QLPLIEVEFLIIKALALGLVKGHID 402 (436)
Q Consensus 369 sf~~i~~~~--~~~~~~ve~lvmka~s~~li~g~id 402 (436)
...+||++| ++|.++|+.-+=.-..+|||+-.=|
T Consensus 41 d~~~iak~l~p~is~~ev~~sL~~L~~~gli~k~~~ 76 (171)
T PF14394_consen 41 DPEWIAKRLRPKISAEEVRDSLEFLEKLGLIKKDGD 76 (171)
T ss_pred CHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEECCC
Confidence 788999999 9999999999999999999986555
No 333
>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=22.13 E-value=2.6e+02 Score=20.15 Aligned_cols=32 Identities=28% Similarity=0.236 Sum_probs=28.9
Q ss_pred cc-CHHHHHHHhCCChhhHHHHHHHHHhCCccc
Q psy3716 301 QL-SFAEISEAAQLPLIEVEFLIIKALALGLVK 332 (436)
Q Consensus 301 ~i-sf~~Ia~~l~i~~~eVE~lvikAi~~gLI~ 332 (436)
.+ +-.+||+.++++...|-..+-+.-..|+|.
T Consensus 24 ~~~~~~~la~~~~is~~~v~~~l~~L~~~G~i~ 56 (66)
T cd07377 24 RLPSERELAEELGVSRTTVREALRELEAEGLVE 56 (66)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 44 499999999999999999999999999986
No 334
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=22.07 E-value=1.2e+02 Score=26.89 Aligned_cols=34 Identities=24% Similarity=0.203 Sum_probs=32.2
Q ss_pred cccCHHHHHHHhCCChhhHHHHHHHHHhCCcccc
Q psy3716 300 HQLSFAEISEAAQLPLIEVEFLIIKALALGLVKG 333 (436)
Q Consensus 300 r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G 333 (436)
+.++-++||+.++++..-|..-|-+.+..|||.=
T Consensus 41 ~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~R 74 (126)
T COG3355 41 GPLTVDELAEILNRSRSTVYRSLQNLLEAGLVER 74 (126)
T ss_pred CCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeee
Confidence 5699999999999999999999999999999975
No 335
>COG5600 Transcription-associated recombination protein [DNA replication, recombination, and repair]
Probab=22.00 E-value=1.2e+02 Score=31.96 Aligned_cols=99 Identities=20% Similarity=0.276 Sum_probs=60.9
Q ss_pred hhHHHHHHHHHhCCccccc---ccCCcc-----EEEEEecc------ccccccchhhccccCCcc-cccHHHHHHHcCC-
Q psy3716 316 IEVEFLIIKALALGLVKGH---IDQVDE-----SFNVTWVQ------PRVLSKDQLAFKKIPGSH-QLSFAEISEAAQL- 379 (436)
Q Consensus 316 ~eVE~lvikAi~~gLI~G~---IDQv~~-----~v~vtwv~------pRvL~l~Qi~~lr~~~~r-~~sf~~i~~~~~~- 379 (436)
-+|-.=+++|+..|.|+|- +.+-.+ .+++|=.- -|.+=..+|.+-... .| .+|.-.|+.+...
