Query 036949
Match_columns 81
No_of_seqs 102 out of 178
Neff 7.1
Searched_HMMs 46136
Date Fri Mar 29 07:02:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036949.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036949hhsearch_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 99.7 2.8E-17 6E-22 105.8 4.3 56 1-56 82-137 (143)
2 KOG4414 COP9 signalosome, subu 99.6 1.3E-15 2.7E-20 100.4 2.3 79 2-81 118-197 (197)
3 KOG3151 26S proteasome regulat 99.2 5.8E-11 1.3E-15 82.8 6.5 53 2-54 178-231 (260)
4 KOG3252 Uncharacterized conser 98.4 1.1E-06 2.3E-11 59.9 5.6 79 1-79 136-216 (217)
5 smart00753 PAM PCI/PINT associ 97.1 0.0013 2.9E-08 38.4 4.7 55 2-56 10-70 (88)
6 smart00088 PINT motif in prote 97.1 0.0013 2.9E-08 38.4 4.7 55 2-56 10-70 (88)
7 PF01399 PCI: PCI domain; Int 97.0 0.0018 4E-08 38.2 4.7 38 2-39 46-83 (105)
8 PF03399 SAC3_GANP: SAC3/GANP/ 96.2 0.0052 1.1E-07 40.7 3.1 27 2-28 177-204 (204)
9 KOG1861 Leucine permease trans 96.2 0.012 2.6E-07 45.2 5.2 58 3-60 464-523 (540)
10 PF03374 ANT: Phage antirepres 95.6 0.047 1E-06 33.3 5.2 49 6-54 14-62 (111)
11 smart00071 Galanin Galanin. Ga 94.1 0.074 1.6E-06 32.5 3.1 21 38-58 10-30 (103)
12 KOG1498 26S proteasome regulat 93.6 0.27 6E-06 37.2 5.9 33 7-39 344-376 (439)
13 COG5071 RPN5 26S proteasome re 93.5 0.24 5.2E-06 36.8 5.4 39 6-44 343-384 (439)
14 KOG2581 26S proteasome regulat 92.9 0.053 1.1E-06 41.2 1.3 30 7-36 368-398 (493)
15 PF03683 UPF0175: Uncharacteri 91.8 0.31 6.7E-06 28.2 3.4 30 15-44 33-62 (76)
16 PF12728 HTH_17: Helix-turn-he 91.5 0.33 7.2E-06 25.4 3.1 23 17-39 2-24 (51)
17 PF10668 Phage_terminase: Phag 91.5 0.62 1.3E-05 26.2 4.3 46 3-48 9-54 (60)
18 PF04800 ETC_C1_NDUFA4: ETC co 91.1 0.17 3.7E-06 31.2 1.9 28 26-57 53-81 (101)
19 PF04760 IF2_N: Translation in 90.6 0.28 6.1E-06 26.3 2.3 29 15-43 2-31 (54)
20 PF02042 RWP-RK: RWP-RK domain 90.6 0.56 1.2E-05 25.7 3.5 29 13-41 12-40 (52)
21 PRK13503 transcriptional activ 89.8 0.84 1.8E-05 31.2 4.7 37 4-40 174-211 (278)
22 PLN03238 probable histone acet 89.1 1.6 3.4E-05 31.7 5.7 52 3-54 210-261 (290)
23 cd01104 HTH_MlrA-CarA Helix-Tu 89.0 2.4 5.2E-05 23.1 5.4 52 18-79 2-54 (68)
24 PF07037 DUF1323: Putative tra 89.0 0.84 1.8E-05 29.1 3.8 29 18-46 2-30 (122)
25 TIGR01764 excise DNA binding d 88.9 0.72 1.6E-05 23.2 3.0 23 17-39 2-24 (49)
26 PF03484 B5: tRNA synthetase B 88.1 3.1 6.6E-05 23.4 5.5 41 16-56 5-48 (70)
27 PF09339 HTH_IclR: IclR helix- 87.4 1.4 3.1E-05 23.2 3.6 40 5-44 7-49 (52)
28 PF13404 HTH_AsnC-type: AsnC-t 87.2 2.8 6E-05 21.6 4.6 33 5-38 7-39 (42)
29 smart00874 B5 tRNA synthetase 87.0 3.7 7.9E-05 22.8 6.7 32 16-47 5-38 (71)
30 PF08727 P3A: Poliovirus 3A pr 86.8 0.43 9.3E-06 26.6 1.4 25 22-46 20-45 (57)
31 PF13463 HTH_27: Winged helix 86.2 2.3 5E-05 23.0 4.2 39 5-43 7-48 (68)
32 smart00550 Zalpha Z-DNA-bindin 86.1 2.6 5.6E-05 23.7 4.5 44 2-45 7-54 (68)
33 PF14056 DUF4250: Domain of un 85.7 2 4.2E-05 23.8 3.6 30 18-47 22-51 (55)
34 cd04762 HTH_MerR-trunc Helix-T 85.5 1.5 3.2E-05 21.8 3.0 22 18-39 2-23 (49)
35 PF12840 HTH_20: Helix-turn-he 85.0 4.1 9E-05 22.0 4.8 36 2-38 11-46 (61)
36 PF00165 HTH_AraC: Bacterial r 84.9 1.7 3.8E-05 21.8 3.1 30 14-43 6-36 (42)
37 COG2522 Predicted transcriptio 84.9 2.5 5.4E-05 26.8 4.3 37 2-40 10-46 (119)
38 smart00342 HTH_ARAC helix_turn 84.7 2.8 6.1E-05 22.8 4.2 28 16-43 50-79 (84)
39 PF08279 HTH_11: HTH domain; 84.6 4.2 9.1E-05 21.3 4.7 35 4-38 3-37 (55)
40 PF01418 HTH_6: Helix-turn-hel 84.2 3.2 6.9E-05 23.7 4.3 39 5-43 20-61 (77)
41 COG3415 Transposase and inacti 84.1 9.1 0.0002 24.8 7.2 67 4-75 9-75 (138)
42 PRK12686 carbamate kinase; Rev 83.9 2.9 6.3E-05 30.5 4.9 21 27-47 133-153 (312)
43 PF05687 DUF822: Plant protein 83.9 1.2 2.6E-05 29.4 2.6 24 29-52 46-70 (150)
44 PF08280 HTH_Mga: M protein tr 83.7 4.8 0.0001 21.9 4.7 35 5-40 9-43 (59)
45 PF01022 HTH_5: Bacterial regu 83.6 3.8 8.2E-05 21.1 4.1 35 2-38 3-37 (47)
46 PF13412 HTH_24: Winged helix- 83.4 4.5 9.7E-05 20.7 4.7 40 2-42 4-46 (48)
47 PF12324 HTH_15: Helix-turn-he 83.3 7.2 0.00016 23.0 5.7 45 6-51 29-74 (77)
48 smart00497 IENR1 Intron encode 83.3 3.4 7.3E-05 21.4 3.9 27 17-44 18-44 (53)
49 PF08220 HTH_DeoR: DeoR-like h 83.2 4.3 9.3E-05 21.9 4.4 40 3-43 2-44 (57)
50 PF01296 Galanin: Galanin; In 83.0 0.77 1.7E-05 22.1 1.1 19 41-59 1-19 (29)
51 KOG3389 NADH:ubiquinone oxidor 82.7 0.71 1.5E-05 30.6 1.2 27 21-47 124-151 (178)
52 smart00418 HTH_ARSR helix_turn 82.5 3.7 8E-05 21.2 3.9 37 6-44 2-41 (66)
53 PF09035 Tn916-Xis: Excisionas 82.3 3.2 6.9E-05 23.8 3.7 37 16-52 13-52 (67)
54 PF06627 DUF1153: Protein of u 82.1 5.1 0.00011 24.3 4.7 37 2-38 35-71 (90)
55 smart00419 HTH_CRP helix_turn_ 81.7 4.9 0.00011 20.0 4.6 35 16-50 8-45 (48)
56 TIGR02702 SufR_cyano iron-sulf 81.4 5.6 0.00012 26.6 5.2 43 1-44 1-46 (203)
57 PF08784 RPA_C: Replication pr 81.3 4 8.6E-05 24.3 4.1 44 2-45 48-97 (102)
58 COG2886 Uncharacterized small 81.0 5.2 0.00011 24.1 4.5 36 8-45 35-70 (88)
59 PF01853 MOZ_SAS: MOZ/SAS fami 80.8 7.4 0.00016 26.6 5.6 49 3-51 135-185 (188)
60 PRK10906 DNA-binding transcrip 80.8 11 0.00025 26.2 6.8 51 3-54 7-60 (252)
61 PRK11511 DNA-binding transcrip 80.8 5.4 0.00012 24.8 4.7 37 4-40 12-49 (127)
62 TIGR02844 spore_III_D sporulat 80.0 4.5 9.8E-05 23.8 3.9 33 3-37 8-40 (80)
63 PF11112 PyocinActivator: Pyoc 80.0 5.5 0.00012 23.3 4.2 54 15-76 13-68 (76)
64 PF14555 UBA_4: UBA-like domai 79.6 2.6 5.6E-05 21.6 2.5 28 19-46 4-31 (43)
65 PF06056 Terminase_5: Putative 79.3 3.4 7.4E-05 22.8 3.1 40 2-44 2-41 (58)
66 COG3645 Uncharacterized phage- 79.3 5.9 0.00013 25.7 4.6 49 6-54 37-85 (135)
67 TIGR03573 WbuX N-acetyl sugar 78.9 3.9 8.6E-05 29.7 4.1 35 2-37 304-342 (343)
68 PF04539 Sigma70_r3: Sigma-70 78.9 7 0.00015 21.8 4.5 29 10-38 13-42 (78)
69 PRK10434 srlR DNA-bindng trans 78.5 5.3 0.00011 27.9 4.5 50 3-53 7-59 (256)
70 PF05584 Sulfolobus_pRN: Sulfo 78.4 10 0.00022 22.0 5.0 34 2-37 6-39 (72)
71 COG5187 RPN7 26S proteasome re 78.4 5.8 0.00013 29.5 4.8 76 2-77 317-403 (412)
72 cd04761 HTH_MerR-SF Helix-Turn 78.3 3.6 7.8E-05 20.8 2.9 24 18-42 2-25 (49)
73 PF00325 Crp: Bacterial regula 78.2 4.3 9.3E-05 19.9 2.9 20 17-36 3-22 (32)
74 PF13730 HTH_36: Helix-turn-he 77.8 4.6 9.9E-05 21.1 3.3 25 18-42 27-54 (55)
75 cd04235 AAK_CK AAK_CK: Carbama 77.4 3.7 8E-05 29.9 3.6 32 28-59 132-167 (308)
76 PF05344 DUF746: Domain of Unk 77.2 2.4 5.2E-05 24.3 2.1 41 10-50 7-50 (65)
77 PRK13500 transcriptional activ 77.2 6 0.00013 28.0 4.6 40 4-43 209-250 (312)
78 PLN03239 histone acetyltransfe 76.9 12 0.00026 27.9 6.2 52 3-54 268-322 (351)
79 PF06971 Put_DNA-bind_N: Putat 76.9 7.6 0.00017 20.9 3.9 27 9-35 21-47 (50)
80 TIGR01610 phage_O_Nterm phage 76.3 13 0.00028 22.1 5.2 42 13-54 44-90 (95)
81 PRK12354 carbamate kinase; Rev 76.0 8.2 0.00018 28.2 5.0 21 28-48 127-147 (307)
82 smart00422 HTH_MERR helix_turn 75.6 5.4 0.00012 21.7 3.3 24 18-42 2-25 (70)
83 PRK13501 transcriptional activ 75.4 7.2 0.00016 27.1 4.5 41 4-44 179-221 (290)
84 PF04967 HTH_10: HTH DNA bindi 75.3 5.7 0.00012 21.6 3.2 24 15-38 22-45 (53)
85 PF12802 MarR_2: MarR family; 75.0 9.1 0.0002 20.2 4.0 40 5-44 9-52 (62)
86 PF13542 HTH_Tnp_ISL3: Helix-t 74.9 9.6 0.00021 19.6 4.1 25 14-38 25-49 (52)
87 COG1349 GlpR Transcriptional r 74.8 17 0.00037 25.3 6.2 56 3-59 7-65 (253)
88 PRK10572 DNA-binding transcrip 74.6 7.9 0.00017 26.7 4.6 36 5-40 187-223 (290)
89 COG5484 Uncharacterized conser 74.5 3.7 8.1E-05 29.5 2.9 27 17-43 20-46 (279)
90 KOG2582 COP9 signalosome, subu 74.4 13 0.00029 28.2 5.9 60 5-64 306-370 (422)
91 COG0549 ArcC Carbamate kinase 74.1 9.7 0.00021 27.9 4.9 41 29-72 136-180 (312)
92 TIGR00122 birA_repr_reg BirA b 73.6 13 0.00028 20.4 6.0 41 4-46 3-46 (69)
93 PF13384 HTH_23: Homeodomain-l 73.2 9.7 0.00021 19.4 3.7 34 3-39 7-40 (50)
94 KOG1497 COP9 signalosome, subu 72.6 5 0.00011 30.1 3.2 32 8-39 309-340 (399)
95 PF03793 PASTA: PASTA domain; 72.6 4.6 9.9E-05 21.7 2.4 22 24-45 5-26 (63)
96 PF01047 MarR: MarR family; I 72.3 12 0.00026 19.6 4.5 38 6-44 8-48 (59)
97 smart00344 HTH_ASNC helix_turn 72.2 16 0.00034 21.6 4.9 40 4-44 6-48 (108)
98 PF06262 DUF1025: Possibl zinc 72.2 2.9 6.3E-05 25.5 1.7 21 18-42 77-97 (97)
99 PF00627 UBA: UBA/TS-N domain; 72.1 5.2 0.00011 19.6 2.4 26 19-45 6-31 (37)
100 PF13545 HTH_Crp_2: Crp-like h 71.7 10 0.00022 20.9 3.8 38 16-53 28-68 (76)
101 PRK11161 fumarate/nitrate redu 71.5 19 0.00041 24.0 5.7 51 2-52 156-223 (235)
102 PF09494 Slx4: Slx4 endonuclea 71.5 5.9 0.00013 22.0 2.7 32 13-44 21-61 (64)
103 cd04763 HTH_MlrA-like Helix-Tu 71.2 7.4 0.00016 21.3 3.1 52 18-79 2-54 (68)
104 COG2207 AraC AraC-type DNA-bin 71.1 16 0.00034 21.3 4.8 34 5-38 24-58 (127)
105 cd00092 HTH_CRP helix_turn_hel 70.9 14 0.0003 19.6 4.7 31 15-45 24-57 (67)
106 PF01710 HTH_Tnp_IS630: Transp 70.8 14 0.00031 22.7 4.6 40 7-46 62-101 (119)
107 PRK10681 DNA-binding transcrip 70.8 12 0.00025 26.0 4.7 41 3-44 9-52 (252)
108 cd04764 HTH_MlrA-like_sg1 Heli 70.5 8 0.00017 21.1 3.2 22 18-39 2-23 (67)
109 smart00420 HTH_DEOR helix_turn 70.2 12 0.00026 18.6 5.4 41 4-45 3-46 (53)
110 PF13411 MerR_1: MerR HTH fami 70.0 7.7 0.00017 21.0 3.0 50 18-78 2-52 (69)
111 PF04703 FaeA: FaeA-like prote 69.8 12 0.00026 21.0 3.7 42 3-44 2-46 (62)
112 PF14791 DNA_pol_B_thumb: DNA 69.8 3.8 8.2E-05 23.0 1.7 20 31-50 13-32 (64)
113 PLN00104 MYST -like histone ac 69.6 20 0.00043 27.6 6.0 51 3-53 361-411 (450)
114 TIGR02297 HpaA 4-hydroxyphenyl 69.5 13 0.00028 25.5 4.7 36 4-39 189-225 (287)
115 TIGR03879 near_KaiC_dom probab 69.1 20 0.00043 20.8 4.7 32 7-38 23-54 (73)
116 PRK12454 carbamate kinase-like 69.1 14 0.0003 27.0 4.9 20 28-47 136-155 (313)
117 PF13601 HTH_34: Winged helix 68.7 20 0.00044 20.7 5.4 74 2-80 1-77 (80)
118 cd08311 Death_p75NR Death doma 68.5 14 0.00029 21.5 3.9 36 3-38 2-37 (77)
119 cd07377 WHTH_GntR Winged helix 68.3 15 0.00033 19.1 4.6 29 16-44 24-56 (66)
120 smart00345 HTH_GNTR helix_turn 68.1 9.3 0.0002 19.6 3.0 29 16-44 19-51 (60)
121 PRK09685 DNA-binding transcrip 68.1 16 0.00035 25.3 4.9 39 4-42 200-240 (302)
122 PRK09391 fixK transcriptional 67.7 16 0.00034 24.6 4.7 43 2-44 155-210 (230)
123 PF13518 HTH_28: Helix-turn-he 67.5 15 0.00032 18.6 4.2 33 3-38 2-34 (52)
124 PF00531 Death: Death domain; 67.5 15 0.00033 20.4 4.0 34 5-39 2-35 (83)
125 PRK13239 alkylmercury lyase; P 67.3 27 0.00058 24.1 5.8 50 2-52 23-73 (206)
126 PF00376 MerR: MerR family reg 66.9 8.3 0.00018 19.3 2.5 24 18-42 1-24 (38)
127 PRK11753 DNA-binding transcrip 66.8 18 0.00039 23.5 4.8 39 16-54 168-209 (211)
128 PF02002 TFIIE_alpha: TFIIE al 66.7 14 0.0003 22.1 3.9 34 5-39 17-50 (105)
129 PF07453 NUMOD1: NUMOD1 domain 66.6 6.6 0.00014 19.2 2.1 18 18-35 18-35 (37)
130 TIGR02010 IscR iron-sulfur clu 66.4 29 0.00063 21.6 6.2 51 5-56 12-70 (135)
131 TIGR02944 suf_reg_Xantho FeS a 66.0 28 0.00061 21.4 6.3 40 5-44 13-56 (130)
132 PRK10163 DNA-binding transcrip 65.1 33 0.00072 23.9 6.1 48 5-52 29-80 (271)
133 PRK13918 CRP/FNR family transc 65.0 34 0.00075 22.0 6.6 52 2-53 121-189 (202)
134 KOG1076 Translation initiation 65.0 6.3 0.00014 32.2 2.6 45 9-54 711-763 (843)
135 PF13986 DUF4224: Domain of un 64.7 19 0.00041 18.9 4.7 34 17-50 3-39 (47)
136 PF04801 Sin_N: Sin-like prote 64.7 9.3 0.0002 28.5 3.4 42 2-44 338-387 (421)
137 COG1522 Lrp Transcriptional re 64.6 19 0.00042 22.4 4.4 35 3-38 10-44 (154)
138 PF01325 Fe_dep_repress: Iron 64.5 20 0.00042 19.6 3.9 32 13-44 19-53 (60)
139 PF07971 Glyco_hydro_92: Glyco 64.2 11 0.00025 29.1 3.8 52 5-57 233-287 (502)
140 PRK15185 transcriptional regul 63.9 16 0.00034 26.8 4.3 42 3-44 208-250 (309)
141 COG1777 Predicted transcriptio 63.3 15 0.00033 25.7 3.9 35 2-38 16-50 (217)
142 PF13591 MerR_2: MerR HTH fami 63.1 13 0.00029 21.6 3.2 27 17-44 1-27 (84)
143 PF13443 HTH_26: Cro/C1-type H 63.0 7.1 0.00015 20.8 1.9 26 15-40 9-34 (63)
144 COG1654 BirA Biotin operon rep 62.9 29 0.00062 20.4 5.4 49 9-57 12-65 (79)
145 COG4004 Uncharacterized protei 62.7 33 0.00071 21.0 5.3 54 27-80 9-79 (96)
146 PF00440 TetR_N: Bacterial reg 62.6 19 0.00042 18.3 3.6 28 9-36 9-36 (47)
147 PRK15482 transcriptional regul 62.3 16 0.00035 25.4 4.1 39 5-43 20-61 (285)
148 cd04766 HTH_HspR Helix-Turn-He 61.6 14 0.00031 21.5 3.2 26 17-43 2-27 (91)
149 PRK15186 AraC family transcrip 61.6 23 0.00051 25.3 4.8 39 3-41 183-222 (291)
150 PHA02591 hypothetical protein; 61.2 13 0.00028 22.2 2.9 23 17-39 60-82 (83)
151 PRK11569 transcriptional repre 60.9 41 0.00089 23.4 5.9 46 5-50 32-81 (274)
152 PRK13502 transcriptional activ 60.7 23 0.0005 24.2 4.6 40 4-43 179-220 (282)
153 PRK10371 DNA-binding transcrip 60.6 23 0.00049 25.1 4.6 37 4-40 194-231 (302)
154 PRK09978 DNA-binding transcrip 60.5 27 0.00059 25.0 5.0 38 4-41 145-183 (274)
155 PF12244 DUF3606: Protein of u 60.4 15 0.00031 20.1 2.9 23 19-41 23-45 (57)
156 smart00796 AHS1 Allophanate hy 60.3 13 0.00029 25.2 3.3 27 18-44 102-128 (201)
157 PF12793 SgrR_N: Sugar transpo 60.1 14 0.0003 23.0 3.1 29 15-43 18-49 (115)
158 TIGR01033 DNA-binding regulato 60.0 21 0.00045 25.0 4.3 47 29-80 176-225 (238)
159 PF02682 AHS1: Allophanate hyd 59.9 12 0.00025 25.5 2.9 30 16-45 99-128 (202)
160 PF10255 Paf67: RNA polymerase 59.8 16 0.00036 27.6 3.9 30 7-36 312-341 (404)
161 PRK11179 DNA-binding transcrip 59.7 26 0.00056 22.3 4.4 34 4-38 12-45 (153)
162 KOG2747 Histone acetyltransfer 59.5 25 0.00054 26.7 4.8 46 3-48 315-361 (396)
163 TIGR02431 pcaR_pcaU beta-ketoa 59.5 41 0.0009 22.9 5.6 41 5-45 13-56 (248)
164 PF08671 SinI: Anti-repressor 59.1 12 0.00027 18.0 2.2 17 22-38 11-27 (30)
165 PRK13509 transcriptional repre 59.0 28 0.00061 24.1 4.8 35 3-38 7-41 (251)
166 PF01709 Transcrip_reg: Transc 58.9 11 0.00024 26.2 2.7 46 31-81 177-222 (234)
167 PRK09411 carbamate kinase; Rev 58.7 31 0.00066 25.2 5.0 22 29-50 129-150 (297)
168 smart00165 UBA Ubiquitin assoc 58.5 2.3 4.9E-05 20.7 -0.6 20 27-46 12-31 (37)
169 PRK10219 DNA-binding transcrip 58.4 36 0.00078 20.0 4.8 40 5-44 9-50 (107)
170 KOG0488 Transcription factor B 58.1 6.4 0.00014 28.6 1.5 25 20-44 203-229 (309)
171 TIGR03697 NtcA_cyano global ni 58.1 46 0.00099 21.1 6.2 53 2-54 115-184 (193)
172 PRK04424 fatty acid biosynthes 57.6 29 0.00063 23.1 4.5 30 3-33 9-38 (185)
173 PF13551 HTH_29: Winged helix- 57.6 27 0.00057 20.3 4.0 34 4-39 2-35 (112)
174 PRK11302 DNA-binding transcrip 57.6 23 0.00049 24.4 4.1 40 4-43 19-61 (284)
175 PRK10046 dpiA two-component re 57.3 24 0.00053 23.3 4.1 34 5-38 166-199 (225)
176 TIGR02337 HpaR homoprotocatech 57.2 33 0.00071 20.6 4.4 39 5-44 32-73 (118)
177 PF09012 FeoC: FeoC like trans 56.8 20 0.00043 19.8 3.1 27 12-38 10-36 (69)
178 COG3413 Predicted DNA binding 56.7 16 0.00034 24.6 3.2 34 5-38 159-200 (215)
179 TIGR01889 Staph_reg_Sar staphy 56.6 39 0.00085 20.2 4.7 39 6-44 30-74 (109)
180 PF01978 TrmB: Sugar-specific 56.3 31 0.00068 18.7 4.4 32 13-44 19-53 (68)
181 PRK15090 DNA-binding transcrip 56.2 50 0.0011 22.7 5.7 39 5-44 18-59 (257)
182 PRK09802 DNA-binding transcrip 56.0 68 0.0015 22.5 8.4 50 3-53 19-71 (269)
183 smart00346 HTH_ICLR helix_turn 55.7 36 0.00077 19.2 4.7 41 5-45 9-52 (91)
184 PF01381 HTH_3: Helix-turn-hel 55.5 20 0.00044 18.3 2.9 24 16-39 9-32 (55)
185 PF05930 Phage_AlpA: Prophage 55.5 20 0.00044 18.7 2.9 23 16-38 3-25 (51)
186 TIGR00370 conserved hypothetic 55.3 18 0.00039 24.7 3.2 29 17-45 91-119 (202)
187 PF01329 Pterin_4a: Pterin 4 a 55.0 25 0.00055 20.8 3.5 19 28-46 5-24 (95)
188 PF04545 Sigma70_r4: Sigma-70, 54.9 27 0.00058 17.8 3.3 23 14-36 18-40 (50)
189 PF12833 HTH_18: Helix-turn-he 54.3 36 0.00078 18.8 4.3 26 14-39 43-69 (81)
190 PF15436 PGBA_N: Plasminogen-b 54.2 36 0.00079 23.8 4.6 37 4-40 102-146 (218)
191 COG1737 RpiR Transcriptional r 53.6 17 0.00036 25.6 3.0 39 5-43 22-63 (281)
192 PRK08558 adenine phosphoribosy 53.5 22 0.00048 24.7 3.5 30 6-38 16-45 (238)
193 PF01465 GRIP: GRIP domain; I 53.2 18 0.0004 18.9 2.4 18 19-36 28-45 (46)
194 PRK00110 hypothetical protein; 53.0 34 0.00073 24.1 4.4 44 33-81 181-224 (245)
195 PF11917 DUF3435: Protein of u 52.7 15 0.00033 27.3 2.8 38 10-47 231-271 (418)
196 PF04769 MAT_Alpha1: Mating-ty 52.7 30 0.00065 23.8 4.0 46 6-54 86-147 (201)
197 PF02954 HTH_8: Bacterial regu 52.2 27 0.00058 17.5 2.9 19 18-36 20-38 (42)
198 PRK11337 DNA-binding transcrip 52.2 29 0.00063 24.2 4.0 39 5-43 32-73 (292)
199 PRK13413 mpi multiple promoter 52.1 38 0.00083 22.4 4.4 35 4-41 163-197 (200)
200 PRK00823 phhB pterin-4-alpha-c 51.8 28 0.00061 20.8 3.4 20 28-47 6-26 (97)
201 PRK09834 DNA-binding transcrip 51.8 77 0.0017 21.9 6.0 44 5-48 15-62 (263)
202 PF08281 Sigma70_r4_2: Sigma-7 51.7 26 0.00056 18.0 2.9 27 12-38 22-48 (54)
203 PRK10402 DNA-binding transcrip 51.5 70 0.0015 21.3 6.3 51 2-52 151-208 (226)
204 PF12668 DUF3791: Protein of u 51.3 27 0.00059 19.1 3.1 23 18-40 7-29 (62)
205 PTZ00064 histone acetyltransfe 51.2 62 0.0013 25.6 5.8 38 17-54 472-509 (552)
206 PF05543 Peptidase_C47: Stapho 50.6 16 0.00035 24.7 2.4 39 8-47 47-85 (175)
207 PF11360 DUF3110: Protein of u 50.3 24 0.00051 21.0 2.8 27 29-55 56-85 (86)
208 PF02082 Rrf2: Transcriptional 50.3 45 0.00097 18.9 4.0 53 5-57 12-72 (83)
209 TIGR00746 arcC carbamate kinas 50.2 33 0.00072 24.9 4.1 20 28-47 133-152 (310)
210 PF10141 ssDNA-exonuc_C: Singl 50.1 56 0.0012 21.8 5.0 46 14-59 110-162 (195)
211 COG1724 Predicted RNA binding 49.8 16 0.00035 20.9 2.0 21 24-44 3-23 (66)
212 COG3357 Predicted transcriptio 49.5 36 0.00078 20.8 3.5 32 2-33 4-36 (97)
213 PRK11557 putative DNA-binding 49.5 36 0.00077 23.5 4.1 39 5-43 16-57 (278)
214 PRK09392 ftrB transcriptional 49.2 55 0.0012 21.7 4.9 37 2-38 149-195 (236)
215 PF02796 HTH_7: Helix-turn-hel 49.0 36 0.00078 17.2 3.5 31 4-37 12-42 (45)
216 TIGR03613 RutR pyrimidine util 48.7 32 0.00069 22.2 3.6 22 9-30 21-42 (202)
217 KOG0687 26S proteasome regulat 48.7 60 0.0013 24.5 5.2 59 2-60 303-367 (393)
218 COG0217 Uncharacterized conser 48.7 43 0.00094 23.8 4.3 46 31-81 181-226 (241)
219 PRK05988 formate dehydrogenase 48.4 49 0.0011 21.6 4.4 33 6-38 28-63 (156)
220 TIGR01958 nuoE_fam NADH-quinon 47.8 48 0.001 21.2 4.2 33 6-38 21-56 (148)
221 PRK10411 DNA-binding transcrip 47.6 91 0.002 21.5 8.6 49 3-52 6-57 (240)
222 PRK12378 hypothetical protein; 47.2 47 0.001 23.3 4.3 43 33-80 180-222 (235)
223 PHA02535 P terminase ATPase su 47.1 35 0.00075 27.2 4.0 40 2-44 7-46 (581)
224 cd00086 homeodomain Homeodomai 46.8 30 0.00066 17.7 2.7 22 19-40 30-51 (59)
225 PRK09940 transcriptional regul 46.7 57 0.0012 23.1 4.8 37 5-41 138-175 (253)
226 PHA00738 putative HTH transcri 46.5 69 0.0015 20.0 4.6 36 2-38 13-48 (108)
227 cd08784 Death_DRs Death Domain 46.2 24 0.00052 20.3 2.4 20 19-38 14-33 (79)
228 COG3604 FhlA Transcriptional r 46.1 43 0.00092 26.5 4.3 40 3-44 508-547 (550)
229 PRK12702 mannosyl-3-phosphogly 45.8 23 0.00049 25.9 2.7 30 12-42 119-148 (302)
230 smart00530 HTH_XRE Helix-turn- 45.5 34 0.00074 16.1 2.7 23 15-37 9-31 (56)
231 PRK09975 DNA-binding transcrip 45.4 35 0.00075 22.2 3.4 22 9-30 24-45 (213)
232 PRK09393 ftrA transcriptional 44.9 56 0.0012 23.1 4.5 40 5-44 222-263 (322)
233 COG2944 Predicted transcriptio 44.7 29 0.00063 21.5 2.7 20 16-35 57-76 (104)
234 cd08318 Death_NMPP84 Death dom 44.6 26 0.00056 20.5 2.4 20 19-38 21-40 (86)
235 PF07022 Phage_CI_repr: Bacter 44.5 32 0.00069 18.9 2.7 28 7-34 3-30 (66)
236 PF13994 PgaD: PgaD-like prote 44.4 31 0.00068 21.9 2.9 24 17-40 101-124 (138)
237 TIGR00498 lexA SOS regulatory 44.4 90 0.0019 20.5 5.5 47 3-49 8-62 (199)
238 TIGR00472 pheT_bact phenylalan 44.3 1.1E+02 0.0023 25.0 6.5 33 16-48 409-443 (798)
239 PRK14584 hmsS hemin storage sy 44.2 93 0.002 20.6 5.2 41 15-55 97-139 (153)
240 PRK03573 transcriptional regul 44.0 73 0.0016 19.7 4.6 39 6-44 36-77 (144)
241 PF12046 DUF3529: Protein of u 44.0 43 0.00093 22.6 3.6 26 31-56 47-75 (173)
242 cd04772 HTH_TioE_rpt1 First He 43.9 69 0.0015 19.0 5.1 46 18-73 2-48 (99)
243 cd01109 HTH_YyaN Helix-Turn-He 43.7 72 0.0016 19.2 5.5 49 18-76 2-51 (113)
244 PRK03902 manganese transport t 43.7 80 0.0017 19.7 5.9 35 10-44 16-53 (142)
245 PF08811 DUF1800: Protein of u 43.5 61 0.0013 24.6 4.8 35 27-61 196-237 (462)
246 PF03752 ALF: Short repeats of 43.4 47 0.001 16.9 3.0 39 3-43 1-40 (43)
247 cd08315 Death_TRAILR_DR4_DR5 D 43.1 55 0.0012 19.6 3.7 21 18-38 21-41 (96)
248 cd01107 HTH_BmrR Helix-Turn-He 42.8 74 0.0016 19.1 5.4 48 18-74 2-50 (108)
249 PF10743 Phage_Cox: Regulatory 42.6 61 0.0013 19.5 3.7 30 10-39 6-35 (87)
250 COG2345 Predicted transcriptio 42.5 65 0.0014 22.5 4.4 36 2-38 12-47 (218)
251 cd00592 HTH_MerR-like Helix-Tu 42.4 45 0.00097 19.4 3.2 24 18-42 2-25 (100)
252 smart00351 PAX Paired Box doma 42.3 83 0.0018 19.5 4.7 35 2-39 22-56 (125)
253 PF01726 LexA_DNA_bind: LexA D 42.3 53 0.0011 18.3 3.3 42 3-44 8-57 (65)
254 KOG2908 26S proteasome regulat 42.2 1.5E+02 0.0033 22.4 7.1 66 5-74 277-355 (380)
255 KOG1464 COP9 signalosome, subu 42.2 50 0.0011 24.7 3.9 38 2-39 350-387 (440)
256 cd08777 Death_RIP1 Death Domai 42.1 30 0.00066 20.3 2.4 20 19-38 16-35 (86)
257 PRK10857 DNA-binding transcrip 41.4 1E+02 0.0022 20.2 6.3 40 16-56 25-70 (164)
258 TIGR02051 MerR Hg(II)-responsi 41.4 63 0.0014 19.9 3.9 19 18-36 1-19 (124)
259 PF09756 DDRGK: DDRGK domain; 41.3 53 0.0012 22.3 3.8 43 15-57 112-160 (188)
260 cd00090 HTH_ARSR Arsenical Res 41.3 53 0.0011 16.9 5.1 40 3-44 9-51 (78)
261 PF00046 Homeobox: Homeobox do 41.1 44 0.00095 17.3 2.8 21 19-39 30-50 (57)
262 PRK14101 bifunctional glucokin 41.0 47 0.001 26.1 3.9 40 4-43 359-401 (638)
263 TIGR02531 yecD_yerC TrpR-relat 41.0 78 0.0017 18.8 4.2 33 3-38 40-72 (88)
264 PF13936 HTH_38: Helix-turn-he 40.9 51 0.0011 16.7 3.5 33 3-38 10-42 (44)
265 PF12643 MazG-like: MazG-like 40.9 67 0.0015 19.5 3.9 32 2-39 37-68 (98)
266 cd04765 HTH_MlrA-like_sg2 Heli 40.8 46 0.001 19.9 3.1 50 18-77 2-52 (99)
267 cd08317 Death_ank Death domain 40.8 40 0.00086 19.4 2.8 22 17-38 16-37 (84)
268 PF13613 HTH_Tnp_4: Helix-turn 40.8 56 0.0012 17.1 4.2 38 1-38 4-41 (53)
269 PF00392 GntR: Bacterial regul 40.8 33 0.00071 18.5 2.3 30 15-44 22-55 (64)
270 COG5340 Predicted transcriptio 40.7 53 0.0012 23.5 3.8 49 9-57 23-75 (269)
271 cd06577 PASTA_pknB PASTA domai 40.5 50 0.0011 16.5 3.8 22 24-45 4-25 (62)
272 TIGR01884 cas_HTH CRISPR locus 40.5 97 0.0021 20.6 5.0 40 5-45 147-189 (203)
273 PRK15121 right oriC-binding tr 40.4 74 0.0016 22.1 4.6 35 5-39 9-44 (289)
274 PF04963 Sigma54_CBD: Sigma-54 40.3 21 0.00045 23.9 1.7 37 11-48 47-83 (194)
275 smart00347 HTH_MARR helix_turn 40.3 67 0.0015 17.9 4.5 40 4-44 13-55 (101)
276 cd01279 HTH_HspR-like Helix-Tu 40.0 50 0.0011 19.6 3.2 25 17-42 2-26 (98)
277 PRK07539 NADH dehydrogenase su 39.6 77 0.0017 20.4 4.3 33 6-38 27-62 (154)
278 cd01105 HTH_GlnR-like Helix-Tu 39.6 44 0.00095 19.4 2.9 21 18-38 3-23 (88)
279 PRK06266 transcription initiat 39.4 85 0.0018 20.9 4.5 35 4-39 25-59 (178)
280 TIGR02394 rpoS_proteo RNA poly 39.3 36 0.00078 23.9 2.8 32 14-45 240-282 (285)
281 smart00513 SAP Putative DNA-bi 39.3 34 0.00073 16.5 2.0 19 27-45 3-21 (35)
282 smart00389 HOX Homeodomain. DN 39.3 47 0.001 16.9 2.7 22 19-40 30-51 (56)
283 PRK15044 transcriptional regul 39.2 91 0.002 22.7 4.9 38 4-41 195-233 (295)
284 KOG1860 Nuclear protein export 39.1 1.1E+02 0.0024 25.9 5.8 56 1-56 367-427 (927)
285 PF02943 FeThRed_B: Ferredoxin 39.1 23 0.00051 22.0 1.7 19 32-50 9-27 (108)
286 PF11972 HTH_13: HTH DNA bindi 39.1 55 0.0012 17.9 3.0 29 13-41 10-38 (54)
287 TIGR00471 pheT_arch phenylalan 39.0 1.2E+02 0.0026 23.6 5.9 33 16-48 281-315 (551)
288 PRK05472 redox-sensing transcr 38.9 70 0.0015 21.4 4.1 33 3-35 18-51 (213)
289 PHA01976 helix-turn-helix prot 38.9 46 0.00099 17.7 2.7 23 14-36 13-35 (67)
290 PRK11920 rirA iron-responsive 38.5 1.1E+02 0.0023 19.7 6.3 53 6-58 13-72 (153)
291 PF07381 DUF1495: Winged helix 38.3 90 0.0019 18.7 4.8 44 2-45 10-54 (90)
292 PF11625 DUF3253: Protein of u 38.1 49 0.0011 19.7 2.9 27 2-28 8-36 (83)
293 PRK09645 RNA polymerase sigma 38.0 66 0.0014 20.2 3.7 23 12-34 130-152 (173)
294 COG4802 FtrB Ferredoxin-thiore 37.7 27 0.00059 21.8 1.8 17 32-48 12-28 (110)
295 COG0072 PheT Phenylalanyl-tRNA 37.4 1.6E+02 0.0035 23.6 6.4 34 16-49 268-303 (650)
296 PRK09616 pheT phenylalanyl-tRN 37.3 1.5E+02 0.0032 23.1 6.1 33 16-48 278-312 (552)
297 PRK12515 RNA polymerase sigma 37.3 53 0.0012 21.1 3.3 22 12-33 143-164 (189)
298 PRK00629 pheT phenylalanyl-tRN 37.3 1.9E+02 0.004 23.7 6.8 33 16-48 404-438 (791)
299 cd08306 Death_FADD Fas-associa 37.1 40 0.00086 19.7 2.4 22 19-40 16-37 (86)
300 PF09840 DUF2067: Uncharacteri 36.9 61 0.0013 22.0 3.6 48 5-52 120-179 (190)
301 PHA01083 hypothetical protein 36.8 89 0.0019 20.7 4.1 35 3-37 3-37 (149)
302 PF01257 2Fe-2S_thioredx: Thio 36.8 85 0.0018 20.0 4.1 33 6-38 18-53 (145)
303 PF08986 DUF1889: Domain of un 36.7 31 0.00067 21.5 1.9 19 26-44 60-80 (119)
304 PRK14996 TetR family transcrip 36.6 47 0.001 21.3 2.9 22 9-30 21-42 (192)
305 smart00421 HTH_LUXR helix_turn 36.6 58 0.0013 16.0 4.6 26 13-38 15-40 (58)
306 TIGR03209 P21_Cbot clostridium 36.5 62 0.0013 19.7 3.3 22 12-33 119-140 (142)
307 PF14898 DUF4491: Domain of un 36.5 67 0.0015 19.6 3.3 34 16-58 54-93 (94)
308 cd08319 Death_RAIDD Death doma 36.3 41 0.0009 19.7 2.4 20 19-38 16-35 (83)
309 PRK09974 putative regulator Pr 36.3 43 0.00093 21.0 2.5 33 40-80 38-70 (111)
310 cd04774 HTH_YfmP Helix-Turn-He 36.2 60 0.0013 19.2 3.1 25 18-43 2-26 (96)
311 TIGR03338 phnR_burk phosphonat 36.2 1.2E+02 0.0027 19.8 5.5 42 3-44 21-65 (212)
312 PF00356 LacI: Bacterial regul 36.1 65 0.0014 16.7 2.9 19 19-37 2-20 (46)
313 PF01171 ATP_bind_3: PP-loop f 36.1 35 0.00076 22.1 2.3 26 22-47 141-166 (182)
314 TIGR00373 conserved hypothetic 36.0 49 0.0011 21.6 2.9 23 16-38 28-50 (158)
315 smart00311 PWI PWI, domain in 35.9 48 0.001 18.7 2.6 20 20-39 15-34 (74)
316 PF04433 SWIRM: SWIRM domain; 35.9 87 0.0019 17.9 5.2 42 2-43 38-84 (86)
317 COG4388 Mu-like prophage I pro 35.7 38 0.00083 25.1 2.5 21 21-41 337-357 (357)
318 PRK11512 DNA-binding transcrip 35.5 1.1E+02 0.0024 19.0 4.7 38 6-44 45-85 (144)
319 TIGR00738 rrf2_super rrf2 fami 34.9 1.1E+02 0.0023 18.6 5.7 39 6-44 13-56 (132)
320 PRK08349 hypothetical protein; 34.6 68 0.0015 21.1 3.5 21 21-41 137-157 (198)
321 PRK00430 fis global DNA-bindin 34.5 67 0.0015 19.2 3.1 23 18-40 70-92 (95)
322 PRK04217 hypothetical protein; 34.4 1.2E+02 0.0025 18.9 4.6 29 8-36 49-78 (110)
323 cd01670 Death Death Domain: a 34.4 83 0.0018 17.2 4.0 31 4-39 3-33 (79)
324 cd04773 HTH_TioE_rpt2 Second H 34.3 59 0.0013 19.6 2.9 21 18-38 2-22 (108)
325 PRK15435 bifunctional DNA-bind 34.3 1E+02 0.0022 22.6 4.6 34 5-39 89-122 (353)
326 TIGR03070 couple_hipB transcri 34.2 67 0.0015 16.1 2.8 23 15-37 14-36 (58)
327 PRK07571 bidirectional hydroge 34.1 1.1E+02 0.0024 20.3 4.4 33 6-38 41-76 (169)
328 cd08779 Death_PIDD Death Domai 34.1 47 0.001 19.4 2.4 21 19-39 16-36 (86)
329 PRK04214 rbn ribonuclease BN/u 33.9 1.6E+02 0.0035 21.9 5.7 53 6-58 297-355 (412)
330 PRK14165 winged helix-turn-hel 33.5 68 0.0015 22.2 3.4 31 14-44 19-52 (217)
331 PRK09685 DNA-binding transcrip 33.3 1E+02 0.0022 21.2 4.3 33 7-39 255-288 (302)
332 PF10702 DUF2507: Protein of u 33.2 33 0.0007 21.9 1.6 24 20-43 29-53 (124)
333 PHA02552 4 head completion pro 33.1 39 0.00086 22.2 2.1 14 31-44 121-134 (151)
334 COG3093 VapI Plasmid maintenan 33.1 60 0.0013 20.1 2.8 25 16-40 23-47 (104)
335 PF07900 DUF1670: Protein of u 33.0 1.2E+02 0.0026 21.2 4.6 36 3-38 89-127 (220)
336 cd01106 HTH_TipAL-Mta Helix-Tu 33.0 64 0.0014 19.1 2.9 23 18-41 2-24 (103)
337 PF10108 DNA_pol_B_exo2: Predi 33.0 48 0.001 22.9 2.6 15 15-29 115-129 (209)
338 PF08383 Maf_N: Maf N-terminal 32.8 44 0.00096 16.8 1.8 15 24-38 19-33 (35)
339 cd00194 UBA Ubiquitin Associat 32.7 35 0.00075 16.3 1.4 20 26-45 11-30 (38)
340 PRK09210 RNA polymerase sigma 32.6 87 0.0019 23.0 4.1 21 18-38 234-254 (367)
341 cd00131 PAX Paired Box domain 32.6 1.3E+02 0.0028 18.8 4.7 34 2-38 22-55 (128)
342 smart00005 DEATH DEATH domain, 32.6 65 0.0014 18.1 2.8 23 17-39 18-40 (88)
343 PF10415 FumaraseC_C: Fumarase 32.5 87 0.0019 16.9 3.9 33 5-37 13-47 (55)
344 PF13413 HTH_25: Helix-turn-he 32.5 43 0.00093 18.4 1.9 15 19-33 48-62 (62)
345 COG1321 TroR Mn-dependent tran 32.4 1.1E+02 0.0024 19.9 4.1 34 11-44 19-55 (154)
346 PRK10141 DNA-binding transcrip 32.3 1.3E+02 0.0028 18.7 4.6 42 2-44 17-61 (117)
347 COG1309 AcrR Transcriptional r 32.1 57 0.0012 19.4 2.6 22 9-30 25-46 (201)
348 PF10165 Ric8: Guanine nucleot 32.1 44 0.00095 25.3 2.5 42 1-43 308-350 (446)
349 TIGR00637 ModE_repress ModE mo 32.0 1.2E+02 0.0025 18.2 4.0 40 5-44 5-44 (99)
350 PF12401 DUF3662: Protein of u 31.9 91 0.002 19.2 3.5 32 16-47 58-96 (116)
351 PRK10360 DNA-binding transcrip 31.5 1.1E+02 0.0024 18.9 4.0 31 5-38 144-174 (196)
352 KOG0259 Tyrosine aminotransfer 31.5 96 0.0021 23.9 4.1 42 37-78 180-230 (447)
353 cd00141 NT_POLXc Nucleotidyltr 31.4 39 0.00084 24.3 2.0 28 22-49 244-276 (307)
354 smart00857 Resolvase Resolvase 31.3 31 0.00068 21.2 1.3 32 13-45 3-36 (148)
355 PHA00542 putative Cro-like pro 31.1 68 0.0015 18.4 2.7 23 16-38 31-53 (82)
356 PRK15340 transcriptional regul 30.9 80 0.0017 21.9 3.4 31 9-39 118-148 (216)
357 PRK13869 plasmid-partitioning 30.8 1.6E+02 0.0035 22.0 5.2 55 13-77 45-100 (405)
358 TIGR02293 TAS_TIGR02293 putati 30.6 89 0.0019 19.6 3.4 30 7-36 16-45 (133)
359 PRK09954 putative kinase; Prov 30.5 1.3E+02 0.0029 21.5 4.6 40 3-43 5-47 (362)
360 TIGR02366 DHAK_reg probable di 30.5 66 0.0014 20.2 2.8 22 9-30 16-37 (176)
361 PRK00215 LexA repressor; Valid 30.4 1.6E+02 0.0035 19.3 4.8 41 4-44 7-55 (205)
362 COG1709 Predicted transcriptio 30.3 46 0.00099 23.6 2.1 16 15-30 39-54 (241)
363 PF09107 SelB-wing_3: Elongati 30.0 94 0.002 16.5 4.8 34 13-46 7-43 (50)
364 KOG2072 Translation initiation 30.0 70 0.0015 26.9 3.3 35 4-38 435-470 (988)
365 PF14821 Thr_synth_N: Threonin 29.9 68 0.0015 18.4 2.5 33 6-38 42-76 (79)
366 PF09278 MerR-DNA-bind: MerR, 29.6 54 0.0012 17.5 2.0 18 21-38 8-25 (65)
367 KOG0848 Transcription factor C 29.5 45 0.00098 24.4 2.0 27 14-40 223-250 (317)
368 cd08804 Death_ank2 Death domai 29.4 79 0.0017 18.4 2.8 20 19-38 18-37 (84)
369 COG3311 AlpA Predicted transcr 29.4 1.2E+02 0.0026 17.4 3.7 43 12-64 9-51 (70)
370 PF11338 DUF3140: Protein of u 29.3 46 0.00099 20.2 1.8 23 23-45 3-30 (92)
371 PF08992 QH-AmDH_gamma: Quinoh 29.3 18 0.00039 21.2 -0.0 12 39-50 11-22 (78)
372 PF10078 DUF2316: Uncharacteri 29.3 79 0.0017 19.0 2.8 33 6-38 11-45 (89)
373 cd00569 HTH_Hin_like Helix-tur 29.2 58 0.0012 13.8 3.9 21 15-35 20-40 (42)
374 TIGR02607 antidote_HigA addict 29.2 81 0.0018 17.2 2.8 24 15-38 17-40 (78)
375 PLN02705 beta-amylase 29.1 53 0.0012 26.6 2.5 26 31-57 122-147 (681)
376 cd04768 HTH_BmrR-like Helix-Tu 29.1 89 0.0019 18.3 3.0 21 18-38 2-22 (96)
377 PRK07921 RNA polymerase sigma 29.1 1.3E+02 0.0028 21.9 4.4 21 18-38 191-211 (324)
378 COG2901 Fis Factor for inversi 29.1 82 0.0018 19.3 2.8 29 13-41 68-96 (98)
379 PRK02101 hypothetical protein; 29.0 1.4E+02 0.0029 21.0 4.4 34 11-44 35-69 (255)
380 PRK01905 DNA-binding protein F 28.9 98 0.0021 17.5 3.1 23 18-40 52-74 (77)
381 cd00118 LysM Lysin domain, fou 28.9 67 0.0015 14.4 2.8 18 19-36 11-28 (46)
382 TIGR03384 betaine_BetI transcr 28.8 92 0.002 19.5 3.3 22 9-30 21-42 (189)
383 PF13560 HTH_31: Helix-turn-he 28.8 83 0.0018 16.7 2.7 24 15-38 13-36 (64)
384 cd04790 HTH_Cfa-like_unk Helix 28.7 1.7E+02 0.0038 19.1 5.4 46 17-72 2-48 (172)
385 PF11242 DUF2774: Protein of u 28.7 1E+02 0.0023 17.4 3.0 20 17-36 14-33 (63)
386 PF09820 AAA-ATPase_like: Pred 28.7 56 0.0012 23.1 2.4 20 21-40 218-237 (284)
387 PLN02265 probable phenylalanyl 28.6 1.2E+02 0.0027 23.9 4.5 31 16-46 313-345 (597)
388 PRK05657 RNA polymerase sigma 28.6 79 0.0017 22.8 3.2 33 13-45 279-322 (325)
389 PF07942 N2227: N2227-like pro 28.5 62 0.0014 23.2 2.6 20 26-45 219-238 (270)
390 smart00755 Grip golgin-97, Ran 28.5 98 0.0021 16.2 3.4 35 3-37 8-44 (46)
391 cd08313 Death_TNFR1 Death doma 28.4 67 0.0015 18.7 2.4 18 19-36 14-31 (80)
392 PF11193 DUF2812: Protein of u 28.4 1.4E+02 0.003 17.8 5.2 32 30-61 53-86 (115)
393 cd04767 HTH_HspR-like_MBC Heli 28.4 94 0.002 19.5 3.2 49 17-77 2-51 (120)
394 PF05491 RuvB_C: Holliday junc 28.2 1.2E+02 0.0026 17.7 3.4 51 3-53 10-67 (76)
395 PF06744 DUF1215: Protein of u 28.0 76 0.0016 19.6 2.7 35 13-47 61-104 (125)
396 PRK10296 DNA-binding transcrip 28.0 1.5E+02 0.0032 20.2 4.4 31 13-43 234-266 (278)
397 PRK10265 chaperone-modulator p 27.9 66 0.0014 19.3 2.3 30 14-44 5-34 (101)
398 PRK07408 RNA polymerase sigma 27.9 1.4E+02 0.0031 20.5 4.3 19 18-36 131-149 (256)
399 cd06170 LuxR_C_like C-terminal 27.8 88 0.0019 15.4 4.6 25 14-38 13-37 (57)
400 KOG2758 Translation initiation 27.7 1.4E+02 0.003 22.7 4.3 52 7-58 340-398 (432)
401 cd04789 HTH_Cfa Helix-Turn-Hel 27.7 98 0.0021 18.4 3.1 46 17-73 2-48 (102)
402 PRK15008 HTH-type transcriptio 27.6 1E+02 0.0022 20.2 3.4 22 9-30 31-52 (212)
403 PF07927 YcfA: YcfA-like prote 27.6 70 0.0015 16.6 2.2 16 31-46 2-17 (56)
404 smart00531 TFIIE Transcription 27.4 85 0.0018 20.0 2.9 25 15-39 14-38 (147)
405 KOG3964 Phosphatidylglycerolph 27.4 24 0.00051 27.2 0.3 44 8-51 341-386 (469)
406 cd04780 HTH_MerR-like_sg5 Heli 27.3 1.4E+02 0.003 17.6 5.1 49 18-76 2-51 (95)
407 PRK00767 transcriptional regul 27.3 1.1E+02 0.0025 19.3 3.5 22 9-30 22-43 (197)
408 PF00690 Cation_ATPase_N: Cati 27.1 1E+02 0.0023 16.6 2.9 29 14-42 1-35 (69)
409 PRK13182 racA polar chromosome 27.0 92 0.002 20.8 3.1 22 18-39 2-23 (175)
410 PRK14000 potassium-transportin 27.0 51 0.0011 22.5 1.9 30 10-39 132-161 (185)
411 smart00354 HTH_LACI helix_turn 27.0 1E+02 0.0022 16.9 2.9 12 33-44 35-46 (70)
412 KOG0483 Transcription factor H 27.0 72 0.0016 21.9 2.6 39 6-44 61-107 (198)
413 PRK07598 RNA polymerase sigma 26.9 1.6E+02 0.0036 22.4 4.7 23 17-39 279-301 (415)
414 PRK15201 fimbriae regulatory p 26.7 1.6E+02 0.0034 20.4 4.2 32 4-38 139-170 (198)
415 PHA00675 hypothetical protein 26.5 1.5E+02 0.0032 17.5 4.2 31 16-46 39-69 (78)
416 COG4753 Response regulator con 26.5 1.4E+02 0.0031 23.2 4.4 37 4-40 375-412 (475)
417 PF08219 TOM13: Outer membrane 26.4 70 0.0015 18.9 2.1 28 24-55 48-75 (77)
418 PHA02943 hypothetical protein; 26.4 1.7E+02 0.0037 19.6 4.2 31 4-36 14-44 (165)
419 PF03943 TAP_C: TAP C-terminal 26.3 13 0.00028 19.8 -0.9 36 20-55 5-40 (51)
420 PRK14003 potassium-transportin 26.2 53 0.0012 22.5 1.9 30 10-39 136-165 (194)
421 TIGR03830 CxxCG_CxxCG_HTH puta 26.2 86 0.0019 18.8 2.7 19 16-34 78-96 (127)
422 PRK13999 potassium-transportin 26.2 54 0.0012 22.7 1.9 30 10-39 142-171 (201)
423 cd04782 HTH_BltR Helix-Turn-He 26.1 1E+02 0.0022 18.1 2.9 21 18-38 2-22 (97)
424 cd00093 HTH_XRE Helix-turn-hel 26.1 85 0.0018 14.7 2.8 24 15-38 11-34 (58)
425 PF10671 TcpQ: Toxin co-regula 26.0 61 0.0013 18.6 1.9 15 30-44 13-27 (84)
426 PF00126 HTH_1: Bacterial regu 26.0 1.1E+02 0.0025 16.1 4.0 30 10-39 7-36 (60)
427 cd00808 GluRS_core catalytic c 26.0 1.5E+02 0.0032 20.8 4.1 35 9-44 162-196 (239)
428 TIGR00027 mthyl_TIGR00027 meth 25.8 77 0.0017 22.2 2.7 20 27-46 228-247 (260)
429 PF04391 DUF533: Protein of un 25.7 1.2E+02 0.0026 20.6 3.5 26 10-39 161-186 (188)
430 PF09743 DUF2042: Uncharacteri 25.7 1.9E+02 0.0041 20.7 4.6 48 2-50 56-108 (272)
431 PLN02627 glutamyl-tRNA synthet 25.7 78 0.0017 25.0 2.9 37 9-46 293-329 (535)
432 PRK00315 potassium-transportin 25.7 55 0.0012 22.4 1.9 30 10-39 133-162 (193)
433 TIGR03826 YvyF flagellar opero 25.6 1.3E+02 0.0028 19.4 3.5 38 17-54 47-84 (137)
434 smart00740 PASTA PASTA domain. 25.5 96 0.0021 15.7 2.5 22 24-45 9-30 (66)
435 PF02413 Caudo_TAP: Caudoviral 25.5 1.4E+02 0.0031 18.5 3.6 33 4-36 69-102 (130)
436 PRK14001 potassium-transportin 25.4 56 0.0012 22.3 1.8 30 10-39 133-162 (189)
437 PF03428 RP-C: Replication pro 25.3 74 0.0016 21.3 2.4 39 19-58 32-76 (177)
438 PF03462 PCRF: PCRF domain; I 25.3 55 0.0012 20.1 1.7 12 34-45 73-84 (115)
439 PF08221 HTH_9: RNA polymerase 24.9 1.3E+02 0.0028 16.4 3.8 32 5-37 17-48 (62)
440 PRK11426 hypothetical protein; 24.9 1.5E+02 0.0032 19.1 3.6 31 8-38 64-94 (132)
441 PF01476 LysM: LysM domain; I 24.9 96 0.0021 14.9 2.5 17 20-36 10-26 (44)
442 PRK10870 transcriptional repre 24.9 1.2E+02 0.0027 19.7 3.4 30 15-44 70-102 (176)
443 TIGR03853 matur_matur probable 24.8 1.6E+02 0.0034 17.3 4.0 29 22-50 39-67 (77)
444 PF00867 XPG_I: XPG I-region; 24.7 1E+02 0.0023 17.9 2.8 25 14-38 65-89 (94)
445 PF07345 DUF1476: Domain of un 24.7 26 0.00057 21.6 0.1 18 22-39 37-54 (103)
446 cd03472 Rieske_RO_Alpha_BPDO_l 24.7 54 0.0012 20.4 1.6 16 39-54 73-89 (128)
447 PF07471 Phage_Nu1: Phage DNA 24.4 74 0.0016 21.1 2.2 23 16-38 2-24 (164)
448 PF07957 DUF3294: Protein of u 24.4 44 0.00095 23.4 1.2 25 5-29 180-208 (216)
449 PF03278 IpaB_EvcA: IpaB/EvcA 24.3 54 0.0012 21.7 1.5 19 2-21 66-84 (152)
450 cd01389 MATA_HMG-box MATA_HMG- 24.3 1.4E+02 0.003 16.5 3.4 41 6-46 32-73 (77)
451 PF07862 Nif11: Nitrogen fixat 24.2 51 0.0011 16.9 1.2 18 29-46 28-45 (49)
452 TIGR02937 sigma70-ECF RNA poly 24.2 1.2E+02 0.0027 17.7 3.1 25 14-38 124-148 (158)
453 KOG1344 Predicted histone deac 24.1 52 0.0011 23.8 1.5 22 33-54 124-145 (324)
454 PF11800 RP-C_C: Replication p 24.1 96 0.0021 20.8 2.8 25 20-44 134-158 (207)
455 PF12844 HTH_19: Helix-turn-he 24.1 1E+02 0.0023 16.1 2.5 23 16-38 12-34 (64)
456 COG3753 Uncharacterized protei 24.1 1.4E+02 0.003 19.6 3.3 32 8-39 82-113 (143)
457 PF01747 ATP-sulfurylase: ATP- 24.0 55 0.0012 22.6 1.6 17 27-43 5-21 (215)
458 PF02669 KdpC: K+-transporting 24.0 66 0.0014 22.0 2.0 30 10-39 132-161 (188)
459 PRK09726 antitoxin HipB; Provi 24.0 1.5E+02 0.0033 16.9 4.4 22 16-37 25-46 (88)
460 PLN03083 E3 UFM1-protein ligas 23.9 1.7E+02 0.0037 24.4 4.5 36 2-38 61-96 (803)
461 TIGR01784 T_den_put_tspse cons 23.9 1.3E+02 0.0029 20.2 3.5 20 16-35 250-269 (270)
462 cd08803 Death_ank3 Death domai 23.9 93 0.002 18.2 2.4 20 19-38 18-37 (84)
463 cd08805 Death_ank1 Death domai 23.7 1.1E+02 0.0025 17.9 2.8 21 19-39 18-38 (84)
464 PF06870 RNA_pol_I_A49: A49-li 23.7 1.5E+02 0.0033 21.7 4.0 40 6-46 310-349 (385)
465 TIGR02395 rpoN_sigma RNA polym 23.6 1.1E+02 0.0024 23.3 3.3 39 11-50 108-146 (429)
466 TIGR03453 partition_RepA plasm 23.5 2.9E+02 0.0062 20.2 5.4 52 16-77 33-85 (387)
467 PRK15429 formate hydrogenlyase 23.3 2E+02 0.0044 22.8 4.8 40 3-42 643-683 (686)
468 cd04775 HTH_Cfa-like Helix-Tur 23.3 1.3E+02 0.0028 17.8 3.0 50 17-77 2-52 (102)
469 TIGR00681 kdpC K+-transporting 23.2 66 0.0014 22.0 1.8 30 10-39 131-160 (187)
470 PF05331 DUF742: Protein of un 23.2 92 0.002 19.5 2.4 31 4-37 46-76 (114)
471 TIGR02989 Sig-70_gvs1 RNA poly 23.1 1.9E+02 0.0041 17.7 4.4 25 12-36 123-147 (159)
472 COG1414 IclR Transcriptional r 23.0 2.3E+02 0.005 19.5 4.6 42 5-46 8-53 (246)
473 cd01388 SOX-TCF_HMG-box SOX-TC 23.0 1.4E+02 0.0031 16.3 3.0 35 9-43 35-70 (72)
474 PF13167 GTP-bdg_N: GTP-bindin 22.9 1.8E+02 0.004 17.5 4.9 46 29-77 9-54 (95)
475 PRK10130 transcriptional regul 22.8 2.2E+02 0.0047 20.9 4.6 35 5-39 244-279 (350)
476 PF07093 SGT1: SGT1 protein; 22.8 1.5E+02 0.0032 23.4 3.9 28 18-45 383-410 (589)
477 PF06224 HTH_42: Winged helix 22.8 2.5E+02 0.0054 19.7 4.8 36 7-42 172-207 (327)
478 PF06322 Phage_NinH: Phage Nin 22.7 1.1E+02 0.0024 17.3 2.4 31 8-40 10-40 (64)
479 smart00760 Bac_DnaA_C Bacteria 22.6 1.3E+02 0.0028 16.0 2.7 18 10-27 39-56 (60)
480 PRK11169 leucine-responsive tr 22.4 1.2E+02 0.0026 19.5 2.9 26 13-38 25-50 (164)
481 PRK09464 pdhR transcriptional 22.2 2.6E+02 0.0056 18.9 4.7 30 15-44 32-65 (254)
482 PRK09490 metH B12-dependent me 22.2 17 0.00038 31.2 -1.3 29 23-51 1193-1224(1229)
483 COG2154 Pterin-4a-carbinolamin 22.2 97 0.0021 19.1 2.3 23 25-47 3-26 (101)
484 PF10678 DUF2492: Protein of u 21.7 1.9E+02 0.004 17.0 3.7 28 23-50 42-69 (78)
485 PRK03975 tfx putative transcri 21.7 2.4E+02 0.0051 18.2 4.4 26 5-33 13-38 (141)
486 COG4840 Uncharacterized protei 21.7 69 0.0015 18.5 1.5 16 26-41 52-67 (71)
487 PF14261 DUF4351: Domain of un 21.6 1.5E+02 0.0034 16.1 4.8 35 4-38 10-44 (59)
488 cd08815 Death_TNFRSF25_DR3 Dea 21.5 98 0.0021 18.2 2.1 16 19-34 14-29 (77)
489 KOG1463 26S proteasome regulat 21.5 1.2E+02 0.0025 23.2 3.0 42 13-54 342-389 (411)
490 PF07742 BTG: BTG family; Int 21.4 53 0.0012 20.6 1.1 33 11-44 54-96 (118)
491 PLN02905 beta-amylase 21.4 74 0.0016 25.9 2.0 22 31-52 124-145 (702)
492 CHL00165 ftrB ferredoxin thior 21.4 80 0.0017 20.0 1.8 17 33-49 20-36 (116)
493 PRK12423 LexA repressor; Provi 21.4 2.6E+02 0.0056 18.6 4.7 42 3-44 8-57 (202)
494 COG1395 Predicted transcriptio 21.4 94 0.002 22.9 2.4 22 15-36 137-158 (313)
495 PF08299 Bac_DnaA_C: Bacterial 21.3 1.6E+02 0.0036 16.3 4.5 31 6-36 35-66 (70)
496 PF09824 ArsR: ArsR transcript 21.3 2.5E+02 0.0054 18.8 4.2 33 4-38 111-143 (160)
497 PF01527 HTH_Tnp_1: Transposas 21.3 1.5E+02 0.0033 15.9 3.9 28 14-41 21-48 (76)
498 PF07499 RuvA_C: RuvA, C-termi 21.3 94 0.002 15.9 1.9 16 24-39 11-26 (47)
499 TIGR00241 CoA_E_activ CoA-subs 21.1 1.2E+02 0.0025 20.7 2.8 24 18-41 129-152 (248)
500 COG5114 Histone acetyltransfer 21.1 2.7E+02 0.0059 21.1 4.8 42 3-44 385-429 (432)
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=99.68 E-value=2.8e-17 Score=105.80 Aligned_cols=56 Identities=29% Similarity=0.577 Sum_probs=41.0
Q ss_pred ChHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHhcCCeEeCCCceEeecCC
Q 036949 1 LYTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQ 56 (81)
Q Consensus 1 ~~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~~~~~p~~~ 56 (81)
.+|++|+.||++||++|+++++++|||++++++.++++++||++|+++.++.|.+.
