Query 043012
Match_columns 151
No_of_seqs 128 out of 612
Neff 7.2
Searched_HMMs 46136
Date Fri Mar 29 11:55:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043012.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043012hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08148 DSHCT: DSHCT (NUC185) 100.0 1.7E-44 3.6E-49 275.7 10.1 142 2-148 28-175 (180)
2 KOG0948 Nuclear exosomal RNA h 100.0 3.1E-39 6.6E-44 283.0 10.3 141 2-149 890-1037(1041)
3 KOG0947 Cytoplasmic exosomal R 100.0 5.9E-35 1.3E-39 260.7 13.5 143 1-150 1095-1245(1248)
4 COG4581 Superfamily II RNA hel 99.9 1.5E-27 3.3E-32 217.3 12.7 144 2-148 888-1036(1041)
5 smart00421 HTH_LUXR helix_turn 90.2 1.6 3.6E-05 25.4 5.8 44 75-118 4-47 (58)
6 PF04545 Sigma70_r4: Sigma-70, 88.8 1.6 3.5E-05 25.7 5.0 37 83-119 14-50 (50)
7 TIGR03643 conserved hypothetic 88.0 0.83 1.8E-05 29.9 3.4 30 84-113 8-37 (72)
8 PF10985 DUF2805: Protein of u 87.8 0.85 1.8E-05 29.9 3.4 30 84-113 7-36 (73)
9 cd06170 LuxR_C_like C-terminal 86.5 3.4 7.3E-05 24.1 5.5 35 81-115 7-41 (57)
10 PRK04217 hypothetical protein; 86.5 3.2 6.9E-05 29.3 6.0 50 73-122 41-91 (110)
11 cd06171 Sigma70_r4 Sigma70, re 82.7 5.1 0.00011 22.6 5.0 31 87-117 24-54 (55)
12 PF13518 HTH_28: Helix-turn-he 82.7 4.8 0.0001 23.4 4.9 35 81-115 4-38 (52)
13 PF13384 HTH_23: Homeodomain-l 79.0 2.1 4.5E-05 25.0 2.3 34 81-114 9-42 (50)
14 PRK00118 putative DNA-binding 76.0 11 0.00024 26.3 5.6 50 76-125 19-69 (104)
15 TIGR02172 Fb_sc_TIGR02172 Fibr 73.3 11 0.00023 29.4 5.6 55 66-123 51-110 (226)
16 PF13936 HTH_38: Helix-turn-he 71.6 9.7 0.00021 22.0 3.9 31 82-112 13-43 (44)
17 PF00196 GerE: Bacterial regul 69.8 15 0.00032 22.1 4.6 45 74-118 3-47 (58)
18 PF13613 HTH_Tnp_4: Helix-turn 69.4 20 0.00043 21.4 5.0 44 77-120 7-50 (53)
19 PF08281 Sigma70_r4_2: Sigma-7 67.4 13 0.00028 21.9 3.9 33 84-116 21-53 (54)
20 PF02796 HTH_7: Helix-turn-hel 66.7 21 0.00045 20.6 4.6 33 78-110 10-42 (45)
21 PF12690 BsuPI: Intracellular 64.1 0.48 1E-05 31.6 -3.3 25 81-105 36-60 (82)
22 smart00351 PAX Paired Box doma 63.2 21 0.00045 25.4 4.9 35 81-115 25-59 (125)
23 TIGR02337 HpaR homoprotocatech 60.3 52 0.0011 22.5 7.2 55 58-116 15-69 (118)
24 PRK06759 RNA polymerase factor 57.9 31 0.00068 24.4 5.2 44 77-120 109-153 (154)
25 PRK03573 transcriptional regul 57.2 67 0.0014 22.7 7.4 48 65-115 25-72 (144)
26 PF13601 HTH_34: Winged helix 57.1 19 0.0004 23.6 3.5 37 78-115 4-40 (80)
27 PF13412 HTH_24: Winged helix- 55.7 22 0.00047 20.4 3.4 29 87-115 15-43 (48)
28 PRK09639 RNA polymerase sigma 55.5 31 0.00066 24.8 4.8 37 83-120 122-158 (166)
29 cd00090 HTH_ARSR Arsenical Res 54.7 37 0.00081 20.2 4.5 31 85-115 16-46 (78)
30 PF00440 TetR_N: Bacterial reg 53.9 11 0.00024 21.7 1.9 33 88-120 15-47 (47)
31 COG0501 HtpX Zn-dependent prot 53.9 5.3 0.00011 31.9 0.5 21 1-21 142-162 (302)
32 PF13730 HTH_36: Helix-turn-he 53.3 24 0.00052 20.7 3.3 25 91-115 27-51 (55)
33 TIGR02985 Sig70_bacteroi1 RNA 53.0 53 0.0012 23.0 5.7 45 75-119 114-159 (161)
34 cd00180 PKc Catalytic domain o 52.7 11 0.00024 26.7 2.0 46 78-123 64-111 (215)
35 PF01527 HTH_Tnp_1: Transposas 52.4 19 0.00041 22.6 2.9 29 86-114 20-48 (76)
36 TIGR02999 Sig-70_X6 RNA polyme 52.3 41 0.00089 24.6 5.1 46 75-120 135-181 (183)
37 PRK12525 RNA polymerase sigma 51.4 43 0.00093 24.3 5.1 35 85-119 130-164 (168)
38 PRK00254 ski2-like helicase; P 51.2 38 0.00082 31.0 5.7 68 78-145 570-640 (720)
39 PRK09642 RNA polymerase sigma 50.5 45 0.00097 23.8 5.0 43 77-119 109-152 (160)
40 PF01047 MarR: MarR family; I 50.2 26 0.00057 20.8 3.2 35 80-115 9-43 (59)
41 TIGR02941 Sigma_B RNA polymera 49.8 40 0.00088 26.4 5.0 37 84-120 216-252 (255)
42 TIGR02937 sigma70-ECF RNA poly 49.6 47 0.001 22.6 4.9 43 77-119 113-156 (158)
43 PRK09648 RNA polymerase sigma 49.0 48 0.001 24.5 5.1 35 86-120 152-186 (189)
44 PF12802 MarR_2: MarR family; 48.5 32 0.0007 20.4 3.4 30 86-115 16-47 (62)
45 PRK05417 glutathione-dependent 48.4 31 0.00067 26.7 4.0 33 52-88 151-183 (191)
46 PRK08583 RNA polymerase sigma 47.7 48 0.001 26.0 5.1 44 77-120 208-252 (257)
47 PRK15345 type III secretion sy 47.5 1.6E+02 0.0034 24.8 8.1 97 44-141 218-321 (326)
48 TIGR02984 Sig-70_plancto1 RNA 47.3 68 0.0015 23.4 5.7 46 75-120 141-187 (189)
49 PRK09047 RNA polymerase factor 47.3 53 0.0011 23.3 5.0 37 84-120 117-153 (161)
50 PRK12522 RNA polymerase sigma 47.1 52 0.0011 23.9 5.0 36 84-119 130-165 (173)
51 PRK02362 ski2-like helicase; P 46.8 25 0.00054 32.3 3.8 66 80-145 581-647 (737)
52 PRK13919 putative RNA polymera 46.6 55 0.0012 24.0 5.1 43 77-119 138-181 (186)
53 PF13463 HTH_27: Winged helix 46.4 28 0.00062 21.1 3.0 29 88-116 17-45 (68)
54 PF13404 HTH_AsnC-type: AsnC-t 46.2 34 0.00074 19.6 3.1 25 90-114 18-42 (42)
55 PF01022 HTH_5: Bacterial regu 46.0 55 0.0012 18.8 4.0 36 80-115 5-41 (47)
56 TIGR02479 FliA_WhiG RNA polyme 45.3 57 0.0012 25.0 5.1 44 77-120 178-222 (224)
57 cd06571 Bac_DnaA_C C-terminal 45.0 89 0.0019 20.6 6.3 45 88-139 43-88 (90)
58 PRK03001 M48 family peptidase; 44.1 9 0.0002 31.0 0.5 20 2-21 110-129 (283)
59 TIGR02511 type_III_tyeA type I 43.8 45 0.00099 21.9 3.8 56 84-139 16-72 (79)
60 PRK11512 DNA-binding transcrip 43.6 1.2E+02 0.0025 21.6 7.7 29 87-115 52-80 (144)
61 PRK12528 RNA polymerase sigma 43.5 68 0.0015 22.9 5.1 35 84-118 124-158 (161)
62 cd05579 STKc_MAST_like Catalyt 43.3 18 0.00039 27.2 2.0 43 81-123 69-112 (265)
63 PF13551 HTH_29: Winged helix- 42.7 67 0.0014 21.2 4.6 34 81-114 3-37 (112)
64 cd00131 PAX Paired Box domain 42.5 71 0.0015 22.8 4.9 33 83-115 27-59 (128)
65 PF04255 DUF433: Protein of un 42.2 40 0.00087 20.4 3.1 32 77-108 19-51 (56)
66 TIGR02989 Sig-70_gvs1 RNA poly 42.2 90 0.0019 22.0 5.5 45 75-119 112-157 (159)
67 PRK12541 RNA polymerase sigma 41.9 71 0.0015 22.8 5.0 38 84-121 123-160 (161)
68 PF00165 HTH_AraC: Bacterial r 41.6 38 0.00082 18.8 2.8 28 86-113 5-32 (42)
69 PRK03982 heat shock protein Ht 41.6 11 0.00024 30.6 0.6 20 2-21 111-130 (288)
70 PF14493 HTH_40: Helix-turn-he 41.4 1E+02 0.0022 20.3 6.3 58 83-140 7-64 (91)
71 PRK12543 RNA polymerase sigma 40.7 52 0.0011 24.1 4.1 33 86-118 130-162 (179)
72 COG1393 ArsC Arsenate reductas 40.6 50 0.0011 23.3 3.8 21 127-147 77-97 (117)
73 smart00418 HTH_ARSR helix_turn 40.4 72 0.0016 18.3 4.5 29 87-115 8-36 (66)
74 PRK06986 fliA flagellar biosyn 40.2 70 0.0015 24.7 5.0 37 84-120 195-231 (236)
75 PRK08301 sporulation sigma fac 39.6 56 0.0012 25.2 4.3 33 87-119 196-228 (234)
76 PF08406 CbbQ_C: CbbQ/NirQ/Nor 39.6 1.1E+02 0.0025 20.3 6.9 64 51-116 17-84 (86)
77 TIGR02948 SigW_bacill RNA poly 38.9 70 0.0015 23.3 4.6 35 86-120 149-183 (187)
78 PF07900 DUF1670: Protein of u 38.8 1.7E+02 0.0037 23.2 6.8 59 54-112 120-186 (220)
79 TIGR03879 near_KaiC_dom probab 38.7 50 0.0011 21.6 3.2 32 82-113 25-56 (73)
80 PRK12511 RNA polymerase sigma 38.6 77 0.0017 23.5 4.8 44 77-120 114-158 (182)
81 PRK12531 RNA polymerase sigma 38.4 86 0.0019 23.3 5.1 36 85-120 153-188 (194)
82 PRK12514 RNA polymerase sigma 38.1 1.1E+02 0.0024 22.2 5.6 45 75-119 130-175 (179)
83 PRK10870 transcriptional repre 37.5 1.7E+02 0.0037 21.8 6.9 52 59-115 43-97 (176)
84 PF13628 DUF4142: Domain of un 37.4 1.5E+02 0.0032 21.0 9.5 81 55-142 46-130 (139)
85 PRK08241 RNA polymerase factor 37.4 1.9E+02 0.0041 23.5 7.4 61 85-145 165-231 (339)
86 PF13822 ACC_epsilon: Acyl-CoA 37.1 29 0.00063 21.7 1.9 16 10-25 10-25 (62)
87 PRK09645 RNA polymerase sigma 36.8 98 0.0021 22.3 5.1 44 77-120 121-165 (173)
88 TIGR02983 SigE-fam_strep RNA p 36.8 90 0.002 22.2 4.8 38 84-121 121-158 (162)
89 PF09339 HTH_IclR: IclR helix- 36.7 45 0.00097 19.5 2.7 28 88-115 17-44 (52)
90 PRK05457 heat shock protein Ht 36.7 15 0.00033 29.9 0.7 20 2-21 120-139 (284)
91 smart00346 HTH_ICLR helix_turn 36.4 1.1E+02 0.0024 19.5 4.8 37 79-115 10-46 (91)
92 PRK13777 transcriptional regul 36.1 2E+02 0.0042 22.0 8.1 47 64-115 38-85 (185)
93 PRK12530 RNA polymerase sigma 35.9 70 0.0015 23.8 4.2 33 87-119 148-180 (189)
94 TIGR02950 SigM_subfam RNA poly 35.9 70 0.0015 22.4 4.1 35 86-120 118-152 (154)
95 TIGR02835 spore_sigmaE RNA pol 35.9 68 0.0015 24.8 4.3 32 88-119 197-228 (234)
96 cd06654 STKc_PAK1 Catalytic do 35.7 37 0.0008 26.7 2.8 44 79-122 91-134 (296)
97 PRK07408 RNA polymerase sigma 35.7 91 0.002 24.6 5.0 37 84-120 214-250 (256)
98 PRK11179 DNA-binding transcrip 35.7 56 0.0012 23.7 3.5 26 90-115 24-49 (153)
99 PF13977 TetR_C_6: Bacterial t 35.6 1.3E+02 0.0027 19.7 6.3 72 45-117 42-113 (115)
100 cd03572 ENTH_epsin_related ENT 35.6 65 0.0014 23.1 3.7 44 99-142 66-118 (122)
101 TIGR02952 Sig70_famx2 RNA poly 35.5 1.1E+02 0.0023 21.8 5.1 34 86-119 135-168 (170)
102 PRK15443 pduE propanediol dehy 35.3 75 0.0016 23.3 4.0 54 87-142 21-78 (138)
103 COG2442 Uncharacterized conser 35.0 91 0.002 20.6 4.1 37 77-113 31-68 (79)
104 PRK07037 extracytoplasmic-func 34.8 80 0.0017 22.5 4.3 36 86-121 122-157 (163)
105 PF04967 HTH_10: HTH DNA bindi 34.8 69 0.0015 19.5 3.3 33 84-116 18-50 (53)
106 PRK12519 RNA polymerase sigma 34.7 78 0.0017 23.4 4.3 33 87-119 155-187 (194)
107 TIGR01889 Staph_reg_Sar staphy 34.2 71 0.0015 21.7 3.7 27 89-115 43-69 (109)
108 PRK07122 RNA polymerase sigma 34.1 95 0.0021 24.7 4.9 36 84-119 226-261 (264)
109 PRK11924 RNA polymerase sigma 34.1 1.1E+02 0.0024 21.8 4.9 35 86-120 138-172 (179)
110 COG3079 Uncharacterized protei 33.9 22 0.00048 27.2 1.1 74 10-89 21-108 (186)
111 cd06656 STKc_PAK3 Catalytic do 33.8 42 0.00092 26.3 2.8 45 79-123 90-134 (297)
112 PRK02870 heat shock protein Ht 33.8 18 0.0004 30.3 0.7 21 1-21 158-178 (336)
113 PF07638 Sigma70_ECF: ECF sigm 33.7 1.5E+02 0.0033 22.0 5.7 44 75-118 136-180 (185)
114 smart00347 HTH_MARR helix_turn 33.5 70 0.0015 20.4 3.5 29 88-116 23-51 (101)
115 PF05584 Sulfolobus_pRN: Sulfo 33.5 1.2E+02 0.0025 19.9 4.3 34 82-115 10-44 (72)
116 PF01471 PG_binding_1: Putativ 33.4 98 0.0021 18.1 3.9 25 58-82 32-56 (57)
117 PRK12523 RNA polymerase sigma 33.3 1.2E+02 0.0027 21.9 5.1 35 85-119 131-165 (172)
118 TIGR02947 SigH_actino RNA poly 33.1 83 0.0018 23.3 4.2 36 84-119 142-177 (193)
119 PRK12542 RNA polymerase sigma 32.9 1.4E+02 0.003 21.9 5.4 48 75-122 123-171 (185)
120 PF14193 DUF4315: Domain of un 32.7 39 0.00084 22.6 2.0 14 10-23 47-60 (83)
121 TIGR02939 RpoE_Sigma70 RNA pol 32.6 87 0.0019 22.8 4.2 34 87-120 152-185 (190)
122 PRK12527 RNA polymerase sigma 32.5 1.3E+02 0.0028 21.3 5.1 44 77-120 108-152 (159)
123 PRK00423 tfb transcription ini 32.5 2.3E+02 0.005 23.2 7.1 67 52-118 235-305 (310)
124 PRK09652 RNA polymerase sigma 32.5 1.2E+02 0.0027 21.6 5.0 36 84-119 139-174 (182)
125 PRK01265 heat shock protein Ht 32.4 18 0.00038 30.3 0.4 21 1-21 125-145 (324)
126 PF13940 Ldr_toxin: Toxin Ldr, 32.3 15 0.00032 20.5 -0.0 19 7-25 10-28 (35)
127 PF03333 PapB: Adhesin biosynt 32.2 83 0.0018 21.4 3.7 45 77-121 40-85 (91)
128 COG3457 Predicted amino acid r 32.0 2.1E+02 0.0045 24.3 6.6 94 50-143 10-117 (353)
129 PRK06930 positive control sigm 32.0 1.6E+02 0.0036 21.9 5.7 46 74-119 114-160 (170)
130 PRK01345 heat shock protein Ht 31.9 18 0.00039 30.0 0.4 20 2-21 110-129 (317)
131 PRK12532 RNA polymerase sigma 31.8 1.2E+02 0.0025 22.5 4.8 36 85-120 148-183 (195)
132 PRK12538 RNA polymerase sigma 31.8 1E+02 0.0022 24.1 4.6 38 84-121 182-219 (233)
133 PRK09191 two-component respons 31.7 1.6E+02 0.0035 22.4 5.8 54 86-139 101-158 (261)
134 PRK12547 RNA polymerase sigma 31.5 1.3E+02 0.0028 21.6 5.0 35 86-120 125-159 (164)
135 PF08158 NUC130_3NT: NUC130/3N 31.4 1.2E+02 0.0027 18.3 4.9 42 100-143 7-48 (52)
136 PF01710 HTH_Tnp_IS630: Transp 31.3 72 0.0016 22.2 3.4 31 82-112 11-41 (119)
137 TIGR02980 SigBFG RNA polymeras 31.3 1.2E+02 0.0027 23.1 5.0 35 86-120 191-225 (227)
138 PRK05602 RNA polymerase sigma 31.2 1.3E+02 0.0027 22.1 4.9 35 86-120 141-175 (186)
139 smart00344 HTH_ASNC helix_turn 31.0 84 0.0018 21.0 3.6 30 89-118 17-48 (108)
140 PF11918 DUF3436: Domain of un 30.8 44 0.00096 20.7 1.9 16 6-21 33-48 (55)
141 PRK11169 leucine-responsive tr 30.7 71 0.0015 23.5 3.4 27 90-116 29-55 (164)
142 PRK09641 RNA polymerase sigma 30.6 1.3E+02 0.0028 21.8 4.9 37 84-120 147-183 (187)
143 PRK03072 heat shock protein Ht 30.4 20 0.00042 29.3 0.4 20 2-21 113-132 (288)
144 PF11994 DUF3489: Protein of u 30.3 1.1E+02 0.0024 19.9 3.9 34 78-111 13-50 (72)
145 TIGR02846 spore_sigmaK RNA pol 30.2 1.7E+02 0.0038 22.4 5.7 32 88-119 193-224 (227)
146 PF03847 TFIID_20kDa: Transcri 30.1 97 0.0021 19.8 3.5 28 111-138 3-30 (68)
147 PRK12539 RNA polymerase sigma 30.1 99 0.0021 22.7 4.2 35 86-120 144-178 (184)
148 PRK10573 type IV pilin biogene 30.0 1.2E+02 0.0026 25.5 5.1 72 63-136 274-363 (399)
149 PRK05803 sporulation sigma fac 29.7 1.3E+02 0.0028 23.2 4.9 34 87-120 193-226 (233)
150 PRK12537 RNA polymerase sigma 29.5 1.5E+02 0.0032 21.7 5.0 36 85-120 145-180 (182)
151 PRK12536 RNA polymerase sigma 29.4 1.1E+02 0.0023 22.5 4.2 35 85-119 141-175 (181)
152 PF04010 DUF357: Protein of un 29.3 48 0.001 21.6 2.0 34 108-141 2-35 (75)
153 PRK09640 RNA polymerase sigma 29.3 90 0.0019 23.0 3.8 36 84-119 145-180 (188)
154 PRK12529 RNA polymerase sigma 29.2 1.1E+02 0.0024 22.4 4.3 33 87-119 141-173 (178)
155 PF01435 Peptidase_M48: Peptid 29.2 10 0.00022 28.7 -1.4 21 2-22 75-95 (226)
156 PRK12512 RNA polymerase sigma 29.1 1.1E+02 0.0023 22.4 4.2 34 87-120 145-178 (184)
157 PRK07670 RNA polymerase sigma 29.1 1.4E+02 0.003 23.4 5.1 35 86-120 214-248 (251)
158 TIGR02957 SigX4 RNA polymerase 29.1 2.3E+02 0.005 22.6 6.4 40 83-122 118-157 (281)
159 PRK12518 RNA polymerase sigma 29.0 1E+02 0.0022 22.2 4.0 36 86-121 133-168 (175)
160 PRK09644 RNA polymerase sigma 28.8 1.6E+02 0.0035 21.0 5.0 48 74-121 108-156 (165)
161 TIGR02850 spore_sigG RNA polym 28.8 1.4E+02 0.003 23.5 5.0 36 84-119 217-252 (254)
162 PF00382 TFIIB: Transcription 28.8 1.5E+02 0.0032 18.4 4.9 55 52-106 13-71 (71)
163 PF01418 HTH_6: Helix-turn-hel 28.6 84 0.0018 20.1 3.1 28 86-113 31-58 (77)
164 PRK08215 sporulation sigma fac 28.4 1.4E+02 0.0031 23.4 5.1 37 84-120 220-256 (258)
165 PRK12520 RNA polymerase sigma 28.3 1.1E+02 0.0024 22.5 4.2 34 87-120 145-178 (191)
166 TIGR02531 yecD_yerC TrpR-relat 28.1 1.3E+02 0.0028 20.2 4.0 36 75-112 37-72 (88)
167 cd07841 STKc_CDK7 Catalytic do 28.0 46 0.00099 25.8 2.1 43 80-123 77-121 (298)
168 TIGR02120 GspF general secreti 28.0 2.2E+02 0.0047 23.9 6.3 87 51-138 61-166 (399)
169 PRK09638 RNA polymerase sigma 27.9 1.1E+02 0.0024 22.0 4.1 32 88-119 141-172 (176)
170 PRK06704 RNA polymerase factor 27.9 98 0.0021 24.3 3.9 34 87-120 130-163 (228)
171 PRK09649 RNA polymerase sigma 27.5 1.6E+02 0.0034 21.7 4.9 43 77-119 133-176 (185)
172 PRK12535 RNA polymerase sigma 27.5 1.1E+02 0.0024 23.0 4.1 36 85-120 145-180 (196)
173 PRK09415 RNA polymerase factor 27.0 1.3E+02 0.0027 22.1 4.3 33 87-119 141-173 (179)
174 smart00419 HTH_CRP helix_turn_ 26.9 1.2E+02 0.0026 16.6 3.4 26 90-115 9-34 (48)
175 PRK04897 heat shock protein Ht 26.9 24 0.00051 28.9 0.3 20 2-21 123-142 (298)
176 cd00092 HTH_CRP helix_turn_hel 26.7 1.3E+02 0.0028 17.8 3.7 27 89-115 25-51 (67)
177 PF11027 DUF2615: Protein of u 26.7 46 0.001 23.3 1.7 18 108-125 16-33 (103)
178 PRK12545 RNA polymerase sigma 26.6 1.2E+02 0.0026 22.7 4.2 35 86-120 152-186 (201)
179 PF02885 Glycos_trans_3N: Glyc 26.6 59 0.0013 20.2 2.1 17 10-26 31-47 (66)
180 smart00345 HTH_GNTR helix_turn 26.5 1.2E+02 0.0027 17.3 3.4 25 91-115 22-46 (60)
181 PRK06288 RNA polymerase sigma 26.4 1.7E+02 0.0036 23.2 5.1 34 86-119 225-258 (268)
182 PF11269 DUF3069: Protein of u 26.4 46 0.001 23.9 1.6 25 113-138 96-120 (121)
183 TIGR02954 Sig70_famx3 RNA poly 26.2 1.3E+02 0.0027 21.6 4.1 42 78-119 123-165 (169)
184 PRK12526 RNA polymerase sigma 26.1 1.3E+02 0.0028 22.7 4.2 43 79-121 158-201 (206)
185 PRK04966 hypothetical protein; 26.1 1.1E+02 0.0023 20.0 3.2 22 8-29 5-26 (72)
186 cd06614 STKc_PAK Catalytic dom 26.0 52 0.0011 25.4 2.1 45 78-122 88-134 (286)
187 TIGR02943 Sig70_famx1 RNA poly 25.9 1.3E+02 0.0029 22.3 4.2 35 86-120 144-178 (188)
188 TIGR02859 spore_sigH RNA polym 25.9 1.3E+02 0.0029 22.0 4.2 36 84-120 161-196 (198)
189 cd00569 HTH_Hin_like Helix-tur 25.8 92 0.002 15.0 3.1 28 82-109 14-41 (42)
190 cd05578 STKc_Yank1 Catalytic d 25.6 49 0.0011 25.0 1.9 44 80-123 75-119 (258)
191 PRK11922 RNA polymerase sigma 25.6 1.3E+02 0.0028 23.1 4.3 35 87-121 163-197 (231)
192 PF01724 DUF29: Domain of unkn 25.5 64 0.0014 23.4 2.4 19 101-119 1-19 (139)
193 cd05122 PKc_STE Catalytic doma 25.4 56 0.0012 24.0 2.1 46 78-123 70-117 (253)
194 PRK09636 RNA polymerase sigma 25.2 3E+02 0.0065 22.0 6.4 55 84-138 126-184 (293)
195 TIGR02394 rpoS_proteo RNA poly 25.1 1.2E+02 0.0027 24.2 4.2 35 87-121 240-274 (285)
196 PRK09413 IS2 repressor TnpA; R 25.1 1.7E+02 0.0036 20.4 4.4 33 82-114 22-54 (121)
197 cd08217 STKc_Nek2 Catalytic do 25.0 78 0.0017 23.6 2.9 42 80-121 76-122 (265)
198 smart00073 HPT Histidine Phosp 24.9 1.8E+02 0.004 18.1 4.7 42 101-142 44-86 (87)
199 cd06630 STKc_MEKK1 Catalytic d 24.9 50 0.0011 25.0 1.8 47 77-123 75-122 (268)
200 PF12840 HTH_20: Helix-turn-he 24.9 1E+02 0.0022 18.5 2.9 29 87-115 22-50 (61)
201 PRK05572 sporulation sigma fac 24.8 1.8E+02 0.0039 22.7 5.0 37 84-120 213-249 (252)
202 PRK12540 RNA polymerase sigma 24.8 1.8E+02 0.0039 21.5 4.8 37 86-122 124-160 (182)
203 PRK00304 hypothetical protein; 24.3 1.7E+02 0.0038 19.2 4.0 22 8-29 5-26 (75)
204 PRK02391 heat shock protein Ht 24.3 28 0.0006 28.6 0.2 20 2-21 119-138 (296)
205 PRK09647 RNA polymerase sigma 24.3 1.4E+02 0.0031 22.6 4.2 35 87-121 152-186 (203)
206 cd04762 HTH_MerR-trunc Helix-T 24.1 1E+02 0.0022 16.7 2.6 22 91-112 2-23 (49)
207 PRK12533 RNA polymerase sigma 24.1 1.8E+02 0.004 22.3 4.8 35 86-120 147-181 (216)
208 PF07374 DUF1492: Protein of u 24.1 2.1E+02 0.0045 19.3 4.6 33 83-115 65-97 (100)
209 PRK12427 flagellar biosynthesi 24.0 1.9E+02 0.0041 22.5 5.0 36 84-119 194-229 (231)
210 smart00221 STYKc Protein kinas 23.9 67 0.0014 23.2 2.2 46 78-123 70-117 (225)
211 PRK11923 algU RNA polymerase s 23.8 1.5E+02 0.0032 21.8 4.2 33 87-119 152-184 (193)
212 PRK09637 RNA polymerase sigma 23.8 2.1E+02 0.0046 21.0 5.0 44 77-120 109-153 (181)
213 PRK06811 RNA polymerase factor 23.7 2.1E+02 0.0046 21.0 5.0 46 74-119 131-177 (189)
214 PF01978 TrmB: Sugar-specific 23.6 68 0.0015 19.7 1.9 27 89-115 22-48 (68)
215 PRK15411 rcsA colanic acid cap 23.5 2.6E+02 0.0057 21.1 5.6 45 74-118 137-181 (207)
216 KOG2163 Centromere/kinetochore 23.1 39 0.00085 30.9 0.9 34 75-110 670-704 (719)
217 cd08777 Death_RIP1 Death Domai 23.0 1.1E+02 0.0024 20.3 2.9 9 79-87 46-54 (86)
218 PF11242 DUF2774: Protein of u 22.9 1.9E+02 0.0041 18.4 3.7 29 87-115 11-39 (63)
219 cd06647 STKc_PAK_I Catalytic d 22.9 59 0.0013 25.4 1.9 46 77-122 88-133 (293)
220 PF12029 DUF3516: Domain of un 22.9 1.9E+02 0.0042 25.4 5.0 47 87-134 250-299 (461)
221 cd06641 STKc_MST3 Catalytic do 22.7 57 0.0012 25.1 1.7 44 80-123 77-120 (277)
222 PRK09643 RNA polymerase sigma 22.7 2.1E+02 0.0046 21.2 4.8 36 85-120 146-181 (192)
223 KOG0180 20S proteasome, regula 22.6 55 0.0012 25.2 1.5 20 10-29 81-100 (204)
224 cd06640 STKc_MST4 Catalytic do 22.5 59 0.0013 25.0 1.8 45 77-121 74-118 (277)
225 PRK12544 RNA polymerase sigma 22.5 2.3E+02 0.0049 21.5 5.1 36 84-119 159-194 (206)
226 cd08215 STKc_Nek Catalytic dom 22.5 57 0.0012 24.2 1.7 46 78-123 72-122 (258)
227 cd05611 STKc_Rim15_like Cataly 22.5 64 0.0014 24.4 2.0 45 79-123 71-116 (260)
228 TIGR02292 ygfB_yecA yecA famil 22.5 3E+02 0.0064 19.7 6.8 20 10-29 17-36 (150)
229 TIGR02959 SigZ RNA polymerase 22.4 1.8E+02 0.0039 21.1 4.3 35 86-120 113-147 (170)
230 PRK09480 slmA division inhibit 22.3 78 0.0017 23.0 2.3 28 89-116 30-57 (194)
231 COG1698 Uncharacterized protei 22.3 1.5E+02 0.0033 20.3 3.4 35 109-143 14-48 (93)
232 PRK15215 fimbriae biosynthesis 22.2 1.9E+02 0.0041 20.1 4.0 47 78-124 49-96 (100)
233 PF13542 HTH_Tnp_ISL3: Helix-t 22.1 1.7E+02 0.0036 16.7 4.4 31 83-113 20-51 (52)
234 COG1510 Predicted transcriptio 22.0 3.5E+02 0.0075 20.8 5.7 57 56-115 11-67 (177)
235 PF01152 Bac_globin: Bacterial 21.9 1.2E+02 0.0027 20.6 3.2 52 92-147 68-119 (120)
236 cd05145 RIO1_like RIO kinase f 21.9 1.1E+02 0.0024 22.6 3.1 57 66-122 78-135 (190)
237 TIGR02960 SigX5 RNA polymerase 21.8 4.2E+02 0.0091 21.2 7.3 38 85-122 154-191 (324)
238 PF06824 DUF1237: Protein of u 21.4 58 0.0013 28.4 1.6 38 106-145 235-272 (424)
239 PRK12524 RNA polymerase sigma 21.3 2.5E+02 0.0055 20.7 5.0 35 86-120 149-183 (196)
240 cd05155 APH_ChoK_like_1 Unchar 21.1 61 0.0013 24.8 1.6 60 58-123 40-106 (235)
241 PRK09651 RNA polymerase sigma 21.0 2E+02 0.0042 20.9 4.3 34 86-119 132-165 (172)
242 PF10975 DUF2802: Protein of u 21.0 2.4E+02 0.0052 18.0 7.2 28 77-104 32-59 (70)
243 PRK12517 RNA polymerase sigma 20.9 1.8E+02 0.0039 21.5 4.2 34 87-120 142-175 (188)
244 PF06794 UPF0270: Uncharacteri 20.9 93 0.002 20.2 2.2 22 8-29 5-26 (70)
245 KOG1379 Serine/threonine prote 20.8 2.6E+02 0.0056 23.6 5.2 46 4-71 253-298 (330)
246 PRK01736 hypothetical protein; 20.7 1.7E+02 0.0038 22.3 4.0 19 9-27 21-39 (190)
247 COG1595 RpoE DNA-directed RNA 20.7 2.4E+02 0.0053 20.5 4.8 39 82-120 136-174 (182)
248 PF09059 TyeA: TyeA; InterPro 20.7 1.9E+02 0.0041 19.5 3.7 55 84-138 18-73 (87)
249 PRK12534 RNA polymerase sigma 20.7 2.7E+02 0.0059 20.2 5.0 35 86-120 150-184 (187)
250 PRK02166 hypothetical protein; 20.7 1.1E+02 0.0024 23.5 2.9 78 10-89 21-108 (184)
251 cd05154 ACAD10_11_like Acyl-Co 20.6 20 0.00044 26.4 -1.2 45 80-124 75-119 (223)
252 cd06606 STKc_MAPKKK Catalytic 20.6 62 0.0013 23.9 1.5 46 78-123 74-120 (260)
253 COG1522 Lrp Transcriptional re 20.5 1.5E+02 0.0033 20.9 3.5 26 90-115 23-48 (154)
254 COG3066 MutH DNA mismatch repa 20.3 3.3E+02 0.0071 21.2 5.3 50 42-91 10-62 (229)
255 PF03195 DUF260: Protein of un 20.3 1E+02 0.0022 21.3 2.4 55 6-64 44-98 (101)
256 PRK14067 exodeoxyribonuclease 20.2 1.5E+02 0.0033 19.6 3.1 18 107-124 10-27 (80)
257 PRK03902 manganese transport t 20.1 3.3E+02 0.0071 19.2 5.2 27 90-116 23-49 (142)
258 TIGR00014 arsC arsenate reduct 20.0 2.1E+02 0.0044 19.7 4.0 20 128-147 77-96 (114)
No 1
>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=1.7e-44 Score=275.68 Aligned_cols=142 Identities=29% Similarity=0.449 Sum_probs=113.3
Q ss_pred ccccCCCCCCCHHHHHHHHHHhhccccccccccCCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHcCC----CCCCCCCc
Q 043012 2 VLRNKILLDLKPAQLAAVCASLVSEGIKVRLWKNNSYIYEPSTTVINVINVLDEHRSSFLELQEKHGV----EIPCCLDS 77 (151)
Q Consensus 2 ~L~~g~f~~L~p~elAAllS~~v~e~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~l~~~~~~~~l----~~~~~~~~ 77 (151)
|||+|+|++|+|+||||++||||||+++++. . ..+.|+..+.++++++.+++++|.++|.+||+ ..+ .++|
T Consensus 28 ~l~~g~f~~L~p~elAa~lS~~v~e~~~~~~--~--~~~~~~~~l~~~~~~l~~~~~~l~~~~~~~~l~~~~~~~-~~~~ 102 (180)
T PF08148_consen 28 LLFSGVFDDLDPAELAALLSCFVYEPRREDE--E--ERYPPSPRLREALEQLQEIAERLAKVEREHGLDEEEYVE-RFDP 102 (180)
T ss_dssp HHHCTCCCCS-HHHHHHHHHHHC-----SS-------------HHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHH-CSTT
T ss_pred HHHcCCCCCCCHHHHHHHHHHhhcccccCcc--c--ccccccHHHHHHHHHHHHHHHHHHHHHHHhCCCCccccc-CCCc
Confidence 7999999999999999999999999997532 1 11223348999999999999999999999999 333 3499
Q ss_pred hHHHHHHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhcCCCCC--CCHHHHHHHHHHHhhcCCCcccc
Q 043012 78 QFSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIPKLPD--VDQRLQKNAVDASNVMDRPPISE 148 (151)
Q Consensus 78 ~l~~~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl~~a~~--~~~~L~~k~~~a~~~i~R~iV~~ 148 (151)
++|++||+||+|+||.+||+.|+++||||||++||++|+||||+++++ +||+|++|+++|+++|||||||+
T Consensus 103 ~l~~~v~~Wa~G~~~~~i~~~t~l~EGdiVR~~rRl~dlLrql~~aa~~~g~~~L~~~~~~a~~~i~R~iV~~ 175 (180)
T PF08148_consen 103 GLMEVVYAWASGASFAEILEMTDLFEGDIVRWIRRLIDLLRQLANAAKIIGDPELAEKAREAIDLIRRDIVFA 175 (180)
T ss_dssp TTHHHHHHHHCT--HHHHCCT-SS-HHHHHHHHHHHHHHHHHHHHHHHCCT-HHHHHHHHHHHHHHSHCCCC-
T ss_pred cHHHHHHHHHCCCCHHHHHhcCCCCchHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhccCCcccc
Confidence 999999999999999999999999999999999999999999999944 59999999999999999999996
No 2
>KOG0948 consensus Nuclear exosomal RNA helicase MTR4, DEAD-box superfamily [RNA processing and modification]
Probab=100.00 E-value=3.1e-39 Score=283.00 Aligned_cols=141 Identities=21% Similarity=0.268 Sum_probs=132.4
Q ss_pred ccccCCCCCCCHHHHHHHHHHhhccccccccccCCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHcCCCCC-----CCCC
Q 043012 2 VLRNKILLDLKPAQLAAVCASLVSEGIKVRLWKNNSYIYEPSTTVINVINVLDEHRSSFLELQEKHGVEIP-----CCLD 76 (151)
Q Consensus 2 ~L~~g~f~~L~p~elAAllS~~v~e~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~l~~~~~~~~l~~~-----~~~~ 76 (151)
.+|+|.|++|+|+|+||+||||||+++..+. ..+.+.|...+..+++.+++|++++.+|++++. .+|+
T Consensus 890 liFnG~Fndl~~eq~aaLLSCfVf~eks~e~-------~~l~~el~~~l~~lqe~ArrIAkVs~ecKlEide~~Yv~sFk 962 (1041)
T KOG0948|consen 890 LIFNGIFNDLPVEQAAALLSCFVFQEKSSEA-------PKLKEELAGPLRQLQESARRIAKVSKECKLEIDEEDYVESFK 962 (1041)
T ss_pred HHHhccccCCCHHHHHHHHhheeehhccccc-------ccchHHHHHHHHHHHHHHHHHHHHHHhhccccCHHHHHHhcC
Confidence 4799999999999999999999999997531 346789999999999999999999999999986 5799
Q ss_pred chHHHHHHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhcCCCCC--CCHHHHHHHHHHHhhcCCCccccc
Q 043012 77 SQFSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIPKLPD--VDQRLQKNAVDASNVMDRPPISEL 149 (151)
Q Consensus 77 ~~l~~~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl~~a~~--~~~~L~~k~~~a~~~i~R~iV~~~ 149 (151)
|.+|++||+|++|+||.+||++|+++||+|||++|||+|||||+.+||+ +|.+|.+|++.++.+|+||||||.