T Consensus 288 ~s~~~~LvkavrsGni~~~~~~l~~ner~~~~~~l~ltl~~~~~~V~~RNL~rk~w~~~~~q-srlp~sil~~~~qls~~ 366 (413)
T COG5600 288 CSVYSPLVKAVRSGNIEDFDLALSRNERKFAKRGLYLTLLAHYPLVCFRNLFRKIWRLHGKQ-SRLPLSILLIVLQLSAI 366 (413)
T ss_pred cchhHHHHHHHHcCCHHHHHHHHHHhHHHHHHcchHHHHHhhccHHHHHHHHHHHHhhcccc-ccCcHHHHHHHHHccCC
Confidence 4566678899999998873 333321 11111111 121222333333222 23 4566666665432
Q ss_pred ----ChhhHHHHHHHHHhcccceeecccccceEEEeeecc
Q psy3716 380 ----PLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQP 415 (436)
Q Consensus 380 ----~~~~ve~lvmka~s~~li~g~idqv~~~v~~~wv~p 415 (436)
|.++||-.+--++++|++||.|---.++|-++--.|
T Consensus 367 dn~~~~~~VEciL~tlI~~G~lrgYis~s~~~vV~sk~~p 406 (413)
T COG5600 367 DNFHSFKEVECILVTLIGLGLLRGYISHSRRTVVFSKKDP 406 (413)
T ss_pred CcccChHHHHHHHHHHHhhhhhhheecccceEEEEecCCC
Confidence 478999999999999999999999999988775444
No 336
>KOG2235|consensus
Probab=21.99 E-value=1.3e+02 Score=33.59 Aligned_cols=92 Identities=18% Similarity=0.263 Sum_probs=72.5
Q ss_pred cccCHHHHHHHhCCChhhHHHHHHHHHhCCcccccccCCccEEEEEeccccccccchhhccccC------CcccccHHHH
Q psy3716 300 HQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPRVLSKDQLAFKKIP------GSHQLSFAEI 373 (436)
Q Consensus 300 r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDQv~~~v~vtwv~pRvL~l~Qi~~lr~~------~~r~~sf~~i 373 (436)
+..+.-++|+.++|+.+-||...=+.++.. + +++-|...+++..=|..++.- ..-.++.+|.
T Consensus 72 gRaslvDla~tlnVDl~hIEk~a~dIv~~d----------~--~v~Lv~geiide~Y~d~iaeEinekLqE~gqvtiaeL 139 (776)
T KOG2235|consen 72 GRASLVDLAVTLNVDLDHIEKTARDIVSTD----------D--EVTLVLGEIIDEEYVDRIAEEINEKLQEQGQVTIAEL 139 (776)
T ss_pred CcchhHHHHHHhCcCHHHHHHHHHHHhhcC----------C--ceEEehhhhhhHHHHHHHHHHHHHHHHHhcchHHHHH
Confidence 478999999999999999998876555432 2 355567777777766655442 2247899999
Q ss_pred HHHcCCChhhHHHHHHHHHhcccceeeccc
Q psy3716 374 SEAAQLPLIEVEFLIIKALALGLVKGHIDQ 403 (436)
Q Consensus 374 ~~~~~~~~~~ve~lvmka~s~~li~g~idq 403 (436)
|...++|-+=+-+++.-=+--.+|+|++|.
T Consensus 140 akq~dl~sellqs~l~ek~lg~iikgr~dg 169 (776)
T KOG2235|consen 140 AKQWDLPSELLQSLLIEKLLGSIIKGRVDG 169 (776)
T ss_pred HHhcCCcHHHHHHHHHHHhhccceeeeecC
Confidence 999999999999999988667899999999
No 337
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=21.98 E-value=99 Score=27.65 Aligned_cols=27 Identities=22% Similarity=0.433 Sum_probs=24.8
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
..|++|||+.+++|..-|...+-+|++
T Consensus 134 g~s~~EIA~~l~is~~tV~~~l~ra~~ 160 (168)
T PRK12525 134 GLTYVEIGERLGVSLSRIHQYMVEAFK 160 (168)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 589999999999999999999988875
No 338
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=21.74 E-value=1e+02 Score=27.97 Aligned_cols=27 Identities=22% Similarity=0.241 Sum_probs=24.3
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
.+|+++||+.+++|+.-|...+-+|..
T Consensus 138 g~s~~EIA~~lgis~~tVk~~l~Rar~ 164 (185)
T PRK12542 138 NLTYQEISSVMGITEANVRKQFERARK 164 (185)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 599999999999999999998877754
No 339
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=21.58 E-value=1.5e+02 Score=21.06 Aligned_cols=24 Identities=13% Similarity=0.077 Sum_probs=20.8
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHH
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIK 324 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvik 324 (436)
.-....||+.++++..+|..|...
T Consensus 27 ~~~~~~la~~~~l~~~qV~~WF~n 50 (56)
T smart00389 27 REEREELAAKLGLSERQVKVWFQN 50 (56)
T ss_pred HHHHHHHHHHHCcCHHHHHHhHHH
Confidence 456789999999999999999865
No 340
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.