T Consensus 82 ~iR~~i~~~i~~aY~sIs~~~la~~Lg~~~~el~~~~~~~gW~~d~~~~~~~~~~~ 137 (143)
T PF10075_consen 82 TIRERIAHLISKAYSSISLSDLAEMLGLSEEELEKFIKSRGWTVDGDGVLFPPNPE 137 (143)
T ss_dssp HHHHHHHHHHHHH-SEE-HHHHHHHTTS-HHHHHHHHHHHT-EE-----EE---HH
T ss_pred HHHHHHHHHHHHHHhHcCHHHHHHHhCCCHHHHHHHHHHcCCEECCCccEEecCCc
Confidence 37999999999999999999999999999999999999999999988766554433
No 2
>KOG4414 consensus COP9 signalosome, subunit CSN8 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=99.56 E-value=1.3e-15 Score=100.38 Aligned_cols=79 Identities=44% Similarity=0.607 Sum_probs=69.4
Q ss_pred hHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHhcCCeEeCCCceE-eecCCCCcccCCCChhHHHHHHhHHHhhc
Q 036949 2 YTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRML-TVKKQPLVTEQKLDPSKMQCLTEYVFHLE 80 (81)
Q Consensus 2 ~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~~~~-~p~~~~~~~~~~~~~~~l~~Lt~~v~~LE 80 (81)
.|.|.|.|+.+||++|-.+++|.+|||+++|+.+++.+.||+.|+.++|. .|+++...+ ..++-..+..||+++.|||
T Consensus 118 ~~kR~FaLl~qAYssI~~~D~A~FlGl~~ddAtk~ilEnGWqaDaasqMasl~kk~V~~a-~~Vd~nK~~~LsE~a~~~~ 196 (197)
T KOG4414|consen 118 TRKRAFALLLQAYSSIIADDFAAFLGLPEDDATKGILENGWQADAASQMASLKKKAVAGA-LDVDFNKFIPLSEPAFHLE 196 (197)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHcccchhhHHHHhhccchhcccc-cccchhhceecCCccCCCC
Confidence 58999999999999999999999999999999999999999999999998 555444443 3337788999999999999
Q ss_pred C
Q 036949 81 H 81 (81)
Q Consensus 81 ~ 81 (81)
+
T Consensus 197 ~ 197 (197)
T KOG4414|consen 197 H 197 (197)
T ss_pred C
Confidence 6
No 3
>KOG3151 consensus 26S proteasome regulatory complex, subunit RPN12/PSMD8 [Posttranslational modification, protein turnover, chaperones]
Probab=99.19 E-value=5.8e-11 Score=82.78 Aligned_cols=53 Identities=15% Similarity=0.331 Sum_probs=47.3
Q ss_pred hHHHHHHHHHHhcccccHHHHHHHhCC-CHHHHHHHHHhcCCeEeCCCceEeec
Q 036949 2 YTKRMFQLLMSAYSTISTQDTALFLGM-NEDDAAYYVQQQGWTLDPASRMLTVK 54 (81)
Q Consensus 2 ~R~~~~~li~~AY~sIs~~~~a~~Lgl-s~~e~~~~~~~~GW~~d~~~~~~~p~ 54 (81)
||++|+.|++|+|..|++++++.||+| +++++.+|+++|+|.+++.+.+.+-.
T Consensus 178 iRdEIA~c~EKsYd~l~~s~a~~~L~f~~~~e~~~~~~~r~W~l~~~~~~~~~~ 231 (260)
T KOG3151|consen 178 IRDEIAGCIEKSYDKLSASDATQMLLFNNDKELKKFATERQWPLDEKGVFSFAS 231 (260)
T ss_pred HHHHHHHHHHHHHhhcCHHHHHHHHhcCChHHHHHHHHhcCCcccccccccchh
Confidence 799999999999999999999999999 89999999999999999555444433
No 4
>KOG3252 consensus Uncharacterized conserved protein [Function unknown]
Probab=98.36 E-value=1.1e-06 Score=59.86 Aligned_cols=79 Identities=13% Similarity=0.272 Sum_probs=64.0
Q ss_pred ChHHHHHHHHHHhcccccHHHHHHHhCC-CHHHHHHHHHhcCCeEeCCCceEeecCCCCcccCCC-ChhHHHHHHhHHHh
Q 036949 1 LYTKRMFQLLMSAYSTISTQDTALFLGM-NEDDAAYYVQQQGWTLDPASRMLTVKKQPLVTEQKL-DPSKMQCLTEYVFH 78 (81)
Q Consensus 1 ~~R~~~~~li~~AY~sIs~~~~a~~Lgl-s~~e~~~~~~~~GW~~d~~~~~~~p~~~~~~~~~~~-~~~~l~~Lt~~v~~ 78 (81)
++|.-+...++-.|.+|.-.-+|++||- +..++..++++-||..+.+|.+++|....+-...-. +..+++..++++..
T Consensus 136 svr~yachvv~iTyQkI~k~lLaellG~~sDs~le~~~~~~GW~a~e~G~ifv~~qE~~iKtkNi~EkI~fd~Va~ima~ 215 (217)
T KOG3252|consen 136 SVRKYACHVVGITYQKIDKWLLAELLGGLSDSQLEVWMTKYGWIADESGQIFVASQEEEIKTKNIVEKIDFDHVASIMAS 215 (217)
T ss_pred HHHHHHHHheechHhhchHHHHHHhhCcccHHHHHHHHHHccceecCCceEEEeccccccccCCccccCCcchHHHHHHh
Confidence 4677788899999999999999999998 899999999999999999997777766553321222 77888888887765
Q ss_pred h
Q 036949 79 L 79 (81)
Q Consensus 79 L 79 (81)
+
T Consensus 216 ~ 216 (217)
T KOG3252|consen 216 L 216 (217)
T ss_pred c
Confidence 4
No 5
>smart00753 PAM PCI/PINT associated module.
Probab=97.12 E-value=0.0013 Score=38.39 Aligned_cols=55 Identities=20% Similarity=0.267 Sum_probs=44.0
Q ss_pred hHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHh------cCCeEeCCCceEeecCC
Q 036949 2 YTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQ------QGWTLDPASRMLTVKKQ 56 (81)
Q Consensus 2 ~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~------~GW~~d~~~~~~~p~~~ 56 (81)
+|.+.+..+.+.|++|++++++..++++.+++..++.+ ...++|..++++.-...
T Consensus 10 ~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~ 70 (88)
T smart00753 10 IRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEV 70 (88)
T ss_pred HHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCC
Confidence 67888899999999999999999999998888777553 25678876666655543
No 6
>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=97.12 E-value=0.0013 Score=38.39 Aligned_cols=55 Identities=20% Similarity=0.267 Sum_probs=44.0
Q ss_pred hHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHh------cCCeEeCCCceEeecCC
Q 036949 2 YTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQ------QGWTLDPASRMLTVKKQ 56 (81)
Q Consensus 2 ~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~------~GW~~d~~~~~~~p~~~ 56 (81)
+|.+.+..+.+.|++|++++++..++++.+++..++.+ ...++|..++++.-...
T Consensus 10 ~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~ 70 (88)
T smart00088 10 IRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEV 70 (88)
T ss_pred HHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCC
Confidence 67888899999999999999999999998888777553 25678876666655543
No 7
>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=97.03 E-value=0.0018 Score=38.22 Aligned_cols=38 Identities=24% Similarity=0.357 Sum_probs=33.0
Q ss_pred hHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHh
Q 036949 2 YTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQ 39 (81)
Q Consensus 2 ~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~ 39 (81)
+|.+.+.-+.+.|++|+++++|..|+++.+++..++.+
T Consensus 46 i~~~~l~~l~~~y~~i~~~~ia~~l~~~~~~vE~~l~~ 83 (105)
T PF01399_consen 46 IRRRNLRQLSKPYSSISISEIAKALQLSEEEVESILID 83 (105)
T ss_dssp HHHHHHHHHHHC-SEEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhcccchHHHHHHhccchHHHHHHHHH
Confidence 57788889999999999999999999999998887654
No 8
>PF03399 SAC3_GANP: SAC3/GANP/Nin1/mts3/eIF-3 p25 family; InterPro: IPR005062 This large family includes diverse proteins involved in large complexes [, , ]. The alignment contains one highly conserved negatively charged residue and one highly conserved positively charged residue that are probably important for the function of these proteins. The family includes the yeast nuclear export factor Sac3 [], and mammalian GANP/MCM3-associated proteins, which facilitate the nuclear localisation of MCM3, a protein that associates with chromatin in the G1 phase of the cell-cycle. The 26S protease (or 26S proteasome) is responsible for degrading ubiquitin conjugates. It consists of 19S regulatory complexes associated with the ends of 20S proteasomes. The 19S regulatory complex is composed of about 20 different polypeptides and confers ATP-dependence and substrate specificity to the 26S enzyme. The conserved region occurs at the C-terminal of the Nin1-like regulatory subunit [, , ]. This family includes several eukaryotic translation initiation factor 3 subunit 11 (eIF-3 p25) proteins. Eukaryotic initiation factor 3 (eIF3) is a multisubunit complex that is required for binding of mRNA to 40 S ribosomal subunits, stabilisation of ternary complex binding to 40 S subunits, and dissociation of 40 and 60 S subunits [].; PDB: 3T5V_D.
Probab=96.23 E-value=0.0052 Score=40.75 Aligned_cols=27 Identities=30% Similarity=0.346 Sum_probs=24.4
Q ss_pred hHHHHHHHHHHhccc-ccHHHHHHHhCC
Q 036949 2 YTKRMFQLLMSAYST-ISTQDTALFLGM 28 (81)
Q Consensus 2 ~R~~~~~li~~AY~s-Is~~~~a~~Lgl 28 (81)
+|.+++.++++||.+ |+++.++++|||
T Consensus 177 iR~~al~~i~~ay~~~i~l~~l~~~L~F 204 (204)
T PF03399_consen 177 IRLRALQSISKAYRSSIPLSFLAELLGF 204 (204)
T ss_dssp HHHHHHHHHHHHS-T-EEHHHHHHHTT-
T ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHcCC
Confidence 799999999999999 999999999996
No 9
>KOG1861 consensus Leucine permease transcriptional regulator [Transcription]
Probab=96.19 E-value=0.012 Score=45.18 Aligned_cols=58 Identities=19% Similarity=0.284 Sum_probs=51.8
Q ss_pred HHHHHHHHHHhcc-cccHHHHHHHhCC-CHHHHHHHHHhcCCeEeCCCceEeecCCCCcc
Q 036949 3 TKRMFQLLMSAYS-TISTQDTALFLGM-NEDDAAYYVQQQGWTLDPASRMLTVKKQPLVT 60 (81)
Q Consensus 3 R~~~~~li~~AY~-sIs~~~~a~~Lgl-s~~e~~~~~~~~GW~~d~~~~~~~p~~~~~~~ 60 (81)
|-..+..|.|+|. +|+++.++..|.| +.+++..|..+.+|+.|+.|..+.+++.....
T Consensus 464 R~~Al~ii~KsyrP~i~~~fi~~~laf~~~e~c~~~l~~~~~~~~~~g~~~~~~~~~s~~ 523 (540)
T KOG1861|consen 464 RKKALTIICKSYRPTITVDFIASELAFDSMEDCVNFLNEQNLTYDSLGPQILDKNASSSN 523 (540)
T ss_pred HHHHHHHHHHHcCCCccHHHHhhhhhhchHHHHHHHHhccCccccccCCccccccccccc
Confidence 5667889999999 9999999999999 78889999999999999999999888776653
No 10
>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=95.57 E-value=0.047 Score=33.25 Aligned_cols=49 Identities=10% Similarity=0.309 Sum_probs=38.3
Q ss_pred HHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHhcCCeEeCCCceEeec
Q 036949 6 MFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVK 54 (81)
Q Consensus 6 ~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~~~~~p~ 54 (81)
.++.+..+=..+++.++|..||+++.++.++..+.||-+...+.-..|.
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 4455555668899999999999999999999999999998322333444
No 11
>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=94.07 E-value=0.074 Score=32.51 Aligned_cols=21 Identities=29% Similarity=0.542 Sum_probs=17.2
Q ss_pred HhcCCeEeCCCceEeecCCCC
Q 036949 38 QQQGWTLDPASRMLTVKKQPL 58 (81)
Q Consensus 38 ~~~GW~~d~~~~~~~p~~~~~ 58 (81)
.+|||++++.|+.+-|-...+
T Consensus 10 eKRgwtlnsagyllgp~aid~ 30 (103)
T smart00071 10 EKRGWTLNSAGYLLGPHAIDN 30 (103)
T ss_pred cccCceeccCceeeCcccccc
Confidence 578999999999998876443
No 12
>KOG1498 consensus 26S proteasome regulatory complex, subunit RPN5/PSMD12 [Posttranslational modification, protein turnover, chaperones]
Probab=93.55 E-value=0.27 Score=37.17 Aligned_cols=33 Identities=15% Similarity=0.360 Sum_probs=30.2
Q ss_pred HHHHHHhcccccHHHHHHHhCCCHHHHHHHHHh
Q 036949 7 FQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQ 39 (81)
Q Consensus 7 ~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~ 39 (81)
++-|++=|++|++.+++..|+++.+++.+|...
T Consensus 344 iRiiA~yYSrIt~~rl~eLLdl~~ee~E~~LS~ 376 (439)
T KOG1498|consen 344 IRIIAKYYSRITLKRLAELLDLPVEEMEKFLSD 376 (439)
T ss_pred HHHHHHHHhhccHHHHHHHhCCCHHHHHHHHHH
Confidence 568999999999999999999999999998664
No 13
>COG5071 RPN5 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=93.46 E-value=0.24 Score=36.79 Aligned_cols=39 Identities=15% Similarity=0.377 Sum_probs=33.7
Q ss_pred HHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH---hcCCeE
Q 036949 6 MFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ---QQGWTL 44 (81)
Q Consensus 6 ~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~---~~GW~~ 44 (81)
-++.|++-|++|++.++.-.|.+++++..+++. .+|--+
T Consensus 343 N~RvI~~yYSrI~~~rl~~lld~~~s~te~~ISdlVN~G~~y 384 (439)
T COG5071 343 NIRVIANYYSRIHCSRLGVLLDMSPSETEQFISDLVNKGHFY 384 (439)
T ss_pred hHhHHHHHhhhhhHHHHHHHHcCCHHHHHHHHHHHHhcCcEE
Confidence 367999999999999999999999999988866 456655
No 14
>KOG2581 consensus 26S proteasome regulatory complex, subunit RPN3/PSMD3 [Posttranslational modification, protein turnover, chaperones]
Probab=92.86 E-value=0.053 Score=41.25 Aligned_cols=30 Identities=43% Similarity=0.602 Sum_probs=24.4
Q ss_pred HHHHHHhcccccHHHHHHHhCC-CHHHHHHH
Q 036949 7 FQLLMSAYSTISTQDTALFLGM-NEDDAAYY 36 (81)
Q Consensus 7 ~~li~~AY~sIs~~~~a~~Lgl-s~~e~~~~ 36 (81)
.+-||-+|++||+.++|.-||+ |++++.-.
T Consensus 368 IR~ISlsYSRISl~DIA~kL~l~Seed~Eyi 398 (493)
T KOG2581|consen 368 IRKISLSYSRISLQDIAKKLGLNSEEDAEYI 398 (493)
T ss_pred hhheeeeeeeccHHHHHHHhcCCCchhHHHH
Confidence 4678999999999999999999 55545433
No 15
>PF03683 UPF0175: Uncharacterised protein family (UPF0175); InterPro: IPR005368 This entry contains small proteins of unknown function.
Probab=91.75 E-value=0.31 Score=28.23 Aligned_cols=30 Identities=20% Similarity=0.264 Sum_probs=26.9
Q ss_pred ccccHHHHHHHhCCCHHHHHHHHHhcCCeE
Q 036949 15 STISTQDTALFLGMNEDDAAYYVQQQGWTL 44 (81)
Q Consensus 15 ~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~ 44 (81)
..||+..+|.++|+|.-++.++..++|=.+
T Consensus 33 g~iS~gkAAelag~s~~eF~~~L~~~gI~~ 62 (76)
T PF03683_consen 33 GKISLGKAAELAGMSRWEFLELLKERGIPI 62 (76)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHCCCCC
Confidence 579999999999999999999999987543
No 16
>PF12728 HTH_17: Helix-turn-helix domain
Probab=91.52 E-value=0.33 Score=25.41 Aligned_cols=23 Identities=17% Similarity=0.481 Sum_probs=20.5
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHh
Q 036949 17 ISTQDTALFLGMNEDDAAYYVQQ 39 (81)
Q Consensus 17 Is~~~~a~~Lgls~~e~~~~~~~ 39 (81)
++++++|.+||+|..-+..++.+
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~~ 24 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIRQ 24 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHc
Confidence 47899999999999999998874
No 17
>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=91.47 E-value=0.62 Score=26.22 Aligned_cols=46 Identities=17% Similarity=0.325 Sum_probs=37.3
Q ss_pred HHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHhcCCeEeCCC
Q 036949 3 TKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPAS 48 (81)
Q Consensus 3 R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~ 48 (81)
|++++.+--..=..|.+.++|..||+|+..+..+=..-.|.-.-.|
T Consensus 9 rdkA~e~y~~~~g~i~lkdIA~~Lgvs~~tIr~WK~~dkW~~~~~~ 54 (60)
T PF10668_consen 9 RDKAFEIYKESNGKIKLKDIAEKLGVSESTIRKWKSRDKWDEKLKG 54 (60)
T ss_pred HHHHHHHHHHhCCCccHHHHHHHHCCCHHHHHHHhhhcchhhHhcc
Confidence 6677777666667899999999999999999988887788764343
No 18
>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=91.08 E-value=0.17 Score=31.23 Aligned_cols=28 Identities=29% Similarity=0.630 Sum_probs=18.9
Q ss_pred hCC-CHHHHHHHHHhcCCeEeCCCceEeecCCC
Q 036949 26 LGM-NEDDAAYYVQQQGWTLDPASRMLTVKKQP 57 (81)
Q Consensus 26 Lgl-s~~e~~~~~~~~GW~~d~~~~~~~p~~~~ 57 (81)
|-| |.+++++||.+.||.+. +.-|....
T Consensus 53 l~F~skE~Ai~yaer~G~~Y~----V~~p~~r~ 81 (101)
T PF04800_consen 53 LKFDSKEDAIAYAERNGWDYE----VEEPKKRK 81 (101)
T ss_dssp EEESSHHHHHHHHHHCT-EEE----EE-STT--
T ss_pred eeeCCHHHHHHHHHHcCCeEE----EeCCCCCc
Confidence 344 89999999999999993 55555443
No 19
>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=90.63 E-value=0.28 Score=26.30 Aligned_cols=29 Identities=17% Similarity=0.216 Sum_probs=23.3
Q ss_pred ccccHHHHHHHhCCCHHHHHHHH-HhcCCe
Q 036949 15 STISTQDTALFLGMNEDDAAYYV-QQQGWT 43 (81)
Q Consensus 15 ~sIs~~~~a~~Lgls~~e~~~~~-~~~GW~ 43 (81)
..|++.++|.-||++.+++.+.+ .+.|=.
T Consensus 2 ~~i~V~elAk~l~v~~~~ii~~l~~~~Gi~ 31 (54)
T PF04760_consen 2 EKIRVSELAKELGVPSKEIIKKLFKELGIM 31 (54)
T ss_dssp -EE-TTHHHHHHSSSHHHHHHHH-HHHTS-
T ss_pred CceEHHHHHHHHCcCHHHHHHHHHHhCCcC
Confidence 35789999999999999999999 557866
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=90.58 E-value=0.56 Score=25.66 Aligned_cols=29 Identities=17% Similarity=0.258 Sum_probs=25.4
Q ss_pred hcccccHHHHHHHhCCCHHHHHHHHHhcC
Q 036949 13 AYSTISTQDTALFLGMNEDDAAYYVQQQG 41 (81)
Q Consensus 13 AY~sIs~~~~a~~Lgls~~e~~~~~~~~G 41 (81)
.|=..++.++|.-||++...+...|.+.|
T Consensus 12 ~~fhlp~~eAA~~Lgv~~T~LKr~CR~~G 40 (52)
T PF02042_consen 12 QYFHLPIKEAAKELGVSVTTLKRRCRRLG 40 (52)
T ss_pred HHhCCCHHHHHHHhCCCHHHHHHHHHHcC
Confidence 46678999999999999999999999876
No 21
>PRK13503 transcriptional activator RhaS; Provisional
Probab=89.85 E-value=0.84 Score=31.24 Aligned_cols=37 Identities=11% Similarity=0.152 Sum_probs=31.6
Q ss_pred HHHHHHHHHhcc-cccHHHHHHHhCCCHHHHHHHHHhc
Q 036949 4 KRMFQLLMSAYS-TISTQDTALFLGMNEDDAAYYVQQQ 40 (81)
Q Consensus 4 ~~~~~li~~AY~-sIs~~~~a~~Lgls~~e~~~~~~~~ 40 (81)
.++.+.|.+.|. .++++++|+.+|+|+.-+...+++.
T Consensus 174 ~~~~~~I~~~~~~~~tl~~lA~~~~lS~~~l~r~Fk~~ 211 (278)
T PRK13503 174 NQLLAWLEDHFAEEVNWEALADQFSLSLRTLHRQLKQQ 211 (278)
T ss_pred HHHHHHHHHhhcCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 357788999998 9999999999999998887777653
No 22
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=89.08 E-value=1.6 Score=31.69 Aligned_cols=52 Identities=15% Similarity=0.142 Sum_probs=42.3
Q ss_pred HHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHhcCCeEeCCCceEeec
Q 036949 3 TKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVK 54 (81)
Q Consensus 3 R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~~~~~p~ 54 (81)
|+.++..+.+...+||+++++...|+..+|+..-.+..|...--.|..++-.
T Consensus 210 ~~~il~~L~~~~~~isi~~is~~T~i~~~Dii~tL~~l~~l~~~~g~~~i~~ 261 (290)
T PLN03238 210 TRVLLEQLRDVKGDVSIKDLSLATGIRGEDIVSTLQSLNLIKYWKGQHVIHV 261 (290)
T ss_pred HHHHHHHHHhcCCCccHHHHHHHhCCCHHHHHHHHHHCCcEEEECCcEEEEe
Confidence 5678888877788999999999999999999999998897654455555544
No 23
>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=89.02 E-value=2.4 Score=23.06 Aligned_cols=52 Identities=12% Similarity=0.094 Sum_probs=32.6
Q ss_pred cHHHHHHHhCCCHHHHHHHHHhcCCeEeCCCceEeecCCCCcccCCC-ChhHHHHHHhHHHhh
Q 036949 18 STQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVTEQKL-DPSKMQCLTEYVFHL 79 (81)
Q Consensus 18 s~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~~~~~p~~~~~~~~~~~-~~~~l~~Lt~~v~~L 79 (81)
++.++|+.+|++..-+..+.++.| ...|. ........ ++.++.+|-.+....
T Consensus 2 s~~eva~~~gvs~~tlr~w~~~~g--------~~~~~--r~~~~~r~yt~~~v~~l~~i~~l~ 54 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAWERRYG--------LPAPQ--RTDGGHRLYSEADVARLRLIRRLT 54 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHhCC--------CCCCC--cCCCCCeecCHHHHHHHHHHHHHH
Confidence 678999999999999998876432 11221 11112222 777777776665443
No 24
>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=88.99 E-value=0.84 Score=29.13 Aligned_cols=29 Identities=21% Similarity=0.607 Sum_probs=25.9
Q ss_pred cHHHHHHHhCCCHHHHHHHHHhcCCeEeC
Q 036949 18 STQDTALFLGMNEDDAAYYVQQQGWTLDP 46 (81)
Q Consensus 18 s~~~~a~~Lgls~~e~~~~~~~~GW~~d~ 46 (81)
..+++|..+|++..-+-.++.+.||+-.+
T Consensus 2 T~eELA~~tG~srQTINrWvRkegW~T~p 30 (122)
T PF07037_consen 2 TPEELAELTGYSRQTINRWVRKEGWKTEP 30 (122)
T ss_pred CHHHHHHHhCccHHHHHHHHHhcCceecc
Confidence 46789999999999999999999999644
No 25
>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=88.88 E-value=0.72 Score=23.19 Aligned_cols=23 Identities=17% Similarity=0.509 Sum_probs=20.4
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHh
Q 036949 17 ISTQDTALFLGMNEDDAAYYVQQ 39 (81)
Q Consensus 17 Is~~~~a~~Lgls~~e~~~~~~~ 39 (81)
+++.++|.+||++..-+..++.+
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~ 24 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHE 24 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHc
Confidence 57899999999999999998864
No 26
>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=88.08 E-value=3.1 Score=23.42 Aligned_cols=41 Identities=17% Similarity=0.353 Sum_probs=30.5
Q ss_pred cccHHHHHHHhCC--CHHHHHHHHHhcCCeEeC-CCceEeecCC
Q 036949 16 TISTQDTALFLGM--NEDDAAYYVQQQGWTLDP-ASRMLTVKKQ 56 (81)
Q Consensus 16 sIs~~~~a~~Lgl--s~~e~~~~~~~~GW~~d~-~~~~~~p~~~ 56 (81)
.++.+.+.++||+ +.+++.+.....|-+++. ++..+....|
T Consensus 5 ~~~~~~i~~~lG~~i~~~~i~~~L~~lg~~~~~~~~~~~~v~vP 48 (70)
T PF03484_consen 5 TLSLDKINKLLGIDISPEEIIKILKRLGFKVEKIDGDTLEVTVP 48 (70)
T ss_dssp EEEHHHHHHHHTS---HHHHHHHHHHTT-EEEE-CTTEEEEEEE
T ss_pred EecHHHHHHHhCCCCCHHHHHHHHHHCCCEEEECCCCEEEEEcC
Confidence 4678899999998 899999999999999887 5544444433
No 27
>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=87.37 E-value=1.4 Score=23.22 Aligned_cols=40 Identities=18% Similarity=0.347 Sum_probs=31.7
Q ss_pred HHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH---hcCCeE
Q 036949 5 RMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ---QQGWTL 44 (81)
Q Consensus 5 ~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~---~~GW~~ 44 (81)
+|++++..+=..+++.++|+-+|++..-+-.+.. +.||-.
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 5778888998999999999999998877655544 568864
No 28
>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=87.17 E-value=2.8 Score=21.57 Aligned_cols=33 Identities=21% Similarity=0.299 Sum_probs=23.9
Q ss_pred HHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH
Q 036949 5 RMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 5 ~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~ 38 (81)
+|+.++..- .+++..++|..+|+|+..+..-..
T Consensus 7 ~Il~~Lq~d-~r~s~~~la~~lglS~~~v~~Ri~ 39 (42)
T PF13404_consen 7 KILRLLQED-GRRSYAELAEELGLSESTVRRRIR 39 (42)
T ss_dssp HHHHHHHH--TTS-HHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHc-CCccHHHHHHHHCcCHHHHHHHHH
Confidence 566666655 889999999999999998876544
No 29
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=86.96 E-value=3.7 Score=22.75 Aligned_cols=32 Identities=13% Similarity=0.395 Sum_probs=27.9
Q ss_pred cccHHHHHHHhCC--CHHHHHHHHHhcCCeEeCC
Q 036949 16 TISTQDTALFLGM--NEDDAAYYVQQQGWTLDPA 47 (81)
Q Consensus 16 sIs~~~~a~~Lgl--s~~e~~~~~~~~GW~~d~~ 47 (81)
+++.+.+.++||+ +.+++.+.....|..++.+
T Consensus 5 ~~~~~~i~~llG~~i~~~ei~~~L~~lg~~~~~~ 38 (71)
T smart00874 5 TLRRERINRLLGLDLSAEEIEEILKRLGFEVEVS 38 (71)
T ss_pred EecHHHHHHHHCCCCCHHHHHHHHHHCCCeEEec
Confidence 4678899999998 7899999999999998653
No 30
>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=86.80 E-value=0.43 Score=26.64 Aligned_cols=25 Identities=24% Similarity=0.522 Sum_probs=14.7
Q ss_pred HHHHhCC-CHHHHHHHHHhcCCeEeC
Q 036949 22 TALFLGM-NEDDAAYYVQQQGWTLDP 46 (81)
Q Consensus 22 ~a~~Lgl-s~~e~~~~~~~~GW~~d~ 46 (81)
++.+|-= ..+|+.+||+++||.+-.
T Consensus 20 I~DLL~SV~~~eV~~YC~~~GWIip~ 45 (57)
T PF08727_consen 20 IADLLRSVDSPEVREYCEEQGWIIPA 45 (57)
T ss_dssp THHHHHHH--HHHHHHHHHHT--TT-
T ss_pred HHHHHHhcCCHHHHHHHHHCCccccC
Confidence 3444433 568899999999999843
No 31
>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=86.17 E-value=2.3 Score=23.01 Aligned_cols=39 Identities=15% Similarity=0.329 Sum_probs=26.5
Q ss_pred HHHHHHHHhcccccHHHHHHHhCCCHHHHHHH---HHhcCCe
Q 036949 5 RMFQLLMSAYSTISTQDTALFLGMNEDDAAYY---VQQQGWT 43 (81)
Q Consensus 5 ~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~---~~~~GW~ 43 (81)
.++.+|......++..+++.++|++...+... ..++||.
T Consensus 7 ~vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv 48 (68)
T PF13463_consen 7 QVLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLV 48 (68)
T ss_dssp HHHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence 46667777889999999999999987665444 4567998
No 32
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=86.11 E-value=2.6 Score=23.66 Aligned_cols=44 Identities=14% Similarity=0.225 Sum_probs=35.4
Q ss_pred hHHHHHHHHHHhcc-cccHHHHHHHhCCCHHHHHHHHH---hcCCeEe
Q 036949 2 YTKRMFQLLMSAYS-TISTQDTALFLGMNEDDAAYYVQ---QQGWTLD 45 (81)
Q Consensus 2 ~R~~~~~li~~AY~-sIs~~~~a~~Lgls~~e~~~~~~---~~GW~~d 45 (81)
.+++|+.++...=. .++..++|..||++...+..+.. +.|+..-
T Consensus 7 ~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~ 54 (68)
T smart00550 7 LEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCK 54 (68)
T ss_pred HHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence 57889999998844 49999999999999888877654 5688653
No 33
>PF14056 DUF4250: Domain of unknown function (DUF4250)
Probab=85.71 E-value=2 Score=23.79 Aligned_cols=30 Identities=10% Similarity=0.216 Sum_probs=28.2
Q ss_pred cHHHHHHHhCCCHHHHHHHHHhcCCeEeCC
Q 036949 18 STQDTALFLGMNEDDAAYYVQQQGWTLDPA 47 (81)
Q Consensus 18 s~~~~a~~Lgls~~e~~~~~~~~GW~~d~~ 47 (81)
|+++++..++++.+++.+-...-|..+|+.
T Consensus 22 sLd~Lc~~~~id~~~l~~kL~~~Gy~Y~~~ 51 (55)
T PF14056_consen 22 SLDELCYDYDIDKEELEEKLASIGYEYDEE 51 (55)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHcCCeEchh
Confidence 889999999999999999999999999875
No 34
>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=85.52 E-value=1.5 Score=21.82 Aligned_cols=22 Identities=23% Similarity=0.465 Sum_probs=19.6
Q ss_pred cHHHHHHHhCCCHHHHHHHHHh
Q 036949 18 STQDTALFLGMNEDDAAYYVQQ 39 (81)
Q Consensus 18 s~~~~a~~Lgls~~e~~~~~~~ 39 (81)
++.++|.+||++..-+..++.+
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~~ 23 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHHc
Confidence 6789999999999999988874
No 35
>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=85.00 E-value=4.1 Score=22.01 Aligned_cols=36 Identities=19% Similarity=0.403 Sum_probs=30.2
Q ss_pred hHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH
Q 036949 2 YTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 2 ~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~ 38 (81)
.|.+|+..+ ......+..++|..||++...+-....
T Consensus 11 ~R~~Il~~L-~~~~~~t~~ela~~l~~~~~t~s~hL~ 46 (61)
T PF12840_consen 11 TRLRILRLL-ASNGPMTVSELAEELGISQSTVSYHLK 46 (61)
T ss_dssp HHHHHHHHH-HHCSTBEHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHH-hcCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 588899988 788999999999999999988766655
No 36
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=84.90 E-value=1.7 Score=21.76 Aligned_cols=30 Identities=17% Similarity=0.217 Sum_probs=21.0
Q ss_pred cccccHHHHHHHhCCCHHHHHHHHHhc-CCe
Q 036949 14 YSTISTQDTALFLGMNEDDAAYYVQQQ-GWT 43 (81)
Q Consensus 14 Y~sIs~~~~a~~Lgls~~e~~~~~~~~-GW~ 43 (81)
-+.++++++|..+|+|+.-+....++. |.+
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 457899999999999998888777755 765
No 37
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=84.87 E-value=2.5 Score=26.83 Aligned_cols=37 Identities=16% Similarity=0.279 Sum_probs=28.7
Q ss_pred hHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHhc
Q 036949 2 YTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQ 40 (81)
Q Consensus 2 ~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~~ 40 (81)
||..++.-+..- -.|-.++|.+||+++..+-+|..++
T Consensus 10 iRa~lA~~L~ee--G~Sq~~iA~LLGltqaAVS~Yls~k 46 (119)
T COG2522 10 IRALLAKELIEE--GLSQYRIAKLLGLTQAAVSQYLSGK 46 (119)
T ss_pred HHHHHHHHHHHc--CCcHHHHHHHhCCCHHHHHHHHccC
Confidence 566666644333 6778899999999999999999854
No 38
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=84.69 E-value=2.8 Score=22.84 Aligned_cols=28 Identities=21% Similarity=0.280 Sum_probs=23.9
Q ss_pred cccHHHHHHHhCC-CHHHHHHHHHhc-CCe
Q 036949 16 TISTQDTALFLGM-NEDDAAYYVQQQ-GWT 43 (81)
Q Consensus 16 sIs~~~~a~~Lgl-s~~e~~~~~~~~-GW~ 43 (81)
.++++++|..+|+ |...+....++. |.+
T Consensus 50 ~~~~~~ia~~~g~~s~~~f~r~Fk~~~g~s 79 (84)
T smart00342 50 DLSVTEIALRVGFSSQSYFSRAFKKLFGVT 79 (84)
T ss_pred CCCHHHHHHHhCCCChHHHHHHHHHHHCcC
Confidence 6999999999999 999998887654 655
No 39
>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=84.58 E-value=4.2 Score=21.28 Aligned_cols=35 Identities=20% Similarity=0.358 Sum_probs=25.5
Q ss_pred HHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH
Q 036949 4 KRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 4 ~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~ 38 (81)
.+++.++-.+=..|+..++|..||+|..-+.....
T Consensus 3 ~~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~ 37 (55)
T PF08279_consen 3 KQILKLLLESKEPITAKELAEELGVSRRTIRRDIK 37 (55)
T ss_dssp HHHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHH
Confidence 46777775444459999999999999877765554
No 40
>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=84.24 E-value=3.2 Score=23.71 Aligned_cols=39 Identities=10% Similarity=0.259 Sum_probs=27.7
Q ss_pred HHHHHHHHhcc---cccHHHHHHHhCCCHHHHHHHHHhcCCe
Q 036949 5 RMFQLLMSAYS---TISTQDTALFLGMNEDDAAYYVQQQGWT 43 (81)
Q Consensus 5 ~~~~li~~AY~---sIs~~~~a~~Lgls~~e~~~~~~~~GW~ 43 (81)
+|++.|-.-+. ..++.++|.-+|.|+.-+..||++.|-.
T Consensus 20 ~Ia~yil~~~~~~~~~si~elA~~~~vS~sti~Rf~kkLG~~ 61 (77)
T PF01418_consen 20 KIADYILENPDEIAFMSISELAEKAGVSPSTIVRFCKKLGFS 61 (77)
T ss_dssp HHHHHHHH-HHHHCT--HHHHHHHCTS-HHHHHHHHHHCTTT
T ss_pred HHHHHHHhCHHHHHHccHHHHHHHcCCCHHHHHHHHHHhCCC
Confidence 45555544443 6789999999999999999999998853
No 41
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=84.11 E-value=9.1 Score=24.79 Aligned_cols=67 Identities=15% Similarity=0.096 Sum_probs=44.3
Q ss_pred HHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHhcCCeEeCCCceEeecCCCCcccCCCChhHHHHHHhH
Q 036949 4 KRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVTEQKLDPSKMQCLTEY 75 (81)
Q Consensus 4 ~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~~~~~p~~~~~~~~~~~~~~~l~~Lt~~ 75 (81)
.|....+.--|.-.|..++|.++|.|..-+..++.. |. ..|.. .|.++....+..++..|++.|-+.
T Consensus 9 ~R~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~r--~~--e~G~~-l~~~~~~GrP~kl~~~q~~~l~e~ 75 (138)
T COG3415 9 LRERVVDAVVGEGLSCREAAKRFGVSISTVYRWVRR--YR--ETGLD-LPPKPRKGRPRKLSEEQLEILLER 75 (138)
T ss_pred HHHHHHHHHHHcCccHHHHHHHhCccHHHHHHHHHH--hc--ccccc-ccCccCCCCCcccCHHHHHHHHHH
Confidence 455556666788999999999999998888877763 11 12222 355555555555577777766544
No 42
>PRK12686 carbamate kinase; Reviewed
Probab=83.94 E-value=2.9 Score=30.49 Aligned_cols=21 Identities=24% Similarity=0.232 Sum_probs=17.8
Q ss_pred CCCHHHHHHHHHhcCCeEeCC
Q 036949 27 GMNEDDAAYYVQQQGWTLDPA 47 (81)
Q Consensus 27 gls~~e~~~~~~~~GW~~d~~ 47 (81)
+++++|+...++++||++-.|
T Consensus 133 ~~~~~~a~~~~~~~g~~~~~d 153 (312)
T PRK12686 133 FYTEEEAKQQAEQPGSTFKED 153 (312)
T ss_pred ccCHHHHHHHHHHcCCccccc
Confidence 458999999999999987666
No 43
>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=83.90 E-value=1.2 Score=29.36 Aligned_cols=24 Identities=17% Similarity=0.587 Sum_probs=18.0
Q ss_pred CHHHHH-HHHHhcCCeEeCCCceEe
Q 036949 29 NEDDAA-YYVQQQGWTLDPASRMLT 52 (81)
Q Consensus 29 s~~e~~-~~~~~~GW~~d~~~~~~~ 52 (81)
+-+|+. ++|.+-||++++||..+-
T Consensus 46 D~NeVLkALc~eAGw~Ve~DGTtyr 70 (150)
T PF05687_consen 46 DNNEVLKALCREAGWTVEPDGTTYR 70 (150)
T ss_pred CHHHHHHHHHHhCCEEEccCCCeec
Confidence 346654 788899999999986643
No 44
>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=83.66 E-value=4.8 Score=21.87 Aligned_cols=35 Identities=17% Similarity=0.278 Sum_probs=28.2
Q ss_pred HHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHhc
Q 036949 5 RMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQ 40 (81)
Q Consensus 5 ~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~~ 40 (81)
+++.++-+ -..+++.++|..||+|..-+..++.+.
T Consensus 9 ~Ll~~L~~-~~~~~~~ela~~l~~S~rti~~~i~~L 43 (59)
T PF08280_consen 9 KLLELLLK-NKWITLKELAKKLNISERTIKNDINEL 43 (59)
T ss_dssp HHHHHHHH-HTSBBHHHHHHHCTS-HHHHHHHHHHH
T ss_pred HHHHHHHc-CCCCcHHHHHHHHCCCHHHHHHHHHHH
Confidence 45667777 889999999999999998888877754
No 45
>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=83.63 E-value=3.8 Score=21.11 Aligned_cols=35 Identities=17% Similarity=0.306 Sum_probs=29.2
Q ss_pred hHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH
Q 036949 2 YTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 2 ~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~ 38 (81)
.|-+|+.++.+ ...++.+++..||++...+-.+..
T Consensus 3 ~R~~Il~~L~~--~~~~~~el~~~l~~s~~~vs~hL~ 37 (47)
T PF01022_consen 3 TRLRILKLLSE--GPLTVSELAEELGLSQSTVSHHLK 37 (47)
T ss_dssp HHHHHHHHHTT--SSEEHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHHHh--CCCchhhHHHhccccchHHHHHHH
Confidence 48889999988 889999999999999988876654
No 46
>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=83.41 E-value=4.5 Score=20.68 Aligned_cols=40 Identities=18% Similarity=0.380 Sum_probs=28.9
Q ss_pred hHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH---hcCC
Q 036949 2 YTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ---QQGW 42 (81)
Q Consensus 2 ~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~---~~GW 42 (81)
.+.+|+.++..--. ++..++|..+|+|..-+..+.. +.||
T Consensus 4 ~~~~Il~~l~~~~~-~t~~ela~~~~is~~tv~~~l~~L~~~g~ 46 (48)
T PF13412_consen 4 TQRKILNYLRENPR-ITQKELAEKLGISRSTVNRYLKKLEEKGL 46 (48)
T ss_dssp HHHHHHHHHHHCTT-S-HHHHHHHHTS-HHHHHHHHHHHHHTTS
T ss_pred HHHHHHHHHHHcCC-CCHHHHHHHhCCCHHHHHHHHHHHHHCcC
Confidence 35678888888444 9999999999999877766655 3465
No 47
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=83.31 E-value=7.2 Score=22.99 Aligned_cols=45 Identities=16% Similarity=0.246 Sum_probs=32.9
Q ss_pred HHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHh-cCCeEeCCCceE
Q 036949 6 MFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQ-QGWTLDPASRML 51 (81)
Q Consensus 6 ~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~-~GW~~d~~~~~~ 51 (81)
+++++.+ =.-+++.++|.-+|.+.+++.+.... -+=++|.+|+++
T Consensus 29 LLr~LA~-G~PVt~~~LA~a~g~~~e~v~~~L~~~p~tEyD~~GrIV 74 (77)
T PF12324_consen 29 LLRLLAK-GQPVTVEQLAAALGWPVEEVRAALAAMPDTEYDDQGRIV 74 (77)
T ss_dssp HHHHHTT-TS-B-HHHHHHHHT--HHHHHHHHHH-TTSEEETTSEEE
T ss_pred HHHHHHc-CCCcCHHHHHHHHCCCHHHHHHHHHhCCCceEcCCCCee
Confidence 4555555 56789999999999999999998776 488999888775
No 48
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=83.29 E-value=3.4 Score=21.39 Aligned_cols=27 Identities=22% Similarity=0.484 Sum_probs=21.9
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHhcCCeE
Q 036949 17 ISTQDTALFLGMNEDDAAYYVQQQGWTL 44 (81)
Q Consensus 17 Is~~~~a~~Lgls~~e~~~~~~~~GW~~ 44 (81)
-|+.+||++||++..-+...+.. |+..
T Consensus 18 ~S~~eAa~~lg~~~~~I~~~~~~-~~~~ 44 (53)
T smart00497 18 SSIREAAKYLGISHSSISKYLNT-GKKF 44 (53)
T ss_pred cCHHHHHHHhCCCHHHHHHHHhC-CCcc
Confidence 37889999999999888888775 5555
No 49
>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=83.19 E-value=4.3 Score=21.93 Aligned_cols=40 Identities=20% Similarity=0.310 Sum_probs=29.6
Q ss_pred HHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHH---HhcCCe
Q 036949 3 TKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYV---QQQGWT 43 (81)
Q Consensus 3 R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~---~~~GW~ 43 (81)
++.|+.++.. -..+++.++|..||.|..-+..-. .+.|.-
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 4677777755 589999999999999987664433 345664
No 50
>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=83.02 E-value=0.77 Score=22.06 Aligned_cols=19 Identities=32% Similarity=0.482 Sum_probs=15.6
Q ss_pred CCeEeCCCceEeecCCCCc
Q 036949 41 GWTLDPASRMLTVKKQPLV 59 (81)
Q Consensus 41 GW~~d~~~~~~~p~~~~~~ 59 (81)
||++++.|..+-|-..++-
T Consensus 1 gwtlnsagyLlGPhaiD~H 19 (29)
T PF01296_consen 1 GWTLNSAGYLLGPHAIDNH 19 (29)
T ss_pred CccccccceEeccccccCc
Confidence 8999999999888766553
No 51
>KOG3389 consensus NADH:ubiquinone oxidoreductase, NDUFS4/18 kDa subunit [Energy production and conversion]
Probab=82.69 E-value=0.71 Score=30.63 Aligned_cols=27 Identities=22% Similarity=0.634 Sum_probs=20.7
Q ss_pred HHHHHhCC-CHHHHHHHHHhcCCeEeCC
Q 036949 21 DTALFLGM-NEDDAAYYVQQQGWTLDPA 47 (81)
Q Consensus 21 ~~a~~Lgl-s~~e~~~~~~~~GW~~d~~ 47 (81)
.+..-|-| +.+++..||.+.||.+|-.
T Consensus 124 Nvgm~L~F~tkEdA~sFaEkngW~ydve 151 (178)
T KOG3389|consen 124 NVGMALAFDTKEDAKSFAEKNGWDYDVE 151 (178)
T ss_pred ccceeeeeccHHHHHHHHHHcCCccccc
Confidence 33344556 7899999999999999754
No 52
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=82.50 E-value=3.7 Score=21.16 Aligned_cols=37 Identities=16% Similarity=0.313 Sum_probs=27.7
Q ss_pred HHHHHHHhcccccHHHHHHHhCCCHHHHHHHH---HhcCCeE
Q 036949 6 MFQLLMSAYSTISTQDTALFLGMNEDDAAYYV---QQQGWTL 44 (81)
Q Consensus 6 ~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~---~~~GW~~ 44 (81)
++.++. -..++..+++..||++...+.... .++||-.
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 455665 677899999999999876665554 4678885
No 53
>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=82.32 E-value=3.2 Score=23.76 Aligned_cols=37 Identities=19% Similarity=0.306 Sum_probs=24.9
Q ss_pred cccHHHHHHHhCCCHHHHHHHH-H--hcCCeEeCCCceEe
Q 036949 16 TISTQDTALFLGMNEDDAAYYV-Q--QQGWTLDPASRMLT 52 (81)
Q Consensus 16 sIs~~~~a~~Lgls~~e~~~~~-~--~~GW~~d~~~~~~~ 52 (81)
.+++++||.|.|+..+-+.+.+ . ..+|.+--++++++
T Consensus 13 ~LTi~EAa~Y~gIG~~klr~l~~~~~~~~f~~~~G~r~lI 52 (67)
T PF09035_consen 13 TLTIEEAAEYFGIGEKKLRELAEENPDCPFVLWIGNRRLI 52 (67)
T ss_dssp EEEHHHHHHHT-S-HHHHHHHHHH-TT-SSEEEETTEEEE
T ss_pred ccCHHHHHHHhCccHHHHHHHHHhCCCCCEEEEECCEEEE
Confidence 4688999999999999999999 3 33666543444443
No 54
>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=82.11 E-value=5.1 Score=24.30 Aligned_cols=37 Identities=11% Similarity=0.150 Sum_probs=30.4
Q ss_pred hHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH
Q 036949 2 YTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 2 ~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~ 38 (81)
.|++..-...-.|.-|+.+++++.-|||.+|+..+..
T Consensus 35 a~RKAaVV~aV~~Glis~~EA~~rY~Ls~eEf~~W~~ 71 (90)
T PF06627_consen 35 ARRKAAVVRAVRGGLISVEEACRRYGLSEEEFESWQR 71 (90)
T ss_dssp HHHHHHHHHHHHCTTS-HHHHHHCTTSSHHHHHHHHH
T ss_pred hhHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 3566666777789999999999999999999998765
No 55
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=81.70 E-value=4.9 Score=19.98 Aligned_cols=35 Identities=17% Similarity=0.404 Sum_probs=24.5
Q ss_pred cccHHHHHHHhCCCHHHHHHHH---HhcCCeEeCCCce
Q 036949 16 TISTQDTALFLGMNEDDAAYYV---QQQGWTLDPASRM 50 (81)
Q Consensus 16 sIs~~~~a~~Lgls~~e~~~~~---~~~GW~~d~~~~~ 50 (81)
.++..++|.++|++...+.... .+.||-.-..+.+
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~~~~~~~ 45 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLEKEGLISREGGRI 45 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCCEE
Confidence 4678899999999887765554 4679975333333
No 56
>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=81.36 E-value=5.6 Score=26.64 Aligned_cols=43 Identities=9% Similarity=0.131 Sum_probs=35.0
Q ss_pred ChHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH---hcCCeE
Q 036949 1 LYTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ---QQGWTL 44 (81)
Q Consensus 1 ~~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~---~~GW~~ 44 (81)
+.|++|+..+.+. ..++..++|..||++..-+..... +.||..
T Consensus 1 ~tr~~IL~~L~~~-~~~t~~eLA~~lgis~~tV~~~L~~Le~~GlV~ 46 (203)
T TIGR02702 1 STKEDILSYLLKQ-GQATAAALAEALAISPQAVRRHLKDLETEGLIE 46 (203)
T ss_pred CHHHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence 3588999988764 779999999999999887766654 569985
No 57
>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=81.34 E-value=4 Score=24.34 Aligned_cols=44 Identities=14% Similarity=0.314 Sum_probs=32.0
Q ss_pred hHHHHHHHHHHhc---ccccHHHHHHHhCCCHHHHHHHHH---hcCCeEe
Q 036949 2 YTKRMFQLLMSAY---STISTQDTALFLGMNEDDAAYYVQ---QQGWTLD 45 (81)
Q Consensus 2 ~R~~~~~li~~AY---~sIs~~~~a~~Lgls~~e~~~~~~---~~GW~~d 45 (81)
++++|+..|.... .=|+++++++.||++.+++.+.+. ..|..+.
T Consensus 48 ~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 97 (102)
T PF08784_consen 48 LQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNEGHIYS 97 (102)
T ss_dssp HHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhCCeEec
Confidence 4778888888733 339999999999999988766655 4577763
No 58
>COG2886 Uncharacterized small protein [Function unknown]
Probab=81.03 E-value=5.2 Score=24.14 Aligned_cols=36 Identities=19% Similarity=0.281 Sum_probs=30.3
Q ss_pred HHHHHhcccccHHHHHHHhCCCHHHHHHHHHhcCCeEe
Q 036949 8 QLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLD 45 (81)
Q Consensus 8 ~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~d 45 (81)
.++.+ ..||+..+|.+.|++..++.....+||=...
T Consensus 35 ~L~qe--g~vSlg~Aaela~~sl~ef~~eL~~R~i~l~ 70 (88)
T COG2886 35 ELFQE--GAVSLGRAAELAGMSLNEFEEELRKRGIPLY 70 (88)
T ss_pred HHHHH--hhhHHHHHHHHhcCCHHHHHHHHHHhCCCcc
Confidence 34444 7899999999999999999999999986653
No 59
>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=80.82 E-value=7.4 Score=26.58 Aligned_cols=49 Identities=18% Similarity=0.223 Sum_probs=37.3
Q ss_pred HHHHHHHHHHhcc--cccHHHHHHHhCCCHHHHHHHHHhcCCeEeCCCceE
Q 036949 3 TKRMFQLLMSAYS--TISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRML 51 (81)
Q Consensus 3 R~~~~~li~~AY~--sIs~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~~~~ 51 (81)
|..+++.+-..-. .|++++++...|+..+|+....+..|+-.--.+..+
T Consensus 135 ~~~i~~~L~~~~~~~~isi~~is~~Tgi~~~DIi~tL~~l~~l~~~~~~~~ 185 (188)
T PF01853_consen 135 RRVILEYLLEFKGKKSISIKDISQETGIRPEDIISTLQQLGMLKYYKGQHI 185 (188)
T ss_dssp HHHHHHHHHHTSSE--EEHHHHHHHH-BTHHHHHHHHHHTT-EEEETTEEE
T ss_pred HHHHHHHHHhcCCCCeEEHHHHHHHHCCCHHHHHHHHHHCCCEEEECCcEE
Confidence 5667777776666 599999999999999999999999999865455443
No 60
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=80.81 E-value=11 Score=26.18 Aligned_cols=51 Identities=10% Similarity=0.089 Sum_probs=38.0
Q ss_pred HHHHHHHHHHhcccccHHHHHHHhCCCHHHHHH---HHHhcCCeEeCCCceEeec
Q 036949 3 TKRMFQLLMSAYSTISTQDTALFLGMNEDDAAY---YVQQQGWTLDPASRMLTVK 54 (81)
Q Consensus 3 R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~---~~~~~GW~~d~~~~~~~p~ 54 (81)
|++|..++ +....+++.++|.+||+|..-+.. ...++|--.-.-|....|.
T Consensus 7 ~~~Il~~l-~~~~~~~~~ela~~l~vS~~TiRRdL~~Le~~g~l~r~~GGa~~~~ 60 (252)
T PRK10906 7 HDAIIELV-KQQGYVSTEELVEHFSVSPQTIRRDLNDLAEQNKILRHHGGAALPS 60 (252)
T ss_pred HHHHHHHH-HHcCCEeHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCEEecC
Confidence 56777888 779999999999999999987755 4456788654445555554
No 61
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=80.75 E-value=5.4 Score=24.77 Aligned_cols=37 Identities=8% Similarity=0.114 Sum_probs=29.5
Q ss_pred HHHHHHHHHhc-ccccHHHHHHHhCCCHHHHHHHHHhc
Q 036949 4 KRMFQLLMSAY-STISTQDTALFLGMNEDDAAYYVQQQ 40 (81)
Q Consensus 4 ~~~~~li~~AY-~sIs~~~~a~~Lgls~~e~~~~~~~~ 40 (81)
.++...|...| ..++++++|+.+|+|+.-+....++.
T Consensus 12 ~~~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 12 HSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 46777887777 56999999999999998886666543
No 62
>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=79.99 E-value=4.5 Score=23.83 Aligned_cols=33 Identities=12% Similarity=0.221 Sum_probs=28.4
Q ss_pred HHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHH
Q 036949 3 TKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYV 37 (81)
Q Consensus 3 R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~ 37 (81)
+.+|+..+.+ .++++.++|..+|+|..-+-...
T Consensus 8 ~~~I~e~l~~--~~~ti~dvA~~~gvS~~TVsr~L 40 (80)
T TIGR02844 8 VLEIGKYIVE--TKATVRETAKVFGVSKSTVHKDV 40 (80)
T ss_pred HHHHHHHHHH--CCCCHHHHHHHhCCCHHHHHHHh
Confidence 5678888888 99999999999999998877644
No 63
>PF11112 PyocinActivator: Pyocin activator protein PrtN
Probab=79.98 E-value=5.5 Score=23.26 Aligned_cols=54 Identities=9% Similarity=0.082 Sum_probs=34.9
Q ss_pred ccccHHHHH-HHh-CCCHHHHHHHHHhcCCeEeCCCceEeecCCCCcccCCCChhHHHHHHhHH
Q 036949 15 STISTQDTA-LFL-GMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVTEQKLDPSKMQCLTEYV 76 (81)
Q Consensus 15 ~sIs~~~~a-~~L-gls~~e~~~~~~~~GW~~d~~~~~~~p~~~~~~~~~~~~~~~l~~Lt~~v 76 (81)
.-|++++++ .|+ ||+++.+..-+.. |.+-+|.-.-..+....--..+..|++|+
T Consensus 13 ~~IpL~~v~~~yf~~lt~~~a~rk~~~--------g~lplPv~rl~~SqKs~~~V~v~dLA~yi 68 (76)
T PF11112_consen 13 PVIPLEEVCEDYFPHLTPKTAKRKANA--------GELPLPVFRLDDSQKSPKFVHVQDLAAYI 68 (76)
T ss_pred CCCcHHHHHHHHHccCCHHHHHHHHHC--------CCCCCceeecCCcccCCceeeHHHHHHHH
Confidence 458888866 888 9999999887773 45544443322222222556777777776
No 64
>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=79.56 E-value=2.6 Score=21.57 Aligned_cols=28 Identities=25% Similarity=0.496 Sum_probs=22.0
Q ss_pred HHHHHHHhCCCHHHHHHHHHhcCCeEeC
Q 036949 19 TQDTALFLGMNEDDAAYYVQQQGWTLDP 46 (81)
Q Consensus 19 ~~~~a~~Lgls~~e~~~~~~~~GW~~d~ 46 (81)
+..+....|.+++.+..+...-+|-++.
T Consensus 4 i~~F~~iTg~~~~~A~~~L~~~~wdle~ 31 (43)
T PF14555_consen 4 IAQFMSITGADEDVAIQYLEANNWDLEA 31 (43)
T ss_dssp HHHHHHHH-SSHHHHHHHHHHTTT-HHH
T ss_pred HHHHHHHHCcCHHHHHHHHHHcCCCHHH
Confidence 4567888899999999999999998864
No 65
>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=79.33 E-value=3.4 Score=22.78 Aligned_cols=40 Identities=15% Similarity=0.207 Sum_probs=30.7
Q ss_pred hHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHhcCCeE
Q 036949 2 YTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTL 44 (81)
Q Consensus 2 ~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~ 44 (81)
+|+.+-.|--+ --++.++|..||++..-+-.+...-||.-
T Consensus 2 ~k~~A~~LY~~---G~~~~eIA~~Lg~~~~TV~~W~~r~~W~~ 41 (58)
T PF06056_consen 2 VKEQARSLYLQ---GWSIKEIAEELGVPRSTVYSWKDRYKWDE 41 (58)
T ss_pred HHHHHHHHHHc---CCCHHHHHHHHCCChHHHHHHHHhhCccc
Confidence 34444444443 45789999999999999999999989973
No 66
>COG3645 Uncharacterized phage-encoded protein [Function unknown]
Probab=79.32 E-value=5.9 Score=25.73 Aligned_cols=49 Identities=10% Similarity=0.137 Sum_probs=41.5
Q ss_pred HHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHhcCCeEeCCCceEeec
Q 036949 6 MFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVK 54 (81)
Q Consensus 6 ~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~~~~~p~ 54 (81)
-++-+..+-.+|.+.++|.+|++.+..+.+|..+.|--+...+....|.
T Consensus 37 f~D~v~~~~gli~~re~AK~lkige~~l~~~L~e~~~l~~~~~~~n~p~ 85 (135)
T COG3645 37 FADAVVEASGLILFRELAKLLKIGENRLFAWLRENKYLIKRGGDKNLPT 85 (135)
T ss_pred HHHHHhcCccceeHHHHHHHHccCHHHHHHHHHHCCEEEEccCCCCCCc
Confidence 4677888999999999999999999999999999998887634555555
No 67
>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=78.94 E-value=3.9 Score=29.73 Aligned_cols=35 Identities=17% Similarity=0.238 Sum_probs=29.6
Q ss_pred hHHHHHHHHHHhccc----ccHHHHHHHhCCCHHHHHHHH
Q 036949 2 YTKRMFQLLMSAYST----ISTQDTALFLGMNEDDAAYYV 37 (81)
Q Consensus 2 ~R~~~~~li~~AY~s----Is~~~~a~~Lgls~~e~~~~~ 37 (81)
-|++.+.+|.+ |.. -.++.++.+||++++|..+++
T Consensus 304 tReeal~~v~~-~d~~~~~~~~~~~~~~lg~t~~ef~~~~ 342 (343)
T TIGR03573 304 TREEAIELVKE-YDGEFPKEDLEYFLKYLGISEEEFWKTV 342 (343)
T ss_pred CHHHHHHHHHH-hcccccHHHHHHHHHHhCCCHHHHHHHh
Confidence 48999999999 765 567889999999999987654
No 68
>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=78.91 E-value=7 Score=21.83 Aligned_cols=29 Identities=17% Similarity=0.221 Sum_probs=20.2
Q ss_pred HHHhc-ccccHHHHHHHhCCCHHHHHHHHH
Q 036949 10 LMSAY-STISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 10 i~~AY-~sIs~~~~a~~Lgls~~e~~~~~~ 38 (81)
+.+.+ +.-+..++|.+||++.+++.....
T Consensus 13 L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~ 42 (78)
T PF04539_consen 13 LEQELGREPTDEEIAEELGISVEEVRELLQ 42 (78)
T ss_dssp HHHHHSS--BHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHhCCCCCHHHHHHHHcccHHHHHHHHH
Confidence 33344 567788899999999999987765
No 69
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=78.46 E-value=5.3 Score=27.87 Aligned_cols=50 Identities=8% Similarity=0.135 Sum_probs=33.7
Q ss_pred HHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHH---HhcCCeEeCCCceEee
Q 036949 3 TKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYV---QQQGWTLDPASRMLTV 53 (81)
Q Consensus 3 R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~---~~~GW~~d~~~~~~~p 53 (81)
|++|+.++.+ +..++++++|.+||+|+.-+..-. .++|--.-.-|..+.+
T Consensus 7 ~~~Il~~L~~-~~~v~v~eLa~~l~VS~~TIRRDL~~Le~~g~l~r~~Gga~~~ 59 (256)
T PRK10434 7 QAAILEYLQK-QGKTSVEELAQYFDTTGTTIRKDLVILEHAGTVIRTYGGVVLN 59 (256)
T ss_pred HHHHHHHHHH-cCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEECCEEcC
Confidence 4566666655 889999999999999987664443 3567654333444433
No 70
>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=78.43 E-value=10 Score=22.05 Aligned_cols=34 Identities=12% Similarity=0.265 Sum_probs=29.0
Q ss_pred hHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHH
Q 036949 2 YTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYV 37 (81)
Q Consensus 2 ~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~ 37 (81)
+.+.|+..+++. .++++++....|++.+++.-+.
T Consensus 6 ~~~~IL~~ls~~--c~TLeeL~ekTgi~k~~LlV~L 39 (72)
T PF05584_consen 6 VTQKILIILSKR--CCTLEELEEKTGISKNTLLVYL 39 (72)
T ss_pred HHHHHHHHHHhc--cCCHHHHHHHHCCCHHHHHHHH
Confidence 467888888888 9999999999999999986553
No 71
>COG5187 RPN7 26S proteasome regulatory complex component, contains PCI domain [Posttranslational modification, protein turnover, chaperones]
Probab=78.40 E-value=5.8 Score=29.53 Aligned_cols=76 Identities=14% Similarity=0.286 Sum_probs=56.5
Q ss_pred hHHHHHHHHHHhcccccHHHHHHHhCCCH----HHHHHHHH-hcCC-eEeCCCceEeecCCCCccc---CCC--ChhHHH
Q 036949 2 YTKRMFQLLMSAYSTISTQDTALFLGMNE----DDAAYYVQ-QQGW-TLDPASRMLTVKKQPLVTE---QKL--DPSKMQ 70 (81)
Q Consensus 2 ~R~~~~~li~~AY~sIs~~~~a~~Lgls~----~e~~~~~~-~~GW-~~d~~~~~~~p~~~~~~~~---~~~--~~~~l~ 70 (81)
+|.|+-.-+=-+|..++++..|.-+|.|. .++.+|+- .+=| .+|--+.++....|++.+. .++ .++-|.
T Consensus 317 MRrrvYaQlLESYr~lsl~sMA~tFgVSV~yvdrDLg~FIp~~~LncvIDRvnGvVetnrpdekn~qy~~vVkqGd~ll~ 396 (412)
T COG5187 317 MRRRVYAQLLESYRLLSLESMAQTFGVSVEYVDRDLGEFIPEGRLNCVIDRVNGVVETNRPDEKNQQYSSVVKQGDDLLR 396 (412)
T ss_pred HHHHHHHHHHHHHHHhhHHHHHHHhCccHHHHhhhHHhhCCCCceeeeeecccceEeccCcchhhhhHHHHHhcchHHHH
Confidence 57777777788999999999999999986 56777766 3444 4566667777777766442 222 888888
Q ss_pred HHHhHHH
Q 036949 71 CLTEYVF 77 (81)
Q Consensus 71 ~Lt~~v~ 77 (81)
+|-+|++
T Consensus 397 klqKy~a 403 (412)
T COG5187 397 KLQKYVA 403 (412)
T ss_pred HHHHHHH
Confidence 8888875
No 72
>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=78.28 E-value=3.6 Score=20.76 Aligned_cols=24 Identities=21% Similarity=0.401 Sum_probs=19.3
Q ss_pred cHHHHHHHhCCCHHHHHHHHHhcCC
Q 036949 18 STQDTALFLGMNEDDAAYYVQQQGW 42 (81)
Q Consensus 18 s~~~~a~~Lgls~~e~~~~~~~~GW 42 (81)
++.++|.++|+++.-+..+.. +|+
T Consensus 2 ~~~e~a~~~gv~~~tlr~~~~-~g~ 25 (49)
T cd04761 2 TIGELAKLTGVSPSTLRYYER-IGL 25 (49)
T ss_pred cHHHHHHHHCcCHHHHHHHHH-CCC
Confidence 578999999999998887754 454
No 73
>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=78.17 E-value=4.3 Score=19.93 Aligned_cols=20 Identities=25% Similarity=0.497 Sum_probs=13.5
Q ss_pred ccHHHHHHHhCCCHHHHHHH
Q 036949 17 ISTQDTALFLGMNEDDAAYY 36 (81)
Q Consensus 17 Is~~~~a~~Lgls~~e~~~~ 36 (81)
++-.++|.|||++.+-+-..
T Consensus 3 mtr~diA~~lG~t~ETVSR~ 22 (32)
T PF00325_consen 3 MTRQDIADYLGLTRETVSRI 22 (32)
T ss_dssp --HHHHHHHHTS-HHHHHHH
T ss_pred cCHHHHHHHhCCcHHHHHHH
Confidence 56789999999988766444
No 74
>PF13730 HTH_36: Helix-turn-helix domain
Probab=77.85 E-value=4.6 Score=21.13 Aligned_cols=25 Identities=20% Similarity=0.284 Sum_probs=19.8
Q ss_pred cHHHHHHHhCCCHHHHHHHHH---hcCC
Q 036949 18 STQDTALFLGMNEDDAAYYVQ---QQGW 42 (81)
Q Consensus 18 s~~~~a~~Lgls~~e~~~~~~---~~GW 42 (81)
|.+.+|..+|++..-+..... ++||
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 789999999999877666544 5687
No 75
>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=77.36 E-value=3.7 Score=29.90 Aligned_cols=32 Identities=22% Similarity=0.472 Sum_probs=24.8
Q ss_pred CCHHHHHHHHHhcCCeEeCCC----ceEeecCCCCc
Q 036949 28 MNEDDAAYYVQQQGWTLDPAS----RMLTVKKQPLV 59 (81)
Q Consensus 28 ls~~e~~~~~~~~GW~~d~~~----~~~~p~~~~~~ 59 (81)
++++|+.+..+++||++-+|+ +-+.|.|.+..
