Query psy396
Match_columns 239
No_of_seqs 118 out of 667
Neff 7.0
Searched_HMMs 46136
Date Fri Aug 16 21:44:29 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy396.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/396hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0687|consensus 100.0 1.1E-61 2.3E-66 428.4 20.3 223 1-239 170-393 (393)
2 COG5187 RPN7 26S proteasome re 100.0 8.1E-51 1.7E-55 355.6 18.1 222 1-237 181-405 (412)
3 KOG0686|consensus 100.0 9.2E-45 2E-49 328.5 19.4 219 9-236 226-445 (466)
4 KOG1463|consensus 100.0 1.1E-33 2.4E-38 251.8 15.1 203 11-236 208-411 (411)
5 COG5159 RPN6 26S proteasome re 100.0 5.1E-29 1.1E-33 218.6 13.6 206 10-238 204-411 (421)
6 KOG1464|consensus 99.9 3.4E-26 7.3E-31 200.2 13.2 174 14-191 233-407 (440)
7 PF10602 RPN7: 26S proteasome 99.8 8.2E-21 1.8E-25 158.7 6.5 73 1-73 102-177 (177)
8 KOG2758|consensus 99.8 2.1E-19 4.7E-24 159.8 12.3 165 49-237 250-421 (432)
9 PF01399 PCI: PCI domain; Int 99.8 5.1E-19 1.1E-23 133.6 12.3 103 89-191 1-103 (105)
10 smart00088 PINT motif in prote 99.5 9.1E-14 2E-18 102.7 9.8 69 125-194 1-69 (88)
11 smart00753 PAM PCI/PINT associ 99.5 9.1E-14 2E-18 102.7 9.8 69 125-194 1-69 (88)
12 KOG2581|consensus 99.1 1E-08 2.2E-13 94.5 16.8 169 12-191 247-421 (493)
13 KOG2908|consensus 99.0 1.2E-07 2.6E-12 85.7 19.3 208 10-237 155-371 (380)
14 KOG1498|consensus 98.8 2.9E-07 6.2E-12 84.6 15.1 176 12-194 210-398 (439)
15 KOG2582|consensus 98.2 4.8E-05 1E-09 69.7 14.8 199 17-234 188-389 (422)
16 COG5071 RPN5 26S proteasome re 98.2 2.8E-05 6E-10 69.9 12.7 176 12-194 210-398 (439)
17 KOG1497|consensus 98.1 3.1E-05 6.7E-10 69.9 11.2 62 130-191 299-360 (399)
18 KOG2753|consensus 98.0 0.00036 7.8E-09 63.3 16.0 162 25-194 178-339 (378)
19 KOG1076|consensus 97.8 0.00037 8.1E-09 68.4 13.5 179 12-194 530-763 (843)
20 PF10075 PCI_Csn8: COP9 signal 97.5 0.00093 2E-08 53.6 9.7 93 89-191 42-134 (143)
21 KOG2688|consensus 97.1 0.0045 9.8E-08 57.7 10.4 164 17-194 210-384 (394)
22 PF09756 DDRGK: DDRGK domain; 96.8 0.0035 7.5E-08 53.0 6.3 59 135-194 100-158 (188)
23 PF03399 SAC3_GANP: SAC3/GANP/ 96.4 0.046 1E-06 45.8 10.8 103 48-159 96-203 (204)
24 COG5600 Transcription-associat 96.4 0.073 1.6E-06 49.4 12.3 165 15-194 223-403 (413)
25 PF10255 Paf67: RNA polymerase 96.3 0.16 3.4E-06 47.9 14.4 146 15-170 167-343 (404)
26 PF09012 FeoC: FeoC like trans 96.2 0.0094 2E-07 41.9 4.6 45 138-182 4-48 (69)
27 PF08220 HTH_DeoR: DeoR-like h 95.6 0.03 6.4E-07 38.0 4.8 44 135-178 1-44 (57)
28 PF14938 SNAP: Soluble NSF att 95.0 0.08 1.7E-06 47.0 7.0 123 6-131 149-278 (282)
29 KOG3054|consensus 94.7 0.15 3.2E-06 44.7 7.6 56 138-194 204-259 (299)
30 smart00345 HTH_GNTR helix_turn 93.3 0.15 3.3E-06 33.5 4.0 49 131-179 2-51 (60)
31 PRK15431 ferrous iron transpor 93.1 0.22 4.8E-06 36.1 4.8 43 138-180 6-48 (78)
32 PF08279 HTH_11: HTH domain; 92.7 0.47 1E-05 31.2 5.8 42 135-176 1-43 (55)
33 KOG1861|consensus 92.7 1.8 3.8E-05 41.5 11.4 107 49-164 385-494 (540)
34 KOG2072|consensus 92.4 1.7 3.7E-05 44.2 11.3 86 107-192 406-492 (988)
35 smart00420 HTH_DEOR helix_turn 92.2 0.57 1.2E-05 29.9 5.6 43 138-180 4-46 (53)
36 PF13412 HTH_24: Winged helix- 91.7 0.67 1.4E-05 29.7 5.4 43 136-178 5-47 (48)
37 PF00392 GntR: Bacterial regul 90.2 0.98 2.1E-05 30.9 5.4 52 128-179 3-55 (64)
38 PF09743 DUF2042: Uncharacteri 90.1 2.4 5.2E-05 37.9 9.1 66 119-191 106-171 (272)
39 PRK10434 srlR DNA-bindng trans 90.1 0.64 1.4E-05 40.9 5.4 45 134-178 5-49 (256)
40 smart00550 Zalpha Z-DNA-bindin 89.1 1.2 2.7E-05 31.1 5.3 45 136-180 8-54 (68)
41 PF08784 RPA_C: Replication pr 88.8 0.54 1.2E-05 35.3 3.5 38 147-184 64-101 (102)
42 PRK10411 DNA-binding transcrip 88.7 0.96 2.1E-05 39.5 5.5 47 133-179 3-49 (240)
43 PRK04424 fatty acid biosynthes 88.1 0.78 1.7E-05 38.5 4.4 46 134-179 7-52 (185)
44 COG1349 GlpR Transcriptional r 87.2 1.2 2.7E-05 39.1 5.2 47 133-179 4-50 (253)
45 PRK10906 DNA-binding transcrip 87.0 1.4 3E-05 38.8 5.4 47 133-179 4-50 (252)
46 PF04703 FaeA: FaeA-like prote 86.7 1.8 3.9E-05 30.0 4.8 41 139-179 5-46 (62)
47 PRK13509 transcriptional repre 86.7 1.5 3.2E-05 38.5 5.5 46 134-179 5-50 (251)
48 PRK09802 DNA-binding transcrip 86.5 1.5 3.2E-05 39.0 5.4 47 133-179 16-62 (269)
49 PRK10681 DNA-binding transcrip 86.4 1.2 2.7E-05 39.0 4.8 41 133-173 6-46 (252)
50 PF01047 MarR: MarR family; I 86.3 3.1 6.7E-05 27.5 5.8 51 137-187 6-56 (59)
51 smart00344 HTH_ASNC helix_turn 85.4 2.5 5.5E-05 31.5 5.5 44 136-179 5-48 (108)
52 PF12802 MarR_2: MarR family; 85.1 4.6 0.0001 26.8 6.2 48 139-186 10-59 (62)
53 PF01984 dsDNA_bind: Double-st 84.8 0.41 8.9E-06 36.9 0.9 53 132-184 31-83 (107)
54 PF01022 HTH_5: Bacterial regu 84.1 3.5 7.6E-05 26.4 5.0 43 134-178 3-45 (47)
55 cd07377 WHTH_GntR Winged helix 82.6 3.8 8.1E-05 27.2 5.0 51 129-179 5-56 (66)
56 KOG3431|consensus 82.4 1.9 4.1E-05 33.9 3.6 53 131-183 38-90 (129)
57 TIGR02844 spore_III_D sporulat 82.2 2.8 6.1E-05 30.5 4.4 34 135-169 7-40 (80)
58 PF10668 Phage_terminase: Phag 81.5 3.2 6.9E-05 28.6 4.2 37 135-171 9-45 (60)
59 PF13518 HTH_28: Helix-turn-he 81.3 4.8 0.0001 25.7 4.9 39 135-176 2-40 (52)
60 KOG4414|consensus 81.3 5.2 0.00011 32.7 6.0 75 92-170 80-154 (197)
61 PF13404 HTH_AsnC-type: AsnC-t 81.3 5 0.00011 25.4 4.8 36 137-172 6-41 (42)
62 PRK11014 transcriptional repre 81.0 4.8 0.0001 31.9 5.8 59 133-191 10-68 (141)
63 PRK04239 hypothetical protein; 80.9 2.1 4.5E-05 33.2 3.4 55 130-184 34-88 (110)
64 smart00346 HTH_ICLR helix_turn 80.4 18 0.0004 25.7 9.1 55 135-191 6-61 (91)
65 KOG2235|consensus 80.4 6.1 0.00013 39.2 7.1 61 124-191 114-174 (776)
66 PF01726 LexA_DNA_bind: LexA D 80.3 5.6 0.00012 27.6 5.2 31 149-179 26-57 (65)
67 KOG3677|consensus 79.0 22 0.00047 34.0 10.0 197 17-236 277-515 (525)
68 cd00090 HTH_ARSR Arsenical Res 78.2 12 0.00026 24.8 6.4 44 140-184 13-56 (78)
69 PRK09954 putative kinase; Prov 77.7 8.9 0.00019 35.0 7.2 56 137-192 6-64 (362)
70 PRK11179 DNA-binding transcrip 77.7 6.7 0.00015 31.5 5.7 49 136-184 11-62 (153)
71 PRK11534 DNA-binding transcrip 77.5 5.4 0.00012 33.8 5.4 64 126-191 8-71 (224)
72 COG2118 DNA-binding protein [G 77.2 3.4 7.3E-05 32.1 3.5 54 131-184 38-91 (116)
73 PF13463 HTH_27: Winged helix 76.8 13 0.00029 24.9 6.3 50 137-186 6-56 (68)
74 smart00419 HTH_CRP helix_turn_ 76.6 5.1 0.00011 24.9 3.8 32 148-179 8-39 (48)
75 cd00092 HTH_CRP helix_turn_hel 75.6 9.3 0.0002 25.5 5.2 34 147-180 24-57 (67)
76 smart00418 HTH_ARSR helix_turn 75.5 12 0.00027 24.0 5.7 44 146-189 8-51 (66)
77 PF13384 HTH_23: Homeodomain-l 74.8 4.8 0.0001 25.7 3.4 39 135-176 7-45 (50)
78 PRK06266 transcription initiat 74.7 32 0.00069 28.7 9.1 62 118-180 5-68 (178)
79 PF02082 Rrf2: Transcriptional 74.7 8.6 0.00019 27.5 5.1 42 149-191 26-67 (83)
80 PRK11169 leucine-responsive tr 74.7 7 0.00015 31.8 5.1 49 136-184 16-67 (164)
81 PF12840 HTH_20: Helix-turn-he 74.5 13 0.00028 24.9 5.6 48 132-180 9-56 (61)
82 PRK03837 transcriptional regul 73.2 8.7 0.00019 32.8 5.6 63 127-191 15-78 (241)
83 TIGR03338 phnR_burk phosphonat 73.1 8 0.00017 32.4 5.3 63 127-191 13-75 (212)
84 COG1802 GntR Transcriptional r 72.2 5.7 0.00012 33.9 4.2 65 125-191 16-80 (230)
85 TIGR03826 YvyF flagellar opero 71.9 6.2 0.00014 31.7 4.0 39 140-182 36-76 (137)
86 PF04545 Sigma70_r4: Sigma-70, 70.7 17 0.00037 23.2 5.3 29 146-174 18-46 (50)
87 PF08280 HTH_Mga: M protein tr 70.1 19 0.00041 24.2 5.6 40 134-173 5-44 (59)
88 TIGR02812 fadR_gamma fatty aci 70.0 13 0.00028 31.7 6.0 63 127-191 8-71 (235)
89 PF09339 HTH_IclR: IclR helix- 69.8 14 0.00029 24.0 4.7 43 136-178 5-48 (52)
90 PF01527 HTH_Tnp_1: Transposas 69.8 14 0.0003 25.5 5.1 43 129-173 6-48 (76)
91 COG2963 Transposase and inacti 69.6 14 0.00031 28.0 5.6 49 129-179 7-56 (116)
92 smart00347 HTH_MARR helix_turn 69.2 36 0.00078 24.1 7.4 48 138-185 14-61 (101)
93 PF01865 PhoU_div: Protein of 68.5 18 0.0004 30.4 6.5 81 88-175 24-104 (214)
94 TIGR02787 codY_Gpos GTP-sensin 68.1 24 0.00051 31.2 7.1 59 124-182 154-232 (251)
95 COG1522 Lrp Transcriptional re 67.8 14 0.00031 29.0 5.4 48 137-184 11-61 (154)
96 PF06163 DUF977: Bacterial pro 67.7 12 0.00027 29.6 4.8 40 139-178 17-56 (127)
97 TIGR03879 near_KaiC_dom probab 67.5 9.8 0.00021 27.3 3.8 35 144-178 28-62 (73)
98 PRK15481 transcriptional regul 66.9 11 0.00024 35.2 5.2 63 127-191 7-70 (431)
99 PF13730 HTH_36: Helix-turn-he 66.8 11 0.00024 24.5 3.8 29 150-178 27-55 (55)
100 KOG3250|consensus 66.7 31 0.00067 30.1 7.3 91 88-191 59-153 (258)
101 PRK10225 DNA-binding transcrip 66.6 14 0.00031 31.9 5.6 64 126-191 10-74 (257)
102 TIGR02337 HpaR homoprotocatech 66.0 55 0.0012 24.7 9.6 49 139-187 33-81 (118)
103 PF01978 TrmB: Sugar-specific 65.8 28 0.00061 23.7 5.9 44 136-180 11-54 (68)
104 PRK10857 DNA-binding transcrip 65.1 19 0.0004 29.7 5.6 44 144-187 21-64 (164)
105 PRK09464 pdhR transcriptional 64.5 15 0.00032 31.7 5.3 63 127-191 12-75 (254)
106 PRK11414 colanic acid/biofilm 64.4 14 0.0003 31.3 5.0 63 127-191 13-75 (221)
107 cd06171 Sigma70_r4 Sigma70, re 64.0 31 0.00067 21.1 5.6 27 147-173 25-51 (55)
108 TIGR00498 lexA SOS regulatory 63.1 17 0.00038 30.2 5.3 47 135-181 7-59 (199)
109 PF07719 TPR_2: Tetratricopept 63.1 11 0.00025 21.2 3.0 27 13-39 2-28 (34)
110 PF13542 HTH_Tnp_ISL3: Helix-t 61.0 21 0.00046 22.8 4.3 23 149-171 28-50 (52)
111 TIGR01884 cas_HTH CRISPR locus 60.7 38 0.00083 28.4 7.0 54 137-191 146-199 (203)
112 PRK09990 DNA-binding transcrip 60.0 20 0.00044 30.8 5.3 63 127-191 9-72 (251)
113 PRK04984 fatty acid metabolism 59.8 21 0.00046 30.4 5.3 62 128-191 10-72 (239)
114 COG2378 Predicted transcriptio 59.4 22 0.00048 32.2 5.6 54 131-187 5-58 (311)
115 COG2345 Predicted transcriptio 59.4 24 0.00052 30.6 5.5 46 136-181 13-58 (218)
116 PF01325 Fe_dep_repress: Iron 59.2 32 0.00069 23.3 5.1 35 145-179 19-53 (60)
117 smart00421 HTH_LUXR helix_turn 58.7 35 0.00076 21.3 5.1 29 146-174 16-44 (58)
118 TIGR02702 SufR_cyano iron-sulf 58.3 72 0.0016 26.7 8.3 45 137-181 4-48 (203)
119 PRK11523 DNA-binding transcrip 58.3 23 0.00049 30.6 5.3 63 127-191 10-73 (253)
120 PF04967 HTH_10: HTH DNA bindi 58.1 15 0.00033 24.5 3.2 34 140-173 15-48 (53)
121 PF13545 HTH_Crp_2: Crp-like h 58.1 19 0.00041 24.8 4.0 40 148-191 28-67 (76)
122 PF10007 DUF2250: Uncharacteri 58.1 27 0.00058 26.1 4.9 42 137-178 10-51 (92)
123 KOG3252|consensus 58.0 1.2E+02 0.0026 25.9 9.7 120 55-191 66-188 (217)
124 smart00351 PAX Paired Box doma 57.9 33 0.00071 26.7 5.7 46 132-180 20-65 (125)
125 PRK11920 rirA iron-responsive 57.9 51 0.0011 26.6 7.0 41 147-187 23-63 (153)
126 PF12324 HTH_15: Helix-turn-he 57.8 22 0.00048 25.7 4.2 35 138-172 28-62 (77)
127 PF09418 DUF2009: Protein of u 57.7 22 0.00048 34.1 5.4 44 22-65 72-116 (458)
128 cd06170 LuxR_C_like C-terminal 57.6 38 0.00082 21.3 5.2 29 146-174 13-41 (57)
129 PF00325 Crp: Bacterial regula 57.1 26 0.00056 21.0 3.8 30 149-178 3-32 (32)
130 TIGR02010 IscR iron-sulfur clu 57.1 41 0.00089 26.3 6.2 41 147-187 24-64 (135)
131 PLN03083 E3 UFM1-protein ligas 56.9 72 0.0016 32.9 9.1 60 124-191 115-174 (803)
132 PF01710 HTH_Tnp_IS630: Transp 56.8 17 0.00038 28.0 3.9 40 136-175 59-98 (119)
133 TIGR00635 ruvB Holliday juncti 56.5 1.4E+02 0.003 26.2 10.4 32 148-179 255-287 (305)
134 PRK06771 hypothetical protein; 56.4 8.2 0.00018 29.0 1.8 31 148-178 36-68 (93)
135 PF13011 LZ_Tnp_IS481: leucine 56.2 37 0.0008 25.1 5.3 31 148-178 25-55 (85)
136 PRK03902 manganese transport t 55.6 99 0.0021 24.2 9.6 49 140-191 14-62 (142)
137 PRK10421 DNA-binding transcrip 55.5 28 0.0006 30.1 5.4 63 127-191 4-67 (253)
138 PF14502 HTH_41: Helix-turn-he 55.4 27 0.0006 22.9 4.0 30 150-179 8-37 (48)
139 KOG1174|consensus 54.8 52 0.0011 31.7 7.2 118 11-142 365-494 (564)
140 PRK00215 LexA repressor; Valid 54.5 33 0.00071 28.7 5.5 56 135-191 5-66 (205)
141 PF06971 Put_DNA-bind_N: Putat 54.2 37 0.0008 22.4 4.5 24 147-170 27-50 (50)
142 PRK05472 redox-sensing transcr 54.2 46 0.00099 28.1 6.4 49 129-177 11-61 (213)
143 PF00515 TPR_1: Tetratricopept 54.0 20 0.00044 20.4 3.0 27 13-39 2-28 (34)
144 PF01476 LysM: LysM domain; I 53.4 15 0.00032 22.5 2.5 19 150-168 8-26 (44)
145 PF08765 Mor: Mor transcriptio 53.4 78 0.0017 23.9 7.0 57 113-172 40-96 (108)
146 PF09743 DUF2042: Uncharacteri 52.4 46 0.001 29.7 6.4 56 129-184 173-228 (272)
147 PRK00080 ruvB Holliday junctio 52.1 1.7E+02 0.0038 26.2 10.2 92 88-179 201-308 (328)
148 COG1959 Predicted transcriptio 51.8 60 0.0013 26.1 6.4 47 145-191 22-68 (150)
149 PHA02943 hypothetical protein; 51.7 42 0.00091 27.6 5.4 44 135-179 12-55 (165)
150 TIGR02018 his_ut_repres histid 51.1 33 0.00071 29.1 5.1 62 128-191 4-66 (230)
151 KOG1586|consensus 51.1 1.3E+02 0.0028 26.8 8.7 109 19-134 161-280 (288)
152 PF13181 TPR_8: Tetratricopept 50.7 25 0.00054 19.9 3.1 27 13-39 2-28 (34)
153 KOG1125|consensus 50.5 28 0.00061 34.3 4.9 52 18-70 504-560 (579)
154 PF08672 APC2: Anaphase promot 50.2 45 0.00098 22.8 4.7 24 158-181 31-54 (60)
155 PRK09391 fixK transcriptional 50.0 1E+02 0.0023 26.0 8.1 40 148-191 179-219 (230)
156 smart00342 HTH_ARAC helix_turn 50.0 76 0.0017 21.3 6.1 42 129-171 32-74 (84)
157 PRK14999 histidine utilization 49.9 38 0.00082 29.0 5.3 63 127-191 14-77 (241)
158 cd00131 PAX Paired Box domain 49.7 55 0.0012 25.6 5.8 45 133-180 21-65 (128)
159 PRK11161 fumarate/nitrate redu 49.5 1.4E+02 0.0031 24.9 8.8 40 148-191 184-223 (235)
160 PF13601 HTH_34: Winged helix 49.5 94 0.002 22.2 8.6 50 138-187 4-53 (80)
161 PRK09764 DNA-binding transcrip 49.3 40 0.00086 28.9 5.3 63 127-191 7-70 (240)
162 TIGR02944 suf_reg_Xantho FeS a 49.2 69 0.0015 24.6 6.3 35 147-181 24-58 (130)
163 PF04760 IF2_N: Translation in 48.1 22 0.00048 23.2 2.8 24 148-171 3-26 (54)
164 PRK14165 winged helix-turn-hel 47.7 81 0.0018 27.2 6.9 52 140-191 13-64 (217)
165 TIGR00153 conserved hypothetic 47.6 1.7E+02 0.0037 24.7 10.1 80 88-174 27-106 (216)
166 PF07106 TBPIP: Tat binding pr 47.6 91 0.002 25.3 7.0 47 144-191 15-61 (169)
167 PRK10141 DNA-binding transcrip 47.5 1.3E+02 0.0029 23.3 9.6 63 128-191 11-73 (117)
168 COG1497 Predicted transcriptio 47.5 46 0.001 29.4 5.3 47 134-180 11-57 (260)
169 PF08281 Sigma70_r4_2: Sigma-7 47.2 48 0.001 21.2 4.3 45 126-173 7-51 (54)
170 cd04761 HTH_MerR-SF Helix-Turn 45.5 53 0.0012 20.3 4.3 27 150-180 2-28 (49)
171 TIGR02675 tape_meas_nterm tape 45.3 29 0.00062 24.7 3.2 27 150-180 46-72 (75)
172 TIGR00373 conserved hypothetic 45.0 1.7E+02 0.0036 23.8 10.4 37 143-179 23-59 (158)
173 PF01710 HTH_Tnp_IS630: Transp 44.9 38 0.00083 26.0 4.1 43 133-179 6-48 (119)
174 PF14493 HTH_40: Helix-turn-he 44.5 36 0.00078 24.8 3.8 33 147-179 12-45 (91)
175 PRK11050 manganese transport r 44.0 1.7E+02 0.0036 23.5 11.0 40 142-181 45-84 (152)
176 KOG3877|consensus 44.0 1.3E+02 0.0028 27.6 7.7 67 98-171 152-237 (393)
177 cd00086 homeodomain Homeodomai 43.5 46 0.001 21.4 3.9 28 144-171 22-50 (59)
178 PRK11753 DNA-binding transcrip 43.4 1.8E+02 0.0039 23.7 9.9 40 148-191 168-207 (211)
179 PF00376 MerR: MerR family reg 42.9 28 0.00061 21.4 2.5 21 150-170 1-21 (38)
180 KOG2165|consensus 42.5 62 0.0013 32.8 6.0 63 137-201 606-669 (765)
181 PF07219 HemY_N: HemY protein 42.5 32 0.0007 26.0 3.3 31 9-39 56-86 (108)
182 COG3063 PilF Tfp pilus assembl 42.5 83 0.0018 27.8 6.1 86 19-114 110-200 (250)
183 PF13551 HTH_29: Winged helix- 42.3 47 0.001 24.3 4.2 27 150-176 14-40 (112)
184 TIGR02325 C_P_lyase_phnF phosp 42.3 61 0.0013 27.4 5.4 63 127-191 10-73 (238)
185 TIGR02404 trehalos_R_Bsub treh 42.1 65 0.0014 27.3 5.5 61 129-191 4-65 (233)
186 PRK09413 IS2 repressor TnpA; R 42.0 75 0.0016 24.4 5.4 44 131-176 14-57 (121)
187 TIGR00738 rrf2_super rrf2 fami 41.7 50 0.0011 25.3 4.4 33 148-180 25-57 (132)
188 TIGR01764 excise DNA binding d 41.6 33 0.00071 21.0 2.8 31 149-183 2-32 (49)
189 PF09182 PuR_N: Bacterial puri 41.6 58 0.0012 23.2 4.2 36 135-170 5-42 (70)
190 PF04157 EAP30: EAP30/Vps36 fa 41.5 44 0.00096 28.6 4.4 43 136-178 176-220 (223)
191 TIGR02859 spore_sigH RNA polym 41.4 70 0.0015 26.0 5.5 46 125-173 145-190 (198)
192 PF13936 HTH_38: Helix-turn-he 41.2 36 0.00079 21.4 2.9 25 147-171 19-43 (44)
193 PF08221 HTH_9: RNA polymerase 41.2 1.1E+02 0.0024 20.7 6.4 49 129-178 9-57 (62)
194 COG3355 Predicted transcriptio 40.7 1.8E+02 0.004 23.0 9.9 56 138-194 32-89 (126)
195 PF10078 DUF2316: Uncharacteri 40.6 32 0.00069 25.6 2.9 23 147-169 22-44 (89)
196 PF13959 DUF4217: Domain of un 40.6 73 0.0016 21.8 4.6 20 142-161 39-58 (65)
197 cd04762 HTH_MerR-trunc Helix-T 39.8 37 0.0008 20.6 2.8 28 150-181 2-29 (49)
198 PF02796 HTH_7: Helix-turn-hel 39.8 58 0.0013 20.4 3.7 21 149-169 22-42 (45)
199 PRK13239 alkylmercury lyase; P 39.7 69 0.0015 27.5 5.2 41 143-188 31-71 (206)
200 cd08809 CARD_CARD9 Caspase act 39.6 39 0.00085 24.9 3.1 68 46-117 14-81 (86)
201 PF06969 HemN_C: HemN C-termin 39.5 1.1E+02 0.0025 20.3 5.6 54 133-191 6-60 (66)
202 PRK11512 DNA-binding transcrip 39.4 76 0.0017 24.8 5.2 42 147-188 53-94 (144)
203 COG3413 Predicted DNA binding 39.1 33 0.00072 29.1 3.2 34 140-173 170-203 (215)
204 PF14947 HTH_45: Winged helix- 39.0 1.4E+02 0.003 21.0 6.8 42 146-191 17-58 (77)
205 PF06056 Terminase_5: Putative 38.8 86 0.0019 21.2 4.6 35 134-171 2-36 (58)
206 PRK09458 pspB phage shock prot 38.7 66 0.0014 23.2 4.1 26 213-238 41-66 (75)
207 PRK10219 DNA-binding transcrip 38.5 85 0.0018 23.1 5.1 26 147-172 20-45 (107)
208 PRK12514 RNA polymerase sigma 38.3 81 0.0018 25.3 5.3 46 125-173 125-170 (179)
209 PRK12423 LexA repressor; Provi 37.9 84 0.0018 26.4 5.5 32 149-180 26-58 (202)
210 smart00028 TPR Tetratricopepti 37.6 33 0.00073 17.4 2.1 25 16-40 5-29 (34)
211 TIGR01610 phage_O_Nterm phage 37.2 91 0.002 22.9 5.0 45 145-191 44-88 (95)
212 PHA00738 putative HTH transcri 37.2 1.9E+02 0.0042 22.3 8.1 57 134-191 13-69 (108)
213 PF03081 Exo70: Exo70 exocyst 37.0 77 0.0017 28.9 5.5 70 102-172 298-371 (371)
214 PF13174 TPR_6: Tetratricopept 36.8 14 0.00031 20.6 0.5 27 17-43 5-31 (33)
215 PF04539 Sigma70_r3: Sigma-70 36.6 94 0.002 21.4 4.8 36 139-174 10-46 (78)
216 PF13176 TPR_7: Tetratricopept 36.3 34 0.00073 20.2 2.1 21 18-38 5-25 (36)
217 PRK00441 argR arginine repress 36.0 72 0.0016 25.8 4.6 41 133-173 3-48 (149)
218 PRK12534 RNA polymerase sigma 35.9 79 0.0017 25.5 4.9 28 146-173 151-178 (187)
219 PF09862 DUF2089: Protein of u 35.8 74 0.0016 24.7 4.3 30 147-176 48-77 (113)
220 PF00440 TetR_N: Bacterial reg 35.7 42 0.0009 21.1 2.6 22 144-165 12-33 (47)
221 TIGR00331 hrcA heat shock gene 35.7 86 0.0019 28.8 5.6 46 134-179 7-54 (337)
222 PF03297 Ribosomal_S25: S25 ri 35.6 1.7E+02 0.0036 22.4 6.2 49 143-191 54-102 (105)
223 PF14549 P22_Cro: DNA-binding 35.2 68 0.0015 21.9 3.6 19 150-168 11-29 (60)
224 cd00569 HTH_Hin_like Helix-tur 34.6 78 0.0017 16.9 3.9 21 148-168 21-41 (42)
225 PF03444 HrcA_DNA-bdg: Winged 34.2 1.8E+02 0.0039 21.1 5.9 56 132-187 7-62 (78)
226 PF10771 DUF2582: Protein of u 34.1 97 0.0021 21.6 4.3 51 139-191 13-63 (65)
227 PRK11886 bifunctional biotin-- 33.9 87 0.0019 28.1 5.3 42 136-177 6-47 (319)
228 TIGR00122 birA_repr_reg BirA b 33.9 1.2E+02 0.0026 20.5 4.9 29 149-177 14-42 (69)
229 PF14069 SpoVIF: Stage VI spor 33.5 63 0.0014 23.5 3.4 28 151-178 37-65 (79)
230 PF13374 TPR_10: Tetratricopep 33.4 39 0.00084 19.7 2.1 22 18-39 8-29 (42)
231 PF05402 PqqD: Coenzyme PQQ sy 33.2 58 0.0013 21.9 3.2 23 152-174 37-59 (68)
232 PRK03573 transcriptional regul 32.7 2.3E+02 0.0051 21.9 8.4 40 148-187 46-85 (144)
233 PRK09392 ftrB transcriptional 32.6 2.3E+02 0.005 23.7 7.5 36 151-191 176-211 (236)
234 PF11972 HTH_13: HTH DNA bindi 32.5 1E+02 0.0022 20.7 4.1 36 139-174 4-39 (54)
235 PF12728 HTH_17: Helix-turn-he 32.4 53 0.0011 20.8 2.7 37 149-191 2-38 (51)
236 PF02042 RWP-RK: RWP-RK domain 31.6 76 0.0016 21.2 3.3 30 142-171 9-38 (52)
237 PRK09334 30S ribosomal protein 31.5 1.5E+02 0.0033 21.9 5.2 38 144-181 37-74 (86)
238 COG2886 Uncharacterized small 31.5 1.3E+02 0.0029 22.2 4.9 25 147-171 40-64 (88)
239 TIGR02976 phageshock_pspB phag 31.3 91 0.002 22.4 3.9 27 212-238 40-66 (75)
240 PF04492 Phage_rep_O: Bacterio 31.2 79 0.0017 23.9 3.8 35 144-178 50-84 (100)
241 PF12793 SgrR_N: Sugar transpo 31.0 1.1E+02 0.0024 23.6 4.7 36 146-181 17-52 (115)
242 PF13613 HTH_Tnp_4: Helix-turn 30.9 1.4E+02 0.003 19.4 4.5 27 147-173 18-44 (53)
243 PRK14584 hmsS hemin storage sy 30.9 1.2E+02 0.0025 24.9 4.9 55 131-191 83-137 (153)
244 PRK10046 dpiA two-component re 30.8 1.1E+02 0.0025 25.4 5.2 41 144-184 173-213 (225)
245 PRK15090 DNA-binding transcrip 30.6 1.1E+02 0.0024 26.5 5.2 55 135-191 15-69 (257)
246 COG3415 Transposase and inacti 30.5 1.2E+02 0.0026 24.3 4.9 45 132-178 7-51 (138)
247 COG4367 Uncharacterized protei 30.4 59 0.0013 24.3 2.8 23 147-169 22-44 (97)
248 PF05043 Mga: Mga helix-turn-h 30.2 1.2E+02 0.0026 21.4 4.6 50 139-191 21-73 (87)
249 KOG0548|consensus 30.1 4.7E+02 0.01 25.8 9.6 79 13-98 427-508 (539)
250 PF12244 DUF3606: Protein of u 30.0 66 0.0014 21.6 2.9 25 147-171 19-43 (57)
251 PF02002 TFIIE_alpha: TFIIE al 29.4 1.2E+02 0.0026 22.4 4.6 38 144-181 23-60 (105)
252 KOG3151|consensus 29.3 4.1E+02 0.0088 23.6 15.4 145 19-177 63-218 (260)
253 PRK06759 RNA polymerase factor 29.0 1.5E+02 0.0032 22.9 5.3 29 146-174 120-148 (154)
254 PF08721 Tn7_Tnp_TnsA_C: TnsA 29.0 1.3E+02 0.0029 20.5 4.5 43 138-180 31-77 (79)
255 PF06224 HTH_42: Winged helix 28.8 1.4E+02 0.003 26.6 5.7 53 131-183 164-217 (327)
256 TIGR02899 spore_safA spore coa 28.6 65 0.0014 19.0 2.5 17 150-166 6-22 (44)
257 KOG1662|consensus 28.5 1.9E+02 0.0042 24.8 6.0 78 108-185 87-177 (210)
258 COG4565 CitB Response regulato 27.6 4E+02 0.0086 23.3 7.8 51 134-184 158-209 (224)
259 PF00046 Homeobox: Homeobox do 27.5 63 0.0014 20.9 2.4 25 147-171 26-50 (57)
260 PF10607 CLTH: CTLH/CRA C-term 27.5 2.6E+02 0.0055 21.6 6.4 51 90-140 4-57 (145)
261 TIGR02392 rpoH_proteo alternat 27.3 1.3E+02 0.0028 26.3 5.1 28 147-174 235-262 (270)
262 PF04190 DUF410: Protein of un 27.3 4.1E+02 0.0088 23.3 8.2 36 4-39 82-117 (260)
263 PF13411 MerR_1: MerR HTH fami 27.1 68 0.0015 21.5 2.6 37 150-190 2-38 (69)
264 PRK11511 DNA-binding transcrip 27.0 1.6E+02 0.0035 22.6 5.1 26 147-172 24-49 (127)
265 TIGR02937 sigma70-ECF RNA poly 26.8 1.6E+02 0.0035 21.8 5.1 27 147-173 125-151 (158)
266 PF03683 UPF0175: Uncharacteri 26.7 2.3E+02 0.005 19.9 5.6 45 126-171 13-57 (76)
267 COG1725 Predicted transcriptio 26.6 2E+02 0.0043 22.7 5.5 65 125-191 11-76 (125)
268 PLN00078 photosystem I reactio 26.5 85 0.0018 24.1 3.2 22 91-112 76-97 (122)
269 cd08050 TAF6 TATA Binding Prot 26.3 3.7E+02 0.008 24.7 8.1 123 46-172 170-313 (343)
270 PF13414 TPR_11: TPR repeat; P 25.9 69 0.0015 21.1 2.5 26 14-39 5-30 (69)
271 PF12833 HTH_18: Helix-turn-he 25.8 1.6E+02 0.0035 20.2 4.5 42 127-168 24-66 (81)
272 PF05331 DUF742: Protein of un 25.8 1.4E+02 0.0031 23.1 4.5 42 137-180 46-87 (114)
273 TIGR03337 phnR transcriptional 25.7 1.6E+02 0.0034 24.7 5.2 62 128-191 4-66 (231)
274 TIGR01889 Staph_reg_Sar staphy 25.0 2.9E+02 0.0063 20.5 9.8 43 145-187 40-82 (109)
275 PF01638 HxlR: HxlR-like helix 25.0 2.6E+02 0.0057 20.0 8.4 61 147-222 17-78 (90)
276 PF05491 RuvB_C: Holliday junc 25.0 94 0.002 22.4 3.0 40 138-177 13-55 (76)
277 PF00126 HTH_1: Bacterial regu 24.8 1.9E+02 0.0041 19.0 4.5 32 141-172 6-37 (60)
278 TIGR03697 NtcA_cyano global ni 24.8 3.6E+02 0.0078 21.4 9.9 40 148-191 143-182 (193)
279 PF00165 HTH_AraC: Bacterial r 24.7 1.1E+02 0.0024 18.5 3.0 25 147-171 7-31 (42)
280 COG1392 Phosphate transport re 24.6 3.2E+02 0.0069 23.5 6.9 80 88-174 26-105 (217)
281 PF14394 DUF4423: Domain of un 24.5 4E+02 0.0086 21.9 9.0 42 150-191 41-88 (171)
282 PF08769 Spo0A_C: Sporulation 24.5 99 0.0022 23.5 3.3 39 151-189 43-81 (106)
283 PRK11924 RNA polymerase sigma 24.5 1.8E+02 0.0039 22.7 5.1 27 147-173 140-166 (179)
284 PF06667 PspB: Phage shock pro 24.4 1.2E+02 0.0027 21.7 3.6 26 213-238 41-66 (75)
285 PF02954 HTH_8: Bacterial regu 24.3 1.8E+02 0.0039 17.8 4.9 35 136-171 7-41 (42)
286 cd08807 CARD_CARD10_CARMA3 Cas 24.3 1.2E+02 0.0026 22.4 3.5 66 47-116 15-80 (86)
287 PRK12547 RNA polymerase sigma 24.0 2E+02 0.0043 22.7 5.3 47 125-174 108-154 (164)
288 PRK12530 RNA polymerase sigma 24.0 1.8E+02 0.0039 23.7 5.1 45 126-173 131-175 (189)
289 PRK14003 potassium-transportin 23.7 1.1E+02 0.0023 26.1 3.7 40 118-176 131-170 (194)
290 PRK09647 RNA polymerase sigma 23.7 1.8E+02 0.0039 24.2 5.2 28 146-173 152-179 (203)
291 smart00389 HOX Homeodomain. DN 23.6 96 0.0021 19.7 2.8 25 147-171 26-50 (56)
292 PRK09652 RNA polymerase sigma 23.5 1.9E+02 0.004 22.8 5.0 27 146-172 142-168 (182)
293 PRK09047 RNA polymerase factor 23.4 2.3E+02 0.005 21.9 5.5 43 128-173 105-147 (161)
294 PRK05574 holA DNA polymerase I 23.4 5.2E+02 0.011 22.8 10.4 73 89-165 216-288 (340)
295 KOG2316|consensus 23.2 1.1E+02 0.0023 27.0 3.6 51 140-191 114-170 (277)
296 PF00356 LacI: Bacterial regul 23.2 1.1E+02 0.0023 19.7 2.8 20 150-169 1-20 (46)
297 PRK10163 DNA-binding transcrip 23.1 1.9E+02 0.004 25.4 5.3 55 135-191 26-81 (271)
298 PRK12537 RNA polymerase sigma 23.1 2.2E+02 0.0047 22.9 5.4 28 146-173 147-174 (182)
299 PHA02591 hypothetical protein; 23.0 99 0.0021 22.6 2.8 23 148-170 59-81 (83)
300 PF08679 DsrD: Dissimilatory s 22.7 2.6E+02 0.0056 19.7 4.8 42 138-179 5-51 (67)
301 PRK00315 potassium-transportin 22.6 1.1E+02 0.0024 26.1 3.5 39 118-175 128-166 (193)
302 TIGR03070 couple_hipB transcri 22.6 2E+02 0.0044 17.9 4.3 23 147-169 14-36 (58)
303 PF13432 TPR_16: Tetratricopep 22.6 64 0.0014 21.0 1.8 26 17-42 2-27 (65)
304 PRK13919 putative RNA polymera 22.5 2.3E+02 0.005 22.7 5.5 28 146-173 149-176 (186)
305 KOG1126|consensus 22.4 3.6E+02 0.0078 27.2 7.4 50 89-138 559-608 (638)
306 PRK12511 RNA polymerase sigma 22.4 2.3E+02 0.0049 23.1 5.4 43 128-173 110-152 (182)
307 PRK10402 DNA-binding transcrip 22.4 4.6E+02 0.01 21.8 8.7 39 149-191 170-208 (226)
308 PRK14001 potassium-transportin 22.3 1.2E+02 0.0025 25.8 3.6 39 118-175 128-166 (189)
309 TIGR02983 SigE-fam_strep RNA p 22.1 2E+02 0.0044 22.4 4.9 29 146-174 124-152 (162)
310 TIGR01636 phage_rinA phage tra 21.9 2.6E+02 0.0056 21.8 5.4 45 128-173 81-125 (134)
311 smart00530 HTH_XRE Helix-turn- 21.8 1.2E+02 0.0025 17.8 2.8 23 147-169 9-31 (56)
312 PF13994 PgaD: PgaD-like prote 21.6 1.8E+02 0.0038 23.0 4.4 53 131-188 84-136 (138)
313 TIGR00681 kdpC K+-transporting 21.3 1.3E+02 0.0027 25.6 3.6 39 118-175 126-164 (187)
314 PF04218 CENP-B_N: CENP-B N-te 21.3 1E+02 0.0022 20.2 2.5 30 139-170 15-44 (53)
315 PRK07037 extracytoplasmic-func 21.1 2.6E+02 0.0056 21.8 5.4 43 128-173 108-150 (163)
316 TIGR02479 FliA_WhiG RNA polyme 21.1 2.5E+02 0.0053 23.6 5.5 38 133-173 179-216 (224)
317 COG2944 Predicted transcriptio 21.0 1.7E+02 0.0036 22.4 3.9 31 130-169 48-78 (104)
318 PRK04217 hypothetical protein; 20.7 1.5E+02 0.0032 22.8 3.7 25 147-171 57-81 (110)
319 PRK13890 conjugal transfer pro 20.7 2.4E+02 0.0053 21.7 4.9 30 134-164 5-34 (120)
320 PRK09863 putative frv operon r 20.7 1.6E+02 0.0035 28.8 4.8 38 134-172 4-41 (584)
321 PF07848 PaaX: PaaX-like prote 20.6 1.2E+02 0.0026 21.3 2.9 34 147-180 22-55 (70)
322 COG1414 IclR Transcriptional r 20.6 2.3E+02 0.005 24.6 5.3 55 135-191 5-60 (246)
323 PF13934 ELYS: Nuclear pore co 20.5 5.4E+02 0.012 22.0 11.0 138 12-177 78-216 (226)
324 PF14056 DUF4250: Domain of un 20.5 1.5E+02 0.0032 20.1 3.1 22 150-171 22-43 (55)
325 PRK13997 potassium-transportin 20.5 1.3E+02 0.0028 25.7 3.5 39 118-175 130-168 (193)
326 COG2522 Predicted transcriptio 20.4 3.2E+02 0.007 21.4 5.5 43 127-171 3-45 (119)
327 PRK12512 RNA polymerase sigma 20.4 2.9E+02 0.0062 22.1 5.6 27 147-173 146-172 (184)
328 KOG3151|consensus 20.3 6.1E+02 0.013 22.5 12.7 125 46-175 51-188 (260)
329 PF03962 Mnd1: Mnd1 family; I 20.3 1.8E+02 0.0039 24.4 4.4 39 145-183 11-51 (188)
330 PRK08301 sporulation sigma fac 20.2 2.5E+02 0.0053 23.7 5.4 28 146-173 196-223 (234)
331 KOG3081|consensus 20.1 6.1E+02 0.013 23.0 7.8 48 18-70 213-260 (299)
332 PRK09642 RNA polymerase sigma 20.0 3E+02 0.0065 21.4 5.5 28 146-173 120-147 (160)
No 1
>KOG0687|consensus
Probab=100.00 E-value=1.1e-61 Score=428.42 Aligned_cols=223 Identities=48% Similarity=0.894 Sum_probs=218.4
Q ss_pred CcccCCchhhhhhhHHHHHHHHchhcCHHHHHHHHhccCCCCCCccccCHhHHHHHHHHHHHHcCChhHHHHccccchhH
Q psy396 1 MSISGGDWSARNKLKAYEGVYCLAIRQYCRAAELFVDVVPTFESYELAEFGTIIRYTVLACMIALPRYNLRKKLMHHGVM 80 (239)
Q Consensus 1 ~~~~~~dw~~~~kl~~~~Gl~~l~~~~y~~Aa~~F~~~~~~f~~~e~~s~~di~~Y~~Lc~Las~~R~elk~~ll~s~~~ 80 (239)
|||+|||||||||+|+|.|+++|+.|||++||.+|+++.+||+++|++++++++.|+++|++.+++|.+||++|+++|++
T Consensus 170 liE~GgDWeRrNRlKvY~Gly~msvR~Fk~Aa~Lfld~vsTFtS~El~~Y~~~v~Ytv~~g~i~leR~dlktKVi~~~Ev 249 (393)
T KOG0687|consen 170 LIEEGGDWERRNRLKVYQGLYCMSVRNFKEAADLFLDSVSTFTSYELMSYETFVRYTVITGLIALERVDLKTKVIKCPEV 249 (393)
T ss_pred HHHhCCChhhhhhHHHHHHHHHHHHHhHHHHHHHHHHHcccccceecccHHHHHHHHHHHhhheeccchHHhhhcCcHHH
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhhhhhHHHHHHHHHHhchHHHHHHHHHHH-HhhhccCcchhHhHHHHHHHHHHHHHHHHhhhhhcccHHHHHHHhC
Q psy396 81 AQALHSQYRDLREYFVSLYDGHYFEFLKCLAAV-EQDMKRDPLLNPHYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFG 159 (239)
Q Consensus 81 ~~~~e~~~p~l~~li~af~~~~y~~~~~~L~~~-~~~l~~D~~L~~h~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg 159 (239)
...++. .|.+++++.++++|+|..|+..|... ...+..|.||+||.+.+.++||.+++.|+++||++++|+.||++||
T Consensus 250 l~vl~~-l~~~~q~l~SLY~C~Y~~Ff~~L~~~~~~~lk~D~~l~~h~~yyvREMR~rvY~QlLESYrsl~l~~MA~aFg 328 (393)
T KOG0687|consen 250 LEVLHK-LPSVSQLLNSLYECDYSDFFNDLAAVEAKQLKDDRYLGPHYRYYVREMRRRVYAQLLESYRSLTLESMAKAFG 328 (393)
T ss_pred HHHhhc-CchHHHHHHHHHhccHHHHHHHHHHHHHHhhccchhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 999998 99999999999999999999999655 7899999999999999999999999999999999999999999999
Q ss_pred CCHHHHHHHHHHHHHcCccceeecccCCEEEEeccccccCCCCCCCccchhhhhHHHHHHHHhhHHHHHHHHHhhhhhcC
Q psy396 160 VSVEFIEKEVARFAAAGRLQCKIDSVAGNVVTTSHISEKGDCRSEAPEASLDRGILYQTTVKRGDIFLNRLKKLARVIDF 239 (239)
Q Consensus 160 ~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~r~~~l~~~~~~ 239 (239)
+|+++|+++|.++|.+|+|+|+||.+||+|++ ++ || +++.+||.+||.|+.++|||||++|+|+.
T Consensus 329 VSVefiDreL~rFI~~grL~ckIDrVnGVVEt-Nr-----------pD---~KN~qyq~vikqGd~LLnriQK~~rvi~~ 393 (393)
T KOG0687|consen 329 VSVEFIDRELGRFIAAGRLHCKIDRVNGVVET-NR-----------PD---EKNAQYQAVIKQGDLLLNRIQKLSRVINL 393 (393)
T ss_pred chHHHHHhHHHHhhccCceeeeeecccceeec-CC-----------cc---ccchHHHHHHhhhHHHHHHHHHHHHHhcC
Confidence 99999999999999999999999999999999 99 99 99999999999999999999999999974
No 2
>COG5187 RPN7 26S proteasome regulatory complex component, contains PCI domain [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=8.1e-51 Score=355.61 Aligned_cols=222 Identities=35% Similarity=0.645 Sum_probs=209.8
Q ss_pred CcccCCchhhhhhhHHHHHHHHchhcCHHHHHHHHhccCCCCCCccccCHhHHHHHHHHHHHHcCChhHHHHccccchhH
Q psy396 1 MSISGGDWSARNKLKAYEGVYCLAIRQYCRAAELFVDVVPTFESYELAEFGTIIRYTVLACMIALPRYNLRKKLMHHGVM 80 (239)
Q Consensus 1 ~~~~~~dw~~~~kl~~~~Gl~~l~~~~y~~Aa~~F~~~~~~f~~~e~~s~~di~~Y~~Lc~Las~~R~elk~~ll~s~~~ 80 (239)
|||+|||||||||+|+|.|++.|..|+|++||.+|.++.++|++.|++++.+++.|+++|++.+++|.++|.+++++||+
T Consensus 181 ~iEkGgDWeRrNRyK~Y~Gi~~m~~RnFkeAa~Ll~d~l~tF~S~El~sY~~~vrYa~~~Gl~~leR~diktki~dspev 260 (412)
T COG5187 181 IIEKGGDWERRNRYKVYKGIFKMMRRNFKEAAILLSDILPTFESSELISYSRAVRYAIFCGLLRLERRDIKTKILDSPEV 260 (412)
T ss_pred HHHhCCCHHhhhhHHHHHHHHHHHHHhhHHHHHHHHHHhccccccccccHHHHHHHHHHhhhheeehhhhhhhhcCCHHH
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhhh--hhHHHHHHHHHHhchHHHHHH-HHHHHHhhhccCcchhHhHHHHHHHHHHHHHHHHhhhhhcccHHHHHHH
Q psy396 81 AQALHSQ--YRDLREYFVSLYDGHYFEFLK-CLAAVEQDMKRDPLLNPHYRHYVQEMRLRAYKQILQAYRSLSLKYMAQC 157 (239)
Q Consensus 81 ~~~~e~~--~p~l~~li~af~~~~y~~~~~-~L~~~~~~l~~D~~L~~h~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~ 157 (239)
..++... -..+..++.+.+.|+|..||. .|.-+.+.|..|.||..|++.+.++||.|++.|.+++|..++|+.||++
T Consensus 261 l~vi~~~e~l~sl~~l~~SLy~cdY~~~F~~ll~~~~n~L~~d~fl~rh~d~fvREMRrrvYaQlLESYr~lsl~sMA~t 340 (412)
T COG5187 261 LDVIGSSEKLGSLVQLATSLYECDYGGDFMNLLYLFCNSLQDDVFLGRHVDLFVREMRRRVYAQLLESYRLLSLESMAQT 340 (412)
T ss_pred HHhccchhhhhhHHHHHHHHHHhccchhhHHHHHHHHhhccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHH
Confidence 9988762 224678899999999996654 4555678999999999999999999999999999999999999999999
Q ss_pred hCCCHHHHHHHHHHHHHcCccceeecccCCEEEEeccccccCCCCCCCccchhhhhHHHHHHHHhhHHHHHHHHHhhhhh
Q psy396 158 FGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVTTSHISEKGDCRSEAPEASLDRGILYQTTVKRGDIFLNRLKKLARVI 237 (239)
Q Consensus 158 fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~r~~~l~~~~ 237 (239)
||+|++.++..|.++|.+|+|+|.||.+||++++ ++ || +++.+|+.++++|+++++++||....|
T Consensus 341 FgVSV~yvdrDLg~FIp~~~LncvIDRvnGvVet-nr-----------pd---ekn~qy~~vVkqGd~ll~klqKy~atv 405 (412)
T COG5187 341 FGVSVEYVDRDLGEFIPEGRLNCVIDRVNGVVET-NR-----------PD---EKNQQYSSVVKQGDDLLRKLQKYVATV 405 (412)
T ss_pred hCccHHHHhhhHHhhCCCCceeeeeecccceEec-cC-----------cc---hhhhhHHHHHhcchHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999 99 99 999999999999999999999988765
No 3
>KOG0686|consensus
Probab=100.00 E-value=9.2e-45 Score=328.49 Aligned_cols=219 Identities=25% Similarity=0.330 Sum_probs=201.1
Q ss_pred hhhhhhHHHHHHHHchhcCHHHHHHHHhccCCCCCCc-cccCHhHHHHHHHHHHHHcCChhHHHHccccchhHHHHhhhh
Q psy396 9 SARNKLKAYEGVYCLAIRQYCRAAELFVDVVPTFESY-ELAEFGTIIRYTVLACMIALPRYNLRKKLMHHGVMAQALHSQ 87 (239)
Q Consensus 9 ~~~~kl~~~~Gl~~l~~~~y~~Aa~~F~~~~~~f~~~-e~~s~~di~~Y~~Lc~Las~~R~elk~~ll~s~~~~~~~e~~ 87 (239)
+..+|++|++|++++..|+|+.|+.+|+.+.++-..+ ++++|.|++.|++||+||||+|.+|+.++++|.+|+.|++.