Probab=21.57 E-value=96 Score=29.50 Aligned_cols=28 Identities=18% Similarity=0.103 Sum_probs=24.5
Q ss_pred ccccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 366 HQLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 366 r~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
..+|.+|||+.+++|..-|...+-+|+.
T Consensus 193 e~~S~~EIAe~lgis~~tV~~~~~rAl~ 220 (227)
T TIGR02846 193 RRKTQREIAKILGISRSYVSRIEKRALM 220 (227)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3589999999999999999999877764
No 341
>TIGR03504 FimV_Cterm FimV C-terminal domain. This protein is found at the extreme C-terminus of FimV from Pseudomonas aeruginosa, and of TspA of Neisseria meningitidis. Disruption of the former blocks twitching motility from type IV pili; Semmler, et al. suggest a role in peptidoglycan layer remodelling required by type IV fimbrial systems.
Probab=21.48 E-value=1.2e+02 Score=21.84 Aligned_cols=25 Identities=20% Similarity=0.349 Sum_probs=20.2
Q ss_pred HHHHHHhhccCCCCCCChHHHHHHHHHHHH
Q psy3716 122 ILQAQMIMNKDADKPGSLDEVEKLIDEIEL 151 (436)
Q Consensus 122 ~~i~~~~l~~~~~~~~~l~~~~~~L~~~~~ 151 (436)
...|..++. .|+.+.++.+|+++-.
T Consensus 3 LdLA~ayie-----~Gd~e~Ar~lL~evl~ 27 (44)
T TIGR03504 3 LDLARAYIE-----MGDLEGARELLEEVIE 27 (44)
T ss_pred hHHHHHHHH-----cCChHHHHHHHHHHHH
Confidence 345667777 9999999999998874
No 342
>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length. Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.
Probab=21.41 E-value=1.1e+03 Score=25.82 Aligned_cols=185 Identities=13% Similarity=0.105 Sum_probs=88.4
Q ss_pred hhcCCchHHHHHHHHHHHHHhhhHH-------------HHHHHHHH-HhcCcccccchhHHHHHHHHHHHHh-hccCchh
Q psy3716 17 AYSKNPEISAQWLNLEELYNKKLWH-------------QLTLAVLA-FVQNPAIQKEGELRDLYHKFVISFE-TKINPVS 81 (436)
Q Consensus 17 ~~~~~~~~~~~~~~l~~l~~~KLWh-------------QLT~~l~~-~~~~p~~~~~~~~~~ly~~fI~~f~-~kin~l~ 81 (436)
.++...++.+.++++--+|.+|..- .|-..+-+ .+--| .++++.|-..+..++ +-.||..
T Consensus 186 ~e~~s~dl~pdyYemilfY~kki~~~d~~~Y~k~~peeeL~s~imqhlfi~p-----~e~l~~~mq~l~~We~~yv~p~~ 260 (549)
T PF07079_consen 186 KESMSSDLYPDYYEMILFYLKKIHAFDQRPYEKFIPEEELFSTIMQHLFIVP-----KERLPPLMQILENWENFYVHPNY 260 (549)
T ss_pred HHhcccccChHHHHHHHHHHHHHHHHhhchHHhhCcHHHHHHHHHHHHHhCC-----HhhccHHHHHHHHHHhhccCCch
Confidence 3455578888899999999888532 11112222 11112 344555555555554 3345554
Q ss_pred HHHHHHHHhccCCCHHHHHHHHHHHHHh-hcCCcchhHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHHHHHhcccChh
Q psy3716 82 LMEIMEVITNHLSDQEEALVLLQSFEDK-VKNNLEAKSLCKILQAQMIMNKDADKPGSLDEVEKLIDEIELLVNDIEGVT 160 (436)
Q Consensus 82 l~~i~~~v~~~~~d~~~aL~~L~~l~~~-l~~~~ea~~~~~~~i~~~~l~~~~~~~~~l~~~~~~L~~~~~~L~~~~~~~ 160 (436)
=-.|-..+-+-+++++.+..|-+.+... +++=.+..+-.+-.+...++. .++-..++. .-+.|..++...