T Consensus 132 y~~~~a~~~~~~~g~~~~~d~~~g~rrvV~SP~P~~ 167 (308)
T cd04235 132 YSEEEAEELAAEKGWTFKEDAGRGYRRVVPSPKPKD 167 (308)
T ss_pred cCHHHHHHHHHHcCCEEEEeCCCCceeeeCCCCCcc
Confidence 488999999999999998876 55666655443
No 76
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=77.22 E-value=2.4 Score=24.26 Aligned_cols=41 Identities=24% Similarity=0.384 Sum_probs=31.4
Q ss_pred HHHhcccccHHHHHHHhCCCHHHHHHHHHh-cCCe--EeCCCce
Q 036949 10 LMSAYSTISTQDTALFLGMNEDDAAYYVQQ-QGWT--LDPASRM 50 (81)
Q Consensus 10 i~~AY~sIs~~~~a~~Lgls~~e~~~~~~~-~GW~--~d~~~~~ 50 (81)
|.---.-|++.++|..||.++..+.+++.. +-|- +||+|.+
T Consensus 7 IrlLs~~~s~~~Aa~~lG~~~~~v~~wv~~fR~wll~LDPSG~~ 50 (65)
T PF05344_consen 7 IRLLSQQISVAQAADRLGTDPGTVRRWVRMFRQWLLQLDPSGHW 50 (65)
T ss_pred HHHhcccccHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCCCCh
Confidence 333445789999999999999999888775 4774 6777754
No 77
>PRK13500 transcriptional activator RhaR; Provisional
Probab=77.20 E-value=6 Score=28.03 Aligned_cols=40 Identities=15% Similarity=0.107 Sum_probs=33.1
Q ss_pred HHHHHHHHHhcc-cccHHHHHHHhCCCHHHHHHHHHhc-CCe
Q 036949 4 KRMFQLLMSAYS-TISTQDTALFLGMNEDDAAYYVQQQ-GWT 43 (81)
Q Consensus 4 ~~~~~li~~AY~-sIs~~~~a~~Lgls~~e~~~~~~~~-GW~ 43 (81)
+++.+.|..-|. .|+++++|..+|+|+.-+...+++. |=+
T Consensus 209 ~~i~~yI~~~~~e~isl~~lA~~~~iS~~~L~r~FK~~tG~T 250 (312)
T PRK13500 209 DKLITRLAASLKSPFALDKFCDEASCSERVLRQQFRQQTGMT 250 (312)
T ss_pred HHHHHHHHHcccCCCCHHHHHHHHCcCHHHHHHHHHHHHCcC
Confidence 467788888877 5999999999999999998887764 543
No 78
>PLN03239 histone acetyltransferase; Provisional
Probab=76.90 E-value=12 Score=27.90 Aligned_cols=52 Identities=15% Similarity=0.149 Sum_probs=39.9
Q ss_pred HHHHHHHHHHhc---ccccHHHHHHHhCCCHHHHHHHHHhcCCeEeCCCceEeec
Q 036949 3 TKRMFQLLMSAY---STISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVK 54 (81)
Q Consensus 3 R~~~~~li~~AY---~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~~~~~p~ 54 (81)
+++++..+...- .+||+++++...|+..+|+..-.+..|.-....|..++-.
T Consensus 268 ~~~il~~L~~~~~~~~~~si~dis~~Tgi~~~DIi~tL~~l~~l~~~~g~~~i~~ 322 (351)
T PLN03239 268 GSTIVDFLLNHSGNDSSLSIMDIAKKTSIMAEDIVFALNQLGILKFINGIYFIAA 322 (351)
T ss_pred HHHHHHHHHhccCCCCCccHHHHHHHhCCCHHHHHHHHHHCCcEEEECCeEEEEe
Confidence 456777765543 4699999999999999999999999997765555554433
No 79
>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=76.86 E-value=7.6 Score=20.87 Aligned_cols=27 Identities=22% Similarity=0.234 Sum_probs=19.5
Q ss_pred HHHHhcccccHHHHHHHhCCCHHHHHH
Q 036949 9 LLMSAYSTISTQDTALFLGMNEDDAAY 35 (81)
Q Consensus 9 li~~AY~sIs~~~~a~~Lgls~~e~~~ 35 (81)
+-..-...||-.++|.++|+++.++.+
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 334456799999999999999988765
No 80
>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=76.33 E-value=13 Score=22.09 Aligned_cols=42 Identities=5% Similarity=0.035 Sum_probs=29.2
Q ss_pred hcccccHHHHHHHhCCCHHHHHH---HHHhcCCeEeCC--CceEeec
Q 036949 13 AYSTISTQDTALFLGMNEDDAAY---YVQQQGWTLDPA--SRMLTVK 54 (81)
Q Consensus 13 AY~sIs~~~~a~~Lgls~~e~~~---~~~~~GW~~d~~--~~~~~p~ 54 (81)
....|+..++|.++|++.+-+-. -..++||-.-.. +.+-+.+
T Consensus 44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~r~~~~~~~~~n~ 90 (95)
T TIGR01610 44 KQDRVTATVIAELTGLSRTHVSDAIKSLARRRIIFRQGMMGIVGVNT 90 (95)
T ss_pred cCCccCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeecCCceeecCC
Confidence 45688899999999997765544 455789997433 4444443
No 81
>PRK12354 carbamate kinase; Reviewed
Probab=75.96 E-value=8.2 Score=28.16 Aligned_cols=21 Identities=29% Similarity=0.730 Sum_probs=18.4
Q ss_pred CCHHHHHHHHHhcCCeEeCCC
Q 036949 28 MNEDDAAYYVQQQGWTLDPAS 48 (81)
Q Consensus 28 ls~~e~~~~~~~~GW~~d~~~ 48 (81)
++++|+.+..+++||++-.++
T Consensus 127 y~~~~a~~~~~e~g~~~~~dg 147 (307)
T PRK12354 127 YDEAEAERLAAEKGWTIKPDG 147 (307)
T ss_pred cCHHHHHHHHHhcCCEEeecC
Confidence 489999999999999987665
No 82
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=75.60 E-value=5.4 Score=21.65 Aligned_cols=24 Identities=21% Similarity=0.390 Sum_probs=20.0
Q ss_pred cHHHHHHHhCCCHHHHHHHHHhcCC
Q 036949 18 STQDTALFLGMNEDDAAYYVQQQGW 42 (81)
Q Consensus 18 s~~~~a~~Lgls~~e~~~~~~~~GW 42 (81)
++.++|+++|+++..+..+.. .|+
T Consensus 2 s~~eva~~~gvs~~tlr~~~~-~gl 25 (70)
T smart00422 2 TIGEVAKLAGVSVRTLRYYER-IGL 25 (70)
T ss_pred CHHHHHHHHCcCHHHHHHHHH-CCC
Confidence 578999999999999998865 454
No 83
>PRK13501 transcriptional activator RhaR; Provisional
Probab=75.40 E-value=7.2 Score=27.06 Aligned_cols=41 Identities=15% Similarity=0.158 Sum_probs=33.4
Q ss_pred HHHHHHHHHhccc-ccHHHHHHHhCCCHHHHHHHHHhc-CCeE
Q 036949 4 KRMFQLLMSAYST-ISTQDTALFLGMNEDDAAYYVQQQ-GWTL 44 (81)
Q Consensus 4 ~~~~~li~~AY~s-Is~~~~a~~Lgls~~e~~~~~~~~-GW~~ 44 (81)
+++++.|.+-|.. |+++++|..+|+|+.-+...+++. |-+.
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 3467778777776 899999999999999998887754 7664
No 84
>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=75.26 E-value=5.7 Score=21.60 Aligned_cols=24 Identities=17% Similarity=0.250 Sum_probs=19.7
Q ss_pred ccccHHHHHHHhCCCHHHHHHHHH
Q 036949 15 STISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 15 ~sIs~~~~a~~Lgls~~e~~~~~~ 38 (81)
..+++.++|..||+|..-+.+...
T Consensus 22 R~~tl~elA~~lgis~st~~~~LR 45 (53)
T PF04967_consen 22 RRITLEELAEELGISKSTVSEHLR 45 (53)
T ss_pred CcCCHHHHHHHhCCCHHHHHHHHH
Confidence 378999999999999887766543
No 85
>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=74.95 E-value=9.1 Score=20.18 Aligned_cols=40 Identities=15% Similarity=0.248 Sum_probs=26.9
Q ss_pred HHHHHHHHhccc-ccHHHHHHHhCCCHHHH---HHHHHhcCCeE
Q 036949 5 RMFQLLMSAYST-ISTQDTALFLGMNEDDA---AYYVQQQGWTL 44 (81)
Q Consensus 5 ~~~~li~~AY~s-Is~~~~a~~Lgls~~e~---~~~~~~~GW~~ 44 (81)
+++..|...=.. ++..++|..+|++..-+ .+-..++||..
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 344444444444 89999999999977655 44455779975
No 86
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=74.89 E-value=9.6 Score=19.58 Aligned_cols=25 Identities=20% Similarity=0.100 Sum_probs=19.9
Q ss_pred cccccHHHHHHHhCCCHHHHHHHHH
Q 036949 14 YSTISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 14 Y~sIs~~~~a~~Lgls~~e~~~~~~ 38 (81)
-...+..++|+.+|+|.+-+.....
T Consensus 25 ~~~~s~~~vA~~~~vs~~TV~ri~~ 49 (52)
T PF13542_consen 25 RESRSFKDVARELGVSWSTVRRIFD 49 (52)
T ss_pred hhcCCHHHHHHHHCCCHHHHHHHHH
Confidence 3346999999999999988776654
No 87
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=74.76 E-value=17 Score=25.35 Aligned_cols=56 Identities=16% Similarity=0.245 Sum_probs=41.8
Q ss_pred HHHHHHHHHHhcccccHHHHHHHhCCCHHHHHH---HHHhcCCeEeCCCceEeecCCCCc
Q 036949 3 TKRMFQLLMSAYSTISTQDTALFLGMNEDDAAY---YVQQQGWTLDPASRMLTVKKQPLV 59 (81)
Q Consensus 3 R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~---~~~~~GW~~d~~~~~~~p~~~~~~ 59 (81)
|++|+.++.+ -.+|+++++|..||.|+.-+.. ...++|=-.-.-|....|.....+
T Consensus 7 ~~~Il~~l~~-~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l~R~hGGa~~~~~~~~~ 65 (253)
T COG1349 7 HQKILELLKE-KGKVSVEELAELFGVSEMTIRRDLNELEEQGLLLRVHGGAVLPDSESEY 65 (253)
T ss_pred HHHHHHHHHH-cCcEEHHHHHHHhCCCHHHHHHhHHHHHHCCcEEEEeCCEecCCCcccc
Confidence 4677777777 8899999999999999977644 455667776556677777666554
No 88
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=74.61 E-value=7.9 Score=26.75 Aligned_cols=36 Identities=17% Similarity=0.167 Sum_probs=29.4
Q ss_pred HHHHHHHHhc-ccccHHHHHHHhCCCHHHHHHHHHhc
Q 036949 5 RMFQLLMSAY-STISTQDTALFLGMNEDDAAYYVQQQ 40 (81)
Q Consensus 5 ~~~~li~~AY-~sIs~~~~a~~Lgls~~e~~~~~~~~ 40 (81)
++.+.|...| ..|+++++|+.+|+|+.-+....++.
T Consensus 187 ~~~~~i~~~~~~~isl~~lA~~~~lS~~~l~r~Fk~~ 223 (290)
T PRK10572 187 EACQYISDHLASEFDIESVAQHVCLSPSRLAHLFRQQ 223 (290)
T ss_pred HHHHHHHhcccCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 4667775555 79999999999999998887777654
No 89
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=74.53 E-value=3.7 Score=29.50 Aligned_cols=27 Identities=22% Similarity=0.538 Sum_probs=25.1
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHhcCCe
Q 036949 17 ISTQDTALFLGMNEDDAAYYVQQQGWT 43 (81)
Q Consensus 17 Is~~~~a~~Lgls~~e~~~~~~~~GW~ 43 (81)
..+.++|.+||+|++.+..+-..-||.
T Consensus 20 mk~~dIAeklGvspntiksWKrr~gWs 46 (279)
T COG5484 20 MKLKDIAEKLGVSPNTIKSWKRRDGWS 46 (279)
T ss_pred ccHHHHHHHhCCChHHHHHHHHhcCCC
Confidence 678899999999999999999999996
No 90
>KOG2582 consensus COP9 signalosome, subunit CSN3 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=74.42 E-value=13 Score=28.18 Aligned_cols=60 Identities=13% Similarity=0.190 Sum_probs=42.2
Q ss_pred HHHHHHHHhcccccHHHHHHHhCC-CHHHHHHHHHhc---C-CeEeCCCceEeecCCCCcccCCC
Q 036949 5 RMFQLLMSAYSTISTQDTALFLGM-NEDDAAYYVQQQ---G-WTLDPASRMLTVKKQPLVTEQKL 64 (81)
Q Consensus 5 ~~~~li~~AY~sIs~~~~a~~Lgl-s~~e~~~~~~~~---G-W~~d~~~~~~~p~~~~~~~~~~~ 64 (81)
+...-+.|.|.+++++++|++..| +.+|+.+++-+. | =..-.+|.+++..++.+...+..
T Consensus 306 ~nI~rltktF~sLsL~dIA~~vQLa~~qevek~Ilqmie~~~i~a~iNG~v~f~~n~e~~~SpeM 370 (422)
T KOG2582|consen 306 KNIQRLTKTFLSLSLSDIASRVQLASAQEVEKYILQMIEDGEIFASINGMVFFTDNPEKYNSPEM 370 (422)
T ss_pred HHHHHHHHHHHHhhHHHHHHHHHhcchHHHHHHHHHHhccCceEEEecceEEEecCcccCCCHHH
Confidence 445567899999999999998888 777777665432 2 22234688888888777655433
No 91
>COG0549 ArcC Carbamate kinase [Amino acid transport and metabolism]
Probab=74.09 E-value=9.7 Score=27.91 Aligned_cols=41 Identities=15% Similarity=0.420 Sum_probs=26.4
Q ss_pred CHHHHHHHHHhcCCeEeCCCce----EeecCCCCcccCCCChhHHHHH
Q 036949 29 NEDDAAYYVQQQGWTLDPASRM----LTVKKQPLVTEQKLDPSKMQCL 72 (81)
Q Consensus 29 s~~e~~~~~~~~GW~~d~~~~~----~~p~~~~~~~~~~~~~~~l~~L 72 (81)
+++|+.+..++.||.+..|+.. +.|.|.+.. +.+.+.+..|
T Consensus 136 ~~eea~~l~~~~gw~~keD~~rG~RRVVpSP~P~~---IvE~~~Ik~L 180 (312)
T COG0549 136 SEEEAEELAKEYGWVFKEDAGRGYRRVVPSPKPVR---IVEAEAIKAL 180 (312)
T ss_pred CHHHHHHHHhhcCcEEEecCCCCeeEecCCCCCcc---chhHHHHHHH
Confidence 8899999999999999766443 444433332 2255555544
No 92
>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=73.58 E-value=13 Score=20.42 Aligned_cols=41 Identities=20% Similarity=0.190 Sum_probs=30.5
Q ss_pred HHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHH---HhcCCeEeC
Q 036949 4 KRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYV---QQQGWTLDP 46 (81)
Q Consensus 4 ~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~---~~~GW~~d~ 46 (81)
.+++.++..++. +.+++|..+|+|..-+.... .+.||.+..
T Consensus 3 ~~il~~L~~~~~--~~~eLa~~l~vS~~tv~~~l~~L~~~g~~i~~ 46 (69)
T TIGR00122 3 LRLLALLADNPF--SGEKLGEALGMSRTAVNKHIQTLREWGVDVLT 46 (69)
T ss_pred HHHHHHHHcCCc--CHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEe
Confidence 367788888874 58999999999887665554 456996543
No 93
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=73.23 E-value=9.7 Score=19.40 Aligned_cols=34 Identities=18% Similarity=0.316 Sum_probs=21.3
Q ss_pred HHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHh
Q 036949 3 TKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQ 39 (81)
Q Consensus 3 R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~ 39 (81)
|..++.+... -.+..++|..||+|..-+..+...
T Consensus 7 R~~ii~l~~~---G~s~~~ia~~lgvs~~Tv~~w~kr 40 (50)
T PF13384_consen 7 RAQIIRLLRE---GWSIREIAKRLGVSRSTVYRWIKR 40 (50)
T ss_dssp ---HHHHHHH---T--HHHHHHHHTS-HHHHHHHHT-
T ss_pred HHHHHHHHHC---CCCHHHHHHHHCcCHHHHHHHHHH
Confidence 4445555544 788999999999999988887653
No 94
>KOG1497 consensus COP9 signalosome, subunit CSN4 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=72.64 E-value=5 Score=30.05 Aligned_cols=32 Identities=19% Similarity=0.243 Sum_probs=28.2
Q ss_pred HHHHHhcccccHHHHHHHhCCCHHHHHHHHHh
Q 036949 8 QLLMSAYSTISTQDTALFLGMNEDDAAYYVQQ 39 (81)
Q Consensus 8 ~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~ 39 (81)
-.+|+=|..|+.+.++..|+++++.+.+.+.+
T Consensus 309 ls~Skly~nisf~~Lg~ll~i~~ekaekiaa~ 340 (399)
T KOG1497|consen 309 LSASKLYNNISFEELGALLKIDAEKAEKIAAQ 340 (399)
T ss_pred HHHHHHHHhccHHHHHHHhCCCHHHHHHHHHH
Confidence 46799999999999999999999988877654
No 95
>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=72.58 E-value=4.6 Score=21.71 Aligned_cols=22 Identities=27% Similarity=0.468 Sum_probs=18.0
Q ss_pred HHhCCCHHHHHHHHHhcCCeEe
Q 036949 24 LFLGMNEDDAAYYVQQQGWTLD 45 (81)
Q Consensus 24 ~~Lgls~~e~~~~~~~~GW~~d 45 (81)
.+.|++.+++.+.+.+.||.+.
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 4679999999999999999653
No 96
>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=72.31 E-value=12 Score=19.58 Aligned_cols=38 Identities=16% Similarity=0.329 Sum_probs=26.8
Q ss_pred HHHHHHHhcccccHHHHHHHhCCCHHHHHHHH---HhcCCeE
Q 036949 6 MFQLLMSAYSTISTQDTALFLGMNEDDAAYYV---QQQGWTL 44 (81)
Q Consensus 6 ~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~---~~~GW~~ 44 (81)
++.+|. .+..++..++|.++|++..-+-..+ .++||-.
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 4677999999999999876665554 4679975
No 97
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=72.20 E-value=16 Score=21.58 Aligned_cols=40 Identities=18% Similarity=0.280 Sum_probs=30.8
Q ss_pred HHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH---hcCCeE
Q 036949 4 KRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ---QQGWTL 44 (81)
Q Consensus 4 ~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~---~~GW~~ 44 (81)
.+|+.++..- ..++.+++|..+|+|+..+..... +.||-.
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 4666777663 679999999999999988766554 568875
No 98
>PF06262 DUF1025: Possibl zinc metallo-peptidase; InterPro: IPR010428 This is a family of bacterial protein with undetermined function.; PDB: 3E11_A.
Probab=72.18 E-value=2.9 Score=25.50 Aligned_cols=21 Identities=24% Similarity=0.623 Sum_probs=14.6
Q ss_pred cHHHHHHHhCCCHHHHHHHHHhcCC
Q 036949 18 STQDTALFLGMNEDDAAYYVQQQGW 42 (81)
Q Consensus 18 s~~~~a~~Lgls~~e~~~~~~~~GW 42 (81)
=+.++|.++|++++++.. .||
T Consensus 77 lvhEiah~fG~~~e~l~~----lg~ 97 (97)
T PF06262_consen 77 LVHEIAHHFGISDEDLDA----LGW 97 (97)
T ss_dssp HHHHHHHHTT--HHHHHC----TT-
T ss_pred HHHHHHHHcCCCHHHhhh----ccC
Confidence 367899999999999875 566
No 99
>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=72.07 E-value=5.2 Score=19.64 Aligned_cols=26 Identities=12% Similarity=0.162 Sum_probs=19.5
Q ss_pred HHHHHHHhCCCHHHHHHHHHhcCCeEe
Q 036949 19 TQDTALFLGMNEDDAAYYVQQQGWTLD 45 (81)
Q Consensus 19 ~~~~a~~Lgls~~e~~~~~~~~GW~~d 45 (81)
+..+..| ||+.+++.+.....||-++
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 4556777 9999999988888888654
No 100
>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=71.65 E-value=10 Score=20.89 Aligned_cols=38 Identities=11% Similarity=0.304 Sum_probs=25.9
Q ss_pred cccHHHHHHHhCCCHHHHH---HHHHhcCCeEeCCCceEee
Q 036949 16 TISTQDTALFLGMNEDDAA---YYVQQQGWTLDPASRMLTV 53 (81)
Q Consensus 16 sIs~~~~a~~Lgls~~e~~---~~~~~~GW~~d~~~~~~~p 53 (81)
.++.+++|.|+|+|..-+. ....+.||---..+.+.++
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 3578899999999876654 4455679985444455443
No 101
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=71.53 E-value=19 Score=23.95 Aligned_cols=51 Identities=14% Similarity=0.217 Sum_probs=32.5
Q ss_pred hHHHHHHHHHHhcc--------------cccHHHHHHHhCCCHHHHHH---HHHhcCCeEeCCCceEe
Q 036949 2 YTKRMFQLLMSAYS--------------TISTQDTALFLGMNEDDAAY---YVQQQGWTLDPASRMLT 52 (81)
Q Consensus 2 ~R~~~~~li~~AY~--------------sIs~~~~a~~Lgls~~e~~~---~~~~~GW~~d~~~~~~~ 52 (81)
.++|++..+-.-+. .++..++|.|||++.+-+-. -..+.||---..+.+.+
T Consensus 156 ~~~Rla~~L~~l~~~~~~~~~~~~~~~~~lt~~~iA~~lG~sr~tvsR~l~~l~~~g~I~~~~~~i~i 223 (235)
T PRK11161 156 AEERLAAFIYNLSRRFAQRGFSPREFRLTMTRGDIGNYLGLTVETISRLLGRFQKSGMLAVKGKYITI 223 (235)
T ss_pred HHHHHHHHHHHHHHHHhhcCCCCceeEccccHHHHHHHhCCcHHHHHHHHHHHHHCCCEEecCCEEEE
Confidence 46777776654221 35678999999998776644 34567886544444443
No 102
>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=71.49 E-value=5.9 Score=22.04 Aligned_cols=32 Identities=19% Similarity=0.362 Sum_probs=26.4
Q ss_pred hcccccHHHHHHHhC--------C-CHHHHHHHHHhcCCeE
Q 036949 13 AYSTISTQDTALFLG--------M-NEDDAAYYVQQQGWTL 44 (81)
Q Consensus 13 AY~sIs~~~~a~~Lg--------l-s~~e~~~~~~~~GW~~ 44 (81)
.|.-|.++++.++|. - +...+.+|+.++|=++
T Consensus 21 ~YePI~L~el~~~L~~~g~~~~~~~~~~~l~~~lD~~gIt~ 61 (64)
T PF09494_consen 21 MYEPINLEELHAWLKASGIGFDRKVDPSKLKEWLDSQGITF 61 (64)
T ss_pred cCCCccHHHHHHHHHHcCCCccceeCHHHHHHHHHHCCcee
Confidence 589999999999997 2 6788999999888554
No 103
>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=71.19 E-value=7.4 Score=21.32 Aligned_cols=52 Identities=12% Similarity=0.197 Sum_probs=33.3
Q ss_pred cHHHHHHHhCCCHHHHHHHHHhcCCeEeCCCceEeecCCCCcccCCC-ChhHHHHHHhHHHhh
Q 036949 18 STQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVTEQKL-DPSKMQCLTEYVFHL 79 (81)
Q Consensus 18 s~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~~~~~p~~~~~~~~~~~-~~~~l~~Lt~~v~~L 79 (81)
++.++|+++|+++.-+..+..+. ..+.|.. ....-.. +.+++..|-.+...+
T Consensus 2 ~i~e~A~~~gVs~~tlr~ye~~~--------gl~~~~r--~~~g~R~yt~~di~~l~~i~~l~ 54 (68)
T cd04763 2 TIGEVALLTGIKPHVLRAWEREF--------GLLKPQR--SDGGHRLFNDADIDRILEIKRWI 54 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHhc--------CCCCCCc--CCCCCcccCHHHHHHHHHHHHHH
Confidence 57899999999999999775532 2222322 1222222 888888877766554
No 104
>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]
Probab=71.06 E-value=16 Score=21.34 Aligned_cols=34 Identities=18% Similarity=0.289 Sum_probs=27.5
Q ss_pred HHHHHHHHhccc-ccHHHHHHHhCCCHHHHHHHHH
Q 036949 5 RMFQLLMSAYST-ISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 5 ~~~~li~~AY~s-Is~~~~a~~Lgls~~e~~~~~~ 38 (81)
++..+|..-|.. ++++++|..+|+|..-+.....
T Consensus 24 ~~~~~i~~~~~~~~~l~~la~~~g~S~~~l~r~f~ 58 (127)
T COG2207 24 RALDYIEENLAEPLTLEDLARRLGMSRRTLSRLFK 58 (127)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 666666666665 8999999999999988877666
No 105
>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=70.93 E-value=14 Score=19.62 Aligned_cols=31 Identities=16% Similarity=0.374 Sum_probs=24.2
Q ss_pred ccccHHHHHHHhCCCHHHHHHHH---HhcCCeEe
Q 036949 15 STISTQDTALFLGMNEDDAAYYV---QQQGWTLD 45 (81)
Q Consensus 15 ~sIs~~~~a~~Lgls~~e~~~~~---~~~GW~~d 45 (81)
..++..++|.++|++..-+.... .+.||-.-
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~ 57 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKELEEEGLISR 57 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence 35899999999999887765554 46799864
No 106
>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=70.82 E-value=14 Score=22.74 Aligned_cols=40 Identities=15% Similarity=0.158 Sum_probs=34.0
Q ss_pred HHHHHHhcccccHHHHHHHhCCCHHHHHHHHHhcCCeEeC
Q 036949 7 FQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDP 46 (81)
Q Consensus 7 ~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~d~ 46 (81)
+.-.-.++..+.+.++|.-||++..-+..+....||+.--
T Consensus 62 L~~~v~~~pd~tl~Ela~~l~Vs~~ti~~~Lkrlg~t~KK 101 (119)
T PF01710_consen 62 LKALVEENPDATLRELAERLGVSPSTIWRALKRLGITRKK 101 (119)
T ss_pred HHHHHHHCCCcCHHHHHHHcCCCHHHHHHHHHHcCchhcc
Confidence 3344456999999999999999999999999999999853
No 107
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=70.82 E-value=12 Score=26.04 Aligned_cols=41 Identities=20% Similarity=0.171 Sum_probs=28.5
Q ss_pred HHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHH---HHhcCCeE
Q 036949 3 TKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYY---VQQQGWTL 44 (81)
Q Consensus 3 R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~---~~~~GW~~ 44 (81)
|++|+..+.+ +.++++.++|.+||.|+.-+..- ..+.|...
T Consensus 9 ~~~I~~~l~~-~~~v~v~eLa~~~~VS~~TIRRDL~~Le~~~~~~ 52 (252)
T PRK10681 9 IGQLLQALKR-SDKLHLKDAAALLGVSEMTIRRDLNAHSAPVVLL 52 (252)
T ss_pred HHHHHHHHHH-cCCCcHHHHHHHhCCCHHHHHHHHHHhhcCeEEE
Confidence 4556666655 99999999999999998654332 22456544
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=70.52 E-value=8 Score=21.08 Aligned_cols=22 Identities=14% Similarity=0.474 Sum_probs=18.9
Q ss_pred cHHHHHHHhCCCHHHHHHHHHh
Q 036949 18 STQDTALFLGMNEDDAAYYVQQ 39 (81)
Q Consensus 18 s~~~~a~~Lgls~~e~~~~~~~ 39 (81)
++.++|+++|+++.-+..+..+
T Consensus 2 ~i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 2 TIKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred CHHHHHHHHCcCHHHHHHHHHh
Confidence 6789999999999999877654
No 109
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=70.18 E-value=12 Score=18.64 Aligned_cols=41 Identities=22% Similarity=0.360 Sum_probs=28.7
Q ss_pred HHHHHHHHHhcccccHHHHHHHhCCCHHHHHHH---HHhcCCeEe
Q 036949 4 KRMFQLLMSAYSTISTQDTALFLGMNEDDAAYY---VQQQGWTLD 45 (81)
Q Consensus 4 ~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~---~~~~GW~~d 45 (81)
..++..+.+ -..++..+++..+|++..-+... ..+.||-.-
T Consensus 3 ~~il~~l~~-~~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~ 46 (53)
T smart00420 3 QQILELLAQ-QGKVSVEELAELLGVSEMTIRRDLNKLEEQGLLTR 46 (53)
T ss_pred HHHHHHHHH-cCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 455666654 36799999999999987665444 446788653
No 110
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=70.00 E-value=7.7 Score=21.04 Aligned_cols=50 Identities=18% Similarity=0.280 Sum_probs=32.0
Q ss_pred cHHHHHHHhCCCHHHHHHHHHhcCCeEeCCCceEeecCCCCcccCCC-ChhHHHHHHhHHHh
Q 036949 18 STQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVTEQKL-DPSKMQCLTEYVFH 78 (81)
Q Consensus 18 s~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~~~~~p~~~~~~~~~~~-~~~~l~~Lt~~v~~ 78 (81)
++.++|.++|+|..-+..|... |. +.|.. ....... +++++..|..+...
T Consensus 2 ti~eva~~~gvs~~tlr~y~~~-gl--------l~~~~--~~~g~r~y~~~dv~~l~~i~~l 52 (69)
T PF13411_consen 2 TIKEVAKLLGVSPSTLRYYERE-GL--------LPPPR--DENGYRYYSEEDVERLREIKEL 52 (69)
T ss_dssp EHHHHHHHTTTTHHHHHHHHHT-TS--------STTBE--STTSSEEE-HHHHHHHHHHHHH
T ss_pred cHHHHHHHHCcCHHHHHHHHHh-cC--------ccccc--ccCceeeccHHHHHHHHHHHHH
Confidence 5789999999999999988663 32 22332 2222222 88888887766543
No 111
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=69.79 E-value=12 Score=20.97 Aligned_cols=42 Identities=19% Similarity=0.397 Sum_probs=32.9
Q ss_pred HHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH---hcCCeE
Q 036949 3 TKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ---QQGWTL 44 (81)
Q Consensus 3 R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~---~~GW~~ 44 (81)
.++|+..|.....-++..++|.-+|+|.-.+..+.. +.|..-
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 467888899989999999999999999999887765 346543
No 112
>PF14791 DNA_pol_B_thumb: DNA polymerase beta thumb ; PDB: 1HUZ_A 3K75_D 1HUO_A 2BPC_A 1RPL_A 1NOM_A 1ZQX_A 1ZQU_A 1ZQZ_A 1ZQV_A ....
Probab=69.77 E-value=3.8 Score=23.03 Aligned_cols=20 Identities=20% Similarity=0.345 Sum_probs=15.8
Q ss_pred HHHHHHHHhcCCeEeCCCce
Q 036949 31 DDAAYYVQQQGWTLDPASRM 50 (81)
Q Consensus 31 ~e~~~~~~~~GW~~d~~~~~ 50 (81)
..+..+|.++||++++.|-+
T Consensus 13 r~lR~~A~~~g~~L~~~Gl~ 32 (64)
T PF14791_consen 13 RDLRQYAKKKGMKLSEYGLF 32 (64)
T ss_dssp HHHHHHHHHTTEEEESSEEE
T ss_pred HHHHHHHHHcCCeeCccccc
Confidence 45788999999999876533
No 113
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=69.59 E-value=20 Score=27.63 Aligned_cols=51 Identities=12% Similarity=0.160 Sum_probs=38.9
Q ss_pred HHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHhcCCeEeCCCceEee
Q 036949 3 TKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTV 53 (81)
Q Consensus 3 R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~~~~~p 53 (81)
+..++..+.+.-..|++++++.+.|+..+|+..-.+..|=-.--.|..++-
T Consensus 361 ~~~i~~~L~~~~~~~si~~is~~T~i~~~Dii~tL~~l~~l~~~kg~~~i~ 411 (450)
T PLN00104 361 TRVLLEILKKHKGNISIKELSDMTAIKAEDIVSTLQSLNLIQYRKGQHVIC 411 (450)
T ss_pred HHHHHHHHHhcCCCccHHHHHHHhCCCHHHHHHHHHHCCCEEecCCcEEEE
Confidence 567788887777899999999999999999998888877332223444443
No 114
>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=69.51 E-value=13 Score=25.47 Aligned_cols=36 Identities=19% Similarity=0.249 Sum_probs=29.7
Q ss_pred HHHHHHHHHhc-ccccHHHHHHHhCCCHHHHHHHHHh
Q 036949 4 KRMFQLLMSAY-STISTQDTALFLGMNEDDAAYYVQQ 39 (81)
Q Consensus 4 ~~~~~li~~AY-~sIs~~~~a~~Lgls~~e~~~~~~~ 39 (81)
.++.+.|..-| ..++++++|..+|+|..-+...+++
T Consensus 189 ~~~~~~I~~~~~~~~sl~~lA~~~~~S~~~l~r~Fk~ 225 (287)
T TIGR02297 189 NRFNFLIEENYKQHLRLPEYADRLGISESRLNDICRR 225 (287)
T ss_pred HHHHHHHHHhhccCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 45667776665 6799999999999999998887776
No 115
>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=69.12 E-value=20 Score=20.82 Aligned_cols=32 Identities=16% Similarity=0.084 Sum_probs=26.1
Q ss_pred HHHHHHhcccccHHHHHHHhCCCHHHHHHHHH
Q 036949 7 FQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 7 ~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~ 38 (81)
+-.+.+-+.-.+..++|..||+|..-+.....
T Consensus 23 af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~ 54 (73)
T TIGR03879 23 AAALAREEAGKTASEIAEELGRTEQTVRNHLK 54 (73)
T ss_pred HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHh
Confidence 33445667999999999999999998887765
No 116
>PRK12454 carbamate kinase-like carbamoyl phosphate synthetase; Reviewed
Probab=69.08 E-value=14 Score=27.04 Aligned_cols=20 Identities=20% Similarity=0.624 Sum_probs=17.3
Q ss_pred CCHHHHHHHHHhcCCeEeCC
Q 036949 28 MNEDDAAYYVQQQGWTLDPA 47 (81)
Q Consensus 28 ls~~e~~~~~~~~GW~~d~~ 47 (81)
++.+|+.+..+++||++-+|
T Consensus 136 y~~~~a~~~~~~~g~~~~~d 155 (313)
T PRK12454 136 YDEEEAKKLAKEKGWIVKED 155 (313)
T ss_pred cCHHHHHHHHHHcCCEEEEc
Confidence 48899999999999998655
No 117
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=68.73 E-value=20 Score=20.66 Aligned_cols=74 Identities=12% Similarity=0.111 Sum_probs=44.2
Q ss_pred hHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHhcCCeEeCCCceEeecCCCCc-ccCCC--ChhHHHHHHhHHHh
Q 036949 2 YTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLV-TEQKL--DPSKMQCLTEYVFH 78 (81)
Q Consensus 2 ~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~~~~~p~~~~~~-~~~~~--~~~~l~~Lt~~v~~ 78 (81)
+|-.|+.++.. -..++..++...||++...+-...... ...|.+-.-+..... +.... ++...+.+-+++..
T Consensus 1 vRl~Il~~L~~-~~~~~f~~L~~~l~lt~g~Ls~hL~~L----e~~GyV~~~k~~~~~~p~t~~~lT~~Gr~~~~~~~~~ 75 (80)
T PF13601_consen 1 VRLAILALLYA-NEEATFSELKEELGLTDGNLSKHLKKL----EEAGYVEVEKEFEGRRPRTWYSLTDKGREAFERYVAA 75 (80)
T ss_dssp HHHHHHHHHHH-HSEEEHHHHHHHTT--HHHHHHHHHHH----HHTTSEEEEEE-SSS--EEEEEE-HHHHHHHHHHHHH
T ss_pred CHHHHHHHHhh-cCCCCHHHHHHHhCcCHHHHHHHHHHH----HHCCCEEEEEeccCCCCeEEEEECHHHHHHHHHHHHH
Confidence 46667777666 678999999999999988877666542 113333333322211 11112 78888888888887
Q ss_pred hc
Q 036949 79 LE 80 (81)
Q Consensus 79 LE 80 (81)
|+
T Consensus 76 L~ 77 (80)
T PF13601_consen 76 LR 77 (80)
T ss_dssp HH
T ss_pred HH
Confidence 75
No 118
>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=68.53 E-value=14 Score=21.50 Aligned_cols=36 Identities=17% Similarity=0.123 Sum_probs=25.5
Q ss_pred HHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH
Q 036949 3 TKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 3 R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~ 38 (81)
|+++-+++...---=.-..+|.-|||+..++..|-.
T Consensus 2 ~~~v~~ll~~~nlG~dW~~LA~~LG~~~~~I~~i~~ 37 (77)
T cd08311 2 QEEVEKLLESGRPGRDWRSLAGELGYEDEAIDTFGR 37 (77)
T ss_pred hHHHHHHHhCCCCccCHHHHHHHcCCCHHHHHHHHc
Confidence 456666665442233467899999999999988854
No 119
>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=68.28 E-value=15 Score=19.15 Aligned_cols=29 Identities=14% Similarity=0.205 Sum_probs=21.3
Q ss_pred ccc-HHHHHHHhCCCHHHHHHHH---HhcCCeE
Q 036949 16 TIS-TQDTALFLGMNEDDAAYYV---QQQGWTL 44 (81)
Q Consensus 16 sIs-~~~~a~~Lgls~~e~~~~~---~~~GW~~ 44 (81)
.++ ..++|..+|+|.+-+.+.. .+.||-.
T Consensus 24 ~~~~~~~la~~~~is~~~v~~~l~~L~~~G~i~ 56 (66)
T cd07377 24 RLPSERELAEELGVSRTTVREALRELEAEGLVE 56 (66)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 344 8899999999887765554 4579953
No 120
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=68.11 E-value=9.3 Score=19.63 Aligned_cols=29 Identities=17% Similarity=0.276 Sum_probs=21.5
Q ss_pred cc-cHHHHHHHhCCCHHHHHHH---HHhcCCeE
Q 036949 16 TI-STQDTALFLGMNEDDAAYY---VQQQGWTL 44 (81)
Q Consensus 16 sI-s~~~~a~~Lgls~~e~~~~---~~~~GW~~ 44 (81)
.+ +..++|..+|+|..-+... ..+.||-.
T Consensus 19 ~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i~ 51 (60)
T smart00345 19 KLPSERELAAQLGVSRTTVREALSRLEAEGLVQ 51 (60)
T ss_pred cCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 36 8999999999987665544 44679853
No 121
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=68.06 E-value=16 Score=25.26 Aligned_cols=39 Identities=15% Similarity=0.175 Sum_probs=32.8
Q ss_pred HHHHHHHHHhccc--ccHHHHHHHhCCCHHHHHHHHHhcCC
Q 036949 4 KRMFQLLMSAYST--ISTQDTALFLGMNEDDAAYYVQQQGW 42 (81)
Q Consensus 4 ~~~~~li~~AY~s--Is~~~~a~~Lgls~~e~~~~~~~~GW 42 (81)
.++.+.|..-|.. ++++++|..+|+|..-+....++.|=
T Consensus 200 ~~~~~~I~~~l~~~~ls~~~lA~~~giS~r~L~r~Fk~~G~ 240 (302)
T PRK09685 200 QKVVALIDQSIQEEILRPEWIAGELGISVRSLYRLFAEQGL 240 (302)
T ss_pred HHHHHHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHHHcCC
Confidence 4778889999975 89999999999999999888776553
No 122
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=67.70 E-value=16 Score=24.65 Aligned_cols=43 Identities=21% Similarity=0.315 Sum_probs=29.5
Q ss_pred hHHHHHHHHHHhcc----------cccHHHHHHHhCCCHHHHHHH---HHhcCCeE
Q 036949 2 YTKRMFQLLMSAYS----------TISTQDTALFLGMNEDDAAYY---VQQQGWTL 44 (81)
Q Consensus 2 ~R~~~~~li~~AY~----------sIs~~~~a~~Lgls~~e~~~~---~~~~GW~~ 44 (81)
.++|++.++-.-+. .++-.++|.|||++.+-+-.. ..+.|+--
T Consensus 155 ~~~Rla~~Ll~l~~~~g~~~~i~i~lt~~~IA~~lGisretlsR~L~~L~~~GlI~ 210 (230)
T PRK09391 155 AMERVAAFLLEMDERLGGAGMMALPMSRRDIADYLGLTIETVSRALSQLQDRGLIG 210 (230)
T ss_pred HHHHHHHHHHHHHHHhCCCCEEEecCCHHHHHHHHCCCHHHHHHHHHHHHHCCcEE
Confidence 56788886665322 245679999999988776544 45678874
No 123
>PF13518 HTH_28: Helix-turn-helix domain
Probab=67.48 E-value=15 Score=18.62 Aligned_cols=33 Identities=12% Similarity=0.269 Sum_probs=25.7
Q ss_pred HHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH
Q 036949 3 TKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 3 R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~ 38 (81)
|.+++.++.. .-++.++|.-+|+|...+..+..
T Consensus 2 r~~iv~~~~~---g~s~~~~a~~~gis~~tv~~w~~ 34 (52)
T PF13518_consen 2 RLQIVELYLE---GESVREIAREFGISRSTVYRWIK 34 (52)
T ss_pred HHHHHHHHHc---CCCHHHHHHHHCCCHhHHHHHHH
Confidence 5566666664 33999999999999988877765
No 124
>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=67.47 E-value=15 Score=20.37 Aligned_cols=34 Identities=21% Similarity=0.278 Sum_probs=22.6
Q ss_pred HHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHh
Q 036949 5 RMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQ 39 (81)
Q Consensus 5 ~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~ 39 (81)
++++++ ..-..-....+|..||++..++..+-..
T Consensus 2 ~l~~~l-~~~~~~~Wk~La~~Lg~~~~~i~~i~~~ 35 (83)
T PF00531_consen 2 KLFDLL-AEDLGSDWKRLARKLGLSESEIENIEEE 35 (83)
T ss_dssp HHHHHH-HHSHSTCHHHHHHHTTS-HHHHHHHHHH
T ss_pred hHHHHH-hhcchhhHHHHHHHhCcCHHHHHHHHHh
Confidence 344444 3334445678999999999999877663
No 125
>PRK13239 alkylmercury lyase; Provisional
Probab=67.35 E-value=27 Score=24.13 Aligned_cols=50 Identities=16% Similarity=0.196 Sum_probs=39.0
Q ss_pred hHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHhc-CCeEeCCCceEe
Q 036949 2 YTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQ-GWTLDPASRMLT 52 (81)
Q Consensus 2 ~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~~-GW~~d~~~~~~~ 52 (81)
++.-+++++. -=+.++++++|+-+|.+.+++.+...+. .=.+|++|+++-
T Consensus 23 ~~~~llr~la-~G~pvt~~~lA~~~~~~~~~v~~~L~~l~~~~~d~~g~iv~ 73 (206)
T PRK13239 23 LLVPLLRLLA-KGRPVSVTTLAAALGWPVEEVEAVLEAMPDTEYDEDGRIIG 73 (206)
T ss_pred HHHHHHHHHH-cCCCCCHHHHHHHhCCCHHHHHHHHHhCCCeEECCCCCEEe
Confidence 3455667766 4577999999999999999999988876 446788877754
No 126
>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=66.86 E-value=8.3 Score=19.31 Aligned_cols=24 Identities=25% Similarity=0.531 Sum_probs=17.8
Q ss_pred cHHHHHHHhCCCHHHHHHHHHhcCC
Q 036949 18 STQDTALFLGMNEDDAAYYVQQQGW 42 (81)
Q Consensus 18 s~~~~a~~Lgls~~e~~~~~~~~GW 42 (81)
++.++|.++|++..-+.-+-.+ |.
T Consensus 1 ti~e~A~~~gvs~~tlR~ye~~-Gl 24 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRYYERE-GL 24 (38)
T ss_dssp EHHHHHHHHTS-HHHHHHHHHT-TS
T ss_pred CHHHHHHHHCCCHHHHHHHHHC-CC
Confidence 4678999999999988876553 54
No 127
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=66.75 E-value=18 Score=23.48 Aligned_cols=39 Identities=13% Similarity=0.233 Sum_probs=23.9
Q ss_pred cccHHHHHHHhCCCHHHHHHHH---HhcCCeEeCCCceEeec
Q 036949 16 TISTQDTALFLGMNEDDAAYYV---QQQGWTLDPASRMLTVK 54 (81)
Q Consensus 16 sIs~~~~a~~Lgls~~e~~~~~---~~~GW~~d~~~~~~~p~ 54 (81)
.++..++|.|||++.+-+-... .+.|=---..+.+.+|.
T Consensus 168 ~~t~~~lA~~lG~tr~tvsR~l~~l~~~gii~~~~~~i~i~~ 209 (211)
T PRK11753 168 KITRQEIGRIVGCSREMVGRVLKMLEDQGLISAHGKTIVVYG 209 (211)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEecCCEEEEec
Confidence 5677999999999887665543 34453211134455554
No 128
>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=66.66 E-value=14 Score=22.07 Aligned_cols=34 Identities=18% Similarity=0.347 Sum_probs=23.1
Q ss_pred HHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHh
Q 036949 5 RMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQ 39 (81)
Q Consensus 5 ~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~ 39 (81)
+|++++.. ..-++-+++|..+|++..++...+.+
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 56676663 46799999999999999999887654
No 129
>PF07453 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases [].
Probab=66.57 E-value=6.6 Score=19.16 Aligned_cols=18 Identities=22% Similarity=0.460 Sum_probs=14.1
Q ss_pred cHHHHHHHhCCCHHHHHH
Q 036949 18 STQDTALFLGMNEDDAAY 35 (81)
Q Consensus 18 s~~~~a~~Lgls~~e~~~ 35 (81)
|+.+||++||++..-+..
T Consensus 18 Si~eAa~~l~i~~~~I~~ 35 (37)
T PF07453_consen 18 SIREAARYLGISHSTISK 35 (37)
T ss_pred CHHHHHHHhCCCHHHHHH
Confidence 678899999998766544
No 130
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=66.38 E-value=29 Score=21.64 Aligned_cols=51 Identities=10% Similarity=0.073 Sum_probs=34.0
Q ss_pred HHHHHHHHhcc--cccHHHHHHHhCCCHHHHHHHHH---hcCCeE---eCCCceEeecCC
Q 036949 5 RMFQLLMSAYS--TISTQDTALFLGMNEDDAAYYVQ---QQGWTL---DPASRMLTVKKQ 56 (81)
Q Consensus 5 ~~~~li~~AY~--sIs~~~~a~~Lgls~~e~~~~~~---~~GW~~---d~~~~~~~p~~~ 56 (81)
+++..++.... .++.+++|..++++..-+.+... +.||.. ++.|.+. |.++
T Consensus 12 ~~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s~~G~~Ggy~-l~~~ 70 (135)
T TIGR02010 12 TAMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKAGLVKSVRGPGGGYQ-LGRP 70 (135)
T ss_pred HHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEeCCCCCEe-ccCC
Confidence 34445554444 48999999999999988777755 459986 3344543 4433
No 131
>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=65.99 E-value=28 Score=21.36 Aligned_cols=40 Identities=15% Similarity=0.139 Sum_probs=29.8
Q ss_pred HHHHHHHHhc-ccccHHHHHHHhCCCHHHHHHHHH---hcCCeE
Q 036949 5 RMFQLLMSAY-STISTQDTALFLGMNEDDAAYYVQ---QQGWTL 44 (81)
Q Consensus 5 ~~~~li~~AY-~sIs~~~~a~~Lgls~~e~~~~~~---~~GW~~ 44 (81)
+++..++++. ..++..++|..+|+|..-+.+... +.||..
T Consensus 13 ~~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~ 56 (130)
T TIGR02944 13 LVLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLSLAGIVT 56 (130)
T ss_pred HHHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHHHCCcEE
Confidence 4555666654 358999999999999877766654 569975
No 132
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=65.14 E-value=33 Score=23.90 Aligned_cols=48 Identities=15% Similarity=0.148 Sum_probs=35.6
Q ss_pred HHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH---hcCCeE-eCCCceEe
Q 036949 5 RMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ---QQGWTL-DPASRMLT 52 (81)
Q Consensus 5 ~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~---~~GW~~-d~~~~~~~ 52 (81)
+|+++++..-..+++.++|+-||++..-+-.+.. +.||-. |+.+..+.
T Consensus 29 ~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~~~~~~~~Y~ 80 (271)
T PRK10163 29 AILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQAADFVYQDSQLGWWH 80 (271)
T ss_pred HHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCCCCeEE
Confidence 5778888877789999999999998877755544 579984 44333333
No 133
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=65.04 E-value=34 Score=22.00 Aligned_cols=52 Identities=10% Similarity=0.147 Sum_probs=33.1
Q ss_pred hHHHHHHHH---HHhc-----------ccccHHHHHHHhCCCHHHHHHH---HHhcCCeEeCCCceEee
Q 036949 2 YTKRMFQLL---MSAY-----------STISTQDTALFLGMNEDDAAYY---VQQQGWTLDPASRMLTV 53 (81)
Q Consensus 2 ~R~~~~~li---~~AY-----------~sIs~~~~a~~Lgls~~e~~~~---~~~~GW~~d~~~~~~~p 53 (81)
.++|++.++ ...| -.++-.++|.|||++.+-+-.. ..+.||---..+.+.++
T Consensus 121 ~~~Rla~~Ll~l~~~~~~~~~~~~~~~~~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~~~~~i~I~ 189 (202)
T PRK13918 121 LKNRIAAALLELSDTPLATQEDSGETMIYATHDELAAAVGSVRETVTKVIGELSREGYIRSGYGKIQLL 189 (202)
T ss_pred hHHHHHHHHHHHHHHhCCCCCCCCeEEecCCHHHHHHHhCccHHHHHHHHHHHHHCCCEEcCCCEEEEE
Confidence 567788754 2222 2367889999999988766444 44568886434444443
No 134
>KOG1076 consensus Translation initiation factor 3, subunit c (eIF-3c) [Translation, ribosomal structure and biogenesis]
Probab=65.02 E-value=6.3 Score=32.19 Aligned_cols=45 Identities=13% Similarity=0.235 Sum_probs=32.2
Q ss_pred HHHHhcccccHHHHHHHhCCCHHHHHHHHHhc--------CCeEeCCCceEeec
Q 036949 9 LLMSAYSTISTQDTALFLGMNEDDAAYYVQQQ--------GWTLDPASRMLTVK 54 (81)
Q Consensus 9 li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~~--------GW~~d~~~~~~~p~ 54 (81)
.-+..|+|||+..+|.|+.|+...+-..+.+. .|- +|.+.+++..
T Consensus 711 tYss~Y~SvSl~~LA~mFdLp~~~VhsIiSkmiineEl~AslD-qpt~~iv~hr 763 (843)
T KOG1076|consen 711 TYSSVYDSVSLAKLADMFDLPEPKVHSIISKMIINEELHASLD-QPTQCIVMHR 763 (843)
T ss_pred HhhhhhhhccHHHHHHHhCCCchhHHHHHHHHHHHHHhhhccC-CCcceEEEee
Confidence 34677999999999999999998876664431 344 3455565555
No 135
>PF13986 DUF4224: Domain of unknown function (DUF4224)
Probab=64.71 E-value=19 Score=18.93 Aligned_cols=34 Identities=9% Similarity=0.280 Sum_probs=25.8
Q ss_pred ccHHHHHHHhCC-CHHHHHHHHHhcCCeE--eCCCce
Q 036949 17 ISTQDTALFLGM-NEDDAAYYVQQQGWTL--DPASRM 50 (81)
Q Consensus 17 Is~~~~a~~Lgl-s~~e~~~~~~~~GW~~--d~~~~~ 50 (81)
++.+++..+.|. ....-+++..+.||-+ +++|..
T Consensus 3 LT~~El~elTG~k~~~~Q~~~L~~~Gi~~~~~~~G~p 39 (47)
T PF13986_consen 3 LTDEELQELTGYKRPSKQIRWLRRNGIPFVVRADGRP 39 (47)
T ss_pred CCHHHHHHHHCCCCHHHHHHHHHHCCCeeEECCCCCE
Confidence 577889999999 6777778888889986 345543
No 136
>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=64.67 E-value=9.3 Score=28.48 Aligned_cols=42 Identities=12% Similarity=0.263 Sum_probs=34.5
Q ss_pred hHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHH----HH----hcCCeE
Q 036949 2 YTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYY----VQ----QQGWTL 44 (81)
Q Consensus 2 ~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~----~~----~~GW~~ 44 (81)
.|+-|+-++.+. ..|+..++....+|+.+++.++ |. .+||++
T Consensus 338 aRD~iL~~F~~~-~~v~r~~l~~~~~l~~~~~~eiL~~~a~~~~~~~~W~l 387 (421)
T PF04801_consen 338 ARDYILLLFTKS-RYVKRKELMSATKLPPEDVKEILKEIAVLRPSNRGWKL 387 (421)
T ss_pred hHHHHHHHhcCC-CceeHHHhhhhcCCCHHHHHHHHHHHhhccCCCCceEE
Confidence 588899999998 7799999999999988887554 32 468887
No 137
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=64.57 E-value=19 Score=22.38 Aligned_cols=35 Identities=20% Similarity=0.327 Sum_probs=27.7
Q ss_pred HHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH
Q 036949 3 TKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 3 R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~ 38 (81)
-.+|+..+.+--. ++..++|..+|+|+..+..-+.
T Consensus 10 D~~IL~~L~~d~r-~~~~eia~~lglS~~~v~~Ri~ 44 (154)
T COG1522 10 DRRILRLLQEDAR-ISNAELAERVGLSPSTVLRRIK 44 (154)
T ss_pred HHHHHHHHHHhCC-CCHHHHHHHHCCCHHHHHHHHH
Confidence 3566776666665 9999999999999998876655
No 138
>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=64.55 E-value=20 Score=19.64 Aligned_cols=32 Identities=19% Similarity=0.226 Sum_probs=22.9
Q ss_pred hcccccHHHHHHHhCCCHHHHHHH---HHhcCCeE
Q 036949 13 AYSTISTQDTALFLGMNEDDAAYY---VQQQGWTL 44 (81)
Q Consensus 13 AY~sIs~~~~a~~Lgls~~e~~~~---~~~~GW~~ 44 (81)
.=..++..++|..||+++.-+-+. ..+.|+..
T Consensus 19 ~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV~ 53 (60)
T PF01325_consen 19 EGGPVRTKDIAERLGVSPPTVTEMLKRLAEKGLVE 53 (60)
T ss_dssp CTSSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred CCCCccHHHHHHHHCCChHHHHHHHHHHHHCCCEE
Confidence 557899999999999977555444 44567753
No 139
>PF07971 Glyco_hydro_92: Glycosyl hydrolase family 92; InterPro: IPR012939 This domain occurs within alpha-1,2-mannosidases, which remove alpha-1,2-linked mannose residues from Man(9)(GlcNAc)(2) by hydrolysis. They are critical for the maturation of N-linked oligosaccharides and ER-associated degradation [].; PDB: 2WW2_C 2WVY_B 2WVZ_B 2WW0_H 2WZS_D 2WVX_B 2WW1_D 2WW3_C.
Probab=64.19 E-value=11 Score=29.13 Aligned_cols=52 Identities=21% Similarity=0.378 Sum_probs=39.3
Q ss_pred HHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH-hcCCe--EeCCCceEeecCCC
Q 036949 5 RMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ-QQGWT--LDPASRMLTVKKQP 57 (81)
Q Consensus 5 ~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~-~~GW~--~d~~~~~~~p~~~~ 57 (81)
-+.+.++-||.-=.+..+|+-||- .++...|.+ ++.|+ +|+++.++.|+...
T Consensus 233 svS~TLEyay~D~~iA~~A~~LG~-~~~~~~~~~Rs~ny~n~fd~~tgf~~pr~~d 287 (502)
T PF07971_consen 233 SVSRTLEYAYDDWAIAQMAKALGK-KEDADKFLKRSQNYRNVFDPETGFFRPRNAD 287 (502)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHTT--HHHHHHHHCCGGGGGGGEETTTTCE--B-TT
T ss_pred cHhHHHHHHHHHHHHHHHHHhcCC-HHHHHHHHHHHHHHHHHcCCccCCccccCCC
Confidence 456788999999999999999994 556677766 56898 89999999998653
No 140
>PRK15185 transcriptional regulator HilD; Provisional
Probab=63.86 E-value=16 Score=26.76 Aligned_cols=42 Identities=14% Similarity=0.215 Sum_probs=33.4
Q ss_pred HHHHHHHHHHhc-ccccHHHHHHHhCCCHHHHHHHHHhcCCeE
Q 036949 3 TKRMFQLLMSAY-STISTQDTALFLGMNEDDAAYYVQQQGWTL 44 (81)
Q Consensus 3 R~~~~~li~~AY-~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~ 44 (81)
.+++...|...| ..++++++|+.+|+|+.-+....++.|-++
T Consensus 208 ~erV~~~I~~n~~~~~SledLA~~lgmS~~tL~R~FK~~G~S~ 250 (309)
T PRK15185 208 KERVYNIISSSPSRQWKLTDVADHIFMSTSTLKRKLAEEGTSF 250 (309)
T ss_pred HHHHHHHHHhCccCCCCHHHHHHHHCcCHHHHHHHHHHcCCCH
Confidence 456667777776 679999999999999999888777656664
No 141
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=63.28 E-value=15 Score=25.66 Aligned_cols=35 Identities=17% Similarity=0.223 Sum_probs=28.0
Q ss_pred hHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH
Q 036949 2 YTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 2 ~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~ 38 (81)
.|++|++++++-= =-...++.+||+++..+.++..
T Consensus 16 tRR~Il~lLt~~p--~yvsEiS~~lgvsqkAVl~HL~ 50 (217)
T COG1777 16 TRRRILQLLTRRP--CYVSEISRELGVSQKAVLKHLR 50 (217)
T ss_pred HHHHHHHHHhcCc--hHHHHHHhhcCcCHHHHHHHHH
Confidence 5899999988754 4466789999999999877743
No 142
>PF13591 MerR_2: MerR HTH family regulatory protein
Probab=63.13 E-value=13 Score=21.60 Aligned_cols=27 Identities=19% Similarity=0.169 Sum_probs=23.0
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHhcCCeE
Q 036949 17 ISTQDTALFLGMNEDDAAYYVQQQGWTL 44 (81)
Q Consensus 17 Is~~~~a~~Lgls~~e~~~~~~~~GW~~ 44 (81)
|++++++...|++++-+..++. .||--
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 7899999999999998887765 68874
No 143
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=63.02 E-value=7.1 Score=20.82 Aligned_cols=26 Identities=15% Similarity=0.207 Sum_probs=17.4
Q ss_pred ccccHHHHHHHhCCCHHHHHHHHHhc
Q 036949 15 STISTQDTALFLGMNEDDAAYYVQQQ 40 (81)
Q Consensus 15 ~sIs~~~~a~~Lgls~~e~~~~~~~~ 40 (81)
..|+..++|+..|++...+-.++..+
T Consensus 9 ~~it~~~La~~~gis~~tl~~~~~~~ 34 (63)
T PF13443_consen 9 RGITQKDLARKTGISRSTLSRILNGK 34 (63)
T ss_dssp TT--HHHHHHHHT--HHHHHHHHTTT
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhcc
Confidence 35688889999999988888887744
No 144
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=62.88 E-value=29 Score=20.35 Aligned_cols=49 Identities=18% Similarity=0.194 Sum_probs=34.9
Q ss_pred HHHHhcccccHHHHHHHhCCCHHHHHHHHH---hcCCeEeCCC--ceEeecCCC
Q 036949 9 LLMSAYSTISTQDTALFLGMNEDDAAYYVQ---QQGWTLDPAS--RMLTVKKQP 57 (81)
Q Consensus 9 li~~AY~sIs~~~~a~~Lgls~~e~~~~~~---~~GW~~d~~~--~~~~p~~~~ 57 (81)
+.-..|.-+|=+.+|+.||+|...+-+.++ +.|=.+++.. .+..|..+.
T Consensus 12 l~~~~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr~~G~~I~s~~~kGY~L~~~~~ 65 (79)
T COG1654 12 LLLLTGNFVSGEKLAEELGISRTAVWKHIQQLREEGVDIESVRGKGYLLPQLPD 65 (79)
T ss_pred HHHcCCCcccHHHHHHHHCccHHHHHHHHHHHHHhCCceEecCCCceeccCccc
Confidence 344567789999999999999888777666 4588877642 455555443
No 145
>COG4004 Uncharacterized protein conserved in archaea [Function unknown]
Probab=62.72 E-value=33 Score=20.98 Aligned_cols=54 Identities=20% Similarity=0.332 Sum_probs=34.0
Q ss_pred CC--CHHHHHHHHHhcCCeEeCCCceEeecCCCC-------cc-----cCCC---ChhHHHHHHhHHHhhc
Q 036949 27 GM--NEDDAAYYVQQQGWTLDPASRMLTVKKQPL-------VT-----EQKL---DPSKMQCLTEYVFHLE 80 (81)
Q Consensus 27 gl--s~~e~~~~~~~~GW~~d~~~~~~~p~~~~~-------~~-----~~~~---~~~~l~~Lt~~v~~LE 80 (81)
|+ .++-+.....+.||++...|..+.-.-|.- +. .... +...|+-+-.|.-|||
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 56 567788888899999988877655443321 11 1111 4667777666776665
No 146
>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=62.65 E-value=19 Score=18.26 Aligned_cols=28 Identities=21% Similarity=0.317 Sum_probs=23.3
Q ss_pred HHHHhcccccHHHHHHHhCCCHHHHHHH
Q 036949 9 LLMSAYSTISTQDTALFLGMNEDDAAYY 36 (81)
Q Consensus 9 li~~AY~sIs~~~~a~~Lgls~~e~~~~ 36 (81)
+..+-|..+++.++|+.+|++..-+-.+
T Consensus 9 ~~~~G~~~~s~~~Ia~~~gvs~~~~y~~ 36 (47)
T PF00440_consen 9 FAEKGYEAVSIRDIARRAGVSKGSFYRY 36 (47)
T ss_dssp HHHHHTTTSSHHHHHHHHTSCHHHHHHH
T ss_pred HHHhCHHhCCHHHHHHHHccchhhHHHH
Confidence 4578999999999999999988665443
No 147
>PRK15482 transcriptional regulator MurR; Provisional
Probab=62.26 E-value=16 Score=25.41 Aligned_cols=39 Identities=21% Similarity=0.348 Sum_probs=27.6
Q ss_pred HHHHHHHHhccc---ccHHHHHHHhCCCHHHHHHHHHhcCCe
Q 036949 5 RMFQLLMSAYST---ISTQDTALFLGMNEDDAAYYVQQQGWT 43 (81)
Q Consensus 5 ~~~~li~~AY~s---Is~~~~a~~Lgls~~e~~~~~~~~GW~ 43 (81)
+|++.|-.-... .++.++|...|.|+.-+..||++.|-.
T Consensus 20 ~Ia~yIl~n~~~v~~~si~elA~~~~vS~aTv~Rf~kkLGf~ 61 (285)
T PRK15482 20 KIADFLRANVSELKSVSSRKMAKQLGISQSSIVKFAQKLGAQ 61 (285)
T ss_pred HHHHHHHhCHHHHHhcCHHHHHHHhCCCHHHHHHHHHHhCCC
Confidence 445544444433 677888999999988888888887654
No 148
>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=61.62 E-value=14 Score=21.51 Aligned_cols=26 Identities=19% Similarity=0.210 Sum_probs=21.4
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHhcCCe
Q 036949 17 ISTQDTALFLGMNEDDAAYYVQQQGWT 43 (81)
Q Consensus 17 Is~~~~a~~Lgls~~e~~~~~~~~GW~ 43 (81)
.++.++|.++|+|+.-+..|.. .||-
T Consensus 2 ~~i~e~A~~~gvs~~tLr~ye~-~Gli 27 (91)
T cd04766 2 YVISVAAELSGMHPQTLRLYER-LGLL 27 (91)
T ss_pred cCHHHHHHHHCcCHHHHHHHHH-CCCc
Confidence 3678999999999999998865 4665
No 149
>PRK15186 AraC family transcriptional regulator; Provisional
Probab=61.57 E-value=23 Score=25.31 Aligned_cols=39 Identities=15% Similarity=0.217 Sum_probs=30.4
Q ss_pred HHHHHHHHHHhcc-cccHHHHHHHhCCCHHHHHHHHHhcC
Q 036949 3 TKRMFQLLMSAYS-TISTQDTALFLGMNEDDAAYYVQQQG 41 (81)
Q Consensus 3 R~~~~~li~~AY~-sIs~~~~a~~Lgls~~e~~~~~~~~G 41 (81)
.+++.+.|..-|. .++++++|..+|+|..-+....++.|
T Consensus 183 ~~~i~~~I~~~~~~~~sl~~lA~~~gmS~stl~R~Fk~~g 222 (291)
T PRK15186 183 AENIYNIIISDISRKWALKDISDSLYMSCSTLKRKLKQEN 222 (291)
T ss_pred HHHHHHHHHhCccCCCCHHHHHHHHCcCHHHHHHHHHHcC
Confidence 3456666766665 79999999999999999888777543
No 150
>PHA02591 hypothetical protein; Provisional
Probab=61.24 E-value=13 Score=22.16 Aligned_cols=23 Identities=17% Similarity=0.392 Sum_probs=19.3
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHh
Q 036949 17 ISTQDTALFLGMNEDDAAYYVQQ 39 (81)
Q Consensus 17 Is~~~~a~~Lgls~~e~~~~~~~ 39 (81)
.+.+++|+.||++.+.+.+|..+
T Consensus 60 lSqeqIA~~LGVsqetVrKYL~~ 82 (83)
T PHA02591 60 FTVEKIASLLGVSVRKVRRYLES 82 (83)
T ss_pred CCHHHHHHHhCCCHHHHHHHHhc
Confidence 35788999999999999988764
No 151
>PRK11569 transcriptional repressor IclR; Provisional
Probab=60.94 E-value=41 Score=23.44 Aligned_cols=46 Identities=11% Similarity=0.204 Sum_probs=34.7
Q ss_pred HHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH---hcCCeE-eCCCce
Q 036949 5 RMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ---QQGWTL-DPASRM 50 (81)
Q Consensus 5 ~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~---~~GW~~-d~~~~~ 50 (81)
+|+++++++=..+++.++|+.||++..-+-.++. +.||-. |+++..
