Query psy7686
Match_columns 243
No_of_seqs 211 out of 445
Neff 5.0
Searched_HMMs 46136
Date Sat Aug 17 00:47:47 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7686.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7686hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2577|consensus 100.0 4.6E-74 9.9E-79 532.6 21.0 231 5-243 64-353 (354)
2 PF02319 E2F_TDP: E2F/DP famil 99.9 7.3E-24 1.6E-28 157.2 6.6 67 9-75 1-71 (71)
3 KOG2578|consensus 99.8 8.7E-21 1.9E-25 174.1 5.1 75 4-79 16-90 (388)
4 KOG2578|consensus 99.3 4.7E-13 1E-17 123.5 4.0 72 8-79 155-241 (388)
5 KOG2829|consensus 99.0 3.5E-09 7.7E-14 97.4 13.4 146 14-179 46-218 (326)
6 PF01978 TrmB: Sugar-specific 95.5 0.031 6.8E-07 40.1 4.8 46 29-75 19-64 (68)
7 PF08279 HTH_11: HTH domain; 93.2 0.27 5.9E-06 33.5 5.3 41 19-61 3-43 (55)
8 PF09339 HTH_IclR: IclR helix- 92.5 0.22 4.9E-06 34.0 4.0 44 21-66 8-51 (52)
9 COG1378 Predicted transcriptio 92.3 0.52 1.1E-05 42.8 7.2 51 21-75 22-72 (247)
10 smart00420 HTH_DEOR helix_turn 91.6 0.45 9.8E-06 31.1 4.6 46 20-68 4-49 (53)
11 cd00092 HTH_CRP helix_turn_hel 91.5 0.64 1.4E-05 32.3 5.5 54 17-71 5-63 (67)
12 smart00550 Zalpha Z-DNA-bindin 91.4 0.5 1.1E-05 34.4 5.1 54 19-73 9-62 (68)
13 smart00346 HTH_ICLR helix_turn 90.5 0.78 1.7E-05 33.9 5.4 47 19-67 8-54 (91)
14 PF12802 MarR_2: MarR family; 89.8 0.82 1.8E-05 31.4 4.8 46 20-66 9-54 (62)
15 PF13412 HTH_24: Winged helix- 88.8 1.1 2.3E-05 29.9 4.6 43 19-64 6-48 (48)
16 COG3355 Predicted transcriptio 88.6 3.3 7.1E-05 34.4 8.2 46 21-69 33-78 (126)
17 PF02082 Rrf2: Transcriptional 86.3 1.9 4.2E-05 32.0 5.2 49 17-66 9-58 (83)
18 smart00418 HTH_ARSR helix_turn 86.1 1.4 3E-05 29.3 4.0 38 30-68 8-45 (66)
19 PF01047 MarR: MarR family; I 84.9 1.7 3.7E-05 29.7 4.0 44 21-67 8-51 (59)
20 TIGR02944 suf_reg_Xantho FeS a 84.9 1.8 4E-05 34.6 4.8 46 20-66 13-58 (130)
21 PF13463 HTH_27: Winged helix 83.7 2.9 6.2E-05 29.1 4.8 37 29-66 15-51 (68)
22 PRK00888 ftsB cell division pr 83.0 4 8.8E-05 32.4 5.9 70 72-155 19-91 (105)
23 PF09012 FeoC: FeoC like trans 82.6 2.4 5.1E-05 30.6 4.1 46 22-70 6-51 (69)
24 PF09079 Cdc6_C: CDC6, C termi 81.9 1.2 2.5E-05 33.3 2.3 32 36-67 26-59 (85)
25 PF01022 HTH_5: Bacterial regu 81.2 3.6 7.8E-05 27.5 4.3 41 21-65 7-47 (47)
26 smart00345 HTH_GNTR helix_turn 80.9 4.1 8.8E-05 27.2 4.6 41 28-69 15-56 (60)
27 cd08768 Cdc6_C Winged-helix do 79.9 1.8 4E-05 31.9 2.8 21 46-66 45-65 (87)
28 cd00090 HTH_ARSR Arsenical Res 79.4 4.8 0.0001 27.3 4.7 46 19-68 10-55 (78)
29 smart00419 HTH_CRP helix_turn_ 78.6 3.3 7.2E-05 26.7 3.4 35 32-67 8-42 (48)
30 PF13730 HTH_36: Helix-turn-he 77.9 3.7 8E-05 27.8 3.6 29 34-63 27-55 (55)
31 PF08220 HTH_DeoR: DeoR-like h 75.8 7.1 0.00015 27.3 4.7 44 20-66 4-47 (57)
32 PRK10163 DNA-binding transcrip 74.4 45 0.00098 30.0 10.8 53 21-75 30-82 (271)
33 PF12840 HTH_20: Helix-turn-he 74.1 7.7 0.00017 27.1 4.5 46 19-67 13-58 (61)
34 PF04182 B-block_TFIIIC: B-blo 73.9 6.4 0.00014 29.0 4.3 48 20-68 6-53 (75)
35 PF00392 GntR: Bacterial regul 73.8 6.7 0.00015 27.6 4.2 49 19-68 7-59 (64)
36 TIGR00738 rrf2_super rrf2 fami 72.5 8.3 0.00018 30.5 4.9 36 30-66 23-58 (132)
37 smart00344 HTH_ASNC helix_turn 71.3 7 0.00015 29.8 4.1 47 17-66 4-50 (108)
38 cd00890 Prefoldin Prefoldin is 71.0 29 0.00063 27.2 7.7 54 67-123 68-121 (129)
39 TIGR02338 gimC_beta prefoldin, 71.0 18 0.00038 28.6 6.4 86 36-123 20-108 (110)
40 PF08781 DP: Transcription fac 70.9 30 0.00065 29.3 8.0 29 148-179 59-87 (142)
41 PF14394 DUF4423: Domain of un 70.2 69 0.0015 27.4 10.6 45 27-72 34-80 (171)
42 PRK09834 DNA-binding transcrip 70.0 9.7 0.00021 34.1 5.3 50 21-72 16-66 (263)
43 PF01920 Prefoldin_2: Prefoldi 69.8 34 0.00074 25.8 7.7 73 48-123 26-103 (106)
44 PF01325 Fe_dep_repress: Iron 68.5 15 0.00033 26.1 5.0 42 24-67 15-56 (60)
45 PF01726 LexA_DNA_bind: LexA D 68.3 8 0.00017 28.1 3.6 47 21-67 14-60 (65)
46 cd07377 WHTH_GntR Winged helix 68.1 16 0.00036 24.6 5.1 38 29-67 21-59 (66)
47 PHA02943 hypothetical protein; 68.1 23 0.00049 30.7 6.8 47 20-70 15-61 (165)
48 KOG3026|consensus 67.8 24 0.00052 32.5 7.3 80 99-179 26-116 (262)
49 PF08784 RPA_C: Replication pr 67.5 12 0.00026 28.7 4.7 50 13-64 44-96 (102)
50 TIGR00122 birA_repr_reg BirA b 67.4 10 0.00022 27.0 4.0 49 20-72 4-53 (69)
51 cd04766 HTH_HspR Helix-Turn-He 66.9 30 0.00066 26.0 6.8 27 33-64 2-28 (91)
52 PRK11414 colanic acid/biofilm 66.8 25 0.00054 30.3 7.0 57 12-69 10-70 (221)
53 cd00632 Prefoldin_beta Prefold 66.7 25 0.00054 27.4 6.4 79 39-122 22-103 (105)
54 COG1414 IclR Transcriptional r 66.5 12 0.00025 33.6 5.1 53 20-75 8-61 (246)
55 PRK09413 IS2 repressor TnpA; R 66.3 53 0.0012 26.1 8.4 30 32-62 29-58 (121)
56 TIGR01610 phage_O_Nterm phage 65.7 15 0.00032 28.3 4.8 38 29-67 44-81 (95)
57 COG1474 CDC6 Cdc6-related prot 65.4 6.5 0.00014 37.6 3.4 29 35-64 304-332 (366)
58 TIGR01889 Staph_reg_Sar staphy 65.0 13 0.00029 28.8 4.6 45 22-67 31-77 (109)
59 PRK10411 DNA-binding transcrip 64.8 44 0.00096 29.9 8.4 53 20-75 8-60 (240)
60 PF01853 MOZ_SAS: MOZ/SAS fami 64.5 15 0.00032 32.6 5.1 48 20-71 137-185 (188)
61 TIGR02702 SufR_cyano iron-sulf 63.2 87 0.0019 27.0 9.7 45 19-66 4-48 (203)
62 smart00347 HTH_MARR helix_turn 63.0 17 0.00036 26.4 4.6 45 19-66 13-57 (101)
63 TIGR02231 conserved hypothetic 62.4 62 0.0013 32.0 9.7 86 87-188 136-226 (525)
64 TIGR02431 pcaR_pcaU beta-ketoa 61.5 16 0.00035 32.3 4.9 44 21-66 14-57 (248)
65 COG4189 Predicted transcriptio 61.4 12 0.00025 34.8 4.1 52 12-66 18-70 (308)
66 cd00584 Prefoldin_alpha Prefol 60.4 49 0.0011 26.3 7.2 54 68-124 69-122 (129)
67 PRK09802 DNA-binding transcrip 60.2 78 0.0017 28.8 9.3 50 19-71 20-69 (269)
68 PF04977 DivIC: Septum formati 59.4 28 0.0006 24.9 5.2 36 90-125 18-53 (80)
69 COG1510 Predicted transcriptio 59.1 30 0.00065 30.4 6.0 36 30-66 39-74 (177)
70 smart00529 HTH_DTXR Helix-turn 58.7 24 0.00051 26.2 4.8 32 35-67 2-33 (96)
71 TIGR02716 C20_methyl_CrtF C-20 58.5 8.8 0.00019 34.9 2.8 37 30-67 21-57 (306)
72 cd04770 HTH_HMRTR Helix-Turn-H 57.8 49 0.0011 26.1 6.7 39 34-77 2-42 (123)
73 TIGR02147 Fsuc_second hypothet 57.7 1.1E+02 0.0023 28.3 9.8 41 28-69 133-175 (271)
74 PRK03947 prefoldin subunit alp 57.4 73 0.0016 25.8 7.8 12 68-79 76-87 (140)
75 TIGR02010 IscR iron-sulfur clu 57.2 23 0.00049 28.7 4.8 37 28-65 21-57 (135)
76 TIGR01764 excise DNA binding d 57.1 9.4 0.0002 24.4 2.1 22 33-55 2-23 (49)
77 TIGR02337 HpaR homoprotocatech 56.8 10 0.00022 29.6 2.6 37 30-67 40-76 (118)
78 COG1522 Lrp Transcriptional re 55.6 21 0.00046 28.6 4.4 50 14-66 6-55 (154)
79 COG2739 Uncharacterized protei 55.6 13 0.00027 30.1 2.9 40 15-55 16-55 (105)
80 COG1382 GimC Prefoldin, chaper 55.0 42 0.00091 27.7 5.9 77 50-127 36-115 (119)
81 PF08280 HTH_Mga: M protein tr 54.5 22 0.00047 24.9 3.7 36 20-58 9-44 (59)
82 COG1846 MarR Transcriptional r 52.7 23 0.0005 26.4 3.9 43 21-66 27-69 (126)
83 PF10779 XhlA: Haemolysin XhlA 52.5 60 0.0013 23.7 6.0 39 87-125 11-49 (71)
84 PRK11050 manganese transport r 52.4 41 0.00088 27.9 5.7 42 30-72 49-90 (152)
85 PRK05014 hscB co-chaperone Hsc 52.3 1.5E+02 0.0032 25.3 11.4 102 7-123 10-137 (171)
86 PRK09343 prefoldin subunit bet 52.3 49 0.0011 26.8 5.9 78 47-125 34-114 (121)
87 PRK11569 transcriptional repre 51.9 1.5E+02 0.0032 26.7 9.6 45 21-67 33-77 (274)
88 cd04789 HTH_Cfa Helix-Turn-Hel 51.9 63 0.0014 25.0 6.3 38 33-75 2-40 (102)
89 PRK09954 putative kinase; Prov 51.8 20 0.00044 33.2 4.1 46 18-66 5-50 (362)
90 KOG2747|consensus 51.2 34 0.00073 33.6 5.6 59 12-76 303-367 (396)
91 TIGR00293 prefoldin, archaeal 51.0 53 0.0012 26.0 5.9 54 68-124 68-121 (126)
92 PRK15090 DNA-binding transcrip 50.5 56 0.0012 29.0 6.6 52 21-75 19-70 (257)
93 TIGR01884 cas_HTH CRISPR locus 50.3 34 0.00073 29.5 5.0 45 21-68 148-192 (203)
94 PRK00215 LexA repressor; Valid 49.3 28 0.00061 29.8 4.3 43 27-69 18-60 (205)
95 PRK10857 DNA-binding transcrip 48.8 26 0.00057 29.8 4.0 38 28-66 21-58 (164)
96 TIGR03338 phnR_burk phosphonat 48.6 95 0.0021 26.3 7.5 40 28-68 30-69 (212)
97 PF12329 TMF_DNA_bd: TATA elem 48.4 49 0.0011 24.7 5.0 37 89-125 12-48 (74)
98 PF13518 HTH_28: Helix-turn-he 48.4 19 0.00042 23.5 2.6 37 21-62 5-41 (52)
99 PRK03902 manganese transport t 48.2 51 0.0011 26.7 5.5 48 19-69 11-58 (142)
100 PRK13509 transcriptional repre 47.8 29 0.00063 31.1 4.4 46 20-68 9-54 (251)
101 PF12269 zf-CpG_bind_C: CpG bi 47.1 31 0.00068 31.5 4.4 51 72-122 15-69 (236)
102 PF07106 TBPIP: Tat binding pr 47.1 1.7E+02 0.0037 24.5 9.6 57 21-79 6-66 (169)
103 PF05491 RuvB_C: Holliday junc 46.7 55 0.0012 25.0 5.0 58 12-70 4-63 (76)
104 PRK11169 leucine-responsive tr 46.2 49 0.0011 27.6 5.3 54 9-65 7-60 (164)
105 COG3093 VapI Plasmid maintenan 46.2 16 0.00036 29.4 2.2 40 9-55 5-45 (104)
106 PLN03239 histone acetyltransfe 46.0 56 0.0012 31.6 6.1 57 5-65 249-313 (351)
107 cd04783 HTH_MerR1 Helix-Turn-H 45.9 1.1E+02 0.0024 24.3 7.1 81 33-124 1-98 (126)
108 PF13545 HTH_Crp_2: Crp-like h 45.7 28 0.00062 24.6 3.3 36 32-68 28-63 (76)
109 TIGR00498 lexA SOS regulatory 45.6 34 0.00073 29.1 4.3 47 20-67 10-60 (199)
110 PF05377 FlaC_arch: Flagella a 45.1 1E+02 0.0022 22.2 5.9 39 86-124 4-42 (55)
111 KOG1318|consensus 44.7 54 0.0012 32.4 5.9 75 46-125 241-319 (411)
112 cd01109 HTH_YyaN Helix-Turn-He 44.6 1E+02 0.0022 24.1 6.5 36 34-74 2-39 (113)
113 PRK03573 transcriptional regul 44.6 39 0.00086 27.1 4.3 34 32-66 46-79 (144)
114 PF09756 DDRGK: DDRGK domain; 44.4 41 0.00088 29.7 4.6 56 17-75 100-157 (188)
115 PRK11014 transcriptional repre 44.3 44 0.00095 27.1 4.6 41 27-68 20-60 (141)
116 TIGR02366 DHAK_reg probable di 43.9 32 0.0007 28.0 3.8 35 16-51 7-41 (176)
117 cd07153 Fur_like Ferric uptake 43.9 45 0.00098 25.6 4.4 45 21-67 6-55 (116)
118 PF03374 ANT: Phage antirepres 43.3 31 0.00067 26.6 3.4 41 21-66 14-54 (111)
119 PHA01750 hypothetical protein 42.8 68 0.0015 24.1 4.9 32 87-118 40-71 (75)
120 PRK14165 winged helix-turn-hel 42.8 49 0.0011 29.7 4.9 48 20-68 8-56 (217)
121 PRK11511 DNA-binding transcrip 42.7 50 0.0011 26.4 4.6 41 15-56 8-48 (127)
122 PRK10870 transcriptional repre 42.7 39 0.00084 28.7 4.1 40 26-66 65-104 (176)
123 COG2919 Septum formation initi 42.6 18 0.00038 29.2 1.9 37 87-124 55-91 (117)
124 PRK11534 DNA-binding transcrip 42.1 1.2E+02 0.0027 25.9 7.3 47 28-75 26-72 (224)
125 COG1802 GntR Transcriptional r 41.3 2E+02 0.0044 24.8 8.6 40 28-68 35-74 (230)
126 cd04790 HTH_Cfa-like_unk Helix 41.0 63 0.0014 27.5 5.2 38 33-77 2-43 (172)
127 PF10018 Med4: Vitamin-D-recep 40.9 1.1E+02 0.0023 26.4 6.7 55 87-141 27-88 (188)
128 cd04775 HTH_Cfa-like Helix-Tur 40.9 1.5E+02 0.0033 22.8 6.9 38 33-75 2-40 (102)
129 TIGR02047 CadR-PbrR Cd(II)/Pb( 40.9 1.2E+02 0.0027 24.3 6.7 81 33-124 1-100 (127)
130 PHA02047 phage lambda Rz1-like 40.3 30 0.00066 27.7 2.8 59 70-133 25-83 (101)
131 COG2894 MinD Septum formation 40.1 7.6 0.00016 35.8 -0.6 27 34-61 42-68 (272)
132 PLN03238 probable histone acet 40.0 82 0.0018 29.7 6.1 55 5-64 191-251 (290)
133 PF09940 DUF2172: Domain of un 39.6 25 0.00054 34.4 2.7 42 21-64 345-386 (386)
134 PF02295 z-alpha: Adenosine de 39.4 1.1E+02 0.0024 22.3 5.5 57 17-74 5-61 (66)
135 PF05732 RepL: Firmicute plasm 39.4 52 0.0011 28.1 4.4 39 32-71 75-113 (165)
136 PF03979 Sigma70_r1_1: Sigma-7 39.4 17 0.00037 27.2 1.3 29 116-146 6-34 (82)
137 PF14817 HAUS5: HAUS augmin-li 39.2 71 0.0015 33.1 6.1 52 68-119 56-109 (632)
138 PRK10219 DNA-binding transcrip 39.1 55 0.0012 24.9 4.2 40 16-56 5-44 (107)
139 cd04762 HTH_MerR-trunc Helix-T 38.8 43 0.00093 20.9 3.0 23 33-56 1-23 (49)
140 PRK11512 DNA-binding transcrip 38.7 33 0.00071 27.7 3.0 37 30-67 52-88 (144)
141 PF14947 HTH_45: Winged helix- 38.5 53 0.0012 24.1 3.9 42 30-73 17-58 (77)
142 COG1321 TroR Mn-dependent tran 38.3 59 0.0013 27.5 4.5 44 29-73 21-64 (154)
143 PF04111 APG6: Autophagy prote 38.2 96 0.0021 29.1 6.4 38 88-125 56-93 (314)
144 PTZ00454 26S protease regulato 37.7 1.6E+02 0.0034 28.6 7.9 71 89-163 22-95 (398)
145 PF01475 FUR: Ferric uptake re 37.6 58 0.0013 25.4 4.2 49 20-69 12-64 (120)
146 PF02954 HTH_8: Bacterial regu 37.3 49 0.0011 21.6 3.1 36 14-52 2-37 (42)
147 PRK00080 ruvB Holliday junctio 36.8 55 0.0012 30.1 4.5 56 12-68 255-312 (328)
148 PF04977 DivIC: Septum formati 36.2 60 0.0013 23.2 3.8 49 86-135 21-69 (80)
149 PRK10869 recombination and rep 36.0 65 0.0014 32.5 5.2 66 37-116 286-351 (553)
150 PF01638 HxlR: HxlR-like helix 35.9 57 0.0012 24.5 3.7 38 29-67 15-53 (90)
151 PF04297 UPF0122: Putative hel 35.9 34 0.00073 27.3 2.5 40 16-56 17-56 (101)
152 PRK09464 pdhR transcriptional 35.7 43 0.00092 29.4 3.4 54 12-66 9-67 (254)
153 COG4519 Uncharacterized protei 35.3 68 0.0015 25.1 4.0 42 21-64 12-53 (95)
154 PRK06266 transcription initiat 34.9 3E+02 0.0065 23.8 8.6 52 20-74 26-84 (178)
155 PF10779 XhlA: Haemolysin XhlA 34.9 1.6E+02 0.0035 21.4 5.9 40 86-125 3-42 (71)
156 COG2512 Predicted membrane-ass 34.7 88 0.0019 28.7 5.4 60 12-73 191-250 (258)
157 PF03444 HrcA_DNA-bdg: Winged 34.7 97 0.0021 23.8 4.7 45 20-66 12-56 (78)
158 KOG3990|consensus 34.3 61 0.0013 30.3 4.2 43 88-130 224-266 (305)
159 PF12728 HTH_17: Helix-turn-he 34.1 35 0.00076 22.6 2.1 22 33-55 2-23 (51)
160 PF04703 FaeA: FaeA-like prote 33.9 1E+02 0.0022 22.4 4.6 52 21-74 5-59 (62)
161 PRK11179 DNA-binding transcrip 33.8 76 0.0017 26.1 4.5 51 13-66 6-56 (153)
162 COG1777 Predicted transcriptio 33.4 3.7E+02 0.0081 24.4 10.0 43 19-65 18-60 (217)
163 PRK09391 fixK transcriptional 33.3 1.2E+02 0.0026 26.3 5.8 39 33-72 180-218 (230)
164 PF10046 BLOC1_2: Biogenesis o 33.0 1.2E+02 0.0026 23.5 5.3 34 89-122 66-99 (99)
165 PRK13922 rod shape-determining 32.7 1.3E+02 0.0028 27.1 6.1 41 86-127 73-113 (276)
166 PF03836 RasGAP_C: RasGAP C-te 32.4 15 0.00032 30.4 0.0 26 46-73 5-30 (142)
167 PRK13729 conjugal transfer pil 32.3 97 0.0021 31.2 5.6 37 89-125 83-119 (475)
168 TIGR02297 HpaA 4-hydroxyphenyl 32.2 54 0.0012 28.9 3.5 43 16-59 186-228 (287)
169 TIGR00373 conserved hypothetic 31.7 2.5E+02 0.0055 23.6 7.4 35 30-65 26-60 (158)
170 PRK03837 transcriptional regul 31.6 55 0.0012 28.3 3.4 54 13-67 13-71 (241)
171 PF05930 Phage_AlpA: Prophage 31.5 49 0.0011 22.4 2.5 24 31-55 2-25 (51)
172 KOG3093|consensus 31.3 2.2E+02 0.0048 25.5 7.1 34 155-193 104-138 (200)
173 PRK06474 hypothetical protein; 31.0 90 0.002 26.7 4.6 47 19-67 14-61 (178)
174 PRK09333 30S ribosomal protein 30.7 57 0.0012 27.9 3.2 38 30-67 65-115 (150)
175 PRK09990 DNA-binding transcrip 30.4 2.6E+02 0.0057 24.3 7.6 48 19-67 14-65 (251)
176 PRK00888 ftsB cell division pr 30.4 1.3E+02 0.0029 23.7 5.2 18 91-108 43-60 (105)
177 PF01710 HTH_Tnp_IS630: Transp 30.0 79 0.0017 25.1 3.8 43 19-67 60-102 (119)
178 PF04218 CENP-B_N: CENP-B N-te 29.9 71 0.0015 22.1 3.1 42 9-55 2-44 (53)
179 PF09904 HTH_43: Winged helix- 29.9 2.7E+02 0.0058 22.0 6.6 30 34-64 23-52 (90)
180 PRK09975 DNA-binding transcrip 29.9 61 0.0013 27.1 3.3 37 15-52 14-50 (213)
181 PF13851 GAS: Growth-arrest sp 29.8 1.1E+02 0.0024 26.9 5.0 38 88-125 26-63 (201)
182 TIGR01242 26Sp45 26S proteasom 29.8 1.6E+02 0.0035 27.4 6.5 67 89-163 6-72 (364)
183 PRK04984 fatty acid metabolism 28.9 66 0.0014 27.9 3.5 38 28-66 26-64 (239)
184 PF02796 HTH_7: Helix-turn-hel 28.9 89 0.0019 20.6 3.3 32 19-55 12-43 (45)
185 PF08181 DegQ: DegQ (SacQ) fam 28.7 1.7E+02 0.0037 20.1 4.6 39 96-134 4-43 (46)
186 PF14257 DUF4349: Domain of un 28.5 1.2E+02 0.0026 27.1 5.2 52 14-66 61-123 (262)
187 PF14830 Haemocyan_bet_s: Haem 28.3 20 0.00044 28.8 0.1 13 51-63 58-70 (103)
188 smart00338 BRLZ basic region l 28.3 2.1E+02 0.0047 20.1 5.5 34 91-124 28-61 (65)
189 TIGR02928 orc1/cdc6 family rep 28.3 43 0.00093 30.7 2.3 32 37-68 319-352 (365)
190 KOG2264|consensus 28.3 89 0.0019 32.6 4.6 40 86-125 97-136 (907)
191 cd04772 HTH_TioE_rpt1 First He 27.9 2.2E+02 0.0048 21.8 5.9 36 34-76 2-41 (99)
192 PF10018 Med4: Vitamin-D-recep 27.6 1.9E+02 0.004 24.9 6.0 38 88-125 21-58 (188)
193 PF08222 HTH_CodY: CodY helix- 27.5 74 0.0016 23.3 2.9 36 31-67 3-38 (61)
194 PLN00104 MYST -like histone ac 27.3 1.6E+02 0.0036 29.4 6.2 55 6-65 343-403 (450)
195 PF11932 DUF3450: Protein of u 27.3 1.9E+02 0.0042 25.7 6.3 29 93-121 88-116 (251)
196 PRK04214 rbn ribonuclease BN/u 26.9 1.3E+02 0.0028 29.1 5.3 43 29-72 307-349 (412)
197 PRK10402 DNA-binding transcrip 26.8 86 0.0019 26.9 3.8 55 16-72 150-207 (226)
198 PF13600 DUF4140: N-terminal d 26.6 1.4E+02 0.0031 22.8 4.6 35 87-121 68-102 (104)
199 PF13551 HTH_29: Winged helix- 26.2 68 0.0015 23.9 2.7 27 34-61 14-40 (112)
200 PF05225 HTH_psq: helix-turn-h 26.1 64 0.0014 21.6 2.3 25 31-56 15-39 (45)
201 PRK11886 bifunctional biotin-- 26.1 1.4E+02 0.0031 27.4 5.3 52 19-73 7-59 (319)
202 PF13384 HTH_23: Homeodomain-l 25.8 81 0.0018 20.6 2.7 36 21-61 10-45 (50)
203 PF14712 Snapin_Pallidin: Snap 25.8 2.3E+02 0.0049 21.1 5.5 38 87-124 12-49 (92)
204 TIGR02063 RNase_R ribonuclease 25.7 1.1E+02 0.0025 31.6 5.0 56 19-74 5-63 (709)
205 PRK10434 srlR DNA-bindng trans 25.5 1.2E+02 0.0027 27.2 4.7 44 20-66 9-52 (256)
206 PF11853 DUF3373: Protein of u 25.3 59 0.0013 32.8 2.8 30 88-117 30-59 (489)
207 cd04776 HTH_GnyR Helix-Turn-He 25.2 1.7E+02 0.0037 23.2 5.0 9 36-44 4-12 (118)
208 PRK10906 DNA-binding transcrip 25.2 1.3E+02 0.0027 27.2 4.7 47 19-68 8-54 (252)
209 COG1730 GIM5 Predicted prefold 25.0 2.3E+02 0.0049 24.0 5.8 39 86-124 10-48 (145)
210 COG1373 Predicted ATPase (AAA+ 24.9 1E+02 0.0022 29.7 4.3 50 16-66 220-270 (398)
211 PF14363 AAA_assoc: Domain ass 24.8 33 0.00073 26.5 0.8 29 212-240 58-86 (98)
212 COG1349 GlpR Transcriptional r 24.8 1.2E+02 0.0027 27.2 4.6 45 19-66 8-52 (253)
213 PF09340 NuA4: Histone acetylt 24.7 1.3E+02 0.0027 22.9 3.9 29 96-124 2-30 (80)
214 PRK01203 prefoldin subunit alp 23.8 2.5E+02 0.0053 23.5 5.8 37 86-122 4-40 (130)
215 PRK10421 DNA-binding transcrip 23.8 1.1E+02 0.0024 26.9 4.0 38 28-66 21-59 (253)
216 PF10141 ssDNA-exonuc_C: Singl 23.6 4.8E+02 0.01 22.5 8.5 46 20-66 102-149 (195)
217 PF05565 Sipho_Gp157: Siphovir 23.5 3E+02 0.0064 23.2 6.4 32 13-44 2-33 (162)
218 PRK10225 DNA-binding transcrip 23.4 5E+02 0.011 22.7 9.8 51 16-67 13-67 (257)
219 cd04769 HTH_MerR2 Helix-Turn-H 23.4 1.2E+02 0.0026 23.8 3.7 26 34-64 2-27 (116)
220 PRK11642 exoribonuclease R; Pr 23.3 1.3E+02 0.0029 32.0 5.1 52 20-72 23-77 (813)
221 PF05158 RNA_pol_Rpc34: RNA po 23.2 2.4E+02 0.0052 26.7 6.3 63 13-76 6-71 (327)
222 TIGR00635 ruvB Holliday juncti 23.1 1.1E+02 0.0024 27.3 4.0 51 17-68 239-291 (305)
223 PF13542 HTH_Tnp_ISL3: Helix-t 23.1 1.1E+02 0.0023 20.2 2.9 37 17-54 12-48 (52)
224 PRK11523 DNA-binding transcrip 22.9 96 0.0021 27.3 3.4 50 17-67 13-66 (253)
225 PF07381 DUF1495: Winged helix 22.9 1.1E+02 0.0024 23.9 3.3 34 18-58 11-44 (90)
226 PRK13626 transcriptional regul 22.8 2.7E+02 0.0059 27.6 6.9 48 16-64 5-54 (552)
227 KOG0718|consensus 22.7 2.7E+02 0.006 28.3 6.8 28 28-55 38-78 (546)
228 PRK11753 DNA-binding transcrip 22.7 1.4E+02 0.003 24.8 4.2 36 32-68 168-203 (211)
229 cd00592 HTH_MerR-like Helix-Tu 22.6 2.8E+02 0.0061 20.7 5.6 21 34-55 2-22 (100)
230 PF08232 Striatin: Striatin fa 22.5 2.5E+02 0.0053 23.2 5.5 39 86-124 29-67 (134)
231 PRK00082 hrcA heat-inducible t 22.4 4.2E+02 0.0091 25.0 7.8 37 29-66 22-60 (339)
232 PF12793 SgrR_N: Sugar transpo 22.4 2.1E+02 0.0046 22.9 5.0 47 17-64 2-50 (115)
233 PF09107 SelB-wing_3: Elongati 22.2 2.1E+02 0.0046 19.7 4.4 37 30-67 8-44 (50)
234 PF09862 DUF2089: Protein of u 22.1 1.3E+02 0.0029 24.4 3.8 38 19-59 39-79 (113)
235 KOG3501|consensus 22.0 3.2E+02 0.007 22.3 5.9 40 86-125 71-110 (114)
236 PRK10130 transcriptional regul 22.0 1E+02 0.0022 29.2 3.6 40 15-55 239-278 (350)
237 KOG4057|consensus 21.6 1.8E+02 0.004 25.2 4.7 37 95-131 8-44 (180)
238 PF08317 Spc7: Spc7 kinetochor 21.5 2.3E+02 0.0049 26.5 5.7 74 90-165 231-310 (325)
239 PHA00738 putative HTH transcri 21.4 4.5E+02 0.0097 21.4 7.1 53 19-74 15-67 (108)
240 PF08172 CASP_C: CASP C termin 21.3 2.5E+02 0.0053 25.7 5.8 39 87-125 84-122 (248)
241 KOG3856|consensus 21.3 1.9E+02 0.0042 24.2 4.6 32 91-122 12-43 (135)
242 PRK15121 right oriC-binding tr 20.9 1.4E+02 0.0031 26.8 4.2 44 17-61 6-49 (289)
243 PRK00411 cdc6 cell division co 20.9 1.1E+02 0.0023 28.5 3.4 36 31-66 314-358 (394)
244 KOG3313|consensus 20.9 1.5E+02 0.0032 26.3 4.0 62 48-126 65-151 (187)
245 TIGR02787 codY_Gpos GTP-sensin 20.8 1.8E+02 0.0038 27.0 4.7 47 19-67 186-232 (251)
246 PRK10884 SH3 domain-containing 20.6 3E+02 0.0065 24.4 6.0 31 68-101 74-105 (206)
247 PRK11920 rirA iron-responsive 20.4 1.8E+02 0.0039 24.2 4.4 42 24-66 16-57 (153)
248 KOG0804|consensus 20.4 95 0.0021 31.2 3.0 61 48-125 389-450 (493)
249 PTZ00064 histone acetyltransfe 20.3 2.5E+02 0.0054 28.8 5.9 30 33-66 472-501 (552)
250 PF06005 DUF904: Protein of un 20.3 3.7E+02 0.0081 20.0 6.2 39 88-126 17-55 (72)
251 PRK09462 fur ferric uptake reg 20.2 2E+02 0.0043 23.5 4.5 46 21-67 22-72 (148)
252 KOG2255|consensus 20.0 46 0.001 30.1 0.8 30 34-66 63-92 (224)
No 1
>KOG2577|consensus
Probab=100.00 E-value=4.6e-74 Score=532.57 Aligned_cols=231 Identities=42% Similarity=0.671 Sum_probs=206.7
Q ss_pred CCCCCCcCcHHHHHHHHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceeccccCceEEeccCCCCchhh
Q psy7686 5 PANSRFEKSLGLLTTKFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNNKNIIRWKALKNKNEEEY 84 (243)
Q Consensus 5 ~~~~R~~~SL~~Lt~kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~sKn~i~W~G~~~~~~~~~ 84 (243)
+.++|+++|||+||+|||.|++++|+|++|||+||++|+| ||||||||||||||||||+|++||+|||+|.+..++.
T Consensus 64 ~~~~R~d~SLglLTkKFv~Llq~s~dGvldLn~aA~~L~V-qKRRIYDITNVLEGI~LIeKksKN~IqW~G~~~~~~~-- 140 (354)
T KOG2577|consen 64 SESTRSDTSLGLLTKKFVDLLQESPDGVLDLNKAAEVLNV-QKRRIYDITNVLEGIGLIEKKSKNNIQWIGGDFNSTG-- 140 (354)
T ss_pred CCcccchhhHHHHHHHHHHHHHhCCCceeeHHHHHHHhcc-ccceeeehhhhhhcccceeeccccceeeecCCCcccc--
Confidence 3568999999999999999999999999999999999999 9999999999999999999999999999999887544
Q ss_pred hHHHHHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhccCccccchhhhhhc--CCCCeEEEEECCCCCeEEec
Q psy7686 85 DLEQSKLIELRDEISDMRNHEAVIDEHIRKCQQSLRNIQEEEVNRKQCYIPTDVILGM--FPDSSLMCLKAPYGTKLHVP 162 (243)
Q Consensus 85 ~~~~~~~~~Lk~El~~L~~~E~~LD~~I~~~~~~l~~l~ed~~n~~~aYVT~~Di~~~--f~~qtviaIkAP~~T~leVp 162 (243)
+...+.+.|++|++.|.++|+.||++|.+|+++|++|++|++|++||||||+||+++ |++|||||||||++|+||||
T Consensus 141 -~~~e~~~~l~~e~~~L~~~E~~LD~~i~~~q~~L~~lted~~n~~laYVT~eDI~~i~~f~~q~vi~vkap~et~levp 219 (354)
T KOG2577|consen 141 -GVPERLNGLEAEVEDLSQEEDDLDQLIRDCQQNLRLLTEDVENRRLAYVTYEDIRSIPGFDEQTVIAVKAPPETRLEVP 219 (354)
T ss_pred -ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcchhcccceeeeHHHHhhccccCCceEEEEecCCcceEecc
Confidence 667788899999999999999999999999999999999999999999999999997 99999999999999999999
Q ss_pred CCCCCCceEEEEEecCCCCCCeEEEEecCCCCCC-CCC------------c--cCCC---C-------C-----------
Q psy7686 163 SISTDENKIKLHVKSSHPEEPVNILLLDTEPKKE-KPQ------------T--RGRK---R-------K----------- 206 (243)
Q Consensus 163 ~p~~~~~~yqi~LkS~~~~GpI~V~L~~~~~~~~-~p~------------~--~~~~---~-------~----------- 206 (243)
+|. +++|+|+|||++ |||+||||+++.... .|. + .+|. . |
T Consensus 220 ~~~--~~~~~i~L~s~~--GpI~v~l~~~e~~~~~~~~~~~~~~~~~~~~~~~~sp~~~~~~~~~~~~p~~~~~~~~~~~ 295 (354)
T KOG2577|consen 220 DPD--EDRYQIRLKSNQ--GPIDVYLCSEEEGEESEPTAKPVGSSSSSEDTISPSPYLPEQPASLALNPQQSEELLDSSN 295 (354)
T ss_pred cCC--CCceEEEeccCC--CceeEEeccccccCccCCCCCCCCCccccccCCCCCCCcCCchhhhhcCcccccchhhccc
Confidence 998 579999999999 999999999987433 211 0 1111 0 0
Q ss_pred -C----------Cc--------cc--cccccCCCCCCCCcccccCCCcchhhhccccC
Q psy7686 207 -W----------SE--------DR--RLIVVPNPPSRKDFLFKLDDDEGISHMFDLIC 243 (243)
Q Consensus 207 -~----------~~--------~~--~~~~lspp~~~~dy~f~l~~~egi~dlfd~~~ 243 (243)
+ ++ +. .+++|+||+.+.||.|+|+++||||||||++|
T Consensus 296 ~~~~~~~~~~~~~~~~~~~~s~~~~~~~i~l~~~~~~~dy~~~l~~~egi~~lfd~~~ 353 (354)
T KOG2577|consen 296 LLSFFPSTSASGSSDIRESFSDDLSEPLISLSPPPRQEDYGFGLKSQEGICDLFDVQF 353 (354)
T ss_pred ccccCccccccCCcceeccccccccCCcccCCCCcccccccccccCCCCccccccccc
Confidence 0 01 11 18999999999999999999999999999997
No 2
>PF02319 E2F_TDP: E2F/DP family winged-helix DNA-binding domain; InterPro: IPR003316 The mammalian transcription factor E2F plays an important role in regulating the expression of genes that are required for passage through the cell cycle. Multiple E2F family members have been identified that bind to DNA as heterodimers, interacting with proteins known as DP - the dimerisation partners [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005667 transcription factor complex; PDB: 1CF7_B.