T Consensus 261 ~LVi~~L~~~f~~~~e~~~~~ce~ia~~~i~~Lke~li~~F~~~Ls~~Vk-----~~~T~~a~q----~l~lL~~ldp~~ 331 (549)
T PF07079_consen 261 DLVIEPLKQQFMSDPEQVGHFCEAIASSKIEKLKEELIDRFGNLLSFKVK-----QVQTEEAKQ----YLALLKILDPRI 331 (549)
T ss_pred hHHHHHHHHHHhcChHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHH-----HHhHHHHHH----HHHHHHhcCCcc
Confidence 2112121222245777777666655332 111111222222222222332 233333332 223444445444
Q ss_pred HHHHHHHHHHHHHHHHhhcHHHHHHHHHHHhccCCCCCCChhHHHHHHHHHHHHH
Q psy3716 161 AIHSRFYLVASTLYRKQAKLSLYYRTALRYLGCVDLNDLTASDQVQHAFLIGLAA 215 (436)
Q Consensus 161 ~v~~~~y~~~a~~~k~~~~~~~~Y~~~L~yL~~~~~~~l~~~e~~~~A~~l~iaA 215 (436)
+++.++-..-...-...-.-...|.+.=.||.-....+....++++++..++..|
T Consensus 332 svs~Kllls~~~lq~Iv~~DD~~~Tklr~yL~lwe~~qs~DiDrqQLvh~L~~~A 386 (549)
T PF07079_consen 332 SVSEKLLLSPKVLQDIVCEDDESYTKLRDYLNLWEEIQSYDIDRQQLVHYLVFGA 386 (549)
T ss_pred hhhhhhhcCHHHHHHHHhcchHHHHHHHHHHHHHHHHHhhcccHHHHHHHHHHHH
Confidence 5666663323333333333356677777787754332233456899999997655
No 343
>PRK00118 putative DNA-binding protein; Validated
Probab=21.37 E-value=1.2e+02 Score=25.96 Aligned_cols=27 Identities=22% Similarity=0.121 Sum_probs=24.5
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
..|+++||+.+|+|..-|..++-+|..
T Consensus 33 g~S~~EIAe~lGIS~~TV~r~L~RArk 59 (104)
T PRK00118 33 DYSLGEIAEEFNVSRQAVYDNIKRTEK 59 (104)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 799999999999999999999887754
No 344
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=21.30 E-value=1e+02 Score=27.07 Aligned_cols=27 Identities=22% Similarity=0.247 Sum_probs=24.6
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
..|.+|||+.+++|..-|...+-+|+.
T Consensus 125 ~~s~~EIA~~lgis~~tV~~~l~ra~~ 151 (163)
T PRK07037 125 GETQKDIARELGVSPTLVNFMIRDALV 151 (163)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 578999999999999999999888865
No 345
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=21.26 E-value=2e+02 Score=29.31 Aligned_cols=37 Identities=27% Similarity=0.370 Sum_probs=34.6
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHhcccceeeccc
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQ 403 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s~~li~g~idq 403 (436)
.+|=+|||++++++---|-.++=+|-..|+|+=+|+.