T Consensus 32 ~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~~G~l~~~~~~~~ 81 (274)
T PRK11569 32 KLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQQGFVRQVGELGH 81 (274)
T ss_pred HHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCCCCe
Confidence 4677888876779999999999998888766554 579984 444333
No 152
>PRK13502 transcriptional activator RhaR; Provisional
Probab=60.65 E-value=23 Score=24.24 Aligned_cols=40 Identities=10% Similarity=0.067 Sum_probs=30.5
Q ss_pred HHHHHHHHHhcc-cccHHHHHHHhCCCHHHHHHHHHh-cCCe
Q 036949 4 KRMFQLLMSAYS-TISTQDTALFLGMNEDDAAYYVQQ-QGWT 43 (81)
Q Consensus 4 ~~~~~li~~AY~-sIs~~~~a~~Lgls~~e~~~~~~~-~GW~ 43 (81)
.++.++|..-|. .|+++++|..+|+|+.-+...+++ .|=+
T Consensus 179 ~~~~~~I~~~~~~~~~~~~lA~~~~iS~~~L~r~fk~~~G~t 220 (282)
T PRK13502 179 DKLITALANSLECPFALDAFCQQEQCSERVLRQQFRAQTGMT 220 (282)
T ss_pred HHHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHHHHCcC
Confidence 456667766554 689999999999999988887775 3544
No 153
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=60.63 E-value=23 Score=25.08 Aligned_cols=37 Identities=19% Similarity=0.313 Sum_probs=29.1
Q ss_pred HHHHHHHHHhc-ccccHHHHHHHhCCCHHHHHHHHHhc
Q 036949 4 KRMFQLLMSAY-STISTQDTALFLGMNEDDAAYYVQQQ 40 (81)
Q Consensus 4 ~~~~~li~~AY-~sIs~~~~a~~Lgls~~e~~~~~~~~ 40 (81)
+++.+.|..-| ..++++++|+.+|+|+..+....++.
T Consensus 194 ~~~~~~i~~~~~~~~tl~~lA~~~~~S~~~l~r~Fk~~ 231 (302)
T PRK10371 194 SQMLGFIAENYDQALTINDVAEHVKLNANYAMGIFQRV 231 (302)
T ss_pred HHHHHHHHHhhcCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 35556666666 47999999999999999888777763
No 154
>PRK09978 DNA-binding transcriptional regulator GadX; Provisional
Probab=60.49 E-value=27 Score=24.98 Aligned_cols=38 Identities=11% Similarity=0.033 Sum_probs=30.0
Q ss_pred HHHHHHHHHhcc-cccHHHHHHHhCCCHHHHHHHHHhcC
Q 036949 4 KRMFQLLMSAYS-TISTQDTALFLGMNEDDAAYYVQQQG 41 (81)
Q Consensus 4 ~~~~~li~~AY~-sIs~~~~a~~Lgls~~e~~~~~~~~G 41 (81)
+++...|..-|. .++++++|..+|+|+.-+....++.|
T Consensus 145 ~~v~~yI~~~~~~~lsl~~lA~~~g~S~~~L~R~Fk~~G 183 (274)
T PRK09978 145 TRVCTVINNNIAHEWTLARIASELLMSPSLLKKKLREEE 183 (274)
T ss_pred HHHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHhcC
Confidence 456666766655 48999999999999999888887644
No 155
>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=60.44 E-value=15 Score=20.13 Aligned_cols=23 Identities=22% Similarity=0.195 Sum_probs=19.0
Q ss_pred HHHHHHHhCCCHHHHHHHHHhcC
Q 036949 19 TQDTALFLGMNEDDAAYYVQQQG 41 (81)
Q Consensus 19 ~~~~a~~Lgls~~e~~~~~~~~G 41 (81)
+...|.-||+|++++.+.+..-|
T Consensus 23 v~ywa~~~gvt~~~L~~AV~~vG 45 (57)
T PF12244_consen 23 VRYWAKRFGVTEEQLREAVRAVG 45 (57)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHC
Confidence 34578899999999999888766
No 156
>smart00796 AHS1 Allophanate hydrolase subunit 1. This domain represents subunit 1 of allophanate hydrolase (AHS1).
Probab=60.33 E-value=13 Score=25.20 Aligned_cols=27 Identities=11% Similarity=0.119 Sum_probs=25.1
Q ss_pred cHHHHHHHhCCCHHHHHHHHHhcCCeE
Q 036949 18 STQDTALFLGMNEDDAAYYVQQQGWTL 44 (81)
Q Consensus 18 s~~~~a~~Lgls~~e~~~~~~~~GW~~ 44 (81)
.++.+|++.|||.+|+++.-.+.-|.+
T Consensus 102 DL~~vA~~~gLs~~evi~~Hs~~~y~V 128 (201)
T smart00796 102 DLEFVARHNGLSVDEVIRLHSAAEYRV 128 (201)
T ss_pred CHHHHHHHhCcCHHHHHHHHhCCCeEE
Confidence 788999999999999999999999986
No 157
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=60.06 E-value=14 Score=23.02 Aligned_cols=29 Identities=17% Similarity=0.392 Sum_probs=23.8
Q ss_pred ccccHHHHHHHhCCCHHHHHHHHH---hcCCe
Q 036949 15 STISTQDTALFLGMNEDDAAYYVQ---QQGWT 43 (81)
Q Consensus 15 ~sIs~~~~a~~Lgls~~e~~~~~~---~~GW~ 43 (81)
.+++++++|..|+.|.-.+....+ +.||-
T Consensus 18 ~~vtl~elA~~l~cS~Rn~r~lLkkm~~~gWi 49 (115)
T PF12793_consen 18 VEVTLDELAELLFCSRRNARTLLKKMQEEGWI 49 (115)
T ss_pred cceeHHHHHHHhCCCHHHHHHHHHHHHHCCCe
Confidence 478999999999999887766655 56997
No 158
>TIGR01033 DNA-binding regulatory protein, YebC/PmpR family. This model describes a minimally characterized protein family, restricted to bacteria excepting for some eukaryotic sequences that have possible transit peptides. YebC from E. coli is crystallized, and PA0964 from Pseudomonas aeruginosa has been shown to be a sequence-specific DNA-binding regulatory protein.
Probab=60.05 E-value=21 Score=25.03 Aligned_cols=47 Identities=13% Similarity=0.188 Sum_probs=32.7
Q ss_pred CHHHH---HHHHHhcCCeEeCCCceEeecCCCCcccCCCChhHHHHHHhHHHhhc
Q 036949 29 NEDDA---AYYVQQQGWTLDPASRMLTVKKQPLVTEQKLDPSKMQCLTEYVFHLE 80 (81)
Q Consensus 29 s~~e~---~~~~~~~GW~~d~~~~~~~p~~~~~~~~~~~~~~~l~~Lt~~v~~LE 80 (81)
+++++ .+...+.||++.......+|..+..- ++++.+++.+++--||
T Consensus 176 ~~~~~~~v~~~L~~~g~~i~~sei~~~P~~~v~l-----~~e~~~~~~~li~~Le 225 (238)
T TIGR01033 176 APEELEKVKEALEAKGFPIESAEITMIPLTTVDL-----DDEQAEKLLKLIDALE 225 (238)
T ss_pred CHHHHHHHHHHHHHcCCCceeeEEEEecCCCccc-----CHHHHHHHHHHHHHHh
Confidence 44444 34455679998877777777744332 6788899999988887
No 159
>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=59.94 E-value=12 Score=25.49 Aligned_cols=30 Identities=7% Similarity=0.091 Sum_probs=24.9
Q ss_pred cccHHHHHHHhCCCHHHHHHHHHhcCCeEe
Q 036949 16 TISTQDTALFLGMNEDDAAYYVQQQGWTLD 45 (81)
Q Consensus 16 sIs~~~~a~~Lgls~~e~~~~~~~~GW~~d 45 (81)
--.++.+|+.+||+.+|+++.-.+.-|.+-
T Consensus 99 g~DL~~vA~~~gls~~evi~~H~~~~y~V~ 128 (202)
T PF02682_consen 99 GPDLEEVAEHNGLSVEEVIRLHSSAEYRVY 128 (202)
T ss_dssp HTTHHHHHHHHTS-HHHHHHHHHTS-EEEE
T ss_pred CCCHHHHHHHhCcCHHHHHHHHHcCchHhh
Confidence 457889999999999999999999999874
No 160
>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=59.78 E-value=16 Score=27.62 Aligned_cols=30 Identities=23% Similarity=0.420 Sum_probs=24.9
Q ss_pred HHHHHHhcccccHHHHHHHhCCCHHHHHHH
Q 036949 7 FQLLMSAYSTISTQDTALFLGMNEDDAAYY 36 (81)
Q Consensus 7 ~~li~~AY~sIs~~~~a~~Lgls~~e~~~~ 36 (81)
++-.-|=|++|+++.+|++|+++++++...
T Consensus 312 lRSyLKLYtti~l~KLA~fl~vd~~~lr~~ 341 (404)
T PF10255_consen 312 LRSYLKLYTTIPLEKLASFLDVDEEELRSQ 341 (404)
T ss_pred HHHHHHhhcCCCHHHHHHHcCCCHHHHHHH
Confidence 445567899999999999999999887554
No 161
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=59.74 E-value=26 Score=22.34 Aligned_cols=34 Identities=15% Similarity=0.236 Sum_probs=27.0
Q ss_pred HHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH
Q 036949 4 KRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 4 ~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~ 38 (81)
.+|+.++.+- .++|..++|+.||+|+..+..-..
T Consensus 12 ~~Il~~Lq~d-~R~s~~eiA~~lglS~~tV~~Ri~ 45 (153)
T PRK11179 12 RGILEALMEN-ARTPYAELAKQFGVSPGTIHVRVE 45 (153)
T ss_pred HHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHH
Confidence 4566666665 899999999999999988866544
No 162
>KOG2747 consensus Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=59.47 E-value=25 Score=26.70 Aligned_cols=46 Identities=17% Similarity=0.114 Sum_probs=35.5
Q ss_pred HHHHHHHHHHhccc-ccHHHHHHHhCCCHHHHHHHHHhcCCeEeCCC
Q 036949 3 TKRMFQLLMSAYST-ISTQDTALFLGMNEDDAAYYVQQQGWTLDPAS 48 (81)
Q Consensus 3 R~~~~~li~~AY~s-Is~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~ 48 (81)
+..++.++-+-=.+ |++++++.+.|+.++|++.-.+..||.---.+
T Consensus 315 ~~~ll~~L~~~~~~~isI~~iS~~Tgi~~~DIisTL~~L~m~~y~k~ 361 (396)
T KOG2747|consen 315 RCVLLELLRKHRGEHISIKEISKETGIRPDDIISTLQSLNMIKYYKG 361 (396)
T ss_pred HHHHHHHHHhcCCCcccHHHHHHhhCCCHHHHHHHHHhhCCccccCC
Confidence 34566666664433 99999999999999999999999898754343
No 163
>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=59.46 E-value=41 Score=22.91 Aligned_cols=41 Identities=12% Similarity=0.240 Sum_probs=32.4
Q ss_pred HHHHHHHHhcccccHHHHHHHhCCCHHHHHHHH---HhcCCeEe
Q 036949 5 RMFQLLMSAYSTISTQDTALFLGMNEDDAAYYV---QQQGWTLD 45 (81)
Q Consensus 5 ~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~---~~~GW~~d 45 (81)
+|+.+++.+=..+++.++|+-+|++..-+-.+. .+.||-.-
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 467777777778999999999999887765554 46799874
No 164
>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=59.06 E-value=12 Score=18.04 Aligned_cols=17 Identities=12% Similarity=0.307 Sum_probs=12.3
Q ss_pred HHHHhCCCHHHHHHHHH
Q 036949 22 TALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 22 ~a~~Lgls~~e~~~~~~ 38 (81)
-|.-+|+|.+|+.+|..
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 46778999999999876
No 165
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=59.01 E-value=28 Score=24.14 Aligned_cols=35 Identities=14% Similarity=0.238 Sum_probs=27.5
Q ss_pred HHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH
Q 036949 3 TKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 3 R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~ 38 (81)
|++|..++. ....+++.++|..||+|..-+.....
T Consensus 7 ~~~Il~~l~-~~~~~~~~ela~~l~vS~~TirRdL~ 41 (251)
T PRK13509 7 HQILLELLA-QLGFVTVEKVIERLGISPATARRDIN 41 (251)
T ss_pred HHHHHHHHH-HcCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 556777777 58999999999999999876654444
No 166
>PF01709 Transcrip_reg: Transcriptional regulator; InterPro: IPR002876 This entry represents the core region of several hypothetical proteins found in bacteria, plants, and yeast proteins. This core region can be subdivided into three domains: a 3-helical bundle domain, and two alpha+beta domains with different folds, where domain 3 (ferredoxin-like fold) is inserted within domain 2. This core region is found in the following hypothetical proteins: YebC from Escherichia coli, HP0162 from Helicobacter pylori (Campylobacter pylori) and aq1575 from Aquifex aeolicus []. The crystal structure of a conserved hypothetical protein, Aq1575, from Aquifex aeolicus has been determined. A structural homology search reveals that this protein has a new fold with no obvious similarity to those of other proteins of known three-dimensional structure. The protein reveals a monomer consisting of three domains arranged along a pseudo threefold symmetry axis. There is a large cleft with approximate dimensions of 10 A x 10 A x 20 A in the centre of the three domains along the symmetry axis. Two possible active sites are suggested based on the structure and multiple sequence alignment. There are several highly conserved residues in these putative active sites [].; PDB: 1LFP_A 1MW7_A 1KON_A.
Probab=58.88 E-value=11 Score=26.24 Aligned_cols=46 Identities=9% Similarity=0.157 Sum_probs=29.5
Q ss_pred HHHHHHHHhcCCeEeCCCceEeecCCCCcccCCCChhHHHHHHhHHHhhcC
Q 036949 31 DDAAYYVQQQGWTLDPASRMLTVKKQPLVTEQKLDPSKMQCLTEYVFHLEH 81 (81)
Q Consensus 31 ~e~~~~~~~~GW~~d~~~~~~~p~~~~~~~~~~~~~~~l~~Lt~~v~~LE~ 81 (81)
..+.+...+.|+++.......+|..+..- +++++.++.+++-.||+
T Consensus 177 ~~v~~~L~~~g~~i~~~e~~~~P~~~v~l-----~~e~~~~~~~lie~Lee 222 (234)
T PF01709_consen 177 SAVKKALEKKGYEIESAELEYIPNNPVEL-----SEEDAEKVEKLIEALEE 222 (234)
T ss_dssp HHHHHHHHHTT---SEEEEEEEESS-EE-------HHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHcCCCeeEEEEEEeCCCCccc-----CHHHHHHHHHHHHHHhC
Confidence 34555666789999877667777755433 67899999999988874
No 167
>PRK09411 carbamate kinase; Reviewed
Probab=58.74 E-value=31 Score=25.16 Aligned_cols=22 Identities=9% Similarity=0.380 Sum_probs=17.7
Q ss_pred CHHHHHHHHHhcCCeEeCCCce
Q 036949 29 NEDDAAYYVQQQGWTLDPASRM 50 (81)
Q Consensus 29 s~~e~~~~~~~~GW~~d~~~~~ 50 (81)
+.+++.+...++||++=.+|+.
T Consensus 129 ~~e~a~~l~~e~g~~~~~dg~g 150 (297)
T PRK09411 129 QPEEQEALEAAYGWQMKRDGKY 150 (297)
T ss_pred CHHHHHHHHHhcCCEEEecCCc
Confidence 7899999989999988655544
No 168
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=58.48 E-value=2.3 Score=20.71 Aligned_cols=20 Identities=10% Similarity=0.255 Sum_probs=16.9
Q ss_pred CCCHHHHHHHHHhcCCeEeC
Q 036949 27 GMNEDDAAYYVQQQGWTLDP 46 (81)
Q Consensus 27 gls~~e~~~~~~~~GW~~d~ 46 (81)
|++.+++.......||.++.
T Consensus 12 Gf~~~~a~~aL~~~~~d~~~ 31 (37)
T smart00165 12 GFSREEALKALRAANGNVER 31 (37)
T ss_pred CCCHHHHHHHHHHhCCCHHH
Confidence 88999999988888987653
No 169
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=58.42 E-value=36 Score=20.01 Aligned_cols=40 Identities=10% Similarity=-0.022 Sum_probs=30.1
Q ss_pred HHHHHHHHhc-ccccHHHHHHHhCCCHHHHHHHHHhc-CCeE
Q 036949 5 RMFQLLMSAY-STISTQDTALFLGMNEDDAAYYVQQQ-GWTL 44 (81)
Q Consensus 5 ~~~~li~~AY-~sIs~~~~a~~Lgls~~e~~~~~~~~-GW~~ 44 (81)
++...|..-| ..++++++|..+|+|..-+...+++. |-+.
T Consensus 9 ~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~f~~~~g~s~ 50 (107)
T PRK10219 9 TLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTVTHQTL 50 (107)
T ss_pred HHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHCcCH
Confidence 4455555555 46899999999999999988777765 6654
No 170
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=58.14 E-value=6.4 Score=28.63 Aligned_cols=25 Identities=20% Similarity=0.441 Sum_probs=22.3
Q ss_pred HHHHHHhCCCHHHHHHHHHhc--CCeE
Q 036949 20 QDTALFLGMNEDDAAYYVQQQ--GWTL 44 (81)
Q Consensus 20 ~~~a~~Lgls~~e~~~~~~~~--GW~~ 44 (81)
.++|..|||+..++..+.+.| .|+=
T Consensus 203 ~~LA~~LgLTdaQVKtWfQNRRtKWKr 229 (309)
T KOG0488|consen 203 IELAASLGLTDAQVKTWFQNRRTKWKR 229 (309)
T ss_pred HHHHHHcCCchhhHHHHHhhhhHHHHH
Confidence 459999999999999999986 8974
No 171
>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=58.07 E-value=46 Score=21.14 Aligned_cols=53 Identities=11% Similarity=0.139 Sum_probs=34.2
Q ss_pred hHHHHHHHHH---Hhc-----------ccccHHHHHHHhCCCHHHHHH---HHHhcCCeEeCCCceEeec
Q 036949 2 YTKRMFQLLM---SAY-----------STISTQDTALFLGMNEDDAAY---YVQQQGWTLDPASRMLTVK 54 (81)
Q Consensus 2 ~R~~~~~li~---~AY-----------~sIs~~~~a~~Lgls~~e~~~---~~~~~GW~~d~~~~~~~p~ 54 (81)
.++|++.++- .-| -.++-.++|.|||++.+-+-. -.++.|+---..+.+.++.
T Consensus 115 ~~~Rla~~L~~l~~~~~~~~~~~~~~~~~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~~~~~i~I~d 184 (193)
T TIGR03697 115 MGSRLVSFLLILCRDFGVPGQRGVTIDLRLSHQAIAEAIGSTRVTITRLLGDLRKKKLISIHKKKITVHD 184 (193)
T ss_pred HHHHHHHHHHHHHHHhCCCCCCeEEecCCCCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEecCCEEEEeC
Confidence 5677777653 222 246788999999998766544 4456798644355555543
No 172
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=57.64 E-value=29 Score=23.05 Aligned_cols=30 Identities=17% Similarity=0.221 Sum_probs=23.6
Q ss_pred HHHHHHHHHHhcccccHHHHHHHhCCCHHHH
Q 036949 3 TKRMFQLLMSAYSTISTQDTALFLGMNEDDA 33 (81)
Q Consensus 3 R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~ 33 (81)
|++|+.++.+ ...+++.++|..||.|..-+
T Consensus 9 ~~~Il~~l~~-~~~~~~~~La~~~~vS~~Ti 38 (185)
T PRK04424 9 QKALQELIEE-NPFITDEELAEKFGVSIQTI 38 (185)
T ss_pred HHHHHHHHHH-CCCEEHHHHHHHHCcCHHHH
Confidence 3456666655 89999999999999998544
No 173
>PF13551 HTH_29: Winged helix-turn helix
Probab=57.57 E-value=27 Score=20.30 Aligned_cols=34 Identities=18% Similarity=0.315 Sum_probs=24.3
Q ss_pred HHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHh
Q 036949 4 KRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQ 39 (81)
Q Consensus 4 ~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~ 39 (81)
-+++.++..--+ +..++|..||+|..-+..+...
T Consensus 2 ~~~l~l~~~g~~--~~~~ia~~lg~s~~Tv~r~~~~ 35 (112)
T PF13551_consen 2 AQILLLLAEGVS--TIAEIARRLGISRRTVYRWLKR 35 (112)
T ss_pred HHHHHHHHcCCC--cHHHHHHHHCcCHHHHHHHHHH
Confidence 344555444443 6999999999999888777664
No 174
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=57.57 E-value=23 Score=24.41 Aligned_cols=40 Identities=10% Similarity=0.171 Sum_probs=29.3
Q ss_pred HHHHHHHHHhccc---ccHHHHHHHhCCCHHHHHHHHHhcCCe
Q 036949 4 KRMFQLLMSAYST---ISTQDTALFLGMNEDDAAYYVQQQGWT 43 (81)
Q Consensus 4 ~~~~~li~~AY~s---Is~~~~a~~Lgls~~e~~~~~~~~GW~ 43 (81)
.+|++.|-+-... .++.++|.-.|.|+.-+..||++.|-.
T Consensus 19 ~~Ia~yil~n~~~v~~~si~~lA~~~~vS~aTv~Rf~kklG~~ 61 (284)
T PRK11302 19 RKVAEVILASPQTAIHSSIATLAKMANVSEPTVNRFCRSLDTK 61 (284)
T ss_pred HHHHHHHHhCHHHHHhcCHHHHHHHhCCCHHHHHHHHHHcCCC
Confidence 3455555554444 578889999999999988888887654
No 175
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=57.34 E-value=24 Score=23.33 Aligned_cols=34 Identities=15% Similarity=0.173 Sum_probs=28.2
Q ss_pred HHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH
Q 036949 5 RMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 5 ~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~ 38 (81)
++++++...+.-.+..++|.-||+|+.-+..+..
T Consensus 166 ~Vl~~~~~g~~g~s~~eIa~~l~iS~~Tv~~~~~ 199 (225)
T PRK10046 166 AVRKLFKEPGVQHTAETVAQALTISRTTARRYLE 199 (225)
T ss_pred HHHHHHHcCCCCcCHHHHHHHhCccHHHHHHHHH
Confidence 7888888877778899999999999888766643
No 176
>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=57.20 E-value=33 Score=20.62 Aligned_cols=39 Identities=10% Similarity=0.137 Sum_probs=28.8
Q ss_pred HHHHHHHHhcccccHHHHHHHhCCCHHHHHHHH---HhcCCeE
Q 036949 5 RMFQLLMSAYSTISTQDTALFLGMNEDDAAYYV---QQQGWTL 44 (81)
Q Consensus 5 ~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~---~~~GW~~ 44 (81)
.++.++.. ...++..++|..+|++..-+-..+ .++||..
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 45566654 678999999999999766655444 4679986
No 177
>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=56.80 E-value=20 Score=19.83 Aligned_cols=27 Identities=11% Similarity=0.185 Sum_probs=19.8
Q ss_pred HhcccccHHHHHHHhCCCHHHHHHHHH
Q 036949 12 SAYSTISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 12 ~AY~sIs~~~~a~~Lgls~~e~~~~~~ 38 (81)
+....+|+.++|.-||++++.+.....
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 456789999999999999988766655
No 178
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=56.68 E-value=16 Score=24.64 Aligned_cols=34 Identities=26% Similarity=0.379 Sum_probs=26.0
Q ss_pred HHHHHHHHhc--------ccccHHHHHHHhCCCHHHHHHHHH
Q 036949 5 RMFQLLMSAY--------STISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 5 ~~~~li~~AY--------~sIs~~~~a~~Lgls~~e~~~~~~ 38 (81)
+-...+..|| +++++.++|..||+|..-+.++..
T Consensus 159 rQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLR 200 (215)
T COG3413 159 RQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLR 200 (215)
T ss_pred HHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHH
Confidence 4445566666 479999999999999988776644
No 179
>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=56.61 E-value=39 Score=20.19 Aligned_cols=39 Identities=5% Similarity=0.123 Sum_probs=27.7
Q ss_pred HHHHHH--Hhc-ccccHHHHHHHhCCCHHHHHHH---HHhcCCeE
Q 036949 6 MFQLLM--SAY-STISTQDTALFLGMNEDDAAYY---VQQQGWTL 44 (81)
Q Consensus 6 ~~~li~--~AY-~sIs~~~~a~~Lgls~~e~~~~---~~~~GW~~ 44 (81)
++.++. ... ..++..++|..++++..-+-.. ..++||-.
T Consensus 30 vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~ 74 (109)
T TIGR01889 30 ILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLSKKGYLS 74 (109)
T ss_pred HHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEe
Confidence 455555 223 3599999999999977665544 45679986
No 180
>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=56.31 E-value=31 Score=18.70 Aligned_cols=32 Identities=13% Similarity=0.190 Sum_probs=25.9
Q ss_pred hcccccHHHHHHHhCCCHHHHHHHH---HhcCCeE
Q 036949 13 AYSTISTQDTALFLGMNEDDAAYYV---QQQGWTL 44 (81)
Q Consensus 13 AY~sIs~~~~a~~Lgls~~e~~~~~---~~~GW~~ 44 (81)
.....+..++|..+|++...+-... .++||.-
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 6778899999999999887765554 4679985
No 181
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=56.16 E-value=50 Score=22.65 Aligned_cols=39 Identities=13% Similarity=0.211 Sum_probs=30.0
Q ss_pred HHHHHHHHhcccccHHHHHHHhCCCHHHHHHHH---HhcCCeE
Q 036949 5 RMFQLLMSAYSTISTQDTALFLGMNEDDAAYYV---QQQGWTL 44 (81)
Q Consensus 5 ~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~---~~~GW~~ 44 (81)
+|+.+++.. ..+++.++|+.||++..-+-.++ .+.||-.
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 466677764 67999999999999887765554 4679974
No 182
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=56.01 E-value=68 Score=22.50 Aligned_cols=50 Identities=14% Similarity=0.280 Sum_probs=33.4
Q ss_pred HHHHHHHHHHhcccccHHHHHHHhCCCHHHHHH---HHHhcCCeEeCCCceEee
Q 036949 3 TKRMFQLLMSAYSTISTQDTALFLGMNEDDAAY---YVQQQGWTLDPASRMLTV 53 (81)
Q Consensus 3 R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~---~~~~~GW~~d~~~~~~~p 53 (81)
+.+|.+++.+ ...++++++|.+||+|..-+.. ...++|+-.-..|..+.+
T Consensus 19 ~~~Il~~L~~-~~~vtv~eLa~~l~VS~~TIRRDL~~Le~~G~l~r~~GGa~~~ 71 (269)
T PRK09802 19 REQIIQRLRQ-QGSVQVNDLSALYGVSTVTIRNDLAFLEKQGIAVRAYGGALIC 71 (269)
T ss_pred HHHHHHHHHH-cCCEeHHHHHHHHCCCHHHHHHHHHHHHhCCCeEEEeCCEEec
Confidence 3455666655 5569999999999999865532 234668876555555443
No 183
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=55.71 E-value=36 Score=19.16 Aligned_cols=41 Identities=17% Similarity=0.268 Sum_probs=29.8
Q ss_pred HHHHHHHHhcccccHHHHHHHhCCCHHHHHHH---HHhcCCeEe
Q 036949 5 RMFQLLMSAYSTISTQDTALFLGMNEDDAAYY---VQQQGWTLD 45 (81)
Q Consensus 5 ~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~---~~~~GW~~d 45 (81)
.|+.++.+.=..+++.++|..+|++..-+-.+ ..+.||-..
T Consensus 9 ~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~ 52 (91)
T smart00346 9 AVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQ 52 (91)
T ss_pred HHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeee
Confidence 45666665435799999999999987766444 456799864
No 184
>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=55.52 E-value=20 Score=18.33 Aligned_cols=24 Identities=17% Similarity=0.191 Sum_probs=17.8
Q ss_pred cccHHHHHHHhCCCHHHHHHHHHh
Q 036949 16 TISTQDTALFLGMNEDDAAYYVQQ 39 (81)
Q Consensus 16 sIs~~~~a~~Lgls~~e~~~~~~~ 39 (81)
.++..++|..+|+|..-+..+...
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 467788999999998888877664
No 185
>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=55.52 E-value=20 Score=18.69 Aligned_cols=23 Identities=13% Similarity=0.296 Sum_probs=18.0
Q ss_pred cccHHHHHHHhCCCHHHHHHHHH
Q 036949 16 TISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 16 sIs~~~~a~~Lgls~~e~~~~~~ 38 (81)
-|++.+++.++|+|..-+-...+
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 37889999999999988877766
No 186
>TIGR00370 conserved hypothetical protein TIGR00370.
Probab=55.34 E-value=18 Score=24.69 Aligned_cols=29 Identities=3% Similarity=0.036 Sum_probs=25.6
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHhcCCeEe
Q 036949 17 ISTQDTALFLGMNEDDAAYYVQQQGWTLD 45 (81)
Q Consensus 17 Is~~~~a~~Lgls~~e~~~~~~~~GW~~d 45 (81)
..++.+|++.|||.+|+++.-.+.-|.+-
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 187
>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=54.97 E-value=25 Score=20.84 Aligned_cols=19 Identities=32% Similarity=0.686 Sum_probs=15.0
Q ss_pred CCHHHHHHHHHhc-CCeEeC
Q 036949 28 MNEDDAAYYVQQQ-GWTLDP 46 (81)
Q Consensus 28 ls~~e~~~~~~~~-GW~~d~ 46 (81)
|+.+|+.....+. ||+++.
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 5788888888876 999986
No 188
>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=54.90 E-value=27 Score=17.83 Aligned_cols=23 Identities=13% Similarity=0.281 Sum_probs=18.9
Q ss_pred cccccHHHHHHHhCCCHHHHHHH
Q 036949 14 YSTISTQDTALFLGMNEDDAAYY 36 (81)
Q Consensus 14 Y~sIs~~~~a~~Lgls~~e~~~~ 36 (81)
|...+..++|..||+|...+...
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 67889999999999998877654
No 189
>PF12833 HTH_18: Helix-turn-helix domain; PDB: 2K9S_A 3LSG_C 3OIO_A 1D5Y_B 3GBG_A 3OOU_A 1BL0_A 1XS9_A 3MN2_B 3MKL_B ....
Probab=54.34 E-value=36 Score=18.79 Aligned_cols=26 Identities=12% Similarity=0.133 Sum_probs=18.6
Q ss_pred cccccHHHHHHHhCC-CHHHHHHHHHh
Q 036949 14 YSTISTQDTALFLGM-NEDDAAYYVQQ 39 (81)
Q Consensus 14 Y~sIs~~~~a~~Lgl-s~~e~~~~~~~ 39 (81)
+...++.++|..+|+ +...+...+.+
T Consensus 43 ~~~~~i~~ia~~~Gf~~~~~f~~~fk~ 69 (81)
T PF12833_consen 43 NTDLSIAEIAEECGFSSQSHFSRAFKR 69 (81)
T ss_dssp HTT--HHHHHHHTT-SSHHHHHHHHHH
T ss_pred hhcccHHHHHHHcCCCCHHHHHHHHHH
Confidence 679999999999999 67777766654
No 190
>PF15436 PGBA_N: Plasminogen-binding protein pgbA N-terminal
Probab=54.22 E-value=36 Score=23.76 Aligned_cols=37 Identities=24% Similarity=0.412 Sum_probs=30.9
Q ss_pred HHHHHHHHHhccc---ccHHHHHHHh---CC--CHHHHHHHHHhc
Q 036949 4 KRMFQLLMSAYST---ISTQDTALFL---GM--NEDDAAYYVQQQ 40 (81)
Q Consensus 4 ~~~~~li~~AY~s---Is~~~~a~~L---gl--s~~e~~~~~~~~ 40 (81)
+++..-|.++|.. |+++-+|.|| |. +.+++.++|.+.
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 4567788899988 7899999999 77 679999999863
No 191
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=53.61 E-value=17 Score=25.62 Aligned_cols=39 Identities=10% Similarity=0.273 Sum_probs=29.4
Q ss_pred HHHHHHHHhccc---ccHHHHHHHhCCCHHHHHHHHHhcCCe
Q 036949 5 RMFQLLMSAYST---ISTQDTALFLGMNEDDAAYYVQQQGWT 43 (81)
Q Consensus 5 ~~~~li~~AY~s---Is~~~~a~~Lgls~~e~~~~~~~~GW~ 43 (81)
+|++.|-.-+.. .++.++|...|+|+.-+..||++.|-.
T Consensus 22 ~iA~yil~~~~~~~~~si~elA~~a~VS~aTv~Rf~~kLGf~ 63 (281)
T COG1737 22 KIADYILANPDEVALLSIAELAERAGVSPATVVRFARKLGFE 63 (281)
T ss_pred HHHHHHHhCHHHHHHHHHHHHHHHhCCCHHHHHHHHHHcCCC
Confidence 355555555543 367889999999999999999998764
No 192
>PRK08558 adenine phosphoribosyltransferase; Provisional
Probab=53.52 E-value=22 Score=24.73 Aligned_cols=30 Identities=20% Similarity=0.377 Sum_probs=21.6
Q ss_pred HHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH
Q 036949 6 MFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 6 ~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~ 38 (81)
+++++.+-| +..++++++|+++..+..|++
T Consensus 16 ~lr~lk~~~---ty~el~~~~g~p~~~l~RYv~ 45 (238)
T PRK08558 16 VLRSLKKTY---TYEELSSITGLPESVLNRYVN 45 (238)
T ss_pred HHHHHhccc---CHHHHHHHHCCCHHHHHHHHc
Confidence 445555555 889999999998877766654
No 193
>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=53.23 E-value=18 Score=18.85 Aligned_cols=18 Identities=11% Similarity=0.095 Sum_probs=12.5
Q ss_pred HHHHHHHhCCCHHHHHHH
Q 036949 19 TQDTALFLGMNEDDAAYY 36 (81)
Q Consensus 19 ~~~~a~~Lgls~~e~~~~ 36 (81)
+.-+++.|.||++|...+
T Consensus 28 lpvi~tlL~fs~~e~~~i 45 (46)
T PF01465_consen 28 LPVIATLLKFSPEEKQKI 45 (46)
T ss_dssp HHHHHHHTT--HHHHHHH
T ss_pred HHHHHHHHCCCHHHHHhh
Confidence 356899999999997653
No 194
>PRK00110 hypothetical protein; Validated
Probab=53.03 E-value=34 Score=24.14 Aligned_cols=44 Identities=14% Similarity=0.135 Sum_probs=30.8
Q ss_pred HHHHHHhcCCeEeCCCceEeecCCCCcccCCCChhHHHHHHhHHHhhcC
Q 036949 33 AAYYVQQQGWTLDPASRMLTVKKQPLVTEQKLDPSKMQCLTEYVFHLEH 81 (81)
Q Consensus 33 ~~~~~~~~GW~~d~~~~~~~p~~~~~~~~~~~~~~~l~~Lt~~v~~LE~ 81 (81)
+.+...+.|+++.......+|..+..- ++++.+++.+++--||.
T Consensus 181 v~~~L~~~g~~~~~sei~~~P~~~v~l-----~~e~~~~~~~li~~Led 224 (245)
T PRK00110 181 VRDALEAAGLEAESAEVTMIPQNTVEL-----DEETAEKLLKLIDALED 224 (245)
T ss_pred HHHHHHHcCCCeeeeEEEEecCCCccc-----CHHHHHHHHHHHHHHhc
Confidence 344456789998877677777643322 67888889999888874
No 195
>PF11917 DUF3435: Protein of unknown function (DUF3435); InterPro: IPR021842 This family of proteins are functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 435 to 791 amino acids in length. This family is related to PF00589 from PFAM suggesting it may be an integrase enzyme.
Probab=52.74 E-value=15 Score=27.34 Aligned_cols=38 Identities=18% Similarity=0.360 Sum_probs=32.3
Q ss_pred HHHhc--ccccHHHHHHHhCC-CHHHHHHHHHhcCCeEeCC
Q 036949 10 LMSAY--STISTQDTALFLGM-NEDDAAYYVQQQGWTLDPA 47 (81)
Q Consensus 10 i~~AY--~sIs~~~~a~~Lgl-s~~e~~~~~~~~GW~~d~~ 47 (81)
..+.| ..|..+.-+.|+|+ +.+++.+.+...+-..|+.
T Consensus 231 f~~~Y~~~~v~~D~qa~~~g~~~~~~l~~~~~~ms~~rDp~ 271 (418)
T PF11917_consen 231 FEKYYLPRNVHVDLQAIFLGLPPREELIRAARSMSRSRDPR 271 (418)
T ss_pred HHHHhhhccCCccHHHHHhCCCchHHHHHHhhhhhhhhCCC
Confidence 34788 66788999999999 7788999999999999876
No 196
>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=52.71 E-value=30 Score=23.75 Aligned_cols=46 Identities=26% Similarity=0.481 Sum_probs=29.3
Q ss_pred HHHHHHHhcccccHH-------------HHHHHhCC-CHHHHHHHHHhcCCeEeCC--CceEeec
Q 036949 6 MFQLLMSAYSTISTQ-------------DTALFLGM-NEDDAAYYVQQQGWTLDPA--SRMLTVK 54 (81)
Q Consensus 6 ~~~li~~AY~sIs~~-------------~~a~~Lgl-s~~e~~~~~~~~GW~~d~~--~~~~~p~ 54 (81)
.-.++.++|+.|.-. -++.++|+ ++ ..|....||++..+ |....-.
T Consensus 86 ~W~l~ak~ys~iRd~~gk~~~~L~~Fl~~~~p~~gi~~p---~~YL~~~Gw~l~~~~~g~~~l~~ 147 (201)
T PF04769_consen 86 KWSLMAKAYSFIRDQLGKDKAPLDQFLAFACPLIGIIPP---EDYLEQLGWQLSQNEEGTITLEQ 147 (201)
T ss_pred HHHHHhhhhhhhccccccccCCHHHHHHHhhhhcCCCCH---HHHHHHcCCeEeeCCCCCEEEEe
Confidence 456888999887643 13445555 33 35778899998554 5555443
No 197
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=52.22 E-value=27 Score=17.51 Aligned_cols=19 Identities=16% Similarity=0.198 Sum_probs=13.4
Q ss_pred cHHHHHHHhCCCHHHHHHH
Q 036949 18 STQDTALFLGMNEDDAAYY 36 (81)
Q Consensus 18 s~~~~a~~Lgls~~e~~~~ 36 (81)
+...+|..||+|..-+-.-
T Consensus 20 n~~~aA~~Lgisr~tL~~k 38 (42)
T PF02954_consen 20 NVSKAARLLGISRRTLYRK 38 (42)
T ss_dssp -HHHHHHHHTS-HHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHH
Confidence 4578999999998776543
No 198
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=52.21 E-value=29 Score=24.16 Aligned_cols=39 Identities=18% Similarity=0.261 Sum_probs=26.8
Q ss_pred HHHHHHHHhcc---cccHHHHHHHhCCCHHHHHHHHHhcCCe
Q 036949 5 RMFQLLMSAYS---TISTQDTALFLGMNEDDAAYYVQQQGWT 43 (81)
Q Consensus 5 ~~~~li~~AY~---sIs~~~~a~~Lgls~~e~~~~~~~~GW~ 43 (81)
+|++.|-+-.. ..++.++|...|.|+.-+..||++.|-.
T Consensus 32 ~Ia~yil~~~~~v~~~si~~lA~~~~vS~aTi~Rf~kkLGf~ 73 (292)
T PRK11337 32 RVVEWLLKPGDLSEATALKDIAEALAVSEAMIVKVAKKLGFS 73 (292)
T ss_pred HHHHHHHhCHHHHHhcCHHHHHHHhCCChHHHHHHHHHcCCC
Confidence 44444443333 3567888888888888888888887654
No 199
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=52.07 E-value=38 Score=22.37 Aligned_cols=35 Identities=23% Similarity=0.372 Sum_probs=26.8
Q ss_pred HHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHhcC
Q 036949 4 KRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQG 41 (81)
Q Consensus 4 ~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~~G 41 (81)
.++..+..+ -.|+..+|+.||+|..-+-.+++.+|
T Consensus 163 ~~i~~~~~~---g~s~~~iak~lgis~~Tv~r~~k~~~ 197 (200)
T PRK13413 163 EKIKKLLDK---GTSKSEIARKLGVSRTTLARFLKTRG 197 (200)
T ss_pred HHHHHHHHC---CCCHHHHHHHHCCCHHHHHHHHHhcc
Confidence 445555443 36999999999999999988888765
No 200
>PRK00823 phhB pterin-4-alpha-carbinolamine dehydratase; Validated
Probab=51.82 E-value=28 Score=20.77 Aligned_cols=20 Identities=30% Similarity=0.599 Sum_probs=15.5
Q ss_pred CCHHHHHHHHHhc-CCeEeCC
Q 036949 28 MNEDDAAYYVQQQ-GWTLDPA 47 (81)
Q Consensus 28 ls~~e~~~~~~~~-GW~~d~~ 47 (81)
|+.+++.++..+. ||+++.+
T Consensus 6 Ls~~ei~~~l~~l~gW~~~~~ 26 (97)
T PRK00823 6 LSDEEIAELLPQLPGWTLVGD 26 (97)
T ss_pred CCHHHHHHHhhcCCCCeEeCC
Confidence 4788888887765 9999755
No 201
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=51.80 E-value=77 Score=21.89 Aligned_cols=44 Identities=11% Similarity=0.163 Sum_probs=31.9
Q ss_pred HHHHHHHHhcccccHHHHHHHhCCCHHHHHHHH---HhcCCeE-eCCC
Q 036949 5 RMFQLLMSAYSTISTQDTALFLGMNEDDAAYYV---QQQGWTL-DPAS 48 (81)
Q Consensus 5 ~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~---~~~GW~~-d~~~ 48 (81)
+|+.+++..=..+++.++++.||++..-+-.+. .+.||-. |+++
T Consensus 15 ~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~~~g~v~~~~~~ 62 (263)
T PRK09834 15 MVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQEEGYVRRSASD 62 (263)
T ss_pred HHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecCC
Confidence 456777765455999999999999877765554 4679985 5443
No 202
>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=51.65 E-value=26 Score=18.03 Aligned_cols=27 Identities=19% Similarity=0.305 Sum_probs=17.9
Q ss_pred HhcccccHHHHHHHhCCCHHHHHHHHH
Q 036949 12 SAYSTISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 12 ~AY~sIs~~~~a~~Lgls~~e~~~~~~ 38 (81)
.-+.-.+..++|..+|+|+..+.....
T Consensus 22 ~~~~g~s~~eIa~~l~~s~~~v~~~l~ 48 (54)
T PF08281_consen 22 RYFQGMSYAEIAEILGISESTVKRRLR 48 (54)
T ss_dssp HHTS---HHHHHHHCTS-HHHHHHHHH
T ss_pred HHHHCcCHHHHHHHHCcCHHHHHHHHH
Confidence 356678889999999999988776543
No 203
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=51.50 E-value=70 Score=21.28 Aligned_cols=51 Identities=16% Similarity=0.272 Sum_probs=32.4
Q ss_pred hHHHHHHHHHHhcc----cccHHHHHHHhCCCHHHHHHHH---HhcCCeEeCCCceEe
Q 036949 2 YTKRMFQLLMSAYS----TISTQDTALFLGMNEDDAAYYV---QQQGWTLDPASRMLT 52 (81)
Q Consensus 2 ~R~~~~~li~~AY~----sIs~~~~a~~Lgls~~e~~~~~---~~~GW~~d~~~~~~~ 52 (81)
+++|++..+-.... ..+..++|.+||++.+-+-... .+.|+--=..+.+.+
T Consensus 151 ~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvsR~L~~L~~~G~I~~~~~~i~I 208 (226)
T PRK10402 151 LENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLLYVLAQFIQDGYLKKSKRGYLI 208 (226)
T ss_pred HHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHHHHHHHHHHCCCEEeeCCEEEE
Confidence 56788887654321 2467899999999887765543 456886433344443
No 204
>PF12668 DUF3791: Protein of unknown function (DUF3791); InterPro: IPR024269 This entry represents proteins of unknown function.
Probab=51.28 E-value=27 Score=19.07 Aligned_cols=23 Identities=17% Similarity=0.306 Sum_probs=19.2
Q ss_pred cHHHHHHHhCCCHHHHHHHHHhc
Q 036949 18 STQDTALFLGMNEDDAAYYVQQQ 40 (81)
Q Consensus 18 s~~~~a~~Lgls~~e~~~~~~~~ 40 (81)
.++.+|.-+|+|++++-++..+-
T Consensus 7 ~Ie~~A~~~~~s~~ea~~~~~~~ 29 (62)
T PF12668_consen 7 CIEEFAKKLNISGEEAYNYFKRS 29 (62)
T ss_pred HHHHHHHHHCcCHHHHHHHHHHc
Confidence 56779999999999998887754
No 205
>PTZ00064 histone acetyltransferase; Provisional
Probab=51.19 E-value=62 Score=25.61 Aligned_cols=38 Identities=8% Similarity=0.089 Sum_probs=30.1
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHhcCCeEeCCCceEeec
Q 036949 17 ISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVK 54 (81)
Q Consensus 17 Is~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~~~~~p~ 54 (81)
|++++++.+.|+..+|++.-.+..|.-..-.|..++-.
T Consensus 472 iSI~dIS~~TgI~~eDII~TLq~L~llky~kgq~~I~~ 509 (552)
T PTZ00064 472 KFIDNVVRSTGIRREDVIRILEENGIMRNIKDQHYIFC 509 (552)
T ss_pred ccHHHHHHHhCCCHHHHHHHHHHCCcEEEeCCCEEEEE
Confidence 89999999999999999998888886544444554444
No 206
>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=50.62 E-value=16 Score=24.71 Aligned_cols=39 Identities=13% Similarity=0.275 Sum_probs=29.2
Q ss_pred HHHHHhcccccHHHHHHHhCCCHHHHHHHHHhcCCeEeCC
Q 036949 8 QLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPA 47 (81)
Q Consensus 8 ~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~d~~ 47 (81)
+.|...|...|.+++... ++++.++.++++++|=..+-.
T Consensus 47 ~iMr~~yPn~s~~~l~~~-~~~~~~~i~y~ks~g~~~~~~ 85 (175)
T PF05543_consen 47 DIMRYLYPNVSEEQLKFT-SLTPNQMIKYAKSQGRNPQYN 85 (175)
T ss_dssp HHHHHHSTTS-CCCHHH---B-HHHHHHHHHHTTEEEEEE
T ss_pred HHHHHHCCCCCHHHHhhc-CCCHHHHHHHHHHcCcchhHh
Confidence 478889999999999665 899999999999988666433
No 207
>PF11360 DUF3110: Protein of unknown function (DUF3110); InterPro: IPR021503 This family of proteins has no known function.
Probab=50.35 E-value=24 Score=21.01 Aligned_cols=27 Identities=7% Similarity=0.326 Sum_probs=19.4
Q ss_pred CHHHHHHHHHhc--CCeEeCCC-ceEeecC
Q 036949 29 NEDDAAYYVQQQ--GWTLDPAS-RMLTVKK 55 (81)
Q Consensus 29 s~~e~~~~~~~~--GW~~d~~~-~~~~p~~ 55 (81)
+.+++..+|.+. +|.+=+.| .+++|..
T Consensus 56 d~~~i~~fC~~~gy~~~iv~~g~~l~~PP~ 85 (86)
T PF11360_consen 56 DPEEIEEFCRSAGYEYEIVPPGRDLLIPPE 85 (86)
T ss_pred CHHHHHHHHHHCCceEEEECCCCCeeCCCC
Confidence 458899999987 56666666 6667653
No 208
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=50.29 E-value=45 Score=18.94 Aligned_cols=53 Identities=15% Similarity=0.165 Sum_probs=32.8
Q ss_pred HHHHHHHHhcc--cccHHHHHHHhCCCHHHHHHHHH---hcCCeE---eCCCceEeecCCC
Q 036949 5 RMFQLLMSAYS--TISTQDTALFLGMNEDDAAYYVQ---QQGWTL---DPASRMLTVKKQP 57 (81)
Q Consensus 5 ~~~~li~~AY~--sIs~~~~a~~Lgls~~e~~~~~~---~~GW~~---d~~~~~~~p~~~~ 57 (81)
+++..+..... .++.+++|..+|+++.-+.+... +.|=-- ++.|.+...++|+
T Consensus 12 ~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~~G~~GGy~L~~~~~ 72 (83)
T PF02082_consen 12 RILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIESSRGRGGGYRLARPPE 72 (83)
T ss_dssp HHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETSTTSEEEESS-CC
T ss_pred HHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEecCCCCCceeecCCHH
Confidence 34445555554 38999999999999988877765 346533 1245565555444
No 209
>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=50.16 E-value=33 Score=24.93 Aligned_cols=20 Identities=20% Similarity=0.572 Sum_probs=16.9
Q ss_pred CCHHHHHHHHHhcCCeEeCC
Q 036949 28 MNEDDAAYYVQQQGWTLDPA 47 (81)
Q Consensus 28 ls~~e~~~~~~~~GW~~d~~ 47 (81)
++.+++.+..++.||++-+|
T Consensus 133 y~~~~a~~~~~~~~~~~~~d 152 (310)
T TIGR00746 133 YTEEEAKRLAAEKGWIVKED 152 (310)
T ss_pred cCHHHHHHHHHHcCCeEeec
Confidence 37899999999999998664
No 210
>PF10141 ssDNA-exonuc_C: Single-strand DNA-specific exonuclease, C terminal domain; InterPro: IPR018779 This entry represents a domain found at the C terminus of a set of single-stranded DNA-specific exonucleases, including RecJ. Its function has not, as yet, been determined.
Probab=50.09 E-value=56 Score=21.83 Aligned_cols=46 Identities=13% Similarity=0.079 Sum_probs=33.1
Q ss_pred cccccH----HHHHHHhCCCHHHH---HHHHHhcCCeEeCCCceEeecCCCCc
Q 036949 14 YSTIST----QDTALFLGMNEDDA---AYYVQQQGWTLDPASRMLTVKKQPLV 59 (81)
Q Consensus 14 Y~sIs~----~~~a~~Lgls~~e~---~~~~~~~GW~~d~~~~~~~p~~~~~~ 59 (81)
...+.+ ..+|.+||++.+.+ .+..-+.|..--.+|.+....+|++.
T Consensus 110 ~~~~~l~~~~~~La~~l~i~~~~l~fml~VF~EL~FVti~~g~i~~~~~p~k~ 162 (195)
T PF10141_consen 110 HPNFDLKEQLQALAKYLGISPDTLKFMLKVFFELGFVTIEDGVISLNPNPEKR 162 (195)
T ss_pred CCCCCHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCcEEEeCCEEEeCCCCCCc
Confidence 355554 67999999998875 56667899987777776665555544
No 211
>COG1724 Predicted RNA binding protein (dsRBD-like fold), HicA family [General function prediction only]
Probab=49.83 E-value=16 Score=20.91 Aligned_cols=21 Identities=14% Similarity=0.319 Sum_probs=18.6
Q ss_pred HHhCCCHHHHHHHHHhcCCeE
Q 036949 24 LFLGMNEDDAAYYVQQQGWTL 44 (81)
Q Consensus 24 ~~Lgls~~e~~~~~~~~GW~~ 44 (81)
.++.++..|+++...+.||.+
T Consensus 3 ~lp~~~~ke~ik~Le~~Gf~~ 23 (66)
T COG1724 3 KLPRMKAKEVIKALEKDGFQL 23 (66)
T ss_pred cCCcCCHHHHHHHHHhCCcEE
Confidence 467789999999999999997
No 212
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=49.54 E-value=36 Score=20.84 Aligned_cols=32 Identities=13% Similarity=0.282 Sum_probs=27.1
Q ss_pred hHHHHHHHHHHhcccccHHHHHHHhCCC-HHHH
Q 036949 2 YTKRMFQLLMSAYSTISTQDTALFLGMN-EDDA 33 (81)
Q Consensus 2 ~R~~~~~li~~AY~sIs~~~~a~~Lgls-~~e~ 33 (81)
.|++|+.++..+=+-..+..+..++|.. ++++
T Consensus 4 ~rEkii~lL~e~~eplt~~ei~~~~~~~~~~~v 36 (97)
T COG3357 4 TREKIISLLLESDEPLTVAEIFELLNGEKEKEV 36 (97)
T ss_pred HHHHHHHHHHcCCCcchHHHHHHHHcCCchHHH
Confidence 6899999998888889999999999994 4444
No 213
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=49.46 E-value=36 Score=23.48 Aligned_cols=39 Identities=21% Similarity=0.344 Sum_probs=25.9
Q ss_pred HHHHHHHHhccc---ccHHHHHHHhCCCHHHHHHHHHhcCCe
Q 036949 5 RMFQLLMSAYST---ISTQDTALFLGMNEDDAAYYVQQQGWT 43 (81)
Q Consensus 5 ~~~~li~~AY~s---Is~~~~a~~Lgls~~e~~~~~~~~GW~ 43 (81)
++++.|-.-+.. .++.++|.-.|.|+.-+..||++.|-+
T Consensus 16 ~ia~yil~n~~~v~~~si~elA~~~~vS~aTv~Rf~kklG~~ 57 (278)
T PRK11557 16 KLADYLLLQPDTARHLSSQQLANEAGVSQSSVVKFAQKLGYK 57 (278)
T ss_pred HHHHHHHhCHHHHHhcCHHHHHHHhCCCHHHHHHHHHHcCCC
Confidence 444544444433 577778888888888888887777653
No 214
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=49.18 E-value=55 Score=21.74 Aligned_cols=37 Identities=19% Similarity=0.295 Sum_probs=23.7
Q ss_pred hHHHHHHHHHHhcc--------ccc--HHHHHHHhCCCHHHHHHHHH
Q 036949 2 YTKRMFQLLMSAYS--------TIS--TQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 2 ~R~~~~~li~~AY~--------sIs--~~~~a~~Lgls~~e~~~~~~ 38 (81)
.++|++..+-.-+. .|+ -.++|.|||++.+-+.....
T Consensus 149 ~~~Rla~~Ll~~~~~~~~~~~~~i~~t~~~iA~~lG~tretvsR~l~ 195 (236)
T PRK09392 149 SAERLANYLLKQSLRQGGADVVTLPYEKRVLASYLGMTPENLSRAFA 195 (236)
T ss_pred HHHHHHHHHHHhccccCCCcEEEeeCCHHHHHHHhCCChhHHHHHHH
Confidence 46777776643222 133 46799999998877655544
No 215
>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=48.97 E-value=36 Score=17.24 Aligned_cols=31 Identities=16% Similarity=0.301 Sum_probs=19.9
Q ss_pred HHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHH
Q 036949 4 KRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYV 37 (81)
Q Consensus 4 ~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~ 37 (81)
+++..+...- +++.++|..+|+|..-+-.+.
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 4455555444 789999999999988776554
No 216
>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=48.74 E-value=32 Score=22.17 Aligned_cols=22 Identities=14% Similarity=0.194 Sum_probs=19.9
Q ss_pred HHHHhcccccHHHHHHHhCCCH
Q 036949 9 LLMSAYSTISTQDTALFLGMNE 30 (81)
Q Consensus 9 li~~AY~sIs~~~~a~~Lgls~ 30 (81)
..++-|...|++++|+-.|+|.
T Consensus 21 f~e~G~~~~s~~~IA~~agvs~ 42 (202)
T TIGR03613 21 FSRFGFHGTSLEQIAELAGVSK 42 (202)
T ss_pred HHHhCcccCCHHHHHHHhCCCH
Confidence 5678899999999999999987
No 217
>KOG0687 consensus 26S proteasome regulatory complex, subunit RPN7/PSMD6 [Posttranslational modification, protein turnover, chaperones]
Probab=48.73 E-value=60 Score=24.52 Aligned_cols=59 Identities=10% Similarity=0.315 Sum_probs=45.8
Q ss_pred hHHHHHHHHHHhcccccHHHHHHHhCCCH----HHHHHHHH-hc-CCeEeCCCceEeecCCCCcc
Q 036949 2 YTKRMFQLLMSAYSTISTQDTALFLGMNE----DDAAYYVQ-QQ-GWTLDPASRMLTVKKQPLVT 60 (81)
Q Consensus 2 ~R~~~~~li~~AY~sIs~~~~a~~Lgls~----~e~~~~~~-~~-GW~~d~~~~~~~p~~~~~~~ 60 (81)
+|.+.-.-+=-+|.+++++-.|.-+|+|. .|+..|+. .+ .=++|.-+.++....|++.+
T Consensus 303 MR~rvY~QlLESYrsl~l~~MA~aFgVSVefiDreL~rFI~~grL~ckIDrVnGVVEtNrpD~KN 367 (393)
T KOG0687|consen 303 MRRRVYAQLLESYRSLTLESMAKAFGVSVEFIDRELGRFIAAGRLHCKIDRVNGVVETNRPDEKN 367 (393)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhCchHHHHHhHHHHhhccCceeeeeecccceeecCCccccc
Confidence 47777777778999999999999999986 56777766 34 44578777788877777665
No 218
>COG0217 Uncharacterized conserved protein [Function unknown]
Probab=48.71 E-value=43 Score=23.78 Aligned_cols=46 Identities=13% Similarity=0.224 Sum_probs=32.9
Q ss_pred HHHHHHHHhcCCeEeCCCceEeecCCCCcccCCCChhHHHHHHhHHHhhcC
Q 036949 31 DDAAYYVQQQGWTLDPASRMLTVKKQPLVTEQKLDPSKMQCLTEYVFHLEH 81 (81)
Q Consensus 31 ~e~~~~~~~~GW~~d~~~~~~~p~~~~~~~~~~~~~~~l~~Lt~~v~~LE~ 81 (81)
..+.+...+.|+++.......+|.+.... +.++.++|-+++-.||.
T Consensus 181 ~~V~~~L~~~g~~~~~ael~~iP~~~v~~-----~~e~a~k~~kLid~LEd 226 (241)
T COG0217 181 NKVKEALEAAGYEIESAELTMIPQNTVEL-----DDEDAEKLEKLIDALED 226 (241)
T ss_pred HHHHHHHHHcCCceeeeeEEEecCCceec-----CHHHHHHHHHHHHHHhc
Confidence 34566677889988766666677654433 45888889889888884
No 219
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=48.38 E-value=49 Score=21.61 Aligned_cols=33 Identities=6% Similarity=0.197 Sum_probs=25.8
Q ss_pred HHHHHHHhcccccHHH---HHHHhCCCHHHHHHHHH
Q 036949 6 MFQLLMSAYSTISTQD---TALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 6 ~~~li~~AY~sIs~~~---~a~~Lgls~~e~~~~~~ 38 (81)
++..+-..|.-|+.+. +|..||+++.++...++
T Consensus 28 ~L~~vQ~~~G~Ip~e~~~~iA~~l~v~~~~V~~vat 63 (156)
T PRK05988 28 ILHAIQDEFGYVPEDAVPVIAEALNLSRAEVHGVIT 63 (156)
T ss_pred HHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHHHHH
Confidence 4567778888888765 89999999988876655
No 220
>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=47.76 E-value=48 Score=21.20 Aligned_cols=33 Identities=9% Similarity=0.011 Sum_probs=25.9
Q ss_pred HHHHHHHhcccccHHH---HHHHhCCCHHHHHHHHH
Q 036949 6 MFQLLMSAYSTISTQD---TALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 6 ~~~li~~AY~sIs~~~---~a~~Lgls~~e~~~~~~ 38 (81)
++..+-..|.-||.+. +|..||++..++...++
T Consensus 21 ~L~~vQ~~~G~i~~~~~~~iA~~l~~~~~~v~~v~t 56 (148)
T TIGR01958 21 ALMIAQEQKGWVTPEAIAAVAEMLGIPPVWVYEVAT 56 (148)
T ss_pred HHHHHHHHhCCCCHHHHHHHHHHhCcCHHHHHHHHh
Confidence 5567778888888766 89999999888766654
No 221
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=47.62 E-value=91 Score=21.48 Aligned_cols=49 Identities=18% Similarity=0.236 Sum_probs=33.8
Q ss_pred HHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH---hcCCeEeCCCceEe
Q 036949 3 TKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ---QQGWTLDPASRMLT 52 (81)
Q Consensus 3 R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~---~~GW~~d~~~~~~~ 52 (81)
+++|...+. ....++..++|.+||+|+.-+..... ++|.-.-..|..+.
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 345666666 58899999999999999876655544 35776544444443
No 222
>PRK12378 hypothetical protein; Provisional
Probab=47.16 E-value=47 Score=23.31 Aligned_cols=43 Identities=9% Similarity=0.052 Sum_probs=30.7
Q ss_pred HHHHHHhcCCeEeCCCceEeecCCCCcccCCCChhHHHHHHhHHHhhc
Q 036949 33 AAYYVQQQGWTLDPASRMLTVKKQPLVTEQKLDPSKMQCLTEYVFHLE 80 (81)
Q Consensus 33 ~~~~~~~~GW~~d~~~~~~~p~~~~~~~~~~~~~~~l~~Lt~~v~~LE 80 (81)
+.+...+.|+.+.......+|..+..- ++++.+++-+++--||
T Consensus 180 v~~~L~~~g~~~~~sei~~~P~~~v~l-----~~e~~~~~~~li~~Le 222 (235)
T PRK12378 180 VKKALEAAGIEFLVAELEMIPQNPVEL-----SGEDLEQFEKLLDALE 222 (235)
T ss_pred HHHHHHHcCCCceeeEEEEecCCCccC-----CHHHHHHHHHHHHHHh
Confidence 344456789988877777777755322 6678888888888887
No 223
>PHA02535 P terminase ATPase subunit; Provisional
Probab=47.06 E-value=35 Score=27.17 Aligned_cols=40 Identities=15% Similarity=0.218 Sum_probs=33.4
Q ss_pred hHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHhcCCeE
Q 036949 2 YTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTL 44 (81)
Q Consensus 2 ~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~ 44 (81)
+|.++..|.-+ --++.++|+.||+++.-+-.++.+-+|.-
T Consensus 7 fK~~Av~Ly~~---G~sv~eIA~~LGv~~~Tl~~W~kr~~w~~ 46 (581)
T PHA02535 7 VRRAAKFLYWQ---GWTVAEIAEELGLKSRTIYSWKERDGWRD 46 (581)
T ss_pred HHHHHHHHHHc---CCCHHHHHHHhCCChhHHHHHhccccccc
Confidence 56667766655 66899999999999999999999999973
No 224
>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=46.76 E-value=30 Score=17.73 Aligned_cols=22 Identities=23% Similarity=0.388 Sum_probs=16.9
Q ss_pred HHHHHHHhCCCHHHHHHHHHhc
Q 036949 19 TQDTALFLGMNEDDAAYYVQQQ 40 (81)
Q Consensus 19 ~~~~a~~Lgls~~e~~~~~~~~ 40 (81)
+..+|.-+||+..++..+...+
T Consensus 30 ~~~la~~~~l~~~qV~~WF~nr 51 (59)
T cd00086 30 REELAKELGLTERQVKIWFQNR 51 (59)
T ss_pred HHHHHHHHCcCHHHHHHHHHHH
Confidence 4568888899888888876643
No 225
>PRK09940 transcriptional regulator YdeO; Provisional
Probab=46.71 E-value=57 Score=23.05 Aligned_cols=37 Identities=11% Similarity=0.047 Sum_probs=28.6
Q ss_pred HHHHHHHHhc-ccccHHHHHHHhCCCHHHHHHHHHhcC
Q 036949 5 RMFQLLMSAY-STISTQDTALFLGMNEDDAAYYVQQQG 41 (81)
Q Consensus 5 ~~~~li~~AY-~sIs~~~~a~~Lgls~~e~~~~~~~~G 41 (81)
++.+.+..-| ..++++++|..+|+|+.-+....++.|
T Consensus 138 kv~~~I~~~~~~~~tl~~LA~~~gmS~s~l~R~FK~~G 175 (253)
T PRK09940 138 KVRNIVNMKLAHPWKLKDICDCLYISESLLKKKLKQEQ 175 (253)
T ss_pred HHHHHHHHhhcCCCCHHHHHHHHCcCHHHHHHHHHHcC
Confidence 5556665555 358999999999999999888877644
No 226
>PHA00738 putative HTH transcription regulator
Probab=46.46 E-value=69 Score=20.01 Aligned_cols=36 Identities=8% Similarity=0.102 Sum_probs=29.1
Q ss_pred hHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH
Q 036949 2 YTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 2 ~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~ 38 (81)
.|.+|+..+.. ....++.+++..++++..-+-....
T Consensus 13 tRr~IL~lL~~-~e~~~V~eLae~l~lSQptVS~HLK 48 (108)
T PHA00738 13 LRRKILELIAE-NYILSASLISHTLLLSYTTVLRHLK 48 (108)
T ss_pred HHHHHHHHHHH-cCCccHHHHHHhhCCCHHHHHHHHH
Confidence 58999999965 3358999999999999888766644
No 227
>cd08784 Death_DRs Death Domain of Death Receptors. Death domain (DD) found in death receptor proteins. Death receptors are members of the tumor necrosis factor (TNF) receptor superfamily, characterized by having a cytoplasmic DD. Known members of the family are Fas (CD95/APO-1), TNF-receptor 1 (TNFR1/TNFRSF1A/p55/CD120a), TNF-related apoptosis-inducing ligand receptor 1 (TRAIL-R1 /DR4), and receptor 2 (TRAIL-R2/DR5/APO-2/KILLER), as well as Death Receptor 3 (DR3/APO-3/TRAMP/WSL-1/LARD). They are involved in apoptosis signaling pathways. 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 adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=46.20 E-value=24 Score=20.28 Aligned_cols=20 Identities=10% Similarity=0.082 Sum_probs=15.8
Q ss_pred HHHHHHHhCCCHHHHHHHHH
Q 036949 19 TQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 19 ~~~~a~~Lgls~~e~~~~~~ 38 (81)
...+++.|||+..++...-.