Probab=99.89 E-value=7.3e-24 Score=157.24 Aligned_cols=67 Identities=51% Similarity=0.844 Sum_probs=62.8
Q ss_pred CCcCcHHHHHHHHHHHHhhCCCCeeeHHHHHhhh---ccc-chhhhhhHHHhhhhccceeccccCceEEec
Q psy7686 9 RFEKSLGLLTTKFVSLLQQAPEGVLHLKYAAENL---EVK-QKRRIYDITNVLEGIGLIEKNNKNIIRWKA 75 (243)
Q Consensus 9 R~~~SL~~Lt~kFi~ll~~~~~g~idL~~aa~~L---~v~-~KRRiYDItNVLEgiglI~K~sKn~i~W~G 75 (243)
|+++||+.||++|++++...+++.++++++|+.| +++ +|||||||+|||||+|+|+|.+|+.|+|+|
T Consensus 1 r~~~sL~~lt~~fi~~~~~~~~~~i~l~~ia~~l~~~~~k~~~RRlYDI~NVLealgli~K~~k~~~~W~G 71 (71)
T PF02319_consen 1 RKEKSLKLLTQRFIQLFESSPDKSISLNEIADKLISENVKTQRRRLYDIINVLEALGLIEKQSKNSYKWIG 71 (71)
T ss_dssp TTTTHHHHHHHHHHHHHHHCCCTEEEHHHHHHHCHHHCCHHHCHHHHHHHHHHHHCTSEEEEETTEEEE--
T ss_pred CCcCCHHHHHHHHHHHHHHCCCCcccHHHHHHHHcccccccccchhhHHHHHHHHhCceeecCCCceEecC
Confidence 7899999999999999999999999999999999 874 899999999999999999999999999998
No 3
>KOG2578|consensus
Probab=99.82 E-value=8.7e-21 Score=174.11 Aligned_cols=75 Identities=41% Similarity=0.616 Sum_probs=70.9
Q ss_pred CCCCCCCcCcHHHHHHHHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceeccccCceEEeccCCC
Q psy7686 4 DPANSRFEKSLGLLTTKFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNNKNIIRWKALKNK 79 (243)
Q Consensus 4 ~~~~~R~~~SL~~Lt~kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~sKn~i~W~G~~~~ 79 (243)
...++|++||||+||.+|+.++..+.-..+-|..||.+||| .|||||||+||||+||++.|.+||.|+|+|++.+
T Consensus 16 lqvysrkekslgvlv~nfl~lynr~dvdlvgLddaA~KlgV-ErRRIYDiVNvlEsig~var~~KnqYsWkGf~ai 90 (388)
T KOG2578|consen 16 LQVYSRKEKSLGVLVQNFLILYNRSDVDLVGLDDAARKLGV-ERRRIYDIVNVLESIGAVARRGKNQYSWKGFGAI 90 (388)
T ss_pred chhhccccchhhHHHHHHHHHhcCCCcceechhhHHHhcCc-hHHHHHHHHHHHHHHHHHHhcccCcccccchhhh
Confidence 35679999999999999999998777788999999999999 9999999999999999999999999999999877
No 4
>KOG2578|consensus
Probab=99.35 E-value=4.7e-13 Score=123.50 Aligned_cols=72 Identities=42% Similarity=0.591 Sum_probs=64.9
Q ss_pred CCCcCcHHHHHHHHHHHHhhCCCC-eeeHHHHHhhhcc--------c-chhhhhhHHHhhhhccceecc-----ccCceE
Q psy7686 8 SRFEKSLGLLTTKFVSLLQQAPEG-VLHLKYAAENLEV--------K-QKRRIYDITNVLEGIGLIEKN-----NKNIIR 72 (243)
Q Consensus 8 ~R~~~SL~~Lt~kFi~ll~~~~~g-~idL~~aa~~L~v--------~-~KRRiYDItNVLEgiglI~K~-----sKn~i~ 72 (243)
.|+++||++||++||+++..+++. .|.|+.||..|-- | .-||+|||.|||-++|||+|+ .|..|+
T Consensus 155 nrkekSL~lL~qnFvklflcs~~~~lvslD~Aak~Ll~ds~~~~~mRtkvRRLYDIANVlssm~LIeKtH~l~trkPafr 234 (388)
T KOG2578|consen 155 NRKEKSLWLLAQNFVKLFLCSDDDILVSLDSAAKALLKDSEDEPPMRTKVRRLYDIANVLSSMNLIEKTHYLFTRKPAFR 234 (388)
T ss_pred chhhhHHHHHHHHHHHheeccccceEEeecHHHHHHhcCCCCCccHHHHHHHHHHHHHHHHHhhhhhhhcccccccchhh
Confidence 578999999999999999999888 8999999988853 2 459999999999999999996 699999
Q ss_pred EeccCCC
Q psy7686 73 WKALKNK 79 (243)
Q Consensus 73 W~G~~~~ 79 (243)
|.|..++
T Consensus 235 wlG~~~~ 241 (388)
T KOG2578|consen 235 WLGSKPI 241 (388)
T ss_pred eeCCCcc
Confidence 9998887
No 5
>KOG2829|consensus
Probab=99.04 E-value=3.5e-09 Score=97.36 Aligned_cols=146 Identities=20% Similarity=0.334 Sum_probs=91.6
Q ss_pred HHHHHHHHHHHHhhCCCCeeeHHHHHhhhccc---------------------chhhhhhHHHhhhhccceeccccCceE
Q psy7686 14 LGLLTTKFVSLLQQAPEGVLHLKYAAENLEVK---------------------QKRRIYDITNVLEGIGLIEKNNKNIIR 72 (243)
Q Consensus 14 L~~Lt~kFi~ll~~~~~g~idL~~aa~~L~v~---------------------~KRRiYDItNVLEgiglI~K~sKn~i~ 72 (243)
|..++.+..+-++ ..|....|++|+.|-.+ .|||+||..|||.++.+|.|. |..|+
T Consensus 46 LRhfs~kVCeKve--~Kg~TtYneVADelVaef~~~n~~~~i~~n~~~yd~KNIRRRVYDALNVlmAmnIIsKd-KKEIr 122 (326)
T KOG2829|consen 46 LRHFSMKVCEKVE--RKGTTTYNEVADELVAEFAGANNYSHICPNEQEYDQKNIRRRVYDALNVLMAMNIISKD-KKEIR 122 (326)
T ss_pred hhhhhHHHHHHHH--hcCCccHHHHHHHHHHHHhccccccccCccccccchHHHHHHHHHHHHHHHHHHHHhcc-cceee
Confidence 4444444444443 47889999999988642 689999999999999999999 77899
Q ss_pred EeccCCCCchhhhHHHHHhHhHHHH----HHHHHHHHHHHHHHHHHHHHHHHhhhhhhhccCccccchhhhhhcCCC--C
Q psy7686 73 WKALKNKNEEEYDLEQSKLIELRDE----ISDMRNHEAVIDEHIRKCQQSLRNIQEEEVNRKQCYIPTDVILGMFPD--S 146 (243)
Q Consensus 73 W~G~~~~~~~~~~~~~~~~~~Lk~E----l~~L~~~E~~LD~~I~~~~~~l~~l~ed~~n~~~aYVT~~Di~~~f~~--q 146 (243)
|+|.+..... + ..+|+.| ++...++-+.|.++|... -.+++|.+ .| +.++.+.. .-..+ =
T Consensus 123 W~GLP~~ss~---d----v~~le~Er~k~~erI~kK~a~lqEl~~q~-~~fknLV~--RN-~~~e~~~~---~P~~~i~L 188 (326)
T KOG2829|consen 123 WIGLPATSSQ---D----VSELEEERKKRMERIKKKAAQLQELIEQV-SAFKNLVQ--RN-RHAESQGQ---PPSENIHL 188 (326)
T ss_pred eeccCccchH---H----HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHH--hh-hhhhhccC---CCCccccc
Confidence 9999875332 2 2222222 222333334455555433 24555555 22 22343310 00111 2
Q ss_pred eEEEEECCCCCeEEecCCCCCCceEEEEEecCC
Q psy7686 147 SLMCLKAPYGTKLHVPSISTDENKIKLHVKSSH 179 (243)
Q Consensus 147 tviaIkAP~~T~leVp~p~~~~~~yqi~LkS~~ 179 (243)
..|.|..-+.|.+++...+ +....+++..+
T Consensus 189 PFiiinT~k~a~Ieceise---Dks~~~F~Fnk 218 (326)
T KOG2829|consen 189 PFIIINTSKKAVIECEISE---DKSEYLFKFNK 218 (326)
T ss_pred ceEEEecCCCceEEEEecc---cceeeeeecCC
Confidence 4689999999999999886 36667777776
No 6
>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=95.46 E-value=0.031 Score=40.07 Aligned_cols=46 Identities=24% Similarity=0.380 Sum_probs=41.2
Q ss_pred CCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceeccccCceEEec
Q psy7686 29 PEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNNKNIIRWKA 75 (243)
Q Consensus 29 ~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~sKn~i~W~G 75 (243)
..|..+..++|+.+++ .+..+|+++|-|+.-|+|++...+.+.|.-
T Consensus 19 ~~~~~t~~eIa~~l~i-~~~~v~~~L~~L~~~GlV~~~~~~~~~Y~a 64 (68)
T PF01978_consen 19 KNGPATAEEIAEELGI-SRSTVYRALKSLEEKGLVEREEGRPKVYRA 64 (68)
T ss_dssp HHCHEEHHHHHHHHTS-SHHHHHHHHHHHHHTTSEEEEEECCEEEEE
T ss_pred HcCCCCHHHHHHHHCc-CHHHHHHHHHHHHHCCCEEEEcCceEEEEE
Confidence 3677999999999999 999999999999999999999777777653
No 7
>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=93.22 E-value=0.27 Score=33.53 Aligned_cols=41 Identities=29% Similarity=0.338 Sum_probs=34.9
Q ss_pred HHHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhcc
Q psy7686 19 TKFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIG 61 (243)
Q Consensus 19 ~kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgig 61 (243)
.+.+.+|..+.+. +...++|+.|+| .+|-|+--++.|+..|
T Consensus 3 ~~il~~L~~~~~~-it~~eLa~~l~v-S~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 3 KQILKLLLESKEP-ITAKELAEELGV-SRRTIRRDIKELREWG 43 (55)
T ss_dssp HHHHHHHHHTTTS-BEHHHHHHHCTS--HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHcCCC-cCHHHHHHHhCC-CHHHHHHHHHHHHHCC
Confidence 4567788666555 999999999999 9999999999999998
No 8
>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=92.49 E-value=0.22 Score=34.04 Aligned_cols=44 Identities=20% Similarity=0.292 Sum_probs=36.7
Q ss_pred HHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceecc
Q psy7686 21 FVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKN 66 (243)
Q Consensus 21 Fi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~ 66 (243)
.++++..++.+ +.+.++|+.+|+ .|--+|-+.+.|+..|+++|.
T Consensus 8 iL~~l~~~~~~-~t~~eia~~~gl-~~stv~r~L~tL~~~g~v~~d 51 (52)
T PF09339_consen 8 ILEALAESGGP-LTLSEIARALGL-PKSTVHRLLQTLVEEGYVERD 51 (52)
T ss_dssp HHHCHHCTBSC-EEHHHHHHHHTS--HHHHHHHHHHHHHTTSEEEC
T ss_pred HHHHHHcCCCC-CCHHHHHHHHCc-CHHHHHHHHHHHHHCcCeecC
Confidence 45566665444 799999999999 999999999999999999874
No 9
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=92.26 E-value=0.52 Score=42.78 Aligned_cols=51 Identities=27% Similarity=0.412 Sum_probs=41.1
Q ss_pred HHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceeccccCceEEec
Q psy7686 21 FVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNNKNIIRWKA 75 (243)
Q Consensus 21 Fi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~sKn~i~W~G 75 (243)
++.|+. -|...-.++|+..|| .+=|+|||++-||+=|+++....+--+++.
T Consensus 22 Y~aLl~---~g~~tA~eis~~sgv-P~~kvY~vl~sLe~kG~v~~~~g~P~~y~a 72 (247)
T COG1378 22 YLALLC---LGEATAKEISEASGV-PRPKVYDVLRSLEKKGLVEVIEGRPKKYRA 72 (247)
T ss_pred HHHHHH---hCCccHHHHHHHcCC-CchhHHHHHHHHHHCCCEEeeCCCCceEEe
Confidence 455554 466788999999999 999999999999999999998554444444
No 10
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=91.64 E-value=0.45 Score=31.14 Aligned_cols=46 Identities=30% Similarity=0.343 Sum_probs=38.8
Q ss_pred HHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceecccc
Q psy7686 20 KFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNNK 68 (243)
Q Consensus 20 kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~sK 68 (243)
.++.++.+. +.+++.++|+.+++ .++.+|-.++-|+..|+|.+..+
T Consensus 4 ~il~~l~~~--~~~s~~~l~~~l~~-s~~tv~~~l~~L~~~g~i~~~~~ 49 (53)
T smart00420 4 QILELLAQQ--GKVSVEELAELLGV-SEMTIRRDLNKLEEQGLLTRVHG 49 (53)
T ss_pred HHHHHHHHc--CCcCHHHHHHHHCC-CHHHHHHHHHHHHHCCCEEEeec
Confidence 456666653 45899999999999 99999999999999999998643
No 11
>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=91.50 E-value=0.64 Score=32.27 Aligned_cols=54 Identities=19% Similarity=0.202 Sum_probs=41.9
Q ss_pred HHHHHHHHHhhC-----CCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceeccccCce
Q psy7686 17 LTTKFVSLLQQA-----PEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNNKNII 71 (243)
Q Consensus 17 Lt~kFi~ll~~~-----~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~sKn~i 71 (243)
+..-|+.+.... ..+.+...++|+.+++ .+.-++-+++.|+.-|+|++.....|
T Consensus 5 ia~~l~~l~~~~~~~~~~~~~~s~~ela~~~g~-s~~tv~r~l~~L~~~g~i~~~~~~~~ 63 (67)
T cd00092 5 LASFLLNLSLRYGAGDLVQLPLTRQEIADYLGL-TRETVSRTLKELEEEGLISRRGRGKY 63 (67)
T ss_pred HHHHHHHHHHHcCCCccccCCcCHHHHHHHHCC-CHHHHHHHHHHHHHCCCEEecCCCeE
Confidence 334455554432 3467899999999999 99999999999999999998763433
No 12
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=91.45 E-value=0.5 Score=34.41 Aligned_cols=54 Identities=20% Similarity=0.286 Sum_probs=45.1
Q ss_pred HHHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceeccccCceEE
Q psy7686 19 TKFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNNKNIIRW 73 (243)
Q Consensus 19 ~kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~sKn~i~W 73 (243)
.+.+.+|..+++..+.+.++|+.||+ .++-+.-+..-|+.-|+|.+.+.+.=.|
T Consensus 9 ~~IL~~L~~~g~~~~ta~eLa~~lgl-~~~~v~r~L~~L~~~G~V~~~~~~~~~W 62 (68)
T smart00550 9 EKILEFLENSGDETSTALQLAKNLGL-PKKEVNRVLYSLEKKGKVCKQGGTPPLW 62 (68)
T ss_pred HHHHHHHHHCCCCCcCHHHHHHHHCC-CHHHHHHHHHHHHHCCCEEecCCCCCce
Confidence 56778888764434999999999999 9999999999999999999976543466
No 13
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=90.49 E-value=0.78 Score=33.89 Aligned_cols=47 Identities=28% Similarity=0.427 Sum_probs=39.7
Q ss_pred HHHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceeccc
Q psy7686 19 TKFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNN 67 (243)
Q Consensus 19 ~kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~s 67 (243)
.+.++++...+ +.+.+.++|+.+++ .+.-+|-+++.|+..|+|++..
T Consensus 8 ~~Il~~l~~~~-~~~t~~~ia~~l~i-~~~tv~r~l~~L~~~g~l~~~~ 54 (91)
T smart00346 8 LAVLRALAEEP-GGLTLAELAERLGL-SKSTAHRLLNTLQELGYVEQDG 54 (91)
T ss_pred HHHHHHHHhCC-CCcCHHHHHHHhCC-CHHHHHHHHHHHHHCCCeeecC
Confidence 34566666543 47999999999999 9999999999999999999864
No 14
>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=89.85 E-value=0.82 Score=31.43 Aligned_cols=46 Identities=28% Similarity=0.389 Sum_probs=40.0
Q ss_pred HHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceecc
Q psy7686 20 KFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKN 66 (243)
Q Consensus 20 kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~ 66 (243)
..+..+...++..+...++|+.+++ .|-.+--+++-|+.-|+|+|.
T Consensus 9 ~vL~~l~~~~~~~~t~~~la~~l~~-~~~~vs~~v~~L~~~Glv~r~ 54 (62)
T PF12802_consen 9 RVLMALARHPGEELTQSELAERLGI-SKSTVSRIVKRLEKKGLVERE 54 (62)
T ss_dssp HHHHHHHHSTTSGEEHHHHHHHHTS--HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHCCCCCcCHHHHHHHHCc-CHHHHHHHHHHHHHCCCEEEe
Confidence 3556667777777999999999999 999999999999999999997
No 15
>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=88.80 E-value=1.1 Score=29.89 Aligned_cols=43 Identities=30% Similarity=0.457 Sum_probs=36.0
Q ss_pred HHHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhcccee
Q psy7686 19 TKFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIE 64 (243)
Q Consensus 19 ~kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~ 64 (243)
++.+.++.+.|. ++..++|+.+|+ .+..++.+++-|+.-|+|+
T Consensus 6 ~~Il~~l~~~~~--~t~~ela~~~~i-s~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 6 RKILNYLRENPR--ITQKELAEKLGI-SRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHCTT--S-HHHHHHHHTS--HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHcCC--CCHHHHHHHhCC-CHHHHHHHHHHHHHCcCcC
Confidence 567788887444 999999999999 9999999999999999985
No 16
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=88.56 E-value=3.3 Score=34.38 Aligned_cols=46 Identities=28% Similarity=0.432 Sum_probs=40.0
Q ss_pred HHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceeccccC
Q psy7686 21 FVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNNKN 69 (243)
Q Consensus 21 Fi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~sKn 69 (243)
|..|+. +.|..+.+++|+.|+. .|=.+|=..|=|...|||.|..-+
T Consensus 33 ~~~LL~--~~~~~tvdelae~lnr-~rStv~rsl~~L~~~GlV~Rek~~ 78 (126)
T COG3355 33 YKALLE--ENGPLTVDELAEILNR-SRSTVYRSLQNLLEAGLVEREKVN 78 (126)
T ss_pred HHHHHh--hcCCcCHHHHHHHHCc-cHHHHHHHHHHHHHcCCeeeeeec
Confidence 555554 5788999999999999 999999999999999999997444
No 17
>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=86.27 E-value=1.9 Score=32.04 Aligned_cols=49 Identities=27% Similarity=0.392 Sum_probs=39.0
Q ss_pred HHHHHHHHHhhCCCC-eeeHHHHHhhhcccchhhhhhHHHhhhhccceecc
Q psy7686 17 LTTKFVSLLQQAPEG-VLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKN 66 (243)
Q Consensus 17 Lt~kFi~ll~~~~~g-~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~ 66 (243)
.+-+++.++...+++ .++..++|+.+++ ..+.+..|++-|..-|+|+..
T Consensus 9 ~Al~~l~~la~~~~~~~~s~~eiA~~~~i-~~~~l~kil~~L~~~Gli~s~ 58 (83)
T PF02082_consen 9 YALRILLYLARHPDGKPVSSKEIAERLGI-SPSYLRKILQKLKKAGLIESS 58 (83)
T ss_dssp HHHHHHHHHHCTTTSC-BEHHHHHHHHTS--HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHhCCCCCCCCHHHHHHHHCc-CHHHHHHHHHHHhhCCeeEec
Confidence 344566666555554 5999999999999 999999999999999999865
No 18
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=86.12 E-value=1.4 Score=29.32 Aligned_cols=38 Identities=26% Similarity=0.307 Sum_probs=34.2
Q ss_pred CCeeeHHHHHhhhcccchhhhhhHHHhhhhccceecccc
Q psy7686 30 EGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNNK 68 (243)
Q Consensus 30 ~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~sK 68 (243)
.+.+++++++..|++ .+..++.+++.|+.-|+|.+..+
T Consensus 8 ~~~~~~~~i~~~l~i-s~~~v~~~l~~L~~~g~i~~~~~ 45 (66)
T smart00418 8 EGELCVCELAEILGL-SQSTVSHHLKKLREAGLVESRRE 45 (66)
T ss_pred cCCccHHHHHHHHCC-CHHHHHHHHHHHHHCCCeeeeec
Confidence 456799999999999 99999999999999999997643
No 19
>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=84.95 E-value=1.7 Score=29.75 Aligned_cols=44 Identities=25% Similarity=0.372 Sum_probs=36.2
Q ss_pred HHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceeccc
Q psy7686 21 FVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNN 67 (243)
Q Consensus 21 Fi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~s 67 (243)
++..+.+.++ +.+.++|+.+++ .+-.+-.+++-|+.-|+|+|..
T Consensus 8 iL~~l~~~~~--~~~~~la~~~~~-~~~~~t~~i~~L~~~g~I~r~~ 51 (59)
T PF01047_consen 8 ILRILYENGG--ITQSELAEKLGI-SRSTVTRIIKRLEKKGLIERER 51 (59)
T ss_dssp HHHHHHHHSS--EEHHHHHHHHTS--HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHcCC--CCHHHHHHHHCC-ChhHHHHHHHHHHHCCCEEecc
Confidence 3444555444 999999999999 9999999999999999999973
No 20
>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=84.92 E-value=1.8 Score=34.56 Aligned_cols=46 Identities=15% Similarity=0.141 Sum_probs=39.9
Q ss_pred HHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceecc
Q psy7686 20 KFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKN 66 (243)
Q Consensus 20 kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~ 66 (243)
+.+.++...+++.+++.++|+.+++ .+..++.+.+.|+.-|+|+..
T Consensus 13 ~~l~~la~~~~~~~s~~eia~~l~i-s~~~v~~~l~~L~~~Gli~~~ 58 (130)
T TIGR02944 13 LVLTTLAQNDSQPYSAAEIAEQTGL-NAPTVSKILKQLSLAGIVTSK 58 (130)
T ss_pred HHHHHHHhCCCCCccHHHHHHHHCc-CHHHHHHHHHHHHHCCcEEec
Confidence 3455565566788999999999999 999999999999999999864
No 21
>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=83.71 E-value=2.9 Score=29.12 Aligned_cols=37 Identities=32% Similarity=0.451 Sum_probs=31.9
Q ss_pred CCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceecc
Q psy7686 29 PEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKN 66 (243)
Q Consensus 29 ~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~ 66 (243)
.++.+.+.++|+.+++ .+--+..+++-|+..|+|+|.
T Consensus 15 ~~~~~t~~~l~~~~~~-~~~~vs~~i~~L~~~glv~~~ 51 (68)
T PF13463_consen 15 SDGPMTQSDLAERLGI-SKSTVSRIIKKLEEKGLVEKE 51 (68)
T ss_dssp -TS-BEHHHHHHHTT---HHHHHHHHHHHHHTTSEEEE
T ss_pred cCCCcCHHHHHHHHCc-CHHHHHHHHHHHHHCCCEEec
Confidence 6888999999999999 999999999999999999887
No 22
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=83.02 E-value=4 Score=32.44 Aligned_cols=70 Identities=7% Similarity=0.061 Sum_probs=35.0
Q ss_pred EEeccCCCCchhhhHHHHHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhccCccccchh---hhhhcCCCCeE
Q psy7686 72 RWKALKNKNEEEYDLEQSKLIELRDEISDMRNHEAVIDEHIRKCQQSLRNIQEEEVNRKQCYIPTD---VILGMFPDSSL 148 (243)
Q Consensus 72 ~W~G~~~~~~~~~~~~~~~~~~Lk~El~~L~~~E~~LD~~I~~~~~~l~~l~ed~~n~~~aYVT~~---Di~~~f~~qtv 148 (243)
-|.|.... ..+.+...++..+++|++.|+++.+.|...|..++ ++. .|+... ++.=+-++.++
T Consensus 19 l~~g~~G~--~~~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~-------~~~-----dyiEe~AR~~Lg~vk~gEiv 84 (105)
T PRK00888 19 LWFGKNGI--LDYWRVNDQVAAQQQTNAKLKARNDQLFAEIDDLK-------GGQ-----EAIEERARNELGMVKPGETF 84 (105)
T ss_pred HhccCCcH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh-------CcH-----HHHHHHHHHHcCCCCCCCEE
Confidence 36565443 11124455555666666666666666655555444 321 232211 11114577888
Q ss_pred EEEECCC
Q psy7686 149 MCLKAPY 155 (243)
Q Consensus 149 iaIkAP~ 155 (243)
+.|.-|.
T Consensus 85 y~~~~~~ 91 (105)
T PRK00888 85 YRIVPDA 91 (105)
T ss_pred EEeCCCC
Confidence 8776553
No 23
>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=82.56 E-value=2.4 Score=30.64 Aligned_cols=46 Identities=17% Similarity=0.221 Sum_probs=36.6
Q ss_pred HHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceeccccCc
Q psy7686 22 VSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNNKNI 70 (243)
Q Consensus 22 i~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~sKn~ 70 (243)
.+++.. .+.+++.++|..|++ ...-+=..+.+|+..|.|+|...+.
T Consensus 6 ~~~l~~--~~~~S~~eLa~~~~~-s~~~ve~mL~~l~~kG~I~~~~~~~ 51 (69)
T PF09012_consen 6 RDYLRE--RGRVSLAELAREFGI-SPEAVEAMLEQLIRKGYIRKVDMSS 51 (69)
T ss_dssp HHHHHH--S-SEEHHHHHHHTT---HHHHHHHHHHHHCCTSCEEEEEE-
T ss_pred HHHHHH--cCCcCHHHHHHHHCc-CHHHHHHHHHHHHHCCcEEEecCCC
Confidence 344554 788999999999999 9999999999999999999985543
No 24
>PF09079 Cdc6_C: CDC6, C terminal ; InterPro: IPR015163 The C-terminal domain of CDC6 assumes a winged helix fold, with a five alpha-helical bundle (alpha15-alpha19) structure, backed on one side by three beta strands (beta6-beta8). It has been shown that this domain acts as a DNA-localisation factor, however its exact function is, as yet, unknown. Putative functions include: (1) mediation of protein-protein interactions and (2) regulation of nucleotide binding and hydrolysis. Mutagenesis studies have shown that this domain is essential for appropriate Cdc6 activity []. ; PDB: 2QBY_A 2V1U_A 1W5T_A 1W5S_B 1FNN_B.
Probab=81.86 E-value=1.2 Score=33.30 Aligned_cols=32 Identities=38% Similarity=0.460 Sum_probs=24.3
Q ss_pred HHHHhhhccc--chhhhhhHHHhhhhccceeccc
Q psy7686 36 KYAAENLEVK--QKRRIYDITNVLEGIGLIEKNN 67 (243)
Q Consensus 36 ~~aa~~L~v~--~KRRiYDItNVLEgiglI~K~s 67 (243)
..+|+.+++. ..||++|+.|-|+.+|+|+-..
T Consensus 26 ~~lc~~~~~~pls~~r~~~~l~eL~~~gli~~~~ 59 (85)
T PF09079_consen 26 EELCESLGVDPLSYRRFSDYLSELEMLGLIESER 59 (85)
T ss_dssp HHHHHHTTS----HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHcCCCCCCHHHHHHHHHHHHhCCCeEEEe
Confidence 3456666653 5799999999999999998763
No 25
>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=81.19 E-value=3.6 Score=27.48 Aligned_cols=41 Identities=29% Similarity=0.432 Sum_probs=34.8
Q ss_pred HHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceec
Q psy7686 21 FVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEK 65 (243)
Q Consensus 21 Fi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K 65 (243)
.+.++.. |.....++|+.+++ .+--++==.+.|+..|+|+|
T Consensus 7 Il~~L~~---~~~~~~el~~~l~~-s~~~vs~hL~~L~~~glV~~ 47 (47)
T PF01022_consen 7 ILKLLSE---GPLTVSELAEELGL-SQSTVSHHLKKLREAGLVEK 47 (47)
T ss_dssp HHHHHTT---SSEEHHHHHHHHTS--HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHh---CCCchhhHHHhccc-cchHHHHHHHHHHHCcCeeC
Confidence 4555543 77999999999999 99999999999999999986
No 26
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=80.90 E-value=4.1 Score=27.15 Aligned_cols=41 Identities=22% Similarity=0.327 Sum_probs=35.5
Q ss_pred CCCCee-eHHHHHhhhcccchhhhhhHHHhhhhccceeccccC
Q psy7686 28 APEGVL-HLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNNKN 69 (243)
Q Consensus 28 ~~~g~i-dL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~sKn 69 (243)
.++..+ +..++|+.+++ .+--+...++-|+.-|+|.+..+.
T Consensus 15 ~~~~~l~s~~~la~~~~v-s~~tv~~~l~~L~~~g~i~~~~~~ 56 (60)
T smart00345 15 RPGDKLPSERELAAQLGV-SRTTVREALSRLEAEGLVQRRPGS 56 (60)
T ss_pred CCCCcCcCHHHHHHHHCC-CHHHHHHHHHHHHHCCCEEEecCC
Confidence 355567 89999999999 999999999999999999876543
No 27
>cd08768 Cdc6_C Winged-helix domain of essential DNA replication protein Cell division control protein (Cdc6), which mediates DNA binding. This model characterizes the winged-helix, C-terminal domain of the Cell division control protein (Cdc6_C). Cdc6 (also known as Cell division cycle 6 or Cdc18) functions as a regulator at the early stages of DNA replication, by helping to recruit and load the Minichromosome Maintenance Complex (MCM) onto DNA and may have additional roles in the control of mitotic entry. Precise duplication of chromosomal DNA is required for genomic stability during replication. Cdc6 has an essential role in DNA replication and irregular expression of Cdc6 may lead to genomic instability. Cdc6 over-expression is observed in many cancerous lesions. DNA replication begins when an origin recognition complex (ORC) binds to a replication origin site on the chromatin. Studies indicate that Cdc6 interacts with ORC through the Orc1 subunit, and that this association increases
Probab=79.91 E-value=1.8 Score=31.88 Aligned_cols=21 Identities=43% Similarity=0.684 Sum_probs=19.4
Q ss_pred chhhhhhHHHhhhhccceecc
Q psy7686 46 QKRRIYDITNVLEGIGLIEKN 66 (243)
Q Consensus 46 ~KRRiYDItNVLEgiglI~K~ 66 (243)
..||++|+.|-|+..|+|+-.
T Consensus 45 ~~~~~~~~l~~L~~~gli~~~ 65 (87)
T cd08768 45 TQRRISDLLSELEMLGLLETE 65 (87)
T ss_pred cHHHHHHHHHHHHHcCCeEEE
Confidence 679999999999999999865
No 28
>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=79.40 E-value=4.8 Score=27.27 Aligned_cols=46 Identities=26% Similarity=0.408 Sum_probs=37.9
Q ss_pred HHHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceecccc
Q psy7686 19 TKFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNNK 68 (243)
Q Consensus 19 ~kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~sK 68 (243)
.+++..+...+ +...++|+.+++ .+.-++-++|.|+.-|+|.+...
T Consensus 10 ~~il~~l~~~~---~~~~ei~~~~~i-~~~~i~~~l~~L~~~g~i~~~~~ 55 (78)
T cd00090 10 LRILRLLLEGP---LTVSELAERLGL-SQSTVSRHLKKLEEAGLVESRRE 55 (78)
T ss_pred HHHHHHHHHCC---cCHHHHHHHHCc-CHhHHHHHHHHHHHCCCeEEEEe
Confidence 44555555533 899999999999 99999999999999999997643
No 29
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=78.64 E-value=3.3 Score=26.67 Aligned_cols=35 Identities=26% Similarity=0.278 Sum_probs=31.9
Q ss_pred eeeHHHHHhhhcccchhhhhhHHHhhhhccceeccc
Q psy7686 32 VLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNN 67 (243)
Q Consensus 32 ~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~s 67 (243)
.+...++|+.+++ .+..++.+++.|+.-|+|++..
T Consensus 8 ~~s~~~la~~l~~-s~~tv~~~l~~L~~~g~l~~~~ 42 (48)
T smart00419 8 PLTRQEIAELLGL-TRETVSRTLKRLEKEGLISREG 42 (48)
T ss_pred ccCHHHHHHHHCC-CHHHHHHHHHHHHHCCCEEEeC
Confidence 3677899999999 9999999999999999999864
No 30
>PF13730 HTH_36: Helix-turn-helix domain
Probab=77.92 E-value=3.7 Score=27.79 Aligned_cols=29 Identities=31% Similarity=0.392 Sum_probs=27.8
Q ss_pred eHHHHHhhhcccchhhhhhHHHhhhhccce
Q psy7686 34 HLKYAAENLEVKQKRRIYDITNVLEGIGLI 63 (243)
Q Consensus 34 dL~~aa~~L~v~~KRRiYDItNVLEgiglI 63 (243)
+...+|+.+|+ .+|.|+-.++.|+..|+|
T Consensus 27 S~~~la~~~g~-s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 27 SQETLAKDLGV-SRRTVQRAIKELEEKGLI 55 (55)
T ss_pred CHHHHHHHHCc-CHHHHHHHHHHHHHCcCC
Confidence 78999999999 999999999999999986
No 31
>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=75.83 E-value=7.1 Score=27.32 Aligned_cols=44 Identities=32% Similarity=0.440 Sum_probs=37.5
Q ss_pred HHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceecc
Q psy7686 20 KFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKN 66 (243)
Q Consensus 20 kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~ 66 (243)
+.++++++ .+.+.+.++|+.|+| ...-|.==+|.|+.-|+|.|.
T Consensus 4 ~Il~~l~~--~~~~s~~ela~~~~V-S~~TiRRDl~~L~~~g~i~r~ 47 (57)
T PF08220_consen 4 QILELLKE--KGKVSVKELAEEFGV-SEMTIRRDLNKLEKQGLIKRT 47 (57)
T ss_pred HHHHHHHH--cCCEEHHHHHHHHCc-CHHHHHHHHHHHHHCCCEEEE
Confidence 45677776 678999999999999 887777777899999999987
No 32
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=74.45 E-value=45 Score=30.04 Aligned_cols=53 Identities=11% Similarity=0.194 Sum_probs=41.7
Q ss_pred HHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceeccccCceEEec
Q psy7686 21 FVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNNKNIIRWKA 75 (243)
Q Consensus 21 Fi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~sKn~i~W~G 75 (243)
.+++|... ++.+.+.++|+.|++ .|=.+|-+.+-|+..|++.+.....--+.|
T Consensus 30 IL~~~~~~-~~~~tl~eIa~~lgl-pkStv~RlL~tL~~~G~l~~~~~~~~Y~lG 82 (271)
T PRK10163 30 ILQYLEKS-GGSSSVSDISLNLDL-PLSTTFRLLKVLQAADFVYQDSQLGWWHIG 82 (271)
T ss_pred HHHHHHhC-CCCcCHHHHHHHHCc-CHHHHHHHHHHHHHCCCEEEcCCCCeEEec
Confidence 55666544 345899999999999 999999999999999999986443333345
No 33
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=74.07 E-value=7.7 Score=27.08 Aligned_cols=46 Identities=26% Similarity=0.368 Sum_probs=38.1
Q ss_pred HHHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceeccc
Q psy7686 19 TKFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNN 67 (243)
Q Consensus 19 ~kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~s 67 (243)
.+.+.++. .++.....++|+.|++ .+--+|-=+++|+..|||+...
T Consensus 13 ~~Il~~L~--~~~~~t~~ela~~l~~-~~~t~s~hL~~L~~aGli~~~~ 58 (61)
T PF12840_consen 13 LRILRLLA--SNGPMTVSELAEELGI-SQSTVSYHLKKLEEAGLIEVER 58 (61)
T ss_dssp HHHHHHHH--HCSTBEHHHHHHHHTS--HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHh--cCCCCCHHHHHHHHCC-CHHHHHHHHHHHHHCCCeEEec
Confidence 34566663 3677999999999999 9999999999999999999764
No 34
>PF04182 B-block_TFIIIC: B-block binding subunit of TFIIIC; InterPro: IPR007309 Yeast transcription factor IIIC (TFIIIC) is a multisubunit protein complex that interacts with two control elements of class III promoters called the A and B blocks. This family represents the subunit within TFIIIC involved in B-block binding []. Although defined as a yeast protein, it is also found in a number of other organisms.
Probab=73.93 E-value=6.4 Score=29.03 Aligned_cols=48 Identities=19% Similarity=0.189 Sum_probs=38.7
Q ss_pred HHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceecccc
Q psy7686 20 KFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNNK 68 (243)
Q Consensus 20 kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~sK 68 (243)
++++.+-.+...-+.-.+++..++. ..|-++=++++|+..|||.|.+-
T Consensus 6 ~~Le~I~rsR~~Gi~q~~L~~~~~~-D~r~i~~~~k~L~~~gLI~k~~~ 53 (75)
T PF04182_consen 6 CLLERIARSRYNGITQSDLSKLLGI-DPRSIFYRLKKLEKKGLIVKQSV 53 (75)
T ss_pred HHHHHHHhcCCCCEehhHHHHHhCC-CchHHHHHHHHHHHCCCEEEEEe
Confidence 4566665555444566778899999 99999999999999999999865
No 35
>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=73.80 E-value=6.7 Score=27.59 Aligned_cols=49 Identities=22% Similarity=0.295 Sum_probs=37.5
Q ss_pred HHHHHHHhh---CCCCee-eHHHHHhhhcccchhhhhhHHHhhhhccceecccc
Q psy7686 19 TKFVSLLQQ---APEGVL-HLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNNK 68 (243)
Q Consensus 19 ~kFi~ll~~---~~~g~i-dL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~sK 68 (243)
..+...+.. .++..+ +..++|+.++| .+.=+....+.|+.-|+|++..+
T Consensus 7 ~~l~~~I~~g~~~~g~~lps~~~la~~~~v-sr~tvr~al~~L~~~g~i~~~~~ 59 (64)
T PF00392_consen 7 DQLRQAILSGRLPPGDRLPSERELAERYGV-SRTTVREALRRLEAEGLIERRPG 59 (64)
T ss_dssp HHHHHHHHTTSS-TTSBE--HHHHHHHHTS--HHHHHHHHHHHHHTTSEEEETT
T ss_pred HHHHHHHHcCCCCCCCEeCCHHHHHHHhcc-CCcHHHHHHHHHHHCCcEEEECC
Confidence 344444443 356678 99999999999 99999999999999999998754
No 36
>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=72.47 E-value=8.3 Score=30.50 Aligned_cols=36 Identities=28% Similarity=0.379 Sum_probs=33.5
Q ss_pred CCeeeHHHHHhhhcccchhhhhhHHHhhhhccceecc
Q psy7686 30 EGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKN 66 (243)
Q Consensus 30 ~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~ 66 (243)
.+.++..++|+.+++ .++.+++|+..|..-|+|...