T Consensus 29 g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~GiV~I~I~~ 65 (318)
T PRK15418 29 GLTQSEIGERLGLTRLKVSRLLEKGRQSGIIRVQINS 65 (318)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHcCcEEEEEeC
Confidence 5788999999999999999999999999999988875
No 346
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=21.25 E-value=2.2e+02 Score=22.38 Aligned_cols=49 Identities=14% Similarity=0.119 Sum_probs=39.9
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHhcccceeecccccceEEEeeecc
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQP 415 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s~~li~g~idqv~~~v~~~wv~p 415 (436)
.++.++|++.++++...|-..|-+-...|+|.-.-++.++....--++|
T Consensus 24 ~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~~~~~~~r~~~~~lT~ 72 (101)
T smart00347 24 PLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRLPSPEDRRSVLVSLTE 72 (101)
T ss_pred CcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEecCCCCCCCeEEEEECH
Confidence 4889999999999999999999999999999877776655554433333
No 347
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=21.22 E-value=3.8e+02 Score=24.35 Aligned_cols=60 Identities=20% Similarity=0.231 Sum_probs=44.2
Q ss_pred ccccHHHHHHHcCCChhhHHHHHHHHHhcccceeec--ccccceEEEeeecccccchhhhhHHHHH
Q psy3716 366 HQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHI--DQVDESFNVTWVQPRVLSKDQVFWSLEE 429 (436)
Q Consensus 366 r~~sf~~i~~~~~~~~~~ve~lvmka~s~~li~g~i--dqv~~~v~~~wv~pr~l~~~q~~~~~~~ 429 (436)
..+|=++||+.+|++.++|-..+-+-...||+...- |.-+|...-.|- ++.+++...++.
T Consensus 27 ~~~tdEeLa~~Lgi~~~~VRk~L~~L~e~~Lv~~~r~r~~~~gw~~Y~w~----i~~~~i~d~Ik~ 88 (158)
T TIGR00373 27 GEFTDEEISLELGIKLNEVRKALYALYDAGLADYKRRKDDETGWYEYTWR----INYEKALDVLKR 88 (158)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCceeeeeeecCCCcEEEEEE----eCHHHHHHHHHH
Confidence 468999999999999999999999999999994332 223344555552 366666655544
No 348
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=21.16 E-value=1e+02 Score=27.82 Aligned_cols=27 Identities=19% Similarity=0.151 Sum_probs=25.0
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
..|+++||+.+++|..-|...+-+|+.
T Consensus 147 g~s~~eIA~~l~is~~tV~~~l~ra~~ 173 (184)
T PRK12512 147 GASIKETAAKLSMSEGAVRVALHRGLA 173 (184)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 589999999999999999999998875
No 349
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=21.08 E-value=1e+02 Score=27.46 Aligned_cols=27 Identities=26% Similarity=0.149 Sum_probs=24.8
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
..|.+|||+.+++|..-|.-.+-+|..
T Consensus 134 g~s~~EIA~~lgis~~tV~~~l~ra~~ 160 (173)
T PRK09645 134 GWSTAQIAADLGIPEGTVKSRLHYALR 160 (173)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 589999999999999999999988874
No 350
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=21.08 E-value=1e+02 Score=29.83 Aligned_cols=27 Identities=19% Similarity=0.228 Sum_probs=24.5
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
..||++||+.+|+|++-|...+-+|..
T Consensus 132 g~S~~EIAe~LgiS~~tVksrL~Rark 158 (228)
T PRK06704 132 QYSIADIAKVCSVSEGAVKASLFRSRN 158 (228)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 589999999999999999999887765
No 351
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=21.01 E-value=1e+02 Score=27.93 Aligned_cols=27 Identities=26% Similarity=0.282 Sum_probs=25.1
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
.+|.+|||+.+++|..-|.-.+.+|+.
T Consensus 143 gls~~EIA~~l~i~~~tVks~l~ra~~ 169 (182)
T COG1595 143 GLSYEEIAEILGISVGTVKSRLHRARK 169 (182)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 589999999999999999999999875
No 352
>TIGR03643 conserved hypothetical protein TIGR03643. This model describes an uncharacterized bacterial protein family. Members average about 90 amino acids in length with several well-conserved uncommon amino acids (Trp, Met). The majority of species are marine bacteria. Few species have more than one copy, but Vibrio cholerae El Tor N16961 has three identical copies.
