Query psy9207
Match_columns 125
No_of_seqs 100 out of 209
Neff 7.5
Searched_HMMs 46136
Date Fri Aug 16 21:38:36 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9207.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9207hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10075 PCI_Csn8: COP9 signal 100.0 1.9E-29 4.1E-34 177.1 6.5 98 3-100 38-137 (143)
2 KOG4414|consensus 99.9 3.1E-28 6.7E-33 170.8 7.0 121 2-124 72-196 (197)
3 KOG3151|consensus 99.8 2.7E-20 5.9E-25 138.9 11.3 88 3-90 134-222 (260)
4 KOG3252|consensus 99.0 1.7E-09 3.6E-14 78.8 7.6 118 3-123 95-216 (217)
5 PF03399 SAC3_GANP: SAC3/GANP/ 99.0 2.9E-09 6.3E-14 77.8 7.8 72 2-73 131-204 (204)
6 PF01399 PCI: PCI domain; Int 98.2 2.2E-05 4.7E-10 51.0 8.6 77 8-84 2-83 (105)
7 KOG1861|consensus 98.1 3.3E-05 7.1E-10 63.4 9.9 99 2-101 419-521 (540)
8 COG5187 RPN7 26S proteasome re 97.4 0.001 2.2E-08 52.4 8.4 119 3-121 267-403 (412)
9 smart00088 PINT motif in prote 97.3 0.00074 1.6E-08 42.9 5.6 63 39-101 2-72 (88)
10 smart00753 PAM PCI/PINT associ 97.3 0.00074 1.6E-08 42.9 5.6 63 39-101 2-72 (88)
11 KOG0687|consensus 96.5 0.017 3.8E-07 46.0 7.9 96 8-103 258-367 (393)
12 KOG2581|consensus 96.4 0.0053 1.1E-07 50.1 4.5 80 5-84 317-400 (493)
13 KOG1076|consensus 95.2 0.11 2.4E-06 45.2 7.6 77 8-84 656-741 (843)
14 KOG1464|consensus 94.3 0.56 1.2E-05 37.2 9.2 83 2-84 300-387 (440)
15 KOG1498|consensus 92.5 0.56 1.2E-05 38.4 6.7 49 36-84 328-376 (439)
16 KOG2908|consensus 92.0 2.5 5.4E-05 34.1 9.7 83 9-94 237-335 (380)
17 COG5071 RPN5 26S proteasome re 91.9 0.97 2.1E-05 36.2 7.3 51 39-89 331-384 (439)
18 PF03374 ANT: Phage antirepres 91.7 0.52 1.1E-05 31.1 4.9 47 51-97 14-62 (111)
19 PF12840 HTH_20: Helix-turn-he 88.5 2.5 5.3E-05 24.8 5.6 45 38-83 2-46 (61)
20 PF02042 RWP-RK: RWP-RK domain 88.0 1.1 2.3E-05 26.3 3.6 29 58-86 12-40 (52)
21 PF07037 DUF1323: Putative tra 86.2 1.1 2.4E-05 30.7 3.4 28 63-90 2-29 (122)
22 PF03683 UPF0175: Uncharacteri 86.1 1.4 3E-05 27.5 3.6 30 60-89 33-62 (76)
23 PF12728 HTH_17: Helix-turn-he 85.8 1.3 2.8E-05 25.0 3.1 24 62-85 2-25 (51)
24 PF10668 Phage_terminase: Phag 85.3 3.3 7.1E-05 24.9 4.8 43 48-90 9-51 (60)
25 PF04760 IF2_N: Translation in 83.5 1.2 2.6E-05 25.7 2.3 28 61-88 3-31 (54)
26 PF10255 Paf67: RNA polymerase 82.8 4.6 0.0001 33.1 6.2 48 34-81 290-341 (404)
27 cd07377 WHTH_GntR Winged helix 81.3 4.2 9.1E-05 23.4 4.2 49 41-89 4-56 (66)
28 PF08727 P3A: Poliovirus 3A pr 80.6 1.1 2.4E-05 26.7 1.4 17 74-90 28-44 (57)
29 COG2522 Predicted transcriptio 80.5 7.4 0.00016 26.6 5.7 43 41-85 4-46 (119)
30 TIGR01764 excise DNA binding d 79.5 3 6.4E-05 22.6 3.0 23 62-84 2-24 (49)
31 TIGR01128 holA DNA polymerase 77.4 20 0.00043 27.1 7.9 80 8-90 182-266 (302)
32 PF08280 HTH_Mga: M protein tr 77.1 12 0.00026 21.8 5.5 34 50-84 9-42 (59)
33 KOG3389|consensus 76.8 1.5 3.2E-05 31.2 1.4 28 63-90 121-149 (178)
34 PF04800 ETC_C1_NDUFA4: ETC co 76.8 3.2 7E-05 27.6 2.9 16 74-89 57-72 (101)
35 PF14555 UBA_4: UBA-like domai 76.4 4 8.6E-05 22.4 2.8 27 64-90 4-30 (43)
36 smart00550 Zalpha Z-DNA-bindin 76.3 12 0.00027 22.5 5.3 45 45-89 5-53 (68)
37 PF13412 HTH_24: Winged helix- 74.7 12 0.00026 20.6 5.1 42 45-87 2-46 (48)
38 PRK13503 transcriptional activ 74.6 7.7 0.00017 29.0 4.9 40 50-89 175-216 (278)
39 PF13463 HTH_27: Winged helix 74.4 8.9 0.00019 22.4 4.3 41 49-89 6-49 (68)
40 cd04762 HTH_MerR-trunc Helix-T 74.0 5.3 0.00011 21.3 3.0 23 62-84 1-23 (49)
41 PF09339 HTH_IclR: IclR helix- 72.1 8.6 0.00019 21.7 3.6 40 50-89 7-49 (52)
42 PF05584 Sulfolobus_pRN: Sulfo 71.8 18 0.0004 22.5 5.2 35 46-82 5-39 (72)
43 PLN03238 probable histone acet 71.3 12 0.00026 29.4 5.3 54 42-95 204-259 (290)
44 COG3357 Predicted transcriptio 70.7 14 0.0003 24.2 4.7 30 45-74 2-31 (97)
45 smart00071 Galanin Galanin. Ga 70.5 6.4 0.00014 25.8 3.0 17 83-99 10-28 (103)
46 PF14056 DUF4250: Domain of un 70.1 11 0.00023 22.3 3.7 28 63-90 22-49 (55)
47 cd01104 HTH_MlrA-CarA Helix-Tu 68.9 21 0.00045 20.9 5.6 53 63-123 2-54 (68)
48 PF06627 DUF1153: Protein of u 68.6 18 0.00039 23.5 4.8 38 47-84 35-72 (90)
49 PF13411 MerR_1: MerR HTH fami 68.5 11 0.00025 22.1 3.8 50 63-122 2-52 (69)
50 smart00345 HTH_GNTR helix_turn 68.3 9.6 0.00021 21.3 3.3 45 45-89 3-51 (60)
51 PF01022 HTH_5: Bacterial regu 67.8 15 0.00033 20.2 4.0 35 46-82 2-36 (47)
52 PF01418 HTH_6: Helix-turn-hel 67.7 13 0.00028 22.9 4.0 29 60-88 33-61 (77)
53 KOG0686|consensus 67.4 36 0.00078 28.3 7.4 83 8-90 307-400 (466)
54 COG5484 Uncharacterized conser 66.7 6.8 0.00015 30.4 3.0 28 62-89 20-47 (279)
55 COG2886 Uncharacterized small 65.0 26 0.00057 22.7 5.1 39 48-88 30-68 (88)
56 smart00422 HTH_MERR helix_turn 64.8 26 0.00056 20.5 5.6 50 63-121 2-52 (70)
57 smart00497 IENR1 Intron encode 63.9 16 0.00035 20.2 3.7 27 62-89 18-44 (53)
58 PF08279 HTH_11: HTH domain; 63.6 24 0.00053 19.7 4.9 41 49-89 3-46 (55)
59 PF08220 HTH_DeoR: DeoR-like h 63.5 26 0.00057 20.2 4.6 40 48-88 2-44 (57)
60 smart00420 HTH_DEOR helix_turn 63.4 22 0.00047 19.2 5.2 39 50-89 4-45 (53)
61 PF00165 HTH_AraC: Bacterial r 63.3 15 0.00032 19.7 3.3 30 59-88 6-36 (42)
62 KOG2582|consensus 63.3 20 0.00044 29.3 5.2 65 37-101 293-364 (422)
63 PF06056 Terminase_5: Putative 62.7 13 0.00028 22.0 3.1 29 61-89 13-41 (58)
64 PF05687 DUF822: Plant protein 62.4 9.9 0.00021 27.0 3.0 23 75-97 47-71 (150)
65 PF13404 HTH_AsnC-type: AsnC-t 62.2 24 0.00053 19.3 5.3 34 49-83 6-39 (42)
66 TIGR03573 WbuX N-acetyl sugar 61.9 14 0.0003 29.4 4.1 37 45-82 302-342 (343)
67 TIGR02844 spore_III_D sporulat 61.4 21 0.00045 22.6 4.1 34 47-82 7-40 (80)
68 PF00392 GntR: Bacterial regul 61.1 22 0.00047 20.8 4.0 48 42-89 4-55 (64)
69 COG1777 Predicted transcriptio 61.0 19 0.00041 27.1 4.4 44 36-81 5-48 (217)
70 KOG1860|consensus 60.8 92 0.002 28.4 9.2 88 3-90 305-416 (927)
71 KOG1497|consensus 60.8 21 0.00046 28.9 4.9 80 43-122 299-389 (399)
72 PF12169 DNA_pol3_gamma3: DNA 60.7 29 0.00063 23.4 5.2 51 7-57 16-68 (143)
73 PRK05629 hypothetical protein; 60.6 62 0.0013 25.1 7.5 82 7-90 195-279 (318)
74 cd04761 HTH_MerR-SF Helix-Turn 60.5 14 0.00029 20.1 2.9 21 63-83 2-22 (49)
75 smart00418 HTH_ARSR helix_turn 60.3 24 0.00053 19.5 4.1 37 51-89 2-41 (66)
76 TIGR00122 birA_repr_reg BirA b 59.8 34 0.00074 20.2 5.8 39 50-90 4-45 (69)
77 PF00627 UBA: UBA/TS-N domain; 59.6 14 0.00031 19.4 2.7 26 64-90 6-31 (37)
78 PF13545 HTH_Crp_2: Crp-like h 59.5 19 0.00041 21.5 3.6 36 61-96 28-68 (76)
79 cd04763 HTH_MlrA-like Helix-Tu 59.5 34 0.00074 20.1 5.9 53 63-124 2-55 (68)
80 PF08784 RPA_C: Replication pr 59.1 23 0.0005 22.7 4.2 45 45-89 46-96 (102)
81 PRK11161 fumarate/nitrate redu 58.8 47 0.001 24.1 6.3 28 62-89 185-215 (235)
82 smart00874 B5 tRNA synthetase 58.3 19 0.00041 21.4 3.5 30 61-90 5-36 (71)
83 KOG2758|consensus 57.8 44 0.00095 27.2 6.2 47 38-84 326-372 (432)
84 PF12802 MarR_2: MarR family; 57.8 33 0.00072 19.4 4.7 40 50-89 9-52 (62)
85 PRK05574 holA DNA polymerase I 57.6 85 0.0019 24.1 9.0 83 7-90 216-301 (340)
86 PF13384 HTH_23: Homeodomain-l 56.8 27 0.00059 19.1 3.8 36 46-84 5-40 (50)
87 PRK00430 fis global DNA-bindin 56.7 52 0.0011 21.3 7.0 59 23-86 34-93 (95)
88 PF09035 Tn916-Xis: Excisionas 56.1 16 0.00035 22.4 2.8 30 61-90 13-45 (67)
89 PF00325 Crp: Bacterial regula 55.7 22 0.00048 18.5 3.0 19 62-80 3-21 (32)
90 PF03484 B5: tRNA synthetase B 55.6 25 0.00055 21.2 3.7 30 61-90 5-36 (70)
91 PRK11511 DNA-binding transcrip 55.3 49 0.0011 22.1 5.5 36 49-84 12-48 (127)
92 PRK07914 hypothetical protein; 54.9 99 0.0021 24.0 8.4 80 7-90 197-279 (320)
93 PF01853 MOZ_SAS: MOZ/SAS fami 54.9 29 0.00063 25.6 4.5 49 41-89 128-178 (188)
94 smart00419 HTH_CRP helix_turn_ 54.7 27 0.0006 18.5 3.5 29 61-89 8-39 (48)
95 PF04433 SWIRM: SWIRM domain; 54.3 51 0.0011 20.5 5.6 43 45-87 36-83 (86)
96 PRK07452 DNA polymerase III su 54.1 1E+02 0.0022 23.8 8.3 82 7-90 201-288 (326)
97 TIGR01610 phage_O_Nterm phage 53.8 45 0.00098 21.3 4.9 32 58-89 44-78 (95)
98 PRK10141 DNA-binding transcrip 53.5 58 0.0013 22.0 5.5 53 36-89 6-61 (117)
99 COG3645 Uncharacterized phage- 53.1 38 0.00081 23.7 4.6 41 50-90 36-76 (135)
100 COG1654 BirA Biotin operon rep 52.5 57 0.0012 20.6 5.8 48 53-100 11-65 (79)
101 PF13542 HTH_Tnp_ISL3: Helix-t 52.4 39 0.00084 18.6 5.3 36 45-83 14-49 (52)
102 PF13730 HTH_36: Helix-turn-he 52.1 28 0.0006 19.5 3.3 25 63-87 27-54 (55)
103 cd04790 HTH_Cfa-like_unk Helix 51.7 66 0.0014 23.0 5.9 47 62-117 2-49 (172)
104 TIGR02702 SufR_cyano iron-sulf 51.4 51 0.0011 23.9 5.4 42 47-89 2-46 (203)
105 PF06250 DUF1016: Protein of u 51.4 48 0.001 26.4 5.5 83 6-90 25-127 (320)
106 PF09551 Spore_II_R: Stage II 50.7 70 0.0015 22.2 5.6 60 41-100 19-88 (130)
107 COG5079 SAC3 Nuclear protein e 50.2 56 0.0012 28.1 5.9 65 22-89 303-376 (646)
108 cd04764 HTH_MlrA-like_sg1 Heli 50.0 29 0.00063 20.3 3.3 49 63-121 2-51 (67)
109 PF04967 HTH_10: HTH DNA bindi 49.7 34 0.00073 19.9 3.4 23 60-82 22-44 (53)
110 PLN00104 MYST -like histone ac 49.0 44 0.00095 28.0 5.1 46 43-88 356-401 (450)
111 PF09494 Slx4: Slx4 endonuclea 48.9 25 0.00054 21.0 2.8 31 58-88 21-60 (64)
112 PF05344 DUF746: Domain of Unk 47.5 20 0.00043 22.0 2.2 32 58-89 10-42 (65)
113 PRK10434 srlR DNA-bindng trans 47.1 47 0.001 25.2 4.8 49 47-96 6-59 (256)
114 smart00342 HTH_ARAC helix_turn 46.8 57 0.0012 18.9 6.0 37 50-88 41-79 (84)
115 PF06971 Put_DNA-bind_N: Putat 46.5 30 0.00066 19.9 2.8 27 54-80 21-47 (50)
116 PRK10906 DNA-binding transcrip 46.2 1.3E+02 0.0028 22.8 7.6 51 46-97 5-60 (252)
117 PF04539 Sigma70_r3: Sigma-70 46.2 64 0.0014 19.3 5.8 25 60-84 19-43 (78)
118 cd04766 HTH_HspR Helix-Turn-He 46.0 74 0.0016 20.0 5.4 25 62-87 2-26 (91)
119 COG1349 GlpR Transcriptional r 45.8 95 0.0021 23.5 6.3 54 47-101 6-64 (253)
120 PF07742 BTG: BTG family; Int 45.8 51 0.0011 22.3 4.3 63 32-95 23-105 (118)
121 PF09756 DDRGK: DDRGK domain; 45.7 28 0.0006 25.7 3.2 54 39-101 100-161 (188)
122 PRK10681 DNA-binding transcrip 45.7 23 0.00051 26.7 2.9 47 45-93 6-56 (252)
123 PRK13500 transcriptional activ 45.5 69 0.0015 24.7 5.6 42 48-89 208-251 (312)
124 PF13518 HTH_28: Helix-turn-he 45.4 51 0.0011 17.9 4.4 34 48-84 2-35 (52)
125 PF11428 DUF3196: Protein of u 45.3 59 0.0013 25.6 5.1 58 9-66 47-109 (286)
126 PF05543 Peptidase_C47: Stapho 44.4 29 0.00062 25.4 3.0 59 31-90 23-83 (175)
127 cd04235 AAK_CK AAK_CK: Carbama 43.9 57 0.0012 25.8 4.9 30 72-101 131-166 (308)
128 PLN03239 histone acetyltransfe 43.7 93 0.002 25.2 6.0 48 43-90 263-313 (351)
129 PRK09392 ftrB transcriptional 43.5 1.2E+02 0.0025 22.1 6.3 39 45-83 147-195 (236)
130 COG2207 AraC AraC-type DNA-bin 43.5 83 0.0018 19.8 5.4 37 46-83 21-58 (127)
131 cd01105 HTH_GlnR-like Helix-Tu 43.3 82 0.0018 19.7 5.4 50 62-120 2-52 (88)
132 PRK09391 fixK transcriptional 43.3 1.3E+02 0.0028 22.0 6.8 44 46-89 154-210 (230)
133 TIGR02837 spore_II_R stage II 43.2 1.1E+02 0.0023 22.3 5.8 61 40-100 53-123 (168)
134 PF01047 MarR: MarR family; I 43.1 61 0.0013 18.2 4.5 38 51-89 8-48 (59)
135 TIGR02297 HpaA 4-hydroxyphenyl 42.6 78 0.0017 23.7 5.4 41 49-89 189-231 (287)
136 COG3415 Transposase and inacti 42.5 1.2E+02 0.0025 21.2 7.6 66 50-119 10-75 (138)
137 PF12244 DUF3606: Protein of u 42.5 39 0.00084 19.8 2.9 25 64-88 23-47 (57)
138 PF04801 Sin_N: Sin-like prote 42.4 48 0.001 27.0 4.4 48 41-89 332-387 (421)
139 PRK13918 CRP/FNR family transc 42.3 1.1E+02 0.0023 21.5 5.9 36 61-96 149-189 (202)
140 KOG1463|consensus 41.6 2E+02 0.0043 23.7 7.6 115 2-118 281-410 (411)
141 PF07453 NUMOD1: NUMOD1 domain 41.6 29 0.00062 18.1 2.1 19 62-80 17-35 (37)
142 COG2901 Fis Factor for inversi 41.5 1E+02 0.0022 20.2 6.5 57 25-86 39-96 (98)
143 PHA02591 hypothetical protein; 41.4 41 0.00088 21.4 3.0 37 45-84 46-82 (83)
144 cd04773 HTH_TioE_rpt2 Second H 41.3 1E+02 0.0022 20.1 5.5 22 62-83 1-22 (108)
145 PF10116 Host_attach: Protein 41.1 33 0.00072 23.3 2.9 39 33-71 100-138 (138)
146 PF04703 FaeA: FaeA-like prote 41.0 71 0.0015 19.1 4.0 42 48-89 2-46 (62)
147 COG1522 Lrp Transcriptional re 41.0 90 0.002 21.0 5.1 39 45-84 7-45 (154)
148 PF03793 PASTA: PASTA domain; 40.9 28 0.00061 20.0 2.2 22 69-90 5-26 (63)
149 PF07964 Red1: Rec10 / Red1; 40.7 80 0.0017 28.0 5.6 48 32-85 657-704 (706)
150 PRK10572 DNA-binding transcrip 40.5 70 0.0015 24.1 4.8 40 50-89 187-228 (290)
151 cd04789 HTH_Cfa Helix-Turn-Hel 40.2 1E+02 0.0022 19.9 5.6 46 62-117 2-48 (102)
152 KOG2747|consensus 40.1 71 0.0015 26.3 5.0 47 43-89 310-357 (396)
153 PRK09685 DNA-binding transcrip 40.0 1.1E+02 0.0023 23.2 5.8 42 48-89 199-242 (302)
154 PRK13501 transcriptional activ 39.9 88 0.0019 23.6 5.3 41 49-89 179-221 (290)
155 smart00165 UBA Ubiquitin assoc 39.6 27 0.00058 18.0 1.8 19 72-90 12-30 (37)
156 PF00376 MerR: MerR family reg 39.6 46 0.00099 17.7 2.7 21 63-83 1-21 (38)
157 PF01710 HTH_Tnp_IS630: Transp 39.3 97 0.0021 20.6 4.9 39 52-90 62-100 (119)
158 PF13443 HTH_26: Cro/C1-type H 38.9 33 0.00071 19.6 2.3 24 61-84 10-33 (63)
159 TIGR03697 NtcA_cyano global ni 38.8 1.3E+02 0.0028 20.8 6.5 36 61-96 143-183 (193)
160 PF13591 MerR_2: MerR HTH fami 38.8 51 0.0011 20.6 3.3 27 62-89 1-27 (84)
161 PRK12686 carbamate kinase; Rev 38.7 67 0.0015 25.5 4.6 18 72-89 133-150 (312)
162 smart00346 HTH_ICLR helix_turn 38.3 93 0.002 18.9 4.9 40 50-89 9-51 (91)
163 PF12793 SgrR_N: Sugar transpo 38.1 51 0.0011 22.1 3.3 32 58-89 16-50 (115)
164 smart00344 HTH_ASNC helix_turn 37.9 1.1E+02 0.0023 19.5 5.3 40 49-89 6-48 (108)
165 cd08311 Death_p75NR Death doma 37.8 84 0.0018 19.6 4.1 36 48-83 2-37 (77)
166 PRK11753 DNA-binding transcrip 37.6 1.4E+02 0.0029 21.1 5.8 38 61-98 168-210 (211)
167 TIGR02394 rpoS_proteo RNA poly 37.4 80 0.0017 24.1 4.8 33 58-90 239-282 (285)
168 PRK09978 DNA-binding transcrip 37.0 1.1E+02 0.0025 23.7 5.6 43 46-88 142-185 (274)
169 PF13551 HTH_29: Winged helix- 37.0 1.1E+02 0.0023 19.2 5.2 22 63-84 14-35 (112)
170 PF04545 Sigma70_r4: Sigma-70, 36.9 74 0.0016 17.4 4.1 23 59-81 18-40 (50)
171 COG5159 RPN6 26S proteasome re 36.9 2.3E+02 0.0049 23.0 8.4 120 3-122 280-412 (421)
172 PF02682 AHS1: Allophanate hyd 36.9 38 0.00082 25.0 2.8 85 6-90 24-128 (202)
173 PF12672 DUF3793: Protein of u 36.9 53 0.0011 23.7 3.5 63 11-85 65-127 (176)
174 PF02002 TFIIE_alpha: TFIIE al 36.8 69 0.0015 20.6 3.8 34 50-84 17-50 (105)
175 PRK12454 carbamate kinase-like 36.6 75 0.0016 25.3 4.5 29 73-101 136-170 (313)
176 cd01109 HTH_YyaN Helix-Turn-He 36.0 1.2E+02 0.0027 19.7 6.0 49 63-120 2-51 (113)
177 PF00356 LacI: Bacterial regul 35.6 69 0.0015 17.9 3.1 12 64-75 2-13 (46)
178 smart00796 AHS1 Allophanate hy 34.9 49 0.0011 24.4 3.1 87 4-90 22-129 (201)
179 COG1448 TyrB Aspartate/tyrosin 34.4 1.7E+02 0.0037 24.2 6.3 18 69-86 349-366 (396)
180 PF06262 DUF1025: Possibl zinc 34.2 30 0.00065 22.7 1.7 17 64-80 78-94 (97)
181 TIGR03879 near_KaiC_dom probab 34.1 1.2E+02 0.0026 18.9 4.7 27 57-83 28-54 (73)
182 PRK15185 transcriptional regul 33.8 1.2E+02 0.0026 24.1 5.3 44 46-89 206-250 (309)
183 cd04772 HTH_TioE_rpt1 First He 33.7 1.3E+02 0.0028 19.3 5.0 46 63-117 2-48 (99)
184 PF12401 DUF3662: Protein of u 33.7 56 0.0012 21.9 3.0 38 55-92 51-96 (116)
185 PRK08558 adenine phosphoribosy 33.5 1.2E+02 0.0026 22.9 5.1 31 50-83 15-45 (238)
186 cd04780 HTH_MerR-like_sg5 Heli 32.9 1.3E+02 0.0029 19.1 5.7 49 63-120 2-51 (95)
187 PF01381 HTH_3: Helix-turn-hel 32.8 63 0.0014 17.8 2.7 24 61-84 9-32 (55)
188 PRK15482 transcriptional regul 32.7 72 0.0016 24.2 3.8 26 62-87 35-60 (285)
189 smart00513 SAP Putative DNA-bi 32.6 56 0.0012 16.8 2.3 19 72-90 3-21 (35)
190 PF11360 DUF3110: Protein of u 32.6 63 0.0014 20.7 3.0 24 74-97 56-84 (86)
191 PRK10402 DNA-binding transcrip 32.5 1.9E+02 0.0042 20.9 6.9 44 46-89 150-200 (226)
192 PF10537 WAC_Acf1_DNA_bd: ATP- 32.5 83 0.0018 20.8 3.6 61 5-68 19-85 (102)
193 cd04774 HTH_YfmP Helix-Turn-He 32.1 1.4E+02 0.003 19.1 5.2 48 63-120 2-50 (96)
194 PF05930 Phage_AlpA: Prophage 32.0 70 0.0015 17.9 2.8 23 61-83 3-25 (51)
195 TIGR03338 phnR_burk phosphonat 31.9 1.9E+02 0.0041 20.6 6.4 49 41-89 14-65 (212)
196 PRK15186 AraC family transcrip 31.8 1.3E+02 0.0028 23.4 5.1 42 45-86 180-222 (291)
197 PF15436 PGBA_N: Plasminogen-b 31.6 96 0.0021 23.4 4.2 37 49-85 102-146 (218)
198 PF13317 DUF4088: Protein of u 31.4 2E+02 0.0044 21.5 5.8 58 8-71 140-197 (229)
199 PRK06585 holA DNA polymerase I 31.4 2.5E+02 0.0054 21.8 7.0 65 7-74 213-281 (343)
200 PF01978 TrmB: Sugar-specific 31.2 1.1E+02 0.0025 17.8 4.3 32 58-89 19-53 (68)
201 PF02269 TFIID-18kDa: Transcri 31.2 78 0.0017 20.4 3.3 27 34-60 19-45 (93)
202 PRK13502 transcriptional activ 31.1 1.2E+02 0.0026 22.7 4.8 41 49-89 179-221 (282)
203 PF09107 SelB-wing_3: Elongati 31.1 1.1E+02 0.0023 17.5 4.9 33 58-90 7-42 (50)
204 PF07304 SRA1: Steroid recepto 30.8 85 0.0018 22.2 3.7 24 2-25 87-110 (157)
205 PF12643 MazG-like: MazG-like 30.7 1.6E+02 0.0034 19.3 6.3 34 45-84 35-68 (98)
206 PRK06266 transcription initiat 30.5 2.1E+02 0.0045 20.6 6.0 39 45-84 21-59 (178)
207 COG3604 FhlA Transcriptional r 30.3 1.3E+02 0.0029 25.8 5.2 50 38-89 498-547 (550)
208 PRK10046 dpiA two-component re 30.3 1.2E+02 0.0027 21.7 4.6 33 50-82 166-198 (225)
209 cd04768 HTH_BmrR-like Helix-Tu 30.1 1.5E+02 0.0032 18.8 5.6 49 63-120 2-51 (96)
210 PRK10371 DNA-binding transcrip 29.9 1.8E+02 0.0038 22.4 5.6 41 49-89 194-236 (302)
211 PRK05988 formate dehydrogenase 29.9 1.3E+02 0.0029 21.2 4.5 32 51-82 28-62 (156)
212 PRK15044 transcriptional regul 29.9 2.3E+02 0.0051 22.4 6.2 41 46-86 192-233 (295)
213 PF00440 TetR_N: Bacterial reg 29.9 99 0.0022 16.7 3.9 25 54-78 9-33 (47)
214 TIGR01958 nuoE_fam NADH-quinon 29.8 1.3E+02 0.0027 20.9 4.4 32 51-82 21-55 (148)
215 COG5114 Histone acetyltransfer 29.7 1.5E+02 0.0031 24.1 5.1 44 46-89 383-429 (432)
216 PRK05657 RNA polymerase sigma 29.6 1.5E+02 0.0033 23.3 5.3 33 58-90 279-322 (325)
217 TIGR00370 conserved hypothetic 29.6 68 0.0015 23.7 3.1 29 62-90 91-119 (202)
218 PRK12515 RNA polymerase sigma 29.6 1.9E+02 0.0041 20.2 5.4 22 57-78 143-164 (189)
219 smart00311 PWI PWI, domain in 29.5 67 0.0015 19.6 2.6 19 66-84 16-34 (74)
220 PF07900 DUF1670: Protein of u 29.5 2.2E+02 0.0048 21.6 5.8 45 43-87 84-135 (220)
221 COG0549 ArcC Carbamate kinase 29.3 1.3E+02 0.0027 24.0 4.6 28 74-101 136-169 (312)
222 PF12668 DUF3791: Protein of u 29.2 90 0.002 18.3 3.1 23 63-85 7-29 (62)
223 PF01296 Galanin: Galanin; In 29.1 34 0.00074 17.4 1.0 16 86-101 1-18 (29)
224 cd01106 HTH_TipAL-Mta Helix-Tu 28.9 1.6E+02 0.0035 18.8 5.6 21 63-83 2-22 (103)
225 PF08671 SinI: Anti-repressor 28.9 69 0.0015 16.4 2.2 17 67-83 11-27 (30)
226 PF07146 DUF1389: Protein of u 28.9 96 0.0021 24.7 4.0 62 7-73 172-234 (314)
227 PRK11302 DNA-binding transcrip 28.7 92 0.002 23.4 3.8 27 62-88 35-61 (284)
228 PRK04424 fatty acid biosynthes 28.7 1.4E+02 0.003 21.5 4.6 29 46-75 7-35 (185)
229 PF01325 Fe_dep_repress: Iron 28.5 1.3E+02 0.0028 17.6 5.9 38 51-89 13-53 (60)
230 TIGR02431 pcaR_pcaU beta-ketoa 28.4 1.3E+02 0.0029 22.3 4.6 41 50-90 13-56 (248)
231 COG4189 Predicted transcriptio 28.3 2.6E+02 0.0057 21.8 6.1 38 38-76 15-52 (308)
232 PRK09645 RNA polymerase sigma 28.2 2E+02 0.0043 19.6 5.4 22 57-78 130-151 (173)
233 KOG3978|consensus 28.2 72 0.0016 26.1 3.2 40 39-90 169-209 (469)
234 cd00256 VATPase_H VATPase_H, r 28.1 2.5E+02 0.0054 23.4 6.4 82 6-88 201-291 (429)
235 PRK10163 DNA-binding transcrip 28.0 1.5E+02 0.0031 22.6 4.8 40 50-89 29-71 (271)
236 COG4004 Uncharacterized protei 27.9 1.8E+02 0.0039 19.1 4.9 53 72-124 9-79 (96)
237 PF09145 Ubiq-assoc: Ubiquitin 27.8 66 0.0014 18.2 2.1 12 45-56 3-15 (46)
238 TIGR02337 HpaR homoprotocatech 27.5 1.7E+02 0.0038 18.9 4.6 39 50-89 32-73 (118)
239 COG1724 Predicted RNA binding 27.4 53 0.0012 20.1 1.8 21 69-89 3-23 (66)
240 COG3413 Predicted DNA binding 27.4 85 0.0019 22.9 3.3 41 42-82 155-199 (215)
241 COG1737 RpiR Transcriptional r 27.1 71 0.0015 24.5 3.0 27 62-88 37-63 (281)
242 PF00531 Death: Death domain; 27.0 1.4E+02 0.0031 17.7 4.5 22 63-84 14-35 (83)
243 PRK07670 RNA polymerase sigma 26.9 2.4E+02 0.0052 20.9 5.8 22 61-82 125-146 (251)
244 cd00092 HTH_CRP helix_turn_hel 26.8 1.3E+02 0.0028 17.0 4.7 30 60-89 24-56 (67)
245 smart00099 btg1 tob/btg1 famil 26.7 2E+02 0.0044 19.3 6.4 51 31-81 22-87 (108)
246 PRK11179 DNA-binding transcrip 26.7 2E+02 0.0042 19.8 4.9 37 46-83 9-45 (153)
247 PF09012 FeoC: FeoC like trans 26.6 1E+02 0.0023 18.2 3.1 27 57-83 10-36 (69)
248 PF10743 Phage_Cox: Regulatory 26.6 1.4E+02 0.0031 19.2 3.8 29 56-84 7-35 (87)
249 PRK14584 hmsS hemin storage sy 26.6 1.2E+02 0.0026 21.6 3.8 39 58-96 95-137 (153)
250 PF08281 Sigma70_r4_2: Sigma-7 26.6 1.1E+02 0.0024 16.8 3.0 26 57-82 22-47 (54)
251 PF13994 PgaD: PgaD-like prote 26.4 81 0.0017 21.7 2.9 28 62-89 101-128 (138)
252 PHA00738 putative HTH transcri 26.4 1.9E+02 0.0041 19.4 4.5 46 44-90 10-58 (108)
253 PRK12354 carbamate kinase; Rev 26.3 1.4E+02 0.0031 23.6 4.6 29 73-101 127-160 (307)
254 PF11237 DUF3038: Protein of u 26.3 2.6E+02 0.0056 20.3 5.8 48 4-51 67-125 (171)
255 PRK11534 DNA-binding transcrip 26.0 2.6E+02 0.0056 20.2 7.4 52 38-89 7-61 (224)
256 PRK13509 transcriptional repre 26.0 1.8E+02 0.0038 21.9 4.9 34 45-79 4-37 (251)
257 cd04782 HTH_BltR Helix-Turn-He 25.9 1.8E+02 0.0039 18.4 6.0 21 63-83 2-22 (97)
258 TIGR02885 spore_sigF RNA polym 25.8 2.6E+02 0.0057 20.3 5.9 23 61-83 113-135 (231)
259 PF04769 MAT_Alpha1: Mating-ty 25.7 1.4E+02 0.0031 22.1 4.2 54 34-89 68-135 (201)
260 PRK06288 RNA polymerase sigma 25.6 2.6E+02 0.0057 21.0 5.8 23 60-82 133-155 (268)
261 TIGR00746 arcC carbamate kinas 25.5 1.3E+02 0.0028 23.8 4.1 27 74-100 134-166 (310)
262 TIGR03613 RutR pyrimidine util 25.4 1.5E+02 0.0032 20.8 4.2 22 54-75 21-42 (202)
263 PF10108 DNA_pol_B_exo2: Predi 25.2 77 0.0017 23.7 2.7 28 60-87 115-148 (209)
264 PF08454 RIH_assoc: RyR and IP 25.1 2.1E+02 0.0046 18.9 6.3 29 4-32 8-36 (109)
265 cd03568 VHS_STAM VHS domain fa 25.1 1.2E+02 0.0026 21.0 3.6 76 9-89 57-135 (144)
266 PHA01083 hypothetical protein 25.0 1.5E+02 0.0033 21.0 4.1 35 49-83 4-38 (149)
267 PRK11337 DNA-binding transcrip 25.0 1.1E+02 0.0024 23.2 3.7 27 62-88 47-73 (292)
268 PRK03573 transcriptional regul 25.0 2.2E+02 0.0047 19.0 4.9 40 50-89 35-77 (144)
269 COG4388 Mu-like prophage I pro 24.9 70 0.0015 25.6 2.5 21 66-86 337-357 (357)
270 PRK07539 NADH dehydrogenase su 24.9 1.8E+02 0.0038 20.3 4.4 32 51-82 27-61 (154)
271 PRK10411 DNA-binding transcrip 24.8 2.1E+02 0.0046 21.4 5.1 47 48-95 6-57 (240)
272 KOG0259|consensus 24.6 1.1E+02 0.0023 25.5 3.6 39 82-122 180-230 (447)
273 KOG2807|consensus 24.5 57 0.0012 26.4 2.0 63 13-75 9-80 (378)
274 TIGR02944 suf_reg_Xantho FeS a 24.5 2.2E+02 0.0047 18.8 4.7 39 51-89 14-56 (130)
275 PRK13749 transcriptional regul 24.5 2.3E+02 0.005 19.2 6.1 49 62-119 4-53 (121)
276 PRK09834 DNA-binding transcrip 24.4 2E+02 0.0042 21.7 4.9 40 50-89 15-57 (263)
277 COG2049 DUR1 Allophanate hydro 24.3 1.9E+02 0.0042 21.9 4.7 87 4-90 20-126 (223)
278 PHA02535 P terminase ATPase su 24.2 1.1E+02 0.0023 26.6 3.7 42 45-89 5-46 (581)
279 PRK11569 transcriptional repre 24.0 1.9E+02 0.0041 21.9 4.8 40 50-89 32-74 (274)
280 COG2944 Predicted transcriptio 23.9 98 0.0021 20.6 2.8 21 61-81 57-77 (104)
281 PF13413 HTH_25: Helix-turn-he 23.8 70 0.0015 18.9 1.9 13 66-78 50-62 (62)
282 TIGR02051 MerR Hg(II)-responsi 23.7 2.3E+02 0.005 18.8 5.4 19 63-81 1-19 (124)
283 PRK03902 manganese transport t 23.7 2.4E+02 0.0051 19.0 4.8 33 57-89 18-53 (142)
284 PF11972 HTH_13: HTH DNA bindi 23.7 1.4E+02 0.003 17.6 3.0 29 58-86 10-38 (54)
285 PF03428 RP-C: Replication pro 23.6 66 0.0014 23.4 2.1 38 64-101 32-76 (177)
286 PRK09975 DNA-binding transcrip 23.5 1.8E+02 0.0039 20.5 4.4 33 43-75 12-45 (213)
287 PRK13413 mpi multiple promoter 23.4 1.9E+02 0.0041 20.7 4.5 25 62-86 173-197 (200)
288 cd00194 UBA Ubiquitin Associat 23.4 73 0.0016 16.3 1.8 20 71-90 11-30 (38)
289 PHA00675 hypothetical protein 23.2 1.6E+02 0.0035 18.6 3.5 46 42-89 22-67 (78)
290 cd06171 Sigma70_r4 Sigma70, re 23.1 1.3E+02 0.0027 15.6 5.3 23 60-82 25-47 (55)
291 PRK15002 redox-sensitivie tran 22.7 2.7E+02 0.0059 19.6 5.0 47 61-117 11-58 (154)
292 cd00090 HTH_ARSR Arsenical Res 22.6 1.5E+02 0.0033 16.4 4.7 41 47-89 8-51 (78)
293 cd04765 HTH_MlrA-like_sg2 Heli 22.5 1.4E+02 0.003 19.2 3.3 50 63-121 2-52 (99)
294 cd01279 HTH_HspR-like Helix-Tu 22.4 2.2E+02 0.0048 18.1 5.2 22 62-83 2-23 (98)
295 PHA01976 helix-turn-helix prot 22.4 1.2E+02 0.0026 17.4 2.8 25 58-82 12-36 (67)
296 cd04788 HTH_NolA-AlbR Helix-Tu 22.3 2.2E+02 0.0047 18.0 5.5 49 63-120 2-51 (96)
297 PRK10219 DNA-binding transcrip 22.3 2.2E+02 0.0047 18.0 5.8 30 60-89 20-50 (107)
298 PRK15090 DNA-binding transcrip 22.3 1.9E+02 0.0042 21.6 4.5 39 50-89 18-59 (257)
299 PF00946 Mononeg_RNA_pol: Mono 22.3 1.3E+02 0.0029 27.8 4.2 50 4-53 249-307 (1072)
300 PF01257 2Fe-2S_thioredx: Thio 22.2 1.9E+02 0.0042 19.8 4.2 31 53-83 20-53 (145)
301 PF01465 GRIP: GRIP domain; I 22.2 1.1E+02 0.0024 17.0 2.4 16 65-80 29-44 (46)
302 PRK12427 flagellar biosynthesi 22.1 3.3E+02 0.0072 20.1 6.8 23 61-83 117-139 (231)
303 PRK14965 DNA polymerase III su 22.1 3.6E+02 0.0078 23.1 6.5 44 8-51 248-293 (576)
304 PRK15429 formate hydrogenlyase 22.0 5.3E+02 0.011 22.4 8.2 41 47-87 642-683 (686)
305 PRK11557 putative DNA-binding 22.0 1.4E+02 0.0031 22.4 3.8 33 43-75 25-58 (278)
306 smart00530 HTH_XRE Helix-turn- 22.0 1.3E+02 0.0027 15.2 2.8 24 60-83 9-32 (56)
307 PRK05685 fliS flagellar protei 21.5 2E+02 0.0044 19.5 4.1 78 6-88 36-122 (132)
308 PF13167 GTP-bdg_N: GTP-bindin 21.5 2.4E+02 0.0052 18.3 4.7 19 76-94 11-29 (95)
309 TIGR01889 Staph_reg_Sar staphy 21.3 2.4E+02 0.0052 18.1 4.9 40 50-89 29-74 (109)
310 COG1309 AcrR Transcriptional r 21.2 1.8E+02 0.0038 18.9 3.8 22 54-75 25-46 (201)
311 PF02796 HTH_7: Helix-turn-hel 21.2 1.6E+02 0.0034 15.9 3.4 31 49-82 12-42 (45)
312 PRK09411 carbamate kinase; Rev 21.1 2.2E+02 0.0049 22.5 4.7 28 74-101 129-161 (297)
313 PF01329 Pterin_4a: Pterin 4 a 21.1 1.3E+02 0.0028 19.2 2.9 19 73-91 5-24 (95)
314 PF07022 Phage_CI_repr: Bacter 21.1 1.4E+02 0.003 17.6 2.9 28 52-79 3-30 (66)
315 cd00086 homeodomain Homeodomai 20.7 1.4E+02 0.0031 16.3 2.8 22 63-84 29-50 (59)
316 PF01527 HTH_Tnp_1: Transposas 20.7 1.9E+02 0.0042 16.8 3.8 39 46-86 10-48 (76)
317 PF05427 FIBP: Acidic fibrobla 20.6 1.6E+02 0.0034 24.0 3.8 57 34-90 247-316 (361)
318 PRK10225 DNA-binding transcrip 20.6 3.6E+02 0.0078 19.9 6.4 51 39-89 10-64 (257)
319 PLN00157 histone H2A; Provisio 20.5 3.1E+02 0.0067 19.1 7.1 71 9-90 29-105 (132)
320 KOG3442|consensus 20.5 3.1E+02 0.0066 19.1 5.5 25 56-80 50-78 (132)
321 TIGR03830 CxxCG_CxxCG_HTH puta 20.4 2.6E+02 0.0056 18.1 6.4 21 61-81 78-98 (127)
322 KOG3054|consensus 20.3 4.3E+02 0.0093 20.7 6.2 52 36-96 198-257 (299)
323 cd01111 HTH_MerD Helix-Turn-He 20.3 2.6E+02 0.0057 18.2 5.5 49 63-120 2-51 (107)
324 PF11112 PyocinActivator: Pyoc 20.3 1.6E+02 0.0035 18.3 3.1 54 60-120 13-68 (76)
325 PRK14950 DNA polymerase III su 20.3 4.1E+02 0.0089 22.7 6.5 45 8-52 249-295 (585)
326 smart00700 JHBP Juvenile hormo 20.2 2.2E+02 0.0047 20.8 4.3 42 26-67 181-222 (225)
327 PTZ00064 histone acetyltransfe 20.1 2.8E+02 0.006 23.9 5.2 28 62-89 472-499 (552)
328 PRK03837 transcriptional regul 20.0 2.7E+02 0.0059 20.2 4.8 50 40-89 15-68 (241)
329 PRK14101 bifunctional glucokin 20.0 3.6E+02 0.0079 23.2 6.2 39 50-88 360-401 (638)
No 1
>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=99.96 E-value=1.9e-29 Score=177.07 Aligned_cols=98 Identities=37% Similarity=0.757 Sum_probs=77.4
Q ss_pred chHHHHHHHHHHHHHcCCchHHHHHhcc-CCcHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHH
Q psy9207 3 HPEIGQVWEVGKHLWNGNYPSIYSTLKR-TWSDDIAHIMKALQDEVQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAI 81 (125)
Q Consensus 3 ~~~l~~~~~l~~~l~~~~y~~v~~~~~~-~~s~~~~~~i~~l~~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~ 81 (125)
||+|+++|.|+++||+|+|++||+.+++ +|++.+.++|..|++++|++++.||++||++|+++++++|||++++|+.++
T Consensus 38 ~~~i~~i~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~iR~~i~~~i~~aY~sIs~~~la~~Lg~~~~el~~~ 117 (143)
T PF10075_consen 38 DPEIKAIWSLGQALWEGDYSKFWQALRSNPWSPDYKPFVPGFEDTIRERIAHLISKAYSSISLSDLAEMLGLSEEELEKF 117 (143)
T ss_dssp -TTHHHHHHHHHHHHTT-HHHHHHHS-TT----HHHHTSTTHHHHHHHHHHHHHHHH-SEE-HHHHHHHTTS-HHHHHHH
T ss_pred hHHHHHHHHHHHHHHCCCHHHHHHHHHhccchHHHHHHHHHHHHHHHHHHHHHHHHHHhHcCHHHHHHHhCCCHHHHHHH
Confidence 6999999999999999999999999998 999999999999999999999999999999999999999999999999999
Q ss_pred HHhcCCeec-CceeeccCCC
Q psy9207 82 AQAEGWTVD-KVYTQPVKKP 100 (125)
Q Consensus 82 ~~~~GW~~d-~~~~~p~~~~ 100 (125)
+.++||++| +..++|.++.
T Consensus 118 ~~~~gW~~d~~~~~~~~~~~ 137 (143)
T PF10075_consen 118 IKSRGWTVDGDGVLFPPNPE 137 (143)
T ss_dssp HHHHT-EE-----EE---HH
T ss_pred HHHcCCEECCCccEEecCCc
Confidence 999999998 5555554443
No 2
>KOG4414|consensus
Probab=99.95 E-value=3.1e-28 Score=170.81 Aligned_cols=121 Identities=29% Similarity=0.612 Sum_probs=110.8
Q ss_pred CchHHHHHHHHHHHHHcCCchHHHHHhcc-CCcHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHH
Q psy9207 2 SHPEIGQVWEVGKHLWNGNYPSIYSTLKR-TWSDDIAHIMKALQDEVQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAA 80 (125)
Q Consensus 2 ~~~~l~~~~~l~~~l~~~~y~~v~~~~~~-~~s~~~~~~i~~l~~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~ 80 (125)
++||+.++|.+||.+|++||+++|.+++. +||+..+++|+.|.|..|.|.|.++.+||+||..+++|.+||++++|+.+
T Consensus 72 ~k~El~aaWgiGQkiWq~Df~GiYeaI~~~dWSeeak~imaAf~D~~~kR~FaLl~qAYssI~~~D~A~FlGl~~ddAtk 151 (197)
T KOG4414|consen 72 AKPELGAAWGIGQKIWQHDFAGIYEAINAHDWSEEAKDIMAAFRDATRKRAFALLLQAYSSIIADDFAAFLGLPEDDATK 151 (197)
T ss_pred cCchhhhhhhhhHHHHhcccchHHHHHhhhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHH
Confidence 47999999999999999999999999999 99999999999999999999999999999999999999999999999999
Q ss_pred HHHhcCCeec--Ccee-eccCCCCCCCCCCCChHHHHHHhhHHHhhc
Q psy9207 81 IAQAEGWTVD--KVYT-QPVKKPEEYATPNITDDQLYILTQYVSFLE 124 (125)
Q Consensus 81 ~~~~~GW~~d--~~~~-~p~~~~~~~~~~~~~~~ql~~Lt~~v~fLE 124 (125)
.+.+.||+.| +++. .|+++.. ....++-..+..||+++-|||
T Consensus 152 ~ilEnGWqaDaasqMasl~kk~V~--~a~~Vd~nK~~~LsE~a~~~~ 196 (197)
T KOG4414|consen 152 GILENGWQADAASQMASLKKKAVA--GALDVDFNKFIPLSEPAFHLE 196 (197)
T ss_pred HHHHcccchhhHHHHhhccchhcc--cccccchhhceecCCccCCCC
Confidence 9999999999 6776 5555544 344457788999999999987
No 3
>KOG3151|consensus
Probab=99.84 E-value=2.7e-20 Score=138.91 Aligned_cols=88 Identities=20% Similarity=0.386 Sum_probs=85.9
Q ss_pred chHHHHHHHHHHHHHcCCchHHHHHhccCCcHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHhCCC-HHHHHHH
Q psy9207 3 HPEIGQVWEVGKHLWNGNYPSIYSTLKRTWSDDIAHIMKALQDEVQKRAISLISKAYSSIPNTSLSEFLGVT-EQEAAAI 81 (125)
Q Consensus 3 ~~~l~~~~~l~~~l~~~~y~~v~~~~~~~~s~~~~~~i~~l~~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~-~~e~~~~ 81 (125)
+|.|+++.+|+|++|+|.|++||.++++.+++.|..||+.+.++||++|+.|++|+|..|++++++.+|+|+ ++|+.+|
T Consensus 134 ~~~I~~~v~LEq~~MEGaYnKv~~a~~s~p~~~y~~FmdIl~~tiRdEIA~c~EKsYd~l~~s~a~~~L~f~~~~e~~~~ 213 (260)
T KOG3151|consen 134 NPYISHPVSLEQSLMEGAYNKVLSAKQSIPSEEYTYFMDILLDTIRDEIAGCIEKSYDKLSASDATQMLLFNNDKELKKF 213 (260)
T ss_pred cchhhhHHHHHHHHHhhHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCHHHHHHHHhcCChHHHHHH
Confidence 589999999999999999999999999988999999999999999999999999999999999999999997 7999999
Q ss_pred HHhcCCeec
Q psy9207 82 AQAEGWTVD 90 (125)
Q Consensus 82 ~~~~GW~~d 90 (125)
+.+++|.++
T Consensus 214 ~~~r~W~l~ 222 (260)
T KOG3151|consen 214 ATERQWPLD 222 (260)
T ss_pred HHhcCCccc
Confidence 999999998
No 4
>KOG3252|consensus
Probab=99.00 E-value=1.7e-09 Score=78.80 Aligned_cols=118 Identities=19% Similarity=0.287 Sum_probs=95.4
Q ss_pred chHHHHHHHHHHHHHcCCchHHHHHhccCCcHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHhCCC-HHHHHHH
Q psy9207 3 HPEIGQVWEVGKHLWNGNYPSIYSTLKRTWSDDIAHIMKALQDEVQKRAISLISKAYSSIPNTSLSEFLGVT-EQEAAAI 81 (125)
Q Consensus 3 ~~~l~~~~~l~~~l~~~~y~~v~~~~~~~~s~~~~~~i~~l~~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~-~~e~~~~ 81 (125)
+..++.|.-|+.+|..|+|..||...+.. ..+-.=|..|+|.||.-+-..++-.|..|.-.-+|.+||=. +.++..+
T Consensus 95 ee~~r~ii~L~~~LEt~~Fq~FW~~~~~N--~~mle~itGFedsvr~yachvv~iTyQkI~k~lLaellG~~sDs~le~~ 172 (217)
T KOG3252|consen 95 EEPFRSIIDLGDYLETCRFQQFWQEADEN--RDMLEGITGFEDSVRKYACHVVGITYQKIDKWLLAELLGGLSDSQLEVW 172 (217)
T ss_pred ccchhHHHhHHHHHhhchHHHHhhhhccc--hHHhcCCCcHHHHHHHHHHHheechHhhchHHHHHHhhCcccHHHHHHH
Confidence 45789999999999999999999876543 55666678999999999999999999999999999999875 7889999
Q ss_pred HHhcCCeec--CceeeccCCCCCCCCCCC-ChHHHHHHhhHHHhh
Q psy9207 82 AQAEGWTVD--KVYTQPVKKPEEYATPNI-TDDQLYILTQYVSFL 123 (125)
Q Consensus 82 ~~~~GW~~d--~~~~~p~~~~~~~~~~~~-~~~ql~~Lt~~v~fL 123 (125)
+++-||..| |.+++|... ..-.++.+ +..+++..+++++.+
T Consensus 173 ~~~~GW~a~e~G~ifv~~qE-~~iKtkNi~EkI~fd~Va~ima~~ 216 (217)
T KOG3252|consen 173 MTKYGWIADESGQIFVASQE-EEIKTKNIVEKIDFDHVASIMASL 216 (217)
T ss_pred HHHccceecCCceEEEeccc-cccccCCccccCCcchHHHHHHhc
Confidence 999999998 434444333 32244445 777888888777654
No 5
>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=98.96 E-value=2.9e-09 Score=77.77 Aligned_cols=72 Identities=33% Similarity=0.479 Sum_probs=63.0
Q ss_pred CchHHHHHHHHHHHHHcCCchHHHHHhcc-CCcHHHHHHHHHHHHHHHHHHHHHHHHhcCC-cchHHHHHHhCC
Q psy9207 2 SHPEIGQVWEVGKHLWNGNYPSIYSTLKR-TWSDDIAHIMKALQDEVQKRAISLISKAYSS-IPNTSLSEFLGV 73 (125)
Q Consensus 2 ~~~~l~~~~~l~~~l~~~~y~~v~~~~~~-~~s~~~~~~i~~l~~~vR~~~~~li~~AY~s-I~~~~~a~~Lgl 73 (125)
.||.++.+..|.+++++|+|.+||+.+++ ..+.....++..+.+.+|.++++++++||.+ |+++.++++|||
T Consensus 131 ~~~~i~~al~l~~a~~~gny~~ff~l~~~~~~~~l~~~l~~~~~~~iR~~al~~i~~ay~~~i~l~~l~~~L~F 204 (204)
T PF03399_consen 131 SSPYIQFALELCRALMEGNYVRFFRLYRSKSAPYLFACLMERFFNRIRLRALQSISKAYRSSIPLSFLAELLGF 204 (204)
T ss_dssp TSHHHHHHHHHHHHH--TTHHHHHHHHT-TTS-HHHHHHHGGGHHHHHHHHHHHHHHHS-T-EEHHHHHHHTT-
T ss_pred cCHHHHHHHHHHHHHHcCCHHHHHHHHhccCCChHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCC
Confidence 58999999999999999999999999955 6778889999999999999999999999999 999999999996
No 6
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=98.17 E-value=2.2e-05 Score=50.96 Aligned_cols=77 Identities=21% Similarity=0.349 Sum_probs=63.9
Q ss_pred HHHHHHHHHHcCCchHHHHHhccC---C--cHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHH
Q psy9207 8 QVWEVGKHLWNGNYPSIYSTLKRT---W--SDDIAHIMKALQDEVQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAIA 82 (125)
Q Consensus 8 ~~~~l~~~l~~~~y~~v~~~~~~~---~--s~~~~~~i~~l~~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~ 82 (125)
+.-.|.+++-+|+|..+...++.- + .+.+...+..+...+|.+.+.-+.+.|++|+++++|+.|+++.+++..++
T Consensus 2 ~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~l~~~i~~~~l~~l~~~y~~i~~~~ia~~l~~~~~~vE~~l 81 (105)
T PF01399_consen 2 PYSELLRAFRSGDLQEFEEFLEKHSESLFKDPFLAEYVEQLKEKIRRRNLRQLSKPYSSISISEIAKALQLSEEEVESIL 81 (105)
T ss_dssp HHHHHHHHHHCT-HHHHHHHHHHTCHHHHHCTTHHHHHHHHHHHHHHHHHHHHHHC-SEEEHHHHHHHHTCCHHHHHHHH
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHhccchHHHHHHH
Confidence 355788999999999998888753 1 24566788999999999999999999999999999999999998888876
Q ss_pred Hh
Q psy9207 83 QA 84 (125)
Q Consensus 83 ~~ 84 (125)
.+
T Consensus 82 ~~ 83 (105)
T PF01399_consen 82 ID 83 (105)
T ss_dssp HH
T ss_pred HH
Confidence 54
No 7
>KOG1861|consensus
Probab=98.10 E-value=3.3e-05 Score=63.42 Aligned_cols=99 Identities=15% Similarity=0.219 Sum_probs=86.7
Q ss_pred CchHHHHHHHHHHHHHcCCchHHHHHhccCCcHHHHHHHHHHHHHHHHHHHHHHHHhcC-CcchHHHHHHhCCC-HHHHH
Q psy9207 2 SHPEIGQVWEVGKHLWNGNYPSIYSTLKRTWSDDIAHIMKALQDEVQKRAISLISKAYS-SIPNTSLSEFLGVT-EQEAA 79 (125)
Q Consensus 2 ~~~~l~~~~~l~~~l~~~~y~~v~~~~~~~~s~~~~~~i~~l~~~vR~~~~~li~~AY~-sI~~~~~a~~Lgl~-~~e~~ 79 (125)
.|+.+.++.+|-.+.--|+|-+||......+ ---..+|+.|.+.-|-..+..|.|+|. +|+++-+++-|.|. .+++.
