Query psy6286
Match_columns 159
No_of_seqs 132 out of 565
Neff 6.4
Searched_HMMs 46136
Date Fri Aug 16 22:33:39 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6286.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6286hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0948|consensus 100.0 4.2E-50 9.2E-55 363.3 10.2 158 2-159 843-1041(1041)
2 PF08148 DSHCT: DSHCT (NUC185) 100.0 2.2E-45 4.7E-50 288.8 9.5 136 22-159 1-180 (180)
3 KOG0947|consensus 100.0 4.9E-43 1.1E-47 322.9 10.7 158 2-159 1049-1248(1248)
4 COG4581 Superfamily II RNA hel 100.0 7.7E-31 1.7E-35 246.6 10.4 156 2-159 841-1041(1041)
5 PF04408 HA2: Helicase associa 88.6 0.39 8.4E-06 34.0 2.4 28 13-40 3-30 (102)
6 smart00421 HTH_LUXR helix_turn 86.0 2.2 4.7E-05 25.5 4.5 41 80-120 5-45 (58)
7 smart00847 HA2 Helicase associ 85.5 0.8 1.7E-05 31.2 2.5 28 13-40 3-30 (92)
8 PRK00254 ski2-like helicase; P 84.5 4.4 9.6E-05 38.0 7.8 73 80-152 568-641 (720)
9 cd06171 Sigma70_r4 Sigma70, re 84.1 2.6 5.6E-05 24.6 4.2 43 79-121 11-54 (55)
10 PRK01172 ski2-like helicase; P 84.0 18 0.00038 33.7 11.4 134 9-151 446-607 (674)
11 PF04545 Sigma70_r4: Sigma-70, 83.6 3.2 7E-05 25.2 4.5 38 86-123 13-50 (50)
12 PRK00118 putative DNA-binding 83.1 8 0.00017 28.0 7.0 55 77-131 16-71 (104)
13 cd06170 LuxR_C_like C-terminal 82.4 3.8 8.1E-05 24.6 4.5 33 85-117 7-39 (57)
14 TIGR03643 conserved hypothetic 82.2 2 4.3E-05 29.2 3.3 30 87-116 7-36 (72)
15 PF13518 HTH_28: Helix-turn-he 82.1 3.7 7.9E-05 24.7 4.3 35 85-119 4-38 (52)
16 PF10985 DUF2805: Protein of u 80.8 2.4 5.1E-05 28.9 3.3 29 88-116 7-35 (73)
17 PRK04217 hypothetical protein; 80.3 7.4 0.00016 28.4 6.0 52 78-129 42-94 (110)
18 PRK02362 ski2-like helicase; P 74.6 12 0.00026 35.3 7.2 139 9-151 467-647 (737)
19 PF13384 HTH_23: Homeodomain-l 74.3 2.4 5.1E-05 25.6 1.7 34 85-118 9-42 (50)
20 PRK12543 RNA polymerase sigma 68.2 11 0.00023 28.6 4.5 44 90-133 130-177 (179)
21 PF14947 HTH_45: Winged helix- 67.0 6.1 0.00013 26.5 2.6 34 5-38 32-68 (77)
22 TIGR02337 HpaR homoprotocatech 65.4 29 0.00064 24.5 6.1 55 56-119 14-68 (118)
23 PF13936 HTH_38: Helix-turn-he 65.1 10 0.00022 22.7 3.1 31 86-116 13-43 (44)
24 cd00180 PKc Catalytic domain o 64.3 5.3 0.00012 28.9 2.1 51 83-133 65-117 (215)
25 smart00351 PAX Paired Box doma 58.3 20 0.00043 26.3 4.2 35 85-119 25-59 (125)
26 PRK03573 transcriptional regul 57.7 41 0.0009 24.5 5.9 37 83-119 36-72 (144)
27 PF00440 TetR_N: Bacterial reg 56.3 8.7 0.00019 23.0 1.7 34 91-124 14-47 (47)
28 PF03333 PapB: Adhesin biosynt 55.7 27 0.00059 24.7 4.3 49 81-129 40-89 (91)
29 PF00196 GerE: Bacterial regul 55.2 25 0.00053 21.8 3.8 43 78-120 3-45 (58)
30 PF06969 HemN_C: HemN C-termin 55.2 11 0.00024 24.0 2.1 29 5-33 34-65 (66)
31 PF13613 HTH_Tnp_4: Helix-turn 54.6 38 0.00083 20.9 4.5 43 82-124 8-50 (53)
32 TIGR02984 Sig-70_plancto1 RNA 54.4 41 0.00089 25.2 5.6 47 78-124 140-187 (189)
33 PRK11512 DNA-binding transcrip 54.2 39 0.00085 24.8 5.3 37 82-119 44-80 (144)
34 PF08281 Sigma70_r4_2: Sigma-7 52.6 22 0.00048 21.5 3.2 30 90-119 23-52 (54)
35 PRK11664 ATP-dependent RNA hel 52.0 16 0.00036 35.2 3.6 34 7-40 384-417 (812)
36 TIGR02985 Sig70_bacteroi1 RNA 51.9 46 0.00099 23.9 5.3 47 77-123 112-159 (161)
37 PRK12514 RNA polymerase sigma 51.9 49 0.0011 24.8 5.7 47 77-123 128-175 (179)
38 PF02796 HTH_7: Helix-turn-hel 50.3 25 0.00055 20.9 3.1 33 82-114 10-42 (45)
39 PRK06759 RNA polymerase factor 50.2 33 0.00073 24.9 4.4 47 77-123 105-152 (154)
40 PF13601 HTH_34: Winged helix 49.7 17 0.00036 24.7 2.4 37 82-119 4-40 (80)
41 CHL00073 chlN photochlorophyll 49.6 24 0.00052 31.9 4.1 53 103-156 68-136 (457)
42 PF12690 BsuPI: Intracellular 49.5 1.5 3.2E-05 30.2 -2.9 25 85-109 36-60 (82)
43 cd05579 STKc_MAST_like Catalyt 49.1 14 0.00029 28.5 2.2 49 85-133 69-118 (265)
44 cd06571 Bac_DnaA_C C-terminal 48.5 81 0.0017 21.5 5.8 45 92-145 43-88 (90)
45 TIGR02989 Sig-70_gvs1 RNA poly 48.3 52 0.0011 23.9 5.2 46 78-123 111-157 (159)
46 PRK09642 RNA polymerase sigma 47.4 44 0.00096 24.5 4.7 47 78-124 106-153 (160)
47 PRK09648 RNA polymerase sigma 47.3 44 0.00094 25.4 4.7 48 78-125 139-187 (189)
48 PRK09639 RNA polymerase sigma 46.9 45 0.00097 24.5 4.7 38 87-125 122-159 (166)
49 PRK12542 RNA polymerase sigma 46.7 92 0.002 23.5 6.5 51 77-127 121-172 (185)
50 TIGR02948 SigW_bacill RNA poly 46.4 56 0.0012 24.4 5.2 35 90-124 149-183 (187)
51 TIGR01970 DEAH_box_HrpB ATP-de 45.9 23 0.0005 34.2 3.6 34 7-40 381-414 (819)
52 PF01527 HTH_Tnp_1: Transposas 45.7 16 0.00034 23.6 1.8 29 90-118 20-48 (76)
53 COG4910 PduE Propanediol dehyd 45.4 33 0.00072 26.3 3.6 64 78-146 44-108 (170)
54 PF03444 HrcA_DNA-bdg: Winged 45.1 22 0.00047 24.5 2.4 28 9-36 40-73 (78)
55 cd00090 HTH_ARSR Arsenical Res 45.0 49 0.0011 20.2 4.0 30 90-119 17-46 (78)
56 TIGR02999 Sig-70_X6 RNA polyme 44.9 48 0.001 24.8 4.6 46 79-124 135-181 (183)
57 PRK13919 putative RNA polymera 44.0 51 0.0011 24.8 4.6 46 78-123 135-181 (186)
58 TIGR02937 sigma70-ECF RNA poly 43.6 53 0.0012 22.8 4.5 45 79-123 111-156 (158)
59 PRK12522 RNA polymerase sigma 43.3 52 0.0011 24.5 4.6 46 79-124 120-166 (173)
60 PF13730 HTH_36: Helix-turn-he 42.2 31 0.00067 20.9 2.6 25 95-119 27-51 (55)
61 PRK09047 RNA polymerase factor 41.7 79 0.0017 23.0 5.3 49 78-126 106-155 (161)
62 TIGR02479 FliA_WhiG RNA polyme 41.3 78 0.0017 24.9 5.5 46 78-123 175-221 (224)
63 cd06654 STKc_PAK1 Catalytic do 41.2 29 0.00063 27.9 3.0 45 84-128 92-136 (296)
64 PRK10573 type IV pilin biogene 40.8 1.6E+02 0.0035 25.3 7.8 55 85-143 304-364 (399)
65 PF13412 HTH_24: Winged helix- 40.8 36 0.00079 20.1 2.8 29 91-119 15-43 (48)
66 cd06656 STKc_PAK3 Catalytic do 40.8 30 0.00065 27.9 3.1 45 84-128 91-135 (297)
67 TIGR02941 Sigma_B RNA polymera 39.8 58 0.0013 26.2 4.6 38 87-124 215-252 (255)
68 PRK12525 RNA polymerase sigma 39.7 91 0.002 23.2 5.4 45 79-123 119-164 (168)
69 PF14493 HTH_40: Helix-turn-he 39.6 81 0.0018 21.5 4.7 35 86-120 6-40 (91)
70 PRK12531 RNA polymerase sigma 39.4 1.1E+02 0.0023 23.4 5.9 49 78-126 141-190 (194)
71 COG1420 HrcA Transcriptional r 39.4 23 0.0005 30.9 2.2 24 9-32 44-72 (346)
72 PF01047 MarR: MarR family; I 39.0 45 0.00098 20.3 3.1 38 81-119 6-43 (59)
73 PF08461 HTH_12: Ribonuclease 38.3 40 0.00088 22.0 2.8 27 7-33 33-63 (66)
74 PF12802 MarR_2: MarR family; 37.7 40 0.00087 20.7 2.7 29 91-119 17-47 (62)
75 PRK06930 positive control sigm 37.0 1E+02 0.0022 23.8 5.4 47 77-123 113-160 (170)
76 PRK13777 transcriptional regul 36.9 1.2E+02 0.0027 23.8 5.9 29 91-119 57-85 (185)
77 PRK09645 RNA polymerase sigma 36.9 1.1E+02 0.0023 22.7 5.4 48 78-125 118-166 (173)
78 PF13463 HTH_27: Winged helix 36.8 34 0.00073 21.4 2.3 28 92-119 17-44 (68)
79 PRK08583 RNA polymerase sigma 36.8 69 0.0015 25.8 4.6 47 78-124 205-252 (257)
80 PF04255 DUF433: Protein of un 36.7 36 0.00077 21.4 2.3 32 80-111 18-50 (56)
81 KOG4456|consensus 36.6 49 0.0011 25.0 3.3 50 88-150 67-117 (134)
82 PF13551 HTH_29: Winged helix- 36.6 66 0.0014 21.9 3.9 34 85-118 3-37 (112)
83 COG1393 ArsC Arsenate reductas 36.2 54 0.0012 23.9 3.5 24 132-155 76-99 (117)
84 TIGR02120 GspF general secreti 35.9 1.3E+02 0.0029 25.8 6.5 57 84-144 304-366 (399)
85 smart00418 HTH_ARSR helix_turn 35.1 85 0.0018 18.5 3.9 29 91-119 8-36 (66)
86 PRK09644 RNA polymerase sigma 34.9 1.2E+02 0.0027 22.3 5.4 51 77-127 107-158 (165)
87 PRK12511 RNA polymerase sigma 34.6 1.2E+02 0.0027 23.0 5.6 49 78-126 111-160 (182)
88 PRK12528 RNA polymerase sigma 34.1 85 0.0018 23.0 4.4 45 78-122 113-158 (161)
89 PRK12541 RNA polymerase sigma 34.0 76 0.0017 23.3 4.1 47 79-125 113-160 (161)
90 PRK13870 transcriptional regul 33.8 78 0.0017 25.6 4.4 60 79-152 174-234 (234)
91 cd00131 PAX Paired Box domain 33.8 78 0.0017 23.3 4.1 34 86-119 26-59 (128)
92 PRK06986 fliA flagellar biosyn 33.3 86 0.0019 24.9 4.6 36 89-124 196-231 (236)
93 TIGR02950 SigM_subfam RNA poly 32.8 72 0.0016 23.0 3.8 35 90-124 118-152 (154)
94 PRK09333 30S ribosomal protein 32.8 36 0.00077 26.3 2.1 25 9-33 98-125 (150)
95 PF07900 DUF1670: Protein of u 32.4 1.3E+02 0.0027 24.8 5.3 66 53-118 120-188 (220)
96 PF09339 HTH_IclR: IclR helix- 32.3 40 0.00087 20.5 2.0 28 92-119 17-44 (52)
97 cd05578 STKc_Yank1 Catalytic d 32.2 33 0.00073 26.5 2.0 49 84-132 75-124 (258)
98 PF13404 HTH_AsnC-type: AsnC-t 32.2 50 0.0011 19.6 2.3 25 94-118 18-42 (42)
99 COG1321 TroR Mn-dependent tran 32.1 47 0.001 25.4 2.7 34 6-39 38-76 (154)
100 PRK15443 pduE propanediol dehy 31.7 77 0.0017 24.1 3.7 54 91-148 21-78 (138)
101 TIGR02846 spore_sigmaK RNA pol 31.6 1.3E+02 0.0029 23.7 5.4 46 78-123 174-224 (227)
102 PRK09413 IS2 repressor TnpA; R 31.4 70 0.0015 23.1 3.5 36 83-118 19-54 (121)
103 PRK09643 RNA polymerase sigma 31.2 1.4E+02 0.0029 22.9 5.3 41 89-129 146-186 (192)
104 PRK12539 RNA polymerase sigma 31.1 1.6E+02 0.0035 22.1 5.6 48 77-124 130-178 (184)
105 smart00221 STYKc Protein kinas 31.0 44 0.00096 24.7 2.4 51 83-133 71-123 (225)
106 TIGR02983 SigE-fam_strep RNA p 31.0 1.1E+02 0.0023 22.4 4.5 37 89-125 122-158 (162)
107 PRK09480 slmA division inhibit 30.9 50 0.0011 24.7 2.7 33 92-124 29-61 (194)
108 PRK05803 sporulation sigma fac 30.9 1.2E+02 0.0025 24.1 5.0 35 91-125 193-227 (233)
109 cd05122 PKc_STE Catalytic doma 30.8 31 0.00068 26.0 1.6 50 84-133 72-123 (253)
110 COG2771 CsgD DNA-binding HTH d 30.6 1.3E+02 0.0028 18.2 4.2 39 82-120 8-46 (65)
111 smart00346 HTH_ICLR helix_turn 30.5 1.1E+02 0.0024 20.1 4.1 37 83-119 10-46 (91)
112 PRK05602 RNA polymerase sigma 30.4 1.4E+02 0.0031 22.4 5.2 50 78-127 128-178 (186)
113 PRK12538 RNA polymerase sigma 30.2 93 0.002 25.0 4.3 49 78-126 171-220 (233)
114 cd07841 STKc_CDK7 Catalytic do 30.1 40 0.00087 26.8 2.2 44 85-129 78-123 (298)
115 PF00165 HTH_AraC: Bacterial r 29.9 52 0.0011 18.9 2.1 28 90-117 5-32 (42)
116 PRK08301 sporulation sigma fac 29.9 92 0.002 24.6 4.2 33 91-123 196-228 (234)
117 PRK12547 RNA polymerase sigma 29.6 1.8E+02 0.0039 21.4 5.6 48 78-125 112-160 (164)
118 cd08215 STKc_Nek Catalytic dom 29.6 35 0.00075 26.0 1.6 52 82-133 72-128 (258)
119 PRK12518 RNA polymerase sigma 29.1 1E+02 0.0023 22.7 4.2 38 90-127 133-170 (175)
120 cd06614 STKc_PAK Catalytic dom 29.0 52 0.0011 26.0 2.7 50 83-132 89-140 (286)
121 TIGR02952 Sig70_famx2 RNA poly 28.9 1.3E+02 0.0027 22.0 4.6 46 78-123 122-168 (170)
122 TIGR02835 spore_sigmaE RNA pol 28.8 1.1E+02 0.0024 24.3 4.5 33 92-124 197-229 (234)
123 PRK07037 extracytoplasmic-func 28.8 1.1E+02 0.0023 22.4 4.1 38 90-127 122-159 (163)
124 PRK12537 RNA polymerase sigma 28.8 1.3E+02 0.0028 22.6 4.7 35 90-124 146-180 (182)
125 cd06606 STKc_MAPKKK Catalytic 28.8 39 0.00084 25.6 1.8 51 83-133 75-126 (260)
126 PRK12519 RNA polymerase sigma 28.7 91 0.002 23.6 3.9 34 91-124 155-188 (194)
127 PRK11202 DNA-binding transcrip 28.6 1.2E+02 0.0026 23.3 4.6 35 92-126 31-65 (203)
128 cd03572 ENTH_epsin_related ENT 28.5 1.3E+02 0.0029 22.2 4.5 44 105-148 68-118 (122)
129 PRK06811 RNA polymerase factor 28.4 1.6E+02 0.0035 22.3 5.2 47 77-123 130-177 (189)
130 cd05611 STKc_Rim15_like Cataly 27.9 48 0.001 25.6 2.2 50 84-133 72-122 (260)
131 PRK12532 RNA polymerase sigma 27.8 1.2E+02 0.0027 23.0 4.5 48 79-126 137-185 (195)
132 COG2442 Uncharacterized conser 27.8 1E+02 0.0022 21.1 3.6 32 84-115 34-66 (79)
133 PRK07408 RNA polymerase sigma 27.8 1.2E+02 0.0026 24.6 4.7 38 87-124 213-250 (256)
134 PRK09641 RNA polymerase sigma 27.8 1.4E+02 0.003 22.2 4.7 37 88-124 147-183 (187)
135 PRK11924 RNA polymerase sigma 27.7 1.4E+02 0.003 21.8 4.6 37 90-126 138-174 (179)
136 PRK13344 spxA transcriptional 27.5 61 0.0013 24.0 2.6 77 79-155 8-98 (132)
137 TIGR02947 SigH_actino RNA poly 27.5 1E+02 0.0022 23.4 4.0 37 89-125 143-179 (193)
138 TIGR02939 RpoE_Sigma70 RNA pol 27.5 94 0.002 23.2 3.7 34 91-124 152-185 (190)
139 cd06630 STKc_MEKK1 Catalytic d 27.3 46 0.001 25.8 2.0 47 82-128 76-123 (268)
140 PF08158 NUC130_3NT: NUC130/3N 27.2 1.2E+02 0.0026 19.1 3.6 40 106-149 9-48 (52)
141 cd00569 HTH_Hin_like Helix-tur 27.0 84 0.0018 15.6 2.5 29 85-113 13-41 (42)
142 COG1202 Superfamily II helicas 26.9 2.2E+02 0.0047 27.3 6.4 60 88-147 761-826 (830)
143 TIGR01889 Staph_reg_Sar staphy 26.8 83 0.0018 22.1 3.1 28 92-119 42-69 (109)
144 cd06640 STKc_MST4 Catalytic do 26.7 49 0.0011 26.1 2.1 46 82-127 75-120 (277)
145 smart00347 HTH_MARR helix_turn 26.5 92 0.002 20.4 3.2 29 91-119 22-50 (101)
146 PRK12523 RNA polymerase sigma 26.3 1.5E+02 0.0032 22.1 4.6 46 78-123 119-165 (172)
147 PF12246 MKT1_C: Temperature d 26.1 30 0.00066 28.3 0.8 28 14-41 1-28 (243)
148 PRK12530 RNA polymerase sigma 26.1 1.5E+02 0.0032 22.6 4.6 35 91-125 148-182 (189)
149 PF01022 HTH_5: Bacterial regu 26.1 1.5E+02 0.0032 17.5 3.7 35 85-119 6-41 (47)
150 TIGR02511 type_III_tyeA type I 25.9 1.4E+02 0.0031 20.2 4.0 56 88-145 16-72 (79)
151 PRK09652 RNA polymerase sigma 25.8 1.5E+02 0.0034 21.6 4.6 36 88-123 139-174 (182)
152 cd08217 STKc_Nek2 Catalytic do 25.6 68 0.0015 24.5 2.7 42 84-125 76-122 (265)
153 TIGR02954 Sig70_famx3 RNA poly 25.6 1.2E+02 0.0026 22.4 4.0 46 78-123 119-165 (169)
154 PF01710 HTH_Tnp_IS630: Transp 25.5 78 0.0017 22.8 2.8 30 86-115 11-40 (119)
155 PRK12526 RNA polymerase sigma 25.5 2.2E+02 0.0047 22.1 5.6 49 77-125 152-201 (206)
156 PRK12540 RNA polymerase sigma 25.4 2.2E+02 0.0047 21.7 5.5 51 77-127 110-161 (182)
157 PRK07122 RNA polymerase sigma 25.1 1.3E+02 0.0028 24.6 4.4 38 87-124 225-262 (264)
158 PRK12527 RNA polymerase sigma 25.1 1.9E+02 0.0042 21.0 5.0 49 78-126 105-154 (159)
159 PRK10870 transcriptional repre 24.9 3.1E+02 0.0067 21.0 6.2 27 93-119 71-97 (176)
160 PF04967 HTH_10: HTH DNA bindi 24.9 87 0.0019 19.8 2.6 32 88-119 18-49 (53)
161 TIGR02980 SigBFG RNA polymeras 24.5 1.5E+02 0.0033 23.1 4.6 35 90-124 191-225 (227)
162 PRK15215 fimbriae biosynthesis 24.5 1.7E+02 0.0036 21.2 4.2 45 84-128 51-96 (100)
163 PRK09638 RNA polymerase sigma 24.4 1.2E+02 0.0026 22.4 3.8 33 91-123 140-172 (176)
164 PRK12534 RNA polymerase sigma 24.3 2.8E+02 0.0061 20.7 5.9 35 90-124 150-184 (187)
165 PRK07670 RNA polymerase sigma 24.2 2.3E+02 0.0049 22.8 5.6 47 78-124 201-248 (251)
166 PRK11923 algU RNA polymerase s 24.2 1.1E+02 0.0024 23.1 3.7 33 91-123 152-184 (193)
167 PRK12512 RNA polymerase sigma 24.2 1.2E+02 0.0026 22.7 3.8 49 78-126 131-180 (184)
168 KOG3337|consensus 24.2 1.6E+02 0.0034 23.7 4.4 100 33-146 64-185 (201)
169 smart00344 HTH_ASNC helix_turn 24.0 1.1E+02 0.0025 20.9 3.4 37 82-119 7-43 (108)
170 cd06632 STKc_MEKK1_plant Catal 23.9 55 0.0012 25.0 1.9 45 84-128 77-122 (258)
171 PF09821 AAA_assoc_C: C-termin 23.6 94 0.002 22.8 2.9 33 5-37 10-45 (120)
172 PRK12546 RNA polymerase sigma 23.5 2.3E+02 0.005 21.7 5.3 51 77-127 112-163 (188)
173 PRK09415 RNA polymerase factor 23.0 1.4E+02 0.003 22.5 3.9 47 78-124 127-174 (179)
174 PRK06704 RNA polymerase factor 22.8 1.2E+02 0.0027 24.5 3.8 48 78-125 116-164 (228)
175 PF11269 DUF3069: Protein of u 22.7 1.4E+02 0.003 22.3 3.6 25 117-144 96-120 (121)
176 cd06641 STKc_MST3 Catalytic do 22.6 45 0.00098 26.3 1.2 45 84-128 77-121 (277)
177 cd06655 STKc_PAK2 Catalytic do 22.5 62 0.0013 26.0 2.0 45 84-128 91-135 (296)
178 PF07638 Sigma70_ECF: ECF sigm 22.4 1.8E+02 0.004 22.2 4.6 45 78-122 135-180 (185)
179 PRK09640 RNA polymerase sigma 22.1 1.4E+02 0.003 22.6 3.8 36 89-124 146-181 (188)
180 TIGR02859 spore_sigH RNA polym 21.7 2.1E+02 0.0046 21.4 4.8 32 92-123 164-195 (198)
181 cd05123 STKc_AGC Catalytic dom 21.6 76 0.0016 24.2 2.2 50 83-132 67-117 (250)
182 cd06659 STKc_PAK6 Catalytic do 21.6 65 0.0014 25.9 1.9 44 85-128 94-137 (297)
183 PRK00794 flbT flagellar biosyn 21.6 3E+02 0.0065 20.6 5.4 43 108-153 68-110 (132)
184 PRK12533 RNA polymerase sigma 21.5 2.2E+02 0.0049 22.5 5.0 48 79-126 135-183 (216)
185 TIGR02943 Sig70_famx1 RNA poly 21.5 1.5E+02 0.0032 22.6 3.9 37 90-126 144-180 (188)
186 PRK11179 DNA-binding transcrip 21.4 1E+02 0.0023 22.9 2.9 34 86-119 14-49 (153)
187 PRK12545 RNA polymerase sigma 21.3 1.5E+02 0.0033 22.8 3.9 37 90-126 152-188 (201)
188 PRK09647 RNA polymerase sigma 21.2 1.7E+02 0.0037 22.8 4.2 37 91-127 152-188 (203)
189 PRK08215 sporulation sigma fac 21.2 1.8E+02 0.004 23.4 4.5 35 89-123 221-255 (258)
190 TIGR03613 RutR pyrimidine util 21.1 93 0.002 23.5 2.6 35 92-126 27-61 (202)
191 cd06647 STKc_PAK_I Catalytic d 21.1 66 0.0014 25.8 1.9 46 83-128 90-135 (293)
192 PRK12536 RNA polymerase sigma 21.1 1.5E+02 0.0032 22.3 3.7 47 77-123 128-175 (181)
193 TIGR01967 DEAH_box_HrpA ATP-de 21.1 1E+02 0.0022 31.6 3.4 33 8-40 450-485 (1283)
194 cd06611 STKc_SLK_like Catalyti 21.0 91 0.002 24.4 2.6 48 82-129 75-124 (280)
195 KOG0578|consensus 21.0 41 0.00088 31.2 0.6 34 82-115 343-376 (550)
196 PRK10359 lipopolysaccharide co 21.0 76 0.0017 25.9 2.2 47 85-138 119-165 (232)
197 cd01043 DPS DPS protein, ferri 20.9 2.7E+02 0.0059 20.0 5.0 44 110-153 91-134 (139)
198 PF11994 DUF3489: Protein of u 20.6 1.6E+02 0.0035 19.9 3.3 28 82-109 13-40 (72)
199 PRK09649 RNA polymerase sigma 20.6 1.9E+02 0.0042 21.8 4.3 47 77-123 129-176 (185)
200 PRK05572 sporulation sigma fac 20.4 2.1E+02 0.0045 23.0 4.6 47 78-124 202-249 (252)
201 cd03565 VHS_Tom1 VHS domain fa 20.4 1.5E+02 0.0032 22.2 3.5 39 113-153 102-140 (141)
202 TIGR02850 spore_sigG RNA polym 20.3 1.9E+02 0.0041 23.3 4.4 35 89-123 218-252 (254)
203 COG1309 AcrR Transcriptional r 20.3 1.2E+02 0.0027 21.1 3.0 37 92-128 31-67 (201)
204 PF11027 DUF2615: Protein of u 20.2 77 0.0017 23.0 1.8 17 112-128 16-32 (103)
205 PRK12535 RNA polymerase sigma 20.1 2.1E+02 0.0046 22.0 4.5 48 77-124 132-180 (196)
No 1
>KOG0948|consensus
Probab=100.00 E-value=4.2e-50 Score=363.32 Aligned_cols=158 Identities=59% Similarity=0.955 Sum_probs=153.0
Q ss_pred cchhHHHHHHHHHHHhhhCCccCCCccchhhHHHhhhcCCCceeeec--cC---------------------------cH
Q psy6286 2 SLLHMEELKCRKRVLRRLGYATEADVIEMKGRVACELSKSEETVILT--IN---------------------------DK 52 (159)
Q Consensus 2 ~~~~~~e~~~~~~vL~~lgyid~~~~vt~kGrva~~I~s~~eLlltE--f~---------------------------p~ 52 (159)
++++++|+++|.+||++|||++.++++.+|||+||||+|+|||++|| |+ |+
T Consensus 843 ~i~~ldELk~RkRVLrrLG~~t~ddvie~KGrvACEIsSgDELlLTEliFnG~Fndl~~eq~aaLLSCfVf~eks~e~~~ 922 (1041)
T KOG0948|consen 843 AILQLDELKNRKRVLRRLGYCTSDDVIELKGRVACEISSGDELLLTELIFNGIFNDLPVEQAAALLSCFVFQEKSSEAPK 922 (1041)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCCCCeEEEcceEEEEecccchHHHHHHHHhccccCCCHHHHHHHHhheeehhccccccc
Confidence 57899999999999999999999999999999999999999999999 44 11
Q ss_pred ------------HHHHHHHHHHHHHcCCCCChhhhhccCCchHHHHHHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHH
Q psy6286 53 ------------LELARHIARISIESKLDLDEDSYVNQFKPSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEV 120 (159)
Q Consensus 53 ------------~~i~~~i~~~~~~~~l~~~~~~~~~~~~~~l~~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~el 120 (159)
++.|++|++++.+|++++++++|+++|+|.+|+|||.|++|+||.+||++|+++||+|||++|||+|+
T Consensus 923 l~~el~~~l~~lqe~ArrIAkVs~ecKlEide~~Yv~sFkp~LMdvVy~W~~GatF~eIckmTdvfEGSiIR~~RRLeEl 1002 (1041)
T KOG0948|consen 923 LKEELAGPLRQLQESARRIAKVSKECKLEIDEEDYVESFKPELMDVVYAWAKGATFAEICKMTDVFEGSIIRTFRRLEEL 1002 (1041)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHhhccccCHHHHHHhcChHHHHHHHHHHccccHHHHHHHhhhhhhHHHHHHHHHHHH
Confidence 79999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhhhhCChHHHHHHHHHHHhhcCCcccccccCC
Q psy6286 121 LRQLVQASRNIGNTLLEEKFNEAIKTVKRDIFLEILENL 159 (159)
Q Consensus 121 Lrql~~a~~~ig~~~L~~k~~~a~~~I~RdIV~~~sl~~ 159 (159)
||||.+||+.|||.+|.+||++++.+|+|||||++||||
T Consensus 1003 LrQl~~AAk~iGnteLe~Kf~~~~~~ikRDIVFAaSLYL 1041 (1041)
T KOG0948|consen 1003 LRQLIDAAKVIGNTELENKFEEAIKKIKRDIVFAASLYL 1041 (1041)
T ss_pred HHHHHHHHHHhcchHHHHHHHHHHHHHhhceeehhhccC
Confidence 999999999999999999999999999999999999997
No 2
>PF08148 DSHCT: DSHCT (NUC185) domain; InterPro: IPR012961 This C-terminal domain is found in DOB1/SK12/helY-like DEAD box helicases [].; GO: 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides; PDB: 4A4Z_A 2XGJ_B 3L9O_A.