T Consensus 23 ~~~~s~~eia~~~~i-~~~~v~~il~~L~~~gli~~~ 58 (132)
T TIGR00738 23 EGPVSVKEIAERQGI-SRSYLEKILRTLRRAGLVESV 58 (132)
T ss_pred CCcCcHHHHHHHHCc-CHHHHHHHHHHHHHCCcEEec
Confidence 458999999999999 999999999999999999864
No 37
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=71.26 E-value=7 Score=29.85 Aligned_cols=47 Identities=19% Similarity=0.277 Sum_probs=41.0
Q ss_pred HHHHHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceecc
Q psy7686 17 LTTKFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKN 66 (243)
Q Consensus 17 Lt~kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~ 66 (243)
+-++.+.+++. ++.+...++|+.+|+ ...-++..++-|+.-|+|.+.
T Consensus 4 ~D~~il~~L~~--~~~~~~~~la~~l~~-s~~tv~~~l~~L~~~g~i~~~ 50 (108)
T smart00344 4 IDRKILEELQK--DARISLAELAKKVGL-SPSTVHNRVKRLEEEGVIKGY 50 (108)
T ss_pred HHHHHHHHHHH--hCCCCHHHHHHHHCc-CHHHHHHHHHHHHHCCCeece
Confidence 34678888887 456899999999999 999999999999999999954
No 38
>cd00890 Prefoldin Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.
Probab=71.03 E-value=29 Score=27.15 Aligned_cols=54 Identities=9% Similarity=0.164 Sum_probs=26.1
Q ss_pred ccCceEEeccCCCCchhhhHHHHHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q psy7686 67 NKNIIRWKALKNKNEEEYDLEQSKLIELRDEISDMRNHEAVIDEHIRKCQQSLRNIQ 123 (243)
Q Consensus 67 sKn~i~W~G~~~~~~~~~~~~~~~~~~Lk~El~~L~~~E~~LD~~I~~~~~~l~~l~ 123 (243)
...-+.|.|.+..-.. ........++..++.|+..-..|+..+..+++++..+.
T Consensus 68 ~~~v~v~iG~~~~ve~---~~~eA~~~l~~r~~~l~~~~~~l~~~~~~~~~~~~~l~ 121 (129)
T cd00890 68 DDKVLVDLGTGVYVEK---SLEEAIEFLKKRLETLEKQIEKLEKQLEKLQDQITELQ 121 (129)
T ss_pred CCEEEEEecCCEEEEe---cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4556889996665111 11112233444444444444445555555555544443
No 39
>TIGR02338 gimC_beta prefoldin, beta subunit, archaeal. Chaperonins are cytosolic, ATP-dependent molecular chaperones, with a conserved toroidal architecture, that assist in the folding of nascent and/or denatured polypeptide chains. The group I chaperonin system consists of GroEL and GroES, and is found (usually) in bacteria and organelles of bacterial origin. The group II chaperonin system, called the thermosome in Archaea and TRiC or CCT in the Eukaryota, is structurally similar but only distantly related. Prefoldin, also called GimC, is a complex in Archaea and Eukaryota, that works with group II chaperonins. Members of this protein family are the archaeal clade of the beta class of prefoldin subunit. Closely related, but outside the scope of this family are the eukaryotic beta-class prefoldin subunits, Gim-1,3,4 and 6. The alpha class prefoldin subunits are more distantly related.
Probab=71.00 E-value=18 Score=28.59 Aligned_cols=86 Identities=10% Similarity=0.156 Sum_probs=52.7
Q ss_pred HHHHhhhcccchhhhhhHHHhhhhccceeccccCceEEeccCCC-Cchhh--hHHHHHhHhHHHHHHHHHHHHHHHHHHH
Q psy7686 36 KYAAENLEVKQKRRIYDITNVLEGIGLIEKNNKNIIRWKALKNK-NEEEY--DLEQSKLIELRDEISDMRNHEAVIDEHI 112 (243)
Q Consensus 36 ~~aa~~L~v~~KRRiYDItNVLEgiglI~K~sKn~i~W~G~~~~-~~~~~--~~~~~~~~~Lk~El~~L~~~E~~LD~~I 112 (243)
..++..+.. -.+.+=....|++.+.-+. .+.+.|+-.|.--+ .+... ..+..++..+...+..|+.+...|...+
T Consensus 20 ~~l~~q~~~-le~~~~E~~~v~~eL~~l~-~d~~vyk~VG~vlv~~~~~e~~~~l~~r~e~ie~~i~~lek~~~~l~~~l 97 (110)
T TIGR02338 20 QAVATQKQQ-VEAQLKEAEKALEELERLP-DDTPVYKSVGNLLVKTDKEEAIQELKEKKETLELRVKTLQRQEERLREQL 97 (110)
T ss_pred HHHHHHHHH-HHHHHHHHHHHHHHHHcCC-CcchhHHHhchhhheecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333433333 3344445556666666555 34555666665433 22211 2455677788888888888888888888
Q ss_pred HHHHHHHHhhh
Q psy7686 113 RKCQQSLRNIQ 123 (243)
Q Consensus 113 ~~~~~~l~~l~ 123 (243)
..++++|+.+.
T Consensus 98 ~e~q~~l~~~~ 108 (110)
T TIGR02338 98 KELQEKIQEAL 108 (110)
T ss_pred HHHHHHHHHHh
Confidence 88888888765
No 40
>PF08781 DP: Transcription factor DP; InterPro: IPR014889 DP forms a heterodimer with E2F and regulates genes involved in cell cycle progression. The transcriptional activity of E2F is inhibited by the retinoblastoma protein which binds to the E2F-DP heterodimer [] and negatively regulates the G1-S transition. ; PDB: 2AZE_A.
Probab=70.90 E-value=30 Score=29.33 Aligned_cols=29 Identities=7% Similarity=0.102 Sum_probs=18.2
Q ss_pred EEEEECCCCCeEEecCCCCCCceEEEEEecCC
Q psy7686 148 LMCLKAPYGTKLHVPSISTDENKIKLHVKSSH 179 (243)
Q Consensus 148 viaIkAP~~T~leVp~p~~~~~~yqi~LkS~~ 179 (243)
.|.|..-+.|.+++-..++ ...+|.+..+
T Consensus 59 FIlV~T~~~a~I~ceiS~D---~~~~~F~Fn~ 87 (142)
T PF08781_consen 59 FILVNTSKKAVIECEISED---KSEYHFDFNS 87 (142)
T ss_dssp -EEEEEESS--EEEEE-TT---SSEEEEEESS
T ss_pred EEEEEecCCcEEEEEEcCC---ccEEEEEcCC
Confidence 4889999999999987763 4455555554
No 41
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=70.18 E-value=69 Score=27.39 Aligned_cols=45 Identities=20% Similarity=0.258 Sum_probs=38.3
Q ss_pred hCCCCeeeHHHHHhhh--cccchhhhhhHHHhhhhccceeccccCceE
Q psy7686 27 QAPEGVLHLKYAAENL--EVKQKRRIYDITNVLEGIGLIEKNNKNIIR 72 (243)
Q Consensus 27 ~~~~g~idL~~aa~~L--~v~~KRRiYDItNVLEgiglI~K~sKn~i~ 72 (243)
.-+++.-|..++|.+| +| .--.+=+.++.|+-+|||+|...+.|.
T Consensus 34 ~l~~~~~d~~~iak~l~p~i-s~~ev~~sL~~L~~~gli~k~~~g~y~ 80 (171)
T PF14394_consen 34 PLMPFAPDPEWIAKRLRPKI-SAEEVRDSLEFLEKLGLIKKDGDGKYV 80 (171)
T ss_pred hcCCCCCCHHHHHHHhcCCC-CHHHHHHHHHHHHHCCCeEECCCCcEE
Confidence 3456667999999999 99 999999999999999999999764443
No 42
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=70.03 E-value=9.7 Score=34.12 Aligned_cols=50 Identities=14% Similarity=0.277 Sum_probs=40.1
Q ss_pred HHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceeccc-cCceE
Q psy7686 21 FVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNN-KNIIR 72 (243)
Q Consensus 21 Fi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~s-Kn~i~ 72 (243)
.+++|... ++.+.+.++|+.|++ .|=-+|-+++-|+..|++++.. .+.|.
T Consensus 16 iL~~l~~~-~~~ls~~eia~~lgl-~kstv~RlL~tL~~~g~v~~~~~~~~Y~ 66 (263)
T PRK09834 16 VLRALNRL-DGGATVGLLAELTGL-HRTTVRRLLETLQEEGYVRRSASDDSFR 66 (263)
T ss_pred HHHHHHhc-CCCCCHHHHHHHHCc-CHHHHHHHHHHHHHCCCEEEecCCCcEE
Confidence 44555544 334999999999999 9999999999999999999863 34454
No 43
>PF01920 Prefoldin_2: Prefoldin subunit; InterPro: IPR002777 Prefoldin (PFD) is a chaperone that interacts exclusively with type II chaperonins, hetero-oligomers lacking an obligate co-chaperonin that are found only in eukaryotes (chaperonin-containing T-complex polypeptide-1 (CCT)) and archaea. Eukaryotic PFD is a multi-subunit complex containing six polypeptides in the molecular mass range of 14-23 kDa. In archaea, on the other hand, PFD is composed of two types of subunits, two alpha and four beta. The six subunits associate to form two back-to-back up-and-down eight-stranded barrels, from which hang six coiled coils. Each subunit contributes one (beta subunits) or two (alpha subunits) beta hairpin turns to the barrels. The coiled coils are formed by the N and C termini of an individual subunit. Overall, this unique arrangement resembles a jellyfish. The eukaryotic PFD hexamer is composed of six different subunits; however, these can be grouped into two alpha-like (PFD3 and -5) and four beta-like (PFD1, -2, -4, and -6) subunits based on amino acid sequence similarity with their archaeal counterparts. Eukaryotic PFD has a six-legged structure similar to that seen in the archaeal homologue [, ]. This family contains the archaeal beta subunit, eukaryotic prefoldin subunits 1, 2, 4 and 6. Eukaryotic PFD has been shown to bind both actin and tubulin co-translationally. The chaperone then delivers the target protein to CCT, interacting with the chaperonin through the tips of the coiled coils. No authentic target proteins of any archaeal PFD have been identified, to date.; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0016272 prefoldin complex; PDB: 2ZDI_B 3AEI_B 2ZQM_A 1FXK_A.
Probab=69.79 E-value=34 Score=25.80 Aligned_cols=73 Identities=12% Similarity=0.312 Sum_probs=37.9
Q ss_pred hhhhhHHHhhhhccceeccccCceEEeccCCC---Cchhh--hHHHHHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy7686 48 RRIYDITNVLEGIGLIEKNNKNIIRWKALKNK---NEEEY--DLEQSKLIELRDEISDMRNHEAVIDEHIRKCQQSLRNI 122 (243)
Q Consensus 48 RRiYDItNVLEgiglI~K~sKn~i~W~G~~~~---~~~~~--~~~~~~~~~Lk~El~~L~~~E~~LD~~I~~~~~~l~~l 122 (243)
+.+-.+.-|++-+..+. .+.-.|.+.+.. .+... ..+..+...++.++..|......+...+..++..|+.+
T Consensus 26 ~~~~~~~~~~~eL~~l~---~~~~~y~~vG~~fv~~~~~~~~~~L~~~~~~~~~~i~~l~~~~~~l~~~l~~~~~~l~~~ 102 (106)
T PF01920_consen 26 RQLRELELTLEELEKLD---DDRKVYKSVGKMFVKQDKEEAIEELEERIEKLEKEIKKLEKQLKYLEKKLKELKKKLYEL 102 (106)
T ss_dssp HHHHHHHHHHHHHHTSS---TT-EEEEEETTEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred HHHHHHHHHHHHHHhCC---CcchhHHHHhHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33344444555444443 334555554444 22211 23445566666667777666666666666666666554
Q ss_pred h
Q psy7686 123 Q 123 (243)
Q Consensus 123 ~ 123 (243)
+
T Consensus 103 ~ 103 (106)
T PF01920_consen 103 F 103 (106)
T ss_dssp C
T ss_pred h
Confidence 3
No 44
>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=68.53 E-value=15 Score=26.13 Aligned_cols=42 Identities=26% Similarity=0.310 Sum_probs=36.5
Q ss_pred HHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceeccc
Q psy7686 24 LLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNN 67 (243)
Q Consensus 24 ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~s 67 (243)
.+.+ .++.+...++|+.|+| .+=-+.+.++-|+.-|||+...
T Consensus 15 ~l~~-~~~~v~~~~iA~~L~v-s~~tvt~ml~~L~~~GlV~~~~ 56 (60)
T PF01325_consen 15 ELSE-EGGPVRTKDIAERLGV-SPPTVTEMLKRLAEKGLVEYEP 56 (60)
T ss_dssp HHHH-CTSSBBHHHHHHHHTS--HHHHHHHHHHHHHTTSEEEET
T ss_pred HHHc-CCCCccHHHHHHHHCC-ChHHHHHHHHHHHHCCCEEecC
Confidence 3344 7889999999999999 9999999999999999999864
No 45
>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=68.30 E-value=8 Score=28.13 Aligned_cols=47 Identities=19% Similarity=0.212 Sum_probs=35.5
Q ss_pred HHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceeccc
Q psy7686 21 FVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNN 67 (243)
Q Consensus 21 Fi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~s 67 (243)
||.-+....+-.-.+.++|+.||++...-++.-+..||.-|+|++..
T Consensus 14 ~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~kG~I~r~~ 60 (65)
T PF01726_consen 14 FIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKALERKGYIRRDP 60 (65)
T ss_dssp HHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHHHHTTSEEEGC
T ss_pred HHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCcCccCCC
Confidence 44333344456679999999999955999999999999999999874
No 46
>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=68.12 E-value=16 Score=24.61 Aligned_cols=38 Identities=29% Similarity=0.403 Sum_probs=32.8
Q ss_pred CCCee-eHHHHHhhhcccchhhhhhHHHhhhhccceeccc
Q psy7686 29 PEGVL-HLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNN 67 (243)
Q Consensus 29 ~~g~i-dL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~s 67 (243)
+++.+ ...++|+.+++ .+=.+...++-|+.-|+|++..
T Consensus 21 ~~~~~~~~~~la~~~~i-s~~~v~~~l~~L~~~G~i~~~~ 59 (66)
T cd07377 21 PGDRLPSERELAEELGV-SRTTVREALRELEAEGLVERRP 59 (66)
T ss_pred CCCCCCCHHHHHHHHCC-CHHHHHHHHHHHHHCCCEEecC
Confidence 34444 59999999999 9999999999999999998764
No 47
>PHA02943 hypothetical protein; Provisional
Probab=68.08 E-value=23 Score=30.72 Aligned_cols=47 Identities=21% Similarity=0.186 Sum_probs=41.1
Q ss_pred HHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceeccccCc
Q psy7686 20 KFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNNKNI 70 (243)
Q Consensus 20 kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~sKn~ 70 (243)
.+++++ ..|.....++|+.||+ .--....++=|||.-|.|++.....
T Consensus 15 eILE~L---k~G~~TtseIAkaLGl-S~~qa~~~LyvLErEG~VkrV~~G~ 61 (165)
T PHA02943 15 KTLRLL---ADGCKTTSRIANKLGV-SHSMARNALYQLAKEGMVLKVEIGR 61 (165)
T ss_pred HHHHHH---hcCCccHHHHHHHHCC-CHHHHHHHHHHHHHcCceEEEeecc
Confidence 477888 4788899999999999 9999999999999999999976553
No 48
>KOG3026|consensus
Probab=67.83 E-value=24 Score=32.53 Aligned_cols=80 Identities=13% Similarity=0.184 Sum_probs=57.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhhhhccCccccchhhhhh-----------cCCCCeEEEEECCCCCeEEecCCCCC
Q psy7686 99 SDMRNHEAVIDEHIRKCQQSLRNIQEEEVNRKQCYIPTDVILG-----------MFPDSSLMCLKAPYGTKLHVPSISTD 167 (243)
Q Consensus 99 ~~L~~~E~~LD~~I~~~~~~l~~l~ed~~n~~~aYVT~~Di~~-----------~f~~qtviaIkAP~~T~leVp~p~~~ 167 (243)
++|...|+.|+++|.--..-|..-.++..+..+++|+.+=++. .|....|-|++=|.|+++.++-++.
T Consensus 26 eEllkLe~DLkEvIsLTedLlqT~~ee~~sss~a~~ssq~~h~s~~~~~~~~~~l~~~~~i~a~~w~vg~K~~A~~~dd- 104 (262)
T KOG3026|consen 26 EELLKLEKDLKEVISLTEDLLQTQKEEDKSSSDAFVSSQPTHSSFTPRWVSGDYLFYPSRITAVGWKVGDKVQAVFSDD- 104 (262)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhhhcccccccccCccccCCCchhhhhhhhccccccchhcccccCCEEEEeecCC-
Confidence 4677788899999974444333333333355688888876665 3677888889999999999999976
Q ss_pred CceEEEEEecCC
Q psy7686 168 ENKIKLHVKSSH 179 (243)
Q Consensus 168 ~~~yqi~LkS~~ 179 (243)
..-|...|.+.+
T Consensus 105 g~~y~AtIe~it 116 (262)
T KOG3026|consen 105 GQIYDATIEHIT 116 (262)
T ss_pred CceEEeehhhcc
Confidence 357778777766
No 49
>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=67.54 E-value=12 Score=28.69 Aligned_cols=50 Identities=24% Similarity=0.405 Sum_probs=40.5
Q ss_pred cHHHHHHHHHHHHhh---CCCCeeeHHHHHhhhcccchhhhhhHHHhhhhcccee
Q psy7686 13 SLGLLTTKFVSLLQQ---APEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIE 64 (243)
Q Consensus 13 SL~~Lt~kFi~ll~~---~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~ 64 (243)
++..+.++.+.+|++ .+.| +.+++++++|++ ....|..++.-|..-|+|=
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~~G-v~v~~I~~~l~~-~~~~v~~al~~L~~eG~IY 96 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQPNSEEG-VHVDEIAQQLGM-SENEVRKALDFLSNEGHIY 96 (102)
T ss_dssp -S-HHHHHHHHHHHC----TTT-EEHHHHHHHSTS--HHHHHHHHHHHHHTTSEE
T ss_pred CCCHHHHHHHHHHHhcCCCCCc-ccHHHHHHHhCc-CHHHHHHHHHHHHhCCeEe
Confidence 688899999999987 2333 899999999999 9999999999999998873
No 50
>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=67.42 E-value=10 Score=27.03 Aligned_cols=49 Identities=14% Similarity=0.193 Sum_probs=36.3
Q ss_pred HHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccc-eeccccCceE
Q psy7686 20 KFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGL-IEKNNKNIIR 72 (243)
Q Consensus 20 kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgigl-I~K~sKn~i~ 72 (243)
+.+.++.+ +....+++|+.++| .++-++--++.|++-|+ |...++..+-
T Consensus 4 ~il~~L~~---~~~~~~eLa~~l~v-S~~tv~~~l~~L~~~g~~i~~~~~g~~l 53 (69)
T TIGR00122 4 RLLALLAD---NPFSGEKLGEALGM-SRTAVNKHIQTLREWGVDVLTVGKGYRL 53 (69)
T ss_pred HHHHHHHc---CCcCHHHHHHHHCC-CHHHHHHHHHHHHHCCCeEEecCCceEe
Confidence 45566654 34669999999999 99999999999988888 3333443333
No 51
>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=66.85 E-value=30 Score=26.03 Aligned_cols=27 Identities=22% Similarity=0.262 Sum_probs=21.0
Q ss_pred eeHHHHHhhhcccchhhhhhHHHhhhhcccee
Q psy7686 33 LHLKYAAENLEVKQKRRIYDITNVLEGIGLIE 64 (243)
Q Consensus 33 idL~~aa~~L~v~~KRRiYDItNVLEgiglI~ 64 (243)
+.+.++|+.+|| ..+-|.-. +..|+|.
T Consensus 2 ~~i~e~A~~~gv-s~~tLr~y----e~~Gli~ 28 (91)
T cd04766 2 YVISVAAELSGM-HPQTLRLY----ERLGLLS 28 (91)
T ss_pred cCHHHHHHHHCc-CHHHHHHH----HHCCCcC
Confidence 467899999999 87766655 5568886
No 52
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=66.81 E-value=25 Score=30.30 Aligned_cols=57 Identities=19% Similarity=0.160 Sum_probs=43.9
Q ss_pred CcHHH-HHHHHHHHHhh---CCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceeccccC
Q psy7686 12 KSLGL-LTTKFVSLLQQ---APEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNNKN 69 (243)
Q Consensus 12 ~SL~~-Lt~kFi~ll~~---~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~sKn 69 (243)
.|+.. +...+.+.+.. .|+..+.-.++|+.||| .|=-+=+.+..|+..|||+.....
T Consensus 10 ~~~~e~v~~~l~~~I~~g~l~pG~~L~e~~La~~lgV-SRtpVREAL~~L~~eGLV~~~~~~ 70 (221)
T PRK11414 10 ISLTLQVENDLKHQLSIGALKPGARLITKNLAEQLGM-SITPVREALLRLVSVNALSVAPAQ 70 (221)
T ss_pred CCHHHHHHHHHHHHHHhCCCCCCCccCHHHHHHHHCC-CchhHHHHHHHHHHCCCEEecCCC
Confidence 34443 33444444433 47888999999999999 999999999999999999976544
No 53
>cd00632 Prefoldin_beta Prefoldin beta; Prefoldin is a hexameric molecular chaperone complex, composed of two evolutionarily related subunits (alpha and beta), which are found in both eukaryotes and archaea. Prefoldin binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The hexameric structure consists of a double beta barrel assembly with six protruding coiled-coils. The alpha prefoldin subunits have two beta hairpin structures while the beta prefoldin subunits (this CD) have only one hairpin that is most similar to the second hairpin of the alpha subunit. The prefoldin hexamer consists of two alpha and four beta subunits and is assembled from the beta hairpins of all six subunits. The alpha subunits initially dimerize providing a structural nucleus for the assembly of the beta subunits. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the st
Probab=66.70 E-value=25 Score=27.41 Aligned_cols=79 Identities=14% Similarity=0.203 Sum_probs=49.0
Q ss_pred HhhhcccchhhhhhHHHhhhhccceeccccCceEEeccCCC-Cchh--hhHHHHHhHhHHHHHHHHHHHHHHHHHHHHHH
Q psy7686 39 AENLEVKQKRRIYDITNVLEGIGLIEKNNKNIIRWKALKNK-NEEE--YDLEQSKLIELRDEISDMRNHEAVIDEHIRKC 115 (243)
Q Consensus 39 a~~L~v~~KRRiYDItNVLEgiglI~K~sKn~i~W~G~~~~-~~~~--~~~~~~~~~~Lk~El~~L~~~E~~LD~~I~~~ 115 (243)
-..|.. +++...++.+-|+.+. ...+.|+=.|.--+ -+.. ...+..++..+..++..|......+...+..+
T Consensus 22 ~~~l~~-~~~E~~~v~~EL~~l~----~d~~vy~~VG~vfv~~~~~ea~~~Le~~~e~le~~i~~l~~~~~~l~~~~~el 96 (105)
T cd00632 22 RQKVEA-QLNENKKALEELEKLA----DDAEVYKLVGNVLVKQEKEEARTELKERLETIELRIKRLERQEEDLQEKLKEL 96 (105)
T ss_pred HHHHHH-HHHHHHHHHHHHHcCC----CcchHHHHhhhHHhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344555 7777788888887775 23344444565443 1111 12345566677777777777777777777777
Q ss_pred HHHHHhh
Q psy7686 116 QQSLRNI 122 (243)
Q Consensus 116 ~~~l~~l 122 (243)
+..|+.+
T Consensus 97 k~~l~~~ 103 (105)
T cd00632 97 QEKIQQA 103 (105)
T ss_pred HHHHHHH
Confidence 7777765
No 54
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=66.50 E-value=12 Score=33.65 Aligned_cols=53 Identities=26% Similarity=0.442 Sum_probs=44.1
Q ss_pred HHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceeccccC-ceEEec
Q psy7686 20 KFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNNKN-IIRWKA 75 (243)
Q Consensus 20 kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~sKn-~i~W~G 75 (243)
..+++|...|.+ +.+.++|+.+|+ .|=-.|=+.+.|+..|++++...+ .|+ .|
T Consensus 8 ~iL~~l~~~~~~-l~l~ela~~~gl-pksT~~RlL~tL~~~G~v~~d~~~g~Y~-Lg 61 (246)
T COG1414 8 AILDLLAEGPGG-LSLAELAERLGL-PKSTVHRLLQTLVELGYVEQDPEDGRYR-LG 61 (246)
T ss_pred HHHHHHHhCCCC-CCHHHHHHHhCc-CHHHHHHHHHHHHHCCCEEEcCCCCcEe-eh
Confidence 466777775554 899999999999 999999999999999999999765 444 45
No 55
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=66.29 E-value=53 Score=26.13 Aligned_cols=30 Identities=10% Similarity=0.092 Sum_probs=25.6
Q ss_pred eeeHHHHHhhhcccchhhhhhHHHhhhhccc
Q psy7686 32 VLHLKYAAENLEVKQKRRIYDITNVLEGIGL 62 (243)
Q Consensus 32 ~idL~~aa~~L~v~~KRRiYDItNVLEgigl 62 (243)
-.++.++|..+|| ..--||-+.+-+..-|.
T Consensus 29 g~sv~evA~e~gI-s~~tl~~W~r~y~~~~~ 58 (121)
T PRK09413 29 GMTVSLVARQHGV-AASQLFLWRKQYQEGSL 58 (121)
T ss_pred CCCHHHHHHHHCc-CHHHHHHHHHHHhhccc
Confidence 3589999999999 99999999998875444
No 56
>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=65.66 E-value=15 Score=28.28 Aligned_cols=38 Identities=13% Similarity=0.128 Sum_probs=34.1
Q ss_pred CCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceeccc
Q psy7686 29 PEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNN 67 (243)
Q Consensus 29 ~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~s 67 (243)
....+.-.++|+.+|+ .|.-+.-+++.||.-|+|++..
T Consensus 44 ~~~~is~~eLa~~~g~-sr~tVsr~L~~Le~~GlI~r~~ 81 (95)
T TIGR01610 44 KQDRVTATVIAELTGL-SRTHVSDAIKSLARRRIIFRQG 81 (95)
T ss_pred cCCccCHHHHHHHHCc-CHHHHHHHHHHHHHCCCeeeec
Confidence 3456888999999999 9999999999999999999764
No 57
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=65.42 E-value=6.5 Score=37.61 Aligned_cols=29 Identities=34% Similarity=0.620 Sum_probs=26.6
Q ss_pred HHHHHhhhcccchhhhhhHHHhhhhcccee
Q psy7686 35 LKYAAENLEVKQKRRIYDITNVLEGIGLIE 64 (243)
Q Consensus 35 L~~aa~~L~v~~KRRiYDItNVLEgiglI~ 64 (243)
+..+++.++. +.||+|||+|-|+++|+|.
T Consensus 304 y~~~~~~~~~-~~~~~~~ii~~L~~lgiv~ 332 (366)
T COG1474 304 YESLCERLRT-SQRRFSDIISELEGLGIVS 332 (366)
T ss_pred HHHHHhhhCc-hHHHHHHHHHHHHhcCeEE
Confidence 4677888888 9999999999999999998
No 58
>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=64.98 E-value=13 Score=28.85 Aligned_cols=45 Identities=22% Similarity=0.339 Sum_probs=39.3
Q ss_pred HHHHh--hCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceeccc
Q psy7686 22 VSLLQ--QAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNN 67 (243)
Q Consensus 22 i~ll~--~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~s 67 (243)
+..+. .++++.+.+.++|+.+++ .+-.+-=+++-||.-|+|.|..
T Consensus 31 L~~l~~~~~~~~~~t~~eL~~~l~~-~~stvs~~i~~Le~kg~I~r~~ 77 (109)
T TIGR01889 31 LYYLGKLENNEGKLTLKEIIKEILI-KQSALVKIIKKLSKKGYLSKER 77 (109)
T ss_pred HHHHHhhhccCCcCcHHHHHHHHCC-CHHHHHHHHHHHHHCCCEeccC
Confidence 44444 567789999999999999 9999999999999999999973
No 59
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=64.79 E-value=44 Score=29.85 Aligned_cols=53 Identities=28% Similarity=0.229 Sum_probs=43.3
Q ss_pred HHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceeccccCceEEec
Q psy7686 20 KFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNNKNIIRWKA 75 (243)
Q Consensus 20 kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~sKn~i~W~G 75 (243)
+.++++++ .+.+...++|+.|+| ..+.|.--++.|+.-|++.+.....+.+.+
T Consensus 8 ~Il~~l~~--~~~~~~~eLa~~l~V-S~~TiRRdL~~L~~~~~l~r~~Gga~~~~~ 60 (240)
T PRK10411 8 AIVDLLLN--HTSLTTEALAEQLNV-SKETIRRDLNELQTQGKILRNHGRAKYIHR 60 (240)
T ss_pred HHHHHHHH--cCCCcHHHHHHHHCc-CHHHHHHHHHHHHHCCCEEEecCeEEEecC
Confidence 45667764 568999999999999 999999999999999999887555555554
No 60
>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=64.47 E-value=15 Score=32.55 Aligned_cols=48 Identities=17% Similarity=0.261 Sum_probs=36.5
Q ss_pred HHHHHHhhCCCC-eeeHHHHHhhhcccchhhhhhHHHhhhhccceeccccCce
Q psy7686 20 KFVSLLQQAPEG-VLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNNKNII 71 (243)
Q Consensus 20 kFi~ll~~~~~g-~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~sKn~i 71 (243)
..++.|....+. .++++++++..++ +--||+..|+.+|++.....+++
T Consensus 137 ~i~~~L~~~~~~~~isi~~is~~Tgi----~~~DIi~tL~~l~~l~~~~~~~~ 185 (188)
T PF01853_consen 137 VILEYLLEFKGKKSISIKDISQETGI----RPEDIISTLQQLGMLKYYKGQHI 185 (188)
T ss_dssp HHHHHHHHTSSE--EEHHHHHHHH-B----THHHHHHHHHHTT-EEEETTEEE
T ss_pred HHHHHHHhcCCCCeEEHHHHHHHHCC----CHHHHHHHHHHCCCEEEECCcEE
Confidence 366677666554 8999999999999 66899999999999998765554
No 61
>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=63.20 E-value=87 Score=26.96 Aligned_cols=45 Identities=27% Similarity=0.277 Sum_probs=37.8
Q ss_pred HHHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceecc
Q psy7686 19 TKFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKN 66 (243)
Q Consensus 19 ~kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~ 66 (243)
.+.+.++... +.++..++|+.|++ .+=-+.-.++.|+.-|+|++.
T Consensus 4 ~~IL~~L~~~--~~~t~~eLA~~lgi-s~~tV~~~L~~Le~~GlV~r~ 48 (203)
T TIGR02702 4 EDILSYLLKQ--GQATAAALAEALAI-SPQAVRRHLKDLETEGLIEYE 48 (203)
T ss_pred HHHHHHHHHc--CCCCHHHHHHHHCc-CHHHHHHHHHHHHHCCCeEEe
Confidence 3466667653 44999999999999 998999999999999999876
No 62
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=62.97 E-value=17 Score=26.44 Aligned_cols=45 Identities=24% Similarity=0.316 Sum_probs=37.7
Q ss_pred HHHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceecc
Q psy7686 19 TKFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKN 66 (243)
Q Consensus 19 ~kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~ 66 (243)
.+.+.++... +.+...++|+.+++ .+.-|+-+++-|+.-|+|++.
T Consensus 13 ~~il~~l~~~--~~~~~~~la~~~~~-s~~~i~~~l~~L~~~g~v~~~ 57 (101)
T smart00347 13 FLVLRILYEE--GPLSVSELAKRLGV-SPSTVTRVLDRLEKKGLIRRL 57 (101)
T ss_pred HHHHHHHHHc--CCcCHHHHHHHHCC-CchhHHHHHHHHHHCCCeEec
Confidence 3445555553 35899999999999 999999999999999999976
No 63
>TIGR02231 conserved hypothetical protein. This family consists of proteins over 500 amino acids long in Caenorhabditis elegans and several bacteria (Pseudomonas aeruginosa, Nostoc sp. PCC 7120, Leptospira interrogans, etc.). The function is unknown.
Probab=62.43 E-value=62 Score=32.01 Aligned_cols=86 Identities=13% Similarity=0.198 Sum_probs=56.1
Q ss_pred HHHHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhccCccccchhhhhhcCCCCeEEEEECCCCC--eEEecCC
Q psy7686 87 EQSKLIELRDEISDMRNHEAVIDEHIRKCQQSLRNIQEEEVNRKQCYIPTDVILGMFPDSSLMCLKAPYGT--KLHVPSI 164 (243)
Q Consensus 87 ~~~~~~~Lk~El~~L~~~E~~LD~~I~~~~~~l~~l~ed~~n~~~aYVT~~Di~~~f~~qtviaIkAP~~T--~leVp~p 164 (243)
...++.++..++.+|+.+.+++++.|..++++|..+...... -.....+.|.+|.+. .|++.--
T Consensus 136 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~l~~l~~~~~~--------------~~~~v~v~l~~~~~g~~~l~lsY~ 201 (525)
T TIGR02231 136 NGSEIERLLTEDREAERRIRELEKQLSELQNELNALLTGKSQ--------------RSHTVLVRLEAPEDAEAELNLTYQ 201 (525)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCcc--------------ceEEEEEEEeccCCceEEEEEEEE
Confidence 445667777888888888888888888888888877663111 011334566666554 3444322
Q ss_pred --CCC-CceEEEEEecCCCCCCeEEEE
Q psy7686 165 --STD-ENKIKLHVKSSHPEEPVNILL 188 (243)
Q Consensus 165 --~~~-~~~yqi~LkS~~~~GpI~V~L 188 (243)
..+ .-.|.++|.+.. +++++-.
T Consensus 202 v~~a~W~P~Ydlrl~~~~--~~~~l~~ 226 (525)
T TIGR02231 202 VGNASWTPSYDARLDTGA--PTVELTY 226 (525)
T ss_pred eCCCcEeeeeEEEecCCC--ceEEEEE
Confidence 222 578999999888 8777654
No 64
>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=61.46 E-value=16 Score=32.26 Aligned_cols=44 Identities=14% Similarity=0.166 Sum_probs=37.6
Q ss_pred HHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceecc
Q psy7686 21 FVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKN 66 (243)
Q Consensus 21 Fi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~ 66 (243)
.+++|..+ .+.+.+.++|+.+|+ .|=.+|-+.+-|+..|++++.
T Consensus 14 IL~~l~~~-~~~~~l~eia~~lgl-pksT~~RlL~tL~~~G~l~~~ 57 (248)
T TIGR02431 14 VIEAFGAE-RPRLTLTDVAEATGL-TRAAARRFLLTLVELGYVTSD 57 (248)
T ss_pred HHHHHhcC-CCCCCHHHHHHHHCc-CHHHHHHHHHHHHHCCCEEeC
Confidence 45555543 456899999999999 999999999999999999985
No 65
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=61.37 E-value=12 Score=34.82 Aligned_cols=52 Identities=29% Similarity=0.401 Sum_probs=41.5
Q ss_pred CcHHHHHH-HHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceecc
Q psy7686 12 KSLGLLTT-KFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKN 66 (243)
Q Consensus 12 ~SL~~Lt~-kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~ 66 (243)
++|+..++ +.+++|.. .+.+++|++|+.||. ..--+--=+-|||-.|||+-.
T Consensus 18 kalaS~vRv~Il~lL~~--k~plNvneiAe~lgL-pqst~s~~ik~Le~aGlirT~ 70 (308)
T COG4189 18 KALASKVRVAILQLLHR--KGPLNVNEIAEALGL-PQSTMSANIKVLEKAGLIRTE 70 (308)
T ss_pred HHHHHHHHHHHHHHHHH--hCCCCHHHHHHHhCC-chhhhhhhHHHHHhcCceeee
Confidence 45666664 45677754 677999999999999 888888888999999999854
No 66
>cd00584 Prefoldin_alpha Prefoldin alpha subunit; Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.
Probab=60.42 E-value=49 Score=26.30 Aligned_cols=54 Identities=7% Similarity=0.116 Sum_probs=28.2
Q ss_pred cCceEEeccCCCCchhhhHHHHHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q psy7686 68 KNIIRWKALKNKNEEEYDLEQSKLIELRDEISDMRNHEAVIDEHIRKCQQSLRNIQE 124 (243)
Q Consensus 68 Kn~i~W~G~~~~~~~~~~~~~~~~~~Lk~El~~L~~~E~~LD~~I~~~~~~l~~l~e 124 (243)
+.-+.|.|.+-.-.. .......-++..++.|++.-+.|.+.+..+++++..+..
T Consensus 69 ~~v~v~iG~g~~vE~---~~~eA~~~l~~r~~~l~~~~~~l~~~l~~l~~~~~~~~~ 122 (129)
T cd00584 69 DKVLVDLGTGYYVEK---DLEEAIEFLDKKIEELTKQIEKLQKELAKLKDQINTLEA 122 (129)
T ss_pred CEEEEEcCCCEEEEe---cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345788887766221 122223344555555555555555555555555555443
No 67
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=60.24 E-value=78 Score=28.78 Aligned_cols=50 Identities=16% Similarity=0.216 Sum_probs=37.1
Q ss_pred HHHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceeccccCce
Q psy7686 19 TKFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNNKNII 71 (243)
Q Consensus 19 ~kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~sKn~i 71 (243)
.+.++++++ .+.+.+.++|+.|+| ..+-|.==++.||.-|++.|.....+
T Consensus 20 ~~Il~~L~~--~~~vtv~eLa~~l~V-S~~TIRRDL~~Le~~G~l~r~~GGa~ 69 (269)
T PRK09802 20 EQIIQRLRQ--QGSVQVNDLSALYGV-STVTIRNDLAFLEKQGIAVRAYGGAL 69 (269)
T ss_pred HHHHHHHHH--cCCEeHHHHHHHHCC-CHHHHHHHHHHHHhCCCeEEEeCCEE
Confidence 346677776 455999999999999 76555444556899999998865543
No 68
>PF04977 DivIC: Septum formation initiator; InterPro: IPR007060 DivIC, from the spore-forming, Gram-positive bacterium Bacillus subtilis, is necessary for both vegetative and sporulation septum formation []. These proteins are mainly composed of an N-terminal coiled-coil. DivIB, DivIC and FtsL inter-depend on each other for stabilisation and localisation. The latter two form a heterodimer. DivIC is always centre cell but the other two associate with it during septation [].; GO: 0007049 cell cycle
Probab=59.42 E-value=28 Score=24.95 Aligned_cols=36 Identities=8% Similarity=0.355 Sum_probs=25.8
Q ss_pred HhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q psy7686 90 KLIELRDEISDMRNHEAVIDEHIRKCQQSLRNIQEE 125 (243)
Q Consensus 90 ~~~~Lk~El~~L~~~E~~LD~~I~~~~~~l~~l~ed 125 (243)
+...++.++..|+.+-+.+.+-+..+++++..+..|
T Consensus 18 ~~~~~~~ei~~l~~~i~~l~~e~~~L~~ei~~l~~~ 53 (80)
T PF04977_consen 18 RYYQLNQEIAELQKEIEELKKENEELKEEIERLKND 53 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 345667777777777777777777788888888443
No 69
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=59.05 E-value=30 Score=30.40 Aligned_cols=36 Identities=25% Similarity=0.200 Sum_probs=34.4
Q ss_pred CCeeeHHHHHhhhcccchhhhhhHHHhhhhccceecc
Q psy7686 30 EGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKN 66 (243)
Q Consensus 30 ~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~ 66 (243)
.+++.|.++++.||+ .|=++-=.+-.|++.||++|+
T Consensus 39 ~~Pmtl~Ei~E~lg~-Sks~vS~~lkkL~~~~lV~~~ 74 (177)
T COG1510 39 RKPLTLDEIAEALGM-SKSNVSMGLKKLQDWNLVKKV 74 (177)
T ss_pred CCCccHHHHHHHHCC-CcchHHHHHHHHHhcchHHhh
Confidence 678999999999999 999999999999999999987
No 70
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=58.66 E-value=24 Score=26.21 Aligned_cols=32 Identities=28% Similarity=0.301 Sum_probs=29.9
Q ss_pred HHHHHhhhcccchhhhhhHHHhhhhccceeccc
Q psy7686 35 LKYAAENLEVKQKRRIYDITNVLEGIGLIEKNN 67 (243)
Q Consensus 35 L~~aa~~L~v~~KRRiYDItNVLEgiglI~K~s 67 (243)
+.++|+.|++ .+=-++-++.-|+.-|+|.+..