Probab=21.01 E-value=1e+02 Score=24.73 Aligned_cols=29 Identities=24% Similarity=0.203 Sum_probs=23.9
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHhcc
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALALG 395 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s~~ 395 (436)
..+|+.|..++|++..+|-.|.=+-|..+
T Consensus 13 RtpFeaI~~~fGL~E~eVi~lMR~~lk~~ 41 (72)
T TIGR03643 13 RTPFEAIEQQFGLSEKEVIKLMRQNLKPS 41 (72)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHhhcChh
Confidence 36999999999999999998876655543
No 353
>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=20.71 E-value=3.9e+02 Score=20.58 Aligned_cols=33 Identities=21% Similarity=0.153 Sum_probs=26.5
Q ss_pred cccCHHHHHHHhCCC-hhhHHHHHHHHHhCCccc
Q psy3716 300 HQLSFAEISEAAQLP-LIEVEFLIIKALALGLVK 332 (436)
Q Consensus 300 r~isf~~Ia~~l~i~-~~eVE~lvikAi~~gLI~ 332 (436)
..-|+.||++++++. ..-|-..+-..-..|+|+
T Consensus 24 ~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~kG~I~ 57 (65)
T PF01726_consen 24 YPPTVREIAEALGLKSTSTVQRHLKALERKGYIR 57 (65)
T ss_dssp S---HHHHHHHHTSSSHHHHHHHHHHHHHTTSEE
T ss_pred CCCCHHHHHHHhCCCChHHHHHHHHHHHHCcCcc
Confidence 356999999999995 899999998888888875
No 354
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=20.71 E-value=2e+02 Score=25.65 Aligned_cols=42 Identities=12% Similarity=0.126 Sum_probs=35.7
Q ss_pred HHHHHHhhcCCCCcccCHHHHHHHhCCChhhHHHHHHHHHhCCccc
Q psy3716 287 CLMELAFKKIPGSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVK 332 (436)
Q Consensus 287 aL~~L~~~~p~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~ 332 (436)
-+++++-. +..+|+.++...+|++-+.|+.++-++...|-|-
T Consensus 16 rIvElVRe----~GRiTi~ql~~~TGasR~Tvk~~lreLVa~G~l~ 57 (127)
T PF06163_consen 16 RIVELVRE----HGRITIKQLVAKTGASRNTVKRYLRELVARGDLY 57 (127)
T ss_pred HHHHHHHH----cCCccHHHHHHHHCCCHHHHHHHHHHHHHcCCeE
Confidence 35566654 4789999999999999999999999999988764
No 355
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=20.70 E-value=1.7e+02 Score=25.66 Aligned_cols=70 Identities=10% Similarity=0.069 Sum_probs=0.0
Q ss_pred ccccccccchhhcccc-CCcccccHHHHHHHcCCChhhHHHHHHHHHhcccceeecccccceEEEeeeccc
Q psy3716 347 VQPRVLSKDQLAFKKI-PGSHQLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPR 416 (436)
Q Consensus 347 v~pRvL~l~Qi~~lr~-~~~r~~sf~~i~~~~~~~~~~ve~lvmka~s~~li~g~idqv~~~v~~~wv~pr 416 (436)
..+-.++..||..+.. .....+|..+||+.++++.--|=.+|=+--..|||+=..|.-|+....=+++|+
T Consensus 33 l~~~glt~~q~~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~~~~~DrR~~~l~LT~~ 103 (144)
T PRK11512 33 LSPLDITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTS 103 (144)
T ss_pred hcccCCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCcccCCeeEeEEChh
No 356
>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=20.65 E-value=1.1e+02 Score=28.15 Aligned_cols=27 Identities=15% Similarity=0.215 Sum_probs=24.1
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
..|++|||+.+++|..-|...+-+|..