Probab=100.00 E-value=2.2e-45 Score=288.78 Aligned_cols=136 Identities=43% Similarity=0.745 Sum_probs=114.8
Q ss_pred ccCCCccchhhHHHhhhcCCCceeeec------cC---c---------------------------H--------HHHHH
Q psy6286 22 ATEADVIEMKGRVACELSKSEETVILT------IN---D---------------------------K--------LELAR 57 (159)
Q Consensus 22 id~~~~vt~kGrva~~I~s~~eLlltE------f~---p---------------------------~--------~~i~~ 57 (159)
||++++||+|||+||+|++++||++|| |+ | . .++++
T Consensus 1 id~~~~vt~kGr~a~~I~~~~eLl~te~l~~g~f~~L~p~elAa~lS~~v~e~~~~~~~~~~~~~~~l~~~~~~l~~~~~ 80 (180)
T PF08148_consen 1 IDEDNVVTLKGRVACEIYSEDELLLTELLFSGVFDDLDPAELAALLSCFVYEPRREDEEERYPPSPRLREALEQLQEIAE 80 (180)
T ss_dssp B-TTS-BSHHHHHHCC--SSTHHHHHHHHHCTCCCCS-HHHHHHHHHHHC-----SS---------HHHHHHHHHHHHHH
T ss_pred CCCCCccCHHHHHHHHHcCcccHHHHHHHHcCCCCCCCHHHHHHHHHHhhcccccCcccccccccHHHHHHHHHHHHHHH
Confidence 688999999999999999999999999 33 1 0 68889
Q ss_pred HHHHHHHHcCCCCChhhhhccCCchHHHHHHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHHhhhhhCChHHH
Q psy6286 58 HIARISIESKLDLDEDSYVNQFKPSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLE 137 (159)
Q Consensus 58 ~i~~~~~~~~l~~~~~~~~~~~~~~l~~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~a~~~ig~~~L~ 137 (159)
+|.+++.+||+ +.++|.+.++|++|+++|+||+|+||++||+.|+++||||||++||++|+||||++|++++|||+|+
T Consensus 81 ~l~~~~~~~~l--~~~~~~~~~~~~l~~~v~~Wa~G~~~~~i~~~t~l~EGdiVR~~rRl~dlLrql~~aa~~~g~~~L~ 158 (180)
T PF08148_consen 81 RLAKVEREHGL--DEEEYVERFDPGLMEVVYAWASGASFAEILEMTDLFEGDIVRWIRRLIDLLRQLANAAKIIGDPELA 158 (180)
T ss_dssp HHHHHHHHTT---HHHHHHHCSTTTTHHHHHHHHCT--HHHHCCT-SS-HHHHHHHHHHHHHHHHHHHHHHHCCT-HHHH
T ss_pred HHHHHHHHhCC--CCcccccCCCccHHHHHHHHHCCCCHHHHHhcCCCCchHHHHHHHHHHHHHHHHHHHHHhcCCHHHH
Confidence 99999999999 5667888889999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhhcCCcccccccCC
Q psy6286 138 EKFNEAIKTVKRDIFLEILENL 159 (159)
Q Consensus 138 ~k~~~a~~~I~RdIV~~~sl~~ 159 (159)
+|+++|+++|||||||++|||+
T Consensus 159 ~~~~~a~~~i~R~iV~~~SLYl 180 (180)
T PF08148_consen 159 EKAREAIDLIRRDIVFASSLYL 180 (180)
T ss_dssp HHHHHHHHHHSHCCCC---TT-
T ss_pred HHHHHHHHhccCCccccccccC
Confidence 9999999999999999999997
No 3
>KOG0947|consensus
Probab=100.00 E-value=4.9e-43 Score=322.95 Aligned_cols=158 Identities=32% Similarity=0.570 Sum_probs=150.1
Q ss_pred cchhHHHHHHHHHHHhhhCCccCCCccchhhHHHhhhcCCCceeeec--cC-------cH--------------------
Q psy6286 2 SLLHMEELKCRKRVLRRLGYATEADVIEMKGRVACELSKSEETVILT--IN-------DK-------------------- 52 (159)
Q Consensus 2 ~~~~~~e~~~~~~vL~~lgyid~~~~vt~kGrva~~I~s~~eLlltE--f~-------p~-------------------- 52 (159)
+|.++|+|.+|++||+.+||+|+..+|++|||+||+|++++||++|| |+ |.
T Consensus 1049 ~L~l~pey~~RlevLk~~g~vD~~~~V~lkGRvAceI~s~~ELllteli~dn~l~~l~peeiaallSslV~e~~~e~~~~ 1128 (1248)
T KOG0947|consen 1049 SLLLSPEYHNRLEVLKPLGFVDEMRTVLLKGRVACEINSGNELLLTELIFDNALVDLSPEEIAALLSSLVCEGKTERPPT 1128 (1248)
T ss_pred hhhhCHHHHHHHHHHhhcCcccccceeeecceeeeeecCCcchhHHHHHHhhhhhhcCHHHHHHHHHHHHhcCccccCCC
Confidence 67889999999999999999999999999999999999999999999 55 21
Q ss_pred ------------HHHHHHHHHHHHHcCCCCChh-hhhccCCchHHHHHHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHH
Q psy6286 53 ------------LELARHIARISIESKLDLDED-SYVNQFKPSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEE 119 (159)
Q Consensus 53 ------------~~i~~~i~~~~~~~~l~~~~~-~~~~~~~~~l~~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~e 119 (159)
.+++.++..++..|++..+++ +|...++|+||++||+||+|.||.+||++|++.||+|||+|+||+|
T Consensus 1129 ~~~~l~k~~e~v~~v~~rl~ev~~~~~~~~~~~e~f~~~lrF~l~evVYeWA~G~sf~eim~~t~~~EG~iVR~I~RLdE 1208 (1248)
T KOG0947|consen 1129 LTPYLKKGKERVRDVAKRLEEVQSSHQLLQTPEEEFPCELRFGLVEVVYEWARGLSFKEIMELTDVLEGLIVRLIQRLDE 1208 (1248)
T ss_pred CChhhhhHHHHHHHHHHHHHHHHHhhccccCchhhccccccccHHHHHHHHHcCCCHHHHHhhhCCcchhHHHHHHHHHH
Confidence 688999999999999988774 6888999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhhhhCChHHHHHHHHHHHhhcCCcccccccCC
Q psy6286 120 VLRQLVQASRNIGNTLLEEKFNEAIKTVKRDIFLEILENL 159 (159)
Q Consensus 120 lLrql~~a~~~ig~~~L~~k~~~a~~~I~RdIV~~~sl~~ 159 (159)
+|||+++|++++|||.|.+||++|.++|||||||++|||+
T Consensus 1209 ~cre~~~aa~ivGd~~L~~Km~~as~~ikRdIVFaaSLY~ 1248 (1248)
T KOG0947|consen 1209 VCRELRNAARIVGDPVLHEKMEAASALIKRDIVFAASLYL 1248 (1248)
T ss_pred HHHhhhccceecCcHHHHHHHHHHHHHhccCccchhhccC
Confidence 9999999999999999999999999999999999999996
No 4
>COG4581 Superfamily II RNA helicase [DNA replication, recombination, and repair]
Probab=99.97 E-value=7.7e-31 Score=246.63 Aligned_cols=156 Identities=39% Similarity=0.665 Sum_probs=145.9
Q ss_pred cchhHHHHHHHHHHHhhhCCccCCCccchhhHHHhhhcCCCceeeec------cC--------------------c----
Q psy6286 2 SLLHMEELKCRKRVLRRLGYATEADVIEMKGRVACELSKSEETVILT------IN--------------------D---- 51 (159)
Q Consensus 2 ~~~~~~e~~~~~~vL~~lgyid~~~~vt~kGrva~~I~s~~eLlltE------f~--------------------p---- 51 (159)
.+.++++|+.+..+|+.+||++.+..++.|||+||+|++++|+++|| |+ |
T Consensus 841 ~~~~l~~~~~l~~~l~~~g~~~~~~~v~~kGr~a~eI~s~~ellL~e~i~~g~f~~l~p~e~aallSa~v~e~~~~d~~~ 920 (1041)
T COG4581 841 ALSFLDDYKTLQEVLKKLGFIEDNAVVLIKGRVAAEISSEDELLLTELIFSGEFNDLEPEELAALLSAFVFEEKTDDGTA 920 (1041)
T ss_pred HhhhhHHHHHHHHHHHhhcCCCcccccccccceeeeecCCCchHHHHHHHcCCccCCCHHHHHHHHHheeeccCCccccc
Confidence 35678999999999999999998889999999999999999999999 43 1
Q ss_pred H---------------HHHHHHHHHHHHHcCCCCChhhhhccCCchHHHHHHHhhCCCCHHHHHhhcCCCccHHHHHHHH
Q psy6286 52 K---------------LELARHIARISIESKLDLDEDSYVNQFKPSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRR 116 (159)
Q Consensus 52 ~---------------~~i~~~i~~~~~~~~l~~~~~~~~~~~~~~l~~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rR 116 (159)
. .+++++|.++++.|++++..+ ++.+.+++|++||.||+|.+|.+||..|++.|||+||+++|
T Consensus 921 ~~~~~~~~l~~~~~~l~e~~~kl~~~~~~~~i~~~~~--l~~~~~~lm~vv~~wa~g~s~~~i~~~~~~~eGs~vR~~~r 998 (1041)
T COG4581 921 EAPEITPALRDALLRLLELARKLNKDQNSSQIEIYPE--LNDFSVGLMEVVYEWARGLSFADICGLTSLLEGSFVRIFRR 998 (1041)
T ss_pred ccccCCHHHHhHHHHHHHHHHHHHHHHHhcCCcCCcc--cccccccHHHHHHHHHhhcchhhhhcCCcccccchhhhhhH
Confidence 0 688999999999999998654 56889999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhhhhhCChHHHHHHHHHHHhhcCCcccccccCC
Q psy6286 117 LEEVLRQLVQASRNIGNTLLEEKFNEAIKTVKRDIFLEILENL 159 (159)
Q Consensus 117 l~elLrql~~a~~~ig~~~L~~k~~~a~~~I~RdIV~~~sl~~ 159 (159)
+.|+|+|+.+++.++||++|.+|+..|+..|||||||..|||+
T Consensus 999 ~~ell~ql~~aa~~ig~~~L~~k~~~~~~~irr~iv~~~sly~ 1041 (1041)
T COG4581 999 LRELLRQLRKAASVIGNPELEEKAYRAIQEIRRDIVFVDSLYL 1041 (1041)
T ss_pred HHHHHHHhhhcccccCCHHHHHHHHHHHHhhhcCeEecccccC
Confidence 9999999999999999999999999999999999999999996
No 5
>PF04408 HA2: Helicase associated domain (HA2); InterPro: IPR007502 This presumed domain is about 90 amino acid residues in length. It is found as a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding.; GO: 0004386 helicase activity; PDB: 3I4U_A 2XAU_B 3KX2_B.
Probab=88.65 E-value=0.39 Score=33.97 Aligned_cols=28 Identities=25% Similarity=0.313 Sum_probs=22.2
Q ss_pred HHHHhhhCCccCCCccchhhHHHhhhcC
Q psy6286 13 KRVLRRLGYATEADVIEMKGRVACELSK 40 (159)
Q Consensus 13 ~~vL~~lgyid~~~~vt~kGrva~~I~s 40 (159)
++.|..+|.+|+++.+|..|+.++.+--
T Consensus 3 ~~~L~~Lgald~~~~lT~lG~~~~~lPl 30 (102)
T PF04408_consen 3 LELLKSLGALDENGNLTPLGRKMSQLPL 30 (102)
T ss_dssp HHHHHHTTSB-TTS-B-HHHHHHTTSSS
T ss_pred HHHHHHCCCCCCCCCcCHHHHHHHHCCC
Confidence 4679999999999999999999998765
No 6
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=86.04 E-value=2.2 Score=25.50 Aligned_cols=41 Identities=15% Similarity=0.196 Sum_probs=32.9
Q ss_pred CchHHHHHHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHH
Q psy6286 80 KPSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEV 120 (159)
Q Consensus 80 ~~~l~~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~el 120 (159)
.+.-..++..+..|.|..+|.+..++.++.+=+.+.|+..-
T Consensus 5 ~~~e~~i~~~~~~g~s~~eia~~l~is~~tv~~~~~~~~~k 45 (58)
T smart00421 5 TPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRK 45 (58)
T ss_pred CHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 33334566678899999999999999999999988877443
No 7
>smart00847 HA2 Helicase associated domain (HA2) Add an annotation. This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding.
Probab=85.50 E-value=0.8 Score=31.18 Aligned_cols=28 Identities=25% Similarity=0.286 Sum_probs=24.7
Q ss_pred HHHHhhhCCccCCCccchhhHHHhhhcC
Q psy6286 13 KRVLRRLGYATEADVIEMKGRVACELSK 40 (159)
Q Consensus 13 ~~vL~~lgyid~~~~vt~kGrva~~I~s 40 (159)
.+.|..+|-+|.++.+|..|+..+++-.
T Consensus 3 ~~~L~~LgAld~~~~lT~lG~~m~~lPl 30 (92)
T smart00847 3 LELLYELGALDDDGRLTPLGRKMAELPL 30 (92)
T ss_pred HHHHHHCCCcCCCCCcCHHHHHHHHCCC
Confidence 4689999999998899999999998754
No 8
>PRK00254 ski2-like helicase; Provisional
Probab=84.53 E-value=4.4 Score=38.03 Aligned_cols=73 Identities=11% Similarity=0.120 Sum_probs=58.3
Q ss_pred CchHHHHHHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHHhhhhhCC-hHHHHHHHHHHHhhcCCcc
Q psy6286 80 KPSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGN-TLLEEKFNEAIKTVKRDIF 152 (159)
Q Consensus 80 ~~~l~~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~a~~~ig~-~~L~~k~~~a~~~I~RdIV 152 (159)
.+...-+.+.|.+|.+...+++..++..||+=+.+.+..-++.-+...+..+|. +++...+.+....|+-|+-
T Consensus 568 ~~k~~~ll~~~~~~~~~~~~~~~~~~~~gd~~~~~~~~~~l~~a~~~i~~~~~~~~~~~~~l~~l~~rl~~g~~ 641 (720)
T PRK00254 568 AFKTAKVLLDWINEVPEGEIVETYNIDPGDLYRILELADWLMYSLIELYKLFEPKQEVLDYLETLHLRVKHGVR 641 (720)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHhCCChHHHHHHHHHHHHHHHHHHHHHHHhCcchhHHHHHHHHHHHHHcCCC
Confidence 345568899999999999999999999999999999999999999988887883 5555666655555555543
No 9
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=84.14 E-value=2.6 Score=24.58 Aligned_cols=43 Identities=19% Similarity=0.252 Sum_probs=32.8
Q ss_pred CCchHHHHHHHhh-CCCCHHHHHhhcCCCccHHHHHHHHHHHHH
Q psy6286 79 FKPSLMDVVHAWC-EGASFLKVCSITDIFEGSIIRCMRRLEEVL 121 (159)
Q Consensus 79 ~~~~l~~~v~~Wa-~G~~f~~i~~~t~l~EG~iVR~~rRl~elL 121 (159)
+.+.--.++.... .|.+..+|.+..++.++.+-+++.+...-|
T Consensus 11 l~~~~~~~~~~~~~~~~~~~~ia~~~~~s~~~i~~~~~~~~~~l 54 (55)
T cd06171 11 LPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54 (55)
T ss_pred CCHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHc
Confidence 4444445555544 999999999999999999999988876543
No 10
>PRK01172 ski2-like helicase; Provisional
Probab=83.95 E-value=18 Score=33.69 Aligned_cols=134 Identities=14% Similarity=0.141 Sum_probs=80.7
Q ss_pred HHHHHHHHhhhCCccCCC--ccchhhHHHhhhcCCCceee--ec-cC-------------------cH----HHHHHHHH
Q psy6286 9 LKCRKRVLRRLGYATEAD--VIEMKGRVACELSKSEETVI--LT-IN-------------------DK----LELARHIA 60 (159)
Q Consensus 9 ~~~~~~vL~~lgyid~~~--~vt~kGrva~~I~s~~eLll--tE-f~-------------------p~----~~i~~~i~ 60 (159)
...-++-|.+.|+|+.++ .+|.-|+++++.+-+-+... .+ ++ |- .+...
T Consensus 446 v~~~l~~L~~~~~i~~~~~~~~t~lG~~~s~~~l~~~t~~~~~~~l~~~~~~~~~l~~~~~~~e~~~~~~~~~~~~~--- 522 (674)
T PRK01172 446 IESSLKFLKENGFIKGDVTLRATRLGKLTSDLYIDPESALILKSAFDHDYDEDLALYYISLCREIIPANTRDDYYAM--- 522 (674)
T ss_pred HHHHHHHHHHCCCcccCCcEeECHHHHHHHHhCCCHHHHHHHHHHhhccCCHHHHHHHhhcCccccccccchHHHHH---
Confidence 467788999999998553 68999999998776322110 00 11 11 11111
Q ss_pred HHHHHcCCCCChhhhhccCCchHHHHHHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHHhhhhhCChHHHHHH
Q psy6286 61 RISIESKLDLDEDSYVNQFKPSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKF 140 (159)
Q Consensus 61 ~~~~~~~l~~~~~~~~~~~~~~l~~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~a~~~ig~~~L~~k~ 140 (159)
.+....+.. +.+ .+...-.-+.++|-++.++.+|.+.-++..|++=+++....-+..-+...++.+ .+++.+.+
T Consensus 523 ~~~~~~~~~---~~~--~~~~k~~~ll~~~~~~~~~~~i~~~~~~~~g~l~~~~~~~~~~~~a~~~~~~~~-~~~~~~~l 596 (674)
T PRK01172 523 EFLEDIGVI---DGD--ISAAKTAMVLRGWISEASMQKITDTYGIAPGDVQARASSADWISYSLARLSSIY-KPEMRRKL 596 (674)
T ss_pred HHHHHhccc---cch--hHHHHHHHHHHHHHcCCCHHHHHHHhCCChHHHHHHHHHHHHHHHHHHHHHHHh-hHHHHHHH
Confidence 112222221 111 123344678999999999999999999999998887544444433444444443 37777776
Q ss_pred HHHHHhhcCCc
Q psy6286 141 NEAIKTVKRDI 151 (159)
Q Consensus 141 ~~a~~~I~RdI 151 (159)
......|.=|+
T Consensus 597 ~~~~~rl~~gv 607 (674)
T PRK01172 597 EILNIRIKEGI 607 (674)
T ss_pred HHHHHHHHcCC
Confidence 65555554443
No 11
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=83.58 E-value=3.2 Score=25.19 Aligned_cols=38 Identities=18% Similarity=0.323 Sum_probs=31.7
Q ss_pred HHHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHH
Q psy6286 86 VVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQ 123 (159)
Q Consensus 86 ~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrq 123 (159)
+...|..|.|+.+|-+..++++|.+=+..+|..+-||+
T Consensus 13 i~~~y~~~~t~~eIa~~lg~s~~~V~~~~~~al~kLR~ 50 (50)
T PF04545_consen 13 IRLRYFEGLTLEEIAERLGISRSTVRRILKRALKKLRK 50 (50)
T ss_dssp HHHHHTST-SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred HHHHhcCCCCHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence 45567899999999999999999999988888877764
No 12
>PRK00118 putative DNA-binding protein; Validated
Probab=83.14 E-value=8 Score=27.97 Aligned_cols=55 Identities=7% Similarity=0.128 Sum_probs=44.6
Q ss_pred ccCCchHHHHHHHh-hCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHHhhhhh
Q psy6286 77 NQFKPSLMDVVHAW-CEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNI 131 (159)
Q Consensus 77 ~~~~~~l~~~v~~W-a~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~a~~~i 131 (159)
+.+.+.--.++..+ ..|.|..+|.+..+++++.+=+.+.|...-|++....-+.+
T Consensus 16 ~~L~ekqRevl~L~y~eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~~~~~ 71 (104)
T PRK00118 16 SLLTEKQRNYMELYYLDDYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKLHLY 71 (104)
T ss_pred ccCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHChH
Confidence 45555555666555 58999999999999999999999999999999977765443
No 13
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=82.36 E-value=3.8 Score=24.58 Aligned_cols=33 Identities=21% Similarity=0.371 Sum_probs=28.4
Q ss_pred HHHHHhhCCCCHHHHHhhcCCCccHHHHHHHHH
Q psy6286 85 DVVHAWCEGASFLKVCSITDIFEGSIIRCMRRL 117 (159)
Q Consensus 85 ~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl 117 (159)
.+++.++.|.|..+|.+..++.++.+-+.+.|+
T Consensus 7 ~i~~~~~~~~s~~eia~~l~~s~~tv~~~~~~~ 39 (57)
T cd06170 7 EVLRLLAEGKTNKEIADILGISEKTVKTHLRNI 39 (57)
T ss_pred HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 355667899999999999999999998888766
No 14
>TIGR03643 conserved hypothetical protein TIGR03643. This model describes an uncharacterized bacterial protein family. Members average about 90 amino acids in length with several well-conserved uncommon amino acids (Trp, Met). The majority of species are marine bacteria. Few species have more than one copy, but Vibrio cholerae El Tor N16961 has three identical copies.
Probab=82.23 E-value=2 Score=29.22 Aligned_cols=30 Identities=23% Similarity=0.387 Sum_probs=27.4
Q ss_pred HHHhhCCCCHHHHHhhcCCCccHHHHHHHH
Q psy6286 87 VHAWCEGASFLKVCSITDIFEGSIIRCMRR 116 (159)
Q Consensus 87 v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rR 116 (159)
--+|.+-.||..|-...++.|+++|..||+
T Consensus 7 eMAweDRtpFeaI~~~fGL~E~eVi~lMR~ 36 (72)
T TIGR03643 7 EMAWEDRTPFEAIEQQFGLSEKEVIKLMRQ 36 (72)
T ss_pred HHHHccCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 357999999999999999999999998886
No 15
>PF13518 HTH_28: Helix-turn-helix domain
Probab=82.10 E-value=3.7 Score=24.67 Aligned_cols=35 Identities=23% Similarity=0.409 Sum_probs=30.8
Q ss_pred HHHHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHH
Q psy6286 85 DVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEE 119 (159)
Q Consensus 85 ~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~e 119 (159)
.++..+.+|.|..+++...++....+-+|+++-.+
T Consensus 4 ~iv~~~~~g~s~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 4 QIVELYLEGESVREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred HHHHHHHcCCCHHHHHHHHCCCHhHHHHHHHHHHh
Confidence 46667779999999999999999999999988765
No 16
>PF10985 DUF2805: Protein of unknown function (DUF2805); InterPro: IPR019882 This entry represents an uncharacterised bacterial protein family. Members average about 90 amino acids in length with several well-conserved uncommon amino acids (Trp, Met). The majority of species are marine bacteria. Few species have more than one copy, but Vibrio cholerae O1 biovar eltor str. N16961 has three identical copies.
Probab=80.82 E-value=2.4 Score=28.94 Aligned_cols=29 Identities=24% Similarity=0.431 Sum_probs=27.0
Q ss_pred HHhhCCCCHHHHHhhcCCCccHHHHHHHH
Q psy6286 88 HAWCEGASFLKVCSITDIFEGSIIRCMRR 116 (159)
Q Consensus 88 ~~Wa~G~~f~~i~~~t~l~EG~iVR~~rR 116 (159)
-+|.+-.||..|-...++.|.+++..||+
T Consensus 7 MAweDRtpFeaI~~qfGl~E~eVi~lMR~ 35 (73)
T PF10985_consen 7 MAWEDRTPFEAIERQFGLSEKEVIKLMRK 35 (73)
T ss_pred HHHccCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 57999999999999999999999998886
No 17
>PRK04217 hypothetical protein; Provisional
Probab=80.29 E-value=7.4 Score=28.42 Aligned_cols=52 Identities=12% Similarity=0.151 Sum_probs=43.9
Q ss_pred cCCchHHHHHHHhh-CCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHHhhh
Q psy6286 78 QFKPSLMDVVHAWC-EGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASR 129 (159)
Q Consensus 78 ~~~~~l~~~v~~Wa-~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~a~~ 129 (159)
.+...--.++..+. .|.|+.+|.+..++.++++=+.+.|....|++......
T Consensus 42 ~Lt~eereai~l~~~eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre~L~~~~ 94 (110)
T PRK04217 42 FMTYEEFEALRLVDYEGLTQEEAGKRMGVSRGTVWRALTSARKKVAQMLVEGR 94 (110)
T ss_pred cCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhcc
Confidence 44555568888887 99999999999999999999999999999988665543
No 18
>PRK02362 ski2-like helicase; Provisional
Probab=74.64 E-value=12 Score=35.30 Aligned_cols=139 Identities=13% Similarity=0.118 Sum_probs=85.9
Q ss_pred HHHHHHHHhhhCCccCCC---ccchhhHHHhhhcCCCce---------------------eee---ccC--c--H--HHH
Q psy6286 9 LKCRKRVLRRLGYATEAD---VIEMKGRVACELSKSEET---------------------VIL---TIN--D--K--LEL 55 (159)
Q Consensus 9 ~~~~~~vL~~lgyid~~~---~vt~kGrva~~I~s~~eL---------------------llt---Ef~--p--~--~~i 55 (159)
....++.|.+.|+|+.++ .+|..|++++..+-.-+- +++ ||+ | . .++
T Consensus 467 v~~~l~~L~~~~~i~~~~~~~~~t~lG~~~s~~~l~~~t~~~~~~~l~~~~~~~~~~~l~~i~~~~e~~~~~~r~~e~~~ 546 (737)
T PRK02362 467 VDDVLDFLERNGMIEEDGETLEATELGHLVSRLYIDPLSAAEIIDGLEAAKKPTDLGLLHLVCSTPDMYELYLRSGDYEW 546 (737)
T ss_pred HHHHHHHHHHCCCeeecCCeEeEChHHHHHHHhcCCHHHHHHHHHHhhhcccCchHHHHHHhhcCccccccccChhHHHH
Confidence 467789999999998654 599999999865541110 010 122 1 1 222
Q ss_pred HHHHHHHHHHcC------CCC--Chhhhhc-cCCchHHHHHHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHH
Q psy6286 56 ARHIARISIESK------LDL--DEDSYVN-QFKPSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQ 126 (159)
Q Consensus 56 ~~~i~~~~~~~~------l~~--~~~~~~~-~~~~~l~~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~ 126 (159)
...+ ..++. ++. ...+|.. .+.+.-.-+.+.|-++.++.+|.+..++..||+-....+..-++..+..
T Consensus 547 l~~~---~~~~~~~~~~~~p~~~~~~~~~~~~~~~k~~~ll~~~i~~~~~~~i~~~~~~~~gdl~~~~~~~~~l~~a~~~ 623 (737)
T PRK02362 547 LNEY---LYEHEDELLGDVPSEFEDDEFEDFLSAVKTALLLEDWIDEVDEERITERYGVGPGDIRGKVETAEWLLHAAER 623 (737)
T ss_pred HHHH---HHhcccchhccCCchhhhhhHHHHHHHHHHHHHHHHHHhCCCHHHHHHHhCCCchHHHHHHHHHHHHHHHHHH
Confidence 2222 22222 111 1111110 0122335678999999999999999999999998888888888888777
Q ss_pred hhhhhCChHHHHHHHHHHHhhcCCc
Q psy6286 127 ASRNIGNTLLEEKFNEAIKTVKRDI 151 (159)
Q Consensus 127 a~~~ig~~~L~~k~~~a~~~I~RdI 151 (159)
.+...| ..++..+.+-...|+-|+
T Consensus 624 i~~~~~-~~~~~~~~~l~~~l~~gv 647 (737)
T PRK02362 624 LASELD-LDLARAARELEKRVEYGV 647 (737)
T ss_pred HHHHhC-ccHHHHHHHHHHHHHhCC
Confidence 777654 455555555555555544
No 19
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=74.31 E-value=2.4 Score=25.59 Aligned_cols=34 Identities=15% Similarity=0.310 Sum_probs=24.4
Q ss_pred HHHHHhhCCCCHHHHHhhcCCCccHHHHHHHHHH
Q psy6286 85 DVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLE 118 (159)
Q Consensus 85 ~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~ 118 (159)
.++..+..|.|-.+|++..++...++=||++|-.