T Consensus 963 p~LMdvVy~W~~GatF~eIckmTdvfEGSiIR~~RRLeElLrQl~~AAk~iGnteLe~Kf~~~~~~ikRDIVFAa 1037 (1041)
T KOG0948|consen 963 PELMDVVYAWAKGATFAEICKMTDVFEGSIIRTFRRLEELLRQLIDAAKVIGNTELENKFEEAIKKIKRDIVFAA 1037 (1041)
T ss_pred hHHHHHHHHHHccccHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHhhceeehh
Confidence 9999999999999999999999999999999999999999999999997 399999999999999999999984
No 3
>KOG0947 consensus Cytoplasmic exosomal RNA helicase SKI2, DEAD-box superfamily [RNA processing and modification]
Probab=100.00 E-value=5.9e-35 Score=260.70 Aligned_cols=143 Identities=22% Similarity=0.327 Sum_probs=132.9
Q ss_pred CccccCCCCCCCHHHHHHHHHHhhccccccccccCCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHcCCCCC------CC
Q 043012 1 MVLRNKILLDLKPAQLAAVCASLVSEGIKVRLWKNNSYIYEPSTTVINVINVLDEHRSSFLELQEKHGVEIP------CC 74 (151)
Q Consensus 1 ~~L~~g~f~~L~p~elAAllS~~v~e~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~l~~~~~~~~l~~~------~~ 74 (151)
++||++.|.+|+|+|+||+||+||||+++. .++..++.+.++-+.+.+++.++.+++..|++.++ ..
T Consensus 1095 eli~dn~l~~l~peeiaallSslV~e~~~e-------~~~~~~~~l~k~~e~v~~v~~rl~ev~~~~~~~~~~~e~f~~~ 1167 (1248)
T KOG0947|consen 1095 ELIFDNALVDLSPEEIAALLSSLVCEGKTE-------RPPTLTPYLKKGKERVRDVAKRLEEVQSSHQLLQTPEEEFPCE 1167 (1248)
T ss_pred HHHHhhhhhhcCHHHHHHHHHHHHhcCccc-------cCCCCChhhhhHHHHHHHHHHHHHHHHHhhccccCchhhcccc
Confidence 379999999999999999999999999863 23456889999999999999999999999998764 56
Q ss_pred CCchHHHHHHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhcCCCCCC--CHHHHHHHHHHHhhcCCCcccccC
Q 043012 75 LDSQFSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIPKLPDV--DQRLQKNAVDASNVMDRPPISELA 150 (151)
Q Consensus 75 ~~~~l~~~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl~~a~~~--~~~L~~k~~~a~~~i~R~iV~~~~ 150 (151)
++|+||++||+||+|.||.+||++|++.||+|||+|+||+|+|||+++|+.+ ||.|.+||++|.++|||||||++.
T Consensus 1168 lrF~l~evVYeWA~G~sf~eim~~t~~~EG~iVR~I~RLdE~cre~~~aa~ivGd~~L~~Km~~as~~ikRdIVFaaS 1245 (1248)
T KOG0947|consen 1168 LRFGLVEVVYEWARGLSFKEIMELTDVLEGLIVRLIQRLDEVCRELRNAARIVGDPVLHEKMEAASALIKRDIVFAAS 1245 (1248)
T ss_pred ccccHHHHHHHHHcCCCHHHHHhhhCCcchhHHHHHHHHHHHHHhhhccceecCcHHHHHHHHHHHHHhccCccchhh
Confidence 8999999999999999999999999999999999999999999999999874 999999999999999999999874
No 4
>COG4581 Superfamily II RNA helicase [DNA replication, recombination, and repair]
Probab=99.95 E-value=1.5e-27 Score=217.27 Aligned_cols=144 Identities=23% Similarity=0.257 Sum_probs=131.1
Q ss_pred ccccCCCCCCCHHHHHHHHHHhhccccccccccCCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHcCCCCCC---CCCch
Q 043012 2 VLRNKILLDLKPAQLAAVCASLVSEGIKVRLWKNNSYIYEPSTTVINVINVLDEHRSSFLELQEKHGVEIPC---CLDSQ 78 (151)
Q Consensus 2 ~L~~g~f~~L~p~elAAllS~~v~e~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~l~~~~~~~~l~~~~---~~~~~ 78 (151)
|+++|.|++|+|+++||++||||||+++++.. ...+.+++.++++...+.+++.+|.+++..|+++++. .+.++
T Consensus 888 ~i~~g~f~~l~p~e~aallSa~v~e~~~~d~~---~~~~~~~~~l~~~~~~l~e~~~kl~~~~~~~~i~~~~~l~~~~~~ 964 (1041)
T COG4581 888 LIFSGEFNDLEPEELAALLSAFVFEEKTDDGT---AEAPEITPALRDALLRLLELARKLNKDQNSSQIEIYPELNDFSVG 964 (1041)
T ss_pred HHHcCCccCCCHHHHHHHHHheeeccCCcccc---cccccCCHHHHhHHHHHHHHHHHHHHHHHhcCCcCCccccccccc
Confidence 68999999999999999999999999875320 1234568999999999999999999999999999864 46689
Q ss_pred HHHHHHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhcCCCCCC--CHHHHHHHHHHHhhcCCCcccc
Q 043012 79 FSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIPKLPDV--DQRLQKNAVDASNVMDRPPISE 148 (151)
Q Consensus 79 l~~~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl~~a~~~--~~~L~~k~~~a~~~i~R~iV~~ 148 (151)
+|++||.||+|.+|.+|+.+|++.|||+||+++|+.|+|+|+.+++.. |++|.+|++.++..|||||||.
T Consensus 965 lm~vv~~wa~g~s~~~i~~~~~~~eGs~vR~~~r~~ell~ql~~aa~~ig~~~L~~k~~~~~~~irr~iv~~ 1036 (1041)
T COG4581 965 LMEVVYEWARGLSFADICGLTSLLEGSFVRIFRRLRELLRQLRKAASVIGNPELEEKAYRAIQEIRRDIVFV 1036 (1041)
T ss_pred HHHHHHHHHhhcchhhhhcCCcccccchhhhhhHHHHHHHHhhhcccccCCHHHHHHHHHHHHhhhcCeEec
Confidence 999999999999999999999999999999999999999999999874 8999999999999999999985
No 5
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=90.25 E-value=1.6 Score=25.36 Aligned_cols=44 Identities=18% Similarity=0.245 Sum_probs=35.8
Q ss_pred CCchHHHHHHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHh
Q 043012 75 LDSQFSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLA 118 (151)
Q Consensus 75 ~~~~l~~~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLr 118 (151)
+++.-..++..+..|.|..+|.+..+++.+.+=+.++|+..-|+
T Consensus 4 l~~~e~~i~~~~~~g~s~~eia~~l~is~~tv~~~~~~~~~kl~ 47 (58)
T smart00421 4 LTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLG 47 (58)
T ss_pred CCHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence 34444556777899999999999999999999999998855543
No 6
>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=88.85 E-value=1.6 Score=25.70 Aligned_cols=37 Identities=22% Similarity=0.377 Sum_probs=32.4
Q ss_pred HHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhh
Q 043012 83 VEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQ 119 (151)
Q Consensus 83 v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQ 119 (151)
...|-.|.|+.||-+..++++|.+=+..+|..+-||+
T Consensus 14 ~~~y~~~~t~~eIa~~lg~s~~~V~~~~~~al~kLR~ 50 (50)
T PF04545_consen 14 RLRYFEGLTLEEIAERLGISRSTVRRILKRALKKLRK 50 (50)
T ss_dssp HHHHTST-SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred HHHhcCCCCHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence 3677899999999999999999999999999888874
No 7
>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=88.02 E-value=0.83 Score=29.86 Aligned_cols=30 Identities=17% Similarity=0.479 Sum_probs=27.8
Q ss_pred HHhhCCCCHHHHHhhcCCChhHHHHHHHHH
Q 043012 84 EAWASGLTWREMMMDCALDDGDLARLLRRT 113 (151)
Q Consensus 84 ~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl 113 (151)
-+|.+-.||..|-...++.|++++..+|+-
T Consensus 8 MAweDRtpFeaI~~~fGL~E~eVi~lMR~~ 37 (72)
T TIGR03643 8 MAWEDRTPFEAIEQQFGLSEKEVIKLMRQN 37 (72)
T ss_pred HHHccCCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 689999999999999999999999998863
No 8
>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=87.82 E-value=0.85 Score=29.90 Aligned_cols=30 Identities=17% Similarity=0.478 Sum_probs=27.8
Q ss_pred HHhhCCCCHHHHHhhcCCChhHHHHHHHHH
Q 043012 84 EAWASGLTWREMMMDCALDDGDLARLLRRT 113 (151)
Q Consensus 84 ~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl 113 (151)
-+|.+-.||..|-...++.|.+++..+|+-
T Consensus 7 MAweDRtpFeaI~~qfGl~E~eVi~lMR~~ 36 (73)
T PF10985_consen 7 MAWEDRTPFEAIERQFGLSEKEVIKLMRKE 36 (73)
T ss_pred HHHccCCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 689999999999999999999999998863
No 9
>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=86.53 E-value=3.4 Score=24.09 Aligned_cols=35 Identities=17% Similarity=0.213 Sum_probs=30.2
Q ss_pred HHHHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHH
Q 043012 81 GMVEAWASGLTWREMMMDCALDDGDLARLLRRTID 115 (151)
Q Consensus 81 ~~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~e 115 (151)
.+++.+..|.|..+|.+..+++++.+-+.++|+..
T Consensus 7 ~i~~~~~~~~s~~eia~~l~~s~~tv~~~~~~~~~ 41 (57)
T cd06170 7 EVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMR 41 (57)
T ss_pred HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 45666889999999999999999999999888744
No 10
>PRK04217 hypothetical protein; Provisional
Probab=86.47 E-value=3.2 Score=29.34 Aligned_cols=50 Identities=18% Similarity=0.101 Sum_probs=42.2
Q ss_pred CCCCchHHHHHHHhh-CCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhcCC
Q 043012 73 CCLDSQFSGMVEAWA-SGLTWREMMMDCALDDGDLARLLRRTIDLLAQIPK 122 (151)
Q Consensus 73 ~~~~~~l~~~v~~Wa-~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl~~ 122 (151)
..++..--+++..+. .|.|+.+|.+..+++.+++-+.++|....|++.-.
T Consensus 41 ~~Lt~eereai~l~~~eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre~L~ 91 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEGLTQEEAGKRMGVSRGTVWRALTSARKKVAQMLV 91 (110)
T ss_pred ccCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 345555567788886 99999999999999999999999999999988543
No 11
>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=82.70 E-value=5.1 Score=22.58 Aligned_cols=31 Identities=19% Similarity=0.377 Sum_probs=27.8
Q ss_pred hCCCCHHHHHhhcCCChhHHHHHHHHHHHHH
Q 043012 87 ASGLTWREMMMDCALDDGDLARLLRRTIDLL 117 (151)
Q Consensus 87 a~G~~f~eil~~t~l~EGdiVR~~rRl~elL 117 (151)
..|.+..+|.+..++.++.+-+++.|...-|
T Consensus 24 ~~~~~~~~ia~~~~~s~~~i~~~~~~~~~~l 54 (55)
T cd06171 24 GEGLSYEEIAEILGISRSTVRQRLHRALKKL 54 (55)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHc
Confidence 4999999999999999999999999876654
No 12
>PF13518 HTH_28: Helix-turn-helix domain
Probab=82.68 E-value=4.8 Score=23.39 Aligned_cols=35 Identities=20% Similarity=0.378 Sum_probs=31.1
Q ss_pred HHHHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHH
Q 043012 81 GMVEAWASGLTWREMMMDCALDDGDLARLLRRTID 115 (151)
Q Consensus 81 ~~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~e 115 (151)
.+|..+.+|.|..++....+++...+-+|+++-.+
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 46677779999999999999999999999998765
No 13
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=78.96 E-value=2.1 Score=25.01 Aligned_cols=34 Identities=15% Similarity=0.272 Sum_probs=24.2
Q ss_pred HHHHHhhCCCCHHHHHhhcCCChhHHHHHHHHHH
Q 043012 81 GMVEAWASGLTWREMMMDCALDDGDLARLLRRTI 114 (151)
Q Consensus 81 ~~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~ 114 (151)
.++..+..|.|-.+|.+..+++..++-||++|-.
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 3566677799999999999999999999998853
No 14
>PRK00118 putative DNA-binding protein; Validated
Probab=75.98 E-value=11 Score=26.31 Aligned_cols=50 Identities=12% Similarity=0.161 Sum_probs=40.2
Q ss_pred CchHHHHHHHh-hCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhcCCCCC
Q 043012 76 DSQFSGMVEAW-ASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIPKLPD 125 (151)
Q Consensus 76 ~~~l~~~v~~W-a~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl~~a~~ 125 (151)
++.--.++..+ ..|.|..+|.+..+++++.+=+.+.|.-..|++.-..-+
T Consensus 19 ~ekqRevl~L~y~eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~~~ 69 (104)
T PRK00118 19 TEKQRNYMELYYLDDYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKLH 69 (104)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHC
Confidence 34444555443 679999999999999999999999999999999755543
No 15
>TIGR02172 Fb_sc_TIGR02172 Fibrobacter succinogenes paralogous family TIGR02172. This model describes a paralogous family of five proteins, likely to be enzymes, in the rumen bacterium Fibrobacter succinogenes S85. Members show homology to proteins described by PFAM model pfam01636, a phosphotransferase enzyme family associated with resistance to aminoglycoside antibiotics. However, members of this family score below the current trusted and noise cutoffs for pfam01636.
Probab=73.31 E-value=11 Score=29.42 Aligned_cols=55 Identities=11% Similarity=0.224 Sum_probs=37.5
Q ss_pred HcCCCCCCCC----CchHHHHHHHhhCCCC-HHHHHhhcCCChhHHHHHHHHHHHHHhhcCCC
Q 043012 66 KHGVEIPCCL----DSQFSGMVEAWASGLT-WREMMMDCALDDGDLARLLRRTIDLLAQIPKL 123 (151)
Q Consensus 66 ~~~l~~~~~~----~~~l~~~v~~Wa~G~~-f~eil~~t~l~EGdiVR~~rRl~elLrQl~~a 123 (151)
..|++.|..+ +.+..+.+++|..|.+ ..+++. ....+.-+...++.+++++|...
T Consensus 51 ~~glpvP~~~~~~~~~~~~glv~e~i~G~~~~~~~~~---~~~~~~~~l~~~la~~l~~lH~~ 110 (226)
T TIGR02172 51 SLGIPTPHPFDLVEDGGRLGLIYELIVGKRSFSRIIS---DNPSRLEEIAKIFAEMAKKLHST 110 (226)
T ss_pred HcCCCCCceEEEEecCCeeeeeeeecCCccchhhhhc---CCHHHHHHHHHHHHHHHHHHhCC
Confidence 7888877544 3333466899999984 555543 34466667778888888887765
No 16
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=71.61 E-value=9.7 Score=22.00 Aligned_cols=31 Identities=19% Similarity=0.324 Sum_probs=22.7
Q ss_pred HHHHhhCCCCHHHHHhhcCCChhHHHHHHHH
Q 043012 82 MVEAWASGLTWREMMMDCALDDGDLARLLRR 112 (151)
Q Consensus 82 ~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rR 112 (151)
+..-|..|.|..+|-+.-+.+..+|-|.++|
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 3445789999999999999999999999987
No 17
>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=69.83 E-value=15 Score=22.13 Aligned_cols=45 Identities=16% Similarity=0.259 Sum_probs=36.5
Q ss_pred CCCchHHHHHHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHh
Q 043012 74 CLDSQFSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLA 118 (151)
Q Consensus 74 ~~~~~l~~~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLr 118 (151)
.+.+.=..++..|+.|.+-.+|.+.-++.+.++-...+++-.-|+
T Consensus 3 ~LT~~E~~vl~~l~~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGMSNKEIAEELGISEKTVKSHRRRIMKKLG 47 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-HHHHHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred ccCHHHHHHHHHHHhcCCcchhHHhcCcchhhHHHHHHHHHHHhC
Confidence 355666788999999999999999999999999988888766543
No 18
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=69.39 E-value=20 Score=21.42 Aligned_cols=44 Identities=18% Similarity=0.287 Sum_probs=39.3
Q ss_pred chHHHHHHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhc
Q 043012 77 SQFSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120 (151)
Q Consensus 77 ~~l~~~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl 120 (151)
-.+.-+...|-.|-++.++-..-++.+..+-|.++...++|.+.
T Consensus 7 d~lll~L~~LR~~~~~~~La~~FgIs~stvsri~~~~~~~L~~~ 50 (53)
T PF13613_consen 7 DQLLLTLMYLRLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQV 50 (53)
T ss_pred HHHHHHHHHHHcCCcHhHHhhheeecHHHHHHHHHHHHHHHHHh
Confidence 35666778899999999999999999999999999999999874
No 19
>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=67.38 E-value=13 Score=21.88 Aligned_cols=33 Identities=18% Similarity=0.324 Sum_probs=23.9
Q ss_pred HHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHH
Q 043012 84 EAWASGLTWREMMMDCALDDGDLARLLRRTIDL 116 (151)
Q Consensus 84 ~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~el 116 (151)
..--.|.|+.||.+..+++++.+=+.+.|--.-
T Consensus 21 l~~~~g~s~~eIa~~l~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 21 LRYFQGMSYAEIAEILGISESTVKRRLRRARKK 53 (54)
T ss_dssp HHHTS---HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred HHHHHCcCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence 335699999999999999999999888886543
No 20
>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=66.72 E-value=21 Score=20.59 Aligned_cols=33 Identities=21% Similarity=0.373 Sum_probs=25.8
Q ss_pred hHHHHHHHhhCCCCHHHHHhhcCCChhHHHHHH
Q 043012 78 QFSGMVEAWASGLTWREMMMDCALDDGDLARLL 110 (151)
Q Consensus 78 ~l~~~v~~Wa~G~~f~eil~~t~l~EGdiVR~~ 110 (151)
..-.++....+|.|-.+|.+.++++-.+|=|.+
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 466777888999999999999999999888865
No 21
>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=64.05 E-value=0.48 Score=31.59 Aligned_cols=25 Identities=20% Similarity=0.493 Sum_probs=13.3
Q ss_pred HHHHHhhCCCCHHHHHhhcCCChhH
Q 043012 81 GMVEAWASGLTWREMMMDCALDDGD 105 (151)
Q Consensus 81 ~~v~~Wa~G~~f~eil~~t~l~EGd 105 (151)
..||+|.+|+.|.+++....+.+|.
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 4589999999999999998888885
No 22
>smart00351 PAX Paired Box domain.
Probab=63.25 E-value=21 Score=25.37 Aligned_cols=35 Identities=17% Similarity=0.284 Sum_probs=30.4
Q ss_pred HHHHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHH
Q 043012 81 GMVEAWASGLTWREMMMDCALDDGDLARLLRRTID 115 (151)
Q Consensus 81 ~~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~e 115 (151)
.+|.....|.|..+|.+..++....+.||++|-.+
T Consensus 25 riv~~~~~G~s~~~iA~~~gvs~~tV~kwi~r~~~ 59 (125)
T smart00351 25 RIVELAQNGVRPCDISRQLCVSHGCVSKILGRYYE 59 (125)
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 34555679999999999999999999999999765
No 23
>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=60.30 E-value=52 Score=22.51 Aligned_cols=55 Identities=13% Similarity=0.201 Sum_probs=38.0
Q ss_pred HHHHHHHHHcCCCCCCCCCchHHHHHHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHH
Q 043012 58 SSFLELQEKHGVEIPCCLDSQFSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDL 116 (151)
Q Consensus 58 ~~l~~~~~~~~l~~~~~~~~~l~~~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~el 116 (151)
..+......+|+..+ .+.+...++. ..|.+..+|.+...+....+.|.+.+|++-
T Consensus 15 ~~~~~~l~~~~lt~~---q~~iL~~l~~-~~~~t~~ela~~~~~~~~tvs~~l~~Le~~ 69 (118)
T TIGR02337 15 SFFRPILAQHGLTEQ---QWRILRILAE-QGSMEFTQLANQACILRPSLTGILARLERD 69 (118)
T ss_pred HHHHHHHHHcCCCHH---HHHHHHHHHH-cCCcCHHHHHHHhCCCchhHHHHHHHHHHC
Confidence 344444556777522 1334444432 456899999999999999999999999873
No 24
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=57.88 E-value=31 Score=24.38 Aligned_cols=44 Identities=11% Similarity=0.220 Sum_probs=36.3
Q ss_pred chHHHHH-HHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhc
Q 043012 77 SQFSGMV-EAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120 (151)
Q Consensus 77 ~~l~~~v-~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl 120 (151)
+.-=.++ ..+-.|.|..||-+..++++|.+-..+.|...-||+.
T Consensus 109 ~~~r~ii~l~~~~~~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~~ 153 (154)
T PRK06759 109 EKEKYIIFERFFVGKTMGEIALETEMTYYQVRWIYRQALEKMRNS 153 (154)
T ss_pred HHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhhc
Confidence 3333444 5688999999999999999999999999988888764
No 25
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=57.18 E-value=67 Score=22.74 Aligned_cols=48 Identities=6% Similarity=0.009 Sum_probs=33.4
Q ss_pred HHcCCCCCCCCCchHHHHHHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHH
Q 043012 65 EKHGVEIPCCLDSQFSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTID 115 (151)
Q Consensus 65 ~~~~l~~~~~~~~~l~~~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~e 115 (151)
..+|+..+ .+.++..++.--.|.+..+|.+...+..+.+.|.+.||++
T Consensus 25 ~~~glt~~---q~~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~ 72 (144)
T PRK03573 25 KPLELTQT---HWVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLEE 72 (144)
T ss_pred HhcCCCHH---HHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHH
Confidence 45665533 1233333333224689999999999999999999999986
No 26
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=57.10 E-value=19 Score=23.63 Aligned_cols=37 Identities=22% Similarity=0.393 Sum_probs=28.8
Q ss_pred hHHHHHHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHH
Q 043012 78 QFSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTID 115 (151)
Q Consensus 78 ~l~~~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~e 115 (151)
.++...+. ..+++|.+|-+..++..|.+=+.++.|+|
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 67799999999999999999999988876
No 27
>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=55.75 E-value=22 Score=20.40 Aligned_cols=29 Identities=14% Similarity=0.292 Sum_probs=23.9
Q ss_pred hCCCCHHHHHhhcCCChhHHHHHHHHHHH
Q 043012 87 ASGLTWREMMMDCALDDGDLARLLRRTID 115 (151)
Q Consensus 87 a~G~~f~eil~~t~l~EGdiVR~~rRl~e 115 (151)
-.+.|..+|.+.++++.+.+=+.++++.+
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 34599999999999999999999999875
No 28
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=55.45 E-value=31 Score=24.75 Aligned_cols=37 Identities=16% Similarity=0.369 Sum_probs=33.1
Q ss_pred HHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhc
Q 043012 83 VEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120 (151)
Q Consensus 83 v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl 120 (151)
.... .|.|..+|-+..++++|.+-..+.|.-.-|++.
T Consensus 122 ~l~~-~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~ 158 (166)
T PRK09639 122 LLRF-SGYSYKEIAEALGIKESSVGTTLARAKKKFRKI 158 (166)
T ss_pred HHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3556 999999999999999999999999998888874
No 29
>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=54.71 E-value=37 Score=20.19 Aligned_cols=31 Identities=19% Similarity=0.245 Sum_probs=25.9
Q ss_pred HhhCCCCHHHHHhhcCCChhHHHHHHHHHHH
Q 043012 85 AWASGLTWREMMMDCALDDGDLARLLRRTID 115 (151)
Q Consensus 85 ~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~e 115 (151)
.|..+.+..+|.+..++..+.+-|.++++.+
T Consensus 16 l~~~~~~~~ei~~~~~i~~~~i~~~l~~L~~ 46 (78)
T cd00090 16 LLEGPLTVSELAERLGLSQSTVSRHLKKLEE 46 (78)
T ss_pred HHHCCcCHHHHHHHHCcCHhHHHHHHHHHHH
Confidence 3555699999999999999999888888754
No 30
>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=53.93 E-value=11 Score=21.74 Aligned_cols=33 Identities=18% Similarity=0.375 Sum_probs=28.8
Q ss_pred CCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhc
Q 043012 88 SGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120 (151)
Q Consensus 88 ~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl 120 (151)
++.|..+|++.+++..|.|-+-+.=-++|++.+
T Consensus 15 ~~~s~~~Ia~~~gvs~~~~y~~f~~k~~l~~a~ 47 (47)
T PF00440_consen 15 EAVSIRDIARRAGVSKGSFYRYFPSKDDLLRAV 47 (47)
T ss_dssp TTSSHHHHHHHHTSCHHHHHHHCSSHHHHHHHH
T ss_pred HhCCHHHHHHHHccchhhHHHHcCCHHHHHhhC
Confidence 678999999999999999999988888887653
No 31
>COG0501 HtpX Zn-dependent protease with chaperone function [Posttranslational modification, protein turnover, chaperones]
Probab=53.92 E-value=5.3 Score=31.92 Aligned_cols=21 Identities=33% Similarity=0.335 Sum_probs=19.0
Q ss_pred CccccCCCCCCCHHHHHHHHH
Q 043012 1 MVLRNKILLDLKPAQLAAVCA 21 (151)
Q Consensus 1 ~~L~~g~f~~L~p~elAAllS 21 (151)
+++++|+++.|+++||+||++
T Consensus 142 V~vt~gLl~~l~~dEl~aVla 162 (302)
T COG0501 142 VVVTTGLLDLLNDDELEAVLA 162 (302)
T ss_pred EEecHHHHhhCCHHHHHHHHH
Confidence 367899999999999999987
No 32
>PF13730 HTH_36: Helix-turn-helix domain
Probab=53.28 E-value=24 Score=20.74 Aligned_cols=25 Identities=8% Similarity=0.191 Sum_probs=22.6
Q ss_pred CHHHHHhhcCCChhHHHHHHHHHHH
Q 043012 91 TWREMMMDCALDDGDLARLLRRTID 115 (151)
Q Consensus 91 ~f~eil~~t~l~EGdiVR~~rRl~e 115 (151)
|-.+|.+.+++..-++.|.+++|+|
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~ 51 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEE 51 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 6788999999999999999999987
No 33
>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=53.05 E-value=53 Score=22.96 Aligned_cols=45 Identities=11% Similarity=0.192 Sum_probs=36.3
Q ss_pred CCchHHHHHHH-hhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhh
Q 043012 75 LDSQFSGMVEA-WASGLTWREMMMDCALDDGDLARLLRRTIDLLAQ 119 (151)
Q Consensus 75 ~~~~l~~~v~~-Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQ 119 (151)
+++.-..+++. ...|.|+.||-+..+++++.+=..+.|.-.-|++
T Consensus 114 L~~~~r~il~l~~~~~~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 114 LPEQCRKIFILSRFEGKSYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 34455556555 6799999999999999999999888888877775
No 34
>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=52.69 E-value=11 Score=26.68 Aligned_cols=46 Identities=13% Similarity=0.296 Sum_probs=39.7
Q ss_pred hHHHHHHHhhCCCCHHHHHhhc--CCChhHHHHHHHHHHHHHhhcCCC
Q 043012 78 QFSGMVEAWASGLTWREMMMDC--ALDDGDLARLLRRTIDLLAQIPKL 123 (151)
Q Consensus 78 ~l~~~v~~Wa~G~~f~eil~~t--~l~EGdiVR~~rRl~elLrQl~~a 123 (151)
....+++.|..|.++.+.+... .+.+..+.++++++...+.++...
