Query psy8528
Match_columns 240
No_of_seqs 267 out of 1285
Neff 4.4
Searched_HMMs 46136
Date Fri Aug 16 21:14:22 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8528.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8528hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3196|consensus 100.0 1.2E-66 2.5E-71 453.3 17.0 194 17-230 9-233 (233)
2 PRK12373 NADH dehydrogenase su 100.0 6.8E-50 1.5E-54 377.9 18.9 160 42-220 9-202 (400)
3 COG1905 NuoE NADH:ubiquinone o 100.0 1.5E-42 3.4E-47 293.9 12.7 128 45-182 2-160 (160)
4 PRK07571 bidirectional hydroge 100.0 2.8E-39 6.1E-44 275.7 15.6 127 43-179 11-168 (169)
5 PRK05988 formate dehydrogenase 100.0 1.9E-38 4.1E-43 266.9 14.3 122 49-180 4-156 (156)
6 PRK07539 NADH dehydrogenase su 100.0 1.7E-37 3.7E-42 259.2 13.6 122 48-179 2-154 (154)
7 TIGR01958 nuoE_fam NADH-quinon 100.0 2.9E-37 6.3E-42 256.1 12.4 117 55-179 1-148 (148)
8 PF01257 2Fe-2S_thioredx: Thio 100.0 4.9E-37 1.1E-41 253.9 11.8 114 56-179 1-145 (145)
9 cd03081 TRX_Fd_NuoE_FDH_gamma 99.2 4E-11 8.6E-16 90.3 5.3 49 130-178 1-80 (80)
10 cd03083 TRX_Fd_NuoE_hoxF TRX-l 99.1 1.6E-10 3.6E-15 86.9 5.4 49 130-178 1-80 (80)
11 cd03082 TRX_Fd_NuoE_W_FDH_beta 98.9 1.8E-09 3.9E-14 80.4 5.6 47 131-177 2-71 (72)
12 cd03064 TRX_Fd_NuoE TRX-like [ 98.8 1E-08 2.2E-13 76.4 5.6 49 130-178 1-80 (80)
13 cd02980 TRX_Fd_family Thioredo 98.5 2.2E-07 4.7E-12 67.6 4.8 47 131-177 1-76 (77)
14 cd03063 TRX_Fd_FDH_beta TRX-li 97.2 0.00061 1.3E-08 53.5 4.9 48 132-179 2-78 (92)
15 cd03062 TRX_Fd_Sucrase TRX-lik 96.0 0.016 3.4E-07 45.2 5.4 54 131-185 2-89 (97)
16 cd00086 homeodomain Homeodomai 85.1 2.3 4.9E-05 28.7 4.7 38 70-107 9-46 (59)
17 PF00046 Homeobox: Homeobox do 84.6 1.9 4E-05 29.5 4.1 35 72-106 11-45 (57)
18 PF06999 Suc_Fer-like: Sucrase 83.8 2.7 5.8E-05 36.7 5.6 57 130-187 132-225 (230)
19 smart00389 HOX Homeodomain. DN 81.3 3.6 7.9E-05 27.6 4.4 37 71-107 10-46 (56)
20 PF14297 DUF4373: Domain of un 81.1 4.7 0.0001 30.5 5.4 65 53-118 11-76 (87)
21 PF10820 DUF2543: Protein of u 75.9 3.1 6.8E-05 32.0 3.0 31 84-114 47-77 (81)
22 PF02797 Chal_sti_synt_C: Chal 75.3 0.84 1.8E-05 38.5 -0.2 37 144-180 67-114 (151)
23 PLN00415 3-ketoacyl-CoA syntha 66.7 3.3 7.1E-05 41.3 1.7 56 143-198 363-429 (466)
24 COG3424 BcsA Predicted naringe 65.0 5.1 0.00011 38.6 2.5 53 144-197 278-341 (356)
25 PF01726 LexA_DNA_bind: LexA D 63.4 8.3 0.00018 28.2 2.9 38 68-107 7-45 (65)
26 PF13404 HTH_AsnC-type: AsnC-t 63.2 7.7 0.00017 26.0 2.5 30 74-107 7-36 (42)
27 PLN03168 chalcone synthase; Pr 63.0 3 6.5E-05 39.9 0.6 43 144-187 303-356 (389)
28 COG1508 RpoN DNA-directed RNA 62.7 24 0.00051 35.2 6.7 126 53-188 93-228 (444)
29 PF13309 HTH_22: HTH domain 59.1 22 0.00047 25.8 4.4 53 55-107 6-61 (64)
30 TIGR01565 homeo_ZF_HD homeobox 56.7 22 0.00048 25.8 4.1 27 79-105 19-49 (58)
31 PLN03172 chalcone synthase fam 54.5 7.9 0.00017 37.2 1.9 37 144-180 304-351 (393)
32 COG3411 Ferredoxin [Energy pro 53.1 14 0.0003 27.7 2.6 25 163-187 29-54 (64)
33 PLN02932 3-ketoacyl-CoA syntha 48.6 9.8 0.00021 38.0 1.6 57 141-197 375-442 (478)
34 PRK09480 slmA division inhibit 47.5 11 0.00025 30.7 1.6 44 68-119 11-55 (194)
35 PLN03173 chalcone synthase; Pr 46.3 13 0.00028 35.7 1.9 37 144-180 304-351 (391)
36 PTZ00397 macrophage migration 45.8 36 0.00079 26.7 4.2 79 88-170 22-107 (116)
37 COG2442 Uncharacterized conser 45.3 23 0.0005 27.2 2.8 44 131-177 15-67 (79)
38 TIGR01764 excise DNA binding d 43.5 25 0.00054 22.3 2.4 20 91-110 4-23 (49)
39 PF04539 Sigma70_r3: Sigma-70 43.2 38 0.00082 24.3 3.6 36 77-114 11-46 (78)
40 PF12728 HTH_17: Helix-turn-he 41.6 27 0.00059 23.2 2.5 20 91-110 4-23 (51)
41 KOG0917|consensus 39.8 35 0.00077 32.5 3.7 29 163-191 125-163 (338)
42 PLN03170 chalcone synthase; Pr 39.7 18 0.00038 34.9 1.8 36 144-179 308-354 (401)
43 TIGR00207 fliG flagellar motor 39.0 67 0.0015 30.4 5.5 89 78-197 26-120 (338)
44 PF04963 Sigma54_CBD: Sigma-54 38.9 3.6 7.7E-05 35.7 -2.8 99 80-188 45-152 (194)
45 PRK12522 RNA polymerase sigma 38.6 56 0.0012 26.6 4.4 49 49-107 106-154 (173)
46 PRK09975 DNA-binding transcrip 38.4 22 0.00048 29.6 2.0 45 68-119 12-56 (213)
47 PLN03169 chalcone synthase fam 37.8 16 0.00036 34.8 1.2 54 144-197 310-377 (391)
48 PF14338 Mrr_N: Mrr N-terminal 37.4 66 0.0014 24.3 4.3 39 70-108 4-43 (92)
49 PF13551 HTH_29: Winged helix- 37.2 1.6E+02 0.0034 21.8 6.4 51 48-98 58-111 (112)
50 PF14261 DUF4351: Domain of un 37.2 27 0.00058 25.2 2.0 30 67-96 4-33 (59)
51 COG1212 KdsB CMP-2-keto-3-deox 36.8 53 0.0011 30.5 4.2 52 130-181 61-120 (247)
52 KOG1719|consensus 36.6 88 0.0019 27.7 5.4 66 49-115 91-170 (183)
53 PLN02192 3-ketoacyl-CoA syntha 36.2 22 0.00047 35.9 1.8 57 141-197 403-470 (511)
54 PF06056 Terminase_5: Putative 35.8 36 0.00079 24.4 2.5 30 91-120 16-45 (58)
55 PF13443 HTH_26: Cro/C1-type H 35.8 17 0.00038 25.0 0.8 24 84-107 36-59 (63)
56 PLN02377 3-ketoacyl-CoA syntha 35.8 22 0.00048 35.8 1.8 56 141-196 399-465 (502)
57 PF13744 HTH_37: Helix-turn-he 35.6 48 0.001 24.5 3.2 37 69-109 16-52 (80)
58 PF14756 Pdase_C33_assoc: Pept 35.2 27 0.00058 29.5 1.9 106 43-182 6-111 (147)
59 PF07845 DUF1636: Protein of u 35.1 59 0.0013 26.6 3.9 47 141-187 16-95 (116)
60 PF05049 IIGP: Interferon-indu 34.9 68 0.0015 31.3 4.9 48 71-119 274-321 (376)
61 PRK09648 RNA polymerase sigma 34.8 33 0.00072 28.4 2.5 49 50-108 127-175 (189)
62 COG1152 CdhA CO dehydrogenase/ 34.7 71 0.0015 33.6 5.1 105 42-155 144-258 (772)
63 TIGR02366 DHAK_reg probable di 34.5 29 0.00063 28.2 2.1 42 71-119 7-48 (176)
64 TIGR02950 SigM_subfam RNA poly 34.1 34 0.00074 27.0 2.3 47 52-108 95-141 (154)
65 PRK09047 RNA polymerase factor 34.0 75 0.0016 25.2 4.3 47 51-107 95-141 (161)
66 TIGR02392 rpoH_proteo alternat 34.0 57 0.0012 29.3 4.0 78 31-110 73-161 (270)
67 PLN02854 3-ketoacyl-CoA syntha 33.8 26 0.00056 35.5 1.9 56 141-196 415-481 (521)
68 PF04472 DUF552: Protein of un 33.8 71 0.0015 23.4 3.8 41 140-180 6-46 (73)
69 PF15508 NAAA-beta: beta subun 33.5 2E+02 0.0043 22.0 6.5 44 70-113 47-94 (95)
70 PF13384 HTH_23: Homeodomain-l 33.4 41 0.0009 22.1 2.3 24 90-113 19-42 (50)
71 PF02796 HTH_7: Helix-turn-hel 31.4 42 0.00091 22.3 2.1 19 90-108 23-41 (45)
72 KOG2251|consensus 31.2 66 0.0014 29.6 3.9 42 45-106 41-82 (228)
73 PF14842 FliG_N: FliG N-termin 30.6 57 0.0012 25.7 3.1 77 78-184 22-104 (108)
74 PRK11924 RNA polymerase sigma 30.5 1E+02 0.0022 24.5 4.6 51 49-109 112-162 (179)
75 PRK10668 DNA-binding transcrip 30.4 38 0.00082 28.4 2.1 44 68-118 12-55 (215)
76 PF07293 DUF1450: Protein of u 29.7 58 0.0013 25.0 2.8 26 132-159 4-29 (78)
77 COG2964 Uncharacterized protei 29.5 95 0.0021 28.4 4.6 24 84-107 186-210 (220)
78 PF14174 YycC: YycC-like prote 28.8 60 0.0013 23.5 2.6 21 86-106 6-26 (53)
79 smart00035 CLa CLUSTERIN alpha 28.8 25 0.00055 32.0 0.8 53 54-113 112-164 (216)
80 PLN02804 chalcone isomerase 28.6 66 0.0014 29.0 3.4 91 85-188 47-141 (206)
81 PF01978 TrmB: Sugar-specific 28.6 54 0.0012 23.1 2.4 22 90-111 24-45 (68)
82 COG3531 Predicted protein-disu 28.0 94 0.002 28.3 4.3 36 73-108 108-148 (212)
83 COG3343 RpoE DNA-directed RNA 27.9 94 0.002 27.5 4.2 49 71-119 15-66 (175)
84 PF13700 DUF4158: Domain of un 27.5 1.5E+02 0.0032 24.6 5.2 57 44-104 23-85 (166)
85 CHL00124 acpP acyl carrier pro 26.8 1.3E+02 0.0028 21.9 4.2 50 89-162 9-58 (82)
86 cd04762 HTH_MerR-trunc Helix-T 26.7 56 0.0012 20.4 2.0 20 91-110 3-22 (49)
87 PRK07194 fliG flagellar motor 26.6 1.5E+02 0.0033 28.0 5.6 87 78-196 24-116 (334)
88 TIGR03830 CxxCG_CxxCG_HTH puta 26.3 1.2E+02 0.0026 23.5 4.3 61 41-106 35-96 (127)
89 PF09999 DUF2240: Uncharacteri 25.8 4.1E+02 0.0088 22.7 7.5 50 56-107 91-142 (144)
90 PRK15480 glucose-1-phosphate t 25.5 55 0.0012 30.1 2.4 51 49-101 229-279 (292)
91 KOG0372|consensus 25.4 1.6E+02 0.0036 27.9 5.5 70 145-226 131-213 (303)
92 PF13936 HTH_38: Helix-turn-he 25.3 72 0.0016 21.2 2.4 21 89-109 21-41 (44)
93 KOG2577|consensus 25.1 62 0.0013 31.5 2.8 56 75-141 80-137 (354)
94 PRK05932 RNA polymerase factor 25.1 82 0.0018 31.2 3.7 127 52-188 103-241 (455)
95 TIGR02985 Sig70_bacteroi1 RNA 25.1 45 0.00098 26.0 1.6 50 50-109 101-150 (161)
96 TIGR01207 rmlA glucose-1-phosp 25.0 72 0.0016 29.1 3.1 51 49-101 225-275 (286)
97 PRK09641 RNA polymerase sigma 24.9 61 0.0013 26.4 2.4 45 54-108 128-172 (187)
98 TIGR02844 spore_III_D sporulat 24.7 1.3E+02 0.0029 23.0 4.0 34 71-109 7-40 (80)
99 PF14779 BBS1: Ciliary BBSome 24.6 1.2E+02 0.0025 28.2 4.4 99 23-139 83-184 (257)
100 PF11165 DUF2949: Protein of u 24.5 88 0.0019 22.9 2.8 34 146-179 2-57 (58)
101 PRK05883 acyl carrier protein; 24.5 1.1E+02 0.0023 23.6 3.6 68 87-178 16-87 (91)
102 PRK12513 RNA polymerase sigma 24.5 71 0.0015 26.5 2.7 47 51-107 128-174 (194)