T Consensus 419 ed~~V~hAL~vR~A~~~GNY~kFFrLY~~AP-~M~~yLmdlF~erER~~Al~ii~KsyrP~i~~~fi~~~laf~~~e~c~ 497 (540)
T KOG1861|consen 419 EDEAVAHALEVRSAVTLGNYHKFFRLYLTAP-NMSGYLMDLFLERERKKALTIICKSYRPTITVDFIASELAFDSMEDCV 497 (540)
T ss_pred cCHHHHHHHHHHHHHHhccHHHHHHHHhhcc-cchhHHHHHHHHHHHHHHHHHHHHHcCCCccHHHHhhhhhhchHHHHH
Confidence 4788999999999999999999999988632 333568999999999999999999999 99999999999998 57788
Q ss_pred HHHHhcCCeec--CceeeccCCCC
Q psy9207 80 AIAQAEGWTVD--KVYTQPVKKPE 101 (125)
Q Consensus 80 ~~~~~~GW~~d--~~~~~p~~~~~ 101 (125)
.|..+++|+.| |..+.++++.+
T Consensus 498 ~~l~~~~~~~~~~g~~~~~~~~~s 521 (540)
T KOG1861|consen 498 NFLNEQNLTYDSLGPQILDKNASS 521 (540)
T ss_pred HHHhccCccccccCCccccccccc
Confidence 89999999997 66777776655
No 8
>COG5187 RPN7 26S proteasome regulatory complex component, contains PCI domain [Posttranslational modification, protein turnover, chaperones]
Probab=97.43 E-value=0.001 Score=52.42 Aligned_cols=119 Identities=16% Similarity=0.223 Sum_probs=90.9
Q ss_pred chHHHHHHHHHHHHHcCCchHHHHHhccC------CcHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHhCCCH-
Q psy9207 3 HPEIGQVWEVGKHLWNGNYPSIYSTLKRT------WSDDIAHIMKALQDEVQKRAISLISKAYSSIPNTSLSEFLGVTE- 75 (125)
Q Consensus 3 ~~~l~~~~~l~~~l~~~~y~~v~~~~~~~------~s~~~~~~i~~l~~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~- 75 (125)
+..++.+-++...|..+||.+.|..+-.. .-.-+...++-|..-.|.|+-.-+--+|..++++..|+-+|+|.
T Consensus 267 ~e~l~sl~~l~~SLy~cdY~~~F~~ll~~~~n~L~~d~fl~rh~d~fvREMRrrvYaQlLESYr~lsl~sMA~tFgVSV~ 346 (412)
T COG5187 267 SEKLGSLVQLATSLYECDYGGDFMNLLYLFCNSLQDDVFLGRHVDLFVREMRRRVYAQLLESYRLLSLESMAQTFGVSVE 346 (412)
T ss_pred hhhhhhHHHHHHHHHHhccchhhHHHHHHHHhhccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhCccHH
Confidence 44677888999999999999887766431 11233456678888889999888889999999999999999995
Q ss_pred ---HHHHHHHHh-cCCee-c--CceeeccCCCCCCCCC---CC-ChHHHHHHhhHHH
Q psy9207 76 ---QEAAAIAQA-EGWTV-D--KVYTQPVKKPEEYATP---NI-TDDQLYILTQYVS 121 (125)
Q Consensus 76 ---~e~~~~~~~-~GW~~-d--~~~~~p~~~~~~~~~~---~~-~~~ql~~Lt~~v~ 121 (125)
.++.+|+-+ +=|.+ | ++++...+|++.+... .. +++-|.+|-++++
T Consensus 347 yvdrDLg~FIp~~~LncvIDRvnGvVetnrpdekn~qy~~vVkqGd~ll~klqKy~a 403 (412)
T COG5187 347 YVDRDLGEFIPEGRLNCVIDRVNGVVETNRPDEKNQQYSSVVKQGDDLLRKLQKYVA 403 (412)
T ss_pred HHhhhHHhhCCCCceeeeeecccceEeccCcchhhhhHHHHHhcchHHHHHHHHHHH
Confidence 678888765 55665 7 8888888887743211 11 8888899988875
No 9
>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=97.33 E-value=0.00074 Score=42.94 Aligned_cols=63 Identities=19% Similarity=0.293 Sum_probs=49.8
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHHHh------cCCeec--CceeeccCCCC
Q psy9207 39 IMKALQDEVQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQA------EGWTVD--KVYTQPVKKPE 101 (125)
Q Consensus 39 ~i~~l~~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~~------~GW~~d--~~~~~p~~~~~ 101 (125)
.+..+...+|.+.+..+.+.|++|++++++..++++.+++..++.+ ...++| ++++......+
T Consensus 2 ~~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~~ 72 (88)
T smart00088 2 LVERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVDP 72 (88)
T ss_pred hHHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCch
Confidence 4577889999999999999999999999999999998887777554 245777 55555544433
No 10
>smart00753 PAM PCI/PINT associated module.
Probab=97.33 E-value=0.00074 Score=42.94 Aligned_cols=63 Identities=19% Similarity=0.293 Sum_probs=49.8
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHHHh------cCCeec--CceeeccCCCC
Q psy9207 39 IMKALQDEVQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQA------EGWTVD--KVYTQPVKKPE 101 (125)
Q Consensus 39 ~i~~l~~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~~------~GW~~d--~~~~~p~~~~~ 101 (125)
.+..+...+|.+.+..+.+.|++|++++++..++++.+++..++.+ ...++| ++++......+
T Consensus 2 ~~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~~ 72 (88)
T smart00753 2 LVERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVDP 72 (88)
T ss_pred hHHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCch
Confidence 4577889999999999999999999999999999998887777554 245777 55555544433
No 11
>KOG0687|consensus
Probab=96.50 E-value=0.017 Score=46.03 Aligned_cols=96 Identities=16% Similarity=0.246 Sum_probs=74.4
Q ss_pred HHHHHHHHHHcCCchHHHHHhccC------CcHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHhCCCH----HH
Q psy9207 8 QVWEVGKHLWNGNYPSIYSTLKRT------WSDDIAHIMKALQDEVQKRAISLISKAYSSIPNTSLSEFLGVTE----QE 77 (125)
Q Consensus 8 ~~~~l~~~l~~~~y~~v~~~~~~~------~s~~~~~~i~~l~~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~----~e 77 (125)
.+-++...|.+|+|..||..+... .---+.|...-+..-+|.++-.-+--+|.+++++..|+-+|+|. .|
T Consensus 258 ~~~q~l~SLY~C~Y~~Ff~~L~~~~~~~lk~D~~l~~h~~yyvREMR~rvY~QlLESYrsl~l~~MA~aFgVSVefiDre 337 (393)
T KOG0687|consen 258 SVSQLLNSLYECDYSDFFNDLAAVEAKQLKDDRYLGPHYRYYVREMRRRVYAQLLESYRSLTLESMAKAFGVSVEFIDRE 337 (393)
T ss_pred hHHHHHHHHHhccHHHHHHHHHHHHHHhhccchhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCchHHHHHhH
Confidence 455678889999999999988431 11123445566677888999888889999999999999999994 88
Q ss_pred HHHHHHh-cCCe-ec--CceeeccCCCCCC
Q psy9207 78 AAAIAQA-EGWT-VD--KVYTQPVKKPEEY 103 (125)
Q Consensus 78 ~~~~~~~-~GW~-~d--~~~~~p~~~~~~~ 103 (125)
+..|+.. +=|. +| ++++...+|++.+
T Consensus 338 L~rFI~~grL~ckIDrVnGVVEtNrpD~KN 367 (393)
T KOG0687|consen 338 LGRFIAAGRLHCKIDRVNGVVETNRPDEKN 367 (393)
T ss_pred HHHhhccCceeeeeecccceeecCCccccc
Confidence 9999775 4454 48 8888888888754
No 12
>KOG2581|consensus
Probab=96.39 E-value=0.0053 Score=50.15 Aligned_cols=80 Identities=23% Similarity=0.321 Sum_probs=63.7
Q ss_pred HHHHHHHHHHHHHcCCchHHHHHhcc-C---CcHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHH
Q psy9207 5 EIGQVWEVGKHLWNGNYPSIYSTLKR-T---WSDDIAHIMKALQDEVQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAA 80 (125)
Q Consensus 5 ~l~~~~~l~~~l~~~~y~~v~~~~~~-~---~s~~~~~~i~~l~~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~ 80 (125)
-|+.-..|-+++--||..+|=..+.+ - -.+..-.++..|.-.|=..-.+.||-+|+.||+.|+|.-||++++|-.+
T Consensus 317 sL~~Yf~Lt~AVr~gdlkkF~~~leq~k~~f~~D~ty~LivRLR~NVIkTgIR~ISlsYSRISl~DIA~kL~l~Seed~E 396 (493)
T KOG2581|consen 317 SLRPYFKLTQAVRLGDLKKFNETLEQFKDKFQADGTYTLIVRLRHNVIKTGIRKISLSYSRISLQDIAKKLGLNSEEDAE 396 (493)
T ss_pred HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHhhCCcchHHHHHHHHHHHHhhhheeeeeeeccHHHHHHHhcCCCchhHH
Confidence 56677888888888888888777664 1 2345556777888888888889999999999999999999999877666
Q ss_pred HHHh
Q psy9207 81 IAQA 84 (125)
Q Consensus 81 ~~~~ 84 (125)
|+.+
T Consensus 397 yiVa 400 (493)
T KOG2581|consen 397 YIVA 400 (493)
T ss_pred HHHH
Confidence 6554
No 13
>KOG1076|consensus
Probab=95.15 E-value=0.11 Score=45.16 Aligned_cols=77 Identities=17% Similarity=0.418 Sum_probs=60.6
Q ss_pred HHHHHHHHHHcCCchHHHH-Hhc-c-CCc--HHHHHHHHHHHHHHHHHHHH----HHHHhcCCcchHHHHHHhCCCHHHH
Q psy9207 8 QVWEVGKHLWNGNYPSIYS-TLK-R-TWS--DDIAHIMKALQDEVQKRAIS----LISKAYSSIPNTSLSEFLGVTEQEA 78 (125)
Q Consensus 8 ~~~~l~~~l~~~~y~~v~~-~~~-~-~~s--~~~~~~i~~l~~~vR~~~~~----li~~AY~sI~~~~~a~~Lgl~~~e~ 78 (125)
++..-.++|..|++.+-+. .++ . +|. +....+.++|.+.|+++.++ .-+..|+|||+..+|.|+.|+...+
T Consensus 656 hVvaAsKAm~~Gnw~~c~~fi~nn~KvW~Lfpn~d~V~~Ml~~rIqEEsLRTYLftYss~Y~SvSl~~LA~mFdLp~~~V 735 (843)
T KOG1076|consen 656 HVVAASKAMQKGNWQKCFEFIVNNIKVWDLFPNADTVLDMLTERIQEESLRTYLFTYSSVYDSVSLAKLADMFDLPEPKV 735 (843)
T ss_pred HHHHHHHHHhcCCHHHHHHHHHhhhhHHHhcccHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhccHHHHHHHhCCCchhH
Confidence 4566688999999999877 344 2 664 45566778899999998887 4578899999999999999998777
Q ss_pred HHHHHh
Q psy9207 79 AAIAQA 84 (125)
Q Consensus 79 ~~~~~~ 84 (125)
-..+.+
T Consensus 736 hsIiSk 741 (843)
T KOG1076|consen 736 HSIISK 741 (843)
T ss_pred HHHHHH
Confidence 666543
No 14
>KOG1464|consensus
Probab=94.31 E-value=0.56 Score=37.17 Aligned_cols=83 Identities=19% Similarity=0.212 Sum_probs=69.8
Q ss_pred CchHHHHHHHHHHHHHcCCchHHHHHhccCCc-----HHHHHHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHhCCCHH
Q psy9207 2 SHPEIGQVWEVGKHLWNGNYPSIYSTLKRTWS-----DDIAHIMKALQDEVQKRAISLISKAYSSIPNTSLSEFLGVTEQ 76 (125)
Q Consensus 2 ~~~~l~~~~~l~~~l~~~~y~~v~~~~~~~~s-----~~~~~~i~~l~~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~ 76 (125)
.+|||-+.-.|.++...++-..|=+.+++.-+ +-+..-+..|...+|..++--+-+-|+.|.+..++.-|++++.
T Consensus 300 NdPEIlAMTnlv~aYQ~NdI~eFE~Il~~~~~~IM~DpFIReh~EdLl~niRTQVLlkLIkPYt~i~Ipfis~~Lnv~~~ 379 (440)
T KOG1464|consen 300 NDPEILAMTNLVAAYQNNDIIEFERILKSNRSNIMDDPFIREHIEDLLRNIRTQVLLKLIKPYTNIGIPFISKELNVPEA 379 (440)
T ss_pred CCHHHHHHHHHHHHHhcccHHHHHHHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHhccccccCchhhHhhcCCCHH
Confidence 37999999999999999998887776665222 3455667889999999999999999999999999999999999
Q ss_pred HHHHHHHh
Q psy9207 77 EAAAIAQA 84 (125)
Q Consensus 77 e~~~~~~~ 84 (125)
|+.....+
T Consensus 380 dV~~LLV~ 387 (440)
T KOG1464|consen 380 DVESLLVS 387 (440)
T ss_pred HHHHHHHH
Confidence 98887655
No 15
>KOG1498|consensus
Probab=92.45 E-value=0.56 Score=38.36 Aligned_cols=49 Identities=22% Similarity=0.269 Sum_probs=42.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHHHh
Q psy9207 36 IAHIMKALQDEVQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQA 84 (125)
Q Consensus 36 ~~~~i~~l~~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~~ 84 (125)
-..-...|..+|=+.=++-+++=|++|+..+++..|+++.+++.+|...
T Consensus 328 gek~~~dL~~RIiEHNiRiiA~yYSrIt~~rl~eLLdl~~ee~E~~LS~ 376 (439)
T KOG1498|consen 328 GEKRWSDLKLRIIEHNIRIIAKYYSRITLKRLAELLDLPVEEMEKFLSD 376 (439)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHhhccHHHHHHHhCCCHHHHHHHHHH
Confidence 3444577888888888999999999999999999999999999888654
No 16
>KOG2908|consensus
Probab=91.96 E-value=2.5 Score=34.11 Aligned_cols=83 Identities=13% Similarity=0.186 Sum_probs=61.0
Q ss_pred HHHHHHHHHcCCchHHHHHhccCCcHHHHHHHHHHHHHHHH--HHHHHHHHhcCC------cchHHHHHHhCCCHHHHHH
Q psy9207 9 VWEVGKHLWNGNYPSIYSTLKRTWSDDIAHIMKALQDEVQK--RAISLISKAYSS------IPNTSLSEFLGVTEQEAAA 80 (125)
Q Consensus 9 ~~~l~~~l~~~~y~~v~~~~~~~~s~~~~~~i~~l~~~vR~--~~~~li~~AY~s------I~~~~~a~~Lgl~~~e~~~ 80 (125)
+..+..++-.||.++|.+... .|+. .|..+.-++.+|+ +...+|+.+|+. ||.++.|+.+-++.+|+.=
T Consensus 237 L~dll~Afn~Gdl~~f~~l~~-~~~~--~p~L~~~e~~L~qKI~LmaLiEi~F~rpa~~R~lsf~~Ia~~tkip~~eVE~ 313 (380)
T KOG2908|consen 237 LKDLLIAFNSGDLKRFESLKG-VWGK--QPDLASNEDFLLQKIRLLALIEITFSRPANERTLSFKEIAEATKIPNKEVEL 313 (380)
T ss_pred HHHHHHHhccCCHHHHHHHHH-Hhcc--CchHHHHHHHHHHHHHHHHHHHHHhcCcchhccccHHHHHHHhCCCHHHHHH
Confidence 567899999999999766655 6655 5555666666666 467889999987 9999999999999888655
Q ss_pred HHHh------cCCeec--Ccee
Q psy9207 81 IAQA------EGWTVD--KVYT 94 (125)
Q Consensus 81 ~~~~------~GW~~d--~~~~ 94 (125)
.+.+ -.|.+| ++++
T Consensus 314 LVMKAlslgLikG~Idqv~~~v 335 (380)
T KOG2908|consen 314 LVMKALSLGLIKGSIDQVEGVV 335 (380)
T ss_pred HHHHHHhccceeeeecccccEE
Confidence 5433 256666 4444
No 17
>COG5071 RPN5 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=91.92 E-value=0.97 Score=36.19 Aligned_cols=51 Identities=22% Similarity=0.305 Sum_probs=42.4
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHHHh---cCCee
Q psy9207 39 IMKALQDEVQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQA---EGWTV 89 (125)
Q Consensus 39 ~i~~l~~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~~---~GW~~ 89 (125)
-...|..++-+.-++.|++-|++|++.++.-.|.++++++.+++.. +|--+
T Consensus 331 ~w~DL~krviEHN~RvI~~yYSrI~~~rl~~lld~~~s~te~~ISdlVN~G~~y 384 (439)
T COG5071 331 RWSDLRKRVIEHNIRVIANYYSRIHCSRLGVLLDMSPSETEQFISDLVNKGHFY 384 (439)
T ss_pred hHHHHHHHHHHhhHhHHHHHhhhhhHHHHHHHHcCCHHHHHHHHHHHHhcCcEE
Confidence 3456667777888999999999999999999999999999888764 46554
No 18
>PF03374 ANT: Phage antirepressor protein KilAC domain; InterPro: IPR005039 This entry is represented by Bacteriophage P1, Ant1 C-terminal domain, which represents the processed Ant2 chain. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Prophages P1 and P7 exist as unit copy DNA plasmids in the bacterial cell. Maintenance of the prophage state requires the continuous expression of two repressors: (i) C1 is a protein which negatively regulates the expression of lytic genes including the C1 inactivator gene coi, and (ii) C4 is an antisense RNA which specifically inhibits the synthesis of an anti-repressor Ant.; GO: 0003677 DNA binding
Probab=91.69 E-value=0.52 Score=31.06 Aligned_cols=47 Identities=13% Similarity=0.183 Sum_probs=37.3
Q ss_pred HHHHHHHhcCCcchHHHHHHhCCCHHHHHHHHHhcCCeec--Cceeecc
Q psy9207 51 AISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQAEGWTVD--KVYTQPV 97 (125)
Q Consensus 51 ~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~~~GW~~d--~~~~~p~ 97 (125)
.++.+..+=.++++.++|+.||++..++.++..+.||-+. ++...|.
T Consensus 14 ~~d~~~~~~~~~ti~~~AK~L~i~~~~l~~~Lr~~g~l~~~~~~~~~p~ 62 (111)
T PF03374_consen 14 FYDAFVDSDGLYTIREAAKLLGIGRNKLFQWLREKGWLYRRGKGRNLPY 62 (111)
T ss_pred HHHHHHcCCCCccHHHHHHHhCCCHHHHHHHHHhCCceEECCCCCcccC
Confidence 3444555558999999999999999999999999999986 3344444
No 19
>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=88.47 E-value=2.5 Score=24.81 Aligned_cols=45 Identities=24% Similarity=0.400 Sum_probs=36.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHHH
Q psy9207 38 HIMKALQDEVQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQ 83 (125)
Q Consensus 38 ~~i~~l~~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~ 83 (125)
.+...|.+..|.+|+..+ ......++.+++.-||++...+-....
T Consensus 2 ~i~~aL~~p~R~~Il~~L-~~~~~~t~~ela~~l~~~~~t~s~hL~ 46 (61)
T PF12840_consen 2 EIFKALSDPTRLRILRLL-ASNGPMTVSELAEELGISQSTVSYHLK 46 (61)
T ss_dssp HHHHHHTSHHHHHHHHHH-HHCSTBEHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHhCCHHHHHHHHHH-hcCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 356778899999999999 888999999999999999876655433
No 20
>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=87.98 E-value=1.1 Score=26.32 Aligned_cols=29 Identities=21% Similarity=0.275 Sum_probs=25.4
Q ss_pred hcCCcchHHHHHHhCCCHHHHHHHHHhcC
Q psy9207 58 AYSSIPNTSLSEFLGVTEQEAAAIAQAEG 86 (125)
Q Consensus 58 AY~sI~~~~~a~~Lgl~~~e~~~~~~~~G 86 (125)
.|=.+++.+||.-||++...+...|.+.|
T Consensus 12 ~~fhlp~~eAA~~Lgv~~T~LKr~CR~~G 40 (52)
T PF02042_consen 12 QYFHLPIKEAAKELGVSVTTLKRRCRRLG 40 (52)
T ss_pred HHhCCCHHHHHHHhCCCHHHHHHHHHHcC
Confidence 46679999999999999999999999876
No 21
>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=86.20 E-value=1.1 Score=30.71 Aligned_cols=28 Identities=25% Similarity=0.520 Sum_probs=25.4
Q ss_pred chHHHHHHhCCCHHHHHHHHHhcCCeec
Q psy9207 63 PNTSLSEFLGVTEQEAAAIAQAEGWTVD 90 (125)
Q Consensus 63 ~~~~~a~~Lgl~~~e~~~~~~~~GW~~d 90 (125)
..+.+|.++|++.+-+-+++.+.||+-.
T Consensus 2 T~eELA~~tG~srQTINrWvRkegW~T~ 29 (122)
T PF07037_consen 2 TPEELAELTGYSRQTINRWVRKEGWKTE 29 (122)
T ss_pred CHHHHHHHhCccHHHHHHHHHhcCceec
Confidence 4678999999999999999999999963
No 22
>PF03683 UPF0175: Uncharacterised protein family (UPF0175); InterPro: IPR005368 This entry contains small proteins of unknown function.
Probab=86.08 E-value=1.4 Score=27.51 Aligned_cols=30 Identities=17% Similarity=0.271 Sum_probs=26.9
Q ss_pred CCcchHHHHHHhCCCHHHHHHHHHhcCCee
Q psy9207 60 SSIPNTSLSEFLGVTEQEAAAIAQAEGWTV 89 (125)
Q Consensus 60 ~sI~~~~~a~~Lgl~~~e~~~~~~~~GW~~ 89 (125)
..||+..+|.++|++.-++.++..++|=.+
T Consensus 33 g~iS~gkAAelag~s~~eF~~~L~~~gI~~ 62 (76)
T PF03683_consen 33 GKISLGKAAELAGMSRWEFLELLKERGIPI 62 (76)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHCCCCC
Confidence 689999999999999999999999987444
No 23
>PF12728 HTH_17: Helix-turn-helix domain
Probab=85.76 E-value=1.3 Score=24.95 Aligned_cols=24 Identities=13% Similarity=0.243 Sum_probs=20.9
Q ss_pred cchHHHHHHhCCCHHHHHHHHHhc
Q psy9207 62 IPNTSLSEFLGVTEQEAAAIAQAE 85 (125)
Q Consensus 62 I~~~~~a~~Lgl~~~e~~~~~~~~ 85 (125)
++++++|.+||++..-+..++.+.
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~~g 25 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIRQG 25 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcC
Confidence 578999999999999999988753
No 24
>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=85.32 E-value=3.3 Score=24.94 Aligned_cols=43 Identities=19% Similarity=0.360 Sum_probs=36.4
Q ss_pred HHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHHHhcCCeec
Q psy9207 48 QKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQAEGWTVD 90 (125)
Q Consensus 48 R~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~~~GW~~d 90 (125)
|+.++.+--..=..|.+.++|..||+++..+..+-..-.|.-.
T Consensus 9 rdkA~e~y~~~~g~i~lkdIA~~Lgvs~~tIr~WK~~dkW~~~ 51 (60)
T PF10668_consen 9 RDKAFEIYKESNGKIKLKDIAEKLGVSESTIRKWKSRDKWDEK 51 (60)
T ss_pred HHHHHHHHHHhCCCccHHHHHHHHCCCHHHHHHHhhhcchhhH
Confidence 6677777766777999999999999999999988887788764
No 25
>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=83.45 E-value=1.2 Score=25.67 Aligned_cols=28 Identities=25% Similarity=0.265 Sum_probs=23.0
Q ss_pred CcchHHHHHHhCCCHHHHHHHH-HhcCCe
Q psy9207 61 SIPNTSLSEFLGVTEQEAAAIA-QAEGWT 88 (125)
Q Consensus 61 sI~~~~~a~~Lgl~~~e~~~~~-~~~GW~ 88 (125)
.+++.++|.-||++..++++.+ .+.|=.
T Consensus 3 ~i~V~elAk~l~v~~~~ii~~l~~~~Gi~ 31 (54)
T PF04760_consen 3 KIRVSELAKELGVPSKEIIKKLFKELGIM 31 (54)
T ss_dssp EE-TTHHHHHHSSSHHHHHHHH-HHHTS-
T ss_pred ceEHHHHHHHHCcCHHHHHHHHHHhCCcC
Confidence 5789999999999999999999 548866
No 26
>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=82.84 E-value=4.6 Score=33.14 Aligned_cols=48 Identities=29% Similarity=0.447 Sum_probs=35.8
Q ss_pred HHHHHHHHHHHHHHHH----HHHHHHHHhcCCcchHHHHHHhCCCHHHHHHH
Q psy9207 34 DDIAHIMKALQDEVQK----RAISLISKAYSSIPNTSLSEFLGVTEQEAAAI 81 (125)
Q Consensus 34 ~~~~~~i~~l~~~vR~----~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~ 81 (125)
+.+..-+..|.+.|+. ..++.--|=|++|+++.+|++|+++++++...
T Consensus 290 e~~~~Ql~~Fl~eV~~q~~l~~lRSyLKLYtti~l~KLA~fl~vd~~~lr~~ 341 (404)
T PF10255_consen 290 EPYRRQLKLFLDEVKQQQKLPTLRSYLKLYTTIPLEKLASFLDVDEEELRSQ 341 (404)
T ss_pred hHHHHHHHHHHHHHHHhhhhhHHHHHHHhhcCCCHHHHHHHcCCCHHHHHHH
Confidence 3444445555555554 56778889999999999999999998876554
No 27
>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=81.33 E-value=4.2 Score=23.36 Aligned_cols=49 Identities=24% Similarity=0.340 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHHHHHHHhcCCcc-hHHHHHHhCCCHHHHHHH---HHhcCCee
Q psy9207 41 KALQDEVQKRAISLISKAYSSIP-NTSLSEFLGVTEQEAAAI---AQAEGWTV 89 (125)
Q Consensus 41 ~~l~~~vR~~~~~li~~AY~sI~-~~~~a~~Lgl~~~e~~~~---~~~~GW~~ 89 (125)
..+.+.+++.+....-..-..++ ..++|..+|++..-+.+. ..+.||-.
T Consensus 4 ~~~~~~i~~~i~~~~~~~~~~~~~~~~la~~~~is~~~v~~~l~~L~~~G~i~ 56 (66)
T cd07377 4 EQIADQLREAILSGELKPGDRLPSERELAEELGVSRTTVREALRELEAEGLVE 56 (66)
T ss_pred HHHHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 34555566665555444445566 999999999997555444 45579943
No 28
>PF08727 P3A: Poliovirus 3A protein like; InterPro: IPR014838 The 3A protein is found in positive-strand RNA viruses. It is a critical component of the poliovirus replication complex, and is also an inhibitor of host cell ER to Golgi transport. ; GO: 0003968 RNA-directed RNA polymerase activity, 0004197 cysteine-type endopeptidase activity, 0017111 nucleoside-triphosphatase activity; PDB: 1NG7_A.
Probab=80.62 E-value=1.1 Score=26.71 Aligned_cols=17 Identities=18% Similarity=0.567 Sum_probs=11.9
Q ss_pred CHHHHHHHHHhcCCeec
Q psy9207 74 TEQEAAAIAQAEGWTVD 90 (125)
Q Consensus 74 ~~~e~~~~~~~~GW~~d 90 (125)
..+|+.+||+++||-+.
T Consensus 28 ~~~eV~~YC~~~GWIip 44 (57)
T PF08727_consen 28 DSPEVREYCEEQGWIIP 44 (57)
T ss_dssp --HHHHHHHHHHT--TT
T ss_pred CCHHHHHHHHHCCcccc
Confidence 35899999999999873
No 29
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=80.53 E-value=7.4 Score=26.61 Aligned_cols=43 Identities=7% Similarity=0.210 Sum_probs=33.9
Q ss_pred HHHHHHHHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHHHhc
Q psy9207 41 KALQDEVQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQAE 85 (125)
Q Consensus 41 ~~l~~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~~~ 85 (125)
..+.-++|..++.-+..- -.|..++|.+||++...+-+|....
T Consensus 4 ~~vlPaiRa~lA~~L~ee--G~Sq~~iA~LLGltqaAVS~Yls~k 46 (119)
T COG2522 4 EEVLPAIRALLAKELIEE--GLSQYRIAKLLGLTQAAVSQYLSGK 46 (119)
T ss_pred HHHHHHHHHHHHHHHHHc--CCcHHHHHHHhCCCHHHHHHHHccC
Confidence 445667888777644443 7889999999999999999998864
No 30
>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=79.52 E-value=3 Score=22.56 Aligned_cols=23 Identities=17% Similarity=0.398 Sum_probs=20.2
Q ss_pred cchHHHHHHhCCCHHHHHHHHHh
Q psy9207 62 IPNTSLSEFLGVTEQEAAAIAQA 84 (125)
Q Consensus 62 I~~~~~a~~Lgl~~~e~~~~~~~ 84 (125)
+++.++|.+||++..-+..++.+
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~ 24 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHE 24 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHc
Confidence 57899999999999999888764
No 31
>TIGR01128 holA DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp.
Probab=77.41 E-value=20 Score=27.11 Aligned_cols=80 Identities=16% Similarity=0.189 Sum_probs=55.4
Q ss_pred HHHHHHHHHHcCCchHHHHHhcc--CCcHHHHHHHHHHHHHHHHH--HHHHHHHhcCCcchHHHHHHhCCCHHHHHHHHH
Q psy9207 8 QVWEVGKHLWNGNYPSIYSTLKR--TWSDDIAHIMKALQDEVQKR--AISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQ 83 (125)
Q Consensus 8 ~~~~l~~~l~~~~y~~v~~~~~~--~~s~~~~~~i~~l~~~vR~~--~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~ 83 (125)
.++.+..++.+|+..+++..++. .-......++..+...+|.- +-.+..+. .+.++++..+|+++.....+..
T Consensus 182 ~if~l~dal~~~~~~~a~~~l~~l~~~~~~~~~il~~l~~~~~~L~~~k~~~~~~---~~~~~i~~~~~~~~~~~~~~~~ 258 (302)
T TIGR01128 182 NVFDLTDALLEGKAARALRILKGLLGEGEEPLILLALLQRQLRLLLQLKRLAQQG---GPLAQLASKLGIWPYRRKLALK 258 (302)
T ss_pred CHHHHHHHHHCCCHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHHHHHHHHHHcC---CCHHHHHHHcCCCHHHHHHHHH
Confidence 58999999999999998888876 22344456677777777762 22333333 3788899999998766655544
Q ss_pred h-cCCeec
Q psy9207 84 A-EGWTVD 90 (125)
Q Consensus 84 ~-~GW~~d 90 (125)
. +.|+.+
T Consensus 259 ~~~~~s~~ 266 (302)
T TIGR01128 259 ALRRLSLA 266 (302)
T ss_pred HHhcCCHH
Confidence 3 678874
No 32
>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=77.13 E-value=12 Score=21.83 Aligned_cols=34 Identities=18% Similarity=0.206 Sum_probs=27.4
Q ss_pred HHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHHHh
Q psy9207 50 RAISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQA 84 (125)
Q Consensus 50 ~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~~ 84 (125)
+++.++.. -..++++++|..||+|.--+...+.+
T Consensus 9 ~Ll~~L~~-~~~~~~~ela~~l~~S~rti~~~i~~ 42 (59)
T PF08280_consen 9 KLLELLLK-NKWITLKELAKKLNISERTIKNDINE 42 (59)
T ss_dssp HHHHHHHH-HTSBBHHHHHHHCTS-HHHHHHHHHH
T ss_pred HHHHHHHc-CCCCcHHHHHHHHCCCHHHHHHHHHH
Confidence 67777777 89999999999999998777666654
No 33
>KOG3389|consensus
Probab=76.81 E-value=1.5 Score=31.20 Aligned_cols=28 Identities=25% Similarity=0.574 Sum_probs=21.4
Q ss_pred chHHHHHHhCCC-HHHHHHHHHhcCCeec
Q psy9207 63 PNTSLSEFLGVT-EQEAAAIAQAEGWTVD 90 (125)
Q Consensus 63 ~~~~~a~~Lgl~-~~e~~~~~~~~GW~~d 90 (125)
+++.+..-|-|+ .+++..||++.||.+|
T Consensus 121 PlsNvgm~L~F~tkEdA~sFaEkngW~yd 149 (178)
T KOG3389|consen 121 PLSNVGMALAFDTKEDAKSFAEKNGWDYD 149 (178)
T ss_pred cccccceeeeeccHHHHHHHHHHcCCccc
Confidence 444555556665 6889999999999998
No 34
>PF04800 ETC_C1_NDUFA4: ETC complex I subunit conserved region; InterPro: IPR006885 This entry represents prokaryotic NADH-ubiquinone oxidoreductase subunits (1.6.5.3 from EC, 1.6.99.3 from EC) from complex I of the electron transport chain initially identified in Neurospora crassa as a 21 kDa protein [].; GO: 0016651 oxidoreductase activity, acting on NADH or NADPH, 0022900 electron transport chain, 0005743 mitochondrial inner membrane; PDB: 2JYA_A 2LJU_A.
Probab=76.75 E-value=3.2 Score=27.55 Aligned_cols=16 Identities=31% Similarity=0.719 Sum_probs=13.9
Q ss_pred CHHHHHHHHHhcCCee
Q psy9207 74 TEQEAAAIAQAEGWTV 89 (125)
Q Consensus 74 ~~~e~~~~~~~~GW~~ 89 (125)
+.+++++||+++||.+
T Consensus 57 skE~Ai~yaer~G~~Y 72 (101)
T PF04800_consen 57 SKEDAIAYAERNGWDY 72 (101)
T ss_dssp SHHHHHHHHHHCT-EE
T ss_pred CHHHHHHHHHHcCCeE
Confidence 4799999999999999
No 35
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=76.38 E-value=4 Score=22.45 Aligned_cols=27 Identities=19% Similarity=0.389 Sum_probs=22.0
Q ss_pred hHHHHHHhCCCHHHHHHHHHhcCCeec
Q psy9207 64 NTSLSEFLGVTEQEAAAIAQAEGWTVD 90 (125)
Q Consensus 64 ~~~~a~~Lgl~~~e~~~~~~~~GW~~d 90 (125)
+.++....|.+++.+..+....+|-++
T Consensus 4 i~~F~~iTg~~~~~A~~~L~~~~wdle 30 (43)
T PF14555_consen 4 IAQFMSITGADEDVAIQYLEANNWDLE 30 (43)
T ss_dssp HHHHHHHH-SSHHHHHHHHHHTTT-HH
T ss_pred HHHHHHHHCcCHHHHHHHHHHcCCCHH
Confidence 567888899999999999999999986
No 36
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=76.32 E-value=12 Score=22.50 Aligned_cols=45 Identities=13% Similarity=0.335 Sum_probs=36.0
Q ss_pred HHHHHHHHHHHHHhcC-CcchHHHHHHhCCCHHHHHHHH---HhcCCee
Q psy9207 45 DEVQKRAISLISKAYS-SIPNTSLSEFLGVTEQEAAAIA---QAEGWTV 89 (125)
Q Consensus 45 ~~vR~~~~~li~~AY~-sI~~~~~a~~Lgl~~~e~~~~~---~~~GW~~ 89 (125)
+..+++|+.++...=. .++..++|..||++...+.... .+.|+..
T Consensus 5 ~~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~ 53 (68)
T smart00550 5 DSLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVC 53 (68)
T ss_pred hHHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 5678899999998844 4999999999999987766664 4568765
No 37
>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=74.75 E-value=12 Score=20.55 Aligned_cols=42 Identities=21% Similarity=0.411 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHHH---hcCC
Q psy9207 45 DEVQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQ---AEGW 87 (125)
Q Consensus 45 ~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~---~~GW 87 (125)
+..+.+|+.++...-. ++..++|..+|++..-+..... +.|+
T Consensus 2 ~~~~~~Il~~l~~~~~-~t~~ela~~~~is~~tv~~~l~~L~~~g~ 46 (48)
T PF13412_consen 2 DETQRKILNYLRENPR-ITQKELAEKLGISRSTVNRYLKKLEEKGL 46 (48)
T ss_dssp -HHHHHHHHHHHHCTT-S-HHHHHHHHTS-HHHHHHHHHHHHHTTS
T ss_pred CHHHHHHHHHHHHcCC-CCHHHHHHHhCCCHHHHHHHHHHHHHCcC
Confidence 4567788888888544 9999999999999766555543 3565
No 38
>PRK13503 transcriptional activator RhaS; Provisional
Probab=74.57 E-value=7.7 Score=29.00 Aligned_cols=40 Identities=8% Similarity=0.215 Sum_probs=31.8
Q ss_pred HHHHHHHHhcC-CcchHHHHHHhCCCHHHHHHHHHhc-CCee
Q psy9207 50 RAISLISKAYS-SIPNTSLSEFLGVTEQEAAAIAQAE-GWTV 89 (125)
Q Consensus 50 ~~~~li~~AY~-sI~~~~~a~~Lgl~~~e~~~~~~~~-GW~~ 89 (125)
++.+.|.+.|+ .++++++|+.+|+|+..+....++. |=+.
T Consensus 175 ~~~~~I~~~~~~~~tl~~lA~~~~lS~~~l~r~Fk~~~G~S~ 216 (278)
T PRK13503 175 QLLAWLEDHFAEEVNWEALADQFSLSLRTLHRQLKQQTGLTP 216 (278)
T ss_pred HHHHHHHHhhcCCCCHHHHHHHHCCCHHHHHHHHHHHhCcCH
Confidence 57778888888 9999999999999997777766553 5443
No 39
>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=74.40 E-value=8.9 Score=22.36 Aligned_cols=41 Identities=12% Similarity=0.283 Sum_probs=27.4
Q ss_pred HHHHHHHHHhcCCcchHHHHHHhCCCHHHHHH---HHHhcCCee
Q psy9207 49 KRAISLISKAYSSIPNTSLSEFLGVTEQEAAA---IAQAEGWTV 89 (125)
Q Consensus 49 ~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~---~~~~~GW~~ 89 (125)
-.++.+|......+++.+++..+|++...+.. -..++||-.
T Consensus 6 ~~vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~ 49 (68)
T PF13463_consen 6 WQVLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLVE 49 (68)
T ss_dssp HHHHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 35677777889999999999999999755444 455689984
No 40
>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=73.97 E-value=5.3 Score=21.33 Aligned_cols=23 Identities=17% Similarity=0.316 Sum_probs=19.6
Q ss_pred cchHHHHHHhCCCHHHHHHHHHh
Q psy9207 62 IPNTSLSEFLGVTEQEAAAIAQA 84 (125)
Q Consensus 62 I~~~~~a~~Lgl~~~e~~~~~~~ 84 (125)
+++.++|.+||++..-+..++.+
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~~~ 23 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHc
Confidence 36789999999999999888774
No 41
>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=72.14 E-value=8.6 Score=21.71 Aligned_cols=40 Identities=13% Similarity=0.312 Sum_probs=31.2
Q ss_pred HHHHHHHHhcCCcchHHHHHHhCCCHHHHHHH---HHhcCCee
Q psy9207 50 RAISLISKAYSSIPNTSLSEFLGVTEQEAAAI---AQAEGWTV 89 (125)
Q Consensus 50 ~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~---~~~~GW~~ 89 (125)
+|++++..+=..+++.+++.-+|++..-+-.+ ..+.||-.
T Consensus 7 ~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~ 49 (52)
T PF09339_consen 7 RILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVEEGYVE 49 (52)
T ss_dssp HHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCee
Confidence 67888999999999999999999997655444 44578864
No 42
>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=71.80 E-value=18 Score=22.52 Aligned_cols=35 Identities=17% Similarity=0.252 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHH
Q psy9207 46 EVQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAIA 82 (125)
Q Consensus 46 ~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~ 82 (125)
++.+.|+..+++. +++++.+....|++.+++.-+.
T Consensus 5 t~~~~IL~~ls~~--c~TLeeL~ekTgi~k~~LlV~L 39 (72)
T PF05584_consen 5 TVTQKILIILSKR--CCTLEELEEKTGISKNTLLVYL 39 (72)
T ss_pred hHHHHHHHHHHhc--cCCHHHHHHHHCCCHHHHHHHH
Confidence 5778888899888 9999999999999998877663
No 43
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=71.28 E-value=12 Score=29.41 Aligned_cols=54 Identities=7% Similarity=0.050 Sum_probs=42.4
Q ss_pred HHHHHHHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHHHhcCCee--cCceee
Q psy9207 42 ALQDEVQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQAEGWTV--DKVYTQ 95 (125)
Q Consensus 42 ~l~~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~~~GW~~--d~~~~~ 95 (125)
.+..-=|+.++..+.+...+|++++++...|+..+|++...+..|.-. +|+.++
T Consensus 204 sY~~YW~~~il~~L~~~~~~isi~~is~~T~i~~~Dii~tL~~l~~l~~~~g~~~i 259 (290)
T PLN03238 204 SFRSYWTRVLLEQLRDVKGDVSIKDLSLATGIRGEDIVSTLQSLNLIKYWKGQHVI 259 (290)
T ss_pred HHHHHHHHHHHHHHHhcCCCccHHHHHHHhCCCHHHHHHHHHHCCcEEEECCcEEE
Confidence 345556677777777777899999999999999999999999988765 255443
No 44
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=70.73 E-value=14 Score=24.20 Aligned_cols=30 Identities=17% Similarity=0.294 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHHHhcCCcchHHHHHHhCCC
Q psy9207 45 DEVQKRAISLISKAYSSIPNTSLSEFLGVT 74 (125)
Q Consensus 45 ~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~ 74 (125)
.+.|++|+.++.-+=+-+.+..++.++|..
T Consensus 2 ~t~rEkii~lL~e~~eplt~~ei~~~~~~~ 31 (97)
T COG3357 2 ETTREKIISLLLESDEPLTVAEIFELLNGE 31 (97)
T ss_pred chHHHHHHHHHHcCCCcchHHHHHHHHcCC
Confidence 468999999998888999999999999997
No 45
>smart00071 Galanin Galanin. Galanin [1,2,3] is a neuropeptide that controls various biological activities: it regulates the release growth hormone, inhibits the release of insulin and somatostatin, contracts smooth muscle of the gastrointestinal and genitourinary tract and may be involved in the control of adrenal secretion
Probab=70.52 E-value=6.4 Score=25.78 Aligned_cols=17 Identities=24% Similarity=0.542 Sum_probs=12.7
Q ss_pred HhcCCeec--CceeeccCC
Q psy9207 83 QAEGWTVD--KVYTQPVKK 99 (125)
Q Consensus 83 ~~~GW~~d--~~~~~p~~~ 99 (125)
.+|||+++ |..+-|...
T Consensus 10 eKRgwtlnsagyllgp~ai 28 (103)
T smart00071 10 EKRGWTLNSAGYLLGPHAI 28 (103)
T ss_pred cccCceeccCceeeCcccc
Confidence 46899998 667777653
No 46
>PF14056 DUF4250: Domain of unknown function (DUF4250)
Probab=70.12 E-value=11 Score=22.33 Aligned_cols=28 Identities=14% Similarity=0.146 Sum_probs=26.6
Q ss_pred chHHHHHHhCCCHHHHHHHHHhcCCeec
Q psy9207 63 PNTSLSEFLGVTEQEAAAIAQAEGWTVD 90 (125)
Q Consensus 63 ~~~~~a~~Lgl~~~e~~~~~~~~GW~~d 90 (125)
|+++++..++++.+++.+-..+-|..+|
T Consensus 22 sLd~Lc~~~~id~~~l~~kL~~~Gy~Y~ 49 (55)
T PF14056_consen 22 SLDELCYDYDIDKEELEEKLASIGYEYD 49 (55)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHcCCeEc
Confidence 8899999999999999999999999997
No 47
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=68.93 E-value=21 Score=20.85 Aligned_cols=53 Identities=11% Similarity=0.138 Sum_probs=32.7
Q ss_pred chHHHHHHhCCCHHHHHHHHHhcCCeecCceeeccCCCCCCCCCCCChHHHHHHhhHHHhh
Q psy9207 63 PNTSLSEFLGVTEQEAAAIAQAEGWTVDKVYTQPVKKPEEYATPNITDDQLYILTQYVSFL 123 (125)
Q Consensus 63 ~~~~~a~~Lgl~~~e~~~~~~~~GW~~d~~~~~p~~~~~~~~~~~~~~~ql~~Lt~~v~fL 123 (125)
++.++|+.+|++..-+..+.++.| ...|.+..+ ..-..+++++.+|-.+....
T Consensus 2 s~~eva~~~gvs~~tlr~w~~~~g------~~~~~r~~~--~~r~yt~~~v~~l~~i~~l~ 54 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAWERRYG------LPAPQRTDG--GHRLYSEADVARLRLIRRLT 54 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHhCC------CCCCCcCCC--CCeecCHHHHHHHHHHHHHH
Confidence 678999999999999988775433 222222111 11122777887776665543
No 48
>PF06627 DUF1153: Protein of unknown function (DUF1153); InterPro: IPR009534 This family consists of several short, hypothetical bacterial proteins of unknown function.; PDB: 2OA4_A 2JRT_A.
Probab=68.58 E-value=18 Score=23.50 Aligned_cols=38 Identities=16% Similarity=0.160 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHHHh
Q psy9207 47 VQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQA 84 (125)
Q Consensus 47 vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~~ 84 (125)
.|++..-...=.|.-|+.++++..-||+.+|+..+...
T Consensus 35 a~RKAaVV~aV~~Glis~~EA~~rY~Ls~eEf~~W~~a 72 (90)
T PF06627_consen 35 ARRKAAVVRAVRGGLISVEEACRRYGLSEEEFESWQRA 72 (90)
T ss_dssp HHHHHHHHHHHHCTTS-HHHHHHCTTSSHHHHHHHHHH
T ss_pred hhHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 45555556666799999999999999999999988664
No 49
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=68.49 E-value=11 Score=22.07 Aligned_cols=50 Identities=12% Similarity=0.195 Sum_probs=31.9
Q ss_pred chHHHHHHhCCCHHHHHHHHHhcCCeecCceeeccCCCCCCCCCCC-ChHHHHHHhhHHHh
Q psy9207 63 PNTSLSEFLGVTEQEAAAIAQAEGWTVDKVYTQPVKKPEEYATPNI-TDDQLYILTQYVSF 122 (125)
Q Consensus 63 ~~~~~a~~Lgl~~~e~~~~~~~~GW~~d~~~~~p~~~~~~~~~~~~-~~~ql~~Lt~~v~f 122 (125)
++.++|.++|++...+..|.. . +.+.|.+..+ .-.. +++++..|..+...