T Consensus 64 ~~~~~~~e~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~l~~lh~~ 111 (215)
T cd00180 64 NHLYLVMEYCEGGSLKDLLKENEGKLSEDEILRILLQILEGLEYLHSN 111 (215)
T ss_pred CeEEEEEecCCCCcHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHHhC
Confidence 3455788899999999999886 799999999999999999888654
No 35
>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=52.42 E-value=19 Score=22.57 Aligned_cols=29 Identities=14% Similarity=0.136 Sum_probs=25.6
Q ss_pred hhCCCCHHHHHhhcCCChhHHHHHHHHHH
Q 043012 86 WASGLTWREMMMDCALDDGDLARLLRRTI 114 (151)
Q Consensus 86 Wa~G~~f~eil~~t~l~EGdiVR~~rRl~ 114 (151)
...|.|..+++...++.+..|-+|+++..
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 47899999999999999999999999987
No 36
>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=52.28 E-value=41 Score=24.56 Aligned_cols=46 Identities=24% Similarity=0.214 Sum_probs=36.8
Q ss_pred CCchHHHHHH-HhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhc
Q 043012 75 LDSQFSGMVE-AWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120 (151)
Q Consensus 75 ~~~~l~~~v~-~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl 120 (151)
+.+.--.++. ..-.|.|..||-+..++++|.+=..+.|.-..|++.
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 3344444553 356999999999999999999999999998888863
No 37
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=51.44 E-value=43 Score=24.32 Aligned_cols=35 Identities=14% Similarity=0.141 Sum_probs=31.7
Q ss_pred HhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhh
Q 043012 85 AWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQ 119 (151)
Q Consensus 85 ~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQ 119 (151)
....|.|..||.+..++++|.+=..++|...-|++
T Consensus 130 ~~~eg~s~~EIA~~l~is~~tV~~~l~ra~~~~~~ 164 (168)
T PRK12525 130 SQLEGLTYVEIGERLGVSLSRIHQYMVEAFKCCYQ 164 (168)
T ss_pred HHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 36899999999999999999999999988888876
No 38
>PRK00254 ski2-like helicase; Provisional
Probab=51.24 E-value=38 Score=31.03 Aligned_cols=68 Identities=16% Similarity=0.170 Sum_probs=44.7
Q ss_pred hHHHHHHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhcCCCCC---CCHHHHHHHHHHHhhcCCCc
Q 043012 78 QFSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIPKLPD---VDQRLQKNAVDASNVMDRPP 145 (151)
Q Consensus 78 ~l~~~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl~~a~~---~~~~L~~k~~~a~~~i~R~i 145 (151)
...-+.++|.+|.+...+++.-++..||+-+.+.+..-++.-+...+. ..+.+...+.+....|.=|+
T Consensus 570 k~~~ll~~~~~~~~~~~~~~~~~~~~gd~~~~~~~~~~l~~a~~~i~~~~~~~~~~~~~l~~l~~rl~~g~ 640 (720)
T PRK00254 570 KTAKVLLDWINEVPEGEIVETYNIDPGDLYRILELADWLMYSLIELYKLFEPKQEVLDYLETLHLRVKHGV 640 (720)
T ss_pred HHHHHHHHHHcCCCHHHHHHHhCCChHHHHHHHHHHHHHHHHHHHHHHHhCcchhHHHHHHHHHHHHHcCC
Confidence 446778999999999999999999999996666666666555444432 12333344444444444444
No 39
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=50.47 E-value=45 Score=23.81 Aligned_cols=43 Identities=9% Similarity=0.245 Sum_probs=33.3
Q ss_pred chHHHHH-HHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhh
Q 043012 77 SQFSGMV-EAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQ 119 (151)
Q Consensus 77 ~~l~~~v-~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQ 119 (151)
+.--.++ ...-.|.|..||-+..++++|.+=..+.|.-..||+
T Consensus 109 ~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 152 (160)
T PRK09642 109 ENYRDVVLAHYLEEKSYQEIALQEKIEVKTVEMKLYRARKWIKK 152 (160)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3333444 557899999999999999999997777777666665
No 40
>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=50.16 E-value=26 Score=20.76 Aligned_cols=35 Identities=14% Similarity=0.295 Sum_probs=27.3
Q ss_pred HHHHHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHH
Q 043012 80 SGMVEAWASGLTWREMMMDCALDDGDLARLLRRTID 115 (151)
Q Consensus 80 ~~~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~e 115 (151)
+..+|. ..|.+..+|-+...+.-+.+-|.+++|++
T Consensus 9 L~~l~~-~~~~~~~~la~~~~~~~~~~t~~i~~L~~ 43 (59)
T PF01047_consen 9 LRILYE-NGGITQSELAEKLGISRSTVTRIIKRLEK 43 (59)
T ss_dssp HHHHHH-HSSEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHH-cCCCCHHHHHHHHCCChhHHHHHHHHHHH
Confidence 333443 34589999999999999999999999975
No 41
>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=49.84 E-value=40 Score=26.42 Aligned_cols=37 Identities=19% Similarity=0.257 Sum_probs=33.5
Q ss_pred HHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhc
Q 043012 84 EAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120 (151)
Q Consensus 84 ~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl 120 (151)
..+..|.|..||-+..++++|.+-+.+.|...-||+.
T Consensus 216 l~~~~g~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~ 252 (255)
T TIGR02941 216 CTFEENLSQKETGERLGISQMHVSRLQRQAISKLKEA 252 (255)
T ss_pred HHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 5568999999999999999999999999999888874
No 42
>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=49.60 E-value=47 Score=22.61 Aligned_cols=43 Identities=19% Similarity=0.322 Sum_probs=34.5
Q ss_pred chHHHHH-HHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhh
Q 043012 77 SQFSGMV-EAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQ 119 (151)
Q Consensus 77 ~~l~~~v-~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQ 119 (151)
+.-..++ +....|.|+.+|.+..++++.++=+...|.-+-|+.
T Consensus 113 ~~~~~ii~~~~~~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 113 EREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred HHHHHHHhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 3333443 445689999999999999999999999998887775
No 43
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=48.97 E-value=48 Score=24.46 Aligned_cols=35 Identities=17% Similarity=0.121 Sum_probs=32.1
Q ss_pred hhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhc
Q 043012 86 WASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120 (151)
Q Consensus 86 Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl 120 (151)
.-.|.|+.||-+..++++|.+-..+.|....||+.
T Consensus 152 ~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 186 (189)
T PRK09648 152 VVVGLSAEETAEAVGSTPGAVRVAQHRALARLRAE 186 (189)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 56799999999999999999999999999988874
No 44
>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=48.46 E-value=32 Score=20.44 Aligned_cols=30 Identities=20% Similarity=0.345 Sum_probs=25.5
Q ss_pred hhCC--CCHHHHHhhcCCChhHHHHHHHHHHH
Q 043012 86 WASG--LTWREMMMDCALDDGDLARLLRRTID 115 (151)
Q Consensus 86 Wa~G--~~f~eil~~t~l~EGdiVR~~rRl~e 115 (151)
...| .+..+|.+.+.+....+-|.+++|++
T Consensus 16 ~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~ 47 (62)
T PF12802_consen 16 RHPGEELTQSELAERLGISKSTVSRIVKRLEK 47 (62)
T ss_dssp HSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4455 79999999999999999999999976
No 45
>PRK05417 glutathione-dependent formaldehyde-activating enzyme; Provisional
Probab=48.35 E-value=31 Score=26.69 Aligned_cols=33 Identities=18% Similarity=0.317 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHHHHHcCCCCCCCCCchHHHHHHHhhC
Q 043012 52 VLDEHRSSFLELQEKHGVEIPCCLDSQFSGMVEAWAS 88 (151)
Q Consensus 52 ~l~~~~~~l~~~~~~~~l~~~~~~~~~l~~~v~~Wa~ 88 (151)
++.++..++. +.|+++...++|.||+++..|..
T Consensus 151 ~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~ 183 (191)
T PRK05417 151 QMDGIRARLK----ELGLEPYDCLSPALMDAIATHVA 183 (191)
T ss_pred HhHHHHHHHH----HcCCCcccccCHHHHHHHHHHHH
Confidence 3555555555 55999999999999999999953
No 46
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=47.68 E-value=48 Score=26.04 Aligned_cols=44 Identities=16% Similarity=0.240 Sum_probs=35.7
Q ss_pred chHHHHH-HHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhc
Q 043012 77 SQFSGMV-EAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120 (151)
Q Consensus 77 ~~l~~~v-~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl 120 (151)
+.--.++ ..+-.|.|+.||-+..++++|.+=+..+|...-||+.
T Consensus 208 ~~~r~vl~l~~~~g~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~ 252 (257)
T PRK08583 208 DREKSIIQCTFIENLSQKETGERLGISQMHVSRLQRQAIKKLREA 252 (257)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3333344 3467999999999999999999999999998888864
No 47
>PRK15345 type III secretion system protein SsaL; Provisional
Probab=47.50 E-value=1.6e+02 Score=24.81 Aligned_cols=97 Identities=10% Similarity=0.039 Sum_probs=68.6
Q ss_pred hhHHHHHHHHHHHHH------HHHHHHHHcCCCCCCCCCchHHHHH-HHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHH
Q 043012 44 TTVINVINVLDEHRS------SFLELQEKHGVEIPCCLDSQFSGMV-EAWASGLTWREMMMDCALDDGDLARLLRRTIDL 116 (151)
Q Consensus 44 ~~l~~~~~~l~~~~~------~l~~~~~~~~l~~~~~~~~~l~~~v-~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~el 116 (151)
.++...+..++++.- .-..+...|+++....+ +...+++ ..|---.-+.+.+..-...++...|.++|+.|+
T Consensus 218 ~rLaa~i~dLrRLLlFLgLEd~C~r~a~a~~l~gd~iL-~~vL~iieQ~Wl~~dWL~~rl~~l~~~~~~~~r~lrrl~el 296 (326)
T PRK15345 218 SRLAAALVRLRRLLLFLGLEKECQREEWICQLPPNTLL-PLLLDIICERWLFSDWLLDRLTAIVSSSKMFNRLLQQLDAQ 296 (326)
T ss_pred chHHHHHHHHHHHHHHhchHHHHHHHHHHhCCChhHHH-HHHHHHHhcccccHHHHHHHHHhhccchHHHHHHHHHHHHH
Confidence 345555555554442 22344455787755444 4455555 678777677777777777788899999999999
Q ss_pred HhhcCCCCCCCHHHHHHHHHHHhhc
Q 043012 117 LAQIPKLPDVDQRLQKNAVDASNVM 141 (151)
Q Consensus 117 LrQl~~a~~~~~~L~~k~~~a~~~i 141 (151)
..=|+.+|-.|++-++.+.++..-+
T Consensus 297 ~~lmPd~CF~D~eQreqIle~lle~ 321 (326)
T PRK15345 297 FMLIPDNCFNDEDQREQILETLREV 321 (326)
T ss_pred HHhCcHHhcCCHHHHHHHHHHHHHH
Confidence 9999999987999998888877654
No 48
>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=47.30 E-value=68 Score=23.35 Aligned_cols=46 Identities=22% Similarity=0.344 Sum_probs=36.2
Q ss_pred CCchHHHHHHH-hhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhc
Q 043012 75 LDSQFSGMVEA-WASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120 (151)
Q Consensus 75 ~~~~l~~~v~~-Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl 120 (151)
+.+.--.++.. .-.|.|..+|.+..++++|.+-+.+.|.-.-||.+
T Consensus 141 L~~~~r~vi~l~~~~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~~ 187 (189)
T TIGR02984 141 LPEDYREVILLRHLEGLSFAEVAERMDRSEGAVSMLWVRGLARLRQI 187 (189)
T ss_pred CCHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 33444444433 56999999999999999999999999988888764
No 49
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=47.27 E-value=53 Score=23.30 Aligned_cols=37 Identities=14% Similarity=0.140 Sum_probs=32.5
Q ss_pred HHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhc
Q 043012 84 EAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120 (151)
Q Consensus 84 ~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl 120 (151)
...-.|.|..||.+..++++|.+=..+.|....||+.
T Consensus 117 l~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 153 (161)
T PRK09047 117 LRYWEDMDVAETAAAMGCSEGSVKTHCSRATHALAKA 153 (161)
T ss_pred HHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3357999999999999999999999999988888763
No 50
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=47.06 E-value=52 Score=23.89 Aligned_cols=36 Identities=11% Similarity=0.089 Sum_probs=31.9
Q ss_pred HHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhh
Q 043012 84 EAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQ 119 (151)
Q Consensus 84 ~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQ 119 (151)
..+-.|.|..||.+..++++|.+-..+.|.-.-||+
T Consensus 130 l~~~~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 165 (173)
T PRK12522 130 LYYYEQYSYKEMSEILNIPIGTVKYRLNYAKKQMRE 165 (173)
T ss_pred HHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 557799999999999999999999888888777776
No 51
>PRK02362 ski2-like helicase; Provisional
Probab=46.78 E-value=25 Score=32.31 Aligned_cols=66 Identities=15% Similarity=0.234 Sum_probs=43.8
Q ss_pred HHHHHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhcCCCCC-CCHHHHHHHHHHHhhcCCCc
Q 043012 80 SGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIPKLPD-VDQRLQKNAVDASNVMDRPP 145 (151)
Q Consensus 80 ~~~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl~~a~~-~~~~L~~k~~~a~~~i~R~i 145 (151)
.-+.++|-++.++.+|.+.-++..||+-.......-++..+...+. +...++..+.+-...|+-|+
T Consensus 581 ~~ll~~~i~~~~~~~i~~~~~~~~gdl~~~~~~~~~l~~a~~~i~~~~~~~~~~~~~~l~~~l~~gv 647 (737)
T PRK02362 581 ALLLEDWIDEVDEERITERYGVGPGDIRGKVETAEWLLHAAERLASELDLDLARAARELEKRVEYGV 647 (737)
T ss_pred HHHHHHHHhCCCHHHHHHHhCCCchHHHHHHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHhCC
Confidence 5667999999999999999999999997666666666444433332 12334444444444444444
No 52
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=46.60 E-value=55 Score=23.99 Aligned_cols=43 Identities=23% Similarity=0.251 Sum_probs=35.0
Q ss_pred chHHHHH-HHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhh
Q 043012 77 SQFSGMV-EAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQ 119 (151)
Q Consensus 77 ~~l~~~v-~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQ 119 (151)
+.--.++ ...-.|.|..||.+..++++|.+-..+.|.-.-||.
T Consensus 138 ~~~r~vl~l~~~~~~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~ 181 (186)
T PRK13919 138 PEERRVIEVLYYQGYTHREAAQLLGLPLGTLKTRARRALSRLKE 181 (186)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4444444 356899999999999999999999988888887775
No 53
>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=46.40 E-value=28 Score=21.09 Aligned_cols=29 Identities=7% Similarity=0.256 Sum_probs=23.6
Q ss_pred CCCCHHHHHhhcCCChhHHHHHHHHHHHH
Q 043012 88 SGLTWREMMMDCALDDGDLARLLRRTIDL 116 (151)
Q Consensus 88 ~G~~f~eil~~t~l~EGdiVR~~rRl~el 116 (151)
.+.+..+|.+.++++.+.+.|.+++|.+.
T Consensus 17 ~~~t~~~l~~~~~~~~~~vs~~i~~L~~~ 45 (68)
T PF13463_consen 17 GPMTQSDLAERLGISKSTVSRIIKKLEEK 45 (68)
T ss_dssp S-BEHHHHHHHTT--HHHHHHHHHHHHHT
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 45889999999999999999999999874
No 54
>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=46.17 E-value=34 Score=19.59 Aligned_cols=25 Identities=20% Similarity=0.371 Sum_probs=21.1
Q ss_pred CCHHHHHhhcCCChhHHHHHHHHHH
Q 043012 90 LTWREMMMDCALDDGDLARLLRRTI 114 (151)
Q Consensus 90 ~~f~eil~~t~l~EGdiVR~~rRl~ 114 (151)
.||.+|-+..++++..+.+-++||.
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 7999999999999999999999874
No 55
>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=45.97 E-value=55 Score=18.75 Aligned_cols=36 Identities=17% Similarity=0.310 Sum_probs=28.4
Q ss_pred HHHHHHhhCC-CCHHHHHhhcCCChhHHHHHHHHHHH
Q 043012 80 SGMVEAWASG-LTWREMMMDCALDDGDLARLLRRTID 115 (151)
Q Consensus 80 ~~~v~~Wa~G-~~f~eil~~t~l~EGdiVR~~rRl~e 115 (151)
..++..=.+| .++.+|.+.++++.+.+-+-++.|.+
T Consensus 5 ~~Il~~L~~~~~~~~el~~~l~~s~~~vs~hL~~L~~ 41 (47)
T PF01022_consen 5 LRILKLLSEGPLTVSELAEELGLSQSTVSHHLKKLRE 41 (47)
T ss_dssp HHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHhCCCchhhHHHhccccchHHHHHHHHHHH
Confidence 4455555555 89999999999999999999988876
No 56
>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=45.33 E-value=57 Score=24.98 Aligned_cols=44 Identities=9% Similarity=0.122 Sum_probs=34.5
Q ss_pred chHHHHHH-HhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhc
Q 043012 77 SQFSGMVE-AWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120 (151)
Q Consensus 77 ~~l~~~v~-~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl 120 (151)
+.--.++. ....|.|+.||.+..++++|.+=+.++|...-|++.
T Consensus 178 ~~~r~il~l~y~~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 222 (224)
T TIGR02479 178 EREQLVLSLYYYEELNLKEIGEVLGLTESRVSQIHSQALKKLRAK 222 (224)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 33334443 357999999999999999999998888888877763
No 57
>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=45.04 E-value=89 Score=20.61 Aligned_cols=45 Identities=20% Similarity=0.360 Sum_probs=37.2
Q ss_pred CCCCHHHHHhhcC-CChhHHHHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHh
Q 043012 88 SGLTWREMMMDCA-LDDGDLARLLRRTIDLLAQIPKLPDVDQRLQKNAVDASN 139 (151)
Q Consensus 88 ~G~~f~eil~~t~-l~EGdiVR~~rRl~elLrQl~~a~~~~~~L~~k~~~a~~ 139 (151)
.|.|+.+|-+.-+ ..--++...++|+.+.+.. |+.++..++....
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 4999999999988 9999999999999998754 5777777666544
No 58
>PRK03001 M48 family peptidase; Provisional
Probab=44.06 E-value=9 Score=31.00 Aligned_cols=20 Identities=25% Similarity=0.223 Sum_probs=18.3
Q ss_pred ccccCCCCCCCHHHHHHHHH
Q 043012 2 VLRNKILLDLKPAQLAAVCA 21 (151)
Q Consensus 2 ~L~~g~f~~L~p~elAAllS 21 (151)
++.+|+++.|+++|++||++
T Consensus 110 vvt~gLl~~l~~~El~aVlA 129 (283)
T PRK03001 110 AATTGILRVLSEREIRGVMA 129 (283)
T ss_pred EecHHHHhhCCHHHHHHHHH
Confidence 67889999999999999987
No 59
>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=43.84 E-value=45 Score=21.89 Aligned_cols=56 Identities=18% Similarity=0.184 Sum_probs=45.1
Q ss_pred HHhhCCCCHHHHHhhcCCChhHH-HHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHh
Q 043012 84 EAWASGLTWREMMMDCALDDGDL-ARLLRRTIDLLAQIPKLPDVDQRLQKNAVDASN 139 (151)
Q Consensus 84 ~~Wa~G~~f~eil~~t~l~EGdi-VR~~rRl~elLrQl~~a~~~~~~L~~k~~~a~~ 139 (151)
..|..-..+..+......++--- |+.++++-++++.++..+=.|++=++++-++..
T Consensus 16 q~Wl~~~~l~~l~~~l~~~~~~~qv~fl~~l~~l~~~lP~~lf~D~eqR~~~L~~~~ 72 (79)
T TIGR02511 16 ERWLGPDWIEQLANALGLPELEHRVAFLQGLKRLLRLLPIALFSDEEQRQNLLQALQ 72 (79)
T ss_pred cccCCHHHHHHHHHHccCccHHHHHHHHHHHHHHHHHCCHHHhCCHHHHHHHHHHHH
Confidence 67888888888888888887667 999999999999999987667777776665543
No 60
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=43.59 E-value=1.2e+02 Score=21.57 Aligned_cols=29 Identities=31% Similarity=0.323 Sum_probs=26.7
Q ss_pred hCCCCHHHHHhhcCCChhHHHHHHHHHHH
Q 043012 87 ASGLTWREMMMDCALDDGDLARLLRRTID 115 (151)
Q Consensus 87 a~G~~f~eil~~t~l~EGdiVR~~rRl~e 115 (151)
-.|.+..+|.+...+..+.+.|.+.||++
T Consensus 52 ~~~~t~~eLa~~l~i~~~tvsr~l~~Le~ 80 (144)
T PRK11512 52 AACITPVELKKVLSVDLGALTRMLDRLVC 80 (144)
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 45689999999999999999999999986
No 61
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=43.50 E-value=68 Score=22.90 Aligned_cols=35 Identities=17% Similarity=0.196 Sum_probs=31.2
Q ss_pred HHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHh
Q 043012 84 EAWASGLTWREMMMDCALDDGDLARLLRRTIDLLA 118 (151)
Q Consensus 84 ~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLr 118 (151)
.....|.|..||.+..+++.|++=..+.|-...|+
T Consensus 124 L~~~~g~s~~EIA~~l~is~~tV~~~l~ra~~~~~ 158 (161)
T PRK12528 124 LAQVDGLGYGEIATELGISLATVKRYLNKAAMRCY 158 (161)
T ss_pred HHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 45679999999999999999999999999887776
No 62
>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=43.27 E-value=18 Score=27.19 Aligned_cols=43 Identities=12% Similarity=0.118 Sum_probs=36.4
Q ss_pred HHHHHhhCCCCHHHHHhh-cCCChhHHHHHHHHHHHHHhhcCCC
Q 043012 81 GMVEAWASGLTWREMMMD-CALDDGDLARLLRRTIDLLAQIPKL 123 (151)
Q Consensus 81 ~~v~~Wa~G~~f~eil~~-t~l~EGdiVR~~rRl~elLrQl~~a 123 (151)
.+++.|..|.++.+++.. ..+.+..+.++++++.+.|..+...
T Consensus 69 ~lv~e~~~~~~L~~~l~~~~~~~~~~~~~i~~qi~~~L~~lH~~ 112 (265)
T cd05579 69 YLVMEYLPGGDLASLLENVGSLDEDVARIYIAEIVLALEYLHSN 112 (265)
T ss_pred EEEEecCCCCcHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHc
Confidence 357789999999999876 4689999999999999999877543
No 63
>PF13551 HTH_29: Winged helix-turn helix
Probab=42.71 E-value=67 Score=21.24 Aligned_cols=34 Identities=18% Similarity=0.235 Sum_probs=29.8
Q ss_pred HHHHHhhCCCC-HHHHHhhcCCChhHHHHHHHHHH
Q 043012 81 GMVEAWASGLT-WREMMMDCALDDGDLARLLRRTI 114 (151)
Q Consensus 81 ~~v~~Wa~G~~-f~eil~~t~l~EGdiVR~~rRl~ 114 (151)
.++...+.|.+ -.++++..++..-++=||+++..
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 46677889995 99999999999999999999943
No 64
>cd00131 PAX Paired Box domain
Probab=42.51 E-value=71 Score=22.76 Aligned_cols=33 Identities=21% Similarity=0.312 Sum_probs=28.9
Q ss_pred HHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHH
Q 043012 83 VEAWASGLTWREMMMDCALDDGDLARLLRRTID 115 (151)
Q Consensus 83 v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~e 115 (151)
+..-..|.|-.+|.+...+..+.+.||++|-.+
T Consensus 27 v~~~~~G~s~~~iA~~~~Vs~~tV~r~i~r~~e 59 (128)
T cd00131 27 VELAQSGIRPCDISRQLRVSHGCVSKILNRYYE 59 (128)
T ss_pred HHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 344468999999999999999999999999876
No 65
>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins.; PDB: 2GA1_B.
Probab=42.20 E-value=40 Score=20.41 Aligned_cols=32 Identities=19% Similarity=0.218 Sum_probs=21.3
Q ss_pred chHHHHHHHhhCCCCHHHHHhhcC-CChhHHHH
Q 043012 77 SQFSGMVEAWASGLTWREMMMDCA-LDDGDLAR 108 (151)
Q Consensus 77 ~~l~~~v~~Wa~G~~f~eil~~t~-l~EGdiVR 108 (151)
-..-.++..|+.|.|..+|++.-. +..-++--
T Consensus 19 I~v~~i~~~~~~G~s~eeI~~~yp~Lt~~~i~a 51 (56)
T PF04255_consen 19 IPVRDILDLLAAGESPEEIAEDYPSLTLEDIRA 51 (56)
T ss_dssp -BHHHHHHHHHTT--HHHHHHHSTT--HHHHHH
T ss_pred ecHHHHHHHHHcCCCHHHHHHHCCCCCHHHHHH
Confidence 356677888899999999999976 77776643
No 66
>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=42.18 E-value=90 Score=22.01 Aligned_cols=45 Identities=11% Similarity=0.149 Sum_probs=35.8
Q ss_pred CCchHHHHHH-HhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhh
Q 043012 75 LDSQFSGMVE-AWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQ 119 (151)
Q Consensus 75 ~~~~l~~~v~-~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQ 119 (151)
+++.--.++. .+..|.|..||.+..++++|.+=..+.|.-.-|++
T Consensus 112 L~~~~r~v~~l~~~~g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 112 LPERQRELLQLRYQRGVSLTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred CCHHHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 3344444443 37899999999999999999999999988877765
No 67
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=41.91 E-value=71 Score=22.80 Aligned_cols=38 Identities=16% Similarity=0.070 Sum_probs=33.2
Q ss_pred HHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhcC
Q 043012 84 EAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIP 121 (151)
Q Consensus 84 ~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl~ 121 (151)
..+..|.|..||.+..++++|.+=..+.|.-.-|+.+.
T Consensus 123 l~~~~~~s~~eIA~~lgis~~tv~~~l~Rar~~L~~~~ 160 (161)
T PRK12541 123 LRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKETKSIK 160 (161)
T ss_pred hHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhc
Confidence 45779999999999999999999888888888887654
No 68
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=41.64 E-value=38 Score=18.84 Aligned_cols=28 Identities=14% Similarity=0.327 Sum_probs=21.3
Q ss_pred hhCCCCHHHHHhhcCCChhHHHHHHHHH
Q 043012 86 WASGLTWREMMMDCALDDGDLARLLRRT 113 (151)
Q Consensus 86 Wa~G~~f~eil~~t~l~EGdiVR~~rRl 113 (151)
+.++.++.+|.....+++.-+.|.+++.
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 5677899999999999999999999875
No 69
>PRK03982 heat shock protein HtpX; Provisional
Probab=41.62 E-value=11 Score=30.57 Aligned_cols=20 Identities=30% Similarity=0.292 Sum_probs=18.1
Q ss_pred ccccCCCCCCCHHHHHHHHH
Q 043012 2 VLRNKILLDLKPAQLAAVCA 21 (151)
Q Consensus 2 ~L~~g~f~~L~p~elAAllS 21 (151)
++.+|+++.|+++|++||++
T Consensus 111 ~vt~gLl~~l~~~El~AVlA 130 (288)
T PRK03982 111 AVTEGILNLLNEDELEGVIA 130 (288)
T ss_pred EeehHHHhhCCHHHHHHHHH
Confidence 57889999999999999987
No 70
>PF14493 HTH_40: Helix-turn-helix domain
Probab=41.39 E-value=1e+02 Score=20.28 Aligned_cols=58 Identities=17% Similarity=0.117 Sum_probs=40.1
Q ss_pred HHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHhh
Q 043012 83 VEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIPKLPDVDQRLQKNAVDASNV 140 (151)
Q Consensus 83 v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl~~a~~~~~~L~~k~~~a~~~ 140 (151)
...|-+|+|..+|.+.-.+.+++|..-+-+....=..+.--.-++++-.+++.++.+.
T Consensus 7 ~~l~~~G~si~eIA~~R~L~~sTI~~HL~~~~~~g~~~~~~~~l~~e~~~~I~~~~~~ 64 (91)
T PF14493_consen 7 YELFQKGLSIEEIAKIRGLKESTIYGHLAELIESGEPLDIEELLSEEEIKQIEDAIEK 64 (91)
T ss_pred HHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHhCCCCCHHHhCCHHHHHHHHHHHHH
Confidence 4568899999999999999999999888777665332221111356666666665544
No 71
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=40.66 E-value=52 Score=24.13 Aligned_cols=33 Identities=9% Similarity=0.129 Sum_probs=24.3
Q ss_pred hhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHh
Q 043012 86 WASGLTWREMMMDCALDDGDLARLLRRTIDLLA 118 (151)
Q Consensus 86 Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLr 118 (151)
--.|.|..||.+..++++|.+=..+.|.-.-||
T Consensus 130 ~~e~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr 162 (179)
T PRK12543 130 YLHDYSQEEIAQLLQIPIGTVKSRIHAALKKLR 162 (179)
T ss_pred HHccCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 458999999999999999995444444433333
No 72
>COG1393 ArsC Arsenate reductase and related proteins, glutaredoxin family [Inorganic ion transport and metabolism]
Probab=40.62 E-value=50 Score=23.34 Aligned_cols=21 Identities=19% Similarity=0.488 Sum_probs=18.1
Q ss_pred CHHHHHHHHHHHhhcCCCccc
Q 043012 127 DQRLQKNAVDASNVMDRPPIS 147 (151)
Q Consensus 127 ~~~L~~k~~~a~~~i~R~iV~ 147 (151)
+.++.+.+-+.-.+|||+||.
T Consensus 77 ~~~~~~~i~~~~~LikRPivv 97 (117)
T COG1393 77 DEELIEALLENPSLIKRPIVV 97 (117)
T ss_pred hHHHHHHHHhChhhccCCeEE
Confidence 778888888888999999997
No 73
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=40.42 E-value=72 Score=18.26 Aligned_cols=29 Identities=14% Similarity=0.152 Sum_probs=25.8
Q ss_pred hCCCCHHHHHhhcCCChhHHHHHHHHHHH
Q 043012 87 ASGLTWREMMMDCALDDGDLARLLRRTID 115 (151)
Q Consensus 87 a~G~~f~eil~~t~l~EGdiVR~~rRl~e 115 (151)
-...++.+|.+..++..+++-+.++++.+
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~ 36 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLRE 36 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 55689999999999999999999988876
No 74
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=40.16 E-value=70 Score=24.73 Aligned_cols=37 Identities=11% Similarity=0.166 Sum_probs=32.2
Q ss_pred HHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhc
Q 043012 84 EAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120 (151)
Q Consensus 84 ~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl 120 (151)
.....|.|+.||.+..++++|.+=+.+.|...-||+.
T Consensus 195 l~~~~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 231 (236)
T PRK06986 195 LYYQEELNLKEIGAVLGVSESRVSQIHSQAIKRLRAR 231 (236)
T ss_pred hHhccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3457999999999999999999998888888888763
No 75
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=39.62 E-value=56 Score=25.19 Aligned_cols=33 Identities=21% Similarity=0.240 Sum_probs=28.9
Q ss_pred hCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhh
Q 043012 87 ASGLTWREMMMDCALDDGDLARLLRRTIDLLAQ 119 (151)
Q Consensus 87 a~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQ 119 (151)
-.|.|..||-+..++++|.+=+.+.|...-||+
T Consensus 196 ~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~ 228 (234)
T PRK08301 196 GEEKTQKEVADMLGISQSYISRLEKRIIKRLKK 228 (234)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 689999999999999999997777777777765
No 76
>PF08406 CbbQ_C: CbbQ/NirQ/NorQ C-terminal ; InterPro: IPR013615 This domain is found at the C terminus of proteins of the CbbQ/NirQ/NorQ family of proteins which play a role in the post-translational activation of Rubisco []. It is also found in the Thauera aromaticaTutH protein which is similar to the CbbQ/NirQ/NorQ family [], as well as in putative chaperones. The ATPase domain associated with various cellular activities (AAA) IPR011704 from INTERPRO is found in the same bacterial and archaeal proteins as the domain described here.