103 PLN02326 3-oxoacyl-[acyl-carri 24.3 66 0.0014 30.3 2.8 52 145-196 308-367 (379)
104 KOG0183|consensus 24.2 94 0.002 28.7 3.6 56 114-180 145-235 (249)
105 COG5469 Predicted metal-bindin 24.2 2.2E+02 0.0048 24.5 5.6 46 130-177 17-105 (143)
106 PRK06596 RNA polymerase factor 24.2 92 0.002 28.4 3.6 69 43-111 96-174 (284)
107 PF04545 Sigma70_r4: Sigma-70, 24.1 76 0.0016 21.0 2.4 23 86-108 18-40 (50)
108 PF05379 Peptidase_C23: Carlav 23.8 75 0.0016 24.7 2.6 21 90-110 6-26 (89)
109 COG1522 Lrp Transcriptional re 23.8 93 0.002 24.8 3.2 45 73-121 11-65 (154)
110 cd00092 HTH_CRP helix_turn_hel 23.8 1.4E+02 0.003 20.2 3.7 23 89-111 26-48 (67)
111 PF13518 HTH_28: Helix-turn-he 23.6 80 0.0017 20.5 2.4 25 90-114 14-38 (52)
112 PF00390 malic: Malic enzyme, 23.4 88 0.0019 27.7 3.2 34 146-179 147-182 (182)
113 KOG2914|consensus 23.3 1.8E+02 0.0039 26.3 5.2 79 53-156 29-107 (222)
114 PRK09566 nirA ferredoxin-nitri 23.3 3.6E+02 0.0079 26.8 7.8 79 100-188 42-133 (513)
115 COG1595 RpoE DNA-directed RNA 23.3 1.2E+02 0.0027 25.0 3.9 49 50-108 115-163 (182)
116 PLN03171 chalcone synthase-lik 23.3 44 0.00094 32.1 1.4 44 144-187 314-370 (399)
117 cd00569 HTH_Hin_like Helix-tur 23.3 85 0.0018 17.2 2.2 19 90-108 23-41 (42)
118 PF06569 DUF1128: Protein of u 23.2 70 0.0015 24.4 2.2 33 147-179 10-67 (71)
119 PF02954 HTH_8: Bacterial regu 23.1 1.6E+02 0.0035 19.2 3.8 28 76-107 10-37 (42)
120 PF04659 Arch_fla_DE: Archaeal 23.1 2.5E+02 0.0054 22.5 5.4 45 51-100 20-64 (99)
121 TIGR02983 SigE-fam_strep RNA p 23.1 1.1E+02 0.0024 24.4 3.5 50 49-108 97-146 (162)
122 PF09339 HTH_IclR: IclR helix- 23.1 81 0.0018 21.2 2.4 36 72-110 5-40 (52)
123 PF01381 HTH_3: Helix-turn-hel 23.0 1E+02 0.0023 20.3 2.9 22 83-104 33-54 (55)
124 COG4227 Antirestriction protei 22.9 1.1E+02 0.0024 29.2 3.8 47 168-216 14-63 (316)
125 PRK01530 hypothetical protein; 22.8 1.7E+02 0.0036 23.7 4.4 35 145-179 54-104 (105)
126 COG3877 Uncharacterized protei 22.7 77 0.0017 26.3 2.5 34 150-183 60-111 (122)
127 PRK12469 RNA polymerase factor 22.6 65 0.0014 32.3 2.5 127 52-188 125-268 (481)
128 PF01325 Fe_dep_repress: Iron 22.5 1.4E+02 0.003 21.2 3.6 35 73-110 10-44 (60)
129 PRK05350 acyl carrier protein; 22.5 1.6E+02 0.0035 21.6 4.1 65 90-178 11-79 (82)
130 PRK12423 LexA repressor; Provi 22.4 82 0.0018 27.2 2.8 51 69-121 8-62 (202)
131 smart00027 EH Eps15 homology d 22.2 2.1E+02 0.0045 21.4 4.7 49 46-109 2-50 (96)
132 PRK11179 DNA-binding transcrip 22.2 78 0.0017 26.0 2.5 95 73-180 12-130 (153)
133 PF04703 FaeA: FaeA-like prote 22.2 90 0.0019 22.9 2.5 33 75-110 5-37 (62)
134 PHA01083 hypothetical protein 22.0 1.2E+02 0.0027 26.1 3.7 20 85-104 43-62 (149)
135 PRK12533 RNA polymerase sigma 21.7 1.6E+02 0.0035 25.7 4.5 51 48-108 120-170 (216)
136 PRK06840 hypothetical protein; 21.4 99 0.0021 28.2 3.3 53 145-197 265-324 (339)
137 cd08789 CARD_IPS-1_RIG-I Caspa 21.4 75 0.0016 24.3 2.1 39 47-88 29-67 (84)
138 PRK09567 nirA ferredoxin-nitri 21.2 4.3E+02 0.0094 27.0 8.0 82 100-190 93-185 (593)
139 PF13560 HTH_31: Helix-turn-he 21.2 1.2E+02 0.0027 20.9 3.1 18 91-108 17-34 (64)
140 PRK12529 RNA polymerase sigma 21.0 1.4E+02 0.0031 24.5 3.9 48 51-108 116-163 (178)
141 PRK09639 RNA polymerase sigma 21.0 1.4E+02 0.003 23.8 3.7 49 50-109 100-148 (166)
142 PRK11202 DNA-binding transcrip 21.0 50 0.0011 27.9 1.2 31 81-118 26-56 (203)
143 COG0735 Fur Fe2+/Zn2+ uptake r 20.9 2.1E+02 0.0045 23.7 4.8 59 53-114 5-67 (145)
144 PRK12534 RNA polymerase sigma 20.8 85 0.0018 25.8 2.5 49 50-108 125-173 (187)
145 smart00803 TAF TATA box bindin 20.8 94 0.002 22.7 2.4 18 84-101 1-18 (65)
146 smart00421 HTH_LUXR helix_turn 20.8 86 0.0019 20.0 2.1 20 90-109 20-39 (58)
147 CHL00203 fabH 3-oxoacyl-acyl-c 20.7 50 0.0011 30.0 1.2 53 144-196 253-313 (326)
148 TIGR02395 rpoN_sigma RNA polym 20.6 1E+02 0.0022 30.3 3.3 126 53-188 79-215 (429)
149 TIGR02684 dnstrm_HI1420 probab 20.5 2.3E+02 0.005 21.9 4.7 45 54-108 19-63 (89)
150 PRK09325 coenzyme F420-reducin 20.5 70 0.0015 29.3 2.1 40 138-177 101-149 (282)
151 cd00831 CHS_like Chalcone and 20.4 59 0.0013 30.0 1.6 53 144-196 288-351 (361)
152 PRK14996 TetR family transcrip 20.1 1.1E+02 0.0023 25.3 2.9 44 68-118 9-52 (192)
No 1
>KOG3196|consensus
Probab=100.00 E-value=1.2e-66 Score=453.28 Aligned_cols=194 Identities=58% Similarity=0.982 Sum_probs=185.9
Q ss_pred cccccccccccCcceeeccCCCCCCCCccccCCHHhHHHHHHHHHhCCCCCCcccHHHHHHHHHHHcCCCCHHHHHHHHH
Q psy8528 17 VRSLSTTQRLNHDALFVHRDTKDDNLDVKFEFTPDNKKRAEAIISIYPVGHERAAVIPLLDLAQRQHGWLPISAMHYVAD 96 (240)
Q Consensus 17 ~~~~~~~~~~~~~~~~~h~~t~~~n~~~~f~ft~e~~~~i~~il~~Yp~~~~rsalIplL~~aQ~q~G~Lp~~am~~VA~ 96 (240)
.|.+..+...+ +.|||||||++||.+.+|+|++||++++++||++||.+++++||||+|+++|+|+||||.+||++||+
T Consensus 9 ~r~l~~~~v~r-~~l~~h~dt~en~~~~~feFt~eN~~rvkAIla~YP~~~k~~AliPLLDLAQRQ~GWlpiSAM~~VA~ 87 (233)
T KOG3196|consen 9 IRRLHLAVVLR-QPLFVHRDTPENNPDLPFEFTPENQKRVKAILAIYPEGHKAGALIPLLDLAQRQHGWLPISAMNEVAE 87 (233)
T ss_pred HHhhhHHHHhh-cccccccCCcccCCCCCcccCHHHHHHHHHHHHHCcccccccchhhhhHHHHHhcCCcCHHHHHHHHH
Confidence 36666666655 99999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HcCCChhhHHHHhhhccCCccccCCcccccccccEEEEecCChhhhhcCHHHHHHHHHHHcCc-----------------
Q psy8528 97 FLNLPKMRVYEVATFYTMFIRKPIGEERIKSILQYHLNWCTTTPCWLRNSDAILEVIKKKCNM----------------- 159 (240)
Q Consensus 97 ~L~lp~~~VyeVATFYtmF~~kP~G~~~~~~~~K~~I~VC~~t~C~lrGs~~Il~~l~~~LgI----------------- 159 (240)
.+++|+++||||||||+||+++|+| ||||+||++||||++|+++|.+++++.||+
T Consensus 88 ~~~v~~mrvyevatfYtmf~r~p~g--------Ky~v~VC~ttpC~lrg~d~i~ea~~k~lgi~~Gett~d~~Ftl~e~e 159 (233)
T KOG3196|consen 88 VLEVPPMRVYEVATFYTMFFRKPVG--------KYHVQVCTTTPCMLRGSDDILEACKKQLGIKVGETTKDGLFTLEEVE 159 (233)
T ss_pred HHcCChHHHHHHHHHHHHhhccCCC--------CceEEEecCcHHhhhccHHHHHHHHHHhCccccccccccceeeecch
Confidence 9999999999999999999999999 999999999999999999999999999999
Q ss_pred ---------e--Ee---ecCCCHHhHHHHHHHHhcCCCCCCCCCCCCCCCcCcCCCccccccCCCCCCccCCCCCCCCCC
Q psy8528 160 ---------M--LE---RQDLEPKDMEQIIDDLKAGKKPAPGPSGYTSGIGSQSGRFCQAREAYHDMTSLTGEPHGPWDS 225 (240)
Q Consensus 160 ---------m--v~---y~~Ltpe~i~~IL~~lk~g~~p~~gp~g~~~~~~~~~gr~~~~~e~~~g~t~l~~~~~~~~~~ 225 (240)
| || |||+|++++.+||++|++||.|++|| ||||+ +|||.||+|||+++|+||||+
T Consensus 160 ClGaCvnaPmi~IND~yyedlt~k~l~eIle~L~~~k~pp~Gp---------rngR~--a~eP~Gg~tsL~~~P~~PgF~ 228 (233)
T KOG3196|consen 160 CLGACVNAPMIAINDDYYEDLTPKKLVEILEDLKAGKKPPAGP---------RNGRF--ASEPKGGLTSLKEEPKGPGFG 228 (233)
T ss_pred hhhhhccCceeeecchhhccCCHHHHHHHHHHHhcCCCCCCCC---------CCCcc--ccCCCCCccccccCCCCCCch
Confidence 3 33 99999999999999999999999999 99999 999999999999999999999
Q ss_pred Ccccc
Q psy8528 226 KRDFC 230 (240)
Q Consensus 226 ~~~~~ 230 (240)
+|+.+
T Consensus 229 ~q~~~ 233 (233)
T KOG3196|consen 229 LQAAL 233 (233)
T ss_pred hcccC
Confidence 99763
No 2
>PRK12373 NADH dehydrogenase subunit E; Provisional
Probab=100.00 E-value=6.8e-50 Score=377.86 Aligned_cols=160 Identities=48% Similarity=0.773 Sum_probs=154.4
Q ss_pred CCccccCCHHhHHHHHHHHHhCCCCCCcccHHHHHHHHHHHcCCCCHHHHHHHHHHcCCChhhHHHHhhhccCCccccCC
Q psy8528 42 LDVKFEFTPDNKKRAEAIISIYPVGHERAAVIPLLDLAQRQHGWLPISAMHYVADFLNLPKMRVYEVATFYTMFIRKPIG 121 (240)
Q Consensus 42 ~~~~f~ft~e~~~~i~~il~~Yp~~~~rsalIplL~~aQ~q~G~Lp~~am~~VA~~L~lp~~~VyeVATFYtmF~~kP~G 121 (240)
++.+|+|++++++++++||++||.++++++|||+||++|+++||||+++|++||+.||||+++||||||||+||+++|+|
T Consensus 9 ~p~~f~f~~e~~~~i~~ii~~yp~~~~~salIplL~~~Qe~~GyIp~~ai~~VAe~Lgvp~~~V~eVATFYtmF~~~P~G 88 (400)
T PRK12373 9 QPDSFAFTPENAAWAEKQITKYPEGRQASAVIPLLMRAQEQEGWVTRAAIEKVADMLDMAYIRVLEVATFYTQFQLQPVG 88 (400)
T ss_pred CCccccCCHHHHHHHHHHHHHCCCccCHHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHHHHHHhhcccccCCC
Confidence 77899999999999999999999888999999999999999999999999999999999999999999999999999999
Q ss_pred ccccccccc-EEEEecCChhhhhcCHHHHHHHHHHHcCc----------------------------eEe---ecCCCHH
Q psy8528 122 EERIKSILQ-YHLNWCTTTPCWLRNSDAILEVIKKKCNM----------------------------MLE---RQDLEPK 169 (240)
Q Consensus 122 ~~~~~~~~K-~~I~VC~~t~C~lrGs~~Il~~l~~~LgI----------------------------mv~---y~~Ltpe 169 (240)
| |||+||+|++||++|+++|+++|+++||| ||| |++||++
T Consensus 89 --------k~~~I~VC~~t~C~l~Ga~~ll~~le~~Lgik~GeTT~DG~FTLe~veCLGaC~~APv~~Ind~~y~~LTpe 160 (400)
T PRK12373 89 --------TRAHIQVCGTTPCMLRGSEALMAVCKSKIHAHPHELNADGTLSWEEVECLGACVNAPMVQIGKDYYEDLTPE 160 (400)
T ss_pred --------CceEEEEcCChHHHhCChHHHHHHHHHHhCCCCCCcCCCCeEEEEeeeecCccCCCCeEEECCEEeCCCCHH
Confidence 9 89999999999999999999999999998 666 9999999
Q ss_pred hHHHHHHHHhcCCCCC--CCCCCCCCCCcCcCCCccccccCCCCCCccCCCCC
Q psy8528 170 DMEQIIDDLKAGKKPA--PGPSGYTSGIGSQSGRFCQAREAYHDMTSLTGEPH 220 (240)
Q Consensus 170 ~i~~IL~~lk~g~~p~--~gp~g~~~~~~~~~gr~~~~~e~~~g~t~l~~~~~ 220 (240)
++++||++|++|+.|+ ||| |+||+ +|||.+|+|||+++..