T Consensus 226 ~v~~kl~C~agLa~L~lkkyk~aa~~fL~~~~~~~d~~~ivtpsdv~iYggLcALAtfdr~~Lk~~vi~n~~Fk~flel- 304 (466)
T KOG0686|consen 226 EVPAKLKCAAGLANLLLKKYKSAAKYFLLAEFDHCDYPEIVTPSDVAIYGGLCALATFDRQDLKLNVIKNESFKLFLEL- 304 (466)
T ss_pred hcCcchHHHHHHHHHHHHHHHHHHHHHHhCCCCccCccceecchhhHHHHhhHhhccCCHHHHHHHHHcchhhhhHHhc-
Confidence 3467999999999999999999999999997664345 89999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHHHHhchHHHHHHHHHHHHhhhccCcchhHhHHHHHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHH
Q psy396 88 YRDLREYFVSLYDGHYFEFLKCLAAVEQDMKRDPLLNPHYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEK 167 (239)
Q Consensus 88 ~p~l~~li~af~~~~y~~~~~~L~~~~~~l~~D~~L~~h~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~ 167 (239)
+|.+++++.+|++++|..|+++|.++++.+++|+||+|||++||..||.|+++||+.||+++++++||.+||+|+.++|+
T Consensus 305 ~Pqlr~il~~fy~sky~~cl~~L~~~k~~llLD~yLaphVd~Ly~~IR~r~llqy~~py~s~~m~~mA~af~~sv~~le~ 384 (466)
T KOG0686|consen 305 EPQLREILFKFYSSKYASCLELLREIKPRLLLDMYLAPHVDNLYSLIRNRALLQYLSPYSSADMSKMAEAFNTSVAILES 384 (466)
T ss_pred ChHHHHHHHHHhhhhHHHHHHHHHHhccceeechhcchhHHHHHHHHHHhhHHHhcCccccchHHHHHHHhcccHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHcCccceeecccCCEEEEeccccccCCCCCCCccchhhhhHHHHHHHHhhHHHHHHHHHhhhh
Q psy396 168 EVARFAAAGRLQCKIDSVAGNVVTTSHISEKGDCRSEAPEASLDRGILYQTTVKRGDIFLNRLKKLARV 236 (239)
Q Consensus 168 ~L~~lI~~g~l~arID~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~r~~~l~~~ 236 (239)
+|.++|.+|+|+||||++++++.+ +|.|+|.++.+..++.+..+++-.+ .+.-|+-.+.+-
T Consensus 385 ~l~~LI~~~~i~~rIDs~~ki~~~-----~~~~~en~~fe~~~~~~~~~~~~~k---al~lr~~~~~~~ 445 (466)
T KOG0686|consen 385 ELLELILEGKISGRIDSHNKILYA-----RDADSENATFERVLPMGKRSQLEAK---ALLLRAALLKNK 445 (466)
T ss_pred HHHHHHHccchheeeccccceeee-----cccccccchhhhcchhhHHHHHHHH---HHHHHHHHHhcc
Confidence 999999999999999999999999 5688898888877788877776544 355555555443
No 4
>KOG1463|consensus
Probab=100.00 E-value=1.1e-33 Score=251.83 Aligned_cols=203 Identities=15% Similarity=0.289 Sum_probs=188.7
Q ss_pred hhhhHHHHHHHHchhcCHHHHHHHHhccCCCCCCcc-ccCHhHHHHHHHHHHHHcCChhHHHHccccchhHHHHhhhhhh
Q psy396 11 RNKLKAYEGVYCLAIRQYCRAAELFVDVVPTFESYE-LAEFGTIIRYTVLACMIALPRYNLRKKLMHHGVMAQALHSQYR 89 (239)
Q Consensus 11 ~~kl~~~~Gl~~l~~~~y~~Aa~~F~~~~~~f~~~e-~~s~~di~~Y~~Lc~Las~~R~elk~~ll~s~~~~~~~e~~~p 89 (239)
.+.++..+|++|+.++||++|++||+|+|++|++.+ -+.+-..++||+||.+|...+++++ .++.++...+|.+.+..
T Consensus 208 Qa~lDLqSGIlha~ekDykTafSYFyEAfEgf~s~~~~v~A~~sLKYMlLcKIMln~~ddv~-~lls~K~~l~y~g~~i~ 286 (411)
T KOG1463|consen 208 QATLDLQSGILHAAEKDYKTAFSYFYEAFEGFDSLDDDVKALTSLKYMLLCKIMLNLPDDVA-ALLSAKLALKYAGRDID 286 (411)
T ss_pred HHHHHHhccceeecccccchHHHHHHHHHccccccCCcHHHHHHHHHHHHHHHHhcCHHHHH-HHHhhHHHHhccCcchH
Confidence 467899999999999999999999999999998863 3566677999999999999999995 69999999998877678
Q ss_pred HHHHHHHHHHhchHHHHHHHHHHHHhhhccCcchhHhHHHHHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHH
Q psy396 90 DLREYFVSLYDGHYFEFLKCLAAVEQDMKRDPLLNPHYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEV 169 (239)
Q Consensus 90 ~l~~li~af~~~~y~~~~~~L~~~~~~l~~D~~L~~h~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L 169 (239)
.|+.+.++|.+++.++|.+.|.++.++|..||+++.|...||+++.++++.+.++|||+|.|+++|+.+|+|+..||+.|
T Consensus 287 AmkavAeA~~nRSLkdF~~AL~~yk~eL~~D~ivr~Hl~~Lyd~lLEknl~riIEPyS~Vei~hIA~~IGl~~~~VEkKL 366 (411)
T KOG1463|consen 287 AMKAVAEAFGNRSLKDFEKALADYKKELAEDPIVRSHLQSLYDNLLEKNLCRIIEPYSRVEISHIAEVIGLDVPQVEKKL 366 (411)
T ss_pred HHHHHHHHhcCCcHHHHHHHHHHhHHHHhcChHHHHHHHHHHHHHHHHhHHHHcCchhhhhHHHHHHHHCCCcHHHHHHH
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHcCccceeecccCCEEEEeccccccCCCCCCCccchhhhhHHHHHHHHhhHHHHHHHHHhhhh
Q psy396 170 ARFAAAGRLQCKIDSVAGNVVTTSHISEKGDCRSEAPEASLDRGILYQTTVKRGDIFLNRLKKLARV 236 (239)
Q Consensus 170 ~~lI~~g~l~arID~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~r~~~l~~~ 236 (239)
++||+++++.|.+|+.+|+|++ ++ .. +.++.|+++++. |+.++.|
T Consensus 367 sqMILDKkf~G~LDQg~g~Liv-~~-----------e~---~~d~~y~~aLet-------I~~m~kV 411 (411)
T KOG1463|consen 367 SQMILDKKFYGTLDQGEGCLIV-FE-----------EP---PADNTYDAALET-------IQNMGKV 411 (411)
T ss_pred HHHHHHHHhhcccccCCCeEEE-eC-----------CC---CcchHHHHHHHH-------HHhccCC
Confidence 9999999999999999999999 87 55 788999999998 7777653
No 5
>COG5159 RPN6 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=99.96 E-value=5.1e-29 Score=218.61 Aligned_cols=206 Identities=13% Similarity=0.256 Sum_probs=184.1
Q ss_pred hhhhhHHHHHHHHchhcCHHHHHHHHhccCCCCCCc-cccCHhHHHHHHHHHHHHcCChhHHHHccccchhHHHHhhh-h
Q psy396 10 ARNKLKAYEGVYCLAIRQYCRAAELFVDVVPTFESY-ELAEFGTIIRYTVLACMIALPRYNLRKKLMHHGVMAQALHS-Q 87 (239)
Q Consensus 10 ~~~kl~~~~Gl~~l~~~~y~~Aa~~F~~~~~~f~~~-e~~s~~di~~Y~~Lc~Las~~R~elk~~ll~s~~~~~~~e~-~ 87 (239)
..+.|+..+|++++..+||++|.++|++++++|+.. ...-+-..++|++|+.+|...|+++| ++++++.+.+.... .
T Consensus 204 lqa~lDL~sGIlhcdd~dyktA~SYF~Ea~Egft~l~~d~kAc~sLkYmlLSkIMlN~~~evk-~vl~~K~t~~~y~~r~ 282 (421)
T COG5159 204 LQAQLDLLSGILHCDDRDYKTASSYFIEALEGFTLLKMDVKACVSLKYMLLSKIMLNRREEVK-AVLRNKNTLKHYDDRM 282 (421)
T ss_pred HHHHHHHhccceeeccccchhHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHhhHHHHH-HHHccchhHhhhhhhh
Confidence 457899999999999999999999999999999875 22233346899999999999999997 59999998885443 3
Q ss_pred hhHHHHHHHHHHhchHHHHHHHHHHHHhhhccCcchhHhHHHHHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHH
Q psy396 88 YRDLREYFVSLYDGHYFEFLKCLAAVEQDMKRDPLLNPHYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEK 167 (239)
Q Consensus 88 ~p~l~~li~af~~~~y~~~~~~L~~~~~~l~~D~~L~~h~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~ 167 (239)
...|+.+.++|.+++..+|.+.|+++.+++..|+|+..|...+|+.+.++++.+.++||++|.++++|+.+|.++..+|.
T Consensus 283 I~am~avaea~~NRsL~df~~aL~qY~~el~~D~~iRsHl~~LYD~LLe~Nl~kiiEPfs~VeishIa~viGldt~qvEg 362 (421)
T COG5159 283 IRAMLAVAEAFGNRSLKDFSDALAQYSDELHQDSFIRSHLQYLYDVLLEKNLVKIIEPFSVVEISHIADVIGLDTNQVEG 362 (421)
T ss_pred HHHHHHHHHHhCCCcHhhHHHHHHHhhHHhccCHHHHHHHHHHHHHHHHhhhhhhcCcceeeehhHHHHHhcccHHHHHH
Confidence 67799999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHcCccceeecccCCEEEEeccccccCCCCCCCccchhhhhHHHHHHHHhhHHHHHHHHHhhhhhc
Q psy396 168 EVARFAAAGRLQCKIDSVAGNVVTTSHISEKGDCRSEAPEASLDRGILYQTTVKRGDIFLNRLKKLARVID 238 (239)
Q Consensus 168 ~L~~lI~~g~l~arID~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~r~~~l~~~~~ 238 (239)
.|++||+++-..|.+|+.+|.++. +. .. ..++.|..+++. +..|..+||
T Consensus 363 KLsqMILDKifyG~LDqg~gcLiv-y~-----------ep---~qd~tyd~ale~-------v~~l~~vVd 411 (421)
T COG5159 363 KLSQMILDKIFYGTLDQGDGCLIV-YG-----------EP---AQDNTYDEALEQ-------VEALDCVVD 411 (421)
T ss_pred HHHHHHHHHHHHhhhccCCceEEE-eC-----------Cc---cccchHHHHHHH-------HHHhhhHHH
Confidence 999999999999999999999999 77 44 677888888886 556665554
No 6
>KOG1464|consensus
Probab=99.94 E-value=3.4e-26 Score=200.22 Aligned_cols=174 Identities=13% Similarity=0.266 Sum_probs=156.7
Q ss_pred hHHHHHHHHchhcCHHHHHHHHhccCCCCCCccccCHhHHHHHHHHHHHHcCChhHHHHccccchhHHHHhhhh-hhHHH
Q psy396 14 LKAYEGVYCLAIRQYCRAAELFVDVVPTFESYELAEFGTIIRYTVLACMIALPRYNLRKKLMHHGVMAQALHSQ-YRDLR 92 (239)
Q Consensus 14 l~~~~Gl~~l~~~~y~~Aa~~F~~~~~~f~~~e~~s~~di~~Y~~Lc~Las~~R~elk~~ll~s~~~~~~~e~~-~p~l~ 92 (239)
+.-+.|.+|+.+|.|.+|+..|+++|.+|+..+.-....+++|++|+.|+..+- + ++++++++++|-... .-.|.
T Consensus 233 IRECGGKMHlreg~fe~AhTDFFEAFKNYDEsGspRRttCLKYLVLANMLmkS~--i--NPFDsQEAKPyKNdPEIlAMT 308 (440)
T KOG1464|consen 233 IRECGGKMHLREGEFEKAHTDFFEAFKNYDESGSPRRTTCLKYLVLANMLMKSG--I--NPFDSQEAKPYKNDPEILAMT 308 (440)
T ss_pred HHHcCCccccccchHHHHHhHHHHHHhcccccCCcchhHHHHHHHHHHHHHHcC--C--CCCcccccCCCCCCHHHHHHH
Confidence 345678999999999999999999966665544334446899999999988644 4 899999999998741 22478
Q ss_pred HHHHHHHhchHHHHHHHHHHHHhhhccCcchhHhHHHHHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHH
Q psy396 93 EYFVSLYDGHYFEFLKCLAAVEQDMKRDPLLNPHYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARF 172 (239)
Q Consensus 93 ~li~af~~~~y~~~~~~L~~~~~~l~~D~~L~~h~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~l 172 (239)
.++.+|.+.+..+|..+|...++.++.|||+..|+..|+++||.+++++.++||..|.|+++++.+++|+.+|+..|+.+
T Consensus 309 nlv~aYQ~NdI~eFE~Il~~~~~~IM~DpFIReh~EdLl~niRTQVLlkLIkPYt~i~Ipfis~~Lnv~~~dV~~LLV~~ 388 (440)
T KOG1464|consen 309 NLVAAYQNNDIIEFERILKSNRSNIMDDPFIREHIEDLLRNIRTQVLLKLIKPYTNIGIPFISKELNVPEADVESLLVSC 388 (440)
T ss_pred HHHHHHhcccHHHHHHHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHhccccccCchhhHhhcCCCHHHHHHHHHHH
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHcCccceeecccCCEEEE
Q psy396 173 AAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 173 I~~g~l~arID~~~~~l~~ 191 (239)
|++..|+|+||.+|+.|..
T Consensus 389 ILD~~i~g~Ide~n~~l~~ 407 (440)
T KOG1464|consen 389 ILDDTIDGRIDEVNQYLEL 407 (440)
T ss_pred HhccccccchHHhhhHhcc
Confidence 9999999999999999999
No 7
>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=99.82 E-value=8.2e-21 Score=158.71 Aligned_cols=73 Identities=44% Similarity=0.710 Sum_probs=69.4
Q ss_pred CcccCCchhhhhhhHHHHHHHHchhcCHHHHHHHHhccCCCCCC---ccccCHhHHHHHHHHHHHHcCChhHHHHc
Q psy396 1 MSISGGDWSARNKLKAYEGVYCLAIRQYCRAAELFVDVVPTFES---YELAEFGTIIRYTVLACMIALPRYNLRKK 73 (239)
Q Consensus 1 ~~~~~~dw~~~~kl~~~~Gl~~l~~~~y~~Aa~~F~~~~~~f~~---~e~~s~~di~~Y~~Lc~Las~~R~elk~~ 73 (239)
++++||||+++|||+||.||++|..|+|++||..|+++.++|++ .+++||+|+++|++||+|+|++|.+||++
T Consensus 102 ~~~~~~d~~~~nrlk~~~gL~~l~~r~f~~AA~~fl~~~~t~~~~~~~el~s~~d~a~Y~~l~aLat~~R~eLk~K 177 (177)
T PF10602_consen 102 LIEKGGDWERRNRLKVYEGLANLAQRDFKEAAELFLDSLSTFTSLQYTELISYNDFAIYGGLCALATLDRSELKKK 177 (177)
T ss_pred HHhccchHHHHHHHHHHHHHHHHHhchHHHHHHHHHccCcCCCCCchhhhcCHHHHHHHHHHHHHHhCCHHHHccC
Confidence 46889999999999999999999999999999999999999987 69999999999999999999999999753
No 8
>KOG2758|consensus
Probab=99.81 E-value=2.1e-19 Score=159.78 Aligned_cols=165 Identities=18% Similarity=0.291 Sum_probs=143.0
Q ss_pred CHhHHHHHHHHHHHHcCCh--hHHHHccccchhHHHHhhhhhhHHHHHHHHHHhchHHHH-----HHHHHHHHhhhccCc
Q psy396 49 EFGTIIRYTVLACMIALPR--YNLRKKLMHHGVMAQALHSQYRDLREYFVSLYDGHYFEF-----LKCLAAVEQDMKRDP 121 (239)
Q Consensus 49 s~~di~~Y~~Lc~Las~~R--~elk~~ll~s~~~~~~~e~~~p~l~~li~af~~~~y~~~-----~~~L~~~~~~l~~D~ 121 (239)
+++.+++|++.+-+....| ..+| ++.++++.+....+++++.|..|-|..| .+.|.+++..+.+|+
T Consensus 250 ~cPhllRYLatAvvtnk~~rr~~lk-------dlvkVIqqE~ysYkDPiteFl~clyvn~DFdgAq~kl~eCeeVl~nDf 322 (432)
T KOG2758|consen 250 SCPHLLRYLATAVVTNKRRRRNRLK-------DLVKVIQQESYSYKDPITEFLECLYVNYDFDGAQKKLRECEEVLVNDF 322 (432)
T ss_pred hCHHHHHHHHHHhhcchHhhHHHHH-------HHHHHHHHhccccCCcHHHHHHHHhhccchHHHHHHHHHHHHHHhcch
Confidence 5678899998776665332 3333 4777777744556777777776666555 899999999999999
Q ss_pred chhHhHHHHHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEEeccccccCCC
Q psy396 122 LLNPHYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVTTSHISEKGDC 201 (239)
Q Consensus 122 ~L~~h~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~~~~~~~~~~~ 201 (239)
||-+.++.|.+..|.-++.-||+.+++|+|+-+|.+++|++++.|.|++.+|.+.+|+||||+..|.|++ ..
T Consensus 323 FLva~l~~F~E~ARl~ifEtfCRIHqcIti~mLA~kLnm~~eeaErwivnlIr~~rl~AkidSklg~Vvm-g~------- 394 (432)
T KOG2758|consen 323 FLVALLDEFLENARLLIFETFCRIHQCITIDMLADKLNMDPEEAERWIVNLIRTARLDAKIDSKLGHVVM-GH------- 394 (432)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHheeHHHHHHHhcCCHHHHHHHHHHHHHHhhhhhhhccccCceee-cC-------
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999 44
Q ss_pred CCCCccchhhhhHHHHHHHHhhHHHHHHHHHhhhhh
Q psy396 202 RSEAPEASLDRGILYQTTVKRGDIFLNRLKKLARVI 237 (239)
Q Consensus 202 ~~~~~~~~~~~~~~~~~~i~~~~~~~~r~~~l~~~~ 237 (239)
+..+.|||++++++.|..|.|+|+..+
T Consensus 395 ---------~~~s~~qQ~ie~tksLS~rsq~la~~l 421 (432)
T KOG2758|consen 395 ---------PTVSPHQQLIEKTKSLSFRSQNLAQQL 421 (432)
T ss_pred ---------CCCCHHHHHHHhccccchhHHHHHHHH
Confidence 678899999999999999999998765
No 9
>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=99.81 E-value=5.1e-19 Score=133.60 Aligned_cols=103 Identities=25% Similarity=0.395 Sum_probs=99.2
Q ss_pred hHHHHHHHHHHhchHHHHHHHHHHHHhhhccCcchhHhHHHHHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHH
Q psy396 89 RDLREYFVSLYDGHYFEFLKCLAAVEQDMKRDPLLNPHYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKE 168 (239)
Q Consensus 89 p~l~~li~af~~~~y~~~~~~L~~~~~~l~~D~~L~~h~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~ 168 (239)
|++.+++++|..++|..|.+.+.++.+.+..|+++.+|+..+.+.++.+++.++..||++|+++.||+.++++.+++|.+
T Consensus 1 ~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~l~~~i~~~~l~~l~~~y~~i~~~~ia~~l~~~~~~vE~~ 80 (105)
T PF01399_consen 1 PPYSELLRAFRSGDLQEFEEFLEKHSESLFKDPFLAEYVEQLKEKIRRRNLRQLSKPYSSISISEIAKALQLSEEEVESI 80 (105)
T ss_dssp HHHHHHHHHHHCT-HHHHHHHHHHTCHHHHHCTTHHHHHHHHHHHHHHHHHHHHHHC-SEEEHHHHHHHHTCCHHHHHHH
T ss_pred CHHHHHHHHHHhCCHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHhccchHHHHHH
Confidence 78999999999999999999999998889999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHcCccceeecccCCEEEE
Q psy396 169 VARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 169 L~~lI~~g~l~arID~~~~~l~~ 191 (239)
|++||.+|.|+|+||+.+|+|+.
T Consensus 81 l~~~I~~~~i~~~ID~~~~~v~~ 103 (105)
T PF01399_consen 81 LIDLISNGLIKAKIDQVNGVVVF 103 (105)
T ss_dssp HHHHHHTTSSEEEEETTTTEEEE
T ss_pred HHHHHHCCCEEEEEECCCCEEEe
Confidence 99999999999999999999987
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=99.52 E-value=9.1e-14 Score=102.67 Aligned_cols=69 Identities=30% Similarity=0.415 Sum_probs=67.0
Q ss_pred HhHHHHHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEEecc
Q psy396 125 PHYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVTTSH 194 (239)
Q Consensus 125 ~h~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~~~~ 194 (239)
+|++.+.+.+|.+++.+|++||++|+++.||+.|++|.+++|.+|+++|.+|.|+|+||+.+|++.. ..
T Consensus 1 ~~~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~-~~ 69 (88)
T smart00088 1 QLVERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEF-EE 69 (88)
T ss_pred ChHHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEE-CC
Confidence 4789999999999999999999999999999999999999999999999999999999999999999 65
No 11
>smart00753 PAM PCI/PINT associated module.
Probab=99.52 E-value=9.1e-14 Score=102.67 Aligned_cols=69 Identities=30% Similarity=0.415 Sum_probs=67.0
Q ss_pred HhHHHHHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEEecc
Q psy396 125 PHYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVTTSH 194 (239)
Q Consensus 125 ~h~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~~~~ 194 (239)
+|++.+.+.+|.+++.+|++||++|+++.||+.|++|.+++|.+|+++|.+|.|+|+||+.+|++.. ..
T Consensus 1 ~~~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~-~~ 69 (88)
T smart00753 1 QLVERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEF-EE 69 (88)
T ss_pred ChHHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEE-CC
Confidence 4789999999999999999999999999999999999999999999999999999999999999999 65
No 12
>KOG2581|consensus
Probab=99.06 E-value=1e-08 Score=94.48 Aligned_cols=169 Identities=18% Similarity=0.197 Sum_probs=130.9
Q ss_pred hhhHHHHHHHHchhcCHHHHHHHHhccCCCCC-CccccCHhHHHHHHHHHHHHcCChhHHHHccccchhHHHHhhhhhhH
Q psy396 12 NKLKAYEGVYCLAIRQYCRAAELFVDVVPTFE-SYELAEFGTIIRYTVLACMIALPRYNLRKKLMHHGVMAQALHSQYRD 90 (239)
Q Consensus 12 ~kl~~~~Gl~~l~~~~y~~Aa~~F~~~~~~f~-~~e~~s~~di~~Y~~Lc~Las~~R~elk~~ll~s~~~~~~~e~~~p~ 90 (239)
+|.--|.|...+-+.+|..|.++|+.+.---+ +..+.-...+-+.+++..+...+=.+. .++.-|..++-+..
T Consensus 247 ARY~yY~GrIkaiqldYssA~~~~~qa~rkapq~~alGf~q~v~k~~ivv~ll~geiPer--s~F~Qp~~~ksL~~---- 320 (493)
T KOG2581|consen 247 ARYLYYLGRIKAIQLDYSSALEYFLQALRKAPQHAALGFRQQVNKLMIVVELLLGEIPER--SVFRQPGMRKSLRP---- 320 (493)
T ss_pred HHHHHHHhhHHHhhcchhHHHHHHHHHHHhCcchhhhhHHHHHHHHHHHHHHHcCCCcch--hhhcCccHHHHHHH----
Confidence 35667999999999999999999999963332 223445567789999999988764443 45666666655543
Q ss_pred HHHHHHHHHhchHHHHHHHHHHHHhhhccCcchhHhHHHHHHHHHHHHHHH----HhhhhhcccHHHHHHHhCCCHHH-H
Q psy396 91 LREYFVSLYDGHYFEFLKCLAAVEQDMKRDPLLNPHYRHYVQEMRLRAYKQ----ILQAYRSLSLKYMAQCFGVSVEF-I 165 (239)
Q Consensus 91 l~~li~af~~~~y~~~~~~L~~~~~~l~~D~~L~~h~~~l~~~ir~~~l~q----yl~pYs~v~l~~mA~~fg~s~~~-l 165 (239)
.-++-++-..++.+.|.+.|.++.+.++.| +.-.++-.+|..+|.. +=-+||+|++..+|+.+|++.++ +
T Consensus 321 Yf~Lt~AVr~gdlkkF~~~leq~k~~f~~D-----~ty~LivRLR~NVIkTgIR~ISlsYSRISl~DIA~kL~l~Seed~ 395 (493)
T KOG2581|consen 321 YFKLTQAVRLGDLKKFNETLEQFKDKFQAD-----GTYTLIVRLRHNVIKTGIRKISLSYSRISLQDIAKKLGLNSEEDA 395 (493)
T ss_pred HHHHHHHHHHhhHHHHHHHHHHHHHHHhhC-----CcchHHHHHHHHHHHHhhhheeeeeeeccHHHHHHHhcCCCchhH
Confidence 556777888999999999999998877666 4445555555555544 44469999999999999996654 9
Q ss_pred HHHHHHHHHcCccceeecccCCEEEE
Q psy396 166 EKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 166 E~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
|--+.+.|.+|-|.|+||..+|.+..
T Consensus 396 EyiVakAIRDGvIea~Id~~~g~m~s 421 (493)
T KOG2581|consen 396 EYIVAKAIRDGVIEAKIDHEDGFMQS 421 (493)
T ss_pred HHHHHHHHHhccceeeeccccCceeh
Confidence 99999999999999999999997776
No 13
>KOG2908|consensus
Probab=98.95 E-value=1.2e-07 Score=85.65 Aligned_cols=208 Identities=19% Similarity=0.219 Sum_probs=151.2
Q ss_pred hhhhhHHHHHHHHchhcCHHHHHHHHhccCCCCCCccccCH--hHHHHHHHHHHHHcCChhHHHHccccchhHHHHhhhh
Q psy396 10 ARNKLKAYEGVYCLAIRQYCRAAELFVDVVPTFESYELAEF--GTIIRYTVLACMIALPRYNLRKKLMHHGVMAQALHSQ 87 (239)
Q Consensus 10 ~~~kl~~~~Gl~~l~~~~y~~Aa~~F~~~~~~f~~~e~~s~--~di~~Y~~Lc~Las~~R~elk~~ll~s~~~~~~~e~~ 87 (239)
-++...-.+..|+=..|||..++..-+.=...-+..++-.. .+.+.-++++||+.-+=-... -++.-|-+....+.+
T Consensus 155 Vh~~fY~lssqYyk~~~d~a~yYr~~L~YL~~~d~~~l~~se~~~lA~~L~~aALLGe~iyNfG-ELL~HPilesL~gT~ 233 (380)
T KOG2908|consen 155 VHSSFYSLSSQYYKKIGDFASYYRHALLYLGCSDIDDLSESEKQDLAFDLSLAALLGENIYNFG-ELLAHPILESLKGTN 233 (380)
T ss_pred hhhhHHHHHHHHHHHHHhHHHHHHHHHHHhccccccccCHHHHHHHHHHHHHHHHhccccccHH-HHHhhHHHHHhcCCc
Confidence 35666667777888888887665543332211111122223 378999999999985432222 135556555555544
Q ss_pred hhHHHHHHHHHHhchHHHHHHHHHHHHhhhccCcchhHhHHHHHHHHHHHHHHHHhhh----hhcccHHHHHHHhCCCHH
Q psy396 88 YRDLREYFVSLYDGHYFEFLKCLAAVEQDMKRDPLLNPHYRHYVQEMRLRAYKQILQA----YRSLSLKYMAQCFGVSVE 163 (239)
Q Consensus 88 ~p~l~~li~af~~~~y~~~~~~L~~~~~~l~~D~~L~~h~~~l~~~ir~~~l~qyl~p----Ys~v~l~~mA~~fg~s~~ 163 (239)
..|+.+++.+|..++...|++..... ..=|-|+.|.+.+.+.||.-+++..+-. -+.|+++.+|++..+|.+
T Consensus 234 ~eWL~dll~Afn~Gdl~~f~~l~~~~----~~~p~L~~~e~~L~qKI~LmaLiEi~F~rpa~~R~lsf~~Ia~~tkip~~ 309 (380)
T KOG2908|consen 234 REWLKDLLIAFNSGDLKRFESLKGVW----GKQPDLASNEDFLLQKIRLLALIEITFSRPANERTLSFKEIAEATKIPNK 309 (380)
T ss_pred HHHHHHHHHHhccCCHHHHHHHHHHh----ccCchHHHHHHHHHHHHHHHHHHHHHhcCcchhccccHHHHHHHhCCCHH
Confidence 67999999999999999998866554 3368899999999999999999987654 578999999999999999
Q ss_pred HHHHHHHHHHHcCccceeecccCCEEEEeccccccCCCCCCCccchhhhhHHHHHHHHhhHH---HHHHHHHhhhhh
Q psy396 164 FIEKEVARFAAAGRLQCKIDSVAGNVVTTSHISEKGDCRSEAPEASLDRGILYQTTVKRGDI---FLNRLKKLARVI 237 (239)
Q Consensus 164 ~lE~~L~~lI~~g~l~arID~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~---~~~r~~~l~~~~ 237 (239)
++|-.+.+.+.-|-|.|.||+++|++++ .- .- ||.-.-+++++-++. -.+.++++...+
T Consensus 310 eVE~LVMKAlslgLikG~Idqv~~~v~~-sw-----------vq---PRvl~~~qI~~Mk~rl~~W~~~v~~me~~v 371 (380)
T KOG2908|consen 310 EVELLVMKALSLGLIKGSIDQVEGVVYM-SW-----------VQ---PRVLDRSQIVKMKDRLDEWNKDVKSMEGLV 371 (380)
T ss_pred HHHHHHHHHHhccceeeeecccccEEEE-ec-----------cc---ccccCHHHHHhHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999 43 33 555556666664443 344566655544
No 14
>KOG1498|consensus
Probab=98.76 E-value=2.9e-07 Score=84.63 Aligned_cols=176 Identities=15% Similarity=0.232 Sum_probs=128.3
Q ss_pred hhhHHHHHHH--HchhcCHHHHHHHHhccCCCCCCccccCHhHHHHHHH-----HHHHHcCChhHHHHccccchhHHHHh
Q psy396 12 NKLKAYEGVY--CLAIRQYCRAAELFVDVVPTFESYELAEFGTIIRYTV-----LACMIALPRYNLRKKLMHHGVMAQAL 84 (239)
Q Consensus 12 ~kl~~~~Gl~--~l~~~~y~~Aa~~F~~~~~~f~~~e~~s~~di~~Y~~-----Lc~Las~~R~elk~~ll~s~~~~~~~ 84 (239)
-||+-|.-+. +++.+.|=+++++.-.+ ++...+-+-+.-.++.+ .|.||..+. .+..++.+..--+-+
T Consensus 210 lKlkyY~lmI~l~lh~~~Yl~v~~~Yrai---y~t~~vk~d~~kw~~vL~~iv~f~~LAp~dn--eQsdll~~is~dKkL 284 (439)
T KOG1498|consen 210 LKLKYYELMIRLGLHDRAYLNVCRSYRAI---YDTGNVKEDPEKWIEVLRSIVSFCVLAPHDN--EQSDLLARISNDKKL 284 (439)
T ss_pred HHHHHHHHHHHhcccccchhhHHHHHHHH---hcccccccChhhhhhhhhhheeEEeecCCCc--HHHHHHHHHhccccc
Confidence 4677777663 55688898988888877 43322322112223333 345665543 334455544443445
Q ss_pred hhhhhHHHHHHHHHHhchHHHHHHHHHHHHhhhccCcch------hHhHHHHHHHHHHHHHHHHhhhhhcccHHHHHHHh
Q psy396 85 HSQYRDLREYFVSLYDGHYFEFLKCLAAVEQDMKRDPLL------NPHYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCF 158 (239)
Q Consensus 85 e~~~p~l~~li~af~~~~y~~~~~~L~~~~~~l~~D~~L------~~h~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~f 158 (239)
+. .|...+++..|.+...-.+-..-+.+.+.+..+.|+ ..|...+-..+-+-++-=.-+-||+|++.+||+.+
T Consensus 285 ~e-~p~~k~lLklfv~~EL~rw~s~~~~yg~~l~~~~~~~~~~~gek~~~dL~~RIiEHNiRiiA~yYSrIt~~rl~eLL 363 (439)
T KOG1498|consen 285 SE-LPDYKELLKLFVTMELIRWVSLVESYGDELRTNDFFDGGEEGEKRWSDLKLRIIEHNIRIIAKYYSRITLKRLAELL 363 (439)
T ss_pred cc-CccHHHHHHHHHhcceeeehhHhhhhHHHHhhcccccccchhhhHHHHHHHHHHHHHHHHHHHHHhhccHHHHHHHh
Confidence 55 899999999999999988887777788877666333 25666666666666666566679999999999999
Q ss_pred CCCHHHHHHHHHHHHHcCccceeecccCCEEEEecc
Q psy396 159 GVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVTTSH 194 (239)
Q Consensus 159 g~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~~~~ 194 (239)
|.|+++.|+.|+.|+.+|.+.||||..+|++.- ..
T Consensus 364 dl~~ee~E~~LS~lv~t~ti~aKidrpsgII~F-~k 398 (439)
T KOG1498|consen 364 DLPVEEMEKFLSDLVVTGTIYAKIDRPSGIINF-QK 398 (439)
T ss_pred CCCHHHHHHHHHHHHhccceEEEecCCCceEEE-Ee
Confidence 999999999999999999999999999999999 44
No 15
>KOG2582|consensus
Probab=98.22 E-value=4.8e-05 Score=69.66 Aligned_cols=199 Identities=15% Similarity=0.239 Sum_probs=135.0
Q ss_pred HHHHHHchhcCHHHHHHHHhccC--CCCCCccccCHhHHHHHHHHHHHHcCChhHHHHccccchhHHHHhhhhhhHHHHH
Q psy396 17 YEGVYCLAIRQYCRAAELFVDVV--PTFESYELAEFGTIIRYTVLACMIALPRYNLRKKLMHHGVMAQALHSQYRDLREY 94 (239)
Q Consensus 17 ~~Gl~~l~~~~y~~Aa~~F~~~~--~~f~~~e~~s~~di~~Y~~Lc~Las~~R~elk~~ll~s~~~~~~~e~~~p~l~~l 94 (239)
|.|..+++.++|+.|.-.|..+. |++.- ..+.-+..=+|+++.=|.+..-.+|-+ -.|+.+.++...-.|...++
T Consensus 188 Ygg~iciglk~fe~Al~~~e~~v~~Pa~~v-s~~hlEaYkkylLvsLI~~GK~~ql~k--~ts~~~~r~~K~ms~pY~ef 264 (422)
T KOG2582|consen 188 YGGMICIGLKRFERALYLLEICVTTPAMAV-SHIHLEAYKKYLLVSLILTGKVFQLPK--NTSQNAGRFFKPMSNPYHEF 264 (422)
T ss_pred hcceeeeccccHHHHHHHHHHHHhcchhHH-HHHHHHHHHHHHHHHhhhcCceeeccc--cchhhhHHhcccCCchHHHH
Confidence 46778999999999987766663 22221 122233334676665555543323311 23344544443325689999
Q ss_pred HHHHHhchHHHHHHHHHHHHhhhccCcchhHhHHHHHHHHHHHHHHHHhhhhhcccHHHHHHHhCC-CHHHHHHHHHHHH
Q psy396 95 FVSLYDGHYFEFLKCLAAVEQDMKRDPLLNPHYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGV-SVEFIEKEVARFA 173 (239)
Q Consensus 95 i~af~~~~y~~~~~~L~~~~~~l~~D~~L~~h~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~-s~~~lE~~L~~lI 173 (239)
+++|.+..-.+....+.+..+.+..|-=.+ .+......+-.+.|..+-+-|++++|+.||+.-.+ +..++|+.+.+||
T Consensus 265 ~~~Y~~~~~~eLr~lVk~~~~rF~kDnnt~-l~k~av~sl~k~nI~rltktF~sLsL~dIA~~vQLa~~qevek~Ilqmi 343 (422)
T KOG2582|consen 265 LNVYLKDSSTELRTLVKKHSERFTKDNNTG-LAKQAVSSLYKKNIQRLTKTFLSLSLSDIASRVQLASAQEVEKYILQMI 343 (422)
T ss_pred HHHHhcCCcHHHHHHHHHHHHHHhhcCcHH-HHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcchHHHHHHHHHHh
Confidence 999999999998888888888888887654 34667778888999999999999999999996554 4578999999999
Q ss_pred HcCccceeecccCCEEEEeccccccCCCCCCCccchhhhhHHHHHHHHhhHHHHHHHHHhh
Q psy396 174 AAGRLQCKIDSVAGNVVTTSHISEKGDCRSEAPEASLDRGILYQTTVKRGDIFLNRLKKLA 234 (239)
Q Consensus 174 ~~g~l~arID~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~r~~~l~ 234 (239)
.+|++-++|| |-+.-.... .++ +..+.+..-+.....+..++++..
T Consensus 344 e~~~i~a~iN---G~v~f~~n~---------e~~---~SpeM~~nk~~~~~~L~e~l~~~e 389 (422)
T KOG2582|consen 344 EDGEIFASIN---GMVFFTDNP---------EKY---NSPEMHENKIDLCIQLIEALKAME 389 (422)
T ss_pred ccCceEEEec---ceEEEecCc---------ccC---CCHHHHhhHHHHHHHHHHHHHhcc
Confidence 9999999999 665551220 022 333444434445555666666543
No 16
>COG5071 RPN5 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=98.21 E-value=2.8e-05 Score=69.93 Aligned_cols=176 Identities=16% Similarity=0.176 Sum_probs=115.4
Q ss_pred hhhHHHHHH--HHchhcCHHHHHHHHhccCCCCCCccccCHhHHHHHHHHHHHHcC----ChhHHHHccccchh-HHHHh
Q psy396 12 NKLKAYEGV--YCLAIRQYCRAAELFVDVVPTFESYELAEFGTIIRYTVLACMIAL----PRYNLRKKLMHHGV-MAQAL 84 (239)
Q Consensus 12 ~kl~~~~Gl--~~l~~~~y~~Aa~~F~~~~~~f~~~e~~s~~di~~Y~~Lc~Las~----~R~elk~~ll~s~~-~~~~~ 84 (239)
-||+-|.=+ .+++.|.|=.|+.++-++-.+.. +-.+..--|-+|+.+..| +=...+.+++.-.. -.+ +
T Consensus 210 lKlkyYeL~V~i~Lh~R~Yl~v~~y~~~vY~t~~----~~~d~Akwk~VLS~~v~F~iLtpy~neq~dlvhKi~~d~k-l 284 (439)
T COG5071 210 LKLKYYELKVRIGLHDRAYLDVCKYYRAVYDTAV----VQEDPAKWKEVLSNVVCFALLTPYDNEQADLLHKINADHK-L 284 (439)
T ss_pred HHHHHHHHhheeecccHHHHHHHHHHHHHHHHHH----hccCcccccchhhcceeeEEecccccHHHHHHHHhhhhhh-h
Confidence 366777666 57789999999988888732210 000001112222221111 00111122222111 112 2
Q ss_pred hhhhhHHHHHHHHHHhchHHHHHHHHHHHHhhhccCcc-hh-----HhHHHHHHHHHHHHHHHHhhhhhcccHHHHHHHh
Q psy396 85 HSQYRDLREYFVSLYDGHYFEFLKCLAAVEQDMKRDPL-LN-----PHYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCF 158 (239)
Q Consensus 85 e~~~p~l~~li~af~~~~y~~~~~~L~~~~~~l~~D~~-L~-----~h~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~f 158 (239)
.. .|...+++.+|.-..+-..-..-..+.+.+..|.| ++ .|.+.|...+-+-++.-+-+-||+|+..++...+
T Consensus 285 ~s-l~~~~~lVk~f~vNelmrwp~V~~~y~~~l~~~~faF~~e~~~~~w~DL~krviEHN~RvI~~yYSrI~~~rl~~ll 363 (439)
T COG5071 285 NS-LPLLQQLVKCFIVNELMRWPKVAEIYGSALRSNVFAFNDEKGEKRWSDLRKRVIEHNIRVIANYYSRIHCSRLGVLL 363 (439)
T ss_pred cc-chhhhhHHHHHHHHHHHhhhHHHHHhHHHHHhhhhhhccchhhhhHHHHHHHHHHhhHhHHHHHhhhhhHHHHHHHH
Confidence 22 56677778887766655554444556666666644 32 6778888888888877777779999999999999
Q ss_pred CCCHHHHHHHHHHHHHcCccceeecccCCEEEEecc
Q psy396 159 GVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVTTSH 194 (239)
Q Consensus 159 g~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~~~~ 194 (239)
++|+++.|+.++.|...|-+.|||++..|+|.- ..
T Consensus 364 d~~~s~te~~ISdlVN~G~~yaKiNrpa~Ii~F-EK 398 (439)
T COG5071 364 DMSPSETEQFISDLVNKGHFYAKINRPAQIISF-EK 398 (439)
T ss_pred cCCHHHHHHHHHHHHhcCcEEEEecCccceEEe-ec
Confidence 999999999999999999999999999999999 55
No 17
>KOG1497|consensus
Probab=98.12 E-value=3.1e-05 Score=69.93 Aligned_cols=62 Identities=16% Similarity=0.220 Sum_probs=55.7
Q ss_pred HHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 130 YVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 130 l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
+-+.+.+-++.-.=+=|-.++.+.+++-|++|.+..|+-..+||.++|++|-||+.+|+|+-
T Consensus 299 l~ra~~EhNlls~Skly~nisf~~Lg~ll~i~~ekaekiaa~MI~qeRmng~IDQ~egiihF 360 (399)
T KOG1497|consen 299 LDRAVIEHNLLSASKLYNNISFEELGALLKIDAEKAEKIAAQMITQERMNGSIDQIEGIIHF 360 (399)
T ss_pred hhhHHHHHhHHHHHHHHHhccHHHHHHHhCCCHHHHHHHHHHHHhHHHhccchHhhcceEee
Confidence 44555666666666779999999999999999999999999999999999999999999999
No 18
>KOG2753|consensus
Probab=98.02 E-value=0.00036 Score=63.25 Aligned_cols=162 Identities=14% Similarity=0.177 Sum_probs=122.3
Q ss_pred hcCHHHHHHHHhccCCCCCCccccCHhHHHHHHHHHHHHcCChhHHHHccccchhHHHHhhhhhhHHHHHHHHHHhchHH
Q psy396 25 IRQYCRAAELFVDVVPTFESYELAEFGTIIRYTVLACMIALPRYNLRKKLMHHGVMAQALHSQYRDLREYFVSLYDGHYF 104 (239)
Q Consensus 25 ~~~y~~Aa~~F~~~~~~f~~~e~~s~~di~~Y~~Lc~Las~~R~elk~~ll~s~~~~~~~e~~~p~l~~li~af~~~~y~ 104 (239)
.+.-+.|+.-|.+-..+|+.-.+..+.+-|+=++.-++..-+--.. +.+++-|.++ +++. ++ +.+++.=|......
T Consensus 178 ~k~~~~s~kvmt~lLgtyt~dnas~AredA~rcV~~av~dP~~F~f-D~Ll~L~pV~-qLE~-d~-i~qLL~IF~s~~L~ 253 (378)
T KOG2753|consen 178 NKSVDESSKVMTELLGTYTEDNASEAREDAMRCVVEAVKDPKIFLF-DHLLTLPPVK-QLEG-DL-IHQLLKIFVSGKLD 253 (378)
T ss_pred cchhhhHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHcCCceecc-chhccCchHH-Hhcc-ch-HHHHHHHHHhcchH
Confidence 3446677777777777887655566777777777888776433222 2245555453 4554 33 88999999988887
Q ss_pred HHHHHHHHHHhhhccCcchhHhHHHHHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecc
Q psy396 105 EFLKCLAAVEQDMKRDPLLNPHYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDS 184 (239)
Q Consensus 105 ~~~~~L~~~~~~l~~D~~L~~h~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~ 184 (239)
+|.+-.++....+..=-+. | ...+..||..-+.+.-+|-..|+...||+.+.+..+++|-|++..|..|-+.||||+
T Consensus 254 aYveF~~~N~~Fvqs~gl~--~-E~~~~KMRLLTlm~LA~es~eisy~~l~k~LqI~edeVE~fVIdaI~aklV~~kidq 330 (378)
T KOG2753|consen 254 AYVEFVAANSGFVQSQGLV--H-EQNMAKMRLLTLMSLAEESNEISYDTLAKELQINEDEVELFVIDAIRAKLVEGKIDQ 330 (378)
T ss_pred HHHHHHHhChHHHHHhccc--H-HHHHHHHHHHHHHHHhccCCCCCHHHHHHHhccCHHHHHHHHHHHHHHHHHHhhHHh
Confidence 7777666654433221122 2 378999999999999999999999999999999999999999999999999999999
Q ss_pred cCCEEEEecc
Q psy396 185 VAGNVVTTSH 194 (239)
Q Consensus 185 ~~~~l~~~~~ 194 (239)
.++++++ .+
T Consensus 331 ~~~~viV-s~ 339 (378)
T KOG2753|consen 331 MNRTVIV-SS 339 (378)
T ss_pred hcceEEe-eh
Confidence 9999999 55
No 19
>KOG1076|consensus
Probab=97.83 E-value=0.00037 Score=68.38 Aligned_cols=179 Identities=13% Similarity=0.147 Sum_probs=119.6
Q ss_pred hhhHHHHHHHHchhcCHHHHHHHHhccCCCCCC-----ccccCH-------h------------------HH--HHHHHH
Q psy396 12 NKLKAYEGVYCLAIRQYCRAAELFVDVVPTFES-----YELAEF-------G------------------TI--IRYTVL 59 (239)
Q Consensus 12 ~kl~~~~Gl~~l~~~~y~~Aa~~F~~~~~~f~~-----~e~~s~-------~------------------di--~~Y~~L 59 (239)
||-=|--||..+..|--++|..++.+...+=.. .++..+ + ++ ++|+ .
T Consensus 530 NRtmvQLGLCAFR~Gmi~EaH~~L~dl~st~r~kELLgQgv~~~~~he~t~eQe~~eR~rQlPyHmHINLELlEcVyL-t 608 (843)
T KOG1076|consen 530 NRTMVQLGLCAFRQGMIKEAHQCLSDLQSTGRVKELLGQGVLQRRQHEKTAEQEKIERRRQLPYHMHINLELLECVYL-T 608 (843)
T ss_pred HHHHHHHHHHHHHcccHHHHHHHHHHHHhcchHHHHHhhhhhhhhhhccChhhHHHHHhhcCchhhhccHHHHHHHHH-H
Confidence 566678899999999999999888887532100 011111 1 11 4665 4
Q ss_pred HHHH-------cCChhHHHHccccchhHHHHhhhh-------hh-----HHHHHHHHHHhchHHHHHHHHHHHHhhhccC
Q psy396 60 ACMI-------ALPRYNLRKKLMHHGVMAQALHSQ-------YR-----DLREYFVSLYDGHYFEFLKCLAAVEQDMKRD 120 (239)
Q Consensus 60 c~La-------s~~R~elk~~ll~s~~~~~~~e~~-------~p-----~l~~li~af~~~~y~~~~~~L~~~~~~l~~D 120 (239)
|+|+ +.. .+-|. ..-++.|+..++.. -| ++.....+...++++.|++.+...-....+=
T Consensus 609 caMLlEIP~MAA~~-~d~Rr-r~iSk~frr~Le~serqsf~gPPEn~RehVvaAsKAm~~Gnw~~c~~fi~nn~KvW~Lf 686 (843)
T KOG1076|consen 609 CAMLLEIPYMAAHE-SDARR-RMISKSFRRQLEHSERQSFTGPPENTREHVVAASKAMQKGNWQKCFEFIVNNIKVWDLF 686 (843)
T ss_pred HHHHHhhhHHhhhh-hhhhc-ccccHHHHHHHHHHhhccccCCchhHHHHHHHHHHHHhcCCHHHHHHHHHhhhhHHHhc
Confidence 6554 221 12222 23345566655531 12 3555778899999999999655522221111
Q ss_pred cchhHhHHHHHHHHHHHHHHHHhhh----hhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEEecc
Q psy396 121 PLLNPHYRHYVQEMRLRAYKQILQA----YRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVTTSH 194 (239)
Q Consensus 121 ~~L~~h~~~l~~~ir~~~l~qyl~p----Ys~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~~~~ 194 (239)
|=--.-.+-+.+.|++-.+.-||-. |.+|+|..+|+.|.+|+..|-.-|++||.+..|.|.+|+.+++|++ ++
T Consensus 687 pn~d~V~~Ml~~rIqEEsLRTYLftYss~Y~SvSl~~LA~mFdLp~~~VhsIiSkmiineEl~AslDqpt~~iv~-hr 763 (843)
T KOG1076|consen 687 PNADTVLDMLTERIQEESLRTYLFTYSSVYDSVSLAKLADMFDLPEPKVHSIISKMIINEELHASLDQPTQCIVM-HR 763 (843)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhccHHHHHHHhCCCchhHHHHHHHHHHHHHhhhccCCCcceEEE-ee
Confidence 1111222456667777777777765 6789999999999999999999999999999999999999999999 77
No 20
>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=97.52 E-value=0.00093 Score=53.62 Aligned_cols=93 Identities=24% Similarity=0.317 Sum_probs=62.9
Q ss_pred hHHHHHHHHHHhchHHHHHHHHHHHHhhhccCcchhHhHHHHHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHH
Q psy396 89 RDLREYFVSLYDGHYFEFLKCLAAVEQDMKRDPLLNPHYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKE 168 (239)
Q Consensus 89 p~l~~li~af~~~~y~~~~~~L~~~~~~l~~D~~L~~h~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~ 168 (239)
..+..+.+...+|+|..|...+.... -.+.+.+.+..|.+.+|.++..-.=..|++|+++.+|+.+|++.+++++.
T Consensus 42 ~~i~~l~~~L~~~~~~~~~~~~~~~~----~~~~~~~~v~~~~~~iR~~i~~~i~~aY~sIs~~~la~~Lg~~~~el~~~ 117 (143)
T PF10075_consen 42 KAIWSLGQALWEGDYSKFWQALRSNP----WSPDYKPFVPGFEDTIRERIAHLISKAYSSISLSDLAEMLGLSEEELEKF 117 (143)
T ss_dssp HHHHHHHHHHHTT-HHHHHHHS-TT--------HHHHTSTTHHHHHHHHHHHHHHHH-SEE-HHHHHHHTTS-HHHHHHH
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHhcc----chHHHHHHHHHHHHHHHHHHHHHHHHHHhHcCHHHHHHHhCCCHHHHHHH
Confidence 34667788899999999998776541 13477888899999999999999999999999999999999997766666
Q ss_pred HHHHHHcCccceeecccCCEEEE
Q psy396 169 VARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 169 L~~lI~~g~l~arID~~~~~l~~ 191 (239)
+.+. +=.+|....++..