T Consensus 2 ~~ela~~l~i-s~stvs~~l~~L~~~glI~r~~ 33 (96)
T smart00529 2 TSEIAERLNV-SPPTVTQMLKKLEKDGLVEYEP 33 (96)
T ss_pred HHHHHHHhCC-ChHHHHHHHHHHHHCCCEEEcC
Confidence 4689999999 9999999999999999999985
No 71
>TIGR02716 C20_methyl_CrtF C-20 methyltransferase BchU. Members of this protein family are the S-adenosylmethionine-depenedent C-20 methyltransferase BchU, part of the pathway of bacteriochlorophyll c production in photosynthetic green sulfur bacteria. The position modified by this enzyme represents the difference between bacteriochlorophylls c and d; strains lacking this protein can only produced bacteriochlorophyll d.
Probab=58.45 E-value=8.8 Score=34.85 Aligned_cols=37 Identities=19% Similarity=0.205 Sum_probs=34.1
Q ss_pred CCeeeHHHHHhhhcccchhhhhhHHHhhhhccceeccc
Q psy7686 30 EGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNN 67 (243)
Q Consensus 30 ~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~s 67 (243)
.|..++.++|+++++ ..|+++-+.+.|.++|++++..
T Consensus 21 ~gp~t~~eLA~~~~~-~~~~~~~lL~~L~~lgll~~~~ 57 (306)
T TIGR02716 21 EGPKDLATLAADTGS-VPPRLEMLLETLRQMRVINLED 57 (306)
T ss_pred cCCCCHHHHHHHcCC-ChHHHHHHHHHHHhCCCeEecC
Confidence 367899999999999 9999999999999999999863
No 72
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=57.80 E-value=49 Score=26.11 Aligned_cols=39 Identities=23% Similarity=0.211 Sum_probs=26.9
Q ss_pred eHHHHHhhhcccchhhhhhHHHhhhhcccee--ccccCceEEeccC
Q psy7686 34 HLKYAAENLEVKQKRRIYDITNVLEGIGLIE--KNNKNIIRWKALK 77 (243)
Q Consensus 34 dL~~aa~~L~v~~KRRiYDItNVLEgiglI~--K~sKn~i~W~G~~ 77 (243)
.+.++|+.+|| ..+-|- -.|..|||. +...|.|+|-...
T Consensus 2 ~I~eva~~~gv-s~~tLR----yYe~~GLl~p~~r~~~gyR~Y~~~ 42 (123)
T cd04770 2 KIGELAKAAGV-SPDTIR----YYERIGLLPPPQRSENGYRLYGEA 42 (123)
T ss_pred CHHHHHHHHCc-CHHHHH----HHHHCCCCCCCCCCCCCCccCCHH
Confidence 57889999999 766442 356788886 3456677775543
No 73
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147. This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.
Probab=57.67 E-value=1.1e+02 Score=28.32 Aligned_cols=41 Identities=20% Similarity=0.208 Sum_probs=35.0
Q ss_pred CCCCeeeHHHHHhhhc--ccchhhhhhHHHhhhhccceeccccC
Q psy7686 28 APEGVLHLKYAAENLE--VKQKRRIYDITNVLEGIGLIEKNNKN 69 (243)
Q Consensus 28 ~~~g~idL~~aa~~L~--v~~KRRiYDItNVLEgiglI~K~sKn 69 (243)
-.++.-|..++|++++ | .--.+=+.++.|+-+|||+|...+
T Consensus 133 ~~~~~~~~~~ia~~l~p~i-s~~ev~~sL~~L~~~glikk~~~g 175 (271)
T TIGR02147 133 VMPFADDPEELAKRCFPKI-SAEQVKESLDLLERLGLIKKNEDG 175 (271)
T ss_pred cCCCCCCHHHHHHHhCCCC-CHHHHHHHHHHHHHCCCeeECCCC
Confidence 3567778999999999 6 778889999999999999998654
No 74
>PRK03947 prefoldin subunit alpha; Reviewed
Probab=57.37 E-value=73 Score=25.81 Aligned_cols=12 Identities=8% Similarity=-0.056 Sum_probs=7.8
Q ss_pred cCceEEeccCCC
Q psy7686 68 KNIIRWKALKNK 79 (243)
Q Consensus 68 Kn~i~W~G~~~~ 79 (243)
...+.|.|.+-.
T Consensus 76 ~kV~v~lG~g~~ 87 (140)
T PRK03947 76 DKVIVSLGAGYS 87 (140)
T ss_pred CeEEEEcCCCEE
Confidence 344678887665
No 75
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=57.20 E-value=23 Score=28.69 Aligned_cols=37 Identities=19% Similarity=0.245 Sum_probs=33.6
Q ss_pred CCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceec
Q psy7686 28 APEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEK 65 (243)
Q Consensus 28 ~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K 65 (243)
..++.+...++|+.+++ ..+-+..|...|.--|+|.-
T Consensus 21 ~~~~~~s~~~ia~~~~i-p~~~l~kil~~L~~~glv~s 57 (135)
T TIGR02010 21 AETGPVTLADISERQGI-SLSYLEQLFAKLRKAGLVKS 57 (135)
T ss_pred CCCCcCcHHHHHHHHCc-CHHHHHHHHHHHHHCCceEE
Confidence 34458999999999999 99999999999999999974
No 76
>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=57.11 E-value=9.4 Score=24.35 Aligned_cols=22 Identities=36% Similarity=0.523 Sum_probs=20.0
Q ss_pred eeHHHHHhhhcccchhhhhhHHH
Q psy7686 33 LHLKYAAENLEVKQKRRIYDITN 55 (243)
Q Consensus 33 idL~~aa~~L~v~~KRRiYDItN 55 (243)
+++.++|+.||| .++.||-.++
T Consensus 2 lt~~e~a~~lgi-s~~ti~~~~~ 23 (49)
T TIGR01764 2 LTVEEAAEYLGV-SKDTVYRLIH 23 (49)
T ss_pred CCHHHHHHHHCC-CHHHHHHHHH
Confidence 578999999999 9999999875
No 77
>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=56.84 E-value=10 Score=29.63 Aligned_cols=37 Identities=19% Similarity=0.280 Sum_probs=33.9
Q ss_pred CCeeeHHHHHhhhcccchhhhhhHHHhhhhccceeccc
Q psy7686 30 EGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNN 67 (243)
Q Consensus 30 ~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~s 67 (243)
.+.+...++|+.+++ .+--+.=+++-||.-|+|++..
T Consensus 40 ~~~~t~~ela~~~~~-~~~tvs~~l~~Le~~GlI~r~~ 76 (118)
T TIGR02337 40 QGSMEFTQLANQACI-LRPSLTGILARLERDGLVTRLK 76 (118)
T ss_pred cCCcCHHHHHHHhCC-CchhHHHHHHHHHHCCCEEecc
Confidence 456899999999999 9999999999999999999973
No 78
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=55.65 E-value=21 Score=28.65 Aligned_cols=50 Identities=20% Similarity=0.262 Sum_probs=43.2
Q ss_pred HHHHHHHHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceecc
Q psy7686 14 LGLLTTKFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKN 66 (243)
Q Consensus 14 L~~Lt~kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~ 66 (243)
|-.+=++-+++|+. ++...+.++|+++|+ ....+...+.-|+.-|+|.+-
T Consensus 6 lD~~D~~IL~~L~~--d~r~~~~eia~~lgl-S~~~v~~Ri~~L~~~GiI~~~ 55 (154)
T COG1522 6 LDDIDRRILRLLQE--DARISNAELAERVGL-SPSTVLRRIKRLEEEGVIKGY 55 (154)
T ss_pred ccHHHHHHHHHHHH--hCCCCHHHHHHHHCC-CHHHHHHHHHHHHHCCceeeE
Confidence 34455778888886 666999999999999 999999999999999999986
No 79
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=55.64 E-value=13 Score=30.11 Aligned_cols=40 Identities=33% Similarity=0.329 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHH
Q psy7686 15 GLLTTKFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITN 55 (243)
Q Consensus 15 ~~Lt~kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItN 55 (243)
++||.|=..++.--=..-++|.++|+.++| .|-.|||=++
T Consensus 16 sLLT~KQ~~Y~~lyy~dDlSl~EIAee~~V-SRqAIyDnIK 55 (105)
T COG2739 16 SLLTKKQKNYLELYYLDDLSLSEIAEEFNV-SRQAIYDNIK 55 (105)
T ss_pred HHHhHHHHHHHHHHHHhhccHHHHHHHhCc-cHHHHHHHHH
Confidence 467766554443322344899999999999 9999999654
No 80
>COG1382 GimC Prefoldin, chaperonin cofactor [Posttranslational modification, protein turnover, chaperones]
Probab=55.01 E-value=42 Score=27.67 Aligned_cols=77 Identities=13% Similarity=0.194 Sum_probs=51.3
Q ss_pred hhhHHHhhhhccceeccccCceEEeccCCC-Cchh--hhHHHHHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhh
Q psy7686 50 IYDITNVLEGIGLIEKNNKNIIRWKALKNK-NEEE--YDLEQSKLIELRDEISDMRNHEAVIDEHIRKCQQSLRNIQEEE 126 (243)
Q Consensus 50 iYDItNVLEgiglI~K~sKn~i~W~G~~~~-~~~~--~~~~~~~~~~Lk~El~~L~~~E~~LD~~I~~~~~~l~~l~ed~ 126 (243)
|-+|.-||+-++.+.--. +-|+-.|.--+ -+.+ .+++..+..-|.-.+..|+.+|+.+.+.++.++..|..+..+.
T Consensus 36 L~E~~~al~Ele~l~eD~-~vYk~VG~llvk~~k~~~~~eL~er~E~Le~ri~tLekQe~~l~e~l~eLq~~i~~~l~~~ 114 (119)
T COG1382 36 LKEIEKALEELEKLDEDA-PVYKKVGNLLVKVSKEEAVDELEERKETLELRIKTLEKQEEKLQERLEELQSEIQKALGDA 114 (119)
T ss_pred HHHHHHHHHHHhcCCccc-HHHHHhhhHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 345667777776665432 33444553333 1111 1356667778888889999999999999999999998887754
Q ss_pred h
Q psy7686 127 V 127 (243)
Q Consensus 127 ~ 127 (243)
.
T Consensus 115 ~ 115 (119)
T COG1382 115 A 115 (119)
T ss_pred c
Confidence 3
No 81
>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=54.53 E-value=22 Score=24.94 Aligned_cols=36 Identities=31% Similarity=0.398 Sum_probs=26.8
Q ss_pred HHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhh
Q psy7686 20 KFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLE 58 (243)
Q Consensus 20 kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLE 58 (243)
+.+++|.. .+.+.+.++|+.|++ ..|-|.--++-|.
T Consensus 9 ~Ll~~L~~--~~~~~~~ela~~l~~-S~rti~~~i~~L~ 44 (59)
T PF08280_consen 9 KLLELLLK--NKWITLKELAKKLNI-SERTIKNDINELN 44 (59)
T ss_dssp HHHHHHHH--HTSBBHHHHHHHCTS--HHHHHHHHHHHH
T ss_pred HHHHHHHc--CCCCcHHHHHHHHCC-CHHHHHHHHHHHH
Confidence 35677766 677899999999999 8887765555554
No 82
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=52.73 E-value=23 Score=26.41 Aligned_cols=43 Identities=28% Similarity=0.299 Sum_probs=34.9
Q ss_pred HHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceecc
Q psy7686 21 FVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKN 66 (243)
Q Consensus 21 Fi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~ 66 (243)
++..+...++... .++|+.+++ .+=-+--+++-||.-|+|++.
T Consensus 27 ~L~~l~~~~~~~~--~~la~~l~i-~~~~vt~~l~~Le~~glv~r~ 69 (126)
T COG1846 27 VLLALYEAGGITV--KELAERLGL-DRSTVTRLLKRLEDKGLIERL 69 (126)
T ss_pred HHHHHHHhCCCcH--HHHHHHHCC-CHHHHHHHHHHHHHCCCeeec
Confidence 3444445444333 999999999 999999999999999999997
No 83
>PF10779 XhlA: Haemolysin XhlA; InterPro: IPR019715 Haemolysin XhlA is a cell-surface associated haemolysin that lyses the two most prevalent types of insect immune cells (granulocytes and plasmatocytes) as well as rabbit and horse erythrocytes [].
Probab=52.53 E-value=60 Score=23.69 Aligned_cols=39 Identities=18% Similarity=0.368 Sum_probs=28.8
Q ss_pred HHHHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q psy7686 87 EQSKLIELRDEISDMRNHEAVIDEHIRKCQQSLRNIQEE 125 (243)
Q Consensus 87 ~~~~~~~Lk~El~~L~~~E~~LD~~I~~~~~~l~~l~ed 125 (243)
...++.++...+..|+.....++..|+.+..+|..+.++
T Consensus 11 ie~~l~~~~~~i~~lE~~~~~~e~~i~~~~~~l~~I~~n 49 (71)
T PF10779_consen 11 IETKLDNHEERIDKLEKRDAANEKDIKNLNKQLEKIKSN 49 (71)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344555666777778888888888888888888888763
No 84
>PRK11050 manganese transport regulator MntR; Provisional
Probab=52.39 E-value=41 Score=27.93 Aligned_cols=42 Identities=19% Similarity=0.119 Sum_probs=36.1
Q ss_pred CCeeeHHHHHhhhcccchhhhhhHHHhhhhccceeccccCceE
Q psy7686 30 EGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNNKNIIR 72 (243)
Q Consensus 30 ~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~sKn~i~ 72 (243)
++.+.+.++|+.|++ .+--+.-+++-|+.-|+|.+.....+.
T Consensus 49 ~~~~t~~eLA~~l~i-s~stVsr~l~~Le~~GlI~r~~~~~v~ 90 (152)
T PRK11050 49 VGEARQVDIAARLGV-SQPTVAKMLKRLARDGLVEMRPYRGVF 90 (152)
T ss_pred cCCCCHHHHHHHHCC-CHHHHHHHHHHHHHCCCEEEecCCceE
Confidence 466899999999999 999999999999999999986543333
No 85
>PRK05014 hscB co-chaperone HscB; Provisional
Probab=52.31 E-value=1.5e+02 Score=25.32 Aligned_cols=102 Identities=20% Similarity=0.320 Sum_probs=58.7
Q ss_pred CCCCcCcHHHHHHHHHHHHhh-CCCCee---------------eHHHHHhhhcccchhhhhhHHHhhhhccceeccccCc
Q psy7686 7 NSRFEKSLGLLTTKFVSLLQQ-APEGVL---------------HLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNNKNI 70 (243)
Q Consensus 7 ~~R~~~SL~~Lt~kFi~ll~~-~~~g~i---------------dL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~sKn~ 70 (243)
+..++.+...|.++|-.+.+. .||... -+|+|=..|.=-.+|+.|+. -|.|+.+.....
T Consensus 10 ~~~~~~d~~~L~~~yr~l~~~~HPDk~~~~~~~~~~~a~~~s~~iN~AY~~L~dp~~Ra~Yll--~l~g~~~~~~~~--- 84 (171)
T PRK05014 10 PARYDIDTQLLASRYQELQRQFHPDKFANASERERLLAVQQAATINDAYQTLKHPLKRAEYLL--SLHGFDLAHEQH--- 84 (171)
T ss_pred CCCCCCCHHHHHHHHHHHHHHhCcCCCCCCcHHHHHHHHHHHHHHHHHHHHHCChhHHHHHHH--HhcCCccccccC---
Confidence 345677888999999988753 566422 26666677766468999985 455766643321
Q ss_pred eEEeccCCCCchhhhHHHHHhHhHHHHHHHH----------HHHHHHHHHHHHHHHHHHHhhh
Q psy7686 71 IRWKALKNKNEEEYDLEQSKLIELRDEISDM----------RNHEAVIDEHIRKCQQSLRNIQ 123 (243)
Q Consensus 71 i~W~G~~~~~~~~~~~~~~~~~~Lk~El~~L----------~~~E~~LD~~I~~~~~~l~~l~ 123 (243)
...+. +.-.++-+++++++.. ...-.++++.++.+.+.|.+..
T Consensus 85 -------~~~d~---efLme~me~rE~le~~~~~~d~~~~l~~l~~~~~~~~~~~~~~l~~~~ 137 (171)
T PRK05014 85 -------TVRDT---AFLMEQMELREELEDIEQSKDPEAALESFIKRVKKMFKTRLQQMVEQL 137 (171)
T ss_pred -------CcCCH---HHHHHHHHHHHHHHhhccccCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 11122 5555555666666544 3333444444444444454444
No 86
>PRK09343 prefoldin subunit beta; Provisional
Probab=52.30 E-value=49 Score=26.76 Aligned_cols=78 Identities=10% Similarity=0.128 Sum_probs=52.5
Q ss_pred hhhhhhHHHhhhhccceeccccCceEEeccCCC-Cchhh--hHHHHHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q psy7686 47 KRRIYDITNVLEGIGLIEKNNKNIIRWKALKNK-NEEEY--DLEQSKLIELRDEISDMRNHEAVIDEHIRKCQQSLRNIQ 123 (243)
Q Consensus 47 KRRiYDItNVLEgiglI~K~sKn~i~W~G~~~~-~~~~~--~~~~~~~~~Lk~El~~L~~~E~~LD~~I~~~~~~l~~l~ 123 (243)
.+.+=..-.|++.+..+.-- -+-|+=.|.--+ .+... .++..++..+..++..|+.++..|...+..++.+|+.+.
T Consensus 34 e~q~~e~~~~~~EL~~L~~d-~~VYk~VG~vlv~qd~~e~~~~l~~r~E~ie~~ik~lekq~~~l~~~l~e~q~~l~~ll 112 (121)
T PRK09343 34 DLELREINKALEELEKLPDD-TPIYKIVGNLLVKVDKTKVEKELKERKELLELRSRTLEKQEKKLREKLKELQAKINEML 112 (121)
T ss_pred HHHHHHHHHHHHHHHcCCCc-chhHHHhhHHHhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455666777777666521 233443443222 22211 356678888999999999999999999999999999987
Q ss_pred hh
Q psy7686 124 EE 125 (243)
Q Consensus 124 ed 125 (243)
.-
T Consensus 113 ~~ 114 (121)
T PRK09343 113 SK 114 (121)
T ss_pred Hh
Confidence 63
No 87
>PRK11569 transcriptional repressor IclR; Provisional
Probab=51.89 E-value=1.5e+02 Score=26.74 Aligned_cols=45 Identities=9% Similarity=0.245 Sum_probs=38.1
Q ss_pred HHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceeccc
Q psy7686 21 FVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNN 67 (243)
Q Consensus 21 Fi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~s 67 (243)
.+++|.. ..+.+.+.++|+.+|+ .|=.+|=+++-|+..|++++..
T Consensus 33 IL~~l~~-~~~~~~lseia~~lgl-pksTv~RlL~tL~~~G~l~~~~ 77 (274)
T PRK11569 33 LLEWIAE-SNGSVALTELAQQAGL-PNSTTHRLLTTMQQQGFVRQVG 77 (274)
T ss_pred HHHHHHh-CCCCcCHHHHHHHHCc-CHHHHHHHHHHHHHCCCEEEcC
Confidence 4455554 3556899999999999 9999999999999999999853
No 88
>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=51.87 E-value=63 Score=25.03 Aligned_cols=38 Identities=24% Similarity=0.300 Sum_probs=24.1
Q ss_pred eeHHHHHhhhcccchhhhhhHHHhhhhccceec-cccCceEEec
Q psy7686 33 LHLKYAAENLEVKQKRRIYDITNVLEGIGLIEK-NNKNIIRWKA 75 (243)
Q Consensus 33 idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K-~sKn~i~W~G 75 (243)
+.+.++|+.+|| ..+-|- -.|..|+|.- ...|.+++-.
T Consensus 2 ~~i~eva~~~gv-s~~tlR----~ye~~Gll~~~r~~~g~R~Y~ 40 (102)
T cd04789 2 YTISELAEKAGI-SRSTLL----YYEKLGLITGTRNANGYRLYP 40 (102)
T ss_pred CCHHHHHHHHCc-CHHHHH----HHHHCCCCCCCcCCCCCeeCC
Confidence 568899999999 765332 3355677762 2345566544
No 89
>PRK09954 putative kinase; Provisional
Probab=51.77 E-value=20 Score=33.19 Aligned_cols=46 Identities=15% Similarity=0.247 Sum_probs=40.3
Q ss_pred HHHHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceecc
Q psy7686 18 TTKFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKN 66 (243)
Q Consensus 18 t~kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~ 66 (243)
-++.+++|++. +.++..++|+.|+| .|..++-.++=|+.-|+|++.
T Consensus 5 ~~~il~~l~~~--~~~s~~~la~~l~~-s~~~v~~~i~~L~~~g~i~~~ 50 (362)
T PRK09954 5 EKEILAILRRN--PLIQQNEIADILQI-SRSRVAAHIMDLMRKGRIKGK 50 (362)
T ss_pred HHHHHHHHHHC--CCCCHHHHHHHHCC-CHHHHHHHHHHHHHCCCcCCc
Confidence 45688888864 47999999999999 999999999999999999764
No 90
>KOG2747|consensus
Probab=51.16 E-value=34 Score=33.58 Aligned_cols=59 Identities=22% Similarity=0.335 Sum_probs=45.9
Q ss_pred CcHHHHHHH------HHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceeccccCceEEecc
Q psy7686 12 KSLGLLTTK------FVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNNKNIIRWKAL 76 (243)
Q Consensus 12 ~SL~~Lt~k------Fi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~sKn~i~W~G~ 76 (243)
.-||+|+=+ .+++|....+..|+|+++|..-++ +.-||++.|+.+++|... |. +.|...
T Consensus 303 SDLGllsYrsYW~~~ll~~L~~~~~~~isI~~iS~~Tgi----~~~DIisTL~~L~m~~y~-k~-~~~~~~ 367 (396)
T KOG2747|consen 303 SDLGLLSYRSYWRCVLLELLRKHRGEHISIKEISKETGI----RPDDIISTLQSLNMIKYY-KG-YIISIC 367 (396)
T ss_pred chhhHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHhhCC----CHHHHHHHHHhhCCcccc-CC-eeEEEe
Confidence 346666632 677777765555999999999999 778999999999999877 33 777653
No 91
>TIGR00293 prefoldin, archaeal alpha subunit/eukaryotic subunit 5. This model finds a set of small proteins from the Archaea and from Aquifex aeolicus that may represent two orthologous groups. The proteins are predicted to be mostly coiled coil, and may hit large numbers of proteins that contain coiled coil regions.
Probab=51.02 E-value=53 Score=26.01 Aligned_cols=54 Identities=7% Similarity=0.117 Sum_probs=33.1
Q ss_pred cCceEEeccCCCCchhhhHHHHHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q psy7686 68 KNIIRWKALKNKNEEEYDLEQSKLIELRDEISDMRNHEAVIDEHIRKCQQSLRNIQE 124 (243)
Q Consensus 68 Kn~i~W~G~~~~~~~~~~~~~~~~~~Lk~El~~L~~~E~~LD~~I~~~~~~l~~l~e 124 (243)
+.-+.|.|.+-.-.. .......-|+..+..|...-+.|.+.+.++++++..+..
T Consensus 68 ~~v~v~iG~g~~vE~---~~~eA~~~l~~~~~~l~~~~~~l~~~l~~l~~~~~~i~~ 121 (126)
T TIGR00293 68 DKVLVSIGSGYYVEK---DAEEAIEFLKKRIEELEKAIEKLQEALAELASRAQQLEQ 121 (126)
T ss_pred CEEEEEcCCCEEEEe---cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455788887766222 233444556666666766666666777776666666544
No 92
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=50.50 E-value=56 Score=28.99 Aligned_cols=52 Identities=10% Similarity=0.226 Sum_probs=41.1
Q ss_pred HHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceeccccCceEEec
Q psy7686 21 FVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNNKNIIRWKA 75 (243)
Q Consensus 21 Fi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~sKn~i~W~G 75 (243)
.+++|.. .+.+.+.++|+.+++ .|=-+|-+++.|+..|++++...+.--..|
T Consensus 19 IL~~l~~--~~~l~l~eia~~lgl-~kstv~Rll~tL~~~G~l~~~~~~~~Y~lG 70 (257)
T PRK15090 19 ILQALGE--EREIGITELSQRVMM-SKSTVYRFLQTMKTLGYVAQEGESEKYSLT 70 (257)
T ss_pred HHHHhhc--CCCCCHHHHHHHHCc-CHHHHHHHHHHHHHCCCEEEcCCCCcEEec
Confidence 5566654 346899999999999 999999999999999999987543322355
No 93
>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=50.32 E-value=34 Score=29.51 Aligned_cols=45 Identities=27% Similarity=0.338 Sum_probs=37.8
Q ss_pred HHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceecccc
Q psy7686 21 FVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNNK 68 (243)
Q Consensus 21 Fi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~sK 68 (243)
.+.++.. .+.+.+.++|+.+++ .+-.++-.++-|+..|+|++..+
T Consensus 148 IL~~l~~--~g~~s~~eia~~l~i-s~stv~r~L~~Le~~GlI~r~~~ 192 (203)
T TIGR01884 148 VLEVLKA--EGEKSVKNIAKKLGK-SLSTISRHLRELEKKGLVEQKGR 192 (203)
T ss_pred HHHHHHH--cCCcCHHHHHHHHCc-CHHHHHHHHHHHHHCCCEEEEcC
Confidence 3444443 356899999999999 99999999999999999999863
No 94
>PRK00215 LexA repressor; Validated
Probab=49.25 E-value=28 Score=29.77 Aligned_cols=43 Identities=14% Similarity=0.178 Sum_probs=37.0
Q ss_pred hCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceeccccC
Q psy7686 27 QAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNNKN 69 (243)
Q Consensus 27 ~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~sKn 69 (243)
...+....+.++|+.++++.|--++.+++-|+.-|+|++....
T Consensus 18 ~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~~~g~i~~~~~~ 60 (205)
T PRK00215 18 EETGYPPSRREIADALGLRSPSAVHEHLKALERKGFIRRDPGR 60 (205)
T ss_pred HHhCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEeCCCC
Confidence 3345668999999999997799999999999999999987544
No 95
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=48.83 E-value=26 Score=29.76 Aligned_cols=38 Identities=16% Similarity=0.183 Sum_probs=34.6
Q ss_pred CCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceecc
Q psy7686 28 APEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKN 66 (243)
Q Consensus 28 ~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~ 66 (243)
..++.+.+.++|+.+++ .++-+..|++-|.--|||.-.
T Consensus 21 ~~~~~vs~~eIA~~~~i-p~~~l~kIl~~L~~aGLv~s~ 58 (164)
T PRK10857 21 SEAGPVPLADISERQGI-SLSYLEQLFSRLRKNGLVSSV 58 (164)
T ss_pred CCCCcCcHHHHHHHHCc-CHHHHHHHHHHHHHCCCEEeC
Confidence 34568999999999999 999999999999999999954
No 96
>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=48.58 E-value=95 Score=26.28 Aligned_cols=40 Identities=23% Similarity=0.334 Sum_probs=36.5
Q ss_pred CCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceecccc
Q psy7686 28 APEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNNK 68 (243)
Q Consensus 28 ~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~sK 68 (243)
.|+..+.-.++|+.||| .|=-+=+.+..|++-|||+...+
T Consensus 30 ~pG~~L~e~~La~~lgV-SRtpVReAL~~L~~eGlv~~~~~ 69 (212)
T TIGR03338 30 PPGAKLNESDIAARLGV-SRGPVREAFRALEEAGLVRNEKN 69 (212)
T ss_pred CCCCEecHHHHHHHhCC-ChHHHHHHHHHHHHCCCEEEecC
Confidence 57888999999999999 99999999999999999997644
No 97
>PF12329 TMF_DNA_bd: TATA element modulatory factor 1 DNA binding; InterPro: IPR022092 This is the middle region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes that contains at its N-terminal section a number of leucine zippers that could potentially form coiled coil structures. The whole proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal [] and plant [] cells.
Probab=48.40 E-value=49 Score=24.68 Aligned_cols=37 Identities=14% Similarity=0.399 Sum_probs=29.9
Q ss_pred HHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q psy7686 89 SKLIELRDEISDMRNHEAVIDEHIRKCQQSLRNIQEE 125 (243)
Q Consensus 89 ~~~~~Lk~El~~L~~~E~~LD~~I~~~~~~l~~l~ed 125 (243)
.++..|..|.+.|...|..+...|+.+..+++.+-..
T Consensus 12 e~Ia~L~eEGekLSk~el~~~~~IKKLr~~~~e~e~~ 48 (74)
T PF12329_consen 12 EQIAQLMEEGEKLSKKELKLNNTIKKLRAKIKELEKQ 48 (74)
T ss_pred HHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHH
Confidence 4677888899999999988888888888887776543
No 98
>PF13518 HTH_28: Helix-turn-helix domain
Probab=48.40 E-value=19 Score=23.55 Aligned_cols=37 Identities=19% Similarity=0.345 Sum_probs=30.2
Q ss_pred HHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccc
Q psy7686 21 FVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGL 62 (243)
Q Consensus 21 Fi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgigl 62 (243)
.|.++. +|. ++.++|..+|| .+..||.+++-++.-|+
T Consensus 5 iv~~~~---~g~-s~~~~a~~~gi-s~~tv~~w~~~y~~~G~ 41 (52)
T PF13518_consen 5 IVELYL---EGE-SVREIAREFGI-SRSTVYRWIKRYREGGI 41 (52)
T ss_pred HHHHHH---cCC-CHHHHHHHHCC-CHhHHHHHHHHHHhcCH
Confidence 455555 244 99999999999 99999999999988664
No 99
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=48.16 E-value=51 Score=26.67 Aligned_cols=48 Identities=15% Similarity=0.191 Sum_probs=38.0
Q ss_pred HHHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceeccccC
Q psy7686 19 TKFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNNKN 69 (243)
Q Consensus 19 ~kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~sKn 69 (243)
+.|..++. .+|.+.+.++|+.|+| .+--+--.++-|+.-|+|.+....
T Consensus 11 ~~I~~l~~--~~~~~~~~ela~~l~v-s~~svs~~l~~L~~~Gli~~~~~~ 58 (142)
T PRK03902 11 EQIYLLIE--EKGYARVSDIAEALSV-HPSSVTKMVQKLDKDEYLIYEKYR 58 (142)
T ss_pred HHHHHHHh--cCCCcCHHHHHHHhCC-ChhHHHHHHHHHHHCCCEEEecCc
Confidence 33444443 3567799999999999 999999999999999999976433
No 100
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=47.84 E-value=29 Score=31.14 Aligned_cols=46 Identities=22% Similarity=0.266 Sum_probs=37.6
Q ss_pred HHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceecccc
Q psy7686 20 KFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNNK 68 (243)
Q Consensus 20 kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~sK 68 (243)
+.++++.+ .+.+.+.++|+.|+| .+.-|+=-++.||..|+|.|..-
T Consensus 9 ~Il~~l~~--~~~~~~~ela~~l~v-S~~TirRdL~~Le~~g~i~r~~g 54 (251)
T PRK13509 9 ILLELLAQ--LGFVTVEKVIERLGI-SPATARRDINKLDESGKLKKVRN 54 (251)
T ss_pred HHHHHHHH--cCCcCHHHHHHHHCc-CHHHHHHHHHHHHHCCCEEEecC
Confidence 35566664 788999999999999 88777766888999999998633
No 101
>PF12269 zf-CpG_bind_C: CpG binding protein zinc finger C terminal domain; InterPro: IPR022056 This domain family is found in eukaryotes, and is approximately 240 amino acids in length. This domain is the zinc finger domain of a CpG binding DNA methyltransferase protein. It contains a CxxC motif which forms the zinc finger and binds to DNA.
Probab=47.14 E-value=31 Score=31.52 Aligned_cols=51 Identities=14% Similarity=0.244 Sum_probs=37.4
Q ss_pred EEeccCCCCchhh----hHHHHHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy7686 72 RWKALKNKNEEEY----DLEQSKLIELRDEISDMRNHEAVIDEHIRKCQQSLRNI 122 (243)
Q Consensus 72 ~W~G~~~~~~~~~----~~~~~~~~~Lk~El~~L~~~E~~LD~~I~~~~~~l~~l 122 (243)
+|...+......+ +++..++...+.++.+|+..+++|+.+|...++.--.-
T Consensus 15 Ew~~~p~~A~E~~r~~Le~Ir~kq~~v~~~l~eLe~~~~el~~~i~~~k~~~~~~ 69 (236)
T PF12269_consen 15 EWQLSPCVAEEQNRKLLEEIRKKQQKVRNRLQELEKRFKELEAIIARAKQFTVDQ 69 (236)
T ss_pred HhcCCCchhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCc
Confidence 5766655532212 45677788889999999999999999999887764443
No 102
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=47.12 E-value=1.7e+02 Score=24.46 Aligned_cols=57 Identities=19% Similarity=0.222 Sum_probs=31.2
Q ss_pred HHHHHhhCCCCeeeHHHHHhhhc--ccchhhhhhHHHhhhhccce-ecc-ccCceEEeccCCC
Q psy7686 21 FVSLLQQAPEGVLHLKYAAENLE--VKQKRRIYDITNVLEGIGLI-EKN-NKNIIRWKALKNK 79 (243)
Q Consensus 21 Fi~ll~~~~~g~idL~~aa~~L~--v~~KRRiYDItNVLEgiglI-~K~-sKn~i~W~G~~~~ 79 (243)
.+++|.. .+.+++.+.+...|+ | .|=-+==+..-|..=|.| .|. +|-.|-|.-.+..
T Consensus 6 Il~y~~~-qNRPys~~di~~nL~~~~-~K~~v~k~Ld~L~~~g~i~~K~~GKqkiY~~~Q~~~ 66 (169)
T PF07106_consen 6 ILEYMKE-QNRPYSAQDIFDNLHNKV-GKTAVQKALDSLVEEGKIVEKEYGKQKIYFANQDEL 66 (169)
T ss_pred HHHHHHH-cCCCCcHHHHHHHHHhhc-cHHHHHHHHHHHHhCCCeeeeeecceEEEeeCcccc
Confidence 3456654 467788888888884 4 443333333333333443 343 6777777554443
No 103
>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=46.69 E-value=55 Score=24.97 Aligned_cols=58 Identities=24% Similarity=0.335 Sum_probs=43.7
Q ss_pred CcHHHHHHHHHHHHhhC-CCCeeeHHHHHhhhcccchhhhhhHHH-hhhhccceeccccCc
Q psy7686 12 KSLGLLTTKFVSLLQQA-PEGVLHLKYAAENLEVKQKRRIYDITN-VLEGIGLIEKNNKNI 70 (243)
Q Consensus 12 ~SL~~Lt~kFi~ll~~~-~~g~idL~~aa~~L~v~~KRRiYDItN-VLEgiglI~K~sKn~ 70 (243)
..|..+=++++..+.+. .+|++-|+.+|..|+. .+.-|=|++- -|--.|+|+|+.+..
T Consensus 4 ~GLd~~D~~yL~~l~~~f~ggPvGl~tlA~~l~e-d~~Tie~v~EPyLiq~G~I~RT~rGR 63 (76)
T PF05491_consen 4 LGLDELDRRYLKTLIENFKGGPVGLDTLAAALGE-DKETIEDVIEPYLIQIGFIQRTPRGR 63 (76)
T ss_dssp TS-BHHHHHHHHHHHHCSTTS-B-HHHHHHHTTS--HHHHHHTTHHHHHHTTSEEEETTEE
T ss_pred ccCCHHHHHHHHHHHHHcCCCCeeHHHHHHHHCC-CHhHHHHHhhHHHHHhhhHhhCccHH
Confidence 34566778899888765 7899999999999999 8888877654 577899999997754
No 104
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=46.24 E-value=49 Score=27.60 Aligned_cols=54 Identities=19% Similarity=0.241 Sum_probs=46.6
Q ss_pred CCcCcHHHHHHHHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceec
Q psy7686 9 RFEKSLGLLTTKFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEK 65 (243)
Q Consensus 9 R~~~SL~~Lt~kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K 65 (243)
.....|-.+=++.+.+|+. ++.+...++|+.+|+ ..--++.=++=|+.-|+|++
T Consensus 7 ~~~~~lD~~D~~IL~~Lq~--d~R~s~~eiA~~lgl-S~~tv~~Ri~rL~~~GvI~~ 60 (164)
T PRK11169 7 RPGKDLDRIDRNILNELQK--DGRISNVELSKRVGL-SPTPCLERVRRLERQGFIQG 60 (164)
T ss_pred cchhhHHHHHHHHHHHhcc--CCCCCHHHHHHHHCc-CHHHHHHHHHHHHHCCCeEE
Confidence 3456677778899999975 888999999999999 88888888899999999986
No 105
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=46.18 E-value=16 Score=29.41 Aligned_cols=40 Identities=30% Similarity=0.340 Sum_probs=29.5
Q ss_pred CCcCcHHH-HHHHHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHH
Q psy7686 9 RFEKSLGL-LTTKFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITN 55 (243)
Q Consensus 9 R~~~SL~~-Lt~kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItN 55 (243)
|+-..-|. |...|++.+. ++.+.+|+.||| .+.+|-.|+|
T Consensus 5 ~~P~~PGEiL~eeflep~g------lt~~~lA~~lgV-~r~~is~lin 45 (104)
T COG3093 5 RKPAHPGEILREEFLEPLG------LTQTELAEALGV-TRNTISELIN 45 (104)
T ss_pred CCCCCchHHHHHHHhcccc------CCHHHHHHHhCC-CHHHHHHHHc
Confidence 44444454 3455665442 789999999999 9999999987
No 106
>PLN03239 histone acetyltransferase; Provisional
Probab=45.97 E-value=56 Score=31.61 Aligned_cols=57 Identities=18% Similarity=0.253 Sum_probs=42.6
Q ss_pred CCCCCCcCcHHHHH------HHHHHHHhhCC--CCeeeHHHHHhhhcccchhhhhhHHHhhhhccceec
Q psy7686 5 PANSRFEKSLGLLT------TKFVSLLQQAP--EGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEK 65 (243)
Q Consensus 5 ~~~~R~~~SL~~Lt------~kFi~ll~~~~--~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K 65 (243)
+++.|-=+-||.++ ...+++|.... ...++++++|...++ |.-||+..|+.+|++..