T Consensus 161 ~v~~IL~~l~ag~~~~~~~g~---------~~~r~--~~~p~~g~t~l~~~~~ 202 (400)
T PRK12373 161 RLEEIIDAFAAGKGPVVKPGP---------QIGRY--ASEPAGGLTSLTEEAG 202 (400)
T ss_pred HHHHHHHHHhCCCCCCCCCCC---------CCCcc--ccCCCCCCcccCCCCC
Confidence 9999999999999988 898 99999 9999999999998643
No 3
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=100.00 E-value=1.5e-42 Score=293.93 Aligned_cols=128 Identities=47% Similarity=0.862 Sum_probs=123.6
Q ss_pred cccCCHHhHHHHHHHHHhCCCCCCcccHHHHHHHHHHHcCCCCHHHHHHHHHHcCCChhhHHHHhhhccCCccccCCccc
Q psy8528 45 KFEFTPDNKKRAEAIISIYPVGHERAAVIPLLDLAQRQHGWLPISAMHYVADFLNLPKMRVYEVATFYTMFIRKPIGEER 124 (240)
Q Consensus 45 ~f~ft~e~~~~i~~il~~Yp~~~~rsalIplL~~aQ~q~G~Lp~~am~~VA~~L~lp~~~VyeVATFYtmF~~kP~G~~~ 124 (240)
.|.|++++.+++++++++|| ++|+||||+||++|+++||||++++++||+.||||+++||||||||+||+++|+|
T Consensus 2 ~~~~~~~~~~~~~~~i~~yp--~~rsAlip~L~~aQ~~~G~l~~~ai~~iA~~L~i~~~~v~~VaTFY~~f~~~P~G--- 76 (160)
T COG1905 2 TFAFSAENLELIEAIIAKYP--DKRSALIPLLHIAQEQFGWLPPEAIEEIADMLGIPRARVYGVATFYTQFFLKPVG--- 76 (160)
T ss_pred CcccchhHHHHHHHHHHHCc--cchhHHHHHHHHHHHHhCCCCHHHHHHHHHHhCCCHHHheeeeeeehhhccCcCC---
Confidence 35599999999999999999 6999999999999999999999999999999999999999999999999999999
Q ss_pred ccccccEEEEecCChhhhhcCHHHHHHHHHHHcCc----------------------------eEe---ecCCCHHhHHH
Q psy8528 125 IKSILQYHLNWCTTTPCWLRNSDAILEVIKKKCNM----------------------------MLE---RQDLEPKDMEQ 173 (240)
Q Consensus 125 ~~~~~K~~I~VC~~t~C~lrGs~~Il~~l~~~LgI----------------------------mv~---y~~Ltpe~i~~ 173 (240)
||+|+||+||+||++|+++|+++|+++||| ||| |+++|||++.+
T Consensus 77 -----r~~i~VC~~t~C~l~Gs~~l~~~l~~~lgi~~gett~DG~ftl~~v~ClGaC~~AP~vmind~~~~~lt~e~l~e 151 (160)
T COG1905 77 -----RHHIRVCTGTACHLKGSEALLKALEKKLGIKPGETTADGKFTLEPVECLGACGQAPVVMINDDVYGRLTPEKLEE 151 (160)
T ss_pred -----CeEEEEeCCcHHhhcChHHHHHHHHHHhCCCCCCcCCCCeEEEeeeeeecccccCCEEEECCchhccCCHHHHHH
Confidence 999999999999999999999999999998 777 99999999999
Q ss_pred HHHHHhcCC
Q psy8528 174 IIDDLKAGK 182 (240)
Q Consensus 174 IL~~lk~g~ 182 (240)
||+++++++
T Consensus 152 il~~~~~~~ 160 (160)
T COG1905 152 ILEKLKAKK 160 (160)
T ss_pred HHHHHhcCC
Confidence 999999874
No 4
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=100.00 E-value=2.8e-39 Score=275.73 Aligned_cols=127 Identities=30% Similarity=0.444 Sum_probs=122.3
Q ss_pred CccccCCHHhHHHHHHHHHhCCCCCCcccHHHHHHHHHHHcCCCCHHHHHHHHHHcCCChhhHHHHhhhccCCccccCCc
Q psy8528 43 DVKFEFTPDNKKRAEAIISIYPVGHERAAVIPLLDLAQRQHGWLPISAMHYVADFLNLPKMRVYEVATFYTMFIRKPIGE 122 (240)
Q Consensus 43 ~~~f~ft~e~~~~i~~il~~Yp~~~~rsalIplL~~aQ~q~G~Lp~~am~~VA~~L~lp~~~VyeVATFYtmF~~kP~G~ 122 (240)
+....++++..+++++|+++|| +++++|||+||++|+++||||++++++||+.||||+++||||||||+||+++|+|
T Consensus 11 ~~~~~~~~~~~~~i~~ii~~~~--~~~~~li~~L~~iQ~~~GyIp~e~~~~iA~~l~v~~a~V~gVatFY~~f~~~P~G- 87 (169)
T PRK07571 11 SATHPSGDKRFKVLEATMKRNQ--YRQDALIEVLHKAQELFGYLERDLLLYVARQLKLPLSRVYGVATFYHLFSLKPSG- 87 (169)
T ss_pred CccCcCcHHHHHHHHHHHHHcC--CCHHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHHHHHHHHccccCcCCCC-
Confidence 4567899999999999999998 5899999999999999999999999999999999999999999999999999999
Q ss_pred ccccccccEEEEecCChhhhhcCHHHHHHHHHHHcCc----------------------------eEe---ecCCCHHhH
Q psy8528 123 ERIKSILQYHLNWCTTTPCWLRNSDAILEVIKKKCNM----------------------------MLE---RQDLEPKDM 171 (240)
Q Consensus 123 ~~~~~~~K~~I~VC~~t~C~lrGs~~Il~~l~~~LgI----------------------------mv~---y~~Ltpe~i 171 (240)
||+|+||+|++|+++|+++|+++++++||| ||| |++||++++
T Consensus 88 -------k~~I~VC~g~aC~~~G~~~ll~~l~~~Lgi~~gett~DG~ftL~~~~ClG~C~~AP~~~Vn~~~~~~lt~e~v 160 (169)
T PRK07571 88 -------EHTCVVCTGTACYVKGSAAILEDLENELGIKAGETTADGKLSLLTARCLGACGIAPAVVFDGKVAGKQTPESV 160 (169)
T ss_pred -------CEEEEEcCChHHHHCCcHHHHHHHHHHhCCCCCCcCCCCeEEEEEecccCccCCCCeEEECCEEeCCCCHHHH
Confidence 999999999999999999999999999998 677 999999999
Q ss_pred HHHHHHHh
Q psy8528 172 EQIIDDLK 179 (240)
Q Consensus 172 ~~IL~~lk 179 (240)
++||++|+
T Consensus 161 ~~il~~~~ 168 (169)
T PRK07571 161 LEKVQGWL 168 (169)
T ss_pred HHHHHHHh
Confidence 99999985
No 5
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=100.00 E-value=1.9e-38 Score=266.93 Aligned_cols=122 Identities=29% Similarity=0.515 Sum_probs=116.5
Q ss_pred CHHhHHHHHHHHHhCCCCCCcccHHHHHHHHHHHcCCCCHHHHHHHHHHcCCChhhHHHHhhhccCCccccCCccccccc
Q psy8528 49 TPDNKKRAEAIISIYPVGHERAAVIPLLDLAQRQHGWLPISAMHYVADFLNLPKMRVYEVATFYTMFIRKPIGEERIKSI 128 (240)
Q Consensus 49 t~e~~~~i~~il~~Yp~~~~rsalIplL~~aQ~q~G~Lp~~am~~VA~~L~lp~~~VyeVATFYtmF~~kP~G~~~~~~~ 128 (240)
+|...+++++|+++|| +++++|||+||++|+++||||++++++||+.||||+++||+|||||+||+++|+|
T Consensus 4 ~~~~~~~i~~ii~~y~--~~~~~li~~L~~vQ~~~G~Ip~e~~~~iA~~l~v~~~~V~~vatFY~~f~~~p~G------- 74 (156)
T PRK05988 4 EPWDAARIAAIIAEHK--HLEGALLPILHAIQDEFGYVPEDAVPVIAEALNLSRAEVHGVITFYHDFRTHPPG------- 74 (156)
T ss_pred chhHHHHHHHHHHHcC--CCHHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHHHHHHhhccCCCCCC-------
Confidence 4567788999999998 5899999999999999999999999999999999999999999999999999999
Q ss_pred ccEEEEecCChhhhhcCHHHHHHHHHHHcCc----------------------------eEe---ecCCCHHhHHHHHHH
Q psy8528 129 LQYHLNWCTTTPCWLRNSDAILEVIKKKCNM----------------------------MLE---RQDLEPKDMEQIIDD 177 (240)
Q Consensus 129 ~K~~I~VC~~t~C~lrGs~~Il~~l~~~LgI----------------------------mv~---y~~Ltpe~i~~IL~~ 177 (240)
||+|+||+|++|+++|+++|+++++++||| ||| |++||++++++||++
T Consensus 75 -k~~I~VC~~~~C~~~G~~~ll~~l~~~Lgi~~gett~Dg~ftL~~~~ClG~C~~aP~~~in~~~~~~lt~~~~~~il~~ 153 (156)
T PRK05988 75 -RHVLKLCRAEACQAMGGDALAAHAKARLGIDFHQTTADGAVTLEPVYCLGLCACSPAAMLDGEVHGRLDPQRLDALLAE 153 (156)
T ss_pred -CEEEEEeCCchhhcCCHHHHHHHHHHHhCCCCCCcCCCCeEEEEeeeecCccCCCCeEEECCEEeCCCCHHHHHHHHHH
Confidence 999999999999999999999999999998 677 999999999999999
Q ss_pred Hhc
Q psy8528 178 LKA 180 (240)
Q Consensus 178 lk~ 180 (240)
+++
T Consensus 154 ~~~ 156 (156)
T PRK05988 154 ARR 156 (156)
T ss_pred hhC
Confidence 874
No 6
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=100.00 E-value=1.7e-37 Score=259.20 Aligned_cols=122 Identities=43% Similarity=0.867 Sum_probs=117.2
Q ss_pred CCHHhHHHHHHHHHhCCCCCCcccHHHHHHHHHHHcCCCCHHHHHHHHHHcCCChhhHHHHhhhccCCccccCCcccccc
Q psy8528 48 FTPDNKKRAEAIISIYPVGHERAAVIPLLDLAQRQHGWLPISAMHYVADFLNLPKMRVYEVATFYTMFIRKPIGEERIKS 127 (240)
Q Consensus 48 ft~e~~~~i~~il~~Yp~~~~rsalIplL~~aQ~q~G~Lp~~am~~VA~~L~lp~~~VyeVATFYtmF~~kP~G~~~~~~ 127 (240)
|+++..+++++|+++|| +++++|||+||++|+++||||+++|++||+.||+|+++||+|||||+||+++|+|
T Consensus 2 ~~~~~~~~~~~i~~~~~--~~~~~ll~~L~~vQ~~~g~ip~~~~~~iA~~l~v~~~~v~~v~tFY~~f~~~p~g------ 73 (154)
T PRK07539 2 LSAEELAAIEREIAKYP--RPRSAVIPALKIVQEQRGWVPDEAIEAVADYLGMPAIDVEEVATFYSMIFRQPVG------ 73 (154)
T ss_pred CCHHHHHHHHHHHHHCC--CCHHHHHHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHHHHHHHHHhhhCcCCCC------
Confidence 78888999999999998 5899999999999999999999999999999999999999999999999999999
Q ss_pred cccEEEEecCChhhhhcCHHHHHHHHHHHcCc----------------------------eEe---ecCCCHHhHHHHHH
Q psy8528 128 ILQYHLNWCTTTPCWLRNSDAILEVIKKKCNM----------------------------MLE---RQDLEPKDMEQIID 176 (240)
Q Consensus 128 ~~K~~I~VC~~t~C~lrGs~~Il~~l~~~LgI----------------------------mv~---y~~Ltpe~i~~IL~ 176 (240)
||+|+||++++|+++|+++|+++|+++||| +|| |+++|++++++||+
T Consensus 74 --k~~I~VC~g~~C~~~Ga~~l~~~l~~~L~i~~g~tt~dg~~~l~~~~ClG~C~~gPvv~V~~~~y~~vt~e~v~~il~ 151 (154)
T PRK07539 74 --RHVIQVCTSTPCWLRGGEAILAALKKKLGIKPGETTADGRFTLLEVECLGACDNAPVVMINDDTYEDLTPEKIDELLD 151 (154)
T ss_pred --CEEEEEcCCchHHHCCHHHHHHHHHHHhCCCCCCcCCCCeEEEEEccccCccCCCCEEEECCEEeCCCCHHHHHHHHH
Confidence 999999999999999999999999999995 566 99999999999999
Q ss_pred HHh
Q psy8528 177 DLK 179 (240)