Probab=39.61 E-value=1.1e+02 Score=20.32 Aligned_cols=64 Identities=22% Similarity=0.209 Sum_probs=41.4
Q ss_pred HHHHHHHHHHHHHHHHcCCCCCCCCCchHHHHHHHhhCCCCHHHHHhhc----CCChhHHHHHHHHHHHH
Q 043012 51 NVLDEHRSSFLELQEKHGVEIPCCLDSQFSGMVEAWASGLTWREMMMDC----ALDDGDLARLLRRTIDL 116 (151)
Q Consensus 51 ~~l~~~~~~l~~~~~~~~l~~~~~~~~~l~~~v~~Wa~G~~f~eil~~t----~l~EGdiVR~~rRl~el 116 (151)
++|.+++.++..+ ..++++.+.+. -.++.....=+.|.++.+.+..+ =-++.|+...++.+++.
T Consensus 17 ~~LV~~A~~iR~l-~~~~L~e~~ST-R~Li~~A~Li~~G~~~~~A~~~ai~~~Ltdd~~~~~al~~~i~~ 84 (86)
T PF08406_consen 17 EKLVKLANAIRNL-KGGGLEETVST-RLLIYAARLIAAGMDPRQACRAAIVEPLTDDPDVREALRELIDA 84 (86)
T ss_pred HHHHHHHHHHHhc-cCCCCCCCCcH-HHHHHHHHHHHcCCCHHHHHHHHHhccCCCCHHHHHHHHHHHHH
Confidence 5677888888877 67777766443 23444444446799999987662 13366666666666553
No 77
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=38.94 E-value=70 Score=23.27 Aligned_cols=35 Identities=17% Similarity=0.225 Sum_probs=31.2
Q ss_pred hhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhc
Q 043012 86 WASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120 (151)
Q Consensus 86 Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl 120 (151)
+..|.|..||.+..++++|.+=..+.|.-.-|++.
T Consensus 149 ~~~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 149 YMEDLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 66899999999999999999999999888777763
No 78
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=38.79 E-value=1.7e+02 Score=23.25 Aligned_cols=59 Identities=15% Similarity=0.246 Sum_probs=45.6
Q ss_pred HHHHHHHHHHHHHcCCCCCC-----CCCchH---HHHHHHhhCCCCHHHHHhhcCCChhHHHHHHHH
Q 043012 54 DEHRSSFLELQEKHGVEIPC-----CLDSQF---SGMVEAWASGLTWREMMMDCALDDGDLARLLRR 112 (151)
Q Consensus 54 ~~~~~~l~~~~~~~~l~~~~-----~~~~~l---~~~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rR 112 (151)
..+...|...|++||+-.|. ..-|++ ..++..|-.|.+..||-..|.-+++.+=|.++-
T Consensus 120 ~TI~~~i~~yq~e~g~vvPtrG~i~DiGp~~tHK~~ii~~~l~g~~~~eiar~t~HS~~av~rYi~~ 186 (220)
T PF07900_consen 120 RTISKDIKEYQKEHGVVVPTRGTIHDIGPGVTHKKIIIRLYLKGKPTPEIARRTNHSPEAVDRYIKD 186 (220)
T ss_pred HHHHHHHHHHHHHcCceeccCCcccccCCcchHHHHHHHHHHcCCCHHHHHHHhccCHHHHHHHHHh
Confidence 35668899999999987661 122332 466888999999999999999999988776654
No 79
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=38.69 E-value=50 Score=21.58 Aligned_cols=32 Identities=13% Similarity=0.110 Sum_probs=26.0
Q ss_pred HHHHhhCCCCHHHHHhhcCCChhHHHHHHHHH
Q 043012 82 MVEAWASGLTWREMMMDCALDDGDLARLLRRT 113 (151)
Q Consensus 82 ~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl 113 (151)
.++.--.|.|..||-+..+++++.+=..++++
T Consensus 25 ~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~~ 56 (73)
T TIGR03879 25 ALAREEAGKTASEIAEELGRTEQTVRNHLKGE 56 (73)
T ss_pred HHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcC
Confidence 33444599999999999999999988877654
No 80
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=38.61 E-value=77 Score=23.55 Aligned_cols=44 Identities=16% Similarity=0.195 Sum_probs=32.7
Q ss_pred chHHHHHH-HhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhc
Q 043012 77 SQFSGMVE-AWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120 (151)
Q Consensus 77 ~~l~~~v~-~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl 120 (151)
+.--.++. ....|.|+.||.+..++++|.+=..+.|.-.-|+.+
T Consensus 114 ~~~R~v~~L~~~eg~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 158 (182)
T PRK12511 114 EEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARAALRAF 158 (182)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 44444443 356999999999999999999877776666666554
No 81
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=38.44 E-value=86 Score=23.30 Aligned_cols=36 Identities=14% Similarity=0.196 Sum_probs=31.9
Q ss_pred HhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhc
Q 043012 85 AWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120 (151)
Q Consensus 85 ~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl 120 (151)
..-.|.|+.||.+..++++|.+=..+.|....||+.
T Consensus 153 ~~~eg~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~ 188 (194)
T PRK12531 153 VYLEELPHQQVAEMFDIPLGTVKSRLRLAVEKLRHS 188 (194)
T ss_pred HHHcCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 356999999999999999999988888888888874
No 82
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=38.13 E-value=1.1e+02 Score=22.17 Aligned_cols=45 Identities=20% Similarity=0.299 Sum_probs=35.3
Q ss_pred CCchHHHHHHHh-hCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhh
Q 043012 75 LDSQFSGMVEAW-ASGLTWREMMMDCALDDGDLARLLRRTIDLLAQ 119 (151)
Q Consensus 75 ~~~~l~~~v~~W-a~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQ 119 (151)
+.+..-.++... -.|.|..||.+..++++|.+-..+.|.-.-||+
T Consensus 130 L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 175 (179)
T PRK12514 130 LEKDRAAAVRRAYLEGLSYKELAERHDVPLNTMRTWLRRSLLKLRE 175 (179)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHHCCChHHHHHHHHHHHHHHHH
Confidence 334555555444 589999999999999999998888888777775
No 83
>PRK10870 transcriptional repressor MprA; Provisional
Probab=37.48 E-value=1.7e+02 Score=21.77 Aligned_cols=52 Identities=8% Similarity=0.102 Sum_probs=37.3
Q ss_pred HHHHHHHHcCCCCCCCCCchHHHHHHHhhC---CCCHHHHHhhcCCChhHHHHHHHHHHH
Q 043012 59 SFLELQEKHGVEIPCCLDSQFSGMVEAWAS---GLTWREMMMDCALDDGDLARLLRRTID 115 (151)
Q Consensus 59 ~l~~~~~~~~l~~~~~~~~~l~~~v~~Wa~---G~~f~eil~~t~l~EGdiVR~~rRl~e 115 (151)
.+.+....+|+..+ .+.-+..-|.. +.+..+|.+...+.-+.+-|.+.||+.
T Consensus 43 ~~~~~l~~~gLt~~-----q~~iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe~ 97 (176)
T PRK10870 43 NRNKMLKAQGINET-----LFMALITLESQENHSIQPSELSCALGSSRTNATRIADELEK 97 (176)
T ss_pred HHHHHHHHCCCCHH-----HHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 34555567777632 33344444532 368899999999999999999999986
No 84
>PF13628 DUF4142: Domain of unknown function (DUF4142)
Probab=37.39 E-value=1.5e+02 Score=20.96 Aligned_cols=81 Identities=16% Similarity=0.275 Sum_probs=60.2
Q ss_pred HHHHHHHHHHHHcCCCCC-CCCCchHHHHHHHh--hCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhh-cCCCCCCCHHH
Q 043012 55 EHRSSFLELQEKHGVEIP-CCLDSQFSGMVEAW--ASGLTWREMMMDCALDDGDLARLLRRTIDLLAQ-IPKLPDVDQRL 130 (151)
Q Consensus 55 ~~~~~l~~~~~~~~l~~~-~~~~~~l~~~v~~W--a~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQ-l~~a~~~~~~L 130 (151)
..-.+|..+....|+++| ..+++.--..+... .+|..|..- +=-..|..-++.+.++.. +...+. |++|
T Consensus 46 ~~~~~l~~la~~~~v~lp~~~~~~~~~~~l~~L~~~~g~~FD~~------yl~~~i~~h~~~l~~~~~~~~~~~~-~~~l 118 (139)
T PF13628_consen 46 QANQQLAALAAKKGVTLPPTALSAEQQAELDRLQKLSGSAFDRA------YLDAQIKAHEKALALFEKQLAASGK-DPEL 118 (139)
T ss_pred HHHHHHHHHHHhcCCCcccccccHhhHHHHHHHHcCchhHHHHH------HHHHHHHHHHHHHHHHHHHhhccCC-CHHH
Confidence 344566677789999999 78888777777666 678888765 233447778888999988 655555 9999
Q ss_pred HHHHHHHHhhcC
Q 043012 131 QKNAVDASNVMD 142 (151)
Q Consensus 131 ~~k~~~a~~~i~ 142 (151)
+.-+.++...|.
T Consensus 119 k~~a~~~lp~l~ 130 (139)
T PF13628_consen 119 KAFAQETLPVLE 130 (139)
T ss_pred HHHHHHHhHHHH
Confidence 999888776654
No 85
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=37.36 E-value=1.9e+02 Score=23.50 Aligned_cols=61 Identities=11% Similarity=-0.046 Sum_probs=44.8
Q ss_pred HhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhcCCC-----CC-CCHHHHHHHHHHHhhcCCCc
Q 043012 85 AWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIPKL-----PD-VDQRLQKNAVDASNVMDRPP 145 (151)
Q Consensus 85 ~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl~~a-----~~-~~~~L~~k~~~a~~~i~R~i 145 (151)
.-..|.|..||.+..++++|.+=..+.|--..||+-... .. ......+.+++-.+++.++=
T Consensus 165 ~~~~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~~~~~~~~~~~~~~~~~~~~v~~~~~A~~~gD 231 (339)
T PRK08241 165 RDVLGWSAAEVAELLDTSVAAVNSALQRARATLAERGPSAADTLREPDDPEERALLARYVAAFEAYD 231 (339)
T ss_pred HHhhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhhcCCCcccccCCCCChHHHHHHHHHHHHHhcCC
Confidence 356999999999999999999999999999999994321 11 13455555555555555543
No 86
>PF13822 ACC_epsilon: Acyl-CoA carboxylase epsilon subunit
Probab=37.11 E-value=29 Score=21.74 Aligned_cols=16 Identities=31% Similarity=0.370 Sum_probs=13.0
Q ss_pred CCCHHHHHHHHHHhhc
Q 043012 10 DLKPAQLAAVCASLVS 25 (151)
Q Consensus 10 ~L~p~elAAllS~~v~ 25 (151)
+-|++|||||...|.-
T Consensus 10 nPt~eElAAL~aVlaa 25 (62)
T PF13822_consen 10 NPTDEELAALTAVLAA 25 (62)
T ss_pred CCCHHHHHHHHHHHHH
Confidence 5689999998887765
No 87
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=36.79 E-value=98 Score=22.29 Aligned_cols=44 Identities=11% Similarity=0.265 Sum_probs=33.7
Q ss_pred chHHHHH-HHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhc
Q 043012 77 SQFSGMV-EAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120 (151)
Q Consensus 77 ~~l~~~v-~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl 120 (151)
+.--.++ ...-.|.|..||.+..++++|.+=..+.|.-..||+.
T Consensus 121 ~~~r~vl~L~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 165 (173)
T PRK09645 121 PEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYALRALRLA 165 (173)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3444444 3367899999999999999999977777777777663
No 88
>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=36.76 E-value=90 Score=22.17 Aligned_cols=38 Identities=13% Similarity=0.175 Sum_probs=33.3
Q ss_pred HHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhcC
Q 043012 84 EAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIP 121 (151)
Q Consensus 84 ~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl~ 121 (151)
.....|.|..||.+..++++|.+=..+.|.-.-|+..-
T Consensus 121 l~~~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 158 (162)
T TIGR02983 121 LRYYEDLSEAQVAEALGISVGTVKSRLSRALARLRELL 158 (162)
T ss_pred hHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 34578999999999999999999999999988888643
No 89
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=36.72 E-value=45 Score=19.55 Aligned_cols=28 Identities=25% Similarity=0.364 Sum_probs=23.0
Q ss_pred CCCCHHHHHhhcCCChhHHHHHHHHHHH
Q 043012 88 SGLTWREMMMDCALDDGDLARLLRRTID 115 (151)
Q Consensus 88 ~G~~f~eil~~t~l~EGdiVR~~rRl~e 115 (151)
.+.++.||.+.++++-.++=|.+.-|.+
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 4468999999999999999998887765
No 90
>PRK05457 heat shock protein HtpX; Provisional
Probab=36.66 E-value=15 Score=29.90 Aligned_cols=20 Identities=20% Similarity=0.341 Sum_probs=17.9
Q ss_pred ccccCCCCCCCHHHHHHHHH
Q 043012 2 VLRNKILLDLKPAQLAAVCA 21 (151)
Q Consensus 2 ~L~~g~f~~L~p~elAAllS 21 (151)
|+..|+++.|+++|++|+++
T Consensus 120 ~vt~gLl~~L~~~El~aVlA 139 (284)
T PRK05457 120 AVSTGLLQNMSRDEVEAVLA 139 (284)
T ss_pred EeehHHhhhCCHHHHHHHHH
Confidence 56788999999999999987
No 91
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=36.45 E-value=1.1e+02 Score=19.51 Aligned_cols=37 Identities=22% Similarity=0.222 Sum_probs=28.7
Q ss_pred HHHHHHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHH
Q 043012 79 FSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTID 115 (151)
Q Consensus 79 l~~~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~e 115 (151)
++..+..-..+.+..+|.+.++++..++-|.+..|.+
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 3344444334689999999999999999999988876
No 92
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=36.08 E-value=2e+02 Score=21.99 Aligned_cols=47 Identities=9% Similarity=0.049 Sum_probs=34.7
Q ss_pred HHHcCCCCCCCCCchHHHHHHHhh-CCCCHHHHHhhcCCChhHHHHHHHHHHH
Q 043012 64 QEKHGVEIPCCLDSQFSGMVEAWA-SGLTWREMMMDCALDDGDLARLLRRTID 115 (151)
Q Consensus 64 ~~~~~l~~~~~~~~~l~~~v~~Wa-~G~~f~eil~~t~l~EGdiVR~~rRl~e 115 (151)
-..+|+..+ .+.-+.+-|. .|.+-.+|.+...+..+++.|.+.||++
T Consensus 38 l~~~gLt~~-----q~~iL~~L~~~~~itq~eLa~~l~l~~sTvtr~l~rLE~ 85 (185)
T PRK13777 38 IKPYDLNIN-----EHHILWIAYHLKGASISEIAKFGVMHVSTAFNFSKKLEE 85 (185)
T ss_pred HHHCCCCHH-----HHHHHHHHHhCCCcCHHHHHHHHCCCHhhHHHHHHHHHH
Confidence 345777643 2222334454 5799999999999999999999999987
No 93
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=35.95 E-value=70 Score=23.78 Aligned_cols=33 Identities=21% Similarity=0.283 Sum_probs=29.1
Q ss_pred hCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhh
Q 043012 87 ASGLTWREMMMDCALDDGDLARLLRRTIDLLAQ 119 (151)
Q Consensus 87 a~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQ 119 (151)
..|.|..||.+..++++|.+=..+.|.-..||+
T Consensus 148 ~~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 180 (189)
T PRK12530 148 YLELSSEQICQECDISTSNLHVLLYRARLQLQA 180 (189)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 579999999999999999998888887777775
No 94
>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=35.94 E-value=70 Score=22.45 Aligned_cols=35 Identities=14% Similarity=0.094 Sum_probs=31.0
Q ss_pred hhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhc
Q 043012 86 WASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120 (151)
Q Consensus 86 Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl 120 (151)
.-.|.|+.||.+..++++|.+-..+.|.-.-|++.
T Consensus 118 ~~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~~ 152 (154)
T TIGR02950 118 EFKEFSYKEIAELLNLSLAKVKSNLFRARKELKKL 152 (154)
T ss_pred hhccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 45899999999999999999999998888877763
No 95
>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=35.90 E-value=68 Score=24.85 Aligned_cols=32 Identities=19% Similarity=0.243 Sum_probs=28.4
Q ss_pred CCCCHHHHHhhcCCChhHHHHHHHHHHHHHhh
Q 043012 88 SGLTWREMMMDCALDDGDLARLLRRTIDLLAQ 119 (151)
Q Consensus 88 ~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQ 119 (151)
.|.|+.||-+..++++|.+-+.+.|...-||+
T Consensus 197 eg~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~ 228 (234)
T TIGR02835 197 TEKTQKEVADMLGISQSYISRLEKRILKRLKK 228 (234)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 78999999999999999998888777777765
No 96
>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=35.73 E-value=37 Score=26.67 Aligned_cols=44 Identities=16% Similarity=0.310 Sum_probs=37.9
Q ss_pred HHHHHHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhcCC
Q 043012 79 FSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIPK 122 (151)
Q Consensus 79 l~~~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl~~ 122 (151)
...+|++|..|.++.+.+....+.++.+.+.++++.+.|..+..
T Consensus 91 ~~~lv~e~~~~~~L~~~~~~~~~~~~~~~~i~~ql~~aL~~LH~ 134 (296)
T cd06654 91 ELWVVMEYLAGGSLTDVVTETCMDEGQIAAVCRECLQALEFLHS 134 (296)
T ss_pred EEEEeecccCCCCHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45578899999999999988889999999999999988877644
No 97
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=35.68 E-value=91 Score=24.62 Aligned_cols=37 Identities=16% Similarity=0.258 Sum_probs=33.3
Q ss_pred HHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhc
Q 043012 84 EAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120 (151)
Q Consensus 84 ~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl 120 (151)
..+..|.|+.+|-+..+++++.+=+.+.|...-||+.
T Consensus 214 l~y~~~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~ 250 (256)
T PRK07408 214 FVFLHDLTQKEAAERLGISPVTVSRRVKKGLDQLKKL 250 (256)
T ss_pred HHHHCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4567899999999999999999999999999888874
No 98
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=35.67 E-value=56 Score=23.74 Aligned_cols=26 Identities=8% Similarity=0.211 Sum_probs=25.0
Q ss_pred CCHHHHHhhcCCChhHHHHHHHHHHH
Q 043012 90 LTWREMMMDCALDDGDLARLLRRTID 115 (151)
Q Consensus 90 ~~f~eil~~t~l~EGdiVR~~rRl~e 115 (151)
.||++|-+..+++++++-|-++||.+
T Consensus 24 ~s~~eiA~~lglS~~tV~~Ri~rL~~ 49 (153)
T PRK11179 24 TPYAELAKQFGVSPGTIHVRVEKMKQ 49 (153)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 89999999999999999999999987
No 99
>PF13977 TetR_C_6: Bacterial transcriptional repressor; PDB: 2NX4_C 3CRJ_C 3E7Q_B 2NP5_A 3QBM_B 2G3B_B 2GFN_A.
Probab=35.64 E-value=1.3e+02 Score=19.68 Aligned_cols=72 Identities=14% Similarity=0.078 Sum_probs=46.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCchHHHHHHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHH
Q 043012 45 TVINVINVLDEHRSSFLELQEKHGVEIPCCLDSQFSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLL 117 (151)
Q Consensus 45 ~l~~~~~~l~~~~~~l~~~~~~~~l~~~~~~~~~l~~~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elL 117 (151)
.+.+.+....+...++..-... |-..+..--..++..+++..+|..+.-.+.-.+.....+++.+++..+.|
T Consensus 42 ~~~~~~~~~~~~l~~~l~~~~~-g~~~~~~~~~~~A~~l~al~~Gl~~~~~~~~~~~~~~~~~~~l~~~l~~l 113 (115)
T PF13977_consen 42 LLREAYARWRSRLAELLRRAVA-GGIRADVDPERLARMLLALLDGLWLQWLLDPDDFDAERARAILRAFLERL 113 (115)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHH-TSSSTTSTHHHHHHHHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHhC-CCCCCCCCHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHH
Confidence 3444555555544444333334 43333222257788889999999888888777788888888888887754
No 100
>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=35.57 E-value=65 Score=23.08 Aligned_cols=44 Identities=14% Similarity=0.296 Sum_probs=32.1
Q ss_pred cCCChhHHHHHHHHHHHHHhhcCCCCC------C---CHHHHHHHHHHHhhcC
Q 043012 99 CALDDGDLARLLRRTIDLLAQIPKLPD------V---DQRLQKNAVDASNVMD 142 (151)
Q Consensus 99 t~l~EGdiVR~~rRl~elLrQl~~a~~------~---~~~L~~k~~~a~~~i~ 142 (151)
+.-..++|+|++++-....++..+-.. + +...+.++++++++|.
T Consensus 66 ~~~G~~~f~~~~~~~~~~Ik~~~~f~g~~Dp~~Gd~~~~~VR~~A~El~~~if 118 (122)
T cd03572 66 CEKGNSDFKRELQRNSAQIRECANYKGPPDPLKGDSLNEKVREEAQELIKAIF 118 (122)
T ss_pred HhhCCHHHHHHHHHhHHHHHHHHHcCCCCCcccCcchhHHHHHHHHHHHHHHh
Confidence 344468999999998888887655432 1 5677888888887763
No 101
>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=35.46 E-value=1.1e+02 Score=21.83 Aligned_cols=34 Identities=24% Similarity=0.248 Sum_probs=31.1
Q ss_pred hhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhh
Q 043012 86 WASGLTWREMMMDCALDDGDLARLLRRTIDLLAQ 119 (151)
Q Consensus 86 Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQ 119 (151)
.-.|.|..||.+..++++|++=..+.|...-||+
T Consensus 135 ~~~g~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 135 FGQNLPIAEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5689999999999999999999999999888876
No 102
>PRK15443 pduE propanediol dehydratase small subunit; Provisional
Probab=35.35 E-value=75 Score=23.32 Aligned_cols=54 Identities=19% Similarity=0.283 Sum_probs=40.4
Q ss_pred hCCCCHHHHHhh----cCCChhHHHHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHhhcC
Q 043012 87 ASGLTWREMMMD----CALDDGDLARLLRRTIDLLAQIPKLPDVDQRLQKNAVDASNVMD 142 (151)
Q Consensus 87 a~G~~f~eil~~----t~l~EGdiVR~~rRl~elLrQl~~a~~~~~~L~~k~~~a~~~i~ 142 (151)
.+|+++++|.-. -++...| +|.-.-+.+.=.||+..+. .+.|+..|++|.++..
T Consensus 21 ~tGk~l~diTle~V~~G~v~~~D-lRItpetL~~QaqiAe~~G-r~~la~NfrRAAELt~ 78 (138)
T PRK15443 21 PTGKSLDDITLENVLSGKVTAED-LRITPETLRMQAQIAEDAG-RPQLAMNFRRAAELTA 78 (138)
T ss_pred CCCCChhHhhHHHHHcCCCCHHH-hccCHHHHHHHHHHHHHcC-CHHHHHHHHHHHhccC
Confidence 578888888533 3455555 4666677777778887765 9999999999999864
No 103
>COG2442 Uncharacterized conserved protein [Function unknown]
Probab=34.99 E-value=91 Score=20.59 Aligned_cols=37 Identities=24% Similarity=0.302 Sum_probs=28.8
Q ss_pred chHHHHHHHhhCCCCHHHHHhhcC-CChhHHHHHHHHH
Q 043012 77 SQFSGMVEAWASGLTWREMMMDCA-LDDGDLARLLRRT 113 (151)
Q Consensus 77 ~~l~~~v~~Wa~G~~f~eil~~t~-l~EGdiVR~~rRl 113 (151)
-..-.++..|+.|.|..||++.-+ +..=||--+++=.
T Consensus 31 I~V~~Il~~l~~G~s~eeil~dyp~Lt~~dI~aal~ya 68 (79)
T COG2442 31 IPVWDILEMLAAGESIEEILADYPDLTLEDIRAALRYA 68 (79)
T ss_pred ecHHHHHHHHHCCCCHHHHHHhCCCCCHHHHHHHHHHH
Confidence 345667899999999999999976 8877776666533
No 104
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=34.83 E-value=80 Score=22.47 Aligned_cols=36 Identities=8% Similarity=0.069 Sum_probs=32.5
Q ss_pred hhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhcC
Q 043012 86 WASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIP 121 (151)
Q Consensus 86 Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl~ 121 (151)
-..|.|-.||.+..++++|.+=+.+.|....||+.-
T Consensus 122 ~~~~~s~~EIA~~lgis~~tV~~~l~ra~~~lr~~l 157 (163)
T PRK07037 122 RLHGETQKDIARELGVSPTLVNFMIRDALVHCRKCL 157 (163)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 357999999999999999999999999999998753
No 105
>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=34.83 E-value=69 Score=19.49 Aligned_cols=33 Identities=15% Similarity=0.176 Sum_probs=28.8
Q ss_pred HHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHH
Q 043012 84 EAWASGLTWREMMMDCALDDGDLARLLRRTIDL 116 (151)
Q Consensus 84 ~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~el 116 (151)
|.|-++.++.++-+.-+++...+-.-+||-+.-
T Consensus 18 fd~PR~~tl~elA~~lgis~st~~~~LRrae~k 50 (53)
T PF04967_consen 18 FDVPRRITLEELAEELGISKSTVSEHLRRAERK 50 (53)
T ss_pred CCCCCcCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 568899999999999999999999999887653
No 106
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=34.69 E-value=78 Score=23.36 Aligned_cols=33 Identities=18% Similarity=0.193 Sum_probs=29.9
Q ss_pred hCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhh
Q 043012 87 ASGLTWREMMMDCALDDGDLARLLRRTIDLLAQ 119 (151)
Q Consensus 87 a~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQ 119 (151)
-.|.|..||.+..+++++.+-..+.|...-|++
T Consensus 155 ~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 187 (194)
T PRK12519 155 YEGLSQSEIAKRLGIPLGTVKARARQGLLKLRE 187 (194)
T ss_pred hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 489999999999999999999888888887776
No 107
>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=34.19 E-value=71 Score=21.73 Aligned_cols=27 Identities=15% Similarity=0.427 Sum_probs=25.7
Q ss_pred CCCHHHHHhhcCCChhHHHHHHHHHHH
Q 043012 89 GLTWREMMMDCALDDGDLARLLRRTID 115 (151)
Q Consensus 89 G~~f~eil~~t~l~EGdiVR~~rRl~e 115 (151)
|.+..+|.+.+.+..+.+-|.+.+|++
T Consensus 43 ~~t~~eL~~~l~~~~stvs~~i~~Le~ 69 (109)
T TIGR01889 43 KLTLKEIIKEILIKQSALVKIIKKLSK 69 (109)
T ss_pred cCcHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 599999999999999999999999987
No 108
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=34.14 E-value=95 Score=24.74 Aligned_cols=36 Identities=17% Similarity=0.266 Sum_probs=32.5
Q ss_pred HHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhh
Q 043012 84 EAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQ 119 (151)
Q Consensus 84 ~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQ 119 (151)
..+..|.|+.||-+..+++++.+=+.+.|...-||+
T Consensus 226 l~y~~~~t~~EIA~~lgis~~~V~~~~~ral~kLr~ 261 (264)
T PRK07122 226 LRFFESMTQTQIAERVGISQMHVSRLLAKTLARLRD 261 (264)
T ss_pred HHhcCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 446799999999999999999999999998888876
No 109
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=34.08 E-value=1.1e+02 Score=21.81 Aligned_cols=35 Identities=29% Similarity=0.460 Sum_probs=32.0
Q ss_pred hhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhc
Q 043012 86 WASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120 (151)
Q Consensus 86 Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl 120 (151)
.-.|.+..+|.+..+++++.+=+.+.|...-||+.
T Consensus 138 ~~~~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~ 172 (179)
T PRK11924 138 YVEGLSYREIAEILGVPVGTVKSRLRRARQLLREC 172 (179)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 46899999999999999999999999999888874
No 110
>COG3079 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.93 E-value=22 Score=27.18 Aligned_cols=74 Identities=18% Similarity=0.394 Sum_probs=42.7
Q ss_pred CCCHHHHHHHHHHhhccccccccc-------cCCCCCCCCchhHHHHHHHHHHH-HHHHHHHHHHcCCC----CC--CCC
Q 043012 10 DLKPAQLAAVCASLVSEGIKVRLW-------KNNSYIYEPSTTVINVINVLDEH-RSSFLELQEKHGVE----IP--CCL 75 (151)
Q Consensus 10 ~L~p~elAAllS~~v~e~~~~~~~-------~~~~~~~~~~~~l~~~~~~l~~~-~~~l~~~~~~~~l~----~~--~~~ 75 (151)
.++|+|+=+.+|.++|-.-.+..| .++. ..++..+..+++++.+. .+.+. +-++. .| ...
T Consensus 21 ~~t~aElHG~LsG~lcgG~~d~sWq~l~~~~tneg--~A~p~~l~~~l~~l~~a~s~~L~----d~~F~f~LlLpe~e~~ 94 (186)
T COG3079 21 GLTPAELHGLLSGLLCGGLNDSSWQPLLHDLTNEG--MAPPHGLLQALEQLLQATSQQLE----DDGFAFQLLLPEGEDV 94 (186)
T ss_pred CCCHHHHHHHHHhhhhcCCCchhHHHHHHHHhhcc--CCCcHHHHHHHHHHHHHHHHHhc----CCCeEEEEecCCCCcH
Confidence 689999999999999955322111 0111 12355566666665542 22333 22322 22 222
Q ss_pred CchHHHHHHHhhCC
Q 043012 76 DSQFSGMVEAWASG 89 (151)
Q Consensus 76 ~~~l~~~v~~Wa~G 89 (151)
=|.-++++..|+++
T Consensus 95 vf~rADAL~eW~nh 108 (186)
T COG3079 95 VFDRADALAEWCNH 108 (186)
T ss_pred HHHHHHHHHHHHHH
Confidence 37889999999985
No 111
>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=33.78 E-value=42 Score=26.33 Aligned_cols=45 Identities=16% Similarity=0.279 Sum_probs=38.5
Q ss_pred HHHHHHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhcCCC
Q 043012 79 FSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIPKL 123 (151)
Q Consensus 79 l~~~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl~~a 123 (151)
...++++|..|.++.+.+....+.+..+.+.++++...|..+...
T Consensus 90 ~~~lv~e~~~~~~L~~~~~~~~~~~~~~~~~~~~l~~~L~~LH~~ 134 (297)
T cd06656 90 ELWVVMEYLAGGSLTDVVTETCMDEGQIAAVCRECLQALDFLHSN 134 (297)
T ss_pred EEEEeecccCCCCHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHC
Confidence 345788999999999999888899999999999999888877543
No 112
>PRK02870 heat shock protein HtpX; Provisional
Probab=33.75 E-value=18 Score=30.33 Aligned_cols=21 Identities=29% Similarity=0.387 Sum_probs=18.9
Q ss_pred CccccCCCCCCCHHHHHHHHH
Q 043012 1 MVLRNKILLDLKPAQLAAVCA 21 (151)
Q Consensus 1 ~~L~~g~f~~L~p~elAAllS 21 (151)
+++.+|+++.|+++|++||++
T Consensus 158 Ivvt~GLL~~L~~dEL~aVlA 178 (336)
T PRK02870 158 VAITTGLLEKLDRDELQAVMA 178 (336)
T ss_pred EEEehHHhhhCCHHHHHHHHH
Confidence 368899999999999999987
No 113
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=33.73 E-value=1.5e+02 Score=22.04 Aligned_cols=44 Identities=25% Similarity=0.339 Sum_probs=35.6
Q ss_pred CCchHHHHH-HHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHh
Q 043012 75 LDSQFSGMV-EAWASGLTWREMMMDCALDDGDLARLLRRTIDLLA 118 (151)
Q Consensus 75 ~~~~l~~~v-~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLr 118 (151)
++|....++ ..|..|.|..||-+..++++.++=|-+++.-.-|+
T Consensus 136 l~~~~~~~v~l~~~~Gls~~EIA~~lgiS~~tV~r~l~~aR~~l~ 180 (185)
T PF07638_consen 136 LDPRQRRVVELRFFEGLSVEEIAERLGISERTVRRRLRRARAWLR 180 (185)
T ss_pred cCHHHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 456666666 56789999999999999999999888887765554
No 114
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=33.53 E-value=70 Score=20.44 Aligned_cols=29 Identities=17% Similarity=0.211 Sum_probs=26.1
Q ss_pred CCCCHHHHHhhcCCChhHHHHHHHHHHHH
Q 043012 88 SGLTWREMMMDCALDDGDLARLLRRTIDL 116 (151)
Q Consensus 88 ~G~~f~eil~~t~l~EGdiVR~~rRl~el 116 (151)
.+.+..+|.+..+++.+.+-+.+++|.+.