T Consensus 249 G~PEkPLSdlG~~sY~~YW~~~il~~L~~~~~~~~~~si~dis~~Tgi----~~~DIi~tL~~l~~l~~ 313 (351)
T PLN03239 249 GSPEKPMSDLGQQAYIPYWGSTIVDFLLNHSGNDSSLSIMDIAKKTSI----MAEDIVFALNQLGILKF 313 (351)
T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHhccCCCCCccHHHHHHHhCC----CHHHHHHHHHHCCcEEE
Confidence 34455556677766 22556665543 357999999999999 78999999999999964
No 107
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. 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=45.90 E-value=1.1e+02 Score=24.32 Aligned_cols=81 Identities=14% Similarity=0.201 Sum_probs=0.0
Q ss_pred eeHHHHHhhhcccchhhhhhHHHhhhhcccee--ccccCceEEeccCCCCchhhhHHHHHhHhHH------HHHHHHHH-
Q psy7686 33 LHLKYAAENLEVKQKRRIYDITNVLEGIGLIE--KNNKNIIRWKALKNKNEEEYDLEQSKLIELR------DEISDMRN- 103 (243)
Q Consensus 33 idL~~aa~~L~v~~KRRiYDItNVLEgiglI~--K~sKn~i~W~G~~~~~~~~~~~~~~~~~~Lk------~El~~L~~- 103 (243)
+.+.++|..+|| ..+-| =-.|.+|||. +...|.|++-+...+ .....+..|+ +|+..+-.
T Consensus 1 m~I~e~a~~~gv-s~~tl----R~Ye~~GLl~~~~r~~~gyR~Y~~~~l------~~l~~I~~lr~~G~sL~eI~~~l~~ 69 (126)
T cd04783 1 LTIGELAKAAGV-NVETI----RYYQRRGLLPEPPRPEGGYRRYPEETV------TRLRFIKRAQELGFTLDEIAELLEL 69 (126)
T ss_pred CCHHHHHHHHCc-CHHHH----HHHHHCCCCCCCCcCCCCCeecCHHHH------HHHHHHHHHHHcCCCHHHHHHHHhc
Q ss_pred --------HHHHHHHHHHHHHHHHHhhhh
Q psy7686 104 --------HEAVIDEHIRKCQQSLRNIQE 124 (243)
Q Consensus 104 --------~E~~LD~~I~~~~~~l~~l~e 124 (243)
....|..++..+++++..|..
T Consensus 70 ~~~~~~~~~~~~l~~~~~~l~~~i~~L~~ 98 (126)
T cd04783 70 DDGTDCSEARELAEQKLAEVDEKIADLQR 98 (126)
T ss_pred ccCCCHHHHHHHHHHHHHHHHHHHHHHHH
No 108
>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=45.71 E-value=28 Score=24.58 Aligned_cols=36 Identities=25% Similarity=0.288 Sum_probs=32.5
Q ss_pred eeeHHHHHhhhcccchhhhhhHHHhhhhccceecccc
Q psy7686 32 VLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNNK 68 (243)
Q Consensus 32 ~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~sK 68 (243)
.++..++|+.+|+ .++.+--+.+-|+.-|+|+...+
T Consensus 28 ~lt~~~iA~~~g~-sr~tv~r~l~~l~~~g~I~~~~~ 63 (76)
T PF13545_consen 28 PLTQEEIADMLGV-SRETVSRILKRLKDEGIIEVKRG 63 (76)
T ss_dssp ESSHHHHHHHHTS-CHHHHHHHHHHHHHTTSEEEETT
T ss_pred cCCHHHHHHHHCC-CHHHHHHHHHHHHHCCCEEEcCC
Confidence 4678999999999 99999999999999999997644
No 109
>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=45.63 E-value=34 Score=29.12 Aligned_cols=47 Identities=15% Similarity=0.232 Sum_probs=37.6
Q ss_pred HHHHHHh---hCCCCeeeHHHHHhhhcccc-hhhhhhHHHhhhhccceeccc
Q psy7686 20 KFVSLLQ---QAPEGVLHLKYAAENLEVKQ-KRRIYDITNVLEGIGLIEKNN 67 (243)
Q Consensus 20 kFi~ll~---~~~~g~idL~~aa~~L~v~~-KRRiYDItNVLEgiglI~K~s 67 (243)
+.+.++. ...+-...+.++|+.+++ . +--++..++.|+..|+|++..
T Consensus 10 ~iL~~l~~~~~~~~~~~~~~ela~~~~~-~s~~tv~~~l~~L~~~g~i~~~~ 60 (199)
T TIGR00498 10 EVLDLIRAHIESTGYPPSIREIARAVGL-RSPSAAEEHLKALERKGYIERDP 60 (199)
T ss_pred HHHHHHHHHHHhcCCCCcHHHHHHHhCC-CChHHHHHHHHHHHHCCCEecCC
Confidence 3444444 333445789999999999 8 999999999999999999974
No 110
>PF05377 FlaC_arch: Flagella accessory protein C (FlaC); InterPro: IPR008039 Although archaeal flagella appear superficially similar to those of bacteria, they are quite distinct []. In several archaea, the flagellin genes are followed immediately by the flagellar accessory genes flaCDEFGHIJ. The gene products may have a role in translocation, secretion, or assembly of the flagellum. FlaC is a protein whose exact role is unknown but it has been shown to be membrane-associated (by immuno-blotting fractionated cells) [].
Probab=45.08 E-value=1e+02 Score=22.16 Aligned_cols=39 Identities=13% Similarity=0.337 Sum_probs=25.6
Q ss_pred HHHHHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q psy7686 86 LEQSKLIELRDEISDMRNHEAVIDEHIRKCQQSLRNIQE 124 (243)
Q Consensus 86 ~~~~~~~~Lk~El~~L~~~E~~LD~~I~~~~~~l~~l~e 124 (243)
++..++..+...+..++.+-+.|-.-+..+.+.++.|..
T Consensus 4 elEn~~~~~~~~i~tvk~en~~i~~~ve~i~envk~ll~ 42 (55)
T PF05377_consen 4 ELENELPRIESSINTVKKENEEISESVEKIEENVKDLLS 42 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455556666666666666666666777777777766655
No 111
>KOG1318|consensus
Probab=44.74 E-value=54 Score=32.35 Aligned_cols=75 Identities=15% Similarity=0.245 Sum_probs=44.7
Q ss_pred chhhhhhHHHhhhhc-cceeccccCceEEeccCCCCchhhhHHHHHhHhHHHH---HHHHHHHHHHHHHHHHHHHHHHHh
Q psy7686 46 QKRRIYDITNVLEGI-GLIEKNNKNIIRWKALKNKNEEEYDLEQSKLIELRDE---ISDMRNHEAVIDEHIRKCQQSLRN 121 (243)
Q Consensus 46 ~KRRiYDItNVLEgi-glI~K~sKn~i~W~G~~~~~~~~~~~~~~~~~~Lk~E---l~~L~~~E~~LD~~I~~~~~~l~~ 121 (243)
.|||=|-|=+-.--+ .||-|.+-+..+|. .+.+-. .....+.+|+++ ..++....+.|+.-++.+.+.+..
T Consensus 241 ERRRR~nIN~~IkeLg~liP~~~~~~~~~n-KgtILk----~s~dYIr~Lqq~~q~~~E~~~rqk~le~~n~~L~~riee 315 (411)
T KOG1318|consen 241 ERRRRENINDRIKELGQLIPKCNSEDMKSN-KGTILK----ASCDYIRELQQTLQRARELENRQKKLESTNQELALRIEE 315 (411)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCCcchhhcc-cchhhH----HHHHHHHHHHHHHHHHHHHHhhhhHHHhHHHHHHHHHHH
Confidence 677755554433333 37888888888996 444411 122334444444 446666677777777777777777
Q ss_pred hhhh
Q psy7686 122 IQEE 125 (243)
Q Consensus 122 l~ed 125 (243)
|..-
T Consensus 316 Lk~~ 319 (411)
T KOG1318|consen 316 LKSE 319 (411)
T ss_pred HHHH
Confidence 7653
No 112
>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=44.63 E-value=1e+02 Score=24.08 Aligned_cols=36 Identities=28% Similarity=0.238 Sum_probs=23.0
Q ss_pred eHHHHHhhhcccchhhhhhHHHhhhhcccee--ccccCceEEe
Q psy7686 34 HLKYAAENLEVKQKRRIYDITNVLEGIGLIE--KNNKNIIRWK 74 (243)
Q Consensus 34 dL~~aa~~L~v~~KRRiYDItNVLEgiglI~--K~sKn~i~W~ 74 (243)
.+.++|+.+|| ..|-|--. |..|||. ....|.+++-
T Consensus 2 ~i~e~a~~~gv-s~~tlr~y----e~~gll~~~~r~~~gyR~Y 39 (113)
T cd01109 2 TIKEVAEKTGL-SADTLRYY----EKEGLLPPVKRDENGIRDF 39 (113)
T ss_pred CHHHHHHHHCc-CHHHHHHH----HHCCCCCCCCcCCCCCccC
Confidence 57889999999 77755322 4678883 2334555543
No 113
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=44.61 E-value=39 Score=27.05 Aligned_cols=34 Identities=18% Similarity=0.230 Sum_probs=31.9
Q ss_pred eeeHHHHHhhhcccchhhhhhHHHhhhhccceecc
Q psy7686 32 VLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKN 66 (243)
Q Consensus 32 ~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~ 66 (243)
.+...++|+.+++ .+--+--+++.||.-|+|+|.
T Consensus 46 ~~t~~eLa~~l~~-~~~tvt~~v~~Le~~GlV~r~ 79 (144)
T PRK03573 46 EQSQIQLAKAIGI-EQPSLVRTLDQLEEKGLISRQ 79 (144)
T ss_pred CCCHHHHHHHhCC-ChhhHHHHHHHHHHCCCEeee
Confidence 3678999999999 999999999999999999997
No 114
>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=44.38 E-value=41 Score=29.66 Aligned_cols=56 Identities=14% Similarity=0.307 Sum_probs=33.7
Q ss_pred HHHHHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceecc--ccCceEEec
Q psy7686 17 LTTKFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKN--NKNIIRWKA 75 (243)
Q Consensus 17 Lt~kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~--sKn~i~W~G 75 (243)
+-..||.+++. ..++.|+.+|..+|+ .--=+-+-++-|+.-|.|+=. ....|.++.
T Consensus 100 lL~~Fi~yIK~--~Kvv~ledla~~f~l-~t~~~i~ri~~L~~~g~ltGv~DdrGkfIyIs 157 (188)
T PF09756_consen 100 LLQEFINYIKE--HKVVNLEDLAAEFGL-RTQDVINRIQELEAEGRLTGVIDDRGKFIYIS 157 (188)
T ss_dssp HHHHHHHHHHH---SEE-HHHHHHHH-S--HHHHHHHHHHHHHHSSS-EEE-TT--EEE--
T ss_pred HHHHHHHHHHH--cceeeHHHHHHHcCC-CHHHHHHHHHHHHHCCCceeeEcCCCCeEEec
Confidence 66779999997 678999999999999 333334556667777766543 233454444
No 115
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=44.27 E-value=44 Score=27.15 Aligned_cols=41 Identities=15% Similarity=0.176 Sum_probs=35.9
Q ss_pred hCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceecccc
Q psy7686 27 QAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNNK 68 (243)
Q Consensus 27 ~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~sK 68 (243)
..++..++..++|+.++| .+.-+-.|...|..-|||+....
T Consensus 20 ~~~g~~~s~~~ia~~~~i-s~~~vrk~l~~L~~~Glv~s~~G 60 (141)
T PRK11014 20 LPEGRMTSISEVTEVYGV-SRNHMVKIINQLSRAGYVTAVRG 60 (141)
T ss_pred CCCCCccCHHHHHHHHCc-CHHHHHHHHHHHHhCCEEEEecC
Confidence 345668999999999999 99999999999999999987643
No 116
>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=43.89 E-value=32 Score=28.01 Aligned_cols=35 Identities=9% Similarity=0.264 Sum_probs=31.3
Q ss_pred HHHHHHHHHHhhCCCCeeeHHHHHhhhcccchhhhh
Q psy7686 16 LLTTKFVSLLQQAPEGVLHLKYAAENLEVKQKRRIY 51 (243)
Q Consensus 16 ~Lt~kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiY 51 (243)
.+..-|++|+.+.+-..+.++++|++-|| .|.-+|
T Consensus 7 ~I~~a~~~Ll~~k~~~~ITV~~I~~~Agv-sR~TFY 41 (176)
T TIGR02366 7 KIAKAFKDLMEVQAFSKISVSDIMSTAQI-RRQTFY 41 (176)
T ss_pred HHHHHHHHHHHHCCCccCCHHHHHHHhCC-CHHHHH
Confidence 46677999999999999999999999999 887776
No 117
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=43.89 E-value=45 Score=25.61 Aligned_cols=45 Identities=22% Similarity=0.406 Sum_probs=37.3
Q ss_pred HHHHHhhCCCCeeeHHHHHhhh-----cccchhhhhhHHHhhhhccceeccc
Q psy7686 21 FVSLLQQAPEGVLHLKYAAENL-----EVKQKRRIYDITNVLEGIGLIEKNN 67 (243)
Q Consensus 21 Fi~ll~~~~~g~idL~~aa~~L-----~v~~KRRiYDItNVLEgiglI~K~s 67 (243)
.+++|..+ ++.++..++.+.| .+ .+=-+|=+.+.|+..|+|.|..
T Consensus 6 Il~~l~~~-~~~~sa~ei~~~l~~~~~~i-~~~TVYR~L~~L~~~Gli~~~~ 55 (116)
T cd07153 6 ILEVLLES-DGHLTAEEIYERLRKKGPSI-SLATVYRTLELLEEAGLVREIE 55 (116)
T ss_pred HHHHHHhC-CCCCCHHHHHHHHHhcCCCC-CHHHHHHHHHHHHhCCCEEEEE
Confidence 45666665 5778999999888 46 7889999999999999999963
No 118
>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=43.32 E-value=31 Score=26.63 Aligned_cols=41 Identities=17% Similarity=0.430 Sum_probs=33.2
Q ss_pred HHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceecc
Q psy7686 21 FVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKN 66 (243)
Q Consensus 21 Fi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~ 66 (243)
|.+-+-++ ++.+.+.++|..|++ ..++++++ |...|++-|.
T Consensus 14 ~~d~~~~~-~~~~ti~~~AK~L~i-~~~~l~~~---Lr~~g~l~~~ 54 (111)
T PF03374_consen 14 FYDAFVDS-DGLYTIREAAKLLGI-GRNKLFQW---LREKGWLYRR 54 (111)
T ss_pred HHHHHHcC-CCCccHHHHHHHhCC-CHHHHHHH---HHhCCceEEC
Confidence 55555554 599999999999999 89999876 6668888883
No 119
>PHA01750 hypothetical protein
Probab=42.78 E-value=68 Score=24.15 Aligned_cols=32 Identities=16% Similarity=0.365 Sum_probs=23.0
Q ss_pred HHHHhHhHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy7686 87 EQSKLIELRDEISDMRNHEAVIDEHIRKCQQS 118 (243)
Q Consensus 87 ~~~~~~~Lk~El~~L~~~E~~LD~~I~~~~~~ 118 (243)
+..++.+|+.|++++....+.|.+.+..+...
T Consensus 40 V~~ELdNL~~ei~~~kikqDnl~~qv~eik~k 71 (75)
T PHA01750 40 VNSELDNLKTEIEELKIKQDELSRQVEEIKRK 71 (75)
T ss_pred HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHh
Confidence 34567888888888887777777777665543
No 120
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=42.76 E-value=49 Score=29.68 Aligned_cols=48 Identities=19% Similarity=0.120 Sum_probs=38.4
Q ss_pred HHHHHHhh-CCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceecccc
Q psy7686 20 KFVSLLQQ-APEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNNK 68 (243)
Q Consensus 20 kFi~ll~~-~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~sK 68 (243)
+-+.++.. +....+...++|+.|++ .+..+.-+++-||.-|+|+|...
T Consensus 8 k~iallg~l~~~~~IS~~eLA~~L~i-S~~Tvsr~Lk~LEe~GlI~R~~~ 56 (217)
T PRK14165 8 KKLALLGAVNNTVKISSSEFANHTGT-SSKTAARILKQLEDEGYITRTIV 56 (217)
T ss_pred HHHHHHhccCCCCCcCHHHHHHHHCc-CHHHHHHHHHHHHHCCCEEEEEc
Confidence 33434433 33446899999999999 99999999999999999999743
No 121
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=42.73 E-value=50 Score=26.39 Aligned_cols=41 Identities=12% Similarity=0.160 Sum_probs=34.0
Q ss_pred HHHHHHHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHh
Q psy7686 15 GLLTTKFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNV 56 (243)
Q Consensus 15 ~~Lt~kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNV 56 (243)
.....+++.++.......+++.++|+.+|+ .+|.+.-+..-
T Consensus 8 ~~~i~~~~~~I~~~~~~~~sl~~lA~~~g~-S~~~l~r~Fk~ 48 (127)
T PRK11511 8 AITIHSILDWIEDNLESPLSLEKVSERSGY-SKWHLQRMFKK 48 (127)
T ss_pred HHHHHHHHHHHHHhcCCCCCHHHHHHHHCc-CHHHHHHHHHH
Confidence 455678999999988889999999999999 88877665543
No 122
>PRK10870 transcriptional repressor MprA; Provisional
Probab=42.70 E-value=39 Score=28.73 Aligned_cols=40 Identities=18% Similarity=0.194 Sum_probs=35.8
Q ss_pred hhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceecc
Q psy7686 26 QQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKN 66 (243)
Q Consensus 26 ~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~ 66 (243)
...+++.+...++|+.+++ .+=-+-=+++-|+.-|+|+|.
T Consensus 65 ~~~~~~~it~~eLa~~l~l-~~~tvsr~v~rLe~kGlV~R~ 104 (176)
T PRK10870 65 ESQENHSIQPSELSCALGS-SRTNATRIADELEKRGWIERR 104 (176)
T ss_pred hcCCCCCcCHHHHHHHHCC-CHHHHHHHHHHHHHCCCEEec
Confidence 3445678999999999999 999999999999999999997
No 123
>COG2919 Septum formation initiator [Cell division and chromosome partitioning]
Probab=42.59 E-value=18 Score=29.16 Aligned_cols=37 Identities=14% Similarity=0.332 Sum_probs=25.7
Q ss_pred HHHHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q psy7686 87 EQSKLIELRDEISDMRNHEAVIDEHIRKCQQSLRNIQE 124 (243)
Q Consensus 87 ~~~~~~~Lk~El~~L~~~E~~LD~~I~~~~~~l~~l~e 124 (243)
...+...+++|++.|.+.+..|...|+.++.. +++.+
T Consensus 55 l~~qi~~~~~e~~~L~~~~~~l~~ei~~L~dg-~~~i~ 91 (117)
T COG2919 55 LQRQIAAQQAELEKLSARNTALEAEIKDLKDG-RDYIE 91 (117)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc-HHHHH
Confidence 44455577788888888888888888777766 33333
No 124
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=42.14 E-value=1.2e+02 Score=25.92 Aligned_cols=47 Identities=13% Similarity=0.136 Sum_probs=39.9
Q ss_pred CCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceeccccCceEEec
Q psy7686 28 APEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNNKNIIRWKA 75 (243)
Q Consensus 28 ~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~sKn~i~W~G 75 (243)
.|+..+...++|+.||| .|==|=+....|+.-|||+...+.-+....
T Consensus 26 ~pG~~L~e~eLae~lgV-SRtpVREAL~~L~~eGlv~~~~~~G~~V~~ 72 (224)
T PRK11534 26 QPDEKLRMSLLTSRYAL-GVGPLREALSQLVAERLVTVVNQKGYRVAS 72 (224)
T ss_pred CCCCcCCHHHHHHHHCC-ChHHHHHHHHHHHHCCCEEEeCCCceEeCC
Confidence 47888999999999999 999999999999999999977555444443
No 125
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=41.27 E-value=2e+02 Score=24.81 Aligned_cols=40 Identities=30% Similarity=0.348 Sum_probs=37.4
Q ss_pred CCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceecccc
Q psy7686 28 APEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNNK 68 (243)
Q Consensus 28 ~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~sK 68 (243)
.|+..++.+++|+.||| .|--|=+....|++-|||+....
T Consensus 35 ~pG~~l~e~~La~~~gv-SrtPVReAL~rL~~eGlv~~~p~ 74 (230)
T COG1802 35 APGERLSEEELAEELGV-SRTPVREALRRLEAEGLVEIEPN 74 (230)
T ss_pred CCCCCccHHHHHHHhCC-CCccHHHHHHHHHHCCCeEecCC
Confidence 58999999999999999 99999999999999999999843
No 126
>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=40.95 E-value=63 Score=27.53 Aligned_cols=38 Identities=18% Similarity=0.340 Sum_probs=26.6
Q ss_pred eeHHHHHhhhcccchh--hhhhHHHhhhhccceec--cccCceEEeccC
Q psy7686 33 LHLKYAAENLEVKQKR--RIYDITNVLEGIGLIEK--NNKNIIRWKALK 77 (243)
Q Consensus 33 idL~~aa~~L~v~~KR--RiYDItNVLEgiglI~K--~sKn~i~W~G~~ 77 (243)
+.+.++|+.+|| .++ |-|| .+|||.- ...|.|++-+..
T Consensus 2 ~~I~evA~~~gv-s~~tLRyYe------~~GLl~p~~r~~~gyR~Y~~~ 43 (172)
T cd04790 2 LTISQLARQFGL-SRSTLLYYE------RIGLLSPSARSESNYRLYGER 43 (172)
T ss_pred CCHHHHHHHHCc-CHHHHHHHH------HCCCCCCCccCCCCCccCCHH
Confidence 467899999999 776 5564 5677753 456777776544
No 127
>PF10018 Med4: Vitamin-D-receptor interacting Mediator subunit 4; InterPro: IPR019258 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Members of this family represent the Med4 subunit of the Mediator (Med) complex [, ]. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=40.94 E-value=1.1e+02 Score=26.41 Aligned_cols=55 Identities=16% Similarity=0.369 Sum_probs=26.8
Q ss_pred HHHHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhh-------hccCccccchhhhhh
Q psy7686 87 EQSKLIELRDEISDMRNHEAVIDEHIRKCQQSLRNIQEEE-------VNRKQCYIPTDVILG 141 (243)
Q Consensus 87 ~~~~~~~Lk~El~~L~~~E~~LD~~I~~~~~~l~~l~ed~-------~n~~~aYVT~~Di~~ 141 (243)
...++..|++|+..|+.+-+.+=..+..|.+.|..+.... ....-.=|++++|.+
T Consensus 27 ~~~~I~~L~~e~~~ld~~i~~~~~~L~~~~~~L~~~~~~~~~~~~~~~~~~~~~v~~~eLL~ 88 (188)
T PF10018_consen 27 NQARIQQLRAEIEELDEQIRDILKQLKEARKELRTLPDQADEKLKSIPKAEKRPVDYEELLS 88 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccCCCCHHHHHH
Confidence 3344445555555554444444444444555555555211 111234577888875
No 128
>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=40.87 E-value=1.5e+02 Score=22.80 Aligned_cols=38 Identities=18% Similarity=0.268 Sum_probs=24.7
Q ss_pred eeHHHHHhhhcccchhhhhhHHHhhhhcccee-ccccCceEEec
Q psy7686 33 LHLKYAAENLEVKQKRRIYDITNVLEGIGLIE-KNNKNIIRWKA 75 (243)
Q Consensus 33 idL~~aa~~L~v~~KRRiYDItNVLEgiglI~-K~sKn~i~W~G 75 (243)
+.+.++|+.+|| ..+-| --.|-.||+. +...|.++.-+
T Consensus 2 ~~i~eva~~~gv-s~~tL----R~ye~~Gll~~~r~~~g~R~Y~ 40 (102)
T cd04775 2 YTIGQMSRKFGV-SRSTL----LYYESIGLIPSARSEANYRLYS 40 (102)
T ss_pred CCHHHHHHHHCc-CHHHH----HHHHHCCCCCCCCCCCCCeeeC
Confidence 468899999999 87766 3445678883 23345555433
No 129
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. 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(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=40.87 E-value=1.2e+02 Score=24.32 Aligned_cols=81 Identities=21% Similarity=0.257 Sum_probs=0.0
Q ss_pred eeHHHHHhhhcccchhhhhhHHHhhhhcccee--ccccCceEEeccCCCCchhhhHHHHHhHhHH------HHHHHH---
Q psy7686 33 LHLKYAAENLEVKQKRRIYDITNVLEGIGLIE--KNNKNIIRWKALKNKNEEEYDLEQSKLIELR------DEISDM--- 101 (243)
Q Consensus 33 idL~~aa~~L~v~~KRRiYDItNVLEgiglI~--K~sKn~i~W~G~~~~~~~~~~~~~~~~~~Lk------~El~~L--- 101 (243)
+.+.++|+.+|| ..+-|.=- |.+||+. +...|.|++-+...+ .....+..|+ +||..+
T Consensus 1 m~I~e~a~~~gv-s~~tlR~Y----e~~GLl~~~~r~~~gyR~Y~~~~l------~~l~~I~~lr~lG~sL~eI~~~l~~ 69 (127)
T TIGR02047 1 MKIGELAQKTGV-SVETIRFY----EKQGLLPPPARTDNNYRVYTVGHV------ERLAFIRNCRTLDMSLAEIRQLLRY 69 (127)
T ss_pred CcHHHHHHHHCc-CHHHHHHH----HHCCCCCCCCcCCCCCCcCCHHHH------HHHHHHHHHHHcCCCHHHHHHHHHh
Q ss_pred --------HHHHHHHHHHHHHHHHHHHhhhh
Q psy7686 102 --------RNHEAVIDEHIRKCQQSLRNIQE 124 (243)
Q Consensus 102 --------~~~E~~LD~~I~~~~~~l~~l~e 124 (243)
......|.+++..+.+++.+|..
T Consensus 70 ~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~ 100 (127)
T TIGR02047 70 QDKPEKSCSDVNALLDEHISHVRARIIKLQA 100 (127)
T ss_pred hhCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
No 130
>PHA02047 phage lambda Rz1-like protein
Probab=40.28 E-value=30 Score=27.70 Aligned_cols=59 Identities=12% Similarity=0.174 Sum_probs=26.1
Q ss_pred ceEEeccCCCCchhhhHHHHHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhccCccc
Q psy7686 70 IIRWKALKNKNEEEYDLEQSKLIELRDEISDMRNHEAVIDEHIRKCQQSLRNIQEEEVNRKQCY 133 (243)
Q Consensus 70 ~i~W~G~~~~~~~~~~~~~~~~~~Lk~El~~L~~~E~~LD~~I~~~~~~l~~l~ed~~n~~~aY 133 (243)
+|+|.|...-.. .....+++.++..+..+.+.-+.|.+.-....+.+++-.+ .|+.|++
T Consensus 25 ~~r~~g~~h~~a---~~la~qLE~a~~r~~~~Q~~V~~l~~kae~~t~Ei~~aL~--~n~~WaD 83 (101)
T PHA02047 25 SYRALGIAHEEA---KRQTARLEALEVRYATLQRHVQAVEARTNTQRQEVDRALD--QNRPWAD 83 (101)
T ss_pred HHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--hCCCccc
Confidence 367877432200 1223334444444444444444444444444445555444 3444443
No 131
>COG2894 MinD Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]
Probab=40.11 E-value=7.6 Score=35.85 Aligned_cols=27 Identities=26% Similarity=0.497 Sum_probs=21.0
Q ss_pred eHHHHHhhhcccchhhhhhHHHhhhhcc
Q psy7686 34 HLKYAAENLEVKQKRRIYDITNVLEGIG 61 (243)
Q Consensus 34 dL~~aa~~L~v~~KRRiYDItNVLEgig 61 (243)
-|.-+=-.+|. .+|=+||.+||++|=-
T Consensus 42 GLRNLDlimGl-E~RiVYd~vdVi~g~~ 68 (272)
T COG2894 42 GLRNLDLIMGL-ENRIVYDLVDVIEGEA 68 (272)
T ss_pred Cchhhhhhhcc-cceeeeeehhhhcCcc
Confidence 34445556788 9999999999999854
No 132
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=39.95 E-value=82 Score=29.75 Aligned_cols=55 Identities=22% Similarity=0.286 Sum_probs=41.6
Q ss_pred CCCCCCcCcHHHHH------HHHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhcccee
Q psy7686 5 PANSRFEKSLGLLT------TKFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIE 64 (243)
Q Consensus 5 ~~~~R~~~SL~~Lt------~kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~ 64 (243)
+++.|-=+-||.++ ...++.|.+ ..+.++++++|...++ +.-||+..|+.+|++.
T Consensus 191 G~PEkPLSdlG~~sY~~YW~~~il~~L~~-~~~~isi~~is~~T~i----~~~Dii~tL~~l~~l~ 251 (290)
T PLN03238 191 GTPERPLSDLGKVSFRSYWTRVLLEQLRD-VKGDVSIKDLSLATGI----RGEDIVSTLQSLNLIK 251 (290)
T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHh-cCCCccHHHHHHHhCC----CHHHHHHHHHHCCcEE
Confidence 34445556677765 225566654 4578999999999999 7789999999999994
No 133
>PF09940 DUF2172: Domain of unknown function (DUF2172); InterPro: IPR012353 The proteins in this entry are encoded by genes located in polysaccharide biosynthesis gene clusters, and are therefore believed to be involved in polysaccharide biosynthesis. The ste gene cluster (for Streptomyces eps) is involved in exopolysaccharide EPS 139A biosynthesis in Streptomyces sp. 139 []. Members of this group exhibit distant sequence similarity to aminopeptidases (IPR007484 from INTERPRO, MEROPS peptidase family M28).; PDB: 3K9T_A.
Probab=39.61 E-value=25 Score=34.37 Aligned_cols=42 Identities=21% Similarity=0.260 Sum_probs=33.3
Q ss_pred HHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhcccee
Q psy7686 21 FVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIE 64 (243)
Q Consensus 21 Fi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~ 64 (243)
++.+|.- .||..+|-++|+++++ .-++++|+.+.|...|||+
T Consensus 345 ~l~~L~~-~DG~~slldIA~~~~~-~~~~~~~~~~~l~~~~Llk 386 (386)
T PF09940_consen 345 MLWVLNY-SDGKNSLLDIAERIGL-PFDELADAARKLLEAGLLK 386 (386)
T ss_dssp HHHHHHH--EEEEEHHHHHHHHT---HHHHHHHHHHHHHTT-EE
T ss_pred HHHHHHh-ccCCCcHHHHHHHHCc-CHHHHHHHHHHHHHcCCCC
Confidence 4455544 5999999999999999 9999999999999999985
No 134
>PF02295 z-alpha: Adenosine deaminase z-alpha domain; InterPro: IPR000607 Double-stranded RNA-specific adenosine deaminase (3.5 from EC) converts multiple adenosines to inosines and creates I/U mismatched base pairs in double-helical RNA substrates without apparent sequence specificity. DRADA has been found to modify adenosines in AU-rich regions more frequently, probably due to the relative ease of melting A/U base pairs compared to G/C base pairs. The protein functions to modify viral RNA genomes, and may be responsible for hypermutation of certain negative-stranded viruses. DRADA edits the mRNAs for the glutamate receptor subunits by site-selective adenosine deamination. The DRADA repeat is also found in viral E3 proteins, which contain a double-stranded RNA-binding domain.; GO: 0003723 RNA binding, 0003726 double-stranded RNA adenosine deaminase activity; PDB: 1OYI_A 3EYI_A 2L4M_A 2HEO_D 1J75_A 1SFU_B 3IRR_B 2ACJ_C 3F22_B 2L54_A ....
Probab=39.43 E-value=1.1e+02 Score=22.28 Aligned_cols=57 Identities=21% Similarity=0.278 Sum_probs=45.6
Q ss_pred HHHHHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceeccccCceEEe
Q psy7686 17 LTTKFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNNKNIIRWK 74 (243)
Q Consensus 17 Lt~kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~sKn~i~W~ 74 (243)
+-.+.+.+|....+....--..|..|.+ .|+.|==+..=|+.=|.|.|.+-+--.|.
T Consensus 5 ~ee~Il~~L~~~g~~~a~~ia~~~~L~~-~kk~VN~~LY~L~k~g~v~k~~~~PP~W~ 61 (66)
T PF02295_consen 5 LEEKILDFLKELGGSTATAIAKALGLSV-PKKEVNRVLYRLEKQGKVCKEGGTPPKWS 61 (66)
T ss_dssp HHHHHHHHHHHHTSSEEEHHHHHHHHTS--HHHHHHHHHHHHHTTSEEEECSSSTEEE
T ss_pred HHHHHHHHHHhcCCccHHHHHHHhCcch-hHHHHHHHHHHHHHCCCEeeCCCCCCceE
Confidence 4466778887766666777777888888 89999999999999999999988888885
No 135
>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This entry consists of proteins thought to be involved in plasmid replication. ; GO: 0006260 DNA replication, 0006276 plasmid maintenance
Probab=39.43 E-value=52 Score=28.11 Aligned_cols=39 Identities=26% Similarity=0.235 Sum_probs=34.9
Q ss_pred eeeHHHHHhhhcccchhhhhhHHHhhhhccceeccccCce
Q psy7686 32 VLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNNKNII 71 (243)
Q Consensus 32 ~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~sKn~i 71 (243)
+.+..++|+.+++ .++-++-.+..|+--|+|.|...+.|
T Consensus 75 ~~t~~~ia~~l~i-S~~Tv~r~ik~L~e~~iI~k~~~G~Y 113 (165)
T PF05732_consen 75 VATQKEIAEKLGI-SKPTVSRAIKELEEKNIIKKIRNGAY 113 (165)
T ss_pred EeeHHHHHHHhCC-CHHHHHHHHHHHHhCCcEEEccCCeE
Confidence 5788999999999 99999999999999999999865544
No 136
>PF03979 Sigma70_r1_1: Sigma-70 factor, region 1.1; InterPro: IPR007127 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. This entry represents Region 1.1 which modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase [, ]. Region 1.1 is also involved in promoter binding.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2K6X_A.
Probab=39.40 E-value=17 Score=27.25 Aligned_cols=29 Identities=21% Similarity=0.478 Sum_probs=16.7
Q ss_pred HHHHHhhhhhhhccCccccchhhhhhcCCCC
Q psy7686 116 QQSLRNIQEEEVNRKQCYIPTDVILGMFPDS 146 (243)
Q Consensus 116 ~~~l~~l~ed~~n~~~aYVT~~Di~~~f~~q 146 (243)
...++.|..-.. +-.||||++|...|+..
T Consensus 6 ~~~i~~Li~~gK--~~G~lT~~eI~~~L~~~ 34 (82)
T PF03979_consen 6 EEAIKKLIEKGK--KKGYLTYDEINDALPED 34 (82)
T ss_dssp HHHHHHHHHHHH--HHSS-BHHHHHHH-S-S
T ss_pred HHHHHHHHHHHh--hcCcCCHHHHHHHcCcc
Confidence 345555655433 34789999999877644
No 137
>PF14817 HAUS5: HAUS augmin-like complex subunit 5
Probab=39.15 E-value=71 Score=33.15 Aligned_cols=52 Identities=15% Similarity=0.328 Sum_probs=31.3
Q ss_pred cCceEEeccCCCC--chhhhHHHHHhHhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy7686 68 KNIIRWKALKNKN--EEEYDLEQSKLIELRDEISDMRNHEAVIDEHIRKCQQSL 119 (243)
Q Consensus 68 Kn~i~W~G~~~~~--~~~~~~~~~~~~~Lk~El~~L~~~E~~LD~~I~~~~~~l 119 (243)
+.++.|.|..... .........+..+|++|++.|+.+-..||..|+....++
T Consensus 56 RgNl~~~~~~~~~~~~~~~e~~~~~r~~L~~everLraei~~l~~~I~~~e~e~ 109 (632)
T PF14817_consen 56 RGNLLWYGHQQSKERKKSRENEARRRRELEKEVERLRAEIQELDKEIESREREV 109 (632)
T ss_pred HcceeeccccccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5668899876652 111111223455677777777777777777776655443
No 138
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=39.10 E-value=55 Score=24.87 Aligned_cols=40 Identities=8% Similarity=0.143 Sum_probs=32.9
Q ss_pred HHHHHHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHh
Q psy7686 16 LLTTKFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNV 56 (243)
Q Consensus 16 ~Lt~kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNV 56 (243)
.+..+++.++.+.....+++.++|+.+++ .+|.+.=+.+=
T Consensus 5 ~~~~~~~~~i~~~~~~~~~~~~lA~~~~~-S~~~l~r~f~~ 44 (107)
T PRK10219 5 KIIQTLIAWIDEHIDQPLNIDVVAKKSGY-SKWYLQRMFRT 44 (107)
T ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHHCC-CHHHHHHHHHH
Confidence 35677888888888888999999999999 88887766543
No 139
>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=38.76 E-value=43 Score=20.93 Aligned_cols=23 Identities=30% Similarity=0.174 Sum_probs=19.5
Q ss_pred eeHHHHHhhhcccchhhhhhHHHh
Q psy7686 33 LHLKYAAENLEVKQKRRIYDITNV 56 (243)
Q Consensus 33 idL~~aa~~L~v~~KRRiYDItNV 56 (243)
+++.++|+.|+| .++-||....-
T Consensus 1 ~s~~e~a~~lgv-s~~tl~~~~~~ 23 (49)
T cd04762 1 LTTKEAAELLGV-SPSTLRRWVKE 23 (49)
T ss_pred CCHHHHHHHHCc-CHHHHHHHHHc
Confidence 367899999999 99999988763
No 140
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=38.70 E-value=33 Score=27.73 Aligned_cols=37 Identities=14% Similarity=0.091 Sum_probs=34.1
Q ss_pred CCeeeHHHHHhhhcccchhhhhhHHHhhhhccceeccc
Q psy7686 30 EGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNN 67 (243)
Q Consensus 30 ~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~s 67 (243)
.+.+...++|+.+++ .+=-+--+++-||.-|+|+|..