Q Consensus 177 ~lk 179 (240)
+++
T Consensus 152 ~~~ 154 (154)
T PRK07539 152 ELK 154 (154)
T ss_pred hcC
Confidence 875
No 7
>TIGR01958 nuoE_fam NADH-quinone oxidoreductase, E subunit. This model describes the E chain of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoB. This model does not identify proteins from chloroplast and cyanobacteria.
Probab=100.00 E-value=2.9e-37 Score=256.06 Aligned_cols=117 Identities=40% Similarity=0.798 Sum_probs=111.0
Q ss_pred HHHHHHHhCCCCCCcccHHHHHHHHHHHcCCCCHHHHHHHHHHcCCChhhHHHHhhhccCCccccCCcccccccccEEEE
Q psy8528 55 RAEAIISIYPVGHERAAVIPLLDLAQRQHGWLPISAMHYVADFLNLPKMRVYEVATFYTMFIRKPIGEERIKSILQYHLN 134 (240)
Q Consensus 55 ~i~~il~~Yp~~~~rsalIplL~~aQ~q~G~Lp~~am~~VA~~L~lp~~~VyeVATFYtmF~~kP~G~~~~~~~~K~~I~ 134 (240)
++++|+++||.+.++++|||+||++|+++||||++++++||+.||||+++||+|||||+||+++|+| ||+|+
T Consensus 1 ~~~~i~~~~~~~~~~~~li~~L~~vQ~~~G~i~~~~~~~iA~~l~~~~~~v~~v~tFY~~f~~~p~g--------k~~I~ 72 (148)
T TIGR01958 1 LIEEIIAKYPDDQKRSAIMPALMIAQEQKGWVTPEAIAAVAEMLGIPPVWVYEVATFYSMFDTEPVG--------RYHLQ 72 (148)
T ss_pred ChHHHHHHCCCCCChhHHHHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHHHHHHhHHhhcCcCCCC--------CEEEE
Confidence 4689999999534899999999999999999999999999999999999999999999999999999 99999
Q ss_pred ecCChhhhhcCHHHHHHHHHHHcCc----------------------------eEe---ecCCCHHhHHHHHHHHh
Q psy8528 135 WCTTTPCWLRNSDAILEVIKKKCNM----------------------------MLE---RQDLEPKDMEQIIDDLK 179 (240)
Q Consensus 135 VC~~t~C~lrGs~~Il~~l~~~LgI----------------------------mv~---y~~Ltpe~i~~IL~~lk 179 (240)
||++++|+++|+++|+++|+++||+ ||| |+++|++++++||++++
T Consensus 73 VC~g~~C~~~Ga~~v~~~l~~~L~i~~g~~t~dg~~~l~~~~ClG~C~~aP~v~V~~~~y~~vt~e~v~~il~~~~ 148 (148)
T TIGR01958 73 VCTNVPCALRGSEALLKYLENKLGIKPGETTPDGRFTLVEVECLGACGNAPVMMINDDYYEFLTPEKLDELLERYE 148 (148)
T ss_pred EcCCchhhhcCHHHHHHHHHHHhCCCCCCCCCCCeEEEEEcCccCccCCCCEEEECCEEeCCCCHHHHHHHHHhcC
Confidence 9999999999999999999999996 666 99999999999999874
No 8
>PF01257 2Fe-2S_thioredx: Thioredoxin-like [2Fe-2S] ferredoxin; InterPro: IPR002023 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. Among the many polypeptide subunits that make up complex I, there is one with a molecular weight of 24 kDa (in mammals), which is a component of the iron-sulphur (IP) fragment of the enzyme. It seems to bind a 2Fe-2S iron-sulphur cluster. The 24 kDa subunit is nuclear encoded, as a precursor form with a transit peptide in mammals and in Neurospora crassa. There is a highly conserved region located in the central section of this subunit that contains two conserved cysteines, that are probably involved in the binding of the 2Fe-2S centre. The 24 kDa subunit is highly similar to [, ]: Subunit E of Escherichia coli NADH-ubiquinone oxidoreductase (gene nuoE) Subunit NQO2 of Paracoccus denitrificans NADH-ubiquinone oxidoreductase ; GO: 0016491 oxidoreductase activity, 0051287 NAD binding, 0055114 oxidation-reduction process; PDB: 1M2D_A 1M2A_B 1F37_B 1M2B_B 2FUG_B 3M9S_B 3IAM_B 3IAS_K 2YBB_2 3I9V_B ....
Probab=100.00 E-value=4.9e-37 Score=253.95 Aligned_cols=114 Identities=36% Similarity=0.754 Sum_probs=100.7
Q ss_pred HHHHHHhCCCCCCcccHHHHHHHHHHHcCCCCHHHHHHHHHHcCCChhhHHHHhhhccCCccccCCcccccccccEEEEe
Q psy8528 56 AEAIISIYPVGHERAAVIPLLDLAQRQHGWLPISAMHYVADFLNLPKMRVYEVATFYTMFIRKPIGEERIKSILQYHLNW 135 (240)
Q Consensus 56 i~~il~~Yp~~~~rsalIplL~~aQ~q~G~Lp~~am~~VA~~L~lp~~~VyeVATFYtmF~~kP~G~~~~~~~~K~~I~V 135 (240)
|++||++|| +++++|||+||++|+++||||++++++||+.|+||+++||+|||||+||+++|.| ||+|.|
T Consensus 1 i~~i~~~~~--~~~~~ll~~L~~~Q~~~g~i~~~~~~~iA~~l~i~~~~v~~v~tFY~~f~~~p~g--------k~~I~V 70 (145)
T PF01257_consen 1 IEEIIARYP--SKRSALLPILHEVQEEYGYIPEEALEEIAEALGIPPAEVYGVATFYSMFRLEPKG--------KHHIRV 70 (145)
T ss_dssp -HHHHHTS----GGGGHHHHHHHHHHHHSS--HHHHHHHHHHHTS-HHHHHHHHHHSSSS-SSS----------SEEEEE
T ss_pred ChHHHHHCC--CCHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHcccCCCC--------CcEEEe
Confidence 689999999 5899999999999999999999999999999999999999999999999999999 999999
Q ss_pred cCChhhhhcCHHHHHHHHHHHcCc----------------------------eEe---ecCCCHHhHHHHHHHHh
Q psy8528 136 CTTTPCWLRNSDAILEVIKKKCNM----------------------------MLE---RQDLEPKDMEQIIDDLK 179 (240)
Q Consensus 136 C~~t~C~lrGs~~Il~~l~~~LgI----------------------------mv~---y~~Ltpe~i~~IL~~lk 179 (240)
|+|++|+++|+++|+++++++||+ +|| |+++|||++++||++||
T Consensus 71 C~g~~C~~~Ga~~l~~~l~~~l~i~~g~~~~dg~~~l~~~~ClG~C~~aP~v~V~~~~y~~vt~e~v~~il~~lk 145 (145)
T PF01257_consen 71 CTGTSCHLRGAEELLEALEEELGIKPGETTEDGKFTLEETGCLGACDQAPVVMVDGEWYGNVTPEKVDEILEELK 145 (145)
T ss_dssp E-SHHHHTTTHHHHHHHHHHHHCTSCCCCSTTTTEEEEEESSSSSGGGSSEEEECCCEEESSSCCHHHHHHHHH-
T ss_pred CCCchHHhCCCHHHHHHHHHHhCCcccccCCCceEEEEECCCccccCCCCEEEECCEEECCCCHHHHHHHHHhcC
Confidence 999999999999999999999986 677 99999999999999986
No 9
>cd03081 TRX_Fd_NuoE_FDH_gamma TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily, NAD-dependent formate dehydrogenase (FDH) gamma subunit; composed of proteins similar to the gamma subunit of NAD-linked FDH of Ralstonia eutropha, a soluble enzyme that catalyzes the irreversible oxidation of formate to carbon dioxide accompanied by the reduction of NAD+ to NADH. FDH is a heteromeric enzyme composed of four nonidentical subunits (alpha, beta, gamma and delta). The FDH gamma subunit is closely related to NuoE, which is part of a multisubunit complex (Nuo) catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. Electrons are transferred from NADH to quinone through a chain of iron-sulfur clusters in Nuo, including the [2Fe-2S] cluster present in NuoE. Similarly, the FDH gamma subunit is hypothesized to be involved in an electron transport chain involving other FDH subunits, upon the oxidat
Probab=99.17 E-value=4e-11 Score=90.26 Aligned_cols=49 Identities=18% Similarity=0.514 Sum_probs=45.5
Q ss_pred cEEEEecCChhhhhcCHHHHHHHHHHHcCc----------------------------eEe---ecCCCHHhHHHHHHHH
Q psy8528 130 QYHLNWCTTTPCWLRNSDAILEVIKKKCNM----------------------------MLE---RQDLEPKDMEQIIDDL 178 (240)
Q Consensus 130 K~~I~VC~~t~C~lrGs~~Il~~l~~~LgI----------------------------mv~---y~~Ltpe~i~~IL~~l 178 (240)
||+|+||++++|+++|+++|+++++++|++ +|| |+++|||++++||++|
T Consensus 1 ~~~i~vC~~~~C~~~G~~~ll~~l~~~l~~~~g~~~~dg~~~l~~~~ClG~C~~gP~~~v~~~~~~~~~~e~i~~il~~~ 80 (80)
T cd03081 1 RHVLKLCRAEACQAMGAEALAAHIKARLGIDFHETTADGSVTLEPVYCLGLCACSPAAMIDGEVHGRVDPEKFDALLAEL 80 (80)
T ss_pred CeEEEEcCChHHHhCCHHHHHHHHHHHhCCCCCCcCCCCeEEEEEeeecCccCCCCEEEECCEEECCCCHHHHHHHHHcC
Confidence 699999999999999999999999999985 566 9999999999999864
No 10
>cd03083 TRX_Fd_NuoE_hoxF TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily, hoxF; composed of proteins similar to the NAD-reducing hydrogenase (hoxS) alpha subunit of Alcaligenes eutrophus H16. HoxS is a cytoplasmic hydrogenase catalyzing the oxidation of molecular hydrogen accompanied by the reduction of NAD. It is composed of four structural subunits encoded by the genes hoxF, hoxU, hoxY and hoxH. The hoxF protein (or alpha subunit) is a fusion protein containing an N-terminal NuoE-like domain and a C-terminal NuoF domain. NuoE and NuoF are components of Nuo, a multisubunit complex catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. Electrons are transferred from NADH to quinone through a chain of iron-sulfur clusters in Nuo, including the [2Fe-2S] cluster in NuoE and the [4Fe-4S] cluster in NuoF. In addition, NuoF is also the NADH- and FMN-binding subunit. HoxF may be involved
Probab=99.08 E-value=1.6e-10 Score=86.91 Aligned_cols=49 Identities=14% Similarity=0.357 Sum_probs=45.2
Q ss_pred cEEEEecCChhhhhcCHHHHHHHHHHHcCc----------------------------eEe---ecCCCHHhHHHHHHHH