T Consensus 23 ~~~~~~~la~~~~~s~~~i~~~l~~L~~~ 51 (101)
T smart00347 23 GPLSVSELAKRLGVSPSTVTRVLDRLEKK 51 (101)
T ss_pred CCcCHHHHHHHHCCCchhHHHHHHHHHHC
Confidence 44899999999999999999999999883
No 115
>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=33.51 E-value=1.2e+02 Score=19.87 Aligned_cols=34 Identities=15% Similarity=0.157 Sum_probs=28.1
Q ss_pred HHHHhhCC-CCHHHHHhhcCCChhHHHHHHHHHHH
Q 043012 82 MVEAWASG-LTWREMMMDCALDDGDLARLLRRTID 115 (151)
Q Consensus 82 ~v~~Wa~G-~~f~eil~~t~l~EGdiVR~~rRl~e 115 (151)
+.-.||.+ .|+.++-+.|++....+...+.||.+
T Consensus 10 IL~~ls~~c~TLeeL~ekTgi~k~~LlV~LsrL~k 44 (72)
T PF05584_consen 10 ILIILSKRCCTLEELEEKTGISKNTLLVYLSRLAK 44 (72)
T ss_pred HHHHHHhccCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 34456555 89999999999999999999988865
No 116
>PF01471 PG_binding_1: Putative peptidoglycan binding domain; InterPro: IPR002477 This entry represents peptidoglycan binding domain (PGBD), as well as related domains that share the same structure. PGBD may have a general peptidoglycan binding function, has a core structure consisting of a closed, three-helical bundle with a left-handed twist. It is found at the N or C terminus of a variety of enzymes involved in bacterial cell wall degradation [, , ]. Examples are: Muramoyl-pentapeptide carboxypeptidase (3.4.17.8 from EC) N-acetylmuramoyl-L-alanine amidase cwlA precursor (cell wall hydrolase, autolysin, 3.5.1.28 from EC) Autolytic lysozyme (1,4-beta-N-acetylmuramidase, autolysin, 3.2.1.17 from EC) Membrane-bound lytic murein transglycosylase B Zinc-containing D-alanyl-D-alanine-cleaving carboxypeptidase, VanX []. Many of the proteins having this domain are as yet uncharacterised. However, some are known to belong to MEROPS peptidase family M15 (clan MD), subfamily M15A metallopeptidases. A number of the proteins belonging to subfamily M15A are non-peptidase homologues as they either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity. Eukaryotic enzymes can contain structurally similar PGBD-like domains. Matrix metalloproteinases (MMP), which catalyse extracellular matrix degradation, have N-terminal domains that resemble PGBD. Examples are gelatinase A (MMP-2), which degrades type IV collagen [], stromelysin-1 (MMP-3), which plays a role in arthritis and tumour invasion [, ], and gelatinase B (MMP-9) secreted by neutrophils as part of the innate immune defence mechanism []. Several MMPs are implicated in cancer progression, since degradation of the extracellular matrix is an essential step in the cascade of metastasis [].; GO: 0008152 metabolic process; PDB: 1L6J_A 3BKH_A 3BKV_A 1GXD_A 1EAK_D 1CK7_A 1SLM_A 1LBU_A 1SU3_B.
Probab=33.37 E-value=98 Score=18.13 Aligned_cols=25 Identities=12% Similarity=0.224 Sum_probs=17.5
Q ss_pred HHHHHHHHHcCCCCCCCCCchHHHH
Q 043012 58 SSFLELQEKHGVEIPCCLDSQFSGM 82 (151)
Q Consensus 58 ~~l~~~~~~~~l~~~~~~~~~l~~~ 82 (151)
..|...|..+|++.+..+|+.....
T Consensus 32 ~Av~~fQ~~~gL~~tG~~d~~T~~~ 56 (57)
T PF01471_consen 32 EAVKAFQKANGLPVTGVVDPETWEA 56 (57)
T ss_dssp HHHHHHHHHTTS-SSSSBCHHHHHH
T ss_pred HHHHHHHHHcCcCCCCccCHHHHhc
Confidence 3355678899999988888776554
No 117
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=33.25 E-value=1.2e+02 Score=21.88 Aligned_cols=35 Identities=9% Similarity=0.076 Sum_probs=29.3
Q ss_pred HhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhh
Q 043012 85 AWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQ 119 (151)
Q Consensus 85 ~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQ 119 (151)
..-.|.|..||.+..++++|.+=..+.|-..-|+.
T Consensus 131 ~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~~~~ 165 (172)
T PRK12523 131 NRLDGMGHAEIAERLGVSVSRVRQYLAQGLRQCYI 165 (172)
T ss_pred HHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46799999999999999999988877776666654
No 118
>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=33.11 E-value=83 Score=23.29 Aligned_cols=36 Identities=19% Similarity=0.178 Sum_probs=31.2
Q ss_pred HHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhh
Q 043012 84 EAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQ 119 (151)
Q Consensus 84 ~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQ 119 (151)
...-.|.|..||.+..++++|.+=..+.|.-..|++
T Consensus 142 L~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 177 (193)
T TIGR02947 142 LADVEGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRK 177 (193)
T ss_pred ehhhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 345699999999999999999998888888777775
No 119
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=32.87 E-value=1.4e+02 Score=21.86 Aligned_cols=48 Identities=10% Similarity=0.180 Sum_probs=39.0
Q ss_pred CCchHHHHHH-HhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhcCC
Q 043012 75 LDSQFSGMVE-AWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIPK 122 (151)
Q Consensus 75 ~~~~l~~~v~-~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl~~ 122 (151)
+.+.--.++. .+-.|.|..||.+..++++|.+=..+.|.-..|++.-.
T Consensus 123 L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 171 (185)
T PRK12542 123 LNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERARKRVQNMIG 171 (185)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHc
Confidence 3344555554 47899999999999999999999999999988888643
No 120
>PF14193 DUF4315: Domain of unknown function (DUF4315)
Probab=32.66 E-value=39 Score=22.65 Aligned_cols=14 Identities=29% Similarity=0.558 Sum_probs=12.8
Q ss_pred CCCHHHHHHHHHHh
Q 043012 10 DLKPAQLAAVCASL 23 (151)
Q Consensus 10 ~L~p~elAAllS~~ 23 (151)
+|+|++|+++|+..
T Consensus 47 ~mtp~eL~~~L~~~ 60 (83)
T PF14193_consen 47 KMTPEELAAFLRAM 60 (83)
T ss_pred CCCHHHHHHHHHHH
Confidence 79999999999876
No 121
>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=32.64 E-value=87 Score=22.83 Aligned_cols=34 Identities=15% Similarity=0.184 Sum_probs=29.8
Q ss_pred hCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhc
Q 043012 87 ASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120 (151)
Q Consensus 87 a~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl 120 (151)
..|.|+.||.+..+++++.+=..+.|.-.-||+.
T Consensus 152 ~~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~ 185 (190)
T TIGR02939 152 LEGLSYEDIARIMDCPVGTVRSRIFRAREAIAIR 185 (190)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4999999999999999999988888887777763
No 122
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=32.53 E-value=1.3e+02 Score=21.31 Aligned_cols=44 Identities=5% Similarity=0.022 Sum_probs=34.6
Q ss_pred chHHHHH-HHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhc
Q 043012 77 SQFSGMV-EAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120 (151)
Q Consensus 77 ~~l~~~v-~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl 120 (151)
+.--.++ ...-.|.|..||-+..++++|.+=..+.|.-.-||+.
T Consensus 108 ~~~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~ 152 (159)
T PRK12527 108 PACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVR 152 (159)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 4444444 3357999999999999999999988888887777764
No 123
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=32.49 E-value=2.3e+02 Score=23.21 Aligned_cols=67 Identities=10% Similarity=0.069 Sum_probs=47.0
Q ss_pred HHHHHHHHHHHHHHHcCCCCCCCCCchHHHHHHHhh--CC--CCHHHHHhhcCCChhHHHHHHHHHHHHHh
Q 043012 52 VLDEHRSSFLELQEKHGVEIPCCLDSQFSGMVEAWA--SG--LTWREMMMDCALDDGDLARLLRRTIDLLA 118 (151)
Q Consensus 52 ~l~~~~~~l~~~~~~~~l~~~~~~~~~l~~~v~~Wa--~G--~~f~eil~~t~l~EGdiVR~~rRl~elLr 118 (151)
.+.+.+.+|.+...+.++-.-..+..=.+.++|-=+ .| .|+.||.+.+++.+++|=+..+-+...|.
T Consensus 235 ~v~~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g~~~t~keIa~v~~Vs~~tI~~~ykel~~~l~ 305 (310)
T PRK00423 235 EVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERRTQREVAEVAGVTEVTVRNRYKELAEKLD 305 (310)
T ss_pred HHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHHHHHhC
Confidence 455666777766666676555556555555555433 33 79999999999999999988887776654
No 124
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=32.46 E-value=1.2e+02 Score=21.59 Aligned_cols=36 Identities=17% Similarity=0.133 Sum_probs=30.0
Q ss_pred HHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhh
Q 043012 84 EAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQ 119 (151)
Q Consensus 84 ~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQ 119 (151)
..+-.|.|..+|-+..+++++.+-..+.|.-.-|+.
T Consensus 139 l~~~~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 174 (182)
T PRK09652 139 LREIEGLSYEEIAEIMGCPIGTVRSRIFRAREALRA 174 (182)
T ss_pred HHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 346799999999999999999998887777666654
No 125
>PRK01265 heat shock protein HtpX; Provisional
Probab=32.37 E-value=18 Score=30.29 Aligned_cols=21 Identities=19% Similarity=0.271 Sum_probs=18.9
Q ss_pred CccccCCCCCCCHHHHHHHHH
Q 043012 1 MVLRNKILLDLKPAQLAAVCA 21 (151)
Q Consensus 1 ~~L~~g~f~~L~p~elAAllS 21 (151)
+++.+|+++.|+++|+.|+++
T Consensus 125 Ivvt~gLl~~l~~~El~aVlA 145 (324)
T PRK01265 125 IAITLPLLKILNRDEIKAVAG 145 (324)
T ss_pred EEEehHHHhhCCHHHHHHHHH
Confidence 368899999999999999987
No 126
>PF13940 Ldr_toxin: Toxin Ldr, type I toxin-antitoxin system
Probab=32.33 E-value=15 Score=20.49 Aligned_cols=19 Identities=32% Similarity=0.419 Sum_probs=15.5
Q ss_pred CCCCCCHHHHHHHHHHhhc
Q 043012 7 ILLDLKPAQLAAVCASLVS 25 (151)
Q Consensus 7 ~f~~L~p~elAAllS~~v~ 25 (151)
+|+||-.+-+|+++.+++-
T Consensus 10 ~WhDLAAP~iagIi~s~iv 28 (35)
T PF13940_consen 10 FWHDLAAPIIAGIIASLIV 28 (35)
T ss_pred HHHHhHhHHHHHHHHHHHH
Confidence 5788999999999887653
No 127
>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=32.20 E-value=83 Score=21.43 Aligned_cols=45 Identities=13% Similarity=0.248 Sum_probs=31.3
Q ss_pred chHHHHHHHh-hCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhcC
Q 043012 77 SQFSGMVEAW-ASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIP 121 (151)
Q Consensus 77 ~~l~~~v~~W-a~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl~ 121 (151)
.....+.+.- ..|.|=.++|+..++..|-|-++++|+...=+-+.
T Consensus 40 ~kiI~AL~dyLV~G~srkeac~~~gV~~syfs~~L~rL~~v~~~V~ 85 (91)
T PF03333_consen 40 EKIIAALRDYLVDGLSRKEACERHGVNQSYFSRALNRLNRVSQIVE 85 (91)
T ss_dssp HHHHHHHHHHHTT---HHHHHHHTT--HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 4555555444 89999999999999999999999999987655443
No 128
>COG3457 Predicted amino acid racemase [Amino acid transport and metabolism]
Probab=32.01 E-value=2.1e+02 Score=24.28 Aligned_cols=94 Identities=13% Similarity=0.147 Sum_probs=68.3
Q ss_pred HHHHHHHHHHHHHHHHHcCCCCC---CC--CCchHHHHHHHhh----CCCCHHHHHhh--cCCC-hhHHHH--HHHHHHH
Q 043012 50 INVLDEHRSSFLELQEKHGVEIP---CC--LDSQFSGMVEAWA----SGLTWREMMMD--CALD-DGDLAR--LLRRTID 115 (151)
Q Consensus 50 ~~~l~~~~~~l~~~~~~~~l~~~---~~--~~~~l~~~v~~Wa----~G~~f~eil~~--t~l~-EGdiVR--~~rRl~e 115 (151)
+.++.+-++.+.+....+|++.. .. =+|.+++.+.+=- --..+.++..+ +++. .|-++| |..+.+|
T Consensus 10 l~~ieeNak~~~~~a~~~gI~~~~vtK~~~g~~~iae~l~~~Gi~~iaesr~~n~~~lr~~g~~~~~~Llr~P~~sei~~ 89 (353)
T COG3457 10 LDKIEENAKVLQETAARYGIELYGVTKQFGGDPFIAEALLALGIEGIAESRIDNAIRLREAGCTIPGHLLRSPCMSEIED 89 (353)
T ss_pred HHHHHHhHHHHHHHHHHcCCEEEEEEeeccCChHHHHHHHhcCcceeeehhHHHHHHHHHcCCCcCceEeecccHHHHHH
Confidence 56788899999999999999964 33 3678888876531 11457777766 3333 389999 8999999
Q ss_pred HHhhcCCCCCCCHHHHHHHHHHHhhcCC
Q 043012 116 LLAQIPKLPDVDQRLQKNAVDASNVMDR 143 (151)
Q Consensus 116 lLrQl~~a~~~~~~L~~k~~~a~~~i~R 143 (151)
.++.+--.-..+++-.+...++...+.|
T Consensus 90 vv~~~Dvs~~sel~~arqlse~A~~~Gk 117 (353)
T COG3457 90 VVRKVDVSTVSELDTARQLSEAAVRMGK 117 (353)
T ss_pred HHHhcCeEEEecHHHHHHHHHHHHHhCc
Confidence 9998764443477888888888777665
No 129
>PRK06930 positive control sigma-like factor; Validated
Probab=31.99 E-value=1.6e+02 Score=21.95 Aligned_cols=46 Identities=13% Similarity=0.206 Sum_probs=37.1
Q ss_pred CCCchHHHHHHH-hhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhh
Q 043012 74 CLDSQFSGMVEA-WASGLTWREMMMDCALDDGDLARLLRRTIDLLAQ 119 (151)
Q Consensus 74 ~~~~~l~~~v~~-Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQ 119 (151)
.+.+.--.++.. -..|.|+.+|.+..++++|.+=..+.|...-|+.
T Consensus 114 ~L~~rer~V~~L~~~eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~ 160 (170)
T PRK06930 114 VLTEREKEVYLMHRGYGLSYSEIADYLNIKKSTVQSMIERAEKKIAR 160 (170)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 455666666654 6899999999999999999998888887776664
No 130
>PRK01345 heat shock protein HtpX; Provisional
Probab=31.88 E-value=18 Score=30.00 Aligned_cols=20 Identities=30% Similarity=0.434 Sum_probs=17.8
Q ss_pred ccccCCCCCCCHHHHHHHHH
Q 043012 2 VLRNKILLDLKPAQLAAVCA 21 (151)
Q Consensus 2 ~L~~g~f~~L~p~elAAllS 21 (151)
++.+|+++.|+++|++||++
T Consensus 110 ~vt~gLL~~L~~dEL~aVlA 129 (317)
T PRK01345 110 AATTGLLQRLSPEEVAGVMA 129 (317)
T ss_pred EechHHHhhCCHHHHHHHHH
Confidence 56779999999999999987
No 131
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=31.81 E-value=1.2e+02 Score=22.54 Aligned_cols=36 Identities=17% Similarity=0.294 Sum_probs=31.1
Q ss_pred HhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhc
Q 043012 85 AWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120 (151)
Q Consensus 85 ~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl 120 (151)
....|.|..||.+..++++|.+=..+.|.-..||+.
T Consensus 148 ~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 183 (195)
T PRK12532 148 KEILGFSSDEIQQMCGISTSNYHTIMHRARESLRQC 183 (195)
T ss_pred HHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 467999999999999999999988888877777764
No 132
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=31.76 E-value=1e+02 Score=24.10 Aligned_cols=38 Identities=13% Similarity=0.132 Sum_probs=33.3
Q ss_pred HHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhcC
Q 043012 84 EAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIP 121 (151)
Q Consensus 84 ~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl~ 121 (151)
...-.|.|..||.+..++++|.+=..+.|.-.-||+.-
T Consensus 182 L~~~eg~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l 219 (233)
T PRK12538 182 LSYHENMSNGEIAEVMDTTVAAVESLLKRGRQQLRDLL 219 (233)
T ss_pred hHHhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 44579999999999999999999999999888888743
No 133
>PRK09191 two-component response regulator; Provisional
Probab=31.68 E-value=1.6e+02 Score=22.37 Aligned_cols=54 Identities=11% Similarity=0.021 Sum_probs=40.1
Q ss_pred hhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhcCCCCC----CCHHHHHHHHHHHh
Q 043012 86 WASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIPKLPD----VDQRLQKNAVDASN 139 (151)
Q Consensus 86 Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl~~a~~----~~~~L~~k~~~a~~ 139 (151)
.-.|.|..||-+..++++|.+-..+.|....|++....-- .++...........
T Consensus 101 ~~~~~s~~eIA~~l~~s~~tV~~~l~ra~~~l~~~~~~~~liidd~~~~~~~l~~~L~ 158 (261)
T PRK09191 101 ALEGFSVEEAAEILGVDPAEAEALLDDARAEIARQVATRVLIIEDEPIIAMDLEQLVE 158 (261)
T ss_pred HHhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHhccCCCeEEEEcCcHHHHHHHHHHHh
Confidence 5689999999999999999999999999998886433211 15555555554443
No 134
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=31.52 E-value=1.3e+02 Score=21.58 Aligned_cols=35 Identities=20% Similarity=0.370 Sum_probs=30.9
Q ss_pred hhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhc
Q 043012 86 WASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120 (151)
Q Consensus 86 Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl 120 (151)
...|.|..||.+..++++|++=..+.|.-.-|+..
T Consensus 125 ~~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 159 (164)
T PRK12547 125 GASGFSYEDAAAICGCAVGTIKSRVSRARNRLQEL 159 (164)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 35999999999999999999999888888877764
No 135
>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=31.45 E-value=1.2e+02 Score=18.30 Aligned_cols=42 Identities=19% Similarity=0.165 Sum_probs=30.9
Q ss_pred CCChhHHHHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHhhcCC
Q 043012 100 ALDDGDLARLLRRTIDLLAQIPKLPDVDQRLQKNAVDASNVMDR 143 (151)
Q Consensus 100 ~l~EGdiVR~~rRl~elLrQl~~a~~~~~~L~~k~~~a~~~i~R 143 (151)
..+.-+...--.++.|+|++=.. ..+|+|+.++-+|.-++|.
T Consensus 7 ~cYp~~~~~Fp~~L~~lL~~~~~--~L~p~lR~~lv~aLiLLRn 48 (52)
T PF08158_consen 7 HCYPKETKDFPQELIDLLRNHHT--VLDPDLRMKLVKALILLRN 48 (52)
T ss_pred cccHHHHHHHHHHHHHHHHhccc--cCCHHHHHHHHHHHHHHHc
Confidence 44555555666788888887555 3499999999999887764
No 136
>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=31.34 E-value=72 Score=22.24 Aligned_cols=31 Identities=19% Similarity=0.281 Sum_probs=24.0
Q ss_pred HHHHhhCCCCHHHHHhhcCCChhHHHHHHHH
Q 043012 82 MVEAWASGLTWREMMMDCALDDGDLARLLRR 112 (151)
Q Consensus 82 ~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rR 112 (151)
|+..+..|.|..++...=.+...++.||++|
T Consensus 11 Vl~~~~~g~s~~eaa~~F~VS~~Tv~~W~k~ 41 (119)
T PF01710_consen 11 VLAYIEKGKSIREAAKRFGVSRNTVYRWLKR 41 (119)
T ss_pred HHHHHHccchHHHHHHHhCcHHHHHHHHHHh
Confidence 4456677888888888888888888888873
No 137
>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=31.28 E-value=1.2e+02 Score=23.07 Aligned_cols=35 Identities=23% Similarity=0.309 Sum_probs=31.4
Q ss_pred hhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhc
Q 043012 86 WASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120 (151)
Q Consensus 86 Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl 120 (151)
.-.|.|..||-+..+++.+.+=+.+.|...-|++.
T Consensus 191 y~~~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~~ 225 (227)
T TIGR02980 191 FFEDKTQSEIAERLGISQMHVSRLLRRALKKLREQ 225 (227)
T ss_pred HhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 35899999999999999999999999998888763
No 138
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=31.25 E-value=1.3e+02 Score=22.09 Aligned_cols=35 Identities=23% Similarity=0.173 Sum_probs=31.8
Q ss_pred hhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhc
Q 043012 86 WASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120 (151)
Q Consensus 86 Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl 120 (151)
.-.|.|+.||.+..+++.|.+=..+.|.-.-||+.
T Consensus 141 ~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 175 (186)
T PRK05602 141 YYQGLSNIEAAAVMDISVDALESLLARGRRALRAQ 175 (186)
T ss_pred HhcCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 56899999999999999999999999988888873
No 139
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=31.04 E-value=84 Score=20.95 Aligned_cols=30 Identities=10% Similarity=0.254 Sum_probs=27.1
Q ss_pred CCCHHHHHhhcCCChhHHHHHHHHHHH--HHh
Q 043012 89 GLTWREMMMDCALDDGDLARLLRRTID--LLA 118 (151)
Q Consensus 89 G~~f~eil~~t~l~EGdiVR~~rRl~e--lLr 118 (151)
..|+.+|.+..++++-.+-|.+++|.+ +++
T Consensus 17 ~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~ 48 (108)
T smart00344 17 RISLAELAKKVGLSPSTVHNRVKRLEEEGVIK 48 (108)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence 489999999999999999999999988 444
No 140
>PF11918 DUF3436: Domain of unknown function (DUF3436); InterPro: IPR024591 This uncharacterised N-terminal domain is associated with the interphotoreceptor retinol-binding protein family. It is about 50 amino acids in length and has two conserved sequence motifs: DPRL and SYEP.
Probab=30.82 E-value=44 Score=20.69 Aligned_cols=16 Identities=38% Similarity=0.459 Sum_probs=13.1
Q ss_pred CCCCCCCHHHHHHHHH
Q 043012 6 KILLDLKPAQLAAVCA 21 (151)
Q Consensus 6 g~f~~L~p~elAAllS 21 (151)
..+.+|+|+||+|++=
T Consensus 33 p~~~~Lt~EqLla~lq 48 (55)
T PF11918_consen 33 PALPNLTPEQLLAMLQ 48 (55)
T ss_pred CCCCCcCHHHHHHHHH
Confidence 3568999999999874
No 141
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=30.69 E-value=71 Score=23.50 Aligned_cols=27 Identities=15% Similarity=0.068 Sum_probs=24.8
Q ss_pred CCHHHHHhhcCCChhHHHHHHHHHHHH
Q 043012 90 LTWREMMMDCALDDGDLARLLRRTIDL 116 (151)
Q Consensus 90 ~~f~eil~~t~l~EGdiVR~~rRl~el 116 (151)
.|+.+|-+..++++..+-|-++||.+-
T Consensus 29 ~s~~eiA~~lglS~~tv~~Ri~rL~~~ 55 (164)
T PRK11169 29 ISNVELSKRVGLSPTPCLERVRRLERQ 55 (164)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 788999999999999999999999873
No 142
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=30.64 E-value=1.3e+02 Score=21.83 Aligned_cols=37 Identities=16% Similarity=0.183 Sum_probs=31.8
Q ss_pred HHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhc
Q 043012 84 EAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120 (151)
Q Consensus 84 ~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl 120 (151)
..+-.|.|..+|.+..++++|.+-..+.|.-.-|++.
T Consensus 147 l~~~~~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T PRK09641 147 LKYIEDLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred hHHhhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3456999999999999999999999988888777763
No 143
>PRK03072 heat shock protein HtpX; Provisional
Probab=30.36 E-value=20 Score=29.26 Aligned_cols=20 Identities=25% Similarity=0.208 Sum_probs=17.7
Q ss_pred ccccCCCCCCCHHHHHHHHH
Q 043012 2 VLRNKILLDLKPAQLAAVCA 21 (151)
Q Consensus 2 ~L~~g~f~~L~p~elAAllS 21 (151)
++.+|+++.|+++|++||++
T Consensus 113 ~vt~gLl~~l~~~El~aVlA 132 (288)
T PRK03072 113 CCTEGILQILNERELRGVLG 132 (288)
T ss_pred EecHHHHHhCCHHHHHHHHH
Confidence 45788999999999999987
No 144
>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=30.25 E-value=1.1e+02 Score=19.92 Aligned_cols=34 Identities=21% Similarity=0.159 Sum_probs=25.1
Q ss_pred hHHHHHHHhhCCCCHHHHHhhcCCCh----hHHHHHHH
Q 043012 78 QFSGMVEAWASGLTWREMMMDCALDD----GDLARLLR 111 (151)
Q Consensus 78 ~l~~~v~~Wa~G~~f~eil~~t~l~E----GdiVR~~r 111 (151)
..+-.+..+..|++..+||+.|+=+. |-|-+.++
T Consensus 13 a~li~mL~rp~GATi~ei~~atGWq~HTvRgalsg~~k 50 (72)
T PF11994_consen 13 AQLIAMLRRPEGATIAEICEATGWQPHTVRGALSGLLK 50 (72)
T ss_pred HHHHHHHcCCCCCCHHHHHHhhCCchhhHHHHHHHHHH
Confidence 44555678999999999999998776 44444443
No 145
>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=30.16 E-value=1.7e+02 Score=22.41 Aligned_cols=32 Identities=19% Similarity=0.185 Sum_probs=28.4
Q ss_pred CCCCHHHHHhhcCCChhHHHHHHHHHHHHHhh
Q 043012 88 SGLTWREMMMDCALDDGDLARLLRRTIDLLAQ 119 (151)
Q Consensus 88 ~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQ 119 (151)
.|.|..||.+..++..|.+-+.+.|..--||+
T Consensus 193 e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~ 224 (227)
T TIGR02846 193 RRKTQREIAKILGISRSYVSRIEKRALMKLYK 224 (227)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 89999999999999999998888887766664
No 146
>PF03847 TFIID_20kDa: Transcription initiation factor TFIID subunit A; InterPro: IPR003228 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription [].; GO: 0006352 transcription initiation, DNA-dependent, 0005669 transcription factor TFIID complex; PDB: 1H3O_B.
Probab=30.12 E-value=97 Score=19.78 Aligned_cols=28 Identities=18% Similarity=0.306 Sum_probs=16.7
Q ss_pred HHHHHHHhhcCCCCCCCHHHHHHHHHHH
Q 043012 111 RRTIDLLAQIPKLPDVDQRLQKNAVDAS 138 (151)
Q Consensus 111 rRl~elLrQl~~a~~~~~~L~~k~~~a~ 138 (151)
+++.||++||---..++|+..+-+-+..
T Consensus 3 ~~l~~Lv~~iDp~~~ld~~vee~Ll~la 30 (68)
T PF03847_consen 3 RKLQELVKQIDPNEKLDPDVEELLLELA 30 (68)
T ss_dssp HHHHHHHHCC-SS----HHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCCCCCHHHHHHHHHHH
Confidence 6899999999766666777666554443
No 147
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=30.07 E-value=99 Score=22.71 Aligned_cols=35 Identities=17% Similarity=0.257 Sum_probs=31.0
Q ss_pred hhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhc
Q 043012 86 WASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120 (151)
Q Consensus 86 Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl 120 (151)
--.|.|..||.+..++++|.+=..+.|.-..|++.
T Consensus 144 ~~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 178 (184)
T PRK12539 144 KLEGLSVAEAATRSGMSESAVKVSVHRGLKALAAL 178 (184)
T ss_pred HHcCCcHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 34899999999999999999999998888888764
No 148
>PRK10573 type IV pilin biogenesis protein; Provisional
Probab=29.95 E-value=1.2e+02 Score=25.48 Aligned_cols=72 Identities=14% Similarity=0.104 Sum_probs=46.9
Q ss_pred HHHHcCCCCCC--------CCCchHH----HHHHHhhCCCCHHHHHhhcCCChhHHHHHHH------HHHHHHhhcCCCC
Q 043012 63 LQEKHGVEIPC--------CLDSQFS----GMVEAWASGLTWREMMMDCALDDGDLARLLR------RTIDLLAQIPKLP 124 (151)
Q Consensus 63 ~~~~~~l~~~~--------~~~~~l~----~~v~~Wa~G~~f~eil~~t~l~EGdiVR~~r------Rl~elLrQl~~a~ 124 (151)
..-+.|++... .-|+.+- .+...=.+|.+|++.++.++.++..+++.++ ++++.|.++++--
T Consensus 274 ~ll~sGi~l~~al~~~~~~~~n~~l~~~~~~i~~~v~~G~sls~al~~~~~fp~~~~~~i~~GE~sG~L~~~L~~la~~~ 353 (399)
T PRK10573 274 LTQSAGLTLLQGLESAAETLRCPYWQQALTQIQQQIAQGIPLWLALKNHPLFPPLCLQLVRVGEESGSLDLMLENLAHWH 353 (399)
T ss_pred HHHHcCCcHHHHHHHHHHHcCCHHHHHHHHHHHHHHHCcccHHHHHhhCCCCcHHHHHHHHHHHhhccHHHHHHHHHHHH
Confidence 34567777531 1234443 3444556899999999999999999999887 4777777775543
Q ss_pred CCCHHHHHHHHH
Q 043012 125 DVDQRLQKNAVD 136 (151)
Q Consensus 125 ~~~~~L~~k~~~ 136 (151)
..++..+.+.
T Consensus 354 --~~~~~~~~~~ 363 (399)
T PRK10573 354 --QEQTQALADN 363 (399)
T ss_pred --HHHHHHHHHH
Confidence 3444444443
No 149
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=29.67 E-value=1.3e+02 Score=23.18 Aligned_cols=34 Identities=18% Similarity=0.225 Sum_probs=29.7
Q ss_pred hCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhc
Q 043012 87 ASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120 (151)
Q Consensus 87 a~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl 120 (151)
-.|.|..||.+..+++++.+-+...|...-||+.
T Consensus 193 ~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~ 226 (233)
T PRK05803 193 GKEKTQREIAKALGISRSYVSRIEKRALKKLFKE 226 (233)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 5889999999999999999999888877777664
No 150
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=29.49 E-value=1.5e+02 Score=21.74 Aligned_cols=36 Identities=17% Similarity=0.316 Sum_probs=32.0
Q ss_pred HhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhc
Q 043012 85 AWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120 (151)
Q Consensus 85 ~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl 120 (151)
.=-.|.|..||.+..++++|.+=..+.|....||+.
T Consensus 145 ~~~~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 180 (182)
T PRK12537 145 AYVDGCSHAEIAQRLGAPLGTVKAWIKRSLKALREC 180 (182)
T ss_pred HHHcCCCHHHHHHHHCCChhhHHHHHHHHHHHHHHH
Confidence 346999999999999999999999999988888764
No 151
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=29.37 E-value=1.1e+02 Score=22.48 Aligned_cols=35 Identities=20% Similarity=0.187 Sum_probs=31.2
Q ss_pred HhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhh
Q 043012 85 AWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQ 119 (151)
Q Consensus 85 ~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQ 119 (151)
.=-.|.|..||.+..++++|.+=..+.|...-|++
T Consensus 141 ~~~~g~s~~EIA~~l~is~~tV~~~l~rar~~Lr~ 175 (181)
T PRK12536 141 VKLEGLSVAETAQLTGLSESAVKVGIHRGLKALAA 175 (181)
T ss_pred HHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34699999999999999999999999988888876
No 152
>PF04010 DUF357: Protein of unknown function (DUF357); InterPro: IPR023140 This domain is found in a family of proteins, which have no known function.; PDB: 2OO2_A 2PMR_A.
Probab=29.34 E-value=48 Score=21.63 Aligned_cols=34 Identities=21% Similarity=0.212 Sum_probs=19.3
Q ss_pred HHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHhhc
Q 043012 108 RLLRRTIDLLAQIPKLPDVDQRLQKNAVDASNVM 141 (151)
Q Consensus 108 R~~rRl~elLrQl~~a~~~~~~L~~k~~~a~~~i 141 (151)
|.++.+.+-|.++..++.-...+...+++..++.