T Consensus 2 ti~eva~~~gvs~~tlr~y~~-~------gll~~~~~~~---g~r~y~~~dv~~l~~i~~l 52 (69)
T PF13411_consen 2 TIKEVAKLLGVSPSTLRYYER-E------GLLPPPRDEN---GYRYYSEEDVERLREIKEL 52 (69)
T ss_dssp EHHHHHHHTTTTHHHHHHHHH-T------TSSTTBESTT---SSEEE-HHHHHHHHHHHHH
T ss_pred cHHHHHHHHCcCHHHHHHHHH-h------cCcccccccC---ceeeccHHHHHHHHHHHHH
Confidence 578999999999988888765 2 2234433111 1122 88888888766544
No 50
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=68.29 E-value=9.6 Score=21.28 Aligned_cols=45 Identities=20% Similarity=0.264 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHHHhcCCc-chHHHHHHhCCCHHH---HHHHHHhcCCee
Q psy9207 45 DEVQKRAISLISKAYSSI-PNTSLSEFLGVTEQE---AAAIAQAEGWTV 89 (125)
Q Consensus 45 ~~vR~~~~~li~~AY~sI-~~~~~a~~Lgl~~~e---~~~~~~~~GW~~ 89 (125)
+.++..+....-..=..+ +..++|..+|+|..- ..+...+.||-.
T Consensus 3 ~~l~~~i~~~~~~~~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i~ 51 (60)
T smart00345 3 ERLREDIVSGELRPGDKLPSERELAAQLGVSRTTVREALSRLEAEGLVQ 51 (60)
T ss_pred HHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 445555544322222346 899999999999644 444455679853
No 51
>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=67.84 E-value=15 Score=20.23 Aligned_cols=35 Identities=20% Similarity=0.350 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHH
Q psy9207 46 EVQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAIA 82 (125)
Q Consensus 46 ~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~ 82 (125)
..|-+|+.++.. ...++.+++.-||++...+-...
T Consensus 2 ~~R~~Il~~L~~--~~~~~~el~~~l~~s~~~vs~hL 36 (47)
T PF01022_consen 2 PTRLRILKLLSE--GPLTVSELAEELGLSQSTVSHHL 36 (47)
T ss_dssp HHHHHHHHHHTT--SSEEHHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHHHh--CCCchhhHHHhccccchHHHHHH
Confidence 468899999998 88999999999999987665543
No 52
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=67.66 E-value=13 Score=22.88 Aligned_cols=29 Identities=17% Similarity=0.296 Sum_probs=22.3
Q ss_pred CCcchHHHHHHhCCCHHHHHHHHHhcCCe
Q psy9207 60 SSIPNTSLSEFLGVTEQEAAAIAQAEGWT 88 (125)
Q Consensus 60 ~sI~~~~~a~~Lgl~~~e~~~~~~~~GW~ 88 (125)
...++.++|.-.|+|+.-+..||++.|-+
T Consensus 33 ~~~si~elA~~~~vS~sti~Rf~kkLG~~ 61 (77)
T PF01418_consen 33 AFMSISELAEKAGVSPSTIVRFCKKLGFS 61 (77)
T ss_dssp CT--HHHHHHHCTS-HHHHHHHHHHCTTT
T ss_pred HHccHHHHHHHcCCCHHHHHHHHHHhCCC
Confidence 47788999999999999999999988753
No 53
>KOG0686|consensus
Probab=67.41 E-value=36 Score=28.34 Aligned_cols=83 Identities=18% Similarity=0.203 Sum_probs=65.8
Q ss_pred HHHHHHHHHHcCCchHHHHHhcc-CCc----HHHHHHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHhCCCH----HHH
Q psy9207 8 QVWEVGKHLWNGNYPSIYSTLKR-TWS----DDIAHIMKALQDEVQKRAISLISKAYSSIPNTSLSEFLGVTE----QEA 78 (125)
Q Consensus 8 ~~~~l~~~l~~~~y~~v~~~~~~-~~s----~~~~~~i~~l~~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~----~e~ 78 (125)
.+|.+.+....+.|..-+..++. .+. --+.|=|+.|-+.||+|.+----.-|.++.....|.-+|.+. .++
T Consensus 307 qlr~il~~fy~sky~~cl~~L~~~k~~llLD~yLaphVd~Ly~~IR~r~llqy~~py~s~~m~~mA~af~~sv~~le~~l 386 (466)
T KOG0686|consen 307 QLREILFKFYSSKYASCLELLREIKPRLLLDMYLAPHVDNLYSLIRNRALLQYLSPYSSADMSKMAEAFNTSVAILESEL 386 (466)
T ss_pred HHHHHHHHHhhhhHHHHHHHHHHhccceeechhcchhHHHHHHHHHHhhHHHhcCccccchHHHHHHHhcccHHHHHHHH
Confidence 35777778889999998888876 322 245677899999999999999999999999999999999985 556
Q ss_pred HHHHHhc--CCeec
Q psy9207 79 AAIAQAE--GWTVD 90 (125)
Q Consensus 79 ~~~~~~~--GW~~d 90 (125)
.+.+.+. .=.+|
T Consensus 387 ~~LI~~~~i~~rID 400 (466)
T KOG0686|consen 387 LELILEGKISGRID 400 (466)
T ss_pred HHHHHccchheeec
Confidence 6666653 34567
No 54
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=66.71 E-value=6.8 Score=30.36 Aligned_cols=28 Identities=21% Similarity=0.513 Sum_probs=26.0
Q ss_pred cchHHHHHHhCCCHHHHHHHHHhcCCee
Q psy9207 62 IPNTSLSEFLGVTEQEAAAIAQAEGWTV 89 (125)
Q Consensus 62 I~~~~~a~~Lgl~~~e~~~~~~~~GW~~ 89 (125)
..+.++|..||+++..+.++....||+.
T Consensus 20 mk~~dIAeklGvspntiksWKrr~gWs~ 47 (279)
T COG5484 20 MKLKDIAEKLGVSPNTIKSWKRRDGWSA 47 (279)
T ss_pred ccHHHHHHHhCCChHHHHHHHHhcCCCc
Confidence 6789999999999999999999999963
No 55
>COG2886 Uncharacterized small protein [Function unknown]
Probab=64.96 E-value=26 Score=22.67 Aligned_cols=39 Identities=18% Similarity=0.229 Sum_probs=30.7
Q ss_pred HHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHHHhcCCe
Q psy9207 48 QKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQAEGWT 88 (125)
Q Consensus 48 R~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~~~GW~ 88 (125)
++-+..++.+ ..+|+..++.+.|++..++..-..+||=.
T Consensus 30 l~iaI~L~qe--g~vSlg~Aaela~~sl~ef~~eL~~R~i~ 68 (88)
T COG2886 30 LEIAIELFQE--GAVSLGRAAELAGMSLNEFEEELRKRGIP 68 (88)
T ss_pred HHHHHHHHHH--hhhHHHHHHHHhcCCHHHHHHHHHHhCCC
Confidence 3344455555 88999999999999999998888887743
No 56
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=64.84 E-value=26 Score=20.46 Aligned_cols=50 Identities=16% Similarity=0.186 Sum_probs=30.5
Q ss_pred chHHHHHHhCCCHHHHHHHHHhcCCeecCceeeccCCCCCCCCCCC-ChHHHHHHhhHHH
Q psy9207 63 PNTSLSEFLGVTEQEAAAIAQAEGWTVDKVYTQPVKKPEEYATPNI-TDDQLYILTQYVS 121 (125)
Q Consensus 63 ~~~~~a~~Lgl~~~e~~~~~~~~GW~~d~~~~~p~~~~~~~~~~~~-~~~ql~~Lt~~v~ 121 (125)
++.++|+++|++...+..+.. .|+ +.|..... ..... +.+++..|-.+..
T Consensus 2 s~~eva~~~gvs~~tlr~~~~-~gl------i~~~~~~~--~g~r~y~~~dl~~l~~i~~ 52 (70)
T smart00422 2 TIGEVAKLAGVSVRTLRYYER-IGL------LPPPIRTE--GGYRLYSDEDLERLRFIKR 52 (70)
T ss_pred CHHHHHHHHCcCHHHHHHHHH-CCC------CCCCccCC--CCCEecCHHHHHHHHHHHH
Confidence 678999999999998888765 333 33321111 11122 7777776655543
No 57
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=63.87 E-value=16 Score=20.23 Aligned_cols=27 Identities=11% Similarity=0.256 Sum_probs=21.0
Q ss_pred cchHHHHHHhCCCHHHHHHHHHhcCCee
Q psy9207 62 IPNTSLSEFLGVTEQEAAAIAQAEGWTV 89 (125)
Q Consensus 62 I~~~~~a~~Lgl~~~e~~~~~~~~GW~~ 89 (125)
-|+.+||++||++..-+...+.. |...
T Consensus 18 ~S~~eAa~~lg~~~~~I~~~~~~-~~~~ 44 (53)
T smart00497 18 SSIREAAKYLGISHSSISKYLNT-GKKF 44 (53)
T ss_pred cCHHHHHHHhCCCHHHHHHHHhC-CCcc
Confidence 47889999999998888777765 4444
No 58
>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=63.61 E-value=24 Score=19.74 Aligned_cols=41 Identities=22% Similarity=0.300 Sum_probs=26.3
Q ss_pred HHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHH---HHhcCCee
Q psy9207 49 KRAISLISKAYSSIPNTSLSEFLGVTEQEAAAI---AQAEGWTV 89 (125)
Q Consensus 49 ~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~---~~~~GW~~ 89 (125)
..++.++-.+=..++.+++|..||+|..-+... ..+.|..+
T Consensus 3 ~~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~~~I 46 (55)
T PF08279_consen 3 KQILKLLLESKEPITAKELAEELGVSRRTIRRDIKELREWGIPI 46 (55)
T ss_dssp HHHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT-EE
T ss_pred HHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeE
Confidence 366777744444599999999999997555444 34456433
No 59
>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=63.48 E-value=26 Score=20.25 Aligned_cols=40 Identities=20% Similarity=0.319 Sum_probs=27.8
Q ss_pred HHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHH---HHhcCCe
Q psy9207 48 QKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAI---AQAEGWT 88 (125)
Q Consensus 48 R~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~---~~~~GW~ 88 (125)
++.|+..+.. -..++++++|..||+|..-+..- ..+.|--
T Consensus 2 ~~~Il~~l~~-~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~i 44 (57)
T PF08220_consen 2 QQQILELLKE-KGKVSVKELAEEFGVSEMTIRRDLNKLEKQGLI 44 (57)
T ss_pred HHHHHHHHHH-cCCEEHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence 3567777754 58999999999999997544332 3345653
No 60
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=63.38 E-value=22 Score=19.15 Aligned_cols=39 Identities=21% Similarity=0.381 Sum_probs=26.2
Q ss_pred HHHHHHHHhcCCcchHHHHHHhCCCHHHH---HHHHHhcCCee
Q psy9207 50 RAISLISKAYSSIPNTSLSEFLGVTEQEA---AAIAQAEGWTV 89 (125)
Q Consensus 50 ~~~~li~~AY~sI~~~~~a~~Lgl~~~e~---~~~~~~~GW~~ 89 (125)
.++..+.+ -..++..+++..+|++..-+ .+...+.||-.
T Consensus 4 ~il~~l~~-~~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~ 45 (53)
T smart00420 4 QILELLAQ-QGKVSVEELAELLGVSEMTIRRDLNKLEEQGLLT 45 (53)
T ss_pred HHHHHHHH-cCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 34444443 35699999999999986444 44455678854
No 61
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=63.28 E-value=15 Score=19.67 Aligned_cols=30 Identities=17% Similarity=0.216 Sum_probs=19.4
Q ss_pred cCCcchHHHHHHhCCCHHHHHHHHHhc-CCe
Q psy9207 59 YSSIPNTSLSEFLGVTEQEAAAIAQAE-GWT 88 (125)
Q Consensus 59 Y~sI~~~~~a~~Lgl~~~e~~~~~~~~-GW~ 88 (125)
-+.++++++|..+|+|..-+....++. |.+
T Consensus 6 ~~~~~l~~iA~~~g~S~~~f~r~Fk~~~g~t 36 (42)
T PF00165_consen 6 QQKLTLEDIAEQAGFSPSYFSRLFKKETGMT 36 (42)
T ss_dssp -SS--HHHHHHHHTS-HHHHHHHHHHHTSS-
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHHCcC
Confidence 357899999999999887777665553 654
No 62
>KOG2582|consensus
Probab=63.27 E-value=20 Score=29.34 Aligned_cols=65 Identities=11% Similarity=0.125 Sum_probs=43.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHhCCC-HHHHHHHHHhc-----CCee-cCceeeccCCCC
Q psy9207 37 AHIMKALQDEVQKRAISLISKAYSSIPNTSLSEFLGVT-EQEAAAIAQAE-----GWTV-DKVYTQPVKKPE 101 (125)
Q Consensus 37 ~~~i~~l~~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~-~~e~~~~~~~~-----GW~~-d~~~~~p~~~~~ 101 (125)
..++.......-.+.+.-+.|.|.||+++++|++..|. .+|+.+++-+. -... ||.+++-.+|..
T Consensus 293 t~l~k~av~sl~k~nI~rltktF~sLsL~dIA~~vQLa~~qevek~Ilqmie~~~i~a~iNG~v~f~~n~e~ 364 (422)
T KOG2582|consen 293 TGLAKQAVSSLYKKNIQRLTKTFLSLSLSDIASRVQLASAQEVEKYILQMIEDGEIFASINGMVFFTDNPEK 364 (422)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcchHHHHHHHHHHhccCceEEEecceEEEecCccc
Confidence 34566666666667777889999999999999987775 57777665542 2222 455555555444
No 63
>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=62.65 E-value=13 Score=21.98 Aligned_cols=29 Identities=17% Similarity=0.235 Sum_probs=25.9
Q ss_pred CcchHHHHHHhCCCHHHHHHHHHhcCCee
Q psy9207 61 SIPNTSLSEFLGVTEQEAAAIAQAEGWTV 89 (125)
Q Consensus 61 sI~~~~~a~~Lgl~~~e~~~~~~~~GW~~ 89 (125)
-.++.++|..||++..-+-.+...-||.-
T Consensus 13 G~~~~eIA~~Lg~~~~TV~~W~~r~~W~~ 41 (58)
T PF06056_consen 13 GWSIKEIAEELGVPRSTVYSWKDRYKWDE 41 (58)
T ss_pred CCCHHHHHHHHCCChHHHHHHHHhhCccc
Confidence 56789999999999999999999999975
No 64
>PF05687 DUF822: Plant protein of unknown function (DUF822); InterPro: IPR008540 This group of proteins contains members of the BZR1/LAT61 family of plant transcriptional repressors involved in controlling the response to Brassinosteroids (BRs). BRs are plant hormones that play essential roles in growth and development. BZR1 binds directly to DNA repressing the synthesis of genes involved in BR synthesis. Phosphorylation of BZR1 by BIN1 targets BZR1 to the 20S proteosome, while dephosphorylation leads to nuclear accumulation of BZR1 [].
Probab=62.41 E-value=9.9 Score=26.96 Aligned_cols=23 Identities=30% Similarity=0.497 Sum_probs=16.3
Q ss_pred HHHHH-HHHHhcCCeec-Cceeecc
Q psy9207 75 EQEAA-AIAQAEGWTVD-KVYTQPV 97 (125)
Q Consensus 75 ~~e~~-~~~~~~GW~~d-~~~~~p~ 97 (125)
.+|++ +.|.+-||+|+ ++..+++
T Consensus 47 ~NeVLkALc~eAGw~Ve~DGTtyr~ 71 (150)
T PF05687_consen 47 NNEVLKALCREAGWTVEPDGTTYRK 71 (150)
T ss_pred HHHHHHHHHHhCCEEEccCCCeecc
Confidence 36655 77999999996 5555554
No 65
>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=62.22 E-value=24 Score=19.28 Aligned_cols=34 Identities=18% Similarity=0.318 Sum_probs=23.6
Q ss_pred HHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHHH
Q psy9207 49 KRAISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQ 83 (125)
Q Consensus 49 ~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~ 83 (125)
.+|+..+.+- ..+|..++|..+|+|+..+..-+.
T Consensus 6 ~~Il~~Lq~d-~r~s~~~la~~lglS~~~v~~Ri~ 39 (42)
T PF13404_consen 6 RKILRLLQED-GRRSYAELAEELGLSESTVRRRIR 39 (42)
T ss_dssp HHHHHHHHH--TTS-HHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHHc-CCccHHHHHHHHCcCHHHHHHHHH
Confidence 4555555555 899999999999999988766443
No 66
>TIGR03573 WbuX N-acetyl sugar amidotransferase. This enzyme has been implicated in the formation of the acetamido moiety (sugar-NC(=NH)CH3) which is found on some exopolysaccharides and is positively charged at neutral pH. The reaction involves ligation of ammonia with a sugar N-acetyl group, displacing water. In E. coli (O145 strain) and Pseudomonas aeruginosa (O12 strain) this gene is known as wbuX and ifnA respectively and likely acts on sialic acid. In Campylobacter jejuni, the gene is known as pseA and acts on pseudaminic acid in the process of flagellin glycosylation. In other Pseudomonas strains and various organisms it is unclear what the identity of the sugar substrate is, and in fact, the phylogenetic tree of this family sports a considerably deep branching suggestive of possible major differences in substrate structure. Nevertheless, the family is characterized by a conserved tetracysteine motif (CxxC.....[GN]xCxxC) possibly indicative of a metal binding site, as well as an
Probab=61.93 E-value=14 Score=29.39 Aligned_cols=37 Identities=22% Similarity=0.352 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHHHhcCC----cchHHHHHHhCCCHHHHHHHH
Q psy9207 45 DEVQKRAISLISKAYSS----IPNTSLSEFLGVTEQEAAAIA 82 (125)
Q Consensus 45 ~~vR~~~~~li~~AY~s----I~~~~~a~~Lgl~~~e~~~~~ 82 (125)
..-|++.+.++.+ |.. -.++.++.+||++.+|+.+.+
T Consensus 302 ~itReeal~~v~~-~d~~~~~~~~~~~~~~lg~t~~ef~~~~ 342 (343)
T TIGR03573 302 RITREEAIELVKE-YDGEFPKEDLEYFLKYLGISEEEFWKTV 342 (343)
T ss_pred CCCHHHHHHHHHH-hcccccHHHHHHHHHHhCCCHHHHHHHh
Confidence 4568999999999 766 457889999999999987654
No 67
>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=61.43 E-value=21 Score=22.64 Aligned_cols=34 Identities=9% Similarity=0.038 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHH
Q psy9207 47 VQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAIA 82 (125)
Q Consensus 47 vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~ 82 (125)
=+.+|+..+.+ .++++.++|..+|+|..-+-...
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 35678888888 99999999999999976655543
No 68
>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=61.13 E-value=22 Score=20.80 Aligned_cols=48 Identities=23% Similarity=0.262 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHHHHHHhcCCc-chHHHHHHhCCCH---HHHHHHHHhcCCee
Q psy9207 42 ALQDEVQKRAISLISKAYSSI-PNTSLSEFLGVTE---QEAAAIAQAEGWTV 89 (125)
Q Consensus 42 ~l~~~vR~~~~~li~~AY~sI-~~~~~a~~Lgl~~---~e~~~~~~~~GW~~ 89 (125)
.+.+.+++.|...--+.=+.+ +..+++..+|+|. .++.....+.|+-.
T Consensus 4 ~i~~~l~~~I~~g~~~~g~~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~ 55 (64)
T PF00392_consen 4 QIYDQLRQAILSGRLPPGDRLPSERELAERYGVSRTTVREALRRLEAEGLIE 55 (64)
T ss_dssp HHHHHHHHHHHTTSS-TTSBE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHcCCCCCCCEeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEE
Confidence 344555555555544555689 9999999999996 55666677789876
No 69
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=60.99 E-value=19 Score=27.13 Aligned_cols=44 Identities=23% Similarity=0.385 Sum_probs=35.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHH
Q psy9207 36 IAHIMKALQDEVQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAI 81 (125)
Q Consensus 36 ~~~~i~~l~~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~ 81 (125)
...+++.|-...|++|++++++-= =-...++.+||+++..+++.
T Consensus 5 ~~~ildvLGNetRR~Il~lLt~~p--~yvsEiS~~lgvsqkAVl~H 48 (217)
T COG1777 5 IDKILDVLGNETRRRILQLLTRRP--CYVSEISRELGVSQKAVLKH 48 (217)
T ss_pred HHHHHHHHcCcHHHHHHHHHhcCc--hHHHHHHhhcCcCHHHHHHH
Confidence 456788999999999999998754 34567889999999777665
No 70
>KOG1860|consensus
Probab=60.82 E-value=92 Score=28.45 Aligned_cols=88 Identities=16% Similarity=0.282 Sum_probs=65.2
Q ss_pred chHHHHHHHHHHHHHcCCchHHHH-----------------Hhcc-CCcHHH-HHHHHHHHHHHHHHHHHHHHHhcCC--
Q psy9207 3 HPEIGQVWEVGKHLWNGNYPSIYS-----------------TLKR-TWSDDI-AHIMKALQDEVQKRAISLISKAYSS-- 61 (125)
Q Consensus 3 ~~~l~~~~~l~~~l~~~~y~~v~~-----------------~~~~-~~s~~~-~~~i~~l~~~vR~~~~~li~~AY~s-- 61 (125)
+++.+=...+-++...++|-.++. .+.+ .-++.+ -.++..|--.+|.-....++.+|.+
T Consensus 305 ~~~Vk~al~~~~a~~~nn~~~~~r~~~~~t~a~~~l~~~~~~l~q~p~~~~L~~~v~~~~f~~ir~~al~~~~~~~~~~~ 384 (927)
T KOG1860|consen 305 DSEVKLALCLRRAFQSNNFRRFFRLSSLRTEALQNLYTRFFKLMQSPALPYLMGCVLELFFPDIRWAALRAMSHAYNSKH 384 (927)
T ss_pred chhHHHHHHHHHHhccCCeeeeeeccchhHHHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhccC
Confidence 345556667778888888877742 1222 223322 3355677888999999999999975
Q ss_pred --cchHHHHHHhCCC-HHHHHHHHHhcCCeec
Q psy9207 62 --IPNTSLSEFLGVT-EQEAAAIAQAEGWTVD 90 (125)
Q Consensus 62 --I~~~~~a~~Lgl~-~~e~~~~~~~~GW~~d 90 (125)
|+...+..+|+++ .+++..++..+|=+++
T Consensus 385 ~~vp~~~l~~~l~f~~~e~~~~~~~~y~Leis 416 (927)
T KOG1860|consen 385 VPVPLGKLDRILLFDGEEELKVVCNYYGLEIS 416 (927)
T ss_pred CCcchhHHHHHHhcCChhhhHhhhhheeeEee
Confidence 8889999999997 6889999999999996
No 71
>KOG1497|consensus
Probab=60.82 E-value=21 Score=28.89 Aligned_cols=80 Identities=20% Similarity=0.189 Sum_probs=50.7
Q ss_pred HHHHHHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHHHh------cCCeec--CceeeccCCCCCC-CCCCC--ChH
Q psy9207 43 LQDEVQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQA------EGWTVD--KVYTQPVKKPEEY-ATPNI--TDD 111 (125)
Q Consensus 43 l~~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~~------~GW~~d--~~~~~p~~~~~~~-~~~~~--~~~ 111 (125)
+...+-+.=+-.+|+=|..|+.+.+++.|+++.+.+.+.+.+ ..=.+| .+++..-+...-. ..+++ --.
T Consensus 299 l~ra~~EhNlls~Skly~nisf~~Lg~ll~i~~ekaekiaa~MI~qeRmng~IDQ~egiihFe~~e~l~~wdkqi~sl~~ 378 (399)
T KOG1497|consen 299 LDRAVIEHNLLSASKLYNNISFEELGALLKIDAEKAEKIAAQMITQERMNGSIDQIEGIIHFEDREELPQWDKQIQSLCN 378 (399)
T ss_pred hhhHHHHHhHHHHHHHHHhccHHHHHHHhCCCHHHHHHHHHHHHhHHHhccchHhhcceEeecchhhhhhhhHHHHHHHH
Confidence 345566666778999999999999999999998777766543 244566 5565554421100 12222 345
Q ss_pred HHHHHhhHHHh
Q psy9207 112 QLYILTQYVSF 122 (125)
Q Consensus 112 ql~~Lt~~v~f 122 (125)
|+.++.+.+++
T Consensus 379 qvNki~~~i~~ 389 (399)
T KOG1497|consen 379 QVNKILDKISH 389 (399)
T ss_pred HHHHHHHHHHH
Confidence 56666665543
No 72
>PF12169 DNA_pol3_gamma3: DNA polymerase III subunits gamma and tau domain III; InterPro: IPR022754 This domain is found in bacteria and eukaryotes, and is approximately 110 amino acids in length. It is found in association with PF00004 from PFAM. This domain is also present in the tau subunit before it undergoes cleavage. Domains I-III are shared between the tau and the gamma subunits, while most of the DnaB-binding Domain IV and all of the alpha-interacting Domain V are unique to tau. ; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G.
Probab=60.72 E-value=29 Score=23.36 Aligned_cols=51 Identities=14% Similarity=0.220 Sum_probs=41.0
Q ss_pred HHHHHHHHHHHcCCchHHHHHhcc--CCcHHHHHHHHHHHHHHHHHHHHHHHH
Q psy9207 7 GQVWEVGKHLWNGNYPSIYSTLKR--TWSDDIAHIMKALQDEVQKRAISLISK 57 (125)
Q Consensus 7 ~~~~~l~~~l~~~~y~~v~~~~~~--~~s~~~~~~i~~l~~~vR~~~~~li~~ 57 (125)
..+.++.+++-+||.+++...++. .-+-+...++..|.+.+|+-..--...
T Consensus 16 ~~i~~l~~ai~~~d~~~~l~~~~~l~~~G~d~~~~l~~L~~~~R~ll~~k~~~ 68 (143)
T PF12169_consen 16 EQIFELLDAILEGDAAEALELLNELLEQGKDPKQFLDDLIEYLRDLLLYKITG 68 (143)
T ss_dssp HHHHHHHHHHHTT-HHHHHHHHHHHHHCT--HHHHHHHHHHHHHHHHHHTTSG
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhCC
Confidence 357889999999999999999998 567789999999999999977765555
No 73
>PRK05629 hypothetical protein; Validated
Probab=60.58 E-value=62 Score=25.08 Aligned_cols=82 Identities=18% Similarity=0.227 Sum_probs=52.1
Q ss_pred HHHHHHHHHHHcCCchHHHHHhcc--CCcHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHHHh
Q psy9207 7 GQVWEVGKHLWNGNYPSIYSTLKR--TWSDDIAHIMKALQDEVQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQA 84 (125)
Q Consensus 7 ~~~~~l~~~l~~~~y~~v~~~~~~--~~s~~~~~~i~~l~~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~~ 84 (125)
..++.+..++-+|+..+....++. .-.+.-..++..+...+|.-. ++.... ..++...+++-+|+.+-.+..+..+
T Consensus 195 ~~iF~l~dAv~~g~~~~Al~~l~~l~~~g~~pi~il~~l~~~~r~l~-~l~~~~-~~~~~~~ia~~l~i~p~~~~~~~~~ 272 (318)
T PRK05629 195 VSGFDIADLACAGQVSKAVASTRRALQLGVSPVALAAALSMKVGQIA-RLYSTR-GRIDSFELAKELGMPPFVVEKTAKV 272 (318)
T ss_pred chHHHHHHHHHcCCHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHHH-HHHhhc-CCCCHHHHHHHcCCChHHHHHHHHH
Confidence 478999999999999998877753 223333456666665555422 222211 2246778999999987544444333
Q ss_pred -cCCeec
Q psy9207 85 -EGWTVD 90 (125)
Q Consensus 85 -~GW~~d 90 (125)
++|+.+
T Consensus 273 ar~~s~~ 279 (318)
T PRK05629 273 ARNWSGD 279 (318)
T ss_pred HhCCCHH
Confidence 699874
No 74
>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=60.55 E-value=14 Score=20.06 Aligned_cols=21 Identities=14% Similarity=0.181 Sum_probs=17.4
Q ss_pred chHHHHHHhCCCHHHHHHHHH
Q psy9207 63 PNTSLSEFLGVTEQEAAAIAQ 83 (125)
Q Consensus 63 ~~~~~a~~Lgl~~~e~~~~~~ 83 (125)
++.++|.++|++..-+..+..
T Consensus 2 ~~~e~a~~~gv~~~tlr~~~~ 22 (49)
T cd04761 2 TIGELAKLTGVSPSTLRYYER 22 (49)
T ss_pred cHHHHHHHHCcCHHHHHHHHH
Confidence 678999999999887776644
No 75
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=60.33 E-value=24 Score=19.47 Aligned_cols=37 Identities=16% Similarity=0.299 Sum_probs=26.6
Q ss_pred HHHHHHHhcCCcchHHHHHHhCCCHHHHHHH---HHhcCCee
Q psy9207 51 AISLISKAYSSIPNTSLSEFLGVTEQEAAAI---AQAEGWTV 89 (125)
Q Consensus 51 ~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~---~~~~GW~~ 89 (125)
++.++. -..++..+++..||++...+... ..+.||-.
T Consensus 2 il~~l~--~~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~ 41 (66)
T smart00418 2 ILKLLA--EGELCVCELAEILGLSQSTVSHHLKKLREAGLVE 41 (66)
T ss_pred HHHHhh--cCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCee
Confidence 445554 56789999999999987554444 55578876
No 76
>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=59.84 E-value=34 Score=20.22 Aligned_cols=39 Identities=21% Similarity=0.245 Sum_probs=28.5
Q ss_pred HHHHHHHHhcCCcchHHHHHHhCCCHHHHHH---HHHhcCCeec
Q psy9207 50 RAISLISKAYSSIPNTSLSEFLGVTEQEAAA---IAQAEGWTVD 90 (125)
Q Consensus 50 ~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~---~~~~~GW~~d 90 (125)
+++..+..++. +.+++|..+|++..-+.. ...+.|+.+.
T Consensus 4 ~il~~L~~~~~--~~~eLa~~l~vS~~tv~~~l~~L~~~g~~i~ 45 (69)
T TIGR00122 4 RLLALLADNPF--SGEKLGEALGMSRTAVNKHIQTLREWGVDVL 45 (69)
T ss_pred HHHHHHHcCCc--CHHHHHHHHCCCHHHHHHHHHHHHHCCCeEE
Confidence 56777777774 589999999999754443 4556799763
No 77
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=59.62 E-value=14 Score=19.37 Aligned_cols=26 Identities=23% Similarity=0.277 Sum_probs=18.9
Q ss_pred hHHHHHHhCCCHHHHHHHHHhcCCeec
Q psy9207 64 NTSLSEFLGVTEQEAAAIAQAEGWTVD 90 (125)
Q Consensus 64 ~~~~a~~Lgl~~~e~~~~~~~~GW~~d 90 (125)
+..+..| ||+.+++.+.....||.++
T Consensus 6 v~~L~~m-Gf~~~~~~~AL~~~~~nve 31 (37)
T PF00627_consen 6 VQQLMEM-GFSREQAREALRACNGNVE 31 (37)
T ss_dssp HHHHHHH-TS-HHHHHHHHHHTTTSHH
T ss_pred HHHHHHc-CCCHHHHHHHHHHcCCCHH
Confidence 3456667 9999888888888888654
No 78
>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=59.47 E-value=19 Score=21.45 Aligned_cols=36 Identities=14% Similarity=0.224 Sum_probs=24.9
Q ss_pred CcchHHHHHHhCCCHHHH---HHHHHhcCCee-c-Cceeec
Q psy9207 61 SIPNTSLSEFLGVTEQEA---AAIAQAEGWTV-D-KVYTQP 96 (125)
Q Consensus 61 sI~~~~~a~~Lgl~~~e~---~~~~~~~GW~~-d-~~~~~p 96 (125)
.++.+++|.++|++.+-+ .....+.||-- + +.+.++
T Consensus 28 ~lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I~~~~~~i~I~ 68 (76)
T PF13545_consen 28 PLTQEEIADMLGVSRETVSRILKRLKDEGIIEVKRGKIIIL 68 (76)
T ss_dssp ESSHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEETTEEEES
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEcCCEEEEC
Confidence 467899999999997554 44455679875 3 444444
No 79
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=59.46 E-value=34 Score=20.11 Aligned_cols=53 Identities=8% Similarity=0.131 Sum_probs=34.1
Q ss_pred chHHHHHHhCCCHHHHHHHHHhcCCeecCceeeccCCCCCCCCCCC-ChHHHHHHhhHHHhhc
Q psy9207 63 PNTSLSEFLGVTEQEAAAIAQAEGWTVDKVYTQPVKKPEEYATPNI-TDDQLYILTQYVSFLE 124 (125)
Q Consensus 63 ~~~~~a~~Lgl~~~e~~~~~~~~GW~~d~~~~~p~~~~~~~~~~~~-~~~ql~~Lt~~v~fLE 124 (125)
++.++|+++|++..-+..+..+. +.+.|.+..+ .-.. +++++..|-.+..+++
T Consensus 2 ~i~e~A~~~gVs~~tlr~ye~~~------gl~~~~r~~~---g~R~yt~~di~~l~~i~~l~~ 55 (68)
T cd04763 2 TIGEVALLTGIKPHVLRAWEREF------GLLKPQRSDG---GHRLFNDADIDRILEIKRWID 55 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHhc------CCCCCCcCCC---CCcccCHHHHHHHHHHHHHHH
Confidence 67899999999998888765432 3333422211 2223 8888888877666543
No 80
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=59.12 E-value=23 Score=22.74 Aligned_cols=45 Identities=18% Similarity=0.345 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHHHhc---CCcchHHHHHHhCCCHHHHHHHHH---hcCCee
Q psy9207 45 DEVQKRAISLISKAY---SSIPNTSLSEFLGVTEQEAAAIAQ---AEGWTV 89 (125)
Q Consensus 45 ~~vR~~~~~li~~AY---~sI~~~~~a~~Lgl~~~e~~~~~~---~~GW~~ 89 (125)
..++++|++.|.... .=++++.+++-||++.+++.+.+. ..|.-+
T Consensus 46 ~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IY 96 (102)
T PF08784_consen 46 SPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNEGHIY 96 (102)
T ss_dssp -HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTTSEE
T ss_pred CHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhCCeEe
Confidence 455666777766622 349999999999999877666544 457766
No 81
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=58.82 E-value=47 Score=24.11 Aligned_cols=28 Identities=18% Similarity=0.396 Sum_probs=20.6
Q ss_pred cchHHHHHHhCCCHHHHHHH---HHhcCCee
Q psy9207 62 IPNTSLSEFLGVTEQEAAAI---AQAEGWTV 89 (125)
Q Consensus 62 I~~~~~a~~Lgl~~~e~~~~---~~~~GW~~ 89 (125)
++..++|.|||++.+-+-.. .++.|+--
T Consensus 185 lt~~~iA~~lG~sr~tvsR~l~~l~~~g~I~ 215 (235)
T PRK11161 185 MTRGDIGNYLGLTVETISRLLGRFQKSGMLA 215 (235)
T ss_pred ccHHHHHHHhCCcHHHHHHHHHHHHHCCCEE
Confidence 66789999999997665444 45578854
No 82
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=58.26 E-value=19 Score=21.43 Aligned_cols=30 Identities=20% Similarity=0.484 Sum_probs=26.2
Q ss_pred CcchHHHHHHhCCC--HHHHHHHHHhcCCeec
Q psy9207 61 SIPNTSLSEFLGVT--EQEAAAIAQAEGWTVD 90 (125)
Q Consensus 61 sI~~~~~a~~Lgl~--~~e~~~~~~~~GW~~d 90 (125)
.++.+.+.++||++ .+++.+.....|.+++
T Consensus 5 ~~~~~~i~~llG~~i~~~ei~~~L~~lg~~~~ 36 (71)
T smart00874 5 TLRRERINRLLGLDLSAEEIEEILKRLGFEVE 36 (71)
T ss_pred EecHHHHHHHHCCCCCHHHHHHHHHHCCCeEE
Confidence 46788999999986 6899999999999985
No 83
>KOG2758|consensus
Probab=57.84 E-value=44 Score=27.22 Aligned_cols=47 Identities=11% Similarity=0.140 Sum_probs=36.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHHHh
Q psy9207 38 HIMKALQDEVQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQA 84 (125)
Q Consensus 38 ~~i~~l~~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~~ 84 (125)
+..+.|.+.-|--||...-+--+.|+++-+|.-|+++++|+..++..
T Consensus 326 a~l~~F~E~ARl~ifEtfCRIHqcIti~mLA~kLnm~~eeaErwivn 372 (432)
T KOG2758|consen 326 ALLDEFLENARLLIFETFCRIHQCITIDMLADKLNMDPEEAERWIVN 372 (432)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHheeHHHHHHHhcCCHHHHHHHHHH
Confidence 34455556666666776667778899999999999999998887554
No 84
>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=57.77 E-value=33 Score=19.42 Aligned_cols=40 Identities=15% Similarity=0.313 Sum_probs=27.4
Q ss_pred HHHHHHHHhcCC-cchHHHHHHhCCCHHH---HHHHHHhcCCee
Q psy9207 50 RAISLISKAYSS-IPNTSLSEFLGVTEQE---AAAIAQAEGWTV 89 (125)
Q Consensus 50 ~~~~li~~AY~s-I~~~~~a~~Lgl~~~e---~~~~~~~~GW~~ 89 (125)
+++..|...=.. ++..+++..+|++..- +++-..++||..
T Consensus 9 ~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~ 52 (62)
T PF12802_consen 9 RVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKKGLVE 52 (62)
T ss_dssp HHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 444455554444 8999999999999744 455566689976
No 85
>PRK05574 holA DNA polymerase III subunit delta; Reviewed
Probab=57.56 E-value=85 Score=24.09 Aligned_cols=83 Identities=16% Similarity=0.132 Sum_probs=55.8
Q ss_pred HHHHHHHHHHHcCCchHHHHHhcc--CCcHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHHHh
Q psy9207 7 GQVWEVGKHLWNGNYPSIYSTLKR--TWSDDIAHIMKALQDEVQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQA 84 (125)
Q Consensus 7 ~~~~~l~~~l~~~~y~~v~~~~~~--~~s~~~~~~i~~l~~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~~ 84 (125)
..+|.+..++-+|+...++..++. .-..+...++..+...+|.-..-....+ ...+.+++++-+|+.+.....+...
T Consensus 216 ~~~f~l~dai~~~~~~~a~~~l~~l~~~~~~~~~il~~l~~~~~~l~~~k~~~~-~g~~~~~~~~~~~i~~~~~~~~~~~ 294 (340)
T PRK05574 216 FDVFDLVDAILAGKIKRALRILDGLRLEGEEPIKLLAALQREFRLLLQLKILSQ-QGYPLQQLAKELRVWPYRVKLALRA 294 (340)
T ss_pred CCHHHHHHHHHCCCHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHHHHHHHHHH-cCCCHHHHHHHcCCChhHHHHHHHH
Confidence 468999999999999998887775 2234445677888777776333222222 2456788999999987555444332
Q ss_pred -cCCeec
Q psy9207 85 -EGWTVD 90 (125)
Q Consensus 85 -~GW~~d 90 (125)
+.|+.+
T Consensus 295 ~~~~s~~ 301 (340)
T PRK05574 295 LQRLSLK 301 (340)
T ss_pred HhCCCHH
Confidence 577764
No 86
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=56.84 E-value=27 Score=19.08 Aligned_cols=36 Identities=17% Similarity=0.230 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHHHh
Q psy9207 46 EVQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQA 84 (125)
Q Consensus 46 ~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~~ 84 (125)
..|.+++.+... -.+..++|..||+|..-+..+...
T Consensus 5 ~~R~~ii~l~~~---G~s~~~ia~~lgvs~~Tv~~w~kr 40 (50)
T PF13384_consen 5 ERRAQIIRLLRE---GWSIREIAKRLGVSRSTVYRWIKR 40 (50)
T ss_dssp -----HHHHHHH---T--HHHHHHHHTS-HHHHHHHHT-
T ss_pred hHHHHHHHHHHC---CCCHHHHHHHHCcCHHHHHHHHHH
Confidence 445666666665 889999999999998888777653
No 87
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=56.70 E-value=52 Score=21.32 Aligned_cols=59 Identities=10% Similarity=0.128 Sum_probs=36.3
Q ss_pred HHHHHhcc-CCcHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHHHhcC
Q psy9207 23 SIYSTLKR-TWSDDIAHIMKALQDEVQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQAEG 86 (125)
Q Consensus 23 ~v~~~~~~-~~s~~~~~~i~~l~~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~~~G 86 (125)
..|..+.. .+++.+...+..++..+ +...+.++ .=....+|..||++..-+.....+.|
T Consensus 34 ~~~~~l~~~~~~~~~~~~l~~~Er~~---i~~aL~~~--~gn~s~AAr~LGIsRsTL~rKLkr~g 93 (95)
T PRK00430 34 NYFAQLNGQDVNDLYELVLAEVEAPL---LDMVMQYT--RGNQTRAALMLGINRGTLRKKLKKYG 93 (95)
T ss_pred HHHHHhcCCCchhHHHHHHHHHHHHH---HHHHHHHc--CCCHHHHHHHhCCCHHHHHHHHHHhC
Confidence 44556666 66677777776665433 22233332 23478899999999877666555433
No 88
>PF09035 Tn916-Xis: Excisionase from transposon Tn916; InterPro: IPR015122 The phage-encoded excisionase protein Tn916-Xis adopts a winged-helix structure that consists of a three-stranded anti-parallel beta-sheet that packs against a helix-turn-helix (HTH) motif and a third C-terminal alpha-helix. It is encoded for by Tn916, which also codes for the integrase Tn916-Int. The protein interacts with DNA by the insertion of helix alpha-2 into the major groove and the contact of the hairpin that connects strands beta-2 and beta-3 with the adjacent phosphodiester backbone and/or minor groove. Tn916-Xis stimulates phage excision and inhibits viral integration by stabilising distorted DNA structures []. ; PDB: 1Y6U_A.
Probab=56.08 E-value=16 Score=22.41 Aligned_cols=30 Identities=13% Similarity=0.308 Sum_probs=22.4
Q ss_pred CcchHHHHHHhCCCHHHHHHHH-H--hcCCeec
Q psy9207 61 SIPNTSLSEFLGVTEQEAAAIA-Q--AEGWTVD 90 (125)
Q Consensus 61 sI~~~~~a~~Lgl~~~e~~~~~-~--~~GW~~d 90 (125)
.++++.||.|.|+...-+.+.+ . ..+|.+-
T Consensus 13 ~LTi~EAa~Y~gIG~~klr~l~~~~~~~~f~~~ 45 (67)
T PF09035_consen 13 TLTIEEAAEYFGIGEKKLRELAEENPDCPFVLW 45 (67)
T ss_dssp EEEHHHHHHHT-S-HHHHHHHHHH-TT-SSEEE
T ss_pred ccCHHHHHHHhCccHHHHHHHHHhCCCCCEEEE
Confidence 5789999999999999999998 3 3578764
No 89
>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=55.71 E-value=22 Score=18.53 Aligned_cols=19 Identities=16% Similarity=0.573 Sum_probs=12.2
Q ss_pred cchHHHHHHhCCCHHHHHH
Q psy9207 62 IPNTSLSEFLGVTEQEAAA 80 (125)
Q Consensus 62 I~~~~~a~~Lgl~~~e~~~ 80 (125)
++-.++|.|||++.+-+-.
T Consensus 3 mtr~diA~~lG~t~ETVSR 21 (32)
T PF00325_consen 3 MTRQDIADYLGLTRETVSR 21 (32)
T ss_dssp --HHHHHHHHTS-HHHHHH
T ss_pred cCHHHHHHHhCCcHHHHHH
Confidence 5678899999999755433
No 90
>PF03484 B5: tRNA synthetase B5 domain; InterPro: IPR005147 Domain B5 is found in phenylalanine-tRNA synthetase beta subunits. This domain has been shown to bind DNA through a winged helix-turn-helix motif []. Phenylalanine-tRNA synthetase may influence common cellular processes via DNA binding, in addition to its aminoacylation function.; GO: 0000287 magnesium ion binding, 0003723 RNA binding, 0005524 ATP binding, 0006432 phenylalanyl-tRNA aminoacylation; PDB: 2AKW_B 1B70_B 1B7Y_B 2ALY_B 2IY5_B 2AMC_B 3PCO_D 2CXI_C 1JJC_B 1EIY_B ....
Probab=55.63 E-value=25 Score=21.16 Aligned_cols=30 Identities=20% Similarity=0.473 Sum_probs=24.6
Q ss_pred CcchHHHHHHhCCC--HHHHHHHHHhcCCeec
Q psy9207 61 SIPNTSLSEFLGVT--EQEAAAIAQAEGWTVD 90 (125)
Q Consensus 61 sI~~~~~a~~Lgl~--~~e~~~~~~~~GW~~d 90 (125)
.++.+.+.++||++ .+++.+.....|-+++
T Consensus 5 ~~~~~~i~~~lG~~i~~~~i~~~L~~lg~~~~ 36 (70)
T PF03484_consen 5 TLSLDKINKLLGIDISPEEIIKILKRLGFKVE 36 (70)
T ss_dssp EEEHHHHHHHHTS---HHHHHHHHHHTT-EEE
T ss_pred EecHHHHHHHhCCCCCHHHHHHHHHHCCCEEE
Confidence 46788999999975 7999999999999985
No 91
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=55.27 E-value=49 Score=22.14 Aligned_cols=36 Identities=14% Similarity=0.158 Sum_probs=25.7
Q ss_pred HHHHHHHHHhc-CCcchHHHHHHhCCCHHHHHHHHHh
Q psy9207 49 KRAISLISKAY-SSIPNTSLSEFLGVTEQEAAAIAQA 84 (125)
Q Consensus 49 ~~~~~li~~AY-~sI~~~~~a~~Lgl~~~e~~~~~~~ 84 (125)
.++...|...| ..++++++|+.+|++..-+....++
T Consensus 12 ~~~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~ 48 (127)
T PRK11511 12 HSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKK 48 (127)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 35566666666 5689999999999998666555443
No 92
>PRK07914 hypothetical protein; Reviewed
Probab=54.90 E-value=99 Score=24.01 Aligned_cols=80 Identities=15% Similarity=0.221 Sum_probs=53.0
Q ss_pred HHHHHHHHHHHcCCchHHHHHhcc--CCcHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHHHh
Q psy9207 7 GQVWEVGKHLWNGNYPSIYSTLKR--TWSDDIAHIMKALQDEVQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQA 84 (125)
Q Consensus 7 ~~~~~l~~~l~~~~y~~v~~~~~~--~~s~~~~~~i~~l~~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~~ 84 (125)
.+++.|..++-+|+..+....++. .-.++...++..|...+|.-. .+ +.... +..++++-+|+.+--+..+.++
T Consensus 197 ~~vf~L~dAi~~g~~~~A~~~l~~L~~~ge~p~~il~~l~~~~r~L~-~~--k~~~~-~~~~i~~~l~i~p~~~~~~~~~ 272 (320)
T PRK07914 197 VKGFDIADKAVAGDVAGAAEALRWAMMRGEPHVVLADALAEAVHTIA-RV--GPLSG-DPYRLAGELGMPPWRVQKAQKQ 272 (320)
T ss_pred chHHHHHHHHHCCCHHHHHHHHHHHHHCCCchHHHHHHHHHHHHHHH-HH--HHhcC-CHHHHHHHcCCCHHHHHHHHHH
Confidence 368999999999999998887764 223444455566666666521 11 11123 7889999999987444444333
Q ss_pred -cCCeec
Q psy9207 85 -EGWTVD 90 (125)
Q Consensus 85 -~GW~~d 90 (125)
++|+.+
T Consensus 273 ~~~~s~~ 279 (320)
T PRK07914 273 ARRWSRD 279 (320)
T ss_pred HcCCCHH
Confidence 699875
No 93
>PF01853 MOZ_SAS: MOZ/SAS family; InterPro: IPR002717 Moz is a monocytic leukemia Zn_finger protein and the SAS protein from Saccharomyces cerevisiae (Baker's yeast) is involved in silencing the Hmr locus. These proteins were reported to be homologous to acetyltransferases [] but this similarity is not supported by standard sequence analysis.; GO: 0016747 transferase activity, transferring acyl groups other than amino-acyl groups, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3TO6_A 1MJA_A 1MJ9_A 3TO7_A 3TO9_A 1MJB_A 1FY7_A 2OZU_A 2RC4_A 2OU2_A ....
Probab=54.89 E-value=29 Score=25.59 Aligned_cols=49 Identities=12% Similarity=0.120 Sum_probs=39.4
Q ss_pred HHHHHHHHHHHHHHHHHhcC--CcchHHHHHHhCCCHHHHHHHHHhcCCee
Q psy9207 41 KALQDEVQKRAISLISKAYS--SIPNTSLSEFLGVTEQEAAAIAQAEGWTV 89 (125)
Q Consensus 41 ~~l~~~vR~~~~~li~~AY~--sI~~~~~a~~Lgl~~~e~~~~~~~~GW~~ 89 (125)
.....-=|..+++.+...-. .|++++++...|+..++++...+..|+-.
T Consensus 128 ~sY~sYW~~~i~~~L~~~~~~~~isi~~is~~Tgi~~~DIi~tL~~l~~l~ 178 (188)
T PF01853_consen 128 LSYRSYWRRVILEYLLEFKGKKSISIKDISQETGIRPEDIISTLQQLGMLK 178 (188)
T ss_dssp HHHHHHHHHHHHHHHHHTSSE--EEHHHHHHHH-BTHHHHHHHHHHTT-EE
T ss_pred HHHHHHHHHHHHHHHHhcCCCCeEEHHHHHHHHCCCHHHHHHHHHHCCCEE
Confidence 34566677788888877777 59999999999999999999999999876
No 94
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=54.74 E-value=27 Score=18.52 Aligned_cols=29 Identities=21% Similarity=0.440 Sum_probs=21.7
Q ss_pred CcchHHHHHHhCCCHHHHHHH---HHhcCCee
Q psy9207 61 SIPNTSLSEFLGVTEQEAAAI---AQAEGWTV 89 (125)
Q Consensus 61 sI~~~~~a~~Lgl~~~e~~~~---~~~~GW~~ 89 (125)
.++..++|.++|++...+... ..+.||-.
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 467889999999997555444 45578875
No 95
>PF04433 SWIRM: SWIRM domain; InterPro: IPR007526 The SWIRM domain is a small alpha-helical domain of about 85 amino acid residues found in eukaryotic chromosomal proteins. It is named after the proteins SWI3, RSC8 and MOIRA in which it was first recognised. This domain is predicted to mediate protein-protein interactions in the assembly of chromatin-protein complexes. The SWIRM domain can be linked to different domains, such as the ZZ-type zinc finger (IPR000433 from INTERPRO), the Myb DNA-binding domain (IPR001005 from INTERPRO), the HORMA domain (IPR003511 from INTERPRO), the amino-oxidase domain, the chromo domain (IPR000953 from INTERPRO), and the JAB1/PAD1 domain.; GO: 0005515 protein binding; PDB: 2Z3Y_A 2UXN_A 2Y48_A 2HKO_A 2XAF_A 2X0L_A 2XAJ_A 2UXX_A 2V1D_A 2L3D_A ....