T Consensus 14 Wk~laR~LGls~~~I~~ie~ 33 (79)
T cd08784 14 HKRFFRKLGLSDNEIKVAEL 33 (79)
T ss_pred HHHHHHHcCCCHHHHHHHHH
Confidence 35799999999998876543
No 228
>COG3604 FhlA Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / Signal transduction mechanisms]
Probab=46.08 E-value=43 Score=26.51 Aligned_cols=40 Identities=15% Similarity=0.223 Sum_probs=33.7
Q ss_pred HHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHhcCCeE
Q 036949 3 TKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTL 44 (81)
Q Consensus 3 R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~ 44 (81)
|++|.++++++=-.+.- +|+.||+....+...+++.|=++
T Consensus 508 R~~I~~aL~~~~~~~a~--AAr~LGl~~~~L~~~~kRlGI~~ 547 (550)
T COG3604 508 RQLIIAALEETNGNWAG--AARRLGLTRRTLLYRMKRLGIKV 547 (550)
T ss_pred HHHHHHHHHHhCCcHHH--HHHHhCCCHHHHHHHHHHcCCCc
Confidence 78899999988776655 99999999999998888778654
No 229
>PRK12702 mannosyl-3-phosphoglycerate phosphatase; Reviewed
Probab=45.80 E-value=23 Score=25.92 Aligned_cols=30 Identities=13% Similarity=0.271 Sum_probs=22.2
Q ss_pred HhcccccHHHHHHHhCCCHHHHHHHHHhcCC
Q 036949 12 SAYSTISTQDTALFLGMNEDDAAYYVQQQGW 42 (81)
Q Consensus 12 ~AY~sIs~~~~a~~Lgls~~e~~~~~~~~GW 42 (81)
+.|...+.++++.+.||+.+++. .|++|-|
T Consensus 119 ~gF~d~t~~ei~~~TGL~~~~A~-~A~~Re~ 148 (302)
T PRK12702 119 IGFGDWTASELAAATGIPLEEAE-RAQKREY 148 (302)
T ss_pred eehhhCCHHHHHHHhCcCHHHHH-HHHhccC
Confidence 35788999999999999987764 3333433
No 230
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=45.55 E-value=34 Score=16.11 Aligned_cols=23 Identities=13% Similarity=0.179 Sum_probs=18.8
Q ss_pred ccccHHHHHHHhCCCHHHHHHHH
Q 036949 15 STISTQDTALFLGMNEDDAAYYV 37 (81)
Q Consensus 15 ~sIs~~~~a~~Lgls~~e~~~~~ 37 (81)
..++..++|..+|++...+..+.
T Consensus 9 ~~~s~~~la~~~~i~~~~i~~~~ 31 (56)
T smart00530 9 KGLTQEELAEKLGVSRSTLSRIE 31 (56)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHH
Confidence 46889999999999988876654
No 231
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=45.38 E-value=35 Score=22.19 Aligned_cols=22 Identities=14% Similarity=0.119 Sum_probs=19.4
Q ss_pred HHHHhcccccHHHHHHHhCCCH
Q 036949 9 LLMSAYSTISTQDTALFLGMNE 30 (81)
Q Consensus 9 li~~AY~sIs~~~~a~~Lgls~ 30 (81)
+.++-|..++++++|+..|+|.
T Consensus 24 f~~~G~~~~ti~~Ia~~agvsk 45 (213)
T PRK09975 24 FALRGVSNTTLNDIADAANVTR 45 (213)
T ss_pred HHHcCcccCCHHHHHHHcCCCH
Confidence 3478899999999999999976
No 232
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=44.94 E-value=56 Score=23.07 Aligned_cols=40 Identities=10% Similarity=0.043 Sum_probs=30.3
Q ss_pred HHHHHHHHhc-ccccHHHHHHHhCCCHHHHHHHHHhc-CCeE
Q 036949 5 RMFQLLMSAY-STISTQDTALFLGMNEDDAAYYVQQQ-GWTL 44 (81)
Q Consensus 5 ~~~~li~~AY-~sIs~~~~a~~Lgls~~e~~~~~~~~-GW~~ 44 (81)
++...|..-| ..++++++|..+|+|+..+...+++. |-+.
T Consensus 222 ~~~~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~~~g~s~ 263 (322)
T PRK09393 222 PLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAATGMTP 263 (322)
T ss_pred HHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCH
Confidence 4455555554 57999999999999999998887764 6543
No 233
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=44.66 E-value=29 Score=21.53 Aligned_cols=20 Identities=20% Similarity=0.218 Sum_probs=15.2
Q ss_pred cccHHHHHHHhCCCHHHHHH
Q 036949 16 TISTQDTALFLGMNEDDAAY 35 (81)
Q Consensus 16 sIs~~~~a~~Lgls~~e~~~ 35 (81)
.+|-+.+|+|||.|..-+.+
T Consensus 57 ~lSQ~vFA~~L~vs~~Tv~~ 76 (104)
T COG2944 57 GLSQPVFARYLGVSVSTVRK 76 (104)
T ss_pred CCCHHHHHHHHCCCHHHHHH
Confidence 46777888888888776654
No 234
>cd08318 Death_NMPP84 Death domain of Nuclear Matrix Protein P84. Death domain (DD) found in the Nuclear Matrix Protein P84 (also known as HPR1 or THOC1). HPR1/p84 resides in the nuclear matrix and is part of the THO complex, also called TREX (transcription/export) complex, which functions in mRNP biogenesis at the interface between transcription and export of mRNA from the nucleus. Mice lacking THOC1 have abnormal testis development and are sterile. 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 adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=44.65 E-value=26 Score=20.48 Aligned_cols=20 Identities=15% Similarity=0.084 Sum_probs=16.3
Q ss_pred HHHHHHHhCCCHHHHHHHHH
Q 036949 19 TQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 19 ~~~~a~~Lgls~~e~~~~~~ 38 (81)
...+|+-|||+..++..+-.
T Consensus 21 Wk~Lar~LGls~~dI~~i~~ 40 (86)
T cd08318 21 WKTLAPHLEMKDKEIRAIES 40 (86)
T ss_pred HHHHHHHcCCCHHHHHHHHh
Confidence 45699999999999977654
No 235
>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=44.54 E-value=32 Score=18.90 Aligned_cols=28 Identities=21% Similarity=0.253 Sum_probs=18.7
Q ss_pred HHHHHHhcccccHHHHHHHhCCCHHHHH
Q 036949 7 FQLLMSAYSTISTQDTALFLGMNEDDAA 34 (81)
Q Consensus 7 ~~li~~AY~sIs~~~~a~~Lgls~~e~~ 34 (81)
++-+-.+|.-=+..++|..||+|..-+-
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 4445566777777899999999888776
No 236
>PF13994 PgaD: PgaD-like protein
Probab=44.44 E-value=31 Score=21.87 Aligned_cols=24 Identities=17% Similarity=0.281 Sum_probs=20.9
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHhc
Q 036949 17 ISTQDTALFLGMNEDDAAYYVQQQ 40 (81)
Q Consensus 17 Is~~~~a~~Lgls~~e~~~~~~~~ 40 (81)
++.+++|++++++++++.+.-+.+
T Consensus 101 ~~~~elA~~f~l~~~~l~~lr~~k 124 (138)
T PF13994_consen 101 VSDEELARSFGLSPEQLQQLRQAK 124 (138)
T ss_pred CCHHHHHHHcCCCHHHHHHHHhCC
Confidence 899999999999999998876654
No 237
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=44.42 E-value=90 Score=20.48 Aligned_cols=47 Identities=13% Similarity=0.267 Sum_probs=33.9
Q ss_pred HHHHHHHHHHhcc----cccHHHHHHHhCCC-HHHHH---HHHHhcCCeEeCCCc
Q 036949 3 TKRMFQLLMSAYS----TISTQDTALFLGMN-EDDAA---YYVQQQGWTLDPASR 49 (81)
Q Consensus 3 R~~~~~li~~AY~----sIs~~~~a~~Lgls-~~e~~---~~~~~~GW~~d~~~~ 49 (81)
+.+++..|...|. ..+..++|..||++ ..-+. +-..++||-.-.+|.
T Consensus 8 q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~g~i~~~~~~ 62 (199)
T TIGR00498 8 QQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALERKGYIERDPGK 62 (199)
T ss_pred HHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHHHCCCEecCCCC
Confidence 5678888887665 37788999999997 65544 344567997755544
No 238
>TIGR00472 pheT_bact phenylalanyl-tRNA synthetase, beta subunit, non-spirochete bacterial. Every known example of the phenylalanyl-tRNA synthetase, except the monomeric form of mitochondrial, is an alpha 2 beta 2 heterotetramer. The beta subunits break into two subfamilies that are considerably different in sequence, length, and pattern of gaps. This model represents the subfamily that includes the beta subunit from Bacteria other than spirochetes, as well as a chloroplast-encoded form from Porphyra purpurea. The chloroplast-derived sequence is considerably shorter at the amino end, however.
Probab=44.30 E-value=1.1e+02 Score=24.99 Aligned_cols=33 Identities=9% Similarity=0.387 Sum_probs=28.3
Q ss_pred cccHHHHHHHhCC--CHHHHHHHHHhcCCeEeCCC
Q 036949 16 TISTQDTALFLGM--NEDDAAYYVQQQGWTLDPAS 48 (81)
Q Consensus 16 sIs~~~~a~~Lgl--s~~e~~~~~~~~GW~~d~~~ 48 (81)
.++.+.+.++||+ +.+++.+..+..|.+++.++
T Consensus 409 ~~~~~~i~~~lG~~i~~~ei~~iL~~Lgf~~~~~~ 443 (798)
T TIGR00472 409 SLRIKKLNKILGISLSDEEVRDILKRLGFKVEKQK 443 (798)
T ss_pred EecHHHHHHHhCCccCHHHHHHHHHHCCCEEEecC
Confidence 3567889999998 89999999999999997554
No 239
>PRK14584 hmsS hemin storage system protein; Provisional
Probab=44.17 E-value=93 Score=20.59 Aligned_cols=41 Identities=17% Similarity=0.220 Sum_probs=30.7
Q ss_pred ccccHHHHHHHhCCCHHHHHHHHHhcCCeE--eCCCceEeecC
Q 036949 15 STISTQDTALFLGMNEDDAAYYVQQQGWTL--DPASRMLTVKK 55 (81)
Q Consensus 15 ~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~--d~~~~~~~p~~ 55 (81)
..++.+++|+++|++++.+.+.-+.+-=++ |..|+++-.+.
T Consensus 97 ~~l~~dElA~sF~l~~e~i~qLr~~kiltVh~De~G~Ii~V~~ 139 (153)
T PRK14584 97 PDLDDDELASSFALSPELIAQLKSGSCLTLYNDEHGHIIDVKE 139 (153)
T ss_pred CCCChHHHHHHcCCCHHHHHHHHhCCeEEEEECCCCCEEEeec
Confidence 457889999999999999988777665443 55666665544
No 240
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=44.01 E-value=73 Score=19.67 Aligned_cols=39 Identities=10% Similarity=0.104 Sum_probs=26.7
Q ss_pred HHHHHHHhcccccHHHHHHHhCCCHHHHH---HHHHhcCCeE
Q 036949 6 MFQLLMSAYSTISTQDTALFLGMNEDDAA---YYVQQQGWTL 44 (81)
Q Consensus 6 ~~~li~~AY~sIs~~~~a~~Lgls~~e~~---~~~~~~GW~~ 44 (81)
++..|...-..++..++|..+|++..-+. +-..++||..
T Consensus 36 vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~ 77 (144)
T PRK03573 36 TLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLEEKGLIS 77 (144)
T ss_pred HHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHHCCCEe
Confidence 34444443346789999999999765554 4455789986
No 241
>PF12046 DUF3529: Protein of unknown function (DUF3529); InterPro: IPR021919 This family of proteins is functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 176 to 190 amino acids in length.
Probab=43.97 E-value=43 Score=22.63 Aligned_cols=26 Identities=12% Similarity=0.312 Sum_probs=18.8
Q ss_pred HHHHHHHHhcCCeEeC---CCceEeecCC
Q 036949 31 DDAAYYVQQQGWTLDP---ASRMLTVKKQ 56 (81)
Q Consensus 31 ~e~~~~~~~~GW~~d~---~~~~~~p~~~ 56 (81)
+++.+|.++|||.+.+ +++.+.-...
T Consensus 47 ~~l~~yf~~r~y~v~~~d~~~~~itFeG~ 75 (173)
T PF12046_consen 47 EQLKAYFEQRNYRVAEGDAEGEVITFEGF 75 (173)
T ss_pred HHHHHHHHhcCceecccCccccEEEEEEE
Confidence 5678899999999865 6656555433
No 242
>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=43.93 E-value=69 Score=19.01 Aligned_cols=46 Identities=13% Similarity=0.192 Sum_probs=28.6
Q ss_pred cHHHHHHHhCCCHHHHHHHHHhcCCeEeCCCceEeecCCCCcccCCC-ChhHHHHHH
Q 036949 18 STQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVTEQKL-DPSKMQCLT 73 (81)
Q Consensus 18 s~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~~~~~p~~~~~~~~~~~-~~~~l~~Lt 73 (81)
++.++|.++|+|..-+.-|-. .|.+ |.+......-.. +++++..|-
T Consensus 2 ~i~e~A~~~gvs~~tlR~Ye~--------~Gll--~~~~r~~~g~R~Y~~~~v~~l~ 48 (99)
T cd04772 2 RTVDLARAIGLSPQTVRNYES--------LGLI--PPAERTANGYRIYTDKHIAALR 48 (99)
T ss_pred CHHHHHHHHCcCHHHHHHHHH--------cCCC--CCCCcCCCCCeecCHHHHHHHH
Confidence 578999999999999987643 2332 322222222222 777777763
No 243
>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=43.74 E-value=72 Score=19.18 Aligned_cols=49 Identities=12% Similarity=0.141 Sum_probs=30.6
Q ss_pred cHHHHHHHhCCCHHHHHHHHHhcCCeEeCCCceEeecCCCCcccCCC-ChhHHHHHHhHH
Q 036949 18 STQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVTEQKL-DPSKMQCLTEYV 76 (81)
Q Consensus 18 s~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~~~~~p~~~~~~~~~~~-~~~~l~~Lt~~v 76 (81)
++.++|.++|+|..-+.-|-.. | . +|.++.+...--. +..++..|..+.
T Consensus 2 ~i~e~a~~~gvs~~tlr~ye~~--------g-l-l~~~~r~~~gyR~Y~~~~l~~l~~I~ 51 (113)
T cd01109 2 TIKEVAEKTGLSADTLRYYEKE--------G-L-LPPVKRDENGIRDFTEEDLEWLEFIK 51 (113)
T ss_pred CHHHHHHHHCcCHHHHHHHHHC--------C-C-CCCCCcCCCCCccCCHHHHHHHHHHH
Confidence 5789999999999999977542 2 2 2222222222222 778888775444
No 244
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=43.70 E-value=80 Score=19.69 Aligned_cols=35 Identities=14% Similarity=0.205 Sum_probs=26.5
Q ss_pred HHHhcccccHHHHHHHhCCCHHHHHHHH---HhcCCeE
Q 036949 10 LMSAYSTISTQDTALFLGMNEDDAAYYV---QQQGWTL 44 (81)
Q Consensus 10 i~~AY~sIs~~~~a~~Lgls~~e~~~~~---~~~GW~~ 44 (81)
+...-..++++++|..||++..-+...+ .+.||..
T Consensus 16 l~~~~~~~~~~ela~~l~vs~~svs~~l~~L~~~Gli~ 53 (142)
T PRK03902 16 LIEEKGYARVSDIAEALSVHPSSVTKMVQKLDKDEYLI 53 (142)
T ss_pred HHhcCCCcCHHHHHHHhCCChhHHHHHHHHHHHCCCEE
Confidence 3445567899999999999877766555 5679986
No 245
>PF08811 DUF1800: Protein of unknown function (DUF1800); InterPro: IPR014917 This is an entry of large bacterial proteins of unknown function.
Probab=43.55 E-value=61 Score=24.63 Aligned_cols=35 Identities=20% Similarity=0.329 Sum_probs=23.8
Q ss_pred CCCHHHHHHHHHhc-CCeEeCC-----CceEeecC-CCCccc
Q 036949 27 GMNEDDAAYYVQQQ-GWTLDPA-----SRMLTVKK-QPLVTE 61 (81)
Q Consensus 27 gls~~e~~~~~~~~-GW~~d~~-----~~~~~p~~-~~~~~~ 61 (81)
|.+++|+.+++.-. ||+++.. +.+.+... -++..+
T Consensus 196 GYtq~DV~e~AR~lTGw~~~~~~~~~~~~~~f~~~~HD~g~K 237 (462)
T PF08811_consen 196 GYTQQDVKEAARALTGWTVDDARGNDTGMFVFRPNRHDPGEK 237 (462)
T ss_pred CcCHHHHHHHHHHHhCCcccCCCCCCCCCeeecccccCCCCc
Confidence 46889999999987 9999862 34554443 444443
No 246
>PF03752 ALF: Short repeats of unknown function; InterPro: IPR005506 This set of repeats is found in a small family of secreted proteins of no known function, which may be involved in signal transduction.
Probab=43.42 E-value=47 Score=16.95 Aligned_cols=39 Identities=15% Similarity=0.161 Sum_probs=24.4
Q ss_pred HHHHHHHHHHhcccccHHHHHHHh-CCCHHHHHHHHHhcCCe
Q 036949 3 TKRMFQLLMSAYSTISTQDTALFL-GMNEDDAAYYVQQQGWT 43 (81)
Q Consensus 3 R~~~~~li~~AY~sIs~~~~a~~L-gls~~e~~~~~~~~GW~ 43 (81)
|..+++++......+.-. +..-| .=+++++.+|... ||.
T Consensus 1 R~~v~~l~~~gG~~vr~A-A~~AL~~G~~~~l~~FL~~-G~~ 40 (43)
T PF03752_consen 1 RVAVVQLLASGGPAVRAA-AQAALDAGTPEALREFLET-GQY 40 (43)
T ss_pred CHHHHHHHHcCCHHHHHH-HHHHHHhCCHHHHHHHHHH-hHH
Confidence 556777777775554443 34444 3388888888774 664
No 247
>cd08315 Death_TRAILR_DR4_DR5 Death domain of Tumor necrosis factor-Related Apoptosis-Inducing Ligand Receptors. Death Domain (DD) found in Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL) Receptors. In mammals, this family includes TRAILR1 (also called DR4 or TNFRSF10A) and TRAILR2 (also called DR5, TNFRSF10B, or KILLER). They function as receptors for the cytokine TRAIL and are involved in apoptosis signaling pathways. TRAIL preferentially induces apoptosis in cancer cells while exhibiting little toxicity in normal cells. 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 adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=43.14 E-value=55 Score=19.62 Aligned_cols=21 Identities=19% Similarity=0.142 Sum_probs=16.7
Q ss_pred cHHHHHHHhCCCHHHHHHHHH
Q 036949 18 STQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 18 s~~~~a~~Lgls~~e~~~~~~ 38 (81)
....+++-||||+.++...-.
T Consensus 21 ~Wk~laR~LGLse~~I~~i~~ 41 (96)
T cd08315 21 SWNRLMRQLGLSENEIDVAKA 41 (96)
T ss_pred HHHHHHHHcCCCHHHHHHHHH
Confidence 366799999999999876544
No 248
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares 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=42.84 E-value=74 Score=19.07 Aligned_cols=48 Identities=13% Similarity=0.146 Sum_probs=30.0
Q ss_pred cHHHHHHHhCCCHHHHHHHHHhcCCeEeCCCceEeecCCCCcccCCC-ChhHHHHHHh
Q 036949 18 STQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVTEQKL-DPSKMQCLTE 74 (81)
Q Consensus 18 s~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~~~~~p~~~~~~~~~~~-~~~~l~~Lt~ 74 (81)
++.++|+++|+|..-+.-|... | ++.|.....+..--. +++++..|..
T Consensus 2 ~i~eva~~~gis~~tlR~ye~~--------G-Li~p~~~~~~ngyR~Y~~~~i~~l~~ 50 (108)
T cd01107 2 TIGEFAKLSNLSIKALRYYDKI--------G-LLKPAYVDPDTGYRYYSAEQLERLNR 50 (108)
T ss_pred CHHHHHHHHCcCHHHHHHHHHc--------C-CCCCCcCCCCCCccccCHHHHHHHHH
Confidence 5789999999999999887663 2 333432222222222 7777777643
No 249
>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=42.58 E-value=61 Score=19.53 Aligned_cols=30 Identities=7% Similarity=0.121 Sum_probs=24.9
Q ss_pred HHHhcccccHHHHHHHhCCCHHHHHHHHHh
Q 036949 10 LMSAYSTISTQDTALFLGMNEDDAAYYVQQ 39 (81)
Q Consensus 10 i~~AY~sIs~~~~a~~Lgls~~e~~~~~~~ 39 (81)
++..-.-++.+.+|.|+|-++..+.+.++.
T Consensus 6 ~~~p~d~v~~~~FA~~IGKt~sAVr~Mi~~ 35 (87)
T PF10743_consen 6 SEYPSDAVTYEKFAEYIGKTPSAVRKMIKA 35 (87)
T ss_pred HhhhccccCHHHHHHHHCCCHHHHHHHHHc
Confidence 334456789999999999999999999885
No 250
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=42.46 E-value=65 Score=22.46 Aligned_cols=36 Identities=19% Similarity=0.257 Sum_probs=28.4
Q ss_pred hHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH
Q 036949 2 YTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 2 ~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~ 38 (81)
.|++|..++.+ -..++..++|.-||+|...+.....
T Consensus 12 tr~~il~lL~~-~g~~sa~elA~~Lgis~~avR~HL~ 47 (218)
T COG2345 12 TRERILELLKK-SGPVSADELAEELGISPMAVRRHLD 47 (218)
T ss_pred HHHHHHHHHhc-cCCccHHHHHHHhCCCHHHHHHHHH
Confidence 46777766654 4678999999999999998876654
No 251
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=42.43 E-value=45 Score=19.42 Aligned_cols=24 Identities=25% Similarity=0.512 Sum_probs=20.0
Q ss_pred cHHHHHHHhCCCHHHHHHHHHhcCC
Q 036949 18 STQDTALFLGMNEDDAAYYVQQQGW 42 (81)
Q Consensus 18 s~~~~a~~Lgls~~e~~~~~~~~GW 42 (81)
++.++|..+|+++.-+..|.. .|+
T Consensus 2 ~~~eva~~~gi~~~tlr~~~~-~Gl 25 (100)
T cd00592 2 TIGEVAKLLGVSVRTLRYYEE-KGL 25 (100)
T ss_pred CHHHHHHHHCcCHHHHHHHHH-CCC
Confidence 578999999999999998865 454
No 252
>smart00351 PAX Paired Box domain.
Probab=42.33 E-value=83 Score=19.48 Aligned_cols=35 Identities=11% Similarity=0.123 Sum_probs=27.9
Q ss_pred hHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHh
Q 036949 2 YTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQ 39 (81)
Q Consensus 2 ~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~ 39 (81)
.|.+|+.+.. .-.+..++|..||+|..-+..+...
T Consensus 22 ~R~riv~~~~---~G~s~~~iA~~~gvs~~tV~kwi~r 56 (125)
T smart00351 22 ERQRIVELAQ---NGVRPCDISRQLCVSHGCVSKILGR 56 (125)
T ss_pred HHHHHHHHHH---cCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 5778877764 4568899999999999888777664
No 253
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=42.27 E-value=53 Score=18.26 Aligned_cols=42 Identities=12% Similarity=0.275 Sum_probs=26.0
Q ss_pred HHHHHHHHHHhcc----cccHHHHHHHhCC-CHHHHHHH---HHhcCCeE
Q 036949 3 TKRMFQLLMSAYS----TISTQDTALFLGM-NEDDAAYY---VQQQGWTL 44 (81)
Q Consensus 3 R~~~~~li~~AY~----sIs~~~~a~~Lgl-s~~e~~~~---~~~~GW~~ 44 (81)
+.+++..|..-+. .=++.++|..||+ |..-+..+ ..++||--
T Consensus 8 Q~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~kG~I~ 57 (65)
T PF01726_consen 8 QKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKALERKGYIR 57 (65)
T ss_dssp HHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCcCcc
Confidence 3456666555433 2477899999999 56665444 44678864
No 254
>KOG2908 consensus 26S proteasome regulatory complex, subunit RPN9/PSMD13 [Posttranslational modification, protein turnover, chaperones]
Probab=42.23 E-value=1.5e+02 Score=22.45 Aligned_cols=66 Identities=14% Similarity=0.256 Sum_probs=42.1
Q ss_pred HHHHHHHHhccc------ccHHHHHHHhCCCHHHHHHHHHh-----c-CCeEeCCCceEeecCCCCcccCCC-ChhHHHH
Q 036949 5 RMFQLLMSAYST------ISTQDTALFLGMNEDDAAYYVQQ-----Q-GWTLDPASRMLTVKKQPLVTEQKL-DPSKMQC 71 (81)
Q Consensus 5 ~~~~li~~AY~s------Is~~~~a~~Lgls~~e~~~~~~~-----~-GW~~d~~~~~~~p~~~~~~~~~~~-~~~~l~~ 71 (81)
+++.+|+-+|++ ||.+++|+.+-++.+++.=.+.+ . .|.+|.-+..+.-. ...+.+ +.+|+-+
T Consensus 277 ~LmaLiEi~F~rpa~~R~lsf~~Ia~~tkip~~eVE~LVMKAlslgLikG~Idqv~~~v~~s----wvqPRvl~~~qI~~ 352 (380)
T KOG2908|consen 277 RLLALIEITFSRPANERTLSFKEIAEATKIPNKEVELLVMKALSLGLIKGSIDQVEGVVYMS----WVQPRVLDRSQIVK 352 (380)
T ss_pred HHHHHHHHHhcCcchhccccHHHHHHHhCCCHHHHHHHHHHHHhccceeeeecccccEEEEe----cccccccCHHHHHh
Confidence 567888888887 99999999999999997655442 2 45556544443332 112222 5566655
Q ss_pred HHh
Q 036949 72 LTE 74 (81)
Q Consensus 72 Lt~ 74 (81)
+.+
T Consensus 353 Mk~ 355 (380)
T KOG2908|consen 353 MKD 355 (380)
T ss_pred HHH
Confidence 543
No 255
>KOG1464 consensus COP9 signalosome, subunit CSN2 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=42.18 E-value=50 Score=24.66 Aligned_cols=38 Identities=16% Similarity=0.201 Sum_probs=31.9
Q ss_pred hHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHh
Q 036949 2 YTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQ 39 (81)
Q Consensus 2 ~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~ 39 (81)
||..++--+-+-|+.|.+..++.-|++++.++.....+
T Consensus 350 iRTQVLlkLIkPYt~i~Ipfis~~Lnv~~~dV~~LLV~ 387 (440)
T KOG1464|consen 350 IRTQVLLKLIKPYTNIGIPFISKELNVPEADVESLLVS 387 (440)
T ss_pred HHHHHHHHHhccccccCchhhHhhcCCCHHHHHHHHHH
Confidence 56666666778999999999999999999998877654
No 256
>cd08777 Death_RIP1 Death Domain of Receptor-Interacting Protein 1. Death domain (DD) found in Receptor-Interacting Protein 1 (RIP1) and related proteins. RIP kinases serve as essential sensors of cellular stress. Vertebrates contain several types containing a homologous N-terminal kinase domain and varying C-terminal domains. RIP1 harbors a C-terminal DD, which binds death receptors (DRs) including TNF receptor 1, Fas, TNF-related apoptosis-inducing ligand receptor 1 (TRAILR1), and TRAILR2. It also interacts with other DD-containing adaptor proteins such as TRADD and FADD. RIP1 plays a crucial role in determining a cell's fate, between survival or death, following exposure to stress signals. It is important in the signaling of NF-kappaB and MAPKs, and it links DR-associated signaling to reactive oxygen species (ROS) production. Abnormal RIP1 function may result in ROS accumulation affecting inflammatory responses, innate immunity, stress responses, and cell survival. In general, DDs ar
Probab=42.10 E-value=30 Score=20.33 Aligned_cols=20 Identities=20% Similarity=0.131 Sum_probs=16.5
Q ss_pred HHHHHHHhCCCHHHHHHHHH
Q 036949 19 TQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 19 ~~~~a~~Lgls~~e~~~~~~ 38 (81)
...+|+-|||+..++..+-.
T Consensus 16 Wk~lar~LG~s~~eI~~ie~ 35 (86)
T cd08777 16 WKRCARKLGFTESEIEEIDH 35 (86)
T ss_pred HHHHHHHcCCCHHHHHHHHH
Confidence 45799999999999887654
No 257
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=41.44 E-value=1e+02 Score=20.20 Aligned_cols=40 Identities=13% Similarity=0.160 Sum_probs=28.8
Q ss_pred cccHHHHHHHhCCCHHHHHHHHH---hcCCeE---eCCCceEeecCC
Q 036949 16 TISTQDTALFLGMNEDDAAYYVQ---QQGWTL---DPASRMLTVKKQ 56 (81)
Q Consensus 16 sIs~~~~a~~Lgls~~e~~~~~~---~~GW~~---d~~~~~~~p~~~ 56 (81)
.++.+++|..+|++..-+.+... +.|+.. +++|.+ .|.++
T Consensus 25 ~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s~rG~~GGy-~Lar~ 70 (164)
T PRK10857 25 PVPLADISERQGISLSYLEQLFSRLRKNGLVSSVRGPGGGY-LLGKD 70 (164)
T ss_pred cCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCCCCCCCe-eccCC
Confidence 58999999999999877666654 559987 344555 44433
No 258
>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=41.38 E-value=63 Score=19.92 Aligned_cols=19 Identities=26% Similarity=0.441 Sum_probs=16.3
Q ss_pred cHHHHHHHhCCCHHHHHHH
Q 036949 18 STQDTALFLGMNEDDAAYY 36 (81)
Q Consensus 18 s~~~~a~~Lgls~~e~~~~ 36 (81)
++.++|+.+|+|.+-+.-|
T Consensus 1 ~I~e~a~~~gvs~~tlR~Y 19 (124)
T TIGR02051 1 TIGELAKAAGVNVETIRYY 19 (124)
T ss_pred CHHHHHHHHCcCHHHHHHH
Confidence 3678999999999988766
No 259
>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=41.30 E-value=53 Score=22.33 Aligned_cols=43 Identities=16% Similarity=0.380 Sum_probs=24.3
Q ss_pred ccccHHHHHHHhCCCHHHHHHHHHh---cCCe---EeCCCceEeecCCC
Q 036949 15 STISTQDTALFLGMNEDDAAYYVQQ---QGWT---LDPASRMLTVKKQP 57 (81)
Q Consensus 15 ~sIs~~~~a~~Lgls~~e~~~~~~~---~GW~---~d~~~~~~~p~~~~ 57 (81)
.-+.++++|.-+||+..+++..+.+ .|-- +|-.|.|++-.+..
T Consensus 112 Kvv~ledla~~f~l~t~~~i~ri~~L~~~g~ltGv~DdrGkfIyIs~eE 160 (188)
T PF09756_consen 112 KVVNLEDLAAEFGLRTQDVINRIQELEAEGRLTGVIDDRGKFIYISEEE 160 (188)
T ss_dssp SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE-----
T ss_pred ceeeHHHHHHHcCCCHHHHHHHHHHHHHCCCceeeEcCCCCeEEecHHH
Confidence 4578999999999999998877664 3553 56567787766544
No 260
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=41.25 E-value=53 Score=16.95 Aligned_cols=40 Identities=18% Similarity=0.334 Sum_probs=27.4
Q ss_pred HHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHH---HhcCCeE
Q 036949 3 TKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYV---QQQGWTL 44 (81)
Q Consensus 3 R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~---~~~GW~~ 44 (81)
+..++..+.. .. ++.++++..+|++...+...+ .+.||-.
T Consensus 9 ~~~il~~l~~-~~-~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~ 51 (78)
T cd00090 9 RLRILRLLLE-GP-LTVSELAERLGLSQSTVSRHLKKLEEAGLVE 51 (78)
T ss_pred HHHHHHHHHH-CC-cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeE
Confidence 3445555444 23 999999999999887765554 4568875
No 261
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=41.14 E-value=44 Score=17.28 Aligned_cols=21 Identities=24% Similarity=0.371 Sum_probs=16.6
Q ss_pred HHHHHHHhCCCHHHHHHHHHh
Q 036949 19 TQDTALFLGMNEDDAAYYVQQ 39 (81)
Q Consensus 19 ~~~~a~~Lgls~~e~~~~~~~ 39 (81)
...+|.-|||+...+..+...
T Consensus 30 ~~~la~~l~l~~~~V~~WF~n 50 (57)
T PF00046_consen 30 REELAKELGLTERQVKNWFQN 50 (57)
T ss_dssp HHHHHHHHTSSHHHHHHHHHH
T ss_pred cccccccccccccccccCHHH
Confidence 455888999999998887654
No 262
>PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional
Probab=41.01 E-value=47 Score=26.10 Aligned_cols=40 Identities=13% Similarity=0.149 Sum_probs=28.6
Q ss_pred HHHHHHHHHhccc---ccHHHHHHHhCCCHHHHHHHHHhcCCe
Q 036949 4 KRMFQLLMSAYST---ISTQDTALFLGMNEDDAAYYVQQQGWT 43 (81)
Q Consensus 4 ~~~~~li~~AY~s---Is~~~~a~~Lgls~~e~~~~~~~~GW~ 43 (81)
++|++.|-+-+.. .++.++|...|.|+.-+..||++.|-.
T Consensus 359 ~~IA~yIl~n~~~v~~~si~eLA~~~~vS~aTV~Rf~kkLGf~ 401 (638)
T PRK14101 359 RRVADLALNHPRSIINDPIVDIARKADVSQPTVIRFCRSLGCQ 401 (638)
T ss_pred HHHHHHHHhCHHHHHhccHHHHHHHhCCCHHHHHHHHHHhCCC
Confidence 4556666555544 477888888888888888888887654
No 263
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=40.97 E-value=78 Score=18.79 Aligned_cols=33 Identities=9% Similarity=0.054 Sum_probs=26.3
Q ss_pred HHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH
Q 036949 3 TKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 3 R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~ 38 (81)
|.+++.++.+- ++..++|..||+|..-+..+..
T Consensus 40 R~~I~~ll~~G---~S~~eIA~~LgISrsTIyRi~R 72 (88)
T TIGR02531 40 RLQVAKMLKQG---KTYSDIEAETGASTATISRVKR 72 (88)
T ss_pred HHHHHHHHHCC---CCHHHHHHHHCcCHHHHHHHHH
Confidence 66777777765 5899999999999988887554
No 264
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=40.91 E-value=51 Score=16.67 Aligned_cols=33 Identities=18% Similarity=0.215 Sum_probs=17.9
Q ss_pred HHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH
Q 036949 3 TKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 3 R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~ 38 (81)
|..|..+.. .-.|...+|..||.+..-+-..+.
T Consensus 10 R~~I~~l~~---~G~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 10 RNQIEALLE---QGMSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp --HHHHHHC---S---HHHHHHHTT--HHHHHHHHH
T ss_pred HHHHHHHHH---cCCCHHHHHHHHCcCcHHHHHHHh
Confidence 455555554 447888899999998876665543
No 265
>PF12643 MazG-like: MazG-like family
Probab=40.87 E-value=67 Score=19.48 Aligned_cols=32 Identities=13% Similarity=0.213 Sum_probs=23.0
Q ss_pred hHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHh
Q 036949 2 YTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQ 39 (81)
Q Consensus 2 ~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~ 39 (81)
+.+.+++.|--+| -+|+-||++..++.+.+.+
T Consensus 37 i~deLAdvii~~y------lLa~rLGid~~~lD~~i~~ 68 (98)
T PF12643_consen 37 IKDELADVIIYCY------LLADRLGIDFRELDEIIKE 68 (98)
T ss_pred HHHHHHHHHHHHH------HHHHHhCCCHHHHHHHHHH
Confidence 4556666666666 4999999997777776664
No 266
>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=40.82 E-value=46 Score=19.88 Aligned_cols=50 Identities=18% Similarity=0.197 Sum_probs=31.0
Q ss_pred cHHHHHHHhCCCHHHHHHHHHhcCCeEeCCCceEeecCCCCcccCCC-ChhHHHHHHhHHH
Q 036949 18 STQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVTEQKL-DPSKMQCLTEYVF 77 (81)
Q Consensus 18 s~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~~~~~p~~~~~~~~~~~-~~~~l~~Lt~~v~ 77 (81)
++.++|..+|+|+.-+..|...-| .+.|.. ....-.. +.+++..|-.+..
T Consensus 2 ti~EvA~~~gVs~~tLR~ye~~~g--------li~p~r--~~~g~R~Yt~~di~~l~~I~~ 52 (99)
T cd04765 2 SIGEVAEILGLPPHVLRYWETEFP--------QLKPVK--RAGGRRYYRPKDVELLLLIKH 52 (99)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHcC--------CCCCcC--CCCCCeeeCHHHHHHHHHHHH
Confidence 578999999999999998765412 122221 1112222 7777777766554
No 267
>cd08317 Death_ank Death domain associated with Ankyrins. Death Domain (DD) associated with Ankyrins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. Ankyrins function as adaptor proteins and they interact, through ANK repeats, with structurally diverse membrane proteins, including ion channels/pumps, calcium release channels, and cell adhesion molecules. They play critical roles in the proper expression and membrane localization of these proteins. In mammals, this family includes ankyrin-R for restricted (or ANK1), ankyrin-B for broadly expressed (or ANK2) and ankyrin-G for general or giant (or ANK3). They are expressed in different combinations in many tissues and play non-overlapping functions. 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-associati
Probab=40.80 E-value=40 Score=19.41 Aligned_cols=22 Identities=23% Similarity=0.132 Sum_probs=17.2
Q ss_pred ccHHHHHHHhCCCHHHHHHHHH
Q 036949 17 ISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 17 Is~~~~a~~Lgls~~e~~~~~~ 38 (81)
.....+|+.|||+..++..+-.
T Consensus 16 ~dW~~LAr~Lg~~~~dI~~i~~ 37 (84)
T cd08317 16 SDWPQLARELGVSETDIDLIKA 37 (84)
T ss_pred hHHHHHHHHcCCCHHHHHHHHH
Confidence 3456799999999988877654
No 268
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=40.76 E-value=56 Score=17.08 Aligned_cols=38 Identities=16% Similarity=0.222 Sum_probs=31.1
Q ss_pred ChHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH
Q 036949 1 LYTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 1 ~~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~ 38 (81)
++.++++-.+-+--...+..++|...|+|..-+..++.
T Consensus 4 s~~d~lll~L~~LR~~~~~~~La~~FgIs~stvsri~~ 41 (53)
T PF13613_consen 4 SLEDQLLLTLMYLRLNLTFQDLAYRFGISQSTVSRIFH 41 (53)
T ss_pred CHHHHHHHHHHHHHcCCcHhHHhhheeecHHHHHHHHH
Confidence 35677888888888889999999999999888776654
No 269
>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=40.75 E-value=33 Score=18.47 Aligned_cols=30 Identities=13% Similarity=0.189 Sum_probs=21.3
Q ss_pred ccc-cHHHHHHHhCCCHHHH---HHHHHhcCCeE
Q 036949 15 STI-STQDTALFLGMNEDDA---AYYVQQQGWTL 44 (81)
Q Consensus 15 ~sI-s~~~~a~~Lgls~~e~---~~~~~~~GW~~ 44 (81)
+.+ +..++|..+|+|..-+ .....+.||-.
T Consensus 22 ~~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~ 55 (64)
T PF00392_consen 22 DRLPSERELAERYGVSRTTVREALRRLEAEGLIE 55 (64)
T ss_dssp SBE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred CEeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEE
Confidence 478 9999999999976554 45556778874
No 270
>COG5340 Predicted transcriptional regulator [Transcription]
Probab=40.65 E-value=53 Score=23.49 Aligned_cols=49 Identities=18% Similarity=0.244 Sum_probs=34.9
Q ss_pred HHHHhcccccHHHHHHHhCCCHHHHHHHHH---hcCCeEeC-CCceEeecCCC
Q 036949 9 LLMSAYSTISTQDTALFLGMNEDDAAYYVQ---QQGWTLDP-ASRMLTVKKQP 57 (81)
Q Consensus 9 li~~AY~sIs~~~~a~~Lgls~~e~~~~~~---~~GW~~d~-~~~~~~p~~~~ 57 (81)
+..+.-.-|++.++|..+|++++.+...+. ++||-.-- .|.++++.-|.
T Consensus 23 laae~hkiiTirdvae~~ev~~n~lr~lasrLekkG~LeRi~rG~YlI~~lpa 75 (269)
T COG5340 23 LAAEGHKIITIRDVAETLEVAPNTLRELASRLEKKGWLERILRGRYLIIPLPA 75 (269)
T ss_pred HHHHhCceEEeHHhhhhccCCHHHHHHHHhhhhhcchhhhhcCccEEEeecCC
Confidence 444555678999999999999999888765 57997321 45666655444
No 271
>cd06577 PASTA_pknB PASTA domain of bacterial serine/threonine kinase pknB-like proteins. PknB is a member of a group of related transmembrane sensor kinases present in many gram positive bacteria, which has been shown to regulate cell shape in Mycobacterium tubercolosis. PknB is a receptor-like transmembrane protein with an extracellular signal sensor domain (containing multiple PASTA domains) and an intracellular, eukaryotic serine/threonine kinase-like domain. The PASTA domain is found at the C-termini of several Penicillin-binding proteins (PBPs) and bacterial serine/threonine kinases. The name PASTA is derived from PBP and Serine/Threonine kinase Associated domain.
Probab=40.48 E-value=50 Score=16.47 Aligned_cols=22 Identities=23% Similarity=0.342 Sum_probs=19.0
Q ss_pred HHhCCCHHHHHHHHHhcCCeEe
Q 036949 24 LFLGMNEDDAAYYVQQQGWTLD 45 (81)
Q Consensus 24 ~~Lgls~~e~~~~~~~~GW~~d 45 (81)
.+.|++.+++.+...+.||.+.
T Consensus 4 ~~~g~~~~~a~~~l~~~g~~~~ 25 (62)
T cd06577 4 DVVGMTLDEAKAALEAAGLKVG 25 (62)
T ss_pred CcCCCCHHHHHHHHHHCCCcee
Confidence 3568899999999999999986
No 272
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.
Probab=40.45 E-value=97 Score=20.57 Aligned_cols=40 Identities=15% Similarity=0.216 Sum_probs=29.4
Q ss_pred HHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH---hcCCeEe
Q 036949 5 RMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ---QQGWTLD 45 (81)
Q Consensus 5 ~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~---~~GW~~d 45 (81)
+++..+.+ ...++..++|..+|+|..-+..... +.||-.-
T Consensus 147 ~IL~~l~~-~g~~s~~eia~~l~is~stv~r~L~~Le~~GlI~r 189 (203)
T TIGR01884 147 KVLEVLKA-EGEKSVKNIAKKLGKSLSTISRHLRELEKKGLVEQ 189 (203)
T ss_pred HHHHHHHH-cCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence 56666654 4679999999999998876655544 5699853
No 273
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=40.44 E-value=74 Score=22.14 Aligned_cols=35 Identities=11% Similarity=0.098 Sum_probs=24.7
Q ss_pred HHHHHHHHhc-ccccHHHHHHHhCCCHHHHHHHHHh
Q 036949 5 RMFQLLMSAY-STISTQDTALFLGMNEDDAAYYVQQ 39 (81)
Q Consensus 5 ~~~~li~~AY-~sIs~~~~a~~Lgls~~e~~~~~~~ 39 (81)
++.+.|..-+ ..++++++|..+|+|.--+....++
T Consensus 9 ~~~~~i~~~~~~~~~l~~lA~~~~~S~~~l~r~F~~ 44 (289)
T PRK15121 9 DLLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKD 44 (289)
T ss_pred HHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 4555555554 4599999999999998776555443
No 274
>PF04963 Sigma54_CBD: Sigma-54 factor, core binding domain; InterPro: IPR007046 This domain makes a direct interaction with the core RNA polymerase, to form an enhancer dependent holoenzyme []. The centre of this domain contains a very weak similarity to a helix-turn-helix motif, which may represent a DNA binding domain.; GO: 0003677 DNA binding, 0006352 transcription initiation, DNA-dependent; PDB: 2K9L_A 2K9M_A.
Probab=40.32 E-value=21 Score=23.93 Aligned_cols=37 Identities=27% Similarity=0.359 Sum_probs=25.9
Q ss_pred HHhcccccHHHHHHHhCCCHHHHHHHHHhcCCeEeCCC
Q 036949 11 MSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPAS 48 (81)
Q Consensus 11 ~~AY~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~ 48 (81)
++-|=.++++++|..+|++.+++.+...... ++||.|
T Consensus 47 ~~GyL~~~~~eia~~l~~~~~~v~~~l~~lQ-~leP~G 83 (194)
T PF04963_consen 47 DDGYLTESLEEIAEELGVSEEEVEKALELLQ-SLEPAG 83 (194)
T ss_dssp TTSTCSS-HHHHHHHCTS-HHHHHHHHHHHH-TTSS--
T ss_pred CCCccCCCHHHHHHHhCCCHHHHHHHHHHHH-cCCCCc
Confidence 4678899999999999999999877765432 467665
No 275
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=40.30 E-value=67 Score=17.87 Aligned_cols=40 Identities=15% Similarity=0.238 Sum_probs=28.4
Q ss_pred HHHHHHHHHhcccccHHHHHHHhCCCHHHHHHH---HHhcCCeE
Q 036949 4 KRMFQLLMSAYSTISTQDTALFLGMNEDDAAYY---VQQQGWTL 44 (81)
Q Consensus 4 ~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~---~~~~GW~~ 44 (81)
-.++.+|.. -..++..+++..++++...+... ..++||-.
T Consensus 13 ~~il~~l~~-~~~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~ 55 (101)
T smart00347 13 FLVLRILYE-EGPLSVSELAKRLGVSPSTVTRVLDRLEKKGLIR 55 (101)
T ss_pred HHHHHHHHH-cCCcCHHHHHHHHCCCchhHHHHHHHHHHCCCeE
Confidence 345666654 34689999999999976655444 45679986
No 276
>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=40.00 E-value=50 Score=19.58 Aligned_cols=25 Identities=20% Similarity=0.283 Sum_probs=20.2
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHhcCC
Q 036949 17 ISTQDTALFLGMNEDDAAYYVQQQGW 42 (81)
Q Consensus 17 Is~~~~a~~Lgls~~e~~~~~~~~GW 42 (81)
.++.++|..+|+|..-+..|.. .|+
T Consensus 2 ~~i~eva~~~gVs~~tLR~ye~-~Gl 26 (98)
T cd01279 2 YPISVAAELLGIHPQTLRVYDR-LGL 26 (98)
T ss_pred cCHHHHHHHHCcCHHHHHHHHH-CCC
Confidence 3688999999999999998754 443
No 277
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=39.62 E-value=77 Score=20.40 Aligned_cols=33 Identities=15% Similarity=0.216 Sum_probs=24.9
Q ss_pred HHHHHHHhcccccHHH---HHHHhCCCHHHHHHHHH
Q 036949 6 MFQLLMSAYSTISTQD---TALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 6 ~~~li~~AY~sIs~~~---~a~~Lgls~~e~~~~~~ 38 (81)
++..+-..|.-|+.+. +|+.||++..++...++
T Consensus 27 ~L~~vQ~~~g~ip~~~~~~iA~~l~v~~~~v~~v~t 62 (154)
T PRK07539 27 ALKIVQEQRGWVPDEAIEAVADYLGMPAIDVEEVAT 62 (154)
T ss_pred HHHHHHHHhCCCCHHHHHHHHHHhCcCHHHHHHHHH
Confidence 4566777888888765 88999998888766554
No 278
>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=39.56 E-value=44 Score=19.39 Aligned_cols=21 Identities=10% Similarity=0.324 Sum_probs=18.0
Q ss_pred cHHHHHHHhCCCHHHHHHHHH
Q 036949 18 STQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 18 s~~~~a~~Lgls~~e~~~~~~ 38 (81)
++.++|+++|++...+.-|..
T Consensus 3 ti~evA~~~gvs~~tLR~ye~ 23 (88)
T cd01105 3 GIGEVSKLTGVSPRQLRYWEE 23 (88)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 678999999999999987743
No 279
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=39.42 E-value=85 Score=20.92 Aligned_cols=35 Identities=9% Similarity=0.169 Sum_probs=26.4
Q ss_pred HHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHh
Q 036949 4 KRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQ 39 (81)
Q Consensus 4 ~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~ 39 (81)
.+++.++-+ -..++-+++|..||++.+++.+.+.+
T Consensus 25 ~~Vl~~L~~-~g~~tdeeLA~~Lgi~~~~VRk~L~~ 59 (178)
T PRK06266 25 FEVLKALIK-KGEVTDEEIAEQTGIKLNTVRKILYK 59 (178)
T ss_pred hHHHHHHHH-cCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 455555442 23699999999999999999888664
No 280
>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=39.35 E-value=36 Score=23.85 Aligned_cols=32 Identities=13% Similarity=0.325 Sum_probs=23.9
Q ss_pred cccccHHHHHHHhCCCHHHH-----------HHHHHhcCCeEe
Q 036949 14 YSTISTQDTALFLGMNEDDA-----------AYYVQQQGWTLD 45 (81)
Q Consensus 14 Y~sIs~~~~a~~Lgls~~e~-----------~~~~~~~GW~~d 45 (81)
|...+..++|..||+|..-+ .+...+.||.++
T Consensus 240 ~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l~~~~~~~~ 282 (285)
T TIGR02394 240 YEPATLEEVAAEVGLTRERVRQIQVEALKKLRRILERDGVDRE 282 (285)
T ss_pred CCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhhhhh
Confidence 67889999999999988654 334455677765
No 281
>smart00513 SAP Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation.
Probab=39.32 E-value=34 Score=16.46 Aligned_cols=19 Identities=5% Similarity=0.170 Sum_probs=16.1
Q ss_pred CCCHHHHHHHHHhcCCeEe
Q 036949 27 GMNEDDAAYYVQQQGWTLD 45 (81)
Q Consensus 27 gls~~e~~~~~~~~GW~~d 45 (81)
.|+.+++.++|..+||...
T Consensus 3 ~l~~~~Lk~~l~~~gl~~~ 21 (35)
T smart00513 3 KLKVSELKDELKKRGLSTS 21 (35)
T ss_pred cCcHHHHHHHHHHcCCCCC
Confidence 4678999999999999863
No 282
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=39.32 E-value=47 Score=16.90 Aligned_cols=22 Identities=23% Similarity=0.410 Sum_probs=17.3
Q ss_pred HHHHHHHhCCCHHHHHHHHHhc
Q 036949 19 TQDTALFLGMNEDDAAYYVQQQ 40 (81)
Q Consensus 19 ~~~~a~~Lgls~~e~~~~~~~~ 40 (81)
...+|.-+|++..++..+...+
T Consensus 30 ~~~la~~~~l~~~qV~~WF~nr 51 (56)
T smart00389 30 REELAAKLGLSERQVKVWFQNR 51 (56)
T ss_pred HHHHHHHHCcCHHHHHHhHHHH
Confidence 5668888999988888876643
No 283
>PRK15044 transcriptional regulator SirC; Provisional
Probab=39.17 E-value=91 Score=22.73 Aligned_cols=38 Identities=13% Similarity=0.181 Sum_probs=29.2
Q ss_pred HHHHHHHHHhcc-cccHHHHHHHhCCCHHHHHHHHHhcC
Q 036949 4 KRMFQLLMSAYS-TISTQDTALFLGMNEDDAAYYVQQQG 41 (81)
Q Consensus 4 ~~~~~li~~AY~-sIs~~~~a~~Lgls~~e~~~~~~~~G 41 (81)
+++.+.|..-|. .++++++|..+|+|+.-+.....+.|
T Consensus 195 ~kV~~~I~~nl~~~~SLeeLA~~lgmS~~tL~R~Fk~eg 233 (295)
T PRK15044 195 EKVYNIIISDLTRKWSQAEVAGKLFMSVSSLKRKLAAEE 233 (295)
T ss_pred HHHHHHHHhCcccCCCHHHHHHHhCCCHHHHHHHHHHcC
Confidence 455565555554 68999999999999999988777654
No 284
>KOG1860 consensus Nuclear protein export factor [Intracellular trafficking, secretion, and vesicular transport; Cell cycle control, cell division, chromosome partitioning]
Probab=39.13 E-value=1.1e+02 Score=25.87 Aligned_cols=56 Identities=9% Similarity=0.097 Sum_probs=43.4
Q ss_pred ChHHHHHHHHHHhccc----ccHHHHHHHhCC-CHHHHHHHHHhcCCeEeCCCceEeecCC
Q 036949 1 LYTKRMFQLLMSAYST----ISTQDTALFLGM-NEDDAAYYVQQQGWTLDPASRMLTVKKQ 56 (81)
Q Consensus 1 ~~R~~~~~li~~AY~s----Is~~~~a~~Lgl-s~~e~~~~~~~~GW~~d~~~~~~~p~~~ 56 (81)
++|.-....++.+|.+ |.+..+..+|++ +.+++..++.-+|=+++.+...+.+.+.
T Consensus 367 ~ir~~al~~~~~~~~~~~~~vp~~~l~~~l~f~~~e~~~~~~~~y~Leis~~~~~~~~~~~ 427 (927)
T KOG1860|consen 367 DIRWAALRAMSHAYNSKHVPVPLGKLDRILLFDGEEELKVVCNYYGLEISVDDKIVLSIGC 427 (927)
T ss_pred HHHHHHHHHHHHHHhccCCCcchhHHHHHHhcCChhhhHhhhhheeeEeeccccccccccC
Confidence 3567777888888865 788899999999 7899999999999999755444444433
No 285
>PF02943 FeThRed_B: Ferredoxin thioredoxin reductase catalytic beta chain; InterPro: IPR004209 Ferredoxin thioredoxin reductase is a [4FE-4S] protein present in organisms performing oxygenic photosynthesis, and plays an important role in the ferredoxin/thioredoxin regulatory chain. It converts an electron signal (photoreduced ferredoxin) to a thiol signal (reduced thioredoxin), regulating enzymes by reduction of specific disulphide groups. It catalyses the light-dependent activation of several photosynthetis enzymes. Ferredoxin thioredoxin reductase is a heterodimer of subunit alpha and subunit beta. Subunit alpha is the variable subunit, and beta is the catalytic chain []. The structure of the beta subunit has been determined and found to fold around the FeS cluster [].; GO: 0008937 ferredoxin-NAD(P) reductase activity, 0055114 oxidation-reduction process; PDB: 2PUK_E 2PVD_A 2PVG_A 2PUO_A 2PU9_A 1DJ7_A 2PVO_A.
Probab=39.13 E-value=23 Score=22.00 Aligned_cols=19 Identities=21% Similarity=0.527 Sum_probs=12.6
Q ss_pred HHHHHHHhcCCeEeCCCce
Q 036949 32 DAAYYVQQQGWTLDPASRM 50 (81)
Q Consensus 32 e~~~~~~~~GW~~d~~~~~ 50 (81)
-+..++.+.||.+++|..+
T Consensus 9 ~~~~~a~~~G~~~NpD~~~ 27 (108)
T PF02943_consen 9 FLEKYAEKSGYKLNPDEEV 27 (108)
T ss_dssp HHHHHHHHTT-B-BSSHHH
T ss_pred HHHHHHHHhCCEECCCHHH
Confidence 3567788899999988544
No 286
>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=39.11 E-value=55 Score=17.93 Aligned_cols=29 Identities=21% Similarity=0.235 Sum_probs=23.6
Q ss_pred hcccccHHHHHHHhCCCHHHHHHHHHhcC
Q 036949 13 AYSTISTQDTALFLGMNEDDAAYYVQQQG 41 (81)
Q Consensus 13 AY~sIs~~~~a~~Lgls~~e~~~~~~~~G 41 (81)
++-=+|...+++-||.|..-+...+.+.|
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 44557888999999999998888877654
No 287
>TIGR00471 pheT_arch phenylalanyl-tRNA synthetase, beta subunit. Every known example of the phenylalanyl-tRNA synthetase, except the monomeric form of mitochondrial, is an alpha 2 beta 2 heterotetramer. The beta subunits break into two subfamilies that are considerably different in sequence, length, and pattern of gaps. This model represents the subfamily that includes the beta subunit from eukaryotic cytosol, the Archaea, and spirochetes.
Probab=38.99 E-value=1.2e+02 Score=23.61 Aligned_cols=33 Identities=15% Similarity=0.221 Sum_probs=27.8
Q ss_pred cccHHHHHHHhCC--CHHHHHHHHHhcCCeEeCCC
Q 036949 16 TISTQDTALFLGM--NEDDAAYYVQQQGWTLDPAS 48 (81)
Q Consensus 16 sIs~~~~a~~Lgl--s~~e~~~~~~~~GW~~d~~~ 48 (81)
.++.+.+.++||+ +.+++.+.....|..+..++
T Consensus 281 ~~~~~~i~~~lG~~l~~~ei~~iL~~Lg~~v~~~~ 315 (551)
T TIGR00471 281 EVSVEYINSLLGLNLSADEIAHSLKKMRLDAVQSD 315 (551)
T ss_pred EecHHHHHHHhCCCCCHHHHHHHHHHhCCCeEecC
Confidence 4677889999998 88999999999999985443
No 288
>PRK05472 redox-sensing transcriptional repressor Rex; Provisional
Probab=38.89 E-value=70 Score=21.39 Aligned_cols=33 Identities=18% Similarity=0.220 Sum_probs=24.0
Q ss_pred HHHHHHHHHHh-cccccHHHHHHHhCCCHHHHHH
Q 036949 3 TKRMFQLLMSA-YSTISTQDTALFLGMNEDDAAY 35 (81)
Q Consensus 3 R~~~~~li~~A-Y~sIs~~~~a~~Lgls~~e~~~ 35 (81)
+.+|+..+... -..|+.+++|.++|+++..+..
T Consensus 18 ~~~il~~l~~~~~~~vs~~~L~~~~~v~~~tirr 51 (213)
T PRK05472 18 YYRYLKELKEEGVERVSSKELAEALGVDSAQIRK 51 (213)
T ss_pred HHHHHHHHHHcCCcEEeHHHHHHHhCcCHHHHHH
Confidence 45666666553 2489999999999998865533
No 289
>PHA01976 helix-turn-helix protein
Probab=38.88 E-value=46 Score=17.74 Aligned_cols=23 Identities=9% Similarity=-0.003 Sum_probs=17.6
Q ss_pred cccccHHHHHHHhCCCHHHHHHH
Q 036949 14 YSTISTQDTALFLGMNEDDAAYY 36 (81)
Q Consensus 14 Y~sIs~~~~a~~Lgls~~e~~~~ 36 (81)
-..++..++|..+|++..-+-.+
T Consensus 13 ~~glt~~~lA~~~gvs~~~v~~~ 35 (67)
T PHA01976 13 ARAWSAPELSRRAGVRHSLIYDF 35 (67)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHH
Confidence 35588899999999987766643
No 290
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=38.50 E-value=1.1e+02 Score=19.69 Aligned_cols=53 Identities=11% Similarity=-0.016 Sum_probs=35.7
Q ss_pred HHHHHHHhccc-ccHHHHHHHhCCCHHHHHHHHH---hcCCeE---eCCCceEeecCCCC
Q 036949 6 MFQLLMSAYST-ISTQDTALFLGMNEDDAAYYVQ---QQGWTL---DPASRMLTVKKQPL 58 (81)
Q Consensus 6 ~~~li~~AY~s-Is~~~~a~~Lgls~~e~~~~~~---~~GW~~---d~~~~~~~p~~~~~ 58 (81)
++-.++..... ++..++|..+|+|..=+.+... +.||.- ++.|.+..-++|..
T Consensus 13 ~L~~LA~~~~~~~s~~eIA~~~~is~~~L~kIl~~L~~aGlv~S~rG~~GGy~La~~p~e 72 (153)
T PRK11920 13 MLMYCAANDGKLSRIPEIARAYGVSELFLFKILQPLVEAGLVETVRGRNGGVRLGRPAAD 72 (153)
T ss_pred HHHHHHhCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeecCCCCCeeecCCHHH
Confidence 34445444444 7899999999999987777755 459875 33466666665543
No 291
>PF07381 DUF1495: Winged helix DNA-binding domain (DUF1495); InterPro: IPR010863 This family consists of several hypothetical archaeal proteins of around 110 residues in length. The function of this family is unknown, although one sequence (Q8U3W1 from SWISSPROT) is described as a putative HTH transcription regulator.
Probab=38.33 E-value=90 Score=18.74 Aligned_cols=44 Identities=16% Similarity=0.228 Sum_probs=35.6
Q ss_pred hHHHHHHHHHHhc-ccccHHHHHHHhCCCHHHHHHHHHhcCCeEe
Q 036949 2 YTKRMFQLLMSAY-STISTQDTALFLGMNEDDAAYYVQQQGWTLD 45 (81)
Q Consensus 2 ~R~~~~~li~~AY-~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~d 45 (81)
+|.+++..+-+.| ....+.++|+..|.+...+.-....-|=.++
T Consensus 10 ~R~~vl~~L~~~yp~~~~~~eIar~v~~~~snV~GaL~G~g~rY~ 54 (90)
T PF07381_consen 10 VRKKVLEYLCSIYPEPAYPSEIARSVGSDYSNVLGALRGDGKRYN 54 (90)
T ss_pred HHHHHHHHHHHcCCCcCCHHHHHHHHCCCHHHHHHHHhcCCCCcC
Confidence 6899999999995 5678899999999999998877665554443
No 292
>PF11625 DUF3253: Protein of unknown function (DUF3253); InterPro: IPR021660 This bacterial family of proteins has no known function. ; PDB: 2NS0_A.
Probab=38.12 E-value=49 Score=19.70 Aligned_cols=27 Identities=26% Similarity=0.283 Sum_probs=18.7
Q ss_pred hHHHHHHHHHHh--cccccHHHHHHHhCC
Q 036949 2 YTKRMFQLLMSA--YSTISTQDTALFLGM 28 (81)
Q Consensus 2 ~R~~~~~li~~A--Y~sIs~~~~a~~Lgl 28 (81)
+++-|+.++++. =.+|+++++|+.|+=
T Consensus 8 l~~~Il~ll~~R~~~ktiCPSevARal~~ 36 (83)
T PF11625_consen 8 LEAAILALLAARGPGKTICPSEVARALGP 36 (83)
T ss_dssp HHHHHHHHHHHS-TT--B-HHHHHHHH-T
T ss_pred HHHHHHHHHHhcCCCCccCHHHHHHHHCc
Confidence 567788888865 479999999999964
No 293
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=37.99 E-value=66 Score=20.23 Aligned_cols=23 Identities=35% Similarity=0.317 Sum_probs=18.8
Q ss_pred HhcccccHHHHHHHhCCCHHHHH
Q 036949 12 SAYSTISTQDTALFLGMNEDDAA 34 (81)
Q Consensus 12 ~AY~sIs~~~~a~~Lgls~~e~~ 34 (81)
+-|...+..++|..||+|..-+.
T Consensus 130 ~~~~g~s~~EIA~~lgis~~tV~ 152 (173)
T PRK09645 130 SYYRGWSTAQIAADLGIPEGTVK 152 (173)
T ss_pred HHHcCCCHHHHHHHHCcCHHHHH
Confidence 45788899999999999886663
No 294
>COG4802 FtrB Ferredoxin-thioredoxin reductase, catalytic subunit [Energy production and conversion]
Probab=37.70 E-value=27 Score=21.79 Aligned_cols=17 Identities=24% Similarity=0.579 Sum_probs=13.7
Q ss_pred HHHHHHHhcCCeEeCCC
Q 036949 32 DAAYYVQQQGWTLDPAS 48 (81)
Q Consensus 32 e~~~~~~~~GW~~d~~~ 48 (81)
.+.+++.+.||.++|+-
T Consensus 12 ~~eq~AeksG~~lnpD~ 28 (110)
T COG4802 12 FTEQYAEKSGYRLNPDR 28 (110)
T ss_pred HHHHHHHhcCceeCCCH
Confidence 35678899999998873
No 295
>COG0072 PheT Phenylalanyl-tRNA synthetase beta subunit [Translation, ribosomal structure and biogenesis]
Probab=37.35 E-value=1.6e+02 Score=23.57 Aligned_cols=34 Identities=9% Similarity=0.330 Sum_probs=29.0
Q ss_pred cccHHHHHHHhCC--CHHHHHHHHHhcCCeEeCCCc
Q 036949 16 TISTQDTALFLGM--NEDDAAYYVQQQGWTLDPASR 49 (81)
Q Consensus 16 sIs~~~~a~~Lgl--s~~e~~~~~~~~GW~~d~~~~ 49 (81)
.++++.+.++||+ +.+++.+..++.|-.+...+.