T Consensus 2 rY~~~l~~al~~i~~~~~~~s~~~~~a~~~~~mA 35 (75)
T PF04010_consen 2 RYIRMLEEALESIEIAPPEGSPLYDAAEEILEMA 35 (75)
T ss_dssp HHHHHHHHHHHHCC-----TS---HCHHHHHHHH
T ss_pred cHHHHHHHHHHHhhhhhccCCcchHHHHHHHHHH
Confidence 6789999999999977654555655555555543
No 153
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=29.28 E-value=90 Score=23.03 Aligned_cols=36 Identities=14% Similarity=0.172 Sum_probs=31.2
Q ss_pred HHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhh
Q 043012 84 EAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQ 119 (151)
Q Consensus 84 ~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQ 119 (151)
.....|.|..||.+..++++|.+=..+.|.-.-||+
T Consensus 145 l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 180 (188)
T PRK09640 145 LRFVAELEFQEIADIMHMGLSATKMRYKRALDKLRE 180 (188)
T ss_pred eHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 346699999999999999999998888888877776
No 154
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=29.20 E-value=1.1e+02 Score=22.43 Aligned_cols=33 Identities=3% Similarity=0.096 Sum_probs=28.1
Q ss_pred hCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhh
Q 043012 87 ASGLTWREMMMDCALDDGDLARLLRRTIDLLAQ 119 (151)
Q Consensus 87 a~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQ 119 (151)
-.|.|+.||-+..++++|.+=..+.|-..-|++
T Consensus 141 ~~g~s~~EIA~~lgis~~tVk~~l~rAl~~~~~ 173 (178)
T PRK12529 141 LDGMKQKDIAQALDIALPTVKKYIHQAYVTCLS 173 (178)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 499999999999999999998777776666654
No 155
>PF01435 Peptidase_M48: Peptidase family M48 This is family M48 in the peptidase classification. ; InterPro: IPR001915 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family M48 (Ste24 endopeptidase family, clan M-); members of both subfamily are represented. The members of this set of proteins are mostly described as probable protease htpX homologue (3.4.24 from EC) or CAAX prenyl protease 1, which proteolytically removes the C-terminal three residues of farnesylated proteins. They are integral membrane proteins associated with the endoplasmic reticulum and Golgi, binding one zinc ion per subunit. In Saccharomyces cerevisiae (Baker's yeast) Ste24p is required for the first NH2-terminal proteolytic processing event within the a-factor precursor, which takes place after COOH-terminal CAAX modification is complete. The Ste24p contains multiple predicted membrane spans, a zinc metalloprotease motif (HEXXH), and a COOH-terminal ER retrieval signal (KKXX). The HEXXH protease motif is critical for Ste24p activity, since Ste24p fails to function when conserved residues within this motif are mutated. The Ste24p homologues occur in a diverse group of organisms, including Escherichia coli, Schizosaccharomyces pombe (Fission yeast), Haemophilus influenzae, and Homo sapiens (Human), which indicates that the gene is highly conserved throughout evolution. Ste24p and the proteins related to it define a subfamily of proteins that are likely to function as intracellular, membrane-associated zinc metalloproteases []. HtpX is a zinc-dependent endoprotease member of the membrane-localized proteolytic system in E. coli, which participates in the proteolytic quality control of membrane proteins in conjunction with FtsH, a membrane-bound and ATP-dependent protease. Biochemical characterisation revealed that HtpX undergoes self-degradation upon cell disruption or membrane solubilization. It can also degraded casein and cleaves solubilized membrane proteins, for example, SecY []. Expression of HtpX in the plasma membrane is under the control of CpxR, with the metalloproteinase active site of HtpX located on the cytosolic side of the membrane. This suggests a potential role for HtpX in the response to mis-folded proteins [].; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis, 0016020 membrane; PDB: 3CQB_A 3C37_B.
Probab=29.19 E-value=10 Score=28.72 Aligned_cols=21 Identities=38% Similarity=0.433 Sum_probs=18.1
Q ss_pred ccccCCCCCCCHHHHHHHHHH
Q 043012 2 VLRNKILLDLKPAQLAAVCAS 22 (151)
Q Consensus 2 ~L~~g~f~~L~p~elAAllS~ 22 (151)
++..|+++.++++|++|+++=
T Consensus 75 ~v~~~ll~~~~~~el~aVlaH 95 (226)
T PF01435_consen 75 VVTSGLLESLSEDELAAVLAH 95 (226)
T ss_dssp EEEHHHHHHSSHHHHHHHHHH
T ss_pred EEeChhhhcccHHHHHHHHHH
Confidence 577888899999999999883
No 156
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=29.08 E-value=1.1e+02 Score=22.37 Aligned_cols=34 Identities=21% Similarity=0.332 Sum_probs=30.7
Q ss_pred hCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhc
Q 043012 87 ASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120 (151)
Q Consensus 87 a~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl 120 (151)
-.|.|+.||.+..+++.|.+-..+.|...-||+.
T Consensus 145 ~~g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~ 178 (184)
T PRK12512 145 VEGASIKETAAKLSMSEGAVRVALHRGLAALAAK 178 (184)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 4699999999999999999999999988888864
No 157
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=29.07 E-value=1.4e+02 Score=23.36 Aligned_cols=35 Identities=14% Similarity=0.227 Sum_probs=31.1
Q ss_pred hhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhc
Q 043012 86 WASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120 (151)
Q Consensus 86 Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl 120 (151)
.-.|.|+.||-+..++++|.+=..++|-..-||+.
T Consensus 214 ~~~~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 248 (251)
T PRK07670 214 YKEELTLTEIGQVLNLSTSRISQIHSKALFKLKKL 248 (251)
T ss_pred HhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 46999999999999999999998888888877763
No 158
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=29.07 E-value=2.3e+02 Score=22.60 Aligned_cols=40 Identities=13% Similarity=0.065 Sum_probs=35.1
Q ss_pred HHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhcCC
Q 043012 83 VEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIPK 122 (151)
Q Consensus 83 v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl~~ 122 (151)
+..-..|.|+.||.+..++++|.+=..+.|.-.-|++...
T Consensus 118 ~L~~~~g~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~~ 157 (281)
T TIGR02957 118 VLREVFDYPYEEIASIVGKSEANCRQLVSRARRHLDARRP 157 (281)
T ss_pred HHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence 3556799999999999999999999999999999998543
No 159
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=28.97 E-value=1e+02 Score=22.25 Aligned_cols=36 Identities=14% Similarity=-0.002 Sum_probs=31.4
Q ss_pred hhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhcC
Q 043012 86 WASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIP 121 (151)
Q Consensus 86 Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl~ 121 (151)
-..|.|..||.+..++++|.+=..+.|.-.-|++.-
T Consensus 133 ~~~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l 168 (175)
T PRK12518 133 DLEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFL 168 (175)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 358999999999999999999988888888887753
No 160
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=28.80 E-value=1.6e+02 Score=21.04 Aligned_cols=48 Identities=17% Similarity=0.018 Sum_probs=38.7
Q ss_pred CCCchHHHHHHHh-hCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhcC
Q 043012 74 CLDSQFSGMVEAW-ASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIP 121 (151)
Q Consensus 74 ~~~~~l~~~v~~W-a~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl~ 121 (151)
.+.+.--.++..+ ..|.|..||.+..++++|.+=-.+.|.-.-|++.-
T Consensus 108 ~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 156 (165)
T PRK09644 108 TLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRLKALL 156 (165)
T ss_pred hCCHHHHHHHHhHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3445566666655 69999999999999999999888888888887754
No 161
>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=28.78 E-value=1.4e+02 Score=23.45 Aligned_cols=36 Identities=14% Similarity=0.264 Sum_probs=31.7
Q ss_pred HHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhh
Q 043012 84 EAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQ 119 (151)
Q Consensus 84 ~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQ 119 (151)
..+..|.|+.+|-+..+++.+.+=+..+|...-||+
T Consensus 217 ~~~~~~~t~~eIA~~lgis~~~V~~~~~ral~kLr~ 252 (254)
T TIGR02850 217 MRFFEGKTQMEVAEEIGISQAQVSRLEKAALKHMRK 252 (254)
T ss_pred HHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHh
Confidence 345689999999999999999999999999888876
No 162
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.
Probab=28.76 E-value=1.5e+02 Score=18.36 Aligned_cols=55 Identities=9% Similarity=0.071 Sum_probs=38.8
Q ss_pred HHHHHHHHHHHHHHHcCCCCCCCCCchHHHHHHHhh----CCCCHHHHHhhcCCChhHH
Q 043012 52 VLDEHRSSFLELQEKHGVEIPCCLDSQFSGMVEAWA----SGLTWREMMMDCALDDGDL 106 (151)
Q Consensus 52 ~l~~~~~~l~~~~~~~~l~~~~~~~~~l~~~v~~Wa----~G~~f~eil~~t~l~EGdi 106 (151)
.+.+.+.+|.+...+.++-.-..++.=.+..+|.=+ ...|+.||.+.+++.+.+|
T Consensus 13 ~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~~~~t~~eIa~~~~Vs~~tI 71 (71)
T PF00382_consen 13 DVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNGVPRTLKEIAEAAGVSEKTI 71 (71)
T ss_dssp HHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTTSSSSHHHHHHHCTSSHHHH
T ss_pred HHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHhCCCCCcC
Confidence 566777788877778887655566555555555443 2378999999999999876
No 163
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=28.64 E-value=84 Score=20.06 Aligned_cols=28 Identities=7% Similarity=0.151 Sum_probs=21.6
Q ss_pred hhCCCCHHHHHhhcCCChhHHHHHHHHH
Q 043012 86 WASGLTWREMMMDCALDDGDLARLLRRT 113 (151)
Q Consensus 86 Wa~G~~f~eil~~t~l~EGdiVR~~rRl 113 (151)
.....|-.+|-+.+.+++-+|+|.++++
T Consensus 31 ~~~~~si~elA~~~~vS~sti~Rf~kkL 58 (77)
T PF01418_consen 31 EIAFMSISELAEKAGVSPSTIVRFCKKL 58 (77)
T ss_dssp HHCT--HHHHHHHCTS-HHHHHHHHHHC
T ss_pred HHHHccHHHHHHHcCCCHHHHHHHHHHh
Confidence 4567788899999999999999998875
No 164
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=28.38 E-value=1.4e+02 Score=23.36 Aligned_cols=37 Identities=14% Similarity=0.243 Sum_probs=31.6
Q ss_pred HHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhc
Q 043012 84 EAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120 (151)
Q Consensus 84 ~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl 120 (151)
..+..|.|..||-+..+++.+.+=+..+|...-||+.
T Consensus 220 ~~~~~~~t~~eIA~~lgis~~~V~~~~~~al~kLr~~ 256 (258)
T PRK08215 220 LRFFQGKTQMEVAEEIGISQAQVSRLEKAALKHMRKY 256 (258)
T ss_pred HHHhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3456899999999999999999988888888888763
No 165
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=28.33 E-value=1.1e+02 Score=22.55 Aligned_cols=34 Identities=18% Similarity=0.044 Sum_probs=29.5
Q ss_pred hCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhc
Q 043012 87 ASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120 (151)
Q Consensus 87 a~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl 120 (151)
-.|.|..||-+..++++|.+=..+.|.-.-||+.
T Consensus 145 ~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 178 (191)
T PRK12520 145 WLELETEEICQELQITATNAWVLLYRARMRLREC 178 (191)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 5799999999999999999988888877777664
No 166
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=28.07 E-value=1.3e+02 Score=20.20 Aligned_cols=36 Identities=14% Similarity=0.347 Sum_probs=29.1
Q ss_pred CCchHHHHHHHhhCCCCHHHHHhhcCCChhHHHHHHHH
Q 043012 75 LDSQFSGMVEAWASGLTWREMMMDCALDDGDLARLLRR 112 (151)
Q Consensus 75 ~~~~l~~~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rR 112 (151)
+++. -.+...+++|.|-.+|.+..+++.-+|-| ++|
T Consensus 37 Ls~R-~~I~~ll~~G~S~~eIA~~LgISrsTIyR-i~R 72 (88)
T TIGR02531 37 LAQR-LQVAKMLKQGKTYSDIEAETGASTATISR-VKR 72 (88)
T ss_pred hhHH-HHHHHHHHCCCCHHHHHHHHCcCHHHHHH-HHH
Confidence 5555 55555569999999999999999999999 444
No 167
>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=28.04 E-value=46 Score=25.84 Aligned_cols=43 Identities=14% Similarity=0.154 Sum_probs=36.0
Q ss_pred HHHHHHhhCCCCHHHHHhhcC--CChhHHHHHHHHHHHHHhhcCCC
Q 043012 80 SGMVEAWASGLTWREMMMDCA--LDDGDLARLLRRTIDLLAQIPKL 123 (151)
Q Consensus 80 ~~~v~~Wa~G~~f~eil~~t~--l~EGdiVR~~rRl~elLrQl~~a 123 (151)
..+|+.|. |.++.+++.... +.+..+.++++|+.+.|..+...
T Consensus 77 ~~lv~e~~-~~~L~~~i~~~~~~~~~~~~~~~~~qi~~al~~lH~~ 121 (298)
T cd07841 77 INLVFEFM-ETDLEKVIKDKSIVLTPADIKSYMLMTLRGLEYLHSN 121 (298)
T ss_pred EEEEEccc-CCCHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHHhC
Confidence 34688888 889999998765 99999999999999999887543
No 168
>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=28.04 E-value=2.2e+02 Score=23.88 Aligned_cols=87 Identities=11% Similarity=0.074 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHHHcCCCCC--------CCCCchHHHHHHHhh----CCCCHHHHHhh-cCCChhHHHHHHH------
Q 043012 51 NVLDEHRSSFLELQEKHGVEIP--------CCLDSQFSGMVEAWA----SGLTWREMMMD-CALDDGDLARLLR------ 111 (151)
Q Consensus 51 ~~l~~~~~~l~~~~~~~~l~~~--------~~~~~~l~~~v~~Wa----~G~~f~eil~~-t~l~EGdiVR~~r------ 111 (151)
+.+....++++.+ -+.|++.. ..-++.+-.+..+.. +|.+|++.++. .+.+.-.++..++
T Consensus 61 ~~~~~f~~~La~l-l~sGi~l~~aL~~l~~~~~~~~~~~~~~~i~~~l~~G~sls~al~~~~~~fp~~~~~~i~~GE~sG 139 (399)
T TIGR02120 61 AELALFTRQLATL-LGAGLPLEEALAALLEQAEKPRLKSVLAAIRSRVLEGKSLADALAQHPRDFPPLYRALVAAGEASG 139 (399)
T ss_pred HHHHHHHHHHHHH-HHcCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHHCCccHHHHHHhCcccCCHHHHHHHHHHhhcC
Q ss_pred HHHHHHhhcCCCCCCCHHHHHHHHHHH
Q 043012 112 RTIDLLAQIPKLPDVDQRLQKNAVDAS 138 (151)
Q Consensus 112 Rl~elLrQl~~a~~~~~~L~~k~~~a~ 138 (151)
++++.|++++.--+-..++++++..|.
T Consensus 140 ~L~~~L~~~a~~~~~~~~~~~~i~~al 166 (399)
T TIGR02120 140 ALDAVLERLADYLEERQALRSKITTAL 166 (399)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHH
No 169
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=27.95 E-value=1.1e+02 Score=22.04 Aligned_cols=32 Identities=19% Similarity=0.324 Sum_probs=28.2
Q ss_pred CCCCHHHHHhhcCCChhHHHHHHHHHHHHHhh
Q 043012 88 SGLTWREMMMDCALDDGDLARLLRRTIDLLAQ 119 (151)
Q Consensus 88 ~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQ 119 (151)
.|.|..+|.+..+++++.+-..+.|...-|++
T Consensus 141 ~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~~ 172 (176)
T PRK09638 141 YGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRK 172 (176)
T ss_pred cCCCHHHHHHHHCCChhHHHHHHHHHHHHHHH
Confidence 79999999999999999988888887777765
No 170
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=27.91 E-value=98 Score=24.34 Aligned_cols=34 Identities=15% Similarity=0.291 Sum_probs=28.7
Q ss_pred hCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhc
Q 043012 87 ASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120 (151)
Q Consensus 87 a~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl 120 (151)
..|.|..||.+..++++|.+=..+.|.-..|++.
T Consensus 130 ~eg~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~ 163 (228)
T PRK06704 130 VFQYSIADIAKVCSVSEGAVKASLFRSRNRLKTV 163 (228)
T ss_pred hhCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 5799999999999999999877777777766664
No 171
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=27.55 E-value=1.6e+02 Score=21.74 Aligned_cols=43 Identities=16% Similarity=0.223 Sum_probs=35.2
Q ss_pred chHHHHH-HHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhh
Q 043012 77 SQFSGMV-EAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQ 119 (151)
Q Consensus 77 ~~l~~~v-~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQ 119 (151)
+.--.++ ..=-.|.|+.||-+..++++|.+=..+.|.-..||+
T Consensus 133 ~~~r~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 133 TDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred HHHhHHhhhHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 3333344 334599999999999999999999999999999998
No 172
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=27.48 E-value=1.1e+02 Score=23.02 Aligned_cols=36 Identities=17% Similarity=0.129 Sum_probs=28.1
Q ss_pred HhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhc
Q 043012 85 AWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120 (151)
Q Consensus 85 ~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl 120 (151)
.-..|.|+.||.+..++++|.+=-.+.|.-..||+.
T Consensus 145 ~~~~g~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~ 180 (196)
T PRK12535 145 TQVLGYTYEEAAKIADVRVGTIRSRVARARADLIAA 180 (196)
T ss_pred HHHhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 345899999999999999999866666665555543
No 173
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=27.04 E-value=1.3e+02 Score=22.07 Aligned_cols=33 Identities=15% Similarity=0.304 Sum_probs=29.5
Q ss_pred hCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhh
Q 043012 87 ASGLTWREMMMDCALDDGDLARLLRRTIDLLAQ 119 (151)
Q Consensus 87 a~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQ 119 (151)
-.|.|..||.+..++++|.+=..+.|.-.-|++
T Consensus 141 ~~g~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~ 173 (179)
T PRK09415 141 YEELSIKEIAEVTGVNENTVKTRLKKAKELLKK 173 (179)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 479999999999999999998888888877776
No 174
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=26.92 E-value=1.2e+02 Score=16.64 Aligned_cols=26 Identities=27% Similarity=0.282 Sum_probs=21.6
Q ss_pred CCHHHHHhhcCCChhHHHHHHHHHHH
Q 043012 90 LTWREMMMDCALDDGDLARLLRRTID 115 (151)
Q Consensus 90 ~~f~eil~~t~l~EGdiVR~~rRl~e 115 (151)
.+..++.+..++....+-|.++++.+
T Consensus 9 ~s~~~la~~l~~s~~tv~~~l~~L~~ 34 (48)
T smart00419 9 LTRQEIAELLGLTRETVSRTLKRLEK 34 (48)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 56778888899999998888888765
No 175
>PRK04897 heat shock protein HtpX; Provisional
Probab=26.89 E-value=24 Score=28.91 Aligned_cols=20 Identities=15% Similarity=0.245 Sum_probs=17.7
Q ss_pred ccccCCCCCCCHHHHHHHHH
Q 043012 2 VLRNKILLDLKPAQLAAVCA 21 (151)
Q Consensus 2 ~L~~g~f~~L~p~elAAllS 21 (151)
++.+|+++.|+++|+.|+++
T Consensus 123 ~vt~gLl~~l~~~El~aVlA 142 (298)
T PRK04897 123 AVTTGLLAIMNREELEGVIG 142 (298)
T ss_pred EeehHHHhhCCHHHHHHHHH
Confidence 56678999999999999987
No 176
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=26.73 E-value=1.3e+02 Score=17.84 Aligned_cols=27 Identities=22% Similarity=0.229 Sum_probs=24.0
Q ss_pred CCCHHHHHhhcCCChhHHHHHHHHHHH
Q 043012 89 GLTWREMMMDCALDDGDLARLLRRTID 115 (151)
Q Consensus 89 G~~f~eil~~t~l~EGdiVR~~rRl~e 115 (151)
..+..++.+..+++...+-|.+++|.+
T Consensus 25 ~~s~~ela~~~g~s~~tv~r~l~~L~~ 51 (67)
T cd00092 25 PLTRQEIADYLGLTRETVSRTLKELEE 51 (67)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 378889999999999999999998876
No 177
>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=26.70 E-value=46 Score=23.26 Aligned_cols=18 Identities=28% Similarity=0.349 Sum_probs=15.0
Q ss_pred HHHHHHHHHHhhcCCCCC
Q 043012 108 RLLRRTIDLLAQIPKLPD 125 (151)
Q Consensus 108 R~~rRl~elLrQl~~a~~ 125 (151)
-.+|||+.+|||=.+.+.
T Consensus 16 ~AMrRLl~~LRqsQ~~CT 33 (103)
T PF11027_consen 16 MAMRRLLNLLRQSQNYCT 33 (103)
T ss_pred HHHHHHHHHHHHhhCccC
Confidence 368999999999877764
No 178
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=26.63 E-value=1.2e+02 Score=22.72 Aligned_cols=35 Identities=14% Similarity=0.078 Sum_probs=28.8
Q ss_pred hhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhc
Q 043012 86 WASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120 (151)
Q Consensus 86 Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl 120 (151)
--.|.|..||.+..++++|.+=..+.|.-..||+.
T Consensus 152 ~~eg~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~ 186 (201)
T PRK12545 152 EFLDFEIDDICTELTLTANHCSVLLYRARTRLRTC 186 (201)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 35999999999999999999986666666666663
No 179
>PF02885 Glycos_trans_3N: Glycosyl transferase family, helical bundle domain Prosite entry for Thymidine and pyrimidine-nucleoside phosphorylases; InterPro: IPR017459 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. The glycosyl transferase family includes anthranilate phosphoribosyltransferase (TrpD, 2.4.2.18 from EC) and thymidine phosphorylase (2.4.2.2 from EC). All these proteins can transfer a phosphorylated ribose substrate. Thymidine phosphorylase (2.4.2.2 from EC) catalyses the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate. This enzyme regulates the availability of thymidine and is therefore essential to nucleic acid metabolism. This N-terminal domain is found in various family 3 glycosyl transferases, including anthranilate phosphoribosyltransferase (TrpD, 2.4.2.18 from EC) and thymidine phosphorylase (2.4.2.2 from EC). All these proteins can transfer a phosphorylated ribose substrate. Thymidine phosphorylase catalyses the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate. This enzyme regulates the availability of thymidine and is therefore essential to nucleic acid metabolism.; PDB: 2DSJ_B 2ELC_B 2BPQ_A 1ZVW_B 3QR9_B 1V8G_B 2WK5_C 2J0F_C 2WK6_B 1UOU_A ....
Probab=26.60 E-value=59 Score=20.20 Aligned_cols=17 Identities=29% Similarity=0.343 Sum_probs=13.8
Q ss_pred CCCHHHHHHHHHHhhcc
Q 043012 10 DLKPAQLAAVCASLVSE 26 (151)
Q Consensus 10 ~L~p~elAAllS~~v~e 26 (151)
+++|.|++|+|.++-..
T Consensus 31 ~~s~~qiaAfL~al~~k 47 (66)
T PF02885_consen 31 EVSDAQIAAFLMALRMK 47 (66)
T ss_dssp SS-HHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHh
Confidence 67899999999998773
No 180
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=26.47 E-value=1.2e+02 Score=17.29 Aligned_cols=25 Identities=16% Similarity=0.166 Sum_probs=22.0
Q ss_pred CHHHHHhhcCCChhHHHHHHHHHHH
Q 043012 91 TWREMMMDCALDDGDLARLLRRTID 115 (151)
Q Consensus 91 ~f~eil~~t~l~EGdiVR~~rRl~e 115 (151)
|..++.+..+++...+-+.+++|.+
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~L~~ 46 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSRLEA 46 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 6788899999999999999998876
No 181
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=26.44 E-value=1.7e+02 Score=23.18 Aligned_cols=34 Identities=15% Similarity=0.236 Sum_probs=27.5
Q ss_pred hhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhh
Q 043012 86 WASGLTWREMMMDCALDDGDLARLLRRTIDLLAQ 119 (151)
Q Consensus 86 Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQ 119 (151)
...|.|+.+|-+..+++++.+=+.+.|...-||.
T Consensus 225 ~~~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~ 258 (268)
T PRK06288 225 YYEDLTLKEIGKVLGVTESRISQLHTKAVLQLRA 258 (268)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4789999999999999999998666665555543
No 182
>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=26.42 E-value=46 Score=23.87 Aligned_cols=25 Identities=16% Similarity=0.235 Sum_probs=20.1
Q ss_pred HHHHHhhcCCCCCCCHHHHHHHHHHH
Q 043012 113 TIDLLAQIPKLPDVDQRLQKNAVDAS 138 (151)
Q Consensus 113 l~elLrQl~~a~~~~~~L~~k~~~a~ 138 (151)
+-|+++||++|.. |+.|.+.|++..
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 4588999999877 999999988754
No 183
>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=26.22 E-value=1.3e+02 Score=21.65 Aligned_cols=42 Identities=17% Similarity=0.296 Sum_probs=33.5
Q ss_pred hHHHHH-HHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhh
Q 043012 78 QFSGMV-EAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQ 119 (151)
Q Consensus 78 ~l~~~v-~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQ 119 (151)
.--.++ ..--.|.|..||.+..++++|.+-..+.|.-.-||.
T Consensus 123 ~~r~i~~l~~~~g~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~ 165 (169)
T TIGR02954 123 KYQTAIILRYYHDLTIKEIAEVMNKPEGTVKTYLHRALKKLKK 165 (169)
T ss_pred HHhHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 333444 334689999999999999999999999988877765
No 184
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=26.09 E-value=1.3e+02 Score=22.70 Aligned_cols=43 Identities=14% Similarity=0.135 Sum_probs=34.3
Q ss_pred HHHHHH-HhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhcC
Q 043012 79 FSGMVE-AWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIP 121 (151)
Q Consensus 79 l~~~v~-~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl~ 121 (151)
--.++. .--.|.|..||.+..++++|.+=..+.|...-|++.-
T Consensus 158 ~r~vl~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 158 QQTVVKGVYFQELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 333443 3568999999999999999999988888888887643
No 185
>PRK04966 hypothetical protein; Provisional
Probab=26.08 E-value=1.1e+02 Score=20.00 Aligned_cols=22 Identities=27% Similarity=0.285 Sum_probs=19.0
Q ss_pred CCCCCHHHHHHHHHHhhccccc
Q 043012 8 LLDLKPAQLAAVCASLVSEGIK 29 (151)
Q Consensus 8 f~~L~p~elAAllS~~v~e~~~ 29 (151)
|+.|+|+-|-+++-.||.-+.+
T Consensus 5 ~~~L~~eTL~nLIeefv~ReGT 26 (72)
T PRK04966 5 WQDLAPETLENLIESFVLREGT 26 (72)
T ss_pred hHhCCHHHHHHHHHHHHhccCc
Confidence 5789999999999999996544
No 186
>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=26.04 E-value=52 Score=25.41 Aligned_cols=45 Identities=11% Similarity=0.190 Sum_probs=39.0
Q ss_pred hHHHHHHHhhCCCCHHHHHhhc--CCChhHHHHHHHHHHHHHhhcCC
Q 043012 78 QFSGMVEAWASGLTWREMMMDC--ALDDGDLARLLRRTIDLLAQIPK 122 (151)
Q Consensus 78 ~l~~~v~~Wa~G~~f~eil~~t--~l~EGdiVR~~rRl~elLrQl~~ 122 (151)
....++++++.|.++.+++... .+.+..+.+.+.++.+.|..+..
T Consensus 88 ~~~~lv~e~~~~~~L~~~l~~~~~~l~~~~~~~i~~~i~~~L~~lH~ 134 (286)
T cd06614 88 DELWVVMEYMDGGSLTDIITQNFVRMNEPQIAYVCREVLQGLEYLHS 134 (286)
T ss_pred CEEEEEEeccCCCcHHHHHHHhccCCCHHHHHHHHHHHHHHHHHHHh
Confidence 4455688899999999999987 79999999999999999988754
No 187
>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=25.88 E-value=1.3e+02 Score=22.28 Aligned_cols=35 Identities=17% Similarity=0.104 Sum_probs=29.1
Q ss_pred hhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhc
Q 043012 86 WASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120 (151)
Q Consensus 86 Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl 120 (151)
--.|.|+.||.+..++++|.+=..+.|.-.-|++.
T Consensus 144 ~~~g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~ 178 (188)
T TIGR02943 144 EVLGFESDEICQELEISTSNCHVLLYRARLSLRAC 178 (188)
T ss_pred HHhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 35899999999999999999977777776666653
No 188
>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=25.88 E-value=1.3e+02 Score=22.05 Aligned_cols=36 Identities=17% Similarity=0.220 Sum_probs=29.8
Q ss_pred HHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhc
Q 043012 84 EAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120 (151)
Q Consensus 84 ~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl 120 (151)
+-| .|.|..||.+..++++|.+=..+.|.-.-|++.
T Consensus 161 ~~~-~~~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~~ 196 (198)
T TIGR02859 161 SYL-DGKSYQEIACDLNRHVKSIDNALQRVKRKLEKY 196 (198)
T ss_pred HHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 335 899999999999999999887777777776653
No 189
>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=25.75 E-value=92 Score=14.99 Aligned_cols=28 Identities=18% Similarity=0.153 Sum_probs=17.5
Q ss_pred HHHHhhCCCCHHHHHhhcCCChhHHHHH
Q 043012 82 MVEAWASGLTWREMMMDCALDDGDLARL 109 (151)
Q Consensus 82 ~v~~Wa~G~~f~eil~~t~l~EGdiVR~ 109 (151)
++..|-+|.+..++.+..++....+-++
T Consensus 14 i~~~~~~~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 14 ARRLLAAGESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred HHHHHHcCCCHHHHHHHHCCCHHHHHHh
Confidence 3344556777777777777766655443
No 190
>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=25.62 E-value=49 Score=24.98 Aligned_cols=44 Identities=9% Similarity=-0.005 Sum_probs=37.4
Q ss_pred HHHHHHhhCCCCHHHHHhhc-CCChhHHHHHHHHHHHHHhhcCCC
Q 043012 80 SGMVEAWASGLTWREMMMDC-ALDDGDLARLLRRTIDLLAQIPKL 123 (151)
Q Consensus 80 ~~~v~~Wa~G~~f~eil~~t-~l~EGdiVR~~rRl~elLrQl~~a 123 (151)
.-+++.+..|.++.+.+... .+.+..+.+++.++.+.|..+...
T Consensus 75 ~~lv~e~~~~~~L~~~l~~~~~l~~~~~~~~~~~i~~~l~~lh~~ 119 (258)
T cd05578 75 MYLVVDLLLGGDLRYHLSQKVKFSEEQVKFWICEIVLALEYLHSK 119 (258)
T ss_pred EEEEEeCCCCCCHHHHHHhcCCcCHHHHHHHHHHHHHHHHHHHhC
Confidence 34567789999999999877 899999999999999999887654
No 191
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=25.57 E-value=1.3e+02 Score=23.15 Aligned_cols=35 Identities=20% Similarity=0.185 Sum_probs=30.9
Q ss_pred hCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhcC
Q 043012 87 ASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIP 121 (151)
Q Consensus 87 a~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl~ 121 (151)
-.|.|..||.+..++++|.+=..+.|.-.-||+.-
T Consensus 163 ~~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l 197 (231)
T PRK11922 163 VEELSVEETAQALGLPEETVKTRLHRARRLLRESL 197 (231)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 57999999999999999999888888888887743
No 192
>PF01724 DUF29: Domain of unknown function DUF29; InterPro: IPR002636 This entry is represented by Ralstonia phage RSS1, Orf11. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of various hypothetical proteins from cyanobacteria, none of which are functionally described. The aligned region is approximately 120-140 amino acids long corresponding to almost the entire length of the proteins in the family.; PDB: 3FCN_A.
Probab=25.52 E-value=64 Score=23.45 Aligned_cols=19 Identities=26% Similarity=0.345 Sum_probs=16.4
Q ss_pred CChhHHHHHHHHHHHHHhh
Q 043012 101 LDDGDLARLLRRTIDLLAQ 119 (151)
Q Consensus 101 l~EGdiVR~~rRl~elLrQ 119 (151)
++|.||+-|+.+..++||+
T Consensus 1 LYe~Df~~W~~~qa~lLr~ 19 (139)
T PF01724_consen 1 LYEQDFYLWLQEQAQLLRE 19 (139)
T ss_dssp -TTT-HHHHHHHHHHHHHH
T ss_pred CchhhHHHHHHHHHHHHHc
Confidence 5789999999999999999
No 193
>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=25.35 E-value=56 Score=24.05 Aligned_cols=46 Identities=13% Similarity=0.203 Sum_probs=39.1
Q ss_pred hHHHHHHHhhCCCCHHHHHhhc--CCChhHHHHHHHHHHHHHhhcCCC
Q 043012 78 QFSGMVEAWASGLTWREMMMDC--ALDDGDLARLLRRTIDLLAQIPKL 123 (151)
Q Consensus 78 ~l~~~v~~Wa~G~~f~eil~~t--~l~EGdiVR~~rRl~elLrQl~~a 123 (151)
....++++|..|.++.+.+... .+.+..+.+.+.++.+.|..+...