Q psy8528 130 QYHLNWCTTTPCWLRNSDAILEVIKKKCNM----------------------------MLE---RQDLEPKDMEQIIDDL 178 (240)
Q Consensus 130 K~~I~VC~~t~C~lrGs~~Il~~l~~~LgI----------------------------mv~---y~~Ltpe~i~~IL~~l 178 (240)
||+|+||++++|+++|+++|+++|+++|++ +|+ |+++|++++++|++.+
T Consensus 1 ~~~i~vC~~~~C~~~Ga~~v~~~l~~~l~~~~~~~t~d~~v~l~~~gClG~C~~~P~v~V~~~~y~~v~~~~v~~iv~~~ 80 (80)
T cd03083 1 KYRIYLSDSITDRMNGYKAVLDALCRELGIRFGEVDEDGMVGLFFTSCTGLCDQGPALLINNRVFTRLTPGRIDQIAELI 80 (80)
T ss_pred CEEEEEcCChHHHhCCHHHHHHHHHHHHCCCCCCcCCCCeEEEEEeceecCcCCCCeEEECCEEECCCCHHHHHHHHhcC
Confidence 699999999999999999999999999985 455 9999999999999864
No 11
>cd03082 TRX_Fd_NuoE_W_FDH_beta TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E family, Tungsten-containing formate dehydrogenase (W-FDH) beta subunit; composed of proteins similar to the W-FDH beta subunit of Methylobacterium extorquens. W-FDH is a heterodimeric NAD-dependent enzyme catalyzing the conversion of formate to carbon dioxide. The beta subunit is a fusion protein containing an N-terminal NuoE domain and a C-terminal NuoF domain. NuoE and NuoF are components of Nuo, a multisubunit complex catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. Electrons are transferred from NADH to quinone through a chain of iron-sulfur clusters in Nuo, including the [2Fe-2S] cluster in NuoE and the [4Fe-4S] cluster in NuoF. In addition, NuoF is also the NADH- and FMN-binding subunit. Similarly, the beta subunit of W-FDH is most likely involved in the electron transport chain during the NAD-dependen
Probab=98.93 E-value=1.8e-09 Score=80.41 Aligned_cols=47 Identities=9% Similarity=0.328 Sum_probs=43.7
Q ss_pred EEEEecCChhhhhcCHHHHHHHHHHHcCc--------------------eEe---ecCCCHHhHHHHHHH
Q psy8528 131 YHLNWCTTTPCWLRNSDAILEVIKKKCNM--------------------MLE---RQDLEPKDMEQIIDD 177 (240)
Q Consensus 131 ~~I~VC~~t~C~lrGs~~Il~~l~~~LgI--------------------mv~---y~~Ltpe~i~~IL~~ 177 (240)
|+|+||++++|+++|+++|+++|+++|++ +|| |+++|++++++++++
T Consensus 2 ~~I~vC~~~~C~~~Ga~~l~~~l~~~L~~~~v~l~~~~ClG~C~~gP~v~V~~~~~~~~t~~~i~~~~~~ 71 (72)
T cd03082 2 LTVRVCDSLSCAMAGAEELLAALEAGLGPEGVRVVRAPCVGRCERAPAALVGQRPVDGATPAAVAAAVEA 71 (72)
T ss_pred eEEEEcCChHHHHCCHHHHHHHHHHHhCCCeEEEEecCcCCccCCCCeEEECCEEeCCcCHHHHHHHHhc
Confidence 78999999999999999999999999997 666 999999999999864
No 12
>cd03064 TRX_Fd_NuoE TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily; Nuo, also called respiratory chain Complex 1, is the entry point for electrons into the respiratory chains of bacteria and the mitochondria of eukaryotes. It is a multisubunit complex with at least 14 core subunits. It catalyzes the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane, providing the proton motive force required for energy-consuming processes. Electrons are transferred from NADH to quinone through a chain of iron-sulfur clusters in Nuo, including the [2Fe-2S] cluster present in NuoE core subunit, also called the 24 kD subunit of Complex 1. This subfamily also include formate dehydrogenases, NiFe hydrogenases and NAD-reducing hydrogenases, that contain a NuoE domain. A subset of these proteins contain both NuoE and NuoF in a single chain. NuoF, also called the 51 kD subunit of Complex 1, contains one [4Fe-4S] clu
Probab=98.79 E-value=1e-08 Score=76.38 Aligned_cols=49 Identities=33% Similarity=0.662 Sum_probs=44.1
Q ss_pred cEEEEecCChhhhhcCHHHHHHHHHHHcCc----------------------------eEe---ecCCCHHhHHHHHHHH
Q psy8528 130 QYHLNWCTTTPCWLRNSDAILEVIKKKCNM----------------------------MLE---RQDLEPKDMEQIIDDL 178 (240)
Q Consensus 130 K~~I~VC~~t~C~lrGs~~Il~~l~~~LgI----------------------------mv~---y~~Ltpe~i~~IL~~l 178 (240)
||+|.||.+++|+.+|++++++++++++++ +|+ |+++|++++++|+++|
T Consensus 1 ~~~v~vC~~~~C~~~Ga~~~~~~l~~~l~~~~~~~~~~~~v~v~~t~ClG~C~~gP~v~v~g~~y~~vt~~~i~~i~~~~ 80 (80)
T cd03064 1 KHVIRVCTGTACHLRGAEALLEALEKKLGIKPGETTPDGRFTLEEVECLGACDLAPVMMINDDVYGRLTPEKVDAILEAL 80 (80)
T ss_pred CEEEEECCCcHHHhCCHHHHHHHHHHHhCCCCCCcCCCCEEEEEEecCcCcCCCCCEEEECCEEECCCCHHHHHHHHHhC
Confidence 689999999999999999999999998763 344 9999999999999864
No 13
>cd02980 TRX_Fd_family Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:ubiquinone oxidoreductase (NuoE). TRX-like Fds are soluble low-potential electron carriers containing a single [2Fe-2S] cluster. The exact role of TRX-like Fd is still unclear. It has been suggested that it may be involved in nitrogen fixation. Its homologous domains in large redox enzymes (such as Nuo and hydrogenases) function as electron carriers.
Probab=98.47 E-value=2.2e-07 Score=67.63 Aligned_cols=47 Identities=30% Similarity=0.636 Sum_probs=42.3
Q ss_pred EEEEecCChhhhhcCHHHHHHHHHHHcCc------------------------eEe-----ecCCCHHhHHHHHHH
Q psy8528 131 YHLNWCTTTPCWLRNSDAILEVIKKKCNM------------------------MLE-----RQDLEPKDMEQIIDD 177 (240)
Q Consensus 131 ~~I~VC~~t~C~lrGs~~Il~~l~~~LgI------------------------mv~-----y~~Ltpe~i~~IL~~ 177 (240)
|+|.||++++|+.+|+++|+++|++.++. +|+ |+++|++++++||++
T Consensus 1 ~~I~VC~~~~C~~~G~~~l~~~l~~~~~~~~~~~~v~v~~~~Clg~C~~~P~v~i~~~~~~y~~v~~~~~~~il~~ 76 (77)
T cd02980 1 HHILVCTGTACGLRGAEELLEALEKELGIRGGDGRVTVERVGCLGACGLAPVVVVYPDGVWYGRVTPEDVEEIVEE 76 (77)
T ss_pred CEEEEccCCCcccCCHHHHHHHHHHHHhhhcCCCeEEEEEcCCcCcccCCCEEEEeCCCeEEccCCHHHHHHHHHh
Confidence 58999999999999999999999998764 344 999999999999986
No 14
>cd03063 TRX_Fd_FDH_beta TRX-like [2Fe-2S] Ferredoxin (Fd) family, NAD-dependent formate dehydrogenase (FDH) beta subunit; composed of proteins similar to the beta subunit of NAD-linked FDH of Ralstonia eutropha, a soluble enzyme that catalyzes the irreversible oxidation of formate to carbon dioxide accompanied by the reduction of NAD to NADH. FDH is a heteromeric enzyme composed of four nonidentical subunits (alpha, beta, gamma and delta). The FDH beta subunit contains a NADH:ubiquinone oxidoreductase (Nuo) F domain C-terminal to a Fd-like domain without the active site cysteines. The absence of conserved metal-binding residues in the putative active site suggests that members of this subfamily have lost the ability to bind iron-sulfur clusters in the N-terminal Fd-like domain. The C-terminal NuoF domain is a component of Nuo, a multisubunit complex catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. NuoF contains one [4Fe-4S] c
Probab=97.20 E-value=0.00061 Score=53.51 Aligned_cols=48 Identities=13% Similarity=0.194 Sum_probs=41.3
Q ss_pred EEEecCChhhhhcCHHHHHHHHHHHcC-----c-----------------eE-------eecCCCHHhHHHHHHHHh
Q psy8528 132 HLNWCTTTPCWLRNSDAILEVIKKKCN-----M-----------------ML-------ERQDLEPKDMEQIIDDLK 179 (240)
Q Consensus 132 ~I~VC~~t~C~lrGs~~Il~~l~~~Lg-----I-----------------mv-------~y~~Ltpe~i~~IL~~lk 179 (240)
+|.||.+|.|...||++++++|++++. + .| -|+++|||++.+|+++.-
T Consensus 2 ~I~Vc~gT~ciAaGA~~V~~al~~ei~~~gl~v~v~~tGC~G~C~~ePlV~V~~p~g~v~Y~~V~~edv~~Iv~~~~ 78 (92)
T cd03063 2 RIYVPRDAAALALGADEVAEAIEAEAAARGLAATIVRNGSRGMYWLEPLVEVETPGGRVAYGPVTPADVASLLDAGA 78 (92)
T ss_pred EEEEeCChhhhhhCHHHHHHHHHHHHHHcCCeEEEEEecCceecCCCCEEEEEeCCCcEEEEeCCHHHHHHHHHHHh
Confidence 589999999999999999999999774 2 12 199999999999998843
No 15
>cd03062 TRX_Fd_Sucrase TRX-like [2Fe-2S] Ferredoxin (Fd) family, Sucrase subfamily; composed of proteins with similarity to a novel plant enzyme, isolated from potato, which contains a Fd-like domain and exhibits sucrolytic activity. The putative active site of the Fd-like domain of the enzyme contains two cysteines and two histidines for possible binding to iron-sulfur clusters, compared to four cysteines present in the active site of Fd.