T Consensus 9 ~ii~l~~~G~s~~~ia~~lgvs~~Tv~~w~kr~~ 42 (50)
T PF13384_consen 9 QIIRLLREGWSIREIAKRLGVSRSTVYRWIKRYR 42 (50)
T ss_dssp -HHHHHHHT--HHHHHHHHTS-HHHHHHHHT---
T ss_pred HHHHHHHCCCCHHHHHHHHCcCHHHHHHHHHHcc
Confidence 4566677799999999999999999999998854
No 20
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=68.21 E-value=11 Score=28.64 Aligned_cols=44 Identities=16% Similarity=0.185 Sum_probs=33.3
Q ss_pred hhCCCCHHHHHhhcCCCccH----HHHHHHHHHHHHHHHHHhhhhhCC
Q psy6286 90 WCEGASFLKVCSITDIFEGS----IIRCMRRLEEVLRQLVQASRNIGN 133 (159)
Q Consensus 90 Wa~G~~f~~i~~~t~l~EG~----iVR~~rRl~elLrql~~a~~~ig~ 133 (159)
--.|.|..||-+..++++|. +-|+.++|-+.|.+....-+-+||
T Consensus 130 ~~e~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~~~~~~~~~ 177 (179)
T PRK12543 130 YLHDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQIEEIFLGEVGN 177 (179)
T ss_pred HHccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcC
Confidence 45999999999999999999 566666666666666655544454
No 21
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=67.00 E-value=6.1 Score=26.52 Aligned_cols=34 Identities=24% Similarity=0.225 Sum_probs=26.4
Q ss_pred hHHHHHHHHHHHhhhCCccCCC---ccchhhHHHhhh
Q psy6286 5 HMEELKCRKRVLRRLGYATEAD---VIEMKGRVACEL 38 (159)
Q Consensus 5 ~~~e~~~~~~vL~~lgyid~~~---~vt~kGrva~~I 38 (159)
-++.+...++.|.+.|+|..++ .+|.||+-+.+.
T Consensus 32 ~~~~~~~yL~~L~~~gLI~~~~~~Y~lTekG~~~l~~ 68 (77)
T PF14947_consen 32 NYSTLKKYLKELEEKGLIKKKDGKYRLTEKGKEFLEE 68 (77)
T ss_dssp -HHHHHHHHHHHHHTTSEEEETTEEEE-HHHHHHHHH
T ss_pred CHHHHHHHHHHHHHCcCeeCCCCEEEECccHHHHHHH
Confidence 4578899999999999997632 899999877654
No 22
>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=65.39 E-value=29 Score=24.52 Aligned_cols=55 Identities=15% Similarity=0.177 Sum_probs=37.3
Q ss_pred HHHHHHHHHHcCCCCChhhhhccCCchHHHHHHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHH
Q psy6286 56 ARHIARISIESKLDLDEDSYVNQFKPSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEE 119 (159)
Q Consensus 56 ~~~i~~~~~~~~l~~~~~~~~~~~~~~l~~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~e 119 (159)
...+......+|+.. ..+.++..++. ..|.+.++|++...+...++.|.+.+|++
T Consensus 14 ~~~~~~~l~~~~lt~--------~q~~iL~~l~~-~~~~t~~ela~~~~~~~~tvs~~l~~Le~ 68 (118)
T TIGR02337 14 MSFFRPILAQHGLTE--------QQWRILRILAE-QGSMEFTQLANQACILRPSLTGILARLER 68 (118)
T ss_pred HHHHHHHHHHcCCCH--------HHHHHHHHHHH-cCCcCHHHHHHHhCCCchhHHHHHHHHHH
Confidence 344444555566542 22344444433 46679999999999999999999988876
No 23
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=65.12 E-value=10 Score=22.73 Aligned_cols=31 Identities=13% Similarity=0.171 Sum_probs=22.6
Q ss_pred HHHHhhCCCCHHHHHhhcCCCccHHHHHHHH
Q psy6286 86 VVHAWCEGASFLKVCSITDIFEGSIIRCMRR 116 (159)
Q Consensus 86 ~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rR 116 (159)
+...|..|.|..+|-+.-+....+|-|.++|
T Consensus 13 I~~l~~~G~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 13 IEALLEQGMSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp HHHHHCS---HHHHHHHTT--HHHHHHHHHH
T ss_pred HHHHHHcCCCHHHHHHHHCcCcHHHHHHHhc
Confidence 4455789999999999999999999999987
No 24
>cd00180 PKc Catalytic domain of Protein Kinases. Protein Kinases (PKs), catalytic (c) domain. PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine or tyrosine residues on protein substrates. The PK family is part of a larger superfamily that includes the catalytic domains of RIO kinases, aminoglycoside phosphotransferase, choline kinase, phosphoinositide 3-kinase (PI3K), and actin-fragmin kinase. PKs make up a large family of serine/threonine kinases, protein tyrosine kinases (PTKs), and dual-specificity PKs that phosphorylate both serine/threonine and tyrosine residues of target proteins. Majority of protein phosphorylation, about 95%, occurs on serine residues while only 1% occurs on tyrosine residues. Protein phosphorylation is a mechanism by which a wide variety of cellular proteins, such as enzymes and membrane channels, are reversibly regulated in response to certain stimuli. PKs often function as components of signal transduction pathways in which
Probab=64.29 E-value=5.3 Score=28.91 Aligned_cols=51 Identities=22% Similarity=0.296 Sum_probs=42.9
Q ss_pred HHHHHHHhhCCCCHHHHHhhc--CCCccHHHHHHHHHHHHHHHHHHhhhhhCC
Q psy6286 83 LMDVVHAWCEGASFLKVCSIT--DIFEGSIIRCMRRLEEVLRQLVQASRNIGN 133 (159)
Q Consensus 83 l~~~v~~Wa~G~~f~~i~~~t--~l~EG~iVR~~rRl~elLrql~~a~~~ig~ 133 (159)
...++++|..|.++.+.+... .+.+....++++++...+..+....-+.||
T Consensus 65 ~~~~~~e~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~l~~lh~~~~~H~d 117 (215)
T cd00180 65 HLYLVMEYCEGGSLKDLLKENEGKLSEDEILRILLQILEGLEYLHSNGIIHRD 117 (215)
T ss_pred eEEEEEecCCCCcHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHHhCCeeccC
Confidence 345778899999999999886 789999999999999999999887655554
No 25
>smart00351 PAX Paired Box domain.
Probab=58.29 E-value=20 Score=26.29 Aligned_cols=35 Identities=14% Similarity=0.157 Sum_probs=30.4
Q ss_pred HHHHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHH
Q psy6286 85 DVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEE 119 (159)
Q Consensus 85 ~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~e 119 (159)
.++.....|.|..+|++..++....+.||++|-.+
T Consensus 25 riv~~~~~G~s~~~iA~~~gvs~~tV~kwi~r~~~ 59 (125)
T smart00351 25 RIVELAQNGVRPCDISRQLCVSHGCVSKILGRYYE 59 (125)
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 45666679999999999999999999999998654
No 26
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=57.66 E-value=41 Score=24.53 Aligned_cols=37 Identities=22% Similarity=0.326 Sum_probs=28.6
Q ss_pred HHHHHHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHH
Q psy6286 83 LMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEE 119 (159)
Q Consensus 83 l~~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~e 119 (159)
++..++.--.|.+..+|.+...+..+++-|.+.||++
T Consensus 36 vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~ 72 (144)
T PRK03573 36 TLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLEE 72 (144)
T ss_pred HHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHH
Confidence 3344433234679999999999999999999999875
No 27
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=56.33 E-value=8.7 Score=23.01 Aligned_cols=34 Identities=21% Similarity=0.370 Sum_probs=29.5
Q ss_pred hCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHH
Q psy6286 91 CEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQL 124 (159)
Q Consensus 91 a~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql 124 (159)
..+.|..+|++.+++..|+|-+-+.--+++++.+
T Consensus 14 ~~~~s~~~Ia~~~gvs~~~~y~~f~~k~~l~~a~ 47 (47)
T PF00440_consen 14 YEAVSIRDIARRAGVSKGSFYRYFPSKDDLLRAV 47 (47)
T ss_dssp TTTSSHHHHHHHHTSCHHHHHHHCSSHHHHHHHH
T ss_pred HHhCCHHHHHHHHccchhhHHHHcCCHHHHHhhC
Confidence 3678999999999999999999988888887654
No 28
>PF03333 PapB: Adhesin biosynthesis transcription regulatory protein; InterPro: IPR004356 P pili, or fimbriae, are ~68A in diameter and 1 micron in length, the bulk of which is a fibre composed of the main structural protein PapA []. At its tip, the pilus is terminated by a fibrillum consisting of repeating units of the PapE protein. This, in turn, is topped by the adhesins, PapF and PapG, both of which are needed for receptor binding. The tip fibrillum is anchored to the main PapA fibre by the PapK pilus-adaptor protein. PapH, an outer membrane protein, then anchors the entire rod in the bacterial envelope []. A cytoplasmic chaperone (PapD) assists in assembling the monomers of the macromolecule in the membrane. All of the functional pap genes are arranged in a cluster (operon) on the Escherichia coli genome. It is believed that selective pressure exerted by the host's urinal and intestinal tract isoreceptors forced the spread of this operon to other strains via lateral transfer []. PapB, encoded within the cluster, acts as a transcriptional regulator of the functional pap genes and is located in the bacterial cytoplasm []. Its mechanism involves differential binding to separate sites in the cluster, suggesting that this protein is both an activator and repressor of pilus-adhesion transcription. The protein shares similarity with other E. coli fimbrial- adhesion transcription regulators, such as AfaA, DaaA and FanB. ; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 3M8J_A.
Probab=55.72 E-value=27 Score=24.71 Aligned_cols=49 Identities=18% Similarity=0.325 Sum_probs=35.7
Q ss_pred chHHHHHHHh-hCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHHhhh
Q psy6286 81 PSLMDVVHAW-CEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASR 129 (159)
Q Consensus 81 ~~l~~~v~~W-a~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~a~~ 129 (159)
.....+.+.- ..|.|=.++|+..++..|-|-++++|+..+=+-+.++..
T Consensus 40 ~kiI~AL~dyLV~G~srkeac~~~gV~~syfs~~L~rL~~v~~~V~~l~~ 89 (91)
T PF03333_consen 40 EKIIAALRDYLVDGLSRKEACERHGVNQSYFSRALNRLNRVSQIVEQLSP 89 (91)
T ss_dssp HHHHHHHHHHHTT---HHHHHHHTT--HHHHHHHHHHHHHHHHHHHHHGG
T ss_pred HHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHhhc
Confidence 3455566655 699999999999999999999999999988877777653
No 29
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=55.17 E-value=25 Score=21.83 Aligned_cols=43 Identities=16% Similarity=0.212 Sum_probs=33.5
Q ss_pred cCCchHHHHHHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHH
Q psy6286 78 QFKPSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEV 120 (159)
Q Consensus 78 ~~~~~l~~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~el 120 (159)
.+.+.=..++..|++|.+-.+|.+.-++.+.++-...+++-.-
T Consensus 3 ~LT~~E~~vl~~l~~G~~~~eIA~~l~is~~tV~~~~~~i~~K 45 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGMSNKEIAEELGISEKTVKSHRRRIMKK 45 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-HHHHHHHHTSHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHhcCCcchhHHhcCcchhhHHHHHHHHHHH
Confidence 3445556889999999999999999999999988877666543
No 30
>PF06969 HemN_C: HemN C-terminal domain; InterPro: IPR010723 Proteins containing this domain are all oxygen-independent coproporphyrinogen-III oxidases (HemN). This enzyme catalyses the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen-IX [], one of the last steps in haem biosynthesis. The function of this domain is unclear, but comparison to other proteins containing a radical SAM domain suggest it may be a substrate binding domain.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin-containing compound biosynthetic process, 0055114 oxidation-reduction process, 0005737 cytoplasm; PDB: 1OLT_A.
Probab=55.16 E-value=11 Score=23.95 Aligned_cols=29 Identities=24% Similarity=0.248 Sum_probs=20.9
Q ss_pred hHHHHHHHHHHHhhhCCccCCC---ccchhhH
Q psy6286 5 HMEELKCRKRVLRRLGYATEAD---VIEMKGR 33 (159)
Q Consensus 5 ~~~e~~~~~~vL~~lgyid~~~---~vt~kGr 33 (159)
+.+.|...++-|.+.|++..++ .+|.+|+
T Consensus 34 ~~~~~~~~l~~l~~~Gll~~~~~~l~lT~~G~ 65 (66)
T PF06969_consen 34 FAEEFQKELEELQEDGLLEIDGGRLRLTEKGR 65 (66)
T ss_dssp THHH-HHHHHHHHHTTSEEE-SSEEEE-TTTG
T ss_pred HHHHHHHHHHHHHHCCCEEEeCCEEEECcccC
Confidence 3466788899999999996543 7899997
No 31
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=54.57 E-value=38 Score=20.86 Aligned_cols=43 Identities=14% Similarity=0.118 Sum_probs=38.7
Q ss_pred hHHHHHHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHH
Q psy6286 82 SLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQL 124 (159)
Q Consensus 82 ~l~~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql 124 (159)
.+.-+...|..|-++.++-..-++.+..+-|++....++|.+.
T Consensus 8 ~lll~L~~LR~~~~~~~La~~FgIs~stvsri~~~~~~~L~~~ 50 (53)
T PF13613_consen 8 QLLLTLMYLRLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQV 50 (53)
T ss_pred HHHHHHHHHHcCCcHhHHhhheeecHHHHHHHHHHHHHHHHHh
Confidence 5666777899999999999999999999999999999999764
No 32
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=54.41 E-value=41 Score=25.17 Aligned_cols=47 Identities=28% Similarity=0.285 Sum_probs=37.3
Q ss_pred cCCchHHHHHHH-hhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHH
Q psy6286 78 QFKPSLMDVVHA-WCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQL 124 (159)
Q Consensus 78 ~~~~~l~~~v~~-Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql 124 (159)
.+.|.--.++.. ...|.|..+|.+..++++|.+-+.+.|.-.-|+.+
T Consensus 140 ~L~~~~r~vi~l~~~~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~~ 187 (189)
T TIGR02984 140 KLPEDYREVILLRHLEGLSFAEVAERMDRSEGAVSMLWVRGLARLRQI 187 (189)
T ss_pred cCCHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 455555455544 66999999999999999999999988888777764
No 33
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=54.22 E-value=39 Score=24.81 Aligned_cols=37 Identities=11% Similarity=0.171 Sum_probs=29.4
Q ss_pred hHHHHHHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHH
Q psy6286 82 SLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEE 119 (159)
Q Consensus 82 ~l~~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~e 119 (159)
.++..++ ...|.+.++|.+...+..+++.|.+.||++
T Consensus 44 ~vL~~l~-~~~~~t~~eLa~~l~i~~~tvsr~l~~Le~ 80 (144)
T PRK11512 44 KVLCSIR-CAACITPVELKKVLSVDLGALTRMLDRLVC 80 (144)
T ss_pred HHHHHHH-HcCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4444443 245689999999999999999999999875
No 34
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=52.58 E-value=22 Score=21.50 Aligned_cols=30 Identities=27% Similarity=0.530 Sum_probs=22.2
Q ss_pred hhCCCCHHHHHhhcCCCccHHHHHHHHHHH
Q psy6286 90 WCEGASFLKVCSITDIFEGSIIRCMRRLEE 119 (159)
Q Consensus 90 Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~e 119 (159)
--.|.|+.+|.+..+++++.+=+.+.|--.
T Consensus 23 ~~~g~s~~eIa~~l~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 23 YFQGMSYAEIAEILGISESTVKRRLRRARK 52 (54)
T ss_dssp HTS---HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred HHHCcCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence 469999999999999999999888877644
No 35
>PRK11664 ATP-dependent RNA helicase HrpB; Provisional
Probab=52.00 E-value=16 Score=35.15 Aligned_cols=34 Identities=26% Similarity=0.431 Sum_probs=30.1
Q ss_pred HHHHHHHHHHhhhCCccCCCccchhhHHHhhhcC
Q psy6286 7 EELKCRKRVLRRLGYATEADVIEMKGRVACELSK 40 (159)
Q Consensus 7 ~e~~~~~~vL~~lgyid~~~~vt~kGrva~~I~s 40 (159)
..+.+-+..|..+|.+|+++.+|..|+..+++-.
T Consensus 384 ~~~~~A~~~L~~lgald~~g~lT~~G~~m~~lp~ 417 (812)
T PRK11664 384 AALAAAKRLLQQLGALDGQGRLTARGRKMAALGN 417 (812)
T ss_pred HHHHHHHHHHHHCCCCCCCCCcCHHHHHHHhcCC
Confidence 4567788999999999999999999999999864
No 36
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=51.88 E-value=46 Score=23.90 Aligned_cols=47 Identities=13% Similarity=0.157 Sum_probs=37.3
Q ss_pred ccCCchHHHHHHH-hhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHH
Q psy6286 77 NQFKPSLMDVVHA-WCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQ 123 (159)
Q Consensus 77 ~~~~~~l~~~v~~-Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrq 123 (159)
..+.+.-..+++. ...|.|+.+|.+..+++++.+=..+.|...-|++
T Consensus 112 ~~L~~~~r~il~l~~~~~~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 112 EKLPEQCRKIFILSRFEGKSYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred HHCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 3455555667666 6799999999999999999988888887776665
No 37
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=51.85 E-value=49 Score=24.76 Aligned_cols=47 Identities=19% Similarity=0.224 Sum_probs=37.5
Q ss_pred ccCCchHHHHHHHh-hCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHH
Q psy6286 77 NQFKPSLMDVVHAW-CEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQ 123 (159)
Q Consensus 77 ~~~~~~l~~~v~~W-a~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrq 123 (159)
..+.+..-.++... -.|.|..+|.+..++++|++=..+.|.-.-|++
T Consensus 128 ~~L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 175 (179)
T PRK12514 128 EELEKDRAAAVRRAYLEGLSYKELAERHDVPLNTMRTWLRRSLLKLRE 175 (179)
T ss_pred HhCCHHHHHHHHHHHHcCCCHHHHHHHHCCChHHHHHHHHHHHHHHHH
Confidence 35555666666655 499999999999999999998888887777766
No 38
>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=50.31 E-value=25 Score=20.94 Aligned_cols=33 Identities=12% Similarity=0.338 Sum_probs=25.6
Q ss_pred hHHHHHHHhhCCCCHHHHHhhcCCCccHHHHHH
Q psy6286 82 SLMDVVHAWCEGASFLKVCSITDIFEGSIIRCM 114 (159)
Q Consensus 82 ~l~~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~ 114 (159)
..-.++...++|.|-.+|++.+++.-.+|=|.+
T Consensus 10 ~~~~i~~l~~~G~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 10 QIEEIKELYAEGMSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp CHHHHHHHHHTT--HHHHHHHTTS-HHHHHHHH
T ss_pred HHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHH
Confidence 456778888999999999999999998888765
No 39
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=50.17 E-value=33 Score=24.86 Aligned_cols=47 Identities=11% Similarity=0.111 Sum_probs=37.6
Q ss_pred ccCCchHHHHH-HHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHH
Q psy6286 77 NQFKPSLMDVV-HAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQ 123 (159)
Q Consensus 77 ~~~~~~l~~~v-~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrq 123 (159)
..+.+.-=.++ ..+-.|.|..||-+..++++|++-..+.|...-||+
T Consensus 105 ~~L~~~~r~ii~l~~~~~~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 105 SVLDEKEKYIIFERFFVGKTMGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred HhCCHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 34555444544 568899999999999999999999999988777765
No 40
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=49.68 E-value=17 Score=24.67 Aligned_cols=37 Identities=22% Similarity=0.443 Sum_probs=27.7
Q ss_pred hHHHHHHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHH
Q psy6286 82 SLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEE 119 (159)
Q Consensus 82 ~l~~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~e 119 (159)
++|...+. ..+.+|++|-+..++..|++=+.++.|+|
T Consensus 4 ~Il~~L~~-~~~~~f~~L~~~l~lt~g~Ls~hL~~Le~ 40 (80)
T PF13601_consen 4 AILALLYA-NEEATFSELKEELGLTDGNLSKHLKKLEE 40 (80)
T ss_dssp HHHHHHHH-HSEEEHHHHHHHTT--HHHHHHHHHHHHH
T ss_pred HHHHHHhh-cCCCCHHHHHHHhCcCHHHHHHHHHHHHH
Confidence 44555555 67889999999999999999888877665
No 41
>CHL00073 chlN photochlorophyllide reductase subunit N
Probab=49.60 E-value=24 Score=31.87 Aligned_cols=53 Identities=17% Similarity=0.118 Sum_probs=40.6
Q ss_pred cCCCccHHH---HHHHHHHHHHHHHHH-------------hhhhhCChHHHHHHHHHHHhhcCCcccccc
Q psy6286 103 TDIFEGSII---RCMRRLEEVLRQLVQ-------------ASRNIGNTLLEEKFNEAIKTVKRDIFLEIL 156 (159)
Q Consensus 103 t~l~EG~iV---R~~rRl~elLrql~~-------------a~~~ig~~~L~~k~~~a~~~I~RdIV~~~s 156 (159)
|++.|+|+| -.-++|..+|+|+.. ++.+||| ++...+.++.+.+.=.||.+.+
T Consensus 68 tdl~E~Di~~~~g~~~~L~~~i~ei~~~~~p~~ifv~~TC~t~iIGd-Dle~va~~~~~~~gipVV~v~~ 136 (457)
T CHL00073 68 AELEEGDISAQLNDYEELKRLCLQIKKDRNPSVIVWIGTCTTEIIKM-DLEGMAPKLEAEIGIPIVVARA 136 (457)
T ss_pred cccCchhhhhhcCCHHHHHHHHHHHHHhCCCCEEEEEccCcHHhhcc-CHHHHHHHHHHhhCCCEEEEeC
Confidence 899999999 666778888888764 3456774 7888888888888777777654
No 42
>PF12690 BsuPI: Intracellular proteinase inhibitor; InterPro: IPR020481 BsuPI is a intracellular proteinase inhibitor that directly regulates the major intracellular proteinase (ISP-1) activity in vivo. It inhibits ISP-1 in the early stages of sporulation and then may be inactivated by a membrane-bound proteinase [].; PDB: 3ISY_A.
Probab=49.47 E-value=1.5 Score=30.23 Aligned_cols=25 Identities=20% Similarity=0.412 Sum_probs=13.6
Q ss_pred HHHHHhhCCCCHHHHHhhcCCCccH
Q psy6286 85 DVVHAWCEGASFLKVCSITDIFEGS 109 (159)
Q Consensus 85 ~~v~~Wa~G~~f~~i~~~t~l~EG~ 109 (159)
..||+|.+|+.|.+.+....+.+|.
T Consensus 36 ~~vwrwS~~~~FtQal~~~~l~pGe 60 (82)
T PF12690_consen 36 KEVWRWSDGKMFTQALQEETLEPGE 60 (82)
T ss_dssp -EEEETTTT-------EEEEE-TT-
T ss_pred CEEEEecCCchhhheeeEEEECCCC
Confidence 6689999999999999998888885
No 43
>cd05579 STKc_MAST_like Catalytic domain of Microtubule-associated serine/threonine kinase-like proteins. Serine/Threonine Kinases (STKs), Microtubule-associated serine/threonine (MAST) kinase subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The MAST kinase subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. The MAST kinase subfamily includes MAST kinases, MAST-like (MASTL) kinases, and fungal kinases with similarity to Saccharomyces cerevisiae Rim15 and Schizosaccharomyces pombe cek1. MAST kinases contain an N-terminal domain of unknown function, a central catalytic domain, and a C-terminal PDZ domain that mediates protein-protein interactions. MASTL kinases carry only a catalytic domain which contains a long insert re
Probab=49.06 E-value=14 Score=28.48 Aligned_cols=49 Identities=10% Similarity=0.023 Sum_probs=39.6
Q ss_pred HHHHHhhCCCCHHHHHhh-cCCCccHHHHHHHHHHHHHHHHHHhhhhhCC
Q psy6286 85 DVVHAWCEGASFLKVCSI-TDIFEGSIIRCMRRLEEVLRQLVQASRNIGN 133 (159)
Q Consensus 85 ~~v~~Wa~G~~f~~i~~~-t~l~EG~iVR~~rRl~elLrql~~a~~~ig~ 133 (159)
-++++|+.|.++.+++.. ..+.+..+.++++|+.+-|..+.+..-+.||
T Consensus 69 ~lv~e~~~~~~L~~~l~~~~~~~~~~~~~i~~qi~~~L~~lH~~~i~H~d 118 (265)
T cd05579 69 YLVMEYLPGGDLASLLENVGSLDEDVARIYIAEIVLALEYLHSNGIIHRD 118 (265)
T ss_pred EEEEecCCCCcHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHcCeecCC
Confidence 357789999999999876 4689999999999999999888766544444
No 44
>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins. The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple copies of DnaA, which is an ATPase, bind to 9-mers at the origin and form an initial complex in which the DNA strands are being separated in an ATP-dependent step.
Probab=48.53 E-value=81 Score=21.51 Aligned_cols=45 Identities=22% Similarity=0.360 Sum_probs=35.7
Q ss_pred CCCCHHHHHhhcC-CCccHHHHHHHHHHHHHHHHHHhhhhhCChHHHHHHHHHHH
Q psy6286 92 EGASFLKVCSITD-IFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKFNEAIK 145 (159)
Q Consensus 92 ~G~~f~~i~~~t~-l~EG~iVR~~rRl~elLrql~~a~~~ig~~~L~~k~~~a~~ 145 (159)
-|.|+.+|-+.-+ -.--++...++|+.+.+.+ |+.+...++....
T Consensus 43 ~~~s~~~Ig~~fg~r~hStV~~a~~ri~~~~~~---------d~~~~~~v~~i~~ 88 (90)
T cd06571 43 TGLSLPEIGRAFGGRDHSTVLHAVRKIEELLEE---------DPELKEDVEELEK 88 (90)
T ss_pred hCCCHHHHHHHhCCCCHhHHHHHHHHHHHHHHh---------CHHHHHHHHHHHH
Confidence 5999999999987 8899999999999987753 4666666655443
No 45
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=48.34 E-value=52 Score=23.88 Aligned_cols=46 Identities=13% Similarity=0.247 Sum_probs=36.7
Q ss_pred cCCchHHHHHHH-hhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHH
Q psy6286 78 QFKPSLMDVVHA-WCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQ 123 (159)
Q Consensus 78 ~~~~~l~~~v~~-Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrq 123 (159)
.+.+.--.++.. +..|.|..+|.+..++++|.+=+.+.|.-.-|++
T Consensus 111 ~L~~~~r~v~~l~~~~g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 111 KLPERQRELLQLRYQRGVSLTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred HCCHHHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 455555555555 7899999999999999999999888887776664
No 46
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=47.37 E-value=44 Score=24.47 Aligned_cols=47 Identities=15% Similarity=0.191 Sum_probs=35.0
Q ss_pred cCCchHHHHH-HHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHH
Q psy6286 78 QFKPSLMDVV-HAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQL 124 (159)
Q Consensus 78 ~~~~~l~~~v-~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql 124 (159)
.+.+.--.++ .....|.|..||.+..++++|.+=..+.|.-..|++.
T Consensus 106 ~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 153 (160)
T PRK09642 106 ELPENYRDVVLAHYLEEKSYQEIALQEKIEVKTVEMKLYRARKWIKKH 153 (160)
T ss_pred hCCHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3444433444 4578999999999999999999977777776666654
No 47
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=47.26 E-value=44 Score=25.37 Aligned_cols=48 Identities=13% Similarity=0.076 Sum_probs=36.9
Q ss_pred cCCchHHHHHHH-hhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHH
Q psy6286 78 QFKPSLMDVVHA-WCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLV 125 (159)
Q Consensus 78 ~~~~~l~~~v~~-Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~ 125 (159)
.+.+.-=.++.. .-.|.|+.||.+..++++|++=..+.|....|++.-
T Consensus 139 ~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 187 (189)
T PRK09648 139 TLPEKQREILILRVVVGLSAEETAEAVGSTPGAVRVAQHRALARLRAEI 187 (189)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 333333344433 468999999999999999999999999888888754
No 48
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=46.90 E-value=45 Score=24.51 Aligned_cols=38 Identities=18% Similarity=0.324 Sum_probs=33.4
Q ss_pred HHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHH
Q psy6286 87 VHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLV 125 (159)
Q Consensus 87 v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~ 125 (159)
.... .|.|..+|-+..++++|.+-+.+.|...-|++.-
T Consensus 122 ~l~~-~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l 159 (166)
T PRK09639 122 LLRF-SGYSYKEIAEALGIKESSVGTTLARAKKKFRKIY 159 (166)
T ss_pred HHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3455 9999999999999999999999999988888754
No 49
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=46.69 E-value=92 Score=23.49 Aligned_cols=51 Identities=12% Similarity=0.229 Sum_probs=41.5
Q ss_pred ccCCchHHHHHHH-hhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHHh
Q psy6286 77 NQFKPSLMDVVHA-WCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQA 127 (159)
Q Consensus 77 ~~~~~~l~~~v~~-Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~a 127 (159)
..+.|.--.++.. +-.|.|..||.+..++++|.+=..+.|.-..|++....