T Consensus 147 g~s~~EIA~~lgis~~tvk~rl~Rar~ 173 (188)
T TIGR02943 147 GFESDEICQELEISTSNCHVLLYRARL 173 (188)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 589999999999999999999888753
No 357
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=20.64 E-value=2.3e+02 Score=26.89 Aligned_cols=60 Identities=15% Similarity=0.199 Sum_probs=47.2
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHhcccceeecccccceEEEeeecccccchhhhhHHHHHHHhhcc
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALALGLVKGHIDQVDESFNVTWVQPRVLSKDQVFWSLEETVATEV 435 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s~~li~g~idqv~~~v~~~wv~pr~l~~~q~~~~~~~~~~~~~ 435 (436)
..-|.+||+..+=+.+.|=.++.+-|+ ..|+||. +.+.+ + --++..+++..|+.-+.+=|
T Consensus 40 i~N~~~i~~~l~R~~~~~~ky~~~ELg---t~~~~~~--~~~ii---~-G~~~~~~i~~~l~~yi~~yV 99 (201)
T PRK12336 40 LTNFGEIADALNRDPDHLMKFLQRELG---TAGKIEG--GRAVF---N-GKFTEEDIQAAIDAYVDEYV 99 (201)
T ss_pred EecHHHHHHHHCCCHHHHHHHHHHHhC---CcceecC--CEEEE---E-eeeCHHHHHHHHHHHHHheE
Confidence 346999999999999999999999988 5899985 43322 2 34788899998888766544
No 358
>PF13730 HTH_36: Helix-turn-helix domain
Probab=20.62 E-value=1.5e+02 Score=21.33 Aligned_cols=29 Identities=17% Similarity=0.129 Sum_probs=24.5
Q ss_pred cHHHHHHHcCCChhhHHHHHHHHHhcccc
Q psy3716 369 SFAEISEAAQLPLIEVEFLIIKALALGLV 397 (436)
Q Consensus 369 sf~~i~~~~~~~~~~ve~lvmka~s~~li 397 (436)
|.++||+.++++.+-|..-+-.-...|+|
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHCcCC
Confidence 78999999999999998887777776664
No 359
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=20.59 E-value=1.1e+02 Score=27.24 Aligned_cols=27 Identities=15% Similarity=0.265 Sum_probs=24.4
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
..|+++||+.+++|..-|...+-+|..
T Consensus 142 g~s~~eIA~~l~is~~~V~~~l~ra~~ 168 (176)
T PRK09638 142 GYTYEEIAKMLNIPEGTVKSRVHHGIK 168 (176)
T ss_pred CCCHHHHHHHHCCChhHHHHHHHHHHH
Confidence 589999999999999999998888764
No 360
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=20.46 E-value=1e+02 Score=26.29 Aligned_cols=27 Identities=30% Similarity=0.225 Sum_probs=20.7
Q ss_pred cccCHHHHHHHhCCChhhHHHHHHHHH
Q psy3716 300 HQLSFAEISEAAQLPLIEVEFLIIKAL 326 (436)
Q Consensus 300 r~isf~~Ia~~l~i~~~eVE~lvikAi 326 (436)
..+|+++||+.++|+-.-|-.++-+|-
T Consensus 32 eDlSlsEIAe~~~iSRqaV~d~ikr~~ 58 (101)
T PF04297_consen 32 EDLSLSEIAEELGISRQAVYDSIKRAE 58 (101)
T ss_dssp S---HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 479999999999999999999888875
No 361
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=20.41 E-value=1.1e+02 Score=27.98 Aligned_cols=27 Identities=19% Similarity=0.273 Sum_probs=24.5
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
.+|++|||+.+++|..-|.-.+-+|..
T Consensus 146 g~s~~EIA~~lgis~~tVk~~l~Rar~ 172 (185)
T PRK09649 146 GLSYADAAAVCGCPVGTIRSRVARARD 172 (185)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 589999999999999999999888765
No 362
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=20.38 E-value=1e+02 Score=29.20 Aligned_cols=28 Identities=7% Similarity=0.083 Sum_probs=25.0
Q ss_pred ccccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 366 HQLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 366 r~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
..+|++|||+.+++|..-|...+-+|+.
T Consensus 197 eg~s~~EIA~~lgis~~tVk~~~~rA~~ 224 (234)
T PRK08301 197 EEKTQKEVADMLGISQSYISRLEKRIIK 224 (234)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3589999999999999999999888865
No 363
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=20.38 E-value=1.1e+02 Score=27.77 Aligned_cols=27 Identities=33% Similarity=0.332 Sum_probs=24.2
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
.+|++|||+.+++|..-|..-+-+|+.
T Consensus 133 ~~s~~EIA~~lgis~~tV~~~l~ra~~ 159 (179)
T PRK12543 133 DYSQEEIAQLLQIPIGTVKSRIHAALK 159 (179)
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 479999999999999999999888754
No 364
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=20.27 E-value=1.2e+02 Score=26.83 Aligned_cols=27 Identities=30% Similarity=0.351 Sum_probs=24.1
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
..++++||+.+|+|.+.|...+=+|..