Probab=96.01 E-value=0.016 Score=45.24 Aligned_cols=54 Identities=17% Similarity=0.314 Sum_probs=41.9
Q ss_pred EEEEecCC----hhhhhcCHHHHHHHHHHHcC------c----------------eE-----e---ecCCCHHhHHHHHH
Q psy8528 131 YHLNWCTT----TPCWLRNSDAILEVIKKKCN------M----------------ML-----E---RQDLEPKDMEQIID 176 (240)
Q Consensus 131 ~~I~VC~~----t~C~lrGs~~Il~~l~~~Lg------I----------------mv-----~---y~~Ltpe~i~~IL~ 176 (240)
.+|.||++ ..|...| .+|+++|++++. + +| + |+.++|+++++|++
T Consensus 2 ~~ilVCth~rrd~~C~~~g-~~l~~~l~~~l~~~~~~~v~v~~~~clG~c~~gp~vvvyP~~~g~wy~~v~p~~v~~Iv~ 80 (97)
T cd03062 2 PLVLVCTHGKRDKRCGICG-PPLAAELRAELPEHGPGGVRVWEVSHVGGHKFAGNVIIYPKGDGIWYGRVTPEHVPPIVD 80 (97)
T ss_pred CEEEEeCCCCCCcChhhcC-HHHHHHHHHHHHHhCCCceEEEeCCcCCccCcCCEEEEEeCCCeeEEeecCHHHHHHHHH
Confidence 48999995 5698888 689999998874 3 33 3 77999999999998
Q ss_pred HHhcCCCCC
Q psy8528 177 DLKAGKKPA 185 (240)
Q Consensus 177 ~lk~g~~p~ 185 (240)
+.-.+..+-
T Consensus 81 ~hl~~g~~v 89 (97)
T cd03062 81 RLILGGKII 89 (97)
T ss_pred HHhcCCcCC
Confidence 765554443
No 16
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=85.14 E-value=2.3 Score=28.71 Aligned_cols=38 Identities=13% Similarity=0.061 Sum_probs=32.0
Q ss_pred ccHHHHHHHHHHHcCCCCHHHHHHHHHHcCCChhhHHH
Q psy8528 70 AAVIPLLDLAQRQHGWLPISAMHYVADFLNLPKMRVYE 107 (240)
Q Consensus 70 salIplL~~aQ~q~G~Lp~~am~~VA~~L~lp~~~Vye 107 (240)
..-+.+|..+-..+.|.+.+.++.+|+.+||+..+|..
T Consensus 9 ~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~ 46 (59)
T cd00086 9 PEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKI 46 (59)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHH
Confidence 34567777777778899999999999999999998864
No 17
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=84.60 E-value=1.9 Score=29.47 Aligned_cols=35 Identities=14% Similarity=0.119 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHHcCCChhhHH
Q psy8528 72 VIPLLDLAQRQHGWLPISAMHYVADFLNLPKMRVY 106 (240)
Q Consensus 72 lIplL~~aQ~q~G~Lp~~am~~VA~~L~lp~~~Vy 106 (240)
-+.+|..+=+...|++.+.++.||..|||+..+|.
T Consensus 11 q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~ 45 (57)
T PF00046_consen 11 QLKVLEEYFQENPYPSKEEREELAKELGLTERQVK 45 (57)
T ss_dssp HHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHH
T ss_pred HHHHHHHHHHHhccccccccccccccccccccccc
Confidence 34555555556789999999999999999999985
No 18
>PF06999 Suc_Fer-like: Sucrase/ferredoxin-like; InterPro: IPR009737 This family contains a number of bacterial and eukaryotic proteins approximately 400 residues long that resemble ferredoxin and appear to have sucrolytic activity [].
Probab=83.79 E-value=2.7 Score=36.72 Aligned_cols=57 Identities=19% Similarity=0.333 Sum_probs=43.0
Q ss_pred cEEEEecCCh----hhhhcCHHHHHHHHHHHcC--------c----------------eE-----e---ecCCCHHhHHH
Q psy8528 130 QYHLNWCTTT----PCWLRNSDAILEVIKKKCN--------M----------------ML-----E---RQDLEPKDMEQ 173 (240)
Q Consensus 130 K~~I~VC~~t----~C~lrGs~~Il~~l~~~Lg--------I----------------mv-----~---y~~Ltpe~i~~ 173 (240)
+.+|-||+-. -|...| ..|.+++++.+. | +. + |++|+|++++.
T Consensus 132 ~~~iLVCtHg~RD~rCg~~G-p~l~~~l~~~~~~~~l~~~~V~~iSHiGGHkfAgNvIiy~~~~p~g~wyGrv~p~~v~~ 210 (230)
T PF06999_consen 132 KPLILVCTHGKRDKRCGILG-PPLARELEKELRERGLSRDRVWEISHIGGHKFAGNVIIYSKPKPDGIWYGRVTPEDVEG 210 (230)
T ss_pred CCEEEEcCCCCcCCchhccc-HHHHHHHHHHhhhcCCccceEEEecccccceecCeEEEEecCCCcEEEEEeeCHHHHHH
Confidence 7899999854 788887 345555555432 2 22 2 89999999999
Q ss_pred HHHH-HhcCCCCCCC
Q psy8528 174 IIDD-LKAGKKPAPG 187 (240)
Q Consensus 174 IL~~-lk~g~~p~~g 187 (240)
|++. +.+|+..+..
T Consensus 211 iv~~t~~~g~vi~~~ 225 (230)
T PF06999_consen 211 IVDATILDGKVIPEL 225 (230)
T ss_pred HHHHHHhCCcCcCcc
Confidence 9999 9999987764
No 19
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=81.34 E-value=3.6 Score=27.60 Aligned_cols=37 Identities=14% Similarity=0.078 Sum_probs=30.2
Q ss_pred cHHHHHHHHHHHcCCCCHHHHHHHHHHcCCChhhHHH
Q psy8528 71 AVIPLLDLAQRQHGWLPISAMHYVADFLNLPKMRVYE 107 (240)
Q Consensus 71 alIplL~~aQ~q~G~Lp~~am~~VA~~L~lp~~~Vye 107 (240)
.-+.+|..+-..+-|.+.+.+..+|+.+|++..+|..
T Consensus 10 ~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~ 46 (56)
T smart00389 10 EQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKV 46 (56)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHH
Confidence 4566777776667799999999999999999887753
No 20
>PF14297 DUF4373: Domain of unknown function (DUF4373)
Probab=81.14 E-value=4.7 Score=30.49 Aligned_cols=65 Identities=18% Similarity=0.240 Sum_probs=52.5
Q ss_pred HHHHHHHHHhCCCCCCcccHHHHHHHHHHHcCC-CCHHHHHHHHHHcCCChhhHHHHhhhccCCccc
Q psy8528 53 KKRAEAIISIYPVGHERAAVIPLLDLAQRQHGW-LPISAMHYVADFLNLPKMRVYEVATFYTMFIRK 118 (240)
Q Consensus 53 ~~~i~~il~~Yp~~~~rsalIplL~~aQ~q~G~-Lp~~am~~VA~~L~lp~~~VyeVATFYtmF~~k 118 (240)
-.+++.+.++|.. .--+..+-+|-.+=++.|| ++-+.+..+|+.++++...|.+|+.=|..|+..
T Consensus 11 D~ki~~l~~~~G~-~G~~~y~~ll~~iy~~~~y~~~~~~~~~~a~~~~~~~~~v~~II~~~~LF~~~ 76 (87)
T PF14297_consen 11 DPKIRRLMAEYGC-EGYGIYWYLLEYIYKQGGYYLWWDKLFLIARKLGVSEEYVEEIINEYGLFDIE 76 (87)
T ss_pred CHHHHHHHHHcCC-chHHHHHHHHHHHHcCCCeEeeHHHHHHHHHHHCcCHHHHHHHHHHhCCcccC
Confidence 4678889999974 2345677788888777775 677779999999999999999999988788743
No 21
>PF10820 DUF2543: Protein of unknown function (DUF2543); InterPro: IPR020251 This entry contains proteins with no known function.
Probab=75.95 E-value=3.1 Score=32.04 Aligned_cols=31 Identities=16% Similarity=0.193 Sum_probs=28.8
Q ss_pred CCCCHHHHHHHHHHcCCChhhHHHHhhhccC
Q psy8528 84 GWLPISAMHYVADFLNLPKMRVYEVATFYTM 114 (240)
Q Consensus 84 G~Lp~~am~~VA~~L~lp~~~VyeVATFYtm 114 (240)
.=||+++.++.|...|+...|+.++|+|-..
T Consensus 47 eeIsEeaQ~EMA~eAgi~~~rID~IA~fLNq 77 (81)
T PF10820_consen 47 EEISEEAQQEMASEAGIDEQRIDDIANFLNQ 77 (81)
T ss_pred HhhhHHHHHHHHHHcCCcHHHHHHHHHHHHH
Confidence 4799999999999999999999999999754
No 22
>PF02797 Chal_sti_synt_C: Chalcone and stilbene synthases, C-terminal domain; InterPro: IPR012328 Synonym(s): Chalcone synthase, Flavonone synthase, 6'-deoxychalcone synthase Naringenin-chalcone synthases (2.3.1.74 from EC) and stilbene synthases (STS) (formerly known as resveratrol synthases) are related plant enzymes. CHS is an important enzyme in flavanoid biosynthesis and STS is a key enzyme in stilbene-type phyloalexin biosynthesis. Both enzymes catalyze the addition of three molecules of malonyl-CoA to a starter CoA ester (a typical example is 4-coumaroyl-CoA), producing either a chalcone (with CHS) or stilbene (with STS) []. These enzymes have a conserved cysteine residue, located in the central section of the protein sequence, which is essential for the catalytic activity of both enzymes and probably represents the binding site for the 4-coumaryl-CoA group []. This domain of chalcone synthase is reported to be structurally similar to domains in thiolase and beta-ketoacyl synthase. The differences in activity are accounted for by differences in the N-terminal domain. ; GO: 0016746 transferase activity, transferring acyl groups; PDB: 3OV2_A 3OV3_B 1Z1F_A 1Z1E_A 3ALE_C 3OIT_A 2H84_A 1TEE_D 1TED_A 2P0U_A ....
Probab=75.30 E-value=0.84 Score=38.54 Aligned_cols=37 Identities=8% Similarity=0.313 Sum_probs=29.4
Q ss_pred cCHHHHHHHHHHHcCc----------eEe-ecCCCHHhHHHHHHHHhc
Q psy8528 144 RNSDAILEVIKKKCNM----------MLE-RQDLEPKDMEQIIDDLKA 180 (240)
Q Consensus 144 rGs~~Il~~l~~~LgI----------mv~-y~~Ltpe~i~~IL~~lk~ 180 (240)
-|+.+|++.+++.||+ ++. |+|++...+--+|+.+++
T Consensus 67 PGG~~ILd~v~~~L~L~~~~l~~Sr~vLr~yGNmSSaTVlfVL~~~~~ 114 (151)
T PF02797_consen 67 PGGRKILDAVEEALGLSPEQLRASREVLREYGNMSSATVLFVLERMRR 114 (151)
T ss_dssp -SSHHHHHHHHHHHTS-GGGGHHHHHHHHHH-B-GGGHHHHHHHHHHH
T ss_pred CChHHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchHHHHHHHHh
Confidence 4779999999999998 222 999999999999988765
No 23
>PLN00415 3-ketoacyl-CoA synthase
Probab=66.71 E-value=3.3 Score=41.28 Aligned_cols=56 Identities=14% Similarity=0.150 Sum_probs=46.3
Q ss_pred hcCHHHHHHHHHHHcCc---------eEe--ecCCCHHhHHHHHHHHhcCCCCCCCCCCCCCCCcCc
Q psy8528 143 LRNSDAILEVIKKKCNM---------MLE--RQDLEPKDMEQIIDDLKAGKKPAPGPSGYTSGIGSQ 198 (240)
Q Consensus 143 lrGs~~Il~~l~~~LgI---------mv~--y~~Ltpe~i~~IL~~lk~g~~p~~gp~g~~~~~~~~ 198 (240)
=-|+.+|++++++.||+ |+- |||++...+--+|+.+.+....++|-+|-.-++||=
T Consensus 363 HpGGraVLdave~~LgL~~~~le~Sr~vL~r~GN~SSsSV~yvL~~~~~~~~~~~Gdrvl~iaFGpG 429 (466)
T PLN00415 363 HAGGRALLDAVEKGLGLSEFDLEPSRMTLHRFGNTSSSSLWYELAYVEAKCRVKRGDRVWQLAFGSG 429 (466)
T ss_pred cCCcHHHHHHHHHHcCCCHHHHHHHHHHHHHhCCchhhhHHHHHHHHHhhccCCCCCEEEEEEEcCc
Confidence 36999999999999998 222 999999999999999987666778877777777663
No 24
>COG3424 BcsA Predicted naringenin-chalcone synthase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=65.02 E-value=5.1 Score=38.58 Aligned_cols=53 Identities=11% Similarity=0.325 Sum_probs=41.5
Q ss_pred cCHHHHHHHHHHHcCc----------eEe-ecCCCHHhHHHHHHHHhcCCCCCCCCCCCCCCCcC
Q psy8528 144 RNSDAILEVIKKKCNM----------MLE-RQDLEPKDMEQIIDDLKAGKKPAPGPSGYTSGIGS 197 (240)
Q Consensus 144 rGs~~Il~~l~~~LgI----------mv~-y~~Ltpe~i~~IL~~lk~g~~p~~gp~g~~~~~~~ 197 (240)
-|+.+|+++.++.||+ .+. |+||+...+--+|++.-+.. +++|.-|....+||
T Consensus 278 PGG~KVida~~~sLgls~e~l~~s~~~L~~~GNMSSatvLfVL~d~l~~~-~~~g~~Gl~~A~GP 341 (356)
T COG3424 278 PGGPKVIDAYEESLGLSPEALELSWDVLREYGNMSSATVLFVLEDTLQKA-PKSGSRGLMFAMGP 341 (356)
T ss_pred CCCchHHHHHHHhcCCCHHHHHHHHHHHHHhCCccchhhHHHHHHHHHhc-CCCCcceeeeecCC
Confidence 3778999999999999 233 99999999999998875433 77787666655555
No 25
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=63.40 E-value=8.3 Score=28.22 Aligned_cols=38 Identities=18% Similarity=0.339 Sum_probs=25.4
Q ss_pred CcccHHHHHHHHHHHcCCCCHHHHHHHHHHcCCC-hhhHHH
Q psy8528 68 ERAAVIPLLDLAQRQHGWLPISAMHYVADFLNLP-KMRVYE 107 (240)
Q Consensus 68 ~rsalIplL~~aQ~q~G~Lp~~am~~VA~~L~lp-~~~Vye 107 (240)
++..++..+..-.+.+||-| .+++||+.||+. ++-|..