T Consensus 268 ~~~~~~i~~llG~~ls~eei~~iL~rLg~~~~~~~~ 303 (650)
T COG0072 268 ELRLERINRLLGLELSAEEIEKILKRLGFKVEVKGD 303 (650)
T ss_pred EecHHHHHHHhCCCCCHHHHHHHHHHcCCeeEecCC
Confidence 4577889999997 999999999999998876544
No 296
>PRK09616 pheT phenylalanyl-tRNA synthetase subunit beta; Reviewed
Probab=37.33 E-value=1.5e+02 Score=23.11 Aligned_cols=33 Identities=9% Similarity=0.256 Sum_probs=27.5
Q ss_pred cccHHHHHHHhCC--CHHHHHHHHHhcCCeEeCCC
Q 036949 16 TISTQDTALFLGM--NEDDAAYYVQQQGWTLDPAS 48 (81)
Q Consensus 16 sIs~~~~a~~Lgl--s~~e~~~~~~~~GW~~d~~~ 48 (81)
.++.+.+.++||+ +.+++.+..+..|.++..++
T Consensus 278 ~l~~~~i~~~lG~~i~~~~i~~iL~~Lgf~~~~~~ 312 (552)
T PRK09616 278 EVSVEYINKLLGIDLSAEEIIELLERMRYDAEIGD 312 (552)
T ss_pred EecHHHHHHHhCCCCCHHHHHHHHHHcCCCcEecC
Confidence 4567889999998 78999999999999985443
No 297
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=37.30 E-value=53 Score=21.13 Aligned_cols=22 Identities=18% Similarity=0.330 Sum_probs=18.5
Q ss_pred HhcccccHHHHHHHhCCCHHHH
Q 036949 12 SAYSTISTQDTALFLGMNEDDA 33 (81)
Q Consensus 12 ~AY~sIs~~~~a~~Lgls~~e~ 33 (81)
+-+...+..++|..||+|+.-+
T Consensus 143 ~~~~~~s~~eIA~~lgis~~tV 164 (189)
T PRK12515 143 VYYHEKSVEEVGEIVGIPESTV 164 (189)
T ss_pred HHHcCCCHHHHHHHHCcCHHHH
Confidence 4568899999999999988665
No 298
>PRK00629 pheT phenylalanyl-tRNA synthetase subunit beta; Reviewed
Probab=37.29 E-value=1.9e+02 Score=23.66 Aligned_cols=33 Identities=12% Similarity=0.346 Sum_probs=28.0
Q ss_pred cccHHHHHHHhCC--CHHHHHHHHHhcCCeEeCCC
Q 036949 16 TISTQDTALFLGM--NEDDAAYYVQQQGWTLDPAS 48 (81)
Q Consensus 16 sIs~~~~a~~Lgl--s~~e~~~~~~~~GW~~d~~~ 48 (81)
.++.+.+.++||+ +.+++.+..+..|.++..++
T Consensus 404 ~~~~~~i~~ilG~~i~~~~i~~iL~~Lgf~~~~~~ 438 (791)
T PRK00629 404 TLRLERINRLLGTEISDEEIVDILKRLGFEVTEVD 438 (791)
T ss_pred EecHHHHHHHhCCCCCHHHHHHHHHHCCCEEEecC
Confidence 4567889999998 78999999999999986544
No 299
>cd08306 Death_FADD Fas-associated Death Domain protein-protein interaction domain. Death domain (DD) found in FAS-associated via death domain (FADD). FADD is a component of the death-inducing signaling complex (DISC) and serves as an adaptor in the signaling pathway of death receptor proteins. It modulates apoptosis as well as non-apoptotic processes such as cell cycle progression, survival, innate immune signaling, and hematopoiesis. FADD contains an N-terminal DED and a C-terminal DD. Its DD interacts with the DD of the activated death receptor, FAS, and its DED recruits the initiator caspases, caspase-8 and -10, to the DISC complex via a homotypic interaction with the N-terminal DED of the caspase. 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),
Probab=37.13 E-value=40 Score=19.71 Aligned_cols=22 Identities=18% Similarity=0.152 Sum_probs=17.6
Q ss_pred HHHHHHHhCCCHHHHHHHHHhc
Q 036949 19 TQDTALFLGMNEDDAAYYVQQQ 40 (81)
Q Consensus 19 ~~~~a~~Lgls~~e~~~~~~~~ 40 (81)
...+|+-||||+.++..+-...
T Consensus 16 Wk~laR~LGlse~~Id~i~~~~ 37 (86)
T cd08306 16 WRKLARKLGLSETKIESIEEAH 37 (86)
T ss_pred HHHHHHHcCCCHHHHHHHHHHC
Confidence 4569999999999998776543
No 300
>PF09840 DUF2067: Uncharacterized protein conserved in archaea (DUF2067); InterPro: IPR019202 This family of archaeal proteins, have no known function.
Probab=36.95 E-value=61 Score=21.98 Aligned_cols=48 Identities=10% Similarity=0.189 Sum_probs=32.3
Q ss_pred HHHHHHHHhcccccHH-----------HHHHHhCCCHHHHHHHHHhcCCe-EeCCCceEe
Q 036949 5 RMFQLLMSAYSTISTQ-----------DTALFLGMNEDDAAYYVQQQGWT-LDPASRMLT 52 (81)
Q Consensus 5 ~~~~li~~AY~sIs~~-----------~~a~~Lgls~~e~~~~~~~~GW~-~d~~~~~~~ 52 (81)
+++.-++.+|..++.. -++-..|++++|+.+.+.+.|=- .+.++.+..
T Consensus 120 ~l~~~Lse~~~e~~~~~~~~~aK~vi~~~s~~~g~~p~evie~~~e~Gll~~~E~~k~~L 179 (190)
T PF09840_consen 120 ELAERLSEIYKELRFQPLGTKAKRVIAAVSYATGLDPEEVIEELLEKGLLEEGEDGKIEL 179 (190)
T ss_pred HHHHHHHHHHHHHhcCccCHHHHHHHHHHHHHhCCCHHHHHHHHHhCcccccCCCceEEE
Confidence 4566677777777655 24556899999999999988743 223443443
No 301
>PHA01083 hypothetical protein
Probab=36.82 E-value=89 Score=20.65 Aligned_cols=35 Identities=14% Similarity=0.170 Sum_probs=29.3
Q ss_pred HHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHH
Q 036949 3 TKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYV 37 (81)
Q Consensus 3 R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~ 37 (81)
-++.++...+++.-++-..+|.-||+++.-+-++=
T Consensus 3 tnkLLda~K~a~~~~sdkqLA~~LGVs~q~IS~~R 37 (149)
T PHA01083 3 TNKLLDAYKKAKNYVQYKQIAHDLGVSPQKISKMR 37 (149)
T ss_pred HHHHHHHHHHHHhhccHHHHHHHhCCCHHHHHHHH
Confidence 36778889999999999999999999887776543
No 302
>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=36.81 E-value=85 Score=19.96 Aligned_cols=33 Identities=15% Similarity=0.200 Sum_probs=23.2
Q ss_pred HHHHHHHhcccccHHH---HHHHhCCCHHHHHHHHH
Q 036949 6 MFQLLMSAYSTISTQD---TALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 6 ~~~li~~AY~sIs~~~---~a~~Lgls~~e~~~~~~ 38 (81)
++..+-..|.-|+.+. +|..||++..++...++
T Consensus 18 ~L~~~Q~~~g~i~~~~~~~iA~~l~i~~~~v~~v~t 53 (145)
T PF01257_consen 18 ILHEVQEEYGYIPEEALEEIAEALGIPPAEVYGVAT 53 (145)
T ss_dssp HHHHHHHHHSS--HHHHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHcCCCCHHHHHHHHHHHCCCHHHHHHHHH
Confidence 4566777888888665 89999999988877665
No 303
>PF08986 DUF1889: Domain of unknown function (DUF1889); InterPro: IPR015079 This family consist of hypothetical bacterial proteins. ; PDB: 2JN8_A 2ES9_A.
Probab=36.70 E-value=31 Score=21.49 Aligned_cols=19 Identities=32% Similarity=0.632 Sum_probs=12.7
Q ss_pred hCC--CHHHHHHHHHhcCCeE
Q 036949 26 LGM--NEDDAAYYVQQQGWTL 44 (81)
Q Consensus 26 Lgl--s~~e~~~~~~~~GW~~ 44 (81)
||. |.+++.+-..+.||.-
T Consensus 60 lGvPasa~dv~aRg~qeGWn~ 80 (119)
T PF08986_consen 60 LGVPASAADVTARGEQEGWNP 80 (119)
T ss_dssp CT----HHHHHHHHHHCT--H
T ss_pred cCCCCCHHHHHHhcccccCCh
Confidence 577 7889999999999974
No 304
>PRK14996 TetR family transcriptional regulator; Provisional
Probab=36.64 E-value=47 Score=21.32 Aligned_cols=22 Identities=9% Similarity=0.149 Sum_probs=19.6
Q ss_pred HHHHhcccccHHHHHHHhCCCH
Q 036949 9 LLMSAYSTISTQDTALFLGMNE 30 (81)
Q Consensus 9 li~~AY~sIs~~~~a~~Lgls~ 30 (81)
..++-|...|++++|+-.|+|.
T Consensus 21 f~e~G~~~tSi~~Ia~~aGvsk 42 (192)
T PRK14996 21 ALAEGFAAMTVRRIASEAQVAA 42 (192)
T ss_pred HHhcChhhccHHHHHHHhCCCc
Confidence 4678899999999999999976
No 305
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=36.60 E-value=58 Score=16.03 Aligned_cols=26 Identities=15% Similarity=0.209 Sum_probs=21.0
Q ss_pred hcccccHHHHHHHhCCCHHHHHHHHH
Q 036949 13 AYSTISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 13 AY~sIs~~~~a~~Lgls~~e~~~~~~ 38 (81)
.+.-.+..++|..||+|...+.....
T Consensus 15 ~~~g~s~~eia~~l~is~~tv~~~~~ 40 (58)
T smart00421 15 LAEGLTNKEIAERLGISEKTVKTHLS 40 (58)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 35668999999999999988776644
No 306
>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR. Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.
Probab=36.51 E-value=62 Score=19.74 Aligned_cols=22 Identities=14% Similarity=0.194 Sum_probs=16.3
Q ss_pred HhcccccHHHHHHHhCCCHHHH
Q 036949 12 SAYSTISTQDTALFLGMNEDDA 33 (81)
Q Consensus 12 ~AY~sIs~~~~a~~Lgls~~e~ 33 (81)
+-|.-.|..++|..||+|..-+
T Consensus 119 ~~~~~~s~~EIA~~l~is~~tV 140 (142)
T TIGR03209 119 KFFEDMKEIDIAKKLHISRQSV 140 (142)
T ss_pred HHHcCCCHHHHHHHHCcCHHhh
Confidence 4567778888888888876543
No 307
>PF14898 DUF4491: Domain of unknown function (DUF4491)
Probab=36.49 E-value=67 Score=19.61 Aligned_cols=34 Identities=15% Similarity=0.172 Sum_probs=21.6
Q ss_pred cccHHHHHHHhCC----CHHHHHHHHH--hcCCeEeCCCceEeecCCCC
Q 036949 16 TISTQDTALFLGM----NEDDAAYYVQ--QQGWTLDPASRMLTVKKQPL 58 (81)
Q Consensus 16 sIs~~~~a~~Lgl----s~~e~~~~~~--~~GW~~d~~~~~~~p~~~~~ 58 (81)
.+-.+.+...+|+ |.-|+.+..+ ++|| +|+||++
T Consensus 54 ~~~~S~llgv~g~s~lWsI~ElfeQ~kRV~kGW---------FP~NPkr 93 (94)
T PF14898_consen 54 NVIWSALLGVLGFSCLWSIGELFEQEKRVEKGW---------FPKNPKR 93 (94)
T ss_pred chHHHHHHHHHHHHHHHhHHHHHHHHHHHHcCC---------CCCCCCC
Confidence 3444556666665 5677776665 5799 5777764
No 308
>cd08319 Death_RAIDD Death domain of RIP-associated ICH-1 homologous protein with a death domain. Death domain (DD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal Caspase Activation and Recruitment Domain (CARD), which interacts with the caspase-2 CARD, and a C-terminal DD, which interacts with the DD of PIDD. 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, DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other pr
Probab=36.29 E-value=41 Score=19.74 Aligned_cols=20 Identities=20% Similarity=0.215 Sum_probs=15.9
Q ss_pred HHHHHHHhCCCHHHHHHHHH
Q 036949 19 TQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 19 ~~~~a~~Lgls~~e~~~~~~ 38 (81)
-..+|..||||..++..+-.
T Consensus 16 W~~Lar~Lgls~~~I~~i~~ 35 (83)
T cd08319 16 WEQVLLDLGLSQTDIYRCKE 35 (83)
T ss_pred HHHHHHHcCCCHHHHHHHHH
Confidence 45689999999999876644
No 309
>PRK09974 putative regulator PrlF; Provisional
Probab=36.26 E-value=43 Score=21.00 Aligned_cols=33 Identities=9% Similarity=0.170 Sum_probs=17.9
Q ss_pred cCCeEeCCCceEeecCCCCcccCCCChhHHHHHHhHHHhhc
Q 036949 40 QGWTLDPASRMLTVKKQPLVTEQKLDPSKMQCLTEYVFHLE 80 (81)
Q Consensus 40 ~GW~~d~~~~~~~p~~~~~~~~~~~~~~~l~~Lt~~v~~LE 80 (81)
--|.+.++|.+++-+....+..+. +..|..|||
T Consensus 38 I~f~i~~dG~V~i~~~~~~~~Dp~--------ig~FL~fLa 70 (111)
T PRK09974 38 IHYEILPGGQVFICRLGDEEEDPV--------LGAFLDFLA 70 (111)
T ss_pred EEEEEeCCCEEEEEECCCCCCCch--------HHHHHHHHH
Confidence 357766666665554433222222 666666665
No 310
>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=36.23 E-value=60 Score=19.24 Aligned_cols=25 Identities=24% Similarity=0.446 Sum_probs=20.2
Q ss_pred cHHHHHHHhCCCHHHHHHHHHhcCCe
Q 036949 18 STQDTALFLGMNEDDAAYYVQQQGWT 43 (81)
Q Consensus 18 s~~~~a~~Lgls~~e~~~~~~~~GW~ 43 (81)
++.++|..+|++..-+.-|.. .|+-
T Consensus 2 ~I~e~a~~~gvs~~tLR~ye~-~Gll 26 (96)
T cd04774 2 KVDEVAKRLGLTKRTLKYYEE-IGLV 26 (96)
T ss_pred CHHHHHHHHCcCHHHHHHHHH-CCCC
Confidence 578999999999999998865 3543
No 311
>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=36.18 E-value=1.2e+02 Score=19.75 Aligned_cols=42 Identities=14% Similarity=0.214 Sum_probs=27.5
Q ss_pred HHHHHHHHHHhcccccHHHHHHHhCCCH---HHHHHHHHhcCCeE
Q 036949 3 TKRMFQLLMSAYSTISTQDTALFLGMNE---DDAAYYVQQQGWTL 44 (81)
Q Consensus 3 R~~~~~li~~AY~sIs~~~~a~~Lgls~---~e~~~~~~~~GW~~ 44 (81)
|++|...-=+.=..|+..++|..||+|. -|+.......|+.-
T Consensus 21 ~~~I~~g~l~pG~~L~e~~La~~lgVSRtpVReAL~~L~~eGlv~ 65 (212)
T TIGR03338 21 ERAILSGELPPGAKLNESDIAARLGVSRGPVREAFRALEEAGLVR 65 (212)
T ss_pred HHHHHcCCCCCCCEecHHHHHHHhCCChHHHHHHHHHHHHCCCEE
Confidence 3344433333445788899999999965 45555666779973
No 312
>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=36.13 E-value=65 Score=16.70 Aligned_cols=19 Identities=16% Similarity=0.195 Sum_probs=11.6
Q ss_pred HHHHHHHhCCCHHHHHHHH
Q 036949 19 TQDTALFLGMNEDDAAYYV 37 (81)
Q Consensus 19 ~~~~a~~Lgls~~e~~~~~ 37 (81)
+.++|+.+|+|..-+-.+.
T Consensus 2 i~dIA~~agvS~~TVSr~l 20 (46)
T PF00356_consen 2 IKDIAREAGVSKSTVSRVL 20 (46)
T ss_dssp HHHHHHHHTSSHHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 5667777777765544433
No 313
>PF01171 ATP_bind_3: PP-loop family; InterPro: IPR011063 This entry represents the PP-loop motif superfamily [,]. The PP-loop motif appears to be a modified version of the P-loop of nucleotide binding domain that is involved in phosphate binding []. Named PP-motif, since it appears to be a part of a previously uncharacterised ATP pyrophophatase domain. ATP sulfurylases, Escherichia coli NtrL, and Bacillus subtilis OutB consist of this domain alone. In other proteins, the pyrophosphatase domain is associated with amidotransferase domains (type I or type II), a putative citrulline-aspartate ligase domain or a nitrilase/amidase domain.; PDB: 3A2K_A 2E89_B 2E21_D 1WY5_B 1NI5_A.
Probab=36.10 E-value=35 Score=22.11 Aligned_cols=26 Identities=15% Similarity=0.245 Sum_probs=18.3
Q ss_pred HHHHhCCCHHHHHHHHHhcCCeEeCC
Q 036949 22 TALFLGMNEDDAAYYVQQQGWTLDPA 47 (81)
Q Consensus 22 ~a~~Lgls~~e~~~~~~~~GW~~d~~ 47 (81)
+--+|.++.+|+.+||...|+.+-.|
T Consensus 141 iRPLl~~~k~ei~~~~~~~~i~~~~D 166 (182)
T PF01171_consen 141 IRPLLYVSKDEIRAYAKENGIPYVED 166 (182)
T ss_dssp E-GGGCS-HHHHHHHHHHTT-SSBS-
T ss_pred CCcchhCCHHHHHHHHHHCCCcEEEC
Confidence 44578899999999999998877444
No 314
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=36.00 E-value=49 Score=21.56 Aligned_cols=23 Identities=13% Similarity=0.273 Sum_probs=20.0
Q ss_pred cccHHHHHHHhCCCHHHHHHHHH
Q 036949 16 TISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 16 sIs~~~~a~~Lgls~~e~~~~~~ 38 (81)
-++-+++|..||++.+++...+.
T Consensus 28 ~~tdEeLa~~Lgi~~~~VRk~L~ 50 (158)
T TIGR00373 28 EFTDEEISLELGIKLNEVRKALY 50 (158)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHH
Confidence 58999999999999999977744
No 315
>smart00311 PWI PWI, domain in splicing factors.
Probab=35.90 E-value=48 Score=18.73 Aligned_cols=20 Identities=25% Similarity=0.498 Sum_probs=16.3
Q ss_pred HHHHHHhCCCHHHHHHHHHh
Q 036949 20 QDTALFLGMNEDDAAYYVQQ 39 (81)
Q Consensus 20 ~~~a~~Lgls~~e~~~~~~~ 39 (81)
+.+-.+||++++.+.+|+.+
T Consensus 15 ~kv~e~LG~~d~~vvd~i~~ 34 (74)
T smart00311 15 KKVIEFLGFEEDTLVEFILS 34 (74)
T ss_pred HHHHHHHCCChHHHHHHHHH
Confidence 34678999999999999864
No 316
>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=35.86 E-value=87 Score=17.89 Aligned_cols=42 Identities=5% Similarity=0.150 Sum_probs=30.5
Q ss_pred hHHHHHHH-HHHhcccccHHHHHHHhC-CCHHH---HHHHHHhcCCe
Q 036949 2 YTKRMFQL-LMSAYSTISTQDTALFLG-MNEDD---AAYYVQQQGWT 43 (81)
Q Consensus 2 ~R~~~~~l-i~~AY~sIs~~~~a~~Lg-ls~~e---~~~~~~~~GW~ 43 (81)
+|+.|+.+ ..+.-..++.+++-..+. ..... +-+|....||-
T Consensus 38 iRn~il~~w~~n~~~~lt~~~~~~~i~~~d~~~~~ri~~FL~~~G~I 84 (86)
T PF04433_consen 38 IRNTILAEWRKNPNKYLTKTDARKLIKGIDVNKIRRIYDFLERWGLI 84 (86)
T ss_dssp HHHHHHHHHHHHTTS---HHHHHHHTTSSSHHHHHHHHHHHHHTTSS
T ss_pred HHHHHHHHHHHCCCCcccHHHHHHHccccCHHHHHHHHHHHHHcCcc
Confidence 68888888 778889999999999998 65544 45667788883
No 317
>COG4388 Mu-like prophage I protein [General function prediction only]
Probab=35.71 E-value=38 Score=25.12 Aligned_cols=21 Identities=29% Similarity=0.476 Sum_probs=16.4
Q ss_pred HHHHHhCCCHHHHHHHHHhcC
Q 036949 21 DTALFLGMNEDDAAYYVQQQG 41 (81)
Q Consensus 21 ~~a~~Lgls~~e~~~~~~~~G 41 (81)
.+|.+||+|++|..+.-.+.|
T Consensus 337 aaAklLGiSeeef~K~kE~~~ 357 (357)
T COG4388 337 AAAKLLGISEEEFAKAKESEG 357 (357)
T ss_pred HHHHHhCcCHHHHHHHHhhcC
Confidence 378999999999887655543
No 318
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=35.45 E-value=1.1e+02 Score=18.95 Aligned_cols=38 Identities=11% Similarity=0.179 Sum_probs=27.0
Q ss_pred HHHHHHHhcccccHHHHHHHhCCCHHHHHH---HHHhcCCeE
Q 036949 6 MFQLLMSAYSTISTQDTALFLGMNEDDAAY---YVQQQGWTL 44 (81)
Q Consensus 6 ~~~li~~AY~sIs~~~~a~~Lgls~~e~~~---~~~~~GW~~ 44 (81)
++..+.. -..++..++|..+|++..-+-. -..++||..
T Consensus 45 vL~~l~~-~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~ 85 (144)
T PRK11512 45 VLCSIRC-AACITPVELKKVLSVDLGALTRMLDRLVCKGWVE 85 (144)
T ss_pred HHHHHHH-cCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 3444432 3569999999999997766544 455789986
No 319
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=34.85 E-value=1.1e+02 Score=18.57 Aligned_cols=39 Identities=13% Similarity=0.084 Sum_probs=28.0
Q ss_pred HHHHHHHhcc--cccHHHHHHHhCCCHHHHHHHHH---hcCCeE
Q 036949 6 MFQLLMSAYS--TISTQDTALFLGMNEDDAAYYVQ---QQGWTL 44 (81)
Q Consensus 6 ~~~li~~AY~--sIs~~~~a~~Lgls~~e~~~~~~---~~GW~~ 44 (81)
++..+++.-. .++.+++|..+|++..-+.+... +.||-.
T Consensus 13 ~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~ 56 (132)
T TIGR00738 13 ALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRRAGLVE 56 (132)
T ss_pred HHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEE
Confidence 3444554333 68999999999999877766654 569975
No 320
>PRK08349 hypothetical protein; Validated
Probab=34.62 E-value=68 Score=21.15 Aligned_cols=21 Identities=10% Similarity=0.325 Sum_probs=18.1
Q ss_pred HHHHHhCCCHHHHHHHHHhcC
Q 036949 21 DTALFLGMNEDDAAYYVQQQG 41 (81)
Q Consensus 21 ~~a~~Lgls~~e~~~~~~~~G 41 (81)
-..-+++++.+|+.+++...|
T Consensus 137 i~rPL~~~~K~eI~~~a~~~g 157 (198)
T PRK08349 137 VLRPLIGLDKEEIVKIAKEIG 157 (198)
T ss_pred EEcCCCCCCHHHHHHHHHHcC
Confidence 455677899999999999999
No 321
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=34.54 E-value=67 Score=19.21 Aligned_cols=23 Identities=22% Similarity=0.345 Sum_probs=17.6
Q ss_pred cHHHHHHHhCCCHHHHHHHHHhc
Q 036949 18 STQDTALFLGMNEDDAAYYVQQQ 40 (81)
Q Consensus 18 s~~~~a~~Lgls~~e~~~~~~~~ 40 (81)
+...+|++||++..-+.....+.
T Consensus 70 n~s~AAr~LGIsRsTL~rKLkr~ 92 (95)
T PRK00430 70 NQTRAALMLGINRGTLRKKLKKY 92 (95)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHh
Confidence 47789999999988776655543
No 322
>PRK04217 hypothetical protein; Provisional
Probab=34.44 E-value=1.2e+02 Score=18.86 Aligned_cols=29 Identities=7% Similarity=0.077 Sum_probs=21.9
Q ss_pred HHHHHhc-ccccHHHHHHHhCCCHHHHHHH
Q 036949 8 QLLMSAY-STISTQDTALFLGMNEDDAAYY 36 (81)
Q Consensus 8 ~li~~AY-~sIs~~~~a~~Lgls~~e~~~~ 36 (81)
.++...| ..++.+++|..||+|..-+...
T Consensus 49 eai~l~~~eGlS~~EIAk~LGIS~sTV~r~ 78 (110)
T PRK04217 49 EALRLVDYEGLTQEEAGKRMGVSRGTVWRA 78 (110)
T ss_pred HHHHHHHHcCCCHHHHHHHHCcCHHHHHHH
Confidence 4444444 8899999999999998766444
No 323
>cd01670 Death Death Domain: a protein-protein interaction domain. Death Domains (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. Structural analysis of DD-DD complexes show that the domains interact with each other in many different ways. DD-containing proteins serve as adaptors in signaling pathways and they can recruit other proteins into signaling complexes. In mammals, they are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways. In invertebrates, they are involved in transcriptional regulation of zygotic patterning genes in insect embryogenesis, and are components of the ToII/NF-kappaB pathway, a conserved innate immune pathway in a
Probab=34.38 E-value=83 Score=17.19 Aligned_cols=31 Identities=13% Similarity=0.143 Sum_probs=21.9
Q ss_pred HHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHh
Q 036949 4 KRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQ 39 (81)
Q Consensus 4 ~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~ 39 (81)
..++..+. -.-..+|.-||++..++..+-.+
T Consensus 3 ~~ia~~lg-----~~W~~la~~Lgl~~~~I~~i~~~ 33 (79)
T cd01670 3 DKLAKKLG-----KDWKKLARKLGLSDGEIDQIEED 33 (79)
T ss_pred HHHHHHHh-----hHHHHHHHHhCCCHHHHHHHHHh
Confidence 34455555 34556999999999998877664
No 324
>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=34.31 E-value=59 Score=19.60 Aligned_cols=21 Identities=14% Similarity=0.237 Sum_probs=18.3
Q ss_pred cHHHHHHHhCCCHHHHHHHHH
Q 036949 18 STQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 18 s~~~~a~~Lgls~~e~~~~~~ 38 (81)
++.++|+++|+|..-+..|..
T Consensus 2 ~i~eva~~~gvs~~tlR~ye~ 22 (108)
T cd04773 2 TIGELAHLLGVPPSTLRHWEK 22 (108)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 678999999999999987754
No 325
>PRK15435 bifunctional DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase; Provisional
Probab=34.27 E-value=1e+02 Score=22.64 Aligned_cols=34 Identities=12% Similarity=0.055 Sum_probs=24.0
Q ss_pred HHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHh
Q 036949 5 RMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQ 39 (81)
Q Consensus 5 ~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~ 39 (81)
++.++|.+ -..++++++|..+|+|+.-+....++
T Consensus 89 ~a~~~I~~-~~~lsl~eLA~~lG~S~~~L~R~Fkk 122 (353)
T PRK15435 89 HACRLLEQ-ETPVTLEALADQVAMSPFHLHRLFKA 122 (353)
T ss_pred HHHHHHHh-CCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 34455555 46789999999999988776555443
No 326
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=34.25 E-value=67 Score=16.08 Aligned_cols=23 Identities=13% Similarity=-0.036 Sum_probs=18.1
Q ss_pred ccccHHHHHHHhCCCHHHHHHHH
Q 036949 15 STISTQDTALFLGMNEDDAAYYV 37 (81)
Q Consensus 15 ~sIs~~~~a~~Lgls~~e~~~~~ 37 (81)
..++..++|..+|++..-+..+-
T Consensus 14 ~gltq~~lA~~~gvs~~~vs~~e 36 (58)
T TIGR03070 14 LGLTQADLADLAGVGLRFIRDVE 36 (58)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHH
Confidence 47788889999999887776654
No 327
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=34.11 E-value=1.1e+02 Score=20.34 Aligned_cols=33 Identities=6% Similarity=-0.043 Sum_probs=24.6
Q ss_pred HHHHHHHhcccccHHH---HHHHhCCCHHHHHHHHH
Q 036949 6 MFQLLMSAYSTISTQD---TALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 6 ~~~li~~AY~sIs~~~---~a~~Lgls~~e~~~~~~ 38 (81)
++..+-..|.-|+.+. +|..||++..++...++
T Consensus 41 ~L~~iQ~~~GyIp~e~~~~iA~~l~v~~a~V~gVat 76 (169)
T PRK07571 41 VLHKAQELFGYLERDLLLYVARQLKLPLSRVYGVAT 76 (169)
T ss_pred HHHHHHHHcCCCCHHHHHHHHHHhCcCHHHHHHHHH
Confidence 4556677788888765 78999998887766654
No 328
>cd08779 Death_PIDD Death Domain of p53-induced protein with a death domain. Death domain (DD) found in PIDD (p53-induced protein with a death domain) and similar proteins. PIDD is a component of the PIDDosome complex, which is an oligomeric caspase-activating complex involved in caspase-2 activation and plays a role in mediating stress-induced apoptosis. The PIDDosome complex is composed of three components, PIDD, RAIDD and caspase-2, which interact through their DDs and DD-like domains. The DD of PIDD interacts with the DD of RAIDD, which also contains a Caspase Activation and Recruitment Domain (CARD) that interacts with the caspase-2 CARD. Autoproteolysis of PIDD determines the downstream signaling event, between pro-survival NF-kB or pro-death caspase-2 activation. 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
Probab=34.10 E-value=47 Score=19.41 Aligned_cols=21 Identities=19% Similarity=0.162 Sum_probs=16.3
Q ss_pred HHHHHHHhCCCHHHHHHHHHh
Q 036949 19 TQDTALFLGMNEDDAAYYVQQ 39 (81)
Q Consensus 19 ~~~~a~~Lgls~~e~~~~~~~ 39 (81)
-..+|+.||||..++..+-.+
T Consensus 16 Wk~lar~LGlse~~Id~Ie~~ 36 (86)
T cd08779 16 WQAIGLHLGLSYRELQRIKYN 36 (86)
T ss_pred HHHHHHHcCCCHHHHHHHHHH
Confidence 367999999999888766443
No 329
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=33.90 E-value=1.6e+02 Score=21.90 Aligned_cols=53 Identities=9% Similarity=0.057 Sum_probs=35.6
Q ss_pred HHHHHHHhcc---cccHHHHHHHhCCCHHHHHHH---HHhcCCeEeCCCceEeecCCCC
Q 036949 6 MFQLLMSAYS---TISTQDTALFLGMNEDDAAYY---VQQQGWTLDPASRMLTVKKQPL 58 (81)
Q Consensus 6 ~~~li~~AY~---sIs~~~~a~~Lgls~~e~~~~---~~~~GW~~d~~~~~~~p~~~~~ 58 (81)
++.++.+++. .++.+++++.++++.+.+.+. ..+.||-...++.-..|..+..
T Consensus 297 iL~~l~~~~~~g~~~t~~~La~~l~~~~~~v~~iL~~L~~agLI~~~~~g~~~l~rd~~ 355 (412)
T PRK04214 297 LLGRLDQARKHGKALDVDEIRRLEPMGYDELGELLCELARIGLLRRGERGQWVLARDLD 355 (412)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCeEecCCCceEecCCHH
Confidence 4456655543 678999999999988766555 4566999865533345665443
No 330
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=33.46 E-value=68 Score=22.19 Aligned_cols=31 Identities=23% Similarity=0.307 Sum_probs=23.7
Q ss_pred cccccHHHHHHHhCCCHHHHHHH---HHhcCCeE
Q 036949 14 YSTISTQDTALFLGMNEDDAAYY---VQQQGWTL 44 (81)
Q Consensus 14 Y~sIs~~~~a~~Lgls~~e~~~~---~~~~GW~~ 44 (81)
...|+..++|..||+|..-+... ..+.||.-
T Consensus 19 ~~~IS~~eLA~~L~iS~~Tvsr~Lk~LEe~GlI~ 52 (217)
T PRK14165 19 TVKISSSEFANHTGTSSKTAARILKQLEDEGYIT 52 (217)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 34699999999999987665544 44679984
No 331
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=33.27 E-value=1e+02 Score=21.23 Aligned_cols=33 Identities=15% Similarity=0.039 Sum_probs=24.0
Q ss_pred HHHHHHhcccccHHHHHHHhCC-CHHHHHHHHHh
Q 036949 7 FQLLMSAYSTISTQDTALFLGM-NEDDAAYYVQQ 39 (81)
Q Consensus 7 ~~li~~AY~sIs~~~~a~~Lgl-s~~e~~~~~~~ 39 (81)
.+++..+++..++.++|.-+|+ +..-.....++
T Consensus 255 ~~lL~~~~~~~sI~eIA~~~GF~d~s~Fsr~Fkk 288 (302)
T PRK09685 255 ADDLRPAADDEKITSIAYKWGFSDSSHFSTAFKQ 288 (302)
T ss_pred HHHhhhhccCCCHHHHHHHhCCCCHHHHHHHHHH
Confidence 4456445788999999999999 56666555544
No 332
>PF10702 DUF2507: Protein of unknown function (DUF2507); InterPro: IPR019642 This entry represents a family of conserved proteins found primarily in Firmicutes. The function is not known. ; PDB: 3NJC_B.
Probab=33.16 E-value=33 Score=21.88 Aligned_cols=24 Identities=21% Similarity=0.416 Sum_probs=18.3
Q ss_pred HHHHHHhCC-CHHHHHHHHHhcCCe
Q 036949 20 QDTALFLGM-NEDDAAYYVQQQGWT 43 (81)
Q Consensus 20 ~~~a~~Lgl-s~~e~~~~~~~~GW~ 43 (81)
.++|+-.-+ +.+|+..|..+-||-
T Consensus 29 K~lARk~pl~s~edl~~FF~~agwG 53 (124)
T PF10702_consen 29 KRLARKFPLASLEDLIEFFEQAGWG 53 (124)
T ss_dssp HHHHHHS--SSGGGHHHHHHHTTS-
T ss_pred HHHHHhCCCCCHHHHHHHHHHcCCc
Confidence 357788888 889999999999995
No 333
>PHA02552 4 head completion protein; Provisional
Probab=33.12 E-value=39 Score=22.21 Aligned_cols=14 Identities=21% Similarity=0.653 Sum_probs=11.9
Q ss_pred HHHHHHHHhcCCeE
Q 036949 31 DDAAYYVQQQGWTL 44 (81)
Q Consensus 31 ~e~~~~~~~~GW~~ 44 (81)
+.+.++|.++||.+
T Consensus 121 ~Aa~~~a~~~Gw~F 134 (151)
T PHA02552 121 KAARALCEKKGWKF 134 (151)
T ss_pred HHHHHHHHHcCCEE
Confidence 45788999999997
No 334
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=33.08 E-value=60 Score=20.15 Aligned_cols=25 Identities=12% Similarity=0.256 Sum_probs=21.0
Q ss_pred cccHHHHHHHhCCCHHHHHHHHHhc
Q 036949 16 TISTQDTALFLGMNEDDAAYYVQQQ 40 (81)
Q Consensus 16 sIs~~~~a~~Lgls~~e~~~~~~~~ 40 (81)
.++...+|..||++...+-+++..+
T Consensus 23 glt~~~lA~~lgV~r~~is~ling~ 47 (104)
T COG3093 23 GLTQTELAEALGVTRNTISELINGR 47 (104)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHcCC
Confidence 3788999999999998888887744
No 335
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=32.99 E-value=1.2e+02 Score=21.24 Aligned_cols=36 Identities=22% Similarity=0.470 Sum_probs=28.8
Q ss_pred HHHHHHHHHHhccc---ccHHHHHHHhCCCHHHHHHHHH
Q 036949 3 TKRMFQLLMSAYST---ISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 3 R~~~~~li~~AY~s---Is~~~~a~~Lgls~~e~~~~~~ 38 (81)
..||++++.-||.. ++..++|-+||+|..-+...++
T Consensus 89 ~~rIvRl~~EAy~QgglLT~~Dla~LL~~S~~TI~~~i~ 127 (220)
T PF07900_consen 89 KHRIVRLTNEAYDQGGLLTQEDLAMLLGISPRTISKDIK 127 (220)
T ss_pred HHHHHHHHHHHHHcCCcccHHHHHHHHCCCHHHHHHHHH
Confidence 46899999999974 8889999999998865544443
No 336
>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=32.99 E-value=64 Score=19.09 Aligned_cols=23 Identities=22% Similarity=0.410 Sum_probs=18.9
Q ss_pred cHHHHHHHhCCCHHHHHHHHHhcC
Q 036949 18 STQDTALFLGMNEDDAAYYVQQQG 41 (81)
Q Consensus 18 s~~~~a~~Lgls~~e~~~~~~~~G 41 (81)
++.++|..+|++..-+.-|.. .|
T Consensus 2 ti~eva~~~gvs~~tlR~ye~-~G 24 (103)
T cd01106 2 TVGEVAKLTGVSVRTLHYYDE-IG 24 (103)
T ss_pred CHHHHHHHHCcCHHHHHHHHH-CC
Confidence 578999999999999996654 44
No 337
>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=32.96 E-value=48 Score=22.90 Aligned_cols=15 Identities=27% Similarity=0.421 Sum_probs=13.6
Q ss_pred ccccHHHHHHHhCCC
Q 036949 15 STISTQDTALFLGMN 29 (81)
Q Consensus 15 ~sIs~~~~a~~Lgls 29 (81)
.++|++.+|.+||++
T Consensus 115 ~~~sLd~la~~lgiP 129 (209)
T PF10108_consen 115 ARTSLDELAALLGIP 129 (209)
T ss_pred ccCCHHHHHHHcCCC
Confidence 589999999999994
No 338
>PF08383 Maf_N: Maf N-terminal region; InterPro: IPR013592 This region is found in various leucine zipper transcription factors of the Maf family. These are implicated in the regulation of insulin gene expression [], in erythroid differentiation [], and in differentiation of the neuroretina [].
Probab=32.81 E-value=44 Score=16.76 Aligned_cols=15 Identities=27% Similarity=0.295 Sum_probs=11.2
Q ss_pred HHhCCCHHHHHHHHH
Q 036949 24 LFLGMNEDDAAYYVQ 38 (81)
Q Consensus 24 ~~Lgls~~e~~~~~~ 38 (81)
.-|||+++|+.+...
T Consensus 19 e~l~LtpEDAvEaLi 33 (35)
T PF08383_consen 19 EALGLTPEDAVEALI 33 (35)
T ss_pred hhcCCCHHHHHHHHh
Confidence 457999999887643
No 339
>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=32.68 E-value=35 Score=16.31 Aligned_cols=20 Identities=10% Similarity=0.337 Sum_probs=15.5
Q ss_pred hCCCHHHHHHHHHhcCCeEe
Q 036949 26 LGMNEDDAAYYVQQQGWTLD 45 (81)
Q Consensus 26 Lgls~~e~~~~~~~~GW~~d 45 (81)
+|++.+++.......||.++
T Consensus 11 mGf~~~~~~~AL~~~~~d~~ 30 (38)
T cd00194 11 MGFSREEARKALRATNNNVE 30 (38)
T ss_pred cCCCHHHHHHHHHHhCCCHH
Confidence 48898888888887788654
No 340
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=32.64 E-value=87 Score=23.01 Aligned_cols=21 Identities=10% Similarity=0.153 Sum_probs=17.0
Q ss_pred cHHHHHHHhCCCHHHHHHHHH
Q 036949 18 STQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 18 s~~~~a~~Lgls~~e~~~~~~ 38 (81)
+.+++|..||++.+++.+...
T Consensus 234 t~~EiA~~l~~~~~~v~~~~~ 254 (367)
T PRK09210 234 TPEEIAEEMDMPPEKVREILK 254 (367)
T ss_pred CHHHHHHHhCcCHHHHHHHHH
Confidence 467899999999999887643
No 341
>cd00131 PAX Paired Box domain
Probab=32.63 E-value=1.3e+02 Score=18.80 Aligned_cols=34 Identities=18% Similarity=0.179 Sum_probs=27.6
Q ss_pred hHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH
Q 036949 2 YTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 2 ~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~ 38 (81)
.|.+|+.+.. .-.+..++|..||+|..-+..+..
T Consensus 22 ~R~rIv~~~~---~G~s~~~iA~~~~Vs~~tV~r~i~ 55 (128)
T cd00131 22 IRQRIVELAQ---SGIRPCDISRQLRVSHGCVSKILN 55 (128)
T ss_pred HHHHHHHHHH---cCCCHHHHHHHHCcCHHHHHHHHH
Confidence 5788887764 568999999999999888777765
No 342
>smart00005 DEATH DEATH domain, found in proteins involved in cell death (apoptosis). Alpha-helical domain present in a variety of proteins with apoptotic functions. Some (but not all) of these domains form homotypic and heterotypic dimers.
Probab=32.58 E-value=65 Score=18.10 Aligned_cols=23 Identities=22% Similarity=0.264 Sum_probs=18.0
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHh
Q 036949 17 ISTQDTALFLGMNEDDAAYYVQQ 39 (81)
Q Consensus 17 Is~~~~a~~Lgls~~e~~~~~~~ 39 (81)
-....+|+.||++..++..+-..
T Consensus 18 ~~W~~la~~Lg~~~~~i~~i~~~ 40 (88)
T smart00005 18 LDWRELARKLGLSEADIDQIRTE 40 (88)
T ss_pred hHHHHHHHHcCCCHHHHHHHHHH
Confidence 35667999999999888776554
No 343
>PF10415 FumaraseC_C: Fumarase C C-terminus; InterPro: IPR018951 Fumarase C catalyses the stereo-specific interconversion of fumarate to L-malate as part of the Krebs cycle. The full-length protein forms a tetramer with visible globular shape. FumaraseC_C is the C-terminal 65 residues referred to as domain 3. The core of the molecule consists of a bundle of 20 alpha-helices from the five-helix bundle of domain 2. The projections from the core of the tetramer are generated from domains 1 and 3 of each subunit []. This entry does not appear to be part of either the active site or the activation site but is helical in structure forming a little bundle. ; GO: 0016829 lyase activity, 0006099 tricarboxylic acid cycle; PDB: 3RRP_A 3OCE_D 3OCF_D 3E04_B 3GTD_A 3R6V_F 3R6Q_F 1J3U_B 1FUR_A 1YFE_A ....
Probab=32.52 E-value=87 Score=16.86 Aligned_cols=33 Identities=15% Similarity=0.216 Sum_probs=22.1
Q ss_pred HHHHHHHHhc-ccccHHHHHHHhCC-CHHHHHHHH
Q 036949 5 RMFQLLMSAY-STISTQDTALFLGM-NEDDAAYYV 37 (81)
Q Consensus 5 ~~~~li~~AY-~sIs~~~~a~~Lgl-s~~e~~~~~ 37 (81)
+.+.+..+|+ +..++.+++.-.|+ +++++.++.
T Consensus 13 ~aa~iAk~A~~~g~svre~v~~~g~lt~ee~d~ll 47 (55)
T PF10415_consen 13 KAAEIAKEALAEGRSVREVVLEEGLLTEEELDELL 47 (55)
T ss_dssp HHHHHHHHHHHHT--HHHHHHHTTSS-HHHHHHHT
T ss_pred HHHHHHHHHHHcCCCHHHHHHHcCCCCHHHHHHHc
Confidence 4455666777 66888888888896 888887764
No 344
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=32.50 E-value=43 Score=18.40 Aligned_cols=15 Identities=33% Similarity=0.607 Sum_probs=7.7
Q ss_pred HHHHHHHhCCCHHHH
Q 036949 19 TQDTALFLGMNEDDA 33 (81)
Q Consensus 19 ~~~~a~~Lgls~~e~ 33 (81)
+...|++||++++++
T Consensus 48 lr~Ya~~Lgld~~~l 62 (62)
T PF13413_consen 48 LRKYARFLGLDPDEL 62 (62)
T ss_dssp HHHHHHHTT--HHHH
T ss_pred HHHHHHHhCcCcccC
Confidence 344677777766653
No 345
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=32.38 E-value=1.1e+02 Score=19.91 Aligned_cols=34 Identities=15% Similarity=0.089 Sum_probs=25.4
Q ss_pred HHhcccccHHHHHHHhCCCHHHH---HHHHHhcCCeE
Q 036949 11 MSAYSTISTQDTALFLGMNEDDA---AYYVQQQGWTL 44 (81)
Q Consensus 11 ~~AY~sIs~~~~a~~Lgls~~e~---~~~~~~~GW~~ 44 (81)
..--..+...++|..||+++.-+ .+-..+.||.-
T Consensus 19 ~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~ 55 (154)
T COG1321 19 LEEKGFARTKDIAERLKVSPPSVTEMLKRLERLGLVE 55 (154)
T ss_pred HhccCcccHHHHHHHhCCCcHHHHHHHHHHHHCCCeE
Confidence 33667789999999999976555 55555679974
No 346
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=32.30 E-value=1.3e+02 Score=18.74 Aligned_cols=42 Identities=14% Similarity=0.148 Sum_probs=32.7
Q ss_pred hHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH---hcCCeE
Q 036949 2 YTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ---QQGWTL 44 (81)
Q Consensus 2 ~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~---~~GW~~ 44 (81)
.|.+|+.++... ...++.+++.-||++..-+-.+.. +-|+.-
T Consensus 17 tRl~IL~~L~~~-~~~~v~ela~~l~lsqstvS~HL~~L~~AGLV~ 61 (117)
T PRK10141 17 TRLGIVLLLRES-GELCVCDLCTALDQSQPKISRHLALLRESGLLL 61 (117)
T ss_pred HHHHHHHHHHHc-CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCceE
Confidence 588999988653 368899999999999888866654 458874
No 347
>COG1309 AcrR Transcriptional regulator [Transcription]
Probab=32.12 E-value=57 Score=19.35 Aligned_cols=22 Identities=14% Similarity=0.303 Sum_probs=19.2
Q ss_pred HHHHhcccccHHHHHHHhCCCH
Q 036949 9 LLMSAYSTISTQDTALFLGMNE 30 (81)
Q Consensus 9 li~~AY~sIs~~~~a~~Lgls~ 30 (81)
...+.|..+++.++|+.+|++.
T Consensus 25 ~~~~G~~~~t~~~Ia~~agvs~ 46 (201)
T COG1309 25 FAEKGYAATTVDEIAKAAGVSK 46 (201)
T ss_pred HHHcCcCCCCHHHHHHHhCCCc
Confidence 4557999999999999999976
No 348
>PF10165 Ric8: Guanine nucleotide exchange factor synembryn; InterPro: IPR019318 Ric8 is involved in the EGL-30 neurotransmitter signalling pathway []. It is a guanine nucleotide exchange factor [] that regulates neurotransmitter secretion.
Probab=32.06 E-value=44 Score=25.30 Aligned_cols=42 Identities=21% Similarity=0.313 Sum_probs=31.3
Q ss_pred ChHHHHHHHHHHhcccccHHHHHHHhCC-CHHHHHHHHHhcCCe
Q 036949 1 LYTKRMFQLLMSAYSTISTQDTALFLGM-NEDDAAYYVQQQGWT 43 (81)
Q Consensus 1 ~~R~~~~~li~~AY~sIs~~~~a~~Lgl-s~~e~~~~~~~~GW~ 43 (81)
.+|.|.++++...+ .---+.+|.+|+. +.+++..|++--|.-
T Consensus 308 tL~~rLlrLmt~~~-~~~k~~vaellf~Lc~~d~~~~v~~~GyG 350 (446)
T PF10165_consen 308 TLRSRLLRLMTSPD-PQLKDAVAELLFVLCKEDASRFVKYVGYG 350 (446)
T ss_pred chHHHHHHHhCCCC-chHHHHHHHHHHHHHhhhHHHHHHHcCch
Confidence 47899999999999 4444556777766 888888887666654
No 349
>TIGR00637 ModE_repress ModE molybdate transport repressor domain. ModE is a molybdate-activated repressor of the molybdate transport operon in E. coli. It consists of the domain represented by this model and two tandem copies of mop-like domain, where Mop proteins are a family of 68-residue molybdenum-pterin binding proteins of Clostridium pasteurianum. This model also represents the full length of a pair of archaeal proteins that lack Mop-like domains. PSI-BLAST analysis shows similarity to helix-turn-helix regulatory proteins.
Probab=32.02 E-value=1.2e+02 Score=18.16 Aligned_cols=40 Identities=20% Similarity=0.078 Sum_probs=30.7
Q ss_pred HHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHhcCCeE
Q 036949 5 RMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTL 44 (81)
Q Consensus 5 ~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~ 44 (81)
+-+.++...+..=|+..+|..||+|..-+-..+.+..-.+
T Consensus 5 ~~l~~~~av~~~gSis~AA~~L~iS~stvs~~I~~LE~~l 44 (99)
T TIGR00637 5 RRVALLKAIARMGSISQAAKDAGISYKSAWDYIRAMNNLS 44 (99)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHCCCHHHHHHHHHHHHHHh
Confidence 3455666777788999999999999988877777665555
No 350
>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=31.86 E-value=91 Score=19.24 Aligned_cols=32 Identities=22% Similarity=0.240 Sum_probs=17.9
Q ss_pred cccHHHHHHHhCCCH-------HHHHHHHHhcCCeEeCC
Q 036949 16 TISTQDTALFLGMNE-------DDAAYYVQQQGWTLDPA 47 (81)
Q Consensus 16 sIs~~~~a~~Lgls~-------~e~~~~~~~~GW~~d~~ 47 (81)
.++..+...+-.+.+ +.+.+++.++||++...
T Consensus 58 ~Ls~~D~~~l~~~~~~l~~el~~~l~~~a~~qgy~~~G~ 96 (116)
T PF12401_consen 58 ELSPEDYERLSPWGDRLARELADYLAEHAREQGYTFVGP 96 (116)
T ss_dssp EEEHHHHHHH-S-SHHHHHHHHHHHHHHHHHHT-B-SS-
T ss_pred EECHHHHHHHhhhHHHHHHHHHHHHHHHHHHCCCeecCC
Confidence 456666666666522 44677788999999643
No 351
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=31.53 E-value=1.1e+02 Score=18.88 Aligned_cols=31 Identities=13% Similarity=0.156 Sum_probs=20.9
Q ss_pred HHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH
Q 036949 5 RMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 5 ~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~ 38 (81)
+++.++++.| +.+++|..||+|..-+..+..
T Consensus 144 ~il~~l~~g~---~~~~Ia~~l~~s~~tv~~~~~ 174 (196)
T PRK10360 144 QVAEKLAQGM---AVKEIAAELGLSPKTVHVHRA 174 (196)
T ss_pred HHHHHHHCCC---CHHHHHHHhCCCHHHHHHHHH
Confidence 4566666654 778888888887766655443
No 352
>KOG0259 consensus Tyrosine aminotransferase [Amino acid transport and metabolism]
Probab=31.48 E-value=96 Score=23.90 Aligned_cols=42 Identities=10% Similarity=0.211 Sum_probs=31.1
Q ss_pred HHhcCCeEe---------CCCceEeecCCCCcccCCCChhHHHHHHhHHHh
Q 036949 37 VQQQGWTLD---------PASRMLTVKKQPLVTEQKLDPSKMQCLTEYVFH 78 (81)
Q Consensus 37 ~~~~GW~~d---------~~~~~~~p~~~~~~~~~~~~~~~l~~Lt~~v~~ 78 (81)
.-+++|.+| .++.-++..+|.|.--.+-+.++|+++.++-..
T Consensus 180 LPe~~weIDL~~veal~DENT~AivviNP~NPcGnVys~~HL~kiae~A~k 230 (447)
T KOG0259|consen 180 LPEKDWEIDLDGVEALADENTVAIVVINPNNPCGNVYSEDHLKKIAETAKK 230 (447)
T ss_pred cCcccceechHHHHHhhccCeeEEEEeCCCCCCcccccHHHHHHHHHHHHH
Confidence 457899974 456667777777776555599999999887543
No 353
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=31.36 E-value=39 Score=24.28 Aligned_cols=28 Identities=14% Similarity=0.151 Sum_probs=20.6
Q ss_pred HHHHhCCCHH-----HHHHHHHhcCCeEeCCCc
Q 036949 22 TALFLGMNED-----DAAYYVQQQGWTLDPASR 49 (81)
Q Consensus 22 ~a~~Lgls~~-----e~~~~~~~~GW~~d~~~~ 49 (81)
.+.+++++++ .+..+|.++||+++..|-
T Consensus 244 ~~all~fTGs~~~nr~lR~~A~~~G~~L~~~GL 276 (307)
T cd00141 244 GAALLYFTGSKQFNRALRRLAKEKGLKLNEYGL 276 (307)
T ss_pred HHHHHHhhCCHHHHHHHHHHHHHcCCeeecccc
Confidence 4667777443 468889999999987653
No 354
>smart00857 Resolvase Resolvase, N terminal domain. The N-terminal domain of the resolvase family contains the active site and the dimer interface. The extended arm at the C-terminus of this domain connects to the C-terminal helix-turn-helix domain of resolvase.
Probab=31.26 E-value=31 Score=21.17 Aligned_cols=32 Identities=25% Similarity=0.476 Sum_probs=20.2
Q ss_pred hcccccHHHHHHHhCC--CHHHHHHHHHhcCCeEe
Q 036949 13 AYSTISTQDTALFLGM--NEDDAAYYVQQQGWTLD 45 (81)
Q Consensus 13 AY~sIs~~~~a~~Lgl--s~~e~~~~~~~~GW~~d 45 (81)
.|.++|.++=.. .++ ..+.+.+||.+.||.++
T Consensus 3 ~Y~RvS~~~q~~-~s~~~Q~~~~~~~a~~~g~~i~ 36 (148)
T smart00857 3 GYARVSTDDQAD-GSLERQLEALRAYAKANGWEVV 36 (148)
T ss_pred EEEEeCchhhcc-CCHHHHHHHHHHHHHHCCCEEE
Confidence 366666554222 123 34668899999999985
No 355
>PHA00542 putative Cro-like protein
Probab=31.08 E-value=68 Score=18.40 Aligned_cols=23 Identities=9% Similarity=-0.055 Sum_probs=20.0
Q ss_pred cccHHHHHHHhCCCHHHHHHHHH
Q 036949 16 TISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 16 sIs~~~~a~~Lgls~~e~~~~~~ 38 (81)
.++..++|..+|++...+-.+..
T Consensus 31 glTq~elA~~lgIs~~tIsr~e~ 53 (82)
T PHA00542 31 GWSQEQIADATDVSQPTICRIYS 53 (82)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHc
Confidence 58999999999999998887765
No 356
>PRK15340 transcriptional regulator InvF; Provisional
Probab=30.88 E-value=80 Score=21.88 Aligned_cols=31 Identities=13% Similarity=0.003 Sum_probs=25.7
Q ss_pred HHHHhcccccHHHHHHHhCCCHHHHHHHHHh
Q 036949 9 LLMSAYSTISTQDTALFLGMNEDDAAYYVQQ 39 (81)
Q Consensus 9 li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~ 39 (81)
+++...+.++++++|+.+|+|+.-+...+.+
T Consensus 118 Ll~~~~~~~sleeLA~~~gvS~r~f~RlFk~ 148 (216)
T PRK15340 118 LLAQSTSGNTMRMLGEDYGVSYTHFRRLCSR 148 (216)
T ss_pred HHhCccCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 3466678899999999999999888777665
No 357
>PRK13869 plasmid-partitioning protein RepA; Provisional
Probab=30.82 E-value=1.6e+02 Score=21.95 Aligned_cols=55 Identities=4% Similarity=0.116 Sum_probs=34.9
Q ss_pred hcccccHHHHHHHhCCCHHHHHHHHHhcCCeEeCCCceEeecCCCCcccCCC-ChhHHHHHHhHHH
Q 036949 13 AYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVTEQKL-DPSKMQCLTEYVF 77 (81)
Q Consensus 13 AY~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~~~~~p~~~~~~~~~~~-~~~~l~~Lt~~v~ 77 (81)
.....+..++|++||++..-+..+..+ |.- |.+...+..-.. +..++..|-++..
T Consensus 45 ~~r~ft~~e~A~~lgvs~~tlr~~~~~-g~~---------~~~~~~~~grR~yt~~di~~lr~~l~ 100 (405)
T PRK13869 45 SLRKFTSGEAARLMKISDSTLRKMTLA-GEG---------PQPELASNGRRFYTLGQINEIRQMLA 100 (405)
T ss_pred CCCCCCHHHHHHHhCcCHHHHHHHHHc-CCC---------CCCccCCCCceeecHHHHHHHHHHHH
Confidence 445678999999999999999988764 321 222222222222 7777777766653
No 358
>TIGR02293 TAS_TIGR02293 putative toxin-antitoxin system antitoxin component, TIGR02293 family. Proteins in this family are found almost exclusively in the Proteobacteria, but also in Gloeobacter violaceus PCC 7421, a cyanobacterium. This family was proposed by Makarova, et al. (2009) to be the antitoxin component of a new class of type 2 toxin-antitoxin system, or addiction module.
Probab=30.58 E-value=89 Score=19.59 Aligned_cols=30 Identities=7% Similarity=0.009 Sum_probs=18.8
Q ss_pred HHHHHHhcccccHHHHHHHhCCCHHHHHHH
Q 036949 7 FQLLMSAYSTISTQDTALFLGMNEDDAAYY 36 (81)
Q Consensus 7 ~~li~~AY~sIs~~~~a~~Lgls~~e~~~~ 36 (81)
...|.+-...-.+..++..+|++.+++...
T Consensus 16 ~~~i~~Glp~~~~~~l~~~l~ls~~el~~~ 45 (133)
T TIGR02293 16 ISRIERGLPIGALDRLAHLLAIGKAEIFKA 45 (133)
T ss_pred HHHHHcCCCHHHHHHHHHHHCCCHHHHHHH
Confidence 344455555555666777778877776554
No 359
>PRK09954 putative kinase; Provisional
Probab=30.48 E-value=1.3e+02 Score=21.50 Aligned_cols=40 Identities=18% Similarity=0.263 Sum_probs=30.7
Q ss_pred HHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH---hcCCe
Q 036949 3 TKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ---QQGWT 43 (81)
Q Consensus 3 R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~---~~GW~ 43 (81)
..+|+.++.+ -..|+..++|..||+|...+..... +.|+.
T Consensus 5 ~~~il~~l~~-~~~~s~~~la~~l~~s~~~v~~~i~~L~~~g~i 47 (362)
T PRK09954 5 EKEILAILRR-NPLIQQNEIADILQISRSRVAAHIMDLMRKGRI 47 (362)
T ss_pred HHHHHHHHHH-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCc
Confidence 4567777664 3589999999999999988877765 44775
No 360
>TIGR02366 DHAK_reg probable dihydroxyacetone kinase regulator. The seed alignment for this family was built from a set of closely related uncharacterized proteins associated with operons for the type of bacterial dihydroxyacetone kinase that transfers PEP-derived phosphate from a phosphoprotein, as in phosphotransferase system transport, rather than from ATP. Members have a TetR transcriptional regulator domain (pfam00440) at the N-terminus and sequence homology throughout.
Probab=30.46 E-value=66 Score=20.24 Aligned_cols=22 Identities=23% Similarity=0.276 Sum_probs=19.2
Q ss_pred HHHHhcccccHHHHHHHhCCCH
Q 036949 9 LLMSAYSTISTQDTALFLGMNE 30 (81)
Q Consensus 9 li~~AY~sIs~~~~a~~Lgls~ 30 (81)
+-++.|..|++++++.--|+|.
T Consensus 16 l~~k~~~~ITV~~I~~~AgvsR 37 (176)
T TIGR02366 16 MEVQAFSKISVSDIMSTAQIRR 37 (176)
T ss_pred HHHCCCccCCHHHHHHHhCCCH
Confidence 4578999999999999999874
No 361
>PRK00215 LexA repressor; Validated
Probab=30.42 E-value=1.6e+02 Score=19.33 Aligned_cols=41 Identities=12% Similarity=0.237 Sum_probs=28.0
Q ss_pred HHHHHHHHHhc----ccccHHHHHHHhCC-CHHHHHHH---HHhcCCeE
Q 036949 4 KRMFQLLMSAY----STISTQDTALFLGM-NEDDAAYY---VQQQGWTL 44 (81)
Q Consensus 4 ~~~~~li~~AY----~sIs~~~~a~~Lgl-s~~e~~~~---~~~~GW~~ 44 (81)
.+++..|...+ ..+++.++|..+|+ +..-+-.+ ..+.||--
T Consensus 7 ~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~~~g~i~ 55 (205)
T PRK00215 7 QEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALERKGFIR 55 (205)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEE
Confidence 45566665432 25789999999999 87665544 44678874
No 362
>COG1709 Predicted transcriptional regulator [Transcription]
Probab=30.26 E-value=46 Score=23.58 Aligned_cols=16 Identities=25% Similarity=0.279 Sum_probs=13.6
Q ss_pred ccccHHHHHHHhCCCH
Q 036949 15 STISTQDTALFLGMNE 30 (81)
Q Consensus 15 ~sIs~~~~a~~Lgls~ 30 (81)
=.+|-.++|++||.|+
T Consensus 39 F~vSQ~elA~~l~vSp 54 (241)
T COG1709 39 FNVSQTELARELGVSP 54 (241)
T ss_pred hCccHHHHHHHhCCCc
Confidence 3578889999999976
No 363
>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=30.01 E-value=94 Score=16.46 Aligned_cols=34 Identities=21% Similarity=0.293 Sum_probs=26.4
Q ss_pred hcccccHHHHHHHhCCCHHHHH---HHHHhcCCeEeC
Q 036949 13 AYSTISTQDTALFLGMNEDDAA---YYVQQQGWTLDP 46 (81)
Q Consensus 13 AY~sIs~~~~a~~Lgls~~e~~---~~~~~~GW~~d~ 46 (81)
....|++.++-.+||+|-.-++ ++....||+.-.
T Consensus 7 ~~~~itv~~~rd~lg~sRK~ai~lLE~lD~~g~T~R~ 43 (50)
T PF09107_consen 7 KNGEITVAEFRDLLGLSRKYAIPLLEYLDREGITRRV 43 (50)
T ss_dssp TTSSBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred cCCcCcHHHHHHHHCccHHHHHHHHHHHhccCCEEEe
Confidence 3789999999999999977654 455678999753
No 364
>KOG2072 consensus Translation initiation factor 3, subunit a (eIF-3a) [Translation, ribosomal structure and biogenesis]
Probab=29.96 E-value=70 Score=26.91 Aligned_cols=35 Identities=14% Similarity=0.140 Sum_probs=26.8
Q ss_pred HHHHHHHHHhcccccHHHHHHHhCC-CHHHHHHHHH
Q 036949 4 KRMFQLLMSAYSTISTQDTALFLGM-NEDDAAYYVQ 38 (81)
Q Consensus 4 ~~~~~li~~AY~sIs~~~~a~~Lgl-s~~e~~~~~~ 38 (81)
-|.++-+|+-|.+|+.+.+-.+--| +.-++..+..
T Consensus 435 ~RllqQvSqiY~sIs~~~l~~La~F~~~~~lEk~~v 470 (988)
T KOG2072|consen 435 LRLLQQVSQIYESISFERLYKLAPFFSAFELEKLLV 470 (988)
T ss_pred HHHHHHHHHHHHHHhHHHHHHHHhhcCHHHHHHHHH
Confidence 3678899999999999987666555 7777766644
No 365
>PF14821 Thr_synth_N: Threonine synthase N terminus; PDB: 3V7N_A 1VB3_A 1KL7_A.
Probab=29.90 E-value=68 Score=18.40 Aligned_cols=33 Identities=18% Similarity=0.337 Sum_probs=23.4
Q ss_pred HHHHHHHhcccccHHHHHHHhC--CCHHHHHHHHH
Q 036949 6 MFQLLMSAYSTISTQDTALFLG--MNEDDAAYYVQ 38 (81)
Q Consensus 6 ~~~li~~AY~sIs~~~~a~~Lg--ls~~e~~~~~~ 38 (81)
+-.+...+|..|...-+..++| ++++++.+.+.
T Consensus 42 l~~l~~~sy~elA~~il~~f~~~di~~~~L~~ii~ 76 (79)
T PF14821_consen 42 LEELKNLSYAELAFEILSPFLGDDIPEEELKEIIE 76 (79)
T ss_dssp HHHHTTS-HHHHHHHHHHHHCCCCS-HHHHHHHHH
T ss_pred HHHHHCCCHHHHHHHHHHHHHccCCCHHHHHHHHH
Confidence 4456677888888888888983 37888877665
No 366
>PF09278 MerR-DNA-bind: MerR, DNA binding; InterPro: IPR015358 This entry represents a family of DNA-binding domains that are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold []. ; PDB: 3QAO_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q09_A 1Q08_B 1Q0A_B 1Q07_A ....
Probab=29.60 E-value=54 Score=17.45 Aligned_cols=18 Identities=11% Similarity=0.137 Sum_probs=13.0
Q ss_pred HHHHHhCCCHHHHHHHHH
Q 036949 21 DTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 21 ~~a~~Lgls~~e~~~~~~ 38 (81)
..++-||||-+|+.++..
T Consensus 8 ~~~r~lGfsL~eI~~~l~ 25 (65)
T PF09278_consen 8 RRLRELGFSLEEIRELLE 25 (65)
T ss_dssp HHHHHTT--HHHHHHHHH
T ss_pred HHHHHcCCCHHHHHHHHh
Confidence 357789999999999983
No 367
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=29.47 E-value=45 Score=24.36 Aligned_cols=27 Identities=30% Similarity=0.490 Sum_probs=19.4
Q ss_pred ccccc-HHHHHHHhCCCHHHHHHHHHhc
Q 036949 14 YSTIS-TQDTALFLGMNEDDAAYYVQQQ 40 (81)
Q Consensus 14 Y~sIs-~~~~a~~Lgls~~e~~~~~~~~ 40 (81)
|=+|. -+++|.+|||++-++.-+.+.|
T Consensus 223 yITirRKSELA~~LgLsERQVKIWFQNR 250 (317)
T KOG0848|consen 223 YITIRRKSELAATLGLSERQVKIWFQNR 250 (317)
T ss_pred ceeeehhHHHHHhhCccHhhhhHhhhhh
Confidence 33443 4579999999999987765543
No 368
>cd08804 Death_ank2 Death domain of Ankyrin-2. Death Domain (DD) of Ankyrin-2 (ANK-2) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-2, also called ankyrin-B (for broadly expressed), is required for proper function of the Na/Ca ion exchanger-1 in cardiomyocytes, and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. Human ANK-2 is associated with "Ankyrin-B syndrome", an atypical arrythmia disorder with risk of sudden cardiac death. It also plays key roles in the brain and striated muscle. Loss of ANK-2 is associated with significant nervous system defects and sarcomere disorganization. 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
Probab=29.38 E-value=79 Score=18.38 Aligned_cols=20 Identities=15% Similarity=-0.002 Sum_probs=16.0
Q ss_pred HHHHHHHhCCCHHHHHHHHH
Q 036949 19 TQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 19 ~~~~a~~Lgls~~e~~~~~~ 38 (81)
...+|+-|||+..++..+-.