T Consensus 118 ~~~~------gW~~d~~~~~~~~ 134 (143)
T PF10075_consen 118 IKSR------GWTVDGDGVLFPP 134 (143)
T ss_dssp HHHH------T-EE-----EE--
T ss_pred HHHc------CCEECCCccEEec
Confidence 6553 2266644444443
No 21
>KOG2688|consensus
Probab=97.10 E-value=0.0045 Score=57.72 Aligned_cols=164 Identities=15% Similarity=0.145 Sum_probs=116.2
Q ss_pred HHHHHHchhcCHHHHHHHHhccCCCCCCccccCHhHHHHHHHHHHHHcCChhHHHHccccchhHHHHhhhhhh--HHHHH
Q psy396 17 YEGVYCLAIRQYCRAAELFVDVVPTFESYELAEFGTIIRYTVLACMIALPRYNLRKKLMHHGVMAQALHSQYR--DLREY 94 (239)
Q Consensus 17 ~~Gl~~l~~~~y~~Aa~~F~~~~~~f~~~e~~s~~di~~Y~~Lc~Las~~R~elk~~ll~s~~~~~~~e~~~p--~l~~l 94 (239)
|-|.+.|.+.||+.|...+.+++..-..--+...+-+++|++-+++.... + ....+++. .+ .+..+
T Consensus 210 ylGr~a~~~~d~~~A~~~L~~af~~cp~~~~~n~~~iliylip~~~llg~--------~---Pt~~lL~~-~~~~~~~~l 277 (394)
T KOG2688|consen 210 YLGRYAMFESDFLNAFLQLNEAFRLCPDLLLKNKRLILIYLIPTGLLLGR--------I---PTKELLDF-YTLDKYSPL 277 (394)
T ss_pred eeeeehhhhhhHHHHHHHHHHHHHhCcHHHHhhhhhHHHHHhHHHHHhcc--------C---cchhhHhH-hhHHhHHHH
Confidence 46788999999999999999994332221233566789999999987643 1 12333443 33 67888
Q ss_pred HHHHHhchHHHHHHHHHHHHhh-hccCcchh--HhHHHHHHHHHHHHHHHHhhhhhcccHHHHHHHhCC------CHHHH
Q psy396 95 FVSLYDGHYFEFLKCLAAVEQD-MKRDPLLN--PHYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGV------SVEFI 165 (239)
Q Consensus 95 i~af~~~~y~~~~~~L~~~~~~-l~~D~~L~--~h~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~------s~~~l 165 (239)
+++...+++..|-..|++.+.. +..-.|+- ..--..++++-.+++ +++.-=+.++++.+-.++.. +.+++
T Consensus 278 v~aVr~Gnl~~f~~al~~~E~~f~~~gi~l~l~~l~lv~yrnL~kkv~-~~~~~~~~lpls~~~~al~~~~~~~~~~dev 356 (394)
T KOG2688|consen 278 VQAVRSGNLRLFDLALADNERFFIRSGIYLTLEKLPLVVYRNLFKKVI-QLWGKTSQLPLSRFLTALQFSGVTDVDLDEV 356 (394)
T ss_pred HHHHHhccHHHHHHHHhhhHHHHHHhccHHHhhhhhHHHHHHHHHHHH-HHhCCCCCCCHHHHHHHHhhcCCCCCchhhH
Confidence 9999999999999999988643 23334432 211244555555553 33312268888888888743 46899
Q ss_pred HHHHHHHHHcCccceeecccCCEEEEecc
Q psy396 166 EKEVARFAAAGRLQCKIDSVAGNVVTTSH 194 (239)
Q Consensus 166 E~~L~~lI~~g~l~arID~~~~~l~~~~~ 194 (239)
|-.|+.+|..|+|.|=|+.+...++. .+
T Consensus 357 eciLa~lI~~G~ikgYish~~~~~V~-sK 384 (394)
T KOG2688|consen 357 ECILANLIDLGRIKGYISHQLQTLVF-SK 384 (394)
T ss_pred HHHHHhhhhhccccchhchhhheEEE-ec
Confidence 99999999999999999999999988 54
No 22
>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=96.79 E-value=0.0035 Score=53.01 Aligned_cols=59 Identities=20% Similarity=0.329 Sum_probs=44.8
Q ss_pred HHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEEecc
Q psy396 135 RLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVTTSH 194 (239)
Q Consensus 135 r~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~~~~ 194 (239)
....+++|++..+.|.|..+|..||++...+.+-|..|..+|.|.|-||-..+.|++ ++
T Consensus 100 lL~~Fi~yIK~~Kvv~ledla~~f~l~t~~~i~ri~~L~~~g~ltGv~DdrGkfIyI-s~ 158 (188)
T PF09756_consen 100 LLQEFINYIKEHKVVNLEDLAAEFGLRTQDVINRIQELEAEGRLTGVIDDRGKFIYI-SE 158 (188)
T ss_dssp HHHHHHHHHHH-SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE----
T ss_pred HHHHHHHHHHHcceeeHHHHHHHcCCCHHHHHHHHHHHHHCCCceeeEcCCCCeEEe-cH
Confidence 345678999999999999999999999999999999999999999999999999999 44
No 23
>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=96.41 E-value=0.046 Score=45.79 Aligned_cols=103 Identities=24% Similarity=0.374 Sum_probs=66.3
Q ss_pred cCHhHHHHHHHHHHHHcCChhHHHHccccchhHHHHhhhhhhH---HHHHHHHHHhchHHHHHHHHHHHHhhhccCcchh
Q psy396 48 AEFGTIIRYTVLACMIALPRYNLRKKLMHHGVMAQALHSQYRD---LREYFVSLYDGHYFEFLKCLAAVEQDMKRDPLLN 124 (239)
Q Consensus 48 ~s~~di~~Y~~Lc~Las~~R~elk~~ll~s~~~~~~~e~~~p~---l~~li~af~~~~y~~~~~~L~~~~~~l~~D~~L~ 124 (239)
..-.++.-|-+|..+...+..++...+..=+ ..... .|. ..++..++.+++|..|++.+.. ...+++.
T Consensus 96 ~~~~ef~~y~lL~~l~~~~~~~~~~~l~~l~---~~~~~-~~~i~~al~l~~a~~~gny~~ff~l~~~-----~~~~~l~ 166 (204)
T PF03399_consen 96 PNEAEFIAYYLLYLLCQNNIPDFHMELELLP---SEILS-SPYIQFALELCRALMEGNYVRFFRLYRS-----KSAPYLF 166 (204)
T ss_dssp TTHHHHHHHHHHHTT-T---THHHHHHTTS----HHHHT-SHHHHHHHHHHHHH--TTHHHHHHHHT------TTS-HHH
T ss_pred CCHHHHHHHHHHHHHHcccchHHHHHHHHCc---hhhhc-CHHHHHHHHHHHHHHcCCHHHHHHHHhc-----cCCChHH
Confidence 3455678888887776654444433222211 11111 343 4567799999999999998832 3556666
Q ss_pred HhHH-HHHHHHHHHHHHHHhhhhhc-ccHHHHHHHhC
Q psy396 125 PHYR-HYVQEMRLRAYKQILQAYRS-LSLKYMAQCFG 159 (239)
Q Consensus 125 ~h~~-~l~~~ir~~~l~qyl~pYs~-v~l~~mA~~fg 159 (239)
.++- .+...+|.+++.-...+|.+ ++++.+++.+|
T Consensus 167 ~~l~~~~~~~iR~~al~~i~~ay~~~i~l~~l~~~L~ 203 (204)
T PF03399_consen 167 ACLMERFFNRIRLRALQSISKAYRSSIPLSFLAELLG 203 (204)
T ss_dssp HHHHGGGHHHHHHHHHHHHHHHS-T-EEHHHHHHHTT
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcC
Confidence 6664 59999999999999999999 99999999886
No 24
>COG5600 Transcription-associated recombination protein [DNA replication, recombination, and repair]
Probab=96.36 E-value=0.073 Score=49.37 Aligned_cols=165 Identities=18% Similarity=0.205 Sum_probs=112.9
Q ss_pred HHHHHHHHchhcCHHHHHHHHhccCCCCCCc-ccc--CHhHHHHHHHHHHHHcCChhHHHHccccchhHHHHhhhhhh--
Q psy396 15 KAYEGVYCLAIRQYCRAAELFVDVVPTFESY-ELA--EFGTIIRYTVLACMIALPRYNLRKKLMHHGVMAQALHSQYR-- 89 (239)
Q Consensus 15 ~~~~Gl~~l~~~~y~~Aa~~F~~~~~~f~~~-e~~--s~~di~~Y~~Lc~Las~~R~elk~~ll~s~~~~~~~e~~~p-- 89 (239)
.-|-|.+++.+.+|++|.-.|-++ |-.+ .+. .-+.++.|.+-.+|....-. .++.+++. .+
T Consensus 223 ~YYLG~~~l~~en~heA~~~L~~a---Fl~c~~l~~~n~~rIl~~~ipt~Llv~~~~----------Ptk~~L~r-~~~~ 288 (413)
T COG5600 223 HYYLGIYYLLNENFHEAFLHLNEA---FLQCPWLITRNRKRILPYYIPTSLLVNKFP----------PTKDLLER-FKRC 288 (413)
T ss_pred hhHHHHHHHHHHhHHHHHHHHHHH---HHhChhhhhcchheehhHHhhHHHHhCCCC----------CchHHHHh-cccc
Confidence 457899999999999999999999 5333 222 33457888888888875332 23445555 33
Q ss_pred -HHHHHHHHHHhchHHHHHHHHHHHHhh-hccCcch--hHhHH-HHHHHHHHHHHHHHhhhhh-cccHHHHHHHhCC---
Q psy396 90 -DLREYFVSLYDGHYFEFLKCLAAVEQD-MKRDPLL--NPHYR-HYVQEMRLRAYKQILQAYR-SLSLKYMAQCFGV--- 160 (239)
Q Consensus 90 -~l~~li~af~~~~y~~~~~~L~~~~~~-l~~D~~L--~~h~~-~l~~~ir~~~l~qyl~pYs-~v~l~~mA~~fg~--- 160 (239)
...-++.+...+++.+|-..|...+.. ...-.|+ -.|.+ -.++++-.+...--.+.=. .+++-..+..+..
T Consensus 289 s~~~~LvkavrsGni~~~~~~l~~ner~~~~~~l~ltl~~~~~~V~~RNL~rk~w~~~~~qsrlp~sil~~~~qls~~dn 368 (413)
T COG5600 289 SVYSPLVKAVRSGNIEDFDLALSRNERKFAKRGLYLTLLAHYPLVCFRNLFRKIWRLHGKQSRLPLSILLIVLQLSAIDN 368 (413)
T ss_pred chhHHHHHHHHcCCHHHHHHHHHHhHHHHHHcchHHHHHhhccHHHHHHHHHHHHhhccccccCcHHHHHHHHHccCCCc
Confidence 355677888899999999999988643 2333333 23332 3344444444433333322 3556666666643
Q ss_pred --CHHHHHHHHHHHHHcCccceeecccCCEEEEecc
Q psy396 161 --SVEFIEKEVARFAAAGRLQCKIDSVAGNVVTTSH 194 (239)
Q Consensus 161 --s~~~lE~~L~~lI~~g~l~arID~~~~~l~~~~~ 194 (239)
|.+.||--|+.+|..|.+.|-|-..+.+++. ..
T Consensus 369 ~~~~~~VEciL~tlI~~G~lrgYis~s~~~vV~-sk 403 (413)
T COG5600 369 FHSFKEVECILVTLIGLGLLRGYISHSRRTVVF-SK 403 (413)
T ss_pred ccChHHHHHHHHHHHhhhhhhheecccceEEEE-ec
Confidence 3689999999999999999999999999988 54
No 25
>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=96.28 E-value=0.16 Score=47.90 Aligned_cols=146 Identities=18% Similarity=0.321 Sum_probs=87.3
Q ss_pred HHHHHHHHchhcCHHHHHHHHhccCCC-------C-C-Cc--cccCHhHHHHHHHHHHHHcCChhHHHHccccchhHHHH
Q psy396 15 KAYEGVYCLAIRQYCRAAELFVDVVPT-------F-E-SY--ELAEFGTIIRYTVLACMIALPRYNLRKKLMHHGVMAQA 83 (239)
Q Consensus 15 ~~~~Gl~~l~~~~y~~Aa~~F~~~~~~-------f-~-~~--e~~s~~di~~Y~~Lc~Las~~R~elk~~ll~s~~~~~~ 83 (239)
-=+-|.++|+.|.|..|...|-.+.-- + . ++ +.+....==+|.+|+-..++....+ +.. +...
T Consensus 167 ~YyvGFaylMlrRY~DAir~f~~iL~yi~r~k~~~~~~~~q~d~i~K~~eqMyaLlAic~~l~p~~l-----de~-i~~~ 240 (404)
T PF10255_consen 167 YYYVGFAYLMLRRYADAIRTFSQILLYIQRTKNQYHQRSYQYDQINKKNEQMYALLAICLSLCPQRL-----DES-ISSQ 240 (404)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhccccchhhHHHhHHHHHHHHHHHHHHhCCCCC-----CHH-HHHH
Confidence 346899999999999999999988621 1 0 11 3322222224443332223333212 211 2222
Q ss_pred hhhhhhHHHHHHHHHHhchHHHHHHHHHHHHhhhcc----------------CcchhHhHHHHHHHHHHH----HHHHHh
Q psy396 84 LHSQYRDLREYFVSLYDGHYFEFLKCLAAVEQDMKR----------------DPLLNPHYRHYVQEMRLR----AYKQIL 143 (239)
Q Consensus 84 ~e~~~p~l~~li~af~~~~y~~~~~~L~~~~~~l~~----------------D~~L~~h~~~l~~~ir~~----~l~qyl 143 (239)
+.. ...+=......++...|.+......|.+.. || ...|++-|+++++.+ .+..|+
T Consensus 241 lke---ky~ek~~kmq~gd~~~f~elF~~acPKFIsp~~pp~~~~~~~~~~~e~-~~~Ql~~Fl~eV~~q~~l~~lRSyL 316 (404)
T PF10255_consen 241 LKE---KYGEKMEKMQRGDEEAFEELFSFACPKFISPVSPPDYDGPSQNKNKEP-YRRQLKLFLDEVKQQQKLPTLRSYL 316 (404)
T ss_pred HHH---HHHHHHHHHHccCHHHHHHHHHhhCCCccCCCCCCCcccccchhhhhH-HHHHHHHHHHHHHHhhhhhHHHHHH
Confidence 221 122333344555677777766666654322 22 234667777777665 678899
Q ss_pred hhhhcccHHHHHHHhCCCHHHHHHHHH
Q psy396 144 QAYRSLSLKYMAQCFGVSVEFIEKEVA 170 (239)
Q Consensus 144 ~pYs~v~l~~mA~~fg~s~~~lE~~L~ 170 (239)
+=|++++++.+|.-++++++++-.+|.
T Consensus 317 KLYtti~l~KLA~fl~vd~~~lr~~Ll 343 (404)
T PF10255_consen 317 KLYTTIPLEKLASFLDVDEEELRSQLL 343 (404)
T ss_pred HhhcCCCHHHHHHHcCCCHHHHHHHHH
Confidence 999999999999999999998776663
No 26
>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=96.22 E-value=0.0094 Score=41.93 Aligned_cols=45 Identities=22% Similarity=0.300 Sum_probs=38.2
Q ss_pred HHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceee
Q psy396 138 AYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKI 182 (239)
Q Consensus 138 ~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arI 182 (239)
.+.+|++-...+++..+|..||+|++.||.-|..+|.-|+|.-.-
T Consensus 4 ~i~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~~ 48 (69)
T PF09012_consen 4 EIRDYLRERGRVSLAELAREFGISPEAVEAMLEQLIRKGYIRKVD 48 (69)
T ss_dssp HHHHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEEEE
T ss_pred HHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEec
Confidence 467899999999999999999999999999999999999997433
No 27
>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=95.59 E-value=0.03 Score=37.99 Aligned_cols=44 Identities=25% Similarity=0.414 Sum_probs=40.4
Q ss_pred HHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCcc
Q psy396 135 RLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRL 178 (239)
Q Consensus 135 r~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l 178 (239)
|...|.++++....++++.+|+.||+|...+...|..|-..|.+
T Consensus 1 R~~~Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~i 44 (57)
T PF08220_consen 1 RQQQILELLKEKGKVSVKELAEEFGVSEMTIRRDLNKLEKQGLI 44 (57)
T ss_pred CHHHHHHHHHHcCCEEHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence 45678899999999999999999999999999999999998864
No 28
>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A.
Probab=94.98 E-value=0.08 Score=46.98 Aligned_cols=123 Identities=13% Similarity=0.108 Sum_probs=77.9
Q ss_pred CchhhhhhhHHHHHHHHchhcCHHHHHHHHhccCCCCCCcccc--CHhHHHHHHHHHHHHcCChhHHHHcccc-----ch
Q psy396 6 GDWSARNKLKAYEGVYCLAIRQYCRAAELFVDVVPTFESYELA--EFGTIIRYTVLACMIALPRYNLRKKLMH-----HG 78 (239)
Q Consensus 6 ~dw~~~~kl~~~~Gl~~l~~~~y~~Aa~~F~~~~~~f~~~e~~--s~~di~~Y~~Lc~Las~~R~elk~~ll~-----s~ 78 (239)
|.....++...-.|-.+...++|.+|...|-++........+. +..+...-.+||-|+..|-...+. .++ .|
T Consensus 149 ~~~~~a~~~~~~~A~l~~~l~~y~~A~~~~e~~~~~~l~~~l~~~~~~~~~l~a~l~~L~~~D~v~A~~-~~~~~~~~~~ 227 (282)
T PF14938_consen 149 GSPHSAAECLLKAADLYARLGRYEEAIEIYEEVAKKCLENNLLKYSAKEYFLKAILCHLAMGDYVAARK-ALERYCSQDP 227 (282)
T ss_dssp T-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTCCCHCTTGHHHHHHHHHHHHHHHHTT-HHHHHH-HHHHHGTTST
T ss_pred CChhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHHHcCCHHHHHH-HHHHHHhhCC
Confidence 3444445555556667888999999999998886555433332 455677778999999977544432 121 12
Q ss_pred hHHHHhhhhhhHHHHHHHHHHhchHHHHHHHHHHHHhhhccCcchhHhHHHHH
Q psy396 79 VMAQALHSQYRDLREYFVSLYDGHYFEFLKCLAAVEQDMKRDPLLNPHYRHYV 131 (239)
Q Consensus 79 ~~~~~~e~~~p~l~~li~af~~~~y~~~~~~L~~~~~~l~~D~~L~~h~~~l~ 131 (239)
.|..--| ..-+.+++.+|.+.+-..|.+.+.++...-.+|++...-+..+-
T Consensus 228 ~F~~s~E--~~~~~~l~~A~~~~D~e~f~~av~~~d~~~~ld~w~~~~l~~~k 278 (282)
T PF14938_consen 228 SFASSRE--YKFLEDLLEAYEEGDVEAFTEAVAEYDSISRLDNWKTKMLLKIK 278 (282)
T ss_dssp TSTTSHH--HHHHHHHHHHHHTT-CCCHHHHCHHHTTSS---HHHHHHHHHHH
T ss_pred CCCCcHH--HHHHHHHHHHHHhCCHHHHHHHHHHHcccCccHHHHHHHHHHHH
Confidence 2211111 23478899999999999999999999988899988765544443
No 29
>KOG3054|consensus
Probab=94.74 E-value=0.15 Score=44.71 Aligned_cols=56 Identities=16% Similarity=0.241 Sum_probs=52.1
Q ss_pred HHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEEecc
Q psy396 138 AYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVTTSH 194 (239)
Q Consensus 138 ~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~~~~ 194 (239)
-+++|++--+.|.|..+|..||+.....-..+..|+.+|.|.|-||--.+.|++ ..
T Consensus 204 eFv~YIk~nKvV~ledLas~f~Lrtqd~inriq~~l~eg~ltGVmDDRGKfIYI-S~ 259 (299)
T KOG3054|consen 204 EFVEYIKKNKVVPLEDLASEFGLRTQDSINRIQELLAEGLLTGVMDDRGKFIYI-SM 259 (299)
T ss_pred HHHHHHHhcCeeeHHHHHHHhCccHHHHHHHHHHHHHhhhheeeecCCCceEEe-cH
Confidence 357999999999999999999999888888999999999999999999999999 44
No 30
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=93.26 E-value=0.15 Score=33.55 Aligned_cols=49 Identities=24% Similarity=0.302 Sum_probs=41.5
Q ss_pred HHHHHHHHHHHHhhhhhcc-cHHHHHHHhCCCHHHHHHHHHHHHHcCccc
Q psy396 131 VQEMRLRAYKQILQAYRSL-SLKYMAQCFGVSVEFIEKEVARFAAAGRLQ 179 (239)
Q Consensus 131 ~~~ir~~~l~qyl~pYs~v-~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~ 179 (239)
++.++.......+.|-..+ +...+|+.||+|...+.+.+..|...|-+.
T Consensus 2 ~~~l~~~i~~~~~~~~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i~ 51 (60)
T smart00345 2 AERLREDIVSGELRPGDKLPSERELAAQLGVSRTTVREALSRLEAEGLVQ 51 (60)
T ss_pred HHHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 4566777777767777778 899999999999999999999999988764
No 31
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=93.13 E-value=0.22 Score=36.15 Aligned_cols=43 Identities=9% Similarity=0.196 Sum_probs=39.5
Q ss_pred HHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccce
Q psy396 138 AYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQC 180 (239)
Q Consensus 138 ~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~a 180 (239)
.+.+|+.-+.++++..+|..|++|++.||.-|..++.-|++.-
T Consensus 6 qlRd~l~~~gr~s~~~Ls~~~~~p~~~VeaMLe~l~~kGkver 48 (78)
T PRK15431 6 QVRDLLALRGRMEAAQISQTLNTPQPMINAMLQQLESMGKAVR 48 (78)
T ss_pred HHHHHHHHcCcccHHHHHHHHCcCHHHHHHHHHHHHHCCCeEe
Confidence 3568889999999999999999999999999999999999854
No 32
>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=92.75 E-value=0.47 Score=31.24 Aligned_cols=42 Identities=21% Similarity=0.381 Sum_probs=33.5
Q ss_pred HHHHHHHHh-hhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcC
Q psy396 135 RLRAYKQIL-QAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAG 176 (239)
Q Consensus 135 r~~~l~qyl-~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g 176 (239)
|.+-+.+++ +.-..++.+.+|+.||+|...+.+.|..+-..|
T Consensus 1 R~~~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 1 RQKQILKLLLESKEPITAKELAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp HHHHHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred CHHHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 455666777 443449999999999999999999999997777
No 33
>KOG1861|consensus
Probab=92.67 E-value=1.8 Score=41.52 Aligned_cols=107 Identities=13% Similarity=0.237 Sum_probs=77.8
Q ss_pred CHhHHHHHHHHHHHHcCChhHHHHccccchhHHHHhhh-hhhHHHHHHHHHHhchHHHHHHHHHHHHhhhccCcchhHhH
Q psy396 49 EFGTIIRYTVLACMIALPRYNLRKKLMHHGVMAQALHS-QYRDLREYFVSLYDGHYFEFLKCLAAVEQDMKRDPLLNPHY 127 (239)
Q Consensus 49 s~~di~~Y~~Lc~Las~~R~elk~~ll~s~~~~~~~e~-~~p~l~~li~af~~~~y~~~~~~L~~~~~~l~~D~~L~~h~ 127 (239)
....++-|-+|--|++.++.++-. ++.+- .....+. ...+..++-.+..-++|..||..-... |-+..|+
T Consensus 385 ~~~EF~AYriLY~i~tkN~~di~s-ll~~l-t~E~ked~~V~hAL~vR~A~~~GNY~kFFrLY~~A-------P~M~~yL 455 (540)
T KOG1861|consen 385 AYLEFTAYRILYYIFTKNYPDILS-LLRDL-TEEDKEDEAVAHALEVRSAVTLGNYHKFFRLYLTA-------PNMSGYL 455 (540)
T ss_pred chhhHHHHHHHHHHHhcCchHHHH-HHHhc-cHhhccCHHHHHHHHHHHHHHhccHHHHHHHHhhc-------ccchhHH
Confidence 477889999999999999987733 33321 0011111 023455667788899999999864332 4555665
Q ss_pred -HHHHHHHHHHHHHHHhhhhh-cccHHHHHHHhCCCHHH
Q psy396 128 -RHYVQEMRLRAYKQILQAYR-SLSLKYMAQCFGVSVEF 164 (239)
Q Consensus 128 -~~l~~~ir~~~l~qyl~pYs-~v~l~~mA~~fg~s~~~ 164 (239)
+.|++.-|.+++.-.+++|. +|+++++++.|.+...+
T Consensus 456 mdlF~erER~~Al~ii~KsyrP~i~~~fi~~~laf~~~e 494 (540)
T KOG1861|consen 456 MDLFLERERKKALTIICKSYRPTITVDFIASELAFDSME 494 (540)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCCccHHHHhhhhhhchHH
Confidence 78999999999999999999 99999999999886543
No 34
>KOG2072|consensus
Probab=92.36 E-value=1.7 Score=44.18 Aligned_cols=86 Identities=20% Similarity=0.178 Sum_probs=74.2
Q ss_pred HHHHHHHHhhhccCcchhHhHHHHHHHHHHHHHHHHhhhhhcccHHHHHHHhC-CCHHHHHHHHHHHHHcCccceeeccc
Q psy396 107 LKCLAAVEQDMKRDPLLNPHYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFG-VSVEFIEKEVARFAAAGRLQCKIDSV 185 (239)
Q Consensus 107 ~~~L~~~~~~l~~D~~L~~h~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg-~s~~~lE~~L~~lI~~g~l~arID~~ 185 (239)
.+.++.+-+.+..-+..++++..|-..+-.+++.|.=..|.+|+++.+-+.-- .+.-++|+.|++....+-+..+||..
T Consensus 406 ~k~lq~ll~~ls~~~~~~QYI~sLq~v~~~RllqQvSqiY~sIs~~~l~~La~F~~~~~lEk~~v~a~k~~~v~iriDH~ 485 (988)
T KOG2072|consen 406 CKKLQPLLDKLSESPDKSQYIPSLQDVIILRLLQQVSQIYESISFERLYKLAPFFSAFELEKLLVEAAKHNDVSIRIDHE 485 (988)
T ss_pred HHHHHHHHHHHHcCCCccccchhHHHHHHHHHHHHHHHHHHHHhHHHHHHHHhhcCHHHHHHHHHHHHhccceeEEeccc
Confidence 34455555556777888999999999999999999999999999998877543 57789999999999999999999999
Q ss_pred CCEEEEe
Q psy396 186 AGNVVTT 192 (239)
Q Consensus 186 ~~~l~~~ 192 (239)
.++|.-|
T Consensus 486 ~~~v~Fg 492 (988)
T KOG2072|consen 486 SNSVSFG 492 (988)
T ss_pred cceeeec
Confidence 9999985
No 35
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=92.22 E-value=0.57 Score=29.86 Aligned_cols=43 Identities=21% Similarity=0.329 Sum_probs=35.7
Q ss_pred HHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccce
Q psy396 138 AYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQC 180 (239)
Q Consensus 138 ~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~a 180 (239)
.+.+++.....+++..+|+.||++...+.+.|..|...|.+..
T Consensus 4 ~il~~l~~~~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~ 46 (53)
T smart00420 4 QILELLAQQGKVSVEELAELLGVSEMTIRRDLNKLEEQGLLTR 46 (53)
T ss_pred HHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 4455555556799999999999999999999999999887753
No 36
>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=91.75 E-value=0.67 Score=29.72 Aligned_cols=43 Identities=16% Similarity=0.288 Sum_probs=35.2
Q ss_pred HHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCcc
Q psy396 136 LRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRL 178 (239)
Q Consensus 136 ~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l 178 (239)
.+.+..++.--..++...+|+.+|+|...+-..|.+|...|-|
T Consensus 5 ~~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~~~g~I 47 (48)
T PF13412_consen 5 QRKILNYLRENPRITQKELAEKLGISRSTVNRYLKKLEEKGLI 47 (48)
T ss_dssp HHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHCcCc
Confidence 3445577777788999999999999999999999999998865
No 37
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=90.20 E-value=0.98 Score=30.85 Aligned_cols=52 Identities=21% Similarity=0.310 Sum_probs=44.8
Q ss_pred HHHHHHHHHHHHHHHhhhhhcc-cHHHHHHHhCCCHHHHHHHHHHHHHcCccc
Q psy396 128 RHYVQEMRLRAYKQILQAYRSL-SLKYMAQCFGVSVEFIEKEVARFAAAGRLQ 179 (239)
Q Consensus 128 ~~l~~~ir~~~l~qyl~pYs~v-~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~ 179 (239)
..+++.|+..+...-+.|=..+ +...+|+.||+|...+.+-+..|..+|-+.
T Consensus 3 ~~i~~~l~~~I~~g~~~~g~~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~ 55 (64)
T PF00392_consen 3 EQIYDQLRQAILSGRLPPGDRLPSERELAERYGVSRTTVREALRRLEAEGLIE 55 (64)
T ss_dssp HHHHHHHHHHHHTTSS-TTSBE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHHcCCCCCCCEeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEE
Confidence 4678888999988899999999 999999999999999999999999998774
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=90.10 E-value=2.4 Score=37.89 Aligned_cols=66 Identities=14% Similarity=0.233 Sum_probs=55.0
Q ss_pred cCcchhHhHHHHHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 119 RDPLLNPHYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 119 ~D~~L~~h~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
.+.+=..+++.+.+++.++. .--..|+++.+|+.|++|.+++.+.+..-...+.|+|++|.. +|++
T Consensus 106 gelit~~Yld~l~~Eine~L-----qe~G~vsi~eLa~~~~Lp~efl~~~li~~~lg~~I~g~~d~~--~lyT 171 (272)
T PF09743_consen 106 GELITDSYLDSLAEEINEKL-----QESGQVSISELAKQYDLPSEFLKEELISKRLGKIIKGRLDGD--VLYT 171 (272)
T ss_pred CEEccHHHHHHHHHHHHHHH-----HHcCeEeHHHHHHhcCCcHHHHHHHHhhhhcCcceeEEEeCC--EEec
Confidence 34444577788888887765 445899999999999999999998888889999999999998 6666
No 39
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=90.07 E-value=0.64 Score=40.94 Aligned_cols=45 Identities=27% Similarity=0.290 Sum_probs=42.7
Q ss_pred HHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCcc
Q psy396 134 MRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRL 178 (239)
Q Consensus 134 ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l 178 (239)
=|.+.|.++++.+..++++.+|+.||+|.+.+-+.|..|-..|.+
T Consensus 5 eR~~~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~Le~~g~l 49 (256)
T PRK10434 5 QRQAAILEYLQKQGKTSVEELAQYFDTTGTTIRKDLVILEHAGTV 49 (256)
T ss_pred HHHHHHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCE
Confidence 488999999999999999999999999999999999999999876
No 40
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=89.15 E-value=1.2 Score=31.06 Aligned_cols=45 Identities=9% Similarity=0.129 Sum_probs=38.6
Q ss_pred HHHHHHHhhhhhc--ccHHHHHHHhCCCHHHHHHHHHHHHHcCccce
Q psy396 136 LRAYKQILQAYRS--LSLKYMAQCFGVSVEFIEKEVARFAAAGRLQC 180 (239)
Q Consensus 136 ~~~l~qyl~pYs~--v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~a 180 (239)
...+.+++..... ++...+|+.+|++...+.+-|..|...|.+..
T Consensus 8 ~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~ 54 (68)
T smart00550 8 EEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCK 54 (68)
T ss_pred HHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence 3456677777666 99999999999999999999999999998843
No 41
>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=88.84 E-value=0.54 Score=35.30 Aligned_cols=38 Identities=21% Similarity=0.354 Sum_probs=34.0
Q ss_pred hcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecc
Q psy396 147 RSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDS 184 (239)
Q Consensus 147 s~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~ 184 (239)
.=|.++.+++.|+++.++|++.|..|+.+|.|-..||-
T Consensus 64 ~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd 101 (102)
T PF08784_consen 64 EGVHVDEIAQQLGMSENEVRKALDFLSNEGHIYSTIDD 101 (102)
T ss_dssp TTEEHHHHHHHSTS-HHHHHHHHHHHHHTTSEEESSST
T ss_pred CcccHHHHHHHhCcCHHHHHHHHHHHHhCCeEecccCC
Confidence 35999999999999999999999999999999888773
No 42
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=88.68 E-value=0.96 Score=39.47 Aligned_cols=47 Identities=23% Similarity=0.351 Sum_probs=43.0
Q ss_pred HHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccc
Q psy396 133 EMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQ 179 (239)
Q Consensus 133 ~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~ 179 (239)
.-|.+.+.+++.....++.+.+|+.||+|...+.+.|..|-..|.+.
T Consensus 3 ~~R~~~Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~~L~~~~~l~ 49 (240)
T PRK10411 3 AARQQAIVDLLLNHTSLTTEALAEQLNVSKETIRRDLNELQTQGKIL 49 (240)
T ss_pred hHHHHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 34788899999999999999999999999999999999999987774
No 43
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=88.13 E-value=0.78 Score=38.50 Aligned_cols=46 Identities=17% Similarity=0.273 Sum_probs=42.9
Q ss_pred HHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccc
Q psy396 134 MRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQ 179 (239)
Q Consensus 134 ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~ 179 (239)
=|.+.|..++.-...+++..+|+.||+|.+.+-..|..|-..|.+.
T Consensus 7 ~R~~~Il~~l~~~~~~~~~~La~~~~vS~~TiRRDl~~L~~~g~~~ 52 (185)
T PRK04424 7 ERQKALQELIEENPFITDEELAEKFGVSIQTIRLDRMELGIPELRE 52 (185)
T ss_pred HHHHHHHHHHHHCCCEEHHHHHHHHCcCHHHHHHHHHHHhcchHHH
Confidence 3889999999999999999999999999999999999999998763
No 44
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=87.16 E-value=1.2 Score=39.12 Aligned_cols=47 Identities=26% Similarity=0.376 Sum_probs=43.6
Q ss_pred HHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccc
Q psy396 133 EMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQ 179 (239)
Q Consensus 133 ~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~ 179 (239)
.-|.+.|.++++....|+++.+|+.||+|.+.+-+.|..|=..|.+.
T Consensus 4 ~eR~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l~ 50 (253)
T COG1349 4 EERHQKILELLKEKGKVSVEELAELFGVSEMTIRRDLNELEEQGLLL 50 (253)
T ss_pred HHHHHHHHHHHHHcCcEEHHHHHHHhCCCHHHHHHhHHHHHHCCcEE
Confidence 34889999999999999999999999999999999999999988774
No 45
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=86.99 E-value=1.4 Score=38.80 Aligned_cols=47 Identities=17% Similarity=0.276 Sum_probs=43.4
Q ss_pred HHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccc
Q psy396 133 EMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQ 179 (239)
Q Consensus 133 ~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~ 179 (239)
.-|.+.|..+++....+++..+|+.||+|.+.+-+.|..|-..|.+.
T Consensus 4 ~~R~~~Il~~l~~~~~~~~~ela~~l~vS~~TiRRdL~~Le~~g~l~ 50 (252)
T PRK10906 4 TQRHDAIIELVKQQGYVSTEELVEHFSVSPQTIRRDLNDLAEQNKIL 50 (252)
T ss_pred HHHHHHHHHHHHHcCCEeHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence 34888999999999999999999999999999999999999998873
No 46
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=86.68 E-value=1.8 Score=30.01 Aligned_cols=41 Identities=12% Similarity=0.276 Sum_probs=35.0
Q ss_pred HHHHhhh-hhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccc
Q psy396 139 YKQILQA-YRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQ 179 (239)
Q Consensus 139 l~qyl~p-Ys~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~ 179 (239)
+++|++. ...++-..+|+++|+|.-.+...|..|-.+|++.
T Consensus 5 Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~ 46 (62)
T PF04703_consen 5 ILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLEKEGKVE 46 (62)
T ss_dssp HHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEE
T ss_pred HHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence 5666666 8889999999999999999999999999999884
No 47
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=86.67 E-value=1.5 Score=38.48 Aligned_cols=46 Identities=13% Similarity=0.343 Sum_probs=42.2
Q ss_pred HHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccc
Q psy396 134 MRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQ 179 (239)
Q Consensus 134 ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~ 179 (239)
=|.+.+..+++....+++..+|+.||+|...+.+.|..|-..|.+.
T Consensus 5 ~R~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le~~g~i~ 50 (251)
T PRK13509 5 QRHQILLELLAQLGFVTVEKVIERLGISPATARRDINKLDESGKLK 50 (251)
T ss_pred HHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 4778899999999999999999999999999999999998887774
No 48
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=86.51 E-value=1.5 Score=38.96 Aligned_cols=47 Identities=21% Similarity=0.230 Sum_probs=43.5
Q ss_pred HHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccc
Q psy396 133 EMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQ 179 (239)
Q Consensus 133 ~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~ 179 (239)
.-|...|.++++....|++..+|+.||+|...+.+.|..|-..|.+.
T Consensus 16 ~eR~~~Il~~L~~~~~vtv~eLa~~l~VS~~TIRRDL~~Le~~G~l~ 62 (269)
T PRK09802 16 SERREQIIQRLRQQGSVQVNDLSALYGVSTVTIRNDLAFLEKQGIAV 62 (269)
T ss_pred HHHHHHHHHHHHHcCCEeHHHHHHHHCCCHHHHHHHHHHHHhCCCeE
Confidence 45889999999999999999999999999999999999998888774
No 49
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=86.38 E-value=1.2 Score=38.97 Aligned_cols=41 Identities=27% Similarity=0.307 Sum_probs=37.8
Q ss_pred HHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHH
Q psy396 133 EMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFA 173 (239)
Q Consensus 133 ~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI 173 (239)
.=|...|.++++.+..|++..+|+.||+|++.+-+.|..|=
T Consensus 6 ~eR~~~I~~~l~~~~~v~v~eLa~~~~VS~~TIRRDL~~Le 46 (252)
T PRK10681 6 DERIGQLLQALKRSDKLHLKDAAALLGVSEMTIRRDLNAHS 46 (252)
T ss_pred HHHHHHHHHHHHHcCCCcHHHHHHHhCCCHHHHHHHHHHhh
Confidence 34899999999999999999999999999999999999744
No 50
>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=86.31 E-value=3.1 Score=27.50 Aligned_cols=51 Identities=16% Similarity=0.206 Sum_probs=42.1
Q ss_pred HHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCC
Q psy396 137 RAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAG 187 (239)
Q Consensus 137 ~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~ 187 (239)
-.++.++..+-.+++..+|+.+|++...+-..+.+|...|-|.-..|+.++
T Consensus 6 ~~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~~~~~D~ 56 (59)
T PF01047_consen 6 FRILRILYENGGITQSELAEKLGISRSTVTRIIKRLEKKGLIERERDPDDR 56 (59)
T ss_dssp HHHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTET
T ss_pred HHHHHHHHHcCCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEeccCCCCC
Confidence 345566677788999999999999999999999999999999777766543
No 51
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=85.36 E-value=2.5 Score=31.53 Aligned_cols=44 Identities=25% Similarity=0.298 Sum_probs=38.8
Q ss_pred HHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccc
Q psy396 136 LRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQ 179 (239)
Q Consensus 136 ~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~ 179 (239)
++.+..++.....++.+.+|+.+|+|...+-+.+.+|...|-+.
T Consensus 5 D~~il~~L~~~~~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~ 48 (108)
T smart00344 5 DRKILEELQKDARISLAELAKKVGLSPSTVHNRVKRLEEEGVIK 48 (108)
T ss_pred HHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence 45566777777899999999999999999999999999999775
No 52
>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=85.14 E-value=4.6 Score=26.76 Aligned_cols=48 Identities=19% Similarity=0.209 Sum_probs=37.7
Q ss_pred HHHHhhhhhc--ccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccC
Q psy396 139 YKQILQAYRS--LSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVA 186 (239)
Q Consensus 139 l~qyl~pYs~--v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~ 186 (239)
+.-++..+.. +++..+|+.+|++...+-..+.+|+..|-+.-.-|..+
T Consensus 10 vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~~~~~D 59 (62)
T PF12802_consen 10 VLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKKGLVERERDPGD 59 (62)
T ss_dssp HHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE-SSS
T ss_pred HHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCCCC
Confidence 4455555555 99999999999999999999999999998866655544
No 53
>PF01984 dsDNA_bind: Double-stranded DNA-binding domain; InterPro: IPR002836 This protein family is found in archaea and eukaryota. The human TFAR19 (TF-1 cell apoptosis-related protein 19) encodes a protein which shares significant homology to the corresponding proteins of species ranging from yeast to mice. TFAR19 exhibits a ubiquitous expression pattern and its expression is up-regulated in the tumour cells undergoing apoptosis. TFAR19 may play a general role in the apoptotic process []. Also included in this family is a DNA-binding protein from the archaea, Methanobacterium thermoautotrophicum.; GO: 0003677 DNA binding; PDB: 1EIJ_A 2K6B_A 2CRU_A 1YYB_A 2JXN_A 2FH0_A.
Probab=84.83 E-value=0.41 Score=36.87 Aligned_cols=53 Identities=25% Similarity=0.305 Sum_probs=40.8
Q ss_pred HHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecc
Q psy396 132 QEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDS 184 (239)
Q Consensus 132 ~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~ 184 (239)
++.+..++.+++.|=..=.|++++-.--=-...||..|.+|...|+|.++||-
T Consensus 31 ee~~~~iL~qiLt~eAreRL~rI~lvkPe~A~~VE~~Liqlaq~G~l~~kI~d 83 (107)
T PF01984_consen 31 EEQRRAILRQILTPEARERLNRIKLVKPEKARQVENQLIQLAQSGQLRGKIDD 83 (107)
T ss_dssp HHCCHHHHHTCB-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSSSS-B-H
T ss_pred HHHHHHHHHHHcCHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHcCCCCCCcCH
Confidence 44566788889999888888888776655567899999999999999998873
No 54
>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=84.05 E-value=3.5 Score=26.37 Aligned_cols=43 Identities=23% Similarity=0.400 Sum_probs=35.2
Q ss_pred HHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCcc
Q psy396 134 MRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRL 178 (239)
Q Consensus 134 ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l 178 (239)
.|.+++....+ ...+...+|+.+|+|...+..-|..|...|-+
T Consensus 3 ~R~~Il~~L~~--~~~~~~el~~~l~~s~~~vs~hL~~L~~~glV 45 (47)
T PF01022_consen 3 TRLRILKLLSE--GPLTVSELAEELGLSQSTVSHHLKKLREAGLV 45 (47)
T ss_dssp HHHHHHHHHTT--SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHHh--CCCchhhHHHhccccchHHHHHHHHHHHCcCe
Confidence 46666555555 78999999999999999999999999998865
No 55
>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=82.60 E-value=3.8 Score=27.20 Aligned_cols=51 Identities=18% Similarity=0.251 Sum_probs=37.1
Q ss_pred HHHHHHHHHHHHHHhhhhhccc-HHHHHHHhCCCHHHHHHHHHHHHHcCccc
Q psy396 129 HYVQEMRLRAYKQILQAYRSLS-LKYMAQCFGVSVEFIEKEVARFAAAGRLQ 179 (239)
Q Consensus 129 ~l~~~ir~~~l~qyl~pYs~v~-l~~mA~~fg~s~~~lE~~L~~lI~~g~l~ 179 (239)
.+++.++...+...+.+-..+. ...+|+.||+|...+.+.|..|-..|-|.
T Consensus 5 ~~~~~i~~~i~~~~~~~~~~~~~~~~la~~~~is~~~v~~~l~~L~~~G~i~ 56 (66)
T cd07377 5 QIADQLREAILSGELKPGDRLPSERELAEELGVSRTTVREALRELEAEGLVE 56 (66)
T ss_pred HHHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 3444455544444344444454 99999999999999999999999988763
No 56
>KOG3431|consensus
Probab=82.37 E-value=1.9 Score=33.91 Aligned_cols=53 Identities=25% Similarity=0.288 Sum_probs=44.7
Q ss_pred HHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeec
Q psy396 131 VQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKID 183 (239)
Q Consensus 131 ~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID 183 (239)
-+++|.-+|.|+|+|=..-.|+++|-.=-=-...||..|.+|+..|.+.+||+
T Consensus 38 q~e~r~~~lsQvLdqqAr~RLsrlAlvkpekAq~VE~~lirma~~gQvs~Kis 90 (129)
T KOG3431|consen 38 QEEMRQSMLSQVLDQQARERLSRLALVKPEKAQAVENYLIRMAQTGQVSHKIS 90 (129)
T ss_pred HHHHHHhHHHHHhhHHHHHHHHhhhhcCHHHHHHHHHHHHHHHHhCCcccccc
Confidence 67899999999999988888888875443344689999999999999998875
No 57
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=82.22 E-value=2.8 Score=30.54 Aligned_cols=34 Identities=24% Similarity=0.376 Sum_probs=31.0
Q ss_pred HHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHH
Q psy396 135 RLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEV 169 (239)
Q Consensus 135 r~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L 169 (239)
|...|.+++.- ..+++..+|+.||+|...+-..|
T Consensus 7 R~~~I~e~l~~-~~~ti~dvA~~~gvS~~TVsr~L 40 (80)
T TIGR02844 7 RVLEIGKYIVE-TKATVRETAKVFGVSKSTVHKDV 40 (80)
T ss_pred HHHHHHHHHHH-CCCCHHHHHHHhCCCHHHHHHHh
Confidence 77888999999 99999999999999999988865
No 58
>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=81.54 E-value=3.2 Score=28.64 Aligned_cols=37 Identities=30% Similarity=0.332 Sum_probs=32.4
Q ss_pred HHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHH
Q psy396 135 RLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVAR 171 (239)
Q Consensus 135 r~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~ 171 (239)
|.+++.-|++.=-.+++..||+.+|+|...|..|=.+
T Consensus 9 rdkA~e~y~~~~g~i~lkdIA~~Lgvs~~tIr~WK~~ 45 (60)
T PF10668_consen 9 RDKAFEIYKESNGKIKLKDIAEKLGVSESTIRKWKSR 45 (60)
T ss_pred HHHHHHHHHHhCCCccHHHHHHHHCCCHHHHHHHhhh
Confidence 6788888988888999999999999999998877554
No 59
>PF13518 HTH_28: Helix-turn-helix domain
Probab=81.31 E-value=4.8 Score=25.68 Aligned_cols=39 Identities=26% Similarity=0.434 Sum_probs=31.9
Q ss_pred HHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcC
Q psy396 135 RLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAG 176 (239)
Q Consensus 135 r~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g 176 (239)
|.+++..|++ ..++..+|+.||+|...|..|+..+=..|
T Consensus 2 r~~iv~~~~~---g~s~~~~a~~~gis~~tv~~w~~~y~~~G 40 (52)
T PF13518_consen 2 RLQIVELYLE---GESVREIAREFGISRSTVYRWIKRYREGG 40 (52)
T ss_pred HHHHHHHHHc---CCCHHHHHHHHCCCHhHHHHHHHHHHhcC
Confidence 3456666664 34999999999999999999999987766
No 60
>KOG4414|consensus
Probab=81.31 E-value=5.2 Score=32.74 Aligned_cols=75 Identities=16% Similarity=0.206 Sum_probs=55.5
Q ss_pred HHHHHHHHhchHHHHHHHHHHHHhhhccCcchhHhHHHHHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHH
Q psy396 92 REYFVSLYDGHYFEFLKCLAAVEQDMKRDPLLNPHYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVA 170 (239)
Q Consensus 92 ~~li~af~~~~y~~~~~~L~~~~~~l~~D~~L~~h~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~ 170 (239)
..+.+.....+|....+.+..+.-. --.++-+..|-+.-|.|++.-.+..|++|.+...|.-+|+|+++.-+-++
T Consensus 80 WgiGQkiWq~Df~GiYeaI~~~dWS----eeak~imaAf~D~~~kR~FaLl~qAYssI~~~D~A~FlGl~~ddAtk~il 154 (197)
T KOG4414|consen 80 WGIGQKIWQHDFAGIYEAINAHDWS----EEAKDIMAAFRDATRKRAFALLLQAYSSIIADDFAAFLGLPEDDATKGIL 154 (197)
T ss_pred hhhhHHHHhcccchHHHHHhhhcch----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHH
Confidence 3456667778888877777665211 01234556777888999999999999999999999999999887555443
No 61
>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=81.28 E-value=5 Score=25.36 Aligned_cols=36 Identities=22% Similarity=0.314 Sum_probs=27.0
Q ss_pred HHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHH
Q psy396 137 RAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARF 172 (239)
Q Consensus 137 ~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~l 172 (239)
+.|++.+..-.+.+...+|+.+|+|...+-.-+.+|
T Consensus 6 ~~Il~~Lq~d~r~s~~~la~~lglS~~~v~~Ri~rL 41 (42)
T PF13404_consen 6 RKILRLLQEDGRRSYAELAEELGLSESTVRRRIRRL 41 (42)
T ss_dssp HHHHHHHHH-TTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHcCCccHHHHHHHHCcCHHHHHHHHHHh
Confidence 455566666689999999999999999998887765
No 62
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=81.05 E-value=4.8 Score=31.92 Aligned_cols=59 Identities=20% Similarity=0.258 Sum_probs=47.1
Q ss_pred HHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 133 EMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 133 ~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
.+|..++.....|=..++...+|+.+|+|...+.+-+..|-..|-+..+=-...|....
T Consensus 10 Al~~~i~la~~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~~G~~GG~~l~ 68 (141)
T PRK11014 10 GLRALIYMASLPEGRMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVRGKNGGIRLG 68 (141)
T ss_pred HHHHHHHHhcCCCCCccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEecCCCCCeeec
Confidence 35666666666776678999999999999999999999999999887666665565444
No 63
>PRK04239 hypothetical protein; Provisional
Probab=80.87 E-value=2.1 Score=33.17 Aligned_cols=55 Identities=22% Similarity=0.257 Sum_probs=41.5
Q ss_pred HHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecc
Q psy396 130 YVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDS 184 (239)
Q Consensus 130 l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~ 184 (239)
-.+..+.-++.|++.|=..=.|++++-.=-=-...||..|.+|..+|+|.++||-
T Consensus 34 ~~e~qk~~iL~qiLt~eAreRL~rI~lvkPe~A~~VE~~liqlAq~G~i~~ki~e 88 (110)
T PRK04239 34 QAEAQKQAILRQILTPEARERLNRIKLVKPEFAEQVEQQLIQLAQSGRIQGPIDD 88 (110)
T ss_pred HHHHHHHHHHHHHCCHHHHHHHHhhhhcCHHHHHHHHHHHHHHHHcCCCCCCcCH
Confidence 3467788889999999777666666532222235899999999999999998863
No 64
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=80.41 E-value=18 Score=25.71 Aligned_cols=55 Identities=20% Similarity=0.193 Sum_probs=42.8
Q ss_pred HHHHHHHHhhhh-hcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 135 RLRAYKQILQAY-RSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 135 r~~~l~qyl~pY-s~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
|...+.+++... ..+++..+|+.+|+|...+...|..|...|-+.- +..+|....
T Consensus 6 r~~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~--~~~~~~y~l 61 (91)
T smart00346 6 RGLAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQ--DGQNGRYRL 61 (91)
T ss_pred HHHHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeee--cCCCCceee
Confidence 455667777666 5799999999999999999999999999988854 233444444
No 65
>KOG2235|consensus
Probab=80.41 E-value=6.1 Score=39.19 Aligned_cols=61 Identities=11% Similarity=0.225 Sum_probs=52.8
Q ss_pred hHhHHHHHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 124 NPHYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 124 ~~h~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
..+++.+-++|+++.-.+ ..|+++.+|+.|++|.+++...|..=.+..-+.|++|. |++++
T Consensus 114 e~Y~d~iaeEinekLqE~-----gqvtiaeLakq~dl~sellqs~l~ek~lg~iikgr~dg--gviyT 174 (776)
T KOG2235|consen 114 EEYVDRIAEEINEKLQEQ-----GQVTIAELAKQWDLPSELLQSLLIEKLLGSIIKGRVDG--GVIYT 174 (776)
T ss_pred HHHHHHHHHHHHHHHHHh-----cchHHHHHHHhcCCcHHHHHHHHHHHhhccceeeeecC--CEEee
Confidence 367788888888876444 79999999999999999999999998777777999999 99988
No 66
>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=80.34 E-value=5.6 Score=27.62 Aligned_cols=31 Identities=10% Similarity=0.382 Sum_probs=26.6
Q ss_pred ccHHHHHHHhCCC-HHHHHHHHHHHHHcCccc
Q psy396 149 LSLKYMAQCFGVS-VEFIEKEVARFAAAGRLQ 179 (239)
Q Consensus 149 v~l~~mA~~fg~s-~~~lE~~L~~lI~~g~l~ 179 (239)
-++..||+.||++ ...+...|..|...|-|.