T Consensus 52 ~~~~t~~eLa~~l~i-~~~tvsr~l~~Le~~GlI~R~~ 88 (144)
T PRK11512 52 AACITPVELKKVLSV-DLGALTRMLDRLVCKGWVERLP 88 (144)
T ss_pred cCCCCHHHHHHHHCC-CHHHHHHHHHHHHHCCCEEecc
Confidence 455899999999999 9999999999999999999973
No 141
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=38.54 E-value=53 Score=24.14 Aligned_cols=42 Identities=19% Similarity=0.162 Sum_probs=32.3
Q ss_pred CCeeeHHHHHhhhcccchhhhhhHHHhhhhccceeccccCceEE
Q psy7686 30 EGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNNKNIIRW 73 (243)
Q Consensus 30 ~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~sKn~i~W 73 (243)
.+......++...++ .-+++..++|-|+.-|||++ .++.|.-
T Consensus 17 ~~~~~~t~i~~~~~L-~~~~~~~yL~~L~~~gLI~~-~~~~Y~l 58 (77)
T PF14947_consen 17 KGGAKKTEIMYKANL-NYSTLKKYLKELEEKGLIKK-KDGKYRL 58 (77)
T ss_dssp TT-B-HHHHHTTST---HHHHHHHHHHHHHTTSEEE-ETTEEEE
T ss_pred cCCCCHHHHHHHhCc-CHHHHHHHHHHHHHCcCeeC-CCCEEEE
Confidence 667788999999999 99999999999999999966 4555553
No 142
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=38.30 E-value=59 Score=27.45 Aligned_cols=44 Identities=25% Similarity=0.327 Sum_probs=38.8
Q ss_pred CCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceeccccCceEE
Q psy7686 29 PEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNNKNIIRW 73 (243)
Q Consensus 29 ~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~sKn~i~W 73 (243)
.+|.+...++|..|+| ..--+-..+|=|+..|+|++.....|+-
T Consensus 21 ~~~~~~~~diA~~L~V-sp~sVt~ml~rL~~~GlV~~~~y~gi~L 64 (154)
T COG1321 21 EKGFARTKDIAERLKV-SPPSVTEMLKRLERLGLVEYEPYGGVTL 64 (154)
T ss_pred ccCcccHHHHHHHhCC-CcHHHHHHHHHHHHCCCeEEecCCCeEE
Confidence 6899999999999999 9999999999999999999975554444
No 143
>PF04111 APG6: Autophagy protein Apg6; InterPro: IPR007243 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway [].; GO: 0006914 autophagy; PDB: 3Q8T_A 3VP7_A 4DDP_A.
Probab=38.20 E-value=96 Score=29.12 Aligned_cols=38 Identities=18% Similarity=0.426 Sum_probs=27.4
Q ss_pred HHHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q psy7686 88 QSKLIELRDEISDMRNHEAVIDEHIRKCQQSLRNIQEE 125 (243)
Q Consensus 88 ~~~~~~Lk~El~~L~~~E~~LD~~I~~~~~~l~~l~ed 125 (243)
..+...|.+|+..|++++..|++.|..++.+...+.+.
T Consensus 56 e~Ee~~l~~eL~~LE~e~~~l~~el~~le~e~~~l~~e 93 (314)
T PF04111_consen 56 EQEEEELLQELEELEKEREELDQELEELEEELEELDEE 93 (314)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34445666777788888888888888887777777554
No 144
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=37.69 E-value=1.6e+02 Score=28.58 Aligned_cols=71 Identities=20% Similarity=0.148 Sum_probs=36.5
Q ss_pred HHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhc---cCccccchhhhhhcCCCCeEEEEECCCCCeEEecC
Q psy7686 89 SKLIELRDEISDMRNHEAVIDEHIRKCQQSLRNIQEEEVN---RKQCYIPTDVILGMFPDSSLMCLKAPYGTKLHVPS 163 (243)
Q Consensus 89 ~~~~~Lk~El~~L~~~E~~LD~~I~~~~~~l~~l~ed~~n---~~~aYVT~~Di~~~f~~qtviaIkAP~~T~leVp~ 163 (243)
.+..+++.++..|+.+.+.|...++.++++++.+.+.-.. ..+.+-|.. ..+.+. -..||+..|...-|..
T Consensus 22 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~-~~~v~~~~~~~~~~~~ 95 (398)
T PTZ00454 22 EKLKELEKELEFLDIQEEYIKEEQKNLKRELIRAKEEVKRIQSVPLVIGQFL---EMIDSN-YGIVSSTSGSNYYVRI 95 (398)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCceEEEEE---EEEcCC-EEEEEcCCCCEEEEec
Confidence 3444555556666666666655555555555554443211 122232222 233333 3458888888777653
No 145
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=37.59 E-value=58 Score=25.41 Aligned_cols=49 Identities=29% Similarity=0.415 Sum_probs=38.3
Q ss_pred HHHHHHhhCCCCeeeHHHHHhhhccc----chhhhhhHHHhhhhccceeccccC
Q psy7686 20 KFVSLLQQAPEGVLHLKYAAENLEVK----QKRRIYDITNVLEGIGLIEKNNKN 69 (243)
Q Consensus 20 kFi~ll~~~~~g~idL~~aa~~L~v~----~KRRiYDItNVLEgiglI~K~sKn 69 (243)
..++++.+++. .++.+++.+.|.-+ .+=-||-.++.|+..|+|.|...+
T Consensus 12 ~Il~~l~~~~~-~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~~~~~ 64 (120)
T PF01475_consen 12 AILELLKESPE-HLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRKIEFG 64 (120)
T ss_dssp HHHHHHHHHSS-SEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEET
T ss_pred HHHHHHHcCCC-CCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEEEEcC
Confidence 36788887766 89999999988631 334599999999999999997433
No 146
>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=37.26 E-value=49 Score=21.57 Aligned_cols=36 Identities=19% Similarity=0.329 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHHhhCCCCeeeHHHHHhhhcccchhhhhh
Q psy7686 14 LGLLTTKFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYD 52 (243)
Q Consensus 14 L~~Lt~kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYD 52 (243)
|..+=+.+|.-.....+| ++..||..||+ .++-||-
T Consensus 2 l~~~E~~~i~~aL~~~~g--n~~~aA~~Lgi-sr~tL~~ 37 (42)
T PF02954_consen 2 LEEFEKQLIRQALERCGG--NVSKAARLLGI-SRRTLYR 37 (42)
T ss_dssp HHHHHHHHHHHHHHHTTT---HHHHHHHHTS--HHHHHH
T ss_pred HHHHHHHHHHHHHHHhCC--CHHHHHHHHCC-CHHHHHH
Confidence 444555666544433343 46899999999 9988875
No 147
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=36.85 E-value=55 Score=30.12 Aligned_cols=56 Identities=20% Similarity=0.328 Sum_probs=45.4
Q ss_pred CcHHHHHHHHHH-HHhhCCCCeeeHHHHHhhhcccchhhhhhHHH-hhhhccceecccc
Q psy7686 12 KSLGLLTTKFVS-LLQQAPEGVLHLKYAAENLEVKQKRRIYDITN-VLEGIGLIEKNNK 68 (243)
Q Consensus 12 ~SL~~Lt~kFi~-ll~~~~~g~idL~~aa~~L~v~~KRRiYDItN-VLEgiglI~K~sK 68 (243)
..|...-++++. ++..-.++.+.+..+|..||. ....+-|++- .|-..|||++.++
T Consensus 255 ~~l~~~~~~~l~~~~~~~~~~~~~~~~~a~~lg~-~~~~~~~~~e~~Li~~~li~~~~~ 312 (328)
T PRK00080 255 LGLDEMDRKYLRTIIEKFGGGPVGLDTLAAALGE-ERDTIEDVYEPYLIQQGFIQRTPR 312 (328)
T ss_pred CCCCHHHHHHHHHHHHHcCCCceeHHHHHHHHCC-CcchHHHHhhHHHHHcCCcccCCc
Confidence 345556777886 666667889999999999999 9888888888 8889999987643
No 148
>PF04977 DivIC: Septum formation initiator; InterPro: IPR007060 DivIC, from the spore-forming, Gram-positive bacterium Bacillus subtilis, is necessary for both vegetative and sporulation septum formation []. These proteins are mainly composed of an N-terminal coiled-coil. DivIB, DivIC and FtsL inter-depend on each other for stabilisation and localisation. The latter two form a heterodimer. DivIC is always centre cell but the other two associate with it during septation [].; GO: 0007049 cell cycle
Probab=36.18 E-value=60 Score=23.16 Aligned_cols=49 Identities=18% Similarity=0.319 Sum_probs=32.3
Q ss_pred HHHHHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhccCccccc
Q psy7686 86 LEQSKLIELRDEISDMRNHEAVIDEHIRKCQQSLRNIQEEEVNRKQCYIP 135 (243)
Q Consensus 86 ~~~~~~~~Lk~El~~L~~~E~~LD~~I~~~~~~l~~l~ed~~n~~~aYVT 135 (243)
....++..|+.+++.|.++-+.|.+.|+.++..-..+ +.-.-.+|.|+.
T Consensus 21 ~~~~ei~~l~~~i~~l~~e~~~L~~ei~~l~~~~~~i-e~~AR~~lgm~~ 69 (80)
T PF04977_consen 21 QLNQEIAELQKEIEELKKENEELKEEIERLKNDPDYI-EKVAREKLGMVK 69 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHH-HHHHHHHcCCcC
Confidence 4556778888889999888888888888874333333 322223455543
No 149
>PRK10869 recombination and repair protein; Provisional
Probab=36.01 E-value=65 Score=32.48 Aligned_cols=66 Identities=9% Similarity=0.147 Sum_probs=34.9
Q ss_pred HHHhhhcccchhhhhhHHHhhhhccceeccccCceEEeccCCCCchhhhHHHHHhHhHHHHHHHHHHHHHHHHHHHHHHH
Q psy7686 37 YAAENLEVKQKRRIYDITNVLEGIGLIEKNNKNIIRWKALKNKNEEEYDLEQSKLIELRDEISDMRNHEAVIDEHIRKCQ 116 (243)
Q Consensus 37 ~aa~~L~v~~KRRiYDItNVLEgiglI~K~sKn~i~W~G~~~~~~~~~~~~~~~~~~Lk~El~~L~~~E~~LD~~I~~~~ 116 (243)
...+.+.+ .-.|+-.|-+=|.-|.=+.|+ .|.+. +++....+++++|++.|...+..+.++.+.+.
T Consensus 286 ~~~~~~~~-dp~~l~~ie~Rl~~l~~L~rK-------yg~~~------~~~~~~~~~l~~eL~~L~~~e~~l~~Le~e~~ 351 (553)
T PRK10869 286 HYLDRLDL-DPNRLAELEQRLSKQISLARK-------HHVSP------EELPQHHQQLLEEQQQLDDQEDDLETLALAVE 351 (553)
T ss_pred HHHhhcCC-CHHHHHHHHHHHHHHHHHHHH-------hCCCH------HHHHHHHHHHHHHHHHhhCCHHHHHHHHHHHH
Confidence 33333344 444455555555555444444 24221 15666677788888877766555444444433
No 150
>PF01638 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002577 The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure. The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde []. The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH []. The crystal structure of ytfH resembles the DNA-binding domains of winged helix proteins, containing a three helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-H2-B1-H3-H4-B2-B3-H5-H6. This topology corresponds with that of the marR-type DNA-binding domain, wherein helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. ; PDB: 2F2E_B 3DF8_A 1Z7U_B 1YYV_A 4A5M_D 4A5N_B 2FSW_A 2HZT_D.
Probab=35.92 E-value=57 Score=24.46 Aligned_cols=38 Identities=18% Similarity=0.287 Sum_probs=33.7
Q ss_pred CCCeeeHHHHHhhh-cccchhhhhhHHHhhhhccceeccc
Q psy7686 29 PEGVLHLKYAAENL-EVKQKRRIYDITNVLEGIGLIEKNN 67 (243)
Q Consensus 29 ~~g~idL~~aa~~L-~v~~KRRiYDItNVLEgiglI~K~s 67 (243)
..|....++....+ ++ ..+=+.+=...|+..|||+|..
T Consensus 15 ~~g~~rf~el~~~l~~i-s~~~L~~~L~~L~~~GLv~r~~ 53 (90)
T PF01638_consen 15 FQGPMRFSELQRRLPGI-SPKVLSQRLKELEEAGLVERRV 53 (90)
T ss_dssp TTSSEEHHHHHHHSTTS--HHHHHHHHHHHHHTTSEEEEE
T ss_pred HhCCCcHHHHHHhcchh-HHHHHHHHHHHHHHcchhhccc
Confidence 34889999999999 89 9999999999999999999973
No 151
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=35.92 E-value=34 Score=27.35 Aligned_cols=40 Identities=33% Similarity=0.369 Sum_probs=23.9
Q ss_pred HHHHHHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHh
Q psy7686 16 LLTTKFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNV 56 (243)
Q Consensus 16 ~Lt~kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNV 56 (243)
+||.|=-+.+.--=..-++|.++|+.+|| .|--+||.+.-
T Consensus 17 LLT~kQ~~~l~lyy~eDlSlsEIAe~~~i-SRqaV~d~ikr 56 (101)
T PF04297_consen 17 LLTEKQREILELYYEEDLSLSEIAEELGI-SRQAVYDSIKR 56 (101)
T ss_dssp GS-HHHHHHHHHHCTS---HHHHHHHCTS--HHHHHHHHHH
T ss_pred HCCHHHHHHHHHHHccCCCHHHHHHHHCC-CHHHHHHHHHH
Confidence 35644333333223455999999999999 99999998753
No 152
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=35.70 E-value=43 Score=29.42 Aligned_cols=54 Identities=19% Similarity=0.284 Sum_probs=43.0
Q ss_pred CcHHH-HHHHHHHHHhh---CCCCee-eHHHHHhhhcccchhhhhhHHHhhhhccceecc
Q psy7686 12 KSLGL-LTTKFVSLLQQ---APEGVL-HLKYAAENLEVKQKRRIYDITNVLEGIGLIEKN 66 (243)
Q Consensus 12 ~SL~~-Lt~kFi~ll~~---~~~g~i-dL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~ 66 (243)
.++.. +...+.+.+.. .|+..+ .-.++|+.||| .|=-+-+....|++.|||+..
T Consensus 9 ~~~~~~v~~~l~~~I~~g~l~pG~~LpsE~eLa~~lgV-SRtpVREAL~~L~~eGlv~~~ 67 (254)
T PRK09464 9 PKLSDVIEQQLEFLILEGTLRPGEKLPPERELAKQFDV-SRPSLREAIQRLEAKGLLLRR 67 (254)
T ss_pred ccHHHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHhCC-CHHHHHHHHHHHHHCCCEEEe
Confidence 45543 44556666543 467778 89999999999 999999999999999999865
No 153
>COG4519 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.34 E-value=68 Score=25.13 Aligned_cols=42 Identities=14% Similarity=0.292 Sum_probs=33.9
Q ss_pred HHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhcccee
Q psy7686 21 FVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIE 64 (243)
Q Consensus 21 Fi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~ 64 (243)
++.+|-+ .....+.-++-..-|. .||-+-|++-.|+|||+.-
T Consensus 12 Yla~Li~-S~e~~nVP~lm~~TGw-PRRT~QDvikAlpglgi~l 53 (95)
T COG4519 12 YLAYLID-SGETANVPELMAATGW-PRRTAQDVIKALPGLGIVL 53 (95)
T ss_pred HHHHHHh-ccccCChHHHHHHcCC-chhHHHHHHHhCcCCCeEE
Confidence 4455544 3567788888889999 9999999999999999863
No 154
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=34.93 E-value=3e+02 Score=23.75 Aligned_cols=52 Identities=19% Similarity=0.240 Sum_probs=39.1
Q ss_pred HHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhcccee--cc-----ccCceEEe
Q psy7686 20 KFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIE--KN-----NKNIIRWK 74 (243)
Q Consensus 20 kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~--K~-----sKn~i~W~ 74 (243)
+++..|. ..|.+.-.++|..||+ ...-+=-+.+-|+.-|||. +. +...|-|.
T Consensus 26 ~Vl~~L~--~~g~~tdeeLA~~Lgi-~~~~VRk~L~~L~e~gLv~~~r~r~~~~Gr~~y~w~ 84 (178)
T PRK06266 26 EVLKALI--KKGEVTDEEIAEQTGI-KLNTVRKILYKLYDARLADYKREKDEETNWYTYTWK 84 (178)
T ss_pred HHHHHHH--HcCCcCHHHHHHHHCC-CHHHHHHHHHHHHHCCCeEEeeeeccCCCcEEEEEE
Confidence 3444444 3567999999999999 8888888899999999999 32 23456675
No 155
>PF10779 XhlA: Haemolysin XhlA; InterPro: IPR019715 Haemolysin XhlA is a cell-surface associated haemolysin that lyses the two most prevalent types of insect immune cells (granulocytes and plasmatocytes) as well as rabbit and horse erythrocytes [].
Probab=34.92 E-value=1.6e+02 Score=21.39 Aligned_cols=40 Identities=8% Similarity=0.216 Sum_probs=32.7
Q ss_pred HHHHHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q psy7686 86 LEQSKLIELRDEISDMRNHEAVIDEHIRKCQQSLRNIQEE 125 (243)
Q Consensus 86 ~~~~~~~~Lk~El~~L~~~E~~LD~~I~~~~~~l~~l~ed 125 (243)
++.+++..++..+.+++.....|++.......+++++.++
T Consensus 3 ~i~e~l~~ie~~l~~~~~~i~~lE~~~~~~e~~i~~~~~~ 42 (71)
T PF10779_consen 3 DIKEKLNRIETKLDNHEERIDKLEKRDAANEKDIKNLNKQ 42 (71)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566778888888888888888888888888888888776
No 156
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=34.72 E-value=88 Score=28.74 Aligned_cols=60 Identities=23% Similarity=0.256 Sum_probs=48.5
Q ss_pred CcHHHHHHHHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceeccccCceEE
Q psy7686 12 KSLGLLTTKFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNNKNIIRW 73 (243)
Q Consensus 12 ~SL~~Lt~kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~sKn~i~W 73 (243)
..|-.-=+.-++++.. .+|.+.-+++...||. .|=-++=|.-=||-.|+|+|..++.=.|
T Consensus 191 ~~L~~~e~~il~~i~~-~GGri~Q~eL~r~lgl-sktTvsR~L~~LEk~GlIe~~K~G~~n~ 250 (258)
T COG2512 191 YDLNEDEKEILDLIRE-RGGRITQAELRRALGL-SKTTVSRILRRLEKRGLIEKEKKGRTNI 250 (258)
T ss_pred CCCCHHHHHHHHHHHH-hCCEEeHHHHHHhhCC-ChHHHHHHHHHHHhCCceEEEEeCCeeE
Confidence 3444445667788876 5899999999999999 9988888888899999999987665444
No 157
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=34.65 E-value=97 Score=23.75 Aligned_cols=45 Identities=27% Similarity=0.276 Sum_probs=36.3
Q ss_pred HHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceecc
Q psy7686 20 KFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKN 66 (243)
Q Consensus 20 kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~ 66 (243)
-.|+++.+ .+..|-=..+|+.|++ .-=-|..+.-.||.+|||+++
T Consensus 12 alV~~Y~~-~~~PVgSk~ia~~l~~-s~aTIRN~M~~Le~lGlve~~ 56 (78)
T PF03444_consen 12 ALVELYIE-TGEPVGSKTIAEELGR-SPATIRNEMADLEELGLVESQ 56 (78)
T ss_pred HHHHHHHh-cCCCcCHHHHHHHHCC-ChHHHHHHHHHHHHCCCccCC
Confidence 34555554 3677888889999999 888888999999999999975
No 158
>KOG3990|consensus
Probab=34.34 E-value=61 Score=30.33 Aligned_cols=43 Identities=19% Similarity=0.324 Sum_probs=37.2
Q ss_pred HHHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhccC
Q psy7686 88 QSKLIELRDEISDMRNHEAVIDEHIRKCQQSLRNIQEEEVNRK 130 (243)
Q Consensus 88 ~~~~~~Lk~El~~L~~~E~~LD~~I~~~~~~l~~l~ed~~n~~ 130 (243)
.-.++.|++||..|+..-..-|++|-.-..+|-+|.-|.++++
T Consensus 224 ~V~i~~lkeeia~Lkk~L~qkdq~ileKdkqisnLKad~e~~~ 266 (305)
T KOG3990|consen 224 MVKIQKLKEEIARLKKLLHQKDQLILEKDKQISNLKADKEYQK 266 (305)
T ss_pred HHHHHHHHHHHHHHHHHHhhhHHHHHhhhhhhhccCcchhHHH
Confidence 3467899999999999999999999999999999999865553
No 159
>PF12728 HTH_17: Helix-turn-helix domain
Probab=34.08 E-value=35 Score=22.62 Aligned_cols=22 Identities=32% Similarity=0.436 Sum_probs=19.9
Q ss_pred eeHHHHHhhhcccchhhhhhHHH
Q psy7686 33 LHLKYAAENLEVKQKRRIYDITN 55 (243)
Q Consensus 33 idL~~aa~~L~v~~KRRiYDItN 55 (243)
++..+||+.|+| .+..||.+++
T Consensus 2 lt~~e~a~~l~i-s~~tv~~~~~ 23 (51)
T PF12728_consen 2 LTVKEAAELLGI-SRSTVYRWIR 23 (51)
T ss_pred CCHHHHHHHHCc-CHHHHHHHHH
Confidence 578999999999 9999999885
No 160
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=33.93 E-value=1e+02 Score=22.39 Aligned_cols=52 Identities=17% Similarity=0.327 Sum_probs=36.1
Q ss_pred HHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceecc--ccCc-eEEe
Q psy7686 21 FVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKN--NKNI-IRWK 74 (243)
Q Consensus 21 Fi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~--sKn~-i~W~ 74 (243)
.+++++.. ++.+.-.++|+.+++ .+-..-=+.+.||.=|.|++. ++.. ..|.
T Consensus 5 Il~~i~~~-~~p~~T~eiA~~~gl-s~~~aR~yL~~Le~eG~V~~~~~~rG~~~~W~ 59 (62)
T PF04703_consen 5 ILEYIKEQ-NGPLKTREIADALGL-SIYQARYYLEKLEKEGKVERSPVRRGKSTYWR 59 (62)
T ss_dssp HHHHHHHH-TS-EEHHHHHHHHTS--HHHHHHHHHHHHHCTSEEEES-SSSSS-EEE
T ss_pred HHHHHHHc-CCCCCHHHHHHHhCC-CHHHHHHHHHHHHHCCCEEEecCCCCcceeee
Confidence 34455543 566899999999999 777777789999999999973 2222 3585
No 161
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=33.80 E-value=76 Score=26.09 Aligned_cols=51 Identities=14% Similarity=0.132 Sum_probs=43.6
Q ss_pred cHHHHHHHHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceecc
Q psy7686 13 SLGLLTTKFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKN 66 (243)
Q Consensus 13 SL~~Lt~kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~ 66 (243)
+|-.+=++.+.+|+. ++.....++|+.||+ ..-.+..=++=|+.-|+|++.
T Consensus 6 ~lD~~D~~Il~~Lq~--d~R~s~~eiA~~lgl-S~~tV~~Ri~rL~~~GvI~~~ 56 (153)
T PRK11179 6 QIDNLDRGILEALME--NARTPYAELAKQFGV-SPGTIHVRVEKMKQAGIITGT 56 (153)
T ss_pred ccCHHHHHHHHHHHH--cCCCCHHHHHHHHCc-CHHHHHHHHHHHHHCCCeeeE
Confidence 355567889999987 688999999999999 888888888999999999864
No 162
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=33.43 E-value=3.7e+02 Score=24.42 Aligned_cols=43 Identities=23% Similarity=0.425 Sum_probs=27.9
Q ss_pred HHHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceec
Q psy7686 19 TKFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEK 65 (243)
Q Consensus 19 ~kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K 65 (243)
++.+.+|.+.|. =..+.+..||| ....|-+=.-.||--|||+-
T Consensus 18 R~Il~lLt~~p~---yvsEiS~~lgv-sqkAVl~HL~~LE~AGlveS 60 (217)
T COG1777 18 RRILQLLTRRPC---YVSEISRELGV-SQKAVLKHLRILERAGLVES 60 (217)
T ss_pred HHHHHHHhcCch---HHHHHHhhcCc-CHHHHHHHHHHHHHcCCchh
Confidence 456777776663 34567777888 66666666666666666653
No 163
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=33.35 E-value=1.2e+02 Score=26.27 Aligned_cols=39 Identities=18% Similarity=0.201 Sum_probs=33.6
Q ss_pred eeHHHHHhhhcccchhhhhhHHHhhhhccceeccccCceE
Q psy7686 33 LHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNNKNIIR 72 (243)
Q Consensus 33 idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~sKn~i~ 72 (243)
++-.++|..||+ .+..+.=+.+-|+--|+|++.+.++|.
T Consensus 180 lt~~~IA~~lGi-sretlsR~L~~L~~~GlI~~~~~~~i~ 218 (230)
T PRK09391 180 MSRRDIADYLGL-TIETVSRALSQLQDRGLIGLSGARQIE 218 (230)
T ss_pred CCHHHHHHHHCC-CHHHHHHHHHHHHHCCcEEecCCceEE
Confidence 445899999999 999999999999999999877555554
No 164
>PF10046 BLOC1_2: Biogenesis of lysosome-related organelles complex-1 subunit 2 ; InterPro: IPR019269 This entry represents a family of proteins that play a role in cellular proliferation, as well as in the biogenesis of specialised organelles of the endosomal-lysosomal system [].
Probab=32.96 E-value=1.2e+02 Score=23.52 Aligned_cols=34 Identities=6% Similarity=0.342 Sum_probs=26.1
Q ss_pred HHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy7686 89 SKLIELRDEISDMRNHEAVIDEHIRKCQQSLRNI 122 (243)
Q Consensus 89 ~~~~~Lk~El~~L~~~E~~LD~~I~~~~~~l~~l 122 (243)
.++..+..++..|++.=..||+..+.+...+++|
T Consensus 66 ~~Id~Ie~~V~~LE~~v~~LD~ysk~LE~k~k~l 99 (99)
T PF10046_consen 66 QQIDQIEEQVTELEQTVYELDEYSKELESKFKKL 99 (99)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcC
Confidence 4455666688888888888999888888877754
No 165
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=32.66 E-value=1.3e+02 Score=27.06 Aligned_cols=41 Identities=12% Similarity=0.142 Sum_probs=28.7
Q ss_pred HHHHHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhh
Q psy7686 86 LEQSKLIELRDEISDMRNHEAVIDEHIRKCQQSLRNIQEEEV 127 (243)
Q Consensus 86 ~~~~~~~~Lk~El~~L~~~E~~LD~~I~~~~~~l~~l~ed~~ 127 (243)
...++.++|++|+..|+.+...++++...- ++|+.+..-..
T Consensus 73 ~l~~en~~L~~e~~~l~~~~~~~~~l~~en-~~L~~lL~~~~ 113 (276)
T PRK13922 73 DLREENEELKKELLELESRLQELEQLEAEN-ARLRELLNLKE 113 (276)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHhcCcc
Confidence 455667788888888888888777666544 46777766443
No 166
>PF03836 RasGAP_C: RasGAP C-terminus; InterPro: IPR000593 Ras GTPase-activating protein (rasGAP) is a major contributor to the down-regulation of ras by facilitating GTP hydrolysis of activated ras. In addition, GAP participates in the down-stream effector system of the ras signalling pathway. Abnormal signal transduction involving activated ras genes plays a major role in the development of a variety of tumours. Depending on the precise genetic alteration, its location within the gene and the effects it exerts on protein function, rasGAP can theoretically function as either an oncogene or as a tumour suppressor gene [].; GO: 0005099 Ras GTPase activator activity, 0007264 small GTPase mediated signal transduction, 0005622 intracellular; PDB: 3ISU_A 3IEZ_A 4EZA_B 1X0H_A.
Probab=32.45 E-value=15 Score=30.37 Aligned_cols=26 Identities=23% Similarity=0.414 Sum_probs=0.0
Q ss_pred chhhhhhHHHhhhhccceeccccCceEE
Q psy7686 46 QKRRIYDITNVLEGIGLIEKNNKNIIRW 73 (243)
Q Consensus 46 ~KRRiYDItNVLEgiglI~K~sKn~i~W 73 (243)
-|+++-+-+..||..|+|.+. |.|+=
T Consensus 5 lk~~~l~~l~~LE~~G~v~~~--n~yQ~ 30 (142)
T PF03836_consen 5 LKKKILENLKELESLGIVSRS--NNYQD 30 (142)
T ss_dssp ----------------------------
T ss_pred HHHHHHHHHHHHHHCCCCCCc--ccHHH
Confidence 577888889999999999987 66664
No 167
>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional
Probab=32.28 E-value=97 Score=31.17 Aligned_cols=37 Identities=19% Similarity=0.247 Sum_probs=19.2
Q ss_pred HHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q psy7686 89 SKLIELRDEISDMRNHEAVIDEHIRKCQQSLRNIQEE 125 (243)
Q Consensus 89 ~~~~~Lk~El~~L~~~E~~LD~~I~~~~~~l~~l~ed 125 (243)
.++..|+.|++.+.++.+.+++.|+.++..++.|..-
T Consensus 83 KqLaaLrqElq~~saq~~dle~KIkeLEaE~~~Lk~Q 119 (475)
T PRK13729 83 KQYEEIRRELDVLNKQRGDDQRRIEKLGQDNAALAEQ 119 (475)
T ss_pred HHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHH
Confidence 3333444444433344455666666666666666553
No 168
>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=32.22 E-value=54 Score=28.90 Aligned_cols=43 Identities=23% Similarity=0.337 Sum_probs=36.0
Q ss_pred HHHHHHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhh
Q psy7686 16 LLTTKFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEG 59 (243)
Q Consensus 16 ~Lt~kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEg 59 (243)
.+..+++.++.+.....+++..+|+.+++ .++.+..+..-..|
T Consensus 186 ~~~~~~~~~I~~~~~~~~sl~~lA~~~~~-S~~~l~r~Fk~~~G 228 (287)
T TIGR02297 186 YLFNRFNFLIEENYKQHLRLPEYADRLGI-SESRLNDICRRFSA 228 (287)
T ss_pred HHHHHHHHHHHHhhccCCCHHHHHHHHCC-CHHHHHHHHHHHhC
Confidence 35678999998888889999999999999 99999887654443
No 169
>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=31.73 E-value=2.5e+02 Score=23.62 Aligned_cols=35 Identities=14% Similarity=0.157 Sum_probs=32.2
Q ss_pred CCeeeHHHHHhhhcccchhhhhhHHHhhhhccceec
Q psy7686 30 EGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEK 65 (243)
Q Consensus 30 ~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K 65 (243)
.+.+.-.++|..||+ +++-+=-+.+.|...|||..
T Consensus 26 ~~~~tdEeLa~~Lgi-~~~~VRk~L~~L~e~~Lv~~ 60 (158)
T TIGR00373 26 KGEFTDEEISLELGI-KLNEVRKALYALYDAGLADY 60 (158)
T ss_pred cCCCCHHHHHHHHCC-CHHHHHHHHHHHHHCCCcee
Confidence 667999999999999 99999999999999999953
No 170
>PRK03837 transcriptional regulator NanR; Provisional
Probab=31.65 E-value=55 Score=28.31 Aligned_cols=54 Identities=13% Similarity=0.252 Sum_probs=42.4
Q ss_pred cHHH-HHHHHHHHHhh---CCCCee-eHHHHHhhhcccchhhhhhHHHhhhhccceeccc
Q psy7686 13 SLGL-LTTKFVSLLQQ---APEGVL-HLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNN 67 (243)
Q Consensus 13 SL~~-Lt~kFi~ll~~---~~~g~i-dL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~s 67 (243)
++.. +...+.+.+.. .|+..+ ...++|+.||| .|--+=+....|+.-|||+...
T Consensus 13 ~~~~~v~~~l~~~I~~g~l~pG~~Lp~E~~Lae~~gV-SRt~VREAL~~L~~eGlv~~~~ 71 (241)
T PRK03837 13 KLSEEVEERLEQMIRSGEFGPGDQLPSERELMAFFGV-GRPAVREALQALKRKGLVQISH 71 (241)
T ss_pred cHHHHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHhCC-CHHHHHHHHHHHHHCCCEEEec
Confidence 4443 44555555543 467778 89999999999 9999999999999999999763
No 171
>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=31.47 E-value=49 Score=22.40 Aligned_cols=24 Identities=33% Similarity=0.492 Sum_probs=19.6
Q ss_pred CeeeHHHHHhhhcccchhhhhhHHH
Q psy7686 31 GVLHLKYAAENLEVKQKRRIYDITN 55 (243)
Q Consensus 31 g~idL~~aa~~L~v~~KRRiYDItN 55 (243)
..++++++++.+|+ .+.-||..++
T Consensus 2 rll~~~ev~~~~g~-s~~ti~~~~k 25 (51)
T PF05930_consen 2 RLLRIKEVAELLGV-SRSTIYRLIK 25 (51)
T ss_dssp -EE-HHHHHHHHSS--HHHHHHHHH
T ss_pred ccccHHHHHHHHCC-CHHHHHHHHh
Confidence 46899999999999 9999999887
No 172
>KOG3093|consensus
Probab=31.27 E-value=2.2e+02 Score=25.48 Aligned_cols=34 Identities=6% Similarity=0.073 Sum_probs=24.0
Q ss_pred CCCeEEecCCCCCCceEEEEEecCCCCC-CeEEEEecCCC
Q psy7686 155 YGTKLHVPSISTDENKIKLHVKSSHPEE-PVNILLLDTEP 193 (243)
Q Consensus 155 ~~T~leVp~p~~~~~~yqi~LkS~~~~G-pI~V~L~~~~~ 193 (243)
|=|.+.+|.|+. +..++..+. + | |||++++|-=.
T Consensus 104 ~~t~w~i~qp~~-~~~re~~~~--t--~~~lDLiivPGvA 138 (200)
T KOG3093|consen 104 PMTSWGIRQPKP-GGPREDALE--T--GHPLDLIIVPGVA 138 (200)
T ss_pred cccccCCCCCCC-CCchhhhcc--C--CCcceEEEecccc
Confidence 447788888876 466666543 3 4 89999998644
No 173
>PRK06474 hypothetical protein; Provisional
Probab=31.01 E-value=90 Score=26.74 Aligned_cols=47 Identities=19% Similarity=0.286 Sum_probs=38.7
Q ss_pred HHHHHHHhhCCCCeeeHHHHHhhh-cccchhhhhhHHHhhhhccceeccc
Q psy7686 19 TKFVSLLQQAPEGVLHLKYAAENL-EVKQKRRIYDITNVLEGIGLIEKNN 67 (243)
Q Consensus 19 ~kFi~ll~~~~~g~idL~~aa~~L-~v~~KRRiYDItNVLEgiglI~K~s 67 (243)
.+.+++|...+.+ ++..++++.| ++ .+=-+|=..++|+-.|||++..
T Consensus 14 ~~Il~~L~~~~~~-~ta~el~~~l~~i-s~aTvYrhL~~L~e~GLI~~~~ 61 (178)
T PRK06474 14 MKICQVLMRNKEG-LTPLELVKILKDV-PQATLYRHLQTMVDSGILHVVK 61 (178)
T ss_pred HHHHHHHHhCCCC-CCHHHHHHHhcCC-CHHHHHHHHHHHHHCCCEEEee
Confidence 3466777665443 8999999999 68 8999999999999999999753
No 174
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=30.72 E-value=57 Score=27.92 Aligned_cols=38 Identities=26% Similarity=0.384 Sum_probs=30.0
Q ss_pred CCeeeHHHHHhhhcccchhh-------------hhhHHHhhhhccceeccc
Q psy7686 30 EGVLHLKYAAENLEVKQKRR-------------IYDITNVLEGIGLIEKNN 67 (243)
Q Consensus 30 ~g~idL~~aa~~L~v~~KRR-------------iYDItNVLEgiglI~K~s 67 (243)
.|.+-+..++..+|.+++|. |=-+...||.+|||+|..
T Consensus 65 ~gpvGV~~L~~~yGg~k~~G~~P~h~~~~sg~iiR~~LqqLE~~glVek~~ 115 (150)
T PRK09333 65 DGPVGVERLRTAYGGRKNRGVRPEHFVKGSGSIIRKILQQLEKAGLVEKTK 115 (150)
T ss_pred cCCccHHHHHHHHCCCcCCCCCCCccccCccHHHHHHHHHHHHCCCeeeCC
Confidence 45677788888888844433 788999999999999863
No 175
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=30.45 E-value=2.6e+02 Score=24.32 Aligned_cols=48 Identities=21% Similarity=0.298 Sum_probs=39.6
Q ss_pred HHHHHHHhh---CCCCee-eHHHHHhhhcccchhhhhhHHHhhhhccceeccc
Q psy7686 19 TKFVSLLQQ---APEGVL-HLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNN 67 (243)
Q Consensus 19 ~kFi~ll~~---~~~g~i-dL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~s 67 (243)
....+.+.. .|+..+ .-.++|+.||| .|==+-+.+..|+.-|||+...
T Consensus 14 ~~i~~~I~~g~l~pG~~LPsE~eLa~~~gV-SRtpVREAL~~L~~eGlV~~~~ 65 (251)
T PRK09990 14 ERIERLIVDGVLKVGQALPSERRLCEKLGF-SRSALREGLTVLRGRGIIETAQ 65 (251)
T ss_pred HHHHHHHHcCCCCCCCcCcCHHHHHHHHCC-CHHHHHHHHHHHHHCCCEEEeC
Confidence 444444433 578889 89999999999 9999999999999999998763
No 176
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=30.43 E-value=1.3e+02 Score=23.72 Aligned_cols=18 Identities=6% Similarity=-0.009 Sum_probs=7.1
Q ss_pred hHhHHHHHHHHHHHHHHH
Q psy7686 91 LIELRDEISDMRNHEAVI 108 (243)
Q Consensus 91 ~~~Lk~El~~L~~~E~~L 108 (243)
.++|+++.+.|..+-+.|
T Consensus 43 ~~~l~~~n~~L~~eI~~L 60 (105)
T PRK00888 43 NAKLKARNDQLFAEIDDL 60 (105)
T ss_pred HHHHHHHHHHHHHHHHHh
Confidence 334444444443333333
No 177
>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=30.01 E-value=79 Score=25.11 Aligned_cols=43 Identities=26% Similarity=0.502 Sum_probs=34.3
Q ss_pred HHHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceeccc
Q psy7686 19 TKFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNN 67 (243)
Q Consensus 19 ~kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~s 67 (243)
..|..++.+.|+ +.+.++|..|+| ....|+ ..|.-+|+.-|+.