T Consensus 70 ~~~~l~~e~~~~~~L~~~~~~~~~~~~~~~~~~i~~~i~~~l~~lh~~ 117 (253)
T cd05122 70 DELWIVMEFCSGGSLKDLLKSTNQTLTESQIAYVCKELLKGLEYLHSN 117 (253)
T ss_pred CeEEEEEecCCCCcHHHHHhhcCCCCCHHHHHHHHHHHHHHHHHhhcC
Confidence 3445678899999999999886 789999999999999999988764
No 194
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=25.22 E-value=3e+02 Score=21.97 Aligned_cols=55 Identities=13% Similarity=0.012 Sum_probs=40.2
Q ss_pred HHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhcCCCCCC----CHHHHHHHHHHH
Q 043012 84 EAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIPKLPDV----DQRLQKNAVDAS 138 (151)
Q Consensus 84 ~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl~~a~~~----~~~L~~k~~~a~ 138 (151)
..-..|.|+.||.+..++++|.+=..+.|--.-|++....... +.++-+.+-+|.
T Consensus 126 L~~~~g~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~~~~~~~~~~~~~~v~~f~~A~ 184 (293)
T PRK09636 126 LHDVFGVPFDEIASTLGRSPAACRQLASRARKHVRAARPRFPVSDEEGAELVEAFFAAL 184 (293)
T ss_pred HHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHHHH
Confidence 4456899999999999999999998889988888885432211 344445554444
No 195
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=25.08 E-value=1.2e+02 Score=24.19 Aligned_cols=35 Identities=14% Similarity=0.171 Sum_probs=32.0
Q ss_pred hCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhcC
Q 043012 87 ASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIP 121 (151)
Q Consensus 87 a~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl~ 121 (151)
-.|.|+.||-+..++++|.+-+.+.|-...||+.-
T Consensus 240 ~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l 274 (285)
T TIGR02394 240 YEPATLEEVAAEVGLTRERVRQIQVEALKKLRRIL 274 (285)
T ss_pred CCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 68999999999999999999999999999988743
No 196
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=25.07 E-value=1.7e+02 Score=20.37 Aligned_cols=33 Identities=9% Similarity=0.123 Sum_probs=22.5
Q ss_pred HHHHhhCCCCHHHHHhhcCCChhHHHHHHHHHH
Q 043012 82 MVEAWASGLTWREMMMDCALDDGDLARLLRRTI 114 (151)
Q Consensus 82 ~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~ 114 (151)
|.+....|.|-.+++..-++.++.+-+|.++..
T Consensus 22 V~~~~~~g~sv~evA~e~gIs~~tl~~W~r~y~ 54 (121)
T PRK09413 22 VQQSFEPGMTVSLVARQHGVAASQLFLWRKQYQ 54 (121)
T ss_pred HHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHh
Confidence 334456677777777777777777777777654
No 197
>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=25.01 E-value=78 Score=23.61 Aligned_cols=42 Identities=12% Similarity=0.141 Sum_probs=36.5
Q ss_pred HHHHHHhhCCCCHHHHHhh-----cCCChhHHHHHHHHHHHHHhhcC
Q 043012 80 SGMVEAWASGLTWREMMMD-----CALDDGDLARLLRRTIDLLAQIP 121 (151)
Q Consensus 80 ~~~v~~Wa~G~~f~eil~~-----t~l~EGdiVR~~rRl~elLrQl~ 121 (151)
..++++|+.|.++.+.+.. ..+.+..+.+++.++.+.|..+.
T Consensus 76 ~~~~~e~~~~~~L~~~l~~~~~~~~~l~~~~~~~~~~~i~~~l~~lH 122 (265)
T cd08217 76 LYIVMEYCEGGDLAQLIQKCKKERKYIEEEFIWRILTQLLLALYECH 122 (265)
T ss_pred EEEEehhccCCCHHHHHHHHhhcccCCCHHHHHHHHHHHHHHHHHHh
Confidence 4578899999999999875 36888999999999999999887
No 198
>smart00073 HPT Histidine Phosphotransfer domain. Contains an active histidine residue that mediates phosphotransfer reactions. Domain detected only in eubacteria. This alignment is an extension to that shown in the Cell structure paper.
Probab=24.94 E-value=1.8e+02 Score=18.14 Aligned_cols=42 Identities=19% Similarity=0.161 Sum_probs=31.4
Q ss_pred CChhHHHHHHHHHHHHHhhcCCCCC-CCHHHHHHHHHHHhhcC
Q 043012 101 LDDGDLARLLRRTIDLLAQIPKLPD-VDQRLQKNAVDASNVMD 142 (151)
Q Consensus 101 l~EGdiVR~~rRl~elLrQl~~a~~-~~~~L~~k~~~a~~~i~ 142 (151)
+.-..+...+.++++.+++...-.. ..+.+.+.+.++.+.|+
T Consensus 44 ~g~~~l~~~~~~lE~~~~~~~~~~~~~~~~l~~~~~~~~~~l~ 86 (87)
T smart00073 44 LGLQQLAQLCHQLENLLDAARSGEVELTPDLLDLLLELVDVLK 86 (87)
T ss_pred cCHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHc
Confidence 4556777888899999988654322 38899999998888764
No 199
>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=24.87 E-value=50 Score=24.99 Aligned_cols=47 Identities=9% Similarity=0.197 Sum_probs=38.2
Q ss_pred chHHHHHHHhhCCCCHHHHHhhc-CCChhHHHHHHHHHHHHHhhcCCC
Q 043012 77 SQFSGMVEAWASGLTWREMMMDC-ALDDGDLARLLRRTIDLLAQIPKL 123 (151)
Q Consensus 77 ~~l~~~v~~Wa~G~~f~eil~~t-~l~EGdiVR~~rRl~elLrQl~~a 123 (151)
.+-..+++.|+.|.++.+++... .+.+-.+.++++++...|..+.+.
T Consensus 75 ~~~~~~v~e~~~~~~L~~~l~~~~~~~~~~~~~~~~ql~~al~~LH~~ 122 (268)
T cd06630 75 DSHFNLFVEWMAGGSVSHLLSKYGAFKEAVIINYTEQLLRGLSYLHEN 122 (268)
T ss_pred CCeEEEEEeccCCCcHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHhC
Confidence 34455788899999999998764 588999999999999988887543
No 200
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=24.86 E-value=1e+02 Score=18.54 Aligned_cols=29 Identities=10% Similarity=0.212 Sum_probs=24.6
Q ss_pred hCCCCHHHHHhhcCCChhHHHHHHHHHHH
Q 043012 87 ASGLTWREMMMDCALDDGDLARLLRRTID 115 (151)
Q Consensus 87 a~G~~f~eil~~t~l~EGdiVR~~rRl~e 115 (151)
..+.++.+|.+..++..+.+-+-++.|.+
T Consensus 22 ~~~~t~~ela~~l~~~~~t~s~hL~~L~~ 50 (61)
T PF12840_consen 22 NGPMTVSELAEELGISQSTVSYHLKKLEE 50 (61)
T ss_dssp CSTBEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 45699999999999999999998888876
No 201
>PRK05572 sporulation sigma factor SigF; Validated
Probab=24.85 E-value=1.8e+02 Score=22.70 Aligned_cols=37 Identities=11% Similarity=0.155 Sum_probs=32.4
Q ss_pred HHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhc
Q 043012 84 EAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120 (151)
Q Consensus 84 ~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl 120 (151)
..+-.|.|..+|-+..+++.+.+-+...|...-||+.
T Consensus 213 l~~~~~~s~~eIA~~lgis~~~V~~~~~ral~kLr~~ 249 (252)
T PRK05572 213 LRYFKDKTQSEVAKRLGISQVQVSRLEKKILKQMKEK 249 (252)
T ss_pred HHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3456899999999999999999999999998888864
No 202
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=24.77 E-value=1.8e+02 Score=21.48 Aligned_cols=37 Identities=19% Similarity=0.295 Sum_probs=31.7
Q ss_pred hhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhcCC
Q 043012 86 WASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIPK 122 (151)
Q Consensus 86 Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl~~ 122 (151)
...|.|..||.+..++++|.+=..+.|.-..||+.-.
T Consensus 124 ~~~g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~ 160 (182)
T PRK12540 124 GASGFSYEDAAAICGCAVGTIKSRVNRARSKLSALLY 160 (182)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 5799999999999999999998888888887776533
No 203
>PRK00304 hypothetical protein; Provisional
Probab=24.33 E-value=1.7e+02 Score=19.20 Aligned_cols=22 Identities=14% Similarity=0.158 Sum_probs=18.8
Q ss_pred CCCCCHHHHHHHHHHhhccccc
Q 043012 8 LLDLKPAQLAAVCASLVSEGIK 29 (151)
Q Consensus 8 f~~L~p~elAAllS~~v~e~~~ 29 (151)
|+.|+|+.|-+++-.||..+.+
T Consensus 5 ~~~L~~eTL~nLIeefv~ReGT 26 (75)
T PRK00304 5 YDQLEADTLTRLIEDFVTRDGT 26 (75)
T ss_pred hHhCCHHHHHHHHHHHHhccCc
Confidence 5679999999999999996544
No 204
>PRK02391 heat shock protein HtpX; Provisional
Probab=24.32 E-value=28 Score=28.57 Aligned_cols=20 Identities=30% Similarity=0.473 Sum_probs=17.4
Q ss_pred ccccCCCCCCCHHHHHHHHH
Q 043012 2 VLRNKILLDLKPAQLAAVCA 21 (151)
Q Consensus 2 ~L~~g~f~~L~p~elAAllS 21 (151)
++.+|+++.|+++|+.|+++
T Consensus 119 ~vt~gLl~~L~~~El~aVla 138 (296)
T PRK02391 119 CVTTGLMRRLDPDELEAVLA 138 (296)
T ss_pred EecHHHHhhCCHHHHHHHHH
Confidence 45688999999999999987
No 205
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=24.30 E-value=1.4e+02 Score=22.56 Aligned_cols=35 Identities=17% Similarity=0.263 Sum_probs=32.0
Q ss_pred hCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhcC
Q 043012 87 ASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIP 121 (151)
Q Consensus 87 a~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl~ 121 (151)
-.|.|..||-+..++++|.+=..+.|.-.-|++.-
T Consensus 152 ~~g~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l 186 (203)
T PRK09647 152 IEGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAAL 186 (203)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 69999999999999999999999999988888753
No 206
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=24.11 E-value=1e+02 Score=16.72 Aligned_cols=22 Identities=18% Similarity=0.172 Sum_probs=18.8
Q ss_pred CHHHHHhhcCCChhHHHHHHHH
Q 043012 91 TWREMMMDCALDDGDLARLLRR 112 (151)
Q Consensus 91 ~f~eil~~t~l~EGdiVR~~rR 112 (151)
|..|+.+..+++..++-+|+++
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~~ 23 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHHc
Confidence 5678888999999999998876
No 207
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=24.09 E-value=1.8e+02 Score=22.35 Aligned_cols=35 Identities=20% Similarity=0.243 Sum_probs=31.7
Q ss_pred hhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhc
Q 043012 86 WASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120 (151)
Q Consensus 86 Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl 120 (151)
.-.|.|+.||.+..++++|.+=..+.|.-..|+..
T Consensus 147 y~eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~ 181 (216)
T PRK12533 147 ELEDMSYREIAAIADVPVGTVMSRLARARRRLAAL 181 (216)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 45899999999999999999999999988888875
No 208
>PF07374 DUF1492: Protein of unknown function (DUF1492); InterPro: IPR010861 This entry is represented by Streptococcus phage 7201, Orf19. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several hypothetical, highly conserved Streptococcal and related phage proteins. The function of this family is unknown.
Probab=24.06 E-value=2.1e+02 Score=19.31 Aligned_cols=33 Identities=12% Similarity=0.372 Sum_probs=28.3
Q ss_pred HHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHH
Q 043012 83 VEAWASGLTWREMMMDCALDDGDLARLLRRTID 115 (151)
Q Consensus 83 v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~e 115 (151)
.+.+-++.+|.+|++.-++++..+-|.-++-..
T Consensus 65 ~~~Yi~~~~~~~I~~~l~~S~~t~yr~~~~Al~ 97 (100)
T PF07374_consen 65 RMRYINKLTWEQIAEELNISRRTYYRIHKKALK 97 (100)
T ss_pred HHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 366779999999999999999999998776554
No 209
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=24.03 E-value=1.9e+02 Score=22.46 Aligned_cols=36 Identities=8% Similarity=0.241 Sum_probs=30.2
Q ss_pred HHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhh
Q 043012 84 EAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQ 119 (151)
Q Consensus 84 ~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQ 119 (151)
..+..|.|+.+|-+..+++++-+-|.-+++.+-||+
T Consensus 194 l~~~~~~t~~EIA~~lgis~~~V~q~~~~~~~kLr~ 229 (231)
T PRK12427 194 LYYQHEMSLKEIALVLDLTEARICQLNKKIAQKIKS 229 (231)
T ss_pred HHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHh
Confidence 335689999999999999999888888888877764
No 210
>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=23.90 E-value=67 Score=23.25 Aligned_cols=46 Identities=15% Similarity=0.198 Sum_probs=38.2
Q ss_pred hHHHHHHHhhCCCCHHHHHhhcC--CChhHHHHHHHHHHHHHhhcCCC
Q 043012 78 QFSGMVEAWASGLTWREMMMDCA--LDDGDLARLLRRTIDLLAQIPKL 123 (151)
Q Consensus 78 ~l~~~v~~Wa~G~~f~eil~~t~--l~EGdiVR~~rRl~elLrQl~~a 123 (151)
....+++.|..|.++.+.+.... +.+.++.+.+.++.+.|..+...
T Consensus 70 ~~~~~v~e~~~~~~L~~~~~~~~~~~~~~~~~~~~~~l~~~l~~lh~~ 117 (225)
T smart00221 70 EPLYLVMEYCEGGDLFDYLRKKGGKLSEEEARFYLRQILEALEYLHSL 117 (225)
T ss_pred CceEEEEeccCCCCHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHhC
Confidence 34557888999999999998765 89999999999999988877554
No 211
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=23.80 E-value=1.5e+02 Score=21.79 Aligned_cols=33 Identities=12% Similarity=0.226 Sum_probs=28.9
Q ss_pred hCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhh
Q 043012 87 ASGLTWREMMMDCALDDGDLARLLRRTIDLLAQ 119 (151)
Q Consensus 87 a~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQ 119 (151)
-.|.|..||.+..++++|.+=..+.|.-.-||.
T Consensus 152 ~~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~ 184 (193)
T PRK11923 152 FDGLSYEDIASVMQCPVGTVRSRIFRAREAIDK 184 (193)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 499999999999999999998888887777665
No 212
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=23.77 E-value=2.1e+02 Score=21.04 Aligned_cols=44 Identities=14% Similarity=0.156 Sum_probs=34.5
Q ss_pred chHHHHH-HHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhc
Q 043012 77 SQFSGMV-EAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120 (151)
Q Consensus 77 ~~l~~~v-~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl 120 (151)
+.--.++ ..--.|.|..||.+..++++|.+=..+.|.-.-|++.
T Consensus 109 ~~~r~i~~l~~~~g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 153 (181)
T PRK09637 109 EKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKEL 153 (181)
T ss_pred HHHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 3344444 3457999999999999999999988888887777764
No 213
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=23.75 E-value=2.1e+02 Score=21.04 Aligned_cols=46 Identities=15% Similarity=0.116 Sum_probs=35.9
Q ss_pred CCCchHHHHHH-HhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhh
Q 043012 74 CLDSQFSGMVE-AWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQ 119 (151)
Q Consensus 74 ~~~~~l~~~v~-~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQ 119 (151)
.+.+.--.++. .+-.|.|..||.+..++++|.+=..+.|.-.-|+.
T Consensus 131 ~L~~~~r~i~~l~~~~g~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~ 177 (189)
T PRK06811 131 DLEKLDREIFIRRYLLGEKIEEIAKKLGLTRSAIDNRLSRGRKKLQK 177 (189)
T ss_pred hCCHHHHHHHHHHHHccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34455555554 36799999999999999999999888888777664
No 214
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=23.59 E-value=68 Score=19.71 Aligned_cols=27 Identities=15% Similarity=0.166 Sum_probs=24.5
Q ss_pred CCCHHHHHhhcCCChhHHHHHHHHHHH
Q 043012 89 GLTWREMMMDCALDDGDLARLLRRTID 115 (151)
Q Consensus 89 G~~f~eil~~t~l~EGdiVR~~rRl~e 115 (151)
+.+-.+|.+.++++...+-+.+++|.+
T Consensus 22 ~~t~~eIa~~l~i~~~~v~~~L~~L~~ 48 (68)
T PF01978_consen 22 PATAEEIAEELGISRSTVYRALKSLEE 48 (68)
T ss_dssp HEEHHHHHHHHTSSHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 388999999999999999999999876
No 215
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=23.54 E-value=2.6e+02 Score=21.15 Aligned_cols=45 Identities=11% Similarity=0.137 Sum_probs=39.8
Q ss_pred CCCchHHHHHHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHh
Q 043012 74 CLDSQFSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLA 118 (151)
Q Consensus 74 ~~~~~l~~~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLr 118 (151)
.+.+.=.++...|++|.|-.||-+.-.+++.++=.-.+++-+=|.
T Consensus 137 ~LT~RE~eVL~lla~G~snkeIA~~L~iS~~TVk~h~~~I~~KL~ 181 (207)
T PRK15411 137 SLSRTESSMLRMWMAGQGTIQISDQMNIKAKTVSSHKGNIKRKIK 181 (207)
T ss_pred cCCHHHHHHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHHhC
Confidence 488888999999999999999999999999999888877766554
No 216
>KOG2163 consensus Centromere/kinetochore protein zw10 involved in mitotic chromosome segregation [Cell cycle control, cell division, chromosome partitioning]
Probab=23.15 E-value=39 Score=30.91 Aligned_cols=34 Identities=15% Similarity=0.325 Sum_probs=26.1
Q ss_pred CCchHHHHHHHhhCCC-CHHHHHhhcCCChhHHHHHH
Q 043012 75 LDSQFSGMVEAWASGL-TWREMMMDCALDDGDLARLL 110 (151)
Q Consensus 75 ~~~~l~~~v~~Wa~G~-~f~eil~~t~l~EGdiVR~~ 110 (151)
++-.+|++.++|.+|+ ||+.-...+++. ++||.+
T Consensus 670 L~asLmeIt~rW~dgkGplaa~fsrsEVk--~lIkAL 704 (719)
T KOG2163|consen 670 LGASLMEITHRWFDGKGPLAAHFSRSEVK--GLIKAL 704 (719)
T ss_pred hCchHhHHHHHHhcCCccHHhhccHHHHH--HHHHHH
Confidence 6889999999999998 888777665543 455554
No 217
>cd08777 Death_RIP1 Death Domain of Receptor-Interacting Protein 1. Death domain (DD) found in Receptor-Interacting Protein 1 (RIP1) and related proteins. RIP kinases serve as essential sensors of cellular stress. Vertebrates contain several types containing a homologous N-terminal kinase domain and varying C-terminal domains. RIP1 harbors a C-terminal DD, which binds death receptors (DRs) including TNF receptor 1, Fas, TNF-related apoptosis-inducing ligand receptor 1 (TRAILR1), and TRAILR2. It also interacts with other DD-containing adaptor proteins such as TRADD and FADD. RIP1 plays a crucial role in determining a cell's fate, between survival or death, following exposure to stress signals. It is important in the signaling of NF-kappaB and MAPKs, and it links DR-associated signaling to reactive oxygen species (ROS) production. Abnormal RIP1 function may result in ROS accumulation affecting inflammatory responses, innate immunity, stress responses, and cell survival. In general, DDs ar
Probab=23.01 E-value=1.1e+02 Score=20.32 Aligned_cols=9 Identities=22% Similarity=0.697 Sum_probs=4.5
Q ss_pred HHHHHHHhh
Q 043012 79 FSGMVEAWA 87 (151)
Q Consensus 79 l~~~v~~Wa 87 (151)
...+...|.
T Consensus 46 ~~~mL~~W~ 54 (86)
T cd08777 46 VHQMLHKWK 54 (86)
T ss_pred HHHHHHHHH
Confidence 444455554
No 218
>PF11242 DUF2774: Protein of unknown function (DUF2774); InterPro: IPR021404 This entry is represented by Bacteriophage T4, Gp24.3; it is a family of uncharacterised viral proteins.
Probab=22.94 E-value=1.9e+02 Score=18.40 Aligned_cols=29 Identities=17% Similarity=0.297 Sum_probs=23.7
Q ss_pred hCCCCHHHHHhhcCCChhHHHHHHHHHHH
Q 043012 87 ASGLTWREMMMDCALDDGDLARLLRRTID 115 (151)
Q Consensus 87 a~G~~f~eil~~t~l~EGdiVR~~rRl~e 115 (151)
-.|.+|.||-+.-++.+-|..-.-..+++
T Consensus 11 E~g~~FveIAr~~~i~a~e~a~~w~~Ve~ 39 (63)
T PF11242_consen 11 ESGLSFVEIARKIGITAKEVAKAWAEVET 39 (63)
T ss_pred HcCCcHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 47999999999999999888776666654
No 219
>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=22.89 E-value=59 Score=25.43 Aligned_cols=46 Identities=15% Similarity=0.306 Sum_probs=38.0
Q ss_pred chHHHHHHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhcCC
Q 043012 77 SQFSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIPK 122 (151)
Q Consensus 77 ~~l~~~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl~~ 122 (151)
.....+|+.|..|.++.+.+....+.++.+...++++...|+.+..
T Consensus 88 ~~~~~lv~e~~~~~~L~~~~~~~~l~~~~~~~i~~~l~~al~~LH~ 133 (293)
T cd06647 88 GDELWVVMEYLAGGSLTDVVTETCMDEGQIAAVCRECLQALEFLHS 133 (293)
T ss_pred CCcEEEEEecCCCCcHHHHHhhcCCCHHHHHHHHHHHHHHHHHHHh
Confidence 3445678899999999999988888999999988888888876643
No 220
>PF12029 DUF3516: Domain of unknown function (DUF3516); InterPro: IPR021904 This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is typically between 460 to 473 amino acids in length. This domain is found associated with PF00270 from PFAM, PF00271 from PFAM.
Probab=22.87 E-value=1.9e+02 Score=25.44 Aligned_cols=47 Identities=21% Similarity=0.333 Sum_probs=34.9
Q ss_pred hCCCCHHHHHhhcCC--ChhHHHHHHHHHHHHHhhc-CCCCCCCHHHHHHH
Q 043012 87 ASGLTWREMMMDCAL--DDGDLARLLRRTIDLLAQI-PKLPDVDQRLQKNA 134 (151)
Q Consensus 87 a~G~~f~eil~~t~l--~EGdiVR~~rRl~elLrQl-~~a~~~~~~L~~k~ 134 (151)
-+|+||++.+...++ +||-+.|.+.-.=-.|+|. ....+ +++|..-.
T Consensus 250 E~amtF~dyV~~YgLaRSEGvlLRYLsDAyraL~qtVP~~~r-teel~dii 299 (461)
T PF12029_consen 250 ERAMTFSDYVSRYGLARSEGVLLRYLSDAYRALRQTVPEDAR-TEELEDII 299 (461)
T ss_pred HhhCCHHHHHHHhCcchhhhHHHHHHHHHHHHHhhhCChhhc-CchHHHHH
Confidence 378899999998775 6999999998888888884 44444 55554433
No 221
>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=22.74 E-value=57 Score=25.08 Aligned_cols=44 Identities=16% Similarity=0.229 Sum_probs=37.9
Q ss_pred HHHHHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhcCCC
Q 043012 80 SGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIPKL 123 (151)
Q Consensus 80 ~~~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl~~a 123 (151)
..+|++|+.|.++.+.+....+.+..+...+.++...|..+...
T Consensus 77 ~~lv~e~~~~~~l~~~i~~~~~~~~~~~~~~~~l~~~l~~lh~~ 120 (277)
T cd06641 77 LWIIMEYLGGGSALDLLEPGPLDETQIATILREILKGLDYLHSE 120 (277)
T ss_pred EEEEEEeCCCCcHHHHHhcCCCCHHHHHHHHHHHHHHHHHHccC
Confidence 45788899999999999888899999999999999988877543
No 222
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=22.70 E-value=2.1e+02 Score=21.19 Aligned_cols=36 Identities=14% Similarity=0.115 Sum_probs=29.9
Q ss_pred HhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhc
Q 043012 85 AWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120 (151)
Q Consensus 85 ~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl 120 (151)
..-.|.|..||.+..++++|.+-..+.|.-.-|+..
T Consensus 146 ~~~~g~s~~EIA~~lg~s~~tV~~rl~rar~~Lr~~ 181 (192)
T PRK09643 146 VDMQGYSVADAARMLGVAEGTVKSRCARGRARLAEL 181 (192)
T ss_pred HHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 456999999999999999999988887766666653
No 223
>KOG0180 consensus 20S proteasome, regulatory subunit beta type PSMB3/PUP3 [Posttranslational modification, protein turnover, chaperones]
Probab=22.56 E-value=55 Score=25.24 Aligned_cols=20 Identities=25% Similarity=0.436 Sum_probs=18.0
Q ss_pred CCCHHHHHHHHHHhhccccc
Q 043012 10 DLKPAQLAAVCASLVSEGIK 29 (151)
Q Consensus 10 ~L~p~elAAllS~~v~e~~~ 29 (151)
++.|+.+++++|.+.||.|-
T Consensus 81 ~i~P~~~s~mvS~~lYekRf 100 (204)
T KOG0180|consen 81 EIKPETFSSMVSSLLYEKRF 100 (204)
T ss_pred ccCcHHHHHHHHHHHHHhhc
Confidence 68999999999999998764
No 224
>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=22.53 E-value=59 Score=24.99 Aligned_cols=45 Identities=11% Similarity=0.168 Sum_probs=37.6
Q ss_pred chHHHHHHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhcC
Q 043012 77 SQFSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIP 121 (151)
Q Consensus 77 ~~l~~~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl~ 121 (151)
....-+|++|..|.++.+.+....+.+..+.+.+.++.+.|..+.
T Consensus 74 ~~~~~lv~e~~~~~~L~~~i~~~~l~~~~~~~~~~~l~~~l~~lh 118 (277)
T cd06640 74 GTKLWIIMEYLGGGSALDLLRAGPFDEFQIATMLKEILKGLDYLH 118 (277)
T ss_pred CCEEEEEEecCCCCcHHHHHhcCCCCHHHHHHHHHHHHHHHHHHH
Confidence 345667888999999999998888999999999999888877664
No 225
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=22.52 E-value=2.3e+02 Score=21.48 Aligned_cols=36 Identities=22% Similarity=0.059 Sum_probs=30.8
Q ss_pred HHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhh
Q 043012 84 EAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQ 119 (151)
Q Consensus 84 ~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQ 119 (151)
...-.|.|..||.+..++++|.+=..+.|.-..||+
T Consensus 159 L~~~~g~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~ 194 (206)
T PRK12544 159 MREFIELETNEICHAVDLSVSNLNVLLYRARLRLRE 194 (206)
T ss_pred HHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 445689999999999999999998888887777766
No 226
>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=22.52 E-value=57 Score=24.19 Aligned_cols=46 Identities=9% Similarity=0.026 Sum_probs=38.6
Q ss_pred hHHHHHHHhhCCCCHHHHHhh-----cCCChhHHHHHHHHHHHHHhhcCCC
Q 043012 78 QFSGMVEAWASGLTWREMMMD-----CALDDGDLARLLRRTIDLLAQIPKL 123 (151)
Q Consensus 78 ~l~~~v~~Wa~G~~f~eil~~-----t~l~EGdiVR~~rRl~elLrQl~~a 123 (151)
....+++.|..|.++.+.+.. ..+.+..+.+.++++...|..+...
T Consensus 72 ~~~~lv~e~~~~~~L~~~l~~~~~~~~~~~~~~~~~i~~~i~~~l~~lh~~ 122 (258)
T cd08215 72 GKLCIVMEYADGGDLSQKIKKQKKEGKPFPEEQILDWFVQLCLALKYLHSR 122 (258)
T ss_pred CEEEEEEEecCCCcHHHHHHHhhccCCCcCHHHHHHHHHHHHHHHHHHHhC
Confidence 445567889999999999876 5689999999999999988888664
No 227
>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=22.48 E-value=64 Score=24.35 Aligned_cols=45 Identities=7% Similarity=0.091 Sum_probs=37.2
Q ss_pred HHHHHHHhhCCCCHHHHHhh-cCCChhHHHHHHHHHHHHHhhcCCC
Q 043012 79 FSGMVEAWASGLTWREMMMD-CALDDGDLARLLRRTIDLLAQIPKL 123 (151)
Q Consensus 79 l~~~v~~Wa~G~~f~eil~~-t~l~EGdiVR~~rRl~elLrQl~~a 123 (151)
...++++|..|.++.+++.. ..+.+..+.+.+.++.+.|..+...
T Consensus 71 ~~~lv~e~~~~~~L~~~l~~~~~~~~~~~~~i~~qi~~aL~~lH~~ 116 (260)
T cd05611 71 YLYLVMEYLNGGDCASLIKTLGGLPEDWAKQYIAEVVLGVEDLHQR 116 (260)
T ss_pred eEEEEEeccCCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHC
Confidence 44577889999999999976 4689999999999999988877543
No 228
>TIGR02292 ygfB_yecA yecA family protein. This family resembles PFAM model pfam03695 (version pfam03695.3), uncharacterised protein family UPF0149, but is broader in scope and includes additional proteins. It includes E. coli proteins YgfB and YecA. The function of this family of proteins is unknown. The crystal structure is known for the member from Haemophilus influenzae (Ygfb, HI0817).
Probab=22.48 E-value=3e+02 Score=19.67 Aligned_cols=20 Identities=15% Similarity=0.094 Sum_probs=16.8
Q ss_pred CCCHHHHHHHHHHhhccccc
Q 043012 10 DLKPAQLAAVCASLVSEGIK 29 (151)
Q Consensus 10 ~L~p~elAAllS~~v~e~~~ 29 (151)
.++++++=++|+++++-+..
T Consensus 17 ~m~~~elhG~L~al~~~p~~ 36 (150)
T TIGR02292 17 CMNLEELDGFLTALLSGPEV 36 (150)
T ss_pred cCCHHHHhhHHHHHHhCCCC
Confidence 68899999999999996543
No 229
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=22.40 E-value=1.8e+02 Score=21.08 Aligned_cols=35 Identities=17% Similarity=0.159 Sum_probs=30.9
Q ss_pred hhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhc
Q 043012 86 WASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120 (151)
Q Consensus 86 Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl 120 (151)
=-.|.|..||.+..++++|.+=..+.|.-.-|++.
T Consensus 113 ~~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 147 (170)
T TIGR02959 113 ELEGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKEL 147 (170)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 36999999999999999999988888888777774
No 230
>PRK09480 slmA division inhibitor protein; Provisional
Probab=22.32 E-value=78 Score=23.02 Aligned_cols=28 Identities=11% Similarity=0.187 Sum_probs=14.4
Q ss_pred CCCHHHHHhhcCCChhHHHHHHHHHHHH
Q 043012 89 GLTWREMMMDCALDDGDLARLLRRTIDL 116 (151)
Q Consensus 89 G~~f~eil~~t~l~EGdiVR~~rRl~el 116 (151)
|.|..+|.+.+++..|+|=+.+.==+||
T Consensus 30 ~~ti~~Ia~~agvs~gt~Y~~F~~K~~L 57 (194)
T PRK09480 30 RITTAKLAARVGVSEAALYRHFPSKARM 57 (194)
T ss_pred ccCHHHHHHHhCCCHhHHHHHCCCHHHH
Confidence 4455555555555555555544444433
No 231
>COG1698 Uncharacterized protein conserved in archaea [Function unknown]
Probab=22.29 E-value=1.5e+02 Score=20.27 Aligned_cols=35 Identities=17% Similarity=0.359 Sum_probs=24.2
Q ss_pred HHHHHHHHHhhcCCCCCCCHHHHHHHHHHHhhcCC
Q 043012 109 LLRRTIDLLAQIPKLPDVDQRLQKNAVDASNVMDR 143 (151)
Q Consensus 109 ~~rRl~elLrQl~~a~~~~~~L~~k~~~a~~~i~R 143 (151)
.|++...+|++|.+=...+-..+..++++.+.++-
T Consensus 14 ~i~q~~~lL~~Ii~DttVPRNIRraA~~a~e~L~~ 48 (93)
T COG1698 14 KINQVMQLLDEIIQDTTVPRNIRRAAEEAKEALNN 48 (93)
T ss_pred HHHHHHHHHHHHHccccccHHHHHHHHHHHHHHhC
Confidence 36777778888766554566777777777776653
No 232
>PRK15215 fimbriae biosynthesis regulatory protein; Provisional
Probab=22.16 E-value=1.9e+02 Score=20.10 Aligned_cols=47 Identities=9% Similarity=0.233 Sum_probs=36.9
Q ss_pred hHHHHHHHh-hCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhcCCCC
Q 043012 78 QFSGMVEAW-ASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIPKLP 124 (151)
Q Consensus 78 ~l~~~v~~W-a~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl~~a~ 124 (151)
....+++.. ..|.|-.++|+..++..|.|=-+++||..+=+.+.++.