T Consensus 26 Pt~rEIa~~~g~~S~~tv~~~L~~Le~kG~I~ 57 (65)
T PF01726_consen 26 PTVREIAEALGLKSTSTVQRHLKALERKGYIR 57 (65)
T ss_dssp --HHHHHHHHTSSSHHHHHHHHHHHHHTTSEE
T ss_pred CCHHHHHHHhCCCChHHHHHHHHHHHHCcCcc
Confidence 4899999999996 999999999999988773
No 67
>KOG3677|consensus
Probab=79.02 E-value=22 Score=34.00 Aligned_cols=197 Identities=15% Similarity=0.241 Sum_probs=108.9
Q ss_pred HHHHHHchhcCHHHHHHHHhccCC------CC---CCc--cccCHhHHHHHHHHHHHHcCChhHHHHccccchhHHHHhh
Q psy396 17 YEGVYCLAIRQYCRAAELFVDVVP------TF---ESY--ELAEFGTIIRYTVLACMIALPRYNLRKKLMHHGVMAQALH 85 (239)
Q Consensus 17 ~~Gl~~l~~~~y~~Aa~~F~~~~~------~f---~~~--e~~s~~di~~Y~~Lc~Las~~R~elk~~ll~s~~~~~~~e 85 (239)
+-|.++|..|+|..|-.-|+++.. .+ .+| +.++.+.=-.+-+|+-..++-...+ + ..+..++.
T Consensus 277 ~VGFayLmmrryadai~~F~niLlyIqrtks~~~~~~y~~d~inKq~eqm~~llai~l~~yPq~i-D-----ESi~s~l~ 350 (525)
T KOG3677|consen 277 QVGFAYLMMRRYADAIRVFLNILLYIQRTKSMFSRTTYQYDMINKQNEQMHHLLAICLSMYPQMI-D-----ESIHSQLA 350 (525)
T ss_pred ehhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcchhhhHhhhhhhHHHHHHHHHHHHHhCchhh-h-----HHHHHHHH
Confidence 569999999999999999998852 22 122 5555554455555543333322222 1 12222222
Q ss_pred hh--hhHHHHHHHHHHhchHHHHHHH------------HHHHHhhhccCcchhHhHHHHHHHHHHH----HHHHHhhhhh
Q psy396 86 SQ--YRDLREYFVSLYDGHYFEFLKC------------LAAVEQDMKRDPLLNPHYRHYVQEMRLR----AYKQILQAYR 147 (239)
Q Consensus 86 ~~--~p~l~~li~af~~~~y~~~~~~------------L~~~~~~l~~D~~L~~h~~~l~~~ir~~----~l~qyl~pYs 147 (239)
.. +|.++. ++-.--.|++++.. ++...+.+..+|++++- ..+...++.+ .+-+|++=|.
T Consensus 351 Ek~~d~ml~m--qng~~q~~ks~f~y~cpkflsp~~~~~dgv~~~y~kePl~~ql-q~fld~v~qq~dl~~~rsylklyT 427 (525)
T KOG3677|consen 351 EKYGDKMLPM--QNGDPQVFKSLFSYLCPKFLSPVVPNYDGVLPNYHKEPLLQQL-QVFLDEVSQQADLPTIRSYLKLYT 427 (525)
T ss_pred HHhcchhhhh--hcCChHHHHHHHHHcCccccCCCCcccccccccccccHHHHHH-HHHhHHHhhhccchHHHHHHHHHH
Confidence 10 111111 00111122222222 23333445567777652 4566666665 4778888899
Q ss_pred cccHHHHHHHhCCCHHHHHHHHHHHHH-----------cCccceeecccCCEE-EEeccccccCCCCCCCccchhhhhHH
Q psy396 148 SLSLKYMAQCFGVSVEFIEKEVARFAA-----------AGRLQCKIDSVAGNV-VTTSHISEKGDCRSEAPEASLDRGIL 215 (239)
Q Consensus 148 ~v~l~~mA~~fg~s~~~lE~~L~~lI~-----------~g~l~arID~~~~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~ 215 (239)
......+|.-.+.+.++=.+-+++|+. +|.....++...+.- -. .- | .||.+- .
T Consensus 428 t~P~kkla~F~D~~d~~~dk~li~Ll~~khkm~nlv~~sg~s~~d~~f~~~s~idf-yi-----d-----~dmi~i---a 493 (525)
T KOG3677|consen 428 TLPVKKLASFLDLTDQERDKFLIQLLVFKHKMKNLVWTSGPSDLDDAFFSRSEIDF-YI-----D-----KDMIHI---A 493 (525)
T ss_pred hccHHHhhhccCCchhhhhhhHHHHHHHHHHHHHHHHhcCCccccccccCcceeeE-Ee-----c-----hhHHHH---H
Confidence 999999999999998887777777764 455556666444422 22 11 1 332222 2
Q ss_pred HHHHHHh-hHHHHHHHHHhhhh
Q psy396 216 YQTTVKR-GDIFLNRLKKLARV 236 (239)
Q Consensus 216 ~~~~i~~-~~~~~~r~~~l~~~ 236 (239)
-+++..+ |+.+...|+|+..+
T Consensus 494 Dtkv~r~~gd~fir~i~kf~El 515 (525)
T KOG3677|consen 494 DTKVARRYGDIFIRQIHKFEEL 515 (525)
T ss_pred hHHHHHHHHHHHHHHHHHHHHH
Confidence 2333333 99999999987643
No 68
>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=78.17 E-value=12 Score=24.85 Aligned_cols=44 Identities=16% Similarity=0.339 Sum_probs=36.4
Q ss_pred HHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecc
Q psy396 140 KQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDS 184 (239)
Q Consensus 140 ~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~ 184 (239)
..++.... ++.+.+|+.+|++...+...|..|...|-+...-+.
T Consensus 13 l~~l~~~~-~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~~~~ 56 (78)
T cd00090 13 LRLLLEGP-LTVSELAERLGLSQSTVSRHLKKLEEAGLVESRREG 56 (78)
T ss_pred HHHHHHCC-cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEEEec
Confidence 34444444 999999999999999999999999999998876555
No 69
>PRK09954 putative kinase; Provisional
Probab=77.66 E-value=8.9 Score=34.98 Aligned_cols=56 Identities=14% Similarity=0.178 Sum_probs=48.1
Q ss_pred HHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccc---eeecccCCEEEEe
Q psy396 137 RAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQ---CKIDSVAGNVVTT 192 (239)
Q Consensus 137 ~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~---arID~~~~~l~~~ 192 (239)
+-++++++-...++...+|+.+|+|...+.+.|.+|..+|.+. ..+|....++.+|
T Consensus 6 ~~il~~l~~~~~~s~~~la~~l~~s~~~v~~~i~~L~~~g~i~~~~~~l~~~~~v~viG 64 (362)
T PRK09954 6 KEILAILRRNPLIQQNEIADILQISRSRVAAHIMDLMRKGRIKGKGYILTEQEYCVVVG 64 (362)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCcCCcEEEEcCCccEEEEE
Confidence 3466777777899999999999999999999999999999885 4888888887774
No 70
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=77.65 E-value=6.7 Score=31.54 Aligned_cols=49 Identities=22% Similarity=0.278 Sum_probs=41.4
Q ss_pred HHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccc---eeecc
Q psy396 136 LRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQ---CKIDS 184 (239)
Q Consensus 136 ~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~---arID~ 184 (239)
.+.|+..|.-=.+.+...+|+.+|+|...+-.-+.+|..+|-|. +.+|+
T Consensus 11 D~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI~~~~~~v~~ 62 (153)
T PRK11179 11 DRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQAGIITGTRVDVNP 62 (153)
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeEEEEECH
Confidence 45556666666899999999999999999999999999999885 45664
No 71
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=77.54 E-value=5.4 Score=33.82 Aligned_cols=64 Identities=9% Similarity=0.106 Sum_probs=55.8
Q ss_pred hHHHHHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 126 HYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 126 h~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
-.+.+++.||..++..-+.|=..++-..+|+.||+|-.-|-+-|..|..+|-+.- -+..|+.+.
T Consensus 8 ~~~~vy~~i~~~I~~g~l~pG~~L~e~eLae~lgVSRtpVREAL~~L~~eGlv~~--~~~~G~~V~ 71 (224)
T PRK11534 8 TALDGYRWLKNDIIRGNFQPDEKLRMSLLTSRYALGVGPLREALSQLVAERLVTV--VNQKGYRVA 71 (224)
T ss_pred hhHHHHHHHHHHHHhCCCCCCCcCCHHHHHHHHCCChHHHHHHHHHHHHCCCEEE--eCCCceEeC
Confidence 3468999999999999999999999999999999999999999999999998864 344565544
No 72
>COG2118 DNA-binding protein [General function prediction only]
Probab=77.16 E-value=3.4 Score=32.12 Aligned_cols=54 Identities=22% Similarity=0.254 Sum_probs=39.3
Q ss_pred HHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecc
Q psy396 131 VQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDS 184 (239)
Q Consensus 131 ~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~ 184 (239)
.+.-+..++.|++.|=..=.|.+++=.=-==.+.+|..|.+|+..|+|..+||-
T Consensus 38 ~eaqkqaiLrqiLtpeAreRL~~irLvRPe~AeavE~qLi~LaqtGri~~~I~e 91 (116)
T COG2118 38 EEAQKQAILRQILTPEARERLARVRLVRPELAEAVENQLIQLAQTGRITHKIDE 91 (116)
T ss_pred HHHHHHHHHHHHCCHHHHHHHHHhhhcCHHHHHHHHHHHHHHHHcCCCCCCCCH
Confidence 456677788899999666666555432211236799999999999999998874
No 73
>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=76.79 E-value=13 Score=24.90 Aligned_cols=50 Identities=12% Similarity=0.196 Sum_probs=37.0
Q ss_pred HHHHHHhh-hhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccC
Q psy396 137 RAYKQILQ-AYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVA 186 (239)
Q Consensus 137 ~~l~qyl~-pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~ 186 (239)
..++.++. +...+++..+|+.+|++...+-+.|.+|+..|-+.=.-|..+
T Consensus 6 ~~vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~~~~~d 56 (68)
T PF13463_consen 6 WQVLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLVEKERDPHD 56 (68)
T ss_dssp HHHHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEESSC
T ss_pred HHHHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecCCCCc
Confidence 34455555 888999999999999999999999999999998855444433
No 74
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=76.61 E-value=5.1 Score=24.92 Aligned_cols=32 Identities=19% Similarity=0.417 Sum_probs=29.3
Q ss_pred cccHHHHHHHhCCCHHHHHHHHHHHHHcCccc
Q psy396 148 SLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQ 179 (239)
Q Consensus 148 ~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~ 179 (239)
.++...+|+.+|+|...+.+.|..|...|-+.
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~ 39 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLEKEGLIS 39 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 47788999999999999999999999998884
No 75
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=75.56 E-value=9.3 Score=25.51 Aligned_cols=34 Identities=15% Similarity=0.313 Sum_probs=30.7
Q ss_pred hcccHHHHHHHhCCCHHHHHHHHHHHHHcCccce
Q psy396 147 RSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQC 180 (239)
Q Consensus 147 s~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~a 180 (239)
..++...+|+.+|+|...+.+.|..|...|-|..
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~ 57 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKELEEEGLISR 57 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence 3589999999999999999999999999988753
No 76
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=75.48 E-value=12 Score=24.02 Aligned_cols=44 Identities=14% Similarity=0.209 Sum_probs=35.5
Q ss_pred hhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEE
Q psy396 146 YRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNV 189 (239)
Q Consensus 146 Ys~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l 189 (239)
-..+++..+++.+|++...+-+.|..|...|-+...-+...+..
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~~~~~~~~~~ 51 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLREAGLVESRREGKRVYY 51 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeeecCCEEEE
Confidence 46789999999999999999999999999998875444333333
No 77
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=74.81 E-value=4.8 Score=25.70 Aligned_cols=39 Identities=21% Similarity=0.371 Sum_probs=22.6
Q ss_pred HHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcC
Q psy396 135 RLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAG 176 (239)
Q Consensus 135 r~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g 176 (239)
|..++..+.+ -.+...+|+.||+|...+..|+.++-..|
T Consensus 7 R~~ii~l~~~---G~s~~~ia~~lgvs~~Tv~~w~kr~~~~G 45 (50)
T PF13384_consen 7 RAQIIRLLRE---GWSIREIAKRLGVSRSTVYRWIKRYREEG 45 (50)
T ss_dssp ---HHHHHHH---T--HHHHHHHHTS-HHHHHHHHT------
T ss_pred HHHHHHHHHC---CCCHHHHHHHHCcCHHHHHHHHHHccccc
Confidence 4445555544 67899999999999999999998876655
No 78
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=74.74 E-value=32 Score=28.74 Aligned_cols=62 Identities=13% Similarity=0.140 Sum_probs=47.1
Q ss_pred ccCcchhHhHHHHH--HHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccce
Q psy396 118 KRDPLLNPHYRHYV--QEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQC 180 (239)
Q Consensus 118 ~~D~~L~~h~~~l~--~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~a 180 (239)
..||.+...+..++ ..-..++ ...+.....++-..+|+.+|++...+-+-|..|-.+|-+..
T Consensus 5 ~~~~~v~~~l~~~~~~~~~~~~V-l~~L~~~g~~tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~~ 68 (178)
T PRK06266 5 LNNPLVQKVLFEIMEGDEEGFEV-LKALIKKGEVTDEEIAEQTGIKLNTVRKILYKLYDARLADY 68 (178)
T ss_pred hcCHHHHHHHHHHhcCCccHhHH-HHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEE
Confidence 45666666555555 3334333 44566778999999999999999999999999999988764
No 79
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=74.67 E-value=8.6 Score=27.55 Aligned_cols=42 Identities=21% Similarity=0.351 Sum_probs=34.3
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 149 LSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 149 v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
++...+|+.+|+|...+++-+..|-..|-+...= ..+|-...
T Consensus 26 ~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~~-G~~GGy~L 67 (83)
T PF02082_consen 26 VSSKEIAERLGISPSYLRKILQKLKKAGLIESSR-GRGGGYRL 67 (83)
T ss_dssp BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET-STTSEEEE
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEecC-CCCCceee
Confidence 9999999999999999999999999999886543 33455555
No 80
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=74.65 E-value=7 Score=31.85 Aligned_cols=49 Identities=20% Similarity=0.157 Sum_probs=42.8
Q ss_pred HHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccc---eeecc
Q psy396 136 LRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQ---CKIDS 184 (239)
Q Consensus 136 ~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~---arID~ 184 (239)
.+.|+..|..-.+++...+|+.+|+|...+-+-+.+|..+|-|. +.+|+
T Consensus 16 D~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~GvI~~~~~~v~p 67 (164)
T PRK11169 16 DRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQGFIQGYTALLNP 67 (164)
T ss_pred HHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEEEECH
Confidence 55667788888999999999999999999999999999999885 45663
No 81
>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=74.46 E-value=13 Score=24.94 Aligned_cols=48 Identities=19% Similarity=0.378 Sum_probs=37.4
Q ss_pred HHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccce
Q psy396 132 QEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQC 180 (239)
Q Consensus 132 ~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~a 180 (239)
+-.|.++ .+++......+...+|+.+|+|...+-.-|..|...|-|..
T Consensus 9 ~p~R~~I-l~~L~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli~~ 56 (61)
T PF12840_consen 9 DPTRLRI-LRLLASNGPMTVSELAEELGISQSTVSYHLKKLEEAGLIEV 56 (61)
T ss_dssp SHHHHHH-HHHHHHCSTBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred CHHHHHH-HHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEE
Confidence 3444444 44456678999999999999999999999999999887754
No 82
>PRK03837 transcriptional regulator NanR; Provisional
Probab=73.21 E-value=8.7 Score=32.78 Aligned_cols=63 Identities=13% Similarity=0.099 Sum_probs=56.0
Q ss_pred HHHHHHHHHHHHHHHHhhhhhcc-cHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 127 YRHYVQEMRLRAYKQILQAYRSL-SLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 127 ~~~l~~~ir~~~l~qyl~pYs~v-~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
.+.+++.|+.+++...+.|=..+ +...+|+.||+|-.-|-+-|..|-.+|-+.-+ +..|+.+.
T Consensus 15 ~~~v~~~l~~~I~~g~l~pG~~Lp~E~~Lae~~gVSRt~VREAL~~L~~eGlv~~~--~~~G~~V~ 78 (241)
T PRK03837 15 SEEVEERLEQMIRSGEFGPGDQLPSERELMAFFGVGRPAVREALQALKRKGLVQIS--HGERARVS 78 (241)
T ss_pred HHHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe--cCCceeEe
Confidence 46899999999999999999999 89999999999999999999999999988654 45566665
No 83
>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Probab=73.10 E-value=8 Score=32.35 Aligned_cols=63 Identities=17% Similarity=0.131 Sum_probs=55.7
Q ss_pred HHHHHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 127 YRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 127 ~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
.+.+++.|+.+++..-+.|=..++-..+|+.||+|-.-|-+-|..|-.+|-+.- -+..|+.+.
T Consensus 13 ~~~v~~~l~~~I~~g~l~pG~~L~e~~La~~lgVSRtpVReAL~~L~~eGlv~~--~~~~G~~V~ 75 (212)
T TIGR03338 13 TTLVQDEIERAILSGELPPGAKLNESDIAARLGVSRGPVREAFRALEEAGLVRN--EKNRGVFVR 75 (212)
T ss_pred HHHHHHHHHHHHHcCCCCCCCEecHHHHHHHhCCChHHHHHHHHHHHHCCCEEE--ecCCCeEEe
Confidence 367899999999999999999999999999999999999999999999998854 345576666
No 84
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=72.23 E-value=5.7 Score=33.89 Aligned_cols=65 Identities=22% Similarity=0.233 Sum_probs=57.8
Q ss_pred HhHHHHHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 125 PHYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 125 ~h~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
+-.+.+|+.+|..++..-+.|=..++-..+|+.||+|-.-|-+-|.+|-.+|-+.-. +..|..+.
T Consensus 16 ~~~~~vy~~Lr~~Il~g~l~pG~~l~e~~La~~~gvSrtPVReAL~rL~~eGlv~~~--p~rG~~V~ 80 (230)
T COG1802 16 TLADQVYEELREAILSGELAPGERLSEEELAEELGVSRTPVREALRRLEAEGLVEIE--PNRGAFVA 80 (230)
T ss_pred cHHHHHHHHHHHHHHhCCCCCCCCccHHHHHHHhCCCCccHHHHHHHHHHCCCeEec--CCCCCeeC
Confidence 345788999999999999999999999999999999999999999999999988655 66666666
No 85
>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=71.92 E-value=6.2 Score=31.71 Aligned_cols=39 Identities=28% Similarity=0.388 Sum_probs=30.3
Q ss_pred HHHhhhhhc--ccHHHHHHHhCCCHHHHHHHHHHHHHcCccceee
Q psy396 140 KQILQAYRS--LSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKI 182 (239)
Q Consensus 140 ~qyl~pYs~--v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arI 182 (239)
.+||.-+-. .++..+|++.|+|+..| .++|.+|||.-.-
T Consensus 36 ~~yLr~~p~~~ati~eV~e~tgVs~~~I----~~~IreGRL~~~~ 76 (137)
T TIGR03826 36 YKFLRKHENRQATVSEIVEETGVSEKLI----LKFIREGRLQLKH 76 (137)
T ss_pred HHHHHHCCCCCCCHHHHHHHHCcCHHHH----HHHHHcCCeeccC
Confidence 577886656 99999999999998765 5556679986544
No 86
>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=70.67 E-value=17 Score=23.21 Aligned_cols=29 Identities=21% Similarity=0.391 Sum_probs=24.1
Q ss_pred hhcccHHHHHHHhCCCHHHHHHHHHHHHH
Q psy396 146 YRSLSLKYMAQCFGVSVEFIEKEVARFAA 174 (239)
Q Consensus 146 Ys~v~l~~mA~~fg~s~~~lE~~L~~lI~ 174 (239)
|...++..+|+.+|+|...+-....+.+.
T Consensus 18 ~~~~t~~eIa~~lg~s~~~V~~~~~~al~ 46 (50)
T PF04545_consen 18 FEGLTLEEIAERLGISRSTVRRILKRALK 46 (50)
T ss_dssp TST-SHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHCCcHHHHHHHHHHHHH
Confidence 77889999999999999999888776653
No 87
>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=70.05 E-value=19 Score=24.18 Aligned_cols=40 Identities=18% Similarity=0.267 Sum_probs=32.1
Q ss_pred HHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHH
Q psy396 134 MRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFA 173 (239)
Q Consensus 134 ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI 173 (239)
.|..-+..++-.-..+++..+|+.+|+|.-.+...|..+=
T Consensus 5 ~rq~~Ll~~L~~~~~~~~~ela~~l~~S~rti~~~i~~L~ 44 (59)
T PF08280_consen 5 KRQLKLLELLLKNKWITLKELAKKLNISERTIKNDINELN 44 (59)
T ss_dssp HHHHHHHHHHHHHTSBBHHHHHHHCTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4555666666668899999999999999999999988764
No 88
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR. Members of this family are FadR, a transcriptional regulator of fatty acid metabolism, including both biosynthesis and beta-oxidation. It is found exclusively in a subset of Gammaproteobacteria, with strictly one copy per genome. It has an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR from this family heterologously expressed in Escherichia coli show differences in regulatory response and fatty acid binding profiles. The family is nevertheless designated equivalog, as all member proteins have at least nominally the same function.
Probab=70.00 E-value=13 Score=31.67 Aligned_cols=63 Identities=13% Similarity=0.111 Sum_probs=55.2
Q ss_pred HHHHHHHHHHHHHHHHhhhhhcc-cHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 127 YRHYVQEMRLRAYKQILQAYRSL-SLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 127 ~~~l~~~ir~~~l~qyl~pYs~v-~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
.+..++.|+.+++..-+.|=..+ +-..+|+.||+|-.-|-+-|..|-.+|-+.- -+..|+.+.
T Consensus 8 ~~~v~~~l~~~I~~g~l~pG~~LpsE~~La~~lgVSRtpVREAL~~Le~eGlV~~--~~~~G~~V~ 71 (235)
T TIGR02812 8 AGFAEEYIVESIWNNRFPPGSILPAERELSELIGVTRTTLREVLQRLARDGWLTI--QHGKPTKVN 71 (235)
T ss_pred HHHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE--eCCCccEec
Confidence 35788999999999999999999 7999999999999999999999999998863 344566665
No 89
>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=69.80 E-value=14 Score=24.02 Aligned_cols=43 Identities=14% Similarity=0.233 Sum_probs=34.1
Q ss_pred HHHHHHHhhhhhc-ccHHHHHHHhCCCHHHHHHHHHHHHHcCcc
Q psy396 136 LRAYKQILQAYRS-LSLKYMAQCFGVSVEFIEKEVARFAAAGRL 178 (239)
Q Consensus 136 ~~~l~qyl~pYs~-v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l 178 (239)
.-.+..++..... +++..+|+.+|+|...+-..|..|...|-+
T Consensus 5 al~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v 48 (52)
T PF09339_consen 5 ALRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVEEGYV 48 (52)
T ss_dssp HHHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCe
Confidence 3345566665555 799999999999999999999999988765
No 90
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=69.78 E-value=14 Score=25.54 Aligned_cols=43 Identities=21% Similarity=0.368 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHH
Q psy396 129 HYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFA 173 (239)
Q Consensus 129 ~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI 173 (239)
.+-.+.+.+++..++.+ -.++..+|..+|+++..+-+|+.++-
T Consensus 6 ~ys~e~K~~~v~~~~~~--g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 6 RYSPEFKLQAVREYLES--GESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp ---HHHHHHHHHHHHHH--HCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHC--CCceEeeecccccccccccHHHHHHh
Confidence 44566778888888776 78999999999999999999999987
No 91
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=69.61 E-value=14 Score=27.96 Aligned_cols=49 Identities=24% Similarity=0.335 Sum_probs=41.0
Q ss_pred HHHHHHHHHHHHHHhhhhhcccHHHHHHHhCC-CHHHHHHHHHHHHHcCccc
Q psy396 129 HYVQEMRLRAYKQILQAYRSLSLKYMAQCFGV-SVEFIEKEVARFAAAGRLQ 179 (239)
Q Consensus 129 ~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~-s~~~lE~~L~~lI~~g~l~ 179 (239)
.+-.+-+.+++.+|++| -.+++.+|..||+ +...+-+|+.++...+...
T Consensus 7 ~~s~EfK~~iv~~~~~~--g~sv~~vAr~~gv~~~~~l~~W~~~~~~~~~~~ 56 (116)
T COG2963 7 KYSPEFKLEAVALYLRG--GDTVSEVAREFGIVSATQLYKWRIQLQKGGGLA 56 (116)
T ss_pred cCCHHHHHHHHHHHHhc--CccHHHHHHHhCCCChHHHHHHHHHHHHccccc
Confidence 34456788999999998 4489999999996 9999999999999976554
No 92
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=69.20 E-value=36 Score=24.12 Aligned_cols=48 Identities=21% Similarity=0.227 Sum_probs=38.5
Q ss_pred HHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeeccc
Q psy396 138 AYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSV 185 (239)
Q Consensus 138 ~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~ 185 (239)
.+.+.+.....++...+|+.++++...+...|..|...|-+...-|..
T Consensus 14 ~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~~~~~ 61 (101)
T smart00347 14 LVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRLPSPE 61 (101)
T ss_pred HHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEecCCCC
Confidence 344555445579999999999999999999999999999987655543
No 93
>PF01865 PhoU_div: Protein of unknown function DUF47; InterPro: IPR018445 This family includes prokaryotic proteins of unknown function, as well as a protein annotated as the pit accessory protein from Rhizobium meliloti (Sinorhizobium meliloti) (O30498 from SWISSPROT). However, the function of this protein is also unknown (Pit stands for Phosphate transport) [].; PDB: 2OLT_C 2IIU_C 3L39_A.
Probab=68.50 E-value=18 Score=30.38 Aligned_cols=81 Identities=16% Similarity=0.283 Sum_probs=61.7
Q ss_pred hhHHHHHHHHHHhchHHHHHHHHHHHHhhhccCcchhHhHHHHHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHH
Q psy396 88 YRDLREYFVSLYDGHYFEFLKCLAAVEQDMKRDPLLNPHYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEK 167 (239)
Q Consensus 88 ~p~l~~li~af~~~~y~~~~~~L~~~~~~l~~D~~L~~h~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~ 167 (239)
.-.+.+++.++.+++|..+...+.++.. +-++.+.+.+.++......++-|+.+-++-.+++.+.-=.+.++.
T Consensus 24 ~~~~~e~l~~~~~~~~~~~~~~~~~i~~-------lE~~aD~i~~~i~~~L~~~fitP~dRedi~~L~~~lD~I~d~i~~ 96 (214)
T PF01865_consen 24 SVLLAELLEAYLEGDYEDVEELLEEIKE-------LEHEADEIKREIREELYKSFITPFDREDILRLISSLDDIADYIED 96 (214)
T ss_dssp HHCHHHHHHHHCTT-CHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHH-SS-SS-HHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHhccCCCcHHHHHHHHHHHHHHHHHHHH
Confidence 3457888899988888888777776633 246779999999999999999999999999999998877777777
Q ss_pred HHHHHHHc
Q psy396 168 EVARFAAA 175 (239)
Q Consensus 168 ~L~~lI~~ 175 (239)
-...+..-
T Consensus 97 ~a~~l~~~ 104 (214)
T PF01865_consen 97 AAKRLSLY 104 (214)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHHh
Confidence 77666553
No 94
>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=68.11 E-value=24 Score=31.21 Aligned_cols=59 Identities=19% Similarity=0.323 Sum_probs=48.3
Q ss_pred hHhHHHHHHHHHHHHHHHH-hh--hhh-----------------cccHHHHHHHhCCCHHHHHHHHHHHHHcCccceee
Q psy396 124 NPHYRHYVQEMRLRAYKQI-LQ--AYR-----------------SLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKI 182 (239)
Q Consensus 124 ~~h~~~l~~~ir~~~l~qy-l~--pYs-----------------~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arI 182 (239)
+.....+=++.|.++..|. +. +|| +++-..+|+.+|+|...+-+-+.+|-..|-|..+-
T Consensus 154 r~~~~~iEee~Rkka~Vq~Ai~tLSySEleAv~~IL~~L~~~egrlse~eLAerlGVSRs~ireAlrkLE~aGvIe~r~ 232 (251)
T TIGR02787 154 RAQAEEIEEEARKKAAVQMAINTLSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRS 232 (251)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhccHhHHHHHHHHHHHhccccccccHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecc
Confidence 3445667788888888887 32 366 78899999999999999999999999999887654
No 95
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=67.84 E-value=14 Score=29.04 Aligned_cols=48 Identities=21% Similarity=0.322 Sum_probs=40.4
Q ss_pred HHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCcc---ceeecc
Q psy396 137 RAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRL---QCKIDS 184 (239)
Q Consensus 137 ~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l---~arID~ 184 (239)
+-+++.++-=.+.++..+|+.+|+|...+-.-+.+|..+|-| .+.+|.
T Consensus 11 ~~IL~~L~~d~r~~~~eia~~lglS~~~v~~Ri~~L~~~GiI~~~~~~v~~ 61 (154)
T COG1522 11 RRILRLLQEDARISNAELAERVGLSPSTVLRRIKRLEEEGVIKGYTAVLDP 61 (154)
T ss_pred HHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCceeeEEEEECH
Confidence 345566666677999999999999999999999999999977 467775
No 96
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=67.67 E-value=12 Score=29.59 Aligned_cols=40 Identities=15% Similarity=0.285 Sum_probs=37.1
Q ss_pred HHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCcc
Q psy396 139 YKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRL 178 (239)
Q Consensus 139 l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l 178 (239)
|+.+++..-.+++..|+..+|.+-..+...+.+|...|.|
T Consensus 17 IvElVRe~GRiTi~ql~~~TGasR~Tvk~~lreLVa~G~l 56 (127)
T PF06163_consen 17 IVELVREHGRITIKQLVAKTGASRNTVKRYLRELVARGDL 56 (127)
T ss_pred HHHHHHHcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCCe
Confidence 4567788899999999999999999999999999999988
No 97
>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=67.46 E-value=9.8 Score=27.25 Aligned_cols=35 Identities=14% Similarity=0.163 Sum_probs=29.9
Q ss_pred hhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCcc
Q psy396 144 QAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRL 178 (239)
Q Consensus 144 ~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l 178 (239)
.-+...+...+|+.+|+|+..+...+..+...|.+
T Consensus 28 R~~eGlS~kEIAe~LGIS~~TVk~~l~~~~~~~~~ 62 (73)
T TIGR03879 28 REEAGKTASEIAEELGRTEQTVRNHLKGETKAGGL 62 (73)
T ss_pred HHHcCCCHHHHHHHHCcCHHHHHHHHhcCcccchH
Confidence 34578899999999999999999999987777655
No 98
>PRK15481 transcriptional regulatory protein PtsJ; Provisional
Probab=66.86 E-value=11 Score=35.22 Aligned_cols=63 Identities=21% Similarity=0.230 Sum_probs=53.4
Q ss_pred HHHHHHHHHHHHHHHHhhhhhcc-cHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 127 YRHYVQEMRLRAYKQILQAYRSL-SLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 127 ~~~l~~~ir~~~l~qyl~pYs~v-~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
-..+++.|+..+....+.|=..+ +...+|+.||+|...+.+.+.+|..+|-|..+- ..|+.+.
T Consensus 7 ~~~~~~~i~~~i~~g~l~~g~~lps~r~la~~~~vsr~tv~~a~~~L~~~g~i~~~~--~~G~~v~ 70 (431)
T PRK15481 7 ANEIFDSIRQLIQAGRLRPGDSLPPVRELASELGVNRNTVAAAYKRLVTAGLAQSQG--RNGTVIR 70 (431)
T ss_pred HHHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeC--CCceEEc
Confidence 46788899999999999998888 799999999999999999999999999886532 3455444
No 99
>PF13730 HTH_36: Helix-turn-helix domain
Probab=66.83 E-value=11 Score=24.50 Aligned_cols=29 Identities=21% Similarity=0.383 Sum_probs=26.4
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHHHHcCcc
Q psy396 150 SLKYMAQCFGVSVEFIEKEVARFAAAGRL 178 (239)
Q Consensus 150 ~l~~mA~~fg~s~~~lE~~L~~lI~~g~l 178 (239)
+.+++|+.+|++...|.+.+..|...|-|
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 79999999999999999999999987743
No 100
>KOG3250|consensus
Probab=66.71 E-value=31 Score=30.10 Aligned_cols=91 Identities=11% Similarity=0.050 Sum_probs=58.1
Q ss_pred hhHHHHHHHHHHhchHHHHHHHHHHHHhhhccCcch---hHhHHHHHHHHHHHHHHHHhhhhhcccHHHHHHHhCC-CHH
Q psy396 88 YRDLREYFVSLYDGHYFEFLKCLAAVEQDMKRDPLL---NPHYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGV-SVE 163 (239)
Q Consensus 88 ~p~l~~li~af~~~~y~~~~~~L~~~~~~l~~D~~L---~~h~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~-s~~ 163 (239)
+..+.++++-|..+.|.+|...-... |.|..+-.+ +.||-.+.. .-+.+.-..+-..+.+ ++-
T Consensus 59 dsa~lrlL~lFa~Gt~~Dy~aea~rl-p~Ls~~q~~kLk~ltV~slas------------~~k~lpy~~Ll~~l~~~nvr 125 (258)
T KOG3250|consen 59 DSAYLRLLELFAYGTYRDYSAEALRL-PKLSLAQLNKLKHLTVVSLAS------------FEKCLPYLVLLRLLPSRNVR 125 (258)
T ss_pred cHHHHHHHHHHhcCchhhhhhhhhcC-CCCCHHHHHhhhcceehhhhh------------hchhhhHHHHHhhccCCchh
Confidence 34578889999999999996543222 222222221 122222222 2222233333445544 567
Q ss_pred HHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 164 FIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 164 ~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
++|+.|.+.+-.+-+.||||+-|.++++
T Consensus 126 elEd~iieamya~IlrGkldqr~q~leV 153 (258)
T KOG3250|consen 126 ELEDLIIEAMYADILRGKLDQRNQTLEV 153 (258)
T ss_pred HHHHHHHHHHHHHHHHhhHHhhcceEee
Confidence 9999999999999999999999999998
No 101
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=66.55 E-value=14 Score=31.94 Aligned_cols=64 Identities=16% Similarity=0.146 Sum_probs=55.9
Q ss_pred hHHHHHHHHHHHHHHHHhhhhhcc-cHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 126 HYRHYVQEMRLRAYKQILQAYRSL-SLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 126 h~~~l~~~ir~~~l~qyl~pYs~v-~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
-.+.+++.||..++..-+.|=..+ +-..+|+.||+|-.-|-+-|..|-..|-+.- .+..|+.+.
T Consensus 10 ~~~~v~~~l~~~I~~g~l~pG~~LpsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~--~~~~G~~V~ 74 (257)
T PRK10225 10 PYQEVGAMIRDLIIKTPYNPGERLPPEREIAEMLDVTRTVVREALIMLEIKGLVEV--RRGAGIYVL 74 (257)
T ss_pred HHHHHHHHHHHHHHhCCCCCCCcCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE--ecCCEEEEe
Confidence 347899999999999999999999 5999999999999999999999999998864 344576666
No 102
>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=66.00 E-value=55 Score=24.67 Aligned_cols=49 Identities=16% Similarity=0.080 Sum_probs=41.1
Q ss_pred HHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCC
Q psy396 139 YKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAG 187 (239)
Q Consensus 139 l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~ 187 (239)
+...+.-...++.+.+|+.+|++...+-..|.+|...|-|...-|+.++
T Consensus 33 iL~~l~~~~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~~~~D~ 81 (118)
T TIGR02337 33 ILRILAEQGSMEFTQLANQACILRPSLTGILARLERDGLVTRLKASNDQ 81 (118)
T ss_pred HHHHHHHcCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeccCCCCC
Confidence 3444445568999999999999999999999999999999888777665
No 103
>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=65.76 E-value=28 Score=23.65 Aligned_cols=44 Identities=14% Similarity=0.261 Sum_probs=36.9
Q ss_pred HHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccce
Q psy396 136 LRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQC 180 (239)
Q Consensus 136 ~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~a 180 (239)
.++|...+ .....+...+|+.+|+|...+.+.|..|...|-+.-
T Consensus 11 ~~vy~~Ll-~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~ 54 (68)
T PF01978_consen 11 AKVYLALL-KNGPATAEEIAEELGISRSTVYRALKSLEEKGLVER 54 (68)
T ss_dssp HHHHHHHH-HHCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHH-HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence 34444444 678999999999999999999999999999998854
No 104
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=65.10 E-value=19 Score=29.66 Aligned_cols=44 Identities=16% Similarity=0.292 Sum_probs=36.2
Q ss_pred hhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCC
Q psy396 144 QAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAG 187 (239)
Q Consensus 144 ~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~ 187 (239)
..-..++++.+|+.+|+|...+++-|..|-..|-+...=....|
T Consensus 21 ~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s~rG~~GG 64 (164)
T PRK10857 21 SEAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSVRGPGGG 64 (164)
T ss_pred CCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCCCCCCC
Confidence 33457999999999999999999999999999988764344444
No 105
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=64.55 E-value=15 Score=31.73 Aligned_cols=63 Identities=21% Similarity=0.247 Sum_probs=55.3
Q ss_pred HHHHHHHHHHHHHHHHhhhhhcc-cHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 127 YRHYVQEMRLRAYKQILQAYRSL-SLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 127 ~~~l~~~ir~~~l~qyl~pYs~v-~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
.+.+++.|+..++..-+.|=..+ +-..+|+.||+|-.-|-+-|..|-..|-|..+ +..|+.+.
T Consensus 12 ~~~v~~~l~~~I~~g~l~pG~~LpsE~eLa~~lgVSRtpVREAL~~L~~eGlv~~~--~~~G~~V~ 75 (254)
T PRK09464 12 SDVIEQQLEFLILEGTLRPGEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRR--QGGGTFVQ 75 (254)
T ss_pred HHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe--cCceeEEe
Confidence 36789999999999999999999 89999999999999999999999999999754 34566665
No 106
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=64.44 E-value=14 Score=31.25 Aligned_cols=63 Identities=14% Similarity=0.179 Sum_probs=54.0
Q ss_pred HHHHHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 127 YRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 127 ~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
.+.+++.||.+++..-+.|=..++-..+|+.||+|-.-|-+-|..|-.+|-+.-+ +..|+.+.
T Consensus 13 ~e~v~~~l~~~I~~g~l~pG~~L~e~~La~~lgVSRtpVREAL~~L~~eGLV~~~--~~~g~~v~ 75 (221)
T PRK11414 13 TLQVENDLKHQLSIGALKPGARLITKNLAEQLGMSITPVREALLRLVSVNALSVA--PAQAFTVP 75 (221)
T ss_pred HHHHHHHHHHHHHhCCCCCCCccCHHHHHHHHCCCchhHHHHHHHHHHCCCEEec--CCCceeec
Confidence 3679999999999999999999999999999999999999999999999988643 33354443
No 107
>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=63.99 E-value=31 Score=21.07 Aligned_cols=27 Identities=22% Similarity=0.353 Sum_probs=23.6
Q ss_pred hcccHHHHHHHhCCCHHHHHHHHHHHH
Q psy396 147 RSLSLKYMAQCFGVSVEFIEKEVARFA 173 (239)
Q Consensus 147 s~v~l~~mA~~fg~s~~~lE~~L~~lI 173 (239)
...+...+|+.+|+|...+..++....
T Consensus 25 ~~~~~~~ia~~~~~s~~~i~~~~~~~~ 51 (55)
T cd06171 25 EGLSYEEIAEILGISRSTVRQRLHRAL 51 (55)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 678999999999999999988887754
No 108
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=63.14 E-value=17 Score=30.21 Aligned_cols=47 Identities=15% Similarity=0.251 Sum_probs=38.1
Q ss_pred HHHHHHHHhhhhhc-----ccHHHHHHHhCCC-HHHHHHHHHHHHHcCcccee
Q psy396 135 RLRAYKQILQAYRS-----LSLKYMAQCFGVS-VEFIEKEVARFAAAGRLQCK 181 (239)
Q Consensus 135 r~~~l~qyl~pYs~-----v~l~~mA~~fg~s-~~~lE~~L~~lI~~g~l~ar 181 (239)
+++.+.+++.-|.. .++..||+.+|++ ...+-..|..|...|-|...
T Consensus 7 ~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~g~i~~~ 59 (199)
T TIGR00498 7 RQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALERKGYIERD 59 (199)
T ss_pred HHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHHHCCCEecC
Confidence 45556666665543 8899999999998 99999999999999988654
No 109
>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]. It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. This repeat includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by IPR001440 from INTERPRO.; PDB: 1XNF_B 3Q15_A 4ABN_A 1OUV_A 3U4T_A 3MA5_C 2KCV_A 2KCL_A 2XEV_A 3NF1_A ....
Probab=63.14 E-value=11 Score=21.23 Aligned_cols=27 Identities=22% Similarity=0.272 Sum_probs=21.5
Q ss_pred hhHHHHHHHHchhcCHHHHHHHHhccC
Q psy396 13 KLKAYEGVYCLAIRQYCRAAELFVDVV 39 (239)
Q Consensus 13 kl~~~~Gl~~l~~~~y~~Aa~~F~~~~ 39 (239)
+.-..-|..++..|+|++|...|-.+.
T Consensus 2 ~~~~~lg~~~~~~~~~~~A~~~~~~al 28 (34)
T PF07719_consen 2 EAWYYLGQAYYQLGNYEEAIEYFEKAL 28 (34)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence 344567899999999999999998874
No 110
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=61.02 E-value=21 Score=22.77 Aligned_cols=23 Identities=30% Similarity=0.327 Sum_probs=20.3
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHH
Q psy396 149 LSLKYMAQCFGVSVEFIEKEVAR 171 (239)
Q Consensus 149 v~l~~mA~~fg~s~~~lE~~L~~ 171 (239)
.++..+|+.+|+|.+.|...+.+
T Consensus 28 ~s~~~vA~~~~vs~~TV~ri~~~ 50 (52)
T PF13542_consen 28 RSFKDVARELGVSWSTVRRIFDR 50 (52)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHh
Confidence 69999999999999998887654
No 111
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.
Probab=60.74 E-value=38 Score=28.39 Aligned_cols=54 Identities=19% Similarity=0.176 Sum_probs=41.2
Q ss_pred HHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 137 RAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 137 ~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
..+..++..+..+++..+|+.+|+|...+.+.|..|...|-+.-.-+ .+..+..
T Consensus 146 ~~IL~~l~~~g~~s~~eia~~l~is~stv~r~L~~Le~~GlI~r~~~-r~~~~~l 199 (203)
T TIGR01884 146 LKVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLRELEKKGLVEQKGR-KGKRYSL 199 (203)
T ss_pred HHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcC-CccEEEe
Confidence 34556666666799999999999999999999999999988865432 3334443
No 112
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=60.00 E-value=20 Score=30.79 Aligned_cols=63 Identities=13% Similarity=0.172 Sum_probs=55.1
Q ss_pred HHHHHHHHHHHHHHHHhhhhhcc-cHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 127 YRHYVQEMRLRAYKQILQAYRSL-SLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 127 ~~~l~~~ir~~~l~qyl~pYs~v-~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
.+.+++.|+..++..-+.|=..+ +-..+|+.||+|-.-|-+-|..|-..|-+..+- ..|+.+.
T Consensus 9 ~~~v~~~i~~~I~~g~l~pG~~LPsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~--~~G~~V~ 72 (251)
T PRK09990 9 ADVVAERIERLIVDGVLKVGQALPSERRLCEKLGFSRSALREGLTVLRGRGIIETAQ--GRGSFVA 72 (251)
T ss_pred HHHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeC--CCeeEEe
Confidence 46789999999999999999999 899999999999999999999999999886543 3466655
No 113
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=59.76 E-value=21 Score=30.40 Aligned_cols=62 Identities=13% Similarity=0.122 Sum_probs=54.1
Q ss_pred HHHHHHHHHHHHHHHhhhhhcc-cHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 128 RHYVQEMRLRAYKQILQAYRSL-SLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 128 ~~l~~~ir~~~l~qyl~pYs~v-~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
+.+++.|+.+++..-+.|=..+ +-..+|+.||+|-..|-+-|..|..+|-|.. -+..|+.+.
T Consensus 10 ~~~~~~l~~~I~~g~l~pG~~LPsE~eLae~~gVSRt~VReAL~~L~~eGlv~~--~~g~G~~V~ 72 (239)
T PRK04984 10 GFAEEYIIESIWNNRFPPGSILPAERELSELIGVTRTTLREVLQRLARDGWLTI--QHGKPTKVN 72 (239)
T ss_pred HHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE--eCCCeeEeC
Confidence 5788999999999999999999 6899999999999999999999999999864 344566665
No 114
>COG2378 Predicted transcriptional regulator [Transcription]
Probab=59.43 E-value=22 Score=32.22 Aligned_cols=54 Identities=33% Similarity=0.388 Sum_probs=45.8
Q ss_pred HHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCC
Q psy396 131 VQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAG 187 (239)
Q Consensus 131 ~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~ 187 (239)
.+..|.-.+++++..+..++...||+.||+|.-.+...+..|=..|-= |+...|
T Consensus 5 ~ka~RL~~ii~~L~~~~~vta~~lA~~~~VS~RTi~RDi~~L~~~gvP---I~~e~G 58 (311)
T COG2378 5 RKAERLLQIIQILRAKETVTAAELADEFEVSVRTIYRDIATLRAAGVP---IEGERG 58 (311)
T ss_pred hHHHHHHHHHHHHHhCccchHHHHHHhcCCCHHHHHHHHHHHHHCCCC---eEeecC
Confidence 456788889999999999999999999999999999999988776533 555555
No 115
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=59.36 E-value=24 Score=30.58 Aligned_cols=46 Identities=15% Similarity=0.259 Sum_probs=40.7
Q ss_pred HHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCcccee
Q psy396 136 LRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCK 181 (239)
Q Consensus 136 ~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~ar 181 (239)
...|.-+|.-...++...||+.+|+|...+-.-|..|..+|-+...
T Consensus 13 r~~il~lL~~~g~~sa~elA~~Lgis~~avR~HL~~Le~~Glv~~~ 58 (218)
T COG2345 13 RERILELLKKSGPVSADELAEELGISPMAVRRHLDDLEAEGLVEVE 58 (218)
T ss_pred HHHHHHHHhccCCccHHHHHHHhCCCHHHHHHHHHHHHhCcceeee
Confidence 3445667777799999999999999999999999999999988877
No 116
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=59.22 E-value=32 Score=23.30 Aligned_cols=35 Identities=23% Similarity=0.291 Sum_probs=30.5
Q ss_pred hhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccc
Q psy396 145 AYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQ 179 (239)
Q Consensus 145 pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~ 179 (239)
.=..|+...+|+.||++...+-+-+.+|-..|-+.
T Consensus 19 ~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV~ 53 (60)
T PF01325_consen 19 EGGPVRTKDIAERLGVSPPTVTEMLKRLAEKGLVE 53 (60)
T ss_dssp CTSSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred CCCCccHHHHHHHHCCChHHHHHHHHHHHHCCCEE
Confidence 45789999999999999999999999999988764
No 117
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=58.68 E-value=35 Score=21.31 Aligned_cols=29 Identities=17% Similarity=0.285 Sum_probs=25.1
Q ss_pred hhcccHHHHHHHhCCCHHHHHHHHHHHHH
Q psy396 146 YRSLSLKYMAQCFGVSVEFIEKEVARFAA 174 (239)
Q Consensus 146 Ys~v~l~~mA~~fg~s~~~lE~~L~~lI~ 174 (239)
+...+...+|+.+|+|...+...+.++..
T Consensus 16 ~~g~s~~eia~~l~is~~tv~~~~~~~~~ 44 (58)
T smart00421 16 AEGLTNKEIAERLGISEKTVKTHLSNIMR 44 (58)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 35679999999999999999999988754
No 118
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=58.32 E-value=72 Score=26.72 Aligned_cols=45 Identities=9% Similarity=0.191 Sum_probs=39.0
Q ss_pred HHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCcccee
Q psy396 137 RAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCK 181 (239)
Q Consensus 137 ~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~ar 181 (239)
+.++.++.....++...||+.+|++...+-+-|..|...|-|.-+
T Consensus 4 ~~IL~~L~~~~~~t~~eLA~~lgis~~tV~~~L~~Le~~GlV~r~ 48 (203)
T TIGR02702 4 EDILSYLLKQGQATAAALAEALAISPQAVRRHLKDLETEGLIEYE 48 (203)
T ss_pred HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEe
Confidence 345666666688999999999999999999999999999999655
No 119
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=58.28 E-value=23 Score=30.63 Aligned_cols=63 Identities=16% Similarity=0.267 Sum_probs=54.5
Q ss_pred HHHHHHHHHHHHHHHHhhhhhccc-HHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 127 YRHYVQEMRLRAYKQILQAYRSLS-LKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 127 ~~~l~~~ir~~~l~qyl~pYs~v~-l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
.+.+++.|+..++..-+.|=..++ -..+|+.||+|-.-|-+-|..|-..|-+.-+ +..|+.+.
T Consensus 10 ~~~v~~~l~~~I~~g~l~pG~~LpsE~eLae~~gVSRtpVREAL~~L~~eGlV~~~--~~~G~~V~ 73 (253)
T PRK11523 10 YQQLAAELKERIEQGVYLVGDKLPAERFIADEKNVSRTVVREAIIMLEVEGYVEVR--KGSGIHVV 73 (253)
T ss_pred HHHHHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe--cCCeeEEe
Confidence 467899999999999999999995 7899999999999999999999999988644 34566665
No 120
>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=58.15 E-value=15 Score=24.53 Aligned_cols=34 Identities=18% Similarity=0.296 Sum_probs=28.7
Q ss_pred HHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHH
Q psy396 140 KQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFA 173 (239)
Q Consensus 140 ~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI 173 (239)
..|++.=..+++..+|+.||+|...+..-|.+..
T Consensus 15 ~GYfd~PR~~tl~elA~~lgis~st~~~~LRrae 48 (53)
T PF04967_consen 15 LGYFDVPRRITLEELAEELGISKSTVSEHLRRAE 48 (53)
T ss_pred cCCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 4577766899999999999999999988887644
No 121
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=58.12 E-value=19 Score=24.77 Aligned_cols=40 Identities=23% Similarity=0.421 Sum_probs=34.5
Q ss_pred cccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 148 SLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 148 ~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
.++...||..+|+|...+.+.|..|..+|-|. ...+.+.+
T Consensus 28 ~lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I~----~~~~~i~I 67 (76)
T PF13545_consen 28 PLTQEEIADMLGVSRETVSRILKRLKDEGIIE----VKRGKIII 67 (76)
T ss_dssp ESSHHHHHHHHTSCHHHHHHHHHHHHHTTSEE----EETTEEEE
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE----EcCCEEEE
Confidence 46889999999999999999999999987664 56677777
No 122
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=58.11 E-value=27 Score=26.11 Aligned_cols=42 Identities=17% Similarity=0.165 Sum_probs=36.3
Q ss_pred HHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCcc
Q psy396 137 RAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRL 178 (239)
Q Consensus 137 ~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l 178 (239)
.-|.+++.-+-.=.-..||..+++|.++++..+.+|..-|-|
T Consensus 10 ~~IL~hl~~~~~Dy~k~ia~~l~~~~~~v~~~l~~Le~~GLl 51 (92)
T PF10007_consen 10 LKILQHLKKAGPDYAKSIARRLKIPLEEVREALEKLEEMGLL 51 (92)
T ss_pred HHHHHHHHHHCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCe
Confidence 446777787777778889999999999999999999998876
No 123
>KOG3252|consensus
Probab=57.98 E-value=1.2e+02 Score=25.90 Aligned_cols=120 Identities=15% Similarity=0.181 Sum_probs=73.3
Q ss_pred HHHHHHHHHcCChhHHH--HccccchhHHHHhhhhhhHHHHHHHHHHhchHHHHHHHHHHHHhhhccCcchhHhHHHHHH
Q psy396 55 RYTVLACMIALPRYNLR--KKLMHHGVMAQALHSQYRDLREYFVSLYDGHYFEFLKCLAAVEQDMKRDPLLNPHYRHYVQ 132 (239)
Q Consensus 55 ~Y~~Lc~Las~~R~elk--~~ll~s~~~~~~~e~~~p~l~~li~af~~~~y~~~~~~L~~~~~~l~~D~~L~~h~~~l~~ 132 (239)
.=..|=+|+.++..+.- .-+++-. . . .+.+...+.++..-...|+|..|-..+++. +.+-+|+.-|-+
T Consensus 66 aqILlKaL~~lP~tDF~l~kcli~~~-~-~-~ee~~r~ii~L~~~LEt~~Fq~FW~~~~~N-------~~mle~itGFed 135 (217)
T KOG3252|consen 66 AQILLKALTNLPHTDFTLAKCLIDER-V-Q-MEEPFRSIIDLGDYLETCRFQQFWQEADEN-------RDMLEGITGFED 135 (217)
T ss_pred HHHHHHHHhcCCCcchhHHHHhcCHH-H-h-cccchhHHHhHHHHHhhchHHHHhhhhccc-------hHHhcCCCcHHH
Confidence 33445667777665431 1122211 1 1 111134566666667899999998766665 444456666666
Q ss_pred HHHHHHHHHHhhhhhcccHHHHHHHhCC-CHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 133 EMRLRAYKQILQAYRSLSLKYMAQCFGV-SVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 133 ~ir~~~l~qyl~pYs~v~l~~mA~~fg~-s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
.+|.-+---.=-.|..|+=.-+|+.+|- +..++|.|+.+ .|=+-..+|.+.+
T Consensus 136 svr~yachvv~iTyQkI~k~lLaellG~~sDs~le~~~~~-------~GW~a~e~G~ifv 188 (217)
T KOG3252|consen 136 SVRKYACHVVGITYQKIDKWLLAELLGGLSDSQLEVWMTK-------YGWIADESGQIFV 188 (217)
T ss_pred HHHHHHHHheechHhhchHHHHHHhhCcccHHHHHHHHHH-------ccceecCCceEEE
Confidence 6654442222234888888889999975 55688888887 6767777777766
No 124
>smart00351 PAX Paired Box domain.