Probab=54.28 E-value=51 Score=20.51 Aligned_cols=43 Identities=5% Similarity=0.086 Sum_probs=32.4
Q ss_pred HHHHHHHHHH-HHHhcCCcchHHHHHHhC-CCH---HHHHHHHHhcCC
Q psy9207 45 DEVQKRAISL-ISKAYSSIPNTSLSEFLG-VTE---QEAAAIAQAEGW 87 (125)
Q Consensus 45 ~~vR~~~~~l-i~~AY~sI~~~~~a~~Lg-l~~---~e~~~~~~~~GW 87 (125)
-.+|+.|+.+ ..+.-..++.+++.+.+. .+. .-+-+|....||
T Consensus 36 l~iRn~il~~w~~n~~~~lt~~~~~~~i~~~d~~~~~ri~~FL~~~G~ 83 (86)
T PF04433_consen 36 LKIRNTILAEWRKNPNKYLTKTDARKLIKGIDVNKIRRIYDFLERWGL 83 (86)
T ss_dssp HHHHHHHHHHHHHHTTS---HHHHHHHTTSSSHHHHHHHHHHHHHTTS
T ss_pred HHHHHHHHHHHHHCCCCcccHHHHHHHccccCHHHHHHHHHHHHHcCc
Confidence 3689999888 677899999999999999 665 446677888888
No 96
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=54.07 E-value=1e+02 Score=23.80 Aligned_cols=82 Identities=11% Similarity=0.179 Sum_probs=49.7
Q ss_pred HHHHHHHHHHHcCCchHHHHHhcc--CCcHHHHHHHHHHHHHHHHHH-H-HHHHHhcCCcchHHHHHHhCCC-HHHHHHH
Q psy9207 7 GQVWEVGKHLWNGNYPSIYSTLKR--TWSDDIAHIMKALQDEVQKRA-I-SLISKAYSSIPNTSLSEFLGVT-EQEAAAI 81 (125)
Q Consensus 7 ~~~~~l~~~l~~~~y~~v~~~~~~--~~s~~~~~~i~~l~~~vR~~~-~-~li~~AY~sI~~~~~a~~Lgl~-~~e~~~~ 81 (125)
..++.+..++-.|+..+++..++. .-.+....++..|...+|.-. + .+..+-+ -+.+.+++-||+. +-.+..+
T Consensus 201 ~~if~l~dai~~~~~~~A~~~l~~L~~~g~~p~~il~~l~~~~r~l~~~k~~~~~G~--~~~~~ia~~lgi~~p~~~~~~ 278 (326)
T PRK07452 201 QNSLQLADALLQGNTGKALALLDDLLDANEPALRIVATLTGQFRTWLWVKLLVESGE--RDVKVIAKAAGIGNPKRIYFL 278 (326)
T ss_pred CcHHHHHHHHHCCCHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHHHHHHHHHHcCC--CcHHHHHHHhCCCCcHHHHHH
Confidence 468999999999999988777765 333445556677777776421 1 1222222 2455688889994 4222211
Q ss_pred H-HhcCCeec
Q psy9207 82 A-QAEGWTVD 90 (125)
Q Consensus 82 ~-~~~GW~~d 90 (125)
. ..++|+.+
T Consensus 279 ~~~~~~~s~~ 288 (326)
T PRK07452 279 RKEVQGLSSQ 288 (326)
T ss_pred HHHHhcCCHH
Confidence 1 12678774
No 97
>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=53.79 E-value=45 Score=21.31 Aligned_cols=32 Identities=13% Similarity=0.169 Sum_probs=25.2
Q ss_pred hcCCcchHHHHHHhCCCHHH---HHHHHHhcCCee
Q psy9207 58 AYSSIPNTSLSEFLGVTEQE---AAAIAQAEGWTV 89 (125)
Q Consensus 58 AY~sI~~~~~a~~Lgl~~~e---~~~~~~~~GW~~ 89 (125)
.-..|+..++|+++|++.+- +++-..++||-.
T Consensus 44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~ 78 (95)
T TIGR01610 44 KQDRVTATVIAELTGLSRTHVSDAIKSLARRRIIF 78 (95)
T ss_pred cCCccCHHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence 56788999999999999644 444556689988
No 98
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=53.52 E-value=58 Score=21.96 Aligned_cols=53 Identities=15% Similarity=0.223 Sum_probs=41.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHH---HHhcCCee
Q psy9207 36 IAHIMKALQDEVQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAI---AQAEGWTV 89 (125)
Q Consensus 36 ~~~~i~~l~~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~---~~~~GW~~ 89 (125)
...+...|.+..|.+|+.++... ...++.+++.-||++..-+-.. ..+-|+..
T Consensus 6 ~~~~fkaLadptRl~IL~~L~~~-~~~~v~ela~~l~lsqstvS~HL~~L~~AGLV~ 61 (117)
T PRK10141 6 PLQLFKILSDETRLGIVLLLRES-GELCVCDLCTALDQSQPKISRHLALLRESGLLL 61 (117)
T ss_pred HHHHHHHhCCHHHHHHHHHHHHc-CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCceE
Confidence 35677888999999999999753 4689999999999997665544 45568886
No 99
>COG3645 Uncharacterized phage-encoded protein [Function unknown]
Probab=53.14 E-value=38 Score=23.72 Aligned_cols=41 Identities=15% Similarity=0.155 Sum_probs=36.4
Q ss_pred HHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHHHhcCCeec
Q psy9207 50 RAISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQAEGWTVD 90 (125)
Q Consensus 50 ~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~~~GW~~d 90 (125)
.-++-+..+-.+|.+.++|++|++.+..+.+|..+.|--+.
T Consensus 36 ~f~D~v~~~~gli~~re~AK~lkige~~l~~~L~e~~~l~~ 76 (135)
T COG3645 36 EFADAVVEASGLILFRELAKLLKIGENRLFAWLRENKYLIK 76 (135)
T ss_pred HHHHHHhcCccceeHHHHHHHHccCHHHHHHHHHHCCEEEE
Confidence 34567788899999999999999999999999999888875
No 100
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=52.50 E-value=57 Score=20.56 Aligned_cols=48 Identities=21% Similarity=0.222 Sum_probs=35.2
Q ss_pred HHHHHhcCCcchHHHHHHhCCCHHHHHHHHHh---cCCeec---C-ceeeccCCC
Q psy9207 53 SLISKAYSSIPNTSLSEFLGVTEQEAAAIAQA---EGWTVD---K-VYTQPVKKP 100 (125)
Q Consensus 53 ~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~~---~GW~~d---~-~~~~p~~~~ 100 (125)
-+.-..|.-+|=+.++..||+|...+-+.+++ .|=.++ + ++..|.++.
T Consensus 11 ll~~~~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr~~G~~I~s~~~kGY~L~~~~~ 65 (79)
T COG1654 11 LLLLLTGNFVSGEKLAEELGISRTAVWKHIQQLREEGVDIESVRGKGYLLPQLPD 65 (79)
T ss_pred HHHHcCCCcccHHHHHHHHCccHHHHHHHHHHHHHhCCceEecCCCceeccCccc
Confidence 34455678899999999999998777666655 577775 3 466666554
No 101
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=52.42 E-value=39 Score=18.60 Aligned_cols=36 Identities=14% Similarity=0.213 Sum_probs=24.9
Q ss_pred HHHHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHHH
Q psy9207 45 DEVQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQ 83 (125)
Q Consensus 45 ~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~ 83 (125)
..++..|+.++... .+..++|..+|++..-+.....
T Consensus 14 ~~~~~~i~~~~~~~---~s~~~vA~~~~vs~~TV~ri~~ 49 (52)
T PF13542_consen 14 KRLEQYILKLLRES---RSFKDVARELGVSWSTVRRIFD 49 (52)
T ss_pred HHHHHHHHHHHhhc---CCHHHHHHHHCCCHHHHHHHHH
Confidence 44455555555444 7999999999999877665543
No 102
>PF13730 HTH_36: Helix-turn-helix domain
Probab=52.10 E-value=28 Score=19.49 Aligned_cols=25 Identities=20% Similarity=0.371 Sum_probs=18.7
Q ss_pred chHHHHHHhCCCHHHHHHH---HHhcCC
Q psy9207 63 PNTSLSEFLGVTEQEAAAI---AQAEGW 87 (125)
Q Consensus 63 ~~~~~a~~Lgl~~~e~~~~---~~~~GW 87 (125)
|.+.+|..+|++..-+... ..++||
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~~G~ 54 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEEKGL 54 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHCcC
Confidence 7899999999997555554 445677
No 103
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain
Probab=51.66 E-value=66 Score=22.98 Aligned_cols=47 Identities=13% Similarity=0.188 Sum_probs=30.6
Q ss_pred cchHHHHHHhCCCHHHHHHHHHhcCCeecCceeeccCCCCCCCCCCC-ChHHHHHHh
Q psy9207 62 IPNTSLSEFLGVTEQEAAAIAQAEGWTVDKVYTQPVKKPEEYATPNI-TDDQLYILT 117 (125)
Q Consensus 62 I~~~~~a~~Lgl~~~e~~~~~~~~GW~~d~~~~~p~~~~~~~~~~~~-~~~ql~~Lt 117 (125)
+++.++|+.+|++..-+.-|-. -+.+.|..... ..-.. +++++.+|.
T Consensus 2 ~~I~evA~~~gvs~~tLRyYe~-------~GLl~p~~r~~--~gyR~Y~~~dl~rL~ 49 (172)
T cd04790 2 LTISQLARQFGLSRSTLLYYER-------IGLLSPSARSE--SNYRLYGERDLERLE 49 (172)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-------CCCCCCCccCC--CCCccCCHHHHHHHH
Confidence 5789999999999888777654 34555532221 12233 788888873
No 104
>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=51.37 E-value=51 Score=23.94 Aligned_cols=42 Identities=19% Similarity=0.272 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHH---HHhcCCee
Q psy9207 47 VQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAI---AQAEGWTV 89 (125)
Q Consensus 47 vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~---~~~~GW~~ 89 (125)
.|++|+..+.+. ..++..++|..||++..-+... ..+.||..
T Consensus 2 tr~~IL~~L~~~-~~~t~~eLA~~lgis~~tV~~~L~~Le~~GlV~ 46 (203)
T TIGR02702 2 TKEDILSYLLKQ-GQATAAALAEALAISPQAVRRHLKDLETEGLIE 46 (203)
T ss_pred HHHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence 478899888764 7799999999999997665554 44579986
No 105
>PF06250 DUF1016: Protein of unknown function (DUF1016); InterPro: IPR009362 This is a family of proteins which is found in viruses, archaea and bacteria. The function of these proteins has not been experimetnally determined, but computational analysis suggests that they may function as nucleases which enhance the activity of nearby restriction endonucleases []. Cooperation of this kind between a restriction endonuclease and exonucleases has been shown to be essential in allowing some restriction enzymes to perform multiple rounds of DNA cleavage [].
Probab=51.36 E-value=48 Score=26.38 Aligned_cols=83 Identities=13% Similarity=0.313 Sum_probs=53.0
Q ss_pred HHHHHHHHHHHHcCCc--------hHHHHHhcc--------CCcHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchHHHHH
Q psy9207 6 IGQVWEVGKHLWNGNY--------PSIYSTLKR--------TWSDDIAHIMKALQDEVQKRAISLISKAYSSIPNTSLSE 69 (125)
Q Consensus 6 l~~~~~l~~~l~~~~y--------~~v~~~~~~--------~~s~~~~~~i~~l~~~vR~~~~~li~~AY~sI~~~~~a~ 69 (125)
+.-=|.||+.+-+..- .++...++. -+|..--.-|.+|-..+-+. ..+...-..||-.+..-
T Consensus 25 ~~lYW~IG~~I~e~~~~g~ra~yG~~vi~~LS~dL~~~fpkGFS~rNL~~MrqFy~~y~~~--~i~~~l~~qLsW~H~~i 102 (320)
T PF06250_consen 25 VLLYWEIGKRIVEKEQQGERAGYGKKVIKRLSKDLTEEFPKGFSRRNLKYMRQFYEAYPDE--EIVQTLVAQLSWHHIRI 102 (320)
T ss_pred HHHHHHHHHHHHHHHhcCcccccchhHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhh--hhccchhcccchhhHhh
Confidence 4455899998887644 334444432 23444444555565555542 24556666888988998
Q ss_pred HhCCCHHHHHHH----HHhcCCeec
Q psy9207 70 FLGVTEQEAAAI----AQAEGWTVD 90 (125)
Q Consensus 70 ~Lgl~~~e~~~~----~~~~GW~~d 90 (125)
+..+...+...| |.+.||+.+
T Consensus 103 L~kikd~~eR~fY~~~ai~~gWS~r 127 (320)
T PF06250_consen 103 LSKIKDPEERLFYIQEAIENGWSRR 127 (320)
T ss_pred hccCCCHHHHHHHHHHHHHhCCCHH
Confidence 888987666555 667899973
No 106
>PF09551 Spore_II_R: Stage II sporulation protein R (spore_II_R); InterPro: IPR014202 This entry is designated stage II sporulation protein R. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species. SpoIIR is a signalling protein that links the activation of sigma E to the transcriptional activity of sigma F during sporulation [, ].
Probab=50.69 E-value=70 Score=22.19 Aligned_cols=60 Identities=20% Similarity=0.227 Sum_probs=42.2
Q ss_pred HHHHHHHHHHHHHHHHHhcC-CcchHHHHHHhCCCHHHHHHH----HHhcCCeec-----CceeeccCCC
Q psy9207 41 KALQDEVQKRAISLISKAYS-SIPNTSLSEFLGVTEQEAAAI----AQAEGWTVD-----KVYTQPVKKP 100 (125)
Q Consensus 41 ~~l~~~vR~~~~~li~~AY~-sI~~~~~a~~Lgl~~~e~~~~----~~~~GW~~d-----~~~~~p~~~~ 100 (125)
+.++-.||++++..+..... +=+.+++-.++.=..+++.+. +.+.|-.++ +.+.||.+..
T Consensus 19 Q~lKl~VRD~Vl~~l~~~~~~~~~~~ea~~~i~~~~~~Ie~~A~~~l~~~G~~y~v~v~~~~~~FPtK~Y 88 (130)
T PF09551_consen 19 QALKLKVRDAVLEYLSPWLSQAKSKEEAREVIRENLPEIEQIAEEVLAEEGYDYPVKVELGRFYFPTKTY 88 (130)
T ss_pred HHHHHHHHHHHHHHHHHHhccCCCHHHHHHHHHHhHHHHHHHHHHHHHHhCCCCcEEEEEEeeeCCCceE
Confidence 67899999999999998765 445666777776665555554 444575553 7778887654
No 107
>COG5079 SAC3 Nuclear protein export factor [Intracellular trafficking and secretion / Cell division and chromosome partitioning]
Probab=50.17 E-value=56 Score=28.11 Aligned_cols=65 Identities=18% Similarity=0.335 Sum_probs=46.7
Q ss_pred hHHHHHhccCCcHHHHHHHHHHHH----HHHHHHHHHHH----HhcCCcchHHHHHHhCCC-HHHHHHHHHhcCCee
Q psy9207 22 PSIYSTLKRTWSDDIAHIMKALQD----EVQKRAISLIS----KAYSSIPNTSLSEFLGVT-EQEAAAIAQAEGWTV 89 (125)
Q Consensus 22 ~~v~~~~~~~~s~~~~~~i~~l~~----~vR~~~~~li~----~AY~sI~~~~~a~~Lgl~-~~e~~~~~~~~GW~~ 89 (125)
..||..++ |+.+..+|..|.+ .||.-++..++ +|-..|+.-++..+|.++ .+|..+||.=.|=++
T Consensus 303 trFfkl~q---Spsv~~lmg~lle~h~~sir~~aLkAm~k~~~sahk~ipf~~l~~il~f~~~~e~~efckyy~lei 376 (646)
T COG5079 303 TRFFKLIQ---SPSVQYLMGCLLEKHNISIRGGALKAMEKEIESAHKNIPFVDLSGILDFEEKGEGEEFCKYYGLEI 376 (646)
T ss_pred HHHHHHHh---CccHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHhhcCCCeehhhhhccccccchhHHHhhhcceee
Confidence 33444443 4556667766655 46666666544 555789999999999997 688999999888887
No 108
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=50.03 E-value=29 Score=20.33 Aligned_cols=49 Identities=18% Similarity=0.240 Sum_probs=29.9
Q ss_pred chHHHHHHhCCCHHHHHHHHHhcCCeecCceeeccCCCCCCCCCCC-ChHHHHHHhhHHH
Q psy9207 63 PNTSLSEFLGVTEQEAAAIAQAEGWTVDKVYTQPVKKPEEYATPNI-TDDQLYILTQYVS 121 (125)
Q Consensus 63 ~~~~~a~~Lgl~~~e~~~~~~~~GW~~d~~~~~p~~~~~~~~~~~~-~~~ql~~Lt~~v~ 121 (125)
++.++|.++|++..-+.-+..+.| ...| ..+ ..-.. +.+++..|-.+..
T Consensus 2 ~i~evA~~~gvs~~tlR~~~~~g~------l~~~---~~~-~g~R~y~~~~l~~l~~i~~ 51 (67)
T cd04764 2 TIKEVSEIIGVKPHTLRYYEKEFN------LYIP---RTE-NGRRYYTDEDIELLKKIKT 51 (67)
T ss_pred CHHHHHHHHCcCHHHHHHHHHhcC------CCCC---CCC-CCceeeCHHHHHHHHHHHH
Confidence 678999999999998887755433 1112 110 11222 7777777665443
No 109
>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=49.71 E-value=34 Score=19.90 Aligned_cols=23 Identities=22% Similarity=0.290 Sum_probs=18.1
Q ss_pred CCcchHHHHHHhCCCHHHHHHHH
Q psy9207 60 SSIPNTSLSEFLGVTEQEAAAIA 82 (125)
Q Consensus 60 ~sI~~~~~a~~Lgl~~~e~~~~~ 82 (125)
..++++++|.-||++..-+....
T Consensus 22 R~~tl~elA~~lgis~st~~~~L 44 (53)
T PF04967_consen 22 RRITLEELAEELGISKSTVSEHL 44 (53)
T ss_pred CcCCHHHHHHHhCCCHHHHHHHH
Confidence 36889999999999986665543
No 110
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=49.04 E-value=44 Score=27.96 Aligned_cols=46 Identities=11% Similarity=0.176 Sum_probs=37.2
Q ss_pred HHHHHHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHHHhcCCe
Q psy9207 43 LQDEVQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQAEGWT 88 (125)
Q Consensus 43 l~~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~~~GW~ 88 (125)
+..-=++.++..+.+.-.+|++++++...|+..++++...+..|=-
T Consensus 356 Y~~YW~~~i~~~L~~~~~~~si~~is~~T~i~~~Dii~tL~~l~~l 401 (450)
T PLN00104 356 YRGYWTRVLLEILKKHKGNISIKELSDMTAIKAEDIVSTLQSLNLI 401 (450)
T ss_pred HHHHHHHHHHHHHHhcCCCccHHHHHHHhCCCHHHHHHHHHHCCCE
Confidence 4455566666666666789999999999999999999999988743
No 111
>PF09494 Slx4: Slx4 endonuclease; InterPro: IPR018574 The Slx4 protein is a heteromeric structure-specific endonuclease found in fungi. Slx4 with Slx1 acts as a nuclease on branched DNA substrates, particularly simple-Y, 5'-flap, or replication fork structures by cleaving the strand bearing the 5' non-homologous arm at the branch junction and thus generating ligatable nicked products from 5'-flap or replication fork substrates [].
Probab=48.91 E-value=25 Score=20.99 Aligned_cols=31 Identities=19% Similarity=0.277 Sum_probs=25.0
Q ss_pred hcCCcchHHHHHHhCC---------CHHHHHHHHHhcCCe
Q psy9207 58 AYSSIPNTSLSEFLGV---------TEQEAAAIAQAEGWT 88 (125)
Q Consensus 58 AY~sI~~~~~a~~Lgl---------~~~e~~~~~~~~GW~ 88 (125)
.|.-|.++++.++|.. +...+.+|+.++|=+
T Consensus 21 ~YePI~L~el~~~L~~~g~~~~~~~~~~~l~~~lD~~gIt 60 (64)
T PF09494_consen 21 MYEPINLEELHAWLKASGIGFDRKVDPSKLKEWLDSQGIT 60 (64)
T ss_pred cCCCccHHHHHHHHHHcCCCccceeCHHHHHHHHHHCCce
Confidence 5899999999999873 357899999888743
No 112
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=47.54 E-value=20 Score=21.95 Aligned_cols=32 Identities=13% Similarity=0.218 Sum_probs=25.8
Q ss_pred hcCCcchHHHHHHhCCCHHHHHHHHHh-cCCee
Q psy9207 58 AYSSIPNTSLSEFLGVTEQEAAAIAQA-EGWTV 89 (125)
Q Consensus 58 AY~sI~~~~~a~~Lgl~~~e~~~~~~~-~GW~~ 89 (125)
--.-+++.++|..||.+..-+.+++.. +.|-.
T Consensus 10 Ls~~~s~~~Aa~~lG~~~~~v~~wv~~fR~wll 42 (65)
T PF05344_consen 10 LSQQISVAQAADRLGTDPGTVRRWVRMFRQWLL 42 (65)
T ss_pred hcccccHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 345689999999999999888888776 56654
No 113
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=47.07 E-value=47 Score=25.19 Aligned_cols=49 Identities=10% Similarity=0.085 Sum_probs=33.4
Q ss_pred HHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHH---HHhcCCeec--Cceeec
Q psy9207 47 VQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAI---AQAEGWTVD--KVYTQP 96 (125)
Q Consensus 47 vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~---~~~~GW~~d--~~~~~p 96 (125)
=|++|++++.+ +..++++++|+.||+|..-+..- ..++|--.- |+.+.+
T Consensus 6 R~~~Il~~L~~-~~~v~v~eLa~~l~VS~~TIRRDL~~Le~~g~l~r~~Gga~~~ 59 (256)
T PRK10434 6 RQAAILEYLQK-QGKTSVEELAQYFDTTGTTIRKDLVILEHAGTVIRTYGGVVLN 59 (256)
T ss_pred HHHHHHHHHHH-cCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEECCEEcC
Confidence 35566666655 88999999999999997444332 345676553 666544
No 114
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=46.79 E-value=57 Score=18.92 Aligned_cols=37 Identities=19% Similarity=0.203 Sum_probs=26.7
Q ss_pred HHHHHHHHhcCCcchHHHHHHhCC-CHHHHHHHHHh-cCCe
Q psy9207 50 RAISLISKAYSSIPNTSLSEFLGV-TEQEAAAIAQA-EGWT 88 (125)
Q Consensus 50 ~~~~li~~AY~sI~~~~~a~~Lgl-~~~e~~~~~~~-~GW~ 88 (125)
++...+... .++++++|..+|+ +...+....++ -|.+
T Consensus 41 ~a~~~l~~~--~~~~~~ia~~~g~~s~~~f~r~Fk~~~g~s 79 (84)
T smart00342 41 RARRLLRDT--DLSVTEIALRVGFSSQSYFSRAFKKLFGVT 79 (84)
T ss_pred HHHHHHHcC--CCCHHHHHHHhCCCChHHHHHHHHHHHCcC
Confidence 344555443 7999999999999 78888777654 3554
No 115
>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=46.52 E-value=30 Score=19.86 Aligned_cols=27 Identities=22% Similarity=0.372 Sum_probs=19.3
Q ss_pred HHHHhcCCcchHHHHHHhCCCHHHHHH
Q psy9207 54 LISKAYSSIPNTSLSEFLGVTEQEAAA 80 (125)
Q Consensus 54 li~~AY~sI~~~~~a~~Lgl~~~e~~~ 80 (125)
+-..-...||-.++|.++|+++.++.+
T Consensus 21 l~~~G~~~vSS~~La~~~gi~~~qVRK 47 (50)
T PF06971_consen 21 LKEEGVERVSSQELAEALGITPAQVRK 47 (50)
T ss_dssp HHHTT-SEE-HHHHHHHHTS-HHHHHH
T ss_pred HHHcCCeeECHHHHHHHHCCCHHHhcc
Confidence 344466799999999999999988764
No 116
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=46.23 E-value=1.3e+02 Score=22.78 Aligned_cols=51 Identities=16% Similarity=0.149 Sum_probs=37.7
Q ss_pred HHHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHH---HHHhcCCeec--Cceeecc
Q psy9207 46 EVQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAA---IAQAEGWTVD--KVYTQPV 97 (125)
Q Consensus 46 ~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~---~~~~~GW~~d--~~~~~p~ 97 (125)
.-|++|++++ +....+++.+++..||+|..-+.. ...++|--.- |+.+.|.
T Consensus 5 ~R~~~Il~~l-~~~~~~~~~ela~~l~vS~~TiRRdL~~Le~~g~l~r~~GGa~~~~ 60 (252)
T PRK10906 5 QRHDAIIELV-KQQGYVSTEELVEHFSVSPQTIRRDLNDLAEQNKILRHHGGAALPS 60 (252)
T ss_pred HHHHHHHHHH-HHcCCEeHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCEEecC
Confidence 4566777877 779999999999999999866544 4455787653 6665554
No 117
>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=46.22 E-value=64 Score=19.30 Aligned_cols=25 Identities=24% Similarity=0.377 Sum_probs=18.3
Q ss_pred CCcchHHHHHHhCCCHHHHHHHHHh
Q psy9207 60 SSIPNTSLSEFLGVTEQEAAAIAQA 84 (125)
Q Consensus 60 ~sI~~~~~a~~Lgl~~~e~~~~~~~ 84 (125)
+.-+...+|..||++.+++......
T Consensus 19 r~Pt~eEiA~~lgis~~~v~~~l~~ 43 (78)
T PF04539_consen 19 REPTDEEIAEELGISVEEVRELLQA 43 (78)
T ss_dssp S--BHHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCCHHHHHHHHcccHHHHHHHHHh
Confidence 6778889999999999888776543
No 118
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=45.96 E-value=74 Score=19.95 Aligned_cols=25 Identities=16% Similarity=0.129 Sum_probs=20.1
Q ss_pred cchHHHHHHhCCCHHHHHHHHHhcCC
Q psy9207 62 IPNTSLSEFLGVTEQEAAAIAQAEGW 87 (125)
Q Consensus 62 I~~~~~a~~Lgl~~~e~~~~~~~~GW 87 (125)
.++.++|..+|++..-+..|.. .|+
T Consensus 2 ~~i~e~A~~~gvs~~tLr~ye~-~Gl 26 (91)
T cd04766 2 YVISVAAELSGMHPQTLRLYER-LGL 26 (91)
T ss_pred cCHHHHHHHHCcCHHHHHHHHH-CCC
Confidence 4688999999999988888755 444
No 119
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=45.78 E-value=95 Score=23.51 Aligned_cols=54 Identities=17% Similarity=0.283 Sum_probs=39.4
Q ss_pred HHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHH---HHHhcCCeec--CceeeccCCCC
Q psy9207 47 VQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAA---IAQAEGWTVD--KVYTQPVKKPE 101 (125)
Q Consensus 47 vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~---~~~~~GW~~d--~~~~~p~~~~~ 101 (125)
=|++|++++.+ -.++++++++..||+|+.-+.. ...++|=-.- |+.+.|.....
T Consensus 6 R~~~Il~~l~~-~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l~R~hGGa~~~~~~~~ 64 (253)
T COG1349 6 RHQKILELLKE-KGKVSVEELAELFGVSEMTIRRDLNELEEQGLLLRVHGGAVLPDSESE 64 (253)
T ss_pred HHHHHHHHHHH-cCcEEHHHHHHHhCCCHHHHHHhHHHHHHCCcEEEEeCCEecCCCccc
Confidence 45677777776 8999999999999999855433 3445666553 77777766655
No 120
>PF07742 BTG: BTG family; InterPro: IPR002087 Anti-proliferative proteins have been shown to include mammalian and avian protein BTG1 (which appears to be involved in negative regulation of cell proliferation) and rat/mouse NGF-inducible protein PC3/TIS21 (BTG2) [, , ]. These proteins have from 158 to 363 amino acid residues, that are highly similar and include 3 conserved cysteine residues. BTG2 seems to have a signal sequence; while the other proteins may lack such a domain. The sequence of the N-terminal half of these proteins is well conserved.; PDB: 3DJU_B 3E9V_A 2Z15_D 2D5R_B 3DJN_B.
Probab=45.77 E-value=51 Score=22.34 Aligned_cols=63 Identities=13% Similarity=0.138 Sum_probs=40.7
Q ss_pred CcHHHHHHHHHHHHHHHHHHHH-------HHHHhcCCcchH----------HHHHHhCCCHHHHHHHHHhcCCee--c-C
Q psy9207 32 WSDDIAHIMKALQDEVQKRAIS-------LISKAYSSIPNT----------SLSEFLGVTEQEAAAIAQAEGWTV--D-K 91 (125)
Q Consensus 32 ~s~~~~~~i~~l~~~vR~~~~~-------li~~AY~sI~~~----------~~a~~Lgl~~~e~~~~~~~~GW~~--d-~ 91 (125)
+.+.+..|...|.+.+.++-.. +=++||+.|.++ ++|.--|++.+++.+.. -..|++ | +
T Consensus 23 ~~~~~~~F~~~L~~~L~~ry~~HW~P~~P~kGsayRcIrin~~~~~Dp~l~~Aa~~sgl~~~~l~~~L-P~eltlWvDPg 101 (118)
T PF07742_consen 23 PRRQVDRFAEELENLLCERYKGHWYPENPSKGSAYRCIRINPGHKMDPVLEQAAKESGLSYEDLRSLL-PRELTLWVDPG 101 (118)
T ss_dssp -HHHHHHHHHHHHHHHHHHHTTS--TTSTTTTHHHH-EEES--SSB-HHHHHHHHHTT--HHHHHHHS--TTEEEEEETT
T ss_pred CHHHHHHHHHHHHHHHHHHHhCCCCCCCCCCCCceEEEEEcCCCCCCHHHHHHHHHhCCCHHHHHHhc-chhcEEEECCC
Confidence 3366666777777776666544 557788888877 68888999988888764 457876 6 5
Q ss_pred ceee
Q psy9207 92 VYTQ 95 (125)
Q Consensus 92 ~~~~ 95 (125)
.+.+
T Consensus 102 eVs~ 105 (118)
T PF07742_consen 102 EVSY 105 (118)
T ss_dssp EEEE
T ss_pred EEEE
Confidence 5443
No 121
>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=45.73 E-value=28 Score=25.67 Aligned_cols=54 Identities=13% Similarity=0.239 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHHHh---cCCe---ec--CceeeccCCCC
Q psy9207 39 IMKALQDEVQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQA---EGWT---VD--KVYTQPVKKPE 101 (125)
Q Consensus 39 ~i~~l~~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~~---~GW~---~d--~~~~~p~~~~~ 101 (125)
++..|.+.|..+ .-+.++++|.-+||+.++++.-+.+ .|-- +| |.+++-.+..-
T Consensus 100 lL~~Fi~yIK~~---------Kvv~ledla~~f~l~t~~~i~ri~~L~~~g~ltGv~DdrGkfIyIs~eE~ 161 (188)
T PF09756_consen 100 LLQEFINYIKEH---------KVVNLEDLAAEFGLRTQDVINRIQELEAEGRLTGVIDDRGKFIYISEEEM 161 (188)
T ss_dssp HHHHHHHHHHH----------SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE------
T ss_pred HHHHHHHHHHHc---------ceeeHHHHHHHcCCCHHHHHHHHHHHHHCCCceeeEcCCCCeEEecHHHH
Confidence 556666665543 5678999999999999999888776 3554 34 77777655443
No 122
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=45.67 E-value=23 Score=26.74 Aligned_cols=47 Identities=17% Similarity=0.174 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHHhcCCcchHHHHHHhCCCHH----HHHHHHHhcCCeecCce
Q psy9207 45 DEVQKRAISLISKAYSSIPNTSLSEFLGVTEQ----EAAAIAQAEGWTVDKVY 93 (125)
Q Consensus 45 ~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~----e~~~~~~~~GW~~d~~~ 93 (125)
+.=|++|++.+.+ +..+++.+++.+||+|++ ++... ++.|....|.+
T Consensus 6 ~eR~~~I~~~l~~-~~~v~v~eLa~~~~VS~~TIRRDL~~L-e~~~~~~gGa~ 56 (252)
T PRK10681 6 DERIGQLLQALKR-SDKLHLKDAAALLGVSEMTIRRDLNAH-SAPVVLLGGYI 56 (252)
T ss_pred HHHHHHHHHHHHH-cCCCcHHHHHHHhCCCHHHHHHHHHHh-hcCeEEECCEE
Confidence 3445566666655 999999999999999963 33332 24564443444
No 123
>PRK13500 transcriptional activator RhaR; Provisional
Probab=45.46 E-value=69 Score=24.72 Aligned_cols=42 Identities=10% Similarity=0.161 Sum_probs=33.7
Q ss_pred HHHHHHHHHHhcC-CcchHHHHHHhCCCHHHHHHHHHhc-CCee
Q psy9207 48 QKRAISLISKAYS-SIPNTSLSEFLGVTEQEAAAIAQAE-GWTV 89 (125)
Q Consensus 48 R~~~~~li~~AY~-sI~~~~~a~~Lgl~~~e~~~~~~~~-GW~~ 89 (125)
-.++.+.|...|. .++++++|..+|+|+.-+...+++. |=+.
T Consensus 208 l~~i~~yI~~~~~e~isl~~lA~~~~iS~~~L~r~FK~~tG~T~ 251 (312)
T PRK13500 208 LDKLITRLAASLKSPFALDKFCDEASCSERVLRQQFRQQTGMTI 251 (312)
T ss_pred HHHHHHHHHHcccCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCH
Confidence 3567788888877 5999999999999998888777764 6554
No 124
>PF13518 HTH_28: Helix-turn-helix domain
Probab=45.37 E-value=51 Score=17.89 Aligned_cols=34 Identities=6% Similarity=0.114 Sum_probs=25.4
Q ss_pred HHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHHHh
Q psy9207 48 QKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQA 84 (125)
Q Consensus 48 R~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~~ 84 (125)
|.+++.++.. .-++.++|.-+|++...+..++..
T Consensus 2 r~~iv~~~~~---g~s~~~~a~~~gis~~tv~~w~~~ 35 (52)
T PF13518_consen 2 RLQIVELYLE---GESVREIAREFGISRSTVYRWIKR 35 (52)
T ss_pred HHHHHHHHHc---CCCHHHHHHHHCCCHhHHHHHHHH
Confidence 4556666654 349999999999998888777653
No 125
>PF11428 DUF3196: Protein of unknown function (DUF3196); InterPro: IPR024503 The entry comprises bacterial proteins of unknown function. One of the proteins in this entry, MPN330, is thought to involved in a cellular function that has yet to be characterised. The protein has 11 helices and a novel fold. No function is currently known for this protein.; PDB: 1TD6_A.
Probab=45.26 E-value=59 Score=25.60 Aligned_cols=58 Identities=16% Similarity=0.194 Sum_probs=37.1
Q ss_pred HHHHHHHHHcCCchHHHHHhccCCcHHHHH-----HHHHHHHHHHHHHHHHHHHhcCCcchHH
Q psy9207 9 VWEVGKHLWNGNYPSIYSTLKRTWSDDIAH-----IMKALQDEVQKRAISLISKAYSSIPNTS 66 (125)
Q Consensus 9 ~~~l~~~l~~~~y~~v~~~~~~~~s~~~~~-----~i~~l~~~vR~~~~~li~~AY~sI~~~~ 66 (125)
+=++.+.+-+++|..++..++.+.+.+|.| ....+...++..+..--.+.+.++....
T Consensus 47 l~~i~~ll~~~~y~~A~~lI~~EL~mPYIP~~~~~~fe~~l~~ik~~~~eq~~~~~~sLd~~~ 109 (286)
T PF11428_consen 47 LKKIKQLLDKKDYKEALELINEELSMPYIPLPLESKFESLLQEIKKDLYEQENKKYESLDKEK 109 (286)
T ss_dssp HHHHHHHHHTT-HHHHHHHHHHHTT-TTS-HHHHHHHHHHHHHHHHHHHHHH-GGGGG--HHH
T ss_pred HHHHHHHHHHhhHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHHhhHhccccHHH
Confidence 446788899999999999999877665544 4555666666666655555566665433
No 126
>PF05543 Peptidase_C47: Staphopain peptidase C47; InterPro: IPR008750 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to the peptidase family C47 (staphopain family, clan CA). The type example are the staphopains, which are one of four major families of proteinases secreted by the Gram-positive Staphylococcus aureus. These staphylococcal cysteine proteases are secreted as preproenzymes that are proteolytically cleaved to generate the mature enzyme [, , ].; GO: 0008234 cysteine-type peptidase activity, 0006508 proteolysis; PDB: 1X9Y_D 1Y4H_B 1PXV_B 1CV8_A.
Probab=44.35 E-value=29 Score=25.36 Aligned_cols=59 Identities=17% Similarity=0.284 Sum_probs=36.9
Q ss_pred CCcHHH--HHHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHHHhcCCeec
Q psy9207 31 TWSDDI--AHIMKALQDEVQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQAEGWTVD 90 (125)
Q Consensus 31 ~~s~~~--~~~i~~l~~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~~~GW~~d 90 (125)
+|-+.+ +.++.....+=+-..=+.+...|.+++.+++... |+++.|++++++++|=..+
T Consensus 23 pWCa~Ya~aailN~~~~~~~~~A~~iMr~~yPn~s~~~l~~~-~~~~~~~i~y~ks~g~~~~ 83 (175)
T PF05543_consen 23 PWCAGYAMAAILNATTNTKIYNAKDIMRYLYPNVSEEQLKFT-SLTPNQMIKYAKSQGRNPQ 83 (175)
T ss_dssp S-HHHHHHHHHHHHHCT-S---HHHHHHHHSTTS-CCCHHH---B-HHHHHHHHHHTTEEEE
T ss_pred cHHHHHHHHHHHHhhhCcCcCCHHHHHHHHCCCCCHHHHhhc-CCCHHHHHHHHHHcCcchh
Confidence 454433 2344444444344556789999999999999666 8999999999999987764
No 127
>cd04235 AAK_CK AAK_CK: Carbamate kinase (CK) catalyzes both the ATP-phosphorylation of carbamate and carbamoyl phosphate (CP) utilization with the production of ATP from ADP and CP. Both CK (this CD) and nonhomologous CP synthetase synthesize carbamoyl phosphate, an essential precursor of arginine and pyrimidine bases, in the presence of ATP, bicarbonate, and ammonia. CK is a homodimer of 33 kDa subunits and is a member of the Amino Acid Kinase Superfamily (AAK).
Probab=43.87 E-value=57 Score=25.81 Aligned_cols=30 Identities=37% Similarity=0.591 Sum_probs=21.8
Q ss_pred CCCHHHHHHHHHhcCCee--cC----ceeeccCCCC
Q psy9207 72 GVTEQEAAAIAQAEGWTV--DK----VYTQPVKKPE 101 (125)
Q Consensus 72 gl~~~e~~~~~~~~GW~~--d~----~~~~p~~~~~ 101 (125)
.++++|+.+..++.||++ |+ +-+.|.|...
T Consensus 131 ~y~~~~a~~~~~~~g~~~~~d~~~g~rrvV~SP~P~ 166 (308)
T cd04235 131 FYSEEEAEELAAEKGWTFKEDAGRGYRRVVPSPKPK 166 (308)
T ss_pred CcCHHHHHHHHHHcCCEEEEeCCCCceeeeCCCCCc
Confidence 346799999999999998 43 3566665544
No 128
>PLN03239 histone acetyltransferase; Provisional
Probab=43.67 E-value=93 Score=25.24 Aligned_cols=48 Identities=6% Similarity=-0.018 Sum_probs=37.5
Q ss_pred HHHHHHHHHHHHHHHhc---CCcchHHHHHHhCCCHHHHHHHHHhcCCeec
Q psy9207 43 LQDEVQKRAISLISKAY---SSIPNTSLSEFLGVTEQEAAAIAQAEGWTVD 90 (125)
Q Consensus 43 l~~~vR~~~~~li~~AY---~sI~~~~~a~~Lgl~~~e~~~~~~~~GW~~d 90 (125)
+..-=++.++..+...- .+|++++++...|+..++++...+..|.-..
T Consensus 263 Y~~YW~~~il~~L~~~~~~~~~~si~dis~~Tgi~~~DIi~tL~~l~~l~~ 313 (351)
T PLN03239 263 YIPYWGSTIVDFLLNHSGNDSSLSIMDIAKKTSIMAEDIVFALNQLGILKF 313 (351)
T ss_pred HHHHHHHHHHHHHHhccCCCCCccHHHHHHHhCCCHHHHHHHHHHCCcEEE
Confidence 44555666666665443 4699999999999999999999999997663
No 129
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=43.54 E-value=1.2e+02 Score=22.05 Aligned_cols=39 Identities=15% Similarity=0.217 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHHHhcC----------CcchHHHHHHhCCCHHHHHHHHH
Q psy9207 45 DEVQKRAISLISKAYS----------SIPNTSLSEFLGVTEQEAAAIAQ 83 (125)
Q Consensus 45 ~~vR~~~~~li~~AY~----------sI~~~~~a~~Lgl~~~e~~~~~~ 83 (125)
...++|++..+-.-.. .++-.++|.+||++.+-+.....
T Consensus 147 ~~~~~Rla~~Ll~~~~~~~~~~~~~i~~t~~~iA~~lG~tretvsR~l~ 195 (236)
T PRK09392 147 RSSAERLANYLLKQSLRQGGADVVTLPYEKRVLASYLGMTPENLSRAFA 195 (236)
T ss_pred CCHHHHHHHHHHHhccccCCCcEEEeeCCHHHHHHHhCCChhHHHHHHH
Confidence 3566777775543221 23346799999999766555433
No 130
>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]
Probab=43.50 E-value=83 Score=19.83 Aligned_cols=37 Identities=16% Similarity=0.345 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHHhcCC-cchHHHHHHhCCCHHHHHHHHH
Q psy9207 46 EVQKRAISLISKAYSS-IPNTSLSEFLGVTEQEAAAIAQ 83 (125)
Q Consensus 46 ~vR~~~~~li~~AY~s-I~~~~~a~~Lgl~~~e~~~~~~ 83 (125)
.++ ++...|...|.. ++++++|..+|++...+.....
T Consensus 21 ~~~-~~~~~i~~~~~~~~~l~~la~~~g~S~~~l~r~f~ 58 (127)
T COG2207 21 RLA-RALDYIEENLAEPLTLEDLARRLGMSRRTLSRLFK 58 (127)
T ss_pred HHH-HHHHHHHHHhcCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 344 566666655554 8999999999999877766554
No 131
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=43.31 E-value=82 Score=19.73 Aligned_cols=50 Identities=12% Similarity=0.129 Sum_probs=30.1
Q ss_pred cchHHHHHHhCCCHHHHHHHHHhcCCeecCceeeccCCCCCCCCCCC-ChHHHHHHhhHH
Q psy9207 62 IPNTSLSEFLGVTEQEAAAIAQAEGWTVDKVYTQPVKKPEEYATPNI-TDDQLYILTQYV 120 (125)
Q Consensus 62 I~~~~~a~~Lgl~~~e~~~~~~~~GW~~d~~~~~p~~~~~~~~~~~~-~~~ql~~Lt~~v 120 (125)
.++.++|+++|++...+.-|.. .| .+.|.+... ..-.. +.+++..|..+.
T Consensus 2 ~ti~evA~~~gvs~~tLR~ye~-~G------ll~p~r~~~--~g~R~Ys~~dv~~l~~I~ 52 (88)
T cd01105 2 IGIGEVSKLTGVSPRQLRYWEE-KG------LIKSIRSDG--GGQRKYSLADVDRLLVIK 52 (88)
T ss_pred cCHHHHHHHHCcCHHHHHHHHH-CC------CCCCCccCC--CCceecCHHHHHHHHHHH
Confidence 3678999999999988877633 23 333422211 11122 777777766544
No 132
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=43.30 E-value=1.3e+02 Score=21.98 Aligned_cols=44 Identities=14% Similarity=0.286 Sum_probs=28.4
Q ss_pred HHHHHHHHHHHHhcC----------CcchHHHHHHhCCCHHHHHH---HHHhcCCee
Q psy9207 46 EVQKRAISLISKAYS----------SIPNTSLSEFLGVTEQEAAA---IAQAEGWTV 89 (125)
Q Consensus 46 ~vR~~~~~li~~AY~----------sI~~~~~a~~Lgl~~~e~~~---~~~~~GW~~ 89 (125)
.+++|++..+..-+. .++..++|.|||++.+-+-. -.++.|+--
T Consensus 154 ~~~~Rla~~Ll~l~~~~g~~~~i~i~lt~~~IA~~lGisretlsR~L~~L~~~GlI~ 210 (230)
T PRK09391 154 TAMERVAAFLLEMDERLGGAGMMALPMSRRDIADYLGLTIETVSRALSQLQDRGLIG 210 (230)
T ss_pred CHHHHHHHHHHHHHHHhCCCCEEEecCCHHHHHHHHCCCHHHHHHHHHHHHHCCcEE
Confidence 456666665544221 25568999999999766544 445578764
No 133
>TIGR02837 spore_II_R stage II sporulation protein R. A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, a member of this panel, is designated stage II sporulation protein R.
Probab=43.22 E-value=1.1e+02 Score=22.30 Aligned_cols=61 Identities=18% Similarity=0.133 Sum_probs=44.0
Q ss_pred HHHHHHHHHHHHHHHHHHhc-CCcchHHHHHHhCCCHHHH----HHHHHhcCCeec-----CceeeccCCC
Q psy9207 40 MKALQDEVQKRAISLISKAY-SSIPNTSLSEFLGVTEQEA----AAIAQAEGWTVD-----KVYTQPVKKP 100 (125)
Q Consensus 40 i~~l~~~vR~~~~~li~~AY-~sI~~~~~a~~Lgl~~~e~----~~~~~~~GW~~d-----~~~~~p~~~~ 100 (125)
=+.|+-.||++++.-+..-. .+-+++++..++.-+-+++ .+.+.+.|-.++ +.+.||.+..
T Consensus 53 DQ~lKl~VRD~Vl~~~~~~~~~~~s~~ea~~~i~~~l~~Ie~~a~~~l~~~G~~y~v~v~~~~~~FPtK~Y 123 (168)
T TIGR02837 53 DQALKLKVRDAVLKEIRPWLSGLKSLEEARRVIRENLPEIERIAESVIKAEGADYKVRVELGKYSFPTKLY 123 (168)
T ss_pred HHHHHHHHHHHHHHHHHHHhccCCCHHHHHHHHHHhhHHHHHHHHHHHHHhCCCCCeEEEEEEEeCCCccc
Confidence 36799999999999988776 5567777777776665554 444556777764 6778887654
No 134
>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=43.08 E-value=61 Score=18.17 Aligned_cols=38 Identities=16% Similarity=0.309 Sum_probs=26.4
Q ss_pred HHHHHHHhcCCcchHHHHHHhCCCHHHHH---HHHHhcCCee
Q psy9207 51 AISLISKAYSSIPNTSLSEFLGVTEQEAA---AIAQAEGWTV 89 (125)
Q Consensus 51 ~~~li~~AY~sI~~~~~a~~Lgl~~~e~~---~~~~~~GW~~ 89 (125)
++.++. .+..++..++|..+|++..-+. +-..++||-.
T Consensus 8 iL~~l~-~~~~~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~ 48 (59)
T PF01047_consen 8 ILRILY-ENGGITQSELAEKLGISRSTVTRIIKRLEKKGLIE 48 (59)
T ss_dssp HHHHHH-HHSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHH-HcCCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEE
Confidence 344443 4677999999999999975544 4455679976
No 135
>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA. This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (pfam02311) and the helix-turn-helix DNA-binding domain (pfam00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway.
Probab=42.63 E-value=78 Score=23.66 Aligned_cols=41 Identities=20% Similarity=0.302 Sum_probs=31.2
Q ss_pred HHHHHHHHHhc-CCcchHHHHHHhCCCHHHHHHHHHh-cCCee
Q psy9207 49 KRAISLISKAY-SSIPNTSLSEFLGVTEQEAAAIAQA-EGWTV 89 (125)
Q Consensus 49 ~~~~~li~~AY-~sI~~~~~a~~Lgl~~~e~~~~~~~-~GW~~ 89 (125)
.++.+.|..-| ..++++++|..+|+|..-+...+++ -|=+.
T Consensus 189 ~~~~~~I~~~~~~~~sl~~lA~~~~~S~~~l~r~Fk~~~G~t~ 231 (287)
T TIGR02297 189 NRFNFLIEENYKQHLRLPEYADRLGISESRLNDICRRFSALSP 231 (287)
T ss_pred HHHHHHHHHhhccCCCHHHHHHHHCCCHHHHHHHHHHHhCCCH
Confidence 45666776665 6799999999999999888777665 45443
No 136
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=42.54 E-value=1.2e+02 Score=21.24 Aligned_cols=66 Identities=14% Similarity=0.144 Sum_probs=38.4
Q ss_pred HHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHHHhcCCeecCceeeccCCCCCCCCCCCChHHHHHHhhH
Q psy9207 50 RAISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQAEGWTVDKVYTQPVKKPEEYATPNITDDQLYILTQY 119 (125)
Q Consensus 50 ~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~~~GW~~d~~~~~p~~~~~~~~~~~~~~~ql~~Lt~~ 119 (125)
|....+.--|.-+|..++|+++|++..-+..++.. |.=.|.. .|.++... .....+..|++.|-+.
T Consensus 10 R~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~r--~~e~G~~-l~~~~~~G-rP~kl~~~q~~~l~e~ 75 (138)
T COG3415 10 RERVVDAVVGEGLSCREAAKRFGVSISTVYRWVRR--YRETGLD-LPPKPRKG-RPRKLSEEQLEILLER 75 (138)
T ss_pred HHHHHHHHHHcCccHHHHHHHhCccHHHHHHHHHH--hcccccc-ccCccCCC-CCcccCHHHHHHHHHH
Confidence 33444455688999999999999998877777663 2222222 33332221 1112266776665443
No 137
>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=42.53 E-value=39 Score=19.82 Aligned_cols=25 Identities=24% Similarity=0.263 Sum_probs=19.6
Q ss_pred hHHHHHHhCCCHHHHHHHHHhcCCe
Q psy9207 64 NTSLSEFLGVTEQEAAAIAQAEGWT 88 (125)
Q Consensus 64 ~~~~a~~Lgl~~~e~~~~~~~~GW~ 88 (125)
+.-.+.-||++++++.+.+..-|=.
T Consensus 23 v~ywa~~~gvt~~~L~~AV~~vG~~ 47 (57)
T PF12244_consen 23 VRYWAKRFGVTEEQLREAVRAVGNS 47 (57)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHCcC
Confidence 3457888999999999988877633
No 138
>PF04801 Sin_N: Sin-like protein conserved region; InterPro: IPR006886 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. RNA polymerase III (Pol III) is a complex consisting of 17 subunits, which synthesizes small RNAs, such as 5S rRNA and tRNAs. Pol III is essential for efficient transcription from both the type 2 VAI and type 3 U6 RNA polymerase III promoters and plays a key role in sensing and limiting infection by intracellular bacteria and DNA viruses. Subunit c5 is a specific peripheric component of RNA polymerase III complex. ; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent, 0005634 nucleus
Probab=42.41 E-value=48 Score=27.02 Aligned_cols=48 Identities=15% Similarity=0.258 Sum_probs=39.4
Q ss_pred HHHHHHHHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHH----HH----hcCCee
Q psy9207 41 KALQDEVQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAI----AQ----AEGWTV 89 (125)
Q Consensus 41 ~~l~~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~----~~----~~GW~~ 89 (125)
+......|+-|+-++.+. ..|+..++....+++.+++.++ |. .+||++
T Consensus 332 ~e~~~~aRD~iL~~F~~~-~~v~r~~l~~~~~l~~~~~~eiL~~~a~~~~~~~~W~l 387 (421)
T PF04801_consen 332 AEQLCRARDYILLLFTKS-RYVKRKELMSATKLPPEDVKEILKEIAVLRPSNRGWKL 387 (421)
T ss_pred chhhhhhHHHHHHHhcCC-CceeHHHhhhhcCCCHHHHHHHHHHHhhccCCCCceEE
Confidence 346779999999999998 7799999999999998776554 22 369988
No 139
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=42.29 E-value=1.1e+02 Score=21.48 Aligned_cols=36 Identities=11% Similarity=0.165 Sum_probs=24.2
Q ss_pred CcchHHHHHHhCCCHHHHHHH---HHhcCCeec--Cceeec
Q psy9207 61 SIPNTSLSEFLGVTEQEAAAI---AQAEGWTVD--KVYTQP 96 (125)
Q Consensus 61 sI~~~~~a~~Lgl~~~e~~~~---~~~~GW~~d--~~~~~p 96 (125)
.++-.++|.|||++.+-+-.. .++.|+--- +.+.++
T Consensus 149 ~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~~~~~i~I~ 189 (202)
T PRK13918 149 YATHDELAAAVGSVRETVTKVIGELSREGYIRSGYGKIQLL 189 (202)
T ss_pred cCCHHHHHHHhCccHHHHHHHHHHHHHCCCEEcCCCEEEEE
Confidence 467889999999997665444 445688762 344444
No 140
>KOG1463|consensus
Probab=41.65 E-value=2e+02 Score=23.66 Aligned_cols=115 Identities=13% Similarity=0.177 Sum_probs=71.4
Q ss_pred CchHHHHHHHHHHHHHcCCchHHHHHhcc-C--C-cH-HHHHHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHhCCCHH
Q psy9207 2 SHPEIGQVWEVGKHLWNGNYPSIYSTLKR-T--W-SD-DIAHIMKALQDEVQKRAISLISKAYSSIPNTSLSEFLGVTEQ 76 (125)
Q Consensus 2 ~~~~l~~~~~l~~~l~~~~y~~v~~~~~~-~--~-s~-~~~~~i~~l~~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~ 76 (125)
..|-|.++-++.++.-+|+...|=.++.+ . . .+ .+..=...|-|+.-+.=+.-|=--|+.+.+.++|..+||+..