T Consensus 141 ~~~~~eIA~~lgis~~tv~~~~~ra~~ 167 (179)
T PRK11924 141 GLSYREIAEILGVPVGTVKSRLRRARQ 167 (179)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 689999999999999999999877654
No 365
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=20.20 E-value=1.1e+02 Score=29.18 Aligned_cols=27 Identities=26% Similarity=0.358 Sum_probs=24.8
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
.+|++|||+.+++|..-|...+.+|..
T Consensus 150 g~s~~EIAe~LgiS~~tVk~~L~RAr~ 176 (216)
T PRK12533 150 DMSYREIAAIADVPVGTVMSRLARARR 176 (216)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 589999999999999999999988765
No 366
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=20.19 E-value=1.1e+02 Score=27.52 Aligned_cols=27 Identities=26% Similarity=0.459 Sum_probs=24.4
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
-.|++|||+.+++|..-|..-+-+|..
T Consensus 145 g~s~~eIA~~lgis~~tV~~~l~Rar~ 171 (179)
T PRK12514 145 GLSYKELAERHDVPLNTMRTWLRRSLL 171 (179)
T ss_pred CCCHHHHHHHHCCChHHHHHHHHHHHH
Confidence 489999999999999999999888764
No 367
>PF12085 DUF3562: Protein of unknown function (DUF3562); InterPro: IPR021945 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 62 to 84 amino acids in length. This protein has two completely conserved residues (A and Y) that may be functionally important.
Probab=20.18 E-value=1.4e+02 Score=23.61 Aligned_cols=25 Identities=16% Similarity=0.167 Sum_probs=21.2
Q ss_pred CHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 303 SFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 303 sf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
....||+.+++|.++|....-+.+.
T Consensus 9 ~i~~iA~~t~~P~e~V~~my~dt~~ 33 (66)
T PF12085_consen 9 VIRSIAEETGTPAETVRRMYDDTMR 33 (66)
T ss_pred HHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5678999999999999998876554
No 368
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=20.17 E-value=1.1e+02 Score=28.04 Aligned_cols=27 Identities=19% Similarity=0.311 Sum_probs=24.4
Q ss_pred cccHHHHHHHcCCChhhHHHHHHHHHh
Q psy3716 367 QLSFAEISEAAQLPLIEVEFLIIKALA 393 (436)
Q Consensus 367 ~~sf~~i~~~~~~~~~~ve~lvmka~s 393 (436)
.+|++|||+.+++|..-|...+-+|..
T Consensus 150 g~s~~EIA~~lgis~~tVk~~l~RAr~ 176 (189)
T PRK12530 150 ELSSEQICQECDISTSNLHVLLYRARL 176 (189)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 589999999999999999999888764
No 369
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=20.16 E-value=1.1e+02 Score=28.09 Aligned_cols=27 Identities=30% Similarity=0.290 Sum_probs=24.6
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
.+|+++||+.+++|..-|...+=+|..
T Consensus 152 g~s~~eIA~~lgis~~tV~~~l~Ra~~ 178 (196)
T PRK12524 152 GLSNPEIAEVMEIGVEAVESLTARGKR 178 (196)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 699999999999999999999888764
No 370
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=20.12 E-value=1.2e+02 Score=27.74 Aligned_cols=27 Identities=26% Similarity=0.418 Sum_probs=24.5
Q ss_pred ccCHHHHHHHhCCChhhHHHHHHHHHh
Q psy3716 301 QLSFAEISEAAQLPLIEVEFLIIKALA 327 (436)
Q Consensus 301 ~isf~~Ia~~l~i~~~eVE~lvikAi~ 327 (436)
..|+++||+.+|+|..-|...+=+|..
T Consensus 150 g~s~~EIA~~lgis~~tV~~~l~Ra~~ 176 (188)
T PRK09640 150 ELEFQEIADIMHMGLSATKMRYKRALD 176 (188)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 589999999999999999999888763
Done!