Probab=57.92 E-value=33 Score=26.71 Aligned_cols=46 Identities=17% Similarity=0.195 Sum_probs=36.9
Q ss_pred HHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccce
Q psy396 132 QEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQC 180 (239)
Q Consensus 132 ~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~a 180 (239)
...|.+++.-|- .-.+...+|+.||+|...+.+|+.++-.+|.+..
T Consensus 20 ~~~R~riv~~~~---~G~s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~p 65 (125)
T smart00351 20 DEERQRIVELAQ---NGVRPCDISRQLCVSHGCVSKILGRYYETGSIRP 65 (125)
T ss_pred HHHHHHHHHHHH---cCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCC
Confidence 346777765553 4568899999999999999999999999887644
No 125
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=57.92 E-value=51 Score=26.61 Aligned_cols=41 Identities=22% Similarity=0.302 Sum_probs=34.6
Q ss_pred hcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCC
Q psy396 147 RSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAG 187 (239)
Q Consensus 147 s~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~ 187 (239)
..++++.||+..|+|..++++-+..|...|-+...=-..-|
T Consensus 23 ~~~s~~eIA~~~~is~~~L~kIl~~L~~aGlv~S~rG~~GG 63 (153)
T PRK11920 23 KLSRIPEIARAYGVSELFLFKILQPLVEAGLVETVRGRNGG 63 (153)
T ss_pred CcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeecCCCCC
Confidence 45899999999999999999999999999988655544444
No 126
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=57.77 E-value=22 Score=25.74 Aligned_cols=35 Identities=17% Similarity=0.303 Sum_probs=25.6
Q ss_pred HHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHH
Q psy396 138 AYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARF 172 (239)
Q Consensus 138 ~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~l 172 (239)
.+.+.+.-=..|+...+|.+.|+|++++...|..+
T Consensus 28 ~LLr~LA~G~PVt~~~LA~a~g~~~e~v~~~L~~~ 62 (77)
T PF12324_consen 28 PLLRLLAKGQPVTVEQLAAALGWPVEEVRAALAAM 62 (77)
T ss_dssp HHHHHHTTTS-B-HHHHHHHHT--HHHHHHHHHH-
T ss_pred HHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHhC
Confidence 35566666788999999999999999999999886
No 127
>PF09418 DUF2009: Protein of unknown function (DUF2009); InterPro: IPR018553 This is a eukaryotic family of proteins with unknown function.
Probab=57.72 E-value=22 Score=34.06 Aligned_cols=44 Identities=23% Similarity=0.323 Sum_probs=30.9
Q ss_pred HchhcCHHHHHHHHhccCCCCCCccccCHhHH-HHHHHHHHHHcC
Q psy396 22 CLAIRQYCRAAELFVDVVPTFESYELAEFGTI-IRYTVLACMIAL 65 (239)
Q Consensus 22 ~l~~~~y~~Aa~~F~~~~~~f~~~e~~s~~di-~~Y~~Lc~Las~ 65 (239)
.+..++|..-+..|-++|+-..-|.++.|+.. --|+=|+=|+--
T Consensus 72 L~~~kdf~~n~~ffQ~vFEIgRRYKIMNPekMRttYGKLmYmLQD 116 (458)
T PF09418_consen 72 LLEDKDFSDNAEFFQDVFEIGRRYKIMNPEKMRTTYGKLMYMLQD 116 (458)
T ss_pred HhcCCChHHHHHHHHHHHHHHHHHhhhCHHHHHHHHHHHHHHHHh
Confidence 44567888888888888554455678888876 578777766543
No 128
>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=57.59 E-value=38 Score=21.30 Aligned_cols=29 Identities=14% Similarity=0.200 Sum_probs=25.1
Q ss_pred hhcccHHHHHHHhCCCHHHHHHHHHHHHH
Q psy396 146 YRSLSLKYMAQCFGVSVEFIEKEVARFAA 174 (239)
Q Consensus 146 Ys~v~l~~mA~~fg~s~~~lE~~L~~lI~ 174 (239)
+.-.+...+|+.+|+|...+...+.++..
T Consensus 13 ~~~~s~~eia~~l~~s~~tv~~~~~~~~~ 41 (57)
T cd06170 13 AEGKTNKEIADILGISEKTVKTHLRNIMR 41 (57)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 35679999999999999999999887654
No 129
>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=57.12 E-value=26 Score=20.98 Aligned_cols=30 Identities=13% Similarity=0.370 Sum_probs=23.7
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHHHHcCcc
Q psy396 149 LSLKYMAQCFGVSVEFIEKEVARFAAAGRL 178 (239)
Q Consensus 149 v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l 178 (239)
++-+.||..+|++.+.+-..|.+|-.+|-|
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 456789999999999999999999887743
No 130
>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=57.08 E-value=41 Score=26.32 Aligned_cols=41 Identities=20% Similarity=0.365 Sum_probs=34.2
Q ss_pred hcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCC
Q psy396 147 RSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAG 187 (239)
Q Consensus 147 s~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~ 187 (239)
..++.+.||+.+++|..++++-+.+|-..|-+..+=....|
T Consensus 24 ~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s~~G~~Gg 64 (135)
T TIGR02010 24 GPVTLADISERQGISLSYLEQLFAKLRKAGLVKSVRGPGGG 64 (135)
T ss_pred CcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEeCCCCC
Confidence 35999999999999999999999999999988654333334
No 131
>PLN03083 E3 UFM1-protein ligase 1 homolog; Provisional
Probab=56.94 E-value=72 Score=32.90 Aligned_cols=60 Identities=17% Similarity=0.277 Sum_probs=47.6
Q ss_pred hHhHHHHHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 124 NPHYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 124 ~~h~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
..+++.+.++|-++ ++--..|+|..+|+.|++|.+++.+.|..- +.+.|+|++ ..++|++
T Consensus 115 ~~Yld~iaeEIne~-----LqE~G~isI~eLa~~~~Lpsefl~~~l~~r-lG~iI~g~~--~g~~lyT 174 (803)
T PLN03083 115 QSYWDSIAEEINER-----LQECSQIALAELARQLQVGSELVTSMLEPR-LGTIVKARL--EGGQLYT 174 (803)
T ss_pred hHHHHHHHHHHHHH-----HHHcCcChHHHHHHhcCChHHHHHHHHHHH-hccceEEEe--cCCEEec
Confidence 45667777766544 455689999999999999999999999887 557889998 4677777
No 132
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=56.80 E-value=17 Score=27.96 Aligned_cols=40 Identities=20% Similarity=0.295 Sum_probs=34.5
Q ss_pred HHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHc
Q psy396 136 LRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAA 175 (239)
Q Consensus 136 ~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~ 175 (239)
...+.++++-+..+++..+|+.||++...|-..|-++=.+
T Consensus 59 ~~~L~~~v~~~pd~tl~Ela~~l~Vs~~ti~~~Lkrlg~t 98 (119)
T PF01710_consen 59 RDELKALVEENPDATLRELAERLGVSPSTIWRALKRLGIT 98 (119)
T ss_pred HHHHHHHHHHCCCcCHHHHHHHcCCCHHHHHHHHHHcCch
Confidence 3557889999999999999999999999999988876444
No 133
>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=56.54 E-value=1.4e+02 Score=26.21 Aligned_cols=32 Identities=28% Similarity=0.360 Sum_probs=28.8
Q ss_pred cccHHHHHHHhCCCHHHHHHHHH-HHHHcCccc
Q psy396 148 SLSLKYMAQCFGVSVEFIEKEVA-RFAAAGRLQ 179 (239)
Q Consensus 148 ~v~l~~mA~~fg~s~~~lE~~L~-~lI~~g~l~ 179 (239)
.++++.+|+.+|+++..++..+. .||..|-|.
T Consensus 255 ~~~~~~ia~~lg~~~~~~~~~~e~~Li~~~li~ 287 (305)
T TIGR00635 255 PVGLKTLAAALGEDADTIEDVYEPYLLQIGFLQ 287 (305)
T ss_pred cccHHHHHHHhCCCcchHHHhhhHHHHHcCCcc
Confidence 48899999999999999999999 699988873
No 134
>PRK06771 hypothetical protein; Provisional
Probab=56.37 E-value=8.2 Score=28.96 Aligned_cols=31 Identities=16% Similarity=0.310 Sum_probs=26.7
Q ss_pred cccHHHHHHHhCCCHH--HHHHHHHHHHHcCcc
Q psy396 148 SLSLKYMAQCFGVSVE--FIEKEVARFAAAGRL 178 (239)
Q Consensus 148 ~v~l~~mA~~fg~s~~--~lE~~L~~lI~~g~l 178 (239)
...++.+++.+|++.. .+.+++.+|+.+|+=
T Consensus 36 e~~L~~I~~~~Gi~~~~~~~~~e~~~Li~~Gkk 68 (93)
T PRK06771 36 EDRLQLITKEMGIVDREPPVNKELRQLMEEGQT 68 (93)
T ss_pred HHHHHHHHHHcCCCCCcccccHHHHHHHHcCCc
Confidence 4578999999999877 788999999999863
No 135
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=56.23 E-value=37 Score=25.06 Aligned_cols=31 Identities=32% Similarity=0.326 Sum_probs=27.9
Q ss_pred cccHHHHHHHhCCCHHHHHHHHHHHHHcCcc
Q psy396 148 SLSLKYMAQCFGVSVEFIEKEVARFAAAGRL 178 (239)
Q Consensus 148 ~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l 178 (239)
-.++...|+.||+|...+.+|+.++-.+|.-
T Consensus 25 g~~~a~aA~~~gVS~~Ta~kW~~Ryra~G~~ 55 (85)
T PF13011_consen 25 GWPVAHAAAEFGVSRRTAYKWLARYRAEGEA 55 (85)
T ss_pred CCcHHHHHHHhCCCHHHHHHHHHHHHHcCcc
Confidence 5678999999999999999999999988753
No 136
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=55.59 E-value=99 Score=24.23 Aligned_cols=49 Identities=12% Similarity=0.106 Sum_probs=37.8
Q ss_pred HHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 140 KQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 140 ~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
..+++....++++.+|+.+|++...+-..|.+|...|-|.-+ ..+.+..
T Consensus 14 ~~l~~~~~~~~~~ela~~l~vs~~svs~~l~~L~~~Gli~~~---~~~~i~L 62 (142)
T PRK03902 14 YLLIEEKGYARVSDIAEALSVHPSSVTKMVQKLDKDEYLIYE---KYRGLVL 62 (142)
T ss_pred HHHHhcCCCcCHHHHHHHhCCChhHHHHHHHHHHHCCCEEEe---cCceEEE
Confidence 334455566789999999999999999999999999987532 1244555
No 137
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=55.53 E-value=28 Score=30.07 Aligned_cols=63 Identities=19% Similarity=0.251 Sum_probs=55.2
Q ss_pred HHHHHHHHHHHHHHHHhhhhhcc-cHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 127 YRHYVQEMRLRAYKQILQAYRSL-SLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 127 ~~~l~~~ir~~~l~qyl~pYs~v-~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
.+.+++.|+..++..=+.|=..+ +-..+|+.||+|-.-|-+-|..|-..|-+..+ +..|+.+.
T Consensus 4 ~~~v~~~L~~~I~~g~l~pG~~LpsE~eLae~~gVSRtpVREAL~~Le~~GlV~~~--~~~G~~V~ 67 (253)
T PRK10421 4 SDEVADRVRALIEEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSR--RGGGTFIR 67 (253)
T ss_pred HHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe--CCCeEEEe
Confidence 36789999999999999999999 68999999999999999999999999998754 44576666
No 138
>PF14502 HTH_41: Helix-turn-helix domain
Probab=55.39 E-value=27 Score=22.94 Aligned_cols=30 Identities=20% Similarity=0.361 Sum_probs=27.2
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHHHHcCccc
Q psy396 150 SLKYMAQCFGVSVEFIEKEVARFAAAGRLQ 179 (239)
Q Consensus 150 ~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~ 179 (239)
+++.+++.|+++...|+..|.-|-.+|-+.
T Consensus 8 tI~e~~~~~~vs~GtiQ~Alk~Le~~gaI~ 37 (48)
T PF14502_consen 8 TISEYSEKFGVSRGTIQNALKFLEENGAIK 37 (48)
T ss_pred CHHHHHHHhCcchhHHHHHHHHHHHCCcEE
Confidence 688999999999999999999998888764
No 139
>KOG1174|consensus
Probab=54.76 E-value=52 Score=31.65 Aligned_cols=118 Identities=14% Similarity=0.172 Sum_probs=65.4
Q ss_pred hhhhHHHHHHH--HchhcCHHHHHHHHhccCCCCCCccccCHhHHHHHHHHHHHHcCChhHHHHccccchhHHHHhhhh-
Q psy396 11 RNKLKAYEGVY--CLAIRQYCRAAELFVDVVPTFESYELAEFGTIIRYTVLACMIALPRYNLRKKLMHHGVMAQALHSQ- 87 (239)
Q Consensus 11 ~~kl~~~~Gl~--~l~~~~y~~Aa~~F~~~~~~f~~~e~~s~~di~~Y~~Lc~Las~~R~elk~~ll~s~~~~~~~e~~- 87 (239)
.-+|+||.||. ++..+.+++|--.=-++..+|.+ ++..+-..+ +...+.-...++ -.++|.+..
T Consensus 365 p~rL~~Y~GL~hsYLA~~~~kEA~~~An~~~~~~~~----sA~~LtL~g---~~V~~~dp~~rE------KAKkf~ek~L 431 (564)
T KOG1174|consen 365 PYRLEIYRGLFHSYLAQKRFKEANALANWTIRLFQN----SARSLTLFG---TLVLFPDPRMRE------KAKKFAEKSL 431 (564)
T ss_pred hhhHHHHHHHHHHHHhhchHHHHHHHHHHHHHHhhc----chhhhhhhc---ceeeccCchhHH------HHHHHHHhhh
Confidence 46899999995 66799999987555555444433 222222222 233332221211 133343321
Q ss_pred --hh----HHHHHHHH-HHhchHHHHHHHHHHHHhhhccCcchhHhHHHHHHH--HHHHHHHHH
Q psy396 88 --YR----DLREYFVS-LYDGHYFEFLKCLAAVEQDMKRDPLLNPHYRHYVQE--MRLRAYKQI 142 (239)
Q Consensus 88 --~p----~l~~li~a-f~~~~y~~~~~~L~~~~~~l~~D~~L~~h~~~l~~~--ir~~~l~qy 142 (239)
.| .+..+.+- -.+..|.+-...|..+-.. ..|..|+.|+..++.. .-+.++.+|
T Consensus 432 ~~~P~Y~~AV~~~AEL~~~Eg~~~D~i~LLe~~L~~-~~D~~LH~~Lgd~~~A~Ne~Q~am~~y 494 (564)
T KOG1174|consen 432 KINPIYTPAVNLIAELCQVEGPTKDIIKLLEKHLII-FPDVNLHNHLGDIMRAQNEPQKAMEYY 494 (564)
T ss_pred ccCCccHHHHHHHHHHHHhhCccchHHHHHHHHHhh-ccccHHHHHHHHHHHHhhhHHHHHHHH
Confidence 33 33333333 3478888888887776433 5678899998887753 344555555
No 140
>PRK00215 LexA repressor; Validated
Probab=54.45 E-value=33 Score=28.68 Aligned_cols=56 Identities=11% Similarity=0.165 Sum_probs=40.4
Q ss_pred HHHHHHHHhhhhh-----cccHHHHHHHhCC-CHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 135 RLRAYKQILQAYR-----SLSLKYMAQCFGV-SVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 135 r~~~l~qyl~pYs-----~v~l~~mA~~fg~-s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
+++.+++++.-|. ..++..||+.+|+ +...+-..|..|...|-|.-.-+. ...+..
T Consensus 5 ~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~~~g~i~~~~~~-~r~~~l 66 (205)
T PRK00215 5 RQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALERKGFIRRDPGR-SRAIEV 66 (205)
T ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEeCCCC-cceEEe
Confidence 3455555555442 4689999999999 999999999999999998544333 334444
No 141
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=54.23 E-value=37 Score=22.40 Aligned_cols=24 Identities=17% Similarity=0.409 Sum_probs=19.4
Q ss_pred hcccHHHHHHHhCCCHHHHHHHHH
Q psy396 147 RSLSLKYMAQCFGVSVEFIEKEVA 170 (239)
Q Consensus 147 s~v~l~~mA~~fg~s~~~lE~~L~ 170 (239)
..|+=..+|+.+|+++..|-+.++
T Consensus 27 ~~vSS~~La~~~gi~~~qVRKDlS 50 (50)
T PF06971_consen 27 ERVSSQELAEALGITPAQVRKDLS 50 (50)
T ss_dssp SEE-HHHHHHHHTS-HHHHHHHHH
T ss_pred eeECHHHHHHHHCCCHHHhcccCC
Confidence 578899999999999999988774
No 142
>PRK05472 redox-sensing transcriptional repressor Rex; Provisional
Probab=54.20 E-value=46 Score=28.13 Aligned_cols=49 Identities=22% Similarity=0.272 Sum_probs=40.8
Q ss_pred HHHHHHHHHHHHHHhhhhh--cccHHHHHHHhCCCHHHHHHHHHHHHHcCc
Q psy396 129 HYVQEMRLRAYKQILQAYR--SLSLKYMAQCFGVSVEFIEKEVARFAAAGR 177 (239)
Q Consensus 129 ~l~~~ir~~~l~qyl~pYs--~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~ 177 (239)
.+-+.=|...+.+++.... .|+.+.+|+.||+++..+-+.|..+=..|+
T Consensus 11 ~~~r~~~~~~il~~l~~~~~~~vs~~~L~~~~~v~~~tirrDl~~l~~~G~ 61 (213)
T PRK05472 11 TIKRLPLYYRYLKELKEEGVERVSSKELAEALGVDSAQIRKDLSYFGEFGK 61 (213)
T ss_pred HHHHhHHHHHHHHHHHHcCCcEEeHHHHHHHhCcCHHHHHHHHHHHHhcCC
Confidence 4446677788888999987 999999999999999999999988855553
No 143
>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]. It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel alpha-helices []. The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees; within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B. ; GO: 0005515 protein binding; PDB: 3SF4_C 2LNI_A 1ELW_A 2C0M_A 1FCH_B 3R9A_B 2J9Q_A 2C0L_A 1KT1_A 3FWV_A ....
Probab=54.03 E-value=20 Score=20.39 Aligned_cols=27 Identities=15% Similarity=0.161 Sum_probs=21.4
Q ss_pred hhHHHHHHHHchhcCHHHHHHHHhccC
Q psy396 13 KLKAYEGVYCLAIRQYCRAAELFVDVV 39 (239)
Q Consensus 13 kl~~~~Gl~~l~~~~y~~Aa~~F~~~~ 39 (239)
+.-.-.|..++..|+|.+|...|-.+.
T Consensus 2 ~~~~~~g~~~~~~~~~~~A~~~~~~al 28 (34)
T PF00515_consen 2 EAYYNLGNAYFQLGDYEEALEYYQRAL 28 (34)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhCCchHHHHHHHHHH
Confidence 344567899999999999999998774
No 144
>PF01476 LysM: LysM domain; InterPro: IPR018392 This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation []. This domain may have a general peptidoglycan binding function.; GO: 0016998 cell wall macromolecule catabolic process; PDB: 2DJP_A 3ZQD_A 1Y7M_B 4A52_A 2L9Y_A 1E0G_A.
Probab=53.39 E-value=15 Score=22.53 Aligned_cols=19 Identities=26% Similarity=0.399 Sum_probs=14.8
Q ss_pred cHHHHHHHhCCCHHHHHHH
Q psy396 150 SLKYMAQCFGVSVEFIEKE 168 (239)
Q Consensus 150 ~l~~mA~~fg~s~~~lE~~ 168 (239)
++..+|+.||++.+++.++
T Consensus 8 tl~~IA~~~~~~~~~l~~~ 26 (44)
T PF01476_consen 8 TLWSIAKRYGISVDELMEL 26 (44)
T ss_dssp -HHHHHHHTTS-HHHHHHH
T ss_pred cHHHHHhhhhhhHhHHHHh
Confidence 5788999999999988764
No 145
>PF08765 Mor: Mor transcription activator family; InterPro: IPR014875 Mor (Middle operon regulator) is a sequence specific DNA binding protein. It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N-terminal region of Mor is the dimerisation region, and the C-terminal contains a helix-turn-helix motif which binds DNA []. ; PDB: 1RR7_A.
Probab=53.37 E-value=78 Score=23.87 Aligned_cols=57 Identities=14% Similarity=0.305 Sum_probs=33.2
Q ss_pred HHhhhccCcchhHhHHHHHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHH
Q psy396 113 VEQDMKRDPLLNPHYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARF 172 (239)
Q Consensus 113 ~~~~l~~D~~L~~h~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~l 172 (239)
+...+....+--|....+...+|.+.|.+-+. --++..+|..+|+|...|-+-|.+.
T Consensus 40 L~~~~gG~~iyiP~~~~~~~~~R~~~I~~~f~---G~n~~eLA~kyglS~r~I~~Ii~~~ 96 (108)
T PF08765_consen 40 LCRYFGGQQIYIPKCDRLLRALRNREIRREFN---GMNVRELARKYGLSERQIYRIIKRV 96 (108)
T ss_dssp HHHHH-SS------SHHHHHHHHHHHHHHH-----SS-HHHHHHHHT--HHHHHHHHHHH
T ss_pred HHHHHCCEeEEeeCccHHHHHHHHHHHHHHhC---CCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 33444555555566677788888876665544 7789999999999998887777654
No 146
>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=52.39 E-value=46 Score=29.71 Aligned_cols=56 Identities=16% Similarity=0.269 Sum_probs=42.5
Q ss_pred HHHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecc
Q psy396 129 HYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDS 184 (239)
Q Consensus 129 ~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~ 184 (239)
.+....+.++---+...=+-++++.+.+.+|++...+-.-+.+||.+|++.|+|-.
T Consensus 173 ayv~r~ka~iRG~l~a~T~Pt~l~~l~~~~~~~~~l~~~il~~Li~~~~l~G~i~G 228 (272)
T PF09743_consen 173 AYVARQKARIRGALSAITRPTPLSSLLKRYGFEEKLFQSILEELIKSGELPGSIVG 228 (272)
T ss_pred HHHHHHHHHHHHHHhcCccceEHHHHHHHhCCcHHHHHHHHHHHHhcCcceEEEEC
Confidence 34444444333333333455899999999999999999999999999999999877
No 147
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=52.09 E-value=1.7e+02 Score=26.19 Aligned_cols=92 Identities=14% Similarity=0.100 Sum_probs=55.3
Q ss_pred hhHHHHHHHHHHhchHHHHHHHHHHHHhh--h-ccCcchhHhHHHHHHHH---------HHHHHHH-Hhhhh--hcccHH
Q psy396 88 YRDLREYFVSLYDGHYFEFLKCLAAVEQD--M-KRDPLLNPHYRHYVQEM---------RLRAYKQ-ILQAY--RSLSLK 152 (239)
Q Consensus 88 ~p~l~~li~af~~~~y~~~~~~L~~~~~~--l-~~D~~L~~h~~~l~~~i---------r~~~l~q-yl~pY--s~v~l~ 152 (239)
.|...+.+-....++.+.....|+..... . ........++....+.+ ..+.+.. ++..| ..++++
T Consensus 201 ~~~~~~~ia~~~~G~pR~a~~~l~~~~~~a~~~~~~~I~~~~v~~~l~~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~~~ 280 (328)
T PRK00080 201 DEEGALEIARRSRGTPRIANRLLRRVRDFAQVKGDGVITKEIADKALDMLGVDELGLDEMDRKYLRTIIEKFGGGPVGLD 280 (328)
T ss_pred CHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCcCCCCHHHHHHHHHHHHHcCCCceeHH
Confidence 34445555556666666665555543221 1 12334444444444433 2223332 44442 469999
Q ss_pred HHHHHhCCCHHHHHHHHH-HHHHcCccc
Q psy396 153 YMAQCFGVSVEFIEKEVA-RFAAAGRLQ 179 (239)
Q Consensus 153 ~mA~~fg~s~~~lE~~L~-~lI~~g~l~ 179 (239)
.+|..+|.+.+.+|+.+. .||..|-|.
T Consensus 281 ~~a~~lg~~~~~~~~~~e~~Li~~~li~ 308 (328)
T PRK00080 281 TLAAALGEERDTIEDVYEPYLIQQGFIQ 308 (328)
T ss_pred HHHHHHCCCcchHHHHhhHHHHHcCCcc
Confidence 999999999999999999 888888773
No 148
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=51.77 E-value=60 Score=26.15 Aligned_cols=47 Identities=19% Similarity=0.246 Sum_probs=38.6
Q ss_pred hhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 145 AYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 145 pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
+..-++++.+|+..|+|...+++-+..|-..|-+..+=-+.-|..-+
T Consensus 22 ~~~~~s~~~IA~~~~is~~~L~kil~~L~kaGlV~S~rG~~GGy~La 68 (150)
T COG1959 22 GGGPVSSAEIAERQGISPSYLEKILSKLRKAGLVKSVRGKGGGYRLA 68 (150)
T ss_pred CCCcccHHHHHHHhCcCHHHHHHHHHHHHHcCCEEeecCCCCCccCC
Confidence 44468999999999999999999999999999887766655554444
No 149
>PHA02943 hypothetical protein; Provisional
Probab=51.67 E-value=42 Score=27.64 Aligned_cols=44 Identities=20% Similarity=0.240 Sum_probs=37.5
Q ss_pred HHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccc
Q psy396 135 RLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQ 179 (239)
Q Consensus 135 r~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~ 179 (239)
|..-+..|+ ..-..+.+.+|+++|+|..+++--|--|=.+|++.
T Consensus 12 R~~eILE~L-k~G~~TtseIAkaLGlS~~qa~~~LyvLErEG~Vk 55 (165)
T PHA02943 12 RMIKTLRLL-ADGCKTTSRIANKLGVSHSMARNALYQLAKEGMVL 55 (165)
T ss_pred HHHHHHHHH-hcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCceE
Confidence 334466777 66788899999999999999999999999999984
No 150
>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial. This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.
Probab=51.13 E-value=33 Score=29.15 Aligned_cols=62 Identities=16% Similarity=0.200 Sum_probs=50.2
Q ss_pred HHHHHHHHHHHHHHHhhhhhcc-cHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 128 RHYVQEMRLRAYKQILQAYRSL-SLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 128 ~~l~~~ir~~~l~qyl~pYs~v-~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
..+.+.|+.++...-+.|=..+ +-..+|+.||+|-..|-+.|..|..+|.|.-+ +..|+.+.
T Consensus 4 ~qi~~~l~~~I~~g~~~~g~~LPsE~eLa~~~~VSR~TVR~Al~~L~~eGli~r~--~G~GtfV~ 66 (230)
T TIGR02018 4 QRIKQDILERIRSGEWPPGHRIPSEHELVAQYGCSRMTVNRALRELTDAGLLERR--QGVGTFVA 66 (230)
T ss_pred HHHHHHHHHHHHhCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe--cCCEEEEc
Confidence 4566777777777777888888 88899999999999999999999999988432 34566665
No 151
>KOG1586|consensus
Probab=51.13 E-value=1.3e+02 Score=26.82 Aligned_cols=109 Identities=9% Similarity=0.123 Sum_probs=71.8
Q ss_pred HHHHchhcCHHHHHHHHhccCC-CCCCc-cccCHhHHHHHHHHHHHHcCChhHHHHccccchhHHHHhhhhhh-------
Q psy396 19 GVYCLAIRQYCRAAELFVDVVP-TFESY-ELAEFGTIIRYTVLACMIALPRYNLRKKLMHHGVMAQALHSQYR------- 89 (239)
Q Consensus 19 Gl~~l~~~~y~~Aa~~F~~~~~-~f~~~-e~~s~~di~~Y~~Lc~Las~~R~elk~~ll~s~~~~~~~e~~~p------- 89 (239)
+-+....++|.+|-..|-++.. +.++. --.+..|-..=.+||=|..-+--..+. .+.+|.+. .|
T Consensus 161 A~yaa~leqY~~Ai~iyeqva~~s~~n~LLKys~KdyflkAgLChl~~~D~v~a~~------ALeky~~~-dP~F~dsRE 233 (288)
T KOG1586|consen 161 AQYAAQLEQYSKAIDIYEQVARSSLDNNLLKYSAKDYFLKAGLCHLCKADEVNAQR------ALEKYQEL-DPAFTDSRE 233 (288)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhccchHHHhHHHHHHHHHHHHhHhcccHHHHHH------HHHHHHhc-CCcccccHH
Confidence 3445556788888887777632 23332 112555666667788887544322222 23445444 44
Q ss_pred --HHHHHHHHHHhchHHHHHHHHHHHHhhhccCcchhHhHHHHHHHH
Q psy396 90 --DLREYFVSLYDGHYFEFLKCLAAVEQDMKRDPLLNPHYRHYVQEM 134 (239)
Q Consensus 90 --~l~~li~af~~~~y~~~~~~L~~~~~~l~~D~~L~~h~~~l~~~i 134 (239)
-+++|+.+..+.+-..|-+...++.+.-.+|-+.-.++-.+-+.|
T Consensus 234 ckflk~L~~aieE~d~e~fte~vkefDsisrLD~W~ttiLlkiK~si 280 (288)
T KOG1586|consen 234 CKFLKDLLDAIEEQDIEKFTEVVKEFDSISRLDQWKTTILLKIKKSI 280 (288)
T ss_pred HHHHHHHHHHHhhhhHHHHHHHHHhhhccchHHHHHHHHHHHHHHHH
Confidence 388899999999999999999999888888888877766555544
No 152
>PF13181 TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_C 2KCV_A 2KCL_A 3FP3_A 3LCA_A 3FP4_A 3FP2_A 1W3B_B 1ELW_A ....
Probab=50.68 E-value=25 Score=19.89 Aligned_cols=27 Identities=19% Similarity=0.155 Sum_probs=22.4
Q ss_pred hhHHHHHHHHchhcCHHHHHHHHhccC
Q psy396 13 KLKAYEGVYCLAIRQYCRAAELFVDVV 39 (239)
Q Consensus 13 kl~~~~Gl~~l~~~~y~~Aa~~F~~~~ 39 (239)
++-...|..+...|+|++|..+|-++.
T Consensus 2 ~~~~~lg~~y~~~~~~~~A~~~~~~a~ 28 (34)
T PF13181_consen 2 EAYYNLGKIYEQLGDYEEALEYFEKAL 28 (34)
T ss_dssp HHHHHHHHHHHHTTSHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence 345667889999999999999998763
No 153
>KOG1125|consensus
Probab=50.49 E-value=28 Score=34.27 Aligned_cols=52 Identities=15% Similarity=0.271 Sum_probs=35.6
Q ss_pred HHHHHchhcCHHHHHHHHhccCC----CCCCccccCH-hHHHHHHHHHHHHcCChhHH
Q psy396 18 EGVYCLAIRQYCRAAELFVDVVP----TFESYELAEF-GTIIRYTVLACMIALPRYNL 70 (239)
Q Consensus 18 ~Gl~~l~~~~y~~Aa~~F~~~~~----~f~~~e~~s~-~di~~Y~~Lc~Las~~R~el 70 (239)
-|+.+|-.|.|++|+.+|++++. +.++-+..-+ +.+--++= .+|.+++|.++
T Consensus 504 lgIS~mNlG~ykEA~~hlL~AL~mq~ks~~~~~~~~~se~iw~tLR-~als~~~~~D~ 560 (579)
T KOG1125|consen 504 LGISCMNLGAYKEAVKHLLEALSMQRKSRNHNKAPMASENIWQTLR-LALSAMNRSDL 560 (579)
T ss_pred hhhhhhhhhhHHHHHHHHHHHHHhhhcccccccCCcchHHHHHHHH-HHHHHcCCchH
Confidence 48999999999999999999963 2322233222 33433333 77888888874
No 154
>PF08672 APC2: Anaphase promoting complex (APC) subunit 2; InterPro: IPR014786 The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome. Anaphase is initiated when the APC triggers the destruction of securin, thereby allowing the protease, separase, to disrupt sister-chromatid cohesion. Securin ubiquitination by the APC is inhibited by cyclin-dependent kinase 1 (Cdk1)-dependent phosphorylation []. Forkhead Box M1 (FoxM1), which is a transcription factor that is over-expressed in many cancers, is degraded in late mitosis and early G1 phase by the APC/cyclosome (APC/C) E3 ubiquitin ligase []. The APC/C targets mitotic cyclins for destruction in mitosis and G1 phase and is then inactivated at S phase. It thereby generates alternating states of high and low cyclin-Cdk activity, which is required for the alternation of mitosis and DNA replication []. The APC/C is composed of at least 13 subunits that stay tightly associated throughout the cell cycle: APC1, APC2, APC4, APC5, APC9, APC11, CDC16, CDC23, CDC26, CDC27, DOC1, MND2 and SWM1[], []. In fission yeast the 13 subunits are known as: Apc1, Apc2, Nuc2, Apc4, Apc5, Cut9, Apc8, Apc10, Apc11, Hcn1, Apc13, Apc14 and Apc15 []. This entry represents a C-terminal domain found in APC subunit 2. ; PDB: 1LDD_A.
Probab=50.23 E-value=45 Score=22.77 Aligned_cols=24 Identities=25% Similarity=0.677 Sum_probs=18.3
Q ss_pred hCCCHHHHHHHHHHHHHcCcccee
Q psy396 158 FGVSVEFIEKEVARFAAAGRLQCK 181 (239)
Q Consensus 158 fg~s~~~lE~~L~~lI~~g~l~ar 181 (239)
++++.++++..|.+++.+|+|.+.
T Consensus 31 ~~~s~~eL~~fL~~lv~e~~L~~~ 54 (60)
T PF08672_consen 31 YDISLEELQEFLDRLVEEGKLECS 54 (60)
T ss_dssp TT--HHHHHHHHHHHHHTTSEE--
T ss_pred CCCCHHHHHHHHHHHHHCCcEEec
Confidence 467899999999999999999764
No 155
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=50.04 E-value=1e+02 Score=26.00 Aligned_cols=40 Identities=13% Similarity=0.338 Sum_probs=32.3
Q ss_pred cccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccC-CEEEE
Q psy396 148 SLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVA-GNVVT 191 (239)
Q Consensus 148 ~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~-~~l~~ 191 (239)
.++-..+|..+|++.+.+-+.|.+|-.+|-| +... +.|++
T Consensus 179 ~lt~~~IA~~lGisretlsR~L~~L~~~GlI----~~~~~~~i~I 219 (230)
T PRK09391 179 PMSRRDIADYLGLTIETVSRALSQLQDRGLI----GLSGARQIEL 219 (230)
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHHCCcE----EecCCceEEE
Confidence 4667899999999999999999999997766 3333 56666
No 156
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=49.96 E-value=76 Score=21.27 Aligned_cols=42 Identities=21% Similarity=0.445 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHHHhhhhhcccHHHHHHHhCC-CHHHHHHHHHH
Q psy396 129 HYVQEMRLRAYKQILQAYRSLSLKYMAQCFGV-SVEFIEKEVAR 171 (239)
Q Consensus 129 ~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~-s~~~lE~~L~~ 171 (239)
.+....|......++... .+++..+|..+|+ +...+.+...+
T Consensus 32 ~~~~~~r~~~a~~~l~~~-~~~~~~ia~~~g~~s~~~f~r~Fk~ 74 (84)
T smart00342 32 QYLRDRRLERARRLLRDT-DLSVTEIALRVGFSSQSYFSRAFKK 74 (84)
T ss_pred HHHHHHHHHHHHHHHHcC-CCCHHHHHHHhCCCChHHHHHHHHH
Confidence 344555666667777664 8999999999999 88777666554
No 157
>PRK14999 histidine utilization repressor; Provisional
Probab=49.86 E-value=38 Score=29.05 Aligned_cols=63 Identities=17% Similarity=0.209 Sum_probs=52.3
Q ss_pred HHHHHHHHHHHHHHHHhhhhhcc-cHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 127 YRHYVQEMRLRAYKQILQAYRSL-SLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 127 ~~~l~~~ir~~~l~qyl~pYs~v-~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
...+.+.|+.++...-+.|=..+ +=..+|+.||+|-..|-+.|..|..+|.|.-+ +..|+.+.
T Consensus 14 y~qi~~~i~~~I~~g~~~~G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~--~GkGTfV~ 77 (241)
T PRK14999 14 YETVKQDICKKIAGGVWQPHDRIPSEAELVAQYGFSRMTINRALRELTDEGWLVRL--QGVGTFVA 77 (241)
T ss_pred HHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe--cCcEEEEC
Confidence 45677788888877788888888 88999999999999999999999999988432 44577766
No 158
>cd00131 PAX Paired Box domain
Probab=49.65 E-value=55 Score=25.62 Aligned_cols=45 Identities=18% Similarity=0.237 Sum_probs=37.7
Q ss_pred HHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccce
Q psy396 133 EMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQC 180 (239)
Q Consensus 133 ~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~a 180 (239)
..|.+++.-| + .-.+...+|+.||+|...|.+|+.++-.+|.+..
T Consensus 21 d~R~rIv~~~-~--~G~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~p 65 (128)
T cd00131 21 SIRQRIVELA-Q--SGIRPCDISRQLRVSHGCVSKILNRYYETGSIRP 65 (128)
T ss_pred HHHHHHHHHH-H--cCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCC
Confidence 4677777554 2 5678999999999999999999999999998754
No 159
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=49.50 E-value=1.4e+02 Score=24.94 Aligned_cols=40 Identities=20% Similarity=0.374 Sum_probs=32.5
Q ss_pred cccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 148 SLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 148 ~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
.++-+.+|+.+|++.+.+-+.+.+|-.+|.|. ...+.+.+
T Consensus 184 ~lt~~~iA~~lG~sr~tvsR~l~~l~~~g~I~----~~~~~i~i 223 (235)
T PRK11161 184 TMTRGDIGNYLGLTVETISRLLGRFQKSGMLA----VKGKYITI 223 (235)
T ss_pred cccHHHHHHHhCCcHHHHHHHHHHHHHCCCEE----ecCCEEEE
Confidence 36778999999999999999999999977664 44456666
No 160
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=49.50 E-value=94 Score=22.18 Aligned_cols=50 Identities=14% Similarity=0.215 Sum_probs=41.2
Q ss_pred HHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCC
Q psy396 138 AYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAG 187 (239)
Q Consensus 138 ~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~ 187 (239)
.+..++..-..++.+.+.+.+|++...+-+-|..|...|-+..+-....+
T Consensus 4 ~Il~~L~~~~~~~f~~L~~~l~lt~g~Ls~hL~~Le~~GyV~~~k~~~~~ 53 (80)
T PF13601_consen 4 AILALLYANEEATFSELKEELGLTDGNLSKHLKKLEEAGYVEVEKEFEGR 53 (80)
T ss_dssp HHHHHHHHHSEEEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEE-SSS
T ss_pred HHHHHHhhcCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEEEeccCC
Confidence 35677777899999999999999999999999999999999887666655
No 161
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=49.26 E-value=40 Score=28.92 Aligned_cols=63 Identities=19% Similarity=0.264 Sum_probs=51.9
Q ss_pred HHHHHHHHHHHHHHHHhhhhhcc-cHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 127 YRHYVQEMRLRAYKQILQAYRSL-SLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 127 ~~~l~~~ir~~~l~qyl~pYs~v-~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
...+.+.|+.++...-+.|=..+ +=..+|+.||+|-..|-+.|..|..+|.|.-+ +..|+.+.
T Consensus 7 y~qi~~~L~~~I~~g~~~~G~~LPsE~eL~~~~~VSR~TvR~Al~~L~~eGli~r~--~G~GtfV~ 70 (240)
T PRK09764 7 YRQIADRIREQIARGELKPGDALPTESALQTEFGVSRVTVRQALRQLVEQQILESI--QGSGTYVK 70 (240)
T ss_pred HHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe--cCceeEEc
Confidence 35677788888888888888888 67999999999999999999999999988543 34566666
No 162
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=49.24 E-value=69 Score=24.64 Aligned_cols=35 Identities=20% Similarity=0.276 Sum_probs=32.2
Q ss_pred hcccHHHHHHHhCCCHHHHHHHHHHHHHcCcccee
Q psy396 147 RSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCK 181 (239)
Q Consensus 147 s~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~ar 181 (239)
..++...||+.+|+|...+.+-|..|...|-+...
T Consensus 24 ~~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~~ 58 (130)
T TIGR02944 24 QPYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTSK 58 (130)
T ss_pred CCccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEec
Confidence 46899999999999999999999999999988664
No 163
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=48.07 E-value=22 Score=23.24 Aligned_cols=24 Identities=21% Similarity=0.310 Sum_probs=19.5
Q ss_pred cccHHHHHHHhCCCHHHHHHHHHH
Q psy396 148 SLSLKYMAQCFGVSVEFIEKEVAR 171 (239)
Q Consensus 148 ~v~l~~mA~~fg~s~~~lE~~L~~ 171 (239)
.+++..+|+.+|+|+.++-+.|.+
T Consensus 3 ~i~V~elAk~l~v~~~~ii~~l~~ 26 (54)
T PF04760_consen 3 KIRVSELAKELGVPSKEIIKKLFK 26 (54)
T ss_dssp EE-TTHHHHHHSSSHHHHHHHH-H
T ss_pred ceEHHHHHHHHCcCHHHHHHHHHH
Confidence 578899999999999998888843
No 164
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=47.73 E-value=81 Score=27.23 Aligned_cols=52 Identities=12% Similarity=0.070 Sum_probs=44.4
Q ss_pred HHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 140 KQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 140 ~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
...+.-...++.+.+|+.+|+|...+-+.|.+|-..|-+.-+.+.....+..
T Consensus 13 lg~l~~~~~IS~~eLA~~L~iS~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~L 64 (217)
T PRK14165 13 LGAVNNTVKISSSEFANHTGTSSKTAARILKQLEDEGYITRTIVPRGQLITI 64 (217)
T ss_pred HhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEEcCCceEEEE
Confidence 3444445678999999999999999999999999999999888887777777
No 165
>TIGR00153 conserved hypothetical protein TIGR00153. An apparent homolog with a suggested function is Pit accessory protein from Sinorhizobium meliloti, which may be involved in phosphate (Pi) transport.
Probab=47.62 E-value=1.7e+02 Score=24.66 Aligned_cols=80 Identities=14% Similarity=0.089 Sum_probs=63.8
Q ss_pred hhHHHHHHHHHHhchHHHHHHHHHHHHhhhccCcchhHhHHHHHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHH
Q psy396 88 YRDLREYFVSLYDGHYFEFLKCLAAVEQDMKRDPLLNPHYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEK 167 (239)
Q Consensus 88 ~p~l~~li~af~~~~y~~~~~~L~~~~~~l~~D~~L~~h~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~ 167 (239)
...+.+++++|.++++..+.+.+.++.. +-+..+.+.++++......++-|+.+=+|-.+++...-=.+.++.
T Consensus 27 ~~~L~~~~~~~~~~~~~~~~~~~~~I~~-------lE~eaD~i~~~i~~~L~~~fitP~dReDi~~L~~~lD~I~D~i~~ 99 (216)
T TIGR00153 27 VQLLIKSFELLKSGNNEKDEELRKEIIE-------IEHEADEIKREIRLNLEKGAFLPNDRRDLLELAELLDEILDSLEH 99 (216)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHHH-------HHHHHHHHHHHHHHhCcccccCcCcHHHHHHHHHHHHHHHHHHHH
Confidence 3457788888888888887766666533 245678999999999999999999999999999998877777777
Q ss_pred HHHHHHH
Q psy396 168 EVARFAA 174 (239)
Q Consensus 168 ~L~~lI~ 174 (239)
-...+..
T Consensus 100 ~a~~l~l 106 (216)
T TIGR00153 100 AAMLYEL 106 (216)
T ss_pred HHHHHhc
Confidence 7766654
No 166
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=47.60 E-value=91 Score=25.33 Aligned_cols=47 Identities=11% Similarity=0.085 Sum_probs=35.3
Q ss_pred hhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 144 QAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 144 ~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
+||+..+|..--+. +++-..+.+.|-.|..+|+|.+|.=.-..+-..
T Consensus 15 RPys~~di~~nL~~-~~~K~~v~k~Ld~L~~~g~i~~K~~GKqkiY~~ 61 (169)
T PF07106_consen 15 RPYSAQDIFDNLHN-KVGKTAVQKALDSLVEEGKIVEKEYGKQKIYFA 61 (169)
T ss_pred CCCcHHHHHHHHHh-hccHHHHHHHHHHHHhCCCeeeeeecceEEEee
Confidence 68888876544333 688899999999999999999996444444444
No 167
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=47.53 E-value=1.3e+02 Score=23.29 Aligned_cols=63 Identities=14% Similarity=0.083 Sum_probs=49.1
Q ss_pred HHHHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 128 RHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 128 ~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
..|-+..|.+++...... ..++...+|+.||+|...+-+-|..|-..|-+..+-+...-....
T Consensus 11 kaLadptRl~IL~~L~~~-~~~~v~ela~~l~lsqstvS~HL~~L~~AGLV~~~r~Gr~~~Y~l 73 (117)
T PRK10141 11 KILSDETRLGIVLLLRES-GELCVCDLCTALDQSQPKISRHLALLRESGLLLDRKQGKWVHYRL 73 (117)
T ss_pred HHhCCHHHHHHHHHHHHc-CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEEEcCEEEEEE
Confidence 455566677776655542 468899999999999999999999999999998887766544444
No 168
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=47.46 E-value=46 Score=29.43 Aligned_cols=47 Identities=13% Similarity=0.293 Sum_probs=37.5
Q ss_pred HHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccce
Q psy396 134 MRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQC 180 (239)
Q Consensus 134 ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~a 180 (239)
.|.+++..+..-.-.+.-+.+|+.+|+++..+-..+.+|+.+|-++-
T Consensus 11 t~fqIL~ei~~~qp~v~q~eIA~~lgiT~QaVsehiK~Lv~eG~i~~ 57 (260)
T COG1497 11 TRFQILSEIAVRQPRVKQKEIAKKLGITLQAVSEHIKELVKEGLIEK 57 (260)
T ss_pred hHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHHHhccceee
Confidence 34455555544446899999999999999999999999999887643
No 169
>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=47.19 E-value=48 Score=21.22 Aligned_cols=45 Identities=13% Similarity=0.200 Sum_probs=27.5
Q ss_pred hHHHHHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHH
Q psy396 126 HYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFA 173 (239)
Q Consensus 126 h~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI 173 (239)
++..+=+.-|.-....|+ ...+...+|+.+|+|+..+...+.+-.
T Consensus 7 ~l~~L~~~~r~i~~l~~~---~g~s~~eIa~~l~~s~~~v~~~l~ra~ 51 (54)
T PF08281_consen 7 ALAQLPERQREIFLLRYF---QGMSYAEIAEILGISESTVKRRLRRAR 51 (54)
T ss_dssp HHHCS-HHHHHHHHHHHT---S---HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred HHHCCCHHHHHHHHHHHH---HCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 333444444444444554 456788999999999999999987643
No 170
>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=45.46 E-value=53 Score=20.28 Aligned_cols=27 Identities=22% Similarity=0.180 Sum_probs=21.7
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHHHHcCccce
Q psy396 150 SLKYMAQCFGVSVEFIEKEVARFAAAGRLQC 180 (239)
Q Consensus 150 ~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~a 180 (239)
+++.+|+.+|+++..+..| +..|.+.+
T Consensus 2 ~~~e~a~~~gv~~~tlr~~----~~~g~l~~ 28 (49)
T cd04761 2 TIGELAKLTGVSPSTLRYY----ERIGLLSP 28 (49)
T ss_pred cHHHHHHHHCcCHHHHHHH----HHCCCCCC
Confidence 6789999999999987777 55677764
No 171
>TIGR02675 tape_meas_nterm tape measure domain. Proteins containing this domain are strictly bacterial, including bacteriophage and prophage regions of bacterial genomes. Most members are 800 to 1800 amino acids long, making them among the longest predicted proteins of their respective phage genomes, where they are encoded in tail protein regions. This roughly 80-residue domain described here usually begins between residue 100 and 250. Many members are known or predicted to act as phage tail tape measure proteins, a minor tail component that regulates tail length.
Probab=45.30 E-value=29 Score=24.67 Aligned_cols=27 Identities=26% Similarity=0.549 Sum_probs=21.7
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHHHHcCccce
Q psy396 150 SLKYMAQCFGVSVEFIEKEVARFAAAGRLQC 180 (239)
Q Consensus 150 ~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~a 180 (239)
-+..+|+.+|++.+ +|.+|+.+|+|.+
T Consensus 46 ~~~~lAk~~G~t~~----~l~~~~~~Gkit~ 72 (75)
T TIGR02675 46 ALQALAKAMGVTRG----ELRKMLSDGKLTA 72 (75)
T ss_pred HHHHHHHHhCCCHH----HHHHHHHCCCCcc
Confidence 35688999999976 5678889999865
No 172
>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=45.00 E-value=1.7e+02 Score=23.79 Aligned_cols=37 Identities=14% Similarity=0.170 Sum_probs=33.0
Q ss_pred hhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccc
Q psy396 143 LQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQ 179 (239)
Q Consensus 143 l~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~ 179 (239)
+-+.+.++-+.+|+.+|++...|-+-|-.|-..|-+.
T Consensus 23 L~~~~~~tdEeLa~~Lgi~~~~VRk~L~~L~e~~Lv~ 59 (158)
T TIGR00373 23 LGIKGEFTDEEISLELGIKLNEVRKALYALYDAGLAD 59 (158)
T ss_pred HhccCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCce
Confidence 3356789999999999999999999999999998874
No 173
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=44.91 E-value=38 Score=26.01 Aligned_cols=43 Identities=23% Similarity=0.358 Sum_probs=34.4
Q ss_pred HHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccc
Q psy396 133 EMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQ 179 (239)
Q Consensus 133 ~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~ 179 (239)
-+|.+++ .|++- .-++...|+.||+|...+..|+. -...|.+.