T Consensus 121 ~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~ 172 (185)
T PRK12542 121 KELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERARKRVQNMIGG 172 (185)
T ss_pred HhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHcc
Confidence 3555555566655 78999999999999999999999999988888886544
No 50
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=46.44 E-value=56 Score=24.44 Aligned_cols=35 Identities=26% Similarity=0.379 Sum_probs=31.3
Q ss_pred hhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHH
Q psy6286 90 WCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQL 124 (159)
Q Consensus 90 Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql 124 (159)
+..|.|..+|.+..++.+|.+=..+.|.-.-|++.
T Consensus 149 ~~~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 149 YMEDLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 67999999999999999999999988888777764
No 51
>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB. This model represents HrpB, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria, but also in a few species of other lineages. The member from Rhizobium meliloti has been designated HelO. HrpB is typically about 800 residues in length, while its paralog HrpA (TIGR01967), also uncharacterized, is about 1300 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing.
Probab=45.92 E-value=23 Score=34.22 Aligned_cols=34 Identities=21% Similarity=0.357 Sum_probs=29.8
Q ss_pred HHHHHHHHHHhhhCCccCCCccchhhHHHhhhcC
Q psy6286 7 EELKCRKRVLRRLGYATEADVIEMKGRVACELSK 40 (159)
Q Consensus 7 ~e~~~~~~vL~~lgyid~~~~vt~kGrva~~I~s 40 (159)
..+..-++.|..+|.+|+++.+|..|+..+++-.
T Consensus 381 ~~i~~a~~~L~~lgald~~~~lT~~G~~~~~lp~ 414 (819)
T TIGR01970 381 VALAAARQLLQRLGALDAQGRLTAHGKAMAALGC 414 (819)
T ss_pred HHHHHHHHHHHHCCCCCCCCCcCHHHHHHHhcCC
Confidence 3467778899999999999999999999999865
No 52
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=45.66 E-value=16 Score=23.63 Aligned_cols=29 Identities=14% Similarity=0.124 Sum_probs=26.2
Q ss_pred hhCCCCHHHHHhhcCCCccHHHHHHHHHH
Q psy6286 90 WCEGASFLKVCSITDIFEGSIIRCMRRLE 118 (159)
Q Consensus 90 Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~ 118 (159)
...|.|..++|...++.+..|-+|+++..
T Consensus 20 ~~~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 20 LESGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp HHHHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHCCCceEeeecccccccccccHHHHHHh
Confidence 47999999999999999999999999886
No 53
>COG4910 PduE Propanediol dehydratase, small subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=45.45 E-value=33 Score=26.29 Aligned_cols=64 Identities=19% Similarity=0.300 Sum_probs=44.5
Q ss_pred cCCchHHHHHHHhhCCCCHHHHHhhcCCCccHHHH-HHHHHHHHHHHHHHhhhhhCChHHHHHHHHHHHh
Q psy6286 78 QFKPSLMDVVHAWCEGASFLKVCSITDIFEGSIIR-CMRRLEEVLRQLVQASRNIGNTLLEEKFNEAIKT 146 (159)
Q Consensus 78 ~~~~~l~~~v~~Wa~G~~f~~i~~~t~l~EG~iVR-~~rRl~elLrql~~a~~~ig~~~L~~k~~~a~~~ 146 (159)
.-.|+.+. =++|+|+.+|.-.+ +-.|++-. -+|=+-+.|+-=++.++-.|-|.|+..|+.|.++
T Consensus 44 ~k~Pe~VK----ta~~KsLddiTL~s-VL~g~vt~eD~RiTpetL~~QA~vArDaGR~tLA~NFERaAEL 108 (170)
T COG4910 44 EKQPEAVK----TARGKSLDDITLDS-VLAGDVTMEDLRITPETLQAQADVARDAGRPTLALNFERAAEL 108 (170)
T ss_pred cCChhhhh----ccccCcHHHhhHHH-HhcCCCcHHHhhcCHHHHHHHHHHHHhcCchHHHhhHHhhhhh
Confidence 34555332 47899999986443 44555533 2444567777777777777999999999998876
No 54
>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=45.06 E-value=22 Score=24.53 Aligned_cols=28 Identities=18% Similarity=0.164 Sum_probs=21.4
Q ss_pred HHHHHHHHhhhCCccC-----CC-ccchhhHHHh
Q psy6286 9 LKCRKRVLRRLGYATE-----AD-VIEMKGRVAC 36 (159)
Q Consensus 9 ~~~~~~vL~~lgyid~-----~~-~vt~kGrva~ 36 (159)
-++-+..|+++||++. .| .+|.||--+-
T Consensus 40 IRN~M~~Le~lGlve~~p~~s~GriPT~~aYr~~ 73 (78)
T PF03444_consen 40 IRNEMADLEELGLVESQPHPSGGRIPTDKAYRAL 73 (78)
T ss_pred HHHHHHHHHHCCCccCCCCCCCCCCcCHHHHHHH
Confidence 4678899999999973 23 8999885543
No 55
>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=44.99 E-value=49 Score=20.17 Aligned_cols=30 Identities=13% Similarity=0.224 Sum_probs=24.6
Q ss_pred hhCCCCHHHHHhhcCCCccHHHHHHHHHHH
Q psy6286 90 WCEGASFLKVCSITDIFEGSIIRCMRRLEE 119 (159)
Q Consensus 90 Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~e 119 (159)
|..+.++.+|.+..++..+++-|.+.++.+
T Consensus 17 ~~~~~~~~ei~~~~~i~~~~i~~~l~~L~~ 46 (78)
T cd00090 17 LEGPLTVSELAERLGLSQSTVSRHLKKLEE 46 (78)
T ss_pred HHCCcCHHHHHHHHCcCHhHHHHHHHHHHH
Confidence 445589999999999999998888877654
No 56
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=44.94 E-value=48 Score=24.84 Aligned_cols=46 Identities=15% Similarity=0.163 Sum_probs=37.9
Q ss_pred CCchHHHHHHHh-hCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHH
Q psy6286 79 FKPSLMDVVHAW-CEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQL 124 (159)
Q Consensus 79 ~~~~l~~~v~~W-a~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql 124 (159)
+.+.--.++... -.|.|..||-+..++++|.+=..+.|.-..|++.
T Consensus 135 Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 181 (183)
T TIGR02999 135 VDPRQAEVVELRFFAGLTVEEIAELLGVSVRTVERDWRFARAWLADE 181 (183)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 555555565554 5999999999999999999999999988888764
No 57
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=43.99 E-value=51 Score=24.82 Aligned_cols=46 Identities=15% Similarity=0.270 Sum_probs=36.2
Q ss_pred cCCchHHHHHH-HhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHH
Q psy6286 78 QFKPSLMDVVH-AWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQ 123 (159)
Q Consensus 78 ~~~~~l~~~v~-~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrq 123 (159)
.+.+.--.++. ....|.|..+|.+..++++|.+-..+.|.-.-|++
T Consensus 135 ~L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~ 181 (186)
T PRK13919 135 ALSPEERRVIEVLYYQGYTHREAAQLLGLPLGTLKTRARRALSRLKE 181 (186)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 44444445554 56899999999999999999999888887777765
No 58
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=43.63 E-value=53 Score=22.82 Aligned_cols=45 Identities=24% Similarity=0.419 Sum_probs=34.4
Q ss_pred CCchHHHHH-HHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHH
Q psy6286 79 FKPSLMDVV-HAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQ 123 (159)
Q Consensus 79 ~~~~l~~~v-~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrq 123 (159)
+.+.-..++ +....|.|..+|.+..++++.++=+...|..+-|+.
T Consensus 111 L~~~~~~ii~~~~~~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 111 LPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred CCHHHHHHHhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 333333443 335689999999999999999999999998777664
No 59
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=43.30 E-value=52 Score=24.55 Aligned_cols=46 Identities=15% Similarity=0.221 Sum_probs=35.3
Q ss_pred CCchHHHHH-HHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHH
Q psy6286 79 FKPSLMDVV-HAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQL 124 (159)
Q Consensus 79 ~~~~l~~~v-~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql 124 (159)
+.+..-.++ ..+..|.|..||.+..++.+|.+=..+.|.-.-|++.
T Consensus 120 L~~~~r~i~~l~~~~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 166 (173)
T PRK12522 120 LNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKKQMREH 166 (173)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 333333333 4467999999999999999999988888887777763
No 60
>PF13730 HTH_36: Helix-turn-helix domain
Probab=42.15 E-value=31 Score=20.92 Aligned_cols=25 Identities=20% Similarity=0.251 Sum_probs=22.4
Q ss_pred CHHHHHhhcCCCccHHHHHHHHHHH
Q psy6286 95 SFLKVCSITDIFEGSIIRCMRRLEE 119 (159)
Q Consensus 95 ~f~~i~~~t~l~EG~iVR~~rRl~e 119 (159)
|...|.+.+++..-++.|.+++|++
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~ 51 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEE 51 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 6789999999999999999998876
No 61
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=41.72 E-value=79 Score=22.95 Aligned_cols=49 Identities=12% Similarity=0.169 Sum_probs=37.3
Q ss_pred cCCchHHHHHHH-hhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHH
Q psy6286 78 QFKPSLMDVVHA-WCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQ 126 (159)
Q Consensus 78 ~~~~~l~~~v~~-Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~ 126 (159)
.+.+.--.++.. .-.|.|..||.+..++++|.+=..+.|...-|++.-.
T Consensus 106 ~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 155 (161)
T PRK09047 106 KLPARQREAFLLRYWEDMDVAETAAAMGCSEGSVKTHCSRATHALAKALE 155 (161)
T ss_pred hCCHHHHHHHHHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 344343344333 5799999999999999999999999998888887543
No 62
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=41.29 E-value=78 Score=24.88 Aligned_cols=46 Identities=11% Similarity=0.133 Sum_probs=34.9
Q ss_pred cCCchHHHHHHH-hhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHH
Q psy6286 78 QFKPSLMDVVHA-WCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQ 123 (159)
Q Consensus 78 ~~~~~l~~~v~~-Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrq 123 (159)
.+.+.--.++.. ...|.|+.+|.+..++.+|.+=+.+.|...-|++
T Consensus 175 ~L~~~~r~il~l~y~~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~ 221 (224)
T TIGR02479 175 SLSEREQLVLSLYYYEELNLKEIGEVLGLTESRVSQIHSQALKKLRA 221 (224)
T ss_pred hCCHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 344444444444 4699999999999999999988888887777665
No 63
>cd06654 STKc_PAK1 Catalytic domain of the Protein Serine/Threonine Kinase, p21-activated kinase 1. Serine/threonine kinases (STKs), p21-activated kinase (PAK) 1, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The PAK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. PAKs are Rho family GTPase-regulated kinases that serve as important mediators in the function of Cdc42 (cell division cycle 42) and Rac. PAKs from higher eukaryotes are classified into two groups (I and II), according to their biochemical and structural features. PAK1 belongs to group I. Group I PAKs contain a PBD (p21-binding domain) overlapping with an AID (autoinhibitory domain), a C-terminal catalytic domain, SH3 binding sites and a non-classical SH3 binding
Probab=41.16 E-value=29 Score=27.94 Aligned_cols=45 Identities=27% Similarity=0.256 Sum_probs=37.6
Q ss_pred HHHHHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHHhh
Q psy6286 84 MDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQAS 128 (159)
Q Consensus 84 ~~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~a~ 128 (159)
..++++|..|.++.+.+....+.++.+.+.+.++.+-|..+.+..
T Consensus 92 ~~lv~e~~~~~~L~~~~~~~~~~~~~~~~i~~ql~~aL~~LH~~g 136 (296)
T cd06654 92 LWVVMEYLAGGSLTDVVTETCMDEGQIAAVCRECLQALEFLHSNQ 136 (296)
T ss_pred EEEeecccCCCCHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHCC
Confidence 457888999999999998888889998888888888887776554
No 64
>PRK10573 type IV pilin biogenesis protein; Provisional
Probab=40.84 E-value=1.6e+02 Score=25.33 Aligned_cols=55 Identities=11% Similarity=0.168 Sum_probs=38.4
Q ss_pred HHHHHhhCCCCHHHHHhhcCCCccHHHHHHH------HHHHHHHHHHHhhhhhCChHHHHHHHHH
Q psy6286 85 DVVHAWCEGASFLKVCSITDIFEGSIIRCMR------RLEEVLRQLVQASRNIGNTLLEEKFNEA 143 (159)
Q Consensus 85 ~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~r------Rl~elLrql~~a~~~ig~~~L~~k~~~a 143 (159)
.+...=.+|.+|++.++.+++++..+++.++ ++++.|.++++--. .++..+.+..
T Consensus 304 ~i~~~v~~G~sls~al~~~~~fp~~~~~~i~~GE~sG~L~~~L~~la~~~~----~~~~~~~~~~ 364 (399)
T PRK10573 304 QIQQQIAQGIPLWLALKNHPLFPPLCLQLVRVGEESGSLDLMLENLAHWHQ----EQTQALADNL 364 (399)
T ss_pred HHHHHHHCcccHHHHHhhCCCCcHHHHHHHHHHHhhccHHHHHHHHHHHHH----HHHHHHHHHH
Confidence 3444445899999999999999999988887 46677776665542 4444444443
No 65
>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=40.83 E-value=36 Score=20.10 Aligned_cols=29 Identities=17% Similarity=0.237 Sum_probs=23.4
Q ss_pred hCCCCHHHHHhhcCCCccHHHHHHHHHHH
Q psy6286 91 CEGASFLKVCSITDIFEGSIIRCMRRLEE 119 (159)
Q Consensus 91 a~G~~f~~i~~~t~l~EG~iVR~~rRl~e 119 (159)
..+.|..+|.+.+++..|.+=+.++++.+
T Consensus 15 ~~~~t~~ela~~~~is~~tv~~~l~~L~~ 43 (48)
T PF13412_consen 15 NPRITQKELAEKLGISRSTVNRYLKKLEE 43 (48)
T ss_dssp CTTS-HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred cCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 45589999999999999999998888765
No 66
>cd06656 STKc_PAK3 Catalytic domain of the Protein Serine/Threonine Kinase, p21-activated kinase 3. Serine/threonine kinases (STKs), p21-activated kinase (PAK) 3, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The PAK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. PAKs are Rho family GTPase-regulated kinases that serve as important mediators in the function of Cdc42 (cell division cycle 42) and Rac. PAKs from higher eukaryotes are classified into two groups (I and II), according to their biochemical and structural features. PAK3 belongs to group I. Group I PAKs contain a PBD (p21-binding domain) overlapping with an AID (autoinhibitory domain), a C-terminal catalytic domain, SH3 binding sites and a non-classical SH3 binding
Probab=40.83 E-value=30 Score=27.86 Aligned_cols=45 Identities=27% Similarity=0.251 Sum_probs=38.4
Q ss_pred HHHHHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHHhh
Q psy6286 84 MDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQAS 128 (159)
Q Consensus 84 ~~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~a~ 128 (159)
..++++|..|.++.+.+....+.+..+.+.+.++..-|..+.+..
T Consensus 91 ~~lv~e~~~~~~L~~~~~~~~~~~~~~~~~~~~l~~~L~~LH~~~ 135 (297)
T cd06656 91 LWVVMEYLAGGSLTDVVTETCMDEGQIAAVCRECLQALDFLHSNQ 135 (297)
T ss_pred EEEeecccCCCCHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHCC
Confidence 356888999999999998888999999998888888888887654
No 67
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=39.82 E-value=58 Score=26.22 Aligned_cols=38 Identities=16% Similarity=0.044 Sum_probs=32.3
Q ss_pred HHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHH
Q psy6286 87 VHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQL 124 (159)
Q Consensus 87 v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql 124 (159)
...+..|.|..+|-+..++.+|.+-+.+.|...-||+.
T Consensus 215 ~l~~~~g~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~ 252 (255)
T TIGR02941 215 HCTFEENLSQKETGERLGISQMHVSRLQRQAISKLKEA 252 (255)
T ss_pred HHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 34568999999999999999999988888888777764
No 68
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=39.75 E-value=91 Score=23.17 Aligned_cols=45 Identities=11% Similarity=0.045 Sum_probs=34.6
Q ss_pred CCchHHHHHHH-hhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHH
Q psy6286 79 FKPSLMDVVHA-WCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQ 123 (159)
Q Consensus 79 ~~~~l~~~v~~-Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrq 123 (159)
+.+..=.++.. ...|.|..||.+..++++|.+=..++|...-|++
T Consensus 119 L~~~~r~v~~L~~~eg~s~~EIA~~l~is~~tV~~~l~ra~~~~~~ 164 (168)
T PRK12525 119 LSGKARAAFLMSQLEGLTYVEIGERLGVSLSRIHQYMVEAFKCCYQ 164 (168)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 44444344433 6899999999999999999988888887777765
No 69
>PF14493 HTH_40: Helix-turn-helix domain
Probab=39.57 E-value=81 Score=21.46 Aligned_cols=35 Identities=20% Similarity=0.265 Sum_probs=28.4
Q ss_pred HHHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHH
Q psy6286 86 VVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEV 120 (159)
Q Consensus 86 ~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~el 120 (159)
-...|.+|+|..+|-+.-++.+++|..-+-+....
T Consensus 6 T~~l~~~G~si~eIA~~R~L~~sTI~~HL~~~~~~ 40 (91)
T PF14493_consen 6 TYELFQKGLSIEEIAKIRGLKESTIYGHLAELIES 40 (91)
T ss_pred HHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHh
Confidence 34568899999999999999999998776655443
No 70
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=39.42 E-value=1.1e+02 Score=23.41 Aligned_cols=49 Identities=22% Similarity=0.296 Sum_probs=36.8
Q ss_pred cCCchHHHHHH-HhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHH
Q psy6286 78 QFKPSLMDVVH-AWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQ 126 (159)
Q Consensus 78 ~~~~~l~~~v~-~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~ 126 (159)
.+.+.--.++. ..-.|.|+.+|.+..++++|.+=..+.|....|++.-.
T Consensus 141 ~Lp~~~r~v~~l~~~eg~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l~ 190 (194)
T PRK12531 141 RLPKAQRDVLQAVYLEELPHQQVAEMFDIPLGTVKSRLRLAVEKLRHSMD 190 (194)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHhh
Confidence 34444444544 35699999999999999999998888888777776543
No 71
>COG1420 HrcA Transcriptional regulator of heat shock gene [Transcription]
Probab=39.40 E-value=23 Score=30.86 Aligned_cols=24 Identities=25% Similarity=0.350 Sum_probs=20.3
Q ss_pred HHHHHHHHhhhCCccCC----C-ccchhh
Q psy6286 9 LKCRKRVLRRLGYATEA----D-VIEMKG 32 (159)
Q Consensus 9 ~~~~~~vL~~lgyid~~----~-~vt~kG 32 (159)
-++.++.|+++|||.+. | .||.+|
T Consensus 44 IRN~Ma~LE~~GlI~k~HtSsGRvPT~~G 72 (346)
T COG1420 44 IRNEMADLEKLGLIEKPHTSSGRVPTDKG 72 (346)
T ss_pred HHHHHHHHHHCCCccCccccCCcCCcHhH
Confidence 47889999999999874 3 799999
No 72
>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=38.97 E-value=45 Score=20.33 Aligned_cols=38 Identities=16% Similarity=0.288 Sum_probs=29.2
Q ss_pred chHHHHHHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHH
Q psy6286 81 PSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEE 119 (159)
Q Consensus 81 ~~l~~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~e 119 (159)
+.++..+++ ..|.+..+|-+..++..+.+-|.+++|++
T Consensus 6 ~~iL~~l~~-~~~~~~~~la~~~~~~~~~~t~~i~~L~~ 43 (59)
T PF01047_consen 6 FRILRILYE-NGGITQSELAEKLGISRSTVTRIIKRLEK 43 (59)
T ss_dssp HHHHHHHHH-HSSEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHH-cCCCCHHHHHHHHCCChhHHHHHHHHHHH
Confidence 344555554 36679999999999999999999998875
No 73
>PF08461 HTH_12: Ribonuclease R winged-helix domain; InterPro: IPR013668 This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaea.
Probab=38.35 E-value=40 Score=22.00 Aligned_cols=27 Identities=30% Similarity=0.473 Sum_probs=21.8
Q ss_pred HHHHHHHHHHhhhCCccCCC----ccchhhH
Q psy6286 7 EELKCRKRVLRRLGYATEAD----VIEMKGR 33 (159)
Q Consensus 7 ~e~~~~~~vL~~lgyid~~~----~vt~kGr 33 (159)
...+++++.|++-||+...+ .+|.||+
T Consensus 33 ~avRrrLr~me~~Glt~~~g~~G~~iT~~G~ 63 (66)
T PF08461_consen 33 EAVRRRLRAMERDGLTRKVGRQGRIITEKGL 63 (66)
T ss_pred HHHHHHHHHHHHCCCccccCCcccccCHHHH
Confidence 56788999999999997632 5888885
No 74
>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=37.67 E-value=40 Score=20.65 Aligned_cols=29 Identities=21% Similarity=0.318 Sum_probs=24.6
Q ss_pred hCC--CCHHHHHhhcCCCccHHHHHHHHHHH
Q psy6286 91 CEG--ASFLKVCSITDIFEGSIIRCMRRLEE 119 (159)
Q Consensus 91 a~G--~~f~~i~~~t~l~EG~iVR~~rRl~e 119 (159)
..| .+..+|.+...+....+-|.+++|++
T Consensus 17 ~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~ 47 (62)
T PF12802_consen 17 HPGEELTQSELAERLGISKSTVSRIVKRLEK 47 (62)
T ss_dssp STTSGEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 445 69999999999999999999999875
No 75
>PRK06930 positive control sigma-like factor; Validated
Probab=36.96 E-value=1e+02 Score=23.83 Aligned_cols=47 Identities=13% Similarity=0.186 Sum_probs=38.7
Q ss_pred ccCCchHHHHHHH-hhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHH
Q psy6286 77 NQFKPSLMDVVHA-WCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQ 123 (159)
Q Consensus 77 ~~~~~~l~~~v~~-Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrq 123 (159)
..+.+.--.++.. ...|.|+.+|.+..++++|.+=..+.|...-|+.
T Consensus 113 ~~L~~rer~V~~L~~~eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~ 160 (170)
T PRK06930 113 SVLTEREKEVYLMHRGYGLSYSEIADYLNIKKSTVQSMIERAEKKIAR 160 (170)
T ss_pred HhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4667766677776 6899999999999999999988888887776665
No 76
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=36.88 E-value=1.2e+02 Score=23.82 Aligned_cols=29 Identities=21% Similarity=0.335 Sum_probs=26.1
Q ss_pred hCCCCHHHHHhhcCCCccHHHHHHHHHHH
Q psy6286 91 CEGASFLKVCSITDIFEGSIIRCMRRLEE 119 (159)
Q Consensus 91 a~G~~f~~i~~~t~l~EG~iVR~~rRl~e 119 (159)
..|.+-++|++...+..+++.|.+.||++
T Consensus 57 ~~~itq~eLa~~l~l~~sTvtr~l~rLE~ 85 (185)
T PRK13777 57 LKGASISEIAKFGVMHVSTAFNFSKKLEE 85 (185)
T ss_pred CCCcCHHHHHHHHCCCHhhHHHHHHHHHH
Confidence 36889999999999999999999999875
No 77
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=36.85 E-value=1.1e+02 Score=22.68 Aligned_cols=48 Identities=21% Similarity=0.242 Sum_probs=36.1
Q ss_pred cCCchHHHHHHH-hhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHH
Q psy6286 78 QFKPSLMDVVHA-WCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLV 125 (159)
Q Consensus 78 ~~~~~l~~~v~~-Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~ 125 (159)
.+.+.--.++.. ...|.|..||.+..++++|.+=..+.|....|++.-
T Consensus 118 ~L~~~~r~vl~L~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 166 (173)
T PRK09645 118 QLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYALRALRLAL 166 (173)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 344444444443 578999999999999999999877777777777643
No 78
>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=36.84 E-value=34 Score=21.40 Aligned_cols=28 Identities=18% Similarity=0.257 Sum_probs=22.4
Q ss_pred CCCCHHHHHhhcCCCccHHHHHHHHHHH
Q psy6286 92 EGASFLKVCSITDIFEGSIIRCMRRLEE 119 (159)
Q Consensus 92 ~G~~f~~i~~~t~l~EG~iVR~~rRl~e 119 (159)
.+.+..+|++.+++..+.+-|.+++|.+
T Consensus 17 ~~~t~~~l~~~~~~~~~~vs~~i~~L~~ 44 (68)
T PF13463_consen 17 GPMTQSDLAERLGISKSTVSRIIKKLEE 44 (68)
T ss_dssp S-BEHHHHHHHTT--HHHHHHHHHHHHH
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 5568999999999999999999988876
No 79
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=36.76 E-value=69 Score=25.81 Aligned_cols=47 Identities=15% Similarity=0.118 Sum_probs=36.0
Q ss_pred cCCchHHHHHH-HhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHH
Q psy6286 78 QFKPSLMDVVH-AWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQL 124 (159)
Q Consensus 78 ~~~~~l~~~v~-~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql 124 (159)
.+.+.--.++. .+..|.|+.+|-+..++++|.+=+...|...-|++.
T Consensus 205 ~L~~~~r~vl~l~~~~g~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~ 252 (257)
T PRK08583 205 VLSDREKSIIQCTFIENLSQKETGERLGISQMHVSRLQRQAIKKLREA 252 (257)
T ss_pred hCCHHHHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 34444434443 357999999999999999999998888888777754
No 80
>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins.; PDB: 2GA1_B.
Probab=36.72 E-value=36 Score=21.41 Aligned_cols=32 Identities=13% Similarity=0.097 Sum_probs=20.9
Q ss_pred CchHHHHHHHhhCCCCHHHHHhhcC-CCccHHH
Q psy6286 80 KPSLMDVVHAWCEGASFLKVCSITD-IFEGSII 111 (159)
Q Consensus 80 ~~~l~~~v~~Wa~G~~f~~i~~~t~-l~EG~iV 111 (159)
+-..-.++..|+.|.|..+|++.-+ +...++-
T Consensus 18 RI~v~~i~~~~~~G~s~eeI~~~yp~Lt~~~i~ 50 (56)
T PF04255_consen 18 RIPVRDILDLLAAGESPEEIAEDYPSLTLEDIR 50 (56)
T ss_dssp S-BHHHHHHHHHTT--HHHHHHHSTT--HHHHH
T ss_pred eecHHHHHHHHHcCCCHHHHHHHCCCCCHHHHH
Confidence 3445678888899999999999976 7766553
No 81
>KOG4456|consensus
Probab=36.60 E-value=49 Score=24.99 Aligned_cols=50 Identities=14% Similarity=0.173 Sum_probs=36.9
Q ss_pred HHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHHhhhhhCChHHHHHHHHHHH-hhcCC
Q psy6286 88 HAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKFNEAIK-TVKRD 150 (159)
Q Consensus 88 ~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~a~~~ig~~~L~~k~~~a~~-~I~Rd 150 (159)
=.||+|+...+-+.......-++|-.+ ..++|-++|.+-|-++.. ..||+
T Consensus 67 PtWar~~v~~eai~~qa~~pp~~v~~F-------------f~~~pkpdLkeIF~~~~p~~~KR~ 117 (134)
T KOG4456|consen 67 PTWARDMVIVEAIEEQAKNPPFNVNTF-------------FGSMPKPDLKEIFGEMVPSKKKRG 117 (134)
T ss_pred chhhhhchHHHHHHHHhhCCchHHHHH-------------hcccCCcCHHHHHHhhhhhhhhcc
Confidence 359999999997766655555555443 344567899999999888 78886
No 82
>PF13551 HTH_29: Winged helix-turn helix
Probab=36.55 E-value=66 Score=21.86 Aligned_cols=34 Identities=18% Similarity=0.341 Sum_probs=29.3
Q ss_pred HHHHHhhCCCC-HHHHHhhcCCCccHHHHHHHHHH
Q psy6286 85 DVVHAWCEGAS-FLKVCSITDIFEGSIIRCMRRLE 118 (159)
Q Consensus 85 ~~v~~Wa~G~~-f~~i~~~t~l~EG~iVR~~rRl~ 118 (159)
.++...+.|.+ -.+|++..++..-++=||+++..
T Consensus 3 ~~l~l~~~g~~~~~~ia~~lg~s~~Tv~r~~~~~~ 37 (112)
T PF13551_consen 3 QILLLLAEGVSTIAEIARRLGISRRTVYRWLKRYR 37 (112)
T ss_pred HHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHH
Confidence 45667889996 99999999999999999999854
No 83
>COG1393 ArsC Arsenate reductase and related proteins, glutaredoxin family [Inorganic ion transport and metabolism]
Probab=36.19 E-value=54 Score=23.95 Aligned_cols=24 Identities=25% Similarity=0.263 Sum_probs=18.0
Q ss_pred CChHHHHHHHHHHHhhcCCccccc
Q psy6286 132 GNTLLEEKFNEAIKTVKRDIFLEI 155 (159)
Q Consensus 132 g~~~L~~k~~~a~~~I~RdIV~~~ 155 (159)
.+.++...+.+.-.+|||-||...