T Consensus 7 rQ~~vL~~I~~~~~~~G~~P--t~rEIa~~~g~~S~~tv~~ 45 (65)
T PF01726_consen 7 RQKEVLEFIREYIEENGYPP--TVREIAEALGLKSTSTVQR 45 (65)
T ss_dssp HHHHHHHHHHHHHHHHSS-----HHHHHHHHTSSSHHHHHH
T ss_pred HHHHHHHHHHHHHHHcCCCC--CHHHHHHHhCCCChHHHHH
Confidence 34566777777777888765 778888888886 666654
No 26
>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=63.22 E-value=7.7 Score=26.04 Aligned_cols=30 Identities=23% Similarity=0.216 Sum_probs=22.0
Q ss_pred HHHHHHHHHcCCCCHHHHHHHHHHcCCChhhHHH
Q psy8528 74 PLLDLAQRQHGWLPISAMHYVADFLNLPKMRVYE 107 (240)
Q Consensus 74 plL~~aQ~q~G~Lp~~am~~VA~~L~lp~~~Vye 107 (240)
-||+.+|+. +......||+.+|++...|..
T Consensus 7 ~Il~~Lq~d----~r~s~~~la~~lglS~~~v~~ 36 (42)
T PF13404_consen 7 KILRLLQED----GRRSYAELAEELGLSESTVRR 36 (42)
T ss_dssp HHHHHHHH-----TTS-HHHHHHHHTS-HHHHHH
T ss_pred HHHHHHHHc----CCccHHHHHHHHCcCHHHHHH
Confidence 477888877 556677899999999999875
No 27
>PLN03168 chalcone synthase; Provisional
Probab=62.97 E-value=3 Score=39.87 Aligned_cols=43 Identities=19% Similarity=0.343 Sum_probs=35.5
Q ss_pred cCHHHHHHHHHHHcCc----e------Ee-ecCCCHHhHHHHHHHHhcCCCCCCC
Q psy8528 144 RNSDAILEVIKKKCNM----M------LE-RQDLEPKDMEQIIDDLKAGKKPAPG 187 (240)
Q Consensus 144 rGs~~Il~~l~~~LgI----m------v~-y~~Ltpe~i~~IL~~lk~g~~p~~g 187 (240)
.|+..|+++++++||+ + +. |||+....+--+|+++.++ ..+.|
T Consensus 303 qgg~~Il~~v~~~Lgl~~ek~~~s~~vl~~yGNtSSaSv~~vL~~~~~~-~~~~g 356 (389)
T PLN03168 303 PGGPAILDQVEAKLKLTKDKMQGSRDILSEFGNMSSASVLFVLDQIRQR-SVKMG 356 (389)
T ss_pred CCcHHHHHHHHHHcCCCHHHHHHHHHHHHHhCccHhhhHHHHHHHHHHH-HhhcC
Confidence 6889999999999999 2 33 9999999999999988765 44444
No 28
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=62.67 E-value=24 Score=35.24 Aligned_cols=126 Identities=14% Similarity=0.240 Sum_probs=72.0
Q ss_pred HHHHHHHHHhCCCCCCcccHHHHHHHHHHHcCCCCHHHHHHHHHHcC-CChhhHHHHhhhccCCccccCCcccccccccE
Q psy8528 53 KKRAEAIISIYPVGHERAAVIPLLDLAQRQHGWLPISAMHYVADFLN-LPKMRVYEVATFYTMFIRKPIGEERIKSILQY 131 (240)
Q Consensus 53 ~~~i~~il~~Yp~~~~rsalIplL~~aQ~q~G~Lp~~am~~VA~~L~-lp~~~VyeVATFYtmF~~kP~G~~~~~~~~K~ 131 (240)
.+-+..-+.-.+.......+--.|-..-+..||+..+ ++.+++.++ +....|..|..-.-.| .|.| +.-.
T Consensus 93 ~e~L~~Ql~~~~~s~~e~~Ia~~lI~~Ldd~GYl~~~-le~~~~~l~~~~~~eve~vl~~iQ~l--dP~G------V~Ar 163 (444)
T COG1508 93 SEYLLEQLRLLPLSDTERAIATYLIDALDDEGYLTES-LEEIAELLGSVDEEEVEKVLARIQSL--DPAG------VGAR 163 (444)
T ss_pred HHHHHHHHhhcCCChHHHHHHHHHHhhcCcCCCcccC-HHHHHHhcccccHHHHHHHHHHHhcC--CCCc------cccC
Confidence 4445555555554222333333444445668999999 999999999 9999999998766555 5777 0012
Q ss_pred EEEecCChhhhh-----cCHHHHHHHHHHHcCc---eEe-ecCCCHHhHHHHHHHHhcCCCCCCCC
Q psy8528 132 HLNWCTTTPCWL-----RNSDAILEVIKKKCNM---MLE-RQDLEPKDMEQIIDDLKAGKKPAPGP 188 (240)
Q Consensus 132 ~I~VC~~t~C~l-----rGs~~Il~~l~~~LgI---mv~-y~~Ltpe~i~~IL~~lk~g~~p~~gp 188 (240)
.++=|--.-=.. .....|+++++....- ++. .-+++.+++.++++.+++ ..|.||-
T Consensus 164 ~l~EcL~lQL~~~~~~~~~~~~v~~~l~lla~~d~~~i~~~~~v~~~dl~~~l~~I~~-l~PrPg~ 228 (444)
T COG1508 164 DLRECLLLQLERRPLDDPALEIVIDHLELLARRDFTTIARELKVDEDELKEALLLIRS-LDPRPGL 228 (444)
T ss_pred cHHHHHHHHHHhcCCCChhHHHHHHHHHHHHhhhHHHHHHHhCCCHHHHHHHHHHHHc-cCCCCcc
Confidence 222221110000 0011122222211111 233 678999999999988874 5677886
No 29
>PF13309 HTH_22: HTH domain
Probab=59.08 E-value=22 Score=25.80 Aligned_cols=53 Identities=19% Similarity=0.218 Sum_probs=34.2
Q ss_pred HHHHHHHhCCCC---CCcccHHHHHHHHHHHcCCCCHHHHHHHHHHcCCChhhHHH
Q psy8528 55 RAEAIISIYPVG---HERAAVIPLLDLAQRQHGWLPISAMHYVADFLNLPKMRVYE 107 (240)
Q Consensus 55 ~i~~il~~Yp~~---~~rsalIplL~~aQ~q~G~Lp~~am~~VA~~L~lp~~~Vye 107 (240)
.+++++.++... -.+.-=+.++..+.++-=|.=..++.+||+.||++..-||-
T Consensus 6 ~i~~~~~~~~~~~~~l~~~~k~~iV~~L~~~G~F~lKgav~~vA~~L~iS~~TVY~ 61 (64)
T PF13309_consen 6 IIEEVIAEVGKPPSRLSKEEKKEIVRQLYEKGIFLLKGAVEYVAEKLGISRATVYR 61 (64)
T ss_pred HHHHHHHHhCCChhhCCHHHHHHHHHHHHHCCCcccCcHHHHHHHHHCCCHHHHHH
Confidence 455666655321 12233344444444433388899999999999999999984
No 30
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=56.65 E-value=22 Score=25.77 Aligned_cols=27 Identities=7% Similarity=0.206 Sum_probs=22.4
Q ss_pred HHHHcCC----CCHHHHHHHHHHcCCChhhH
Q psy8528 79 AQRQHGW----LPISAMHYVADFLNLPKMRV 105 (240)
Q Consensus 79 aQ~q~G~----Lp~~am~~VA~~L~lp~~~V 105 (240)
.=+..|| ++.+..+++|..|||+...|
T Consensus 19 ~fe~~~y~~~~~~~~~r~~la~~lgl~~~vv 49 (58)
T TIGR01565 19 FAEKLGWKLKDKRREEVREFCEEIGVTRKVF 49 (58)
T ss_pred HHHHcCCCCCCCCHHHHHHHHHHhCCCHHHe
Confidence 3345689 99999999999999998765
No 31
>PLN03172 chalcone synthase family protein; Provisional
Probab=54.54 E-value=7.9 Score=37.18 Aligned_cols=37 Identities=19% Similarity=0.374 Sum_probs=32.2
Q ss_pred cCHHHHHHHHHHHcCc----e------Ee-ecCCCHHhHHHHHHHHhc
Q psy8528 144 RNSDAILEVIKKKCNM----M------LE-RQDLEPKDMEQIIDDLKA 180 (240)
Q Consensus 144 rGs~~Il~~l~~~LgI----m------v~-y~~Ltpe~i~~IL~~lk~ 180 (240)
.|+..|++.++++||+ + +. |||+....+--+|+++.+
T Consensus 304 qgg~~Il~~v~~~Lgl~~~~~~~s~~vl~~yGNtSSaSv~~vL~~~~~ 351 (393)
T PLN03172 304 PGGPAILDQVEIKLDLKEEKLRATRHVLSDYGNMSSACVLFILDEMRK 351 (393)
T ss_pred CCcHHHHHHHHHHcCCCHHHHHHHHHHHHHhCccHHhHHHHHHHHHHh
Confidence 6889999999999999 2 33 999999999999998863
No 32
>COG3411 Ferredoxin [Energy production and conversion]
Probab=53.10 E-value=14 Score=27.71 Aligned_cols=25 Identities=16% Similarity=0.323 Sum_probs=20.8
Q ss_pred ecCCCHHhHHHHHHHH-hcCCCCCCC
Q psy8528 163 RQDLEPKDMEQIIDDL-KAGKKPAPG 187 (240)
Q Consensus 163 y~~Ltpe~i~~IL~~l-k~g~~p~~g 187 (240)
|.+++|+++++|+++. ..|+++...