T Consensus 6 DlR~rVl-~~~~~--g~s~~eaa~~F~VS~~Tv~~W~k-~~~~G~~~ 48 (119)
T PF01710_consen 6 DLRQRVL-AYIEK--GKSIREAAKRFGVSRNTVYRWLK-RKETGDLE 48 (119)
T ss_pred HHHHHHH-HHHHc--cchHHHHHHHhCcHHHHHHHHHH-hccccccc
Confidence 3677776 46666 45899999999999999999999 67777663
No 174
>PF14493 HTH_40: Helix-turn-helix domain
Probab=44.52 E-value=36 Score=24.76 Aligned_cols=33 Identities=24% Similarity=0.372 Sum_probs=30.3
Q ss_pred hcccHHHHHHHhCCCHHHHHHHHHHHHHcCc-cc
Q psy396 147 RSLSLKYMAQCFGVSVEFIEKEVARFAAAGR-LQ 179 (239)
Q Consensus 147 s~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~-l~ 179 (239)
.-.+++.+|+.-|+++..|+.-|.+++..|. ++
T Consensus 12 ~G~si~eIA~~R~L~~sTI~~HL~~~~~~g~~~~ 45 (91)
T PF14493_consen 12 KGLSIEEIAKIRGLKESTIYGHLAELIESGEPLD 45 (91)
T ss_pred cCCCHHHHHHHcCCCHHHHHHHHHHHHHhCCCCC
Confidence 4689999999999999999999999999988 54
No 175
>PRK11050 manganese transport regulator MntR; Provisional
Probab=44.03 E-value=1.7e+02 Score=23.46 Aligned_cols=40 Identities=20% Similarity=0.269 Sum_probs=33.3
Q ss_pred HhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCcccee
Q psy396 142 ILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCK 181 (239)
Q Consensus 142 yl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~ar 181 (239)
++.-...+++..+|+.||++...+-..|.+|...|-+.-+
T Consensus 45 ~l~~~~~~t~~eLA~~l~is~stVsr~l~~Le~~GlI~r~ 84 (152)
T PRK11050 45 LIAEVGEARQVDIAARLGVSQPTVAKMLKRLARDGLVEMR 84 (152)
T ss_pred HHHhcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 3333356899999999999999999999999999877543
No 176
>KOG3877|consensus
Probab=44.01 E-value=1.3e+02 Score=27.56 Aligned_cols=67 Identities=19% Similarity=0.324 Sum_probs=49.9
Q ss_pred HHhchHHHHHHHHHHHHhh-----h----ccCc----------chhHhHHHHHHHHHHHHHHHHhhhhhcccHHHHHHHh
Q psy396 98 LYDGHYFEFLKCLAAVEQD-----M----KRDP----------LLNPHYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCF 158 (239)
Q Consensus 98 f~~~~y~~~~~~L~~~~~~-----l----~~D~----------~L~~h~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~f 158 (239)
.++|.|.+|.++|+.+-.. | -.|+ |++.....-|.++|...|-|++.|+-.|-|
T Consensus 152 ~y~~R~~QY~dAL~HiL~TGQGVVLERsp~SDFVF~eAM~~qgyi~~~~~~hYnevr~nti~~ll~PHLViYl------- 224 (393)
T KOG3877|consen 152 IYNCRFDQYLDALAHILNTGQGVVLERSPHSDFVFAEAMRDQGYIGHEYFKHYNEVRKNTIPQLLWPHLVIYL------- 224 (393)
T ss_pred HHHhHHHHHHHHHHHHHhcCCeEEEecCcchhHHHHHHHHhcCcchhHHHHHHHHHHhhhhhhhcCccEEEEE-------
Confidence 5789999999998876432 2 2233 455666778999999999999999888875
Q ss_pred CCCHHHHHHHHHH
Q psy396 159 GVSVEFIEKEVAR 171 (239)
Q Consensus 159 g~s~~~lE~~L~~ 171 (239)
++|++++.+.|.+
T Consensus 225 d~Pv~~v~~~Ik~ 237 (393)
T KOG3877|consen 225 DTPVNKVLENIKR 237 (393)
T ss_pred cCCcHHHHHHHHh
Confidence 6788877766544
No 177
>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=43.53 E-value=46 Score=21.36 Aligned_cols=28 Identities=11% Similarity=0.141 Sum_probs=23.7
Q ss_pred hhh-hcccHHHHHHHhCCCHHHHHHHHHH
Q psy396 144 QAY-RSLSLKYMAQCFGVSVEFIEKEVAR 171 (239)
Q Consensus 144 ~pY-s~v~l~~mA~~fg~s~~~lE~~L~~ 171 (239)
.|| +.-.+..||..+|++...|..|...
T Consensus 22 ~~~P~~~~~~~la~~~~l~~~qV~~WF~n 50 (59)
T cd00086 22 NPYPSREEREELAKELGLTERQVKIWFQN 50 (59)
T ss_pred CCCCCHHHHHHHHHHHCcCHHHHHHHHHH
Confidence 555 6677999999999999999999764
No 178
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=43.40 E-value=1.8e+02 Score=23.68 Aligned_cols=40 Identities=13% Similarity=0.282 Sum_probs=32.6
Q ss_pred cccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 148 SLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 148 ~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
.++-..+|+.+|++...+-+.+.+|-.+|.|. ...+.|.+
T Consensus 168 ~~t~~~lA~~lG~tr~tvsR~l~~l~~~gii~----~~~~~i~i 207 (211)
T PRK11753 168 KITRQEIGRIVGCSREMVGRVLKMLEDQGLIS----AHGKTIVV 207 (211)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE----ecCCEEEE
Confidence 57789999999999999999999999988763 23455555
No 179
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=42.94 E-value=28 Score=21.39 Aligned_cols=21 Identities=19% Similarity=0.176 Sum_probs=16.2
Q ss_pred cHHHHHHHhCCCHHHHHHHHH
Q psy396 150 SLKYMAQCFGVSVEFIEKEVA 170 (239)
Q Consensus 150 ~l~~mA~~fg~s~~~lE~~L~ 170 (239)
+|+.+|+.+|+|+..|-.+=.
T Consensus 1 ti~e~A~~~gvs~~tlR~ye~ 21 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRYYER 21 (38)
T ss_dssp EHHHHHHHHTS-HHHHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 578999999999998766544
No 180
>KOG2165|consensus
Probab=42.53 E-value=62 Score=32.80 Aligned_cols=63 Identities=14% Similarity=0.202 Sum_probs=51.4
Q ss_pred HHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCcc-ceeecccCCEEEEeccccccCCC
Q psy396 137 RAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRL-QCKIDSVAGNVVTTSHISEKGDC 201 (239)
Q Consensus 137 ~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l-~arID~~~~~l~~~~~~~~~~~~ 201 (239)
-.|.+|-++ .+-++..+|+.+|+|++.+.+-|.=.|..|-| .--|++.+|++.. .+...|.+|
T Consensus 606 ~iI~~Fqek-~twt~eelse~l~ip~~~lrrrL~fWi~~GvL~e~~~~s~tgt~T~-iEse~d~~q 669 (765)
T KOG2165|consen 606 AIINLFQEK-NTWTLEELSESLGIPVPALRRRLSFWIQKGVLREEPIISDTGTLTV-IESEMDFDQ 669 (765)
T ss_pred HHHHHhcCc-ccccHHHHHHHhCCCHHHHHHHHHHHHHcCeeecCCCCCCCceeee-ccccccccc
Confidence 344555555 78999999999999999999999999999998 4466699999998 773366666
No 181
>PF07219 HemY_N: HemY protein N-terminus; InterPro: IPR010817 This entry represents the N terminus (approximately 150 residues) of bacterial HemY porphyrin biosynthesis proteins. These are membrane protein involved in a late step of protoheme IX synthesis [].
Probab=42.49 E-value=32 Score=25.97 Aligned_cols=31 Identities=19% Similarity=0.285 Sum_probs=27.0
Q ss_pred hhhhhhHHHHHHHHchhcCHHHHHHHHhccC
Q psy396 9 SARNKLKAYEGVYCLAIRQYCRAAELFVDVV 39 (239)
Q Consensus 9 ~~~~kl~~~~Gl~~l~~~~y~~Aa~~F~~~~ 39 (239)
.+|.+-....|+..+.+|||+.|...+..+.
T Consensus 56 ~~ka~~al~~Gl~al~~G~~~~A~k~~~~a~ 86 (108)
T PF07219_consen 56 RRKAQRALSRGLIALAEGDWQRAEKLLAKAA 86 (108)
T ss_pred HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4566777889999999999999999999983
No 182
>COG3063 PilF Tfp pilus assembly protein PilF [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=42.46 E-value=83 Score=27.79 Aligned_cols=86 Identities=15% Similarity=0.079 Sum_probs=51.5
Q ss_pred HHHHchhcCHHHHHHHHhccCCCCCCccccCHhHHHHHHHHHHH----HcCChhHHHHccccchhHHHHhhhhhhHHHHH
Q psy396 19 GVYCLAIRQYCRAAELFVDVVPTFESYELAEFGTIIRYTVLACM----IALPRYNLRKKLMHHGVMAQALHSQYRDLREY 94 (239)
Q Consensus 19 Gl~~l~~~~y~~Aa~~F~~~~~~f~~~e~~s~~di~~Y~~Lc~L----as~~R~elk~~ll~s~~~~~~~e~~~p~l~~l 94 (239)
|=..|.+|.|.+|-..|-.+... ....++.+..-=.++|++ ....+..+++.+--+|.+ .|.+.++
T Consensus 110 G~FLC~qg~~~eA~q~F~~Al~~---P~Y~~~s~t~eN~G~Cal~~gq~~~A~~~l~raL~~dp~~-------~~~~l~~ 179 (250)
T COG3063 110 GAFLCAQGRPEEAMQQFERALAD---PAYGEPSDTLENLGLCALKAGQFDQAEEYLKRALELDPQF-------PPALLEL 179 (250)
T ss_pred hHHHHhCCChHHHHHHHHHHHhC---CCCCCcchhhhhhHHHHhhcCCchhHHHHHHHHHHhCcCC-------ChHHHHH
Confidence 66788999999999999999532 112334444555678999 333344444433222222 3344454
Q ss_pred HHH-HHhchHHHHHHHHHHHH
Q psy396 95 FVS-LYDGHYFEFLKCLAAVE 114 (239)
Q Consensus 95 i~a-f~~~~y~~~~~~L~~~~ 114 (239)
... |..++|..-.-.++.+.
T Consensus 180 a~~~~~~~~y~~Ar~~~~~~~ 200 (250)
T COG3063 180 ARLHYKAGDYAPARLYLERYQ 200 (250)
T ss_pred HHHHHhcccchHHHHHHHHHH
Confidence 444 56888887766666553
No 183
>PF13551 HTH_29: Winged helix-turn helix
Probab=42.33 E-value=47 Score=24.27 Aligned_cols=27 Identities=19% Similarity=0.396 Sum_probs=25.1
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHHHHcC
Q psy396 150 SLKYMAQCFGVSVEFIEKEVARFAAAG 176 (239)
Q Consensus 150 ~l~~mA~~fg~s~~~lE~~L~~lI~~g 176 (239)
++..+|+.+|+|...+.+++.++=.+|
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~~~G 40 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYREGG 40 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHccc
Confidence 699999999999999999999988777
No 184
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
Probab=42.28 E-value=61 Score=27.41 Aligned_cols=63 Identities=21% Similarity=0.308 Sum_probs=50.6
Q ss_pred HHHHHHHHHHHHHHHHhhhhhcc-cHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 127 YRHYVQEMRLRAYKQILQAYRSL-SLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 127 ~~~l~~~ir~~~l~qyl~pYs~v-~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
...+.+.|+.++...-+.|=+.+ +-..+|+.||+|-..+-+.|..|..+|-|.-+ +..|+.+.
T Consensus 10 y~~i~~~l~~~I~~g~~~~G~~LPsE~eLa~~~~VSR~TvR~Al~~L~~eGli~r~--~G~GtfV~ 73 (238)
T TIGR02325 10 WRQIADKIEQEIAAGHLRAGDYLPAEMQLAERFGVNRHTVRRAIAALVERGLLRAE--QGRGTFVA 73 (238)
T ss_pred HHHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe--cCCEEEEC
Confidence 35666777777777667776667 77899999999999999999999999998654 55666666
No 185
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=42.12 E-value=65 Score=27.32 Aligned_cols=61 Identities=20% Similarity=0.222 Sum_probs=48.4
Q ss_pred HHHHHHHHHHHHHHhhhhhcc-cHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 129 HYVQEMRLRAYKQILQAYRSL-SLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 129 ~l~~~ir~~~l~qyl~pYs~v-~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
.+.+.|+.++...-+.|=..+ +-..+|+.||+|-..|-+.|..|+.+|-|.-+ +..|+.+.
T Consensus 4 qi~~~l~~~I~~g~~~~G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~--~G~GTfV~ 65 (233)
T TIGR02404 4 QIYQDLEQKITHGQYKEGDYLPSEHELMDQYGASRETVRKALNLLTEAGYIQKI--QGKGSIVL 65 (233)
T ss_pred HHHHHHHHHHHhCCCCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe--CCceEEEe
Confidence 456677777777677776666 68899999999999999999999999988554 44566665
No 186
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=41.96 E-value=75 Score=24.39 Aligned_cols=44 Identities=9% Similarity=0.191 Sum_probs=35.8
Q ss_pred HHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcC
Q psy396 131 VQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAG 176 (239)
Q Consensus 131 ~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g 176 (239)
-.+-+..++.+++++ ..+...+|..||++...+-.|+.++-..|
T Consensus 14 s~EfK~~aV~~~~~~--g~sv~evA~e~gIs~~tl~~W~r~y~~~~ 57 (121)
T PRK09413 14 TTQEKIAIVQQSFEP--GMTVSLVARQHGVAASQLFLWRKQYQEGS 57 (121)
T ss_pred CHHHHHHHHHHHHcC--CCCHHHHHHHHCcCHHHHHHHHHHHhhcc
Confidence 344567777777776 77899999999999999999999986543
No 187
>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=41.69 E-value=50 Score=25.32 Aligned_cols=33 Identities=27% Similarity=0.433 Sum_probs=31.0
Q ss_pred cccHHHHHHHhCCCHHHHHHHHHHHHHcCccce
Q psy396 148 SLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQC 180 (239)
Q Consensus 148 ~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~a 180 (239)
.++.+.+|+.+|+|...+.+-+..|...|-|..
T Consensus 25 ~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~ 57 (132)
T TIGR00738 25 PVSVKEIAERQGISRSYLEKILRTLRRAGLVES 57 (132)
T ss_pred cCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEe
Confidence 799999999999999999999999999998865
No 188
>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=41.63 E-value=33 Score=20.99 Aligned_cols=31 Identities=23% Similarity=0.263 Sum_probs=24.1
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeec
Q psy396 149 LSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKID 183 (239)
Q Consensus 149 v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID 183 (239)
+++..+|+.||+|...+.++ +.+|++.+...
T Consensus 2 lt~~e~a~~lgis~~ti~~~----~~~g~i~~~~~ 32 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRL----IHEGELPAYRV 32 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHH----HHcCCCCeEEe
Confidence 47889999999998876555 56799987543
No 189
>PF09182 PuR_N: Bacterial purine repressor, N-terminal; InterPro: IPR015265 The N-terminal domain of the bacterial purine repressor PuR is a winged-helix domain, a subdivision of the HTH structural family. It consists of a canonical arrangement of secondary structures: a1-b1-a2-T-a3-b2-W-b3, where a2-T-a3 is the HTH motif, a3 is the recognition helix, and W is the wing. The domain allows for recognition of a conserved CGAA sequence in the centre of a DNA PurBox, resulting in binding to the major groove of DNA []. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1O57_B 1P4A_D.
Probab=41.59 E-value=58 Score=23.16 Aligned_cols=36 Identities=31% Similarity=0.514 Sum_probs=24.2
Q ss_pred HHHHHHHHh--hhhhcccHHHHHHHhCCCHHHHHHHHH
Q psy396 135 RLRAYKQIL--QAYRSLSLKYMAQCFGVSVEFIEKEVA 170 (239)
Q Consensus 135 r~~~l~qyl--~pYs~v~l~~mA~~fg~s~~~lE~~L~ 170 (239)
|.-++.+|| .|+.-++|.+.|+.|+..-..+-+.|.
T Consensus 5 Rlv~it~~L~~~P~~lisL~~Fae~f~~AKSsISEDl~ 42 (70)
T PF09182_consen 5 RLVAITKYLLENPNKLISLTYFAERFGAAKSSISEDLS 42 (70)
T ss_dssp HHHHHHHHHHTSTT--EEHHHHHHHHT--HHHHHHHHH
T ss_pred HHHHHHHHHHcCCcceEcHHHHHHHhcccccchHHHHH
Confidence 444556665 689999999999999997777766653
No 190
>PF04157 EAP30: EAP30/Vps36 family; InterPro: IPR007286 EAP30 is a subunit of the ELL complex. The ELL is an 80kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity. ; PDB: 2ZME_A 3CUQ_A 1W7P_D 1U5T_B.
Probab=41.53 E-value=44 Score=28.60 Aligned_cols=43 Identities=16% Similarity=0.189 Sum_probs=36.1
Q ss_pred HHHHHHHh--hhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCcc
Q psy396 136 LRAYKQIL--QAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRL 178 (239)
Q Consensus 136 ~~~l~qyl--~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l 178 (239)
...+.+++ .....++...+|+.+|||..-....|..++.+|-+
T Consensus 176 ~~~il~~~~~~~~g~vt~~~l~~~~~ws~~~a~~~L~~~~~~G~l 220 (223)
T PF04157_consen 176 QSRILELAEEENGGGVTASELAEKLGWSVERAKEALEELEREGLL 220 (223)
T ss_dssp HHHHHHHH--TTTSEEEHHHHHHHHTB-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHhhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCE
Confidence 34456677 77889999999999999999999999999999865
No 191
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=41.38 E-value=70 Score=25.98 Aligned_cols=46 Identities=11% Similarity=0.192 Sum_probs=31.8
Q ss_pred HhHHHHHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHH
Q psy396 125 PHYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFA 173 (239)
Q Consensus 125 ~h~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI 173 (239)
..++.+...-+..++..| |...++..+|+.+|+|+..|...+.+..
T Consensus 145 ~~l~~Ll~~~~~~i~~~~---~~~~s~~eIA~~l~~s~~tV~~~l~r~r 190 (198)
T TIGR02859 145 SKMNELLSDLEWKVLQSY---LDGKSYQEIACDLNRHVKSIDNALQRVK 190 (198)
T ss_pred HHHHHhcCHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 344444444444444433 5789999999999999999987776643
No 192
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=41.25 E-value=36 Score=21.40 Aligned_cols=25 Identities=24% Similarity=0.460 Sum_probs=17.5
Q ss_pred hcccHHHHHHHhCCCHHHHHHHHHH
Q psy396 147 RSLSLKYMAQCFGVSVEFIEKEVAR 171 (239)
Q Consensus 147 s~v~l~~mA~~fg~s~~~lE~~L~~ 171 (239)
.-.++..||+.||.+...|-.+|.+
T Consensus 19 ~G~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 19 QGMSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp S---HHHHHHHTT--HHHHHHHHHH
T ss_pred cCCCHHHHHHHHCcCcHHHHHHHhc
Confidence 5688999999999999999888754
No 193
>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=41.25 E-value=1.1e+02 Score=20.71 Aligned_cols=49 Identities=14% Similarity=0.215 Sum_probs=35.4
Q ss_pred HHHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCcc
Q psy396 129 HYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRL 178 (239)
Q Consensus 129 ~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l 178 (239)
..+..+-.++ ..++-.+-+.++..+++.-++|...+.+-|+-||.-+-+
T Consensus 9 ~~fG~~~~~V-~~~Ll~~G~ltl~~i~~~t~l~~~~Vk~~L~~LiQh~~v 57 (62)
T PF08221_consen 9 EHFGEIVAKV-GEVLLSRGRLTLREIVRRTGLSPKQVKKALVVLIQHNLV 57 (62)
T ss_dssp HHHHHHHHHH-HHHHHHC-SEEHHHHHHHHT--HHHHHHHHHHHHHTTSE
T ss_pred HHcChHHHHH-HHHHHHcCCcCHHHHHHHhCCCHHHHHHHHHHHHHcCCe
Confidence 3344444444 455667789999999999999999999999999987644
No 194
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=40.66 E-value=1.8e+02 Score=22.98 Aligned_cols=56 Identities=18% Similarity=0.283 Sum_probs=42.2
Q ss_pred HHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccce-eec-ccCCEEEEecc
Q psy396 138 AYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQC-KID-SVAGNVVTTSH 194 (239)
Q Consensus 138 ~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~a-rID-~~~~~l~~~~~ 194 (239)
+|..++++---.+...+|+.+|.+-..+.+-|.+|+..|-+.= +.. ..-|--++ +.
T Consensus 32 v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~~~~Ggy~yi-Y~ 89 (126)
T COG3355 32 VYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVNLKGGGYYYL-YK 89 (126)
T ss_pred HHHHHHhhcCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeeccCCCceeEE-Ee
Confidence 4445555667889999999999999999999999999998842 333 34455555 54
No 195
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=40.65 E-value=32 Score=25.62 Aligned_cols=23 Identities=35% Similarity=0.460 Sum_probs=21.2
Q ss_pred hcccHHHHHHHhCCCHHHHHHHH
Q psy396 147 RSLSLKYMAQCFGVSVEFIEKEV 169 (239)
Q Consensus 147 s~v~l~~mA~~fg~s~~~lE~~L 169 (239)
+.++++.+|+.+|+|++.+|+.|
T Consensus 22 ~~ls~~~ia~dL~~s~~~le~vL 44 (89)
T PF10078_consen 22 SGLSLEQIAADLGTSPEHLEQVL 44 (89)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHH
Confidence 68999999999999999999876
No 196
>PF13959 DUF4217: Domain of unknown function (DUF4217)
Probab=40.62 E-value=73 Score=21.84 Aligned_cols=20 Identities=25% Similarity=0.386 Sum_probs=16.1
Q ss_pred HhhhhhcccHHHHHHHhCCC
Q psy396 142 ILQAYRSLSLKYMAQCFGVS 161 (239)
Q Consensus 142 yl~pYs~v~l~~mA~~fg~s 161 (239)
.+-..+.+++..+|+.||+.
T Consensus 39 ~iF~~~~L~l~~~A~sfGL~ 58 (65)
T PF13959_consen 39 DIFNVKKLDLGHLAKSFGLL 58 (65)
T ss_pred hhCCcccCCHHHHHHHcCCC
Confidence 44455789999999999984
No 197
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=39.82 E-value=37 Score=20.57 Aligned_cols=28 Identities=29% Similarity=0.368 Sum_probs=21.9
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHHHHcCcccee
Q psy396 150 SLKYMAQCFGVSVEFIEKEVARFAAAGRLQCK 181 (239)
Q Consensus 150 ~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~ar 181 (239)
++..+|+.+|+|...+..++. .|.+.+.
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~----~g~~~~~ 29 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVK----EGKLKAI 29 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHH----cCCCCce
Confidence 678899999999888776655 4777654
No 198
>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=39.76 E-value=58 Score=20.44 Aligned_cols=21 Identities=29% Similarity=0.415 Sum_probs=15.9
Q ss_pred ccHHHHHHHhCCCHHHHHHHH
Q psy396 149 LSLKYMAQCFGVSVEFIEKEV 169 (239)
Q Consensus 149 v~l~~mA~~fg~s~~~lE~~L 169 (239)
.++..+|+.||+|...|-..+
T Consensus 22 ~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 22 MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp --HHHHHHHTTS-HHHHHHHH
T ss_pred CCHHHHHHHHCcCHHHHHHHH
Confidence 889999999999998887665
No 199
>PRK13239 alkylmercury lyase; Provisional
Probab=39.67 E-value=69 Score=27.54 Aligned_cols=41 Identities=22% Similarity=0.250 Sum_probs=31.8
Q ss_pred hhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCE
Q psy396 143 LQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGN 188 (239)
Q Consensus 143 l~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~ 188 (239)
+.-=+.+++..+|+.+|.|++++++-|..+. .-.+|....+
T Consensus 31 la~G~pvt~~~lA~~~~~~~~~v~~~L~~l~-----~~~~d~~g~i 71 (206)
T PRK13239 31 LAKGRPVSVTTLAAALGWPVEEVEAVLEAMP-----DTEYDEDGRI 71 (206)
T ss_pred HHcCCCCCHHHHHHHhCCCHHHHHHHHHhCC-----CeEECCCCCE
Confidence 3344789999999999999999999999864 2256664444
No 200
>cd08809 CARD_CARD9 Caspase activation and recruitment domain of CARD9-like proteins. Caspase activation and recruitment domain (CARD) similar to that found in CARD9. CARD9 is a central regulator of innate immunity and is highly expressed in dendritic cells and macrophages. Together with BCL10 (B-cell lymphoma 10) and Malt1 (mucosa-associated lymphoid tissue-lymphoma-translocation gene 1), it forms the M-CBM signalosome (the CBM complex in myeloid immune cells), which mediates activation of NF-kB and MAPK by ITAM-coupled receptors expressed on immune cells. CARD9 associates with BCL10 via a CARD-CARD interaction. In general, CARDs are death domains (DDs) found 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 heterodimers by associating wi
Probab=39.62 E-value=39 Score=24.94 Aligned_cols=68 Identities=10% Similarity=0.065 Sum_probs=48.1
Q ss_pred cccCHhHHHHHHHHHHHHcCChhHHHHccccchhHHHHhhhhhhHHHHHHHHHHhchHHHHHHHHHHHHhhh
Q psy396 46 ELAEFGTIIRYTVLACMIALPRYNLRKKLMHHGVMAQALHSQYRDLREYFVSLYDGHYFEFLKCLAAVEQDM 117 (239)
Q Consensus 46 e~~s~~di~~Y~~Lc~Las~~R~elk~~ll~s~~~~~~~e~~~p~l~~li~af~~~~y~~~~~~L~~~~~~l 117 (239)
..++|..+.-|+-=|++++.+-.| .+++++.+...... .-.+.+++..==..-|..|++.|+...|.+
T Consensus 14 ~~i~p~rl~pyLrQ~~Vl~~~deE---eI~~~~~~~~~~~k-vg~LLDIL~~rG~~~f~aFLeSLE~~yP~l 81 (86)
T cd08809 14 SVIDPSRITPYLRQCKVLNSDDEE---QVLNDPSLVIRKRK-VGVLLDILQRTGLKGYEAFLESLELYYPQL 81 (86)
T ss_pred eeeCHhhcChHHHHhCCCChhhHH---HHHcCcccchHHHH-HHHHHHHHHhcCchHHHHHHHHHHHHHHHH
Confidence 357899999999999999876533 35666554443444 556778887777778889999998655543
No 201
>PF06969 HemN_C: HemN C-terminal domain; InterPro: IPR010723 Proteins containing this domain are all oxygen-independent coproporphyrinogen-III oxidases (HemN). This enzyme catalyses the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen-IX [], one of the last steps in haem biosynthesis. The function of this domain is unclear, but comparison to other proteins containing a radical SAM domain suggest it may be a substrate binding domain.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin-containing compound biosynthetic process, 0055114 oxidation-reduction process, 0005737 cytoplasm; PDB: 1OLT_A.
Probab=39.46 E-value=1.1e+02 Score=20.29 Aligned_cols=54 Identities=19% Similarity=0.264 Sum_probs=35.7
Q ss_pred HHHHHHHHHHhhhhhcccHHHHHHHhCCCHHH-HHHHHHHHHHcCccceeecccCCEEEE
Q psy396 133 EMRLRAYKQILQAYRSLSLKYMAQCFGVSVEF-IEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 133 ~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~-lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
.+++.++...-. ..-|+++...+.||.+... ..+.|..++.+|-+ ...++.|..
T Consensus 6 ~~~e~i~~~LR~-~~Gi~~~~~~~~~g~~~~~~~~~~l~~l~~~Gll----~~~~~~l~l 60 (66)
T PF06969_consen 6 RLREYIMLGLRC-NEGIDLSEFEQRFGIDFAEEFQKELEELQEDGLL----EIDGGRLRL 60 (66)
T ss_dssp HHHHHHHHHHHH-HSEEEHHHHHHHTT--THHH-HHHHHHHHHTTSE----EE-SSEEEE
T ss_pred HHHHHHHHHHHh-HCCcCHHHHHHHHCcCHHHHHHHHHHHHHHCCCE----EEeCCEEEE
Confidence 445555555433 4789999999999998644 48889999998766 334456655
No 202
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=39.37 E-value=76 Score=24.84 Aligned_cols=42 Identities=7% Similarity=0.150 Sum_probs=37.9
Q ss_pred hcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCE
Q psy396 147 RSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGN 188 (239)
Q Consensus 147 s~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~ 188 (239)
..++.+.+|+.+|++...+-..|.+|...|-|.-..|+.++-
T Consensus 53 ~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~~~~~DrR 94 (144)
T PRK11512 53 ACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNPNDKR 94 (144)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCcccCC
Confidence 479999999999999999999999999999998877777763
No 203
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=39.08 E-value=33 Score=29.05 Aligned_cols=34 Identities=24% Similarity=0.291 Sum_probs=29.3
Q ss_pred HHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHH
Q psy396 140 KQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFA 173 (239)
Q Consensus 140 ~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI 173 (239)
..|++.=.++++..+|+.||+|...+++-|.+..
T Consensus 170 ~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrAe 203 (215)
T COG3413 170 MGYFDYPRRVSLKDLAKELGISKSTLSEHLRRAE 203 (215)
T ss_pred cCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 4688888999999999999999999888887644
No 204
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=38.97 E-value=1.4e+02 Score=21.02 Aligned_cols=42 Identities=7% Similarity=0.028 Sum_probs=32.2
Q ss_pred hhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 146 YRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 146 Ys~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
....+...++..-|+|...+.+.|..|+..|-+ ...++...+
T Consensus 17 ~~~~~~t~i~~~~~L~~~~~~~yL~~L~~~gLI----~~~~~~Y~l 58 (77)
T PF14947_consen 17 KGGAKKTEIMYKANLNYSTLKKYLKELEEKGLI----KKKDGKYRL 58 (77)
T ss_dssp TT-B-HHHHHTTST--HHHHHHHHHHHHHTTSE----EEETTEEEE
T ss_pred cCCCCHHHHHHHhCcCHHHHHHHHHHHHHCcCe----eCCCCEEEE
Confidence 477889999999999999999999999999998 335566666
No 205
>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=38.80 E-value=86 Score=21.16 Aligned_cols=35 Identities=26% Similarity=0.232 Sum_probs=28.8
Q ss_pred HHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHH
Q psy396 134 MRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVAR 171 (239)
Q Consensus 134 ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~ 171 (239)
+|.++..=|++ -.++..+|+.+|+|...|..|..+
T Consensus 2 ~k~~A~~LY~~---G~~~~eIA~~Lg~~~~TV~~W~~r 36 (58)
T PF06056_consen 2 VKEQARSLYLQ---GWSIKEIAEELGVPRSTVYSWKDR 36 (58)
T ss_pred HHHHHHHHHHc---CCCHHHHHHHHCCChHHHHHHHHh
Confidence 56677777775 567899999999999999998876
No 206
>PRK09458 pspB phage shock protein B; Provisional
Probab=38.71 E-value=66 Score=23.19 Aligned_cols=26 Identities=12% Similarity=0.271 Sum_probs=21.8
Q ss_pred hHHHHHHHHhhHHHHHHHHHhhhhhc
Q psy396 213 GILYQTTVKRGDIFLNRLKKLARVID 238 (239)
Q Consensus 213 ~~~~~~~i~~~~~~~~r~~~l~~~~~ 238 (239)
....++..++++.+..||+.|.+++|
T Consensus 41 ~~~L~~L~~~A~rm~~RI~tLE~ILD 66 (75)
T PRK09458 41 QQRLAQLTEKAERMRERIQALEAILD 66 (75)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 33456677889999999999999998
No 207
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=38.53 E-value=85 Score=23.09 Aligned_cols=26 Identities=15% Similarity=0.262 Sum_probs=21.7
Q ss_pred hcccHHHHHHHhCCCHHHHHHHHHHH
Q psy396 147 RSLSLKYMAQCFGVSVEFIEKEVARF 172 (239)
Q Consensus 147 s~v~l~~mA~~fg~s~~~lE~~L~~l 172 (239)
..++++.||+.+|+|...+.....+.
T Consensus 20 ~~~~~~~lA~~~~~S~~~l~r~f~~~ 45 (107)
T PRK10219 20 QPLNIDVVAKKSGYSKWYLQRMFRTV 45 (107)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 45999999999999999887777664
No 208
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=38.34 E-value=81 Score=25.28 Aligned_cols=46 Identities=15% Similarity=0.141 Sum_probs=32.4
Q ss_pred HhHHHHHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHH
Q psy396 125 PHYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFA 173 (239)
Q Consensus 125 ~h~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI 173 (239)
..++.|-..-|.-.+..|+ ...+.+.+|+.+|+|+..|...+.+..
T Consensus 125 ~~l~~L~~~~r~i~~l~~~---~g~s~~eIA~~lgis~~tV~~~l~Rar 170 (179)
T PRK12514 125 ACLEELEKDRAAAVRRAYL---EGLSYKELAERHDVPLNTMRTWLRRSL 170 (179)
T ss_pred HHHHhCCHHHHHHHHHHHH---cCCCHHHHHHHHCCChHHHHHHHHHHH
Confidence 3444444455555555564 456799999999999999988887643
No 209
>PRK12423 LexA repressor; Provisional
Probab=37.89 E-value=84 Score=26.40 Aligned_cols=32 Identities=38% Similarity=0.466 Sum_probs=28.3
Q ss_pred ccHHHHHHHhC-CCHHHHHHHHHHHHHcCccce
Q psy396 149 LSLKYMAQCFG-VSVEFIEKEVARFAAAGRLQC 180 (239)
Q Consensus 149 v~l~~mA~~fg-~s~~~lE~~L~~lI~~g~l~a 180 (239)
-++..||+.|| .|...+-+.|..|-..|-|.-
T Consensus 26 Ps~~eia~~~g~~s~~~v~~~l~~L~~~G~l~~ 58 (202)
T PRK12423 26 PSLAEIAQAFGFASRSVARKHVQALAEAGLIEV 58 (202)
T ss_pred CCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEe
Confidence 49999999999 588999999999999988864
No 210
>smart00028 TPR Tetratricopeptide repeats. Repeats present in 4 or more copies in proteins. Contain a minimum of 34 amino acids each and self-associate via a "knobs and holes" mechanism.
Probab=37.58 E-value=33 Score=17.41 Aligned_cols=25 Identities=20% Similarity=0.222 Sum_probs=20.4
Q ss_pred HHHHHHHchhcCHHHHHHHHhccCC
Q psy396 16 AYEGVYCLAIRQYCRAAELFVDVVP 40 (239)
Q Consensus 16 ~~~Gl~~l~~~~y~~Aa~~F~~~~~ 40 (239)
...|..++..++|..|...|-.+..
T Consensus 5 ~~~a~~~~~~~~~~~a~~~~~~~~~ 29 (34)
T smart00028 5 YNLGNAYLKLGDYDEALEYYEKALE 29 (34)
T ss_pred HHHHHHHHHHhhHHHHHHHHHHHHc
Confidence 3467888899999999999987753
No 211
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=37.23 E-value=91 Score=22.93 Aligned_cols=45 Identities=13% Similarity=0.149 Sum_probs=37.0
Q ss_pred hhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 145 AYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 145 pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
....++-+.+|+.+|++.+.+-+.|.+|...|-|. .+...|++-+
T Consensus 44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~--r~~~~~~~~~ 88 (95)
T TIGR01610 44 KQDRVTATVIAELTGLSRTHVSDAIKSLARRRIIF--RQGMMGIVGV 88 (95)
T ss_pred cCCccCHHHHHHHHCcCHHHHHHHHHHHHHCCCee--eecCCceeec
Confidence 44678899999999999999999999999999885 3344566655
No 212
>PHA00738 putative HTH transcription regulator
Probab=37.18 E-value=1.9e+02 Score=22.26 Aligned_cols=57 Identities=9% Similarity=0.096 Sum_probs=44.3
Q ss_pred HHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 134 MRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 134 ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
.|.++ +.++..........+++.|+++...|-+-|.-|=..|-|..+-+...-....
T Consensus 13 tRr~I-L~lL~~~e~~~V~eLae~l~lSQptVS~HLKvLreAGLV~srK~Gr~vyY~L 69 (108)
T PHA00738 13 LRRKI-LELIAENYILSASLISHTLLLSYTTVLRHLKILNEQGYIELYKEGRTLYAKI 69 (108)
T ss_pred HHHHH-HHHHHHcCCccHHHHHHhhCCCHHHHHHHHHHHHHCCceEEEEECCEEEEEE
Confidence 34444 4444444468888999999999999999999999999998877776666555
No 213
>PF03081 Exo70: Exo70 exocyst complex subunit; InterPro: IPR004140 The Exo70 protein forms one subunit of the exocyst complex. First discovered in Saccharomyces cerevisiae [], Exo70 and other exocyst proteins have been observed in several other eukaryotes, including humans. In S. cerevisiae, the exocyst complex is involved in the late stages of exocytosis, and is localized at the tip of the bud, the major site of exocytosis in yeast []. Exo70 interacts with the Rho3 GTPase []. This interaction mediates one of the three known functions of Rho3 in cell polarity: vesicle docking and fusion with the plasma membrane (the other two functions are regulation of actin polarity and transport of exocytic vesicles from the mother cell to the bud) []. In humans, the functions of Exo70 and the exocyst complex are less well characterised: Exo70 is expressed in several tissues and is thought to also be involved in exocytosis [].; GO: 0006887 exocytosis, 0000145 exocyst; PDB: 2PFV_A 2B7M_B 2B1E_A 2PFT_A.
Probab=37.05 E-value=77 Score=28.85 Aligned_cols=70 Identities=19% Similarity=0.352 Sum_probs=49.7
Q ss_pred hHHHHHHHHHHH---Hhhhc-cCcchhHhHHHHHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHH
Q psy396 102 HYFEFLKCLAAV---EQDMK-RDPLLNPHYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARF 172 (239)
Q Consensus 102 ~y~~~~~~L~~~---~~~l~-~D~~L~~h~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~l 172 (239)
.++.|.+.+++. ...+. -|+-|...+..=+..+-..+|..|++-|..+.. +-.+-+..+++++|+.|.+|
T Consensus 298 ~f~~Fn~~fee~~~~q~~~~vpD~~LR~~Lr~~i~~~v~p~Y~~F~~~~~~~~~-~~~Kyikyt~~~le~~l~~L 371 (371)
T PF03081_consen 298 KFKKFNSAFEEIYKAQKTWKVPDPELREELRREIKEKVVPAYRRFYERYRNSQF-NPEKYIKYTPEDLENMLNEL 371 (371)
T ss_dssp HHHHHHHHHHHHHHHHTT---S-HHHHHHHHHHHHHHHHHHHHHHHHHCCCCSS-SHCCC-SS-HHHHHHHHHTC
T ss_pred HHHHHHHHHHHHHHcCcceecCCHHHHHHHHHHHHHHHHHHHHHHHHHhccccc-CCCCCCccCHHHHHHHHHcC
Confidence 455554444443 23333 499999999999999999999999999999998 55566788999999988653
No 214
>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A.
Probab=36.82 E-value=14 Score=20.56 Aligned_cols=27 Identities=15% Similarity=0.240 Sum_probs=21.1
Q ss_pred HHHHHHchhcCHHHHHHHHhccCCCCC
Q psy396 17 YEGVYCLAIRQYCRAAELFVDVVPTFE 43 (239)
Q Consensus 17 ~~Gl~~l~~~~y~~Aa~~F~~~~~~f~ 43 (239)
..|..+...|++.+|...|-.....|.
T Consensus 5 ~~a~~~~~~g~~~~A~~~~~~~~~~~P 31 (33)
T PF13174_consen 5 RLARCYYKLGDYDEAIEYFQRLIKRYP 31 (33)
T ss_dssp HHHHHHHHHCHHHHHHHHHHHHHHHST
T ss_pred HHHHHHHHccCHHHHHHHHHHHHHHCc
Confidence 357777789999999999988765553
No 215
>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=36.58 E-value=94 Score=21.42 Aligned_cols=36 Identities=19% Similarity=0.218 Sum_probs=24.3
Q ss_pred HHHHhhhh-hcccHHHHHHHhCCCHHHHHHHHHHHHH
Q psy396 139 YKQILQAY-RSLSLKYMAQCFGVSVEFIEKEVARFAA 174 (239)
Q Consensus 139 l~qyl~pY-s~v~l~~mA~~fg~s~~~lE~~L~~lI~ 174 (239)
..++-.-+ ..-+...+|+.+|+|++.+.+.+...-.
T Consensus 10 ~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~~~~ 46 (78)
T PF04539_consen 10 RRELEQELGREPTDEEIAEELGISVEEVRELLQASRR 46 (78)
T ss_dssp HHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHHHSC
T ss_pred HHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHhCCC
Confidence 33444444 5678999999999999999988875433
No 216
>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A.
Probab=36.33 E-value=34 Score=20.20 Aligned_cols=21 Identities=19% Similarity=0.210 Sum_probs=16.6
Q ss_pred HHHHHchhcCHHHHHHHHhcc
Q psy396 18 EGVYCLAIRQYCRAAELFVDV 38 (239)
Q Consensus 18 ~Gl~~l~~~~y~~Aa~~F~~~ 38 (239)
-|-.+...|+|++|.++|-.+
T Consensus 5 Lg~~~~~~g~~~~Ai~~y~~a 25 (36)
T PF13176_consen 5 LGRIYRQQGDYEKAIEYYEQA 25 (36)
T ss_dssp HHHHHHHCT-HHHHHHHHHHH
T ss_pred HHHHHHHcCCHHHHHHHHHHH
Confidence 456788899999999999874
No 217
>PRK00441 argR arginine repressor; Provisional
Probab=36.05 E-value=72 Score=25.81 Aligned_cols=41 Identities=10% Similarity=0.154 Sum_probs=36.5
Q ss_pred HHHHHHHHHHhhhhhcccHHHHHHHh-----CCCHHHHHHHHHHHH
Q psy396 133 EMRLRAYKQILQAYRSLSLKYMAQCF-----GVSVEFIEKEVARFA 173 (239)
Q Consensus 133 ~ir~~~l~qyl~pYs~v~l~~mA~~f-----g~s~~~lE~~L~~lI 173 (239)
.-|...+.+++..+...+...+++.| ++|...+-..|.+|=
T Consensus 3 ~~R~~~I~~ll~~~~~~~q~eL~~~L~~~G~~vSqaTisRDl~~L~ 48 (149)
T PRK00441 3 VSRHAKILEIINSKEIETQEELAEELKKMGFDVTQATVSRDIKELK 48 (149)
T ss_pred HHHHHHHHHHHHHcCCCcHHHHHHHHHhcCCCcCHHHHHHHHHHcC
Confidence 45888999999999999999999996 999999999998764
No 218
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=35.90 E-value=79 Score=25.55 Aligned_cols=28 Identities=7% Similarity=0.131 Sum_probs=24.1
Q ss_pred hhcccHHHHHHHhCCCHHHHHHHHHHHH
Q psy396 146 YRSLSLKYMAQCFGVSVEFIEKEVARFA 173 (239)
Q Consensus 146 Ys~v~l~~mA~~fg~s~~~lE~~L~~lI 173 (239)
+...+...+|+.||+|+..+...|.+..
T Consensus 151 ~~g~s~~eIA~~lgis~~~v~~~l~Rar 178 (187)
T PRK12534 151 FEGITYEELAARTDTPIGTVKSWIRRGL 178 (187)
T ss_pred HcCCCHHHHHHHhCCChhHHHHHHHHHH
Confidence 4778999999999999999998887643
No 219
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=35.78 E-value=74 Score=24.72 Aligned_cols=30 Identities=17% Similarity=0.205 Sum_probs=27.0
Q ss_pred hcccHHHHHHHhCCCHHHHHHHHHHHHHcC
Q psy396 147 RSLSLKYMAQCFGVSVEFIEKEVARFAAAG 176 (239)
Q Consensus 147 s~v~l~~mA~~fg~s~~~lE~~L~~lI~~g 176 (239)
++-+|+.||+.+|+|-..+-..|-++|..=
T Consensus 48 ~rGnlKe~e~~lgiSYPTvR~rLd~ii~~l 77 (113)
T PF09862_consen 48 NRGNLKEMEKELGISYPTVRNRLDKIIEKL 77 (113)
T ss_pred hcCCHHHHHHHHCCCcHHHHHHHHHHHHHh
Confidence 488999999999999999999999998853
No 220
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=35.72 E-value=42 Score=21.13 Aligned_cols=22 Identities=27% Similarity=0.422 Sum_probs=19.8
Q ss_pred hhhhcccHHHHHHHhCCCHHHH
Q psy396 144 QAYRSLSLKYMAQCFGVSVEFI 165 (239)
Q Consensus 144 ~pYs~v~l~~mA~~fg~s~~~l 165 (239)
++|..+++..+|+..|+|...+
T Consensus 12 ~G~~~~s~~~Ia~~~gvs~~~~ 33 (47)
T PF00440_consen 12 KGYEAVSIRDIARRAGVSKGSF 33 (47)
T ss_dssp HHTTTSSHHHHHHHHTSCHHHH
T ss_pred hCHHhCCHHHHHHHHccchhhH
Confidence 5799999999999999998765
No 221
>TIGR00331 hrcA heat shock gene repressor HrcA. In Bacillus subtilis, hrcA is the first gene of the dnaK operon and so is itself a heat shock gene.
Probab=35.70 E-value=86 Score=28.77 Aligned_cols=46 Identities=13% Similarity=0.234 Sum_probs=39.9
Q ss_pred HHHHHHHHHhhhhhcccHHHHHHH--hCCCHHHHHHHHHHHHHcCccc
Q psy396 134 MRLRAYKQILQAYRSLSLKYMAQC--FGVSVEFIEKEVARFAAAGRLQ 179 (239)
Q Consensus 134 ir~~~l~qyl~pYs~v~l~~mA~~--fg~s~~~lE~~L~~lI~~g~l~ 179 (239)
|-.-++..|+..-..|+...+|+. +|+|.+.+-.++.+|-..|.|.
T Consensus 7 il~aIV~~~l~~~~pv~s~~l~~~~~~~vS~aTiR~d~~~Le~~G~l~ 54 (337)
T TIGR00331 7 ILKAIVEEYIKTGQPVGSKTLLEKYNLGLSSATIRNDMADLEDLGFIE 54 (337)
T ss_pred HHHHHHHHHHhcCCCcCHHHHHhhcCCCCChHHHHHHHHHHHHCCCcc
Confidence 333445579999999999999999 9999999999999999998873
No 222
>PF03297 Ribosomal_S25: S25 ribosomal protein; InterPro: IPR004977 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S25 ribosomal protein is a component of the 40S ribosomal subunit.; PDB: 2XZM_8 2XZN_8 3O30_Q 3U5G_Z 3IZB_V 3U5C_Z 3O2Z_Q 3IZ6_V.
Probab=35.57 E-value=1.7e+02 Score=22.42 Aligned_cols=49 Identities=6% Similarity=0.141 Sum_probs=41.9
Q ss_pred hhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 143 LQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 143 l~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
+..|+-|+-..+|+.|+++..-.-.-|..|-..|.|.--.-.....|++
T Consensus 54 V~~~K~ITp~~lserlkI~~SlAr~~Lr~L~~kG~Ik~V~k~~~~~IYt 102 (105)
T PF03297_consen 54 VPKMKLITPSVLSERLKINGSLARKALRELESKGLIKPVSKHHRQRIYT 102 (105)
T ss_dssp CTTSSCECHHHHHHHHCCSCHHHHHHHHHHHHCCSSEEEECCTTCEEEE
T ss_pred hccCcEeeHHHHHHhHhhHHHHHHHHHHHHHHCCCEEEEeccCCeEEEe
Confidence 3568999999999999999999999999999999997766666666666
No 223
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=35.23 E-value=68 Score=21.92 Aligned_cols=19 Identities=21% Similarity=0.288 Sum_probs=16.2
Q ss_pred cHHHHHHHhCCCHHHHHHH
Q psy396 150 SLKYMAQCFGVSVEFIEKE 168 (239)
Q Consensus 150 ~l~~mA~~fg~s~~~lE~~ 168 (239)
+...+|+++|++...|-+|
T Consensus 11 ~~~~lAkalGVs~~aVs~W 29 (60)
T PF14549_consen 11 GQSKLAKALGVSPQAVSQW 29 (60)
T ss_dssp SHHHHHHHHTS-HHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHh
Confidence 4568999999999999999
No 224
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=34.64 E-value=78 Score=16.94 Aligned_cols=21 Identities=24% Similarity=0.208 Sum_probs=16.9
Q ss_pred cccHHHHHHHhCCCHHHHHHH
Q psy396 148 SLSLKYMAQCFGVSVEFIEKE 168 (239)
Q Consensus 148 ~v~l~~mA~~fg~s~~~lE~~ 168 (239)
..+...+|+.||++...+-.+
T Consensus 21 ~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 21 GESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCCHHHHHHHHCCCHHHHHHh
Confidence 348899999999998877654
No 225
>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=34.21 E-value=1.8e+02 Score=21.08 Aligned_cols=56 Identities=18% Similarity=0.229 Sum_probs=43.6
Q ss_pred HHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCC
Q psy396 132 QEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAG 187 (239)
Q Consensus 132 ~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~ 187 (239)
++|..-.+..|.+.=.-|.=..+|+.+|+|...|-.++..|-.-|-+.++--.-.|
T Consensus 7 ~~IL~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~~Le~lGlve~~p~~s~G 62 (78)
T PF03444_consen 7 REILKALVELYIETGEPVGSKTIAEELGRSPATIRNEMADLEELGLVESQPHPSGG 62 (78)
T ss_pred HHHHHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHHHHHHHCCCccCCCCCCCC
Confidence 34455566677777788999999999999999999999999998877654333333
No 226
>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=34.06 E-value=97 Score=21.57 Aligned_cols=51 Identities=14% Similarity=0.218 Sum_probs=41.2
Q ss_pred HHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 139 YKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 139 l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
+=+++..-...+++.+++..|++..++-.-|-=|..+++|. ++..++.+++
T Consensus 13 Vw~~L~~~~~~s~~el~k~~~l~~~~~~~AiGWLarE~KI~--~~~~~~~~~v 63 (65)
T PF10771_consen 13 VWQLLNENGEWSVSELKKATGLSDKEVYLAIGWLARENKIE--FEEKNGELYV 63 (65)
T ss_dssp HHHHHCCSSSEEHHHHHHHCT-SCHHHHHHHHHHHCTTSEE--EEEETTEEEE
T ss_pred HHHHHhhCCCcCHHHHHHHhCcCHHHHHHHHHHHhccCcee--EEeeCCEEEE
Confidence 45777778899999999999999999999999999999994 4466665554
No 227
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=33.86 E-value=87 Score=28.14 Aligned_cols=42 Identities=17% Similarity=0.109 Sum_probs=33.9
Q ss_pred HHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCc
Q psy396 136 LRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGR 177 (239)
Q Consensus 136 ~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~ 177 (239)
.+.++.++..-..++.+.+|+.||+|...+-+.|..|-..|-
T Consensus 6 ~~~il~~L~~~~~~s~~~LA~~lgvsr~tV~~~l~~L~~~G~ 47 (319)
T PRK11886 6 MLQLLSLLADGDFHSGEQLGEELGISRAAIWKHIQTLEEWGL 47 (319)
T ss_pred HHHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCC
Confidence 444555555545678889999999999999999999998876
No 228
>TIGR00122 birA_repr_reg BirA biotin operon repressor domain. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.
Probab=33.85 E-value=1.2e+02 Score=20.53 Aligned_cols=29 Identities=17% Similarity=0.290 Sum_probs=25.6
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHHHHcCc
Q psy396 149 LSLKYMAQCFGVSVEFIEKEVARFAAAGR 177 (239)
Q Consensus 149 v~l~~mA~~fg~s~~~lE~~L~~lI~~g~ 177 (239)
.+...+|+.||+|...+.+.+..|-..|-
T Consensus 14 ~~~~eLa~~l~vS~~tv~~~l~~L~~~g~ 42 (69)
T TIGR00122 14 FSGEKLGEALGMSRTAVNKHIQTLREWGV 42 (69)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHHCCC
Confidence 45889999999999999999999877655
No 229
>PF14069 SpoVIF: Stage VI sporulation protein F
Probab=33.45 E-value=63 Score=23.50 Aligned_cols=28 Identities=14% Similarity=0.180 Sum_probs=23.0
Q ss_pred HHHHHHHhCCCH-HHHHHHHHHHHHcCcc
Q psy396 151 LKYMAQCFGVSV-EFIEKEVARFAAAGRL 178 (239)
Q Consensus 151 l~~mA~~fg~s~-~~lE~~L~~lI~~g~l 178 (239)
|..+|...|.|+ ++.|+.|+++|..+++
T Consensus 37 Ik~vs~~an~~Vs~~~ed~IV~~I~~~~~ 65 (79)
T PF14069_consen 37 IKQVSQIANKPVSKEQEDQIVQAIINQKI 65 (79)
T ss_pred HHHHHHHhCCCCCHHHHHHHHHHHHhCCC
Confidence 345677888887 6899999999999877
No 230
>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A.
Probab=33.40 E-value=39 Score=19.68 Aligned_cols=22 Identities=23% Similarity=0.158 Sum_probs=17.6
Q ss_pred HHHHHchhcCHHHHHHHHhccC
Q psy396 18 EGVYCLAIRQYCRAAELFVDVV 39 (239)
Q Consensus 18 ~Gl~~l~~~~y~~Aa~~F~~~~ 39 (239)
-|.++...|+|.+|..++-++.