T Consensus 76 ~~~~~~~~i~~~~~LikRPivv~~ 99 (117)
T COG1393 76 SDEELIEALLENPSLIKRPIVVDN 99 (117)
T ss_pred ChHHHHHHHHhChhhccCCeEEeC
Confidence 356667777777789999998754
No 84
>TIGR02120 GspF general secretion pathway protein F. This membrane protein is a component of the terminal branch complex of the general secretion pathway (GSP), also known as the"Type II" secretion pathway. The GSP transports proteins (generally virulence-associated cell wall hydrolases) across the outer membrase of the bacterial cell. Transport across the inner membrane is often, but not exclusively handled by the Sec system. This model was constructed from the broader subfamily model, pfam00482 which includes components of pilin complexes (PilC) as well as other related genes. GspF is nearly always gene clustered with other GSP subunits. Some genes from Xylella and Xanthomonas strains score below the trusted cutoff due to excessive divergence from the family such that a sequence from Deinococcus which does not appear to be GspF scores higher.
Probab=35.86 E-value=1.3e+02 Score=25.84 Aligned_cols=57 Identities=18% Similarity=0.274 Sum_probs=38.5
Q ss_pred HHHHHHhhCCCCHHHHHhhcCCCccHHHHHHH------HHHHHHHHHHHhhhhhCChHHHHHHHHHH
Q psy6286 84 MDVVHAWCEGASFLKVCSITDIFEGSIIRCMR------RLEEVLRQLVQASRNIGNTLLEEKFNEAI 144 (159)
Q Consensus 84 ~~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~r------Rl~elLrql~~a~~~ig~~~L~~k~~~a~ 144 (159)
-.+...=.+|.+|++.++.+++++..+++.++ ++++.|.++++-.. .++..+.+...
T Consensus 304 ~~i~~~l~~G~sls~al~~~~~fp~~~~~mi~~GE~sG~L~~~L~~~a~~~~----~~~~~~~~~~~ 366 (399)
T TIGR02120 304 EDAAARVREGGSLSRALRATGLFPPLLVHMIASGEKSGQLETMLERAADNQE----REFERRIATLT 366 (399)
T ss_pred HHHHHHHHCCccHHHHHhcCCCCCHHHHHHHHHHhhhccHHHHHHHHHHHHH----HHHHHHHHHHH
Confidence 34444445899999999999999988888775 46666666666542 44454444433
No 85
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=35.11 E-value=85 Score=18.47 Aligned_cols=29 Identities=10% Similarity=0.229 Sum_probs=24.4
Q ss_pred hCCCCHHHHHhhcCCCccHHHHHHHHHHH
Q psy6286 91 CEGASFLKVCSITDIFEGSIIRCMRRLEE 119 (159)
Q Consensus 91 a~G~~f~~i~~~t~l~EG~iVR~~rRl~e 119 (159)
....++.+|.+..++..+++-+.++++.+
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~ 36 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLRE 36 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 56679999999999999988888877765
No 86
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=34.88 E-value=1.2e+02 Score=22.26 Aligned_cols=51 Identities=10% Similarity=0.105 Sum_probs=41.6
Q ss_pred ccCCchHHHHHHHh-hCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHHh
Q psy6286 77 NQFKPSLMDVVHAW-CEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQA 127 (159)
Q Consensus 77 ~~~~~~l~~~v~~W-a~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~a 127 (159)
..+.+.--.++... ..|.|..+|.+..++.+|.+=..+.|.-.-|++...-
T Consensus 107 ~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~ 158 (165)
T PRK09644 107 HTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLKE 158 (165)
T ss_pred HhCCHHHHHHHHhHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 35666666777766 5999999999999999999988888888888876543
No 87
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=34.63 E-value=1.2e+02 Score=23.05 Aligned_cols=49 Identities=18% Similarity=0.302 Sum_probs=37.0
Q ss_pred cCCchHHHHHHH-hhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHH
Q psy6286 78 QFKPSLMDVVHA-WCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQ 126 (159)
Q Consensus 78 ~~~~~l~~~v~~-Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~ 126 (159)
.+.+..-.++.. ...|.|+.||.+..++++|++=..+.|.-.-|+..-.
T Consensus 111 ~Lp~~~R~v~~L~~~eg~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~ 160 (182)
T PRK12511 111 DLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARAALRAFEE 160 (182)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 445555555544 5699999999999999999998777777777766444
No 88
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=34.05 E-value=85 Score=23.00 Aligned_cols=45 Identities=11% Similarity=0.139 Sum_probs=34.2
Q ss_pred cCCchHHHHH-HHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHH
Q psy6286 78 QFKPSLMDVV-HAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLR 122 (159)
Q Consensus 78 ~~~~~l~~~v-~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLr 122 (159)
.+.+.-=.++ .....|.|..||.+..++++|++=..+.|-...|+
T Consensus 113 ~L~~~~r~v~~L~~~~g~s~~EIA~~l~is~~tV~~~l~ra~~~~~ 158 (161)
T PRK12528 113 GLPPLVKRAFLLAQVDGLGYGEIATELGISLATVKRYLNKAAMRCY 158 (161)
T ss_pred HCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 3444333444 34579999999999999999999888888766665
No 89
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=33.95 E-value=76 Score=23.25 Aligned_cols=47 Identities=11% Similarity=0.076 Sum_probs=35.3
Q ss_pred CCchHHHHHHH-hhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHH
Q psy6286 79 FKPSLMDVVHA-WCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLV 125 (159)
Q Consensus 79 ~~~~l~~~v~~-Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~ 125 (159)
+.+.--.++.. +..|.|..+|.+..++++|.+=..+.|.-.-|+.+.
T Consensus 113 L~~~~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~Rar~~L~~~~ 160 (161)
T PRK12541 113 LPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKETKSIK 160 (161)
T ss_pred CCHHHHHHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhc
Confidence 44433344443 679999999999999999998888888777777653
No 90
>PRK13870 transcriptional regulator TraR; Provisional
Probab=33.80 E-value=78 Score=25.57 Aligned_cols=60 Identities=13% Similarity=0.288 Sum_probs=38.0
Q ss_pred CCchHHHHHHHh-hCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHHhhhhhCChHHHHHHHHHHHhhcCCcc
Q psy6286 79 FKPSLMDVVHAW-CEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKFNEAIKTVKRDIF 152 (159)
Q Consensus 79 ~~~~l~~~v~~W-a~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~a~~~ig~~~L~~k~~~a~~~I~RdIV 152 (159)
+.+.=.+ +-.| |.|+|-.||-..-++.|.++---++ +|.+=+|- ..+...+..++++|.+
T Consensus 174 LT~RE~E-~L~W~A~GKT~~EIa~ILgISe~TV~~Hl~----------na~~KLga---~nr~qAVa~Ai~~gLI 234 (234)
T PRK13870 174 LDPKEAT-YLRWIAVGKTMEEIADVEGVKYNSVRVKLR----------EAMKRFDV---RSKAHLTALAIRRKLI 234 (234)
T ss_pred CCHHHHH-HHHHHHcCCCHHHHHHHHCCCHHHHHHHHH----------HHHHHcCC---CCHHHHHHHHHHcCCC
Confidence 3443344 4457 6999999999999999998775443 33322222 3455556666766653
No 91
>cd00131 PAX Paired Box domain
Probab=33.78 E-value=78 Score=23.27 Aligned_cols=34 Identities=15% Similarity=0.190 Sum_probs=28.9
Q ss_pred HHHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHH
Q psy6286 86 VVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEE 119 (159)
Q Consensus 86 ~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~e 119 (159)
++..-+.|.|-.+|.+..++..+.+.||++|-.+
T Consensus 26 Iv~~~~~G~s~~~iA~~~~Vs~~tV~r~i~r~~e 59 (128)
T cd00131 26 IVELAQSGIRPCDISRQLRVSHGCVSKILNRYYE 59 (128)
T ss_pred HHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3444469999999999999999999999998665
No 92
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=33.34 E-value=86 Score=24.90 Aligned_cols=36 Identities=11% Similarity=0.137 Sum_probs=31.5
Q ss_pred HhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHH
Q psy6286 89 AWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQL 124 (159)
Q Consensus 89 ~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql 124 (159)
....|.|+.+|.+..++.+|.+=+.+.|...-|++.
T Consensus 196 ~~~~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 231 (236)
T PRK06986 196 YYQEELNLKEIGAVLGVSESRVSQIHSQAIKRLRAR 231 (236)
T ss_pred HhccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 357999999999999999999998888888877764
No 93
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=32.84 E-value=72 Score=22.99 Aligned_cols=35 Identities=11% Similarity=0.180 Sum_probs=30.8
Q ss_pred hhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHH
Q psy6286 90 WCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQL 124 (159)
Q Consensus 90 Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql 124 (159)
...|.|+.+|.+..++++|.+-..+.|...-|++.
T Consensus 118 ~~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~~ 152 (154)
T TIGR02950 118 EFKEFSYKEIAELLNLSLAKVKSNLFRARKELKKL 152 (154)
T ss_pred hhccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 45899999999999999999999888887777764
No 94
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=32.78 E-value=36 Score=26.32 Aligned_cols=25 Identities=28% Similarity=0.428 Sum_probs=19.1
Q ss_pred HHHHHHHHhhhCCccCC--C-ccchhhH
Q psy6286 9 LKCRKRVLRRLGYATEA--D-VIEMKGR 33 (159)
Q Consensus 9 ~~~~~~vL~~lgyid~~--~-~vt~kGr 33 (159)
-+..++.|++.|||+.+ | ++|.+|+
T Consensus 98 iR~~LqqLE~~glVek~~~GR~lT~~G~ 125 (150)
T PRK09333 98 IRKILQQLEKAGLVEKTKKGRVITPKGR 125 (150)
T ss_pred HHHHHHHHHHCCCeeeCCCCCEeCHHHH
Confidence 35678999999999753 3 7788873
No 95
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=32.42 E-value=1.3e+02 Score=24.81 Aligned_cols=66 Identities=9% Similarity=0.209 Sum_probs=50.5
Q ss_pred HHHHHHHHHHHHHcCCCCChhhhhccCCchH---HHHHHHhhCCCCHHHHHhhcCCCccHHHHHHHHHH
Q psy6286 53 LELARHIARISIESKLDLDEDSYVNQFKPSL---MDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLE 118 (159)
Q Consensus 53 ~~i~~~i~~~~~~~~l~~~~~~~~~~~~~~l---~~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~ 118 (159)
.-+.+.|...+++||+-++.--.....-|++ ..++..|-+|.+..+|-..|.-+++.+=|.++--.
T Consensus 120 ~TI~~~i~~yq~e~g~vvPtrG~i~DiGp~~tHK~~ii~~~l~g~~~~eiar~t~HS~~av~rYi~~F~ 188 (220)
T PF07900_consen 120 RTISKDIKEYQKEHGVVVPTRGTIHDIGPGVTHKKIIIRLYLKGKPTPEIARRTNHSPEAVDRYIKDFK 188 (220)
T ss_pred HHHHHHHHHHHHHcCceeccCCcccccCCcchHHHHHHHHHHcCCCHHHHHHHhccCHHHHHHHHHhhH
Confidence 6788899999999997654322223444555 47899999999999999999999998877765443
No 96
>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=32.33 E-value=40 Score=20.47 Aligned_cols=28 Identities=11% Similarity=0.197 Sum_probs=22.5
Q ss_pred CCCCHHHHHhhcCCCccHHHHHHHHHHH
Q psy6286 92 EGASFLKVCSITDIFEGSIIRCMRRLEE 119 (159)
Q Consensus 92 ~G~~f~~i~~~t~l~EG~iVR~~rRl~e 119 (159)
.|.++.+|.+.+++.-.++-|.+..|.+
T Consensus 17 ~~~t~~eia~~~gl~~stv~r~L~tL~~ 44 (52)
T PF09339_consen 17 GPLTLSEIARALGLPKSTVHRLLQTLVE 44 (52)
T ss_dssp SCEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4568999999999999999988877654
No 97
>cd05578 STKc_Yank1 Catalytic domain of the Protein Serine/Threonine Kinase, Yank1. Serine/Threonine Kinases (STKs), Yank1 or STK32A subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The Yank1 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. This subfamily contains uncharacterized STKs with similarity to the human protein designated Yank1 or STK32A.
Probab=32.23 E-value=33 Score=26.52 Aligned_cols=49 Identities=14% Similarity=-0.028 Sum_probs=39.8
Q ss_pred HHHHHHhhCCCCHHHHHhhc-CCCccHHHHHHHHHHHHHHHHHHhhhhhC
Q psy6286 84 MDVVHAWCEGASFLKVCSIT-DIFEGSIIRCMRRLEEVLRQLVQASRNIG 132 (159)
Q Consensus 84 ~~~v~~Wa~G~~f~~i~~~t-~l~EG~iVR~~rRl~elLrql~~a~~~ig 132 (159)
.-++++++.|.++.+.+... .+.+..+.+++.++.+-|..+.+..-+.|
T Consensus 75 ~~lv~e~~~~~~L~~~l~~~~~l~~~~~~~~~~~i~~~l~~lh~~~i~h~ 124 (258)
T cd05578 75 MYLVVDLLLGGDLRYHLSQKVKFSEEQVKFWICEIVLALEYLHSKGIIHR 124 (258)
T ss_pred EEEEEeCCCCCCHHHHHHhcCCcCHHHHHHHHHHHHHHHHHHHhCCeecc
Confidence 34567789999999999877 89999999999999999988887643333
No 98
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=32.22 E-value=50 Score=19.61 Aligned_cols=25 Identities=28% Similarity=0.448 Sum_probs=20.7
Q ss_pred CCHHHHHhhcCCCccHHHHHHHHHH
Q psy6286 94 ASFLKVCSITDIFEGSIIRCMRRLE 118 (159)
Q Consensus 94 ~~f~~i~~~t~l~EG~iVR~~rRl~ 118 (159)
.||.+|-+..++.+..+.+-++|+.
T Consensus 18 ~s~~~la~~lglS~~~v~~Ri~rL~ 42 (42)
T PF13404_consen 18 RSYAELAEELGLSESTVRRRIRRLE 42 (42)
T ss_dssp S-HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred ccHHHHHHHHCcCHHHHHHHHHHhC
Confidence 5999999999999999999998874
No 99
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=32.05 E-value=47 Score=25.41 Aligned_cols=34 Identities=29% Similarity=0.284 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHhhhCCccCC---C-ccchhhH-HHhhhc
Q psy6286 6 MEELKCRKRVLRRLGYATEA---D-VIEMKGR-VACELS 39 (159)
Q Consensus 6 ~~e~~~~~~vL~~lgyid~~---~-~vt~kGr-va~~I~ 39 (159)
.+.=..|++=|.+.||++.. + .+|.+|+ .|..+.
T Consensus 38 p~sVt~ml~rL~~~GlV~~~~y~gi~LT~~G~~~a~~~~ 76 (154)
T COG1321 38 PPSVTEMLKRLERLGLVEYEPYGGVTLTEKGREKAKELL 76 (154)
T ss_pred cHHHHHHHHHHHHCCCeEEecCCCeEEChhhHHHHHHHH
Confidence 35556788999999999763 2 8999999 555544
No 100
>PRK15443 pduE propanediol dehydratase small subunit; Provisional
Probab=31.72 E-value=77 Score=24.12 Aligned_cols=54 Identities=15% Similarity=0.161 Sum_probs=36.1
Q ss_pred hCCCCHHHHHhh----cCCCccHHHHHHHHHHHHHHHHHHhhhhhCChHHHHHHHHHHHhhc
Q psy6286 91 CEGASFLKVCSI----TDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKFNEAIKTVK 148 (159)
Q Consensus 91 a~G~~f~~i~~~----t~l~EG~iVR~~rRl~elLrql~~a~~~ig~~~L~~k~~~a~~~I~ 148 (159)
..|+++++|--. -++...|+ |.-..+-..=.||+.. .|++.|+..|+.|.+++.
T Consensus 21 ~tGk~l~diTle~V~~G~v~~~Dl-RItpetL~~QaqiAe~---~Gr~~la~NfrRAAELt~ 78 (138)
T PRK15443 21 PTGKSLDDITLENVLSGKVTAEDL-RITPETLRMQAQIAED---AGRPQLAMNFRRAAELTA 78 (138)
T ss_pred CCCCChhHhhHHHHHcCCCCHHHh-ccCHHHHHHHHHHHHH---cCCHHHHHHHHHHHhccC
Confidence 589999998633 24555553 4444444444445444 499999999999998754
No 101
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.
Probab=31.63 E-value=1.3e+02 Score=23.72 Aligned_cols=46 Identities=13% Similarity=0.084 Sum_probs=34.3
Q ss_pred cCCchHHHHHHHhh-----CCCCHHHHHhhcCCCccHHHHHHHHHHHHHHH
Q psy6286 78 QFKPSLMDVVHAWC-----EGASFLKVCSITDIFEGSIIRCMRRLEEVLRQ 123 (159)
Q Consensus 78 ~~~~~l~~~v~~Wa-----~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrq 123 (159)
.+.+.-=.++.... .|.|..||.+..++.+|++-+.+.|..--|++
T Consensus 174 ~L~~~~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~ 224 (227)
T TIGR02846 174 VLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMKLYK 224 (227)
T ss_pred hCCHHHHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 44444445555543 89999999999999999998877776655554
No 102
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=31.43 E-value=70 Score=23.07 Aligned_cols=36 Identities=8% Similarity=0.129 Sum_probs=30.3
Q ss_pred HHHHHHHhhCCCCHHHHHhhcCCCccHHHHHHHHHH
Q psy6286 83 LMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLE 118 (159)
Q Consensus 83 l~~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~ 118 (159)
...|.....+|.|-.+++..-++.++.+-+|.++..
T Consensus 19 ~~aV~~~~~~g~sv~evA~e~gIs~~tl~~W~r~y~ 54 (121)
T PRK09413 19 IAIVQQSFEPGMTVSLVARQHGVAASQLFLWRKQYQ 54 (121)
T ss_pred HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHh
Confidence 345555677999999999999999999999999864
No 103
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=31.24 E-value=1.4e+02 Score=22.87 Aligned_cols=41 Identities=20% Similarity=0.181 Sum_probs=33.4
Q ss_pred HhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHHhhh
Q psy6286 89 AWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASR 129 (159)
Q Consensus 89 ~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~a~~ 129 (159)
....|.|..||.+..++++|.+-..+.|.-.-|+..-....
T Consensus 146 ~~~~g~s~~EIA~~lg~s~~tV~~rl~rar~~Lr~~l~~~~ 186 (192)
T PRK09643 146 VDMQGYSVADAARMLGVAEGTVKSRCARGRARLAELLGYLR 186 (192)
T ss_pred HHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHhc
Confidence 35699999999999999999998888887777776555433
No 104
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=31.12 E-value=1.6e+02 Score=22.15 Aligned_cols=48 Identities=17% Similarity=0.181 Sum_probs=36.4
Q ss_pred ccCCchHHHHHHH-hhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHH
Q psy6286 77 NQFKPSLMDVVHA-WCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQL 124 (159)
Q Consensus 77 ~~~~~~l~~~v~~-Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql 124 (159)
..+.+.--.++.. --.|.|..+|.+..++++|++=..+.|...-|++.
T Consensus 130 ~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 178 (184)
T PRK12539 130 ARLPEKMRLAIQAVKLEGLSVAEAATRSGMSESAVKVSVHRGLKALAAL 178 (184)
T ss_pred HhCCHHHHHHHHHHHHcCCcHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3454444445542 34899999999999999999998888888777764
No 105
>smart00221 STYKc Protein kinase; unclassified specificity. Phosphotransferases. The specificity of this class of kinases can not be predicted. Possible dual-specificity Ser/Thr/Tyr kinase.
Probab=31.03 E-value=44 Score=24.75 Aligned_cols=51 Identities=18% Similarity=0.234 Sum_probs=40.2
Q ss_pred HHHHHHHhhCCCCHHHHHhhcC--CCccHHHHHHHHHHHHHHHHHHhhhhhCC
Q psy6286 83 LMDVVHAWCEGASFLKVCSITD--IFEGSIIRCMRRLEEVLRQLVQASRNIGN 133 (159)
Q Consensus 83 l~~~v~~Wa~G~~f~~i~~~t~--l~EG~iVR~~rRl~elLrql~~a~~~ig~ 133 (159)
...++++|+.|.++.+.+.... +.+..+.+.+.++.+.|..+.+..-..||
T Consensus 71 ~~~~v~e~~~~~~L~~~~~~~~~~~~~~~~~~~~~~l~~~l~~lh~~~i~h~d 123 (225)
T smart00221 71 PLYLVMEYCEGGDLFDYLRKKGGKLSEEEARFYLRQILEALEYLHSLGIVHRD 123 (225)
T ss_pred ceEEEEeccCCCCHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHhCCeecCC
Confidence 3456888999999999987765 88999999999999988888776444343
No 106
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=31.02 E-value=1.1e+02 Score=22.40 Aligned_cols=37 Identities=24% Similarity=0.269 Sum_probs=32.4
Q ss_pred HhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHH
Q psy6286 89 AWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLV 125 (159)
Q Consensus 89 ~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~ 125 (159)
....|.|..+|.+..++++|++=..+.|...-|+..-
T Consensus 122 ~~~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 158 (162)
T TIGR02983 122 RYYEDLSEAQVAEALGISVGTVKSRLSRALARLRELL 158 (162)
T ss_pred HHHhcCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 3578999999999999999999999999888887643
No 107
>PRK09480 slmA division inhibitor protein; Provisional
Probab=30.89 E-value=50 Score=24.70 Aligned_cols=33 Identities=15% Similarity=0.214 Sum_probs=27.5
Q ss_pred CCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHH
Q psy6286 92 EGASFLKVCSITDIFEGSIIRCMRRLEEVLRQL 124 (159)
Q Consensus 92 ~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql 124 (159)
+|.|..+|.+.+++..|+|-+.+.-=++|+.++
T Consensus 29 ~~~ti~~Ia~~agvs~gt~Y~~F~~K~~L~~~v 61 (194)
T PRK09480 29 ERITTAKLAARVGVSEAALYRHFPSKARMFEGL 61 (194)
T ss_pred CccCHHHHHHHhCCCHhHHHHHCCCHHHHHHHH
Confidence 477999999999999999998888777766555
No 108
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=30.85 E-value=1.2e+02 Score=24.10 Aligned_cols=35 Identities=11% Similarity=0.048 Sum_probs=29.8
Q ss_pred hCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHH
Q psy6286 91 CEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLV 125 (159)
Q Consensus 91 a~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~ 125 (159)
-.|.|..+|.+..+++++.+-+...|...-|++..
T Consensus 193 ~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~l 227 (233)
T PRK05803 193 GKEKTQREIAKALGISRSYVSRIEKRALKKLFKEL 227 (233)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 58899999999999999999888878777666643
No 109
>cd05122 PKc_STE Catalytic domain of STE family Protein Kinases. Protein Kinases (PKs), STE family, catalytic (c) domain. PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine or tyrosine residues on protein substrates. The STE family is part of a larger superfamily that includes the catalytic domains of other protein serine/threonine kinases (STKs), protein tyrosine kinases (PTKs), RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase (PI3K). This family is composed of STKs, and some dual-specificity PKs that phosphorylate both threonine and tyrosine residues of target proteins. Most members are kinases involved in mitogen-activated protein kinase (MAPK) signaling cascades, acting as MAPK kinases (MAPKKs), MAPK kinase kinases (MAPKKKs), or MAPK kinase kinase kinases (MAP4Ks). The MAPK signaling pathways are important mediators of cellular responses to extracellular signals. The pathways involve a triple kinase core
Probab=30.83 E-value=31 Score=25.99 Aligned_cols=50 Identities=20% Similarity=0.236 Sum_probs=40.6
Q ss_pred HHHHHHhhCCCCHHHHHhhc--CCCccHHHHHHHHHHHHHHHHHHhhhhhCC
Q psy6286 84 MDVVHAWCEGASFLKVCSIT--DIFEGSIIRCMRRLEEVLRQLVQASRNIGN 133 (159)
Q Consensus 84 ~~~v~~Wa~G~~f~~i~~~t--~l~EG~iVR~~rRl~elLrql~~a~~~ig~ 133 (159)
..+++++..|.++.+.+... .+.+..+.+.+.++.+.|..+....-+.||
T Consensus 72 ~~l~~e~~~~~~L~~~~~~~~~~~~~~~~~~i~~~i~~~l~~lh~~~i~h~d 123 (253)
T cd05122 72 LWIVMEFCSGGSLKDLLKSTNQTLTESQIAYVCKELLKGLEYLHSNGIIHRD 123 (253)
T ss_pred EEEEEecCCCCcHHHHHhhcCCCCCHHHHHHHHHHHHHHHHHhhcCCEecCC
Confidence 34677889999999998776 789999999999999999988886544444
No 110
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=30.60 E-value=1.3e+02 Score=18.20 Aligned_cols=39 Identities=15% Similarity=0.208 Sum_probs=31.2
Q ss_pred hHHHHHHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHH
Q psy6286 82 SLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEV 120 (159)
Q Consensus 82 ~l~~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~el 120 (159)
.=.++...++.|.|..+|...-++.+..+---.+++..-
T Consensus 8 rE~~v~~l~~~G~s~~eia~~l~is~~tV~~h~~~i~~K 46 (65)
T COG2771 8 REREILRLVAQGKSNKEIARILGISEETVKTHLRNIYRK 46 (65)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 334677788999999999999999999887776665443
No 111
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=30.52 E-value=1.1e+02 Score=20.09 Aligned_cols=37 Identities=11% Similarity=0.187 Sum_probs=28.5
Q ss_pred HHHHHHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHH
Q psy6286 83 LMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEE 119 (159)
Q Consensus 83 l~~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~e 119 (159)
++..+.+-..+.+..+|.+..++...++-|.+..|.+
T Consensus 10 Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~ 46 (91)
T smart00346 10 VLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQE 46 (91)
T ss_pred HHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3444444335689999999999999999888888765
No 112
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=30.40 E-value=1.4e+02 Score=22.42 Aligned_cols=50 Identities=14% Similarity=0.229 Sum_probs=38.3
Q ss_pred cCCchHHHHHH-HhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHHh
Q psy6286 78 QFKPSLMDVVH-AWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQA 127 (159)
Q Consensus 78 ~~~~~l~~~v~-~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~a 127 (159)
.+.+.--.++. ..-.|.|+.||.+..+++.|.+=..+.|.-.-|++.-..
T Consensus 128 ~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 178 (186)
T PRK05602 128 ALPERQREAIVLQYYQGLSNIEAAAVMDISVDALESLLARGRRALRAQLAD 178 (186)
T ss_pred hCCHHHHHHhhHHHhcCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHh
Confidence 34444444443 357999999999999999999999999998888874443
No 113
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=30.22 E-value=93 Score=24.97 Aligned_cols=49 Identities=14% Similarity=0.205 Sum_probs=37.6
Q ss_pred cCCchHHHH-HHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHH
Q psy6286 78 QFKPSLMDV-VHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQ 126 (159)
Q Consensus 78 ~~~~~l~~~-v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~ 126 (159)
.+.+.--.+ ......|.|..||.+..++++|.+=..+.|...-|++.-.
T Consensus 171 ~Lp~~~R~v~~L~~~eg~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l~ 220 (233)
T PRK12538 171 RLPEQQRIAVILSYHENMSNGEIAEVMDTTVAAVESLLKRGRQQLRDLLR 220 (233)
T ss_pred hCCHHHHHHhhhHHhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 343333343 3445799999999999999999999988888888887544
No 114
>cd07841 STKc_CDK7 Catalytic domain of the Serine/Threonine Kinase, Cyclin-Dependent protein Kinase 7. Serine/Threonine Kinases (STKs), Cyclin-Dependent protein Kinase 7 (CDK7) subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The CDK7 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. CDKs belong to a large family of STKs that are regulated by their cognate cyclins. Together, they are involved in the control of cell-cycle progression, transcription, and neuronal function. CDK7 plays essential roles in the cell cycle and in transcription. It associates with cyclin H and MAT1 and acts as a CDK-Activating Kinase (CAK) by phosphorylating and activating cell cycle CDKs (CDK1/2/4/6). In the brain, it activates CDK5. CDK7 is
Probab=30.06 E-value=40 Score=26.76 Aligned_cols=44 Identities=16% Similarity=0.051 Sum_probs=36.6
Q ss_pred HHHHHhhCCCCHHHHHhhcC--CCccHHHHHHHHHHHHHHHHHHhhh
Q psy6286 85 DVVHAWCEGASFLKVCSITD--IFEGSIIRCMRRLEEVLRQLVQASR 129 (159)
Q Consensus 85 ~~v~~Wa~G~~f~~i~~~t~--l~EG~iVR~~rRl~elLrql~~a~~ 129 (159)
-+|++|. |.++.+++.... +.+..+++++.|+.+.|..+....-
T Consensus 78 ~lv~e~~-~~~L~~~i~~~~~~~~~~~~~~~~~qi~~al~~lH~~~i 123 (298)
T cd07841 78 NLVFEFM-ETDLEKVIKDKSIVLTPADIKSYMLMTLRGLEYLHSNWI 123 (298)
T ss_pred EEEEccc-CCCHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHHhCCe
Confidence 4688888 779999997765 8999999999999999988876653
No 115
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=29.94 E-value=52 Score=18.91 Aligned_cols=28 Identities=4% Similarity=0.037 Sum_probs=20.2
Q ss_pred hhCCCCHHHHHhhcCCCccHHHHHHHHH
Q psy6286 90 WCEGASFLKVCSITDIFEGSIIRCMRRL 117 (159)
Q Consensus 90 Wa~G~~f~~i~~~t~l~EG~iVR~~rRl 117 (159)
++++.++.+|.+..++.+.-+.|.+++.