T Consensus 281 ~g~~i~AmkavAeA~~nRSLkdF~~AL~~yk~eL~~D~ivr~Hl~~Lyd~lLEknl~riIEPyS~Vei~hIA~~IGl~~~ 360 (411)
T KOG1463|consen 281 AGRDIDAMKAVAEAFGNRSLKDFEKALADYKKELAEDPIVRSHLQSLYDNLLEKNLCRIIEPYSRVEISHIAEVIGLDVP 360 (411)
T ss_pred cCcchHHHHHHHHHhcCCcHHHHHHHHHHhHHHHhcChHHHHHHHHHHHHHHHHhHHHHcCchhhhhHHHHHHHHCCCcH
Confidence 35778899999999999988887777764 2 1 12 222233556666666555555668999999999999999965
Q ss_pred HHH----HHHHhc--CCeec--Cc--eeeccCCCCCCCCCCCChHHHHHHhh
Q psy9207 77 EAA----AIAQAE--GWTVD--KV--YTQPVKKPEEYATPNITDDQLYILTQ 118 (125)
Q Consensus 77 e~~----~~~~~~--GW~~d--~~--~~~p~~~~~~~~~~~~~~~ql~~Lt~ 118 (125)
.+. +.+..+ -=++| ++ ++++.|+.. .+-....++++.|++
T Consensus 361 ~VEkKLsqMILDKkf~G~LDQg~g~Liv~~e~~~d--~~y~~aLetI~~m~k 410 (411)
T KOG1463|consen 361 QVEKKLSQMILDKKFYGTLDQGEGCLIVFEEPPAD--NTYDAALETIQNMGK 410 (411)
T ss_pred HHHHHHHHHHHHHHhhcccccCCCeEEEeCCCCcc--hHHHHHHHHHHhccC
Confidence 544 344433 22456 33 345544443 221225555555543
No 141
>PF07453 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases [].
Probab=41.57 E-value=29 Score=18.07 Aligned_cols=19 Identities=11% Similarity=0.261 Sum_probs=14.0
Q ss_pred cchHHHHHHhCCCHHHHHH
Q psy9207 62 IPNTSLSEFLGVTEQEAAA 80 (125)
Q Consensus 62 I~~~~~a~~Lgl~~~e~~~ 80 (125)
-|+.+||.+||++..-+..
T Consensus 17 ~Si~eAa~~l~i~~~~I~~ 35 (37)
T PF07453_consen 17 DSIREAARYLGISHSTISK 35 (37)
T ss_pred cCHHHHHHHhCCCHHHHHH
Confidence 3678899999998655443
No 142
>COG2901 Fis Factor for inversion stimulation Fis, transcriptional activator [Transcription / DNA replication, recombination, and repair]
Probab=41.48 E-value=1e+02 Score=20.20 Aligned_cols=57 Identities=12% Similarity=0.214 Sum_probs=36.3
Q ss_pred HHHhcc-CCcHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHHHhcC
Q psy9207 25 YSTLKR-TWSDDIAHIMKALQDEVQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQAEG 86 (125)
Q Consensus 25 ~~~~~~-~~s~~~~~~i~~l~~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~~~G 86 (125)
|+-++. +..+.|.-....++.-.-+.+. -|.+=.-..||.|||++..-+.+-.++.|
T Consensus 39 ~~~L~G~~v~~lY~mVL~evE~PLL~~vM-----~~~~gNQtrAa~mLGinR~TLRKKLkqyg 96 (98)
T COG2901 39 FADLNGQDVNDLYEMVLAEVEQPLLDMVM-----QYTRGNQTRAALMLGINRGTLRKKLKKYG 96 (98)
T ss_pred HHHcCCCChhhHHHHHHHHHHhHHHHHHH-----HHhcccHHHHHHHHcccHHHHHHHHHHhC
Confidence 445555 5666665555555544444333 35666778899999999877776665544
No 143
>PHA02591 hypothetical protein; Provisional
Probab=41.35 E-value=41 Score=21.45 Aligned_cols=37 Identities=16% Similarity=0.288 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHHHh
Q psy9207 45 DEVQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQA 84 (125)
Q Consensus 45 ~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~~ 84 (125)
|..+.-+-.+.++- .+..+.|..||++.+.+.++..+
T Consensus 46 dd~~~vA~eL~eqG---lSqeqIA~~LGVsqetVrKYL~~ 82 (83)
T PHA02591 46 DDLISVTHELARKG---FTVEKIASLLGVSVRKVRRYLES 82 (83)
T ss_pred chHHHHHHHHHHcC---CCHHHHHHHhCCCHHHHHHHHhc
Confidence 44445455555554 46889999999999998888764
No 144
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=41.31 E-value=1e+02 Score=20.14 Aligned_cols=22 Identities=18% Similarity=0.262 Sum_probs=18.0
Q ss_pred cchHHHHHHhCCCHHHHHHHHH
Q psy9207 62 IPNTSLSEFLGVTEQEAAAIAQ 83 (125)
Q Consensus 62 I~~~~~a~~Lgl~~~e~~~~~~ 83 (125)
.++.++|+++|+|..-+.-|..
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~ 22 (108)
T cd04773 1 MTIGELAHLLGVPPSTLRHWEK 22 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 3688999999999888877644
No 145
>PF10116 Host_attach: Protein required for attachment to host cells; InterPro: IPR019291 Members of this family of bacterial proteins are required for the attachment of the bacterium to host cells [, ].
Probab=41.10 E-value=33 Score=23.31 Aligned_cols=39 Identities=21% Similarity=0.379 Sum_probs=32.5
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHh
Q psy9207 33 SDDIAHIMKALQDEVQKRAISLISKAYSSIPNTSLSEFL 71 (125)
Q Consensus 33 s~~~~~~i~~l~~~vR~~~~~li~~AY~sI~~~~~a~~L 71 (125)
+.-+-.+-..|...++..+..-|.|-++.++..++.+.|
T Consensus 100 p~~LG~LR~~L~~~~~~~V~~ei~kDlt~~~~~ei~~~l 138 (138)
T PF10116_consen 100 PRFLGLLREHLSKAVRKRVVGEIDKDLTKLPADEIEKHL 138 (138)
T ss_pred HHHHHHHHHHhCHHHHHHHHHHHhhhhhcCCHHHHHhhC
Confidence 345566778899999999999999999999999887654
No 146
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=41.03 E-value=71 Score=19.12 Aligned_cols=42 Identities=14% Similarity=0.272 Sum_probs=30.9
Q ss_pred HHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHHH---hcCCee
Q psy9207 48 QKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQ---AEGWTV 89 (125)
Q Consensus 48 R~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~---~~GW~~ 89 (125)
.++|+.-|.....-++..++|.-+|++.-.+..+.. +.|...
T Consensus 2 ke~Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~ 46 (62)
T PF04703_consen 2 KEKILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLEKEGKVE 46 (62)
T ss_dssp HHCHHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEE
T ss_pred cHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence 356778888889999999999999999888777644 346543
No 147
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=40.98 E-value=90 Score=21.05 Aligned_cols=39 Identities=21% Similarity=0.411 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHHHh
Q psy9207 45 DEVQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQA 84 (125)
Q Consensus 45 ~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~~ 84 (125)
|.+-.+|+..+.+--. +|..++|..+|+|...+..-+.+
T Consensus 7 D~~D~~IL~~L~~d~r-~~~~eia~~lglS~~~v~~Ri~~ 45 (154)
T COG1522 7 DDIDRRILRLLQEDAR-ISNAELAERVGLSPSTVLRRIKR 45 (154)
T ss_pred cHHHHHHHHHHHHhCC-CCHHHHHHHHCCCHHHHHHHHHH
Confidence 4455667777766666 99999999999998777665543
No 148
>PF03793 PASTA: PASTA domain; InterPro: IPR005543 The PASTA domain is found at the C-termini of several Penicillin-binding proteins (PBP) and bacterial serine/threonine kinases. It binds the beta-lactam stem, which implicates it in sensing D-alanyl-D-alanine - the PBP transpeptidase substrate. In PknB of Mycobacterium tuberculosis (P71584 from SWISSPROT), all of the extracellular portion is predicted to be made up of four PASTA domains, which strongly suggests that it is a signal-binding sensor domain. The domain has also been found in proteins involved in cell wall biosynthesis, where it is implicated in localizing the biosynthesis complex to unlinked peptidoglycan. PASTA is a small globular fold consisting of 3 beta-sheets and an alpha-helix, with a loop region of variable length between the first and second beta-strands. The name PASTA is derived from PBP and Serine/Threonine kinase Associated domain [].; GO: 0008658 penicillin binding; PDB: 2ZC3_C 1QME_A 1RP5_B 2Z2M_C 2Z2L_F 2ZC4_C 1QMF_A 3M9G_A 3PY9_A 1K25_B ....
Probab=40.86 E-value=28 Score=20.03 Aligned_cols=22 Identities=41% Similarity=0.652 Sum_probs=17.9
Q ss_pred HHhCCCHHHHHHHHHhcCCeec
Q psy9207 69 EFLGVTEQEAAAIAQAEGWTVD 90 (125)
Q Consensus 69 ~~Lgl~~~e~~~~~~~~GW~~d 90 (125)
.+.|++.+++.+...+.||.+.
T Consensus 5 d~~g~~~~~a~~~l~~~g~~~~ 26 (63)
T PF03793_consen 5 DLVGMTYDEAKSILEAAGLTVN 26 (63)
T ss_dssp TTTTSBHHHHHHHHHHTT-EEE
T ss_pred CcCCCcHHHHHHHHHHCCCEEE
Confidence 3678999999999999999653
No 149
>PF07964 Red1: Rec10 / Red1; InterPro: IPR012491 Rec10 / Red1 is involved in meiotic recombination and chromosome segregation during homologous chromosome formation. This protein localises to the synaptonemal complex in Saccharomyces cerevisiae and the analogous structures (linear elements) in Schizosaccharomyces pombe []. This family is currently only found in fungi. ; GO: 0007059 chromosome segregation, 0007131 reciprocal meiotic recombination
Probab=40.68 E-value=80 Score=28.01 Aligned_cols=48 Identities=17% Similarity=0.304 Sum_probs=33.9
Q ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHHHhc
Q psy9207 32 WSDDIAHIMKALQDEVQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQAE 85 (125)
Q Consensus 32 ~s~~~~~~i~~l~~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~~~ 85 (125)
.|+-|+.+...|...++..+=..+. -+.++..||.|+++|++..+..+
T Consensus 657 LSeKYQ~LF~eLQ~sFqnDteeM~~------FvgEiKdml~LPEdeLV~~IR~r 704 (706)
T PF07964_consen 657 LSEKYQRLFKELQKSFQNDTEEMLK------FVGEIKDMLNLPEDELVKVIRNR 704 (706)
T ss_pred HHHHHHHHHHHHHHHHhhhHHHHHH------HHHHHHHHhcCCHHHHHHHHHhc
Confidence 4566666666666666654443333 35678999999999999999876
No 150
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=40.50 E-value=70 Score=24.10 Aligned_cols=40 Identities=20% Similarity=0.261 Sum_probs=30.3
Q ss_pred HHHHHHHHhc-CCcchHHHHHHhCCCHHHHHHHHHhc-CCee
Q psy9207 50 RAISLISKAY-SSIPNTSLSEFLGVTEQEAAAIAQAE-GWTV 89 (125)
Q Consensus 50 ~~~~li~~AY-~sI~~~~~a~~Lgl~~~e~~~~~~~~-GW~~ 89 (125)
++.+.|...| ..|+++++|+.+|+|+.-+....++. |=+.
T Consensus 187 ~~~~~i~~~~~~~isl~~lA~~~~lS~~~l~r~Fk~~~G~tp 228 (290)
T PRK10572 187 EACQYISDHLASEFDIESVAQHVCLSPSRLAHLFRQQLGISV 228 (290)
T ss_pred HHHHHHHhcccCCCCHHHHHHHHCCCHHHHHHHHHHHHCcCH
Confidence 4667775555 79999999999999998877766653 5443
No 151
>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator. Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of 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=40.21 E-value=1e+02 Score=19.89 Aligned_cols=46 Identities=13% Similarity=0.112 Sum_probs=29.5
Q ss_pred cchHHHHHHhCCCHHHHHHHHHhcCCeecCceeeccCCCCCCCCCCC-ChHHHHHHh
Q psy9207 62 IPNTSLSEFLGVTEQEAAAIAQAEGWTVDKVYTQPVKKPEEYATPNI-TDDQLYILT 117 (125)
Q Consensus 62 I~~~~~a~~Lgl~~~e~~~~~~~~GW~~d~~~~~p~~~~~~~~~~~~-~~~ql~~Lt 117 (125)
.++.++|+.+|++..-+.-|.. -+.+.|.+..+ .-.. +++++..|-
T Consensus 2 ~~i~eva~~~gvs~~tlR~ye~-------~Gll~~~r~~~---g~R~Y~~~~l~~l~ 48 (102)
T cd04789 2 YTISELAEKAGISRSTLLYYEK-------LGLITGTRNAN---GYRLYPDSDLQRLL 48 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-------CCCCCCCcCCC---CCeeCCHHHHHHHH
Confidence 4789999999999888775544 34444422111 2222 888888776
No 152
>KOG2747|consensus
Probab=40.14 E-value=71 Score=26.33 Aligned_cols=47 Identities=13% Similarity=0.104 Sum_probs=36.7
Q ss_pred HHHHHHHHHHHHHHHhcCC-cchHHHHHHhCCCHHHHHHHHHhcCCee
Q psy9207 43 LQDEVQKRAISLISKAYSS-IPNTSLSEFLGVTEQEAAAIAQAEGWTV 89 (125)
Q Consensus 43 l~~~vR~~~~~li~~AY~s-I~~~~~a~~Lgl~~~e~~~~~~~~GW~~ 89 (125)
...-=+..++.++-+-=.+ |++++++...|+..+|++...+..||--
T Consensus 310 YrsYW~~~ll~~L~~~~~~~isI~~iS~~Tgi~~~DIisTL~~L~m~~ 357 (396)
T KOG2747|consen 310 YRSYWRCVLLELLRKHRGEHISIKEISKETGIRPDDIISTLQSLNMIK 357 (396)
T ss_pred HHHHHHHHHHHHHHhcCCCcccHHHHHHhhCCCHHHHHHHHHhhCCcc
Confidence 3445556666666664433 9999999999999999999999988876
No 153
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=39.99 E-value=1.1e+02 Score=23.18 Aligned_cols=42 Identities=14% Similarity=0.286 Sum_probs=34.1
Q ss_pred HHHHHHHHHHhcCC--cchHHHHHHhCCCHHHHHHHHHhcCCee
Q psy9207 48 QKRAISLISKAYSS--IPNTSLSEFLGVTEQEAAAIAQAEGWTV 89 (125)
Q Consensus 48 R~~~~~li~~AY~s--I~~~~~a~~Lgl~~~e~~~~~~~~GW~~ 89 (125)
..++.+.|..-|.. ++++++|..+|+|.--+....++.|=++
T Consensus 199 l~~~~~~I~~~l~~~~ls~~~lA~~~giS~r~L~r~Fk~~G~T~ 242 (302)
T PRK09685 199 FQKVVALIDQSIQEEILRPEWIAGELGISVRSLYRLFAEQGLVV 242 (302)
T ss_pred HHHHHHHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHHHcCCCH
Confidence 34788889999975 8999999999999988877776666543
No 154
>PRK13501 transcriptional activator RhaR; Provisional
Probab=39.90 E-value=88 Score=23.62 Aligned_cols=41 Identities=7% Similarity=0.162 Sum_probs=32.3
Q ss_pred HHHHHHHHHhcCC-cchHHHHHHhCCCHHHHHHHHHh-cCCee
Q psy9207 49 KRAISLISKAYSS-IPNTSLSEFLGVTEQEAAAIAQA-EGWTV 89 (125)
Q Consensus 49 ~~~~~li~~AY~s-I~~~~~a~~Lgl~~~e~~~~~~~-~GW~~ 89 (125)
+++.+.|.+-|.. |+++++|..+|+|+..+....++ -|-+.
T Consensus 179 ~~i~~~I~~~~~e~~sl~~lA~~~~lS~~~l~r~Fk~~~G~T~ 221 (290)
T PRK13501 179 DLIMSALQQSLGAYFDMADFCHKNQLVERSLKQLFRQQTGMSI 221 (290)
T ss_pred HHHHHHHHHhhccCCCHHHHHHHHCcCHHHHHHHHHHHHCcCH
Confidence 3467777777776 89999999999999888777665 37665
No 155
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=39.61 E-value=27 Score=17.98 Aligned_cols=19 Identities=26% Similarity=0.345 Sum_probs=16.5
Q ss_pred CCCHHHHHHHHHhcCCeec
Q psy9207 72 GVTEQEAAAIAQAEGWTVD 90 (125)
Q Consensus 72 gl~~~e~~~~~~~~GW~~d 90 (125)
|++.+++.......||.++
T Consensus 12 Gf~~~~a~~aL~~~~~d~~ 30 (37)
T smart00165 12 GFSREEALKALRAANGNVE 30 (37)
T ss_pred CCCHHHHHHHHHHhCCCHH
Confidence 9999999999888898765
No 156
>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=39.56 E-value=46 Score=17.75 Aligned_cols=21 Identities=14% Similarity=0.251 Sum_probs=15.5
Q ss_pred chHHHHHHhCCCHHHHHHHHH
Q psy9207 63 PNTSLSEFLGVTEQEAAAIAQ 83 (125)
Q Consensus 63 ~~~~~a~~Lgl~~~e~~~~~~ 83 (125)
++.++|+++|++..-+.-+-.
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 467899999999877766544
No 157
>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=39.34 E-value=97 Score=20.56 Aligned_cols=39 Identities=18% Similarity=0.156 Sum_probs=33.3
Q ss_pred HHHHHHhcCCcchHHHHHHhCCCHHHHHHHHHhcCCeec
Q psy9207 52 ISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQAEGWTVD 90 (125)
Q Consensus 52 ~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~~~GW~~d 90 (125)
+.-.-.++.-+.+.++|.-||++..-+..+....|++.-
T Consensus 62 L~~~v~~~pd~tl~Ela~~l~Vs~~ti~~~Lkrlg~t~K 100 (119)
T PF01710_consen 62 LKALVEENPDATLRELAERLGVSPSTIWRALKRLGITRK 100 (119)
T ss_pred HHHHHHHCCCcCHHHHHHHcCCCHHHHHHHHHHcCchhc
Confidence 333345599999999999999999999999999999995
No 158
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=38.92 E-value=33 Score=19.64 Aligned_cols=24 Identities=17% Similarity=0.303 Sum_probs=12.6
Q ss_pred CcchHHHHHHhCCCHHHHHHHHHh
Q psy9207 61 SIPNTSLSEFLGVTEQEAAAIAQA 84 (125)
Q Consensus 61 sI~~~~~a~~Lgl~~~e~~~~~~~ 84 (125)
.|+..++|...|++...+-.++..
T Consensus 10 ~it~~~La~~~gis~~tl~~~~~~ 33 (63)
T PF13443_consen 10 GITQKDLARKTGISRSTLSRILNG 33 (63)
T ss_dssp T--HHHHHHHHT--HHHHHHHHTT
T ss_pred CCCHHHHHHHHCcCHHHHHHHHhc
Confidence 456666667777766666666554
No 159
>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=38.83 E-value=1.3e+02 Score=20.78 Aligned_cols=36 Identities=14% Similarity=0.136 Sum_probs=25.1
Q ss_pred CcchHHHHHHhCCCHHHHHH---HHHhcCCee-c-Cceeec
Q psy9207 61 SIPNTSLSEFLGVTEQEAAA---IAQAEGWTV-D-KVYTQP 96 (125)
Q Consensus 61 sI~~~~~a~~Lgl~~~e~~~---~~~~~GW~~-d-~~~~~p 96 (125)
.++-.++|.|||++.+-+-. -.++.|+-- . +.+.++
T Consensus 143 ~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~~~~~i~I~ 183 (193)
T TIGR03697 143 RLSHQAIAEAIGSTRVTITRLLGDLRKKKLISIHKKKITVH 183 (193)
T ss_pred CCCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEecCCEEEEe
Confidence 46788999999999755444 455678854 4 555555
No 160
>PF13591 MerR_2: MerR HTH family regulatory protein
Probab=38.80 E-value=51 Score=20.64 Aligned_cols=27 Identities=19% Similarity=0.250 Sum_probs=21.4
Q ss_pred cchHHHHHHhCCCHHHHHHHHHhcCCee
Q psy9207 62 IPNTSLSEFLGVTEQEAAAIAQAEGWTV 89 (125)
Q Consensus 62 I~~~~~a~~Lgl~~~e~~~~~~~~GW~~ 89 (125)
|++++++...|++.+.+..++. .||--
T Consensus 1 is~~e~~~~~~i~~~~l~~lve-~Gli~ 27 (84)
T PF13591_consen 1 ISLEEFCEACGIEPEFLRELVE-EGLIE 27 (84)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCCee
Confidence 6889999999999877777655 67654
No 161
>PRK12686 carbamate kinase; Reviewed
Probab=38.66 E-value=67 Score=25.48 Aligned_cols=18 Identities=39% Similarity=0.266 Sum_probs=15.0
Q ss_pred CCCHHHHHHHHHhcCCee
Q psy9207 72 GVTEQEAAAIAQAEGWTV 89 (125)
Q Consensus 72 gl~~~e~~~~~~~~GW~~ 89 (125)
+++++|+...++++||++
T Consensus 133 ~~~~~~a~~~~~~~g~~~ 150 (312)
T PRK12686 133 FYTEEEAKQQAEQPGSTF 150 (312)
T ss_pred ccCHHHHHHHHHHcCCcc
Confidence 347799999999999977
No 162
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=38.34 E-value=93 Score=18.92 Aligned_cols=40 Identities=18% Similarity=0.276 Sum_probs=28.9
Q ss_pred HHHHHHHHhcCCcchHHHHHHhCCCHHHH---HHHHHhcCCee
Q psy9207 50 RAISLISKAYSSIPNTSLSEFLGVTEQEA---AAIAQAEGWTV 89 (125)
Q Consensus 50 ~~~~li~~AY~sI~~~~~a~~Lgl~~~e~---~~~~~~~GW~~ 89 (125)
.|+.++.+.=..+++.+++..+|++..-+ .....+.||-.
T Consensus 9 ~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~ 51 (91)
T smart00346 9 AVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQELGYVE 51 (91)
T ss_pred HHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCee
Confidence 45666665435799999999999997554 44455678886
No 163
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=38.14 E-value=51 Score=22.13 Aligned_cols=32 Identities=25% Similarity=0.429 Sum_probs=23.9
Q ss_pred hcCCcchHHHHHHhCCCHHHHHHH---HHhcCCee
Q psy9207 58 AYSSIPNTSLSEFLGVTEQEAAAI---AQAEGWTV 89 (125)
Q Consensus 58 AY~sI~~~~~a~~Lgl~~~e~~~~---~~~~GW~~ 89 (125)
.-.+++++++|..|.+|.--+... -.+.||--
T Consensus 16 ~~~~vtl~elA~~l~cS~Rn~r~lLkkm~~~gWi~ 50 (115)
T PF12793_consen 16 QPVEVTLDELAELLFCSRRNARTLLKKMQEEGWIT 50 (115)
T ss_pred CCcceeHHHHHHHhCCCHHHHHHHHHHHHHCCCee
Confidence 345789999999999997554444 45579975
No 164
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=37.90 E-value=1.1e+02 Score=19.46 Aligned_cols=40 Identities=15% Similarity=0.267 Sum_probs=29.6
Q ss_pred HHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHH---HhcCCee
Q psy9207 49 KRAISLISKAYSSIPNTSLSEFLGVTEQEAAAIA---QAEGWTV 89 (125)
Q Consensus 49 ~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~---~~~GW~~ 89 (125)
.+++.++..- ..++..++|..+|++...+.... .+.||-.
T Consensus 6 ~~il~~L~~~-~~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~ 48 (108)
T smart00344 6 RKILEELQKD-ARISLAELAKKVGLSPSTVHNRVKRLEEEGVIK 48 (108)
T ss_pred HHHHHHHHHh-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence 4666666653 67999999999999987765554 4468866
No 165
>cd08311 Death_p75NR Death domain of p75 Neurotophin Receptor. Death Domain (DD) found in p75 neurotrophin receptor (p75NTR, NGFR, TNFRSF16). p75NTR binds members of the neurotrophin (NT) family including nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), and NT3, among others. It contains an NT-binding extracellular region that bears four cysteine-rich repeats, a transmembrane domain, and an intracellular DD. p75NTR plays roles in the immune, vascular, and nervous systems, and has been shown to promote cell death or survival, and to induce neurite outgrowth or collapse depending on its ligands and co-receptors. In general, 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 with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptor
Probab=37.82 E-value=84 Score=19.56 Aligned_cols=36 Identities=17% Similarity=0.191 Sum_probs=23.1
Q ss_pred HHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHHH
Q psy9207 48 QKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQ 83 (125)
Q Consensus 48 R~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~ 83 (125)
|+++-+++..-----.-..+|.-|||+..++..+..
T Consensus 2 ~~~v~~ll~~~nlG~dW~~LA~~LG~~~~~I~~i~~ 37 (77)
T cd08311 2 QEEVEKLLESGRPGRDWRSLAGELGYEDEAIDTFGR 37 (77)
T ss_pred hHHHHHHHhCCCCccCHHHHHHHcCCCHHHHHHHHc
Confidence 455555554332222346799999999888877753
No 166
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=37.64 E-value=1.4e+02 Score=21.08 Aligned_cols=38 Identities=11% Similarity=0.238 Sum_probs=24.1
Q ss_pred CcchHHHHHHhCCCHHHHHHH---HHhcCC-eec-CceeeccC
Q psy9207 61 SIPNTSLSEFLGVTEQEAAAI---AQAEGW-TVD-KVYTQPVK 98 (125)
Q Consensus 61 sI~~~~~a~~Lgl~~~e~~~~---~~~~GW-~~d-~~~~~p~~ 98 (125)
.++..++|++||++.+-+-.. ..+.|= +++ +.+.+|.+
T Consensus 168 ~~t~~~lA~~lG~tr~tvsR~l~~l~~~gii~~~~~~i~i~~~ 210 (211)
T PRK11753 168 KITRQEIGRIVGCSREMVGRVLKMLEDQGLISAHGKTIVVYGT 210 (211)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEecCCEEEEecC
Confidence 577799999999997655443 344562 223 44666643
No 167
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=37.43 E-value=80 Score=24.13 Aligned_cols=33 Identities=15% Similarity=0.302 Sum_probs=23.6
Q ss_pred hcCCcchHHHHHHhCCCHHHH-----------HHHHHhcCCeec
Q psy9207 58 AYSSIPNTSLSEFLGVTEQEA-----------AAIAQAEGWTVD 90 (125)
Q Consensus 58 AY~sI~~~~~a~~Lgl~~~e~-----------~~~~~~~GW~~d 90 (125)
-|...+..++|..||+|..-+ .+...+.||.++
T Consensus 239 ~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l~~~~~~~~ 282 (285)
T TIGR02394 239 GYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRILERDGVDRE 282 (285)
T ss_pred CCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhhhhh
Confidence 368899999999999997433 333445677664
No 168
>PRK09978 DNA-binding transcriptional regulator GadX; Provisional
Probab=37.03 E-value=1.1e+02 Score=23.68 Aligned_cols=43 Identities=9% Similarity=0.074 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHHhcCC-cchHHHHHHhCCCHHHHHHHHHhcCCe
Q psy9207 46 EVQKRAISLISKAYSS-IPNTSLSEFLGVTEQEAAAIAQAEGWT 88 (125)
Q Consensus 46 ~vR~~~~~li~~AY~s-I~~~~~a~~Lgl~~~e~~~~~~~~GW~ 88 (125)
...+++.+.|..-|.. ++++++|..+|+|..-+....++.|=+
T Consensus 142 ~~~~~v~~yI~~~~~~~lsl~~lA~~~g~S~~~L~R~Fk~~G~S 185 (274)
T PRK09978 142 NMRTRVCTVINNNIAHEWTLARIASELLMSPSLLKKKLREEETS 185 (274)
T ss_pred HHHHHHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHhcCCC
Confidence 3455677777776654 899999999999998877776655533
No 169
>PF13551 HTH_29: Winged helix-turn helix
Probab=36.99 E-value=1.1e+02 Score=19.23 Aligned_cols=22 Identities=9% Similarity=0.175 Sum_probs=18.5
Q ss_pred chHHHHHHhCCCHHHHHHHHHh
Q psy9207 63 PNTSLSEFLGVTEQEAAAIAQA 84 (125)
Q Consensus 63 ~~~~~a~~Lgl~~~e~~~~~~~ 84 (125)
++.++|..||++..-+-.+...
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~ 35 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKR 35 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHH
Confidence 5999999999998877777663
No 170
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=36.94 E-value=74 Score=17.39 Aligned_cols=23 Identities=17% Similarity=0.416 Sum_probs=18.6
Q ss_pred cCCcchHHHHHHhCCCHHHHHHH
Q psy9207 59 YSSIPNTSLSEFLGVTEQEAAAI 81 (125)
Q Consensus 59 Y~sI~~~~~a~~Lgl~~~e~~~~ 81 (125)
|...+..++|..||+|.+.+...
T Consensus 18 ~~~~t~~eIa~~lg~s~~~V~~~ 40 (50)
T PF04545_consen 18 FEGLTLEEIAERLGISRSTVRRI 40 (50)
T ss_dssp TST-SHHHHHHHHTSCHHHHHHH
T ss_pred cCCCCHHHHHHHHCCcHHHHHHH
Confidence 78999999999999998666544
No 171
>COG5159 RPN6 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=36.94 E-value=2.3e+02 Score=22.98 Aligned_cols=120 Identities=14% Similarity=0.151 Sum_probs=71.9
Q ss_pred chHHHHHHHHHHHHHcCCchHHHHHhcc-CC---cHHH-HHHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHhCCCHHH
Q psy9207 3 HPEIGQVWEVGKHLWNGNYPSIYSTLKR-TW---SDDI-AHIMKALQDEVQKRAISLISKAYSSIPNTSLSEFLGVTEQE 77 (125)
Q Consensus 3 ~~~l~~~~~l~~~l~~~~y~~v~~~~~~-~~---s~~~-~~~i~~l~~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e 77 (125)
+.-|++..++.++.-+|+...|=.++.+ .. ++++ ..-...|-|..-+.-+--|---|+.+.+.++|..+||+..+
T Consensus 280 ~r~I~am~avaea~~NRsL~df~~aL~qY~~el~~D~~iRsHl~~LYD~LLe~Nl~kiiEPfs~VeishIa~viGldt~q 359 (421)
T COG5159 280 DRMIRAMLAVAEAFGNRSLKDFSDALAQYSDELHQDSFIRSHLQYLYDVLLEKNLVKIIEPFSVVEISHIADVIGLDTNQ 359 (421)
T ss_pred hhhHHHHHHHHHHhCCCcHhhHHHHHHHhhHHhccCHHHHHHHHHHHHHHHHhhhhhhcCcceeeehhHHHHHhcccHHH
Confidence 4457888999999999987777666664 32 2222 22335555665565555566689999999999999999755
Q ss_pred HH----HHHHhc--CCeec--CceeeccCCCCCCCCCCCChHHHHHHhhHHHh
Q psy9207 78 AA----AIAQAE--GWTVD--KVYTQPVKKPEEYATPNITDDQLYILTQYVSF 122 (125)
Q Consensus 78 ~~----~~~~~~--GW~~d--~~~~~p~~~~~~~~~~~~~~~ql~~Lt~~v~f 122 (125)
+. +.+..+ -=++| ++-++.-..++++.+-....+++..|..+|.-
T Consensus 360 vEgKLsqMILDKifyG~LDqg~gcLivy~ep~qd~tyd~ale~v~~l~~vVd~ 412 (421)
T COG5159 360 VEGKLSQMILDKIFYGTLDQGDGCLIVYGEPAQDNTYDEALEQVEALDCVVDS 412 (421)
T ss_pred HHHHHHHHHHHHHHHhhhccCCceEEEeCCccccchHHHHHHHHHHhhhHHHH
Confidence 43 333332 11334 23333322222112222266777777777743
No 172
>PF02682 AHS1: Allophanate hydrolase subunit 1; InterPro: IPR003833 Allophanate hydrolase catalyses the second reaction in an ATP-dependent, two-step degradation of urea to ammonia and C02. This follows the action of the biotin-containing urea carboxylase. Saccharomyces cerevisiae can use urea as a sole nitrogen source via this degradation pathway []. In yeast, the fusion of allophanate hydrolase to urea carboxylase is called urea amidolyase. In bacteria, the second step in the urea degradation pathway is also the ATP-dependent allophanate hydrolase. The gene encoding this enzyme is found adjacent to the urea carboxylase gene []. Allophanate hydrolase has strict substrate specificity, as analogues of allophanate are not hydrolysed by it []. This domain represents subunit 1 of allophanate hydrolase (AHS1), which is found in urea carboxylase.; PDB: 3VA7_A 3MML_H 3OEP_A 3OPF_C 3ORE_A 2ZP2_A 2KWA_A 2PHC_B.
Probab=36.88 E-value=38 Score=24.99 Aligned_cols=85 Identities=18% Similarity=0.199 Sum_probs=48.8
Q ss_pred HHHHHHHHHHHHcCCchHHHHHhcc--------CCcH-HHHHHHHHHHHHHHHHHHH--------HHHHhcC---CcchH
Q psy9207 6 IGQVWEVGKHLWNGNYPSIYSTLKR--------TWSD-DIAHIMKALQDEVQKRAIS--------LISKAYS---SIPNT 65 (125)
Q Consensus 6 l~~~~~l~~~l~~~~y~~v~~~~~~--------~~s~-~~~~~i~~l~~~vR~~~~~--------li~~AY~---sI~~~ 65 (125)
...++.+.++|.+...+.+....-+ ++.. ....+.+.|.+...+.... -|.-+|. --.++
T Consensus 24 ~~~v~al~~~l~~~~~~gi~e~vp~~~sllV~fdp~~~~~~~l~~~l~~~~~~~~~~~~~~~r~~~iPV~Y~~~~g~DL~ 103 (202)
T PF02682_consen 24 NARVLALARALRAAPLPGIVEVVPAYRSLLVHFDPLRIDRAALRAALEELLASPQPSEKPPSRLIEIPVCYDGEFGPDLE 103 (202)
T ss_dssp HHHHHHHHHHHHHHT-TTEEEEEEESSEEEEEESTTTSHHHHHHHHHHHHHCCCCSSCCCCEEEEEEEEEESTTTHTTHH
T ss_pred HHHHHHHHHHHhcCCCCCeEEeeccccEEEEEEcCCcCCHHHHHHHHHHhhhhccccccCCCceEEEEEEECCCCCCCHH
Confidence 4667888888888776665433221 1111 2333333333332220000 1112466 67889
Q ss_pred HHHHHhCCCHHHHHHHHHhcCCeec
Q psy9207 66 SLSEFLGVTEQEAAAIAQAEGWTVD 90 (125)
Q Consensus 66 ~~a~~Lgl~~~e~~~~~~~~GW~~d 90 (125)
.+|+..||+.+|+++.-.+.-|.+-
T Consensus 104 ~vA~~~gls~~evi~~H~~~~y~V~ 128 (202)
T PF02682_consen 104 EVAEHNGLSVEEVIRLHSSAEYRVY 128 (202)
T ss_dssp HHHHHHTS-HHHHHHHHHTS-EEEE
T ss_pred HHHHHhCcCHHHHHHHHHcCchHhh
Confidence 9999999999999999999999884
No 173
>PF12672 DUF3793: Protein of unknown function (DUF3793); InterPro: IPR024523 This family of bacterial proteins is functionally uncharacterised. The proteins in this family contain two conserved sequence motifs: PHE and LGYP.
Probab=36.88 E-value=53 Score=23.71 Aligned_cols=63 Identities=10% Similarity=0.119 Sum_probs=41.6
Q ss_pred HHHHHHHcCCchHHHHHhccCCcHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHHHhc
Q psy9207 11 EVGKHLWNGNYPSIYSTLKRTWSDDIAHIMKALQDEVQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQAE 85 (125)
Q Consensus 11 ~l~~~l~~~~y~~v~~~~~~~~s~~~~~~i~~l~~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~~~ 85 (125)
.|.+.|.+.+-..|.+.+.- ....+..++..|..+++ .. =-+..+.=+||.+-+|+.-|+...
T Consensus 65 ~L~~~L~~~~~~~fL~~~GY-~~~~~~~~L~~L~~R~~---------~~--~FPHEIGiFLGYPleDV~GFI~~~ 127 (176)
T PF12672_consen 65 LLERYLSDPEVRSFLKSYGY-PDSSLEDCLEHLKKRFE---------SG--EFPHEIGIFLGYPLEDVKGFIENK 127 (176)
T ss_pred HHHHHHCCHHHHHHHHHCCc-CCCCHHHHHHHHHHHhc---------CC--CCCchhHhccCCCHHHHHHHHhCC
Confidence 35566666666666666655 44555555555555541 11 178889999999999999998653
No 174
>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=36.78 E-value=69 Score=20.62 Aligned_cols=34 Identities=18% Similarity=0.328 Sum_probs=21.8
Q ss_pred HHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHHHh
Q psy9207 50 RAISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQA 84 (125)
Q Consensus 50 ~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~~ 84 (125)
+|++++.. ...++-+++|..+|++..++...+..
T Consensus 17 ~Il~~L~~-~~~l~de~la~~~~l~~~~vRkiL~~ 50 (105)
T PF02002_consen 17 RILDALLR-KGELTDEDLAKKLGLKPKEVRKILYK 50 (105)
T ss_dssp HHHHHHHH-H--B-HHHHHHTT-S-HHHHHHHHHH
T ss_pred HHHHHHHH-cCCcCHHHHHHHhCCCHHHHHHHHHH
Confidence 45555553 35688999999999999998887554
No 175
>PRK12454 carbamate kinase-like carbamoyl phosphate synthetase; Reviewed
Probab=36.59 E-value=75 Score=25.27 Aligned_cols=29 Identities=34% Similarity=0.581 Sum_probs=20.9
Q ss_pred CCHHHHHHHHHhcCCee--c-Cc---eeeccCCCC
Q psy9207 73 VTEQEAAAIAQAEGWTV--D-KV---YTQPVKKPE 101 (125)
Q Consensus 73 l~~~e~~~~~~~~GW~~--d-~~---~~~p~~~~~ 101 (125)
++.+|+.+..+++||++ | ++ .+.|.|...
T Consensus 136 y~~~~a~~~~~~~g~~~~~d~g~g~RrvV~SP~P~ 170 (313)
T PRK12454 136 YDEEEAKKLAKEKGWIVKEDAGRGWRRVVPSPDPL 170 (313)
T ss_pred cCHHHHHHHHHHcCCEEEEcCCCceEEEeCCCCCc
Confidence 46799999999999998 5 32 456655443
No 176
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of 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=36.00 E-value=1.2e+02 Score=19.69 Aligned_cols=49 Identities=16% Similarity=0.109 Sum_probs=30.0
Q ss_pred chHHHHHHhCCCHHHHHHHHHhcCCeecCceeeccCCCCCCCCCCC-ChHHHHHHhhHH
Q psy9207 63 PNTSLSEFLGVTEQEAAAIAQAEGWTVDKVYTQPVKKPEEYATPNI-TDDQLYILTQYV 120 (125)
Q Consensus 63 ~~~~~a~~Lgl~~~e~~~~~~~~GW~~d~~~~~p~~~~~~~~~~~~-~~~ql~~Lt~~v 120 (125)
++.++|+++|++..-+.-|.. -+. +|.++.++ ..-.. +.+++..|..+.
T Consensus 2 ~i~e~a~~~gvs~~tlr~ye~-------~gl-l~~~~r~~-~gyR~Y~~~~l~~l~~I~ 51 (113)
T cd01109 2 TIKEVAEKTGLSADTLRYYEK-------EGL-LPPVKRDE-NGIRDFTEEDLEWLEFIK 51 (113)
T ss_pred CHHHHHHHHCcCHHHHHHHHH-------CCC-CCCCCcCC-CCCccCCHHHHHHHHHHH
Confidence 678999999999988877654 233 33222221 12223 778888775443
No 177
>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=35.60 E-value=69 Score=17.87 Aligned_cols=12 Identities=17% Similarity=0.271 Sum_probs=7.5
Q ss_pred hHHHHHHhCCCH
Q psy9207 64 NTSLSEFLGVTE 75 (125)
Q Consensus 64 ~~~~a~~Lgl~~ 75 (125)
+.++|..+|+|.
T Consensus 2 i~dIA~~agvS~ 13 (46)
T PF00356_consen 2 IKDIAREAGVSK 13 (46)
T ss_dssp HHHHHHHHTSSH
T ss_pred HHHHHHHHCcCH
Confidence 456666666664
No 178
>smart00796 AHS1 Allophanate hydrolase subunit 1. This domain represents subunit 1 of allophanate hydrolase (AHS1).
Probab=34.92 E-value=49 Score=24.36 Aligned_cols=87 Identities=15% Similarity=0.113 Sum_probs=52.1
Q ss_pred hHHHHHHHHHHHHHcCCchHHHHHhcc--------CC-cHHHHHHHHHHHHHHHHH-HHH--------HHHHhcC---Cc
Q psy9207 4 PEIGQVWEVGKHLWNGNYPSIYSTLKR--------TW-SDDIAHIMKALQDEVQKR-AIS--------LISKAYS---SI 62 (125)
Q Consensus 4 ~~l~~~~~l~~~l~~~~y~~v~~~~~~--------~~-s~~~~~~i~~l~~~vR~~-~~~--------li~~AY~---sI 62 (125)
.-...++.+.++|-+...+.+....-+ ++ .-....+++.|+...... ... -|--.|. -.
T Consensus 22 ~~~~~v~~l~~~l~~~~~~gi~e~vp~~~sllv~fdp~~~~~~~l~~~l~~~~~~~~~~~~~~~~r~~~IPV~Y~~~~gp 101 (201)
T smart00796 22 ALNRRVLALARALRAAPLPGVVELVPGYRSLLVHFDPLVIDPAALLARLRALEALPLAEALEVPGRIIEIPVCYGGEFGP 101 (201)
T ss_pred HHHHHHHHHHHHHHhcCCCCeEEccccceEEEEEEcCCCCCHHHHHHHHHHHHhcccccccCCCCcEEEEeeEeCCCCCC
Confidence 345778999999988877765443321 11 112233333333322110 000 0222344 34
Q ss_pred chHHHHHHhCCCHHHHHHHHHhcCCeec
Q psy9207 63 PNTSLSEFLGVTEQEAAAIAQAEGWTVD 90 (125)
Q Consensus 63 ~~~~~a~~Lgl~~~e~~~~~~~~GW~~d 90 (125)
.++.+|+..||+.+|+++.-.+.-|.+.
T Consensus 102 DL~~vA~~~gLs~~evi~~Hs~~~y~V~ 129 (201)
T smart00796 102 DLEFVARHNGLSVDEVIRLHSAAEYRVY 129 (201)
T ss_pred CHHHHHHHhCcCHHHHHHHHhCCCeEEE
Confidence 7899999999999999999998888874
No 179
>COG1448 TyrB Aspartate/tyrosine/aromatic aminotransferase [Amino acid transport and metabolism]
Probab=34.44 E-value=1.7e+02 Score=24.16 Aligned_cols=18 Identities=11% Similarity=0.420 Sum_probs=14.3
Q ss_pred HHhCCCHHHHHHHHHhcC
Q psy9207 69 EFLGVTEQEAAAIAQAEG 86 (125)
Q Consensus 69 ~~Lgl~~~e~~~~~~~~G 86 (125)
+|.|||++++...-.+.|
T Consensus 349 sy~Gls~~QV~rLree~~ 366 (396)
T COG1448 349 SYTGLSPEQVDRLREEFG 366 (396)
T ss_pred ecCCCCHHHHHHHHHhcc
Confidence 577999999888777665
No 180
>PF06262 DUF1025: Possibl zinc metallo-peptidase; InterPro: IPR010428 This is a family of bacterial protein with undetermined function.; PDB: 3E11_A.
Probab=34.19 E-value=30 Score=22.69 Aligned_cols=17 Identities=12% Similarity=0.454 Sum_probs=11.4
Q ss_pred hHHHHHHhCCCHHHHHH
Q psy9207 64 NTSLSEFLGVTEQEAAA 80 (125)
Q Consensus 64 ~~~~a~~Lgl~~~e~~~ 80 (125)
+.++|.++|++++++..
T Consensus 78 vhEiah~fG~~~e~l~~ 94 (97)
T PF06262_consen 78 VHEIAHHFGISDEDLDA 94 (97)
T ss_dssp HHHHHHHTT--HHHHHC
T ss_pred HHHHHHHcCCCHHHhhh
Confidence 45678899999988754
No 181
>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=34.07 E-value=1.2e+02 Score=18.87 Aligned_cols=27 Identities=22% Similarity=0.238 Sum_probs=22.7
Q ss_pred HhcCCcchHHHHHHhCCCHHHHHHHHH
Q psy9207 57 KAYSSIPNTSLSEFLGVTEQEAAAIAQ 83 (125)
Q Consensus 57 ~AY~sI~~~~~a~~Lgl~~~e~~~~~~ 83 (125)
+-+.-.+..++|..||+|..-+.....
T Consensus 28 R~~eGlS~kEIAe~LGIS~~TVk~~l~ 54 (73)
T TIGR03879 28 REEAGKTASEIAEELGRTEQTVRNHLK 54 (73)
T ss_pred HHHcCCCHHHHHHHHCcCHHHHHHHHh
Confidence 666999999999999999877776654
No 182
>PRK15185 transcriptional regulator HilD; Provisional
Probab=33.83 E-value=1.2e+02 Score=24.08 Aligned_cols=44 Identities=14% Similarity=0.175 Sum_probs=34.0
Q ss_pred HHHHHHHHHHHHhc-CCcchHHHHHHhCCCHHHHHHHHHhcCCee
Q psy9207 46 EVQKRAISLISKAY-SSIPNTSLSEFLGVTEQEAAAIAQAEGWTV 89 (125)
Q Consensus 46 ~vR~~~~~li~~AY-~sI~~~~~a~~Lgl~~~e~~~~~~~~GW~~ 89 (125)
...+++...|...| ..++++++|+.+|+|+.-+....++.|-++
T Consensus 206 ~~~erV~~~I~~n~~~~~SledLA~~lgmS~~tL~R~FK~~G~S~ 250 (309)
T PRK15185 206 TLKERVYNIISSSPSRQWKLTDVADHIFMSTSTLKRKLAEEGTSF 250 (309)
T ss_pred HHHHHHHHHHHhCccCCCCHHHHHHHHCcCHHHHHHHHHHcCCCH
Confidence 34456666676676 679999999999999988877766667775
No 183
>cd04772 HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.
Probab=33.72 E-value=1.3e+02 Score=19.27 Aligned_cols=46 Identities=17% Similarity=0.252 Sum_probs=28.3
Q ss_pred chHHHHHHhCCCHHHHHHHHHhcCCeecCceeeccCCCCCCCCCCC-ChHHHHHHh
Q psy9207 63 PNTSLSEFLGVTEQEAAAIAQAEGWTVDKVYTQPVKKPEEYATPNI-TDDQLYILT 117 (125)
Q Consensus 63 ~~~~~a~~Lgl~~~e~~~~~~~~GW~~d~~~~~p~~~~~~~~~~~~-~~~ql~~Lt 117 (125)
++.++|.++|++..-+.-|.. .+.+.|..... ..-.. +++++..|.
T Consensus 2 ~i~e~A~~~gvs~~tlR~Ye~-------~Gll~~~~r~~--~g~R~Y~~~~v~~l~ 48 (99)
T cd04772 2 RTVDLARAIGLSPQTVRNYES-------LGLIPPAERTA--NGYRIYTDKHIAALR 48 (99)
T ss_pred CHHHHHHHHCcCHHHHHHHHH-------cCCCCCCCcCC--CCCeecCHHHHHHHH
Confidence 578999999999888876633 33333322211 12222 888887764
No 184
>PF12401 DUF3662: Protein of unknown function (DUF2662) ; InterPro: IPR022128 This domain family is found in bacteria, and is approximately 120 amino acids in length. The family is found in association with PF00498 from PFAM. ; PDB: 2LC0_A.
Probab=33.71 E-value=56 Score=21.91 Aligned_cols=38 Identities=13% Similarity=0.185 Sum_probs=22.3
Q ss_pred HHHhcC-CcchHHHHHHhCCCH-------HHHHHHHHhcCCeecCc
Q psy9207 55 ISKAYS-SIPNTSLSEFLGVTE-------QEAAAIAQAEGWTVDKV 92 (125)
Q Consensus 55 i~~AY~-sI~~~~~a~~Lgl~~-------~e~~~~~~~~GW~~d~~ 92 (125)
+...|. .++..|...+-...+ +.+.+++.++||++.|.
T Consensus 51 aPN~y~V~Ls~~D~~~l~~~~~~l~~el~~~l~~~a~~qgy~~~G~ 96 (116)
T PF12401_consen 51 APNVYTVELSPEDYERLSPWGDRLARELADYLAEHAREQGYTFVGP 96 (116)
T ss_dssp ---EEEEEEEHHHHHHH-S-SHHHHHHHHHHHHHHHHHHT-B-SS-
T ss_pred cCeeEEEEECHHHHHHHhhhHHHHHHHHHHHHHHHHHHCCCeecCC
Confidence 566665 688899988888753 44566788899999744
No 185
>PRK08558 adenine phosphoribosyltransferase; Provisional
Probab=33.49 E-value=1.2e+02 Score=22.93 Aligned_cols=31 Identities=23% Similarity=0.357 Sum_probs=23.6
Q ss_pred HHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHHH
Q psy9207 50 RAISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQ 83 (125)
Q Consensus 50 ~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~ 83 (125)
++++++.+-| +.+++++++|+++..+..|++
T Consensus 15 ~~lr~lk~~~---ty~el~~~~g~p~~~l~RYv~ 45 (238)
T PRK08558 15 RVLRSLKKTY---TYEELSSITGLPESVLNRYVN 45 (238)
T ss_pred HHHHHHhccc---CHHHHHHHHCCCHHHHHHHHc
Confidence 4555666655 899999999999877777755
No 186
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=32.91 E-value=1.3e+02 Score=19.15 Aligned_cols=49 Identities=10% Similarity=0.008 Sum_probs=30.1
Q ss_pred chHHHHHHhCCCHHHHHHHHHhcCCeecCceeeccCCCCCCCCCCC-ChHHHHHHhhHH
Q psy9207 63 PNTSLSEFLGVTEQEAAAIAQAEGWTVDKVYTQPVKKPEEYATPNI-TDDQLYILTQYV 120 (125)
Q Consensus 63 ~~~~~a~~Lgl~~~e~~~~~~~~GW~~d~~~~~p~~~~~~~~~~~~-~~~ql~~Lt~~v 120 (125)
++.++|+.+|++..-+.-|.. -+.+.|..... ..-.. +++++..|-.+.