T Consensus 8 la~~~~~~g~~~~A~~~~~~al 29 (42)
T PF13374_consen 8 LANAYRAQGRYEEALELLEEAL 29 (42)
T ss_dssp HHHHHHHCT-HHHHHHHHHHHH
T ss_pred HHHHHHhhhhcchhhHHHHHHH
Confidence 3567888999999999998884
No 231
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=33.22 E-value=58 Score=21.89 Aligned_cols=23 Identities=26% Similarity=0.371 Sum_probs=16.7
Q ss_pred HHHHHHhCCCHHHHHHHHHHHHH
Q psy396 152 KYMAQCFGVSVEFIEKEVARFAA 174 (239)
Q Consensus 152 ~~mA~~fg~s~~~lE~~L~~lI~ 174 (239)
+.+++.|+++.+.+++.+..++.
T Consensus 37 ~~l~~~y~~~~~~~~~dv~~fl~ 59 (68)
T PF05402_consen 37 DALAEEYDVDPEEAEEDVEEFLE 59 (68)
T ss_dssp HHHHHHTT--HHHHHHHHHHHHH
T ss_pred HHHHHHcCCCHHHHHHHHHHHHH
Confidence 45677889999988888888775
No 232
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=32.74 E-value=2.3e+02 Score=21.87 Aligned_cols=40 Identities=10% Similarity=0.156 Sum_probs=35.7
Q ss_pred cccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCC
Q psy396 148 SLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAG 187 (239)
Q Consensus 148 ~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~ 187 (239)
.++.+.+|+.+|++...+-..+.+|...|-+.-.-|+.++
T Consensus 46 ~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~~~~Dr 85 (144)
T PRK03573 46 EQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQTCASDR 85 (144)
T ss_pred CCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeecCCCCc
Confidence 4678999999999999999999999999999887776666
No 233
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=32.63 E-value=2.3e+02 Score=23.69 Aligned_cols=36 Identities=19% Similarity=0.369 Sum_probs=29.8
Q ss_pred HHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 151 LKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 151 l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
-+.+|..+|++.+.+-..|.+|-..| + .+ ..|.|.+
T Consensus 176 ~~~iA~~lG~tretvsR~l~~L~~~g-l--~~--~~~~i~I 211 (236)
T PRK09392 176 KRVLASYLGMTPENLSRAFAALASHG-V--HV--DGSAVTI 211 (236)
T ss_pred HHHHHHHhCCChhHHHHHHHHHHhCC-e--Ee--eCCEEEE
Confidence 36799999999999999999999998 5 23 3467777
No 234
>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=32.55 E-value=1e+02 Score=20.74 Aligned_cols=36 Identities=17% Similarity=0.223 Sum_probs=29.9
Q ss_pred HHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHH
Q psy396 139 YKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAA 174 (239)
Q Consensus 139 l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~ 174 (239)
+++.+-.+=-|+..-+|+.+|+|.....+.+.++-.
T Consensus 4 Lidll~~~P~Vsa~mva~~L~vT~~~A~~li~eLg~ 39 (54)
T PF11972_consen 4 LIDLLLSRPLVSAPMVAKELGVTPQAAQRLIAELGL 39 (54)
T ss_pred HHHHHHhCccccHHHHHHHhCCCHHHHHHHHHHhhc
Confidence 456666667899999999999999999998877655
No 235
>PF12728 HTH_17: Helix-turn-helix domain
Probab=32.43 E-value=53 Score=20.82 Aligned_cols=37 Identities=16% Similarity=0.258 Sum_probs=26.5
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 149 LSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 149 v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
++.+.+|+.+|+|...+.+ ++..|.|.+- ...+....
T Consensus 2 lt~~e~a~~l~is~~tv~~----~~~~g~i~~~--~~g~~~~~ 38 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYR----WIRQGKIPPF--KIGRKWRI 38 (51)
T ss_pred CCHHHHHHHHCcCHHHHHH----HHHcCCCCeE--EeCCEEEE
Confidence 4678999999999887665 4567999765 24444444
No 236
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=31.55 E-value=76 Score=21.15 Aligned_cols=30 Identities=33% Similarity=0.434 Sum_probs=22.7
Q ss_pred HhhhhhcccHHHHHHHhCCCHHHHHHHHHH
Q psy396 142 ILQAYRSLSLKYMAQCFGVSVEFIEKEVAR 171 (239)
Q Consensus 142 yl~pYs~v~l~~mA~~fg~s~~~lE~~L~~ 171 (239)
-+.+|-.+++...|+.+|++...+-+-..+
T Consensus 9 ~L~~~fhlp~~eAA~~Lgv~~T~LKr~CR~ 38 (52)
T PF02042_consen 9 DLSQYFHLPIKEAAKELGVSVTTLKRRCRR 38 (52)
T ss_pred HHHHHhCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 356677889999999999998776655443
No 237
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=31.53 E-value=1.5e+02 Score=21.86 Aligned_cols=38 Identities=13% Similarity=0.221 Sum_probs=34.0
Q ss_pred hhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCcccee
Q psy396 144 QAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCK 181 (239)
Q Consensus 144 ~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~ar 181 (239)
..|+-|+-+.+|+.+++...-.-.-|..|-..|-|..-
T Consensus 37 ~~~K~ITps~lserlkI~~SlAr~~Lr~L~~kG~Ik~V 74 (86)
T PRK09334 37 KKEKIVTPYTLASKYGIKISVAKKVLRELEKRGVLVLY 74 (86)
T ss_pred ccCcEEcHHHHHHHhcchHHHHHHHHHHHHHCCCEEEE
Confidence 34899999999999999999999999999999988654
No 238
>COG2886 Uncharacterized small protein [Function unknown]
Probab=31.50 E-value=1.3e+02 Score=22.24 Aligned_cols=25 Identities=28% Similarity=0.365 Sum_probs=24.0
Q ss_pred hcccHHHHHHHhCCCHHHHHHHHHH
Q psy396 147 RSLSLKYMAQCFGVSVEFIEKEVAR 171 (239)
Q Consensus 147 s~v~l~~mA~~fg~s~~~lE~~L~~ 171 (239)
..|++..+|+-.|+|..+.+.+|.+
T Consensus 40 g~vSlg~Aaela~~sl~ef~~eL~~ 64 (88)
T COG2886 40 GAVSLGRAAELAGMSLNEFEEELRK 64 (88)
T ss_pred hhhHHHHHHHHhcCCHHHHHHHHHH
Confidence 8999999999999999999999987
No 239
>TIGR02976 phageshock_pspB phage shock protein B. This model describes the PspB protein of the psp (phage shock protein) operon, as found in Escherichia coli and many related species. Expression of a phage protein called secretin protein IV, and a number of other stresses including ethanol, heat shock, and defects in protein secretion trigger sigma-54-dependent expression of the phage shock regulon. PspB is both a regulator and an effector protein of the phage shock response.
Probab=31.27 E-value=91 Score=22.39 Aligned_cols=27 Identities=26% Similarity=0.429 Sum_probs=21.8
Q ss_pred hhHHHHHHHHhhHHHHHHHHHhhhhhc
Q psy396 212 RGILYQTTVKRGDIFLNRLKKLARVID 238 (239)
Q Consensus 212 ~~~~~~~~i~~~~~~~~r~~~l~~~~~ 238 (239)
....-++...+++.+..||+.|.+++|
T Consensus 40 d~~~L~~L~~~a~rm~eRI~tLE~ILd 66 (75)
T TIGR02976 40 DQALLQELYAKADRLEERIDTLERILD 66 (75)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 334456677789999999999999997
No 240
>PF04492 Phage_rep_O: Bacteriophage replication protein O ; InterPro: IPR006497 This entry is represented by the N-terminal domain of Bacteriophage lambda, GpO. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0006260 DNA replication
Probab=31.19 E-value=79 Score=23.86 Aligned_cols=35 Identities=17% Similarity=0.300 Sum_probs=33.5
Q ss_pred hhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCcc
Q psy396 144 QAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRL 178 (239)
Q Consensus 144 ~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l 178 (239)
++...|+.+.+|+.-|++.+.+.+.+..||..|-|
T Consensus 50 Kk~d~Is~sq~~e~tg~~~~~V~~al~~Li~~~vI 84 (100)
T PF04492_consen 50 KKMDRISNSQIAEMTGLSRDHVSKALNELIRRGVI 84 (100)
T ss_pred CccceeeHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence 77889999999999999999999999999999988
No 241
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=31.00 E-value=1.1e+02 Score=23.56 Aligned_cols=36 Identities=11% Similarity=0.100 Sum_probs=32.1
Q ss_pred hhcccHHHHHHHhCCCHHHHHHHHHHHHHcCcccee
Q psy396 146 YRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCK 181 (239)
Q Consensus 146 Ys~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~ar 181 (239)
-..|+|+.+|+.|..|.--+-..|.+|-..|-|.=+
T Consensus 17 ~~~vtl~elA~~l~cS~Rn~r~lLkkm~~~gWi~W~ 52 (115)
T PF12793_consen 17 PVEVTLDELAELLFCSRRNARTLLKKMQEEGWITWQ 52 (115)
T ss_pred CcceeHHHHHHHhCCCHHHHHHHHHHHHHCCCeeee
Confidence 347899999999999999999999999999988533
No 242
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=30.93 E-value=1.4e+02 Score=19.38 Aligned_cols=27 Identities=19% Similarity=0.340 Sum_probs=22.0
Q ss_pred hcccHHHHHHHhCCCHHHHHHHHHHHH
Q psy396 147 RSLSLKYMAQCFGVSVEFIEKEVARFA 173 (239)
Q Consensus 147 s~v~l~~mA~~fg~s~~~lE~~L~~lI 173 (239)
...+...+|..||+|...+.+.+...+
T Consensus 18 ~~~~~~~La~~FgIs~stvsri~~~~~ 44 (53)
T PF13613_consen 18 LNLTFQDLAYRFGISQSTVSRIFHEWI 44 (53)
T ss_pred cCCcHhHHhhheeecHHHHHHHHHHHH
Confidence 467889999999999988877766554
No 243
>PRK14584 hmsS hemin storage system protein; Provisional
Probab=30.87 E-value=1.2e+02 Score=24.92 Aligned_cols=55 Identities=18% Similarity=0.200 Sum_probs=39.8
Q ss_pred HHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 131 VQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 131 ~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
|+..|-+. .+--.| ..++.+.+|+.|+++.+.+ .++-..+.+..-.|...+++.+
T Consensus 83 YN~~RF~~-eRR~~~-~~l~~dElA~sF~l~~e~i----~qLr~~kiltVh~De~G~Ii~V 137 (153)
T PRK14584 83 YNQVRFQV-ERRGHR-PDLDDDELASSFALSPELI----AQLKSGSCLTLYNDEHGHIIDV 137 (153)
T ss_pred HHHHHhcc-cccCCC-CCCChHHHHHHcCCCHHHH----HHHHhCCeEEEEECCCCCEEEe
Confidence 34444443 444444 6899999999999998765 3444556668899999999998
No 244
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=30.78 E-value=1.1e+02 Score=25.40 Aligned_cols=41 Identities=12% Similarity=0.040 Sum_probs=35.0
Q ss_pred hhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecc
Q psy396 144 QAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDS 184 (239)
Q Consensus 144 ~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~ 184 (239)
+.++-.+.+.+|+.+|+|...++..+..+-..|.+...+.-
T Consensus 173 ~g~~g~s~~eIa~~l~iS~~Tv~~~~~~~~~~~~~~~~~~~ 213 (225)
T PRK10046 173 EPGVQHTAETVAQALTISRTTARRYLEYCASRHLIIAEIVH 213 (225)
T ss_pred cCCCCcCHHHHHHHhCccHHHHHHHHHHHHhCCeEEEEeec
Confidence 33345789999999999999999999999999988877765
No 245
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=30.55 E-value=1.1e+02 Score=26.50 Aligned_cols=55 Identities=11% Similarity=0.091 Sum_probs=42.0
Q ss_pred HHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 135 RLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 135 r~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
|.-.+++++.....++++.||+.+|+|...+-..|..|...|=+.- |..++....
T Consensus 15 r~l~IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~~--~~~~~~Y~l 69 (257)
T PRK15090 15 KVFGILQALGEEREIGITELSQRVMMSKSTVYRFLQTMKTLGYVAQ--EGESEKYSL 69 (257)
T ss_pred HHHHHHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE--cCCCCcEEe
Confidence 4444556665556799999999999999999999999999988743 344554444
No 246
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=30.50 E-value=1.2e+02 Score=24.34 Aligned_cols=45 Identities=27% Similarity=0.383 Sum_probs=36.1
Q ss_pred HHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCcc
Q psy396 132 QEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRL 178 (239)
Q Consensus 132 ~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l 178 (239)
+..|.++++.+. |.-.+...+|+.||++...+..|+.+.=..|-+
T Consensus 7 ~~~R~~~~~~~~--~~G~S~re~Ak~~gvs~sTvy~wv~r~~e~G~~ 51 (138)
T COG3415 7 NDLRERVVDAVV--GEGLSCREAAKRFGVSISTVYRWVRRYRETGLD 51 (138)
T ss_pred HHHHHHHHHHHH--HcCccHHHHHHHhCccHHHHHHHHHHhcccccc
Confidence 455666665553 568899999999999999999999998776655
No 247
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.37 E-value=59 Score=24.26 Aligned_cols=23 Identities=22% Similarity=0.107 Sum_probs=21.0
Q ss_pred hcccHHHHHHHhCCCHHHHHHHH
Q psy396 147 RSLSLKYMAQCFGVSVEFIEKEV 169 (239)
Q Consensus 147 s~v~l~~mA~~fg~s~~~lE~~L 169 (239)
..++.+.+|+++|++...+|+-|
T Consensus 22 ~~LS~~~iA~~Ln~t~~~lekil 44 (97)
T COG4367 22 CPLSDEEIATALNWTEVKLEKIL 44 (97)
T ss_pred ccccHHHHHHHhCCCHHHHHHHH
Confidence 57899999999999999999877
No 248
>PF05043 Mga: Mga helix-turn-helix domain; InterPro: IPR007737 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions []. The family also contains VirR like proteins which match only at the C terminus of the alignment.; PDB: 3SQN_A.
Probab=30.22 E-value=1.2e+02 Score=21.42 Aligned_cols=50 Identities=18% Similarity=0.225 Sum_probs=30.4
Q ss_pred HHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHH---HHcCccceeecccCCEEEE
Q psy396 139 YKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARF---AAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 139 l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~l---I~~g~l~arID~~~~~l~~ 191 (239)
+..++--...+++..+|+.+++|...+-+.+.++ +. +.+.+| ...|.-..
T Consensus 21 ll~~ll~~~~~s~~~la~~~~iS~sti~~~i~~l~~~l~--~~~l~i-~~~~~~l~ 73 (87)
T PF05043_consen 21 LLKLLLNNEYVSIEDLAEELFISRSTIYRDIKKLNKYLK--KYGLKI-SKKGYRLE 73 (87)
T ss_dssp HHHHHHH-SEEEHHHHHHHHT--HHHHHHHHHHHHHHHH--CCT-EE--SSEEEEE
T ss_pred HHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHH--HcCeEE-eCCCeEEE
Confidence 3344446689999999999999999887766543 33 446677 44444444
No 249
>KOG0548|consensus
Probab=30.05 E-value=4.7e+02 Score=25.81 Aligned_cols=79 Identities=13% Similarity=0.095 Sum_probs=50.3
Q ss_pred hhHHHHHHHHchhcCHHHHHHHHhccCCCCCCccccCHhHHHHHHHHHHHH---cCChhHHHHccccchhHHHHhhhhhh
Q psy396 13 KLKAYEGVYCLAIRQYCRAAELFVDVVPTFESYELAEFGTIIRYTVLACMI---ALPRYNLRKKLMHHGVMAQALHSQYR 89 (239)
Q Consensus 13 kl~~~~Gl~~l~~~~y~~Aa~~F~~~~~~f~~~e~~s~~di~~Y~~Lc~La---s~~R~elk~~ll~s~~~~~~~e~~~p 89 (239)
|-....|..+...++|.+|.+.|.++..--. +...+.--.-=|..+ ..+..+++++.+.+|+++.++. +|
T Consensus 427 kgy~RKg~al~~mk~ydkAleay~eale~dp-----~~~e~~~~~~rc~~a~~~~~~~ee~~~r~~~dpev~~il~--d~ 499 (539)
T KOG0548|consen 427 KAYLRKGAALRAMKEYDKALEAYQEALELDP-----SNAEAIDGYRRCVEAQRGDETPEETKRRAMADPEVQAILQ--DP 499 (539)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCc-----hhHHHHHHHHHHHHHhhcCCCHHHHHHhhccCHHHHHHHc--CH
Confidence 3444578899999999999999998832111 111222222234444 3445688888888888888876 47
Q ss_pred HHHHHHHHH
Q psy396 90 DLREYFVSL 98 (239)
Q Consensus 90 ~l~~li~af 98 (239)
.++.++..+
T Consensus 500 ~m~~~l~q~ 508 (539)
T KOG0548|consen 500 AMRQILEQM 508 (539)
T ss_pred HHHHHHHHH
Confidence 777544433
No 250
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=29.95 E-value=66 Score=21.63 Aligned_cols=25 Identities=28% Similarity=0.510 Sum_probs=19.6
Q ss_pred hcccHHHHHHHhCCCHHHHHHHHHH
Q psy396 147 RSLSLKYMAQCFGVSVEFIEKEVAR 171 (239)
Q Consensus 147 s~v~l~~mA~~fg~s~~~lE~~L~~ 171 (239)
..-.+.+-|+.||+|.+++..-+.+
T Consensus 19 e~~ev~ywa~~~gvt~~~L~~AV~~ 43 (57)
T PF12244_consen 19 EPYEVRYWAKRFGVTEEQLREAVRA 43 (57)
T ss_pred CHHHHHHHHHHHCcCHHHHHHHHHH
Confidence 3446788999999999988877654
No 251
>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=29.36 E-value=1.2e+02 Score=22.45 Aligned_cols=38 Identities=13% Similarity=0.169 Sum_probs=28.0
Q ss_pred hhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCcccee
Q psy396 144 QAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCK 181 (239)
Q Consensus 144 ~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~ar 181 (239)
-.+..++=+.||+..|++..++-+-|..|-.+|-+..+
T Consensus 23 ~~~~~l~de~la~~~~l~~~~vRkiL~~L~~~~lv~~~ 60 (105)
T PF02002_consen 23 LRKGELTDEDLAKKLGLKPKEVRKILYKLYEDGLVSYR 60 (105)
T ss_dssp HHH--B-HHHHHHTT-S-HHHHHHHHHHHHHHSS-EEE
T ss_pred HHcCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeEEE
Confidence 34567888999999999999999999999999888553
No 252
>KOG3151|consensus
Probab=29.32 E-value=4.1e+02 Score=23.59 Aligned_cols=145 Identities=16% Similarity=0.187 Sum_probs=93.8
Q ss_pred HHHHchhcCHHHHHHHHhccCCCCCCc-cccCHh-HHHHHHH--HHHHHcCChh-----HHHHccccchhHHHHhhh--h
Q psy396 19 GVYCLAIRQYCRAAELFVDVVPTFESY-ELAEFG-TIIRYTV--LACMIALPRY-----NLRKKLMHHGVMAQALHS--Q 87 (239)
Q Consensus 19 Gl~~l~~~~y~~Aa~~F~~~~~~f~~~-e~~s~~-di~~Y~~--Lc~Las~~R~-----elk~~ll~s~~~~~~~e~--~ 87 (239)
.+..+...||..=..+|-+.-+=|..+ +.++.+ .--+.++ |.-|++.+|- +|. .+.... ++. -
T Consensus 63 vl~SI~t~D~~sFerY~~Qlk~YY~d~~~~l~~S~~~~~l~GLnLL~LLsqNRiaeFHteLe--~lp~~~----l~~~~~ 136 (260)
T KOG3151|consen 63 VLLSILTKDFESFERYMNQLKPYYFDYNEKLSESEKKHKLLGLNLLYLLSQNRIAEFHTELE--LLPKKI----LQHNPY 136 (260)
T ss_pred HHHHHHhccHHHHHHHHHHhcchhcccccccCcchhhhHHHHHHHHHHHHhccHHHHHHHHH--hccHHH----hhccch
Confidence 345556778877777887776654443 333332 2222222 4566676662 221 111111 111 0
Q ss_pred hhHHHHHHHHHHhchHHHHHHHHHHHHhhhccCcchhHhHHHHHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHH
Q psy396 88 YRDLREYFVSLYDGHYFEFLKCLAAVEQDMKRDPLLNPHYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEK 167 (239)
Q Consensus 88 ~p~l~~li~af~~~~y~~~~~~L~~~~~~l~~D~~L~~h~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~ 167 (239)
..+...+=+.+-++.|...+...+.+ .++...-..+-+.+.||.-+=.-.=++|..++++..++.++.+.+ +
T Consensus 137 I~~~v~LEq~~MEGaYnKv~~a~~s~-----p~~~y~~FmdIl~~tiRdEIA~c~EKsYd~l~~s~a~~~L~f~~~---~ 208 (260)
T KOG3151|consen 137 ISHPVSLEQSLMEGAYNKVLSAKQSI-----PSEEYTYFMDILLDTIRDEIAGCIEKSYDKLSASDATQMLLFNND---K 208 (260)
T ss_pred hhhHHHHHHHHHhhHHHHHHHHHhcC-----CcHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCHHHHHHHHhcCCh---H
Confidence 22345556677889998888877765 267778888999999999988888889999999999999999854 4
Q ss_pred HHHHHHHcCc
Q psy396 168 EVARFAAAGR 177 (239)
Q Consensus 168 ~L~~lI~~g~ 177 (239)
++..+-..+.
T Consensus 209 e~~~~~~~r~ 218 (260)
T KOG3151|consen 209 ELKKFATERQ 218 (260)
T ss_pred HHHHHHHhcC
Confidence 6666666666
No 253
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=29.01 E-value=1.5e+02 Score=22.90 Aligned_cols=29 Identities=3% Similarity=-0.118 Sum_probs=24.5
Q ss_pred hhcccHHHHHHHhCCCHHHHHHHHHHHHH
Q psy396 146 YRSLSLKYMAQCFGVSVEFIEKEVARFAA 174 (239)
Q Consensus 146 Ys~v~l~~mA~~fg~s~~~lE~~L~~lI~ 174 (239)
+...+...||+.+|+|+..|...+.+.+.
T Consensus 120 ~~~~s~~EIA~~l~is~~tV~~~~~ra~~ 148 (154)
T PRK06759 120 FVGKTMGEIALETEMTYYQVRWIYRQALE 148 (154)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 35678999999999999999999877543
No 254
>PF08721 Tn7_Tnp_TnsA_C: TnsA endonuclease C terminal; InterPro: IPR014832 The Tn7 transposase is composed of proteins TnsA and TnsB. DNA breakage at the 5'-end of the transposon is carried out by TnsA, and breakage and joining at the 3'-end is carried out by TnsB. The C-terminal domain of TnsA binds DNA. ; PDB: 1F1Z_B 1T0F_B.
Probab=28.96 E-value=1.3e+02 Score=20.51 Aligned_cols=43 Identities=9% Similarity=0.103 Sum_probs=34.5
Q ss_pred HHHHHhhhhhcccHHHHHHHh----CCCHHHHHHHHHHHHHcCccce
Q psy396 138 AYKQILQAYRSLSLKYMAQCF----GVSVEFIEKEVARFAAAGRLQC 180 (239)
Q Consensus 138 ~l~qyl~pYs~v~l~~mA~~f----g~s~~~lE~~L~~lI~~g~l~a 180 (239)
.+...+......++..+.+.| +++....-..+-.||..+.+.+
T Consensus 31 ~i~~~l~~~~~~tl~~l~~~~d~~~~l~~g~~L~~l~~LiA~k~i~~ 77 (79)
T PF08721_consen 31 LILARLRKNPTMTLRDLCKELDKDYELEPGTALPLLRHLIATKRIKV 77 (79)
T ss_dssp HHHHHHHHTTTSBHHHHHHHHHHHCT--TTHHHHHHHHHHHTTSEE-
T ss_pred HHHHHHHHcCCCCHHHHHHHHHHhcCCCcCChHHHHHHHHhCChhcc
Confidence 467777777789999999888 8999999999999999988754
No 255
>PF06224 HTH_42: Winged helix DNA-binding domain; InterPro: IPR009351 This is a family of conserved bacterial proteins with unknown function.
Probab=28.77 E-value=1.4e+02 Score=26.63 Aligned_cols=53 Identities=19% Similarity=0.308 Sum_probs=47.6
Q ss_pred HHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCcc-ceeec
Q psy396 131 VQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRL-QCKID 183 (239)
Q Consensus 131 ~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l-~arID 183 (239)
-+......+..|+..|--++...+|.=+|+++..+...+.++-..|.| ...++
T Consensus 164 ~~ea~~~Lv~Ryl~~~GPat~~d~a~w~gl~~~~~r~~l~~l~~~~~L~~v~~~ 217 (327)
T PF06224_consen 164 REEALAELVRRYLRAYGPATLADFAWWSGLPKTQARRALAQLVEEGELVEVEVE 217 (327)
T ss_pred HHHHHHHHHHHHHHHcCCccHHHHHHHhccCHHHHHHHHHhhccCCcEEEEEEc
Confidence 677788889999999999999999999999999999999999877777 66777
No 256
>TIGR02899 spore_safA spore coat assembly protein SafA. in which one of which is found in most examples of endospore-forming bacteria. Lysin motifs are repeated in many proteins.
Probab=28.55 E-value=65 Score=19.03 Aligned_cols=17 Identities=24% Similarity=0.356 Sum_probs=14.0
Q ss_pred cHHHHHHHhCCCHHHHH
Q psy396 150 SLKYMAQCFGVSVEFIE 166 (239)
Q Consensus 150 ~l~~mA~~fg~s~~~lE 166 (239)
++..+|+.||++.+.+.
T Consensus 6 tl~~IA~~~~~~~~~l~ 22 (44)
T TIGR02899 6 TLWKIAKKYGVDFDELI 22 (44)
T ss_pred CHHHHHHHHCcCHHHHH
Confidence 57789999999977664
No 257
>KOG1662|consensus
Probab=28.54 E-value=1.9e+02 Score=24.80 Aligned_cols=78 Identities=17% Similarity=0.318 Sum_probs=56.2
Q ss_pred HHHHHHHhhhccCcchhHhHHHHHHHHHHHHHHHHhhhhhcccHHHHHHHhC-------C---CHHHHHHHHHHHHHcCc
Q psy396 108 KCLAAVEQDMKRDPLLNPHYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFG-------V---SVEFIEKEVARFAAAGR 177 (239)
Q Consensus 108 ~~L~~~~~~l~~D~~L~~h~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg-------~---s~~~lE~~L~~lI~~g~ 177 (239)
..+.+..+....+++....+.-|.++=|..++......|+.+.=.+=-+.+. + ...++|+.|..++..|+
T Consensus 87 ~~i~di~~~~~~~~~t~NflnlLaeNgRL~~l~~Ivk~F~~lm~ahrGev~~~VtSa~pLd~~~~k~l~~~l~k~l~~gk 166 (210)
T KOG1662|consen 87 TAIDDIVEKLKLAPLTKNFLNLLAENGRLNNLTEIVKAFETLMNAHRGEVKVEVTSAEPLDAKQLKQLEKALQKILGGGK 166 (210)
T ss_pred HHHHHHHHHhcccHhHHHHHHHHHHcCchhhHHHHHHHHHHHHHHhCCceEEEEEecccCChHHHHHHHHHHHHHhcCCc
Confidence 4455566667888888899999999999999999999998775333222221 1 22478899999888886
Q ss_pred ---cceeeccc
Q psy396 178 ---LQCKIDSV 185 (239)
Q Consensus 178 ---l~arID~~ 185 (239)
+..+||+.
T Consensus 167 ~l~v~~~vdPS 177 (210)
T KOG1662|consen 167 KLKVENKVDPS 177 (210)
T ss_pred eEEEEeecChh
Confidence 46788863
No 258
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=27.61 E-value=4e+02 Score=23.26 Aligned_cols=51 Identities=20% Similarity=0.331 Sum_probs=41.3
Q ss_pred HHHHHHHHHhh-hhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecc
Q psy396 134 MRLRAYKQILQ-AYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDS 184 (239)
Q Consensus 134 ir~~~l~qyl~-pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~ 184 (239)
.-.+.+.+.++ |=...+...+|++.|+|--.+.+.|.-|+..|.+++.|-.
T Consensus 158 ~Tl~~i~~~~~~~~~~~Taeela~~~giSRvTaRRYLeyl~~~~~l~a~i~y 209 (224)
T COG4565 158 LTLQKVREALKEPDQELTAEELAQALGISRVTARRYLEYLVSNGILEAEIHY 209 (224)
T ss_pred HHHHHHHHHHhCcCCccCHHHHHHHhCccHHHHHHHHHHHHhcCeeeEEeec
Confidence 34445555555 5568899999999999999999999999999999887643
No 259
>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=27.54 E-value=63 Score=20.87 Aligned_cols=25 Identities=8% Similarity=0.084 Sum_probs=20.7
Q ss_pred hcccHHHHHHHhCCCHHHHHHHHHH
Q psy396 147 RSLSLKYMAQCFGVSVEFIEKEVAR 171 (239)
Q Consensus 147 s~v~l~~mA~~fg~s~~~lE~~L~~ 171 (239)
+.-.+..||..+|+|...|..|-..
T Consensus 26 ~~~~~~~la~~l~l~~~~V~~WF~n 50 (57)
T PF00046_consen 26 SKEEREELAKELGLTERQVKNWFQN 50 (57)
T ss_dssp HHHHHHHHHHHHTSSHHHHHHHHHH
T ss_pred cccccccccccccccccccccCHHH
Confidence 4456889999999999999988653
No 260
>PF10607 CLTH: CTLH/CRA C-terminal to LisH motif domain; InterPro: IPR019589 This entry represents the CRA (or CT11-RanBPM) domain, which is a protein-protein interaction domain present in crown eukaryotes (plants, animals, fungi) and which is found in Ran-binding proteins such as Ran-binding protein 9 (RanBP9 or RanBPM) and RanBP10. RanBPM is a scaffolding protein important in regulating cellular function in both the immune system and the nervous system, and may act as an adapter protein to couple membrane receptors to intracellular signaling pathways. This domain is at the C terminus of the proteins and is the binding domain for the CRA motif, which is comprised of approximately 100 amino acids at the C-terminal of RanBPM. It was found to be important for the interaction of RanBPM with fragile X mental retardation protein (FMRP), but its functional significance has yet to be determined [].
Probab=27.47 E-value=2.6e+02 Score=21.59 Aligned_cols=51 Identities=6% Similarity=0.099 Sum_probs=38.4
Q ss_pred HHHHHHHHHHhchHHHHHHHHHHHHhhhc---cCcchhHhHHHHHHHHHHHHHH
Q psy396 90 DLREYFVSLYDGHYFEFLKCLAAVEQDMK---RDPLLNPHYRHYVQEMRLRAYK 140 (239)
Q Consensus 90 ~l~~li~af~~~~y~~~~~~L~~~~~~l~---~D~~L~~h~~~l~~~ir~~~l~ 140 (239)
...++.++..+++...+++.++...+.+. .+..+.=|.-.+++.+|...+.
T Consensus 4 ~r~~I~~~I~~g~i~~Ai~w~~~~~~~l~~~~~~L~f~L~~q~fiell~~~~~~ 57 (145)
T PF10607_consen 4 ERKKIRQAILNGDIDPAIEWLNENFPELLKRNSSLEFELRCQQFIELLREGDIM 57 (145)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHcCHHHHhcCCchhHHHHHHHHHHHHHHHhHH
Confidence 45677778889999999999998888765 3455667777888888875443
No 261
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=27.29 E-value=1.3e+02 Score=26.33 Aligned_cols=28 Identities=29% Similarity=0.307 Sum_probs=23.5
Q ss_pred hcccHHHHHHHhCCCHHHHHHHHHHHHH
Q psy396 147 RSLSLKYMAQCFGVSVEFIEKEVARFAA 174 (239)
Q Consensus 147 s~v~l~~mA~~fg~s~~~lE~~L~~lI~ 174 (239)
...++..+|+.+|+|.+.|.+...+.+.
T Consensus 235 ~~~t~~eIA~~lgvS~~~V~q~~~~Al~ 262 (270)
T TIGR02392 235 DKLTLQELAAEYGVSAERIRQIEKNAMK 262 (270)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4689999999999999999877766554
No 262
>PF04190 DUF410: Protein of unknown function (DUF410) ; InterPro: IPR007317 This is a family of conserved eukaryotic proteins with undetermined function.; PDB: 3LKU_E 2WPV_G.
Probab=27.26 E-value=4.1e+02 Score=23.27 Aligned_cols=36 Identities=14% Similarity=-0.020 Sum_probs=26.9
Q ss_pred cCCchhhhhhhHHHHHHHHchhcCHHHHHHHHhccC
Q psy396 4 SGGDWSARNKLKAYEGVYCLAIRQYCRAAELFVDVV 39 (239)
Q Consensus 4 ~~~dw~~~~kl~~~~Gl~~l~~~~y~~Aa~~F~~~~ 39 (239)
.|+...--+.|.-.-|..+..+++|..|..+|+-+.
T Consensus 82 ~~~~~~Gdp~LH~~~a~~~~~e~~~~~A~~Hfl~~~ 117 (260)
T PF04190_consen 82 FGSYKFGDPELHHLLAEKLWKEGNYYEAERHFLLGT 117 (260)
T ss_dssp TSS-TT--HHHHHHHHHHHHHTT-HHHHHHHHHTS-
T ss_pred cCCCCCCCHHHHHHHHHHHHhhccHHHHHHHHHhcC
Confidence 355555668899999999999999999999998874
No 263
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=27.07 E-value=68 Score=21.49 Aligned_cols=37 Identities=22% Similarity=0.136 Sum_probs=25.6
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEE
Q psy396 150 SLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVV 190 (239)
Q Consensus 150 ~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~ 190 (239)
+++.+|+.+|+|...|..|... |.+...-+..+....
T Consensus 2 ti~eva~~~gvs~~tlr~y~~~----gll~~~~~~~g~r~y 38 (69)
T PF13411_consen 2 TIKEVAKLLGVSPSTLRYYERE----GLLPPPRDENGYRYY 38 (69)
T ss_dssp EHHHHHHHTTTTHHHHHHHHHT----TSSTTBESTTSSEEE
T ss_pred cHHHHHHHHCcCHHHHHHHHHh----cCcccccccCceeec
Confidence 5789999999999988777554 667654433333333
No 264
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=26.98 E-value=1.6e+02 Score=22.58 Aligned_cols=26 Identities=19% Similarity=0.184 Sum_probs=21.6
Q ss_pred hcccHHHHHHHhCCCHHHHHHHHHHH
Q psy396 147 RSLSLKYMAQCFGVSVEFIEKEVARF 172 (239)
Q Consensus 147 s~v~l~~mA~~fg~s~~~lE~~L~~l 172 (239)
..++++.+|+.+|+|+..+.....+.
T Consensus 24 ~~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 24 SPLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 45899999999999999887776553
No 265
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=26.76 E-value=1.6e+02 Score=21.83 Aligned_cols=27 Identities=30% Similarity=0.469 Sum_probs=23.0
Q ss_pred hcccHHHHHHHhCCCHHHHHHHHHHHH
Q psy396 147 RSLSLKYMAQCFGVSVEFIEKEVARFA 173 (239)
Q Consensus 147 s~v~l~~mA~~fg~s~~~lE~~L~~lI 173 (239)
.-.++..+|+.+|+|...|...+.+..
T Consensus 125 ~g~s~~eIA~~l~~s~~~v~~~~~~~~ 151 (158)
T TIGR02937 125 EGLSYKEIAEILGISVGTVKRRLKRAR 151 (158)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 467899999999999999988887643
No 266
>PF03683 UPF0175: Uncharacterised protein family (UPF0175); InterPro: IPR005368 This entry contains small proteins of unknown function.
Probab=26.68 E-value=2.3e+02 Score=19.91 Aligned_cols=45 Identities=18% Similarity=0.113 Sum_probs=34.6
Q ss_pred hHHHHHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHH
Q psy396 126 HYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVAR 171 (239)
Q Consensus 126 h~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~ 171 (239)
.-..+-+.+|...-..+.+- ..|+++.-|+..|+|..++.+.|.+
T Consensus 13 ~~~e~~~~~r~~~Ai~lY~~-g~iS~gkAAelag~s~~eF~~~L~~ 57 (76)
T PF03683_consen 13 TPDEFEQELREELAIKLYEE-GKISLGKAAELAGMSRWEFLELLKE 57 (76)
T ss_pred CHHHHHHHHHHHHHHHHHHc-CCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 33566677776655555554 7999999999999999888888776
No 267
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=26.58 E-value=2e+02 Score=22.71 Aligned_cols=65 Identities=17% Similarity=0.296 Sum_probs=51.6
Q ss_pred HhHHHHHHHHHHHHHHHHhhh-hhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 125 PHYRHYVQEMRLRAYKQILQA-YRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 125 ~h~~~l~~~ir~~~l~qyl~p-Ys~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
|-...+.+.|+..++..-+.| .+-=+...||..+|+++..+.+.-..|=.+|-+.. ....|+.+.
T Consensus 11 PIY~QI~~qIk~~I~~g~l~pGdkLPSvRelA~~~~VNpnTv~raY~eLE~eG~i~t--~rg~G~fV~ 76 (125)
T COG1725 11 PIYEQIANQIKEQIASGELKPGDKLPSVRELAKDLGVNPNTVQRAYQELEREGIVET--KRGKGTFVT 76 (125)
T ss_pred CHHHHHHHHHHHHHHhCCcCCCCCCCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE--ecCeeEEEc
Confidence 344567777788888888888 66678999999999999999999999999887743 345566666
No 268
>PLN00078 photosystem I reaction center subunit N (PsaN); Provisional
Probab=26.45 E-value=85 Score=24.12 Aligned_cols=22 Identities=14% Similarity=0.359 Sum_probs=17.9
Q ss_pred HHHHHHHHHhchHHHHHHHHHH
Q psy396 91 LREYFVSLYDGHYFEFLKCLAA 112 (239)
Q Consensus 91 l~~li~af~~~~y~~~~~~L~~ 112 (239)
=++=+..||.++|++||+....
T Consensus 76 dkERLDdYYKRNykDYF~fveG 97 (122)
T PLN00078 76 DKERLDDYYKRNYKDYFGLIEG 97 (122)
T ss_pred HHHHHHHHHHHhHHHHHHHhcc
Confidence 4667899999999999987653
No 269
>cd08050 TAF6 TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving as
Probab=26.30 E-value=3.7e+02 Score=24.66 Aligned_cols=123 Identities=8% Similarity=0.122 Sum_probs=75.6
Q ss_pred cccCHhHHHHHHHHHHHHcCChhHHHHcccc----chhHHHHhhhhhhHHHHHHHHHHhchHH----HH---HHHHHHH-
Q psy396 46 ELAEFGTIIRYTVLACMIALPRYNLRKKLMH----HGVMAQALHSQYRDLREYFVSLYDGHYF----EF---LKCLAAV- 113 (239)
Q Consensus 46 e~~s~~di~~Y~~Lc~Las~~R~elk~~ll~----s~~~~~~~e~~~p~l~~li~af~~~~y~----~~---~~~L~~~- 113 (239)
..+|.+.-..|--++.....+-...+...+. ++.+. .. .|.+..+|..-...+.. .. ++.+...
T Consensus 170 ~~LS~Elq~yf~~It~a~~~~~~~~r~~aL~sL~tD~gl~---~L-lPyf~~fI~~~v~~n~~~nl~~L~~lm~~v~ALl 245 (343)
T cd08050 170 HVLSKELQLYFEEITEALVGSNEEKRREALQSLRTDPGLQ---QL-LPYFVRFIAEGVTVNLDQNLALLIYLMRMVRALL 245 (343)
T ss_pred cccCHHHHHHHHHHHHHHhCCCHHHHHHHHHHhccCCCch---hh-hhHHHHHHHHHHHhhhcccHHHHHHHHHHHHHHh
Confidence 4567777777776766554333333222222 22221 12 56666666665554444 11 2222222
Q ss_pred -HhhhccCcchhHhHHHHHHHHHHHHHHH--------HhhhhhcccHHHHHHHhCCCHHHHHHHHHHH
Q psy396 114 -EQDMKRDPLLNPHYRHYVQEMRLRAYKQ--------ILQAYRSLSLKYMAQCFGVSVEFIEKEVARF 172 (239)
Q Consensus 114 -~~~l~~D~~L~~h~~~l~~~ir~~~l~q--------yl~pYs~v~l~~mA~~fg~s~~~lE~~L~~l 172 (239)
.+.+..++||++-+..++.++..+-+.. .++-|++--|..+.+.|+-+...+...|.+.
T Consensus 246 ~N~~l~le~Ylh~Lip~vltclv~~~l~~~~~~~~h~~LRd~AA~ll~~i~~~f~~~y~~l~~ri~~t 313 (343)
T cd08050 246 DNPNLHLEPYLHQLIPSVLTCLVAKQLCSRPPDDNHWALRDYAARLLAQICRKFSTSYNTLQPRITRT 313 (343)
T ss_pred cCCCCchHHhHHHHHHHHHHHhhhHhhcCCCCCchHHHHHHHHHHHHHHHHHHcCCCCCcHHHHHHHH
Confidence 2456778888888888888887777665 5677899999999999998877777666643
No 270
>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A ....
Probab=25.87 E-value=69 Score=21.06 Aligned_cols=26 Identities=19% Similarity=0.153 Sum_probs=22.4
Q ss_pred hHHHHHHHHchhcCHHHHHHHHhccC
Q psy396 14 LKAYEGVYCLAIRQYCRAAELFVDVV 39 (239)
Q Consensus 14 l~~~~Gl~~l~~~~y~~Aa~~F~~~~ 39 (239)
.-...|..++..|+|++|..+|-.+.
T Consensus 5 ~~~~~g~~~~~~~~~~~A~~~~~~ai 30 (69)
T PF13414_consen 5 AWYNLGQIYFQQGDYEEAIEYFEKAI 30 (69)
T ss_dssp HHHHHHHHHHHTTHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence 34567899999999999999999993
No 271
>PF12833 HTH_18: Helix-turn-helix domain; PDB: 2K9S_A 3LSG_C 3OIO_A 1D5Y_B 3GBG_A 3OOU_A 1BL0_A 1XS9_A 3MN2_B 3MKL_B ....
Probab=25.76 E-value=1.6e+02 Score=20.18 Aligned_cols=42 Identities=26% Similarity=0.524 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHHHHHHhhhhhcccHHHHHHHhCCC-HHHHHHH
Q psy396 127 YRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVS-VEFIEKE 168 (239)
Q Consensus 127 ~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s-~~~lE~~ 168 (239)
...++...|.......+.-+...++..+|...|.+ ...+-+.
T Consensus 24 ~~~~~~~~R~~~a~~~L~~~~~~~i~~ia~~~Gf~~~~~f~~~ 66 (81)
T PF12833_consen 24 FKQYLRELRLQRAKELLRQNTDLSIAEIAEECGFSSQSHFSRA 66 (81)
T ss_dssp HHHHHHHHHHHHHHHHHHHHTT--HHHHHHHTT-SSHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHhhcccHHHHHHHcCCCCHHHHHHH
Confidence 34666777777777777546799999999999985 3444333
No 272
>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=25.76 E-value=1.4e+02 Score=23.08 Aligned_cols=42 Identities=24% Similarity=0.361 Sum_probs=36.5
Q ss_pred HHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccce
Q psy396 137 RAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQC 180 (239)
Q Consensus 137 ~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~a 180 (239)
+.|...|.. ..++..+|..+++|..-+-=.+..|+..|.+..
T Consensus 46 ~~Il~lC~~--~~SVAEiAA~L~lPlgVvrVLvsDL~~~G~v~v 87 (114)
T PF05331_consen 46 RAILELCRR--PLSVAEIAARLGLPLGVVRVLVSDLADAGLVRV 87 (114)
T ss_pred HHHHHHHCC--CccHHHHHHhhCCCchhhhhhHHHHHhCCCEEE
Confidence 445677777 788999999999999999999999999998855
No 273
>TIGR03337 phnR transcriptional regulator protein. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Salmonella, Vibrio Aeromonas hydrophila, Hahella chejuensis and Psychromonas ingrahamii.
Probab=25.67 E-value=1.6e+02 Score=24.73 Aligned_cols=62 Identities=15% Similarity=0.121 Sum_probs=45.9
Q ss_pred HHHHHHHHHHHHHHHhhhhhcc-cHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 128 RHYVQEMRLRAYKQILQAYRSL-SLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 128 ~~l~~~ir~~~l~qyl~pYs~v-~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
..+.+.++.++-..=+.|=+.+ +-..+|+.||+|-..+-+.|..|..+|-|..+-- .|+.+.
T Consensus 4 ~qi~~~l~~~I~~g~~~~g~~lPsE~eLa~~~~Vsr~Tvr~Al~~L~~eGli~~~~g--~Gt~V~ 66 (231)
T TIGR03337 4 LYIKDHLSYQIRAGALLPGDKLPSERDLGERFNTTRVTIREALQQLEAEGLIYREDR--RGWFVS 66 (231)
T ss_pred HHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCeEEEeCC--CEEEEC
Confidence 3455666666666666776666 6789999999999999999999999998865322 344444
No 274
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=25.00 E-value=2.9e+02 Score=20.47 Aligned_cols=43 Identities=14% Similarity=0.105 Sum_probs=36.9
Q ss_pred hhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCC
Q psy396 145 AYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAG 187 (239)
Q Consensus 145 pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~ 187 (239)
+-..+++..+|+.++++...+-.-+.+|...|-|.=.-|..++
T Consensus 40 ~~~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~r~~~~~D~ 82 (109)
T TIGR01889 40 NEGKLTLKEIIKEILIKQSALVKIIKKLSKKGYLSKERSEDDE 82 (109)
T ss_pred cCCcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEeccCCcccC
Confidence 3357999999999999999999999999999988766666555
No 275
>PF01638 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002577 The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure. The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde []. The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH []. The crystal structure of ytfH resembles the DNA-binding domains of winged helix proteins, containing a three helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-H2-B1-H3-H4-B2-B3-H5-H6. This topology corresponds with that of the marR-type DNA-binding domain, wherein helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. ; PDB: 2F2E_B 3DF8_A 1Z7U_B 1YYV_A 4A5M_D 4A5N_B 2FSW_A 2HZT_D.
Probab=24.98 E-value=2.6e+02 Score=19.98 Aligned_cols=61 Identities=10% Similarity=0.206 Sum_probs=46.2
Q ss_pred hcccHHHHHHHh-CCCHHHHHHHHHHHHHcCccceeecccCCEEEEeccccccCCCCCCCccchhhhhHHHHHHHHh
Q psy396 147 RSLSLKYMAQCF-GVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVTTSHISEKGDCRSEAPEASLDRGILYQTTVKR 222 (239)
Q Consensus 147 s~v~l~~mA~~f-g~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~ 222 (239)
....++.+.+.+ |+|...+-+.|..|...|-+.-++......-.. +. .. +++..+..++..
T Consensus 17 g~~rf~el~~~l~~is~~~L~~~L~~L~~~GLv~r~~~~~~p~~v~-Y~-----------LT---~~G~~l~~~l~~ 78 (90)
T PF01638_consen 17 GPMRFSELQRRLPGISPKVLSQRLKELEEAGLVERRVYPEVPPRVE-YS-----------LT---EKGKELLPVLEA 78 (90)
T ss_dssp SSEEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSSSEEE-EE-----------E----HHHHHHHHHHHH
T ss_pred CCCcHHHHHHhcchhHHHHHHHHHHHHHHcchhhcccccCCCCCCc-cC-----------CC---cCHHHHHHHHHH
Confidence 678899999999 999999999999999999998877765554333 44 44 677776666654
No 276
>PF05491 RuvB_C: Holliday junction DNA helicase ruvB C-terminus; InterPro: IPR008823 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the C-terminal region of the proteins; it is thought to be a helicase DNA-binding domain.; GO: 0003677 DNA binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 3PFI_B 1IXR_C 1HQC_B 1IXS_B 1IN8_A 1IN4_A 1IN5_A 1J7K_A 1IN6_A 1IN7_A.
Probab=24.98 E-value=94 Score=22.44 Aligned_cols=40 Identities=20% Similarity=0.405 Sum_probs=26.9
Q ss_pred HHHHHhhhhh--cccHHHHHHHhCCCHHHHHHHHHHH-HHcCc
Q psy396 138 AYKQILQAYR--SLSLKYMAQCFGVSVEFIEKEVARF-AAAGR 177 (239)
Q Consensus 138 ~l~qyl~pYs--~v~l~~mA~~fg~s~~~lE~~L~~l-I~~g~ 177 (239)
.+.-..+-|+ -|.|+.+|.++|.+.+.+|+.+.-+ |..|-
T Consensus 13 yL~~l~~~f~ggPvGl~tlA~~l~ed~~Tie~v~EPyLiq~G~ 55 (76)
T PF05491_consen 13 YLKTLIENFKGGPVGLDTLAAALGEDKETIEDVIEPYLIQIGF 55 (76)
T ss_dssp HHHHHHHCSTTS-B-HHHHHHHTTS-HHHHHHTTHHHHHHTTS
T ss_pred HHHHHHHHcCCCCeeHHHHHHHHCCCHhHHHHHhhHHHHHhhh
Confidence 3344445455 7999999999999999999988765 44443
No 277
>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI [, , , , ]. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....
Probab=24.84 E-value=1.9e+02 Score=19.02 Aligned_cols=32 Identities=16% Similarity=0.272 Sum_probs=25.2
Q ss_pred HHhhhhhcccHHHHHHHhCCCHHHHHHHHHHH
Q psy396 141 QILQAYRSLSLKYMAQCFGVSVEFIEKEVARF 172 (239)
Q Consensus 141 qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~l 172 (239)
-++.-+..=++..-|+.+|+|...+-+.|.++
T Consensus 6 ~f~~v~~~gs~~~AA~~l~is~~~vs~~i~~L 37 (60)
T PF00126_consen 6 YFLAVAETGSISAAAEELGISQSAVSRQIKQL 37 (60)
T ss_dssp HHHHHHHHSSHHHHHHHCTSSHHHHHHHHHHH
T ss_pred HHHHHHHhCCHHHHHHHhhccchHHHHHHHHH
Confidence 34444566789999999999999988887764
No 278
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=24.77 E-value=3.6e+02 Score=21.44 Aligned_cols=40 Identities=13% Similarity=0.151 Sum_probs=33.4
Q ss_pred cccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 148 SLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 148 ~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
.++-..+|..+|++.+.+-+.|.+|-.+|-|.. ..+.|++
T Consensus 143 ~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~----~~~~i~I 182 (193)
T TIGR03697 143 RLSHQAIAEAIGSTRVTITRLLGDLRKKKLISI----HKKKITV 182 (193)
T ss_pred CCCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEe----cCCEEEE
Confidence 478899999999999999999999999877743 3566666
No 279
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=24.67 E-value=1.1e+02 Score=18.54 Aligned_cols=25 Identities=20% Similarity=0.365 Sum_probs=17.1
Q ss_pred hcccHHHHHHHhCCCHHHHHHHHHH
Q psy396 147 RSLSLKYMAQCFGVSVEFIEKEVAR 171 (239)
Q Consensus 147 s~v~l~~mA~~fg~s~~~lE~~L~~ 171 (239)
..+++..||+.+|+|..-+-+...+
T Consensus 7 ~~~~l~~iA~~~g~S~~~f~r~Fk~ 31 (42)
T PF00165_consen 7 QKLTLEDIAEQAGFSPSYFSRLFKK 31 (42)
T ss_dssp SS--HHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 5689999999999988776665543
No 280
>COG1392 Phosphate transport regulator (distant homolog of PhoU) [Inorganic ion transport and metabolism]
Probab=24.55 E-value=3.2e+02 Score=23.51 Aligned_cols=80 Identities=16% Similarity=0.202 Sum_probs=62.8
Q ss_pred hhHHHHHHHHHHhchHHHHHHHHHHHHhhhccCcchhHhHHHHHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHH
Q psy396 88 YRDLREYFVSLYDGHYFEFLKCLAAVEQDMKRDPLLNPHYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEK 167 (239)
Q Consensus 88 ~p~l~~li~af~~~~y~~~~~~L~~~~~~l~~D~~L~~h~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~ 167 (239)
...+.+.+.+|..++|....+.+..+.. +-.+.+.+-+++|......++-|+.+=+|-.+.+...=-.+.+|+
T Consensus 26 v~~~~~~f~~~~~g~~~~~e~~~~~I~~-------lE~~aD~ik~~i~~~l~~~~flP~~R~Dil~L~~~~D~i~D~~ed 98 (217)
T COG1392 26 VKLLAPAFEALRRGDYEDAEELLKEIKD-------LEHEADEIKREIRLELYKGFFLPFDREDILELIESQDDIADAAED 98 (217)
T ss_pred HHHHHHHHHHHHcCCchhHHHHHHHHHH-------HHHHhhHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 3456777888888888888777776633 356789999999999999999999999999999888766667666
Q ss_pred HHHHHHH
Q psy396 168 EVARFAA 174 (239)
Q Consensus 168 ~L~~lI~ 174 (239)
-...+..