T Consensus 5 ~~~~~~l~~iA~~~g~S~~~f~r~Fk~~ 32 (42)
T PF00165_consen 5 LQQKLTLEDIAEQAGFSPSYFSRLFKKE 32 (42)
T ss_dssp T-SS--HHHHHHHHTS-HHHHHHHHHHH
T ss_pred ccCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 5677888899999999999998888764
No 116
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=29.86 E-value=92 Score=24.61 Aligned_cols=33 Identities=21% Similarity=0.242 Sum_probs=28.1
Q ss_pred hCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHH
Q psy6286 91 CEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQ 123 (159)
Q Consensus 91 a~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrq 123 (159)
-.|.|..||-+..++++|++=+.+.|...-||+
T Consensus 196 ~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~ 228 (234)
T PRK08301 196 GEEKTQKEVADMLGISQSYISRLEKRIIKRLKK 228 (234)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 589999999999999999997777777666665
No 117
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=29.65 E-value=1.8e+02 Score=21.43 Aligned_cols=48 Identities=17% Similarity=0.219 Sum_probs=36.7
Q ss_pred cCCchHHHHHHH-hhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHH
Q psy6286 78 QFKPSLMDVVHA-WCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLV 125 (159)
Q Consensus 78 ~~~~~l~~~v~~-Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~ 125 (159)
.+.+.--.++.. ...|.|..||.+..++.+|++=..+.|...-|+..-
T Consensus 112 ~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 160 (164)
T PRK12547 112 LLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARNRLQELL 160 (164)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 444444454444 359999999999999999999988888887777643
No 118
>cd08215 STKc_Nek Catalytic domain of the Protein Serine/Threonine Kinase, Never In Mitosis gene A-related kinase. Serine/Threonine Kinases (STKs), Never In Mitosis gene A (NIMA)-related kinase (Nek) family, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The Nek family is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. The Nek family is composed of 11 different mammalian members (Nek1-11) with similarity to the catalytic domain of Aspergillus nidulans NIMA kinase, the founding member of the Nek family which was identified in a screen for cell cycle mutants that were prevented from entering mitosis. Neks contain a conserved N-terminal catalytic domain and a more divergent C-terminal regulatory region of various sizes and structures. They
Probab=29.64 E-value=35 Score=25.98 Aligned_cols=52 Identities=13% Similarity=0.126 Sum_probs=41.4
Q ss_pred hHHHHHHHhhCCCCHHHHHhh-----cCCCccHHHHHHHHHHHHHHHHHHhhhhhCC
Q psy6286 82 SLMDVVHAWCEGASFLKVCSI-----TDIFEGSIIRCMRRLEEVLRQLVQASRNIGN 133 (159)
Q Consensus 82 ~l~~~v~~Wa~G~~f~~i~~~-----t~l~EG~iVR~~rRl~elLrql~~a~~~ig~ 133 (159)
+...++++|..|.++.+.+.. ..+.+..+.+.+.++.+-|..+....-+.||
T Consensus 72 ~~~~lv~e~~~~~~L~~~l~~~~~~~~~~~~~~~~~i~~~i~~~l~~lh~~~~~H~d 128 (258)
T cd08215 72 GKLCIVMEYADGGDLSQKIKKQKKEGKPFPEEQILDWFVQLCLALKYLHSRKILHRD 128 (258)
T ss_pred CEEEEEEEecCCCcHHHHHHHhhccCCCcCHHHHHHHHHHHHHHHHHHHhCCEeccc
Confidence 344567889999999999876 5688999999999999999888877544443
No 119
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=29.09 E-value=1e+02 Score=22.75 Aligned_cols=38 Identities=18% Similarity=0.167 Sum_probs=33.3
Q ss_pred hhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHHh
Q psy6286 90 WCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQA 127 (159)
Q Consensus 90 Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~a 127 (159)
-..|.|..+|.+..++++|.+=..+.|.-.-|++.-..
T Consensus 133 ~~~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~~ 170 (175)
T PRK12518 133 DLEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQQ 170 (175)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 35899999999999999999999999998888886554
No 120
>cd06614 STKc_PAK Catalytic domain of the Protein Serine/Threonine Kinase, p21-activated kinase. Serine/threonine kinases (STKs), p21-activated kinase (PAK) subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The PAK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. PAKs are Rho family GTPase-regulated kinases that serve as important mediators in the function of Cdc42 (cell division cycle 42) and Rac. PAKs are implicated in the regulation of many cellular processes including growth factor receptor-mediated proliferation, cell polarity, cell motility, cell death and survival, and actin cytoskeleton organization. PAK deregulation is associated with tumor development. PAKs from higher eukaryotes are classified into two grou
Probab=29.00 E-value=52 Score=25.97 Aligned_cols=50 Identities=18% Similarity=0.140 Sum_probs=41.0
Q ss_pred HHHHHHHhhCCCCHHHHHhhc--CCCccHHHHHHHHHHHHHHHHHHhhhhhC
Q psy6286 83 LMDVVHAWCEGASFLKVCSIT--DIFEGSIIRCMRRLEEVLRQLVQASRNIG 132 (159)
Q Consensus 83 l~~~v~~Wa~G~~f~~i~~~t--~l~EG~iVR~~rRl~elLrql~~a~~~ig 132 (159)
...++++++.|.++.+++... .+.+..+.+.+.++.+.|..+....-+.|
T Consensus 89 ~~~lv~e~~~~~~L~~~l~~~~~~l~~~~~~~i~~~i~~~L~~lH~~gi~H~ 140 (286)
T cd06614 89 ELWVVMEYMDGGSLTDIITQNFVRMNEPQIAYVCREVLQGLEYLHSQNVIHR 140 (286)
T ss_pred EEEEEEeccCCCcHHHHHHHhccCCCHHHHHHHHHHHHHHHHHHHhCCeeeC
Confidence 345678899999999999887 79999999999999999998876544333
No 121
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=28.90 E-value=1.3e+02 Score=22.01 Aligned_cols=46 Identities=17% Similarity=0.188 Sum_probs=34.6
Q ss_pred cCCchHHHHHHH-hhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHH
Q psy6286 78 QFKPSLMDVVHA-WCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQ 123 (159)
Q Consensus 78 ~~~~~l~~~v~~-Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrq 123 (159)
.+.|.-=.++.. .-.|.|..+|.+..++++|++=..+.|...-|++
T Consensus 122 ~L~~~~r~vl~l~~~~g~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 122 ILTPKQQHVIALRFGQNLPIAEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred hCCHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 344433333333 5699999999999999999998888888877775
No 122
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.
Probab=28.81 E-value=1.1e+02 Score=24.32 Aligned_cols=33 Identities=18% Similarity=0.196 Sum_probs=28.7
Q ss_pred CCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHH
Q psy6286 92 EGASFLKVCSITDIFEGSIIRCMRRLEEVLRQL 124 (159)
Q Consensus 92 ~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql 124 (159)
.|.|+.||-+..++++|.+-+.+.|...-||+.
T Consensus 197 eg~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~ 229 (234)
T TIGR02835 197 TEKTQKEVADMLGISQSYISRLEKRILKRLKKE 229 (234)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 799999999999999999988887777776663
No 123
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=28.78 E-value=1.1e+02 Score=22.43 Aligned_cols=38 Identities=11% Similarity=0.010 Sum_probs=33.3
Q ss_pred hhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHHh
Q psy6286 90 WCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQA 127 (159)
Q Consensus 90 Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~a 127 (159)
-..|.|-.||.+..++++|.+=+.+.|....||+.-..
T Consensus 122 ~~~~~s~~EIA~~lgis~~tV~~~l~ra~~~lr~~l~~ 159 (163)
T PRK07037 122 RLHGETQKDIARELGVSPTLVNFMIRDALVHCRKCLDA 159 (163)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 35899999999999999999999999998888875443
No 124
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=28.76 E-value=1.3e+02 Score=22.63 Aligned_cols=35 Identities=17% Similarity=0.301 Sum_probs=31.1
Q ss_pred hhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHH
Q psy6286 90 WCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQL 124 (159)
Q Consensus 90 Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql 124 (159)
-..|.|..+|.+..++++|.+=..+.|...-||+.
T Consensus 146 ~~~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 180 (182)
T PRK12537 146 YVDGCSHAEIAQRLGAPLGTVKAWIKRSLKALREC 180 (182)
T ss_pred HHcCCCHHHHHHHHCCChhhHHHHHHHHHHHHHHH
Confidence 46999999999999999999999888888877764
No 125
>cd06606 STKc_MAPKKK Catalytic domain of the Protein Serine/Threonine Kinase, Mitogen-Activated Protein Kinase Kinase Kinase. Serine/threonine kinases (STKs), mitogen-activated protein kinase (MAPK) kinase kinase (MAPKKK) subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The MAPKKK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. MAPKKKs (MKKKs or MAP3Ks) are also called MAP/ERK kinase kinases (MEKKs) in some cases. They phosphorylate and activate MAPK kinases (MAPKKs or MKKs or MAP2Ks), which in turn phosphorylate and activate MAPKs during signaling cascades that are important in mediating cellular responses to extracellular signals. This subfamily is composed of the Apoptosis Signal-regulating Kinases ASK1 (or MAPKK
Probab=28.75 E-value=39 Score=25.57 Aligned_cols=51 Identities=16% Similarity=0.154 Sum_probs=40.5
Q ss_pred HHHHHHHhhCCCCHHHHHhhc-CCCccHHHHHHHHHHHHHHHHHHhhhhhCC
Q psy6286 83 LMDVVHAWCEGASFLKVCSIT-DIFEGSIIRCMRRLEEVLRQLVQASRNIGN 133 (159)
Q Consensus 83 l~~~v~~Wa~G~~f~~i~~~t-~l~EG~iVR~~rRl~elLrql~~a~~~ig~ 133 (159)
...++++|..|.++.+.+... .+.+-.+.+++.++.+.|..+.+..-+.||
T Consensus 75 ~~~lv~e~~~~~~L~~~~~~~~~~~~~~~~~~~~~l~~~l~~lh~~~~~h~d 126 (260)
T cd06606 75 TLNIFLEYVSGGSLSSLLKKFGKLPEPVIRKYTRQILEGLAYLHSNGIVHRD 126 (260)
T ss_pred eEEEEEEecCCCcHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHCCccccC
Confidence 345678899999999998776 788889999999999999888776544444
No 126
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=28.75 E-value=91 Score=23.61 Aligned_cols=34 Identities=26% Similarity=0.190 Sum_probs=30.5
Q ss_pred hCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHH
Q psy6286 91 CEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQL 124 (159)
Q Consensus 91 a~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql 124 (159)
-.|.|..||.+..++.++++-..+.|...-|++.
T Consensus 155 ~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 188 (194)
T PRK12519 155 YEGLSQSEIAKRLGIPLGTVKARARQGLLKLREL 188 (194)
T ss_pred hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 4899999999999999999999888888877774
No 127
>PRK11202 DNA-binding transcriptional repressor FabR; Provisional
Probab=28.61 E-value=1.2e+02 Score=23.32 Aligned_cols=35 Identities=23% Similarity=0.265 Sum_probs=29.7
Q ss_pred CCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHH
Q psy6286 92 EGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQ 126 (159)
Q Consensus 92 ~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~ 126 (159)
.|.|..+|++..++..|.|-+-+.--++|+.++..
T Consensus 31 ~~~si~~IA~~Agvs~~t~Y~hF~sKe~L~~av~~ 65 (203)
T PRK11202 31 SSLSLREVAREAGIAPTSFYRHFRDMDELGLTMVD 65 (203)
T ss_pred ccCCHHHHHHHhCCCcchHHHHCCCHHHHHHHHHH
Confidence 57799999999999999999988877777776543
No 128
>cd03572 ENTH_epsin_related ENTH domain, Epsin Related family; composed of hypothetical proteins containing an ENTH-like domain. The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. ENTH and ANTH (E/ANTH) domains are structurally similar to the VHS domain and are composed of a superhelix of eight alpha helices. E/ANTH domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membranes. ENTH domains also function in the development of membrane curvature through lipid remodeling during the formation of clathrin-coated vesicles. E/ANTH-bearing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the t
Probab=28.53 E-value=1.3e+02 Score=22.21 Aligned_cols=44 Identities=20% Similarity=0.194 Sum_probs=31.3
Q ss_pred CCccHHHHHHHHHHHHHHHHHHhhhhh----C---ChHHHHHHHHHHHhhc
Q psy6286 105 IFEGSIIRCMRRLEEVLRQLVQASRNI----G---NTLLEEKFNEAIKTVK 148 (159)
Q Consensus 105 l~EG~iVR~~rRl~elLrql~~a~~~i----g---~~~L~~k~~~a~~~I~ 148 (159)
-..++|+|++++-....++..+-.... | +...+.++.+++++|.
T Consensus 68 ~G~~~f~~~~~~~~~~Ik~~~~f~g~~Dp~~Gd~~~~~VR~~A~El~~~if 118 (122)
T cd03572 68 KGNSDFKRELQRNSAQIRECANYKGPPDPLKGDSLNEKVREEAQELIKAIF 118 (122)
T ss_pred hCCHHHHHHHHHhHHHHHHHHHcCCCCCcccCcchhHHHHHHHHHHHHHHh
Confidence 346799999999998888877765422 2 2456777777777663
No 129
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=28.39 E-value=1.6e+02 Score=22.32 Aligned_cols=47 Identities=11% Similarity=0.140 Sum_probs=36.1
Q ss_pred ccCCchHHHHHHH-hhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHH
Q psy6286 77 NQFKPSLMDVVHA-WCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQ 123 (159)
Q Consensus 77 ~~~~~~l~~~v~~-Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrq 123 (159)
..+.|.--.++.. +..|.|..||.+..++++|.+=..+.|.-.-|+.
T Consensus 130 ~~L~~~~r~i~~l~~~~g~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~ 177 (189)
T PRK06811 130 NDLEKLDREIFIRRYLLGEKIEEIAKKLGLTRSAIDNRLSRGRKKLQK 177 (189)
T ss_pred HhCCHHHHHHHHHHHHccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3555555566653 5799999999999999999988888887666553
No 130
>cd05611 STKc_Rim15_like Catalytic domain of fungal Rim15-like Protein Serine/Threonine Kinases. Serine/Threonine Kinases (STKs), Microtubule-associated serine/threonine (MAST) kinase subfamily, fungal Rim15-like kinases, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The MAST kinase subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. Members of this group include Saccharomyces cerevisiae Rim15, Schizosaccharomyces pombe cek1, and similar fungal proteins. They contain a central catalytic domain, which contains an insert relative to MAST kinases. In addition, Rim15 contains a C-terminal signal receiver (REC) domain while cek1 contains an N-terminal PAS domain. Rim15 (or Rim15p) functions as a regulator of meiosis. It acts as a do
Probab=27.88 E-value=48 Score=25.65 Aligned_cols=50 Identities=10% Similarity=0.051 Sum_probs=38.7
Q ss_pred HHHHHHhhCCCCHHHHHhh-cCCCccHHHHHHHHHHHHHHHHHHhhhhhCC
Q psy6286 84 MDVVHAWCEGASFLKVCSI-TDIFEGSIIRCMRRLEEVLRQLVQASRNIGN 133 (159)
Q Consensus 84 ~~~v~~Wa~G~~f~~i~~~-t~l~EG~iVR~~rRl~elLrql~~a~~~ig~ 133 (159)
.-++++|+.|.++.+++.. ..+.+..+.+.+.++.+-|..+....-+-||
T Consensus 72 ~~lv~e~~~~~~L~~~l~~~~~~~~~~~~~i~~qi~~aL~~lH~~~i~H~d 122 (260)
T cd05611 72 LYLVMEYLNGGDCASLIKTLGGLPEDWAKQYIAEVVLGVEDLHQRGIIHRD 122 (260)
T ss_pred EEEEEeccCCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHCCeecCC
Confidence 3467789999999999876 4688999999999998888877765433333
No 131
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=27.85 E-value=1.2e+02 Score=22.98 Aligned_cols=48 Identities=23% Similarity=0.155 Sum_probs=36.5
Q ss_pred CCchHHHHHH-HhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHH
Q psy6286 79 FKPSLMDVVH-AWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQ 126 (159)
Q Consensus 79 ~~~~l~~~v~-~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~ 126 (159)
+.+.--.++. ....|.|..+|.+..++++|.+=..+.|.-..|++...
T Consensus 137 L~~~~r~i~~L~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 185 (195)
T PRK12532 137 LPENTARVFTLKEILGFSSDEIQQMCGISTSNYHTIMHRARESLRQCLQ 185 (195)
T ss_pred CCHHHHHHhhhHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 3333334443 46799999999999999999998888888887777543
No 132
>COG2442 Uncharacterized conserved protein [Function unknown]
Probab=27.81 E-value=1e+02 Score=21.07 Aligned_cols=32 Identities=16% Similarity=0.201 Sum_probs=25.2
Q ss_pred HHHHHHhhCCCCHHHHHhhcC-CCccHHHHHHH
Q psy6286 84 MDVVHAWCEGASFLKVCSITD-IFEGSIIRCMR 115 (159)
Q Consensus 84 ~~~v~~Wa~G~~f~~i~~~t~-l~EG~iVR~~r 115 (159)
-.++..|+.|.|..||++..+ +..=|+-=+++
T Consensus 34 ~~Il~~l~~G~s~eeil~dyp~Lt~~dI~aal~ 66 (79)
T COG2442 34 WDILEMLAAGESIEEILADYPDLTLEDIRAALR 66 (79)
T ss_pred HHHHHHHHCCCCHHHHHHhCCCCCHHHHHHHHH
Confidence 478899999999999999987 77665554443
No 133
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=27.79 E-value=1.2e+02 Score=24.59 Aligned_cols=38 Identities=11% Similarity=0.095 Sum_probs=32.5
Q ss_pred HHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHH
Q psy6286 87 VHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQL 124 (159)
Q Consensus 87 v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql 124 (159)
...+..|.|+.+|-+..++.++.+=+...|...-|++.
T Consensus 213 ~l~y~~~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~ 250 (256)
T PRK07408 213 EFVFLHDLTQKEAAERLGISPVTVSRRVKKGLDQLKKL 250 (256)
T ss_pred HHHHHCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 34567899999999999999999999888888887764
No 134
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=27.77 E-value=1.4e+02 Score=22.23 Aligned_cols=37 Identities=24% Similarity=0.337 Sum_probs=31.6
Q ss_pred HHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHH
Q psy6286 88 HAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQL 124 (159)
Q Consensus 88 ~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql 124 (159)
..+..|.|..+|.+..++.+|.+-..+.|.-.-|++.
T Consensus 147 l~~~~~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T PRK09641 147 LKYIEDLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred hHHhhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3456999999999999999999998888887777764
No 135
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=27.70 E-value=1.4e+02 Score=21.78 Aligned_cols=37 Identities=24% Similarity=0.518 Sum_probs=32.8
Q ss_pred hhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHH
Q psy6286 90 WCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQ 126 (159)
Q Consensus 90 Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~ 126 (159)
...|.+..+|.+.-+++++.+=+.+.|...-|++...
T Consensus 138 ~~~~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l~ 174 (179)
T PRK11924 138 YVEGLSYREIAEILGVPVGTVKSRLRRARQLLRECLE 174 (179)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4689999999999999999999999999888887543
No 136
>PRK13344 spxA transcriptional regulator Spx; Reviewed
Probab=27.55 E-value=61 Score=23.99 Aligned_cols=77 Identities=9% Similarity=0.170 Sum_probs=38.3
Q ss_pred CCchHHHHHHHh--hCCCCHHHH-HhhcCCCccHHHHHHHHH----HHHHHHHHHhhhhhCC-------hHHHHHHHHHH
Q psy6286 79 FKPSLMDVVHAW--CEGASFLKV-CSITDIFEGSIIRCMRRL----EEVLRQLVQASRNIGN-------TLLEEKFNEAI 144 (159)
Q Consensus 79 ~~~~l~~~v~~W--a~G~~f~~i-~~~t~l~EG~iVR~~rRl----~elLrql~~a~~~ig~-------~~L~~k~~~a~ 144 (159)
++.+-+.-+.+| .+|.+|..+ ...+.+....+.+++.++ +++++.=....+-.|. .++-+.+.+=-
T Consensus 8 ~~C~~crkA~~~L~~~~i~~~~~d~~~~~~s~~eL~~~l~~~~~~~~~lin~~~~~~k~L~~~~~~ls~~e~i~ll~~~P 87 (132)
T PRK13344 8 SSCTSCKKAKTWLNAHQLSYKEQNLGKEPLTKEEILAILTKTENGIESIVSSKNRYAKALDCDIEELSVNEVIDLIQENP 87 (132)
T ss_pred CCCHHHHHHHHHHHHcCCCeEEEECCCCCCCHHHHHHHHHHhCCCHHHhhccCcHHHHhCCcchhcCCHHHHHHHHHhCc
Confidence 445555566666 355555544 234456666666666663 4555433333332221 22222222223
Q ss_pred HhhcCCccccc
Q psy6286 145 KTVKRDIFLEI 155 (159)
Q Consensus 145 ~~I~RdIV~~~ 155 (159)
.+|||-||...
T Consensus 88 ~LikRPIv~~~ 98 (132)
T PRK13344 88 RILKSPILIDD 98 (132)
T ss_pred cceeCcEEEeC
Confidence 36899988653
No 137
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=27.53 E-value=1e+02 Score=23.38 Aligned_cols=37 Identities=22% Similarity=0.327 Sum_probs=31.9
Q ss_pred HhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHH
Q psy6286 89 AWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLV 125 (159)
Q Consensus 89 ~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~ 125 (159)
..-.|.|..||.+..++++|.+=..+.|.-.-|++.-
T Consensus 143 ~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 179 (193)
T TIGR02947 143 ADVEGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQL 179 (193)
T ss_pred hhhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3469999999999999999999988888888777643
No 138
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=27.47 E-value=94 Score=23.25 Aligned_cols=34 Identities=24% Similarity=0.282 Sum_probs=29.5
Q ss_pred hCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHH
Q psy6286 91 CEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQL 124 (159)
Q Consensus 91 a~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql 124 (159)
..|.|+.+|.+..++.+|.+=..+.|.-.-|++.
T Consensus 152 ~~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~ 185 (190)
T TIGR02939 152 LEGLSYEDIARIMDCPVGTVRSRIFRAREAIAIR 185 (190)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4999999999999999999988888877777664
No 139
>cd06630 STKc_MEKK1 Catalytic domain of the Protein Serine/Threonine Kinase, MAP/ERK kinase kinase 1. Serine/threonine kinases (STKs), MAP/ERK kinase kinase 1 (MEKK1) subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The MEKK1 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. MEKK1 is a mitogen-activated protein kinase (MAPK) kinase kinase (MAPKKK or MKKK or MAP3K), that phosphorylates and activates MAPK kinases (MAPKKs or MKKs or MAP2Ks), which in turn phosphorylate and activate MAPKs during signaling cascades that are important in mediating cellular responses to extracellular signals. MEKK1 activates the extracellular signal-regulated kinase 1/2 (ERK1/2) and c-Jun N-terminal kinase (JNK) pathways by activating their
Probab=27.33 E-value=46 Score=25.75 Aligned_cols=47 Identities=23% Similarity=0.266 Sum_probs=37.3
Q ss_pred hHHHHHHHhhCCCCHHHHHhhc-CCCccHHHHHHHHHHHHHHHHHHhh
Q psy6286 82 SLMDVVHAWCEGASFLKVCSIT-DIFEGSIIRCMRRLEEVLRQLVQAS 128 (159)
Q Consensus 82 ~l~~~v~~Wa~G~~f~~i~~~t-~l~EG~iVR~~rRl~elLrql~~a~ 128 (159)
+-..++++|+.|.++.+++... .+.+-.+.++++++..-|.-+.+..
T Consensus 76 ~~~~~v~e~~~~~~L~~~l~~~~~~~~~~~~~~~~ql~~al~~LH~~~ 123 (268)
T cd06630 76 SHFNLFVEWMAGGSVSHLLSKYGAFKEAVIINYTEQLLRGLSYLHENQ 123 (268)
T ss_pred CeEEEEEeccCCCcHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHhCC
Confidence 3345778899999999998764 5788888888988888888886654
No 140
>PF08158 NUC130_3NT: NUC130/3NT domain; InterPro: IPR012977 This N-terminal domain is found in a novel nucleolar protein family defined by NUC130/133 [].
Probab=27.19 E-value=1.2e+02 Score=19.06 Aligned_cols=40 Identities=15% Similarity=0.151 Sum_probs=26.5
Q ss_pred CccHHHHHHHHHHHHHHHHHHhhhhhCChHHHHHHHHHHHhhcC
Q psy6286 106 FEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKFNEAIKTVKR 149 (159)
Q Consensus 106 ~EG~iVR~~rRl~elLrql~~a~~~ig~~~L~~k~~~a~~~I~R 149 (159)
++-+.-.--.++.|+|++=... =+|+|+.++-+|.-++|.
T Consensus 9 Yp~~~~~Fp~~L~~lL~~~~~~----L~p~lR~~lv~aLiLLRn 48 (52)
T PF08158_consen 9 YPKETKDFPQELIDLLRNHHTV----LDPDLRMKLVKALILLRN 48 (52)
T ss_pred cHHHHHHHHHHHHHHHHhcccc----CCHHHHHHHHHHHHHHHc
Confidence 3333444445667777665443 289999999999887653
No 141
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=27.01 E-value=84 Score=15.62 Aligned_cols=29 Identities=10% Similarity=0.204 Sum_probs=20.7
Q ss_pred HHHHHhhCCCCHHHHHhhcCCCccHHHHH
Q psy6286 85 DVVHAWCEGASFLKVCSITDIFEGSIIRC 113 (159)
Q Consensus 85 ~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~ 113 (159)
.++..+-+|.+..++.+..++....+-++
T Consensus 13 ~i~~~~~~~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 13 EARRLLAAGESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred HHHHHHHcCCCHHHHHHHHCCCHHHHHHh
Confidence 44445668889999998888776665544
No 142
>COG1202 Superfamily II helicase, archaea-specific [General function prediction only]
Probab=26.88 E-value=2.2e+02 Score=27.35 Aligned_cols=60 Identities=17% Similarity=0.251 Sum_probs=46.7
Q ss_pred HHhhCCCCHHHHHhh------cCCCccHHHHHHHHHHHHHHHHHHhhhhhCChHHHHHHHHHHHhh
Q psy6286 88 HAWCEGASFLKVCSI------TDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKFNEAIKTV 147 (159)
Q Consensus 88 ~~Wa~G~~f~~i~~~------t~l~EG~iVR~~rRl~elLrql~~a~~~ig~~~L~~k~~~a~~~I 147 (159)
..=-.|.+-.+|-+. -..++|||.-|+-.+..+|.-+...|++++-++....+....+.|
T Consensus 761 ~lR~~gk~p~~Isr~l~~~Ygi~aYpgDif~wLd~~vr~Lea~~rIArvf~kr~~~~ea~~lk~~i 826 (830)
T COG1202 761 ELRIEGKDPSQISRILEKRYGIQAYPGDIFTWLDTLVRLLEAIGRIARVFKKREVEAEAKALKKKI 826 (830)
T ss_pred HHHhcCCCHHHHHHHHHHhhCeeecChhHHHHHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHh
Confidence 334588888888765 358899999999999999999999999888777776666555444
No 143
>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=26.77 E-value=83 Score=22.06 Aligned_cols=28 Identities=7% Similarity=0.228 Sum_probs=25.6
Q ss_pred CCCCHHHHHhhcCCCccHHHHHHHHHHH
Q psy6286 92 EGASFLKVCSITDIFEGSIIRCMRRLEE 119 (159)
Q Consensus 92 ~G~~f~~i~~~t~l~EG~iVR~~rRl~e 119 (159)
.|.+..+|++..++..+.+-|.+.+|++
T Consensus 42 ~~~t~~eL~~~l~~~~stvs~~i~~Le~ 69 (109)
T TIGR01889 42 GKLTLKEIIKEILIKQSALVKIIKKLSK 69 (109)
T ss_pred CcCcHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3589999999999999999999999876
No 144
>cd06640 STKc_MST4 Catalytic domain of the Protein Serine/Threonine Kinase, Mammalian Ste20-like protein kinase 4. Serine/threonine kinases (STKs), mammalian Ste20-like protein kinase 4 (MST4) subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The MST4 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. MST4 is sometimes referred to as MASK (MST3 and SOK1-related kinase). It plays a role in mitogen-activated protein kinase (MAPK) signaling during cytoskeletal rearrangement, morphogenesis, and apoptosis. It influences cell growth and transformation by modulating the extracellular signal-regulated kinase (ERK) pathway. MST4 may also play a role in tumor formation and progression. It localizes in the Golgi apparatus by inter
Probab=26.73 E-value=49 Score=26.09 Aligned_cols=46 Identities=15% Similarity=0.132 Sum_probs=36.6
Q ss_pred hHHHHHHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHHh
Q psy6286 82 SLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQA 127 (159)
Q Consensus 82 ~l~~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~a 127 (159)
+..-++++|+.|.++.+.+....+.+..+.+.+.++.+.|..+...