T Consensus 18 Wk~LAr~Lg~se~dI~~i~~ 37 (84)
T cd08804 18 WTELARELDFTEEQIHQIRI 37 (84)
T ss_pred HHHHHHHcCCCHHHHHHHHH
Confidence 45789999999999877544
No 369
>COG3311 AlpA Predicted transcriptional regulator [Transcription]
Probab=29.36 E-value=1.2e+02 Score=17.43 Aligned_cols=43 Identities=9% Similarity=0.040 Sum_probs=30.6
Q ss_pred HhcccccHHHHHHHhCCCHHHHHHHHHhcCCeEeCCCceEeecCCCCcccCCC
Q 036949 12 SAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVTEQKL 64 (81)
Q Consensus 12 ~AY~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~~~~~p~~~~~~~~~~~ 64 (81)
.+..-|.+.+++.++|||..-+=.+.++. -||++..-....+.
T Consensus 9 ~~~r~lrl~ev~~~~GlSrstiYr~i~~~----------~FPkpvklG~r~v~ 51 (70)
T COG3311 9 HTDRLLRLPEVAQLTGLSRSTIYRLIKDG----------TFPKPVKLGGRSVA 51 (70)
T ss_pred ccchhhhHHHHHHHHCccHHHHHHHHccC----------CCCCCeecCccccc
Confidence 35566889999999999999888877743 36776554443333
No 370
>PF11338 DUF3140: Protein of unknown function (DUF3140); InterPro: IPR021487 Some members in this family of proteins are annotated as DNA binding proteins. No function is currently known.
Probab=29.33 E-value=46 Score=20.23 Aligned_cols=23 Identities=13% Similarity=0.183 Sum_probs=17.7
Q ss_pred HHHhCCCHHHHHHHHH-----hcCCeEe
Q 036949 23 ALFLGMNEDDAAYYVQ-----QQGWTLD 45 (81)
Q Consensus 23 a~~Lgls~~e~~~~~~-----~~GW~~d 45 (81)
-...||++.|+.++.. +.||..|
T Consensus 3 ~~~VNMt~~EL~~WL~t~~S~~~g~~~~ 30 (92)
T PF11338_consen 3 HEVVNMTPAELEDWLRTDESKSVGEKKD 30 (92)
T ss_pred hhhhCCCHHHHHHHHcCccccccccCCC
Confidence 4567889999998854 4599985
No 371
>PF08992 QH-AmDH_gamma: Quinohemoprotein amine dehydrogenase, gamma subunit; InterPro: IPR015084 Quinohemoprotein amine dehydrogenases (QHNDH) 1.4.99 from EC) are enzymes produced in the periplasmic space of certain Gram-negative bacteria, such as Paracoccus denitrificans and Pseudomonas putida, in response to primary amines, including n-butylamine and benzylamine. QHNDH catalyses the oxidative deamination of a wide range of aliphatic and aromatic amines through formation of a Schiff-base intermediate involving one of the quinone O atoms []. Catalysis requires the presence of a novel redox cofactor, cysteine tryptophylquinone (CTQ). CTQ is derived from the post-translational modification of specific residues, which involves the oxidation of the indole ring of a tryptophan residue to form tryptophylquinone, followed by covalent cross-linking with a cysteine residue []. There is one CTQ per subunit in QHNDH. In addition to CTQ, two haem c cofactors are present in QHNDH that mediate the transfer of the substrate-derived electrons from CTQ to an external electron acceptor, cytochrome c-550 [, ]. QHNDH is a heterotrimer of alpha, beta and gamma subunits. The alpha and beta subunits contain signal peptides necessary for the translocation of QHNDH to the periplasm. The alpha subunit is composed of four domains - domain 1 forming a dihaem cytochrome, and domains 2-4 forming antiparallel beta-barrel structures; the beta subunit is a 7-bladed beta-propeller that provides part of the active site; and the small, catalytic gamma subunit contains the novel cross-linked CTQ cofactor, in addition to additional thioester cross-links between Cys and Asp/Glu residues that encage CTQ. The gamma subunit assumes a globular secondary structure with two short alpha-helices having many turns and bends []. This entry represents the main structural domain of the QHNDH gamma subunit.; GO: 0016638 oxidoreductase activity, acting on the CH-NH2 group of donors, 0055114 oxidation-reduction process; PDB: 1JJU_C 1PBY_C 1JMX_G 1JMZ_G.
Probab=29.32 E-value=18 Score=21.23 Aligned_cols=12 Identities=25% Similarity=0.747 Sum_probs=9.3
Q ss_pred hcCCeEeCCCce
Q 036949 39 QQGWTLDPASRM 50 (81)
Q Consensus 39 ~~GW~~d~~~~~ 50 (81)
.-||++|+.|.+
T Consensus 11 dPGWEvD~fGG~ 22 (78)
T PF08992_consen 11 DPGWEVDAFGGV 22 (78)
T ss_dssp SSBSSSBTTSSS
T ss_pred CCCceecCCccH
Confidence 459999987654
No 372
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=29.28 E-value=79 Score=19.02 Aligned_cols=33 Identities=21% Similarity=0.209 Sum_probs=23.6
Q ss_pred HHHHHHHhc--ccccHHHHHHHhCCCHHHHHHHHH
Q 036949 6 MFQLLMSAY--STISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 6 ~~~li~~AY--~sIs~~~~a~~Lgls~~e~~~~~~ 38 (81)
+..-+...| +.++.+++|.=||+|++++.+...
T Consensus 11 T~~ELq~nf~~~~ls~~~ia~dL~~s~~~le~vL~ 45 (89)
T PF10078_consen 11 TRQELQANFELSGLSLEQIAADLGTSPEHLEQVLN 45 (89)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 333344444 457888999999999999887754
No 373
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=29.22 E-value=58 Score=13.77 Aligned_cols=21 Identities=19% Similarity=0.116 Sum_probs=15.0
Q ss_pred ccccHHHHHHHhCCCHHHHHH
Q 036949 15 STISTQDTALFLGMNEDDAAY 35 (81)
Q Consensus 15 ~sIs~~~~a~~Lgls~~e~~~ 35 (81)
...+..++|..+|++..-+..
T Consensus 20 ~~~s~~~ia~~~~is~~tv~~ 40 (42)
T cd00569 20 AGESVAEIARRLGVSRSTLYR 40 (42)
T ss_pred cCCCHHHHHHHHCCCHHHHHH
Confidence 345888889999987765543
No 374
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=29.21 E-value=81 Score=17.18 Aligned_cols=24 Identities=21% Similarity=0.205 Sum_probs=18.5
Q ss_pred ccccHHHHHHHhCCCHHHHHHHHH
Q 036949 15 STISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 15 ~sIs~~~~a~~Lgls~~e~~~~~~ 38 (81)
..++..++|..+|++..-+-.+..
T Consensus 17 ~~~t~~~lA~~~gis~~tis~~~~ 40 (78)
T TIGR02607 17 LGLSIRALAKALGVSRSTLSRIVN 40 (78)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHc
Confidence 457788999999998877776544
No 375
>PLN02705 beta-amylase
Probab=29.14 E-value=53 Score=26.59 Aligned_cols=26 Identities=19% Similarity=0.392 Sum_probs=18.1
Q ss_pred HHHHHHHHhcCCeEeCCCceEeecCCC
Q 036949 31 DDAAYYVQQQGWTLDPASRMLTVKKQP 57 (81)
Q Consensus 31 ~e~~~~~~~~GW~~d~~~~~~~p~~~~ 57 (81)
+-+...|.+.||+++++|... .+.++
T Consensus 122 ~vl~al~~eagw~v~~dg~~y-r~~~~ 147 (681)
T PLN02705 122 DVLAALAREAGWTVEADGTTY-RQSPQ 147 (681)
T ss_pred HHHHHHHHhcCcEEcCCCCcc-cCCCC
Confidence 335677888999999987654 34443
No 376
>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=29.14 E-value=89 Score=18.33 Aligned_cols=21 Identities=14% Similarity=0.151 Sum_probs=18.0
Q ss_pred cHHHHHHHhCCCHHHHHHHHH
Q 036949 18 STQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 18 s~~~~a~~Lgls~~e~~~~~~ 38 (81)
++.++|.++|+|..-+.-|-.
T Consensus 2 ti~eva~~~gvs~~tLRyye~ 22 (96)
T cd04768 2 TIGEFAKLAGVSIRTLRHYDD 22 (96)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 678999999999999887655
No 377
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=29.13 E-value=1.3e+02 Score=21.86 Aligned_cols=21 Identities=19% Similarity=0.248 Sum_probs=17.1
Q ss_pred cHHHHHHHhCCCHHHHHHHHH
Q 036949 18 STQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 18 s~~~~a~~Lgls~~e~~~~~~ 38 (81)
+.+++|..||++.+++.....
T Consensus 191 t~~EiA~~lgi~~~~v~~~~~ 211 (324)
T PRK07921 191 TDEELAEESGIPEEKIADLLE 211 (324)
T ss_pred CHHHHHHHhCcCHHHHHHHHH
Confidence 467899999999999887643
No 378
>COG2901 Fis Factor for inversion stimulation Fis, transcriptional activator [Transcription / DNA replication, recombination, and repair]
Probab=29.11 E-value=82 Score=19.26 Aligned_cols=29 Identities=24% Similarity=0.400 Sum_probs=21.5
Q ss_pred hcccccHHHHHHHhCCCHHHHHHHHHhcC
Q 036949 13 AYSTISTQDTALFLGMNEDDAAYYVQQQG 41 (81)
Q Consensus 13 AY~sIs~~~~a~~Lgls~~e~~~~~~~~G 41 (81)
-|.+=.-+.||.|||++-.-+.+=.++-|
T Consensus 68 ~~~~gNQtrAa~mLGinR~TLRKKLkqyg 96 (98)
T COG2901 68 QYTRGNQTRAALMLGINRGTLRKKLKKYG 96 (98)
T ss_pred HHhcccHHHHHHHHcccHHHHHHHHHHhC
Confidence 46666778899999998877776655544
No 379
>PRK02101 hypothetical protein; Validated
Probab=28.99 E-value=1.4e+02 Score=21.00 Aligned_cols=34 Identities=21% Similarity=0.344 Sum_probs=25.8
Q ss_pred HHhcccccHHHHHHHhCCCHHHHHHHHH-hcCCeE
Q 036949 11 MSAYSTISTQDTALFLGMNEDDAAYYVQ-QQGWTL 44 (81)
Q Consensus 11 ~~AY~sIs~~~~a~~Lgls~~e~~~~~~-~~GW~~ 44 (81)
-.++.+.+.++++.++|++++-+.+... =+.|..
T Consensus 35 l~~l~~~s~~el~~l~~vs~~la~~~~~~~~~~~~ 69 (255)
T PRK02101 35 LDALRELSPDDLASLMKISDKLAGLNAARFQDWQP 69 (255)
T ss_pred HHHHHhCCHHHHHHHhCCCHHHHHHHHHHHHhhcc
Confidence 3677778999999999999888765444 347753
No 380
>PRK01905 DNA-binding protein Fis; Provisional
Probab=28.95 E-value=98 Score=17.53 Aligned_cols=23 Identities=26% Similarity=0.354 Sum_probs=17.3
Q ss_pred cHHHHHHHhCCCHHHHHHHHHhc
Q 036949 18 STQDTALFLGMNEDDAAYYVQQQ 40 (81)
Q Consensus 18 s~~~~a~~Lgls~~e~~~~~~~~ 40 (81)
+...+|+.||++..-+.....+.
T Consensus 52 n~s~aAr~LGIsrstL~rklkk~ 74 (77)
T PRK01905 52 NQSLAAEYLGINRNTLRKKLQQH 74 (77)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHh
Confidence 47789999999988776655543
No 381
>cd00118 LysM Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function.
Probab=28.90 E-value=67 Score=14.43 Aligned_cols=18 Identities=11% Similarity=0.102 Sum_probs=11.3
Q ss_pred HHHHHHHhCCCHHHHHHH
Q 036949 19 TQDTALFLGMNEDDAAYY 36 (81)
Q Consensus 19 ~~~~a~~Lgls~~e~~~~ 36 (81)
+..++...|++.+++.+.
T Consensus 11 ~~~ia~~~~~~~~~~~~~ 28 (46)
T cd00118 11 LSSIAQRYGISVEELLKL 28 (46)
T ss_pred HHHHHHHHCcCHHHHHHH
Confidence 445666667777776544
No 382
>TIGR03384 betaine_BetI transcriptional repressor BetI. BetI is a DNA-binding transcriptional repressor of the bet (betaine) regulon. In sequence, it is related to TetR (pfam00440). Choline, through BetI, induces the expression of the betaine biosynthesis genes betA and betB by derepression. The choline porter gene betT is also part of this regulon in Escherichia coli. Note that a different transcriptional regulator, ArcA, controls the expression of bet regulon genes in response to oxygen, as BetA is an oxygen-dependent enzyme.
Probab=28.79 E-value=92 Score=19.53 Aligned_cols=22 Identities=9% Similarity=0.031 Sum_probs=19.5
Q ss_pred HHHHhcccccHHHHHHHhCCCH
Q 036949 9 LLMSAYSTISTQDTALFLGMNE 30 (81)
Q Consensus 9 li~~AY~sIs~~~~a~~Lgls~ 30 (81)
+..+-|...+++++|+-.|+|.
T Consensus 21 f~~~G~~~~s~~~IA~~agvsk 42 (189)
T TIGR03384 21 IGERGSLDVTIAQIARRAGVSS 42 (189)
T ss_pred HHhcCcccCCHHHHHHHhCCCH
Confidence 5677899999999999999976
No 383
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=28.79 E-value=83 Score=16.71 Aligned_cols=24 Identities=17% Similarity=0.185 Sum_probs=17.4
Q ss_pred ccccHHHHHHHhCCCHHHHHHHHH
Q 036949 15 STISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 15 ~sIs~~~~a~~Lgls~~e~~~~~~ 38 (81)
..++..++|..+|+|..-+..+-.
T Consensus 13 ~gls~~~lA~~~g~s~s~v~~iE~ 36 (64)
T PF13560_consen 13 AGLSQAQLADRLGVSQSTVSRIER 36 (64)
T ss_dssp HTS-HHHHHHHHTS-HHHHHHHHT
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHC
Confidence 468889999999999887776544
No 384
>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=28.69 E-value=1.7e+02 Score=19.13 Aligned_cols=46 Identities=15% Similarity=0.312 Sum_probs=29.5
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHhcCCeEeCCCceEeecCCCCcccCCC-ChhHHHHH
Q 036949 17 ISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVTEQKL-DPSKMQCL 72 (81)
Q Consensus 17 Is~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~~~~~p~~~~~~~~~~~-~~~~l~~L 72 (81)
.++.++|..+|+|..-+.-|-.. | ++.|... .+..--. +++++.+|
T Consensus 2 ~~I~evA~~~gvs~~tLRyYe~~--------G-Ll~p~~r-~~~gyR~Y~~~dl~rL 48 (172)
T cd04790 2 LTISQLARQFGLSRSTLLYYERI--------G-LLSPSAR-SESNYRLYGERDLERL 48 (172)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC--------C-CCCCCcc-CCCCCccCCHHHHHHH
Confidence 47889999999999999877552 2 3334321 1222222 77888877
No 385
>PF11242 DUF2774: Protein of unknown function (DUF2774); InterPro: IPR021404 This entry is represented by Bacteriophage T4, Gp24.3; it is a family of uncharacterised viral proteins.
Probab=28.69 E-value=1e+02 Score=17.42 Aligned_cols=20 Identities=20% Similarity=0.237 Sum_probs=15.7
Q ss_pred ccHHHHHHHhCCCHHHHHHH
Q 036949 17 ISTQDTALFLGMNEDDAAYY 36 (81)
Q Consensus 17 Is~~~~a~~Lgls~~e~~~~ 36 (81)
.+.-++|+++|+++.|+..+
T Consensus 14 ~~FveIAr~~~i~a~e~a~~ 33 (63)
T PF11242_consen 14 LSFVEIARKIGITAKEVAKA 33 (63)
T ss_pred CcHHHHHHHhCCCHHHHHHH
Confidence 45667899999998887665
No 386
>PF09820 AAA-ATPase_like: Predicted AAA-ATPase; InterPro: IPR018631 This entry is predicted to be an AAA-ATPase domain []. It is usually found together with IPR012547 from INTERPRO.
Probab=28.66 E-value=56 Score=23.07 Aligned_cols=20 Identities=10% Similarity=0.313 Sum_probs=16.7
Q ss_pred HHHHHhCCCHHHHHHHHHhc
Q 036949 21 DTALFLGMNEDDAAYYVQQQ 40 (81)
Q Consensus 21 ~~a~~Lgls~~e~~~~~~~~ 40 (81)
..+.|+|++++|+.+.+..-
T Consensus 218 ~f~~~~GFT~~Ev~~ll~~~ 237 (284)
T PF09820_consen 218 RFSEYFGFTEEEVETLLKYY 237 (284)
T ss_pred hHhhhcCcCHHHHHHHHHHH
Confidence 78999999999998776643
No 387
>PLN02265 probable phenylalanyl-tRNA synthetase beta chain
Probab=28.62 E-value=1.2e+02 Score=23.89 Aligned_cols=31 Identities=6% Similarity=0.170 Sum_probs=27.0
Q ss_pred cccHHHHHHHhCC--CHHHHHHHHHhcCCeEeC
Q 036949 16 TISTQDTALFLGM--NEDDAAYYVQQQGWTLDP 46 (81)
Q Consensus 16 sIs~~~~a~~Lgl--s~~e~~~~~~~~GW~~d~ 46 (81)
.++.+.+.++||+ +.+++.+...+.|..+..
T Consensus 313 ~~~~~~i~~~lG~~l~~~ei~~iL~~l~~~~~~ 345 (597)
T PLN02265 313 EVDLSYINSSIGVSLDAEEVASLLNKMQLQAEQ 345 (597)
T ss_pred EeeHHHHHHHhCCCCCHHHHHHHHHHCCCCeEe
Confidence 4677889999998 899999999999998853
No 388
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=28.57 E-value=79 Score=22.85 Aligned_cols=33 Identities=21% Similarity=0.434 Sum_probs=24.1
Q ss_pred hcccccHHHHHHHhCCCHHHH-----------HHHHHhcCCeEe
Q 036949 13 AYSTISTQDTALFLGMNEDDA-----------AYYVQQQGWTLD 45 (81)
Q Consensus 13 AY~sIs~~~~a~~Lgls~~e~-----------~~~~~~~GW~~d 45 (81)
.|.-.+..++|..||+|..-+ .+.....||..|
T Consensus 279 ~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l~~~~~~~~ 322 (325)
T PRK05657 279 GYEAATLEDVAREIGLTRERVRQIQVEALRRLREILQTQGLSIE 322 (325)
T ss_pred CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhCccchh
Confidence 357789999999999988554 444555677654
No 389
>PF07942 N2227: N2227-like protein; InterPro: IPR012901 This family features sequences that are similar to a region of hypothetical yeast gene product N2227 (P53934 from SWISSPROT). This is thought to be expressed during meiosis and may be involved in the defence response to stressful conditions [].
Probab=28.53 E-value=62 Score=23.15 Aligned_cols=20 Identities=5% Similarity=0.396 Sum_probs=18.2
Q ss_pred hCCCHHHHHHHHHhcCCeEe
Q 036949 26 LGMNEDDAAYYVQQQGWTLD 45 (81)
Q Consensus 26 Lgls~~e~~~~~~~~GW~~d 45 (81)
+-||-+|+...+.++||++-
T Consensus 219 veLs~eEi~~l~~~~GF~~~ 238 (270)
T PF07942_consen 219 VELSLEEIKELIEKLGFEIE 238 (270)
T ss_pred cCCCHHHHHHHHHHCCCEEE
Confidence 67799999999999999985
No 390
>smart00755 Grip golgin-97, RanBP2alpha,Imh1p and p230/golgin-245.
Probab=28.48 E-value=98 Score=16.19 Aligned_cols=35 Identities=11% Similarity=0.124 Sum_probs=21.5
Q ss_pred HHHHHHHHHHhcc--cccHHHHHHHhCCCHHHHHHHH
Q 036949 3 TKRMFQLLMSAYS--TISTQDTALFLGMNEDDAAYYV 37 (81)
Q Consensus 3 R~~~~~li~~AY~--sIs~~~~a~~Lgls~~e~~~~~ 37 (81)
|+-+++-+..-.. .-=+.-+++.|.||++|...+.
T Consensus 8 KNVll~fl~~~e~~r~~ll~vi~tlL~fs~~e~~~~~ 44 (46)
T smart00755 8 KNVLLQFLTLRESERETLLKVISTVLQLSPEEMQKLL 44 (46)
T ss_pred HHHHHHHhccCcchHHHHHHHHHHHhCCCHHHHHHHH
Confidence 4444554444443 2223458999999999876543
No 391
>cd08313 Death_TNFR1 Death domain of Tumor Necrosis Factor Receptor 1. Death Domain (DD) found in tumor necrosis factor receptor-1 (TNFR-1). TNFR-1 has many names including TNFRSF1A, CD120a, p55, p60, and TNFR60. It activates two major intracellular signaling pathways that lead to the activation of the transcription factor NF-kB and the induction of cell death. Upon binding of its ligand TNF, TNFR-1 trimerizes which leads to the recruitment of an adaptor protein named TNFR-associated death domain protein (TRADD) through a DD/DD interaction. Mutations in the TNFRSF1A gene causes TNFR-associated periodic syndrome (TRAPS), a rare disorder characterized recurrent fever, myalgia, abdominal pain, conjunctivitis and skin eruptions. 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 a
Probab=28.44 E-value=67 Score=18.74 Aligned_cols=18 Identities=11% Similarity=0.213 Sum_probs=14.6
Q ss_pred HHHHHHHhCCCHHHHHHH
Q 036949 19 TQDTALFLGMNEDDAAYY 36 (81)
Q Consensus 19 ~~~~a~~Lgls~~e~~~~ 36 (81)
...+++-||||+.++...
T Consensus 14 wk~~~R~LGlse~~Id~i 31 (80)
T cd08313 14 WKEFVRRLGLSDNEIERV 31 (80)
T ss_pred HHHHHHHcCCCHHHHHHH
Confidence 456999999999888654
No 392
>PF11193 DUF2812: Protein of unknown function (DUF2812); InterPro: IPR021359 This is a bacterial family of uncharacterised proteins, however some members of this family are annotated as membrane proteins.
Probab=28.43 E-value=1.4e+02 Score=17.83 Aligned_cols=32 Identities=9% Similarity=0.190 Sum_probs=21.9
Q ss_pred HHHHHHHHHhcCCeEe-C-CCceEeecCCCCccc
Q 036949 30 EDDAAYYVQQQGWTLD-P-ASRMLTVKKQPLVTE 61 (81)
Q Consensus 30 ~~e~~~~~~~~GW~~d-~-~~~~~~p~~~~~~~~ 61 (81)
.++-.+++.+.||++= . .+.+.+-..+....+
T Consensus 53 ~~~y~~~~e~~GW~~v~~~~~~~~if~~~~~~~~ 86 (115)
T PF11193_consen 53 QKEYLEFFEEAGWEYVYSNFGGWQIFRKEEDDGP 86 (115)
T ss_pred hHHHHHHHHHCCCEEEeccCcEEEEEEEcCCCCC
Confidence 4566778999999976 3 566666666655544
No 393
>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators. Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). 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 spe
Probab=28.35 E-value=94 Score=19.54 Aligned_cols=49 Identities=12% Similarity=0.137 Sum_probs=31.3
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHhcCCeEeCCCceEeecCCCCcccCCC-ChhHHHHHHhHHH
Q 036949 17 ISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVTEQKL-DPSKMQCLTEYVF 77 (81)
Q Consensus 17 Is~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~~~~~p~~~~~~~~~~~-~~~~l~~Lt~~v~ 77 (81)
.++.++|.++|+++.-+.-+.. +|+- .|.. ...... ++.++..|--+..
T Consensus 2 ysI~eVA~~~GVs~~TLR~wE~-~GLl--------~p~r---~~G~R~Ys~~dv~rL~~I~~ 51 (120)
T cd04767 2 YPIGVVAELLNIHPETLRIWER-HGLI--------KPAR---RNGQRLYSNNDLKRLRFIKK 51 (120)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCCC--------CCcC---CCCcEEECHHHHHHHHHHHH
Confidence 3688999999999998886655 3443 3432 122222 7777777655443
No 394
>PF05491 RuvB_C: Holliday junction DNA helicase ruvB C-terminus; InterPro: IPR008823 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the C-terminal region of the proteins; it is thought to be a helicase DNA-binding domain.; GO: 0003677 DNA binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 3PFI_B 1IXR_C 1HQC_B 1IXS_B 1IN8_A 1IN4_A 1IN5_A 1J7K_A 1IN6_A 1IN7_A.
Probab=28.20 E-value=1.2e+02 Score=17.71 Aligned_cols=51 Identities=22% Similarity=0.408 Sum_probs=32.8
Q ss_pred HHHHHHHHHHhcc--cccHHHHHHHhCCCHHHH----HHHHHhcCCeE-eCCCceEee
Q 036949 3 TKRMFQLLMSAYS--TISTQDTALFLGMNEDDA----AYYVQQQGWTL-DPASRMLTV 53 (81)
Q Consensus 3 R~~~~~li~~AY~--sIs~~~~a~~Lgls~~e~----~~~~~~~GW~~-d~~~~~~~p 53 (81)
-.+++.++-..|. -+.++.+|..||.+.+-+ ..|.-+.|--. .+.|+++.+
T Consensus 10 D~~yL~~l~~~f~ggPvGl~tlA~~l~ed~~Tie~v~EPyLiq~G~I~RT~rGR~~T~ 67 (76)
T PF05491_consen 10 DRRYLKTLIENFKGGPVGLDTLAAALGEDKETIEDVIEPYLIQIGFIQRTPRGRVATP 67 (76)
T ss_dssp HHHHHHHHHHCSTTS-B-HHHHHHHTTS-HHHHHHTTHHHHHHTTSEEEETTEEEE-H
T ss_pred HHHHHHHHHHHcCCCCeeHHHHHHHHCCCHhHHHHHhhHHHHHhhhHhhCccHHHhHH
Confidence 3577888888887 788999999999976554 45566677654 233444433
No 395
>PF06744 DUF1215: Protein of unknown function (DUF1215); InterPro: IPR010623 This domain represents a conserved region situated towards the C-terminal end of several hypothetical bacterial proteins of unknown function. A few members resemble the ImcF protein, which has been proposed [] to be involved in Vibrio cholerae cell surface reorganisation that results in increased adherence to epithelial cells line and increased conjugation frequency.
Probab=28.00 E-value=76 Score=19.56 Aligned_cols=35 Identities=23% Similarity=0.390 Sum_probs=24.5
Q ss_pred hcccccHHHHHHHhCCCH-------HHHHHHHHhc--CCeEeCC
Q 036949 13 AYSTISTQDTALFLGMNE-------DDAAYYVQQQ--GWTLDPA 47 (81)
Q Consensus 13 AY~sIs~~~~a~~Lgls~-------~e~~~~~~~~--GW~~d~~ 47 (81)
|=..|+++++++++|=.+ +.+..|+... .|.+.+.
T Consensus 61 s~~dv~l~Df~~fF~p~G~ld~F~~~~L~~fvd~~~~~w~~~~~ 104 (125)
T PF06744_consen 61 SSRDVSLADFARFFGPGGVLDQFFNQYLKPFVDTSGNPWRWRPG 104 (125)
T ss_pred CcccCCHHHHHHHhcCCCcHHHHHHHHHHHHHhCCCCcceeCCC
Confidence 445789999999999743 4566666655 4887543
No 396
>PRK10296 DNA-binding transcriptional regulator ChbR; Provisional
Probab=27.98 E-value=1.5e+02 Score=20.23 Aligned_cols=31 Identities=16% Similarity=0.119 Sum_probs=24.3
Q ss_pred hcccccHHHHHHHhCC-CHHHHHHHHHhc-CCe
Q 036949 13 AYSTISTQDTALFLGM-NEDDAAYYVQQQ-GWT 43 (81)
Q Consensus 13 AY~sIs~~~~a~~Lgl-s~~e~~~~~~~~-GW~ 43 (81)
.++..++.++|..+|+ +..-...+.++. |-+
T Consensus 234 ~~t~~sI~eIA~~~GF~~~s~F~r~FKk~~G~T 266 (278)
T PRK10296 234 EMTNYSVTDIAFEAGYSSPSLFIKTFKKLTSFT 266 (278)
T ss_pred HcCCCCHHHHHHHhCCCCHHHHHHHHHHHHCcC
Confidence 6688999999999999 777777777654 543
No 397
>PRK10265 chaperone-modulator protein CbpM; Provisional
Probab=27.94 E-value=66 Score=19.32 Aligned_cols=30 Identities=20% Similarity=0.221 Sum_probs=24.6
Q ss_pred cccccHHHHHHHhCCCHHHHHHHHHhcCCeE
Q 036949 14 YSTISTQDTALFLGMNEDDAAYYVQQQGWTL 44 (81)
Q Consensus 14 Y~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~ 44 (81)
-..+++++++..-|++++.+.+++. .||--
T Consensus 5 ~~~lt~~Elc~~~gi~~~~l~eLve-~GlIe 34 (101)
T PRK10265 5 TVTFTITEFCLHTGVSEEELNEIVG-LGVIE 34 (101)
T ss_pred EEEeeHHHHHHHHCcCHHHHHHHHH-CCCee
Confidence 3468999999999999999988766 68853
No 398
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=27.86 E-value=1.4e+02 Score=20.53 Aligned_cols=19 Identities=16% Similarity=0.137 Sum_probs=15.9
Q ss_pred cHHHHHHHhCCCHHHHHHH
Q 036949 18 STQDTALFLGMNEDDAAYY 36 (81)
Q Consensus 18 s~~~~a~~Lgls~~e~~~~ 36 (81)
+.+++|..||++.+++.+.
T Consensus 131 t~~elA~~lgi~~~~v~~~ 149 (256)
T PRK07408 131 TDQEIAQALDISLEEWQEI 149 (256)
T ss_pred CHHHHHHHcCCCHHHHHHH
Confidence 4678999999999988765
No 399
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=27.85 E-value=88 Score=15.44 Aligned_cols=25 Identities=16% Similarity=0.226 Sum_probs=20.9
Q ss_pred cccccHHHHHHHhCCCHHHHHHHHH
Q 036949 14 YSTISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 14 Y~sIs~~~~a~~Lgls~~e~~~~~~ 38 (81)
+.-.+..++|..+|+|..-+.....
T Consensus 13 ~~~~s~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 13 AEGKTNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 5778999999999999888776654
No 400
>KOG2758 consensus Translation initiation factor 3, subunit e (eIF-3e) [Translation, ribosomal structure and biogenesis]
Probab=27.71 E-value=1.4e+02 Score=22.71 Aligned_cols=52 Identities=13% Similarity=0.148 Sum_probs=32.8
Q ss_pred HHHHHHhcccccHHHHHHHhCCCHHHHHHHHHhc------CCeEeC-CCceEeecCCCC
Q 036949 7 FQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQ------GWTLDP-ASRMLTVKKQPL 58 (81)
Q Consensus 7 ~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~~------GW~~d~-~~~~~~p~~~~~ 58 (81)
|...-+--+-|+++-+|.-|+|+++|+..++... .=++|+ .|.+++-.++.+
T Consensus 340 fEtfCRIHqcIti~mLA~kLnm~~eeaErwivnlIr~~rl~AkidSklg~Vvmg~~~~s 398 (432)
T KOG2758|consen 340 FETFCRIHQCITIDMLADKLNMDPEEAERWIVNLIRTARLDAKIDSKLGHVVMGHPTVS 398 (432)
T ss_pred HHHHHHHHHheeHHHHHHHhcCCHHHHHHHHHHHHHHhhhhhhhccccCceeecCCCCC
Confidence 3333344466899999999999999998775532 223333 255555444444
No 401
>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=27.66 E-value=98 Score=18.40 Aligned_cols=46 Identities=20% Similarity=0.237 Sum_probs=29.2
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHhcCCeEeCCCceEeecCCCCcccCCC-ChhHHHHHH
Q 036949 17 ISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVTEQKL-DPSKMQCLT 73 (81)
Q Consensus 17 Is~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~~~~~p~~~~~~~~~~~-~~~~l~~Lt 73 (81)
.++.++|+.+|+|+.-+.-|-.. | .+.|. ..+..-.. +++++..|-
T Consensus 2 ~~i~eva~~~gvs~~tlR~ye~~--------G-ll~~~--r~~~g~R~Y~~~~l~~l~ 48 (102)
T cd04789 2 YTISELAEKAGISRSTLLYYEKL--------G-LITGT--RNANGYRLYPDSDLQRLL 48 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC--------C-CCCCC--cCCCCCeeCCHHHHHHHH
Confidence 46889999999999999866552 2 33332 12222222 777777766
No 402
>PRK15008 HTH-type transcriptional regulator RutR; Provisional
Probab=27.61 E-value=1e+02 Score=20.23 Aligned_cols=22 Identities=9% Similarity=0.169 Sum_probs=19.5
Q ss_pred HHHHhcccccHHHHHHHhCCCH
Q 036949 9 LLMSAYSTISTQDTALFLGMNE 30 (81)
Q Consensus 9 li~~AY~sIs~~~~a~~Lgls~ 30 (81)
...+-|...+++++|+-.|+|.
T Consensus 31 f~e~Gy~~~s~~dIA~~aGvs~ 52 (212)
T PRK15008 31 FSQFGFHGTRLEQIAELAGVSK 52 (212)
T ss_pred HHHhCcccCCHHHHHHHhCcCH
Confidence 4578899999999999999976
No 403
>PF07927 YcfA: YcfA-like protein; InterPro: IPR012933 This entry represents UPF0395, which contains viral, archaeal and bacterial proteins. It includes YncN of Escherichia coli K12. Most of these proteins are hypothetical proteins of unknown function. ; GO: 0016788 hydrolase activity, acting on ester bonds; PDB: 1WHZ_A.
Probab=27.57 E-value=70 Score=16.56 Aligned_cols=16 Identities=6% Similarity=0.140 Sum_probs=12.4
Q ss_pred HHHHHHHHhcCCeEeC
Q 036949 31 DDAAYYVQQQGWTLDP 46 (81)
Q Consensus 31 ~e~~~~~~~~GW~~d~ 46 (81)
.|+.....+.||++..
T Consensus 2 ~el~k~L~~~G~~~~r 17 (56)
T PF07927_consen 2 RELIKLLEKAGFEEVR 17 (56)
T ss_dssp HHHHHHHHHTT-EEEE
T ss_pred hHHHHHHHHCCCEEec
Confidence 5788899999999864
No 404
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=27.36 E-value=85 Score=20.01 Aligned_cols=25 Identities=16% Similarity=0.295 Sum_probs=21.3
Q ss_pred ccccHHHHHHHhCCCHHHHHHHHHh
Q 036949 15 STISTQDTALFLGMNEDDAAYYVQQ 39 (81)
Q Consensus 15 ~sIs~~~~a~~Lgls~~e~~~~~~~ 39 (81)
.-++-+++|..||++.+++...+..
T Consensus 14 ~~~~dedLa~~l~i~~n~vRkiL~~ 38 (147)
T smart00531 14 GCVTEEDLAELLGIKQKQLRKILYL 38 (147)
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHH
Confidence 4689999999999999998877554
No 405
>KOG3964 consensus Phosphatidylglycerolphosphate synthase [Lipid transport and metabolism]
Probab=27.35 E-value=24 Score=27.16 Aligned_cols=44 Identities=18% Similarity=0.281 Sum_probs=32.6
Q ss_pred HHHHHhcccccHHHHHHHhCCCHHHHHHHHH--hcCCeEeCCCceE
Q 036949 8 QLLMSAYSTISTQDTALFLGMNEDDAAYYVQ--QQGWTLDPASRML 51 (81)
Q Consensus 8 ~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~--~~GW~~d~~~~~~ 51 (81)
..|.-||.-|.-..+.+.--+..++.+++-+ ++||++.+.|...
T Consensus 341 ~~ip~aY~yi~rqflesv~~~~q~h~v~l~E~q~~GwtyHaKGlW~ 386 (469)
T KOG3964|consen 341 GAIPPAYVYIARQFLESVCRLKQNHRVQLQEYQRRGWTYHAKGLWL 386 (469)
T ss_pred ccCcHHHHHHHHHHHHHHHhhcccccchHHHhhcCCcceeccceee
Confidence 4567788888888887777776665554443 6799999988766
No 406
>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=27.34 E-value=1.4e+02 Score=17.59 Aligned_cols=49 Identities=14% Similarity=0.215 Sum_probs=30.2
Q ss_pred cHHHHHHHhCCCHHHHHHHHHhcCCeEeCCCceEeecCCCCcccCCC-ChhHHHHHHhHH
Q 036949 18 STQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVTEQKL-DPSKMQCLTEYV 76 (81)
Q Consensus 18 s~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~~~~~p~~~~~~~~~~~-~~~~l~~Lt~~v 76 (81)
++.++|.++|++...+.-|... | .+.|. ......... +++++..|-.+.
T Consensus 2 ~I~eva~~~gvs~~tlR~Ye~~--------G-Ll~p~-~r~~~g~r~Y~~~dv~~l~~I~ 51 (95)
T cd04780 2 RMSELSKRSGVSVATIKYYLRE--------G-LLPEG-RRLAPNQAEYSEAHVERLRLIR 51 (95)
T ss_pred CHHHHHHHHCcCHHHHHHHHHC--------C-CCCCC-cCCCCCCeecCHHHHHHHHHHH
Confidence 5789999999999988877652 2 33332 222222223 777777765543
No 407
>PRK00767 transcriptional regulator BetI; Validated
Probab=27.28 E-value=1.1e+02 Score=19.28 Aligned_cols=22 Identities=9% Similarity=-0.016 Sum_probs=19.3
Q ss_pred HHHHhcccccHHHHHHHhCCCH
Q 036949 9 LLMSAYSTISTQDTALFLGMNE 30 (81)
Q Consensus 9 li~~AY~sIs~~~~a~~Lgls~ 30 (81)
...+-|...+++++|+-.|+|.
T Consensus 22 f~~~G~~~~s~~~Ia~~aGvs~ 43 (197)
T PRK00767 22 IGEVGLLDATIAQIARRAGVST 43 (197)
T ss_pred HHHcCcccCCHHHHHHHhCCCH
Confidence 4568899999999999999976
No 408
>PF00690 Cation_ATPase_N: Cation transporter/ATPase, N-terminus; InterPro: IPR004014 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. P-ATPases (sometime known as E1-E2 ATPases) (3.6.3.- from EC) are found in bacteria and in a number of eukaryotic plasma membranes and organelles []. P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, each of which transports a specific type of ion: H+, Na+, K+, Mg2+, Ca2+, Ag+ and Ag2+, Zn2+, Co2+, Pb2+, Ni2+, Cd2+, Cu+ and Cu2+. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2. This entry represents the conserved N-terminal region found in several classes of cation-transporting P-type ATPases, including those that transport H+ (3.6.3.6 from EC), Na+ (3.6.3.7 from EC), Ca2+ (3.6.3.8 from EC), Na+/K+ (3.6.3.9 from EC), and H+/K+ (3.6.3.10 from EC). In the H+/K+- and Na+/K+-exchange P-ATPases, this domain is found in the catalytic alpha chain. In gastric H+/K+-ATPases, this domain undergoes reversible sequential phosphorylation inducing conformational changes that may be important for regulating the function of these ATPases [, ]. More information about this protein can be found at Protein of the Month: ATP Synthases [].; PDB: 3KDP_C 3N2F_A 3B8E_A 3N23_A 2XZB_A 1MHS_B 3A3Y_A 2ZXE_A 3B8C_A 3B9B_A ....
Probab=27.12 E-value=1e+02 Score=16.64 Aligned_cols=29 Identities=10% Similarity=0.197 Sum_probs=20.5
Q ss_pred cccccHHHHHHHhC------CCHHHHHHHHHhcCC
Q 036949 14 YSTISTQDTALFLG------MNEDDAAYYVQQQGW 42 (81)
Q Consensus 14 Y~sIs~~~~a~~Lg------ls~~e~~~~~~~~GW 42 (81)
|...+.+++...|+ |+.+|+.+--++-|-
T Consensus 1 w~~~~~~~v~~~l~t~~~~GLs~~ev~~r~~~~G~ 35 (69)
T PF00690_consen 1 WHQLSVEEVLKRLNTSSSQGLSSEEVEERRKKYGP 35 (69)
T ss_dssp -TTSSHHHHHHHHTTBTSSBBTHHHHHHHHHHHSS
T ss_pred CCCCCHHHHHHHHCcCCCCCCCHHHHHHHHHhccc
Confidence 45667777777774 788888887776564
No 409
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=27.03 E-value=92 Score=20.82 Aligned_cols=22 Identities=27% Similarity=0.271 Sum_probs=19.4
Q ss_pred cHHHHHHHhCCCHHHHHHHHHh
Q 036949 18 STQDTALFLGMNEDDAAYYVQQ 39 (81)
Q Consensus 18 s~~~~a~~Lgls~~e~~~~~~~ 39 (81)
++.++|..+|+|..-+..|..+
T Consensus 2 ti~evA~~lGVS~~TLRrw~k~ 23 (175)
T PRK13182 2 KTPFVAKKLGVSPKTVQRWVKQ 23 (175)
T ss_pred CHHHHHHHHCcCHHHHHHHHHc
Confidence 5789999999999999888874
No 410
>PRK14000 potassium-transporting ATPase subunit C; Provisional
Probab=26.98 E-value=51 Score=22.48 Aligned_cols=30 Identities=3% Similarity=0.028 Sum_probs=24.7
Q ss_pred HHHhcccccHHHHHHHhCCCHHHHHHHHHh
Q 036949 10 LMSAYSTISTQDTALFLGMNEDDAAYYVQQ 39 (81)
Q Consensus 10 i~~AY~sIs~~~~a~~Lgls~~e~~~~~~~ 39 (81)
||-++..+.+..+|+--||+++++.+.+.+
T Consensus 132 ISp~aA~~Qv~RVA~argls~~~v~~LV~~ 161 (185)
T PRK14000 132 ITVDNAKQQVKRIAKERNIDASKINHLIDE 161 (185)
T ss_pred CCHHHHHHHHHHHHHHhCcCHHHHHHHHHH
Confidence 455677778888999999999999888775
No 411
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=26.98 E-value=1e+02 Score=16.87 Aligned_cols=12 Identities=8% Similarity=0.160 Sum_probs=7.0
Q ss_pred HHHHHHhcCCeE
Q 036949 33 AAYYVQQQGWTL 44 (81)
Q Consensus 33 ~~~~~~~~GW~~ 44 (81)
+.+.+.+.|...
T Consensus 35 i~~~~~~~gy~~ 46 (70)
T smart00354 35 VLAAMEELGYIP 46 (70)
T ss_pred HHHHHHHhCCCC
Confidence 455566667654
No 412
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=26.95 E-value=72 Score=21.88 Aligned_cols=39 Identities=18% Similarity=0.374 Sum_probs=28.2
Q ss_pred HHHHHHHhccc------ccHHHHHHHhCCCHHHHHHHHHhc--CCeE
Q 036949 6 MFQLLMSAYST------ISTQDTALFLGMNEDDAAYYVQQQ--GWTL 44 (81)
Q Consensus 6 ~~~li~~AY~s------Is~~~~a~~Lgls~~e~~~~~~~~--GW~~ 44 (81)
-+..++++|.. .....+|..|||++=++..+.+.| -|+.
T Consensus 61 Q~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~ 107 (198)
T KOG0483|consen 61 QVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKT 107 (198)
T ss_pred HHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccc
Confidence 34445555542 334569999999999999999976 8874
No 413
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=26.85 E-value=1.6e+02 Score=22.37 Aligned_cols=23 Identities=17% Similarity=0.101 Sum_probs=18.7
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHh
Q 036949 17 ISTQDTALFLGMNEDDAAYYVQQ 39 (81)
Q Consensus 17 Is~~~~a~~Lgls~~e~~~~~~~ 39 (81)
-+..++|..||++.+++.+....
T Consensus 279 pt~~EiA~~l~is~~~vr~~l~~ 301 (415)
T PRK07598 279 PTIEDIAQELEMTPTQVREVLLR 301 (415)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Confidence 34678999999999999887653
No 414
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=26.72 E-value=1.6e+02 Score=20.35 Aligned_cols=32 Identities=22% Similarity=0.484 Sum_probs=24.4
Q ss_pred HHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH
Q 036949 4 KRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 4 ~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~ 38 (81)
.+++.++++.++ ..++|..||+|+.-+..+..
T Consensus 139 rEVLrLLAqGkT---nKEIAe~L~IS~rTVkth~s 170 (198)
T PRK15201 139 RHLLKLIASGYH---LSETAALLSLSEEQTKSLRR 170 (198)
T ss_pred HHHHHHHHCCCC---HHHHHHHhCCCHHHHHHHHH
Confidence 357778887765 67889999999888776654
No 415
>PHA00675 hypothetical protein
Probab=26.54 E-value=1.5e+02 Score=17.54 Aligned_cols=31 Identities=10% Similarity=-0.142 Sum_probs=26.2
Q ss_pred cccHHHHHHHhCCCHHHHHHHHHhcCCeEeC
Q 036949 16 TISTQDTALFLGMNEDDAAYYVQQQGWTLDP 46 (81)
Q Consensus 16 sIs~~~~a~~Lgls~~e~~~~~~~~GW~~d~ 46 (81)
--|...+|.-+|+|..-+...+..+.|..-.
T Consensus 39 G~s~~~IA~~fGVsrstV~~I~~gk~W~~~~ 69 (78)
T PHA00675 39 GMSYAVLAEKFEQSKGAIAKICRYERRGQFA 69 (78)
T ss_pred CccHHHHHHHhCCCHHHHHHHHccchhhhee
Confidence 3477789999999999999999999998643
No 416
>COG4753 Response regulator containing CheY-like receiver domain and AraC-type DNA-binding domain [Signal transduction mechanisms]
Probab=26.47 E-value=1.4e+02 Score=23.23 Aligned_cols=37 Identities=11% Similarity=0.260 Sum_probs=31.8
Q ss_pred HHHHHHHHHhcc-cccHHHHHHHhCCCHHHHHHHHHhc
Q 036949 4 KRMFQLLMSAYS-TISTQDTALFLGMNEDDAAYYVQQQ 40 (81)
Q Consensus 4 ~~~~~li~~AY~-sIs~~~~a~~Lgls~~e~~~~~~~~ 40 (81)
+.++++|.+-|+ .++++++|..+++++.-+-+..++.
T Consensus 375 ~~~l~~I~~h~se~LtL~~la~~f~in~~Ylgqlfk~~ 412 (475)
T COG4753 375 QKVLDYIHKHFSENLTLKDLAKVFHINPVYLGQLFKKE 412 (475)
T ss_pred HHHHHHHHHHhcCCCCHHHHHHHhCcCHHHHHHHHHHH
Confidence 467889999997 5999999999999999888887753
No 417
>PF08219 TOM13: Outer membrane protein TOM13; InterPro: IPR013262 The TOM13 family of proteins are mitochondrial outer membrane proteins that mediate the assembly of beta-barrel proteins [].; GO: 0005741 mitochondrial outer membrane
Probab=26.44 E-value=70 Score=18.85 Aligned_cols=28 Identities=21% Similarity=0.341 Sum_probs=19.4
Q ss_pred HHhCCCHHHHHHHHHhcCCeEeCCCceEeecC
Q 036949 24 LFLGMNEDDAAYYVQQQGWTLDPASRMLTVKK 55 (81)
Q Consensus 24 ~~Lgls~~e~~~~~~~~GW~~d~~~~~~~p~~ 55 (81)
-||||.+==+-+++=..|| .|.-++|..
T Consensus 48 ~MLGFGEl~AhE~~fr~gW----~g~ki~P~~ 75 (77)
T PF08219_consen 48 MMLGFGELFAHEIAFRLGW----SGTKIFPES 75 (77)
T ss_pred hhHhHHHHHHHHHHHHhcc----CcceecCcc
Confidence 4788876666666777789 456677753
No 418
>PHA02943 hypothetical protein; Provisional
Probab=26.41 E-value=1.7e+02 Score=19.59 Aligned_cols=31 Identities=26% Similarity=0.190 Sum_probs=24.8
Q ss_pred HHHHHHHHHhcccccHHHHHHHhCCCHHHHHHH
Q 036949 4 KRMFQLLMSAYSTISTQDTALFLGMNEDDAAYY 36 (81)
Q Consensus 4 ~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~ 36 (81)
++|+..+ ....-+.+++|.-||+|-.++.-+
T Consensus 14 ~eILE~L--k~G~~TtseIAkaLGlS~~qa~~~ 44 (165)
T PHA02943 14 IKTLRLL--ADGCKTTSRIANKLGVSHSMARNA 44 (165)
T ss_pred HHHHHHH--hcCCccHHHHHHHHCCCHHHHHHH
Confidence 3566677 777788999999999998887655
No 419
>PF03943 TAP_C: TAP C-terminal domain; InterPro: IPR005637 This entry contains the NXF family of shuttling transport receptors for nuclear export of mRNA, which include: vertebrate mRNA export factor TAP or nuclear RNA export factor 1 (NXF1). Caenorhabditis elegans nuclear RNA export factor 1 (nxf-1). yeast mRNA export factor MEX67. Members of the NXF family have a modular structure. A nuclear localization sequence and a noncanonical RNA recognition motif (RRM) (see PDOC00030 from PROSITEDOC) followed by four LRR repeats are located in its N-terminal half. The C-terminal half contains a NTF2 domain (see PDOC50177 from PROSITEDOC) followed by a second domain, TAP-C. The TAP-C domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate nuclear shuttling [,]. The Tap-C domain is made of four alpha helices packed against each other. The arrangement of helices 1, 2 and 3 is similar to that seen in a UBA fold. and is joined to the next module by flexible 12-residue Pro-rich linker [, ].; GO: 0051028 mRNA transport, 0005634 nucleus; PDB: 1OAI_A 1GO5_A 2KHH_A 2JP7_A.
Probab=26.33 E-value=13 Score=19.84 Aligned_cols=36 Identities=19% Similarity=0.258 Sum_probs=23.4
Q ss_pred HHHHHHhCCCHHHHHHHHHhcCCeEeCCCceEeecC
Q 036949 20 QDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKK 55 (81)
Q Consensus 20 ~~~a~~Lgls~~e~~~~~~~~GW~~d~~~~~~~p~~ 55 (81)
..++...||+.+=......+-||-++.....+....
T Consensus 5 ~~~s~~Tgmn~~~s~~CL~~n~Wd~~~A~~~F~~l~ 40 (51)
T PF03943_consen 5 QQFSQQTGMNLEWSQKCLEENNWDYERALQNFEELK 40 (51)
T ss_dssp HHHHHHCSS-CCHHHHHHHHTTT-CCHHHHHHHHCC
T ss_pred HHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence 456777888877777778888999976544443333
No 420
>PRK14003 potassium-transporting ATPase subunit C; Provisional
Probab=26.23 E-value=53 Score=22.55 Aligned_cols=30 Identities=10% Similarity=0.144 Sum_probs=25.2
Q ss_pred HHHhcccccHHHHHHHhCCCHHHHHHHHHh
Q 036949 10 LMSAYSTISTQDTALFLGMNEDDAAYYVQQ 39 (81)
Q Consensus 10 i~~AY~sIs~~~~a~~Lgls~~e~~~~~~~ 39 (81)
||-+|..+.+..+|+--|++++++.+.+.+
T Consensus 136 ISp~aA~~Qv~RVA~argl~~~~v~~LI~~ 165 (194)
T PRK14003 136 ISPEAARAQIERVAKARGLPPDQLEILITK 165 (194)
T ss_pred CCHHHHHHHHHHHHHHhCcCHHHHHHHHHH
Confidence 456777888899999999999999888775
No 421
>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=26.21 E-value=86 Score=18.80 Aligned_cols=19 Identities=21% Similarity=0.293 Sum_probs=8.9
Q ss_pred cccHHHHHHHhCCCHHHHH
Q 036949 16 TISTQDTALFLGMNEDDAA 34 (81)
Q Consensus 16 sIs~~~~a~~Lgls~~e~~ 34 (81)
.++..++|..+|++...+.
T Consensus 78 gltq~~lA~~lg~~~~tis 96 (127)
T TIGR03830 78 GLSQREAAELLGGGVNAFS 96 (127)
T ss_pred CCCHHHHHHHhCCCHHHHH
Confidence 3444455555555544433
No 422
>PRK13999 potassium-transporting ATPase subunit C; Provisional
Probab=26.18 E-value=54 Score=22.67 Aligned_cols=30 Identities=17% Similarity=0.122 Sum_probs=24.6
Q ss_pred HHHhcccccHHHHHHHhCCCHHHHHHHHHh
Q 036949 10 LMSAYSTISTQDTALFLGMNEDDAAYYVQQ 39 (81)
Q Consensus 10 i~~AY~sIs~~~~a~~Lgls~~e~~~~~~~ 39 (81)
||-+|..+.+..+|+--|++++++.+.+.+
T Consensus 142 ISp~aA~~Qv~RVA~argls~~~v~~LV~~ 171 (201)
T PRK13999 142 ISPEAALFQVPRVAKARGLPEDRLRDLVAA 171 (201)
T ss_pred CCHHHHHHHHHHHHHHhCcCHHHHHHHHHH
Confidence 455677788888999999999999888775
No 423
>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=26.14 E-value=1e+02 Score=18.11 Aligned_cols=21 Identities=19% Similarity=0.273 Sum_probs=18.0
Q ss_pred cHHHHHHHhCCCHHHHHHHHH
Q 036949 18 STQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 18 s~~~~a~~Lgls~~e~~~~~~ 38 (81)
++.++|.++|+|..-+.-|-.
T Consensus 2 ~i~eva~~~gvs~~tlR~ye~ 22 (97)
T cd04782 2 TTGEFAKLCGISKQTLFHYDK 22 (97)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 578999999999999987754
No 424
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=26.08 E-value=85 Score=14.69 Aligned_cols=24 Identities=13% Similarity=0.187 Sum_probs=18.7
Q ss_pred ccccHHHHHHHhCCCHHHHHHHHH
Q 036949 15 STISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 15 ~sIs~~~~a~~Lgls~~e~~~~~~ 38 (81)
..++..++|+.+|++..-+..+..
T Consensus 11 ~~~s~~~~a~~~~~~~~~v~~~~~ 34 (58)
T cd00093 11 KGLTQEELAEKLGVSRSTISRIEN 34 (58)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHc
Confidence 368888999999999877766543
No 425
>PF10671 TcpQ: Toxin co-regulated pilus biosynthesis protein Q; InterPro: IPR018927 The toxin-coregulated pilus (TCP) of Vibrio cholerae and the soluble TcpF protein that is secreted via the TCP biogenesis apparatus are essential for intestinal colonisation in the disease of cholera. TCP fibres are homopolymers of TcpA pilin, encoded by the first gene in the tcp biogenesis operon. TcpQ is part of an outer membrane complex of the TCP biogenesis apparatus, comprised of TcpC and TcpQ. TcpQ is required for proper localisation of TcpC to the outer membrane [, ]. This entry represents a C-terminal domain found in TcpQ and other pilus biosynthesis proteins.; PDB: 3OV5_A 2L4W_A.
Probab=26.01 E-value=61 Score=18.63 Aligned_cols=15 Identities=33% Similarity=0.784 Sum_probs=11.6
Q ss_pred HHHHHHHHHhcCCeE
Q 036949 30 EDDAAYYVQQQGWTL 44 (81)
Q Consensus 30 ~~e~~~~~~~~GW~~ 44 (81)
.+.+..++.+.||++
T Consensus 13 ~~~L~~Wa~~aGw~l 27 (84)
T PF10671_consen 13 REALERWAKQAGWTL 27 (84)
T ss_dssp HHHHHHHHHCTT-EE
T ss_pred HHHHHHHHHHCCCEE
Confidence 356888999999997
No 426
>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI [, , , , ]. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....
Probab=25.99 E-value=1.1e+02 Score=16.08 Aligned_cols=30 Identities=20% Similarity=0.232 Sum_probs=21.6
Q ss_pred HHHhcccccHHHHHHHhCCCHHHHHHHHHh
Q 036949 10 LMSAYSTISTQDTALFLGMNEDDAAYYVQQ 39 (81)
Q Consensus 10 i~~AY~sIs~~~~a~~Lgls~~e~~~~~~~ 39 (81)
+-..+..=|+..+|..||+|..-+-..+.+
T Consensus 7 f~~v~~~gs~~~AA~~l~is~~~vs~~i~~ 36 (60)
T PF00126_consen 7 FLAVAETGSISAAAEELGISQSAVSRQIKQ 36 (60)
T ss_dssp HHHHHHHSSHHHHHHHCTSSHHHHHHHHHH
T ss_pred HHHHHHhCCHHHHHHHhhccchHHHHHHHH
Confidence 334444558999999999998877665553
No 427
>cd00808 GluRS_core catalytic core domain of discriminating glutamyl-tRNA synthetase. Discriminating Glutamyl-tRNA synthetase (GluRS) catalytic core domain . The discriminating form of GluRS is only found in bacteria and cellular organelles. GluRS is a monomer that attaches Glu to the appropriate tRNA. Like other class I tRNA synthetases, GluRS aminoacylates the 2'-OH of the nucleotide at the 3' end of the tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding.
Probab=25.98 E-value=1.5e+02 Score=20.76 Aligned_cols=35 Identities=20% Similarity=0.218 Sum_probs=28.4
Q ss_pred HHHHhcccccHHHHHHHhCCCHHHHHHHHHhcCCeE
Q 036949 9 LLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTL 44 (81)
Q Consensus 9 li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~ 44 (81)
-+||.....++..+.+. |+.++.+..|+...||.-
T Consensus 162 KLSKR~~~~~l~~lr~~-G~~p~ai~~~l~~lG~~~ 196 (239)
T cd00808 162 KLSKRKGDTSISDYREE-GYLPEALLNYLALLGWSP 196 (239)
T ss_pred cccCCCCCccHHHHHHC-CCCHHHHHHHHHHcCCCC
Confidence 46777777777777553 999999999999999974
No 428
>TIGR00027 mthyl_TIGR00027 methyltransferase, putative, TIGR00027 family. This model represents a set of probable methyltransferases, about 300 amino acids long, with essentially full length homology. Members share an N-terminal region described by Pfam model pfam02409. Included are a paralogous family of 12 proteins in Mycobacterium tuberculosis, plus close homologs in related species, a family of 8 in the archaeon Methanosarcina acetivorans, and small numbers of members in other species, including plants.
Probab=25.78 E-value=77 Score=22.15 Aligned_cols=20 Identities=25% Similarity=0.737 Sum_probs=17.2
Q ss_pred CCCHHHHHHHHHhcCCeEeC
Q 036949 27 GMNEDDAAYYVQQQGWTLDP 46 (81)
Q Consensus 27 gls~~e~~~~~~~~GW~~d~ 46 (81)
|++++++.++..+.||+...
T Consensus 228 ~~~~~~~~~~l~~~Gw~~~~ 247 (260)
T TIGR00027 228 GIDRADVAEWLAERGWRASE 247 (260)
T ss_pred CCChhhHHHHHHHCCCeeec
Confidence 45889999999999999853
No 429
>PF04391 DUF533: Protein of unknown function (DUF533); InterPro: IPR007486 Some family members may be secreted or integral membrane proteins.
Probab=25.74 E-value=1.2e+02 Score=20.56 Aligned_cols=26 Identities=35% Similarity=0.340 Sum_probs=19.5
Q ss_pred HHHhcccccHHHHHHHhCCCHHHHHHHHHh
Q 036949 10 LMSAYSTISTQDTALFLGMNEDDAAYYVQQ 39 (81)
Q Consensus 10 i~~AY~sIs~~~~a~~Lgls~~e~~~~~~~ 39 (81)
.+++| ++.+|.-|||+++-+..+-.+
T Consensus 161 ~Er~Y----L~~LA~aL~L~~~lv~~le~~ 186 (188)
T PF04391_consen 161 AERAY----LDELAQALGLDPDLVAQLEQQ 186 (188)
T ss_pred HHHHH----HHHHHHHhCcCHHHHHHHHHH
Confidence 46666 899999999988777655443
No 430
>PF09743 DUF2042: Uncharacterized conserved protein (DUF2042); InterPro: IPR018611 The ubiquitin fold modifier 1 (Ufm1) is the most recently discovered ubiquitin-like modifier whose conjugation (ufmylation) system is conserved in multicellular organisms. Ufm1 is known to covalently attach with cellular protein(s) via a specific E1-activating enzyme (Uba5), an E2-conjugating enzyme (Ufc1), and a E3-ligating enzyme []. This entry represents E3 UFM1-protein ligase 1.
Probab=25.74 E-value=1.9e+02 Score=20.66 Aligned_cols=48 Identities=17% Similarity=0.130 Sum_probs=35.1
Q ss_pred hHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHH----HHhc-CCeEeCCCce
Q 036949 2 YTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYY----VQQQ-GWTLDPASRM 50 (81)
Q Consensus 2 ~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~----~~~~-GW~~d~~~~~ 50 (81)
++.+|-+-+-.+=.+|++.+++..||++...+... +.+. ++.+. .|.+
T Consensus 56 L~~EI~~el~~~gGRv~~~dL~~~LnVd~~~ie~~~~~i~~~~~~~~l~-~gel 108 (272)
T PF09743_consen 56 LEKEIKDELYVHGGRVNLVDLAQALNVDLDHIERRAQEIVKSDKSLQLV-QGEL 108 (272)
T ss_pred HHHHHHHHHHHcCCceEHHHHHHhcCcCHHHHHHHHHHHHhCCCcEEEE-CCEE
Confidence 57788888888889999999999999987665443 3333 66664 3443
No 431
>PLN02627 glutamyl-tRNA synthetase
Probab=25.73 E-value=78 Score=24.96 Aligned_cols=37 Identities=19% Similarity=0.230 Sum_probs=30.3
Q ss_pred HHHHhcccccHHHHHHHhCCCHHHHHHHHHhcCCeEeC
Q 036949 9 LLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDP 46 (81)
Q Consensus 9 li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~d~ 46 (81)
-+||.-..+++..+-.. |+.++.+..|+...||....
T Consensus 293 KLSKR~~~~~v~~~r~~-G~~PeAi~nyla~LGws~~~ 329 (535)
T PLN02627 293 KLSKRHGATSVGQFREM-GYLPDAMVNYLALLGWNDGT 329 (535)
T ss_pred ccccccCCccHHHHHHC-CCCHHHHHHHHHHhCCCCCC
Confidence 45777778888887665 99999999999999998653
No 432
>PRK00315 potassium-transporting ATPase subunit C; Reviewed
Probab=25.68 E-value=55 Score=22.44 Aligned_cols=30 Identities=13% Similarity=0.060 Sum_probs=24.5
Q ss_pred HHHhcccccHHHHHHHhCCCHHHHHHHHHh
Q 036949 10 LMSAYSTISTQDTALFLGMNEDDAAYYVQQ 39 (81)
Q Consensus 10 i~~AY~sIs~~~~a~~Lgls~~e~~~~~~~ 39 (81)
||-+|..+.+..+|+--|++++++.+.+.+
T Consensus 133 IS~~aA~~Qv~RVA~argl~~~~v~~LI~~ 162 (193)
T PRK00315 133 ISPAAAAYQIPRVAAARQLPVEQVAQLVAA 162 (193)
T ss_pred CCHHHHHHHHHHHHHHhCcCHHHHHHHHHH
Confidence 455677788888999999999999888775
No 433
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=25.56 E-value=1.3e+02 Score=19.40 Aligned_cols=38 Identities=8% Similarity=0.025 Sum_probs=27.7
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHhcCCeEeCCCceEeec
Q 036949 17 ISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVK 54 (81)
Q Consensus 17 Is~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~~~~~p~ 54 (81)
-++.+++..+|++.+.+..|+.+-.=.+-....+.+|-
T Consensus 47 ati~eV~e~tgVs~~~I~~~IreGRL~~~~~~nl~~~C 84 (137)
T TIGR03826 47 ATVSEIVEETGVSEKLILKFIREGRLQLKHFPNLGYPC 84 (137)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCeeccCCCCCcCcc
Confidence 78899999999999999999996444443333344443
No 434
>smart00740 PASTA PASTA domain.
Probab=25.51 E-value=96 Score=15.68 Aligned_cols=22 Identities=14% Similarity=0.421 Sum_probs=18.4
Q ss_pred HHhCCCHHHHHHHHHhcCCeEe
Q 036949 24 LFLGMNEDDAAYYVQQQGWTLD 45 (81)
Q Consensus 24 ~~Lgls~~e~~~~~~~~GW~~d 45 (81)
.+.|++.+++.+.+.+.|+.+.
T Consensus 9 ~~~g~~~~~a~~~l~~~g~~~~ 30 (66)
T smart00740 9 DVIGLSKEEAKKLLKALGLKVE 30 (66)
T ss_pred CcCCCCHHHHHHHHHHCCCEEE
Confidence 4668999999999999998763
No 435
>PF02413 Caudo_TAP: Caudovirales tail fibre assembly protein; InterPro: IPR003458 This family contains Bacteriophage T4 gp38 and related bacterial prophage and phage proteins. Gene 38 of phage T4 codes for a protein containing 183 amino acid residues with molecular weight of 22.3 kDa. Together with genes 36 and 37, whose products are structural proteins of the fibre distal part, gene 38 forms one transcription unit. Gp38, is a chaperone, which is required for assembly of the distal part of the long fibres and which is absent from the mature phage particle. In the absence of gp38 gp37, which is a component of the distal part of the long tail fibre, fails to oligomerise. The carboxy-terminal region of gp37 forms the tip of the distal fibre that interacts with the cell receptors. Functionally the role of gp38 can be replaced by pTfa of Bacteriophage lambda [, , ]. The function of many of the other members of this family remain to be elucidated.