T Consensus 2 ~I~eva~~~gvs~~tlR~Ye~-------~GLl~p~~r~~--~g~r~Y~~~dv~~l~~I~ 51 (95)
T cd04780 2 RMSELSKRSGVSVATIKYYLR-------EGLLPEGRRLA--PNQAEYSEAHVERLRLIR 51 (95)
T ss_pred CHHHHHHHHCcCHHHHHHHHH-------CCCCCCCcCCC--CCCeecCHHHHHHHHHHH
Confidence 578999999999887776655 33444432221 11122 777777765543
No 187
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=32.82 E-value=63 Score=17.78 Aligned_cols=24 Identities=21% Similarity=0.426 Sum_probs=17.4
Q ss_pred CcchHHHHHHhCCCHHHHHHHHHh
Q psy9207 61 SIPNTSLSEFLGVTEQEAAAIAQA 84 (125)
Q Consensus 61 sI~~~~~a~~Lgl~~~e~~~~~~~ 84 (125)
.++..++|..+|++..-+-.+...
T Consensus 9 gls~~~la~~~gis~~~i~~~~~g 32 (55)
T PF01381_consen 9 GLSQKELAEKLGISRSTISRIENG 32 (55)
T ss_dssp TS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred CCCHHHHHHHhCCCcchhHHHhcC
Confidence 567788999999988887777664
No 188
>PRK15482 transcriptional regulator MurR; Provisional
Probab=32.68 E-value=72 Score=24.23 Aligned_cols=26 Identities=19% Similarity=0.372 Sum_probs=15.8
Q ss_pred cchHHHHHHhCCCHHHHHHHHHhcCC
Q psy9207 62 IPNTSLSEFLGVTEQEAAAIAQAEGW 87 (125)
Q Consensus 62 I~~~~~a~~Lgl~~~e~~~~~~~~GW 87 (125)
.++.++|.-.|.|+.-+..||++.|-
T Consensus 35 ~si~elA~~~~vS~aTv~Rf~kkLGf 60 (285)
T PRK15482 35 VSSRKMAKQLGISQSSIVKFAQKLGA 60 (285)
T ss_pred cCHHHHHHHhCCCHHHHHHHHHHhCC
Confidence 45566666666666666666666543
No 189
>smart00513 SAP Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation.
Probab=32.65 E-value=56 Score=16.83 Aligned_cols=19 Identities=11% Similarity=0.113 Sum_probs=15.7
Q ss_pred CCCHHHHHHHHHhcCCeec
Q psy9207 72 GVTEQEAAAIAQAEGWTVD 90 (125)
Q Consensus 72 gl~~~e~~~~~~~~GW~~d 90 (125)
.++.+++.+.|.++|+...
T Consensus 3 ~l~~~~Lk~~l~~~gl~~~ 21 (35)
T smart00513 3 KLKVSELKDELKKRGLSTS 21 (35)
T ss_pred cCcHHHHHHHHHHcCCCCC
Confidence 4567889999999999875
No 190
>PF11360 DUF3110: Protein of unknown function (DUF3110); InterPro: IPR021503 This family of proteins has no known function.
Probab=32.58 E-value=63 Score=20.65 Aligned_cols=24 Identities=13% Similarity=0.217 Sum_probs=17.3
Q ss_pred CHHHHHHHHHhcCCee---c-C-ceeecc
Q psy9207 74 TEQEAAAIAQAEGWTV---D-K-VYTQPV 97 (125)
Q Consensus 74 ~~~e~~~~~~~~GW~~---d-~-~~~~p~ 97 (125)
+.+++..+|.+.|-.+ . | .+++|.
T Consensus 56 d~~~i~~fC~~~gy~~~iv~~g~~l~~PP 84 (86)
T PF11360_consen 56 DPEEIEEFCRSAGYEYEIVPPGRDLLIPP 84 (86)
T ss_pred CHHHHHHHHHHCCceEEEECCCCCeeCCC
Confidence 4589999999986555 2 5 566764
No 191
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=32.55 E-value=1.9e+02 Score=20.89 Aligned_cols=44 Identities=18% Similarity=0.280 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHHhcC----CcchHHHHHHhCCCHHHHHHH---HHhcCCee
Q psy9207 46 EVQKRAISLISKAYS----SIPNTSLSEFLGVTEQEAAAI---AQAEGWTV 89 (125)
Q Consensus 46 ~vR~~~~~li~~AY~----sI~~~~~a~~Lgl~~~e~~~~---~~~~GW~~ 89 (125)
.+++|++..+-.... .++..++|.+||++.+-+... ..+.|+--
T Consensus 150 ~~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvsR~L~~L~~~G~I~ 200 (226)
T PRK10402 150 PLENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLLYVLAQFIQDGYLK 200 (226)
T ss_pred hHHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHHHHHHHHHHCCCEE
Confidence 567888886654321 246789999999997665544 44468754
No 192
>PF10537 WAC_Acf1_DNA_bd: ATP-utilising chromatin assembly and remodelling N-terminal; InterPro: IPR013136 ACF (for ATP-utilising chromatin assembly and remodeling factor) is a chromatin-remodeling complex that catalyzes the ATP-dependent assembly of periodic nucleosome arrays. This reaction utilises the energy of ATP hydrolysis by ISWI, the smaller of the two subunits of ACF. Acf1, the large subunit of ACF, is essential for the full activity of the complex. The WAC (WSTF/Acf1/cbp146) domain is an ~110-residue module present at the N-termini of Acf1-related proteins in a variety of organisms. It is found in association with other domains such as the bromodomain, the PHD-type zinc finger, DDT or WAKS. The DNA-binding region of Acf1 includes the WAC domain, which is necessary for the efficient binding of ACF complex to DNA. It seems probable that the WAC domain will be involved in DNA binding in other related factors [, ]. Some proteins known to contain a WAC domain are the Drosophila melanogaster (Fruit fly) ATP-dependent chromatin assembly factor large subunit Acf1, human WSTF (Williams syndrome transcription factor), mouse cbp146, yeast imitation switch two complex protein 1 (ITC1 or YGL133w), and yeast protein YPL216w.
Probab=32.45 E-value=83 Score=20.76 Aligned_cols=61 Identities=10% Similarity=0.277 Sum_probs=37.2
Q ss_pred HHHHHHHHHHHHHcCCchH-----HHHHhccCCcHHHHHHHHHHHHHHHHHHHHHHHHhcCCcc-hHHHH
Q psy9207 5 EIGQVWEVGKHLWNGNYPS-----IYSTLKRTWSDDIAHIMKALQDEVQKRAISLISKAYSSIP-NTSLS 68 (125)
Q Consensus 5 ~l~~~~~l~~~l~~~~y~~-----v~~~~~~~~s~~~~~~i~~l~~~vR~~~~~li~~AY~sI~-~~~~a 68 (125)
+++.+--..+..|.|...+ ...|+.++- .....+-+.|-+.+|.-++..+. ++.++ ++++.
T Consensus 19 Y~~R~~~y~~~vwtC~~TGk~~LTy~eAl~SE~-~a~~~l~~~fP~~l~~piL~~v~--~s~~~rld~Lv 85 (102)
T PF10537_consen 19 YLKRMILYNQRVWTCEITGKSNLTYFEALESEK-EARKKLEERFPEELREPILRLVQ--FSTRSRLDDLV 85 (102)
T ss_pred HHHHHHHHhCCeeEEecCCCCCCCHHHHHHHHH-HHHHHHHHHCCHHHHHHHHHHHH--ccccccHHHHH
Confidence 4455555666677776655 455555431 12223334488888888888888 77776 77663
No 193
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=32.10 E-value=1.4e+02 Score=19.08 Aligned_cols=48 Identities=15% Similarity=0.260 Sum_probs=29.9
Q ss_pred chHHHHHHhCCCHHHHHHHHHhcCCeecCceeeccCCCCCCCCCCC-ChHHHHHHhhHH
Q psy9207 63 PNTSLSEFLGVTEQEAAAIAQAEGWTVDKVYTQPVKKPEEYATPNI-TDDQLYILTQYV 120 (125)
Q Consensus 63 ~~~~~a~~Lgl~~~e~~~~~~~~GW~~d~~~~~p~~~~~~~~~~~~-~~~ql~~Lt~~v 120 (125)
++.++|..+|++..-+.-|.. .|+ +.|.+..+ .-.. ++..+..|..+.
T Consensus 2 ~I~e~a~~~gvs~~tLR~ye~-~Gl------l~p~r~~~---g~R~Y~~~dv~~l~~I~ 50 (96)
T cd04774 2 KVDEVAKRLGLTKRTLKYYEE-IGL------VSPERSEG---RYRLYSEEDLKRLERIL 50 (96)
T ss_pred CHHHHHHHHCcCHHHHHHHHH-CCC------CCCCcCCC---CCEEECHHHHHHHHHHH
Confidence 578999999999988888754 243 33433221 1112 667777665544
No 194
>PF05930 Phage_AlpA: Prophage CP4-57 regulatory protein (AlpA); InterPro: IPR010260 This entry is represents phage P4, Orf88. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. In Escherichia coli phage P4 Orf 88 is similar to AlpA of the CP4-57 cryptic prophage []. AlpA acts as a positive transcriptional regulator of slpA, a gene linked to alpA and necessary for suppression of lon mutants [, ]. The sequence of slpA suggests that it encodes an integrase gene closely related to phage P4 int and that both alpA and slpA are part of a cryptic P4-like prophage. Increase in alpA expression increases SlpA synthesis. Increased SlpA leads, in turn, to the excision and loss of the cryptic prophage. ; PDB: 1Z4H_A.
Probab=32.04 E-value=70 Score=17.88 Aligned_cols=23 Identities=17% Similarity=0.316 Sum_probs=17.1
Q ss_pred CcchHHHHHHhCCCHHHHHHHHH
Q psy9207 61 SIPNTSLSEFLGVTEQEAAAIAQ 83 (125)
Q Consensus 61 sI~~~~~a~~Lgl~~~e~~~~~~ 83 (125)
-|++.+++.++|++..-+-..++
T Consensus 3 ll~~~ev~~~~g~s~~ti~~~~k 25 (51)
T PF05930_consen 3 LLRIKEVAELLGVSRSTIYRLIK 25 (51)
T ss_dssp EE-HHHHHHHHSS-HHHHHHHHH
T ss_pred cccHHHHHHHHCCCHHHHHHHHh
Confidence 37889999999999877776655
No 195
>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=31.88 E-value=1.9e+02 Score=20.61 Aligned_cols=49 Identities=20% Similarity=0.274 Sum_probs=38.6
Q ss_pred HHHHHHHHHHHHHHHHHhcCCcchHHHHHHhCCCH---HHHHHHHHhcCCee
Q psy9207 41 KALQDEVQKRAISLISKAYSSIPNTSLSEFLGVTE---QEAAAIAQAEGWTV 89 (125)
Q Consensus 41 ~~l~~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~---~e~~~~~~~~GW~~ 89 (125)
..+.+.+|++|...-=+.=..|+-.++|..||+|. -|+.......|+..
T Consensus 14 ~~v~~~l~~~I~~g~l~pG~~L~e~~La~~lgVSRtpVReAL~~L~~eGlv~ 65 (212)
T TIGR03338 14 TLVQDEIERAILSGELPPGAKLNESDIAARLGVSRGPVREAFRALEEAGLVR 65 (212)
T ss_pred HHHHHHHHHHHHcCCCCCCCEecHHHHHHHhCCChHHHHHHHHHHHHCCCEE
Confidence 45667888888887667777889999999999985 55666666789875
No 196
>PRK15186 AraC family transcriptional regulator; Provisional
Probab=31.77 E-value=1.3e+02 Score=23.43 Aligned_cols=42 Identities=12% Similarity=0.097 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHHHhcC-CcchHHHHHHhCCCHHHHHHHHHhcC
Q psy9207 45 DEVQKRAISLISKAYS-SIPNTSLSEFLGVTEQEAAAIAQAEG 86 (125)
Q Consensus 45 ~~vR~~~~~li~~AY~-sI~~~~~a~~Lgl~~~e~~~~~~~~G 86 (125)
+...+++.+.|...|. .++++++|..+|+|..-+....++.|
T Consensus 180 ~~~~~~i~~~I~~~~~~~~sl~~lA~~~gmS~stl~R~Fk~~g 222 (291)
T PRK15186 180 NTLAENIYNIIISDISRKWALKDISDSLYMSCSTLKRKLKQEN 222 (291)
T ss_pred chHHHHHHHHHHhCccCCCCHHHHHHHHCcCHHHHHHHHHHcC
Confidence 3344455566666665 79999999999999877766655544
No 197
>PF15436 PGBA_N: Plasminogen-binding protein pgbA N-terminal
Probab=31.63 E-value=96 Score=23.44 Aligned_cols=37 Identities=16% Similarity=0.305 Sum_probs=30.2
Q ss_pred HHHHHHHHHhcCC---cchHHHHHHh---CCC--HHHHHHHHHhc
Q psy9207 49 KRAISLISKAYSS---IPNTSLSEFL---GVT--EQEAAAIAQAE 85 (125)
Q Consensus 49 ~~~~~li~~AY~s---I~~~~~a~~L---gl~--~~e~~~~~~~~ 85 (125)
+++-.-|.++|.. |++|-++++| |.+ .+++.++|.+.
T Consensus 102 ~e~Y~~i~~~~~~i~fihpDl~aa~L~~~g~~P~~~dfrkfc~~~ 146 (218)
T PF15436_consen 102 QETYEKIKSSYPNINFIHPDLFAAFLSENGHDPTREDFRKFCNQY 146 (218)
T ss_pred HHHHHHHHHhCCCceEecHHHHHHHHHhcCCCCCHHHHHHHHHHh
Confidence 4566778888887 7899999999 765 49999999873
No 198
>PF13317 DUF4088: Protein of unknown function (DUF4088)
Probab=31.43 E-value=2e+02 Score=21.54 Aligned_cols=58 Identities=17% Similarity=0.319 Sum_probs=34.5
Q ss_pred HHHHHHHHHHcCCchHHHHHhccCCcHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHh
Q psy9207 8 QVWEVGKHLWNGNYPSIYSTLKRTWSDDIAHIMKALQDEVQKRAISLISKAYSSIPNTSLSEFL 71 (125)
Q Consensus 8 ~~~~l~~~l~~~~y~~v~~~~~~~~s~~~~~~i~~l~~~vR~~~~~li~~AY~sI~~~~~a~~L 71 (125)
..|.|...|.++-|...|..-..+=+..-..-+..| |.+--++.+|.||+...++..+
T Consensus 140 PAwrlAeslrQr~ye~~~a~et~~~~~a~R~klGel------R~lL~L~~~yGs~q~~eaq~vm 197 (229)
T PF13317_consen 140 PAWRLAESLRQRVYEAMYACETEVGSTAGREKLGEL------RGLLRLGLAYGSVQKQEAQRVM 197 (229)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhccchHhHHHHHHHH------HHHHHHHHHhCCcCHHHHHHHH
Confidence 358888888888777766553332111111222222 2334478899999999886654
No 199
>PRK06585 holA DNA polymerase III subunit delta; Reviewed
Probab=31.40 E-value=2.5e+02 Score=21.78 Aligned_cols=65 Identities=11% Similarity=0.041 Sum_probs=42.6
Q ss_pred HHHHHHHHHHHcCCchHHHHHhcc--CCcHHHHHHHHHHHHHHHHH--HHHHHHHhcCCcchHHHHHHhCCC
Q psy9207 7 GQVWEVGKHLWNGNYPSIYSTLKR--TWSDDIAHIMKALQDEVQKR--AISLISKAYSSIPNTSLSEFLGVT 74 (125)
Q Consensus 7 ~~~~~l~~~l~~~~y~~v~~~~~~--~~s~~~~~~i~~l~~~vR~~--~~~li~~AY~sI~~~~~a~~Lgl~ 74 (125)
..++.+..++..|+..+++..++. .-.++-..++..|...+|.- +..++. ...+.+++++-+|.+
T Consensus 213 ~~if~l~dai~~~~~~~a~~~l~~ll~~g~~p~~il~~L~~~~r~L~~~~~~~~---~g~~~~~~~~~~~~~ 281 (343)
T PRK06585 213 LSLDDAADAALAGDLAAFERALDRALAEGTAPVLILRAALRHFQRLHIVRLKVE---NGKSAEQAIASLRPP 281 (343)
T ss_pred ccHHHHHHHHHCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHh---cCCCHHHHHHhhCCC
Confidence 468999999999999998887765 33344456777777777762 222221 223556677777654
No 200
>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=31.19 E-value=1.1e+02 Score=17.77 Aligned_cols=32 Identities=13% Similarity=0.206 Sum_probs=25.8
Q ss_pred hcCCcchHHHHHHhCCCHHHHHHH---HHhcCCee
Q psy9207 58 AYSSIPNTSLSEFLGVTEQEAAAI---AQAEGWTV 89 (125)
Q Consensus 58 AY~sI~~~~~a~~Lgl~~~e~~~~---~~~~GW~~ 89 (125)
.....+..++|.-+|++...+-.. ..++||.-
T Consensus 19 ~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~ 53 (68)
T PF01978_consen 19 KNGPATAEEIAEELGISRSTVYRALKSLEEKGLVE 53 (68)
T ss_dssp HHCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE
T ss_pred HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 677889999999999997665555 45589987
No 201
>PF02269 TFIID-18kDa: Transcription initiation factor IID, 18kD subunit; InterPro: IPR003195 This family includes the Spt3 yeast transcription factors and the 18 kDa subunit from human transcription initiation factor IID (TFIID-18). Determination of the crystal structure reveals an atypical histone fold [].; GO: 0006366 transcription from RNA polymerase II promoter; PDB: 1BH9_A 1BH8_A.
Probab=31.17 E-value=78 Score=20.36 Aligned_cols=27 Identities=19% Similarity=0.319 Sum_probs=21.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcC
Q psy9207 34 DDIAHIMKALQDEVQKRAISLISKAYS 60 (125)
Q Consensus 34 ~~~~~~i~~l~~~vR~~~~~li~~AY~ 60 (125)
.+....+..+++.+++.+..++.+|..
T Consensus 19 ~P~~eTv~lvE~iv~~~i~~l~~~A~~ 45 (93)
T PF02269_consen 19 EPLPETVDLVEDIVREYIIELCQEAME 45 (93)
T ss_dssp S--HHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred CCcHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456677888899999999999998873
No 202
>PRK13502 transcriptional activator RhaR; Provisional
Probab=31.15 E-value=1.2e+02 Score=22.66 Aligned_cols=41 Identities=12% Similarity=0.189 Sum_probs=30.3
Q ss_pred HHHHHHHHHhcC-CcchHHHHHHhCCCHHHHHHHHHh-cCCee
Q psy9207 49 KRAISLISKAYS-SIPNTSLSEFLGVTEQEAAAIAQA-EGWTV 89 (125)
Q Consensus 49 ~~~~~li~~AY~-sI~~~~~a~~Lgl~~~e~~~~~~~-~GW~~ 89 (125)
.++.++|..-|. .++++++|..+|+|+.-+...+++ -|=+.
T Consensus 179 ~~~~~~I~~~~~~~~~~~~lA~~~~iS~~~L~r~fk~~~G~t~ 221 (282)
T PRK13502 179 DKLITALANSLECPFALDAFCQQEQCSERVLRQQFRAQTGMTI 221 (282)
T ss_pred HHHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCH
Confidence 455566666544 689999999999999888777765 46554
No 203
>PF09107 SelB-wing_3: Elongation factor SelB, winged helix ; InterPro: IPR015191 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []. Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 3". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0005525 GTP binding, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2PJP_A 2UWM_A 1WSU_B 1LVA_A 2PLY_A.
Probab=31.06 E-value=1.1e+02 Score=17.46 Aligned_cols=33 Identities=18% Similarity=0.249 Sum_probs=26.2
Q ss_pred hcCCcchHHHHHHhCCCH---HHHHHHHHhcCCeec
Q psy9207 58 AYSSIPNTSLSEFLGVTE---QEAAAIAQAEGWTVD 90 (125)
Q Consensus 58 AY~sI~~~~~a~~Lgl~~---~e~~~~~~~~GW~~d 90 (125)
....|++.++-..+|+|- -.+.++.-..||+.-
T Consensus 7 ~~~~itv~~~rd~lg~sRK~ai~lLE~lD~~g~T~R 42 (50)
T PF09107_consen 7 KNGEITVAEFRDLLGLSRKYAIPLLEYLDREGITRR 42 (50)
T ss_dssp TTSSBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred cCCcCcHHHHHHHHCccHHHHHHHHHHHhccCCEEE
Confidence 378999999999999996 445666777899983
No 204
>PF07304 SRA1: Steroid receptor RNA activator (SRA1); InterPro: IPR009917 This entry consists of several hypothetical mammalian steroid receptor RNA activator proteins. The SRA-RNAs encode stable proteins that are widely expressed and upregulated in breast cancer cell lines. SRA-RNA is a steroid receptor co-activator which acts as a functional RNA. This domain is also found at the C terminus of Sec31, a component of the coat protein complex II (COPII, which promotes the formation of transport vesicles from the endoplasmic reticulum (ER). COPII has two main functions, the physical deformation of the endoplasmic reticulum membrane into vesicles and the selection of cargo molecules. ; PDB: 2YRU_A.
Probab=30.80 E-value=85 Score=22.21 Aligned_cols=24 Identities=17% Similarity=0.358 Sum_probs=18.4
Q ss_pred CchHHHHHHHHHHHHHcCCchHHH
Q psy9207 2 SHPEIGQVWEVGKHLWNGNYPSIY 25 (125)
Q Consensus 2 ~~~~l~~~~~l~~~l~~~~y~~v~ 25 (125)
+.|.+..+..|.++|-.|||....
T Consensus 87 s~~v~~~L~~L~~aL~~~d~~~A~ 110 (157)
T PF07304_consen 87 SKPVVDKLHQLAQALQARDYDAAD 110 (157)
T ss_dssp -HHHHHHHHHHHHHHHHT-HHHHH
T ss_pred CHHHHHHHHHHHHHHHcCCHHHHH
Confidence 467788899999999999998843
No 205
>PF12643 MazG-like: MazG-like family
Probab=30.72 E-value=1.6e+02 Score=19.27 Aligned_cols=34 Identities=21% Similarity=0.369 Sum_probs=26.1
Q ss_pred HHHHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHHHh
Q psy9207 45 DEVQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQA 84 (125)
Q Consensus 45 ~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~~ 84 (125)
+.+.+.+++.+--+| -+|.-||++..++.+.+.+
T Consensus 35 e~i~deLAdvii~~y------lLa~rLGid~~~lD~~i~~ 68 (98)
T PF12643_consen 35 EAIKDELADVIIYCY------LLADRLGIDFRELDEIIKE 68 (98)
T ss_pred HHHHHHHHHHHHHHH------HHHHHhCCCHHHHHHHHHH
Confidence 677888888887777 5899999997666665554
No 206
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=30.52 E-value=2.1e+02 Score=20.64 Aligned_cols=39 Identities=15% Similarity=0.203 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHHHh
Q psy9207 45 DEVQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQA 84 (125)
Q Consensus 45 ~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~~ 84 (125)
+..+.+++.++-+ -..++-+++|..||++..++.+.+..
T Consensus 21 ~~~~~~Vl~~L~~-~g~~tdeeLA~~Lgi~~~~VRk~L~~ 59 (178)
T PRK06266 21 DEEGFEVLKALIK-KGEVTDEEIAEQTGIKLNTVRKILYK 59 (178)
T ss_pred CccHhHHHHHHHH-cCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 4445666665553 23699999999999999888877543
No 207
>COG3604 FhlA Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / Signal transduction mechanisms]
Probab=30.34 E-value=1.3e+02 Score=25.75 Aligned_cols=50 Identities=14% Similarity=0.147 Sum_probs=42.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHHHhcCCee
Q psy9207 38 HIMKALQDEVQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQAEGWTV 89 (125)
Q Consensus 38 ~~i~~l~~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~~~GW~~ 89 (125)
.+.....+.-|++|.++++++=-.+.- +|+.||++...+...++..|=++
T Consensus 498 ~l~~~~~~~eR~~I~~aL~~~~~~~a~--AAr~LGl~~~~L~~~~kRlGI~~ 547 (550)
T COG3604 498 TLREATEEFERQLIIAALEETNGNWAG--AARRLGLTRRTLLYRMKRLGIKV 547 (550)
T ss_pred cchhhhHHHHHHHHHHHHHHhCCcHHH--HHHHhCCCHHHHHHHHHHcCCCc
Confidence 456788899999999999998776655 99999999999988888777544
No 208
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=30.32 E-value=1.2e+02 Score=21.75 Aligned_cols=33 Identities=9% Similarity=0.077 Sum_probs=28.0
Q ss_pred HHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHH
Q psy9207 50 RAISLISKAYSSIPNTSLSEFLGVTEQEAAAIA 82 (125)
Q Consensus 50 ~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~ 82 (125)
++++++...+.-.+..++|.-||+|..-+..+.
T Consensus 166 ~Vl~~~~~g~~g~s~~eIa~~l~iS~~Tv~~~~ 198 (225)
T PRK10046 166 AVRKLFKEPGVQHTAETVAQALTISRTTARRYL 198 (225)
T ss_pred HHHHHHHcCCCCcCHHHHHHHhCccHHHHHHHH
Confidence 899999988778899999999999986665553
No 209
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=30.12 E-value=1.5e+02 Score=18.81 Aligned_cols=49 Identities=18% Similarity=0.167 Sum_probs=29.6
Q ss_pred chHHHHHHhCCCHHHHHHHHHhcCCeecCceeeccCCCCCCCCCCC-ChHHHHHHhhHH
Q psy9207 63 PNTSLSEFLGVTEQEAAAIAQAEGWTVDKVYTQPVKKPEEYATPNI-TDDQLYILTQYV 120 (125)
Q Consensus 63 ~~~~~a~~Lgl~~~e~~~~~~~~GW~~d~~~~~p~~~~~~~~~~~~-~~~ql~~Lt~~v 120 (125)
++.++|..+|++..-+.-|.. -+.+.|..... ..-.. +..++..|..+.
T Consensus 2 ti~eva~~~gvs~~tLRyye~-------~Gll~p~~~~~--~gyR~Y~~~~l~~l~~I~ 51 (96)
T cd04768 2 TIGEFAKLAGVSIRTLRHYDD-------IGLFKPAKIAE--NGYRYYSYAQLYQLQFIL 51 (96)
T ss_pred CHHHHHHHHCcCHHHHHHHHH-------CCCCCCCccCC--CCeeeCCHHHHHHHHHHH
Confidence 678999999999877766554 34444543221 11122 667777665443
No 210
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=29.95 E-value=1.8e+02 Score=22.42 Aligned_cols=41 Identities=17% Similarity=0.298 Sum_probs=30.7
Q ss_pred HHHHHHHHHhcC-CcchHHHHHHhCCCHHHHHHHHHhc-CCee
Q psy9207 49 KRAISLISKAYS-SIPNTSLSEFLGVTEQEAAAIAQAE-GWTV 89 (125)
Q Consensus 49 ~~~~~li~~AY~-sI~~~~~a~~Lgl~~~e~~~~~~~~-GW~~ 89 (125)
+++.+.|..-|. .++++++|..+|+|...+....++. |=++
T Consensus 194 ~~~~~~i~~~~~~~~tl~~lA~~~~~S~~~l~r~Fk~~~G~t~ 236 (302)
T PRK10371 194 SQMLGFIAENYDQALTINDVAEHVKLNANYAMGIFQRVMQLTM 236 (302)
T ss_pred HHHHHHHHHhhcCCCCHHHHHHHHCcCHHHHHHHHHHHhCCCH
Confidence 456666666664 7999999999999998877776653 5443
No 211
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=29.90 E-value=1.3e+02 Score=21.20 Aligned_cols=32 Identities=16% Similarity=0.422 Sum_probs=22.9
Q ss_pred HHHHHHHhcCCcchHH---HHHHhCCCHHHHHHHH
Q psy9207 51 AISLISKAYSSIPNTS---LSEFLGVTEQEAAAIA 82 (125)
Q Consensus 51 ~~~li~~AY~sI~~~~---~a~~Lgl~~~e~~~~~ 82 (125)
++..+...|..||.+. +|..||++..++...+
T Consensus 28 ~L~~vQ~~~G~Ip~e~~~~iA~~l~v~~~~V~~va 62 (156)
T PRK05988 28 ILHAIQDEFGYVPEDAVPVIAEALNLSRAEVHGVI 62 (156)
T ss_pred HHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHHHH
Confidence 4445667788888765 8899999986665543
No 212
>PRK15044 transcriptional regulator SirC; Provisional
Probab=29.87 E-value=2.3e+02 Score=22.36 Aligned_cols=41 Identities=10% Similarity=0.090 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHHhcC-CcchHHHHHHhCCCHHHHHHHHHhcC
Q psy9207 46 EVQKRAISLISKAYS-SIPNTSLSEFLGVTEQEAAAIAQAEG 86 (125)
Q Consensus 46 ~vR~~~~~li~~AY~-sI~~~~~a~~Lgl~~~e~~~~~~~~G 86 (125)
...+++.+.|..-|. .++++++|..+|+|..-+.....+.|
T Consensus 192 s~~~kV~~~I~~nl~~~~SLeeLA~~lgmS~~tL~R~Fk~eg 233 (295)
T PRK15044 192 TTKEKVYNIIISDLTRKWSQAEVAGKLFMSVSSLKRKLAAEE 233 (295)
T ss_pred hHHHHHHHHHHhCcccCCCHHHHHHHhCCCHHHHHHHHHHcC
Confidence 345566666666554 69999999999999988877666554
No 213
>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=29.87 E-value=99 Score=16.71 Aligned_cols=25 Identities=16% Similarity=0.331 Sum_probs=21.1
Q ss_pred HHHHhcCCcchHHHHHHhCCCHHHH
Q psy9207 54 LISKAYSSIPNTSLSEFLGVTEQEA 78 (125)
Q Consensus 54 li~~AY~sI~~~~~a~~Lgl~~~e~ 78 (125)
+..+-|..++++++++-.|++..-+
T Consensus 9 ~~~~G~~~~s~~~Ia~~~gvs~~~~ 33 (47)
T PF00440_consen 9 FAEKGYEAVSIRDIARRAGVSKGSF 33 (47)
T ss_dssp HHHHHTTTSSHHHHHHHHTSCHHHH
T ss_pred HHHhCHHhCCHHHHHHHHccchhhH
Confidence 3478999999999999999997544
No 214
>TIGR01958 nuoE_fam NADH-quinone oxidoreductase, E subunit. This model describes the E chain of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoB. This model does not identify proteins from chloroplast and cyanobacteria.
Probab=29.80 E-value=1.3e+02 Score=20.90 Aligned_cols=32 Identities=16% Similarity=0.255 Sum_probs=22.4
Q ss_pred HHHHHHHhcCCcchHH---HHHHhCCCHHHHHHHH
Q psy9207 51 AISLISKAYSSIPNTS---LSEFLGVTEQEAAAIA 82 (125)
Q Consensus 51 ~~~li~~AY~sI~~~~---~a~~Lgl~~~e~~~~~ 82 (125)
++..+...|.-||.+. +|..||++..++...+
T Consensus 21 ~L~~vQ~~~G~i~~~~~~~iA~~l~~~~~~v~~v~ 55 (148)
T TIGR01958 21 ALMIAQEQKGWVTPEAIAAVAEMLGIPPVWVYEVA 55 (148)
T ss_pred HHHHHHHHhCCCCHHHHHHHHHHhCcCHHHHHHHH
Confidence 3445566788888765 8899999986655443
No 215
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=29.74 E-value=1.5e+02 Score=24.12 Aligned_cols=44 Identities=16% Similarity=0.363 Sum_probs=37.9
Q ss_pred HHHHHHHHHHHHhcCCcchHHHHHHhCCC---HHHHHHHHHhcCCee
Q psy9207 46 EVQKRAISLISKAYSSIPNTSLSEFLGVT---EQEAAAIAQAEGWTV 89 (125)
Q Consensus 46 ~vR~~~~~li~~AY~sI~~~~~a~~Lgl~---~~e~~~~~~~~GW~~ 89 (125)
.+...+++|.-++-...+-+++-.++|+. .+.+-+|..++||--
T Consensus 383 ~LK~~~is~~l~t~g~f~K~d~~~Lf~id~~ka~~~YdfF~~~~Wi~ 429 (432)
T COG5114 383 ELKKEVISCFLRTRGEFTKEDFNRLFGIDLGKADGLYDFFLERGWIH 429 (432)
T ss_pred HHHHHHHHHHHHhCCCccHHHHHHHhCcCcchhhHHHHHHHhccccC
Confidence 46778889999999999999999999986 377889999999953
No 216
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=29.64 E-value=1.5e+02 Score=23.28 Aligned_cols=33 Identities=18% Similarity=0.416 Sum_probs=23.7
Q ss_pred hcCCcchHHHHHHhCCCHHH-----------HHHHHHhcCCeec
Q psy9207 58 AYSSIPNTSLSEFLGVTEQE-----------AAAIAQAEGWTVD 90 (125)
Q Consensus 58 AY~sI~~~~~a~~Lgl~~~e-----------~~~~~~~~GW~~d 90 (125)
-|.-.+...+|..||++..- +.+.....||..|
T Consensus 279 ~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l~~~~~~~~ 322 (325)
T PRK05657 279 GYEAATLEDVAREIGLTRERVRQIQVEALRRLREILQTQGLSIE 322 (325)
T ss_pred CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhCccchh
Confidence 46789999999999999633 3344555677653
No 217
>TIGR00370 conserved hypothetical protein TIGR00370.
Probab=29.60 E-value=68 Score=23.73 Aligned_cols=29 Identities=10% Similarity=0.097 Sum_probs=25.5
Q ss_pred cchHHHHHHhCCCHHHHHHHHHhcCCeec
Q psy9207 62 IPNTSLSEFLGVTEQEAAAIAQAEGWTVD 90 (125)
Q Consensus 62 I~~~~~a~~Lgl~~~e~~~~~~~~GW~~d 90 (125)
..++.+|+..||+.+|+++.-.+.-|.+-
T Consensus 91 ~DL~~vA~~~gLs~eevi~~Hs~~~y~V~ 119 (202)
T TIGR00370 91 PDLEEVAKINQLSPEEVIDIHSNGEYVVY 119 (202)
T ss_pred CCHHHHHHHhCcCHHHHHHHHhCCceEEE
Confidence 47889999999999999999888888863
No 218
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=29.57 E-value=1.9e+02 Score=20.22 Aligned_cols=22 Identities=18% Similarity=0.339 Sum_probs=18.0
Q ss_pred HhcCCcchHHHHHHhCCCHHHH
Q psy9207 57 KAYSSIPNTSLSEFLGVTEQEA 78 (125)
Q Consensus 57 ~AY~sI~~~~~a~~Lgl~~~e~ 78 (125)
+-+...+.+++|..||+|..-+
T Consensus 143 ~~~~~~s~~eIA~~lgis~~tV 164 (189)
T PRK12515 143 VYYHEKSVEEVGEIVGIPESTV 164 (189)
T ss_pred HHHcCCCHHHHHHHHCcCHHHH
Confidence 3568999999999999997443
No 219
>smart00311 PWI PWI, domain in splicing factors.
Probab=29.52 E-value=67 Score=19.60 Aligned_cols=19 Identities=26% Similarity=0.427 Sum_probs=15.1
Q ss_pred HHHHHhCCCHHHHHHHHHh
Q psy9207 66 SLSEFLGVTEQEAAAIAQA 84 (125)
Q Consensus 66 ~~a~~Lgl~~~e~~~~~~~ 84 (125)
.+-.+||++++.+++|+.+
T Consensus 16 kv~e~LG~~d~~vvd~i~~ 34 (74)
T smart00311 16 KVIEFLGFEEDTLVEFILS 34 (74)
T ss_pred HHHHHHCCChHHHHHHHHH
Confidence 3456999999999999764
No 220
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=29.46 E-value=2.2e+02 Score=21.57 Aligned_cols=45 Identities=20% Similarity=0.423 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHHHHHhcC---CcchHHHHHHhCCCH----HHHHHHHHhcCC
Q psy9207 43 LQDEVQKRAISLISKAYS---SIPNTSLSEFLGVTE----QEAAAIAQAEGW 87 (125)
Q Consensus 43 l~~~vR~~~~~li~~AY~---sI~~~~~a~~Lgl~~----~e~~~~~~~~GW 87 (125)
+.+.-..+|++++.-||. -++..|+|.+||+|. .++.++-.+.|=
T Consensus 84 ~~elr~~rIvRl~~EAy~QgglLT~~Dla~LL~~S~~TI~~~i~~yq~e~g~ 135 (220)
T PF07900_consen 84 LSELRKHRIVRLTNEAYDQGGLLTQEDLAMLLGISPRTISKDIKEYQKEHGV 135 (220)
T ss_pred HHHHHHHHHHHHHHHHHHcCCcccHHHHHHHHCCCHHHHHHHHHHHHHHcCc
Confidence 345556699999999996 589999999999996 444555444343
No 221
>COG0549 ArcC Carbamate kinase [Amino acid transport and metabolism]
Probab=29.27 E-value=1.3e+02 Score=24.02 Aligned_cols=28 Identities=36% Similarity=0.607 Sum_probs=19.9
Q ss_pred CHHHHHHHHHhcCCee--c-Cc---eeeccCCCC
Q psy9207 74 TEQEAAAIAQAEGWTV--D-KV---YTQPVKKPE 101 (125)
Q Consensus 74 ~~~e~~~~~~~~GW~~--d-~~---~~~p~~~~~ 101 (125)
+++|+.+...+.||.+ | ++ -+.|.|...
T Consensus 136 ~~eea~~l~~~~gw~~keD~~rG~RRVVpSP~P~ 169 (312)
T COG0549 136 SEEEAEELAKEYGWVFKEDAGRGYRRVVPSPKPV 169 (312)
T ss_pred CHHHHHHHHhhcCcEEEecCCCCeeEecCCCCCc
Confidence 5689999999999999 4 33 455655443
No 222
>PF12668 DUF3791: Protein of unknown function (DUF3791); InterPro: IPR024269 This entry represents proteins of unknown function.
Probab=29.23 E-value=90 Score=18.29 Aligned_cols=23 Identities=13% Similarity=0.099 Sum_probs=18.7
Q ss_pred chHHHHHHhCCCHHHHHHHHHhc
Q psy9207 63 PNTSLSEFLGVTEQEAAAIAQAE 85 (125)
Q Consensus 63 ~~~~~a~~Lgl~~~e~~~~~~~~ 85 (125)
.++.+|.-+|++++|+.+...+-
T Consensus 7 ~Ie~~A~~~~~s~~ea~~~~~~~ 29 (62)
T PF12668_consen 7 CIEEFAKKLNISGEEAYNYFKRS 29 (62)
T ss_pred HHHHHHHHHCcCHHHHHHHHHHc
Confidence 56788999999999988877653
No 223
>PF01296 Galanin: Galanin; InterPro: IPR008174 Galanin is a peptide hormone that controls various biological activities []. Galanin-like immuno-reactivity has been found in the central and peripheral nervous systems of mammals, with high concentrations demonstrated in discrete regions of the central nervous system, including the median eminence, hypothalamus, arcuate nucleus, septum, neuro-intermediate lobe of the pituitary, and the spinal cord. Its localisation within neurosecretory granules suggests that galanin may function as a neurotransmitter, and it has been shown to coexist with a variety of other peptide and amine neurotransmitters within individual neurons []. Although the precise physiological role of galanin is uncertain, it has a number of pharmacological properties: it stimulates food intake, when injected into the third ventricle of rats; it increases levels of plasma growth hormone and prolactin, and decreases dopamine levels in the median eminence []; and infusion into humans results in hyperglycemia and glucose intolerance, and inhibits pancreatic release of insulin, somatostatin and pancreatic peptide. Galanin also modulates smooth muscle contractility within the gastro-intestinal and genito-urinary tracts, all such activities suggesting that the hormone may play an important role in the nervous modulation of endocrine and smooth muscle function []. Galanin is a 29 amino acid peptide processed from a larger precursor protein. Except in human, galanin is C-terminally amidated. Its sequence is highly conserved and the first 14 residues are identical in all currently known sequences.; GO: 0005179 hormone activity, 0005576 extracellular region
Probab=29.09 E-value=34 Score=17.36 Aligned_cols=16 Identities=25% Similarity=0.544 Sum_probs=12.1
Q ss_pred CCeec--CceeeccCCCC
Q psy9207 86 GWTVD--KVYTQPVKKPE 101 (125)
Q Consensus 86 GW~~d--~~~~~p~~~~~ 101 (125)
||+++ +..+-|...++
T Consensus 1 gwtlnsagyLlGPhaiD~ 18 (29)
T PF01296_consen 1 GWTLNSAGYLLGPHAIDN 18 (29)
T ss_pred CccccccceEeccccccC
Confidence 89997 66777776665
No 224
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=28.94 E-value=1.6e+02 Score=18.79 Aligned_cols=21 Identities=10% Similarity=0.150 Sum_probs=17.4
Q ss_pred chHHHHHHhCCCHHHHHHHHH
Q psy9207 63 PNTSLSEFLGVTEQEAAAIAQ 83 (125)
Q Consensus 63 ~~~~~a~~Lgl~~~e~~~~~~ 83 (125)
++.++|..+|++..-+.-|..
T Consensus 2 ti~eva~~~gvs~~tlR~ye~ 22 (103)
T cd01106 2 TVGEVAKLTGVSVRTLHYYDE 22 (103)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 678999999999888876654
No 225
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=28.92 E-value=69 Score=16.44 Aligned_cols=17 Identities=12% Similarity=0.198 Sum_probs=11.2
Q ss_pred HHHHhCCCHHHHHHHHH
Q psy9207 67 LSEFLGVTEQEAAAIAQ 83 (125)
Q Consensus 67 ~a~~Lgl~~~e~~~~~~ 83 (125)
-|.-.|++.+|+.+|..
T Consensus 11 eA~~~Gls~eeir~FL~ 27 (30)
T PF08671_consen 11 EAKESGLSKEEIREFLE 27 (30)
T ss_dssp HHHHTT--HHHHHHHHH
T ss_pred HHHHcCCCHHHHHHHHH
Confidence 35567999999888865
No 226
>PF07146 DUF1389: Protein of unknown function (DUF1389); InterPro: IPR010792 This family consists of several hypothetical bacterial proteins, which seem to be specific to Chlamydia pneumoniae (Chlamydophila pneumoniae). Members of this family are typically around 400 residues in length. The function of this family is unknown.
Probab=28.90 E-value=96 Score=24.71 Aligned_cols=62 Identities=13% Similarity=0.329 Sum_probs=39.2
Q ss_pred HHHHHHHHHHHcCCchHHHHHhcc-CCcHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHhCC
Q psy9207 7 GQVWEVGKHLWNGNYPSIYSTLKR-TWSDDIAHIMKALQDEVQKRAISLISKAYSSIPNTSLSEFLGV 73 (125)
Q Consensus 7 ~~~~~l~~~l~~~~y~~v~~~~~~-~~s~~~~~~i~~l~~~vR~~~~~li~~AY~sI~~~~~a~~Lgl 73 (125)
...|-|.|-+-+.+|.......++ .|... . .+..++|+|+..|++.-|....-.+-...+.+
T Consensus 172 ~~~~~l~~~vS~eey~~L~~hA~n~tW~~~-~----~~V~~i~~rl~~~l~~~~~~~~~~~~~~~~~~ 234 (314)
T PF07146_consen 172 PHTWLLAQIVSEEEYSTLKNHARNNTWDQQ-Q----DIVSAIVDRLIACLGNYYQYSFENDKVILLSL 234 (314)
T ss_pred chHHHHHHHccHHHHHHHHHHHhhCCccch-h----hHHHHHHHHHHhhhhhhhhhhhccchhHHHHh
Confidence 367999999999999998877776 89542 2 23355556665666665554444333333333
No 227
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=28.73 E-value=92 Score=23.39 Aligned_cols=27 Identities=11% Similarity=0.131 Sum_probs=16.9
Q ss_pred cchHHHHHHhCCCHHHHHHHHHhcCCe
Q psy9207 62 IPNTSLSEFLGVTEQEAAAIAQAEGWT 88 (125)
Q Consensus 62 I~~~~~a~~Lgl~~~e~~~~~~~~GW~ 88 (125)
.++.++|.-.|.|+.-+..||++.|-+
T Consensus 35 ~si~~lA~~~~vS~aTv~Rf~kklG~~ 61 (284)
T PRK11302 35 SSIATLAKMANVSEPTVNRFCRSLDTK 61 (284)
T ss_pred cCHHHHHHHhCCCHHHHHHHHHHcCCC
Confidence 456666666666666666666665443
No 228
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=28.65 E-value=1.4e+02 Score=21.49 Aligned_cols=29 Identities=34% Similarity=0.371 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHHhcCCcchHHHHHHhCCCH
Q psy9207 46 EVQKRAISLISKAYSSIPNTSLSEFLGVTE 75 (125)
Q Consensus 46 ~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~ 75 (125)
.-|++|+.++.+ ...+++.+++..||+|.
T Consensus 7 ~R~~~Il~~l~~-~~~~~~~~La~~~~vS~ 35 (185)
T PRK04424 7 ERQKALQELIEE-NPFITDEELAEKFGVSI 35 (185)
T ss_pred HHHHHHHHHHHH-CCCEEHHHHHHHHCcCH
Confidence 334556666655 99999999999999996
No 229
>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=28.47 E-value=1.3e+02 Score=17.57 Aligned_cols=38 Identities=16% Similarity=0.178 Sum_probs=25.8
Q ss_pred HHHHHHHhcCCcchHHHHHHhCCCHHHH---HHHHHhcCCee
Q psy9207 51 AISLISKAYSSIPNTSLSEFLGVTEQEA---AAIAQAEGWTV 89 (125)
Q Consensus 51 ~~~li~~AY~sI~~~~~a~~Lgl~~~e~---~~~~~~~GW~~ 89 (125)
|..+.. .=..++..++|..||+++.-+ ++-..+.|+..
T Consensus 13 Iy~l~~-~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV~ 53 (60)
T PF01325_consen 13 IYELSE-EGGPVRTKDIAERLGVSPPTVTEMLKRLAEKGLVE 53 (60)
T ss_dssp HHHHHH-CTSSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHc-CCCCccHHHHHHHHCCChHHHHHHHHHHHHCCCEE
Confidence 444444 668899999999999997444 44455567764
No 230
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=28.40 E-value=1.3e+02 Score=22.28 Aligned_cols=41 Identities=17% Similarity=0.206 Sum_probs=32.4
Q ss_pred HHHHHHHHhcCCcchHHHHHHhCCCHHHHHH---HHHhcCCeec
Q psy9207 50 RAISLISKAYSSIPNTSLSEFLGVTEQEAAA---IAQAEGWTVD 90 (125)
Q Consensus 50 ~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~---~~~~~GW~~d 90 (125)
+|+++++.+=..+++.++|.-+|++..-+-. -..+.||-..
T Consensus 13 ~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~~G~l~~ 56 (248)
T TIGR02431 13 AVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVELGYVTS 56 (248)
T ss_pred HHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe
Confidence 6788888877789999999999999755444 4556799873
No 231
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=28.33 E-value=2.6e+02 Score=21.79 Aligned_cols=38 Identities=21% Similarity=0.456 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHhCCCHH
Q psy9207 38 HIMKALQDEVQKRAISLISKAYSSIPNTSLSEFLGVTEQ 76 (125)
Q Consensus 38 ~~i~~l~~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~ 76 (125)
+.+.+|...+|-+|++++.+. .-+.++++|.-|||+..
T Consensus 15 dv~kalaS~vRv~Il~lL~~k-~plNvneiAe~lgLpqs 52 (308)
T COG4189 15 DVLKALASKVRVAILQLLHRK-GPLNVNEIAEALGLPQS 52 (308)
T ss_pred hHHHHHHHHHHHHHHHHHHHh-CCCCHHHHHHHhCCchh
Confidence 567889999999999999876 34889999999999853
No 232
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=28.19 E-value=2e+02 Score=19.64 Aligned_cols=22 Identities=18% Similarity=0.329 Sum_probs=18.3
Q ss_pred HhcCCcchHHHHHHhCCCHHHH
Q psy9207 57 KAYSSIPNTSLSEFLGVTEQEA 78 (125)
Q Consensus 57 ~AY~sI~~~~~a~~Lgl~~~e~ 78 (125)
+-|...+..++|..||++..-+
T Consensus 130 ~~~~g~s~~EIA~~lgis~~tV 151 (173)
T PRK09645 130 SYYRGWSTAQIAADLGIPEGTV 151 (173)
T ss_pred HHHcCCCHHHHHHHHCcCHHHH
Confidence 4578999999999999997544
No 233
>KOG3978|consensus
Probab=28.18 E-value=72 Score=26.14 Aligned_cols=40 Identities=18% Similarity=0.395 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHHHHHH-HHHhcCCcchHHHHHHhCCCHHHHHHHHHhcCCeec
Q psy9207 39 IMKALQDEVQKRAISL-ISKAYSSIPNTSLSEFLGVTEQEAAAIAQAEGWTVD 90 (125)
Q Consensus 39 ~i~~l~~~vR~~~~~l-i~~AY~sI~~~~~a~~Lgl~~~e~~~~~~~~GW~~d 90 (125)
+.+.+...+|+||++. ++-||.|.+ .-+.+|.+++||-.+
T Consensus 169 L~amiv~~v~erile~gle~ayas~s------------~n~~~fl~~qGl~~~ 209 (469)
T KOG3978|consen 169 LFAMIVAMVSERILEIGLEEAYASLS------------TNIADFLESQGLFDN 209 (469)
T ss_pred HHHHHHHHHHHHHHHhcchHHHHHHh------------hhHHHHHHhcCCCcC
Confidence 5688889999999984 677777664 346678889999764
No 234
>cd00256 VATPase_H VATPase_H, regulatory vacuolar ATP synthase subunit H (Vma13p); activation component of the peripheral V1 complex of V-ATPase, a heteromultimeric enzyme which uses ATP to actively transport protons into organelles and extracellular compartments. The topology is that of a superhelical spiral, in part the geometry is similar to superhelices composed of armadillo repeat motifs, as found in importins for example.
Probab=28.09 E-value=2.5e+02 Score=23.38 Aligned_cols=82 Identities=6% Similarity=0.133 Sum_probs=52.8
Q ss_pred HHHHHHHHHHHHcCCchHHHHHhccCCcHHHHHHHHHHHHHHHHHHHHHHHHhcCCcch---------HHHHHHhCCCHH
Q psy9207 6 IGQVWEVGKHLWNGNYPSIYSTLKRTWSDDIAHIMKALQDEVQKRAISLISKAYSSIPN---------TSLSEFLGVTEQ 76 (125)
Q Consensus 6 l~~~~~l~~~l~~~~y~~v~~~~~~~~s~~~~~~i~~l~~~vR~~~~~li~~AY~sI~~---------~~~a~~Lgl~~~ 76 (125)
++-.+.+.-.+|.=+|..-..... .-.+.+..+++.+.+..++++.+++-....++-- ..+..|++..-.