T Consensus 75 ~~~~lv~e~~~~~~L~~~i~~~~l~~~~~~~~~~~l~~~l~~lh~~ 120 (277)
T cd06640 75 TKLWIIMEYLGGGSALDLLRAGPFDEFQIATMLKEILKGLDYLHSE 120 (277)
T ss_pred CEEEEEEecCCCCcHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHhC
Confidence 3356788899999999999888888888888888887777766544
No 145
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=26.53 E-value=92 Score=20.39 Aligned_cols=29 Identities=17% Similarity=0.214 Sum_probs=25.7
Q ss_pred hCCCCHHHHHhhcCCCccHHHHHHHHHHH
Q psy6286 91 CEGASFLKVCSITDIFEGSIIRCMRRLEE 119 (159)
Q Consensus 91 a~G~~f~~i~~~t~l~EG~iVR~~rRl~e 119 (159)
..+.+..+|.+..++..+.+-|.+++|.+
T Consensus 22 ~~~~~~~~la~~~~~s~~~i~~~l~~L~~ 50 (101)
T smart00347 22 EGPLSVSELAKRLGVSPSTVTRVLDRLEK 50 (101)
T ss_pred cCCcCHHHHHHHHCCCchhHHHHHHHHHH
Confidence 34579999999999999999999999887
No 146
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=26.26 E-value=1.5e+02 Score=22.08 Aligned_cols=46 Identities=2% Similarity=-0.031 Sum_probs=33.5
Q ss_pred cCCchHHHHHH-HhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHH
Q psy6286 78 QFKPSLMDVVH-AWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQ 123 (159)
Q Consensus 78 ~~~~~l~~~v~-~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrq 123 (159)
.+.+.--.++. ....|.|..||.+..++.+|.+=..+.|-..-|+.
T Consensus 119 ~Lp~~~r~v~~L~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~~~~ 165 (172)
T PRK12523 119 KLSSKARAAFLYNRLDGMGHAEIAERLGVSVSRVRQYLAQGLRQCYI 165 (172)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 44444445544 35799999999999999999988777775555543
No 147
>PF12246 MKT1_C: Temperature dependent protein affecting M2 dsRNA replication; InterPro: IPR022039 This domain family is found in eukaryotes, and is typically between 231 and 255 amino acids in length. There is a single completely conserved residue P that may be functionally important. MKT1 is required for maintenance of K2 toxin above 30 degrees C in strains with the L-A-HN variant of the L-A double-stranded RNA virus of Saccharomyces cerevisiae. MKT1 is a 93 kDa protein with serine-rich regions and the retroviral protease signature, DTG. This family is the C-terminal region of MKT1.
Probab=26.14 E-value=30 Score=28.28 Aligned_cols=28 Identities=25% Similarity=0.335 Sum_probs=24.1
Q ss_pred HHHhhhCCccCCCccchhhHHHhhhcCC
Q psy6286 14 RVLRRLGYATEADVIEMKGRVACELSKS 41 (159)
Q Consensus 14 ~vL~~lgyid~~~~vt~kGrva~~I~s~ 41 (159)
+.|.-+||+|+.+.+|.-|+++....+.
T Consensus 1 R~L~l~Gyi~~~~~lT~wGk~L~~~~~~ 28 (243)
T PF12246_consen 1 RFLELRGYIDKSHELTPWGKALAKALKS 28 (243)
T ss_pred CchhHHhHhcCCCCcCHHHHHHHHHHhc
Confidence 3578899999989999999999887753
No 148
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=26.09 E-value=1.5e+02 Score=22.64 Aligned_cols=35 Identities=17% Similarity=0.143 Sum_probs=30.8
Q ss_pred hCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHH
Q psy6286 91 CEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLV 125 (159)
Q Consensus 91 a~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~ 125 (159)
..|.|..||.+..++++|++=..+.|.-..|++.-
T Consensus 148 ~~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 182 (189)
T PRK12530 148 YLELSSEQICQECDISTSNLHVLLYRARLQLQACL 182 (189)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 57999999999999999999888888887777654
No 149
>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=26.06 E-value=1.5e+02 Score=17.49 Aligned_cols=35 Identities=11% Similarity=0.322 Sum_probs=26.1
Q ss_pred HHHHHhhCCC-CHHHHHhhcCCCccHHHHHHHHHHH
Q psy6286 85 DVVHAWCEGA-SFLKVCSITDIFEGSIIRCMRRLEE 119 (159)
Q Consensus 85 ~~v~~Wa~G~-~f~~i~~~t~l~EG~iVR~~rRl~e 119 (159)
.++..=++|. ++.+|.+.+++..+.+-+-++.|.+
T Consensus 6 ~Il~~L~~~~~~~~el~~~l~~s~~~vs~hL~~L~~ 41 (47)
T PF01022_consen 6 RILKLLSEGPLTVSELAEELGLSQSTVSHHLKKLRE 41 (47)
T ss_dssp HHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHhCCCchhhHHHhccccchHHHHHHHHHHH
Confidence 4444444444 8999999999999999998887765
No 150
>TIGR02511 type_III_tyeA type III secretion effector delivery regulator, TyeA family. Members of this family include both small proteins, about 90 amino acids, in which this model covers the whole, and longer proteins of about 360 residues which match in the C-terminal region. The longer proteins (HrpJ) have N-terminal regions that match Pfam model pfam07201. Members of this family belong to bacterial type III secretion systems, and include TyeA from the well-studied Yersinia systems. TyeA appears involved in calcium-responsive regulation of the delivery of type III effectors.
Probab=25.89 E-value=1.4e+02 Score=20.20 Aligned_cols=56 Identities=14% Similarity=0.199 Sum_probs=43.6
Q ss_pred HHhhCCCCHHHHHhhcCCCccHH-HHHHHHHHHHHHHHHHhhhhhCChHHHHHHHHHHH
Q psy6286 88 HAWCEGASFLKVCSITDIFEGSI-IRCMRRLEEVLRQLVQASRNIGNTLLEEKFNEAIK 145 (159)
Q Consensus 88 ~~Wa~G~~f~~i~~~t~l~EG~i-VR~~rRl~elLrql~~a~~~ig~~~L~~k~~~a~~ 145 (159)
..|..-..+..+.......+--- |+.++++.++++.+..++ +.|++=++++-+|..
T Consensus 16 q~Wl~~~~l~~l~~~l~~~~~~~qv~fl~~l~~l~~~lP~~l--f~D~eqR~~~L~~~~ 72 (79)
T TIGR02511 16 ERWLGPDWIEQLANALGLPELEHRVAFLQGLKRLLRLLPIAL--FSDEEQRQNLLQALQ 72 (79)
T ss_pred cccCCHHHHHHHHHHccCccHHHHHHHHHHHHHHHHHCCHHH--hCCHHHHHHHHHHHH
Confidence 45777777888888888887667 999999999999998886 467777776666544
No 151
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=25.84 E-value=1.5e+02 Score=21.58 Aligned_cols=36 Identities=25% Similarity=0.264 Sum_probs=29.8
Q ss_pred HHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHH
Q psy6286 88 HAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQ 123 (159)
Q Consensus 88 ~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrq 123 (159)
..+-.|.|..+|-+..+++++.+-+.+.|.-.-|+.
T Consensus 139 l~~~~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 174 (182)
T PRK09652 139 LREIEGLSYEEIAEIMGCPIGTVRSRIFRAREALRA 174 (182)
T ss_pred HHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 335699999999999999999998887776666655
No 152
>cd08217 STKc_Nek2 Catalytic domain of the Protein Serine/Threonine Kinase, Never In Mitosis gene A-related kinase 2. Serine/Threonine Kinases (STKs), Never In Mitosis gene A (NIMA)-related kinase 2 (Nek2) subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The Nek2 subfamily is one of a family of 11 different Neks (Nek1-11) that are involved in cell cycle control. The Nek family is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. The Nek2 subfamily includes Aspergillus nidulans NIMA kinase, the founding member of the Nek family, which was identified in a screen for cell cycle mutants prevented from entering mitosis. NIMA is essential for mitotic entry and progression through mitosis, and its degradation is essential for mitotic exi
Probab=25.62 E-value=68 Score=24.46 Aligned_cols=42 Identities=24% Similarity=0.313 Sum_probs=35.7
Q ss_pred HHHHHHhhCCCCHHHHHhh-----cCCCccHHHHHHHHHHHHHHHHH
Q psy6286 84 MDVVHAWCEGASFLKVCSI-----TDIFEGSIIRCMRRLEEVLRQLV 125 (159)
Q Consensus 84 ~~~v~~Wa~G~~f~~i~~~-----t~l~EG~iVR~~rRl~elLrql~ 125 (159)
..++++|+.|.++.+.+.. ..+.+..+++++.++.+.|..+.
T Consensus 76 ~~~~~e~~~~~~L~~~l~~~~~~~~~l~~~~~~~~~~~i~~~l~~lH 122 (265)
T cd08217 76 LYIVMEYCEGGDLAQLIQKCKKERKYIEEEFIWRILTQLLLALYECH 122 (265)
T ss_pred EEEEehhccCCCHHHHHHHHhhcccCCCHHHHHHHHHHHHHHHHHHh
Confidence 4578899999999999875 36788889999999999998887
No 153
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=25.59 E-value=1.2e+02 Score=22.39 Aligned_cols=46 Identities=9% Similarity=0.239 Sum_probs=35.2
Q ss_pred cCCchHHHHH-HHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHH
Q psy6286 78 QFKPSLMDVV-HAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQ 123 (159)
Q Consensus 78 ~~~~~l~~~v-~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrq 123 (159)
.+.+.--.++ ..--.|.|..+|.+..++++|.+-..+.|.-.-|+.
T Consensus 119 ~L~~~~r~i~~l~~~~g~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~ 165 (169)
T TIGR02954 119 TLNDKYQTAIILRYYHDLTIKEIAEVMNKPEGTVKTYLHRALKKLKK 165 (169)
T ss_pred hCCHHHhHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3444444444 334689999999999999999999988888777765
No 154
>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=25.55 E-value=78 Score=22.77 Aligned_cols=30 Identities=13% Similarity=0.195 Sum_probs=22.6
Q ss_pred HHHHhhCCCCHHHHHhhcCCCccHHHHHHH
Q psy6286 86 VVHAWCEGASFLKVCSITDIFEGSIIRCMR 115 (159)
Q Consensus 86 ~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~r 115 (159)
|+..+..|.|..+++..-++...++.||++
T Consensus 11 Vl~~~~~g~s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 11 VLAYIEKGKSIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred HHHHHHccchHHHHHHHhCcHHHHHHHHHH
Confidence 445566778888888877888888888877
No 155
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=25.53 E-value=2.2e+02 Score=22.05 Aligned_cols=49 Identities=12% Similarity=0.139 Sum_probs=37.8
Q ss_pred ccCCchHHHHHH-HhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHH
Q psy6286 77 NQFKPSLMDVVH-AWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLV 125 (159)
Q Consensus 77 ~~~~~~l~~~v~-~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~ 125 (159)
..+.+.--.++. .-..|.|..+|.+..++++|.+=..+.|...-|++..
T Consensus 152 ~~L~~~~r~vl~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 152 EKLPEAQQTVVKGVYFQELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred HhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 345555555555 3569999999999999999999888888887777654
No 156
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=25.36 E-value=2.2e+02 Score=21.65 Aligned_cols=51 Identities=16% Similarity=0.191 Sum_probs=39.7
Q ss_pred ccCCchHHHHHHH-hhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHHh
Q psy6286 77 NQFKPSLMDVVHA-WCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQA 127 (159)
Q Consensus 77 ~~~~~~l~~~v~~-Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~a 127 (159)
..+.+.--.++.. ...|.|..||.+..++.+|.+=..+.|.-.-|++.-..
T Consensus 110 ~~Lp~~~R~v~~L~~~~g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~~ 161 (182)
T PRK12540 110 DKLPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRARSKLSALLYV 161 (182)
T ss_pred HhCCHHHHHHhhHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 3455555555544 46999999999999999999988888888888876554
No 157
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=25.07 E-value=1.3e+02 Score=24.64 Aligned_cols=38 Identities=16% Similarity=0.161 Sum_probs=31.9
Q ss_pred HHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHH
Q psy6286 87 VHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQL 124 (159)
Q Consensus 87 v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql 124 (159)
...+..|.|+.+|.+..++.++.+=+.+.|...-|++.
T Consensus 225 ~l~y~~~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~ 262 (264)
T PRK07122 225 VLRFFESMTQTQIAERVGISQMHVSRLLAKTLARLRDQ 262 (264)
T ss_pred HHHhcCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 33467999999999999999999999888888777753
No 158
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=25.06 E-value=1.9e+02 Score=20.98 Aligned_cols=49 Identities=14% Similarity=0.116 Sum_probs=37.4
Q ss_pred cCCchHHHHHHH-hhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHH
Q psy6286 78 QFKPSLMDVVHA-WCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQ 126 (159)
Q Consensus 78 ~~~~~l~~~v~~-Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~ 126 (159)
.+.+.--.++.. .-.|.|..+|.+..++++|.+=..+.|.-.-|++...
T Consensus 105 ~L~~~~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l~ 154 (159)
T PRK12527 105 ELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMR 154 (159)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 344444455544 4699999999999999999998888888877777544
No 159
>PRK10870 transcriptional repressor MprA; Provisional
Probab=24.88 E-value=3.1e+02 Score=21.01 Aligned_cols=27 Identities=11% Similarity=0.016 Sum_probs=23.8
Q ss_pred CCCHHHHHhhcCCCccHHHHHHHHHHH
Q psy6286 93 GASFLKVCSITDIFEGSIIRCMRRLEE 119 (159)
Q Consensus 93 G~~f~~i~~~t~l~EG~iVR~~rRl~e 119 (159)
+.+..+|.+...+.-+++-|.+.||+.
T Consensus 71 ~it~~eLa~~l~l~~~tvsr~v~rLe~ 97 (176)
T PRK10870 71 SIQPSELSCALGSSRTNATRIADELEK 97 (176)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 357899999999999999999998864
No 160
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=24.87 E-value=87 Score=19.76 Aligned_cols=32 Identities=13% Similarity=0.134 Sum_probs=27.5
Q ss_pred HHhhCCCCHHHHHhhcCCCccHHHHHHHHHHH
Q psy6286 88 HAWCEGASFLKVCSITDIFEGSIIRCMRRLEE 119 (159)
Q Consensus 88 ~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~e 119 (159)
|.|-++.++.++-+.-++....+-.-+||-+.
T Consensus 18 fd~PR~~tl~elA~~lgis~st~~~~LRrae~ 49 (53)
T PF04967_consen 18 FDVPRRITLEELAEELGISKSTVSEHLRRAER 49 (53)
T ss_pred CCCCCcCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 45889999999999999999999888888664
No 161
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=24.54 E-value=1.5e+02 Score=23.13 Aligned_cols=35 Identities=20% Similarity=0.235 Sum_probs=30.7
Q ss_pred hhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHH
Q psy6286 90 WCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQL 124 (159)
Q Consensus 90 Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql 124 (159)
...|.|..+|.+..++.++.+=+.+.|...-|++.
T Consensus 191 y~~~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~~ 225 (227)
T TIGR02980 191 FFEDKTQSEIAERLGISQMHVSRLLRRALKKLREQ 225 (227)
T ss_pred HhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 35899999999999999999999999888877763
No 162
>PRK15215 fimbriae biosynthesis regulatory protein; Provisional
Probab=24.50 E-value=1.7e+02 Score=21.16 Aligned_cols=45 Identities=18% Similarity=0.318 Sum_probs=37.4
Q ss_pred HHHHHHh-hCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHHhh
Q psy6286 84 MDVVHAW-CEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQAS 128 (159)
Q Consensus 84 ~~~v~~W-a~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~a~ 128 (159)
..+.++. ..|.|-.++|+..++..|.|=-+++||..+=+.+.+.+
T Consensus 51 I~AL~dyLV~G~trkevCe~~~Vn~gYfS~~L~rL~~i~~~V~~L~ 96 (100)
T PRK15215 51 IQALRDYLVFGVSRKDVCERYEVNNGYFSTSLNRLSRISQAAAQMV 96 (100)
T ss_pred HHHHHHHHHcCccHHHHHHccCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 3444444 69999999999999999999999999998877777664
No 163
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=24.41 E-value=1.2e+02 Score=22.43 Aligned_cols=33 Identities=18% Similarity=0.298 Sum_probs=28.9
Q ss_pred hCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHH
Q psy6286 91 CEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQ 123 (159)
Q Consensus 91 a~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrq 123 (159)
-.|.|..+|.+..++.++.+-..+.|..+-|++
T Consensus 140 ~~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~~ 172 (176)
T PRK09638 140 YYGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRK 172 (176)
T ss_pred hcCCCHHHHHHHHCCChhHHHHHHHHHHHHHHH
Confidence 379999999999999999998888887777776
No 164
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=24.26 E-value=2.8e+02 Score=20.71 Aligned_cols=35 Identities=23% Similarity=0.327 Sum_probs=30.6
Q ss_pred hhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHH
Q psy6286 90 WCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQL 124 (159)
Q Consensus 90 Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql 124 (159)
...|.|..+|.+..++++|.+=..+.|.-.-|+..
T Consensus 150 ~~~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 184 (187)
T PRK12534 150 FFEGITYEELAARTDTPIGTVKSWIRRGLAKLKAC 184 (187)
T ss_pred HHcCCCHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Confidence 36999999999999999999998888887777764
No 165
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=24.23 E-value=2.3e+02 Score=22.75 Aligned_cols=47 Identities=13% Similarity=0.142 Sum_probs=35.1
Q ss_pred cCCchHHHHHHH-hhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHH
Q psy6286 78 QFKPSLMDVVHA-WCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQL 124 (159)
Q Consensus 78 ~~~~~l~~~v~~-Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql 124 (159)
.+.+..=.++.. .-.|.|+.+|-+..++++|.+=+.+.|...-|++.
T Consensus 201 ~L~~~~r~vl~l~~~~~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 248 (251)
T PRK07670 201 QLSEKEQLVISLFYKEELTLTEIGQVLNLSTSRISQIHSKALFKLKKL 248 (251)
T ss_pred cCCHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 344443344443 46999999999999999999988888877777653
No 166
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=24.22 E-value=1.1e+02 Score=23.07 Aligned_cols=33 Identities=18% Similarity=0.325 Sum_probs=29.3
Q ss_pred hCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHH
Q psy6286 91 CEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQ 123 (159)
Q Consensus 91 a~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrq 123 (159)
-.|.|..+|.+..++.+|.+=..+.|.-.-|+.
T Consensus 152 ~~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~ 184 (193)
T PRK11923 152 FDGLSYEDIASVMQCPVGTVRSRIFRAREAIDK 184 (193)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 499999999999999999998888887777766
No 167
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=24.19 E-value=1.2e+02 Score=22.70 Aligned_cols=49 Identities=24% Similarity=0.297 Sum_probs=36.1
Q ss_pred cCCchHHHHHHH-hhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHH
Q psy6286 78 QFKPSLMDVVHA-WCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQ 126 (159)
Q Consensus 78 ~~~~~l~~~v~~-Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~ 126 (159)
.+.+.--.++.. -..|.|+.+|.+..+++.|.+-..+.|...-|++.-.
T Consensus 131 ~L~~~~r~v~~l~~~~g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l~ 180 (184)
T PRK12512 131 TLPPRQRDVVQSISVEGASIKETAAKLSMSEGAVRVALHRGLAALAAKFR 180 (184)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Confidence 333333334333 2479999999999999999999999888888876443
No 168
>KOG3337|consensus
Probab=24.15 E-value=1.6e+02 Score=23.66 Aligned_cols=100 Identities=15% Similarity=0.167 Sum_probs=64.6
Q ss_pred HHHhhhcCCCceeeec---cCcH-H-------H-HHHHHHHHHHHcC----------CCCChhhhhccCCchHHHHHHHh
Q psy6286 33 RVACELSKSEETVILT---INDK-L-------E-LARHIARISIESK----------LDLDEDSYVNQFKPSLMDVVHAW 90 (159)
Q Consensus 33 rva~~I~s~~eLlltE---f~p~-~-------~-i~~~i~~~~~~~~----------l~~~~~~~~~~~~~~l~~~v~~W 90 (159)
|||.++...+...+-| .||. + . -+..|-.+++.|- +......|+.++++|.+..|++|
T Consensus 64 rWasrll~i~~v~viE~SVvdp~nqtmkTyTrNldH~~lm~v~Erc~y~~ssdns~ti~d~~~kfvss~~~G~~r~Vqe~ 143 (201)
T KOG3337|consen 64 RWASRLLDIQVVYVIEESVVDPVNQTMKTYTRNLDHARLMVVEERCVYCVSSDNSGTIEDRREKFVSSSLFGVSRAVQEF 143 (201)
T ss_pred hhhhhhcccceeEEeeeeecCccccceeeeeeccccceeeEEEEEEEEEecCCCCcchhHHHHHHhhhhhhhhHHHHHHH
Confidence 6788888888888888 6653 0 0 0111112222221 11123457789999999999999
Q ss_pred hCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHHhhhhhCChHHHHHHHHHHHh
Q psy6286 91 CEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKFNEAIKT 146 (159)
Q Consensus 91 a~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~a~~~ig~~~L~~k~~~a~~~ 146 (159)
. =+-|.+=+. .+.+=+...|.|+-.-+ .++.+..++-+|-..
T Consensus 144 s-l~rFkenv~----------ktrkGl~yvlqk~fg~a---~~~~~~~~~~~~k~~ 185 (201)
T KOG3337|consen 144 S-LARFKENVT----------KTRKGLEYVLQKLFGEA---NSKTLKMTAIEAKEK 185 (201)
T ss_pred H-HHHHHHHHH----------HHHhhHHHHHHHHhccc---cchHHHHHHHHHHHH
Confidence 7 455665443 44566888899988776 378888888777554
No 169
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=23.97 E-value=1.1e+02 Score=20.87 Aligned_cols=37 Identities=14% Similarity=0.248 Sum_probs=29.5
Q ss_pred hHHHHHHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHH
Q psy6286 82 SLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEE 119 (159)
Q Consensus 82 ~l~~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~e 119 (159)
.+.....+. ...|+.+|.+..++.+-.+-|.+++|.+
T Consensus 7 ~il~~L~~~-~~~~~~~la~~l~~s~~tv~~~l~~L~~ 43 (108)
T smart00344 7 KILEELQKD-ARISLAELAKKVGLSPSTVHNRVKRLEE 43 (108)
T ss_pred HHHHHHHHh-CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 444444443 3479999999999999999999999988
No 170
>cd06632 STKc_MEKK1_plant Catalytic domain of the Protein Serine/Threonine Kinase, Plant MAP/ERK kinase kinase 1. Serine/threonine kinases (STKs), plant MAP/ERK kinase kinase 1 (MEKK1)-like subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The plant MEKK1 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. This subfamily is composed of plant mitogen-activated protein kinase (MAPK) kinase kinases (MAPKKKs or MKKKs or MAP3Ks) including Arabidopsis thaliana MEKK1 and MAPKKK3. MEKK1 is a MAPKKK that phosphorylates and activates MAPK kinases (MAPKKs or MKKs or MAP2Ks), which in turn phosphorylate and activate MAPKs during signaling cascades that are important in mediating cellular responses to extracellular signals. Arabidops
Probab=23.86 E-value=55 Score=25.02 Aligned_cols=45 Identities=18% Similarity=0.094 Sum_probs=35.5
Q ss_pred HHHHHHhhCCCCHHHHHhhcC-CCccHHHHHHHHHHHHHHHHHHhh
Q psy6286 84 MDVVHAWCEGASFLKVCSITD-IFEGSIIRCMRRLEEVLRQLVQAS 128 (159)
Q Consensus 84 ~~~v~~Wa~G~~f~~i~~~t~-l~EG~iVR~~rRl~elLrql~~a~ 128 (159)
..++++|..|.++.+.+.... +.+..+...+.|+.+.|..+....
T Consensus 77 ~~lv~e~~~~~~L~~~~~~~~~~~~~~~~~~~~~i~~~l~~lH~~~ 122 (258)
T cd06632 77 LYIFLELVPGGSLAKLLKKYGSFPEPVIRLYTRQILLGLEYLHDRN 122 (258)
T ss_pred EEEEEEecCCCcHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHCC
Confidence 346788999999999987665 778888888888888888776554
No 171
>PF09821 AAA_assoc_C: C-terminal AAA-associated domain; InterPro: IPR018632 Members of this family are found in various prokaryotic ABC transporters, predominantly involved in nitrate, sulphonate and bicarbonate translocation.
Probab=23.55 E-value=94 Score=22.81 Aligned_cols=33 Identities=21% Similarity=0.244 Sum_probs=26.7
Q ss_pred hHHHHHHHHHHHhhhCCccCC-C--ccchhhHHHhh
Q psy6286 5 HMEELKCRKRVLRRLGYATEA-D--VIEMKGRVACE 37 (159)
Q Consensus 5 ~~~e~~~~~~vL~~lgyid~~-~--~vt~kGrva~~ 37 (159)
..+++...++.++-|||++-. | .+|..|+...+
T Consensus 10 eiDdL~p~~eAaelLgf~~~~~Gdi~LT~~G~~f~~ 45 (120)
T PF09821_consen 10 EIDDLLPIVEAAELLGFAEVEEGDIRLTPLGRRFAE 45 (120)
T ss_pred cHHHHHHHHHHHHHcCCeeecCCcEEeccchHHHHH
Confidence 358899999999999999653 2 78899987765
No 172
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=23.53 E-value=2.3e+02 Score=21.68 Aligned_cols=51 Identities=16% Similarity=0.209 Sum_probs=41.1
Q ss_pred ccCCchHHHHHHHh-hCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHHh
Q psy6286 77 NQFKPSLMDVVHAW-CEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQA 127 (159)
Q Consensus 77 ~~~~~~l~~~v~~W-a~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~a 127 (159)
..+.|.--.++... ..|.|..+|.+..++++|.+=..+.|.-.-|++....
T Consensus 112 ~~Lp~~~r~v~~L~~~~g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~~ 163 (188)
T PRK12546 112 AQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARARLAELLQL 163 (188)
T ss_pred HhCCHHHhHHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 45555555666555 4999999999999999999999999999888875543
No 173
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=23.03 E-value=1.4e+02 Score=22.46 Aligned_cols=47 Identities=15% Similarity=0.297 Sum_probs=35.0
Q ss_pred cCCchHHHHHHH-hhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHH
Q psy6286 78 QFKPSLMDVVHA-WCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQL 124 (159)
Q Consensus 78 ~~~~~l~~~v~~-Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql 124 (159)
.+.+.--.++.. --.|.|..+|.+..++++|++=..+.|.-.-|++.
T Consensus 127 ~L~~~~r~v~~l~~~~g~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~ 174 (179)
T PRK09415 127 SLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKELLKKG 174 (179)
T ss_pred hCCHHHhhHhHhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 344444444333 34899999999999999999988888887777763
No 174
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=22.82 E-value=1.2e+02 Score=24.47 Aligned_cols=48 Identities=10% Similarity=0.139 Sum_probs=36.0
Q ss_pred cCCchHHHHHHHh-hCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHH
Q psy6286 78 QFKPSLMDVVHAW-CEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLV 125 (159)
Q Consensus 78 ~~~~~l~~~v~~W-a~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~ 125 (159)
.+.+.--.++... ..|.|+.||.+..++++|.+=..+.|.-..|++..
T Consensus 116 ~Lp~~~R~v~lL~~~eg~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l 164 (228)
T PRK06704 116 SLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRLKTVS 164 (228)
T ss_pred hCCHHHhhHhhhHHhhCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4444444444443 47999999999999999999888888877777654
No 175
>PF11269 DUF3069: Protein of unknown function (DUF3069); InterPro: IPR021422 This family of proteins with unknown function appear to be restricted to Gammaproteobacteria. ; PDB: 2PV4_A.
Probab=22.74 E-value=1.4e+02 Score=22.27 Aligned_cols=25 Identities=28% Similarity=0.602 Sum_probs=20.0
Q ss_pred HHHHHHHHHHhhhhhCChHHHHHHHHHH
Q psy6286 117 LEEVLRQLVQASRNIGNTLLEEKFNEAI 144 (159)
Q Consensus 117 l~elLrql~~a~~~ig~~~L~~k~~~a~ 144 (159)
+.|.++||+.|-+ |+.|.+-|.+..
T Consensus 96 lKd~vKqLKKAR~---d~~mk~~f~~V~ 120 (121)
T PF11269_consen 96 LKDMVKQLKKARR---DPSMKNSFKEVF 120 (121)
T ss_dssp HHHHHHHHHHHTT----HHHHHHHHHHH
T ss_pred HHHHHHHHHHHcc---CHHHHHHHHHHh
Confidence 5789999999975 899998888754
No 176
>cd06641 STKc_MST3 Catalytic domain of the Protein Serine/Threonine Kinase, Mammalian Ste20-like protein kinase 3. Serine/threonine kinases (STKs), mammalian Ste20-like protein kinase 3 (MST3) subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The MST3 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. MST3 phosphorylates the STK NDR and may play a role in cell cycle progression and cell morphology. It may also regulate paxillin and consequently, cell migration. MST3 is present in human placenta, where it plays an essential role in the oxidative stress-induced apoptosis of trophoblasts in normal spontaneous delivery. Dysregulation of trophoblast apoptosis may result in pregnancy complications such as preeclampsia and int
Probab=22.57 E-value=45 Score=26.25 Aligned_cols=45 Identities=18% Similarity=0.186 Sum_probs=37.0
Q ss_pred HHHHHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHHhh
Q psy6286 84 MDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQAS 128 (159)
Q Consensus 84 ~~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~a~ 128 (159)
..++++|+.|.++.+.+....+.+..+...+.++...+..+....