Probab=25.45 E-value=1.4e+02 Score=18.51 Aligned_cols=33 Identities=24% Similarity=0.329 Sum_probs=26.4
Q ss_pred HHHHHHHHHhcccccHHHHHHHhCC-CHHHHHHH
Q 036949 4 KRMFQLLMSAYSTISTQDTALFLGM-NEDDAAYY 36 (81)
Q Consensus 4 ~~~~~li~~AY~sIs~~~~a~~Lgl-s~~e~~~~ 36 (81)
.+--++|+.|...|..=.=+-.||+ +.+|...+
T Consensus 69 ~~k~~ll~~A~~~I~~lqda~~lg~atd~e~~~L 102 (130)
T PF02413_consen 69 AEKQRLLAEASEAIAPLQDAVDLGIATDEEKARL 102 (130)
T ss_pred HHHHHHHHHHHHHHHHhHHHHHhccCChHHHHHH
Confidence 4456799999999999888889998 77776544
No 436
>PRK14001 potassium-transporting ATPase subunit C; Provisional
Probab=25.35 E-value=56 Score=22.34 Aligned_cols=30 Identities=3% Similarity=0.062 Sum_probs=23.2
Q ss_pred HHHhcccccHHHHHHHhCCCHHHHHHHHHh
Q 036949 10 LMSAYSTISTQDTALFLGMNEDDAAYYVQQ 39 (81)
Q Consensus 10 i~~AY~sIs~~~~a~~Lgls~~e~~~~~~~ 39 (81)
||-++..+.+..+|+--|++++++.+.+.+
T Consensus 133 IS~~aA~~Qv~RVA~argl~~~~v~~LV~~ 162 (189)
T PRK14001 133 ISVVNAKLQAPRVAQARNISIRQVERLIED 162 (189)
T ss_pred CCHHHHHHHHHHHHHHhCcCHHHHHHHHHH
Confidence 345666677788899999999998887764
No 437
>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=25.30 E-value=74 Score=21.32 Aligned_cols=39 Identities=10% Similarity=0.267 Sum_probs=26.0
Q ss_pred HHHHHHHhCCCHHH------HHHHHHhcCCeEeCCCceEeecCCCC
Q 036949 19 TQDTALFLGMNEDD------AAYYVQQQGWTLDPASRMLTVKKQPL 58 (81)
Q Consensus 19 ~~~~a~~Lgls~~e------~~~~~~~~GW~~d~~~~~~~p~~~~~ 58 (81)
+..++..||+++-. +..|....-|+-+ ..-+++|.|..-
T Consensus 32 l~~a~~~lgl~~~~l~vL~aLls~~~~~d~~~~-~~piVfpSN~~L 76 (177)
T PF03428_consen 32 LKEARPALGLSDRALAVLDALLSFTPPDDWEPG-RRPIVFPSNAQL 76 (177)
T ss_pred HHHHHHhcCCChhHHHHHHHHHHhCCcccccCC-CCceeecCHHHH
Confidence 45688999997744 4556667788543 456777775543
No 438
>PF03462 PCRF: PCRF domain; InterPro: IPR005139 This domain is found in peptide chain release factors. Peptide chain release factors are important for protein synthesis since they direct the termination of translation in response to the peptide chain termination codons UAG and UAA. These are structurally distinct but both contain the PCRF domain [].; GO: 0016149 translation release factor activity, codon specific, 0006415 translational termination, 0005737 cytoplasm; PDB: 3D5A_X 3D5C_X 3MR8_V 3MS0_V 3F1G_X 3F1E_X 1ZBT_A 2IHR_1 2X9R_Y 2X9T_Y ....
Probab=25.26 E-value=55 Score=20.11 Aligned_cols=12 Identities=25% Similarity=0.999 Sum_probs=9.3
Q ss_pred HHHHHhcCCeEe
Q 036949 34 AYYVQQQGWTLD 45 (81)
Q Consensus 34 ~~~~~~~GW~~d 45 (81)
..||..+||++.
T Consensus 73 ~~~a~~~gw~~~ 84 (115)
T PF03462_consen 73 QRYAERRGWKVE 84 (115)
T ss_dssp HHHHHHTT-EEE
T ss_pred HHHHHHcCCEEE
Confidence 678999999985
No 439
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=24.95 E-value=1.3e+02 Score=16.38 Aligned_cols=32 Identities=6% Similarity=0.131 Sum_probs=21.6
Q ss_pred HHHHHHHHhcccccHHHHHHHhCCCHHHHHHHH
Q 036949 5 RMFQLLMSAYSTISTQDTALFLGMNEDDAAYYV 37 (81)
Q Consensus 5 ~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~ 37 (81)
+++.++ -.+...++.++.+..+++.+++....
T Consensus 17 ~V~~~L-l~~G~ltl~~i~~~t~l~~~~Vk~~L 48 (62)
T PF08221_consen 17 KVGEVL-LSRGRLTLREIVRRTGLSPKQVKKAL 48 (62)
T ss_dssp HHHHHH-HHC-SEEHHHHHHHHT--HHHHHHHH
T ss_pred HHHHHH-HHcCCcCHHHHHHHhCCCHHHHHHHH
Confidence 444444 45778899999999999998876643
No 440
>PRK11426 hypothetical protein; Provisional
Probab=24.93 E-value=1.5e+02 Score=19.14 Aligned_cols=31 Identities=26% Similarity=0.272 Sum_probs=20.4
Q ss_pred HHHHHhcccccHHHHHHHhCCCHHHHHHHHH
Q 036949 8 QLLMSAYSTISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 8 ~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~ 38 (81)
.-|..++.+=.+..+|.-+|++++++.....
T Consensus 64 ~ql~~~lG~d~i~~lA~q~Gl~~~~~~~~LA 94 (132)
T PRK11426 64 EQLESALGTNAVSDLGQKLGVDTSTASSLLA 94 (132)
T ss_pred HHHHHHhChHHHHHHHHHHCcCHHHHHHHHH
Confidence 3455666666677777777777777655544
No 441
>PF01476 LysM: LysM domain; InterPro: IPR018392 This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation []. This domain may have a general peptidoglycan binding function.; GO: 0016998 cell wall macromolecule catabolic process; PDB: 2DJP_A 3ZQD_A 1Y7M_B 4A52_A 2L9Y_A 1E0G_A.
Probab=24.89 E-value=96 Score=14.89 Aligned_cols=17 Identities=18% Similarity=0.104 Sum_probs=8.7
Q ss_pred HHHHHHhCCCHHHHHHH
Q 036949 20 QDTALFLGMNEDDAAYY 36 (81)
Q Consensus 20 ~~~a~~Lgls~~e~~~~ 36 (81)
..+|...|++.+++.++
T Consensus 10 ~~IA~~~~~~~~~l~~~ 26 (44)
T PF01476_consen 10 WSIAKRYGISVDELMEL 26 (44)
T ss_dssp HHHHHHTTS-HHHHHHH
T ss_pred HHHHhhhhhhHhHHHHh
Confidence 34455556666666553
No 442
>PRK10870 transcriptional repressor MprA; Provisional
Probab=24.87 E-value=1.2e+02 Score=19.73 Aligned_cols=30 Identities=20% Similarity=0.430 Sum_probs=23.2
Q ss_pred ccccHHHHHHHhCCCHHHHH---HHHHhcCCeE
Q 036949 15 STISTQDTALFLGMNEDDAA---YYVQQQGWTL 44 (81)
Q Consensus 15 ~sIs~~~~a~~Lgls~~e~~---~~~~~~GW~~ 44 (81)
..++..++|..+|++..-+- +-..++||..
T Consensus 70 ~~it~~eLa~~l~l~~~tvsr~v~rLe~kGlV~ 102 (176)
T PRK10870 70 HSIQPSELSCALGSSRTNATRIADELEKRGWIE 102 (176)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 35888999999999776654 4455789986
No 443
>TIGR03853 matur_matur probable metal-binding protein. This protein family was identified by searching with a phylogenetic profile based on an anaerobic sulfatase-maturase enzyme, which contains multiple 4Fe-4S clusters. The linkages by phylogenetic profiling and by iron-sulfur cluster-related motifs together suggest this protein may be an accessory protein to certain maturases in sulfatase/maturase systems.
Probab=24.83 E-value=1.6e+02 Score=17.33 Aligned_cols=29 Identities=17% Similarity=0.304 Sum_probs=20.8
Q ss_pred HHHHhCCCHHHHHHHHHhcCCeEeCCCce
Q 036949 22 TALFLGMNEDDAAYYVQQQGWTLDPASRM 50 (81)
Q Consensus 22 ~a~~Lgls~~e~~~~~~~~GW~~d~~~~~ 50 (81)
.++.=||+.+++.+|..++|=-+..++.+
T Consensus 39 TCSa~~m~a~~Li~FL~~kgKfi~~~~gf 67 (77)
T TIGR03853 39 TCSAEGMTADELLQFLLKKGKFIESDGGF 67 (77)
T ss_pred ecccccCCHHHHHHHHHHCCCEeecCCcE
Confidence 34556889999999999887655555444
No 444
>PF00867 XPG_I: XPG I-region; InterPro: IPR006086 This entry represents endonucleases that cleave the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA. The endonuclease binds 2 magnesium ions per subunit. which probably participate in the reaction catalyzed by the enzyme. May bind an additional third magnesium ion after substrate binding.; GO: 0004518 nuclease activity, 0006281 DNA repair; PDB: 1UL1_Z 3Q8K_A 3Q8M_A 3Q8L_A 2IZO_A 1A77_A 1A76_A 3QEA_Z 3QE9_Y 3QEB_Z ....
Probab=24.68 E-value=1e+02 Score=17.91 Aligned_cols=25 Identities=16% Similarity=0.138 Sum_probs=21.8
Q ss_pred cccccHHHHHHHhCCCHHHHHHHHH
Q 036949 14 YSTISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 14 Y~sIs~~~~a~~Lgls~~e~~~~~~ 38 (81)
...++.+.+...||++.+++..+|.
T Consensus 65 ~~~~~~~~i~~~l~l~~~~fi~~~i 89 (94)
T PF00867_consen 65 VEVIDLDDILKELGLTREQFIDLCI 89 (94)
T ss_dssp EEEEEHHHHHHHHTTSHHHHHHHHH
T ss_pred eEEEEHHHHHHHcCCCHHHHHHHhe
Confidence 5678889999999999999998875
No 445
>PF07345 DUF1476: Domain of unknown function (DUF1476); InterPro: IPR009945 This family consists of several hypothetical bacterial proteins of around 100 residues in length. Members of this family are found in Bradyrhizobium, Rhizobium, Brucella and Caulobacter species. The function of this family is unknown.; PDB: 2KZC_A 2LL0_A.
Probab=24.67 E-value=26 Score=21.63 Aligned_cols=18 Identities=33% Similarity=0.630 Sum_probs=14.1
Q ss_pred HHHHhCCCHHHHHHHHHh
Q 036949 22 TALFLGMNEDDAAYYVQQ 39 (81)
Q Consensus 22 ~a~~Lgls~~e~~~~~~~ 39 (81)
+|..||++++++..|+..
T Consensus 37 AAe~lGl~g~~a~~Ya~~ 54 (103)
T PF07345_consen 37 AAELLGLTGEDAEAYAKE 54 (103)
T ss_dssp HHHHHT--CCHHHHHHCC
T ss_pred HHHHcCCCHHHHHHHHHH
Confidence 788999999999999875
No 446
>cd03472 Rieske_RO_Alpha_BPDO_like Rieske non-heme iron oxygenase (RO) family, Biphenyl dioxygenase (BPDO)-like subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; composed of the oxygenase alpha subunits of BPDO and similar proteins including cumene dioxygenase (CumDO), nitrobenzene dioxygenase (NBDO), alkylbenzene dioxygenase (AkbDO) and dibenzofuran 4,4a-dioxygenase (DFDO). ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. BPDO degrades biphenyls and polychlorinated biphenyls (PCB's) while CumDO degrades cumene (isopropylbenzene), an aromatic hydrocarbon that is i
Probab=24.66 E-value=54 Score=20.44 Aligned_cols=16 Identities=25% Similarity=0.590 Sum_probs=12.4
Q ss_pred hcCCeEeCCCceE-eec
Q 036949 39 QQGWTLDPASRML-TVK 54 (81)
Q Consensus 39 ~~GW~~d~~~~~~-~p~ 54 (81)
=.||++|.+|..+ .|.
T Consensus 73 ~Hgw~fd~~G~~~~~P~ 89 (128)
T cd03472 73 YHGWAYDTAGNLVNVPF 89 (128)
T ss_pred cCCeEECCCcCEEeccC
Confidence 3599999998887 444
No 447
>PF07471 Phage_Nu1: Phage DNA packaging protein Nu1; InterPro: IPR010906 This entry is represented by the Bacteriophage lambda, Nu1, terminase small subunit. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Terminase, the DNA packaging enzyme of bacteriophage lambda, is a heteromultimer composed of subunits Nu1 and A. The smaller Nu1 terminase subunit has a low-affinity ATPase stimulated by non-specific DNA [].; PDB: 1J9I_A.
Probab=24.43 E-value=74 Score=21.07 Aligned_cols=23 Identities=13% Similarity=0.335 Sum_probs=17.6
Q ss_pred cccHHHHHHHhCCCHHHHHHHHH
Q 036949 16 TISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 16 sIs~~~~a~~Lgls~~e~~~~~~ 38 (81)
.++-.++|..||+|+.-+.++..
T Consensus 2 ~vnk~~lA~i~gvS~~ti~~W~~ 24 (164)
T PF07471_consen 2 KVNKKELAEIFGVSERTIDKWQR 24 (164)
T ss_dssp EEEHHHHHHHTT--HHHHHHHTT
T ss_pred CCCHHHHHHHHCCCHHHHHHHHH
Confidence 36778999999999999998853
No 448
>PF07957 DUF3294: Protein of unknown function (DUF3294); InterPro: IPR012917 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This is a family of mitochondrial ribosomal proteins, which appears to be fungal specific [].
Probab=24.42 E-value=44 Score=23.38 Aligned_cols=25 Identities=20% Similarity=0.340 Sum_probs=15.7
Q ss_pred HHHHHHHHhccccc----HHHHHHHhCCC
Q 036949 5 RMFQLLMSAYSTIS----TQDTALFLGMN 29 (81)
Q Consensus 5 ~~~~li~~AY~sIs----~~~~a~~Lgls 29 (81)
.-+.--.+.|+.-- .+++|+|||+.
T Consensus 180 ~~i~~~~k~~s~~eld~ifdelARylGlr 208 (216)
T PF07957_consen 180 EEIEKELKKYSKEELDEIFDELARYLGLR 208 (216)
T ss_pred HHHHHHHHhcCHHHHHHHHHHHHHHhCch
Confidence 33444455565544 56799999983
No 449
>PF03278 IpaB_EvcA: IpaB/EvcA family; InterPro: IPR004959 The IpgB family includes the invasion plasmid antigen from Shigella flexneri [], as well as related proteins from Escherichia coli species. Members of this family seem to be involved in pathogenicity of some enterobacteria. However the exact function of these proteins is unclear.; GO: 0009405 pathogenesis; PDB: 3LYQ_A 3LW8_G 3LWN_F 3LXR_F 3GCG_B.
Probab=24.34 E-value=54 Score=21.68 Aligned_cols=19 Identities=21% Similarity=0.434 Sum_probs=13.1
Q ss_pred hHHHHHHHHHHhcccccHHH
Q 036949 2 YTKRMFQLLMSAYSTISTQD 21 (81)
Q Consensus 2 ~R~~~~~li~~AY~sIs~~~ 21 (81)
.|.++|.+|++.| .++++.
T Consensus 66 ~k~~IF~~i~~~~-~~~LD~ 84 (152)
T PF03278_consen 66 TKQRIFKLIEKKF-GIKLDV 84 (152)
T ss_dssp HHHHHHHHHHHHH-T----T
T ss_pred HHHHHHHHHHHHh-CCccch
Confidence 5899999999998 777665
No 450
>cd01389 MATA_HMG-box MATA_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include the fungal mating type gene products MC, MATA1 and Ste11.
Probab=24.27 E-value=1.4e+02 Score=16.52 Aligned_cols=41 Identities=10% Similarity=0.258 Sum_probs=22.4
Q ss_pred HHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHhc-CCeEeC
Q 036949 6 MFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQ-GWTLDP 46 (81)
Q Consensus 6 ~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~~-GW~~d~ 46 (81)
|...|+.....++-++=+.|..+...+-..+..+. +|.+.+
T Consensus 32 isk~~g~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~p~Yky~p 73 (77)
T cd01389 32 ISRIIGRMWRSESPEVKAYYKELAEEEKERHAREYPDYKYTP 73 (77)
T ss_pred HHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHCCCCcccC
Confidence 44455555555555555555555555555666554 676643
No 451
>PF07862 Nif11: Nitrogen fixation protein of unknown function; InterPro: IPR012903 This domain is found in the cyanobacteria, and the nitrogen-fixing proteobacterium Azotobacter vinelandii and may be involved in nitrogen fixation, but no role has been assigned [].
Probab=24.24 E-value=51 Score=16.90 Aligned_cols=18 Identities=11% Similarity=0.409 Sum_probs=15.6
Q ss_pred CHHHHHHHHHhcCCeEeC
Q 036949 29 NEDDAAYYVQQQGWTLDP 46 (81)
Q Consensus 29 s~~e~~~~~~~~GW~~d~ 46 (81)
+++++.+++.+.|-.+++
T Consensus 28 ~~~e~~~lA~~~Gy~ft~ 45 (49)
T PF07862_consen 28 NPEEVVALAREAGYDFTE 45 (49)
T ss_pred CHHHHHHHHHHcCCCCCH
Confidence 889999999999988753
No 452
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=24.20 E-value=1.2e+02 Score=17.67 Aligned_cols=25 Identities=16% Similarity=0.242 Sum_probs=18.7
Q ss_pred cccccHHHHHHHhCCCHHHHHHHHH
Q 036949 14 YSTISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 14 Y~sIs~~~~a~~Lgls~~e~~~~~~ 38 (81)
+.-.+..++|..||+|...+.....
T Consensus 124 ~~g~s~~eIA~~l~~s~~~v~~~~~ 148 (158)
T TIGR02937 124 LEGLSYKEIAEILGISVGTVKRRLK 148 (158)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3567888899999998877765543
No 453
>KOG1344 consensus Predicted histone deacetylase [Chromatin structure and dynamics]
Probab=24.15 E-value=52 Score=23.82 Aligned_cols=22 Identities=18% Similarity=0.432 Sum_probs=17.0
Q ss_pred HHHHHHhcCCeEeCCCceEeec
Q 036949 33 AAYYVQQQGWTLDPASRMLTVK 54 (81)
Q Consensus 33 ~~~~~~~~GW~~d~~~~~~~p~ 54 (81)
+.+.+.++||.++-.|.+..-.
T Consensus 124 A~kLAle~GWAINvGGGFHHcs 145 (324)
T KOG1344|consen 124 AAKLALERGWAINVGGGFHHCS 145 (324)
T ss_pred hhhhhhhcCeEEeecCccceec
Confidence 3567889999999888876543
No 454
>PF11800 RP-C_C: Replication protein C C-terminal region; InterPro: IPR021760 Replication protein C is involved in the early stages of viral DNA replication.
Probab=24.13 E-value=96 Score=20.85 Aligned_cols=25 Identities=12% Similarity=0.114 Sum_probs=20.3
Q ss_pred HHHHHHhCCCHHHHHHHHHhcCCeE
Q 036949 20 QDTALFLGMNEDDAAYYVQQQGWTL 44 (81)
Q Consensus 20 ~~~a~~Lgls~~e~~~~~~~~GW~~ 44 (81)
..++.|||+|+.--.+.+...|...
T Consensus 134 ~~lr~mlGIs~~aw~~A~~~mG~~~ 158 (207)
T PF11800_consen 134 DQLRPMLGISPSAWEEACRAMGREA 158 (207)
T ss_pred HHHHHHcCCCHHHHHHHHHHhChHH
Confidence 3588999999988888888778763
No 455
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=24.07 E-value=1e+02 Score=16.09 Aligned_cols=23 Identities=17% Similarity=0.228 Sum_probs=15.4
Q ss_pred cccHHHHHHHhCCCHHHHHHHHH
Q 036949 16 TISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 16 sIs~~~~a~~Lgls~~e~~~~~~ 38 (81)
.++..++|..+|++...+-.+-.
T Consensus 12 ~lt~~~~a~~~~i~~~~i~~~e~ 34 (64)
T PF12844_consen 12 GLTQKDLAEKLGISRSTISKIEN 34 (64)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHT
T ss_pred CCCHHHHHHHHCcCHHHHHHHHC
Confidence 67888999999998777766544
No 456
>COG3753 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.06 E-value=1.4e+02 Score=19.58 Aligned_cols=32 Identities=22% Similarity=0.185 Sum_probs=25.7
Q ss_pred HHHHHhcccccHHHHHHHhCCCHHHHHHHHHh
Q 036949 8 QLLMSAYSTISTQDTALFLGMNEDDAAYYVQQ 39 (81)
Q Consensus 8 ~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~ 39 (81)
.-++.|..+=.++++|.-+|++.+|+.+...+
T Consensus 82 ~ql~~aiG~~~l~~la~~~Gld~~El~~~Ls~ 113 (143)
T COG3753 82 EQLESAIGTDTLSQLAQKTGLDEQELLKQLSE 113 (143)
T ss_pred HHHHHHhchhHHHHHHHHhCCCHHHHHHHHHH
Confidence 35677888888899999999999988776553
No 457
>PF01747 ATP-sulfurylase: ATP-sulfurylase; InterPro: IPR002650 This entry consists of sulphate adenylyltransferase or ATP-sulfurylase (2.7.7.4 from EC) some of which are part of a bifunctional polypeptide chain associated with adenosyl phosphosulphate (APS) kinase, IPR002891 from INTERPRO. Both enzymes are required for PAPS (phosphoadenosine-phosphosulphate) synthesis from inorganic sulphate []. ATP sulfurylase catalyses the synthesis of adenosine-phosphosulphate APS from ATP and inorganic sulphate [].; GO: 0004781 sulfate adenylyltransferase (ATP) activity, 0000103 sulfate assimilation; PDB: 3CR8_B 1M8P_C 1I2D_B 1JHD_A 1V47_B 1X6V_B 1XNJ_A 1XJQ_B 2QJF_A 2GKS_B ....
Probab=24.02 E-value=55 Score=22.61 Aligned_cols=17 Identities=12% Similarity=0.528 Sum_probs=12.5
Q ss_pred CCCHHHHHHHHHhcCCe
Q 036949 27 GMNEDDAAYYVQQQGWT 43 (81)
Q Consensus 27 gls~~e~~~~~~~~GW~ 43 (81)
-+++.|+.+..+++||.
T Consensus 5 r~tP~e~r~~~~~~gw~ 21 (215)
T PF01747_consen 5 RLTPAETRELFKEKGWR 21 (215)
T ss_dssp B--HHHHHHHHHHTT-S
T ss_pred hCCHHHHHHHHHhcCCC
Confidence 35899999999999997
No 458
>PF02669 KdpC: K+-transporting ATPase, c chain; InterPro: IPR003820 Kdp, the high affinity ATP-driven K+-transport system of Escherichia coli, is a complex of the membrane-bound subunits KdpA, KdpB, KdpC and the small peptide KdpF. KdpC forms strong interactions with the KdpA subunit, serving to assemble and stabilise the Kdp complex []. It has been suggested that KdpC could be one of the connecting links between the energy providing subunit KdpB and the K+- transporting subunit KdpA []. The K+ transport system actively transports K+ ions via ATP hydrolysis.; GO: 0008556 potassium-transporting ATPase activity, 0006813 potassium ion transport, 0016020 membrane
Probab=24.01 E-value=66 Score=21.96 Aligned_cols=30 Identities=17% Similarity=0.268 Sum_probs=24.5
Q ss_pred HHHhcccccHHHHHHHhCCCHHHHHHHHHh
Q 036949 10 LMSAYSTISTQDTALFLGMNEDDAAYYVQQ 39 (81)
Q Consensus 10 i~~AY~sIs~~~~a~~Lgls~~e~~~~~~~ 39 (81)
|+-++..+.++.+|+--|++++++.+++.+
T Consensus 132 IS~~aA~~Qv~RVA~argl~~~~v~~li~~ 161 (188)
T PF02669_consen 132 ISPAAALIQVPRVAKARGLSEEEVEALIDK 161 (188)
T ss_pred cCHHHHHHHHHHHHHHhCcCHHHHHHHHHH
Confidence 455677788889999999999998888764
No 459
>PRK09726 antitoxin HipB; Provisional
Probab=23.99 E-value=1.5e+02 Score=16.91 Aligned_cols=22 Identities=9% Similarity=0.205 Sum_probs=16.6
Q ss_pred cccHHHHHHHhCCCHHHHHHHH
Q 036949 16 TISTQDTALFLGMNEDDAAYYV 37 (81)
Q Consensus 16 sIs~~~~a~~Lgls~~e~~~~~ 37 (81)
.++..++|..+|++...+..+.
T Consensus 25 gltq~elA~~~gvs~~tis~~e 46 (88)
T PRK09726 25 GWTQSELAKKIGIKQATISNFE 46 (88)
T ss_pred CCCHHHHHHHHCcCHHHHHHHH
Confidence 6788889999988876665543
No 460
>PLN03083 E3 UFM1-protein ligase 1 homolog; Provisional
Probab=23.92 E-value=1.7e+02 Score=24.41 Aligned_cols=36 Identities=14% Similarity=0.084 Sum_probs=29.4
Q ss_pred hHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH
Q 036949 2 YTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 2 ~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~ 38 (81)
+|++|.+.| .+..+|++-+++..||+....+...+.
T Consensus 61 L~~EI~~El-~~gGRvnlvdLa~~LnVD~~hiEr~~~ 96 (803)
T PLN03083 61 LRNEIEAEI-KKLGRVSLVDLADTIGVDLYHVERQAQ 96 (803)
T ss_pred HHHHHHHHH-HhCCCeeHHHHhhhcCCCHHHHHHHHH
Confidence 578888888 468999999999999998766655444
No 461
>TIGR01784 T_den_put_tspse conserved hypothetical protein (putative transposase or invertase). Several lines of evidence suggest that members of this family (loaded as a fragment mode model to find part-length matches) are associated with transposition, inversion, or recombination. Members are found in small numbers of genomes, but in large copy numbers in many of those species, including over 30 full length and fragmentary members in Treponema denticola. The strongest similarities are usually within rather than between species. PSI-BLAST shows similarity to proteins designated as possible transposases, DNA invertases (resolvases), and recombinases. In the oral pathogenic spirochete Treponema denticola, full-length members are often found near transporters or other membrane proteins. This family includes members of the putative transposase family pfam04754.
Probab=23.91 E-value=1.3e+02 Score=20.20 Aligned_cols=20 Identities=10% Similarity=0.175 Sum_probs=16.2
Q ss_pred cccHHHHHHHhCCCHHHHHH
Q 036949 16 TISTQDTALFLGMNEDDAAY 35 (81)
Q Consensus 16 sIs~~~~a~~Lgls~~e~~~ 35 (81)
-++.+.++.+.|||.+++.+
T Consensus 250 g~~~~~i~~~~~Ls~eei~~ 269 (270)
T TIGR01784 250 GLTLEQVAEATGLSVEELEE 269 (270)
T ss_pred CCCHHHHHHHHCcCHHHHhh
Confidence 48888888888888888765
No 462
>cd08803 Death_ank3 Death domain of Ankyrin-3. Death Domain (DD) of the human protein ankyrin-3 (ANK-3) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-3, also called anykyrin-G (for general or giant), is found in neurons and at least one splice variant has been shown to be essential for propagation of action potentials as a binding partner to neurofascin and voltage-gated sodium channels. It is required for maintaining axo-dendritic polarity, and may be a genetic risk factor associated with bipolar disorder. ANK-3 may also play roles in other cell types. Mutations affecting ANK-3 pathways for Na channel localization are associated with Brugada syndrome, a potentially fata arrythmia. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by se
Probab=23.88 E-value=93 Score=18.22 Aligned_cols=20 Identities=15% Similarity=-0.004 Sum_probs=15.8
Q ss_pred HHHHHHHhCCCHHHHHHHHH
Q 036949 19 TQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 19 ~~~~a~~Lgls~~e~~~~~~ 38 (81)
-..+|.-||++..++..+-.
T Consensus 18 W~~LA~eLg~s~~dI~~i~~ 37 (84)
T cd08803 18 WTELARELNFSVDEINQIRV 37 (84)
T ss_pred HHHHHHHcCCCHHHHHHHHH
Confidence 35689999999999887743
No 463
>cd08805 Death_ank1 Death domain of Ankyrin-1. Death Domain (DD) of the human protein ankyrin-1 (ANK-1) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-1, also called ankyrin-R (for restricted), is found in brain, muscle, and erythrocytes and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. It plays a critical nonredundant role in erythroid development and is associated with hereditary spherocytosis (HS), a common disorder of the red cell membrane. The small alternatively-spliced variant, sANK-1, found in striated muscle and concentrated in the sarcoplasmic reticulum (SR) binds obscurin and titin, which facilitates the anchoring of the network SR to the contractile apparatus. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common featur
Probab=23.73 E-value=1.1e+02 Score=17.91 Aligned_cols=21 Identities=14% Similarity=-0.004 Sum_probs=15.6
Q ss_pred HHHHHHHhCCCHHHHHHHHHh
Q 036949 19 TQDTALFLGMNEDDAAYYVQQ 39 (81)
Q Consensus 19 ~~~~a~~Lgls~~e~~~~~~~ 39 (81)
-..+|.-||+|..++..+-.+
T Consensus 18 W~~Lar~L~vs~~dI~~I~~e 38 (84)
T cd08805 18 WAELARELQFSVEDINRIRVE 38 (84)
T ss_pred HHHHHHHcCCCHHHHHHHHHh
Confidence 456888899988888766544
No 464
>PF06870 RNA_pol_I_A49: A49-like RNA polymerase I associated factor ; InterPro: IPR009668 Saccharomyces cerevisiae A49 is a specific subunit associated with RNA polymerase I (Pol I) in eukaryotes. Pol I maintains transcription activities in A49 deletion mutants. However, such mutants are deficient in transcription activity at low temperatures. Deletion analysis of the fusion yeast homologue indicates that only the C-terminal two thirds are required for function. Transcript analysis has demonstrated that A49 is maximising transcription of ribosomal DNA [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent, 0005634 nucleus; PDB: 3NFG_A 3NFH_B.
Probab=23.73 E-value=1.5e+02 Score=21.66 Aligned_cols=40 Identities=18% Similarity=0.310 Sum_probs=31.1
Q ss_pred HHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHhcCCeEeC
Q 036949 6 MFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDP 46 (81)
Q Consensus 6 ~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~d~ 46 (81)
++.|+-.-|+ +.+++++.=|++++..+.+++...|=++..
T Consensus 310 ~LaL~id~f~-~d~~~L~~dLkl~~~~l~~~~r~LGC~v~~ 349 (385)
T PF06870_consen 310 ALALHIDNFS-VDITDLARDLKLSPKKLTQYFRELGCKVKK 349 (385)
T ss_dssp HHHHHHTTTE-EEHHHHHHHHT--HHHHHHHHHHTT-EEEE
T ss_pred HHHHHhcCcc-cChHHHHHHhCCCHHHHHHHHHHhCCEecc
Confidence 3445556676 689999999999999999999999999865
No 465
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=23.65 E-value=1.1e+02 Score=23.25 Aligned_cols=39 Identities=23% Similarity=0.245 Sum_probs=30.6
Q ss_pred HHhcccccHHHHHHHhCCCHHHHHHHHHhcCCeEeCCCce
Q 036949 11 MSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRM 50 (81)
Q Consensus 11 ~~AY~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~~~ 50 (81)
.+-|=..+++++|..||++.+++.+..... .++||.|..
T Consensus 108 ~~GyL~~~~~eia~~l~~~~~~ve~~l~~i-q~leP~GIg 146 (429)
T TIGR02395 108 EDGYLEIDLEEIADELEVSEEEVEKVLELI-QRLDPAGVG 146 (429)
T ss_pred CCCCCCCCHHHHHHHcCCCHHHHHHHHHHH-hcCCCCccC
Confidence 467889999999999999998888765543 358887644
No 466
>TIGR03453 partition_RepA plasmid partitioning protein RepA. Members of this family are the RepA (or ParA) protein involved in replicon partitioning. All known examples occur in bacterial species with two or more replicons, on a plasmid or the smaller chromosome. Note that an apparent exception may be seen as a pseudomolecule from assembly of an incompletely sequenced genome. Members of this family belong to a larger family that also includes the enzyme cobyrinic acid a,c-diamide synthase, but assignment of that name to members of this family would be in error.
Probab=23.51 E-value=2.9e+02 Score=20.20 Aligned_cols=52 Identities=12% Similarity=0.174 Sum_probs=32.2
Q ss_pred cccHHHHHHHhCCCHHHHHHHHHhcCCeEeCCCceEeecCCCCcccCCC-ChhHHHHHHhHHH
Q 036949 16 TISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVTEQKL-DPSKMQCLTEYVF 77 (81)
Q Consensus 16 sIs~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~~~~~p~~~~~~~~~~~-~~~~l~~Lt~~v~ 77 (81)
..++.++|+++|++..-+..+ .++|.- |.+...+..... +.+++..|...+.
T Consensus 33 ~~~i~eva~~~gv~~~tlr~~-e~~~~~---------~~~~r~~~g~r~yt~~di~~l~~~~~ 85 (387)
T TIGR03453 33 KFTSGEVAKLLGVSDSYLRQL-SLEGKG---------PEPETLSNGRRSYTLEQINELRRHLA 85 (387)
T ss_pred cCCHHHHHHHHCcCHHHHHHH-HHcCCC---------CCCCcCCCCceeeCHHHHHHHHHHHH
Confidence 458999999999999988865 444442 111111111222 7777777776553
No 467
>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional
Probab=23.33 E-value=2e+02 Score=22.78 Aligned_cols=40 Identities=13% Similarity=0.219 Sum_probs=29.4
Q ss_pred HHHHHHHHHHhccccc-HHHHHHHhCCCHHHHHHHHHhcCC
Q 036949 3 TKRMFQLLMSAYSTIS-TQDTALFLGMNEDDAAYYVQQQGW 42 (81)
Q Consensus 3 R~~~~~li~~AY~sIs-~~~~a~~Lgls~~e~~~~~~~~GW 42 (81)
|+.|...+..+-..++ .+.+|+.||++..-+-.-.++.|-
T Consensus 643 r~~I~~aL~~~~gn~~~~~~aA~~LGi~R~tL~rklk~~gi 683 (686)
T PRK15429 643 YQLIVRVLKETNGVVAGPKGAAQRLGLKRTTLLSRMKRLGI 683 (686)
T ss_pred HHHHHHHHHHcCCCcccHHHHHHHhCCCHHHHHHHHHHcCC
Confidence 4556666677666665 679999999998887766666665
No 468
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, 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 dissimil
Probab=23.31 E-value=1.3e+02 Score=17.85 Aligned_cols=50 Identities=14% Similarity=0.280 Sum_probs=30.7
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHhcCCeEeCCCceEeecCCCCcccCCC-ChhHHHHHHhHHH
Q 036949 17 ISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVTEQKL-DPSKMQCLTEYVF 77 (81)
Q Consensus 17 Is~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~~~~~p~~~~~~~~~~~-~~~~l~~Lt~~v~ 77 (81)
.++.++|+.+|+|..-+.-|-.. | .+ |... .+..--. +++++..|..+..
T Consensus 2 ~~i~eva~~~gvs~~tLR~ye~~--------G-ll-~~~r-~~~g~R~Y~~~dl~~l~~I~~ 52 (102)
T cd04775 2 YTIGQMSRKFGVSRSTLLYYESI--------G-LI-PSAR-SEANYRLYSEADLSRLEKIVF 52 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC--------C-CC-CCCC-CCCCCeeeCHHHHHHHHHHHH
Confidence 36889999999999999765552 3 22 3221 1121122 7777777765543
No 469
>TIGR00681 kdpC K+-transporting ATPase, C subunit. This chain has a single predicted transmembrane region near the amino end. It is part of a K+-transport ATPase that contains two other membrane-bound subunits, KdpA and KdpB, and a small subunit KdpF. KdpA is the K+-translocating subunit, KdpB the ATP-hydrolyzing subunit. During assembly of the complex, KdpA and KdpC bind to each other. This interaction is thought to stabilize the complex [PubMed:9858692]. Data indicates that KdpC might connect the KdpA, the K+-transporting subunit, to KdpB, the ATP-hydrolyzing (energy providing) subunit [PubMed:9858692].
Probab=23.17 E-value=66 Score=21.96 Aligned_cols=30 Identities=7% Similarity=0.025 Sum_probs=24.1
Q ss_pred HHHhcccccHHHHHHHhCCCHHHHHHHHHh
Q 036949 10 LMSAYSTISTQDTALFLGMNEDDAAYYVQQ 39 (81)
Q Consensus 10 i~~AY~sIs~~~~a~~Lgls~~e~~~~~~~ 39 (81)
||-+|..+.+..+|+--||+++++.+.+.+
T Consensus 131 ISp~aA~~Qv~RVA~argl~~~~v~~LI~~ 160 (187)
T TIGR00681 131 ISPAAAQAQFPRVAKARNISPQQLQSLITK 160 (187)
T ss_pred CCHHHHHHHHHHHHHHhCcCHHHHHHHHHH
Confidence 455667778888999999999999888764
No 470
>PF05331 DUF742: Protein of unknown function (DUF742); InterPro: IPR007995 This family consists of several uncharacterised Streptomyces proteins as well as one from Mycobacterium tuberculosis. The function of these proteins is unknown.
Probab=23.16 E-value=92 Score=19.47 Aligned_cols=31 Identities=19% Similarity=0.245 Sum_probs=21.7
Q ss_pred HHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHH
Q 036949 4 KRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYV 37 (81)
Q Consensus 4 ~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~ 37 (81)
.+|+++... .+|+.++|..|+++..-+.-.+
T Consensus 46 ~~Il~lC~~---~~SVAEiAA~L~lPlgVvrVLv 76 (114)
T PF05331_consen 46 RAILELCRR---PLSVAEIAARLGLPLGVVRVLV 76 (114)
T ss_pred HHHHHHHCC---CccHHHHHHhhCCCchhhhhhH
Confidence 445555555 8999999999999765544333
No 471
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=23.15 E-value=1.9e+02 Score=17.65 Aligned_cols=25 Identities=16% Similarity=-0.037 Sum_probs=18.7
Q ss_pred HhcccccHHHHHHHhCCCHHHHHHH
Q 036949 12 SAYSTISTQDTALFLGMNEDDAAYY 36 (81)
Q Consensus 12 ~AY~sIs~~~~a~~Lgls~~e~~~~ 36 (81)
+-|.-.+..++|..||+|...+...
T Consensus 123 ~~~~g~~~~eIA~~l~is~~tv~~~ 147 (159)
T TIGR02989 123 RYQRGVSLTALAEQLGRTVNAVYKA 147 (159)
T ss_pred HHhcCCCHHHHHHHhCCCHHHHHHH
Confidence 3567788888888888888766544
No 472
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=23.00 E-value=2.3e+02 Score=19.52 Aligned_cols=42 Identities=21% Similarity=0.339 Sum_probs=30.9
Q ss_pred HHHHHHHHhcccccHHHHHHHhCCCHHHHHHHH---HhcCCeE-eC
Q 036949 5 RMFQLLMSAYSTISTQDTALFLGMNEDDAAYYV---QQQGWTL-DP 46 (81)
Q Consensus 5 ~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~---~~~GW~~-d~ 46 (81)
++++++...=..+++.++|+-+|++..-+-.+. .+.||.- |+
T Consensus 8 ~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL~~~G~v~~d~ 53 (246)
T COG1414 8 AILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTLVELGYVEQDP 53 (246)
T ss_pred HHHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEcC
Confidence 467777773334789999999999888765554 4679985 44
No 473
>cd01388 SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and transcription factor-like proteins, TCF-1, -3, -4, and LEF-1. They appear to bind the minor groove of the A/T C A A A G/C-motif.
Probab=22.97 E-value=1.4e+02 Score=16.26 Aligned_cols=35 Identities=6% Similarity=0.161 Sum_probs=14.5
Q ss_pred HHHHhcccccHHHHHHHhCCCHHHHHHHHHhc-CCe
Q 036949 9 LLMSAYSTISTQDTALFLGMNEDDAAYYVQQQ-GWT 43 (81)
Q Consensus 9 li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~~-GW~ 43 (81)
.++......+.++-..|.-....+...+..+. +|.
T Consensus 35 ~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~p~y~ 70 (72)
T cd01388 35 ILGDRWKALSNEEKQPYYEEAKKLKELHMKLYPDYK 70 (72)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHCcCCC
Confidence 33444444444444444333334444444433 443
No 474
>PF13167 GTP-bdg_N: GTP-binding GTPase N-terminal
Probab=22.94 E-value=1.8e+02 Score=17.46 Aligned_cols=46 Identities=7% Similarity=0.169 Sum_probs=24.6
Q ss_pred CHHHHHHHHHhcCCeEeCCCceEeecCCCCcccCCCChhHHHHHHhHHH
Q 036949 29 NEDDAAYYVQQQGWTLDPASRMLTVKKQPLVTEQKLDPSKMQCLTEYVF 77 (81)
Q Consensus 29 s~~e~~~~~~~~GW~~d~~~~~~~p~~~~~~~~~~~~~~~l~~Lt~~v~ 77 (81)
+-+|+...|...||++= +.++.. ...+.+..-.+.-+++.|.+.+.
T Consensus 9 ~l~El~~L~~t~g~~vv--~~~~q~-~~~~~p~~~iG~GK~eei~~~~~ 54 (95)
T PF13167_consen 9 SLEELEELAETAGYEVV--GTVVQK-RRKPDPKTYIGSGKVEEIKELIE 54 (95)
T ss_pred HHHHHHHHHHHCCCeEE--EEEEec-CCCCCcceeechhHHHHHHHHHh
Confidence 35788899999999983 333332 22222221124455555555443
No 475
>PRK10130 transcriptional regulator EutR; Provisional
Probab=22.83 E-value=2.2e+02 Score=20.87 Aligned_cols=35 Identities=9% Similarity=0.095 Sum_probs=25.7
Q ss_pred HHHHHHHHhc-ccccHHHHHHHhCCCHHHHHHHHHh
Q 036949 5 RMFQLLMSAY-STISTQDTALFLGMNEDDAAYYVQQ 39 (81)
Q Consensus 5 ~~~~li~~AY-~sIs~~~~a~~Lgls~~e~~~~~~~ 39 (81)
++.+.|..-| ..|+++++|..+|+|.--+....++
T Consensus 244 ~~~~~i~~~~~~~ltv~~lA~~~gvS~r~L~r~Fk~ 279 (350)
T PRK10130 244 RAREYVLENMSEPVTVLDLCNQLHVSRRTLQNAFHA 279 (350)
T ss_pred HHHHHHHhhhcCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 3445555555 4599999999999999888666654
No 476
>PF07093 SGT1: SGT1 protein; InterPro: IPR010770 This family consists of several eukaryotic SGT1 proteins. Human SGT1 or hSGT1 is known to suppress GCR2 and is highly expressed in the muscle and heart. The function of this family is unknown although it has been speculated that SGT1 may be functionally analogous to the Gcr2p protein of Saccharomyces cerevisiae which is known to be a regulatory factor of glycolytic gene expression [].
Probab=22.80 E-value=1.5e+02 Score=23.39 Aligned_cols=28 Identities=14% Similarity=0.290 Sum_probs=22.4
Q ss_pred cHHHHHHHhCCCHHHHHHHHHhcCCeEe
Q 036949 18 STQDTALFLGMNEDDAAYYVQQQGWTLD 45 (81)
Q Consensus 18 s~~~~a~~Lgls~~e~~~~~~~~GW~~d 45 (81)
..++=-+||.++++++.+...++++...
T Consensus 383 ~~eDdDsWL~i~~edLe~~L~er~~~~~ 410 (589)
T PF07093_consen 383 PPEDDDSWLDIDPEDLERELQERQGKMK 410 (589)
T ss_pred CCCCChhhhhCCHHHHHHHHHHHhcccc
Confidence 3444568999999999999999877764
No 477
>PF06224 HTH_42: Winged helix DNA-binding domain; InterPro: IPR009351 This is a family of conserved bacterial proteins with unknown function.
Probab=22.76 E-value=2.5e+02 Score=19.73 Aligned_cols=36 Identities=19% Similarity=0.197 Sum_probs=28.7
Q ss_pred HHHHHHhcccccHHHHHHHhCCCHHHHHHHHHhcCC
Q 036949 7 FQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGW 42 (81)
Q Consensus 7 ~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~~GW 42 (81)
+.---++|.=.++.++|.|+|++..++.....+.+-
T Consensus 172 v~Ryl~~~GPat~~d~a~w~gl~~~~~r~~l~~l~~ 207 (327)
T PF06224_consen 172 VRRYLRAYGPATLADFAWWSGLPKTQARRALAQLVE 207 (327)
T ss_pred HHHHHHHcCCccHHHHHHHhccCHHHHHHHHHhhcc
Confidence 333446788899999999999999999888876643
No 478
>PF06322 Phage_NinH: Phage NinH protein; InterPro: IPR010454 This entry is represented by Bacteriophage 933W, NinH. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=22.67 E-value=1.1e+02 Score=17.34 Aligned_cols=31 Identities=26% Similarity=0.464 Sum_probs=23.7
Q ss_pred HHHHHhcccccHHHHHHHhCCCHHHHHHHHHhc
Q 036949 8 QLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQ 40 (81)
Q Consensus 8 ~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~~ 40 (81)
.++-++|.. ..++|++||.+.+-+.+|+...
T Consensus 10 elLi~~~Gn--qtEvaR~l~c~R~TVrKY~~D~ 40 (64)
T PF06322_consen 10 ELLIETYGN--QTEVARRLGCNRATVRKYSRDK 40 (64)
T ss_pred HHHHHHhCc--HHHHHHHhcccHHHHHHHhccc
Confidence 345556654 5689999999999999998754
No 479
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=22.60 E-value=1.3e+02 Score=15.99 Aligned_cols=18 Identities=17% Similarity=0.338 Sum_probs=8.7
Q ss_pred HHHhcccccHHHHHHHhC
Q 036949 10 LMSAYSTISTQDTALFLG 27 (81)
Q Consensus 10 i~~AY~sIs~~~~a~~Lg 27 (81)
+.+-+...|+.+++.+||
T Consensus 39 la~~~~~~sl~~Ig~~fg 56 (60)
T smart00760 39 LARELTDLSLPEIGKIFG 56 (60)
T ss_pred HHHHHHCCCHHHHHHHhC
Confidence 344444455555555554
No 480
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=22.37 E-value=1.2e+02 Score=19.47 Aligned_cols=26 Identities=15% Similarity=0.130 Sum_probs=21.0
Q ss_pred hcccccHHHHHHHhCCCHHHHHHHHH
Q 036949 13 AYSTISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 13 AY~sIs~~~~a~~Lgls~~e~~~~~~ 38 (81)
--.++|..++|+-+|+|+.-+..-.+
T Consensus 25 ~d~R~s~~eiA~~lglS~~tv~~Ri~ 50 (164)
T PRK11169 25 KDGRISNVELSKRVGLSPTPCLERVR 50 (164)
T ss_pred cCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 34678999999999999988766544
No 481
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=22.22 E-value=2.6e+02 Score=18.87 Aligned_cols=30 Identities=13% Similarity=0.252 Sum_probs=22.5
Q ss_pred ccc-cHHHHHHHhCCCHH---HHHHHHHhcCCeE
Q 036949 15 STI-STQDTALFLGMNED---DAAYYVQQQGWTL 44 (81)
Q Consensus 15 ~sI-s~~~~a~~Lgls~~---e~~~~~~~~GW~~ 44 (81)
..| +-.++|..||+|-. |+.......|+..
T Consensus 32 ~~LpsE~eLa~~lgVSRtpVREAL~~L~~eGlv~ 65 (254)
T PRK09464 32 EKLPPERELAKQFDVSRPSLREAIQRLEAKGLLL 65 (254)
T ss_pred CcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence 567 78899999999754 4555556779984
No 482
>PRK09490 metH B12-dependent methionine synthase; Provisional
Probab=22.17 E-value=17 Score=31.21 Aligned_cols=29 Identities=17% Similarity=0.480 Sum_probs=23.0
Q ss_pred HHHhCC---CHHHHHHHHHhcCCeEeCCCceE
Q 036949 23 ALFLGM---NEDDAAYYVQQQGWTLDPASRML 51 (81)
Q Consensus 23 a~~Lgl---s~~e~~~~~~~~GW~~d~~~~~~ 51 (81)
|+|+++ ..+++.+|+..+||+++..-+.+
T Consensus 1193 a~YF~vg~i~~dq~~dya~r~~~~~~~~~~~l 1224 (1229)
T PRK09490 1193 SKYFAVGKIGRDQVEDYAARKGMSVEEVERWL 1224 (1229)
T ss_pred CCcccCCCCCHHHHHHHHHhCCCCHHHHHHHh
Confidence 678887 78999999999999986544443
No 483
>COG2154 Pterin-4a-carbinolamine dehydratase [Coenzyme metabolism]
Probab=22.15 E-value=97 Score=19.07 Aligned_cols=23 Identities=17% Similarity=0.426 Sum_probs=17.0
Q ss_pred HhCCCHHHHHHHHHhc-CCeEeCC
Q 036949 25 FLGMNEDDAAYYVQQQ-GWTLDPA 47 (81)
Q Consensus 25 ~Lgls~~e~~~~~~~~-GW~~d~~ 47 (81)
+..|+.+++.....+. ||.+..+
T Consensus 3 ~~~lt~~~~~~~l~~l~gW~l~~~ 26 (101)
T COG2154 3 ASKLTDEELAELLRALPGWELADD 26 (101)
T ss_pred ccccCHHHHHHHhcCCCCCEEecC
Confidence 3456778888777776 9999755
No 484
>PF10678 DUF2492: Protein of unknown function (DUF2492); InterPro: IPR019620 This entry describes a family of small cytosolic proteins, about 80 amino acids in length, in which the eight invariant residues include three His residues and two Cys residues. Two pairs of these invariant residues occur in motifs HxH (where x is A or G) and CxH, both of which suggest metal-binding activity. This protein family was identified by searching with a phylogenetic profile based on an anaerobic sulphatase-maturase enzyme, which contains multiple 4Fe-4S clusters. The linkages by phylogenetic profiling and by iron-sulphur cluster-related motifs together suggest this protein may be an accessory protein to certain maturases in sulphatase/maturase systems.
Probab=21.68 E-value=1.9e+02 Score=17.01 Aligned_cols=28 Identities=14% Similarity=0.290 Sum_probs=19.7
Q ss_pred HHHhCCCHHHHHHHHHhcCCeEeCCCce
Q 036949 23 ALFLGMNEDDAAYYVQQQGWTLDPASRM 50 (81)
Q Consensus 23 a~~Lgls~~e~~~~~~~~GW~~d~~~~~ 50 (81)
++-=||+.+++.+|..+||=-+..++.+
T Consensus 42 CSae~m~a~eLv~FL~~rgKfi~~~~g~ 69 (78)
T PF10678_consen 42 CSAEGMTADELVDFLEERGKFIPSDDGF 69 (78)
T ss_pred cCCCCCCHHHHHHHHHHcCCEeecCCCE
Confidence 4455788999999998886555444444
No 485
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=21.67 E-value=2.4e+02 Score=18.24 Aligned_cols=26 Identities=19% Similarity=0.344 Sum_probs=19.8
Q ss_pred HHHHHHHHhcccccHHHHHHHhCCCHHHH
Q 036949 5 RMFQLLMSAYSTISTQDTALFLGMNEDDA 33 (81)
Q Consensus 5 ~~~~li~~AY~sIs~~~~a~~Lgls~~e~ 33 (81)
+++.+ -+.-.+..++|..||+|..-+
T Consensus 13 eVL~l---r~~GlTq~EIAe~LGiS~~tV 38 (141)
T PRK03975 13 EVLRL---RERGLTQQEIADILGTSRANV 38 (141)
T ss_pred HHHHH---HHcCCCHHHHHHHHCCCHHHH
Confidence 44444 368899999999999988554
No 486
>COG4840 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.67 E-value=69 Score=18.47 Aligned_cols=16 Identities=6% Similarity=0.142 Sum_probs=12.8
Q ss_pred hCCCHHHHHHHHHhcC
Q 036949 26 LGMNEDDAAYYVQQQG 41 (81)
Q Consensus 26 Lgls~~e~~~~~~~~G 41 (81)
=+||+.|+..+|.+.|
T Consensus 52 enfSpsEmqaiA~eL~ 67 (71)
T COG4840 52 ENFSPSEMQAIADELG 67 (71)
T ss_pred ccCCHHHHHHHHHHHH
Confidence 4679999998888765
No 487
>PF14261 DUF4351: Domain of unknown function (DUF4351)
Probab=21.61 E-value=1.5e+02 Score=16.09 Aligned_cols=35 Identities=6% Similarity=0.184 Sum_probs=29.4
Q ss_pred HHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH
Q 036949 4 KRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 4 ~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~ 38 (81)
.-+.+++.+-|..|+....+..=.+|.+++..++.
T Consensus 10 ~lllRlL~rrFG~lp~~~~~~I~~l~~eqLE~l~e 44 (59)
T PF14261_consen 10 RLLLRLLTRRFGELPPEIQERIQQLSLEQLEALAE 44 (59)
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHcCCHHHHHHHHH
Confidence 45678999999999999888888889888877765
No 488
>cd08815 Death_TNFRSF25_DR3 Death domain of Tumor Necrosis Factor Receptor superfamily 25. Death Domain (DD) found in Tumor Necrosis Factor (TNF) receptor superfamily 25 (TNFRSF25), also known as TRAMP (TNF receptor-related apoptosis-mediating protein), LARD, APO-3, WSL-1, or DR3 (Death Receptor-3). TNFRSF25 is primarily expressed in T cells, is activated by binding to its ligand TL1A, and plays an important role in T-cell function. 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 adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=21.48 E-value=98 Score=18.18 Aligned_cols=16 Identities=19% Similarity=0.275 Sum_probs=12.8
Q ss_pred HHHHHHHhCCCHHHHH
Q 036949 19 TQDTALFLGMNEDDAA 34 (81)
Q Consensus 19 ~~~~a~~Lgls~~e~~ 34 (81)
.+++.+.||+|++++.
T Consensus 14 wk~F~R~LGLsdn~Ie 29 (77)
T cd08815 14 WKEFVRTLGLREAEIE 29 (77)
T ss_pred HHHHHHHcCCcHhHHH
Confidence 3568999999998854
No 489
>KOG1463 consensus 26S proteasome regulatory complex, subunit RPN6/PSMD11 [Posttranslational modification, protein turnover, chaperones]
Probab=21.45 E-value=1.2e+02 Score=23.18 Aligned_cols=42 Identities=21% Similarity=0.257 Sum_probs=27.6
Q ss_pred hcccccHHHHHHHhCCCHHHHHH----HHHhc--CCeEeCCCceEeec
Q 036949 13 AYSTISTQDTALFLGMNEDDAAY----YVQQQ--GWTLDPASRMLTVK 54 (81)
Q Consensus 13 AY~sIs~~~~a~~Lgls~~e~~~----~~~~~--GW~~d~~~~~~~p~ 54 (81)
-|+.+-++++|..+||+.+.+.. .+-.+ -=++|..+..++.-
T Consensus 342 PyS~Vei~hIA~~IGl~~~~VEkKLsqMILDKkf~G~LDQg~g~Liv~ 389 (411)
T KOG1463|consen 342 PYSRVEISHIAEVIGLDVPQVEKKLSQMILDKKFYGTLDQGEGCLIVF 389 (411)
T ss_pred chhhhhHHHHHHHHCCCcHHHHHHHHHHHHHHHhhcccccCCCeEEEe
Confidence 59999999999999998766543 33322 23566554444444
No 490
>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=21.41 E-value=53 Score=20.57 Aligned_cols=33 Identities=27% Similarity=0.277 Sum_probs=21.7
Q ss_pred HHhcccccHH----------HHHHHhCCCHHHHHHHHHhcCCeE
Q 036949 11 MSAYSTISTQ----------DTALFLGMNEDDAAYYVQQQGWTL 44 (81)
Q Consensus 11 ~~AY~sIs~~----------~~a~~Lgls~~e~~~~~~~~GW~~ 44 (81)
++||+.|.++ .+|.--|++.+++.+.. -..|++
T Consensus 54 GsayRcIrin~~~~~Dp~l~~Aa~~sgl~~~~l~~~L-P~eltl 96 (118)
T PF07742_consen 54 GSAYRCIRINPGHKMDPVLEQAAKESGLSYEDLRSLL-PRELTL 96 (118)
T ss_dssp THHHH-EEES--SSB-HHHHHHHHHTT--HHHHHHHS--TTEEE
T ss_pred CCceEEEEEcCCCCCCHHHHHHHHHhCCCHHHHHHhc-chhcEE
Confidence 3567777666 68899999999988765 457774
No 491
>PLN02905 beta-amylase
Probab=21.38 E-value=74 Score=25.90 Aligned_cols=22 Identities=23% Similarity=0.484 Sum_probs=16.5
Q ss_pred HHHHHHHHhcCCeEeCCCceEe
Q 036949 31 DDAAYYVQQQGWTLDPASRMLT 52 (81)
Q Consensus 31 ~e~~~~~~~~GW~~d~~~~~~~ 52 (81)
+-+.+.|.+.||+++++|..+-
T Consensus 124 ~v~~~l~~eag~~v~~dg~~y~ 145 (702)
T PLN02905 124 DVIAALAREAGWVVLPDGTTFP 145 (702)
T ss_pred HHHHHHHHhcCcEEcCCCCccc
Confidence 3356778889999999876643
No 492
>CHL00165 ftrB ferredoxin thioreductase subunit beta; Validated
Probab=21.38 E-value=80 Score=19.98 Aligned_cols=17 Identities=12% Similarity=0.055 Sum_probs=12.5
Q ss_pred HHHHHHhcCCeEeCCCc
Q 036949 33 AAYYVQQQGWTLDPASR 49 (81)
Q Consensus 33 ~~~~~~~~GW~~d~~~~ 49 (81)
+.+++.+.||.+++|..
T Consensus 20 ~ekya~~~G~~fnpD~~ 36 (116)
T CHL00165 20 AETYAKRTNTFFCSDLS 36 (116)
T ss_pred HHHHHHHhCCeeCCCHH
Confidence 45667788999988743
No 493
>PRK12423 LexA repressor; Provisional
Probab=21.36 E-value=2.6e+02 Score=18.57 Aligned_cols=42 Identities=10% Similarity=0.148 Sum_probs=29.4
Q ss_pred HHHHHHHHHHhccc----ccHHHHHHHhCC-CHH---HHHHHHHhcCCeE
Q 036949 3 TKRMFQLLMSAYST----ISTQDTALFLGM-NED---DAAYYVQQQGWTL 44 (81)
Q Consensus 3 R~~~~~li~~AY~s----Is~~~~a~~Lgl-s~~---e~~~~~~~~GW~~ 44 (81)
|+++++.|...+.+ =+..++|..||+ |.. +..+...+.|+--
T Consensus 8 q~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~~l~~L~~~G~l~ 57 (202)
T PRK12423 8 RAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKHVQALAEAGLIE 57 (202)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEE
Confidence 67788877766433 388999999997 664 4444555667765
No 494
>COG1395 Predicted transcriptional regulator [Transcription]
Probab=21.35 E-value=94 Score=22.94 Aligned_cols=22 Identities=27% Similarity=0.363 Sum_probs=17.9
Q ss_pred ccccHHHHHHHhCCCHHHHHHH
Q 036949 15 STISTQDTALFLGMNEDDAAYY 36 (81)
Q Consensus 15 ~sIs~~~~a~~Lgls~~e~~~~ 36 (81)
..+|+.++|.|||.|...+-.|
T Consensus 137 ~glSlG~lA~~lgVSRktV~~Y 158 (313)
T COG1395 137 MGLSLGDLATMLGVSRKTVYKY 158 (313)
T ss_pred cCcCHHHHHHHhCccHHHHHHh
Confidence 3579999999999998776554
No 495
>PF08299 Bac_DnaA_C: Bacterial dnaA protein helix-turn-helix; InterPro: IPR013159 This entry represents the C-terminal domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication. DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; GO: 0005524 ATP binding, 0043565 sequence-specific DNA binding, 0006270 DNA-dependent DNA replication initiation, 0006275 regulation of DNA replication; PDB: 2HCB_B 3R8F_C 1L8Q_A 3PVP_B 3PVV_A 1J1V_A.
Probab=21.35 E-value=1.6e+02 Score=16.27 Aligned_cols=31 Identities=10% Similarity=0.175 Sum_probs=18.9
Q ss_pred HHHHHHHhcccccHHHHHHHhC-CCHHHHHHH
Q 036949 6 MFQLLMSAYSTISTQDTALFLG-MNEDDAAYY 36 (81)
Q Consensus 6 ~~~li~~AY~sIs~~~~a~~Lg-ls~~e~~~~ 36 (81)
++--+.+-+...|++++++++| -+-.-+...
T Consensus 35 va~yL~r~~~~~sl~~Ig~~fg~rdHstV~~a 66 (70)
T PF08299_consen 35 VAMYLARELTGLSLSEIGRYFGGRDHSTVIHA 66 (70)
T ss_dssp HHHHHHHHHS---HHHHHHHCTSSTHHHHHHH
T ss_pred HHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHH
Confidence 3445667777889999999998 565555443
No 496
>PF09824 ArsR: ArsR transcriptional regulator; InterPro: IPR014517 Members of this family of archaeal proteins are conserved transcriptional regulators belonging to the ArsR family.
Probab=21.32 E-value=2.5e+02 Score=18.80 Aligned_cols=33 Identities=12% Similarity=0.051 Sum_probs=25.9
Q ss_pred HHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH
Q 036949 4 KRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ 38 (81)
Q Consensus 4 ~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~ 38 (81)
+++-..|.. ...|+.++++-||+|+-=+...|+
T Consensus 111 e~i~~~v~~--Gn~Sl~~lsr~l~~sp~firglAK 143 (160)
T PF09824_consen 111 EKIEKEVEA--GNTSLSDLSRKLGISPVFIRGLAK 143 (160)
T ss_pred HHHHHHHHc--CCCcHHHHHHHhCCCHHHHHHHHH
Confidence 455556666 889999999999999987777666
No 497
>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=21.31 E-value=1.5e+02 Score=15.92 Aligned_cols=28 Identities=18% Similarity=0.073 Sum_probs=23.3
Q ss_pred cccccHHHHHHHhCCCHHHHHHHHHhcC
Q 036949 14 YSTISTQDTALFLGMNEDDAAYYVQQQG 41 (81)
Q Consensus 14 Y~sIs~~~~a~~Lgls~~e~~~~~~~~G 41 (81)
-.-.++.++|.-+|+++..+-.+..+..
T Consensus 21 ~~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 21 ESGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp HHHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HCCCceEeeecccccccccccHHHHHHh
Confidence 4578999999999999999999888653
No 498
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.
Probab=21.29 E-value=94 Score=15.90 Aligned_cols=16 Identities=25% Similarity=0.374 Sum_probs=9.4
Q ss_pred HHhCCCHHHHHHHHHh
Q 036949 24 LFLGMNEDDAAYYVQQ 39 (81)
Q Consensus 24 ~~Lgls~~e~~~~~~~ 39 (81)
.-||++..++.+.+.+
T Consensus 11 ~~LGy~~~e~~~av~~ 26 (47)
T PF07499_consen 11 ISLGYSKAEAQKAVSK 26 (47)
T ss_dssp HHTTS-HHHHHHHHHH
T ss_pred HHcCCCHHHHHHHHHH
Confidence 4467777777666553
No 499
>TIGR00241 CoA_E_activ CoA-substrate-specific enzyme activase, putative. This domain may be involved in generating or regenerating the active sites of enzymes related to (R)-2-hydroxyglutaryl-CoA dehydratase and benzoyl-CoA reductase.
Probab=21.14 E-value=1.2e+02 Score=20.73 Aligned_cols=24 Identities=17% Similarity=0.160 Sum_probs=19.4
Q ss_pred cHHHHHHHhCCCHHHHHHHHHhcC
Q 036949 18 STQDTALFLGMNEDDAAYYVQQQG 41 (81)
Q Consensus 18 s~~~~a~~Lgls~~e~~~~~~~~G 41 (81)
-++.+|+.||++.+|+.+++.+..
T Consensus 129 f~e~~a~~l~~~~~e~~~~~~~~~ 152 (248)
T TIGR00241 129 FLEVTARRLGVSVEELGSLAEKAD 152 (248)
T ss_pred HHHHHHHHcCCCHHHHHHHHhcCC
Confidence 357789999999999998877643
No 500
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=21.09 E-value=2.7e+02 Score=21.06 Aligned_cols=42 Identities=14% Similarity=0.414 Sum_probs=33.7
Q ss_pred HHHHHHHHHHhcccccHHHHHHHhCCC---HHHHHHHHHhcCCeE
Q 036949 3 TKRMFQLLMSAYSTISTQDTALFLGMN---EDDAAYYVQQQGWTL 44 (81)
Q Consensus 3 R~~~~~li~~AY~sIs~~~~a~~Lgls---~~e~~~~~~~~GW~~ 44 (81)
...+++|.-+.-...+-+++-.++|+. .+.+-.|..++||--
T Consensus 385 K~~~is~~l~t~g~f~K~d~~~Lf~id~~ka~~~YdfF~~~~Wi~ 429 (432)
T COG5114 385 KKEVISCFLRTRGEFTKEDFNRLFGIDLGKADGLYDFFLERGWIH 429 (432)
T ss_pred HHHHHHHHHHhCCCccHHHHHHHhCcCcchhhHHHHHHHhccccC
Confidence 456777777778888899999999984 456778899999974
Done!