T Consensus 60 ~~L~~~v~~~pd--~tl~Ela~~l~V-s~~ti~---~~Lkrlg~t~KK~ 102 (119)
T PF01710_consen 60 DELKALVEENPD--ATLRELAERLGV-SPSTIW---RALKRLGITRKKK 102 (119)
T ss_pred HHHHHHHHHCCC--cCHHHHHHHcCC-CHHHHH---HHHHHcCchhccC
Confidence 457778888777 677899999999 777766 6788889988874
No 178
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=29.91 E-value=71 Score=22.06 Aligned_cols=42 Identities=26% Similarity=0.325 Sum_probs=24.9
Q ss_pred CCcCcHHHHHH-HHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHH
Q psy7686 9 RFEKSLGLLTT-KFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITN 55 (243)
Q Consensus 9 R~~~SL~~Lt~-kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItN 55 (243)
|+-++|.+--+ ..|..+. .|. ...++|..+|| .+.-|++|..
T Consensus 2 rkR~~LTl~eK~~iI~~~e---~g~-s~~~ia~~fgv-~~sTv~~I~K 44 (53)
T PF04218_consen 2 RKRKSLTLEEKLEIIKRLE---EGE-SKRDIAREFGV-SRSTVSTILK 44 (53)
T ss_dssp SSSSS--HHHHHHHHHHHH---CTT--HHHHHHHHT---CCHHHHHHH
T ss_pred CCCccCCHHHHHHHHHHHH---cCC-CHHHHHHHhCC-CHHHHHHHHH
Confidence 34445544432 2445544 444 89999999999 9999999975
No 179
>PF09904 HTH_43: Winged helix-turn helix; InterPro: IPR017162 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.; PDB: 3KE2_B.
Probab=29.87 E-value=2.7e+02 Score=21.96 Aligned_cols=30 Identities=20% Similarity=0.268 Sum_probs=22.8
Q ss_pred eHHHHHhhhcccchhhhhhHHHhhhhcccee
Q psy7686 34 HLKYAAENLEVKQKRRIYDITNVLEGIGLIE 64 (243)
Q Consensus 34 dL~~aa~~L~v~~KRRiYDItNVLEgiglI~ 64 (243)
++..+-+.-|. .||-+.|.++.|.++|+.-
T Consensus 23 nvp~L~~~TGm-PrRT~Qd~i~aL~~~~I~~ 52 (90)
T PF09904_consen 23 NVPALMEATGM-PRRTIQDTIKALPELGIEC 52 (90)
T ss_dssp -HHHHHHHH----HHHHHHHHHGGGGGT-EE
T ss_pred cHHHHHHHhCC-CHhHHHHHHHHhhcCCeEE
Confidence 88888889999 9999999999999999754
No 180
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=29.87 E-value=61 Score=27.12 Aligned_cols=37 Identities=16% Similarity=0.087 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHhhCCCCeeeHHHHHhhhcccchhhhhh
Q psy7686 15 GLLTTKFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYD 52 (243)
Q Consensus 15 ~~Lt~kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYD 52 (243)
..+...+++++.+..-.-+.++++|+..|| .|+-||-
T Consensus 14 ~~Il~aa~~lf~~~G~~~~ti~~Ia~~agv-sk~t~Y~ 50 (213)
T PRK09975 14 QELIETAIAQFALRGVSNTTLNDIADAANV-TRGAIYW 50 (213)
T ss_pred HHHHHHHHHHHHHcCcccCCHHHHHHHcCC-CHHHHHH
Confidence 456677889998876678999999999999 9999984
No 181
>PF13851 GAS: Growth-arrest specific micro-tubule binding
Probab=29.84 E-value=1.1e+02 Score=26.86 Aligned_cols=38 Identities=18% Similarity=0.340 Sum_probs=31.8
Q ss_pred HHHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q psy7686 88 QSKLIELRDEISDMRNHEAVIDEHIRKCQQSLRNIQEE 125 (243)
Q Consensus 88 ~~~~~~Lk~El~~L~~~E~~LD~~I~~~~~~l~~l~ed 125 (243)
-.-+..|++|+.++...+...+..+..+.+..+.|++-
T Consensus 26 L~lIksLKeei~emkk~e~~~~k~m~ei~~eN~~L~ep 63 (201)
T PF13851_consen 26 LELIKSLKEEIAEMKKKEERNEKLMAEISQENKRLSEP 63 (201)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHH
Confidence 34567899999999999999999999988888888774
No 182
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=29.77 E-value=1.6e+02 Score=27.44 Aligned_cols=67 Identities=12% Similarity=0.318 Sum_probs=41.6
Q ss_pred HHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhccCccccchhhhhhcCCCCeEEEEECCCCCeEEecC
Q psy7686 89 SKLIELRDEISDMRNHEAVIDEHIRKCQQSLRNIQEEEVNRKQCYIPTDVILGMFPDSSLMCLKAPYGTKLHVPS 163 (243)
Q Consensus 89 ~~~~~Lk~El~~L~~~E~~LD~~I~~~~~~l~~l~ed~~n~~~aYVT~~Di~~~f~~qtviaIkAP~~T~leVp~ 163 (243)
.+.++|++++..+..+...+.+.+..+++.|+.+...+. +...+...+.+. -.++|..+|++.-+..
T Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~-~~~~~~~~~~~~~~~~ 72 (364)
T TIGR01242 6 VRIRKLEDEKRSLEKEKIRLERELERLRSEIERLRSPPL-------IVGTVLEVLDDN-RVVVKSSTGPNFVVNV 72 (364)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCe-------EEEEEEEEecCC-EEEEEeCCCCEEEEec
Confidence 456677777777777777777778777777766655321 222233333333 3458888888876643
No 183
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=28.91 E-value=66 Score=27.88 Aligned_cols=38 Identities=16% Similarity=0.263 Sum_probs=34.8
Q ss_pred CCCCee-eHHHHHhhhcccchhhhhhHHHhhhhccceecc
Q psy7686 28 APEGVL-HLKYAAENLEVKQKRRIYDITNVLEGIGLIEKN 66 (243)
Q Consensus 28 ~~~g~i-dL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~ 66 (243)
.|+..+ .-.++|+.||| .|=-+-+-+..|+.-|||+..
T Consensus 26 ~pG~~LPsE~eLae~~gV-SRt~VReAL~~L~~eGlv~~~ 64 (239)
T PRK04984 26 PPGSILPAERELSELIGV-TRTTLREVLQRLARDGWLTIQ 64 (239)
T ss_pred CCCCcCCCHHHHHHHHCC-CHHHHHHHHHHHHHCCCEEEe
Confidence 467778 79999999999 999999999999999999975
No 184
>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=28.87 E-value=89 Score=20.58 Aligned_cols=32 Identities=22% Similarity=0.417 Sum_probs=22.0
Q ss_pred HHHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHH
Q psy7686 19 TKFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITN 55 (243)
Q Consensus 19 ~kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItN 55 (243)
...++|+. .| +.+.++|..+|| .+.-||=+.|
T Consensus 12 ~~i~~l~~---~G-~si~~IA~~~gv-sr~TvyR~l~ 43 (45)
T PF02796_consen 12 EEIKELYA---EG-MSIAEIAKQFGV-SRSTVYRYLN 43 (45)
T ss_dssp HHHHHHHH---TT---HHHHHHHTTS--HHHHHHHHC
T ss_pred HHHHHHHH---CC-CCHHHHHHHHCc-CHHHHHHHHh
Confidence 44556665 34 899999999999 9999987653
No 185
>PF08181 DegQ: DegQ (SacQ) family; InterPro: IPR012554 This family consists of the DegQ (formerly sacQ) regulatory peptides. The DegQ family of peptides control the rates of synthesis of a class of both secreted and intracellular degradative enzymes in Bacillus subtilis. DegQ is 46 amino acids long and activates the synthesis of degradative enzymes. The expression of this peptide was shown to be subjected both to catabolite repression and DegS-DegU-mediated control. Thus allowing an increase in the rate of synthesis of degQ under conditions of nitrogen starvation [].
Probab=28.74 E-value=1.7e+02 Score=20.05 Aligned_cols=39 Identities=26% Similarity=0.410 Sum_probs=23.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhhhh-hccCcccc
Q psy7686 96 DEISDMRNHEAVIDEHIRKCQQSLRNIQEEE-VNRKQCYI 134 (243)
Q Consensus 96 ~El~~L~~~E~~LD~~I~~~~~~l~~l~ed~-~n~~~aYV 134 (243)
.++++|.+.-=+|+.-|+.-..+|+++...- .-.+|.|+
T Consensus 4 ~~ieelkqll~rle~eirett~sl~ninksidq~dk~~y~ 43 (46)
T PF08181_consen 4 KKIEELKQLLWRLENEIRETTDSLRNINKSIDQYDKYTYM 43 (46)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHhchhhh
Confidence 3455555555666677777777777765432 23356665
No 186
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=28.55 E-value=1.2e+02 Score=27.07 Aligned_cols=52 Identities=12% Similarity=0.122 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHHhhCCCCeeeHHH-----------HHhhhcccchhhhhhHHHhhhhccceecc
Q psy7686 14 LGLLTTKFVSLLQQAPEGVLHLKY-----------AAENLEVKQKRRIYDITNVLEGIGLIEKN 66 (243)
Q Consensus 14 L~~Lt~kFi~ll~~~~~g~idL~~-----------aa~~L~v~~KRRiYDItNVLEgiglI~K~ 66 (243)
+....++...++....+.+..-+. +.-.+.| ..-++-+..+-|.++|-+...
T Consensus 61 ~~~a~~~i~~~~~~~gG~i~~~~~~~~~~~~~~~~~~ltiRV-P~~~~~~~l~~l~~~g~v~~~ 123 (262)
T PF14257_consen 61 VEKAVKKIENLVESYGGYIESSSSSSSGGSDDERSASLTIRV-PADKFDSFLDELSELGKVTSR 123 (262)
T ss_pred HHHHHHHHHHHHHHcCCEEEEEeeecccCCCCcceEEEEEEE-CHHHHHHHHHHHhccCceeee
Confidence 444455555666655444433332 2334556 789999999999999976554
No 187
>PF14830 Haemocyan_bet_s: Haemocyanin beta-sandwich; PDB: 1JS8_B 3QJO_A 1LNL_A.
Probab=28.31 E-value=20 Score=28.79 Aligned_cols=13 Identities=54% Similarity=0.938 Sum_probs=9.6
Q ss_pred hhHHHhhhhccce
Q psy7686 51 YDITNVLEGIGLI 63 (243)
Q Consensus 51 YDItNVLEgiglI 63 (243)
||||.+|+.+||=
T Consensus 58 ydIT~~l~~l~l~ 70 (103)
T PF14830_consen 58 YDITDALKKLGLH 70 (103)
T ss_dssp EE-HHHHHHCT--
T ss_pred hhHHHHHHHcCCC
Confidence 8999999999985
No 188
>smart00338 BRLZ basic region leucin zipper.
Probab=28.29 E-value=2.1e+02 Score=20.05 Aligned_cols=34 Identities=12% Similarity=0.382 Sum_probs=19.3
Q ss_pred hHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q psy7686 91 LIELRDEISDMRNHEAVIDEHIRKCQQSLRNIQE 124 (243)
Q Consensus 91 ~~~Lk~El~~L~~~E~~LD~~I~~~~~~l~~l~e 124 (243)
+..|..++..|..+-..|-..+..+..++..|.+
T Consensus 28 ~~~Le~~~~~L~~en~~L~~~~~~l~~e~~~lk~ 61 (65)
T smart00338 28 IEELERKVEQLEAENERLKKEIERLRRELEKLKS 61 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455566666666655566666655555555443
No 189
>TIGR02928 orc1/cdc6 family replication initiation protein. Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.
Probab=28.29 E-value=43 Score=30.70 Aligned_cols=32 Identities=34% Similarity=0.606 Sum_probs=25.4
Q ss_pred HHHhhhccc--chhhhhhHHHhhhhccceecccc
Q psy7686 37 YAAENLEVK--QKRRIYDITNVLEGIGLIEKNNK 68 (243)
Q Consensus 37 ~aa~~L~v~--~KRRiYDItNVLEgiglI~K~sK 68 (243)
.+++..++. ..|++|++.+-|+.+|||+-..+
T Consensus 319 ~~~~~~~~~~~~~~~~~~~l~~l~~~gli~~~~~ 352 (365)
T TIGR02928 319 EVCEDIGVDPLTQRRISDLLNELDMLGLVEAEER 352 (365)
T ss_pred HHHHhcCCCCCcHHHHHHHHHHHHhcCCeEEEEE
Confidence 556666642 56999999999999999997643
No 190
>KOG2264|consensus
Probab=28.26 E-value=89 Score=32.61 Aligned_cols=40 Identities=23% Similarity=0.234 Sum_probs=29.3
Q ss_pred HHHHHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q psy7686 86 LEQSKLIELRDEISDMRNHEAVIDEHIRKCQQSLRNIQEE 125 (243)
Q Consensus 86 ~~~~~~~~Lk~El~~L~~~E~~LD~~I~~~~~~l~~l~ed 125 (243)
+.+.+.++|+.||+++..+-++|.++|...++.|..|.-.
T Consensus 97 ele~krqel~seI~~~n~kiEelk~~i~~~q~eL~~Lk~~ 136 (907)
T KOG2264|consen 97 ELEVKRQELNSEIEEINTKIEELKRLIPQKQLELSALKGE 136 (907)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHHHHHHHHhHHHHHHHHhH
Confidence 5666777888888888888778888777777766665443
No 191
>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=27.91 E-value=2.2e+02 Score=21.82 Aligned_cols=36 Identities=25% Similarity=0.255 Sum_probs=24.2
Q ss_pred eHHHHHhhhcccchh--hhhhHHHhhhhccceec--cccCceEEecc
Q psy7686 34 HLKYAAENLEVKQKR--RIYDITNVLEGIGLIEK--NNKNIIRWKAL 76 (243)
Q Consensus 34 dL~~aa~~L~v~~KR--RiYDItNVLEgiglI~K--~sKn~i~W~G~ 76 (243)
.+.++|+.+|| ..+ |.| |..|++.. ...|.++|-..
T Consensus 2 ~i~e~A~~~gv-s~~tlR~Y------e~~Gll~~~~r~~~g~R~Y~~ 41 (99)
T cd04772 2 RTVDLARAIGL-SPQTVRNY------ESLGLIPPAERTANGYRIYTD 41 (99)
T ss_pred CHHHHHHHHCc-CHHHHHHH------HHcCCCCCCCcCCCCCeecCH
Confidence 46789999999 654 344 67888863 45666766543
No 192
>PF10018 Med4: Vitamin-D-receptor interacting Mediator subunit 4; InterPro: IPR019258 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Members of this family represent the Med4 subunit of the Mediator (Med) complex [, ]. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=27.64 E-value=1.9e+02 Score=24.93 Aligned_cols=38 Identities=24% Similarity=0.351 Sum_probs=30.6
Q ss_pred HHHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q psy7686 88 QSKLIELRDEISDMRNHEAVIDEHIRKCQQSLRNIQEE 125 (243)
Q Consensus 88 ~~~~~~Lk~El~~L~~~E~~LD~~I~~~~~~l~~l~ed 125 (243)
..+++++..+|..|.++-..||..|+.+..+|...-.+
T Consensus 21 l~~hq~~~~~I~~L~~e~~~ld~~i~~~~~~L~~~~~~ 58 (188)
T PF10018_consen 21 LQEHQENQARIQQLRAEIEELDEQIRDILKQLKEARKE 58 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34566788999999999999999999888877776554
No 193
>PF08222 HTH_CodY: CodY helix-turn-helix domain; InterPro: IPR013198 This family consists of the C-terminal helix-turn-helix domain found in several bacterial GTP-sensing transcriptional pleiotropic repressor CodY proteins. CodY has been found to repress the dipeptide transport operon (dpp) of Bacillus subtilis in nutrient-rich conditions []. The CodY protein also has a repressor effect on many genes in Lactococcus lactis during growth in milk [].; PDB: 2B0L_C.
Probab=27.46 E-value=74 Score=23.33 Aligned_cols=36 Identities=25% Similarity=0.360 Sum_probs=28.0
Q ss_pred CeeeHHHHHhhhcccchhhhhhHHHhhhhccceeccc
Q psy7686 31 GVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNN 67 (243)
Q Consensus 31 g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~s 67 (243)
|.+--..+|++.|+ .|.-|---.-=||+.|+|+-.|
T Consensus 3 g~lvas~iAd~~Gi-TRSvIVNALRKleSaGvIesrS 38 (61)
T PF08222_consen 3 GRLVASKIADRVGI-TRSVIVNALRKLESAGVIESRS 38 (61)
T ss_dssp EEE-HHHHHHHHT---HHHHHHHHHHHHHTTSEEEEE
T ss_pred ceehHHHHHHHhCc-cHHHHHHHHHHHHhcCceeecc
Confidence 55667789999999 9998888888899999999654
No 194
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=27.30 E-value=1.6e+02 Score=29.39 Aligned_cols=55 Identities=22% Similarity=0.407 Sum_probs=41.4
Q ss_pred CCCCCcCcHHHHH------HHHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceec
Q psy7686 6 ANSRFEKSLGLLT------TKFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEK 65 (243)
Q Consensus 6 ~~~R~~~SL~~Lt------~kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K 65 (243)
+..|-=+-||.++ ...+++|... .+.++|++++...++ +.-||+..|+.+|++..
T Consensus 343 ~PEkPLSdlG~~sY~~YW~~~i~~~L~~~-~~~~si~~is~~T~i----~~~Dii~tL~~l~~l~~ 403 (450)
T PLN00104 343 TPERPLSDLGLVSYRGYWTRVLLEILKKH-KGNISIKELSDMTAI----KAEDIVSTLQSLNLIQY 403 (450)
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHhc-CCCccHHHHHHHhCC----CHHHHHHHHHHCCCEEe
Confidence 3445455677765 2255666543 468999999999999 77899999999999964
No 195
>PF11932 DUF3450: Protein of unknown function (DUF3450); InterPro: IPR016866 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. However, they are found in an operon along with components of a TonB transport system (typified by Vibrio cholerae TonB2 [], and are predicted to be localized to the periplasmic space. Caution: the low-complexity nature of these sequences produces spurious BLAST hits to chromosome segregation ATPases (which are much longer in length and contain canonical Walker motifs). Accordingly, some members are misidentified as such.
Probab=27.25 E-value=1.9e+02 Score=25.72 Aligned_cols=29 Identities=10% Similarity=0.225 Sum_probs=11.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy7686 93 ELRDEISDMRNHEAVIDEHIRKCQQSLRN 121 (243)
Q Consensus 93 ~Lk~El~~L~~~E~~LD~~I~~~~~~l~~ 121 (243)
.|+.+++.++..++.|.-++..+-..|..
T Consensus 88 ~L~~qi~~~~~~~~~l~p~m~~m~~~L~~ 116 (251)
T PF11932_consen 88 SLEQQIEQIEETRQELVPLMEQMIDELEQ 116 (251)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33333333333344444444444444444
No 196
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=26.86 E-value=1.3e+02 Score=29.05 Aligned_cols=43 Identities=12% Similarity=0.110 Sum_probs=37.5
Q ss_pred CCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceeccccCceE
Q psy7686 29 PEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNNKNIIR 72 (243)
Q Consensus 29 ~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~sKn~i~ 72 (243)
.+..++..++|+.+++ .-+.+-+|.+-|+..|+|.+...+.|.
T Consensus 307 ~g~~~t~~~La~~l~~-~~~~v~~iL~~L~~agLI~~~~~g~~~ 349 (412)
T PRK04214 307 HGKALDVDEIRRLEPM-GYDELGELLCELARIGLLRRGERGQWV 349 (412)
T ss_pred cCCCCCHHHHHHHhCC-CHHHHHHHHHHHHhCCCeEecCCCceE
Confidence 4567899999999999 999999999999999999987656443
No 197
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=26.81 E-value=86 Score=26.95 Aligned_cols=55 Identities=16% Similarity=0.108 Sum_probs=41.0
Q ss_pred HHHHHHHHHHhhC-C--CCeeeHHHHHhhhcccchhhhhhHHHhhhhccceeccccCceE
Q psy7686 16 LLTTKFVSLLQQA-P--EGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNNKNIIR 72 (243)
Q Consensus 16 ~Lt~kFi~ll~~~-~--~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~sKn~i~ 72 (243)
.+..|+..+|... . ....+-.++|+.||+ .++-+.=+.+-|+--|+|++..+ .|.
T Consensus 150 ~~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~-sretvsR~L~~L~~~G~I~~~~~-~i~ 207 (226)
T PRK10402 150 PLENRLAAFILLTQEGDLYHEKHTQAAEYLGV-SYRHLLYVLAQFIQDGYLKKSKR-GYL 207 (226)
T ss_pred hHHHHHHHHHHhcccCCcccchHHHHHHHHCC-cHHHHHHHHHHHHHCCCEEeeCC-EEE
Confidence 3456666665432 1 123567999999999 99999999999999999998743 443
No 198
>PF13600 DUF4140: N-terminal domain of unknown function (DUF4140)
Probab=26.64 E-value=1.4e+02 Score=22.75 Aligned_cols=35 Identities=17% Similarity=0.383 Sum_probs=24.6
Q ss_pred HHHHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy7686 87 EQSKLIELRDEISDMRNHEAVIDEHIRKCQQSLRN 121 (243)
Q Consensus 87 ~~~~~~~Lk~El~~L~~~E~~LD~~I~~~~~~l~~ 121 (243)
...++..|+++++.|+.+-..+...+.-+..++.-
T Consensus 68 ~~~~~~~l~~~l~~l~~~~~~~~~~~~~~~~~~~~ 102 (104)
T PF13600_consen 68 DSPELKELEEELEALEDELAALQDEIQALEAQIAF 102 (104)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 34566777788888877777777777776666553
No 199
>PF13551 HTH_29: Winged helix-turn helix
Probab=26.16 E-value=68 Score=23.93 Aligned_cols=27 Identities=19% Similarity=0.290 Sum_probs=25.6
Q ss_pred eHHHHHhhhcccchhhhhhHHHhhhhcc
Q psy7686 34 HLKYAAENLEVKQKRRIYDITNVLEGIG 61 (243)
Q Consensus 34 dL~~aa~~L~v~~KRRiYDItNVLEgig 61 (243)
...++|..||+ .++-+|.+.+-++.=|
T Consensus 14 ~~~~ia~~lg~-s~~Tv~r~~~~~~~~G 40 (112)
T PF13551_consen 14 TIAEIARRLGI-SRRTVYRWLKRYREGG 40 (112)
T ss_pred cHHHHHHHHCc-CHHHHHHHHHHHHccc
Confidence 79999999999 9999999999998877
No 200
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=26.11 E-value=64 Score=21.65 Aligned_cols=25 Identities=16% Similarity=0.220 Sum_probs=18.5
Q ss_pred CeeeHHHHHhhhcccchhhhhhHHHh
Q psy7686 31 GVLHLKYAAENLEVKQKRRIYDITNV 56 (243)
Q Consensus 31 g~idL~~aa~~L~v~~KRRiYDItNV 56 (243)
|.+++..||..+|| .+.-|+|-.+-
T Consensus 15 g~~S~r~AA~~ygV-p~sTL~~r~~g 39 (45)
T PF05225_consen 15 GKMSIRKAAKKYGV-PRSTLRRRLRG 39 (45)
T ss_dssp TSS-HHHHHHHHT---HHHHHHHHHH
T ss_pred CCCCHHHHHHHHCc-CHHHHHHHHcC
Confidence 34999999999999 99999987663
No 201
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=26.07 E-value=1.4e+02 Score=27.41 Aligned_cols=52 Identities=23% Similarity=0.248 Sum_probs=40.8
Q ss_pred HHHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccc-eeccccCceEE
Q psy7686 19 TKFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGL-IEKNNKNIIRW 73 (243)
Q Consensus 19 ~kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgigl-I~K~sKn~i~W 73 (243)
.+.+.++.+ +..+...++|+.|++ .|.-++=.+..|+.-|+ |.......|..
T Consensus 7 ~~il~~L~~--~~~~s~~~LA~~lgv-sr~tV~~~l~~L~~~G~~i~~~~~~Gy~L 59 (319)
T PRK11886 7 LQLLSLLAD--GDFHSGEQLGEELGI-SRAAIWKHIQTLEEWGLDIFSVKGKGYRL 59 (319)
T ss_pred HHHHHHHHc--CCCcCHHHHHHHHCC-CHHHHHHHHHHHHHCCCceEEecCCeEEe
Confidence 456677764 566888899999999 99999999999999999 55443334655
No 202
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=25.83 E-value=81 Score=20.57 Aligned_cols=36 Identities=19% Similarity=0.338 Sum_probs=21.9
Q ss_pred HHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhcc
Q psy7686 21 FVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIG 61 (243)
Q Consensus 21 Fi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgig 61 (243)
.+.++.+ -....++|+.||| .++-+|-|.+=...-|
T Consensus 10 ii~l~~~----G~s~~~ia~~lgv-s~~Tv~~w~kr~~~~G 45 (50)
T PF13384_consen 10 IIRLLRE----GWSIREIAKRLGV-SRSTVYRWIKRYREEG 45 (50)
T ss_dssp HHHHHHH----T--HHHHHHHHTS--HHHHHHHHT------
T ss_pred HHHHHHC----CCCHHHHHHHHCc-CHHHHHHHHHHccccc
Confidence 4455554 3688999999999 9999999987664333
No 203
>PF14712 Snapin_Pallidin: Snapin/Pallidin
Probab=25.79 E-value=2.3e+02 Score=21.15 Aligned_cols=38 Identities=16% Similarity=0.387 Sum_probs=33.5
Q ss_pred HHHHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q psy7686 87 EQSKLIELRDEISDMRNHEAVIDEHIRKCQQSLRNIQE 124 (243)
Q Consensus 87 ~~~~~~~Lk~El~~L~~~E~~LD~~I~~~~~~l~~l~e 124 (243)
..+.+..+++.+.+|.+....|-..|......|+.+.+
T Consensus 12 l~P~l~~~~~~l~el~~sQ~~L~~~i~~~~~~L~~~~~ 49 (92)
T PF14712_consen 12 LEPDLDRLDQQLQELRQSQEELLQQIDRLNEKLKELNE 49 (92)
T ss_pred HhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45567888999999999999999999999999998888
No 204
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=25.74 E-value=1.1e+02 Score=31.57 Aligned_cols=56 Identities=21% Similarity=0.329 Sum_probs=46.1
Q ss_pred HHHHHHHhhCCCCeeeHHHHHhhhccc---chhhhhhHHHhhhhccceeccccCceEEe
Q psy7686 19 TKFVSLLQQAPEGVLHLKYAAENLEVK---QKRRIYDITNVLEGIGLIEKNNKNIIRWK 74 (243)
Q Consensus 19 ~kFi~ll~~~~~g~idL~~aa~~L~v~---~KRRiYDItNVLEgiglI~K~sKn~i~W~ 74 (243)
.+.++++...+...+..++++..|++. .|.-++.+++-|+.-|.|.|..++.|...
T Consensus 5 ~~il~~l~~~~~~~~~~~~l~~~l~~~~~~~~~~l~~~l~~l~~~g~l~~~~~~~~~~~ 63 (709)
T TIGR02063 5 ELILEFLKSKKGKPISLKELAKAFHLKGADEKKALRKRLRALEDDGLVKKNRRGLYALP 63 (709)
T ss_pred HHHHHHHHhCCCCCCCHHHHHHHhCCCChHHHHHHHHHHHHHHHCCCEEEcCCceEecC
Confidence 356778887788899999999999993 34569999999999999998877766554
No 205
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=25.47 E-value=1.2e+02 Score=27.19 Aligned_cols=44 Identities=18% Similarity=0.257 Sum_probs=32.3
Q ss_pred HHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceecc
Q psy7686 20 KFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKN 66 (243)
Q Consensus 20 kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~ 66 (243)
+.++++++ .+.+.++++|+.|+| ..--|.==++.||.-|+|.|.
T Consensus 9 ~Il~~L~~--~~~v~v~eLa~~l~V-S~~TIRRDL~~Le~~g~l~r~ 52 (256)
T PRK10434 9 AILEYLQK--QGKTSVEELAQYFDT-TGTTIRKDLVILEHAGTVIRT 52 (256)
T ss_pred HHHHHHHH--cCCEEHHHHHHHHCC-CHHHHHHHHHHHHHCCCEEEE
Confidence 35566665 678999999999999 532221115679999999998
No 206
>PF11853 DUF3373: Protein of unknown function (DUF3373); InterPro: IPR021803 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 472 to 574 amino acids in length.
Probab=25.34 E-value=59 Score=32.78 Aligned_cols=30 Identities=10% Similarity=0.433 Sum_probs=20.0
Q ss_pred HHHhHhHHHHHHHHHHHHHHHHHHHHHHHH
Q psy7686 88 QSKLIELRDEISDMRNHEAVIDEHIRKCQQ 117 (243)
Q Consensus 88 ~~~~~~Lk~El~~L~~~E~~LD~~I~~~~~ 117 (243)
.+++++|++||++|+++-..|++.+...++
T Consensus 30 ~qkie~L~kql~~Lk~q~~~l~~~v~k~e~ 59 (489)
T PF11853_consen 30 LQKIEALKKQLEELKAQQDDLNDRVDKVEK 59 (489)
T ss_pred HHHHHHHHHHHHHHHHhhcccccccchhhH
Confidence 347778888888887776666666654443
No 207
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. 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=25.20 E-value=1.7e+02 Score=23.24 Aligned_cols=9 Identities=22% Similarity=0.298 Sum_probs=3.7
Q ss_pred HHHHhhhcc
Q psy7686 36 KYAAENLEV 44 (243)
Q Consensus 36 ~~aa~~L~v 44 (243)
.++|+..||
T Consensus 4 geva~~~gv 12 (118)
T cd04776 4 SELAREFDV 12 (118)
T ss_pred HHHHHHHCc
Confidence 334444443
No 208
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=25.19 E-value=1.3e+02 Score=27.15 Aligned_cols=47 Identities=19% Similarity=0.233 Sum_probs=36.8
Q ss_pred HHHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceecccc
Q psy7686 19 TKFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNNK 68 (243)
Q Consensus 19 ~kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~sK 68 (243)
.+.++++++ .+.+.+.++|+.|+| ...-|+==...||.-|++.|...
T Consensus 8 ~~Il~~l~~--~~~~~~~ela~~l~v-S~~TiRRdL~~Le~~g~l~r~~G 54 (252)
T PRK10906 8 DAIIELVKQ--QGYVSTEELVEHFSV-SPQTIRRDLNDLAEQNKILRHHG 54 (252)
T ss_pred HHHHHHHHH--cCCEeHHHHHHHhCC-CHHHHHHHHHHHHHCCCEEEecC
Confidence 345677765 678999999999999 76655555888999999998733
No 209
>COG1730 GIM5 Predicted prefoldin, molecular chaperone implicated in de novo protein folding [Posttranslational modification, protein turnover, chaperones]
Probab=24.98 E-value=2.3e+02 Score=24.04 Aligned_cols=39 Identities=15% Similarity=0.294 Sum_probs=24.3
Q ss_pred HHHHHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q psy7686 86 LEQSKLIELRDEISDMRNHEAVIDEHIRKCQQSLRNIQE 124 (243)
Q Consensus 86 ~~~~~~~~Lk~El~~L~~~E~~LD~~I~~~~~~l~~l~e 124 (243)
++..+++.++++++.|.+.-..|...|..++..+..|..
T Consensus 10 ~l~a~lq~l~~qie~L~~~i~~l~~~~~e~~~~~~tl~~ 48 (145)
T COG1730 10 ELAAQLQILQSQIESLQAQIAALNAAISELQTAIETLEN 48 (145)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445566666667777766666666666666665554443
No 210
>COG1373 Predicted ATPase (AAA+ superfamily) [General function prediction only]
Probab=24.88 E-value=1e+02 Score=29.66 Aligned_cols=50 Identities=18% Similarity=0.129 Sum_probs=46.0
Q ss_pred HHHHHHHHHHhhCCCCeeeHHHHHhhh-cccchhhhhhHHHhhhhccceecc
Q psy7686 16 LLTTKFVSLLQQAPEGVLHLKYAAENL-EVKQKRRIYDITNVLEGIGLIEKN 66 (243)
Q Consensus 16 ~Lt~kFi~ll~~~~~g~idL~~aa~~L-~v~~KRRiYDItNVLEgiglI~K~ 66 (243)
.+.++++.++....+..++.+.+|..+ ++ .++-++.=++.||..-++-..
T Consensus 220 ~~~k~i~~~l~~~~g~~~s~~~la~~l~~i-s~~Ti~~Yl~~le~~fll~~~ 270 (398)
T COG1373 220 DLMKRILRFLASNIGSPISYSSLARELKGI-SKDTIRKYLSYLEDAFLLFLV 270 (398)
T ss_pred HHHHHHHHHHHhhcCCccCHHHHHHHHhcc-chHHHHHHHHHHHHhhheEEe
Confidence 577889999999999999999999999 79 899999999999999999843
No 211
>PF14363 AAA_assoc: Domain associated at C-terminal with AAA
Probab=24.81 E-value=33 Score=26.52 Aligned_cols=29 Identities=24% Similarity=0.539 Sum_probs=25.2
Q ss_pred cccccCCCCCCCCcccccCCCcchhhhcc
Q psy7686 212 RLIVVPNPPSRKDFLFKLDDDEGISHMFD 240 (243)
Q Consensus 212 ~~~~lspp~~~~dy~f~l~~~egi~dlfd 240 (243)
..++++-+....+..++||++|-|.|-|+
T Consensus 58 ~rL~~~~~~~~~~~~l~l~~~e~V~D~F~ 86 (98)
T PF14363_consen 58 RRLKASKSKNSKNLVLSLDDGEEVVDVFE 86 (98)
T ss_pred ceeeecccCCCCceEEecCCCCEEEEEEC
Confidence 56677777788899999999999999986
No 212
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=24.77 E-value=1.2e+02 Score=27.18 Aligned_cols=45 Identities=29% Similarity=0.342 Sum_probs=36.0
Q ss_pred HHHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceecc
Q psy7686 19 TKFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKN 66 (243)
Q Consensus 19 ~kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~ 66 (243)
++.++++++ .|.+.+.++|+.|+| ..--|.==+|-||.-|++.|.
T Consensus 8 ~~Il~~l~~--~g~v~v~eLa~~~~V-S~~TIRRDL~~Le~~g~l~R~ 52 (253)
T COG1349 8 QKILELLKE--KGKVSVEELAELFGV-SEMTIRRDLNELEEQGLLLRV 52 (253)
T ss_pred HHHHHHHHH--cCcEEHHHHHHHhCC-CHHHHHHhHHHHHHCCcEEEE
Confidence 456788876 789999999999999 653333336899999999998
No 213
>PF09340 NuA4: Histone acetyltransferase subunit NuA4; InterPro: IPR015418 The NuA4 histone acetyltransferase (HAT) multisubunit complex is responsible for acetylation of histone H4 and H2A N-terminal tails in yeast []. NuA4 complexes are highly conserved in eukaryotes and play primary roles in transcription, cellular response to DNA damage, and cell cycle control [].
Probab=24.71 E-value=1.3e+02 Score=22.85 Aligned_cols=29 Identities=3% Similarity=0.280 Sum_probs=20.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q psy7686 96 DEISDMRNHEAVIDEHIRKCQQSLRNIQE 124 (243)
Q Consensus 96 ~El~~L~~~E~~LD~~I~~~~~~l~~l~e 124 (243)
++|.+|.+.-+.|+..+..++++|-++-.
T Consensus 2 ~~L~~l~~~k~~Le~~L~~lE~qIy~~Et 30 (80)
T PF09340_consen 2 KELKELLQKKKKLEKDLAALEKQIYDKET 30 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45667777777788888888887766644
No 214
>PRK01203 prefoldin subunit alpha; Provisional
Probab=23.83 E-value=2.5e+02 Score=23.46 Aligned_cols=37 Identities=14% Similarity=0.207 Sum_probs=20.1
Q ss_pred HHHHHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy7686 86 LEQSKLIELRDEISDMRNHEAVIDEHIRKCQQSLRNI 122 (243)
Q Consensus 86 ~~~~~~~~Lk~El~~L~~~E~~LD~~I~~~~~~l~~l 122 (243)
++..+++.++++++.|.++-..|...+.....++..|
T Consensus 4 ~~~~~~~~~~~q~e~l~~ql~~L~~a~se~~~~ie~L 40 (130)
T PRK01203 4 DVEAQLNYIESLISSVDSQIDSLNKTLSEVQQTISFL 40 (130)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445566666666666655555555555544444333
No 215
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=23.79 E-value=1.1e+02 Score=26.88 Aligned_cols=38 Identities=16% Similarity=0.120 Sum_probs=34.5
Q ss_pred CCCCee-eHHHHHhhhcccchhhhhhHHHhhhhccceecc
Q psy7686 28 APEGVL-HLKYAAENLEVKQKRRIYDITNVLEGIGLIEKN 66 (243)
Q Consensus 28 ~~~g~i-dL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~ 66 (243)
.|+..+ .-.++|+.||| .|=-+=+.+..|++.|||+..
T Consensus 21 ~pG~~LpsE~eLae~~gV-SRtpVREAL~~Le~~GlV~~~ 59 (253)
T PRK10421 21 EAGMKLPAERQLAMQLGV-SRNSLREALAKLVSEGVLLSR 59 (253)
T ss_pred CCCCcCCCHHHHHHHhCC-CHHHHHHHHHHHHHCCCEEEe
Confidence 467778 69999999999 999999999999999999865
No 216
>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=23.62 E-value=4.8e+02 Score=22.47 Aligned_cols=46 Identities=22% Similarity=0.298 Sum_probs=35.9
Q ss_pred HHHHHHhhCCCCee--eHHHHHhhhcccchhhhhhHHHhhhhccceecc
Q psy7686 20 KFVSLLQQAPEGVL--HLKYAAENLEVKQKRRIYDITNVLEGIGLIEKN 66 (243)
Q Consensus 20 kFi~ll~~~~~g~i--dL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~ 66 (243)
++..++...+.-.+ .+..+|..||+ .++-|-=++.|+.-+|+|+-.
T Consensus 102 ~~Y~~l~~~~~~~l~~~~~~La~~l~i-~~~~l~fml~VF~EL~FVti~ 149 (195)
T PF10141_consen 102 KLYKFLKQHPNFDLKEQLQALAKYLGI-SPDTLKFMLKVFFELGFVTIE 149 (195)
T ss_pred HHHHHHHhCCCCCHHHHHHHHHHHHCc-CHHHHHHHHHHHHHcCcEEEe
Confidence 35556666544321 45789999999 999999999999999999866
No 217
>PF05565 Sipho_Gp157: Siphovirus Gp157; InterPro: IPR008840 This family contains both viral and bacterial proteins which are related to the Gp157 protein of the Streptococcus thermophilus SFi bacteriophage. It is thought that bacteria possessing the gene coding for this protein have an increased resistance to the bacteriophage [].