T Consensus 99 ~A~~l~l 105 (217)
T COG1392 99 AAKLLLL 105 (217)
T ss_pred HHHHHHc
Confidence 5555444
No 281
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=24.55 E-value=4e+02 Score=21.88 Aligned_cols=42 Identities=14% Similarity=0.218 Sum_probs=34.6
Q ss_pred cHHHHHHHh--CCCHHHHHHHHHHHHHcCccc----eeecccCCEEEE
Q psy396 150 SLKYMAQCF--GVSVEFIEKEVARFAAAGRLQ----CKIDSVAGNVVT 191 (239)
Q Consensus 150 ~l~~mA~~f--g~s~~~lE~~L~~lI~~g~l~----arID~~~~~l~~ 191 (239)
+...||+.+ ++|.+++++-|.-|..-|-|. |+.-+.++.|..
T Consensus 41 d~~~iak~l~p~is~~ev~~sL~~L~~~gli~k~~~g~y~~t~~~l~~ 88 (171)
T PF14394_consen 41 DPEWIAKRLRPKISAEEVRDSLEFLEKLGLIKKDGDGKYVQTDKSLTT 88 (171)
T ss_pred CHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEECCCCcEEEecceeeC
Confidence 899999999 999999999999999999883 355555555543
No 282
>PF08769 Spo0A_C: Sporulation initiation factor Spo0A C terminal; InterPro: IPR014879 The response regulator Spo0A is comprised of a phophoacceptor domain and a transcription activation domain. This domain corresponds to the transcription activation domain and forms an alpha helical structure comprising of 6 alpha helices. The structure contains a helix-turn-helix and binds DNA [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0005509 calcium ion binding, 0006355 regulation of transcription, DNA-dependent, 0042173 regulation of sporulation resulting in formation of a cellular spore, 0005737 cytoplasm; PDB: 1FC3_C 1LQ1_D.
Probab=24.46 E-value=99 Score=23.52 Aligned_cols=39 Identities=8% Similarity=0.105 Sum_probs=28.6
Q ss_pred HHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEE
Q psy396 151 LKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNV 189 (239)
Q Consensus 151 l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l 189 (239)
-..+|+.+|.++..||+.+...|...--+|..|....+.
T Consensus 43 Yp~IA~k~~TT~s~VERaIR~aI~~~w~~g~~~~l~~i~ 81 (106)
T PF08769_consen 43 YPDIAKKYGTTPSRVERAIRHAIEVAWTRGNPELLEKIF 81 (106)
T ss_dssp HHHHHHHTTS-HHHHHHHHHHHHHHHHHCS-CCCCHHCC
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHh
Confidence 467899999999999999999998765555544444433
No 283
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=24.46 E-value=1.8e+02 Score=22.74 Aligned_cols=27 Identities=26% Similarity=0.410 Sum_probs=23.0
Q ss_pred hcccHHHHHHHhCCCHHHHHHHHHHHH
Q psy396 147 RSLSLKYMAQCFGVSVEFIEKEVARFA 173 (239)
Q Consensus 147 s~v~l~~mA~~fg~s~~~lE~~L~~lI 173 (239)
...+...+|+.+|+|+..|...+.+..
T Consensus 140 ~~~~~~eIA~~lgis~~tv~~~~~ra~ 166 (179)
T PRK11924 140 EGLSYREIAEILGVPVGTVKSRLRRAR 166 (179)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 578889999999999999988876643
No 284
>PF06667 PspB: Phage shock protein B; InterPro: IPR009554 This family consists of several bacterial phage shock protein B (PspB) sequences. The phage shock protein (psp) operon is induced in response to heat, ethanol, osmotic shock and infection by filamentous bacteriophages []. Expression of the operon requires the alternative sigma factor sigma54 and the transcriptional activator PspF. In addition, PspA plays a negative regulatory role, and the integral-membrane proteins PspB and PspC play a positive one [].; GO: 0006355 regulation of transcription, DNA-dependent, 0009271 phage shock
Probab=24.39 E-value=1.2e+02 Score=21.70 Aligned_cols=26 Identities=19% Similarity=0.342 Sum_probs=21.5
Q ss_pred hHHHHHHHHhhHHHHHHHHHhhhhhc
Q psy396 213 GILYQTTVKRGDIFLNRLKKLARVID 238 (239)
Q Consensus 213 ~~~~~~~i~~~~~~~~r~~~l~~~~~ 238 (239)
....++...+++.+..||+.|.+++|
T Consensus 41 ~~~L~~L~~~a~rm~eRI~tLE~ILd 66 (75)
T PF06667_consen 41 EQRLQELYEQAERMEERIETLERILD 66 (75)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 34456677789999999999999997
No 285
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=24.29 E-value=1.8e+02 Score=17.83 Aligned_cols=35 Identities=14% Similarity=0.208 Sum_probs=23.2
Q ss_pred HHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHH
Q psy396 136 LRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVAR 171 (239)
Q Consensus 136 ~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~ 171 (239)
...|.+-++- ..-.+...|+.+|+|...+-..|.+
T Consensus 7 ~~~i~~aL~~-~~gn~~~aA~~Lgisr~tL~~klkk 41 (42)
T PF02954_consen 7 KQLIRQALER-CGGNVSKAARLLGISRRTLYRKLKK 41 (42)
T ss_dssp HHHHHHHHHH-TTT-HHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHHH-hCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 3344444444 3456789999999999988887754
No 286
>cd08807 CARD_CARD10_CARMA3 Caspase activation and recruitment domain of CARD10-like proteins. Caspase activation and recruitment domain (CARD) similar to that found in CARD10, also known as CARMA3 (caspase recruitment domain-containing membrane-associated guanylate kinase protein 3) or BIMP1. The CARMA3-BCL10-MALT1 signalosome plays a role in the GPCR-induced NF-kB activation. CARMA3 is more widely expressed than CARMA1, which is found only in hematopoietic cells. In endothelial and smooth muscle cells, CARMA3-mediated NF-kB activation induces pro-inflammatory signals within the vasculature and is a key factor in atherogenesis. In bronchial epithelial cells, CARMA3-mediated NF-kB signaling is important for the development of allergic airway inflammation. In general, CARDs are death domains (DDs) found 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 fo
Probab=24.26 E-value=1.2e+02 Score=22.41 Aligned_cols=66 Identities=11% Similarity=0.062 Sum_probs=46.8
Q ss_pred ccCHhHHHHHHHHHHHHcCChhHHHHccccchhHHHHhhhhhhHHHHHHHHHHhchHHHHHHHHHHHHhh
Q psy396 47 LAEFGTIIRYTVLACMIALPRYNLRKKLMHHGVMAQALHSQYRDLREYFVSLYDGHYFEFLKCLAAVEQD 116 (239)
Q Consensus 47 ~~s~~di~~Y~~Lc~Las~~R~elk~~ll~s~~~~~~~e~~~p~l~~li~af~~~~y~~~~~~L~~~~~~ 116 (239)
.+.|.++.-|+-=|++++.+-.| .+++++.+...... .-.+.+++..==..-|..|++.|+...|+
T Consensus 15 ~l~p~~vtpYLrQ~~VL~~~deE---EI~~~~~~~~~~~k-~~~LLDIL~trG~~gf~aFLeSLE~~yp~ 80 (86)
T cd08807 15 ALNPAKLTPYLRQCRVIDEQDEE---EVLNSYRFPCRINR-TGRLMDILRGRGKRGYEAFLEALEFYYPE 80 (86)
T ss_pred hhcHhhccHHHHHhCCCChhhHH---HHHhccchhhHHHH-HHHHHHHHHhcCchHHHHHHHHHHhhhHH
Confidence 45677788899889998876533 35666655444444 55678888777778889999999965554
No 287
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=24.01 E-value=2e+02 Score=22.70 Aligned_cols=47 Identities=17% Similarity=0.072 Sum_probs=32.6
Q ss_pred HhHHHHHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHH
Q psy396 125 PHYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAA 174 (239)
Q Consensus 125 ~h~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~ 174 (239)
..+..|=..-|+-.+..|+ ...+.+.+|+.+|+|+..+...|.+...
T Consensus 108 ~~l~~L~~~~r~v~~l~~~---~g~s~~eIA~~lgis~~tV~~~l~Rar~ 154 (164)
T PRK12547 108 KALNLLSADQREAIILIGA---SGFSYEDAAAICGCAVGTIKSRVSRARN 154 (164)
T ss_pred HHHHhCCHHHHHHHHHHHH---cCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3444444444444444454 5677999999999999999998877553
No 288
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=23.95 E-value=1.8e+02 Score=23.72 Aligned_cols=45 Identities=13% Similarity=0.002 Sum_probs=31.7
Q ss_pred hHHHHHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHH
Q psy396 126 HYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFA 173 (239)
Q Consensus 126 h~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI 173 (239)
.+..|=..-|+-.+..|+ .-.+...+|+.+|+|+..|...|.+..
T Consensus 131 ~l~~Lp~~~R~v~~L~~~---~g~s~~EIA~~lgis~~tVk~~l~RAr 175 (189)
T PRK12530 131 CLNHLPAQQARVFMMREY---LELSSEQICQECDISTSNLHVLLYRAR 175 (189)
T ss_pred HHHhCCHHHHHHHhHHHH---cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 344444455555555554 467899999999999999988876543
No 289
>PRK14003 potassium-transporting ATPase subunit C; Provisional
Probab=23.74 E-value=1.1e+02 Score=26.13 Aligned_cols=40 Identities=15% Similarity=0.264 Sum_probs=32.3
Q ss_pred ccCcchhHhHHHHHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcC
Q psy396 118 KRDPLLNPHYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAG 176 (239)
Q Consensus 118 ~~D~~L~~h~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g 176 (239)
-+||++++. +..+++.++|++=|+|+++|++.+.+.....
T Consensus 131 GLDPhISp~-------------------aA~~Qv~RVA~argl~~~~v~~LI~~~t~~~ 170 (194)
T PRK14003 131 GLDPHISPE-------------------AARAQIERVAKARGLPPDQLEILITKNTDGR 170 (194)
T ss_pred cCCCCCCHH-------------------HHHHHHHHHHHHhCcCHHHHHHHHHHHhhCC
Confidence 468888876 3456789999999999999999888877643
No 290
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=23.72 E-value=1.8e+02 Score=24.22 Aligned_cols=28 Identities=21% Similarity=0.300 Sum_probs=23.6
Q ss_pred hhcccHHHHHHHhCCCHHHHHHHHHHHH
Q psy396 146 YRSLSLKYMAQCFGVSVEFIEKEVARFA 173 (239)
Q Consensus 146 Ys~v~l~~mA~~fg~s~~~lE~~L~~lI 173 (239)
+.-.+...||+.+|+|+..|...|.+..
T Consensus 152 ~~g~s~~EIA~~Lgis~~tV~~~l~RAr 179 (203)
T PRK09647 152 IEGLSYEEIAATLGVKLGTVRSRIHRGR 179 (203)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 5678899999999999999988887643
No 291
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=23.57 E-value=96 Score=19.67 Aligned_cols=25 Identities=12% Similarity=0.036 Sum_probs=21.6
Q ss_pred hcccHHHHHHHhCCCHHHHHHHHHH
Q psy396 147 RSLSLKYMAQCFGVSVEFIEKEVAR 171 (239)
Q Consensus 147 s~v~l~~mA~~fg~s~~~lE~~L~~ 171 (239)
+.-.+..+|+.+|++...|..|...
T Consensus 26 ~~~~~~~la~~~~l~~~qV~~WF~n 50 (56)
T smart00389 26 SREEREELAAKLGLSERQVKVWFQN 50 (56)
T ss_pred CHHHHHHHHHHHCcCHHHHHHhHHH
Confidence 5667899999999999999998764
No 292
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=23.47 E-value=1.9e+02 Score=22.76 Aligned_cols=27 Identities=19% Similarity=0.325 Sum_probs=23.2
Q ss_pred hhcccHHHHHHHhCCCHHHHHHHHHHH
Q psy396 146 YRSLSLKYMAQCFGVSVEFIEKEVARF 172 (239)
Q Consensus 146 Ys~v~l~~mA~~fg~s~~~lE~~L~~l 172 (239)
+...+.+.+|+.+|+|+..|...+.+.
T Consensus 142 ~~~~s~~eIA~~lgis~~tV~~~l~ra 168 (182)
T PRK09652 142 IEGLSYEEIAEIMGCPIGTVRSRIFRA 168 (182)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 367899999999999999998887653
No 293
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=23.38 E-value=2.3e+02 Score=21.91 Aligned_cols=43 Identities=12% Similarity=0.121 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHH
Q psy396 128 RHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFA 173 (239)
Q Consensus 128 ~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI 173 (239)
..|=..-|.-....|+ ...+...+|+.+|+|+..+...+.+.+
T Consensus 105 ~~Lp~~~r~v~~l~~~---~g~s~~EIA~~lgis~~tV~~~l~ra~ 147 (161)
T PRK09047 105 QKLPARQREAFLLRYW---EDMDVAETAAAMGCSEGSVKTHCSRAT 147 (161)
T ss_pred HhCCHHHHHHHHHHHH---hcCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3333444444444454 567799999999999999988776644
No 294
>PRK05574 holA DNA polymerase III subunit delta; Reviewed
Probab=23.35 E-value=5.2e+02 Score=22.79 Aligned_cols=73 Identities=18% Similarity=0.225 Sum_probs=46.5
Q ss_pred hHHHHHHHHHHhchHHHHHHHHHHHHhhhccCcchhHhHHHHHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHH
Q psy396 89 RDLREYFVSLYDGHYFEFLKCLAAVEQDMKRDPLLNPHYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFI 165 (239)
Q Consensus 89 p~l~~li~af~~~~y~~~~~~L~~~~~~l~~D~~L~~h~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~l 165 (239)
..+-+++.++..++....++.+..+... ..||+ .-+..+.+.+|.-...+.+.. ...+.+.+++.+|+++..+
T Consensus 216 ~~~f~l~dai~~~~~~~a~~~l~~l~~~-~~~~~--~il~~l~~~~~~l~~~k~~~~-~g~~~~~~~~~~~i~~~~~ 288 (340)
T PRK05574 216 FDVFDLVDAILAGKIKRALRILDGLRLE-GEEPI--KLLAALQREFRLLLQLKILSQ-QGYPLQQLAKELRVWPYRV 288 (340)
T ss_pred CCHHHHHHHHHCCCHHHHHHHHHHHHHC-CCcHH--HHHHHHHHHHHHHHHHHHHHH-cCCCHHHHHHHcCCChhHH
Confidence 4578899999999999998888876543 34443 344555555555544444332 2345677777777765443
No 295
>KOG2316|consensus
Probab=23.21 E-value=1.1e+02 Score=27.00 Aligned_cols=51 Identities=22% Similarity=0.356 Sum_probs=36.9
Q ss_pred HHHhhhhhcccHHHHHHHhCC-CHHHH-----HHHHHHHHHcCccceeecccCCEEEE
Q psy396 140 KQILQAYRSLSLKYMAQCFGV-SVEFI-----EKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 140 ~qyl~pYs~v~l~~mA~~fg~-s~~~l-----E~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
-.++..|+++..+++.+.+|+ +..++ +..|.+||.+| ++|+|=.+.-+--.
T Consensus 114 GAIlS~YQr~RVEnVC~RL~L~~Ls~LW~rdQ~~LL~eMi~~g-~~AiiiKVAAigL~ 170 (277)
T KOG2316|consen 114 GAILSDYQRTRVENVCSRLGLVSLSYLWQRDQEELLQEMILSG-LDAIIIKVAAIGLG 170 (277)
T ss_pred hhhHhHHHHHHHHHHHhhhCceeehHHHhccHHHHHHHHHHcC-CCeEEEEEeecccC
Confidence 346777888888888888886 33333 66788999987 88888777655443
No 296
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=23.16 E-value=1.1e+02 Score=19.66 Aligned_cols=20 Identities=25% Similarity=0.338 Sum_probs=15.5
Q ss_pred cHHHHHHHhCCCHHHHHHHH
Q psy396 150 SLKYMAQCFGVSVEFIEKEV 169 (239)
Q Consensus 150 ~l~~mA~~fg~s~~~lE~~L 169 (239)
+|..+|+..|+|...+-..|
T Consensus 1 Ti~dIA~~agvS~~TVSr~l 20 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVL 20 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHH
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 57889999999988765544
No 297
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=23.07 E-value=1.9e+02 Score=25.39 Aligned_cols=55 Identities=20% Similarity=0.036 Sum_probs=42.2
Q ss_pred HHHHHHHHhhhh-hcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 135 RLRAYKQILQAY-RSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 135 r~~~l~qyl~pY-s~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
|.-.++++|... ..+++..+|+.+|+|...+-..|..|...|-+.- |..++....
T Consensus 26 r~l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~~--~~~~~~Y~l 81 (271)
T PRK10163 26 RGIAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQAADFVYQ--DSQLGWWHI 81 (271)
T ss_pred HHHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE--cCCCCeEEe
Confidence 444556666554 4689999999999999999999999999998832 555565554
No 298
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=23.07 E-value=2.2e+02 Score=22.91 Aligned_cols=28 Identities=18% Similarity=0.133 Sum_probs=24.6
Q ss_pred hhcccHHHHHHHhCCCHHHHHHHHHHHH
Q psy396 146 YRSLSLKYMAQCFGVSVEFIEKEVARFA 173 (239)
Q Consensus 146 Ys~v~l~~mA~~fg~s~~~lE~~L~~lI 173 (239)
+...+.+.+|+.+|+|+..|...+.+..
T Consensus 147 ~~~~s~~eIA~~lgis~~tV~~~l~ra~ 174 (182)
T PRK12537 147 VDGCSHAEIAQRLGAPLGTVKAWIKRSL 174 (182)
T ss_pred HcCCCHHHHHHHHCCChhhHHHHHHHHH
Confidence 4678999999999999999999887754
No 299
>PHA02591 hypothetical protein; Provisional
Probab=22.96 E-value=99 Score=22.56 Aligned_cols=23 Identities=22% Similarity=0.413 Sum_probs=19.9
Q ss_pred cccHHHHHHHhCCCHHHHHHHHH
Q psy396 148 SLSLKYMAQCFGVSVEFIEKEVA 170 (239)
Q Consensus 148 ~v~l~~mA~~fg~s~~~lE~~L~ 170 (239)
-.+.+.+|+.+|+|++.|-+.+.
T Consensus 59 GlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 59 GFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHh
Confidence 56889999999999999888764
No 300
>PF08679 DsrD: Dissimilatory sulfite reductase D (DsrD); InterPro: IPR014793 The structure of the dissimilatory sulphite reductase D (DsrD) protein has shown it to contain a winged-helix motif similar to those found in DNA binding proteins []. The structure suggests a possible role for DsrD in transcription or translation of genes, which catalyse dissimilatory sulphite reduction. ; PDB: 1WQ2_B 1UCR_B.
Probab=22.75 E-value=2.6e+02 Score=19.71 Aligned_cols=42 Identities=17% Similarity=0.268 Sum_probs=30.7
Q ss_pred HHHHHhh----hhhcccHHHHHHHh-CCCHHHHHHHHHHHHHcCccc
Q psy396 138 AYKQILQ----AYRSLSLKYMAQCF-GVSVEFIEKEVARFAAAGRLQ 179 (239)
Q Consensus 138 ~l~qyl~----pYs~v~l~~mA~~f-g~s~~~lE~~L~~lI~~g~l~ 179 (239)
.++.+|+ +=+..-+..+++.| ++.+-++-+.+.+||.+|+|.
T Consensus 5 ~Ile~L~~k~~~KskfYfkD~~k~~pd~k~R~vKKi~~~LV~Eg~l~ 51 (67)
T PF08679_consen 5 KILEFLEAKKKKKSKFYFKDFYKAFPDAKPREVKKIVNELVNEGKLE 51 (67)
T ss_dssp HHHHHHSSCCCHSS-EEHHHHHHH-TTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHhccCCCCceeHHHHHHHCCCcCHHHHHHHHHHHHhhCeEE
Confidence 4455555 34567788888865 788899999999999999984
No 301
>PRK00315 potassium-transporting ATPase subunit C; Reviewed
Probab=22.65 E-value=1.1e+02 Score=26.06 Aligned_cols=39 Identities=21% Similarity=0.311 Sum_probs=31.7
Q ss_pred ccCcchhHhHHHHHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHc
Q psy396 118 KRDPLLNPHYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAA 175 (239)
Q Consensus 118 ~~D~~L~~h~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~ 175 (239)
-+||++++. +..+++.++|++=|+|+++|++.+.+....
T Consensus 128 GLDPhIS~~-------------------aA~~Qv~RVA~argl~~~~v~~LI~~~t~~ 166 (193)
T PRK00315 128 GLDPHISPA-------------------AAAYQIPRVAAARQLPVEQVAQLVAAYTQG 166 (193)
T ss_pred CCCCCCCHH-------------------HHHHHHHHHHHHhCcCHHHHHHHHHHHhcC
Confidence 468888876 345678999999999999999888887664
No 302
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=22.58 E-value=2e+02 Score=17.85 Aligned_cols=23 Identities=26% Similarity=0.319 Sum_probs=19.3
Q ss_pred hcccHHHHHHHhCCCHHHHHHHH
Q psy396 147 RSLSLKYMAQCFGVSVEFIEKEV 169 (239)
Q Consensus 147 s~v~l~~mA~~fg~s~~~lE~~L 169 (239)
..++...+|+..|++...+-++.
T Consensus 14 ~gltq~~lA~~~gvs~~~vs~~e 36 (58)
T TIGR03070 14 LGLTQADLADLAGVGLRFIRDVE 36 (58)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHH
Confidence 48899999999999988776664
No 303
>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B.
Probab=22.55 E-value=64 Score=21.04 Aligned_cols=26 Identities=12% Similarity=-0.051 Sum_probs=22.3
Q ss_pred HHHHHHchhcCHHHHHHHHhccCCCC
Q psy396 17 YEGVYCLAIRQYCRAAELFVDVVPTF 42 (239)
Q Consensus 17 ~~Gl~~l~~~~y~~Aa~~F~~~~~~f 42 (239)
..|..++..|+|.+|...|-.+...+
T Consensus 2 ~~a~~~~~~g~~~~A~~~~~~~l~~~ 27 (65)
T PF13432_consen 2 ALARALYQQGDYDEAIAAFEQALKQD 27 (65)
T ss_dssp HHHHHHHHCTHHHHHHHHHHHHHCCS
T ss_pred hHHHHHHHcCCHHHHHHHHHHHHHHC
Confidence 36888999999999999999996555
No 304
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=22.52 E-value=2.3e+02 Score=22.65 Aligned_cols=28 Identities=18% Similarity=0.323 Sum_probs=24.2
Q ss_pred hhcccHHHHHHHhCCCHHHHHHHHHHHH
Q psy396 146 YRSLSLKYMAQCFGVSVEFIEKEVARFA 173 (239)
Q Consensus 146 Ys~v~l~~mA~~fg~s~~~lE~~L~~lI 173 (239)
|...+.+.+|+.+|+|+..|...+.+..
T Consensus 149 ~~~~s~~eIA~~lgis~~~V~~~l~ra~ 176 (186)
T PRK13919 149 YQGYTHREAAQLLGLPLGTLKTRARRAL 176 (186)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 5678999999999999999998887654
No 305
>KOG1126|consensus
Probab=22.44 E-value=3.6e+02 Score=27.20 Aligned_cols=50 Identities=10% Similarity=0.093 Sum_probs=37.7
Q ss_pred hHHHHHHHHHHhchHHHHHHHHHHHHhhhccCcchhHhHHHHHHHHHHHH
Q psy396 89 RDLREYFVSLYDGHYFEFLKCLAAVEQDMKRDPLLNPHYRHYVQEMRLRA 138 (239)
Q Consensus 89 p~l~~li~af~~~~y~~~~~~L~~~~~~l~~D~~L~~h~~~l~~~ir~~~ 138 (239)
+.+...---|...+|.+++..|++.+.....+-...--...+++.++..-
T Consensus 559 ~~~~~~~il~~~~~~~eal~~LEeLk~~vP~es~v~~llgki~k~~~~~~ 608 (638)
T KOG1126|consen 559 CKYHRASILFSLGRYVEALQELEELKELVPQESSVFALLGKIYKRLGNTD 608 (638)
T ss_pred hHHHHHHHHHhhcchHHHHHHHHHHHHhCcchHHHHHHHHHHHHHHccch
Confidence 34555566677889999999999998887777777766677777776543
No 306
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=22.41 E-value=2.3e+02 Score=23.07 Aligned_cols=43 Identities=16% Similarity=0.186 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHH
Q psy396 128 RHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFA 173 (239)
Q Consensus 128 ~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI 173 (239)
..|=..-|+-....|+ ...+.+.+|+.+|+|+..+...+.+..
T Consensus 110 ~~Lp~~~R~v~~L~~~---eg~s~~EIA~~lgis~~tV~~~l~Rar 152 (182)
T PRK12511 110 FDLPEEQRAALHLVAI---EGLSYQEAAAVLGIPIGTLMSRIGRAR 152 (182)
T ss_pred HhCCHHHHHHHHHHHH---cCCCHHHHHHHhCcCHHHHHHHHHHHH
Confidence 3333444444444454 467899999999999999988876543
No 307
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=22.39 E-value=4.6e+02 Score=21.84 Aligned_cols=39 Identities=21% Similarity=0.199 Sum_probs=32.6
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 149 LSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 149 v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
.+-..+|+.+|++.+.+-+.|.+|-.+|-|.- ..+.|++
T Consensus 170 ~t~~~lA~~lG~sretvsR~L~~L~~~G~I~~----~~~~i~I 208 (226)
T PRK10402 170 EKHTQAAEYLGVSYRHLLYVLAQFIQDGYLKK----SKRGYLI 208 (226)
T ss_pred chHHHHHHHHCCcHHHHHHHHHHHHHCCCEEe----eCCEEEE
Confidence 46789999999999999999999999877643 4566777
No 308
>PRK14001 potassium-transporting ATPase subunit C; Provisional
Probab=22.30 E-value=1.2e+02 Score=25.80 Aligned_cols=39 Identities=21% Similarity=0.250 Sum_probs=32.0
Q ss_pred ccCcchhHhHHHHHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHc
Q psy396 118 KRDPLLNPHYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAA 175 (239)
Q Consensus 118 ~~D~~L~~h~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~ 175 (239)
-+||++++.. ..+++.++|++=|+|+++|++.+.+....
T Consensus 128 GLDPhIS~~a-------------------A~~Qv~RVA~argl~~~~v~~LV~~~t~~ 166 (189)
T PRK14001 128 GLDPAISVVN-------------------AKLQAPRVAQARNISIRQVERLIEDHTDA 166 (189)
T ss_pred cCCCCCCHHH-------------------HHHHHHHHHHHhCcCHHHHHHHHHHHhcC
Confidence 4688888763 35678999999999999999988887664
No 309
>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=22.05 E-value=2e+02 Score=22.36 Aligned_cols=29 Identities=31% Similarity=0.481 Sum_probs=24.8
Q ss_pred hhcccHHHHHHHhCCCHHHHHHHHHHHHH
Q psy396 146 YRSLSLKYMAQCFGVSVEFIEKEVARFAA 174 (239)
Q Consensus 146 Ys~v~l~~mA~~fg~s~~~lE~~L~~lI~ 174 (239)
+...+.+.+|+.+|+|+..|...+.+...
T Consensus 124 ~~g~s~~eIA~~lgis~~tV~~~l~ra~~ 152 (162)
T TIGR02983 124 YEDLSEAQVAEALGISVGTVKSRLSRALA 152 (162)
T ss_pred HhcCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 56789999999999999999988877543
No 310
>TIGR01636 phage_rinA phage transcriptional activator, RinA family. This model represents a family of phage proteins, including RinA, a transcriptional activator in staphylococcal phage phi 11. This family shows similarity to ArpU, a phage-related putative autolysin regulator, and to some sporulation-specific sigma factors.
Probab=21.94 E-value=2.6e+02 Score=21.84 Aligned_cols=45 Identities=13% Similarity=0.022 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHH
Q psy396 128 RHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFA 173 (239)
Q Consensus 128 ~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI 173 (239)
..|-+.-|.-+...|+.+.. .+...+|..+|+|...+-+.-.+++
T Consensus 81 ~~Ld~~er~II~~rY~~~~~-~t~~~Ia~~l~iS~~t~~r~r~~~l 125 (134)
T TIGR01636 81 NEADEQTRVIIQELYMKKRP-LTLVGLAQQLFISKSTAYRLRNHII 125 (134)
T ss_pred HhCCHHHHHHHHHHHccCCC-CCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 34444455555567787755 7999999999999998876655544
No 311
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=21.80 E-value=1.2e+02 Score=17.85 Aligned_cols=23 Identities=22% Similarity=0.304 Sum_probs=19.2
Q ss_pred hcccHHHHHHHhCCCHHHHHHHH
Q psy396 147 RSLSLKYMAQCFGVSVEFIEKEV 169 (239)
Q Consensus 147 s~v~l~~mA~~fg~s~~~lE~~L 169 (239)
..++...+|+..|++...+.++.
T Consensus 9 ~~~s~~~la~~~~i~~~~i~~~~ 31 (56)
T smart00530 9 KGLTQEELAEKLGVSRSTLSRIE 31 (56)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHH
Confidence 47889999999999988886654
No 312
>PF13994 PgaD: PgaD-like protein
Probab=21.56 E-value=1.8e+02 Score=23.00 Aligned_cols=53 Identities=21% Similarity=0.265 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCE
Q psy396 131 VQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGN 188 (239)
Q Consensus 131 ~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~ 188 (239)
|+..|-+.-.+=-.| ..++.+.+|+.|+++++. +.++-..+.+-.--|...++
T Consensus 84 yn~~Rf~~~~rr~~~-~~~~~~elA~~f~l~~~~----l~~lr~~k~~~V~~d~~G~I 136 (138)
T PF13994_consen 84 YNRLRFRGRRRRRRP-PPVSDEELARSFGLSPEQ----LQQLRQAKVLTVHHDDHGRI 136 (138)
T ss_pred HHHHHhcchhhccCC-CCCCHHHHHHHcCCCHHH----HHHHHhCCeEEEEeCCCCCc
Confidence 344444444444344 239999999999999655 44555555555555555444
No 313
>TIGR00681 kdpC K+-transporting ATPase, C subunit. This chain has a single predicted transmembrane region near the amino end. It is part of a K+-transport ATPase that contains two other membrane-bound subunits, KdpA and KdpB, and a small subunit KdpF. KdpA is the K+-translocating subunit, KdpB the ATP-hydrolyzing subunit. During assembly of the complex, KdpA and KdpC bind to each other. This interaction is thought to stabilize the complex [PubMed:9858692]. Data indicates that KdpC might connect the KdpA, the K+-transporting subunit, to KdpB, the ATP-hydrolyzing (energy providing) subunit [PubMed:9858692].
Probab=21.34 E-value=1.3e+02 Score=25.56 Aligned_cols=39 Identities=13% Similarity=0.246 Sum_probs=32.0
Q ss_pred ccCcchhHhHHHHHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHc
Q psy396 118 KRDPLLNPHYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAA 175 (239)
Q Consensus 118 ~~D~~L~~h~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~ 175 (239)
-+||++++.. ..+++.++|++=|+|+++|++.+.+....
T Consensus 126 GLDPhISp~a-------------------A~~Qv~RVA~argl~~~~v~~LI~~~t~~ 164 (187)
T TIGR00681 126 GLDPHISPAA-------------------AQAQFPRVAKARNISPQQLQSLITKHTEG 164 (187)
T ss_pred cCCCCCCHHH-------------------HHHHHHHHHHHhCcCHHHHHHHHHHHhcC
Confidence 4688888763 45678999999999999999988887764
No 314
>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=21.25 E-value=1e+02 Score=20.23 Aligned_cols=30 Identities=23% Similarity=0.214 Sum_probs=19.4
Q ss_pred HHHHhhhhhcccHHHHHHHhCCCHHHHHHHHH
Q psy396 139 YKQILQAYRSLSLKYMAQCFGVSVEFIEKEVA 170 (239)
Q Consensus 139 l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~ 170 (239)
+++.++.-. +...+|..||++...|-+++-
T Consensus 15 iI~~~e~g~--s~~~ia~~fgv~~sTv~~I~K 44 (53)
T PF04218_consen 15 IIKRLEEGE--SKRDIAREFGVSRSTVSTILK 44 (53)
T ss_dssp HHHHHHCTT---HHHHHHHHT--CCHHHHHHH
T ss_pred HHHHHHcCC--CHHHHHHHhCCCHHHHHHHHH
Confidence 344455533 789999999999988877663
No 315
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=21.12 E-value=2.6e+02 Score=21.79 Aligned_cols=43 Identities=16% Similarity=0.074 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHH
Q psy396 128 RHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFA 173 (239)
Q Consensus 128 ~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI 173 (239)
..|=..-|.-....|+ ...+.+.+|+.+|+|+..|...+.+.+
T Consensus 108 ~~L~~~~r~v~~l~~~---~~~s~~EIA~~lgis~~tV~~~l~ra~ 150 (163)
T PRK07037 108 SELPARTRYAFEMYRL---HGETQKDIARELGVSPTLVNFMIRDAL 150 (163)
T ss_pred HhCCHHHHHHHHHHHH---cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3333333333333444 467799999999999999988876543
No 316
>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=21.10 E-value=2.5e+02 Score=23.58 Aligned_cols=38 Identities=13% Similarity=0.135 Sum_probs=27.4
Q ss_pred HHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHH
Q psy396 133 EMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFA 173 (239)
Q Consensus 133 ~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI 173 (239)
.-|.-....|+ .-.++..+|+.+|+|...+...+.+.+
T Consensus 179 ~~r~il~l~y~---~~~s~~eIA~~lgis~~tV~~~~~ra~ 216 (224)
T TIGR02479 179 REQLVLSLYYY---EELNLKEIGEVLGLTESRVSQIHSQAL 216 (224)
T ss_pred HHHHHHHHHHh---CCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 33444444454 556899999999999999988776544
No 317
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=21.05 E-value=1.7e+02 Score=22.45 Aligned_cols=31 Identities=29% Similarity=0.348 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHH
Q psy396 130 YVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEV 169 (239)
Q Consensus 130 l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L 169 (239)
=++.||++. .++-+..|..+|+|+..|.+|=
T Consensus 48 eIk~iRe~~---------~lSQ~vFA~~L~vs~~Tv~~WE 78 (104)
T COG2944 48 EIKAIREKL---------GLSQPVFARYLGVSVSTVRKWE 78 (104)
T ss_pred HHHHHHHHh---------CCCHHHHHHHHCCCHHHHHHHH
Confidence 345566554 8899999999999999999883
No 318
>PRK04217 hypothetical protein; Provisional
Probab=20.75 E-value=1.5e+02 Score=22.81 Aligned_cols=25 Identities=16% Similarity=0.199 Sum_probs=20.7
Q ss_pred hcccHHHHHHHhCCCHHHHHHHHHH
Q psy396 147 RSLSLKYMAQCFGVSVEFIEKEVAR 171 (239)
Q Consensus 147 s~v~l~~mA~~fg~s~~~lE~~L~~ 171 (239)
..++.+.+|+.+|+|...|...+.+
T Consensus 57 eGlS~~EIAk~LGIS~sTV~r~L~R 81 (110)
T PRK04217 57 EGLTQEEAGKRMGVSRGTVWRALTS 81 (110)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 6679999999999999987666543
No 319
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=20.74 E-value=2.4e+02 Score=21.68 Aligned_cols=30 Identities=23% Similarity=0.383 Sum_probs=13.8
Q ss_pred HHHHHHHHHhhhhhcccHHHHHHHhCCCHHH
Q psy396 134 MRLRAYKQILQAYRSLSLKYMAQCFGVSVEF 164 (239)
Q Consensus 134 ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~ 164 (239)
|.-..+.++++ ...++...+|+..|+|...
T Consensus 5 i~~~~l~~ll~-~~Glsq~eLA~~~Gis~~~ 34 (120)
T PRK13890 5 IFFTNVLRLLD-ERHMTKKELSERSGVSISF 34 (120)
T ss_pred HHHHHHHHHHH-HcCCCHHHHHHHHCcCHHH
Confidence 33333444443 2345555555555555433
No 320
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=20.69 E-value=1.6e+02 Score=28.80 Aligned_cols=38 Identities=26% Similarity=0.230 Sum_probs=31.0
Q ss_pred HHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHH
Q psy396 134 MRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARF 172 (239)
Q Consensus 134 ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~l 172 (239)
-|.+.+.+++.. ..++.+.+|+.||+|.-.|-.++..+
T Consensus 4 ~R~~~iL~~L~~-~~~t~~~LA~~l~VS~RTIr~dI~~i 41 (584)
T PRK09863 4 ERELKIVDLLEQ-QDRSGGELAQQLGVSRRTIVRDIAYI 41 (584)
T ss_pred HHHHHHHHHHHc-CCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 466667777754 67999999999999999988888765
No 321
>PF07848 PaaX: PaaX-like protein; InterPro: IPR012906 This entry describes the N-terminal region of proteins that are similar to, and nclude, the product of the paaX gene of Escherichia coli (P76086 from SWISSPROT). PaaX is a transcriptional regulator that is always found in association with operons believed to be involved in the degradation of phenylacetic acid []. The gene product has been shown to bind to the promoter sites and repress their transcription []. ; PDB: 3KFW_X 3L09_B.
Probab=20.65 E-value=1.2e+02 Score=21.26 Aligned_cols=34 Identities=26% Similarity=0.379 Sum_probs=27.0
Q ss_pred hcccHHHHHHHhCCCHHHHHHHHHHHHHcCccce
Q psy396 147 RSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQC 180 (239)
Q Consensus 147 s~v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~a 180 (239)
..-+|-.+.+.||++...+-.-|.+|-.+|-|..
T Consensus 22 ~~~~Li~ll~~~Gv~e~avR~alsRl~~~G~L~~ 55 (70)
T PF07848_consen 22 WVASLIRLLAAFGVSESAVRTALSRLVRRGWLES 55 (70)
T ss_dssp EHHHHHHHHCCTT--HHHHHHHHHHHHHTTSEEE
T ss_pred eHHHHHHHHHHcCCChHHHHHHHHHHHHcCceee
Confidence 3445667888899999999999999999999865
No 322
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=20.59 E-value=2.3e+02 Score=24.56 Aligned_cols=55 Identities=20% Similarity=0.243 Sum_probs=41.1
Q ss_pred HHHHHHHHhhhhhc-ccHHHHHHHhCCCHHHHHHHHHHHHHcCccceeecccCCEEEE
Q psy396 135 RLRAYKQILQAYRS-LSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191 (239)
Q Consensus 135 r~~~l~qyl~pYs~-v~l~~mA~~fg~s~~~lE~~L~~lI~~g~l~arID~~~~~l~~ 191 (239)
|--.++.+|..... +++..+|+.+|+|...+-..|..|+..|-+ +-|..+|....
T Consensus 5 ral~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL~~~G~v--~~d~~~g~Y~L 60 (246)
T COG1414 5 RALAILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTLVELGYV--EQDPEDGRYRL 60 (246)
T ss_pred HHHHHHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCE--EEcCCCCcEee
Confidence 34455666666444 679999999999999999999999998876 23444555554
No 323
>PF13934 ELYS: Nuclear pore complex assembly
Probab=20.54 E-value=5.4e+02 Score=21.99 Aligned_cols=138 Identities=14% Similarity=0.184 Sum_probs=69.0
Q ss_pred hhhHHHHHHHHchhcCHHHHHHHHhccCCCCCCccccCHhHHHHHHHHHHHHcCChhHHHHccccchhHHHHhhhhhhHH
Q psy396 12 NKLKAYEGVYCLAIRQYCRAAELFVDVVPTFESYELAEFGTIIRYTVLACMIALPRYNLRKKLMHHGVMAQALHSQYRDL 91 (239)
Q Consensus 12 ~kl~~~~Gl~~l~~~~y~~Aa~~F~~~~~~f~~~e~~s~~di~~Y~~Lc~Las~~R~elk~~ll~s~~~~~~~e~~~p~l 91 (239)
+=.+...|+.+|..++|++|.+++.+..-. . --+.+ ++.+|+...+..+--..+.. +...+.. ...+
T Consensus 78 ~~~~~~~g~W~LD~~~~~~A~~~L~~ps~~--~---~~~~~-----Il~~L~~~~~~~lAL~y~~~--~~p~l~s-~~~~ 144 (226)
T PF13934_consen 78 KYIKFIQGFWLLDHGDFEEALELLSHPSLI--P---WFPDK-----ILQALLRRGDPKLALRYLRA--VGPPLSS-PEAL 144 (226)
T ss_pred HHHHHHHHHHHhChHhHHHHHHHhCCCCCC--c---ccHHH-----HHHHHHHCCChhHHHHHHHh--cCCCCCC-HHHH
Confidence 345678999999999999999999776211 1 01112 23334433333321111111 1111111 1223
Q ss_pred HHHHHHHHhchHHHHHHHHHHHHhhhccCcchhHhHHHHHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHH-HHH
Q psy396 92 REYFVSLYDGHYFEFLKCLAAVEQDMKRDPLLNPHYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEK-EVA 170 (239)
Q Consensus 92 ~~li~af~~~~y~~~~~~L~~~~~~l~~D~~L~~h~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~-~L~ 170 (239)
.-.+....++...+.+.....+.+... +...++.+...+++-. ..+.+.+.+++|-+.-|+ ++.
T Consensus 145 ~~~~~~La~~~v~EAf~~~R~~~~~~~-------------~~l~e~l~~~~~~~~~--~~~~~~~Ll~LPl~~~EE~~l~ 209 (226)
T PF13934_consen 145 TLYFVALANGLVTEAFSFQRSYPDELR-------------RRLFEQLLEHCLEECA--RSGRLDELLSLPLDEEEEQWLE 209 (226)
T ss_pred HHHHHHHHcCCHHHHHHHHHhCchhhh-------------HHHHHHHHHHHHHHhh--hhhHHHHHHhCCCChHHHHHHH
Confidence 444445556666666665444322111 2222333333332211 567788888988866554 556
Q ss_pred HHHHcCc
Q psy396 171 RFAAAGR 177 (239)
Q Consensus 171 ~lI~~g~ 177 (239)
++..+++
T Consensus 210 ~~L~~~~ 216 (226)
T PF13934_consen 210 KYLRESP 216 (226)
T ss_pred HHHccCC
Confidence 6665543
No 324
>PF14056 DUF4250: Domain of unknown function (DUF4250)
Probab=20.50 E-value=1.5e+02 Score=20.06 Aligned_cols=22 Identities=23% Similarity=0.335 Sum_probs=20.3
Q ss_pred cHHHHHHHhCCCHHHHHHHHHH
Q psy396 150 SLKYMAQCFGVSVEFIEKEVAR 171 (239)
Q Consensus 150 ~l~~mA~~fg~s~~~lE~~L~~ 171 (239)
+++.+...++++.+++++.|..
T Consensus 22 sLd~Lc~~~~id~~~l~~kL~~ 43 (55)
T PF14056_consen 22 SLDELCYDYDIDKEELEEKLAS 43 (55)
T ss_pred CHHHHHHHhCCCHHHHHHHHHH
Confidence 8999999999999999998875
No 325
>PRK13997 potassium-transporting ATPase subunit C; Provisional
Probab=20.45 E-value=1.3e+02 Score=25.67 Aligned_cols=39 Identities=13% Similarity=0.255 Sum_probs=31.9
Q ss_pred ccCcchhHhHHHHHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHc
Q psy396 118 KRDPLLNPHYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAA 175 (239)
Q Consensus 118 ~~D~~L~~h~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~ 175 (239)
-+||++++.. ..+++.++|++=|+|++++++.+.+....
T Consensus 130 GLDPhISp~a-------------------A~~Qv~RVA~argls~~~v~~LV~~~t~~ 168 (193)
T PRK13997 130 GLDPDISPKA-------------------ASVQVERISKLTNIPKETLDQLIKDQTEG 168 (193)
T ss_pred CCCCCCCHHH-------------------HHHHHHHHHHHhCcCHHHHHHHHHHHccC
Confidence 4688888763 45678999999999999999988887664
No 326
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=20.40 E-value=3.2e+02 Score=21.37 Aligned_cols=43 Identities=14% Similarity=0.241 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHH
Q psy396 127 YRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVAR 171 (239)
Q Consensus 127 ~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~ 171 (239)
++.++..||...-....+- -.+=..+|+.+|+|+..|-+.|..
T Consensus 3 ~~~vlPaiRa~lA~~L~ee--G~Sq~~iA~LLGltqaAVS~Yls~ 45 (119)
T COG2522 3 VEEVLPAIRALLAKELIEE--GLSQYRIAKLLGLTQAAVSQYLSG 45 (119)
T ss_pred hHHHHHHHHHHHHHHHHHc--CCcHHHHHHHhCCCHHHHHHHHcc
Confidence 3556666776665555554 566678999999999988777654
No 327
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=20.37 E-value=2.9e+02 Score=22.10 Aligned_cols=27 Identities=19% Similarity=0.079 Sum_probs=23.5
Q ss_pred hcccHHHHHHHhCCCHHHHHHHHHHHH
Q psy396 147 RSLSLKYMAQCFGVSVEFIEKEVARFA 173 (239)
Q Consensus 147 s~v~l~~mA~~fg~s~~~lE~~L~~lI 173 (239)
...+...+|+.||+|+..|...+.+..
T Consensus 146 ~g~s~~eIA~~l~is~~tV~~~l~ra~ 172 (184)
T PRK12512 146 EGASIKETAAKLSMSEGAVRVALHRGL 172 (184)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 588999999999999999988887644
No 328
>KOG3151|consensus
Probab=20.34 E-value=6.1e+02 Score=22.50 Aligned_cols=125 Identities=15% Similarity=0.164 Sum_probs=85.4
Q ss_pred cccCHhHHHHHHHHHHHHcCChhHH-------HHccccchhHHHHhhhhhhH-----HHHHHHHHHhchHHHHHHHHHHH
Q psy396 46 ELAEFGTIIRYTVLACMIALPRYNL-------RKKLMHHGVMAQALHSQYRD-----LREYFVSLYDGHYFEFLKCLAAV 113 (239)
Q Consensus 46 e~~s~~di~~Y~~Lc~Las~~R~el-------k~~ll~s~~~~~~~e~~~p~-----l~~li~af~~~~y~~~~~~L~~~ 113 (239)
.++-+.|+.-++++.++.+.|-... +.=-.++.+ .++. .+. -..++.-....+..+|...|+..
T Consensus 51 ~l~~aR~ilEi~vl~SI~t~D~~sFerY~~Qlk~YY~d~~~---~l~~-S~~~~~l~GLnLL~LLsqNRiaeFHteLe~l 126 (260)
T KOG3151|consen 51 QLIIARDILEIGVLLSILTKDFESFERYMNQLKPYYFDYNE---KLSE-SEKKHKLLGLNLLYLLSQNRIAEFHTELELL 126 (260)
T ss_pred HHHHHHHHHHHHHHHHHHhccHHHHHHHHHHhcchhccccc---ccCc-chhhhHHHHHHHHHHHHhccHHHHHHHHHhc
Confidence 5677889999999999998765432 111122221 1111 222 23456667788999999999887
Q ss_pred Hh-hhccCcchhHhHHHHHHHHHHHHHHHHhhhhhcccHHHHHHHhCCCHHHHHHHHHHHHHc
Q psy396 114 EQ-DMKRDPLLNPHYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAA 175 (239)
Q Consensus 114 ~~-~l~~D~~L~~h~~~l~~~ir~~~l~qyl~pYs~v~l~~mA~~fg~s~~~lE~~L~~lI~~ 175 (239)
-. .+..++|+++ +=.|=+.+-+-++.+.+..=++++.+.-.--..+=.+.+.++|+..|.-
T Consensus 127 p~~~l~~~~~I~~-~v~LEq~~MEGaYnKv~~a~~s~p~~~y~~FmdIl~~tiRdEIA~c~EK 188 (260)
T KOG3151|consen 127 PKKILQHNPYISH-PVSLEQSLMEGAYNKVLSAKQSIPSEEYTYFMDILLDTIRDEIAGCIEK 188 (260)
T ss_pred cHHHhhccchhhh-HHHHHHHHHhhHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 54 4556677764 4567777778888888888888887777666677777888888888764
No 329
>PF03962 Mnd1: Mnd1 family; InterPro: IPR005647 This family of proteins includes meiotic nuclear division protein 1 (MND1) from Saccharomyces cerevisiae (Baker's yeast). The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair [].
Probab=20.29 E-value=1.8e+02 Score=24.38 Aligned_cols=39 Identities=18% Similarity=0.230 Sum_probs=30.3
Q ss_pred hhhcccHHHHHHH-hCCCHHHHHHHHHHHHHcCccce-eec
Q psy396 145 AYRSLSLKYMAQC-FGVSVEFIEKEVARFAAAGRLQC-KID 183 (239)
Q Consensus 145 pYs~v~l~~mA~~-fg~s~~~lE~~L~~lI~~g~l~a-rID 183 (239)
+|+-=+|..+|-. =|+++..|.+.|..||-+|.+++ ||-
T Consensus 11 ~y~lKELEK~~pK~~gI~~~~VKdvlq~LvDDglV~~EKiG 51 (188)
T PF03962_consen 11 FYTLKELEKLAPKEKGIVSMSVKDVLQSLVDDGLVHVEKIG 51 (188)
T ss_pred cccHHHHHHHcccccCCchhhHHHHHHHHhccccchhhhcc
Confidence 4555566777665 69999999999999999999965 553
No 330
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=20.16 E-value=2.5e+02 Score=23.71 Aligned_cols=28 Identities=21% Similarity=0.279 Sum_probs=24.2
Q ss_pred hhcccHHHHHHHhCCCHHHHHHHHHHHH
Q psy396 146 YRSLSLKYMAQCFGVSVEFIEKEVARFA 173 (239)
Q Consensus 146 Ys~v~l~~mA~~fg~s~~~lE~~L~~lI 173 (239)
+...+...+|+.+|+|+..|...+.+.+
T Consensus 196 ~eg~s~~EIA~~lgis~~tVk~~~~rA~ 223 (234)
T PRK08301 196 GEEKTQKEVADMLGISQSYISRLEKRII 223 (234)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4688999999999999999988876654
No 331
>KOG3081|consensus
Probab=20.15 E-value=6.1e+02 Score=23.02 Aligned_cols=48 Identities=10% Similarity=0.110 Sum_probs=33.2
Q ss_pred HHHHHchhcCHHHHHHHHhccCCCCCCccccCHhHHHHHHHHHHHHcCChhHH
Q psy396 18 EGVYCLAIRQYCRAAELFVDVVPTFESYELAEFGTIIRYTVLACMIALPRYNL 70 (239)
Q Consensus 18 ~Gl~~l~~~~y~~Aa~~F~~~~~~f~~~e~~s~~di~~Y~~Lc~Las~~R~el 70 (239)
.+..+|..|+|++|-+...++.....++ ++.+.=++.|++......+.
T Consensus 213 ~Av~~l~~~~~eeAe~lL~eaL~kd~~d-----petL~Nliv~a~~~Gkd~~~ 260 (299)
T KOG3081|consen 213 QAVCHLQLGRYEEAESLLEEALDKDAKD-----PETLANLIVLALHLGKDAEV 260 (299)
T ss_pred HHHHHHHhcCHHHHHHHHHHHHhccCCC-----HHHHHHHHHHHHHhCCChHH
Confidence 4457889999999999999995544332 55566666777776554333
No 332
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=20.01 E-value=3e+02 Score=21.35 Aligned_cols=28 Identities=18% Similarity=0.109 Sum_probs=23.6
Q ss_pred hhcccHHHHHHHhCCCHHHHHHHHHHHH
Q psy396 146 YRSLSLKYMAQCFGVSVEFIEKEVARFA 173 (239)
Q Consensus 146 Ys~v~l~~mA~~fg~s~~~lE~~L~~lI 173 (239)
|.-.+...+|+.+|+|+..|...+.+..
T Consensus 120 ~~g~s~~EIA~~lgis~~tV~~~l~Rar 147 (160)
T PRK09642 120 LEEKSYQEIALQEKIEVKTVEMKLYRAR 147 (160)
T ss_pred HhCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4678899999999999999988876543
Done!