T Consensus 201 ~Ql~Y~~ll~lWlLSF~~~~~~~~-~~~~~i~~l~~i~k~s~KEKvvRv~l~~l~Nll~~~~~~~~~~~~~~~mv~~~l~ 279 (429)
T cd00256 201 FQLQYQSIFCIWLLTFNPHAAEVL-KRLSLIQDLSDILKESTKEKVIRIVLAIFRNLISKRVDREVKKTAALQMVQCKVL 279 (429)
T ss_pred HHHHHHHHHHHHHHhccHHHHHhh-ccccHHHHHHHHHHhhhhHHHHHHHHHHHHHHhhcccccchhhhHHHHHHHcChH
Confidence 455677777788777776422222 2235677788999999999999977666655543 235566665555
Q ss_pred HHHHHHHhcCCe
Q psy9207 77 EAAAIAQAEGWT 88 (125)
Q Consensus 77 e~~~~~~~~GW~ 88 (125)
.+.+-...++|+
T Consensus 280 ~~l~~L~~rk~~ 291 (429)
T cd00256 280 KTLQSLEQRKYD 291 (429)
T ss_pred HHHHHHhcCCCC
Confidence 555555666664
No 235
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=28.02 E-value=1.5e+02 Score=22.56 Aligned_cols=40 Identities=15% Similarity=0.130 Sum_probs=32.4
Q ss_pred HHHHHHHHhcCCcchHHHHHHhCCCHHHHHHH---HHhcCCee
Q psy9207 50 RAISLISKAYSSIPNTSLSEFLGVTEQEAAAI---AQAEGWTV 89 (125)
Q Consensus 50 ~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~---~~~~GW~~ 89 (125)
+|+++++..-..+++.++|+-||++..-+-.+ ..+.||-.
T Consensus 29 ~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~ 71 (271)
T PRK10163 29 AILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQAADFVY 71 (271)
T ss_pred HHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 57888888878899999999999997665444 55679986
No 236
>COG4004 Uncharacterized protein conserved in archaea [Function unknown]
Probab=27.90 E-value=1.8e+02 Score=19.06 Aligned_cols=53 Identities=25% Similarity=0.330 Sum_probs=29.9
Q ss_pred CCC--HHHHHHHHHhcCCeec--Cceee---cc------CCCCCC---CCCCC--ChHHHHHHhhHHHhhc
Q psy9207 72 GVT--EQEAAAIAQAEGWTVD--KVYTQ---PV------KKPEEY---ATPNI--TDDQLYILTQYVSFLE 124 (125)
Q Consensus 72 gl~--~~e~~~~~~~~GW~~d--~~~~~---p~------~~~~~~---~~~~~--~~~ql~~Lt~~v~fLE 124 (125)
|+. ++-+....+++||++. |..+. |. ++.+.. .+... ....|+.+--|.-|||
T Consensus 9 Gf~~~~dri~~~l~e~g~~v~~eGD~ivas~pgis~ieik~E~kkL~v~t~~~~~d~~~l~~~ktyndfle 79 (96)
T COG4004 9 GFKPDPDRIMRGLSELGWTVSEEGDRIVASSPGISRIEIKPENKKLLVNTTDYTDDETKLQTAKTYNDFLE 79 (96)
T ss_pred CCCCCHHHHHHHHHHhCeeEeecccEEEEecCCceEEEEecccceEEEecccccCchhHHHHHHHHHHHHH
Confidence 564 4678888999999995 44332 21 122211 11111 4666776666666665
No 237
>PF09145 Ubiq-assoc: Ubiquitin-associated; InterPro: IPR015228 Ubiquitin-associated domains contain approximately 40 residues and bind ubiquitin noncovalently. They adopt a secondary structure consisting of three alpha-helices, and have been identified in various modular proteins involved in protein trafficking, clathrin assembly/disassembly, DNA repair, proteasomal degradation, and cell cycle regulation []. ; PDB: 1PGY_A.
Probab=27.79 E-value=66 Score=18.22 Aligned_cols=12 Identities=42% Similarity=0.592 Sum_probs=7.3
Q ss_pred HHHHH-HHHHHHH
Q psy9207 45 DEVQK-RAISLIS 56 (125)
Q Consensus 45 ~~vR~-~~~~li~ 56 (125)
|-+++ ++++++|
T Consensus 3 DEVkDMEiAkLMS 15 (46)
T PF09145_consen 3 DEVKDMEIAKLMS 15 (46)
T ss_dssp HHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHH
Confidence 34444 6777776
No 238
>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=27.52 E-value=1.7e+02 Score=18.87 Aligned_cols=39 Identities=15% Similarity=0.273 Sum_probs=28.9
Q ss_pred HHHHHHHHhcCCcchHHHHHHhCCCHHHHHHH---HHhcCCee
Q psy9207 50 RAISLISKAYSSIPNTSLSEFLGVTEQEAAAI---AQAEGWTV 89 (125)
Q Consensus 50 ~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~---~~~~GW~~ 89 (125)
.++.++.. ...++..+++..+|++..-+... ..+.||..
T Consensus 32 ~iL~~l~~-~~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~ 73 (118)
T TIGR02337 32 RILRILAE-QGSMEFTQLANQACILRPSLTGILARLERDGLVT 73 (118)
T ss_pred HHHHHHHH-cCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEE
Confidence 56666654 67899999999999986554444 45579987
No 239
>COG1724 Predicted RNA binding protein (dsRBD-like fold), HicA family [General function prediction only]
Probab=27.40 E-value=53 Score=20.12 Aligned_cols=21 Identities=10% Similarity=0.313 Sum_probs=18.8
Q ss_pred HHhCCCHHHHHHHHHhcCCee
Q psy9207 69 EFLGVTEQEAAAIAQAEGWTV 89 (125)
Q Consensus 69 ~~Lgl~~~e~~~~~~~~GW~~ 89 (125)
.++.++..|+++..+..||..
T Consensus 3 ~lp~~~~ke~ik~Le~~Gf~~ 23 (66)
T COG1724 3 KLPRMKAKEVIKALEKDGFQL 23 (66)
T ss_pred cCCcCCHHHHHHHHHhCCcEE
Confidence 467788999999999999998
No 240
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=27.39 E-value=85 Score=22.95 Aligned_cols=41 Identities=15% Similarity=0.168 Sum_probs=26.5
Q ss_pred HHHHHHHHHHHHHHHHhc----CCcchHHHHHHhCCCHHHHHHHH
Q psy9207 42 ALQDEVQKRAISLISKAY----SSIPNTSLSEFLGVTEQEAAAIA 82 (125)
Q Consensus 42 ~l~~~vR~~~~~li~~AY----~sI~~~~~a~~Lgl~~~e~~~~~ 82 (125)
.|.+.-|+-+-.....-| +.+++.++|+.||++..-+.+..
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehL 199 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHL 199 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHH
Confidence 344444444444444444 57899999999999986655543
No 241
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=27.15 E-value=71 Score=24.48 Aligned_cols=27 Identities=22% Similarity=0.342 Sum_probs=21.9
Q ss_pred cchHHHHHHhCCCHHHHHHHHHhcCCe
Q psy9207 62 IPNTSLSEFLGVTEQEAAAIAQAEGWT 88 (125)
Q Consensus 62 I~~~~~a~~Lgl~~~e~~~~~~~~GW~ 88 (125)
.++.++|...|+|+.-+..||++.|-+
T Consensus 37 ~si~elA~~a~VS~aTv~Rf~~kLGf~ 63 (281)
T COG1737 37 LSIAELAERAGVSPATVVRFARKLGFE 63 (281)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHHcCCC
Confidence 466788888999988899999887654
No 242
>PF00531 Death: Death domain; InterPro: IPR000488 The death domain (DD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. DD is related in sequence and structure to the death effector domain (DED, see IPR001875 from INTERPRO) and the caspase recruitment domain (CARD, see IPR001315 from INTERPRO), which work in similar pathways and show similar interaction properties []. DD bind each other forming oligomers. Mammals have numerous and diverse DD-containing proteins []. Within these proteins, the DD domains can be found in combination with other domains, including: CARDs, DEDs, ankyrin repeats (IPR002110 from INTERPRO), caspase-like folds, kinase domains, leucine zippers (IPR002158 from INTERPRO), leucine-rich repeats (LRR) (IPR001611 from INTERPRO), TIR domains (IPR000157 from INTERPRO), and ZU5 domains (IPR000906 from INTERPRO) []. Some DD-containing proteins are involved in the regulation of apoptosis and inflammation through their activation of caspases and NF-kappaB, which typically involves interactions with TNF (tumour necrosis factor) cytokine receptors [, ]. In humans, eight of the over 30 known TNF receptors contain DD in their cytoplasmic tails; several of these TNF receptors use caspase activation as a signalling mechanism. The DD mediates self-association of these receptors, thus giving the signal to downstream events that lead to apoptosis. Other DD-containing proteins, such as ankyrin, MyD88 and pelle, are probably not directly involved in cell death signalling. DD-containing proteins also have links to innate immunity, communicating with Toll family receptors through bipartite adapter proteins such as MyD88 [].; GO: 0005515 protein binding, 0007165 signal transduction; PDB: 3OQ9_L 3EZQ_F 1E41_A 1E3Y_A 2GF5_A 2OF5_L 3EWV_E 3G5B_A 3MOP_L 2A9I_A ....
Probab=27.03 E-value=1.4e+02 Score=17.65 Aligned_cols=22 Identities=27% Similarity=0.360 Sum_probs=15.4
Q ss_pred chHHHHHHhCCCHHHHHHHHHh
Q psy9207 63 PNTSLSEFLGVTEQEAAAIAQA 84 (125)
Q Consensus 63 ~~~~~a~~Lgl~~~e~~~~~~~ 84 (125)
.-..+|..||++..++..+-..
T Consensus 14 ~Wk~La~~Lg~~~~~i~~i~~~ 35 (83)
T PF00531_consen 14 DWKRLARKLGLSESEIENIEEE 35 (83)
T ss_dssp CHHHHHHHTTS-HHHHHHHHHH
T ss_pred hHHHHHHHhCcCHHHHHHHHHh
Confidence 4567888889988777776554
No 243
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=26.94 E-value=2.4e+02 Score=20.93 Aligned_cols=22 Identities=27% Similarity=0.415 Sum_probs=16.4
Q ss_pred CcchHHHHHHhCCCHHHHHHHH
Q psy9207 61 SIPNTSLSEFLGVTEQEAAAIA 82 (125)
Q Consensus 61 sI~~~~~a~~Lgl~~~e~~~~~ 82 (125)
..+..++|..||++.+++....
T Consensus 125 ~~~~~eia~~l~~~~~~v~~~~ 146 (251)
T PRK07670 125 NVTPKEVAAELGMTEEEVEATM 146 (251)
T ss_pred CCCHHHHHHHhCcCHHHHHHHH
Confidence 4456788888999887776654
No 244
>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=26.79 E-value=1.3e+02 Score=16.99 Aligned_cols=30 Identities=17% Similarity=0.431 Sum_probs=23.1
Q ss_pred CCcchHHHHHHhCCCHHHHHHH---HHhcCCee
Q psy9207 60 SSIPNTSLSEFLGVTEQEAAAI---AQAEGWTV 89 (125)
Q Consensus 60 ~sI~~~~~a~~Lgl~~~e~~~~---~~~~GW~~ 89 (125)
..++..++|..+|++..-+... ..+.||-.
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~ 56 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKELEEEGLIS 56 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 4689999999999997555444 45578886
No 245
>smart00099 btg1 tob/btg1 family. The tob/btg1 is a family of proteins that inhibit cell proliferation.
Probab=26.75 E-value=2e+02 Score=19.25 Aligned_cols=51 Identities=6% Similarity=0.044 Sum_probs=37.6
Q ss_pred CCcHHHHHHHHHHHHHHHHHHHH-------HHHHhcCCcch--------HHHHHHhCCCHHHHHHH
Q psy9207 31 TWSDDIAHIMKALQDEVQKRAIS-------LISKAYSSIPN--------TSLSEFLGVTEQEAAAI 81 (125)
Q Consensus 31 ~~s~~~~~~i~~l~~~vR~~~~~-------li~~AY~sI~~--------~~~a~~Lgl~~~e~~~~ 81 (125)
-+...+..|.+.|.+.++++.-. .-+.||+.|.+ .+||.-.|++.+|+.+.
T Consensus 22 l~~~~v~~F~~~L~~~L~~~y~~HWyP~~P~kGqayRCIrIn~~~Dp~l~~Aa~~sGl~~~~l~~~ 87 (108)
T smart00099 22 LSKRRVEIFAEKLTRLLKEKYKNHWYPEKPYKGSGFRCIRINQKVDPVIEQACKESGLDIDDLGGN 87 (108)
T ss_pred CCHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCcceEEEEECCcCCHHHHHHHHHhCCCHHHHHHh
Confidence 44577788888888888887776 56788998865 45777778877777653
No 246
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=26.67 E-value=2e+02 Score=19.81 Aligned_cols=37 Identities=11% Similarity=0.267 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHHH
Q psy9207 46 EVQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQ 83 (125)
Q Consensus 46 ~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~ 83 (125)
.+=.+|+.++.+- ..+|..++|.-||+|+..+..-++
T Consensus 9 ~~D~~Il~~Lq~d-~R~s~~eiA~~lglS~~tV~~Ri~ 45 (153)
T PRK11179 9 NLDRGILEALMEN-ARTPYAELAKQFGVSPGTIHVRVE 45 (153)
T ss_pred HHHHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3445666666665 899999999999999877655433
No 247
>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=26.64 E-value=1e+02 Score=18.21 Aligned_cols=27 Identities=11% Similarity=0.297 Sum_probs=19.2
Q ss_pred HhcCCcchHHHHHHhCCCHHHHHHHHH
Q psy9207 57 KAYSSIPNTSLSEFLGVTEQEAAAIAQ 83 (125)
Q Consensus 57 ~AY~sI~~~~~a~~Lgl~~~e~~~~~~ 83 (125)
+.-..+|++++|.-||++++.+.....
T Consensus 10 ~~~~~~S~~eLa~~~~~s~~~ve~mL~ 36 (69)
T PF09012_consen 10 RERGRVSLAELAREFGISPEAVEAMLE 36 (69)
T ss_dssp HHS-SEEHHHHHHHTT--HHHHHHHHH
T ss_pred HHcCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 346789999999999999877766654
No 248
>PF10743 Phage_Cox: Regulatory phage protein cox; InterPro: IPR019679 Phage Cox proteins are expressed by Enterobacteria phages. The Cox protein is a 79-residue basic protein with a predicted strong helix-turn-helix DNA-binding motif. It inhibits integrative recombination and it activates site-specific excision of the HP1 genome from the Haemophilus influenzae chromosome, Hp1. Cox appears to function as a tetramer. Cox binding sites consist of two direct repeats of the consensus motif 5'-GGTMAWWWWA, one Cox tetramer binding to each motif. Cox binding interferes with the interaction of HP1 integrase with one of its binding sites, IBS5. This competition is central to directional control. Both Cox binding sites are needed for full inhibition of integration and for activating excision, because it plays a positive role in assembling the nucleoprotein complexes that produce excisive recombination, by inducing the formation of a critical conformation in those complexes [].
Probab=26.59 E-value=1.4e+02 Score=19.24 Aligned_cols=29 Identities=14% Similarity=0.304 Sum_probs=24.1
Q ss_pred HHhcCCcchHHHHHHhCCCHHHHHHHHHh
Q psy9207 56 SKAYSSIPNTSLSEFLGVTEQEAAAIAQA 84 (125)
Q Consensus 56 ~~AY~sI~~~~~a~~Lgl~~~e~~~~~~~ 84 (125)
+..-.-++.+.+|.|+|-++..+.+.+..
T Consensus 7 ~~p~d~v~~~~FA~~IGKt~sAVr~Mi~~ 35 (87)
T PF10743_consen 7 EYPSDAVTYEKFAEYIGKTPSAVRKMIKA 35 (87)
T ss_pred hhhccccCHHHHHHHHCCCHHHHHHHHHc
Confidence 34456689999999999999999998874
No 249
>PRK14584 hmsS hemin storage system protein; Provisional
Probab=26.59 E-value=1.2e+02 Score=21.64 Aligned_cols=39 Identities=10% Similarity=0.132 Sum_probs=30.2
Q ss_pred hcCCcchHHHHHHhCCCHHHHHHHHHhcCCee--c--Cceeec
Q psy9207 58 AYSSIPNTSLSEFLGVTEQEAAAIAQAEGWTV--D--KVYTQP 96 (125)
Q Consensus 58 AY~sI~~~~~a~~Lgl~~~e~~~~~~~~GW~~--d--~~~~~p 96 (125)
.=..++.+++|+++|++++.+.+.-+.+-=++ | |+.+-.
T Consensus 95 ~~~~l~~dElA~sF~l~~e~i~qLr~~kiltVh~De~G~Ii~V 137 (153)
T PRK14584 95 HRPDLDDDELASSFALSPELIAQLKSGSCLTLYNDEHGHIIDV 137 (153)
T ss_pred CCCCCChHHHHHHcCCCHHHHHHHHhCCeEEEEECCCCCEEEe
Confidence 44578899999999999999988877777776 3 555443
No 250
>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=26.57 E-value=1.1e+02 Score=16.83 Aligned_cols=26 Identities=15% Similarity=0.404 Sum_probs=17.0
Q ss_pred HhcCCcchHHHHHHhCCCHHHHHHHH
Q psy9207 57 KAYSSIPNTSLSEFLGVTEQEAAAIA 82 (125)
Q Consensus 57 ~AY~sI~~~~~a~~Lgl~~~e~~~~~ 82 (125)
.-+.-.+..++|..+|+|...+....
T Consensus 22 ~~~~g~s~~eIa~~l~~s~~~v~~~l 47 (54)
T PF08281_consen 22 RYFQGMSYAEIAEILGISESTVKRRL 47 (54)
T ss_dssp HHTS---HHHHHHHCTS-HHHHHHHH
T ss_pred HHHHCcCHHHHHHHHCcCHHHHHHHH
Confidence 45677889999999999987766543
No 251
>PF13994 PgaD: PgaD-like protein
Probab=26.45 E-value=81 Score=21.66 Aligned_cols=28 Identities=21% Similarity=0.383 Sum_probs=23.3
Q ss_pred cchHHHHHHhCCCHHHHHHHHHhcCCee
Q psy9207 62 IPNTSLSEFLGVTEQEAAAIAQAEGWTV 89 (125)
Q Consensus 62 I~~~~~a~~Lgl~~~e~~~~~~~~GW~~ 89 (125)
++.+++|++++++++++.+.-+++-=++
T Consensus 101 ~~~~elA~~f~l~~~~l~~lr~~k~~~V 128 (138)
T PF13994_consen 101 VSDEELARSFGLSPEQLQQLRQAKVLTV 128 (138)
T ss_pred CCHHHHHHHcCCCHHHHHHHHhCCeEEE
Confidence 9999999999999998888766654444
No 252
>PHA00738 putative HTH transcription regulator
Probab=26.35 E-value=1.9e+02 Score=19.45 Aligned_cols=46 Identities=11% Similarity=0.153 Sum_probs=34.0
Q ss_pred HHHHHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHH---HHhcCCeec
Q psy9207 44 QDEVQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAI---AQAEGWTVD 90 (125)
Q Consensus 44 ~~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~---~~~~GW~~d 90 (125)
.|..|.+|+..+.. ....++.+++..++++..-+-.. ..+.|=...
T Consensus 10 ~dptRr~IL~lL~~-~e~~~V~eLae~l~lSQptVS~HLKvLreAGLV~s 58 (108)
T PHA00738 10 AKILRRKILELIAE-NYILSASLISHTLLLSYTTVLRHLKILNEQGYIEL 58 (108)
T ss_pred CCHHHHHHHHHHHH-cCCccHHHHHHhhCCCHHHHHHHHHHHHHCCceEE
Confidence 36789999999965 33599999999999997655444 445566553
No 253
>PRK12354 carbamate kinase; Reviewed
Probab=26.34 E-value=1.4e+02 Score=23.59 Aligned_cols=29 Identities=34% Similarity=0.645 Sum_probs=21.2
Q ss_pred CCHHHHHHHHHhcCCee--cC---ceeeccCCCC
Q psy9207 73 VTEQEAAAIAQAEGWTV--DK---VYTQPVKKPE 101 (125)
Q Consensus 73 l~~~e~~~~~~~~GW~~--d~---~~~~p~~~~~ 101 (125)
++++|+.+..+++||++ |+ +.+.|.|...
T Consensus 127 y~~~~a~~~~~e~g~~~~~dg~g~rrVv~SP~P~ 160 (307)
T PRK12354 127 YDEAEAERLAAEKGWTIKPDGDYFRRVVPSPRPK 160 (307)
T ss_pred cCHHHHHHHHHhcCCEEeecCCceEEEecCCCCc
Confidence 36799999999999988 32 3566665544
No 254
>PF11237 DUF3038: Protein of unknown function (DUF3038); InterPro: IPR021399 This family of proteins with unknown function appear to be restricted to Cyanobacteria.
Probab=26.31 E-value=2.6e+02 Score=20.32 Aligned_cols=48 Identities=15% Similarity=0.012 Sum_probs=35.2
Q ss_pred hHHHHHHHHHHHHHcCCchHHHHHh------cc-CCcH----HHHHHHHHHHHHHHHHH
Q psy9207 4 PEIGQVWEVGKHLWNGNYPSIYSTL------KR-TWSD----DIAHIMKALQDEVQKRA 51 (125)
Q Consensus 4 ~~l~~~~~l~~~l~~~~y~~v~~~~------~~-~~s~----~~~~~i~~l~~~vR~~~ 51 (125)
.|.+++..|.-++-++.|+-+-+++ .+ ...+ ....+.+.|.+.+++|+
T Consensus 67 eearaLV~Iic~lA~~~~~lIRqll~~~eQ~~~~~~~~~~~~ll~~Yl~rF~~~~~~Rm 125 (171)
T PF11237_consen 67 EEARALVLIICYLAKQLQPLIRQLLLLLEQMSSQEPPPHQNQLLGDYLDRFRSLYQERM 125 (171)
T ss_pred HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhcCCChhhHHHHHHHHHHHHHHHHHHc
Confidence 5788999999999999999999988 44 4433 44455566666666654
No 255
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=25.99 E-value=2.6e+02 Score=20.19 Aligned_cols=52 Identities=12% Similarity=-0.077 Sum_probs=40.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHhCCCH---HHHHHHHHhcCCee
Q psy9207 38 HIMKALQDEVQKRAISLISKAYSSIPNTSLSEFLGVTE---QEAAAIAQAEGWTV 89 (125)
Q Consensus 38 ~~i~~l~~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~---~e~~~~~~~~GW~~ 89 (125)
++.+..-+.+|+.|+..-=+.=..|+..++|..||+|. =|+.......|...
T Consensus 7 ~~~~~vy~~i~~~I~~g~l~pG~~L~e~eLae~lgVSRtpVREAL~~L~~eGlv~ 61 (224)
T PRK11534 7 ITALDGYRWLKNDIIRGNFQPDEKLRMSLLTSRYALGVGPLREALSQLVAERLVT 61 (224)
T ss_pred hhhHHHHHHHHHHHHhCCCCCCCcCCHHHHHHHHCCChHHHHHHHHHHHHCCCEE
Confidence 45566778888888887777778999999999999985 55666666778875
No 256
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=25.98 E-value=1.8e+02 Score=21.94 Aligned_cols=34 Identities=15% Similarity=0.241 Sum_probs=26.3
Q ss_pred HHHHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHH
Q psy9207 45 DEVQKRAISLISKAYSSIPNTSLSEFLGVTEQEAA 79 (125)
Q Consensus 45 ~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~ 79 (125)
+.-|++|++.+. ....+++.+++..||+|..-+.
T Consensus 4 ~~R~~~Il~~l~-~~~~~~~~ela~~l~vS~~Tir 37 (251)
T PRK13509 4 AQRHQILLELLA-QLGFVTVEKVIERLGISPATAR 37 (251)
T ss_pred HHHHHHHHHHHH-HcCCcCHHHHHHHHCcCHHHHH
Confidence 345567777777 5899999999999999974443
No 257
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=25.91 E-value=1.8e+02 Score=18.44 Aligned_cols=21 Identities=10% Similarity=0.251 Sum_probs=17.1
Q ss_pred chHHHHHHhCCCHHHHHHHHH
Q psy9207 63 PNTSLSEFLGVTEQEAAAIAQ 83 (125)
Q Consensus 63 ~~~~~a~~Lgl~~~e~~~~~~ 83 (125)
++.++|..+|++..-+.-|..
T Consensus 2 ~i~eva~~~gvs~~tlR~ye~ 22 (97)
T cd04782 2 TTGEFAKLCGISKQTLFHYDK 22 (97)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 678999999999887776644
No 258
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=25.77 E-value=2.6e+02 Score=20.27 Aligned_cols=23 Identities=26% Similarity=0.300 Sum_probs=17.3
Q ss_pred CcchHHHHHHhCCCHHHHHHHHH
Q psy9207 61 SIPNTSLSEFLGVTEQEAAAIAQ 83 (125)
Q Consensus 61 sI~~~~~a~~Lgl~~~e~~~~~~ 83 (125)
.-+.+.+|..||++.+++.....
T Consensus 113 ~pt~~ela~~l~~~~~~v~~~~~ 135 (231)
T TIGR02885 113 EPTINELAEALGVSPEEIVMALE 135 (231)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHH
Confidence 34467899999999888776543
No 259
>PF04769 MAT_Alpha1: Mating-type protein MAT alpha 1; InterPro: IPR006856 This family includes Saccharomyces cerevisiae (Baker's yeast) mating type protein alpha 1 (P01365 from SWISSPROT). MAT alpha 1 is a transcription activator that activates mating-type alpha-specific genes with the help of the MADS-box containing MCM1 transcription factor, which together bind cooperatively to PQ elements upstream of alpha-specific genes. The MCM1-MATalpha1 complex is required for the proper DNA-bending that is needed for transcriptional activation []. Alpha 1 interacts in vivo with STE12, linking expression of alpha-specific genes to the alpha-pheromone (IPR006742 from INTERPRO) response pathway [].; GO: 0000772 mating pheromone activity, 0003677 DNA binding, 0045895 positive regulation of transcription, mating-type specific, 0005634 nucleus
Probab=25.74 E-value=1.4e+02 Score=22.11 Aligned_cols=54 Identities=24% Similarity=0.465 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHH-HHHHHHHHHHHHhcCCcchH---------H----HHHHhCCCHHHHHHHHHhcCCee
Q psy9207 34 DDIAHIMKALQD-EVQKRAISLISKAYSSIPNT---------S----LSEFLGVTEQEAAAIAQAEGWTV 89 (125)
Q Consensus 34 ~~~~~~i~~l~~-~vR~~~~~li~~AY~sI~~~---------~----~a~~Lgl~~~e~~~~~~~~GW~~ 89 (125)
..+..++..+-. .--+..-.++.++|+.|.-. . ++.++|+- +-..|....||++
T Consensus 68 k~~S~~l~~lW~~dp~k~~W~l~ak~ys~iRd~~gk~~~~L~~Fl~~~~p~~gi~--~p~~YL~~~Gw~l 135 (201)
T PF04769_consen 68 KELSGILTKLWEKDPFKNKWSLMAKAYSFIRDQLGKDKAPLDQFLAFACPLIGII--PPEDYLEQLGWQL 135 (201)
T ss_pred HHHHHHHHHHHhCCccHhHHHHHhhhhhhhccccccccCCHHHHHHHhhhhcCCC--CHHHHHHHcCCeE
Confidence 445555555432 12234466777777766433 1 33444443 2346788899999
No 260
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=25.64 E-value=2.6e+02 Score=20.98 Aligned_cols=23 Identities=13% Similarity=0.320 Sum_probs=18.1
Q ss_pred CCcchHHHHHHhCCCHHHHHHHH
Q psy9207 60 SSIPNTSLSEFLGVTEQEAAAIA 82 (125)
Q Consensus 60 ~sI~~~~~a~~Lgl~~~e~~~~~ 82 (125)
...+.+.+|..||++.+++.+..
T Consensus 133 ~~pt~~eia~~lg~~~~~v~~~~ 155 (268)
T PRK06288 133 RTPSDEEIADELGISLEEYNSLL 155 (268)
T ss_pred CCCCHHHHHHHcCCCHHHHHHHH
Confidence 45678899999999987776654
No 261
>TIGR00746 arcC carbamate kinase. The seed alignment for this model includes experimentally confirmed examples from a set of phylogenetically distinct species. In a neighbor-joining tree constructed from an alignment of candidate carbamate kinases and several acetylglutamate kinases, the latter group forms a clear outgroup which roots the tree of carbamate kinase-like proteins. This analysis suggests that in E. coli, the ArcC paralog YqeA may be a second isozyme, while the paralog YahI branches as an outlier and is less likely to be an authentic carbamate kinase. The homolog from Mycoplasma pneumoniae likewise branches outside the set containing known carbamate kinases and also scores below the trusted cutoff.
Probab=25.53 E-value=1.3e+02 Score=23.82 Aligned_cols=27 Identities=41% Similarity=0.706 Sum_probs=19.1
Q ss_pred CHHHHHHHHHhcCCee--c-Cc---eeeccCCC
Q psy9207 74 TEQEAAAIAQAEGWTV--D-KV---YTQPVKKP 100 (125)
Q Consensus 74 ~~~e~~~~~~~~GW~~--d-~~---~~~p~~~~ 100 (125)
+.+|+.+..++.||++ | ++ -+.|.|..
T Consensus 134 ~~~~a~~~~~~~~~~~~~d~~~~~rrvv~sp~p 166 (310)
T TIGR00746 134 TEEEAKRLAAEKGWIVKEDAGRGWRRVVPSPRP 166 (310)
T ss_pred CHHHHHHHHHHcCCeEeecCCCcceEeecCCCc
Confidence 5688999999999998 3 32 45555543
No 262
>TIGR03613 RutR pyrimidine utilization regulatory protein R. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the TetR family of transcriptional regulators defined by the N-teminal model pfam00440 and the C-terminal model pfam08362 (YcdC-like protein, C-terminal region).
Probab=25.40 E-value=1.5e+02 Score=20.76 Aligned_cols=22 Identities=14% Similarity=0.311 Sum_probs=19.8
Q ss_pred HHHHhcCCcchHHHHHHhCCCH
Q psy9207 54 LISKAYSSIPNTSLSEFLGVTE 75 (125)
Q Consensus 54 li~~AY~sI~~~~~a~~Lgl~~ 75 (125)
..++-|...+++++|+-.|+|.
T Consensus 21 f~e~G~~~~s~~~IA~~agvs~ 42 (202)
T TIGR03613 21 FSRFGFHGTSLEQIAELAGVSK 42 (202)
T ss_pred HHHhCcccCCHHHHHHHhCCCH
Confidence 4578899999999999999986
No 263
>PF10108 DNA_pol_B_exo2: Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; InterPro: IPR019288 This entry represents various prokaryotic 3'-5' exonucleases and hypothetical proteins.
Probab=25.19 E-value=77 Score=23.71 Aligned_cols=28 Identities=18% Similarity=0.278 Sum_probs=20.1
Q ss_pred CCcchHHHHHHhCCCH------HHHHHHHHhcCC
Q psy9207 60 SSIPNTSLSEFLGVTE------QEAAAIAQAEGW 87 (125)
Q Consensus 60 ~sI~~~~~a~~Lgl~~------~e~~~~~~~~GW 87 (125)
.+.|++.+|++||+++ +++.+...+..|
T Consensus 115 ~~~sLd~la~~lgiPgK~~idGs~V~~~y~~g~i 148 (209)
T PF10108_consen 115 ARTSLDELAALLGIPGKDDIDGSQVAELYQEGDI 148 (209)
T ss_pred ccCCHHHHHHHcCCCCCCCCCHHHHHHHHHcCCH
Confidence 5899999999999963 555555444333
No 264
>PF08454 RIH_assoc: RyR and IP3R Homology associated; InterPro: IPR013662 This eukaryotic domain is found in ryanodine receptors (RyR) and inositol 1, 4, 5-trisphosphate receptors (IP3R) which together form a superfamily of homotetrameric ligand-gated intracellular Ca2+ channels []. There seems to be no known function for this domain []. Also see the IP3-binding domain IPR000699 from INTERPRO and IPR003608 from INTERPRO.
Probab=25.11 E-value=2.1e+02 Score=18.92 Aligned_cols=29 Identities=14% Similarity=0.131 Sum_probs=24.6
Q ss_pred hHHHHHHHHHHHHHcCCchHHHHHhccCC
Q psy9207 4 PEIGQVWEVGKHLWNGNYPSIYSTLKRTW 32 (125)
Q Consensus 4 ~~l~~~~~l~~~l~~~~y~~v~~~~~~~~ 32 (125)
..+..+.++.|.|-+|.|..+=..++..+
T Consensus 8 ~~~~~ilr~LQLlCEghn~~lQnylR~Q~ 36 (109)
T PF08454_consen 8 EIIQRILRFLQLLCEGHNLDLQNYLRQQP 36 (109)
T ss_pred HHHHHHHHHHHHHHCcCCHHHHHHHhcCC
Confidence 34678899999999999999988888744
No 265
>cd03568 VHS_STAM VHS domain family, STAM subfamily; members include STAM (Signal Transducing Adaptor Molecule), EAST (EGFR-associated protein with SH3 and TAM domains) and Hbp (Hrs-binding protein). Collectively, they are referred to as STAM. All STAMs have at their N-termini a VHS domain, which is involved in cytokine-mediated intracellular signal transduction and has a superhelical structure similar to the structure of ARM (Armadillo) repeats, followed by a SH3 (Src homology 3) domain, a well-established protein-protein interaction domain. At the C-termini of most vertebrate STAMS, an ITAM (Immunoreceptor Tyrosine-based Activation) motif is present, which mediates the binding of HRS (hepatocyte growth factor-regulated tyrosine kinase substrate) in endocytic and exocytic machineries.
Probab=25.08 E-value=1.2e+02 Score=21.03 Aligned_cols=76 Identities=4% Similarity=0.058 Sum_probs=47.3
Q ss_pred HHHHHHHHHcCCchHHHHHhcc-CCcHHHHHHHHH-HHHHHHHHHHHHHHHhcCCcchHHHHHHhCCC-HHHHHHHHHhc
Q psy9207 9 VWEVGKHLWNGNYPSIYSTLKR-TWSDDIAHIMKA-LQDEVQKRAISLISKAYSSIPNTSLSEFLGVT-EQEAAAIAQAE 85 (125)
Q Consensus 9 ~~~l~~~l~~~~y~~v~~~~~~-~~s~~~~~~i~~-l~~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~-~~e~~~~~~~~ 85 (125)
.+.|...++++.=..|+..+.+ ..-+.+..++.. ....||++++.+|..=+.... ..-+++ -.++-.....+
T Consensus 57 AL~LLe~~vkNCG~~fh~evask~Fl~eL~kl~~~~~~~~Vk~kil~li~~W~~~f~-----~~~~l~~i~~~y~~L~~~ 131 (144)
T cd03568 57 ALTLLDACAENCGKRFHQEVASRDFTQELKKLINDRVHPTVKEKLREVVKQWADEFK-----NDPSLSLMSDLYKKLKNE 131 (144)
T ss_pred HHHHHHHHHHHCCHHHHHHHhhHHHHHHHHHHhcccCCHHHHHHHHHHHHHHHHHhC-----CCcccHHHHHHHHHHHHc
Confidence 4566667777777777777766 555666666655 677899999888766433332 111222 25566666667
Q ss_pred CCee
Q psy9207 86 GWTV 89 (125)
Q Consensus 86 GW~~ 89 (125)
|..+
T Consensus 132 G~~f 135 (144)
T cd03568 132 GPDL 135 (144)
T ss_pred CCCC
Confidence 7766
No 266
>PHA01083 hypothetical protein
Probab=25.05 E-value=1.5e+02 Score=21.03 Aligned_cols=35 Identities=17% Similarity=0.274 Sum_probs=26.5
Q ss_pred HHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHHH
Q psy9207 49 KRAISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQ 83 (125)
Q Consensus 49 ~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~ 83 (125)
++.++...+++..++-.++|.-||++++-+-++=.
T Consensus 4 nkLLda~K~a~~~~sdkqLA~~LGVs~q~IS~~R~ 38 (149)
T PHA01083 4 NKLLDAYKKAKNYVQYKQIAHDLGVSPQKISKMRT 38 (149)
T ss_pred HHHHHHHHHHHhhccHHHHHHHhCCCHHHHHHHHc
Confidence 45667777888888888888888888766665543
No 267
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=25.01 E-value=1.1e+02 Score=23.22 Aligned_cols=27 Identities=22% Similarity=0.343 Sum_probs=18.3
Q ss_pred cchHHHHHHhCCCHHHHHHHHHhcCCe
Q psy9207 62 IPNTSLSEFLGVTEQEAAAIAQAEGWT 88 (125)
Q Consensus 62 I~~~~~a~~Lgl~~~e~~~~~~~~GW~ 88 (125)
.++.++|.-.|.|..-+..||++.|-+
T Consensus 47 ~si~~lA~~~~vS~aTi~Rf~kkLGf~ 73 (292)
T PRK11337 47 TALKDIAEALAVSEAMIVKVAKKLGFS 73 (292)
T ss_pred cCHHHHHHHhCCChHHHHHHHHHcCCC
Confidence 466677777777777777777776544
No 268
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=24.99 E-value=2.2e+02 Score=19.04 Aligned_cols=40 Identities=10% Similarity=0.168 Sum_probs=27.9
Q ss_pred HHHHHHHHhcCCcchHHHHHHhCCCHHH---HHHHHHhcCCee
Q psy9207 50 RAISLISKAYSSIPNTSLSEFLGVTEQE---AAAIAQAEGWTV 89 (125)
Q Consensus 50 ~~~~li~~AY~sI~~~~~a~~Lgl~~~e---~~~~~~~~GW~~ 89 (125)
.++..|...-..++..+++..+|++..- +++-..++||..
T Consensus 35 ~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~ 77 (144)
T PRK03573 35 VTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLEEKGLIS 77 (144)
T ss_pred HHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHHCCCEe
Confidence 3444554443467889999999998644 444556689987
No 269
>COG4388 Mu-like prophage I protein [General function prediction only]
Probab=24.93 E-value=70 Score=25.57 Aligned_cols=21 Identities=33% Similarity=0.632 Sum_probs=16.8
Q ss_pred HHHHHhCCCHHHHHHHHHhcC
Q psy9207 66 SLSEFLGVTEQEAAAIAQAEG 86 (125)
Q Consensus 66 ~~a~~Lgl~~~e~~~~~~~~G 86 (125)
.+|++||+|++|..+.-.+.|
T Consensus 337 aaAklLGiSeeef~K~kE~~~ 357 (357)
T COG4388 337 AAAKLLGISEEEFAKAKESEG 357 (357)
T ss_pred HHHHHhCcCHHHHHHHHhhcC
Confidence 378999999999888766544
No 270
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=24.89 E-value=1.8e+02 Score=20.32 Aligned_cols=32 Identities=16% Similarity=0.532 Sum_probs=22.7
Q ss_pred HHHHHHHhcCCcchHH---HHHHhCCCHHHHHHHH
Q psy9207 51 AISLISKAYSSIPNTS---LSEFLGVTEQEAAAIA 82 (125)
Q Consensus 51 ~~~li~~AY~sI~~~~---~a~~Lgl~~~e~~~~~ 82 (125)
++..+...|.-||.+. +|..||++..++-..+
T Consensus 27 ~L~~vQ~~~g~ip~~~~~~iA~~l~v~~~~v~~v~ 61 (154)
T PRK07539 27 ALKIVQEQRGWVPDEAIEAVADYLGMPAIDVEEVA 61 (154)
T ss_pred HHHHHHHHhCCCCHHHHHHHHHHhCcCHHHHHHHH
Confidence 4445667788888765 7899999986655443
No 271
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=24.81 E-value=2.1e+02 Score=21.41 Aligned_cols=47 Identities=17% Similarity=0.201 Sum_probs=31.4
Q ss_pred HHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHHH---hcCCeec--Cceee
Q psy9207 48 QKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQ---AEGWTVD--KVYTQ 95 (125)
Q Consensus 48 R~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~---~~GW~~d--~~~~~ 95 (125)
+++|+..+. ....++.++++.+||+|..-+..... ++|.-.- |+.+.
T Consensus 6 ~~~Il~~l~-~~~~~~~~eLa~~l~VS~~TiRRdL~~L~~~~~l~r~~Gga~~ 57 (240)
T PRK10411 6 QQAIVDLLL-NHTSLTTEALAEQLNVSKETIRRDLNELQTQGKILRNHGRAKY 57 (240)
T ss_pred HHHHHHHHH-HcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecCeEEE
Confidence 345666665 57899999999999999754444333 3576553 55443
No 272
>KOG0259|consensus
Probab=24.59 E-value=1.1e+02 Score=25.49 Aligned_cols=39 Identities=15% Similarity=0.323 Sum_probs=27.7
Q ss_pred HHhcCCeec-----------CceeeccCCCCCCCCCCC-ChHHHHHHhhHHHh
Q psy9207 82 AQAEGWTVD-----------KVYTQPVKKPEEYATPNI-TDDQLYILTQYVSF 122 (125)
Q Consensus 82 ~~~~GW~~d-----------~~~~~p~~~~~~~~~~~~-~~~ql~~Lt~~v~f 122 (125)
.-+++|++| +..++..+|.| ..... +.++|+++.++-..
T Consensus 180 LPe~~weIDL~~veal~DENT~AivviNP~N--PcGnVys~~HL~kiae~A~k 230 (447)
T KOG0259|consen 180 LPEKDWEIDLDGVEALADENTVAIVVINPNN--PCGNVYSEDHLKKIAETAKK 230 (447)
T ss_pred cCcccceechHHHHHhhccCeeEEEEeCCCC--CCcccccHHHHHHHHHHHHH
Confidence 456899986 23456667777 55555 99999999887543
No 273
>KOG2807|consensus
Probab=24.52 E-value=57 Score=26.37 Aligned_cols=63 Identities=21% Similarity=0.328 Sum_probs=40.7
Q ss_pred HHHHHcCCchHHHHHhccCCcHHHHHHHHHHHHH-HHHHHHH--------HHHHhcCCcchHHHHHHhCCCH
Q psy9207 13 GKHLWNGNYPSIYSTLKRTWSDDIAHIMKALQDE-VQKRAIS--------LISKAYSSIPNTSLSEFLGVTE 75 (125)
Q Consensus 13 ~~~l~~~~y~~v~~~~~~~~s~~~~~~i~~l~~~-vR~~~~~--------li~~AY~sI~~~~~a~~Lgl~~ 75 (125)
+.+-|++.|...|..++.+=+..+...++.+... -|++.+. .|..-|--|..+++..=-.|.+
T Consensus 9 ~~y~WE~eY~RsWe~l~ede~Gsl~~~ia~~v~~~krk~~~~~~t~~r~GiiRhl~iviD~S~am~e~Df~P 80 (378)
T KOG2807|consen 9 KGYTWEGEYKRSWEILKEDESGSLEKSIASIVNEAKRKRRLRYSTRIRKGIIRHLYIVIDCSRAMEEKDFRP 80 (378)
T ss_pred cccchhhhhhhhHHHhhcccccchHHHHHHHHHHHHHhhhhhccchhhhhhheeEEEEEEhhhhhhhccCCc
Confidence 5678999999999999986666777766655433 3333333 3344455666666665555543
No 274
>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=24.47 E-value=2.2e+02 Score=18.83 Aligned_cols=39 Identities=10% Similarity=0.222 Sum_probs=27.2
Q ss_pred HHHHHHHhc-CCcchHHHHHHhCCCHHHHHHH---HHhcCCee
Q psy9207 51 AISLISKAY-SSIPNTSLSEFLGVTEQEAAAI---AQAEGWTV 89 (125)
Q Consensus 51 ~~~li~~AY-~sI~~~~~a~~Lgl~~~e~~~~---~~~~GW~~ 89 (125)
++..++++. ..++.+++|..+|++..-+.+. ..+.|+-.
T Consensus 14 ~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~ 56 (130)
T TIGR02944 14 VLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLSLAGIVT 56 (130)
T ss_pred HHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHHHCCcEE
Confidence 444555543 3589999999999997555444 55578875
No 275
>PRK13749 transcriptional regulator MerD; Provisional
Probab=24.46 E-value=2.3e+02 Score=19.15 Aligned_cols=49 Identities=16% Similarity=0.068 Sum_probs=30.7
Q ss_pred cchHHHHHHhCCCHHHHHHHHHhcCCeecCceeeccCCCCCCCCCCC-ChHHHHHHhhH
Q psy9207 62 IPNTSLSEFLGVTEQEAAAIAQAEGWTVDKVYTQPVKKPEEYATPNI-TDDQLYILTQY 119 (125)
Q Consensus 62 I~~~~~a~~Lgl~~~e~~~~~~~~GW~~d~~~~~p~~~~~~~~~~~~-~~~ql~~Lt~~ 119 (125)
.++.++|+..|+|..-+.-|-. -+.+-|...+. ..-.. ++.++..|.-+
T Consensus 4 ~tIgelA~~~gvS~~tiR~YE~-------~GLl~p~~r~~--~gyR~Y~~~~l~rL~~I 53 (121)
T PRK13749 4 YTVSRLALDAGVSVHIVRDYLL-------RGLLRPVACTT--GGYGLFDDAALQRLCFV 53 (121)
T ss_pred CcHHHHHHHHCCCHHHHHHHHH-------CCCCCCCCcCC--CCCccCCHHHHHHHHHH
Confidence 5789999999999877766544 23444432222 22233 88888877443
No 276
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=24.38 E-value=2e+02 Score=21.67 Aligned_cols=40 Identities=15% Similarity=0.225 Sum_probs=30.6
Q ss_pred HHHHHHHHhcCCcchHHHHHHhCCCHHHH---HHHHHhcCCee
Q psy9207 50 RAISLISKAYSSIPNTSLSEFLGVTEQEA---AAIAQAEGWTV 89 (125)
Q Consensus 50 ~~~~li~~AY~sI~~~~~a~~Lgl~~~e~---~~~~~~~GW~~ 89 (125)
+|+.+++..=..+++.+++..||++..-+ .+...+.||-.
T Consensus 15 ~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~~~g~v~ 57 (263)
T PRK09834 15 MVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQEEGYVR 57 (263)
T ss_pred HHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 56777776655699999999999997554 45556689986
No 277
>COG2049 DUR1 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]
Probab=24.29 E-value=1.9e+02 Score=21.86 Aligned_cols=87 Identities=11% Similarity=0.175 Sum_probs=55.0
Q ss_pred hHHHHHHHHHHHHHcCCchHHHHHhcc--------C-CcHHHHHHHHHHHHHHHHHHHH--------HHHHhcC---Ccc
Q psy9207 4 PEIGQVWEVGKHLWNGNYPSIYSTLKR--------T-WSDDIAHIMKALQDEVQKRAIS--------LISKAYS---SIP 63 (125)
Q Consensus 4 ~~l~~~~~l~~~l~~~~y~~v~~~~~~--------~-~s~~~~~~i~~l~~~vR~~~~~--------li~~AY~---sI~ 63 (125)
.-...+|++.++|.+..++.|-...-+ + ..-....+.+.|+....+-.+. -|.-+|. --.
T Consensus 20 ~~~~~i~al~~~l~~~~~~gvve~vP~~~sllv~~d~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~IeIPV~Y~~~~GpD 99 (223)
T COG2049 20 ELQRRIWALARALEAAPLPGVVEIVPGYRSLLVIYDPPRLDPQELLERLRALWEEIEALEAAGIRLIEIPVVYGGEYGPD 99 (223)
T ss_pred HHHHHHHHHHHHHHhcCCCCeEEecccceeEEEEecccccCHHHHHHHHHHHHhchhhhccccCCEEEEeeEeCCCCCCC
Confidence 345789999999999998887554432 0 0111122223222222111111 1234676 777
Q ss_pred hHHHHHHhCCCHHHHHHHHHhcCCeec
Q psy9207 64 NTSLSEFLGVTEQEAAAIAQAEGWTVD 90 (125)
Q Consensus 64 ~~~~a~~Lgl~~~e~~~~~~~~GW~~d 90 (125)
+.++|+.-|+|.+|+++.-.+..|.+-
T Consensus 100 L~~va~~~gls~~evI~~Hs~~~Y~V~ 126 (223)
T COG2049 100 LAEVARHNGLSVEEVIELHSSTEYRVY 126 (223)
T ss_pred HHHHHHHcCCCHHHHHHHhcCCceEEE
Confidence 889999999999999999888888883
No 278
>PHA02535 P terminase ATPase subunit; Provisional
Probab=24.21 E-value=1.1e+02 Score=26.63 Aligned_cols=42 Identities=21% Similarity=0.365 Sum_probs=35.5
Q ss_pred HHHHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHHHhcCCee
Q psy9207 45 DEVQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQAEGWTV 89 (125)
Q Consensus 45 ~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~~~GW~~ 89 (125)
.-+|.++..+.-+ --++.++|..||++..-+-.++.+-+|.-
T Consensus 5 ~EfK~~Av~Ly~~---G~sv~eIA~~LGv~~~Tl~~W~kr~~w~~ 46 (581)
T PHA02535 5 DDVRRAAKFLYWQ---GWTVAEIAEELGLKSRTIYSWKERDGWRD 46 (581)
T ss_pred HHHHHHHHHHHHc---CCCHHHHHHHhCCChhHHHHHhccccccc
Confidence 3477777777766 67899999999999999999999999974
No 279
>PRK11569 transcriptional repressor IclR; Provisional
Probab=23.96 E-value=1.9e+02 Score=21.95 Aligned_cols=40 Identities=18% Similarity=0.349 Sum_probs=31.9
Q ss_pred HHHHHHHHhcCCcchHHHHHHhCCCHHHHHHH---HHhcCCee
Q psy9207 50 RAISLISKAYSSIPNTSLSEFLGVTEQEAAAI---AQAEGWTV 89 (125)
Q Consensus 50 ~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~---~~~~GW~~ 89 (125)
+|+++++++=..+++.+++.-+|++..-+-.+ ..+.||-.
T Consensus 32 ~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~~G~l~ 74 (274)
T PRK11569 32 KLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQQGFVR 74 (274)
T ss_pred HHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 57788888777799999999999997665554 45579986
No 280
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=23.89 E-value=98 Score=20.64 Aligned_cols=21 Identities=14% Similarity=0.366 Sum_probs=15.5
Q ss_pred CcchHHHHHHhCCCHHHHHHH
Q psy9207 61 SIPNTSLSEFLGVTEQEAAAI 81 (125)
Q Consensus 61 sI~~~~~a~~Lgl~~~e~~~~ 81 (125)
.+|.+.+|.|||.+..-+.+|
T Consensus 57 ~lSQ~vFA~~L~vs~~Tv~~W 77 (104)
T COG2944 57 GLSQPVFARYLGVSVSTVRKW 77 (104)
T ss_pred CCCHHHHHHHHCCCHHHHHHH
Confidence 467777888888887766654
No 281
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=23.76 E-value=70 Score=18.91 Aligned_cols=13 Identities=31% Similarity=0.611 Sum_probs=7.6
Q ss_pred HHHHHhCCCHHHH
Q psy9207 66 SLSEFLGVTEQEA 78 (125)
Q Consensus 66 ~~a~~Lgl~~~e~ 78 (125)
..|++||++++++
T Consensus 50 ~Ya~~Lgld~~~l 62 (62)
T PF13413_consen 50 KYARFLGLDPDEL 62 (62)
T ss_dssp HHHHHTT--HHHH
T ss_pred HHHHHhCcCcccC
Confidence 4577888887664
No 282
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator. This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=23.73 E-value=2.3e+02 Score=18.85 Aligned_cols=19 Identities=16% Similarity=0.092 Sum_probs=15.5
Q ss_pred chHHHHHHhCCCHHHHHHH
Q psy9207 63 PNTSLSEFLGVTEQEAAAI 81 (125)
Q Consensus 63 ~~~~~a~~Lgl~~~e~~~~ 81 (125)
++.++|+.+|++..-+.-|
T Consensus 1 ~I~e~a~~~gvs~~tlR~Y 19 (124)
T TIGR02051 1 TIGELAKAAGVNVETIRYY 19 (124)
T ss_pred CHHHHHHHHCcCHHHHHHH
Confidence 4678999999998877665
No 283
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=23.70 E-value=2.4e+02 Score=19.04 Aligned_cols=33 Identities=9% Similarity=0.199 Sum_probs=24.4
Q ss_pred HhcCCcchHHHHHHhCCCHHHHHHHH---HhcCCee
Q psy9207 57 KAYSSIPNTSLSEFLGVTEQEAAAIA---QAEGWTV 89 (125)
Q Consensus 57 ~AY~sI~~~~~a~~Lgl~~~e~~~~~---~~~GW~~ 89 (125)
..-..++++++|..||++..-+...+ .+.||-.