Probab=23.47 E-value=3e+02 Score=23.20 Aligned_cols=32 Identities=34% Similarity=0.395 Sum_probs=22.3
Q ss_pred cHHHHHHHHHHHHhhCCCCeeeHHHHHhhhcc
Q psy7686 13 SLGLLTTKFVSLLQQAPEGVLHLKYAAENLEV 44 (243)
Q Consensus 13 SL~~Lt~kFi~ll~~~~~g~idL~~aa~~L~v 44 (243)
+|..|+..|..++.-...+..|-..+++.|.-
T Consensus 2 ~LYel~~~~~~l~~~~e~~~~d~e~~~dtLe~ 33 (162)
T PF05565_consen 2 KLYELTDEYLELLELLEEGDLDEEAIADTLES 33 (162)
T ss_pred CHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHH
Confidence 57788888888886655555776666666543
No 218
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=23.43 E-value=5e+02 Score=22.67 Aligned_cols=51 Identities=24% Similarity=0.252 Sum_probs=40.8
Q ss_pred HHHHHHHHHHhh---CCCCee-eHHHHHhhhcccchhhhhhHHHhhhhccceeccc
Q psy7686 16 LLTTKFVSLLQQ---APEGVL-HLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNN 67 (243)
Q Consensus 16 ~Lt~kFi~ll~~---~~~g~i-dL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~s 67 (243)
.+...+.+.+.. .|+..+ +-.++|+.||| .|==+=+.+..|++-|||+...
T Consensus 13 ~v~~~l~~~I~~g~l~pG~~LpsE~eLa~~~gV-SRtpVREAL~~L~~eGlV~~~~ 67 (257)
T PRK10225 13 EVGAMIRDLIIKTPYNPGERLPPEREIAEMLDV-TRTVVREALIMLEIKGLVEVRR 67 (257)
T ss_pred HHHHHHHHHHHhCCCCCCCcCcCHHHHHHHhCC-CHHHHHHHHHHHHHCCCEEEec
Confidence 344445544433 578888 69999999999 9999999999999999998663
No 219
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. 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 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=23.39 E-value=1.2e+02 Score=23.84 Aligned_cols=26 Identities=23% Similarity=0.276 Sum_probs=15.1
Q ss_pred eHHHHHhhhcccchhhhhhHHHhhhhcccee
Q psy7686 34 HLKYAAENLEVKQKRRIYDITNVLEGIGLIE 64 (243)
Q Consensus 34 dL~~aa~~L~v~~KRRiYDItNVLEgiglI~ 64 (243)
.+.++|+.+|| .++-| --.|.+|||.
T Consensus 2 ~ige~a~~~gv-s~~tL----ryYe~~GLi~ 27 (116)
T cd04769 2 YIGELAQQTGV-TIKAI----RLYEEKGLLP 27 (116)
T ss_pred CHHHHHHHHCc-CHHHH----HHHHHCCCCC
Confidence 46777777777 55422 2234566665
No 220
>PRK11642 exoribonuclease R; Provisional
Probab=23.34 E-value=1.3e+02 Score=31.98 Aligned_cols=52 Identities=13% Similarity=0.074 Sum_probs=41.6
Q ss_pred HHHHHHhhCCCCeeeHHHHHhhhccc---chhhhhhHHHhhhhccceeccccCceE
Q psy7686 20 KFVSLLQQAPEGVLHLKYAAENLEVK---QKRRIYDITNVLEGIGLIEKNNKNIIR 72 (243)
Q Consensus 20 kFi~ll~~~~~g~idL~~aa~~L~v~---~KRRiYDItNVLEgiglI~K~sKn~i~ 72 (243)
+.+++|.. .+..+.++++|..|++. .++.+..+++-|+..|.|.+..++.|.
T Consensus 23 ~Il~~l~~-~~~~~~~~~L~~~l~l~~~~~~~~l~~~L~~L~~~g~l~~~~~~~~~ 77 (813)
T PRK11642 23 FILEHLTK-REKPASREELAVELNIEGEEQLEALRRRLRAMERDGQLVFTRRQCYA 77 (813)
T ss_pred HHHHHHHh-cCCCCCHHHHHHHhCCCChHHHHHHHHHHHHHHHCCCEEEcCCceEe
Confidence 35566665 34889999999999993 246699999999999999988777664
No 221
>PF05158 RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; InterPro: IPR007832 The family comprises a subunit specific to RNA Pol III, the tRNA specific polymerase. The C34 subunit of Saccharomyces cerevisiae RNA Pol III is part of a subcomplex of three subunits which have no counterpart in the other two nuclear RNA polymerases. This subunit interacts with TFIIIB70 and therefore participates in Pol III recruitment [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2DK8_A 2DK5_A 2YU3_A.
Probab=23.21 E-value=2.4e+02 Score=26.69 Aligned_cols=63 Identities=16% Similarity=0.165 Sum_probs=45.8
Q ss_pred cHHHHHHHHHHHHhhC-CCCeeeHHHHHhh-hcccchhhhhhHHHhhhhccceecc-ccCceEEecc
Q psy7686 13 SLGLLTTKFVSLLQQA-PEGVLHLKYAAEN-LEVKQKRRIYDITNVLEGIGLIEKN-NKNIIRWKAL 76 (243)
Q Consensus 13 SL~~Lt~kFi~ll~~~-~~g~idL~~aa~~-L~v~~KRRiYDItNVLEgiglI~K~-sKn~i~W~G~ 76 (243)
+|..+.+++..++..+ +...+...++... .+. ...-+-.++|-|..-|+++=. ..+.+.|+-.
T Consensus 6 ~~~~~~~~l~~~~~~~~~~~~~~~~~L~~~~~~~-~~~~~~~~in~Ll~~~~~~~~~~~~~l~~~~~ 71 (327)
T PF05158_consen 6 KLSELEKKLLELCRENPSPKGFSQEDLQQLIPGL-DLQELVKAINELLSSGLLKLLKKGGGLSYKAV 71 (327)
T ss_dssp -HHHHHHHHHHHHHH---SS-EEHHHHHHH-TTS--HHHHHHHHHHHHHHTSEEEEE-SSSEEEEE-
T ss_pred hHHHHHHHHHHHHHHhcCCCCcCHHHHHhhcCCC-CHHHHHHHHHHHHhCCCEEEEEcCCEEEEEEe
Confidence 7888999999999987 5667888888887 566 888899999999999988732 4455666554
No 222
>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=23.09 E-value=1.1e+02 Score=27.28 Aligned_cols=51 Identities=27% Similarity=0.404 Sum_probs=37.8
Q ss_pred HHHHHHH-HHhhCCCCeeeHHHHHhhhcccchhhhhhHHH-hhhhccceecccc
Q psy7686 17 LTTKFVS-LLQQAPEGVLHLKYAAENLEVKQKRRIYDITN-VLEGIGLIEKNNK 68 (243)
Q Consensus 17 Lt~kFi~-ll~~~~~g~idL~~aa~~L~v~~KRRiYDItN-VLEgiglI~K~sK 68 (243)
--+.++. ++..-.++.+.+.++|..||+ ..+.+..++- .|-..|||++.+.
T Consensus 239 ~~~~~L~al~~~~~~~~~~~~~ia~~lg~-~~~~~~~~~e~~Li~~~li~~~~~ 291 (305)
T TIGR00635 239 IDRKLLSVLIEQFQGGPVGLKTLAAALGE-DADTIEDVYEPYLLQIGFLQRTPR 291 (305)
T ss_pred HHHHHHHHHHHHhCCCcccHHHHHHHhCC-CcchHHHhhhHHHHHcCCcccCCc
Confidence 3444555 445445667889999999999 8888888776 6888899976643
No 223
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=23.05 E-value=1.1e+02 Score=20.18 Aligned_cols=37 Identities=16% Similarity=0.143 Sum_probs=23.0
Q ss_pred HHHHHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHH
Q psy7686 17 LTTKFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDIT 54 (243)
Q Consensus 17 Lt~kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDIt 54 (243)
+|++|...+...-....++..+|..+|| .--.+..|.
T Consensus 12 ~T~~~~~~i~~~~~~~~s~~~vA~~~~v-s~~TV~ri~ 48 (52)
T PF13542_consen 12 ITKRLEQYILKLLRESRSFKDVARELGV-SWSTVRRIF 48 (52)
T ss_pred HHHHHHHHHHHHHhhcCCHHHHHHHHCC-CHHHHHHHH
Confidence 4566665554322223799999999999 544444443
No 224
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=22.90 E-value=96 Score=27.26 Aligned_cols=50 Identities=18% Similarity=0.258 Sum_probs=39.5
Q ss_pred HHHHHHHHHhh---CCCCee-eHHHHHhhhcccchhhhhhHHHhhhhccceeccc
Q psy7686 17 LTTKFVSLLQQ---APEGVL-HLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNN 67 (243)
Q Consensus 17 Lt~kFi~ll~~---~~~g~i-dL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~s 67 (243)
+...+.+.+.. .|+..+ .-.++|+.||| .|==+=+-+..|++-|||+...
T Consensus 13 v~~~l~~~I~~g~l~pG~~LpsE~eLae~~gV-SRtpVREAL~~L~~eGlV~~~~ 66 (253)
T PRK11523 13 LAAELKERIEQGVYLVGDKLPAERFIADEKNV-SRTVVREAIIMLEVEGYVEVRK 66 (253)
T ss_pred HHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCC-CHHHHHHHHHHHHHCCCEEEec
Confidence 33444444433 477788 48999999999 9999999999999999998663
No 225
>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=22.86 E-value=1.1e+02 Score=23.92 Aligned_cols=34 Identities=21% Similarity=0.105 Sum_probs=27.3
Q ss_pred HHHHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhh
Q psy7686 18 TTKFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLE 58 (243)
Q Consensus 18 t~kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLE 58 (243)
=++.+.+|.........+.++|...++ |.+||+-
T Consensus 11 R~~vl~~L~~~yp~~~~~~eIar~v~~-------~~snV~G 44 (90)
T PF07381_consen 11 RKKVLEYLCSIYPEPAYPSEIARSVGS-------DYSNVLG 44 (90)
T ss_pred HHHHHHHHHHcCCCcCCHHHHHHHHCC-------CHHHHHH
Confidence 356778888887888999999999998 7777753
No 226
>PRK13626 transcriptional regulator SgrR; Provisional
Probab=22.79 E-value=2.7e+02 Score=27.63 Aligned_cols=48 Identities=23% Similarity=0.315 Sum_probs=41.3
Q ss_pred HHHHHHHHHHhhCC--CCeeeHHHHHhhhcccchhhhhhHHHhhhhcccee
Q psy7686 16 LLTTKFVSLLQQAP--EGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIE 64 (243)
Q Consensus 16 ~Lt~kFi~ll~~~~--~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~ 64 (243)
.|-+.|+.|.+... ...+.|.++|+.|.+ .+|-.==|+|-|+.-|.|+
T Consensus 5 ~~~~~~~~L~~~~~~~~~~~~l~~la~~l~c-s~R~~~~~l~~~~~~gwl~ 54 (552)
T PRK13626 5 RLQQQFIRLWQCCEGKSQETTLNELAELLNC-SRRHMRTLLNTMQQRGWLT 54 (552)
T ss_pred HHHHHHHHHHHhcCCCcceeeHHHHHHHhcC-ChhHHHHHHHHHHHCCCee
Confidence 56678999987643 457999999999999 9999999999999999876
No 227
>KOG0718|consensus
Probab=22.75 E-value=2.7e+02 Score=28.33 Aligned_cols=28 Identities=39% Similarity=0.379 Sum_probs=19.0
Q ss_pred CCCCee--eHHHHHhhhccc-----------chhhhhhHHH
Q psy7686 28 APEGVL--HLKYAAENLEVK-----------QKRRIYDITN 55 (243)
Q Consensus 28 ~~~g~i--dL~~aa~~L~v~-----------~KRRiYDItN 55 (243)
.||.-. |..++|++.=.+ +||-|||+.-
T Consensus 38 HPDkh~dpd~K~~AE~~F~~i~~AyEVLsDp~kRaIYD~~G 78 (546)
T KOG0718|consen 38 HPDKHTDPDQKKAAEEKFQRIQRAYEVLSDPQKRAIYDNYG 78 (546)
T ss_pred CCcccCChhHHHHHHHHHHHHHHHHHHhcChHHHHHHHHhh
Confidence 566654 566777665432 8999999864
No 228
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=22.66 E-value=1.4e+02 Score=24.81 Aligned_cols=36 Identities=17% Similarity=0.236 Sum_probs=32.2
Q ss_pred eeeHHHHHhhhcccchhhhhhHHHhhhhccceecccc
Q psy7686 32 VLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNNK 68 (243)
Q Consensus 32 ~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~sK 68 (243)
.+.-.++|..||+ .++.+.=+.+-|+.-|+|+...+
T Consensus 168 ~~t~~~lA~~lG~-tr~tvsR~l~~l~~~gii~~~~~ 203 (211)
T PRK11753 168 KITRQEIGRIVGC-SREMVGRVLKMLEDQGLISAHGK 203 (211)
T ss_pred CCCHHHHHHHhCC-CHHHHHHHHHHHHHCCCEEecCC
Confidence 4666999999999 99999999999999999987743
No 229
>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=22.55 E-value=2.8e+02 Score=20.70 Aligned_cols=21 Identities=19% Similarity=0.118 Sum_probs=15.2
Q ss_pred eHHHHHhhhcccchhhhhhHHH
Q psy7686 34 HLKYAAENLEVKQKRRIYDITN 55 (243)
Q Consensus 34 dL~~aa~~L~v~~KRRiYDItN 55 (243)
.+.++|+.+|| ..+.|--..+
T Consensus 2 ~~~eva~~~gi-~~~tlr~~~~ 22 (100)
T cd00592 2 TIGEVAKLLGV-SVRTLRYYEE 22 (100)
T ss_pred CHHHHHHHHCc-CHHHHHHHHH
Confidence 57789999999 7766655544
No 230
>PF08232 Striatin: Striatin family; InterPro: IPR013258 This domain is associated with the N terminus of striatin. Striatin is an intracellular protein which has a caveolin-binding motif, a coiled-coil structure, a calmodulin-binding site, and a WD (IPR001680 from INTERPRO) repeat domain []. It acts as a scaffold protein [] and is involved in signalling pathways [, ].
Probab=22.48 E-value=2.5e+02 Score=23.17 Aligned_cols=39 Identities=13% Similarity=0.163 Sum_probs=32.9
Q ss_pred HHHHHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q psy7686 86 LEQSKLIELRDEISDMRNHEAVIDEHIRKCQQSLRNIQE 124 (243)
Q Consensus 86 ~~~~~~~~Lk~El~~L~~~E~~LD~~I~~~~~~l~~l~e 124 (243)
|+..++..|+.|...++..-..|-..|+.+...|++-..
T Consensus 29 EmkarIa~LEGE~r~~e~l~~dL~rrIkMLE~aLkqER~ 67 (134)
T PF08232_consen 29 EMKARIAFLEGERRGQENLKKDLKRRIKMLEYALKQERA 67 (134)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 667778888888888888888899999999998888766
No 231
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=22.41 E-value=4.2e+02 Score=25.04 Aligned_cols=37 Identities=27% Similarity=0.267 Sum_probs=31.2
Q ss_pred CCCeeeHHHHHhh--hcccchhhhhhHHHhhhhccceecc
Q psy7686 29 PEGVLHLKYAAEN--LEVKQKRRIYDITNVLEGIGLIEKN 66 (243)
Q Consensus 29 ~~g~idL~~aa~~--L~v~~KRRiYDItNVLEgiglI~K~ 66 (243)
.++++....+|+. |++ .-=-|.-....||..|+++|.
T Consensus 22 ~~~pv~s~~l~~~~~l~~-S~aTIR~dm~~Le~~G~l~~~ 60 (339)
T PRK00082 22 TGEPVGSKTLSKRYGLGV-SSATIRNDMADLEELGLLEKP 60 (339)
T ss_pred cCCCcCHHHHHHHhCCCC-ChHHHHHHHHHHHhCCCcCCC
Confidence 4788999999966 888 776676777899999999986
No 232
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=22.37 E-value=2.1e+02 Score=22.91 Aligned_cols=47 Identities=21% Similarity=0.208 Sum_probs=38.7
Q ss_pred HHHHHHHHHhhCCCC--eeeHHHHHhhhcccchhhhhhHHHhhhhcccee
Q psy7686 17 LTTKFVSLLQQAPEG--VLHLKYAAENLEVKQKRRIYDITNVLEGIGLIE 64 (243)
Q Consensus 17 Lt~kFi~ll~~~~~g--~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~ 64 (243)
+...|..|.+..+++ .+.|.++|+.|.+ .+|-.==|++=|+..|.|+
T Consensus 2 l~~~y~~L~~~~~~~~~~vtl~elA~~l~c-S~Rn~r~lLkkm~~~gWi~ 50 (115)
T PF12793_consen 2 LLEQYQRLWQHYGGQPVEVTLDELAELLFC-SRRNARTLLKKMQEEGWIT 50 (115)
T ss_pred HHHHHHHHHHHcCCCCcceeHHHHHHHhCC-CHHHHHHHHHHHHHCCCee
Confidence 346678888765544 5899999999999 9999988999999988865
No 233
>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=22.18 E-value=2.1e+02 Score=19.74 Aligned_cols=37 Identities=11% Similarity=0.223 Sum_probs=34.1
Q ss_pred CCeeeHHHHHhhhcccchhhhhhHHHhhhhccceeccc
Q psy7686 30 EGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNN 67 (243)
Q Consensus 30 ~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~s 67 (243)
++.+++.++-+.+|. .|+-.-=+..-|...|+..+.+
T Consensus 8 ~~~itv~~~rd~lg~-sRK~ai~lLE~lD~~g~T~R~g 44 (50)
T PF09107_consen 8 NGEITVAEFRDLLGL-SRKYAIPLLEYLDREGITRRVG 44 (50)
T ss_dssp TSSBEHHHHHHHHTS--HHHHHHHHHHHHHTTSEEEET
T ss_pred CCcCcHHHHHHHHCc-cHHHHHHHHHHHhccCCEEEeC
Confidence 889999999999999 9999999999999999999875
No 234
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=22.07 E-value=1.3e+02 Score=24.44 Aligned_cols=38 Identities=21% Similarity=0.315 Sum_probs=30.3
Q ss_pred HHHHHHHhhCCCCeeeHHHHHhhhccc---chhhhhhHHHhhhh
Q psy7686 19 TKFVSLLQQAPEGVLHLKYAAENLEVK---QKRRIYDITNVLEG 59 (243)
Q Consensus 19 ~kFi~ll~~~~~g~idL~~aa~~L~v~---~KRRiYDItNVLEg 59 (243)
..||..|-.+.+ +|++++..|||- .|-|+.+|+..|..
T Consensus 39 ~~Fi~~Fi~~rG---nlKe~e~~lgiSYPTvR~rLd~ii~~lg~ 79 (113)
T PF09862_consen 39 LEFIKLFIKNRG---NLKEMEKELGISYPTVRNRLDKIIEKLGY 79 (113)
T ss_pred HHHHHHHHHhcC---CHHHHHHHHCCCcHHHHHHHHHHHHHhCC
Confidence 458888876665 799999999983 59999998876644
No 235
>KOG3501|consensus
Probab=21.98 E-value=3.2e+02 Score=22.31 Aligned_cols=40 Identities=13% Similarity=0.366 Sum_probs=33.3
Q ss_pred HHHHHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q psy7686 86 LEQSKLIELRDEISDMRNHEAVIDEHIRKCQQSLRNIQEE 125 (243)
Q Consensus 86 ~~~~~~~~Lk~El~~L~~~E~~LD~~I~~~~~~l~~l~ed 125 (243)
....++..+++.++.|+....-|+.....+.+.|+.|...
T Consensus 71 ~leak~k~see~IeaLqkkK~YlEk~v~eaE~nLrellqs 110 (114)
T KOG3501|consen 71 HLEAKMKSSEEKIEALQKKKTYLEKTVSEAEQNLRELLQS 110 (114)
T ss_pred HHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3445666778889999999999999999999999998874
No 236
>PRK10130 transcriptional regulator EutR; Provisional
Probab=21.96 E-value=1e+02 Score=29.25 Aligned_cols=40 Identities=10% Similarity=0.105 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHH
Q psy7686 15 GLLTTKFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITN 55 (243)
Q Consensus 15 ~~Lt~kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItN 55 (243)
..+.++..+++.+..+..+++.++|+.++| .+|.|+-...
T Consensus 239 ~~~v~~~~~~i~~~~~~~ltv~~lA~~~gv-S~r~L~r~Fk 278 (350)
T PRK10130 239 RRLLSRAREYVLENMSEPVTVLDLCNQLHV-SRRTLQNAFH 278 (350)
T ss_pred HHHHHHHHHHHHhhhcCCCCHHHHHHHHCC-CHHHHHHHHH
Confidence 456778889998888888999999999999 9998876653
No 237
>KOG4057|consensus
Probab=21.62 E-value=1.8e+02 Score=25.22 Aligned_cols=37 Identities=22% Similarity=0.293 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhccCc
Q psy7686 95 RDEISDMRNHEAVIDEHIRKCQQSLRNIQEEEVNRKQ 131 (243)
Q Consensus 95 k~El~~L~~~E~~LD~~I~~~~~~l~~l~ed~~n~~~ 131 (243)
...|..|...|++++.+++.+-+-|.+|-..+.+.+.
T Consensus 8 ~dri~Al~~iEkeI~~~mq~Ag~iiqeLgKEK~~~kn 44 (180)
T KOG4057|consen 8 TDRIQALVTIEKEIDEMMQCAGEIIQELGKEKQIGKN 44 (180)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHhhhhhh
Confidence 3456678888888888888888888888777666553
No 238
>PF08317 Spc7: Spc7 kinetochore protein; InterPro: IPR013253 This entry consists of cell division proteins which are required for kinetochore-spindle association [].
Probab=21.52 E-value=2.3e+02 Score=26.50 Aligned_cols=74 Identities=9% Similarity=0.170 Sum_probs=39.7
Q ss_pred HhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhccCccccchhhhhhc------CCCCeEEEEECCCCCeEEecC
Q psy7686 90 KLIELRDEISDMRNHEAVIDEHIRKCQQSLRNIQEEEVNRKQCYIPTDVILGM------FPDSSLMCLKAPYGTKLHVPS 163 (243)
Q Consensus 90 ~~~~Lk~El~~L~~~E~~LD~~I~~~~~~l~~l~ed~~n~~~aYVT~~Di~~~------f~~qtviaIkAP~~T~leVp~ 163 (243)
.+..|+.+++.+...-+.+...+..+..+|.++....... -.| |..+|... +...|=+.|..=.|+.|++--
T Consensus 231 ~l~el~~el~~l~~~i~~~~~~k~~l~~eI~e~~~~~~~~-r~~-t~~Ev~~Lk~~~~~Le~~~gw~~~~~~~~~l~~~~ 308 (325)
T PF08317_consen 231 ELAELQEELEELEEKIEELEEQKQELLAEIAEAEKIREEC-RGW-TRSEVKRLKAKVDALEKLTGWKIVSISGSTLEFRY 308 (325)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCC-CHHHHHHHHHHHHHHHHHHCcEEEEEeCCeEEEEE
Confidence 3445555555665555666666666666666655443211 123 77777652 333333333333377777765
Q ss_pred CC
Q psy7686 164 IS 165 (243)
Q Consensus 164 p~ 165 (243)
..
T Consensus 309 ~~ 310 (325)
T PF08317_consen 309 KD 310 (325)
T ss_pred cC
Confidence 54
No 239
>PHA00738 putative HTH transcription regulator
Probab=21.40 E-value=4.5e+02 Score=21.35 Aligned_cols=53 Identities=15% Similarity=0.228 Sum_probs=40.4
Q ss_pred HHHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceeccccCceEEe
Q psy7686 19 TKFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNNKNIIRWK 74 (243)
Q Consensus 19 ~kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~sKn~i~W~ 74 (243)
++.+.+|.. ++.+...++|+.+++ .+=.|-==..||+..|||+........+-
T Consensus 15 r~IL~lL~~--~e~~~V~eLae~l~l-SQptVS~HLKvLreAGLV~srK~Gr~vyY 67 (108)
T PHA00738 15 RKILELIAE--NYILSASLISHTLLL-SYTTVLRHLKILNEQGYIELYKEGRTLYA 67 (108)
T ss_pred HHHHHHHHH--cCCccHHHHHHhhCC-CHHHHHHHHHHHHHCCceEEEEECCEEEE
Confidence 345666754 334888899999999 88888888899999999998765554443
No 240
>PF08172 CASP_C: CASP C terminal; InterPro: IPR012955 This domain is the C-terminal region of the CASP family of proteins. These are Golgi membrane proteins which are thought to have a role in vesicle transport [].; GO: 0006891 intra-Golgi vesicle-mediated transport, 0030173 integral to Golgi membrane
Probab=21.34 E-value=2.5e+02 Score=25.69 Aligned_cols=39 Identities=8% Similarity=0.179 Sum_probs=35.4
Q ss_pred HHHHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q psy7686 87 EQSKLIELRDEISDMRNHEAVIDEHIRKCQQSLRNIQEE 125 (243)
Q Consensus 87 ~~~~~~~Lk~El~~L~~~E~~LD~~I~~~~~~l~~l~ed 125 (243)
+..+.+.+++...+|+++-+.+-+.|..+++++..|..|
T Consensus 84 VtsQRDRFR~Rn~ELE~elr~~~~~~~~L~~Ev~~L~~D 122 (248)
T PF08172_consen 84 VTSQRDRFRQRNAELEEELRKQQQTISSLRREVESLRAD 122 (248)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 566788999999999999999999999999999999887
No 241
>KOG3856|consensus
Probab=21.26 E-value=1.9e+02 Score=24.25 Aligned_cols=32 Identities=6% Similarity=0.281 Sum_probs=26.5
Q ss_pred hHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy7686 91 LIELRDEISDMRNHEAVIDEHIRKCQQSLRNI 122 (243)
Q Consensus 91 ~~~Lk~El~~L~~~E~~LD~~I~~~~~~l~~l 122 (243)
...+++||.+|-+.-++|.+.+..++++|-.+
T Consensus 12 ye~~kaEL~elikkrqe~eetl~nLe~qIY~~ 43 (135)
T KOG3856|consen 12 YEDTKAELAELIKKRQELEETLANLERQIYAF 43 (135)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45788999999988888888888888888654
No 242
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=20.95 E-value=1.4e+02 Score=26.76 Aligned_cols=44 Identities=14% Similarity=0.157 Sum_probs=34.3
Q ss_pred HHHHHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhcc
Q psy7686 17 LTTKFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIG 61 (243)
Q Consensus 17 Lt~kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgig 61 (243)
...+.+.++.......++|.++|+.+++ .+|.+.=+..-.-|+.
T Consensus 6 ~i~~~~~~i~~~~~~~~~l~~lA~~~~~-S~~~l~r~F~~~~g~s 49 (289)
T PRK15121 6 IIRDLLIWLEGHLDQPLSLDNVAAKAGY-SKWHLQRMFKDVTGHA 49 (289)
T ss_pred HHHHHHHHHHhcccCCCCHHHHHHHHCc-CHHHHHHHHHHHHCcC
Confidence 4567888999888999999999999999 7776666655544443
No 243
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=20.92 E-value=1.1e+02 Score=28.51 Aligned_cols=36 Identities=22% Similarity=0.357 Sum_probs=27.1
Q ss_pred CeeeHHHHH-------hhhccc--chhhhhhHHHhhhhccceecc
Q psy7686 31 GVLHLKYAA-------ENLEVK--QKRRIYDITNVLEGIGLIEKN 66 (243)
Q Consensus 31 g~idL~~aa-------~~L~v~--~KRRiYDItNVLEgiglI~K~ 66 (243)
+.+...++. +.+++. .+|+++|+.|-|+..|||+-.
T Consensus 314 ~~~~~~~i~~~y~~l~~~~~~~~~~~~~~~~~l~~L~~~glI~~~ 358 (394)
T PRK00411 314 DEVTTGEVYEEYKELCEELGYEPRTHTRFYEYINKLDMLGIINTR 358 (394)
T ss_pred CcccHHHHHHHHHHHHHHcCCCcCcHHHHHHHHHHHHhcCCeEEE
Confidence 456666665 446772 249999999999999999854
No 244
>KOG3313|consensus
Probab=20.90 E-value=1.5e+02 Score=26.34 Aligned_cols=62 Identities=23% Similarity=0.351 Sum_probs=39.2
Q ss_pred hhhhhHHHhhhhccceecc-------------------------ccCceEEeccCCCCchhhhHHHHHhHhHHHHHHHHH
Q psy7686 48 RRIYDITNVLEGIGLIEKN-------------------------NKNIIRWKALKNKNEEEYDLEQSKLIELRDEISDMR 102 (243)
Q Consensus 48 RRiYDItNVLEgiglI~K~-------------------------sKn~i~W~G~~~~~~~~~~~~~~~~~~Lk~El~~L~ 102 (243)
-||=||-|-||-+....++ ..+-+-|.|.+.+-.. .|+
T Consensus 65 ~kIPd~entLeiv~~l~~~~~~~~s~~t~f~lsd~vy~ka~V~~~~kV~LWLGAnVMlEY-----------------~le 127 (187)
T KOG3313|consen 65 TKIPDIENTLEIVQTLIAKKDEGESFETTFLLSDGVYTKASVPPTDKVYLWLGANVMLEY-----------------DLE 127 (187)
T ss_pred hhchHHHHHHHHHHHHHhCcccCcceeEEEEecccceeeeecCCcCeEEEEecceeEEEe-----------------cHH
Confidence 4678999999988755443 1345778887766211 244
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhhh
Q psy7686 103 NHEAVIDEHIRKCQQSLRNIQEEE 126 (243)
Q Consensus 103 ~~E~~LD~~I~~~~~~l~~l~ed~ 126 (243)
+.|+-|++-|.++.+++..+.+|-
T Consensus 128 EAeaLLkknl~sa~k~l~~~~~Dl 151 (187)
T KOG3313|consen 128 EAEALLKKNLTSAVKSLDVLEEDL 151 (187)
T ss_pred HHHHHHHhhHHHHHHHHHHHHHHH
Confidence 555556666666666666666654
No 245
>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY. This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.
Probab=20.78 E-value=1.8e+02 Score=27.02 Aligned_cols=47 Identities=23% Similarity=0.353 Sum_probs=39.1
Q ss_pred HHHHHHHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceeccc
Q psy7686 19 TKFVSLLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKNN 67 (243)
Q Consensus 19 ~kFi~ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~s 67 (243)
++.+..|+ ..+|.+.-.++|+++|| .|=-+-.-+-.||.-|+|+-.+
T Consensus 186 ~~IL~~L~-~~egrlse~eLAerlGV-SRs~ireAlrkLE~aGvIe~r~ 232 (251)
T TIGR02787 186 EHIFEELD-GNEGLLVASKIADRVGI-TRSVIVNALRKLESAGVIESRS 232 (251)
T ss_pred HHHHHHhc-cccccccHHHHHHHHCC-CHHHHHHHHHHHHHCCCEEecc
Confidence 34455554 34689999999999999 9988999999999999999886
No 246
>PRK10884 SH3 domain-containing protein; Provisional
Probab=20.55 E-value=3e+02 Score=24.43 Aligned_cols=31 Identities=16% Similarity=0.379 Sum_probs=13.9
Q ss_pred cCceEEeccCCC-CchhhhHHHHHhHhHHHHHHHH
Q psy7686 68 KNIIRWKALKNK-NEEEYDLEQSKLIELRDEISDM 101 (243)
Q Consensus 68 Kn~i~W~G~~~~-~~~~~~~~~~~~~~Lk~El~~L 101 (243)
++..-|.-..-. ... ....++.+|++|++.|
T Consensus 74 ~G~~GWV~~~~Ls~~p---~~~~rlp~le~el~~l 105 (206)
T PRK10884 74 KGRTAWIPLKQLSTTP---SLRTRVPDLENQVKTL 105 (206)
T ss_pred CCCEEeEEHHHhcCCc---cHHHHHHHHHHHHHHH
Confidence 444566554433 222 2333444555555544
No 247
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=20.44 E-value=1.8e+02 Score=24.18 Aligned_cols=42 Identities=17% Similarity=0.169 Sum_probs=31.1
Q ss_pred HHhhCCCCeeeHHHHHhhhcccchhhhhhHHHhhhhccceecc
Q psy7686 24 LLQQAPEGVLHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKN 66 (243)
Q Consensus 24 ll~~~~~g~idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~ 66 (243)
++-..+++.+...++|+.+++ .+.-+.=|+.-|.--|+|+-.
T Consensus 16 ~LA~~~~~~~s~~eIA~~~~i-s~~~L~kIl~~L~~aGlv~S~ 57 (153)
T PRK11920 16 YCAANDGKLSRIPEIARAYGV-SELFLFKILQPLVEAGLVETV 57 (153)
T ss_pred HHHhCCCCcCcHHHHHHHHCc-CHHHHHHHHHHHHHCCCEEee
Confidence 333456677899999999998 777777777777777777654
No 248
>KOG0804|consensus
Probab=20.36 E-value=95 Score=31.19 Aligned_cols=61 Identities=20% Similarity=0.205 Sum_probs=40.7
Q ss_pred hhhhhHHHhhhhccceecc-ccCceEEeccCCCCchhhhHHHHHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q psy7686 48 RRIYDITNVLEGIGLIEKN-NKNIIRWKALKNKNEEEYDLEQSKLIELRDEISDMRNHEAVIDEHIRKCQQSLRNIQEE 125 (243)
Q Consensus 48 RRiYDItNVLEgiglI~K~-sKn~i~W~G~~~~~~~~~~~~~~~~~~Lk~El~~L~~~E~~LD~~I~~~~~~l~~l~ed 125 (243)
-++-++.|-|.++-=+.|. .||.-.|+| +|++..+.+.+.-...|+.|..++.||++|+--
T Consensus 389 ~k~~k~~kel~~~~E~n~~l~knq~vw~~-----------------kl~~~~e~~~~~~~s~d~~I~dLqEQlrDlmf~ 450 (493)
T KOG0804|consen 389 TKLKKCQKELKEEREENKKLIKNQDVWRG-----------------KLKELEEREKEALGSKDEKITDLQEQLRDLMFF 450 (493)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhHHHHHH-----------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhee
Confidence 3566677777766544332 456666655 344444556666677899999999999998753
No 249
>PTZ00064 histone acetyltransferase; Provisional
Probab=20.33 E-value=2.5e+02 Score=28.81 Aligned_cols=30 Identities=17% Similarity=0.298 Sum_probs=27.7
Q ss_pred eeHHHHHhhhcccchhhhhhHHHhhhhccceecc
Q psy7686 33 LHLKYAAENLEVKQKRRIYDITNVLEGIGLIEKN 66 (243)
Q Consensus 33 idL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~ 66 (243)
++|++++...++ +..||+..|+.+|++...
T Consensus 472 iSI~dIS~~TgI----~~eDII~TLq~L~llky~ 501 (552)
T PTZ00064 472 KFIDNVVRSTGI----RREDVIRILEENGIMRNI 501 (552)
T ss_pred ccHHHHHHHhCC----CHHHHHHHHHHCCcEEEe
Confidence 899999999999 789999999999999754
No 250
>PF06005 DUF904: Protein of unknown function (DUF904); InterPro: IPR009252 Cell division protein ZapB is a non-essential, abundant cell division factor that is required for proper Z-ring formation. It is recruited early to the divisome by direct interaction with FtsZ, stimulating Z-ring assembly and thereby promoting cell division earlier in the cell cycle. Its recruitment to the Z-ring requires functional FtsA or ZipA.; GO: 0000917 barrier septum formation, 0043093 cytokinesis by binary fission, 0005737 cytoplasm; PDB: 2JEE_A.
Probab=20.29 E-value=3.7e+02 Score=19.98 Aligned_cols=39 Identities=10% Similarity=0.224 Sum_probs=28.1
Q ss_pred HHHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhh
Q psy7686 88 QSKLIELRDEISDMRNHEAVIDEHIRKCQQSLRNIQEEE 126 (243)
Q Consensus 88 ~~~~~~Lk~El~~L~~~E~~LD~~I~~~~~~l~~l~ed~ 126 (243)
...+..|+.|++.|..+-..|.+....+.+....+.++.
T Consensus 17 veti~~Lq~e~eeLke~n~~L~~e~~~L~~en~~L~~e~ 55 (72)
T PF06005_consen 17 VETIALLQMENEELKEKNNELKEENEELKEENEQLKQER 55 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHH
Confidence 345667888888888877777777777777777666553
No 251
>PRK09462 fur ferric uptake regulator; Provisional
Probab=20.16 E-value=2e+02 Score=23.48 Aligned_cols=46 Identities=15% Similarity=0.338 Sum_probs=37.1
Q ss_pred HHHHHhhCCCCeeeHHHHHhhhc-----ccchhhhhhHHHhhhhccceeccc
Q psy7686 21 FVSLLQQAPEGVLHLKYAAENLE-----VKQKRRIYDITNVLEGIGLIEKNN 67 (243)
Q Consensus 21 Fi~ll~~~~~g~idL~~aa~~L~-----v~~KRRiYDItNVLEgiglI~K~s 67 (243)
.+++|.+++++.++..++-+.|. + .+=-+|-+.+.|+..|+|.|..
T Consensus 22 Il~~l~~~~~~h~sa~eI~~~l~~~~~~i-~~aTVYR~L~~L~e~Gli~~~~ 72 (148)
T PRK09462 22 ILEVLQEPDNHHVSAEDLYKRLIDMGEEI-GLATVYRVLNQFDDAGIVTRHN 72 (148)
T ss_pred HHHHHHhCCCCCCCHHHHHHHHHhhCCCC-CHHHHHHHHHHHHHCCCEEEEE
Confidence 56677766667789988888874 3 5678999999999999999863
No 252
>KOG2255|consensus
Probab=20.04 E-value=46 Score=30.07 Aligned_cols=30 Identities=33% Similarity=0.464 Sum_probs=26.7
Q ss_pred eHHHHHhhhcccchhhhhhHHHhhhhccceecc
Q psy7686 34 HLKYAAENLEVKQKRRIYDITNVLEGIGLIEKN 66 (243)
Q Consensus 34 dL~~aa~~L~v~~KRRiYDItNVLEgiglI~K~ 66 (243)
=|..+|++|+| +.+++-+ |.+++||+|+-.
T Consensus 63 Ml~~larrlgv-~~nt~s~--~a~~~l~~v~d~ 92 (224)
T KOG2255|consen 63 MLDMLARRLGV-PMNTISS--KALEGLGLVGDV 92 (224)
T ss_pred HHHHHHHHhCC-cccccCc--ccccceeeecce
Confidence 36789999999 9999999 999999998764
Done!