T Consensus 77 ~~lv~e~~~~~~l~~~i~~~~~~~~~~~~~~~~l~~~l~~lh~~~ 121 (277)
T cd06641 77 LWIIMEYLGGGSALDLLEPGPLDETQIATILREILKGLDYLHSEK 121 (277)
T ss_pred EEEEEEeCCCCcHHHHHhcCCCCHHHHHHHHHHHHHHHHHHccCC
Confidence 347888999999999998888888888888888888887775544
No 177
>cd06655 STKc_PAK2 Catalytic domain of the Protein Serine/Threonine Kinase, p21-activated kinase 2. Serine/threonine kinases (STKs), p21-activated kinase (PAK) 2, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The PAK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. PAKs are Rho family GTPase-regulated kinases that serve as important mediators in the function of Cdc42 (cell division cycle 42) and Rac. PAKs from higher eukaryotes are classified into two groups (I and II), according to their biochemical and structural features. PAK2 belongs to group I. Group I PAKs contain a PBD (p21-binding domain) overlapping with an AID (autoinhibitory domain), a C-terminal catalytic domain, SH3 binding sites and a non-classical SH3 binding
Probab=22.51 E-value=62 Score=26.02 Aligned_cols=45 Identities=24% Similarity=0.213 Sum_probs=37.2
Q ss_pred HHHHHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHHhh
Q psy6286 84 MDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQAS 128 (159)
Q Consensus 84 ~~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~a~ 128 (159)
..++++|..|.++.+.+....+.+..+.+.+.++..-+..+....
T Consensus 91 ~~lv~e~~~~~~L~~~~~~~~l~~~~~~~i~~~l~~al~~LH~~~ 135 (296)
T cd06655 91 LFVVMEYLAGGSLTDVVTETCMDEAQIAAVCRECLQALEFLHANQ 135 (296)
T ss_pred EEEEEEecCCCcHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHCC
Confidence 456788999999999998888899989988888888777776544
No 178
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=22.40 E-value=1.8e+02 Score=22.19 Aligned_cols=45 Identities=29% Similarity=0.365 Sum_probs=35.5
Q ss_pred cCCchHHHHH-HHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHH
Q psy6286 78 QFKPSLMDVV-HAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLR 122 (159)
Q Consensus 78 ~~~~~l~~~v-~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLr 122 (159)
.++|....++ ..|..|.|..||.+..++++.++=|-.++.-.-|+
T Consensus 135 ~l~~~~~~~v~l~~~~Gls~~EIA~~lgiS~~tV~r~l~~aR~~l~ 180 (185)
T PF07638_consen 135 ALDPRQRRVVELRFFEGLSVEEIAERLGISERTVRRRLRRARAWLR 180 (185)
T ss_pred ccCHHHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 3566666666 45789999999999999999998888877765554
No 179
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=22.11 E-value=1.4e+02 Score=22.62 Aligned_cols=36 Identities=14% Similarity=0.165 Sum_probs=31.2
Q ss_pred HhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHH
Q psy6286 89 AWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQL 124 (159)
Q Consensus 89 ~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql 124 (159)
....|.|..||.+..++++|.+=..+.|...-|++.
T Consensus 146 ~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 181 (188)
T PRK09640 146 RFVAELEFQEIADIMHMGLSATKMRYKRALDKLREK 181 (188)
T ss_pred HHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 466999999999999999999988888888777774
No 180
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=21.66 E-value=2.1e+02 Score=21.45 Aligned_cols=32 Identities=19% Similarity=0.323 Sum_probs=26.8
Q ss_pred CCCCHHHHHhhcCCCccHHHHHHHHHHHHHHH
Q psy6286 92 EGASFLKVCSITDIFEGSIIRCMRRLEEVLRQ 123 (159)
Q Consensus 92 ~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrq 123 (159)
.|.|..+|.+..++++|++=..+.|.-.-|++
T Consensus 164 ~~~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~ 195 (198)
T TIGR02859 164 DGKSYQEIACDLNRHVKSIDNALQRVKRKLEK 195 (198)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 89999999999999999987666666666554
No 181
>cd05123 STKc_AGC Catalytic domain of AGC family Protein Serine/Threonine Kinases. Serine/Threonine Kinases (STKs), AGC (Protein Kinases A, G and C) family, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The AGC family is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and Phosphoinositide 3-Kinase (PI3K). Members of this family include cAMP-dependent Protein Kinase (PKA), cGMP-dependent Protein Kinase (PKG), Protein Kinase C (PKC), Protein Kinase B (PKB), G protein-coupled Receptor Kinase (GRK), Serum- and Glucocorticoid-induced Kinase (SGK), and 70 kDa ribosomal Protein S6 Kinase (p70S6K or S6K), among others. AGC kinases share an activation mechanism based on the phosphorylation of up to three sites: the activation loop (A-loop), the hydrophobic motif (HM) and the
Probab=21.63 E-value=76 Score=24.16 Aligned_cols=50 Identities=12% Similarity=0.011 Sum_probs=38.7
Q ss_pred HHHHHHHhhCCCCHHHHHhhc-CCCccHHHHHHHHHHHHHHHHHHhhhhhC
Q psy6286 83 LMDVVHAWCEGASFLKVCSIT-DIFEGSIIRCMRRLEEVLRQLVQASRNIG 132 (159)
Q Consensus 83 l~~~v~~Wa~G~~f~~i~~~t-~l~EG~iVR~~rRl~elLrql~~a~~~ig 132 (159)
..-++++|..|.++.+.+... .+.+-.+.+++.++.+-|..+....-+.|
T Consensus 67 ~~~~v~e~~~~~~L~~~l~~~~~l~~~~~~~~~~qi~~~l~~lh~~~~~H~ 117 (250)
T cd05123 67 KLYLVLEYAPGGELFSHLSKEGRFSEERARFYAAEIVLALEYLHSLGIIYR 117 (250)
T ss_pred eeEEEEecCCCCcHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHCCceec
Confidence 345577799899999888765 68899999999999988888877544433
No 182
>cd06659 STKc_PAK6 Catalytic domain of the Protein Serine/Threonine Kinase, p21-activated kinase 6. Serine/threonine kinases (STKs), p21-activated kinase (PAK) 6, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The PAK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. PAKs are Rho family GTPase-regulated kinases that serve as important mediators in the function of Cdc42 (cell division cycle 42) and Rac. PAKs from higher eukaryotes are classified into two groups (I and II), according to their biochemical and structural features. PAK6 belongs to group II. Group II PAKs contain a PBD (p21-binding domain) and a C-terminal catalytic domain, but do not harbor an AID (autoinhibitory domain) or SH3 binding sites. PAK6 may play a role i
Probab=21.59 E-value=65 Score=25.94 Aligned_cols=44 Identities=18% Similarity=0.197 Sum_probs=37.0
Q ss_pred HHHHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHHhh
Q psy6286 85 DVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQAS 128 (159)
Q Consensus 85 ~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~a~ 128 (159)
.++++|+.|.++.+++....+.+-.+.+++.++.+-|..+.+..
T Consensus 94 ~iv~e~~~~~~L~~~~~~~~~~~~~~~~~~~qi~~~L~~LH~~~ 137 (297)
T cd06659 94 WVLMEFLQGGALTDIVSQTRLNEEQIATVCESVLQALCYLHSQG 137 (297)
T ss_pred EEEEecCCCCCHHHHHhhcCCCHHHHHHHHHHHHHHHHHHHhCC
Confidence 45777899999999998888899999999999888888776654
No 183
>PRK00794 flbT flagellar biosynthesis repressor FlbT; Reviewed
Probab=21.56 E-value=3e+02 Score=20.62 Aligned_cols=43 Identities=9% Similarity=0.057 Sum_probs=27.9
Q ss_pred cHHHHHHHHHHHHHHHHHHhhhhhCChHHHHHHHHHHHhhcCCccc
Q psy6286 108 GSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKFNEAIKTVKRDIFL 153 (159)
Q Consensus 108 G~iVR~~rRl~elLrql~~a~~~ig~~~L~~k~~~a~~~I~RdIV~ 153 (159)
++-=.+..+..+.+.|+..+. +||+..+.+.++.+.|..|=.|
T Consensus 68 ~~~~~~~~~~~~~~~~l~~~~---~~p~~~~~l~~i~~~V~~g~~y 110 (132)
T PRK00794 68 AGAEDARAEFARRLEQLLAVF---TDPDILAGLKAIDELVEAGRYY 110 (132)
T ss_pred cchHHHHHHHHHHHHHHHHHH---CCHHHHHHHHHHHHHHHCCcHH
Confidence 333344555555666666665 5888888888888887766443
No 184
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=21.50 E-value=2.2e+02 Score=22.49 Aligned_cols=48 Identities=19% Similarity=0.290 Sum_probs=36.4
Q ss_pred CCchHHHHHHH-hhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHH
Q psy6286 79 FKPSLMDVVHA-WCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQ 126 (159)
Q Consensus 79 ~~~~l~~~v~~-Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~ 126 (159)
+.+.--.++.. ...|.|+.||.+..++++|.+=..+.|.-..|+..-.
T Consensus 135 Lp~~~R~v~~L~y~eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l~ 183 (216)
T PRK12533 135 LPVEYREVLVLRELEDMSYREIAAIADVPVGTVMSRLARARRRLAALLG 183 (216)
T ss_pred CCHHHHhHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHc
Confidence 33333344433 4599999999999999999998888888888877543
No 185
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=21.48 E-value=1.5e+02 Score=22.59 Aligned_cols=37 Identities=16% Similarity=0.101 Sum_probs=30.5
Q ss_pred hhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHH
Q psy6286 90 WCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQ 126 (159)
Q Consensus 90 Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~ 126 (159)
-..|.|+.+|.+..++++|++=..+.|.-.-|++.-.
T Consensus 144 ~~~g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~ 180 (188)
T TIGR02943 144 EVLGFESDEICQELEISTSNCHVLLYRARLSLRACLS 180 (188)
T ss_pred HHhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 3589999999999999999997777777777766543
No 186
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=21.39 E-value=1e+02 Score=22.94 Aligned_cols=34 Identities=9% Similarity=0.275 Sum_probs=27.5
Q ss_pred HHHHhh-CC-CCHHHHHhhcCCCccHHHHHHHHHHH
Q psy6286 86 VVHAWC-EG-ASFLKVCSITDIFEGSIIRCMRRLEE 119 (159)
Q Consensus 86 ~v~~Wa-~G-~~f~~i~~~t~l~EG~iVR~~rRl~e 119 (159)
++..+. +| .|+++|-+..+++++++-|-++||.+
T Consensus 14 Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~ 49 (153)
T PRK11179 14 ILEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQ 49 (153)
T ss_pred HHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 334443 33 59999999999999999999999877
No 187
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=21.30 E-value=1.5e+02 Score=22.84 Aligned_cols=37 Identities=11% Similarity=0.057 Sum_probs=30.8
Q ss_pred hhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHH
Q psy6286 90 WCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQ 126 (159)
Q Consensus 90 Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~ 126 (159)
-..|.|..||.+..++++|.+=..+.|.-..||+.-.
T Consensus 152 ~~eg~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~ 188 (201)
T PRK12545 152 EFLDFEIDDICTELTLTANHCSVLLYRARTRLRTCLS 188 (201)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 3599999999999999999998777777777776543
No 188
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=21.19 E-value=1.7e+02 Score=22.78 Aligned_cols=37 Identities=22% Similarity=0.319 Sum_probs=33.2
Q ss_pred hCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHHh
Q psy6286 91 CEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQA 127 (159)
Q Consensus 91 a~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~a 127 (159)
..|.|..+|.+..++.+|++=..+.|...-|++....
T Consensus 152 ~~g~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~~ 188 (203)
T PRK09647 152 IEGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAALAA 188 (203)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 6999999999999999999999999998888876554
No 189
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=21.17 E-value=1.8e+02 Score=23.39 Aligned_cols=35 Identities=14% Similarity=0.252 Sum_probs=28.5
Q ss_pred HhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHH
Q psy6286 89 AWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQ 123 (159)
Q Consensus 89 ~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrq 123 (159)
.+..|.|..+|-+..+++.+.+=+..+|...-|++
T Consensus 221 ~~~~~~t~~eIA~~lgis~~~V~~~~~~al~kLr~ 255 (258)
T PRK08215 221 RFFQGKTQMEVAEEIGISQAQVSRLEKAALKHMRK 255 (258)
T ss_pred HHhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 34689999999999999999888877777776665
No 190
>TIGR03613 RutR pyrimidine utilization regulatory protein R. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the TetR family of transcriptional regulators defined by the N-teminal model pfam00440 and the C-terminal model pfam08362 (YcdC-like protein, C-terminal region).
Probab=21.14 E-value=93 Score=23.53 Aligned_cols=35 Identities=6% Similarity=0.268 Sum_probs=24.7
Q ss_pred CCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHH
Q psy6286 92 EGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQ 126 (159)
Q Consensus 92 ~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~ 126 (159)
+|.|..+|++.+++..|.|=+.+.==++|+..+..
T Consensus 27 ~~~s~~~IA~~agvs~~~lY~hF~sKe~L~~av~~ 61 (202)
T TIGR03613 27 HGTSLEQIAELAGVSKTNLLYYFPSKDALYLAVLR 61 (202)
T ss_pred ccCCHHHHHHHhCCCHHHHHHHcCCHHHHHHHHHH
Confidence 56778888888888888777776666666655543
No 191
>cd06647 STKc_PAK_I Catalytic domain of the Protein Serine/Threonine Kinase, Group I p21-activated kinase. Serine/threonine kinases (STKs), p21-activated kinase (PAK) subfamily, Group I, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The PAK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. PAKs are Rho family GTPase-regulated kinases that serve as important mediators in the function of Cdc42 (cell division cycle 42) and Rac. PAKs are implicated in the regulation of many cellular processes including growth factor receptor-mediated proliferation, cell polarity, cell motility, cell death and survival, and actin cytoskeleton organization. PAKs from higher eukaryotes are classified into two groups (I and II), according to their bi
Probab=21.12 E-value=66 Score=25.77 Aligned_cols=46 Identities=26% Similarity=0.230 Sum_probs=37.0
Q ss_pred HHHHHHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHHhh
Q psy6286 83 LMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQAS 128 (159)
Q Consensus 83 l~~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~a~ 128 (159)
...++++|..|.++.+.+....+.++.+...++++..-|..+.+..
T Consensus 90 ~~~lv~e~~~~~~L~~~~~~~~l~~~~~~~i~~~l~~al~~LH~~g 135 (293)
T cd06647 90 ELWVVMEYLAGGSLTDVVTETCMDEGQIAAVCRECLQALEFLHSNQ 135 (293)
T ss_pred cEEEEEecCCCCcHHHHHhhcCCCHHHHHHHHHHHHHHHHHHHhCC
Confidence 4457888999999999998888888888888888887777776543
No 192
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=21.11 E-value=1.5e+02 Score=22.33 Aligned_cols=47 Identities=17% Similarity=0.114 Sum_probs=35.5
Q ss_pred ccCCchHHHHHH-HhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHH
Q psy6286 77 NQFKPSLMDVVH-AWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQ 123 (159)
Q Consensus 77 ~~~~~~l~~~v~-~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrq 123 (159)
..+.+.--.++. .--.|.|..||.+..++++|.+=..+.|...-|++
T Consensus 128 ~~L~~~~r~v~~l~~~~g~s~~EIA~~l~is~~tV~~~l~rar~~Lr~ 175 (181)
T PRK12536 128 EQLPDRQRLPIVHVKLEGLSVAETAQLTGLSESAVKVGIHRGLKALAA 175 (181)
T ss_pred HHCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 345444444432 33699999999999999999999888887777766
No 193
>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA. This model represents HrpA, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria and a few high-GC Gram-positive bacteria. HrpA is about 1300 amino acids long, while its paralog HrpB, also uncharacterized, is about 800 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing.
Probab=21.09 E-value=1e+02 Score=31.63 Aligned_cols=33 Identities=21% Similarity=0.323 Sum_probs=28.9
Q ss_pred HHHHHHHHHhhhCCccCCC---ccchhhHHHhhhcC
Q psy6286 8 ELKCRKRVLRRLGYATEAD---VIEMKGRVACELSK 40 (159)
Q Consensus 8 e~~~~~~vL~~lgyid~~~---~vt~kGrva~~I~s 40 (159)
.+..-+..|..+|.||+++ .+|..|+..+++--
T Consensus 450 ~i~~A~~~L~~LGAld~~~~~~~LT~lGr~ma~LPl 485 (1283)
T TIGR01967 450 AIRDGFRLLEELGALDDDEAEPQLTPIGRQLAQLPV 485 (1283)
T ss_pred HHHHHHHHHHHCCCCCCCCCCccccHHHHHHhhcCC
Confidence 4667788999999999887 79999999999875
No 194
>cd06611 STKc_SLK_like Catalytic domain of Ste20-like kinase-like Protein Serine/Threonine Kinases. Serine/threonine kinases (STKs), Ste20-like kinase (SLK)-like subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The SLK-like subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. Members of the subfamily include SLK, STK10 (also called LOK for lymphocyte-oriented kinase), SmSLK (Schistosoma mansoni SLK), and related proteins. SLK promotes apoptosis through apoptosis signal-regulating kinase 1 (ASK1) and the mitogen-activated protein kinase (MAPK) p38. It also plays a role in mediating actin reorganization. STK10 is responsible in regulating the CD28 responsive element in T cells, as well as leukocyte function associated anti
Probab=21.01 E-value=91 Score=24.42 Aligned_cols=48 Identities=17% Similarity=0.225 Sum_probs=38.5
Q ss_pred hHHHHHHHhhCCCCHHHHHhhc--CCCccHHHHHHHHHHHHHHHHHHhhh
Q psy6286 82 SLMDVVHAWCEGASFLKVCSIT--DIFEGSIIRCMRRLEEVLRQLVQASR 129 (159)
Q Consensus 82 ~l~~~v~~Wa~G~~f~~i~~~t--~l~EG~iVR~~rRl~elLrql~~a~~ 129 (159)
+...++.+++.|.++.+++... .+.+..+.+.+.++.+.|.-+.+..-
T Consensus 75 ~~~~lv~e~~~~~~L~~~~~~~~~~l~~~~~~~~~~ql~~~l~~lh~~~i 124 (280)
T cd06611 75 NKLWILIEFCDGGALDSIMLELERGLTEPQIRYVCRQMLEALNFLHSHKV 124 (280)
T ss_pred CeEEEEeeccCCCcHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHCCc
Confidence 3345677899999999998764 58999999999999999888776543
No 195
>KOG0578|consensus
Probab=21.01 E-value=41 Score=31.21 Aligned_cols=34 Identities=32% Similarity=0.385 Sum_probs=27.1
Q ss_pred hHHHHHHHhhCCCCHHHHHhhcCCCccHHHHHHH
Q psy6286 82 SLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMR 115 (159)
Q Consensus 82 ~l~~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~r 115 (159)
+-.|+|.+..+|-++.+|+..+-+.||-|-..+|
T Consensus 343 deLWVVMEym~ggsLTDvVt~~~~~E~qIA~Icr 376 (550)
T KOG0578|consen 343 DELWVVMEYMEGGSLTDVVTKTRMTEGQIAAICR 376 (550)
T ss_pred ceeEEEEeecCCCchhhhhhcccccHHHHHHHHH
Confidence 3357777888999999999999999996655443
No 196
>PRK10359 lipopolysaccharide core biosynthesis protein; Provisional
Probab=21.01 E-value=76 Score=25.95 Aligned_cols=47 Identities=15% Similarity=0.174 Sum_probs=32.6
Q ss_pred HHHHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHHhhhhhCChHHHH
Q psy6286 85 DVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEE 138 (159)
Q Consensus 85 ~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~a~~~ig~~~L~~ 138 (159)
.++.+|..|.++.++... .+ ....++.+.++++....-+.||+...+
T Consensus 119 ~lvmEyi~G~tL~~~~~~---~~----~~~~~i~~~l~~lH~~gi~H~Dikp~N 165 (232)
T PRK10359 119 IMLIEYIEGVELNDMPEI---SE----DVKAKIKASIESLHQHGMVSGDPHKGN 165 (232)
T ss_pred EEEEEEECCccHHHhhhc---cH----HHHHHHHHHHHHHHHcCCccCCCChHH
Confidence 447889999999998432 22 235577777888877766667766554
No 197
>cd01043 DPS DPS protein, ferritin-like diiron-binding domain. DPS (DNA Protecting protein under Starved conditions) domain is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins. Some DPS proteins nonspecifically bind DNA, protecting it from cleavage caused by reactive oxygen species such as the hydroxyl radicals produced during oxidation of Fe(II) by hydrogen peroxide. These proteins assemble into dodecameric structures, some form DPS-DNA co-crystalline complexes, and possess iron and H2O2 detoxification capabilities. Expression of DPS is induced by oxidative or nutritional stress, including metal ion starvation. Members of the DPS family are homopolymers formed by 12 four-helix bundle subunits that assemble with 23 symmetry into a hollow shell. The DPS ferroxidase site is unusual in that it is not located in a four-helix bundle as in ferritin, but is shared by 2-fold symmetry-related subunits providing the iron ligands. Many DPS sequences (e.g., E. coli) disp
Probab=20.87 E-value=2.7e+02 Score=19.95 Aligned_cols=44 Identities=16% Similarity=0.385 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHHHHHHHhhhhhCChHHHHHHHHHHHhhcCCccc
Q psy6286 110 IIRCMRRLEEVLRQLVQASRNIGNTLLEEKFNEAIKTVKRDIFL 153 (159)
Q Consensus 110 iVR~~rRl~elLrql~~a~~~ig~~~L~~k~~~a~~~I~RdIV~ 153 (159)
++.....+.+.+++....|.-.||+..+.-+.+.+...-+.+.|
T Consensus 91 ~~~~~~~~i~~~~~~i~~a~~~~D~~t~~ll~~il~~~ek~~w~ 134 (139)
T cd01043 91 LLEDYETLIEELREAIELADEAGDPATADLLTEIIRELEKQAWM 134 (139)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHH
Confidence 34445555556666666555457888888887776655544443
No 198
>PF11994 DUF3489: Protein of unknown function (DUF3489); InterPro: IPR021880 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 84 to 211 amino acids in length. This protein has a single completely conserved residue W that may be functionally important.
Probab=20.63 E-value=1.6e+02 Score=19.95 Aligned_cols=28 Identities=18% Similarity=0.239 Sum_probs=22.6
Q ss_pred hHHHHHHHhhCCCCHHHHHhhcCCCccH
Q psy6286 82 SLMDVVHAWCEGASFLKVCSITDIFEGS 109 (159)
Q Consensus 82 ~l~~~v~~Wa~G~~f~~i~~~t~l~EG~ 109 (159)
..+-.+..+..|++..+||+.|+=+.=+
T Consensus 13 a~li~mL~rp~GATi~ei~~atGWq~HT 40 (72)
T PF11994_consen 13 AQLIAMLRRPEGATIAEICEATGWQPHT 40 (72)
T ss_pred HHHHHHHcCCCCCCHHHHHHhhCCchhh
Confidence 4556678899999999999999877633
No 199
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=20.55 E-value=1.9e+02 Score=21.85 Aligned_cols=47 Identities=13% Similarity=0.143 Sum_probs=37.6
Q ss_pred ccCCchHHHHHHHh-hCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHH
Q psy6286 77 NQFKPSLMDVVHAW-CEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQ 123 (159)
Q Consensus 77 ~~~~~~l~~~v~~W-a~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrq 123 (159)
..+.+.--.++..- ..|.|+.||.+..++++|++=..+.|.-..|++
T Consensus 129 ~~Lp~~~r~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 129 ADLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred HhCCHHHhHHhhhHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 34555554555443 599999999999999999999999999888887
No 200
>PRK05572 sporulation sigma factor SigF; Validated
Probab=20.41 E-value=2.1e+02 Score=23.01 Aligned_cols=47 Identities=9% Similarity=0.102 Sum_probs=35.4
Q ss_pred cCCchHHHHH-HHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHH
Q psy6286 78 QFKPSLMDVV-HAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQL 124 (159)
Q Consensus 78 ~~~~~l~~~v-~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql 124 (159)
.+.+.--.++ ..+..|.|..+|-+..+++.+.+=+...|...-|++.
T Consensus 202 ~L~~~~~~v~~l~~~~~~s~~eIA~~lgis~~~V~~~~~ral~kLr~~ 249 (252)
T PRK05572 202 ELDERERLIVYLRYFKDKTQSEVAKRLGISQVQVSRLEKKILKQMKEK 249 (252)
T ss_pred cCCHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3443333333 3446899999999999999999999888888888764
No 201
>cd03565 VHS_Tom1 VHS domain family, Tom1 subfamily; The VHS domain is an essential part of Tom1 (Target of myb1 - retroviral oncogene) protein. The VHS domain has a superhelical structure similar to the structure of the ARM repeats and is present at the very N-termini of proteins. It is a right-handed superhelix of eight alpha helices. The VHS domain has been found in a number of proteins, some of which have been implicated in intracellular trafficking and sorting. The VHS domain of the Tom1 protein is essential for the negative regulation of Interleukin-1 and Tumor Necrosis Factor-induced signaling pathways.
Probab=20.39 E-value=1.5e+02 Score=22.17 Aligned_cols=39 Identities=15% Similarity=0.148 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHHHHhhhhhCChHHHHHHHHHHHhhcCCccc
Q psy6286 113 CMRRLEEVLRQLVQASRNIGNTLLEEKFNEAIKTVKRDIFL 153 (159)
Q Consensus 113 ~~rRl~elLrql~~a~~~ig~~~L~~k~~~a~~~I~RdIV~ 153 (159)
.-.|+.+++++...+.+ ++|.|..-.+.-..+.++|+.|
T Consensus 102 Vk~kil~li~~W~~~f~--~~~~l~~i~~~y~~L~~~G~~F 140 (141)
T cd03565 102 VQEKVLALIQAWADAFR--GSPDLTGVVEVYEELKKKGIEF 140 (141)
T ss_pred HHHHHHHHHHHHHHHhC--CCccchHHHHHHHHHHHcCCCC
Confidence 34788999999998876 6777665444444455667766
No 202
>TIGR02850 spore_sigG RNA polymerase sigma-G factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.
Probab=20.31 E-value=1.9e+02 Score=23.29 Aligned_cols=35 Identities=17% Similarity=0.270 Sum_probs=29.0
Q ss_pred HhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHH
Q psy6286 89 AWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQ 123 (159)
Q Consensus 89 ~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrq 123 (159)
.+..|.|+.+|-+..+++.+.+=+..+|...-|++
T Consensus 218 ~~~~~~t~~eIA~~lgis~~~V~~~~~ral~kLr~ 252 (254)
T TIGR02850 218 RFFEGKTQMEVAEEIGISQAQVSRLEKAALKHMRK 252 (254)
T ss_pred HHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHh
Confidence 45688999999999999999888888887777765
No 203
>COG1309 AcrR Transcriptional regulator [Transcription]
Probab=20.30 E-value=1.2e+02 Score=21.06 Aligned_cols=37 Identities=14% Similarity=0.314 Sum_probs=29.5
Q ss_pred CCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHHhh
Q psy6286 92 EGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQAS 128 (159)
Q Consensus 92 ~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~a~ 128 (159)
.|.|..+|++..++..|+|=|.+.--++++.++..-.
T Consensus 31 ~~~t~~~Ia~~agvs~~~~Y~~f~~K~~l~~~~~~~~ 67 (201)
T COG1309 31 AATTVDEIAKAAGVSKGTLYRHFPSKEDLLLALLERA 67 (201)
T ss_pred CCCCHHHHHHHhCCCcchhHHHcCCHHHHHHHHHHHH
Confidence 4568889999999999999988888777777665543
No 204
>PF11027 DUF2615: Protein of unknown function (DUF2615); InterPro: IPR020309 This entry represents a group of uncharacterised protein from the Metazoa, including CD034 (or C4orf34) and YQF4 (or C34C12.4).
Probab=20.23 E-value=77 Score=22.96 Aligned_cols=17 Identities=41% Similarity=0.448 Sum_probs=14.6
Q ss_pred HHHHHHHHHHHHHHHhh
Q psy6286 112 RCMRRLEEVLRQLVQAS 128 (159)
Q Consensus 112 R~~rRl~elLrql~~a~ 128 (159)
-.+|||..+|||=.+.+
T Consensus 16 ~AMrRLl~~LRqsQ~~C 32 (103)
T PF11027_consen 16 MAMRRLLNLLRQSQNYC 32 (103)
T ss_pred HHHHHHHHHHHHhhCcc
Confidence 47999999999987776
No 205
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=20.12 E-value=2.1e+02 Score=22.05 Aligned_cols=48 Identities=17% Similarity=0.224 Sum_probs=33.2
Q ss_pred ccCCchHHHHH-HHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHH
Q psy6286 77 NQFKPSLMDVV-HAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQL 124 (159)
Q Consensus 77 ~~~~~~l~~~v-~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql 124 (159)
..+.+.--.++ ..-..|.|+.||.+..++.+|.+=-.+.|.-..||+.
T Consensus 132 ~~Lp~~~r~v~~l~~~~g~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~ 180 (196)
T PRK12535 132 DALPPERREALILTQVLGYTYEEAAKIADVRVGTIRSRVARARADLIAA 180 (196)
T ss_pred HcCCHHHHHHhhhHHHhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 34444444444 2335999999999999999999866666665555543
Done!