T Consensus 18 ~~~~~~~~~ela~~l~vs~~svs~~l~~L~~~Gli~ 53 (142)
T PRK03902 18 EEKGYARVSDIAEALSVHPSSVTKMVQKLDKDEYLI 53 (142)
T ss_pred hcCCCcCHHHHHHHhCCChhHHHHHHHHHHHCCCEE
Confidence 34466788999999999975555544 5579876
No 284
>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=23.70 E-value=1.4e+02 Score=17.56 Aligned_cols=29 Identities=24% Similarity=0.296 Sum_probs=23.0
Q ss_pred hcCCcchHHHHHHhCCCHHHHHHHHHhcC
Q psy9207 58 AYSSIPNTSLSEFLGVTEQEAAAIAQAEG 86 (125)
Q Consensus 58 AY~sI~~~~~a~~Lgl~~~e~~~~~~~~G 86 (125)
+.-=+|..-+++-||++.+-+...+.+.|
T Consensus 10 ~~P~Vsa~mva~~L~vT~~~A~~li~eLg 38 (54)
T PF11972_consen 10 SRPLVSAPMVAKELGVTPQAAQRLIAELG 38 (54)
T ss_pred hCccccHHHHHHHhCCCHHHHHHHHHHhh
Confidence 45567888999999999988888776654
No 285
>PF03428 RP-C: Replication protein C N-terminal domain; InterPro: IPR005090 Proteins in this group have homology with the RepC protein of Agrobacterium Ri and Ti plasmids []. They may be involved in plasmid replication and stabilisation functions.
Probab=23.56 E-value=66 Score=23.36 Aligned_cols=38 Identities=11% Similarity=0.246 Sum_probs=26.3
Q ss_pred hHHHHHHhCCCH------HHHHHHHHhcCCeec-CceeeccCCCC
Q psy9207 64 NTSLSEFLGVTE------QEAAAIAQAEGWTVD-KVYTQPVKKPE 101 (125)
Q Consensus 64 ~~~~a~~Lgl~~------~e~~~~~~~~GW~~d-~~~~~p~~~~~ 101 (125)
+..++..||+++ +-++.|.....|+=+ .-+|+|.|..-
T Consensus 32 l~~a~~~lgl~~~~l~vL~aLls~~~~~d~~~~~~piVfpSN~~L 76 (177)
T PF03428_consen 32 LKEARPALGLSDRALAVLDALLSFTPPDDWEPGRRPIVFPSNAQL 76 (177)
T ss_pred HHHHHHhcCCChhHHHHHHHHHHhCCcccccCCCCceeecCHHHH
Confidence 456788999986 445666666788665 44888876543
No 286
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=23.50 E-value=1.8e+02 Score=20.50 Aligned_cols=33 Identities=18% Similarity=0.233 Sum_probs=25.0
Q ss_pred HHHHHHHHHHHHH-HHhcCCcchHHHHHHhCCCH
Q psy9207 43 LQDEVQKRAISLI-SKAYSSIPNTSLSEFLGVTE 75 (125)
Q Consensus 43 l~~~vR~~~~~li-~~AY~sI~~~~~a~~Lgl~~ 75 (125)
-+..+.+-+..++ ++-|..++++++|+-.|+|.
T Consensus 12 ~r~~Il~aa~~lf~~~G~~~~ti~~Ia~~agvsk 45 (213)
T PRK09975 12 TRQELIETAIAQFALRGVSNTTLNDIADAANVTR 45 (213)
T ss_pred HHHHHHHHHHHHHHHcCcccCCHHHHHHHcCCCH
Confidence 3444555555554 78899999999999999985
No 287
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=23.40 E-value=1.9e+02 Score=20.73 Aligned_cols=25 Identities=20% Similarity=0.383 Sum_probs=19.9
Q ss_pred cchHHHHHHhCCCHHHHHHHHHhcC
Q psy9207 62 IPNTSLSEFLGVTEQEAAAIAQAEG 86 (125)
Q Consensus 62 I~~~~~a~~Lgl~~~e~~~~~~~~G 86 (125)
.|+..+|+.||++..-+-.++..+|
T Consensus 173 ~s~~~iak~lgis~~Tv~r~~k~~~ 197 (200)
T PRK13413 173 TSKSEIARKLGVSRTTLARFLKTRG 197 (200)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHhcc
Confidence 5888888999998887777777655
No 288
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=23.40 E-value=73 Score=16.30 Aligned_cols=20 Identities=25% Similarity=0.390 Sum_probs=15.6
Q ss_pred hCCCHHHHHHHHHhcCCeec
Q psy9207 71 LGVTEQEAAAIAQAEGWTVD 90 (125)
Q Consensus 71 Lgl~~~e~~~~~~~~GW~~d 90 (125)
+|++.+++.......||.++
T Consensus 11 mGf~~~~~~~AL~~~~~d~~ 30 (38)
T cd00194 11 MGFSREEARKALRATNNNVE 30 (38)
T ss_pred cCCCHHHHHHHHHHhCCCHH
Confidence 48888888888888888664
No 289
>PHA00675 hypothetical protein
Probab=23.24 E-value=1.6e+02 Score=18.61 Aligned_cols=46 Identities=20% Similarity=0.151 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHHHhcCCee
Q psy9207 42 ALQDEVQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQAEGWTV 89 (125)
Q Consensus 42 ~l~~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~~~GW~~ 89 (125)
.|.+..=++|..+.+ +.-.|...+|.-+|++..-+...+..+.|..
T Consensus 22 KLt~~qV~~IR~l~~--r~G~s~~~IA~~fGVsrstV~~I~~gk~W~~ 67 (78)
T PHA00675 22 KLTDAEVERIRELHE--VEGMSYAVLAEKFEQSKGAIAKICRYERRGQ 67 (78)
T ss_pred ccCHHHHHHHHHHHH--hcCccHHHHHHHhCCCHHHHHHHHccchhhh
Confidence 344444445555544 3344788999999999999999999889975
No 290
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=23.14 E-value=1.3e+02 Score=15.59 Aligned_cols=23 Identities=13% Similarity=0.326 Sum_probs=18.9
Q ss_pred CCcchHHHHHHhCCCHHHHHHHH
Q psy9207 60 SSIPNTSLSEFLGVTEQEAAAIA 82 (125)
Q Consensus 60 ~sI~~~~~a~~Lgl~~~e~~~~~ 82 (125)
...+..++|.-+|++..-+....
T Consensus 25 ~~~~~~~ia~~~~~s~~~i~~~~ 47 (55)
T cd06171 25 EGLSYEEIAEILGISRSTVRQRL 47 (55)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHH
Confidence 88899999999999987665543
No 291
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=22.69 E-value=2.7e+02 Score=19.57 Aligned_cols=47 Identities=11% Similarity=0.094 Sum_probs=28.8
Q ss_pred CcchHHHHHHhCCCHHHHHHHHHhcCCeecCceeeccCCCCCCCCCCC-ChHHHHHHh
Q psy9207 61 SIPNTSLSEFLGVTEQEAAAIAQAEGWTVDKVYTQPVKKPEEYATPNI-TDDQLYILT 117 (125)
Q Consensus 61 sI~~~~~a~~Lgl~~~e~~~~~~~~GW~~d~~~~~p~~~~~~~~~~~~-~~~ql~~Lt 117 (125)
-.++.++|+.+|++..-+.-|.. -+.+.|.+..+ .-.. +++++..|.
T Consensus 11 ~~~IgevAk~~gvs~~TlRyYE~-------~GLi~~~r~~~---g~R~Y~~~~i~~L~ 58 (154)
T PRK15002 11 LLTPGEVAKRSGVAVSALHFYES-------KGLITSIRNSG---NQRRYKRDVLRYVA 58 (154)
T ss_pred cccHHHHHHHHCcCHHHHHHHHH-------CCCCCCccCCC---CCEEECHHHHHHHH
Confidence 36889999999999877766554 34444422221 1122 666666663
No 292
>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=22.59 E-value=1.5e+02 Score=16.43 Aligned_cols=41 Identities=17% Similarity=0.284 Sum_probs=27.4
Q ss_pred HHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHH---HHhcCCee
Q psy9207 47 VQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAI---AQAEGWTV 89 (125)
Q Consensus 47 vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~---~~~~GW~~ 89 (125)
.+..++..+.. .. ++.++++..+|++...+... ..+.||-.
T Consensus 8 ~~~~il~~l~~-~~-~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~ 51 (78)
T cd00090 8 TRLRILRLLLE-GP-LTVSELAERLGLSQSTVSRHLKKLEEAGLVE 51 (78)
T ss_pred HHHHHHHHHHH-CC-cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeE
Confidence 34455555444 23 99999999999997554444 45578876
No 293
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=22.52 E-value=1.4e+02 Score=19.24 Aligned_cols=50 Identities=14% Similarity=0.118 Sum_probs=30.3
Q ss_pred chHHHHHHhCCCHHHHHHHHHhcCCeecCceeeccCCCCCCCCCCC-ChHHHHHHhhHHH
Q psy9207 63 PNTSLSEFLGVTEQEAAAIAQAEGWTVDKVYTQPVKKPEEYATPNI-TDDQLYILTQYVS 121 (125)
Q Consensus 63 ~~~~~a~~Lgl~~~e~~~~~~~~GW~~d~~~~~p~~~~~~~~~~~~-~~~ql~~Lt~~v~ 121 (125)
++.++|..+|++..-+.-|.... +.+.|.+..+ .-.. +.+++.+|-.+..
T Consensus 2 ti~EvA~~~gVs~~tLR~ye~~~------gli~p~r~~~---g~R~Yt~~di~~l~~I~~ 52 (99)
T cd04765 2 SIGEVAEILGLPPHVLRYWETEF------PQLKPVKRAG---GRRYYRPKDVELLLLIKH 52 (99)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHc------CCCCCcCCCC---CCeeeCHHHHHHHHHHHH
Confidence 57899999999998888765531 2223322111 1122 7777777766554
No 294
>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator HspR and related proteins, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=22.41 E-value=2.2e+02 Score=18.14 Aligned_cols=22 Identities=23% Similarity=0.371 Sum_probs=18.5
Q ss_pred cchHHHHHHhCCCHHHHHHHHH
Q psy9207 62 IPNTSLSEFLGVTEQEAAAIAQ 83 (125)
Q Consensus 62 I~~~~~a~~Lgl~~~e~~~~~~ 83 (125)
.++.++|..+|++..-+..+..
T Consensus 2 ~~i~eva~~~gVs~~tLR~ye~ 23 (98)
T cd01279 2 YPISVAAELLGIHPQTLRVYDR 23 (98)
T ss_pred cCHHHHHHHHCcCHHHHHHHHH
Confidence 3688999999999988887754
No 295
>PHA01976 helix-turn-helix protein
Probab=22.41 E-value=1.2e+02 Score=17.39 Aligned_cols=25 Identities=16% Similarity=0.062 Sum_probs=18.9
Q ss_pred hcCCcchHHHHHHhCCCHHHHHHHH
Q psy9207 58 AYSSIPNTSLSEFLGVTEQEAAAIA 82 (125)
Q Consensus 58 AY~sI~~~~~a~~Lgl~~~e~~~~~ 82 (125)
.-..++..++|..+|++..-+-.+-
T Consensus 12 ~~~glt~~~lA~~~gvs~~~v~~~e 36 (67)
T PHA01976 12 NARAWSAPELSRRAGVRHSLIYDFE 36 (67)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHH
Confidence 3456889999999999976666543
No 296
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=22.34 E-value=2.2e+02 Score=18.04 Aligned_cols=49 Identities=12% Similarity=0.142 Sum_probs=29.2
Q ss_pred chHHHHHHhCCCHHHHHHHHHhcCCeecCceeeccCCCCCCCCCCC-ChHHHHHHhhHH
Q psy9207 63 PNTSLSEFLGVTEQEAAAIAQAEGWTVDKVYTQPVKKPEEYATPNI-TDDQLYILTQYV 120 (125)
Q Consensus 63 ~~~~~a~~Lgl~~~e~~~~~~~~GW~~d~~~~~p~~~~~~~~~~~~-~~~ql~~Lt~~v 120 (125)
++.++|..+|++..-+.-|.. -+.+.|..... ..-.. +++++..|..+.
T Consensus 2 ~i~eva~~~gvs~~tlR~ye~-------~Gll~p~~r~~--~gyR~Y~~~~l~~l~~I~ 51 (96)
T cd04788 2 KIGELARRTGLSVRTLHHYDH-------IGLLSPSQRTE--GGHRLYDRADIRRLHQII 51 (96)
T ss_pred CHHHHHHHHCcCHHHHHHHHH-------CCCCCCCccCC--CCceeeCHHHHHHHHHHH
Confidence 578999999999877766544 33444432111 11122 777777665443
No 297
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=22.34 E-value=2.2e+02 Score=18.01 Aligned_cols=30 Identities=7% Similarity=-0.011 Sum_probs=23.9
Q ss_pred CCcchHHHHHHhCCCHHHHHHHHHhc-CCee
Q psy9207 60 SSIPNTSLSEFLGVTEQEAAAIAQAE-GWTV 89 (125)
Q Consensus 60 ~sI~~~~~a~~Lgl~~~e~~~~~~~~-GW~~ 89 (125)
..++++++|..+|+|..-+...+++. |-+.
T Consensus 20 ~~~~~~~lA~~~~~S~~~l~r~f~~~~g~s~ 50 (107)
T PRK10219 20 QPLNIDVVAKKSGYSKWYLQRMFRTVTHQTL 50 (107)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHCcCH
Confidence 45899999999999988877766654 7665
No 298
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=22.27 E-value=1.9e+02 Score=21.55 Aligned_cols=39 Identities=13% Similarity=0.187 Sum_probs=29.5
Q ss_pred HHHHHHHHhcCCcchHHHHHHhCCCHHHH---HHHHHhcCCee
Q psy9207 50 RAISLISKAYSSIPNTSLSEFLGVTEQEA---AAIAQAEGWTV 89 (125)
Q Consensus 50 ~~~~li~~AY~sI~~~~~a~~Lgl~~~e~---~~~~~~~GW~~ 89 (125)
+|+++++.. ..+++.++++-+|++..-+ ..-..+.||-.
T Consensus 18 ~IL~~l~~~-~~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~ 59 (257)
T PRK15090 18 GILQALGEE-REIGITELSQRVMMSKSTVYRFLQTMKTLGYVA 59 (257)
T ss_pred HHHHHhhcC-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 566777654 6799999999999997554 44455689975
No 299
>PF00946 Mononeg_RNA_pol: Mononegavirales RNA dependent RNA polymerase ; InterPro: IPR014023 RNA-directed RNA polymerase (RdRp) (2.7.7.48 from EC) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage [, ]. It catalyses synthesis of the RNA strand complementary to a given RNA template, but the precise molecular mechanism remains unclear. The postulated RNA replication process is a two-step mechanism. First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer-independent (de novo) mechanism. The de novo initiation consists in the addition of a nucleotide tri-phosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product []. All the RNA-directed RNA polymerases, and many DNA-directed polymerases, employ a fold whose organisation has been likened to the shape of a right hand with three subdomains termed fingers, palm and thumb []. Only the catalytic palm subdomain, composed of a four-stranded antiparallel beta-sheet with two alpha-helices, is well conserved among all of these enzymes. In RdRp, the palm subdomain comprises three well conserved motifs (A, B and C). Motif A (D-x(4,5)-D) and motif C (GDD) are spatially juxtaposed; the Asp residues of these motifs are implied in the binding of Mg2+ and/or Mn2+. The Asn residue of motif B is involved in selection of ribonucleoside triphosphates over dNTPs and thus determines whether RNA is synthesised rather than DNA []. The domain organisation [] and the 3D structure of the catalytic centre of a wide range of RdPp's, even those with a low overall sequence homology, are conserved. The catalytic centre is formed by several motifs containing a number of conserved amino acid residues. There are 4 superfamilies of viruses that cover all RNA containing viruses with no DNA stage: Viruses containing positive-strand RNA or double-strand RNA, except retroviruses and Birnaviridae: viral RNA-directed RNA polymerases including all positive-strand RNA viruses with no DNA stage, double-strand RNA viruses, and the Cystoviridae, Reoviridae, Hypoviridae, Partitiviridae, Totiviridae families. Mononegavirales (negative-strand RNA viruses with non-segmented genomes). Negative-strand RNA viruses with segmented genomes, i.e. Orthomyxoviruses (including influenza A, B, and C viruses, Thogotoviruses, and the infectious salmon anemia virus), Arenaviruses, Bunyaviruses, Hantaviruses, Nairoviruses, Phleboviruses, Tenuiviruses and Tospoviruses. Birnaviridae family of dsRNA viruses. The RNA-directed RNA polymerases in the first of the above superfamilies can be divided into the following three subgroups: All positive-strand RNA eukaryotic viruses with no DNA stage. All RNA-containing bacteriophages -there are two families of RNA-containing bacteriophages: Leviviridae (positive ssRNA phages) and Cystoviridae (dsRNA phages). Reoviridae family of dsRNA viruses. This entry represents the catalytic domain RNA-directed RNA polymerase.; GO: 0003968 RNA-directed RNA polymerase activity, 0004482 mRNA (guanine-N7-)-methyltransferase activity, 0005524 ATP binding, 0006370 mRNA capping, 0005737 cytoplasm, 0019012 virion
Probab=22.26 E-value=1.3e+02 Score=27.83 Aligned_cols=50 Identities=12% Similarity=0.175 Sum_probs=35.6
Q ss_pred hHHHHHHHHHHHHHcCCchHHHHHhcc-CC--------cHHHHHHHHHHHHHHHHHHHH
Q psy9207 4 PEIGQVWEVGKHLWNGNYPSIYSTLKR-TW--------SDDIAHIMKALQDEVQKRAIS 53 (125)
Q Consensus 4 ~~l~~~~~l~~~l~~~~y~~v~~~~~~-~~--------s~~~~~~i~~l~~~vR~~~~~ 53 (125)
+.+..+|.++..+-..--+..|..++. ++ .+...++...|...+++++.+
T Consensus 249 ~~~~~l~~~gD~~l~~~Gn~~Y~~ik~lE~l~~~~lql~~~~~~~~~~F~~~~~~~~~~ 307 (1072)
T PF00946_consen 249 SRIEKLYRLGDSLLSRLGNEGYDVIKLLEPLCNGRLQLADESRPLIGRFLNFILNEIQE 307 (1072)
T ss_pred HHHHHHHHHHHHHHHHcChhHHHHHHHHHHHHHHHHHhcCCcccchHHHHHHHHHHHHH
Confidence 456889999999988888888888875 32 233444556677777777766
No 300
>PF01257 2Fe-2S_thioredx: Thioredoxin-like [2Fe-2S] ferredoxin; InterPro: IPR002023 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. Among the many polypeptide subunits that make up complex I, there is one with a molecular weight of 24 kDa (in mammals), which is a component of the iron-sulphur (IP) fragment of the enzyme. It seems to bind a 2Fe-2S iron-sulphur cluster. The 24 kDa subunit is nuclear encoded, as a precursor form with a transit peptide in mammals and in Neurospora crassa. There is a highly conserved region located in the central section of this subunit that contains two conserved cysteines, that are probably involved in the binding of the 2Fe-2S centre. The 24 kDa subunit is highly similar to [, ]: Subunit E of Escherichia coli NADH-ubiquinone oxidoreductase (gene nuoE) Subunit NQO2 of Paracoccus denitrificans NADH-ubiquinone oxidoreductase ; GO: 0016491 oxidoreductase activity, 0051287 NAD binding, 0055114 oxidation-reduction process; PDB: 1M2D_A 1M2A_B 1F37_B 1M2B_B 2FUG_B 3M9S_B 3IAM_B 3IAS_K 2YBB_2 3I9V_B ....
Probab=22.19 E-value=1.9e+02 Score=19.84 Aligned_cols=31 Identities=26% Similarity=0.507 Sum_probs=17.7
Q ss_pred HHHHHhcCCcchHH---HHHHhCCCHHHHHHHHH
Q psy9207 53 SLISKAYSSIPNTS---LSEFLGVTEQEAAAIAQ 83 (125)
Q Consensus 53 ~li~~AY~sI~~~~---~a~~Lgl~~~e~~~~~~ 83 (125)
..+...|.-||.+. +|..||++..++...+.
T Consensus 20 ~~~Q~~~g~i~~~~~~~iA~~l~i~~~~v~~v~t 53 (145)
T PF01257_consen 20 HEVQEEYGYIPEEALEEIAEALGIPPAEVYGVAT 53 (145)
T ss_dssp HHHHHHHSS--HHHHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHcCCCCHHHHHHHHHHHCCCHHHHHHHHH
Confidence 34455577777554 78888888766655443
No 301
>PF01465 GRIP: GRIP domain; InterPro: IPR000237 The GRIP (golgin-97, RanBP2alpha,Imh1p and p230/golgin-245) domain [, , ] is found in many large coiled-coil proteins. It has been shown to be sufficient for targeting to the Golgi []. The GRIP domain contains a completely conserved tyrosine residue.; GO: 0005515 protein binding, 0000042 protein targeting to Golgi; PDB: 1R4A_H 1UPT_B.
Probab=22.16 E-value=1.1e+02 Score=17.01 Aligned_cols=16 Identities=13% Similarity=0.277 Sum_probs=10.1
Q ss_pred HHHHHHhCCCHHHHHH
Q psy9207 65 TSLSEFLGVTEQEAAA 80 (125)
Q Consensus 65 ~~~a~~Lgl~~~e~~~ 80 (125)
.-+++.|+|+++|...
T Consensus 29 pvi~tlL~fs~~e~~~ 44 (46)
T PF01465_consen 29 PVIATLLKFSPEEKQK 44 (46)
T ss_dssp HHHHHHTT--HHHHHH
T ss_pred HHHHHHHCCCHHHHHh
Confidence 4478889999887654
No 302
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=22.14 E-value=3.3e+02 Score=20.09 Aligned_cols=23 Identities=17% Similarity=0.045 Sum_probs=18.4
Q ss_pred CcchHHHHHHhCCCHHHHHHHHH
Q psy9207 61 SIPNTSLSEFLGVTEQEAAAIAQ 83 (125)
Q Consensus 61 sI~~~~~a~~Lgl~~~e~~~~~~ 83 (125)
.-+.+++|..||++.+++.+...
T Consensus 117 ~pt~~eiA~~lg~~~~~v~~~~~ 139 (231)
T PRK12427 117 EPNFEEISAELNLTAEEYQEYLL 139 (231)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHH
Confidence 45578899999999988877644
No 303
>PRK14965 DNA polymerase III subunits gamma and tau; Provisional
Probab=22.07 E-value=3.6e+02 Score=23.09 Aligned_cols=44 Identities=7% Similarity=0.283 Sum_probs=33.3
Q ss_pred HHHHHHHHHHcCCchHHHHHhcc--CCcHHHHHHHHHHHHHHHHHH
Q psy9207 8 QVWEVGKHLWNGNYPSIYSTLKR--TWSDDIAHIMKALQDEVQKRA 51 (125)
Q Consensus 8 ~~~~l~~~l~~~~y~~v~~~~~~--~~s~~~~~~i~~l~~~vR~~~ 51 (125)
.+..+..++..+++.++...++. .-+.....++..|...+|+-.
T Consensus 248 ~l~~ll~al~~~d~~~al~~l~~l~~~G~~~~~~l~~Ll~~~RdLl 293 (576)
T PRK14965 248 LLLDISAAVFGRDTRALLEIVERVDEFGYNMRQFCQELIDHLRNLV 293 (576)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 36788899999999998887775 345566677777777777644
No 304
>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional
Probab=22.01 E-value=5.3e+02 Score=22.40 Aligned_cols=41 Identities=7% Similarity=0.124 Sum_probs=24.9
Q ss_pred HHHHHHHHHHHhcCCcc-hHHHHHHhCCCHHHHHHHHHhcCC
Q psy9207 47 VQKRAISLISKAYSSIP-NTSLSEFLGVTEQEAAAIAQAEGW 87 (125)
Q Consensus 47 vR~~~~~li~~AY~sI~-~~~~a~~Lgl~~~e~~~~~~~~GW 87 (125)
=|+.|...+..+-.+++ .+.+|+.||++..-+-.-.++.|-
T Consensus 642 Er~~I~~aL~~~~gn~~~~~~aA~~LGi~R~tL~rklk~~gi 683 (686)
T PRK15429 642 EYQLIVRVLKETNGVVAGPKGAAQRLGLKRTTLLSRMKRLGI 683 (686)
T ss_pred HHHHHHHHHHHcCCCcccHHHHHHHhCCCHHHHHHHHHHcCC
Confidence 34555556666666654 567777777776666555555443
No 305
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=22.00 E-value=1.4e+02 Score=22.36 Aligned_cols=33 Identities=15% Similarity=0.069 Sum_probs=14.7
Q ss_pred HHHHHHHHHHHHHHHhcCC-cchHHHHHHhCCCH
Q psy9207 43 LQDEVQKRAISLISKAYSS-IPNTSLSEFLGVTE 75 (125)
Q Consensus 43 l~~~vR~~~~~li~~AY~s-I~~~~~a~~Lgl~~ 75 (125)
..+....-+-.+-.+++.| -++.++++-||+++
T Consensus 25 ~~~v~~~si~elA~~~~vS~aTv~Rf~kklG~~G 58 (278)
T PRK11557 25 PDTARHLSSQQLANEAGVSQSSVVKFAQKLGYKG 58 (278)
T ss_pred HHHHHhcCHHHHHHHhCCCHHHHHHHHHHcCCCC
Confidence 3333333344444444443 23445555555553
No 306
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=21.95 E-value=1.3e+02 Score=15.19 Aligned_cols=24 Identities=25% Similarity=0.412 Sum_probs=18.3
Q ss_pred CCcchHHHHHHhCCCHHHHHHHHH
Q psy9207 60 SSIPNTSLSEFLGVTEQEAAAIAQ 83 (125)
Q Consensus 60 ~sI~~~~~a~~Lgl~~~e~~~~~~ 83 (125)
..++..+++..+|++...+..+..
T Consensus 9 ~~~s~~~la~~~~i~~~~i~~~~~ 32 (56)
T smart00530 9 KGLTQEELAEKLGVSRSTLSRIEN 32 (56)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHC
Confidence 467888999999998777766543
No 307
>PRK05685 fliS flagellar protein FliS; Validated
Probab=21.55 E-value=2e+02 Score=19.52 Aligned_cols=78 Identities=14% Similarity=0.222 Sum_probs=49.7
Q ss_pred HHHHHHHHHHHHcCCchHHHHHhccCCcHHHHHHHHHHHHHHH----HHHHHHHHHhcCCcchHHHHHHhCCCH---HHH
Q psy9207 6 IGQVWEVGKHLWNGNYPSIYSTLKRTWSDDIAHIMKALQDEVQ----KRAISLISKAYSSIPNTSLSEFLGVTE---QEA 78 (125)
Q Consensus 6 l~~~~~l~~~l~~~~y~~v~~~~~~~~s~~~~~~i~~l~~~vR----~~~~~li~~AY~sI~~~~~a~~Lgl~~---~e~ 78 (125)
|+.+-.-..++.++++.+....+.. ...++..|...+. .+++.-+..=|..+...-....+.-+. +++
T Consensus 36 i~~l~~A~~ai~~~~~~~~~~~l~k-----a~~Ii~eL~~sLd~e~ggeiA~~L~~LY~y~~~~L~~A~~~~d~~~l~ev 110 (132)
T PRK05685 36 LSFLAQAKLAIEQGDIEAKGEYLSK-----AINIINGLRNSLDMEKGGEVAKNLSALYDYMIRRLLEANLRNDVQAIDEV 110 (132)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHH-----HHHHHHHHHhhcCCccccHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHH
Confidence 3444444567788888887776654 2344455555443 377888888888887777777777664 455
Q ss_pred HHHHHh--cCCe
Q psy9207 79 AAIAQA--EGWT 88 (125)
Q Consensus 79 ~~~~~~--~GW~ 88 (125)
...... -||.
T Consensus 111 ~~il~~LreaW~ 122 (132)
T PRK05685 111 EGLLREIKEAWK 122 (132)
T ss_pred HHHHHHHHHHHH
Confidence 555554 3775
No 308
>PF13167 GTP-bdg_N: GTP-binding GTPase N-terminal
Probab=21.53 E-value=2.4e+02 Score=18.29 Aligned_cols=19 Identities=21% Similarity=0.361 Sum_probs=14.7
Q ss_pred HHHHHHHHhcCCeecCcee
Q psy9207 76 QEAAAIAQAEGWTVDKVYT 94 (125)
Q Consensus 76 ~e~~~~~~~~GW~~d~~~~ 94 (125)
+|+...+...||++=+.++
T Consensus 11 ~El~~L~~t~g~~vv~~~~ 29 (95)
T PF13167_consen 11 EELEELAETAGYEVVGTVV 29 (95)
T ss_pred HHHHHHHHHCCCeEEEEEE
Confidence 7888899999999854433
No 309
>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=21.30 E-value=2.4e+02 Score=18.13 Aligned_cols=40 Identities=5% Similarity=0.083 Sum_probs=28.6
Q ss_pred HHHHHHHH--hc-CCcchHHHHHHhCCCHHHHHH---HHHhcCCee
Q psy9207 50 RAISLISK--AY-SSIPNTSLSEFLGVTEQEAAA---IAQAEGWTV 89 (125)
Q Consensus 50 ~~~~li~~--AY-~sI~~~~~a~~Lgl~~~e~~~---~~~~~GW~~ 89 (125)
.++.++.+ .. ..++..+++..++++..-+-. -..++||-.
T Consensus 29 ~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~ 74 (109)
T TIGR01889 29 LILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLSKKGYLS 74 (109)
T ss_pred HHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEe
Confidence 45666663 33 459999999999999755444 455689987
No 310
>COG1309 AcrR Transcriptional regulator [Transcription]
Probab=21.21 E-value=1.8e+02 Score=18.86 Aligned_cols=22 Identities=18% Similarity=0.409 Sum_probs=19.1
Q ss_pred HHHHhcCCcchHHHHHHhCCCH
Q psy9207 54 LISKAYSSIPNTSLSEFLGVTE 75 (125)
Q Consensus 54 li~~AY~sI~~~~~a~~Lgl~~ 75 (125)
...+.|..+++.++|+-+|++.
T Consensus 25 ~~~~G~~~~t~~~Ia~~agvs~ 46 (201)
T COG1309 25 FAEKGYAATTVDEIAKAAGVSK 46 (201)
T ss_pred HHHcCcCCCCHHHHHHHhCCCc
Confidence 3448999999999999999975
No 311
>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=21.18 E-value=1.6e+02 Score=15.94 Aligned_cols=31 Identities=10% Similarity=0.193 Sum_probs=18.6
Q ss_pred HHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHH
Q psy9207 49 KRAISLISKAYSSIPNTSLSEFLGVTEQEAAAIA 82 (125)
Q Consensus 49 ~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~ 82 (125)
+++..+...- .++.++|..+|+|..-+-.+.
T Consensus 12 ~~i~~l~~~G---~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 12 EEIKELYAEG---MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp HHHHHHHHTT-----HHHHHHHTTS-HHHHHHHH
T ss_pred HHHHHHHHCC---CCHHHHHHHHCcCHHHHHHHH
Confidence 3444444443 789999999999977665543
No 312
>PRK09411 carbamate kinase; Reviewed
Probab=21.14 E-value=2.2e+02 Score=22.46 Aligned_cols=28 Identities=25% Similarity=0.456 Sum_probs=19.3
Q ss_pred CHHHHHHHHHhcCCee--cC---ceeeccCCCC
Q psy9207 74 TEQEAAAIAQAEGWTV--DK---VYTQPVKKPE 101 (125)
Q Consensus 74 ~~~e~~~~~~~~GW~~--d~---~~~~p~~~~~ 101 (125)
+.++..+...++||++ |+ +.+.|.|...
T Consensus 129 ~~e~a~~l~~e~g~~~~~dg~g~rrVVpSP~P~ 161 (297)
T PRK09411 129 QPEEQEALEAAYGWQMKRDGKYLRRVVASPQPR 161 (297)
T ss_pred CHHHHHHHHHhcCCEEEecCCceEEEccCCCCc
Confidence 5588888888899988 42 3566655443
No 313
>PF01329 Pterin_4a: Pterin 4 alpha carbinolamine dehydratase; InterPro: IPR001533 DCoH is the dimerisation cofactor of hepatocyte nuclear factor 1 (HNF-1) that functions as both a transcriptional coactivator and a pterin dehydratase []. X-ray crystallographic studies have shown that the ligand binds at four sites per tetrameric enzyme, with little apparent conformational change in the protein.; GO: 0008124 4-alpha-hydroxytetrahydrobiopterin dehydratase activity, 0006729 tetrahydrobiopterin biosynthetic process; PDB: 2V6T_B 2V6U_A 2V6S_B 2EBB_A 1USM_A 1F93_B 1DCP_C 1DCH_E 3HXA_E 1DCO_C ....
Probab=21.12 E-value=1.3e+02 Score=19.17 Aligned_cols=19 Identities=32% Similarity=0.657 Sum_probs=13.7
Q ss_pred CCHHHHHHHHHh-cCCeecC
Q psy9207 73 VTEQEAAAIAQA-EGWTVDK 91 (125)
Q Consensus 73 l~~~e~~~~~~~-~GW~~d~ 91 (125)
|+.+|+.+...+ .||++++
T Consensus 5 Ls~~ei~~~L~~l~~W~~~~ 24 (95)
T PF01329_consen 5 LSEEEIAEALAELPGWKLDG 24 (95)
T ss_dssp -THHHHHHHHHTSTTSEEET
T ss_pred CCHHHHHHhhhcCcCCEECC
Confidence 567777777776 5999974
No 314
>PF07022 Phage_CI_repr: Bacteriophage CI repressor helix-turn-helix domain; InterPro: IPR010744 This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic [].; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2FJR_B.
Probab=21.10 E-value=1.4e+02 Score=17.57 Aligned_cols=28 Identities=21% Similarity=0.366 Sum_probs=17.1
Q ss_pred HHHHHHhcCCcchHHHHHHhCCCHHHHH
Q psy9207 52 ISLISKAYSSIPNTSLSEFLGVTEQEAA 79 (125)
Q Consensus 52 ~~li~~AY~sI~~~~~a~~Lgl~~~e~~ 79 (125)
++-+-.+|.-=+..++|..||++.+-+-
T Consensus 3 i~rl~~~~g~~~~~~lA~~lgis~st~s 30 (66)
T PF07022_consen 3 IERLKEALGVKSDKELAERLGISKSTLS 30 (66)
T ss_dssp HHHHHHHHT-SSCHHHHCCTT--HHHHH
T ss_pred HHHHHHHhCCCCHHHHHHHhCcCHHHhh
Confidence 3445556666677788888888876555
No 315
>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=20.69 E-value=1.4e+02 Score=16.34 Aligned_cols=22 Identities=27% Similarity=0.323 Sum_probs=17.1
Q ss_pred chHHHHHHhCCCHHHHHHHHHh
Q psy9207 63 PNTSLSEFLGVTEQEAAAIAQA 84 (125)
Q Consensus 63 ~~~~~a~~Lgl~~~e~~~~~~~ 84 (125)
.+..+|.-+|++..++..+...
T Consensus 29 ~~~~la~~~~l~~~qV~~WF~n 50 (59)
T cd00086 29 EREELAKELGLTERQVKIWFQN 50 (59)
T ss_pred HHHHHHHHHCcCHHHHHHHHHH
Confidence 3566888899999888887654
No 316
>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=20.67 E-value=1.9e+02 Score=16.85 Aligned_cols=39 Identities=10% Similarity=0.037 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHHHhcC
Q psy9207 46 EVQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQAEG 86 (125)
Q Consensus 46 ~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~~~G 86 (125)
.++.+++... --.-.++.++|.-+|++...+-.+..+..
T Consensus 10 e~K~~~v~~~--~~~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 10 EFKLQAVREY--LESGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp HHHHHHHHHH--HHHHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHH--HHCCCceEeeecccccccccccHHHHHHh
Confidence 3444444443 12357899999999999999999888753
No 317
>PF05427 FIBP: Acidic fibroblast growth factor binding (FIBP) ; InterPro: IPR008614 Acidic fibroblast growth factor (aFGF) intracellular binding protein (FIBP) is a protein found mainly in the nucleus that is thought to be involved in the intracellular function of aFGF [].; GO: 0017134 fibroblast growth factor binding
Probab=20.61 E-value=1.6e+02 Score=24.02 Aligned_cols=57 Identities=18% Similarity=0.423 Sum_probs=43.2
Q ss_pred HHHHH-HHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHhCCC-HHHH-----------HHHHHhcCCeec
Q psy9207 34 DDIAH-IMKALQDEVQKRAISLISKAYSSIPNTSLSEFLGVT-EQEA-----------AAIAQAEGWTVD 90 (125)
Q Consensus 34 ~~~~~-~i~~l~~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~-~~e~-----------~~~~~~~GW~~d 90 (125)
+.+.. ++..|..++-++++.-++..|.+++..-++=--||+ +.|+ ++=+.+.||+.+
T Consensus 247 d~hk~lV~~~L~~~l~~~~l~elesnFK~l~Ralv~Ia~gLs~sKElRdlF~DLvEK~IEPlr~~~Wt~~ 316 (361)
T PF05427_consen 247 DQHKHLVCRRLKGKLSERSLQELESNFKSLSRALVNIASGLSHSKELRDLFEDLVEKFIEPLRQAGWTKE 316 (361)
T ss_pred HHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHHhHHHHHCCCCHH
Confidence 44444 457788899999999999999999988888888887 3333 334667899985
No 318
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=20.57 E-value=3.6e+02 Score=19.92 Aligned_cols=51 Identities=18% Similarity=0.253 Sum_probs=39.7
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCCc-chHHHHHHhCCCH---HHHHHHHHhcCCee
Q psy9207 39 IMKALQDEVQKRAISLISKAYSSI-PNTSLSEFLGVTE---QEAAAIAQAEGWTV 89 (125)
Q Consensus 39 ~i~~l~~~vR~~~~~li~~AY~sI-~~~~~a~~Lgl~~---~e~~~~~~~~GW~~ 89 (125)
....+.+.+|+.|+.--=+.=..| +-.++|..||+|. -|+.......|...
T Consensus 10 ~~~~v~~~l~~~I~~g~l~pG~~LpsE~eLa~~~gVSRtpVREAL~~L~~eGlV~ 64 (257)
T PRK10225 10 PYQEVGAMIRDLIIKTPYNPGERLPPEREIAEMLDVTRTVVREALIMLEIKGLVE 64 (257)
T ss_pred HHHHHHHHHHHHHHhCCCCCCCcCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence 456777888888887666667788 4889999999995 56666677789886
No 319
>PLN00157 histone H2A; Provisional
Probab=20.49 E-value=3.1e+02 Score=19.09 Aligned_cols=71 Identities=20% Similarity=0.302 Sum_probs=44.2
Q ss_pred HHHHHHHHHcCCchHHHHHhccCCcHHHHHHHHHHHHHHHHHHHHHHHHhc-----CCcchHHHHHHhCC-CHHHHHHHH
Q psy9207 9 VWEVGKHLWNGNYPSIYSTLKRTWSDDIAHIMKALQDEVQKRAISLISKAY-----SSIPNTSLSEFLGV-TEQEAAAIA 82 (125)
Q Consensus 9 ~~~l~~~l~~~~y~~v~~~~~~~~s~~~~~~i~~l~~~vR~~~~~li~~AY-----~sI~~~~~a~~Lgl-~~~e~~~~~ 82 (125)
+=.+.++|.+|+|.. .+.. ....++++..+.+-.+|+.+...+- ..|.+.++. |.+ +++|+.++.
T Consensus 29 VgRi~R~Lk~g~~a~---RIg~----~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~--lAI~nDeEL~~Ll 99 (132)
T PLN00157 29 VGRIARYLKAGKYAT---RVGA----GAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQ--LAVRNDEELSKLL 99 (132)
T ss_pred hHHHHHHHhcCchhh---hcCC----CcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHh--hcccCcHHHHHHH
Confidence 346788899988875 2222 2233555566666666777666652 366666653 334 357888777
Q ss_pred HhcCCeec
Q psy9207 83 QAEGWTVD 90 (125)
Q Consensus 83 ~~~GW~~d 90 (125)
. |+++.
T Consensus 100 ~--~vtIa 105 (132)
T PLN00157 100 G--GVTIA 105 (132)
T ss_pred c--Cceec
Confidence 6 78886
No 320
>KOG3442|consensus
Probab=20.49 E-value=3.1e+02 Score=19.06 Aligned_cols=25 Identities=20% Similarity=0.278 Sum_probs=19.3
Q ss_pred HHhcCCcchHHHHHHhCCCH----HHHHH
Q psy9207 56 SKAYSSIPNTSLSEFLGVTE----QEAAA 80 (125)
Q Consensus 56 ~~AY~sI~~~~~a~~Lgl~~----~e~~~ 80 (125)
+.+|..|++..+...||+++ +++.+
T Consensus 50 ~~~~~~iTlqEa~qILnV~~~ln~eei~k 78 (132)
T KOG3442|consen 50 ANSNGKITLQEAQQILNVKEPLNREEIEK 78 (132)
T ss_pred ccccccccHHHHhhHhCCCCCCCHHHHHH
Confidence 34578899999999999973 55544
No 321
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=20.39 E-value=2.6e+02 Score=18.15 Aligned_cols=21 Identities=14% Similarity=0.197 Sum_probs=14.4
Q ss_pred CcchHHHHHHhCCCHHHHHHH
Q psy9207 61 SIPNTSLSEFLGVTEQEAAAI 81 (125)
Q Consensus 61 sI~~~~~a~~Lgl~~~e~~~~ 81 (125)
.++..++|..+|++..-+..+
T Consensus 78 gltq~~lA~~lg~~~~tis~~ 98 (127)
T TIGR03830 78 GLSQREAAELLGGGVNAFSRY 98 (127)
T ss_pred CCCHHHHHHHhCCCHHHHHHH
Confidence 667777777777776555554
No 322
>KOG3054|consensus
Probab=20.31 E-value=4.3e+02 Score=20.67 Aligned_cols=52 Identities=13% Similarity=0.224 Sum_probs=36.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHhCCCHHHHHHHHHh--cCCee----c--Cceeec
Q psy9207 36 IAHIMKALQDEVQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAIAQA--EGWTV----D--KVYTQP 96 (125)
Q Consensus 36 ~~~~i~~l~~~vR~~~~~li~~AY~sI~~~~~a~~Lgl~~~e~~~~~~~--~GW~~----d--~~~~~p 96 (125)
-..++..|.+.|+.. .-+.++++|+-+||-.++.+.-++. ..|++ | |.+++-
T Consensus 198 qdnll~eFv~YIk~n---------KvV~ledLas~f~Lrtqd~inriq~~l~eg~ltGVmDDRGKfIYI 257 (299)
T KOG3054|consen 198 QDNLLSEFVEYIKKN---------KVVPLEDLASEFGLRTQDSINRIQELLAEGLLTGVMDDRGKFIYI 257 (299)
T ss_pred HHHHHHHHHHHHHhc---------CeeeHHHHHHHhCccHHHHHHHHHHHHHhhhheeeecCCCceEEe
Confidence 345777777777653 4578999999999988887776665 26776 3 555554
No 323
>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator. Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs,
Probab=20.27 E-value=2.6e+02 Score=18.19 Aligned_cols=49 Identities=18% Similarity=0.103 Sum_probs=29.9
Q ss_pred chHHHHHHhCCCHHHHHHHHHhcCCeecCceeeccCCCCCCCCCCC-ChHHHHHHhhHH
Q psy9207 63 PNTSLSEFLGVTEQEAAAIAQAEGWTVDKVYTQPVKKPEEYATPNI-TDDQLYILTQYV 120 (125)
Q Consensus 63 ~~~~~a~~Lgl~~~e~~~~~~~~GW~~d~~~~~p~~~~~~~~~~~~-~~~ql~~Lt~~v 120 (125)
++.++|+.+|++..-+.-|.. -+.+-|..... ..-.. +++++.+|.-+.
T Consensus 2 ~Ige~A~~~gvs~~tlR~ye~-------~GLl~p~~r~~--~g~R~Y~~~~l~~l~~I~ 51 (107)
T cd01111 2 SISQLALDAGVSVHIVRDYLL-------RGLLHPVARTE--GGYGLFDDCALQRLRFVR 51 (107)
T ss_pred CHHHHHHHHCcCHHHHHHHHH-------CCCCCCCCcCC--CCCeecCHHHHHHHHHHH
Confidence 578999999999877766554 34444432221 12222 777777765443
No 324
>PF11112 PyocinActivator: Pyocin activator protein PrtN
Probab=20.26 E-value=1.6e+02 Score=18.34 Aligned_cols=54 Identities=19% Similarity=0.225 Sum_probs=32.3
Q ss_pred CCcchHHHH-HHh-CCCHHHHHHHHHhcCCeecCceeeccCCCCCCCCCCCChHHHHHHhhHH
Q psy9207 60 SSIPNTSLS-EFL-GVTEQEAAAIAQAEGWTVDKVYTQPVKKPEEYATPNITDDQLYILTQYV 120 (125)
Q Consensus 60 ~sI~~~~~a-~~L-gl~~~e~~~~~~~~GW~~d~~~~~p~~~~~~~~~~~~~~~ql~~Lt~~v 120 (125)
..|++++++ .|+ |++++.+..-+.+ |.+=+|.-.-. ++.+..--..+..|++|+
T Consensus 13 ~~IpL~~v~~~yf~~lt~~~a~rk~~~------g~lplPv~rl~-~SqKs~~~V~v~dLA~yi 68 (76)
T PF11112_consen 13 PVIPLEEVCEDYFPHLTPKTAKRKANA------GELPLPVFRLD-DSQKSPKFVHVQDLAAYI 68 (76)
T ss_pred CCCcHHHHHHHHHccCCHHHHHHHHHC------CCCCCceeecC-CcccCCceeeHHHHHHHH
Confidence 468898876 889 9999888887664 33333332221 022222455666677665
No 325
>PRK14950 DNA polymerase III subunits gamma and tau; Provisional
Probab=20.26 E-value=4.1e+02 Score=22.71 Aligned_cols=45 Identities=13% Similarity=0.212 Sum_probs=33.4
Q ss_pred HHHHHHHHHHcCCchHHHHHhcc--CCcHHHHHHHHHHHHHHHHHHH
Q psy9207 8 QVWEVGKHLWNGNYPSIYSTLKR--TWSDDIAHIMKALQDEVQKRAI 52 (125)
Q Consensus 8 ~~~~l~~~l~~~~y~~v~~~~~~--~~s~~~~~~i~~l~~~vR~~~~ 52 (125)
.+..+..++..||+.+++..++. ........++..|...+|+-..
T Consensus 249 ~vf~Lidal~~~d~~~al~~l~~L~~~g~~~~~il~~L~~~lR~Ll~ 295 (585)
T PRK14950 249 EVKALAEALLAKDLKAALRTLNAVAADGADLRQFTRDLVEYLRQVML 295 (585)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHH
Confidence 46678889999999998888765 4455667777777777776543
No 326
>smart00700 JHBP Juvenile hormone binding protein domains in insects. The juvenile hormone exerts pleiotropic functions during insect life cycles and its binding proteins regulate these functions.
Probab=20.16 E-value=2.2e+02 Score=20.78 Aligned_cols=42 Identities=17% Similarity=0.479 Sum_probs=32.6
Q ss_pred HHhccCCcHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchHHH
Q psy9207 26 STLKRTWSDDIAHIMKALQDEVQKRAISLISKAYSSIPNTSL 67 (125)
Q Consensus 26 ~~~~~~~s~~~~~~i~~l~~~vR~~~~~li~~AY~sI~~~~~ 67 (125)
..++..|.+-+..+-..+.+.+...+...+.+.+..++.+++
T Consensus 181 ~~lNen~~~i~~e~~p~i~~~~~~~~~~~~n~~~~~vp~~~~ 222 (225)
T smart00700 181 KFLNENWKALINELLPAIVEKLESIFLDLVNKVFAKVPIDEF 222 (225)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHh
Confidence 344446777777777888888888888888888888888765
No 327
>PTZ00064 histone acetyltransferase; Provisional
Probab=20.07 E-value=2.8e+02 Score=23.88 Aligned_cols=28 Identities=11% Similarity=0.120 Sum_probs=25.7
Q ss_pred cchHHHHHHhCCCHHHHHHHHHhcCCee
Q psy9207 62 IPNTSLSEFLGVTEQEAAAIAQAEGWTV 89 (125)
Q Consensus 62 I~~~~~a~~Lgl~~~e~~~~~~~~GW~~ 89 (125)
|++++++...|+..+|++...+..|.-.
T Consensus 472 iSI~dIS~~TgI~~eDII~TLq~L~llk 499 (552)
T PTZ00064 472 KFIDNVVRSTGIRREDVIRILEENGIMR 499 (552)
T ss_pred ccHHHHHHHhCCCHHHHHHHHHHCCcEE
Confidence 8999999999999999999999988554
No 328
>PRK03837 transcriptional regulator NanR; Provisional
Probab=20.03 E-value=2.7e+02 Score=20.22 Aligned_cols=50 Identities=16% Similarity=0.204 Sum_probs=36.4
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCc-chHHHHHHhCCCH---HHHHHHHHhcCCee
Q psy9207 40 MKALQDEVQKRAISLISKAYSSI-PNTSLSEFLGVTE---QEAAAIAQAEGWTV 89 (125)
Q Consensus 40 i~~l~~~vR~~~~~li~~AY~sI-~~~~~a~~Lgl~~---~e~~~~~~~~GW~~ 89 (125)
.+.+.+.+|+.|..--=+.=..| +..++|..||+|. -|+.......|+--
T Consensus 15 ~~~v~~~l~~~I~~g~l~pG~~Lp~E~~Lae~~gVSRt~VREAL~~L~~eGlv~ 68 (241)
T PRK03837 15 SEEVEERLEQMIRSGEFGPGDQLPSERELMAFFGVGRPAVREALQALKRKGLVQ 68 (241)
T ss_pred HHHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence 35566667777666555555678 7899999999995 56666677789976
No 329
>PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional
Probab=20.01 E-value=3.6e+02 Score=23.19 Aligned_cols=39 Identities=13% Similarity=0.143 Sum_probs=25.1
Q ss_pred HHHHHHHHhcC---CcchHHHHHHhCCCHHHHHHHHHhcCCe
Q psy9207 50 RAISLISKAYS---SIPNTSLSEFLGVTEQEAAAIAQAEGWT 88 (125)
Q Consensus 50 ~~~~li~~AY~---sI~~~~~a~~Lgl~~~e~~~~~~~~GW~ 88 (125)
+|++.|-+-+. ..++.++|+-.|.|+.-+..||++.|-+
T Consensus 360 ~IA~yIl~n~~~v~~~si~eLA~~~~vS~aTV~Rf~kkLGf~ 401 (638)
T PRK14101 360 RVADLALNHPRSIINDPIVDIARKADVSQPTVIRFCRSLGCQ 401 (638)
T ss_pred HHHHHHHhCHHHHHhccHHHHHHHhCCCHHHHHHHHHHhCCC
Confidence 45555544443 3467777777777777777777776554
Done!