T Consensus 49 KvI~AL~dyLV~G~trkevCe~~~Vn~gYfS~~L~rL~~i~~~V~~L~ 96 (100)
T PRK15215 49 KIIQALRDYLVFGVSRKDVCERYEVNNGYFSTSLNRLSRISQAAAQMV 96 (100)
T ss_pred HHHHHHHHHHHcCccHHHHHHccCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 444444443 79999999999999999999999999988766665543
No 233
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=22.08 E-value=1.7e+02 Score=16.67 Aligned_cols=31 Identities=6% Similarity=0.185 Sum_probs=23.5
Q ss_pred HHHhhCCC-CHHHHHhhcCCChhHHHHHHHHH
Q 043012 83 VEAWASGL-TWREMMMDCALDDGDLARLLRRT 113 (151)
Q Consensus 83 v~~Wa~G~-~f~eil~~t~l~EGdiVR~~rRl 113 (151)
+..=+... |+.+|-+.++++...+-|.+.|-
T Consensus 20 i~~~~~~~~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 20 ILKLLRESRSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred HHHHHhhcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 33334444 99999999999999999988763
No 234
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=22.01 E-value=3.5e+02 Score=20.78 Aligned_cols=57 Identities=18% Similarity=0.225 Sum_probs=43.6
Q ss_pred HHHHHHHHHHHcCCCCCCCCCchHHHHHHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHH
Q 043012 56 HRSSFLELQEKHGVEIPCCLDSQFSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTID 115 (151)
Q Consensus 56 ~~~~l~~~~~~~~l~~~~~~~~~l~~~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~e 115 (151)
+...+++.+..+|++.+.. .+.+++|.=-.-++++||.+.++++-+.+=..++-|.+
T Consensus 11 ~Ie~fae~m~r~G~nrtVG---~iYgilyls~~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~ 67 (177)
T COG1510 11 FIEHFAETMSRWGINRTVG---QIYGILYLSRKPLTLDEIAEALGMSKSNVSMGLKKLQD 67 (177)
T ss_pred HHHHHHHHHHHhCCcchHH---HHhhhheecCCCccHHHHHHHHCCCcchHHHHHHHHHh
Confidence 4566788889999986632 33444454445589999999999999999999988876
No 235
>PF01152 Bac_globin: Bacterial-like globin; InterPro: IPR001486 Globins are haem-containing proteins involved in binding and/or transporting oxygen. They belong to a very large and well studied family that is widely distributed in many organisms []. Globins have evolved from a common ancestor and can be divided into three groups: single-domain globins, and two types of chimeric globins, flavohaemoglobins and globin-coupled sensors. Bacteria have all three types of globins, while archaea lack flavohaemoglobins, and eukaryotes lack globin-coupled sensors []. Several functionally different haemoglobins can coexist in the same species. The major types of globins include: Haemoglobin (Hb): trimer of two alpha and two beta chains, although embryonic and foetal forms can substitute the alpha or beta chain for ones with higher oxygen affinity, such as gamma, delta, epsilon or zeta chains. Hb transports oxygen from lungs to other tissues in vertebrates []. Hb proteins are also present in unicellular organisms where they act as enzymes or sensors []. Myoglobin (Mb): monomeric protein responsible for oxygen storage in vertebrate muscle []. Neuroglobin: a myoglobin-like haemprotein expressed in vertebrate brain and retina, where it is involved in neuroprotection from damage due to hypoxia or ischemia []. Neuroglobin belongs to a branch of the globin family that diverged early in evolution. Cytoglobin: an oxygen sensor expressed in multiple tissues. Related to neuroglobin []. Erythrocruorin: highly cooperative extracellular respiratory proteins found in annelids and arthropods that are assembled from as many as 180 subunit into hexagonal bilayers []. Leghaemoglobin (legHb or symbiotic Hb): occurs in the root nodules of leguminous plants, where it facilitates the diffusion of oxygen to symbiotic bacteriods in order to promote nitrogen fixation. Non-symbiotic haemoglobin (NsHb): occurs in non-leguminous plants, and can be over-expressed in stressed plants []. Flavohaemoglobins (FHb): chimeric, with an N-terminal globin domain and a C-terminal ferredoxin reductase-like NAD/FAD-binding domain. FHb provides protection against nitric oxide via its C-terminal domain, which transfers electrons to haem in the globin []. Globin-coupled sensors: chimeric, with an N-terminal myoglobin-like domain and a C-terminal domain that resembles the cytoplasmic signalling domain of bacterial chemoreceptors. They bind oxygen, and act to initiate an aerotactic response or regulate gene expression [, ]. Protoglobin: a single domain globin found in archaea that is related to the N-terminal domain of globin-coupled sensors []. Truncated 2/2 globin: lack the first helix, giving them a 2-over-2 instead of the canonical 3-over-3 alpha-helical sandwich fold. Can be divided into three main groups (I, II and II) based on structural features []. This entry represents a group of haemoglobin-like proteins found in eubacteria, cyanobacteria, protozoa, algae and plants, but not in animals or yeast. These proteins have a truncated 2-over-2 rather than the canonical 3-over-3 alpha-helical sandwich fold []. This entry includes: HbN (or GlbN): a truncated haemoglobin-like protein that binds oxygen cooperatively with a very high affinity and a slow dissociation rate, which may exclude it from oxygen transport. It appears to be involved in bacterial nitric oxide detoxification and in nitrosative stress []. Cyanoglobin (or GlbN): a truncated haemoprotein found in cyanobacteria that has high oxygen affinity, and which appears to serve as part of a terminal oxidase, rather than as a respiratory pigment []. HbO (or GlbO): a truncated haemoglobin-like protein with a lower oxygen affinity than HbN. HbO associates with the bacterial cell membrane, where it significantly increases oxygen uptake over membranes lacking this protein. HbO appears to interact with a terminal oxidase, and could participate in an oxygen/electron-transfer process that facilitates oxygen transfer during aerobic metabolism []. Glb3: a nuclear-encoded truncated haemoglobin from plants that appears more closely related to HbO than HbN. Glb3 from Arabidopsis thaliana (Mouse-ear cress) exhibits an unusual concentration-independent binding of oxygen and carbon dioxide []. ; GO: 0019825 oxygen binding, 0015671 oxygen transport; PDB: 2BKM_B 1UVY_A 1DLW_A 2XYK_B 2IG3_A 2GKM_B 1S61_A 1S56_B 1RTE_B 2GLN_A ....
Probab=21.92 E-value=1.2e+02 Score=20.61 Aligned_cols=52 Identities=12% Similarity=0.153 Sum_probs=40.0
Q ss_pred HHHHHhhcCCChhHHHHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHhhcCCCccc
Q 043012 92 WREMMMDCALDDGDLARLLRRTIDLLAQIPKLPDVDQRLQKNAVDASNVMDRPPIS 147 (151)
Q Consensus 92 f~eil~~t~l~EGdiVR~~rRl~elLrQl~~a~~~~~~L~~k~~~a~~~i~R~iV~ 147 (151)
+.+.=..-.+.+..+-+|+.=+.+.|.++.. ++.+.+.+.+..+.+|.+||+
T Consensus 68 m~~~H~~l~it~~~f~~~~~~~~~al~~~~v----~~~~~~~~~~~~~~~~~~i~n 119 (120)
T PF01152_consen 68 MREAHAHLGITEEHFDRWLELLKQALDELGV----PEELIDELLARLESLRDDIVN 119 (120)
T ss_dssp HHHHHTTS-BBHHHHHHHHHHHHHHHHHTTC----THHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHhCCCCCHHHHHHHHHHHHHHHHHhCC----CHHHHHHHHHHHHHHHHHhcC
Confidence 4455555689999999999988888888744 678888888888888877764
No 236
>cd05145 RIO1_like RIO kinase family; RIO1, RIO3 and similar proteins, catalytic domain. The RIO kinase catalytic domain family is part of a larger superfamily, that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase (PI3K). RIO kinases are atypical protein serine kinases containing a kinase catalytic signature, but otherwise show very little sequence similarity to typical PKs. Serine kinases catalyze the transfer of the gamma-phosphoryl group from ATP to serine residues in protein substrates. The RIO catalytic domain is truncated compared to the catalytic domains of typical PKs, with deletions of the loops responsible for substrate binding. RIO1 is present in archaea, bacteria and eukaryotes. In addition, RIO3 is present in multicellular eukaryotes. RIO1 is essential for survival and is required for 18S rRNA processing, proper cell cycle pro
Probab=21.89 E-value=1.1e+02 Score=22.55 Aligned_cols=57 Identities=12% Similarity=0.208 Sum_probs=39.2
Q ss_pred HcCCCCCCCCCchHHHHHHHhhCCCCH-HHHHhhcCCChhHHHHHHHHHHHHHhhcCC
Q 043012 66 KHGVEIPCCLDSQFSGMVEAWASGLTW-REMMMDCALDDGDLARLLRRTIDLLAQIPK 122 (151)
Q Consensus 66 ~~~l~~~~~~~~~l~~~v~~Wa~G~~f-~eil~~t~l~EGdiVR~~rRl~elLrQl~~ 122 (151)
..++..|..+...---+|.+|..|.++ ...+....+++.+..+.+.++.+.+.++..
T Consensus 78 ~~~i~~p~~~~~~~~~lVmE~~~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~l~~lH~ 135 (190)
T cd05145 78 EAGVPVPEPILLKKNVLVMEFIGDDGSPAPRLKDVPLEEEEAEELYEQVVEQMRRLYQ 135 (190)
T ss_pred hCCCCCceEEEecCCEEEEEEecCCCchhhhhhhccCCHHHHHHHHHHHHHHHHHHHH
Confidence 356655533211112367899999754 444666788899999999999999988854
No 237
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 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=21.77 E-value=4.2e+02 Score=21.17 Aligned_cols=38 Identities=13% Similarity=0.024 Sum_probs=33.2
Q ss_pred HhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhcCC
Q 043012 85 AWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIPK 122 (151)
Q Consensus 85 ~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl~~ 122 (151)
.-..|.|..||-+..++++|.+=..+.|.-..||+.-.
T Consensus 154 ~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 191 (324)
T TIGR02960 154 RDVLGWRAAETAELLGTSTASVNSALQRARATLDEVGP 191 (324)
T ss_pred HHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhcc
Confidence 34699999999999999999999999998888888544
No 238
>PF06824 DUF1237: Protein of unknown function (DUF1237); InterPro: IPR008313 There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.; PDB: 2P0V_B 3QSP_B 3QPF_A 3QRY_A 3ON6_A 3QT9_A 3QT3_A 2NVP_A 3P2C_B.
Probab=21.36 E-value=58 Score=28.35 Aligned_cols=38 Identities=11% Similarity=0.017 Sum_probs=26.5
Q ss_pred HHHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHhhcCCCc
Q 043012 106 LARLLRRTIDLLAQIPKLPDVDQRLQKNAVDASNVMDRPP 145 (151)
Q Consensus 106 iVR~~rRl~elLrQl~~a~~~~~~L~~k~~~a~~~i~R~i 145 (151)
.++.++++.|+++++.... +.+|++++++-.+-|+.+|
T Consensus 235 a~v~L~~laei~~~~~~~~--~~~la~~~~~la~eI~~gI 272 (424)
T PF06824_consen 235 AVVALEYLAEILRALGWDD--SAELAERARALADEIRAGI 272 (424)
T ss_dssp HHHHHHHHHHHHHHTT-TH--HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhccch--HHHHHHHHHHHHHHHHHHH
Confidence 6899999999999876632 2467777666666665544
No 239
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=21.32 E-value=2.5e+02 Score=20.73 Aligned_cols=35 Identities=20% Similarity=0.168 Sum_probs=30.6
Q ss_pred hhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhc
Q 043012 86 WASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120 (151)
Q Consensus 86 Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl 120 (151)
.-.|.|..||.+..++++|.+=..+.|.-.-|+..
T Consensus 149 ~~~g~s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~ 183 (196)
T PRK12524 149 HIEGLSNPEIAEVMEIGVEAVESLTARGKRALAAL 183 (196)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 45999999999999999999999888887777753
No 240
>cd05155 APH_ChoK_like_1 Uncharacterized bacterial proteins with similarity to Aminoglycoside 3'-phosphotransferase (APH) and Choline kinase (ChoK) family members. The APH/ChoK subfamily is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase (AFK), and phosphoinositide 3-kinase (PI3K). This family is composed of APH, ChoK, ethanolamine kinase (ETNK), macrolide 2'-phosphotransferase (MPH2'), an unusual homoserine kinase, and uncharacterized proteins with similarity to the N-terminal domain of acyl-CoA dehydrogenase 10 (ACAD10). The members of this family catalyze the transfer of the gamma-phosphoryl group from ATP (or CTP) to small molecule substrates, such as aminoglycosides, macrolides, choline, ethanolamine, and homoserine. Phosphorylation of the antibiotics, aminoglycosides, and macrolides leads to their inactivation and to bacterial antibiotic resista
Probab=21.11 E-value=61 Score=24.80 Aligned_cols=60 Identities=20% Similarity=0.254 Sum_probs=34.2
Q ss_pred HHHHHHHHHcCCCCCCCCCch-------HHHHHHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhcCCC
Q 043012 58 SSFLELQEKHGVEIPCCLDSQ-------FSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIPKL 123 (151)
Q Consensus 58 ~~l~~~~~~~~l~~~~~~~~~-------l~~~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl~~a 123 (151)
+-+..+....+++.|..+..+ ...+++.|..|.++.+.. +.. --+..+++-++|.+|...
T Consensus 40 ~~l~~L~~~~~v~vP~~~~~~~~~~~~~~~~~l~~~i~G~~l~~~~----~~~--~~~l~~~la~~l~~LH~i 106 (235)
T cd05155 40 RWLPRLAPHLPLPVPEPLGKGEPGEGYPWPWSVYRWLEGETATAAA----LSD--PSEFAEDLADFLAALRQI 106 (235)
T ss_pred HHHHHHhccCCCCCCceeecCCCccCCCcceEEEEeecCCCCCccc----cCC--HHHHHHHHHHHHHHHhCC
Confidence 334444333567776443221 234679999999997752 121 225566666666666554
No 241
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=21.03 E-value=2e+02 Score=20.85 Aligned_cols=34 Identities=12% Similarity=0.217 Sum_probs=29.5
Q ss_pred hhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhh
Q 043012 86 WASGLTWREMMMDCALDDGDLARLLRRTIDLLAQ 119 (151)
Q Consensus 86 Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQ 119 (151)
=-.|.|..||.+.+++++|++=..+.|...-|+.
T Consensus 132 ~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~ 165 (172)
T PRK09651 132 QLDGLTYSEIAHKLGVSVSSVKKYVAKATEHCLL 165 (172)
T ss_pred hccCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 4589999999999999999998888887776654
No 242
>PF10975 DUF2802: Protein of unknown function (DUF2802); InterPro: IPR021244 This bacterial family of proteins has no known function.
Probab=20.97 E-value=2.4e+02 Score=18.02 Aligned_cols=28 Identities=21% Similarity=0.445 Sum_probs=23.5
Q ss_pred chHHHHHHHhhCCCCHHHHHhhcCCChh
Q 043012 77 SQFSGMVEAWASGLTWREMMMDCALDDG 104 (151)
Q Consensus 77 ~~l~~~v~~Wa~G~~f~eil~~t~l~EG 104 (151)
+.+-.++.-=..|+|-.||++.|+++.+
T Consensus 32 ~~Y~~A~klv~~Ga~~~el~~~CgL~~a 59 (70)
T PF10975_consen 32 PLYSQAIKLVRQGASVEELMEECGLSRA 59 (70)
T ss_pred chHHHHHHHHHcCCCHHHHHHHcCCCHH
Confidence 4666777777899999999999999865
No 243
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=20.95 E-value=1.8e+02 Score=21.53 Aligned_cols=34 Identities=18% Similarity=0.183 Sum_probs=29.3
Q ss_pred hCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhc
Q 043012 87 ASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120 (151)
Q Consensus 87 a~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl 120 (151)
-.|.|..||.+.+++.+|.+=..+.|...-|++.
T Consensus 142 ~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 175 (188)
T PRK12517 142 IGGFSGEEIAEILDLNKNTVMTRLFRARNQLKEA 175 (188)
T ss_pred HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 5899999999999999999988887777777654
No 244
>PF06794 UPF0270: Uncharacterised protein family (UPF0270); InterPro: IPR010648 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.; PDB: 1Y0N_A.
Probab=20.90 E-value=93 Score=20.15 Aligned_cols=22 Identities=18% Similarity=0.200 Sum_probs=15.6
Q ss_pred CCCCCHHHHHHHHHHhhccccc
Q 043012 8 LLDLKPAQLAAVCASLVSEGIK 29 (151)
Q Consensus 8 f~~L~p~elAAllS~~v~e~~~ 29 (151)
|+.|+|+-|-+++-.||..+.+
T Consensus 5 ~~~L~~eTL~nLIeefv~ReGT 26 (70)
T PF06794_consen 5 YQQLPPETLNNLIEEFVLREGT 26 (70)
T ss_dssp GGGS-HHHHHHHHHHHHH----
T ss_pred hHHCCHHHHHHHHHHHHHccCc
Confidence 4689999999999999986554
No 245
>KOG1379 consensus Serine/threonine protein phosphatase [Signal transduction mechanisms]
Probab=20.82 E-value=2.6e+02 Score=23.60 Aligned_cols=46 Identities=11% Similarity=0.108 Sum_probs=31.7
Q ss_pred ccCCCCCCCHHHHHHHHHHhhccccccccccCCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHcCCCC
Q 043012 4 RNKILLDLKPAQLAAVCASLVSEGIKVRLWKNNSYIYEPSTTVINVINVLDEHRSSFLELQEKHGVEI 71 (151)
Q Consensus 4 ~~g~f~~L~p~elAAllS~~v~e~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~l~~~~~~~~l~~ 71 (151)
.+|+|++|...+|-.++....... ...++.++++|+...+++..+.
T Consensus 253 TDGlfDNl~e~~Il~il~~~~~~~----------------------~~~lq~~A~~ia~~Ar~ls~d~ 298 (330)
T KOG1379|consen 253 TDGLFDNLPEKEILSILKGLDARG----------------------NLDLQVTAQKIAEKARELSRDP 298 (330)
T ss_pred cccccccccHHHHHHHHHHhhccc----------------------cccHHHHHHHHHHHHHHhccCc
Confidence 589999999999999988655421 0125566666776666665553
No 246
>PRK01736 hypothetical protein; Reviewed
Probab=20.75 E-value=1.7e+02 Score=22.33 Aligned_cols=19 Identities=21% Similarity=0.586 Sum_probs=16.7
Q ss_pred CCCCHHHHHHHHHHhhccc
Q 043012 9 LDLKPAQLAAVCASLVSEG 27 (151)
Q Consensus 9 ~~L~p~elAAllS~~v~e~ 27 (151)
..++|+|+=++++++++-+
T Consensus 21 ~~~s~sElHG~L~Gll~gg 39 (190)
T PRK01736 21 VALTPAEMHGLLSGMICGG 39 (190)
T ss_pred CCCCHHHHHHHHHHhhhCC
Confidence 4679999999999999965
No 247
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=20.73 E-value=2.4e+02 Score=20.54 Aligned_cols=39 Identities=18% Similarity=0.287 Sum_probs=33.8
Q ss_pred HHHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhc
Q 043012 82 MVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120 (151)
Q Consensus 82 ~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl 120 (151)
++...-.|.|-.||-+..++++|.+=..+.|--.-|++.
T Consensus 136 ~~l~~~~gls~~EIA~~l~i~~~tVks~l~ra~~~l~~~ 174 (182)
T COG1595 136 FLLRYLEGLSYEEIAEILGISVGTVKSRLHRARKKLREQ 174 (182)
T ss_pred hhhHhhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 457788999999999999999999988888887777764
No 248
>PF09059 TyeA: TyeA; InterPro: IPR015144 This domain is composed of two pairs of parallel alpha-helices, and interacts with the bacterial protein YopN via hydrophobic residues located on the helices. Association of TyeA with the C terminus of YopN is accompanied by conformational changes in both polypeptides that create order out of disorder: the resulting structure then serves as an impediment to type III secretion of YopN []. ; PDB: 1XL3_D.
Probab=20.68 E-value=1.9e+02 Score=19.49 Aligned_cols=55 Identities=20% Similarity=0.260 Sum_probs=35.7
Q ss_pred HHhhCCCCHHHHHhhcCCCh-hHHHHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHH
Q 043012 84 EAWASGLTWREMMMDCALDD-GDLARLLRRTIDLLAQIPKLPDVDQRLQKNAVDAS 138 (151)
Q Consensus 84 ~~Wa~G~~f~eil~~t~l~E-GdiVR~~rRl~elLrQl~~a~~~~~~L~~k~~~a~ 138 (151)
..|.....+.-+.+..++.. =.=|.-+|++-+++|.+...+--|++-+++.-.|.
T Consensus 18 q~Wi~~~~i~~l~~~~~~~d~e~qI~Flrel~~l~r~~Pv~vF~D~EqR~~vL~a~ 73 (87)
T PF09059_consen 18 QRWIGPSQIERLAEALGLPDIEQQILFLRELKELFRLMPVDVFNDEEQRQNVLDAV 73 (87)
T ss_dssp STT--HHHHHHHHHCT--SSHHHHHHHHHHHHHHHHTS-GGGSS-HHHHHHHHHHH
T ss_pred CcCcCHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHCcHHhcCCHHHHHHHHHHH
Confidence 35777777777776665544 56788999999999999887654776666655443
No 249
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=20.67 E-value=2.7e+02 Score=20.21 Aligned_cols=35 Identities=20% Similarity=0.353 Sum_probs=31.0
Q ss_pred hhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhc
Q 043012 86 WASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120 (151)
Q Consensus 86 Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl 120 (151)
...|.|..||.+..++++|.+=..+.|.-.-||..
T Consensus 150 ~~~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 184 (187)
T PRK12534 150 FFEGITYEELAARTDTPIGTVKSWIRRGLAKLKAC 184 (187)
T ss_pred HHcCCCHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Confidence 36999999999999999999999999888887763
No 250
>PRK02166 hypothetical protein; Reviewed
Probab=20.67 E-value=1.1e+02 Score=23.45 Aligned_cols=78 Identities=18% Similarity=0.264 Sum_probs=39.1
Q ss_pred CCCHHHHHHHHHHhhcccccc--ccccC---CCCCCCCchhHHHHHHHHHH-HHHHHHHHHHHcCCC--CCC--CCCchH
Q 043012 10 DLKPAQLAAVCASLVSEGIKV--RLWKN---NSYIYEPSTTVINVINVLDE-HRSSFLELQEKHGVE--IPC--CLDSQF 79 (151)
Q Consensus 10 ~L~p~elAAllS~~v~e~~~~--~~~~~---~~~~~~~~~~l~~~~~~l~~-~~~~l~~~~~~~~l~--~~~--~~~~~l 79 (151)
..+|+|+=++|+++++-.... +.+-. +......+..+...+..+.+ +...+... ..++. .|. ..=+.-
T Consensus 21 ~~spaElHG~L~Gll~gG~~~~~~~W~~~l~~~~~~~~~~~~~~~l~~ly~~t~~~L~d~--~~~F~lLLPddd~~l~~R 98 (184)
T PRK02166 21 PVSPAELHGLLLGRSCAGAGFDADAWLADAAELLEGEPGDNVRAALIGLQEMVKGELTAD--DVAVVLLLPDDDAPLTER 98 (184)
T ss_pred CCCHHHHHHHHHHHHcCCCCCChHHHHHHHHHHhccccCHHHHHHHHHHHHHHHHHhCcC--CCeEEeeCCCCCCcHHHH
Confidence 359999999999999854321 11100 00001223444444444432 22223321 22222 231 112577
Q ss_pred HHHHHHhhCC
Q 043012 80 SGMVEAWASG 89 (151)
Q Consensus 80 ~~~v~~Wa~G 89 (151)
+..+..|++|
T Consensus 99 a~AL~~W~~g 108 (184)
T PRK02166 99 AAALGQWCQG 108 (184)
T ss_pred HHHHHHHHHH
Confidence 8889999998
No 251
>cd05154 ACAD10_11_like Acyl-CoA dehydrogenase (ACAD) 10 and 11, N-terminal domain, and similar proteins. This subfamily is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase (AFK), and phosphoinositide 3-kinase (PI3K). This subfamily is composed of bacterial and eukaryotic proteins with similarity to the N-terminal domains of vertebrate ACAD10 and ACAD11. ACADs are a family of flavoproteins that are involved in the beta-oxidation of fatty acyl-CoA derivatives. ACAD deficiency can cause metabolic disorders including muscle fatigue, hypoglycemia, and hepatic lipidosis, among them. There are at least 11 distinct ACADs, some of which show distinct substrate specificities to either straight-chain or branched-chain fatty acids. ACAD10 is widely expressed in human tissues and is highly expressed in liver, kidney, pancreas, and spleen. ACAD10 and ACAD11 contain
Probab=20.62 E-value=20 Score=26.43 Aligned_cols=45 Identities=20% Similarity=0.199 Sum_probs=36.2
Q ss_pred HHHHHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhcCCCC
Q 043012 80 SGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIPKLP 124 (151)
Q Consensus 80 ~~~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl~~a~ 124 (151)
..++++|..|.++.+......+.+.+..+..+++.+.|.++..+.
T Consensus 75 ~~~v~e~i~G~~l~~~~~~~~~~~~~~~~i~~~i~~~l~~lH~~~ 119 (223)
T cd05154 75 PFYVMERVDGRVLRDRLLRPELSPEERRALARALADTLAALHSVD 119 (223)
T ss_pred ceEEEEEeCCEecCCCCCCCCCCHHHHHHHHHHHHHHHHHHhCCC
Confidence 357899999999988764356788888888889999999887664
No 252
>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=20.61 E-value=62 Score=23.91 Aligned_cols=46 Identities=13% Similarity=0.182 Sum_probs=38.7
Q ss_pred hHHHHHHHhhCCCCHHHHHhhc-CCChhHHHHHHHHHHHHHhhcCCC
Q 043012 78 QFSGMVEAWASGLTWREMMMDC-ALDDGDLARLLRRTIDLLAQIPKL 123 (151)
Q Consensus 78 ~l~~~v~~Wa~G~~f~eil~~t-~l~EGdiVR~~rRl~elLrQl~~a 123 (151)
....+++.|..|.++.+.+... .+.+-.+.+++.++.+.|..+.+.
T Consensus 74 ~~~~lv~e~~~~~~L~~~~~~~~~~~~~~~~~~~~~l~~~l~~lh~~ 120 (260)
T cd06606 74 NTLNIFLEYVSGGSLSSLLKKFGKLPEPVIRKYTRQILEGLAYLHSN 120 (260)
T ss_pred CeEEEEEEecCCCcHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHC
Confidence 4556788899999999998876 789999999999999999887553
No 253
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=20.51 E-value=1.5e+02 Score=20.89 Aligned_cols=26 Identities=15% Similarity=0.261 Sum_probs=24.4
Q ss_pred CCHHHHHhhcCCChhHHHHHHHHHHH
Q 043012 90 LTWREMMMDCALDDGDLARLLRRTID 115 (151)
Q Consensus 90 ~~f~eil~~t~l~EGdiVR~~rRl~e 115 (151)
.|+.+|-+..++++..+-+-++||.+
T Consensus 23 ~~~~eia~~lglS~~~v~~Ri~~L~~ 48 (154)
T COG1522 23 ISNAELAERVGLSPSTVLRRIKRLEE 48 (154)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 78999999999999999999999987
No 254
>COG3066 MutH DNA mismatch repair protein [DNA replication, recombination, and repair]
Probab=20.34 E-value=3.3e+02 Score=21.15 Aligned_cols=50 Identities=22% Similarity=0.311 Sum_probs=37.4
Q ss_pred CchhHHHHHHHHHHHHH-HHHHHHHHcCCCCCCCC--CchHHHHHHHhhCCCC
Q 043012 42 PSTTVINVINVLDEHRS-SFLELQEKHGVEIPCCL--DSQFSGMVEAWASGLT 91 (151)
Q Consensus 42 ~~~~l~~~~~~l~~~~~-~l~~~~~~~~l~~~~~~--~~~l~~~v~~Wa~G~~ 91 (151)
|+....+.+.+-++++. .+.++..+.++..|+.+ |-|-+++..+|+-|+|
T Consensus 10 ~P~te~~Ll~~Aq~isG~t~gELA~~~~~~vP~dLkrdKGWvG~LlE~~LGAs 62 (229)
T COG3066 10 PPQTEEQLLAQAQQLSGLTLGELAAEAGMVVPPDLKRDKGWVGMLLEIWLGAS 62 (229)
T ss_pred CCchHHHHHHHHHHHhCccHHHHHHhcCCCCCccccccccHHHHHHHHHhccc
Confidence 44556666777766653 47788888999888654 6799999999998875
No 255
>PF03195 DUF260: Protein of unknown function DUF260; InterPro: IPR004883 The lateral organ boundaries (LOB) gene is expressed at the adaxial base of initiating lateral organs and encodes a plant-specific protein of unknown function. The N-terminal one half of the LOB protein contains a conserved approximately 100-amino acid domain (the LOB domain) that is present in 42 other Arabidopsis thaliana proteins and in proteins from a variety of other plant species. Genes encoding LOB domain (LBD) proteins are expressed in a variety of temporal- and tissue-specific patterns, suggesting that they may function in diverse processes [] The LOB domain contains conserved blocks of amino acids that identify the LBD gene family. In particular, a conserved C-x(2)-C-x(6)-C-x(3)-C motif, which is defining feature of the LOB domain, is present in all LBD proteins. It is possible that this motif forms a new zinc finger [].
Probab=20.31 E-value=1e+02 Score=21.34 Aligned_cols=55 Identities=20% Similarity=0.235 Sum_probs=34.3
Q ss_pred CCCCCCCHHHHHHHHHHhhccccccccccCCCCCCCCchhHHHHHHHHHHHHHHHHHHH
Q 043012 6 KILLDLKPAQLAAVCASLVSEGIKVRLWKNNSYIYEPSTTVINVINVLDEHRSSFLELQ 64 (151)
Q Consensus 6 g~f~~L~p~elAAllS~~v~e~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~l~~~~ 64 (151)
.++.+++|++=...+.+++||...-. . ...+...+.+...-.++.+...++..+.
T Consensus 44 k~L~~~~~~~R~~a~~Sl~yEA~~R~---~-dPv~Gc~G~i~~L~~ql~~~~~el~~~~ 98 (101)
T PF03195_consen 44 KMLQELPPEQREDAMRSLVYEANARA---R-DPVYGCVGIISQLQQQLQQLQAELALVR 98 (101)
T ss_pred HHHHhCCccchhhHHHHHHHHHHhhc---c-CCCcchHHHHHHHHHHHHHHHHHHHHHH
Confidence 34667888888888999999876421 1 1123344555555566666666666543
No 256
>PRK14067 exodeoxyribonuclease VII small subunit; Provisional
Probab=20.19 E-value=1.5e+02 Score=19.58 Aligned_cols=18 Identities=11% Similarity=0.145 Sum_probs=13.3
Q ss_pred HHHHHHHHHHHhhcCCCC
Q 043012 107 ARLLRRTIDLLAQIPKLP 124 (151)
Q Consensus 107 VR~~rRl~elLrQl~~a~ 124 (151)
=-.+.||+++++||-+-.
T Consensus 10 Eeal~~LEeIV~~LE~~~ 27 (80)
T PRK14067 10 EQQLARLQEIVDALEGGD 27 (80)
T ss_pred HHHHHHHHHHHHHHHCCC
Confidence 345788999999987653
No 257
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=20.10 E-value=3.3e+02 Score=19.24 Aligned_cols=27 Identities=0% Similarity=0.068 Sum_probs=17.7
Q ss_pred CCHHHHHhhcCCChhHHHHHHHHHHHH
Q 043012 90 LTWREMMMDCALDDGDLARLLRRTIDL 116 (151)
Q Consensus 90 ~~f~eil~~t~l~EGdiVR~~rRl~el 116 (151)
.+..+|.+..++..+++.+.+++|.+-
T Consensus 23 ~~~~ela~~l~vs~~svs~~l~~L~~~ 49 (142)
T PRK03902 23 ARVSDIAEALSVHPSSVTKMVQKLDKD 49 (142)
T ss_pred cCHHHHHHHhCCChhHHHHHHHHHHHC
Confidence 355666666667777777777666654
No 258
>TIGR00014 arsC arsenate reductase (glutaredoxin). composed of two polypeptides, the products of the arsA and arsB genes. The pump alone produces resistance to arsenite and antimonite. This protein, ArsC, catalyzes the reduction of arsenate to arsenite, and thus extends resistance to include arsenate.
Probab=20.00 E-value=2.1e+02 Score=19.72 Aligned_cols=20 Identities=25% Similarity=0.401 Sum_probs=13.2
Q ss_pred HHHHHHHHHHHhhcCCCccc
Q 043012 128 QRLQKNAVDASNVMDRPPIS 147 (151)
Q Consensus 128 ~~L~~k~~~a~~~i~R~iV~ 147 (151)
.++-+.+.+==.+|||+||.
T Consensus 77 ~e~i~~l~~~P~LikRPIi~ 96 (114)
T TIGR00014 77 QELLDAMVAHPILLERPIVV 96 (114)
T ss_pred HHHHHHHHHCcCcccCCeEE
Confidence 44555555555689999986
Done!