T Consensus 29 Y~~V~p~~a~rIv~~hl~~Gr~Ve~~ 54 (64)
T COG3411 29 YTRVDPEDARRIVQSHLLGGRPVEEL 54 (64)
T ss_pred EeccCHHHHHHHHHHHHhCCCcchhh
Confidence 9999999999999874 567777654
No 33
>PLN02932 3-ketoacyl-CoA synthase
Probab=48.61 E-value=9.8 Score=37.96 Aligned_cols=57 Identities=14% Similarity=0.218 Sum_probs=44.4
Q ss_pred hhhcCHHHHHHHHHHHcCc----------eEe-ecCCCHHhHHHHHHHHhcCCCCCCCCCCCCCCCcC
Q psy8528 141 CWLRNSDAILEVIKKKCNM----------MLE-RQDLEPKDMEQIIDDLKAGKKPAPGPSGYTSGIGS 197 (240)
Q Consensus 141 C~lrGs~~Il~~l~~~LgI----------mv~-y~~Ltpe~i~~IL~~lk~g~~p~~gp~g~~~~~~~ 197 (240)
|-=.|+..|++++++.||+ .+. ||+.....+-=.|+.+.+....++|-++-..|.|+
T Consensus 375 ~iHqggr~IIdav~k~LgL~~~~~e~s~~tL~rfGNTSSaSI~~~L~~~ea~grik~Gd~vl~iaFGs 442 (478)
T PLN02932 375 CIHAGGRALIDEMEKNLHLTPLDVEASRMTLHRFGNTSSSSIWYELAYTEAKGRMKKGDRIWQIALGS 442 (478)
T ss_pred EEccCCHHHHHHHHHHcCCChHHHHHHHHHHHHhCChhhhHHHHHHHHHHHcCCCCCCCEEEEEEEec
Confidence 3447999999999999999 122 99999999998888887655677887665655554
No 34
>PRK09480 slmA division inhibitor protein; Provisional
Probab=47.50 E-value=11 Score=30.66 Aligned_cols=44 Identities=18% Similarity=0.269 Sum_probs=32.1
Q ss_pred CcccHHHHHHHH-HHHcCCCCHHHHHHHHHHcCCChhhHHHHhhhccCCcccc
Q psy8528 68 ERAAVIPLLDLA-QRQHGWLPISAMHYVADFLNLPKMRVYEVATFYTMFIRKP 119 (240)
Q Consensus 68 ~rsalIplL~~a-Q~q~G~Lp~~am~~VA~~L~lp~~~VyeVATFYtmF~~kP 119 (240)
++..++.....+ -++.| ..-.++.||+..|+++ .|||.+|..|.
T Consensus 11 ~r~~Il~aa~~l~~~~~G--~~~ti~~Ia~~agvs~------gt~Y~~F~~K~ 55 (194)
T PRK09480 11 RREQILQALAQMLESPPG--ERITTAKLAARVGVSE------AALYRHFPSKA 55 (194)
T ss_pred HHHHHHHHHHHHHHhcCC--CccCHHHHHHHhCCCH------hHHHHHCCCHH
Confidence 455666654443 44446 7889999999999997 58889998765
No 35
>PLN03173 chalcone synthase; Provisional
Probab=46.31 E-value=13 Score=35.73 Aligned_cols=37 Identities=19% Similarity=0.367 Sum_probs=31.7
Q ss_pred cCHHHHHHHHHHHcCc----e------Ee-ecCCCHHhHHHHHHHHhc
Q psy8528 144 RNSDAILEVIKKKCNM----M------LE-RQDLEPKDMEQIIDDLKA 180 (240)
Q Consensus 144 rGs~~Il~~l~~~LgI----m------v~-y~~Ltpe~i~~IL~~lk~ 180 (240)
.|+..|++++++.||+ + +. |||+....+--+|+++.+
T Consensus 304 qgg~~Il~~v~~~LgL~~ekl~~s~~vl~~yGNtSSaSv~~vL~~~~~ 351 (391)
T PLN03173 304 PGGPAILDQVEAKLALKPEKLRATRHVLSEYGNMSSACVLFILDEMRK 351 (391)
T ss_pred CCcHHHHHHHHHHcCCChHHHHHHHHHHHHhCcchhhHHHHHHHHHHH
Confidence 5888999999999998 1 33 999999999999998874
No 36
>PTZ00397 macrophage migration inhibition factor-like protein; Provisional
Probab=45.77 E-value=36 Score=26.69 Aligned_cols=79 Identities=13% Similarity=0.096 Sum_probs=43.9
Q ss_pred HHHHHHHHHHcCCChhhHHHHhhhccCCccccCCcccccccccEEEEecCChh--hhhcCHHHHHHHHHHHcCc-----e
Q psy8528 88 ISAMHYVADFLNLPKMRVYEVATFYTMFIRKPIGEERIKSILQYHLNWCTTTP--CWLRNSDAILEVIKKKCNM-----M 160 (240)
Q Consensus 88 ~~am~~VA~~L~lp~~~VyeVATFYtmF~~kP~G~~~~~~~~K~~I~VC~~t~--C~lrGs~~Il~~l~~~LgI-----m 160 (240)
.+.-+.+|+.||.|.. |=++++..--.+-=-|..+ |..+ .+|..=.+.. =.-+=+.+|-+.|+++||| +
T Consensus 22 ~~~~~~l~~~lgkPe~--~~~v~~~~~~~m~f~g~~~-p~a~-v~i~~~g~~~~e~k~~l~~~i~~~l~~~lgi~~~rv~ 97 (116)
T PTZ00397 22 SDIENAIADVLGKPLS--YIMSGYDYQKHMRFGGSHD-GCCF-VRVTSIGGISRSNNSSIAAAITKILASHLKVKSERVY 97 (116)
T ss_pred HHHHHHHHHHhCCChH--HEEEEEeCCceEEECCCCC-ceEE-EEEEEecCCCHHHHHHHHHHHHHHHHHHhCcCcccEE
Confidence 3455679999999999 7677776432221113222 1111 1222112211 0011256788889999999 6
Q ss_pred EeecCCCHHh
Q psy8528 161 LERQDLEPKD 170 (240)
Q Consensus 161 v~y~~Ltpe~ 170 (240)
|+|.++.+++
T Consensus 98 I~f~~~~~~~ 107 (116)
T PTZ00397 98 IEFKDCSAQN 107 (116)
T ss_pred EEEEECChhh
Confidence 7788887764
No 37
>COG2442 Uncharacterized conserved protein [Function unknown]
Probab=45.27 E-value=23 Score=27.20 Aligned_cols=44 Identities=23% Similarity=0.424 Sum_probs=32.2
Q ss_pred EEEEecCChhhhhcC----HHHHHHHHHHHcCc-----eEeecCCCHHhHHHHHHH
Q psy8528 131 YHLNWCTTTPCWLRN----SDAILEVIKKKCNM-----MLERQDLEPKDMEQIIDD 177 (240)
Q Consensus 131 ~~I~VC~~t~C~lrG----s~~Il~~l~~~LgI-----mv~y~~Ltpe~i~~IL~~ 177 (240)
..-.+|.|-|| ++| -..|++.+. .|. .-+|.+||.+++.+.|+-
T Consensus 15 ~~P~i~gGkP~-I~GtRI~V~~Il~~l~--~G~s~eeil~dyp~Lt~~dI~aal~y 67 (79)
T COG2442 15 ITPGICGGKPC-IRGTRIPVWDILEMLA--AGESIEEILADYPDLTLEDIRAALRY 67 (79)
T ss_pred eCCcccCCcce-EeCceecHHHHHHHHH--CCCCHHHHHHhCCCCCHHHHHHHHHH
Confidence 34579999999 455 456777776 454 223999999999998863
No 38
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=43.46 E-value=25 Score=22.30 Aligned_cols=20 Identities=25% Similarity=0.476 Sum_probs=17.3
Q ss_pred HHHHHHHcCCChhhHHHHhh
Q psy8528 91 MHYVADFLNLPKMRVYEVAT 110 (240)
Q Consensus 91 m~~VA~~L~lp~~~VyeVAT 110 (240)
+.++|+.||++...||..+.
T Consensus 4 ~~e~a~~lgis~~ti~~~~~ 23 (49)
T TIGR01764 4 VEEAAEYLGVSKDTVYRLIH 23 (49)
T ss_pred HHHHHHHHCCCHHHHHHHHH
Confidence 56899999999999998773
No 39
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=43.24 E-value=38 Score=24.33 Aligned_cols=36 Identities=14% Similarity=0.049 Sum_probs=25.4
Q ss_pred HHHHHHcCCCCHHHHHHHHHHcCCChhhHHHHhhhccC
Q psy8528 77 DLAQRQHGWLPISAMHYVADFLNLPKMRVYEVATFYTM 114 (240)
Q Consensus 77 ~~aQ~q~G~Lp~~am~~VA~~L~lp~~~VyeVATFYtm 114 (240)
+.++.++|. .+..++||+.|||+..+|..+..+-..
T Consensus 11 ~~L~~~lgr--~Pt~eEiA~~lgis~~~v~~~l~~~~~ 46 (78)
T PF04539_consen 11 RELEQELGR--EPTDEEIAEELGISVEEVRELLQASRR 46 (78)
T ss_dssp HHHHHHHSS----BHHHHHHHHTS-HHHHHHHHHHHSC
T ss_pred HHHHHHhCC--CCCHHHHHHHHcccHHHHHHHHHhCCC
Confidence 444556665 456789999999999999999876443
No 40
>PF12728 HTH_17: Helix-turn-helix domain
Probab=41.57 E-value=27 Score=23.24 Aligned_cols=20 Identities=20% Similarity=0.391 Sum_probs=17.6
Q ss_pred HHHHHHHcCCChhhHHHHhh
Q psy8528 91 MHYVADFLNLPKMRVYEVAT 110 (240)
Q Consensus 91 m~~VA~~L~lp~~~VyeVAT 110 (240)
..++|+.||++...||..+.
T Consensus 4 ~~e~a~~l~is~~tv~~~~~ 23 (51)
T PF12728_consen 4 VKEAAELLGISRSTVYRWIR 23 (51)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46899999999999999875
No 41
>KOG0917|consensus
Probab=39.83 E-value=35 Score=32.53 Aligned_cols=29 Identities=34% Similarity=0.580 Sum_probs=24.2
Q ss_pred ecCCCHHh----------HHHHHHHHhcCCCCCCCCCCC
Q psy8528 163 RQDLEPKD----------MEQIIDDLKAGKKPAPGPSGY 191 (240)
Q Consensus 163 y~~Ltpe~----------i~~IL~~lk~g~~p~~gp~g~ 191 (240)
||.|+++- ...|-..||+|++|.|||-|.
T Consensus 125 FGel~e~~l~~rKYAkWKat~I~~clk~G~~p~Pg~~~d 163 (338)
T KOG0917|consen 125 FGELTEENLKHRKYAKWKATYIHNCLKNGETPQPGPVGD 163 (338)
T ss_pred hcCCChHHHhhhHHhHHHHHHHHHHHhCCCCCCCCCCCC
Confidence 89999874 457888999999999999554
No 42
>PLN03170 chalcone synthase; Provisional
Probab=39.74 E-value=18 Score=34.86 Aligned_cols=36 Identities=22% Similarity=0.415 Sum_probs=31.1
Q ss_pred cCHHHHHHHHHHHcCc----e------Ee-ecCCCHHhHHHHHHHHh
Q psy8528 144 RNSDAILEVIKKKCNM----M------LE-RQDLEPKDMEQIIDDLK 179 (240)
Q Consensus 144 rGs~~Il~~l~~~LgI----m------v~-y~~Ltpe~i~~IL~~lk 179 (240)
.|+..|++.+++.||+ + +. ||++....+--.|+++.
T Consensus 308 qgg~~il~~v~~~Lgl~~~~~~~s~~~l~~~GNtsSasv~~vL~~~~ 354 (401)
T PLN03170 308 PGGPAILDQVEAKVGLEKERMRATRHVLSEYGNMSSACVLFILDEMR 354 (401)
T ss_pred CCcHHHHHHHHHHcCCChHHHHHHHHHHHHhCccHHhHHHHHHHHHH
Confidence 5789999999999998 2 22 99999999999999885
No 43
>TIGR00207 fliG flagellar motor switch protein FliG. The fliG protein along with fliM and fliN interact to form the switch complex of the bacterial flagellar motor located at the base of the basal body. This complex interacts with chemotaxis proteins (eg CHEY). In addition the complex interacts with other components of the motor that determine the direction of flagellar rotation. The model contains putative members of the fliG family at scores of less than 100 from Agrobacterium radiobacter and Sinorhizobium meliloti as well as fliG-like genes from treponema pallidum and Borrelia burgdorferi. That is why the suggested cutoff is set at 20 but was set at 100 to construct the family.
Probab=39.01 E-value=67 Score=30.40 Aligned_cols=89 Identities=12% Similarity=0.095 Sum_probs=60.8
Q ss_pred HHHHHcCCCCHHHHHHHHHH----cCCChhhHHHHh-hhccCCccccCCcccccccccEEEEecCChhhhhcCHHHH-HH
Q psy8528 78 LAQRQHGWLPISAMHYVADF----LNLPKMRVYEVA-TFYTMFIRKPIGEERIKSILQYHLNWCTTTPCWLRNSDAI-LE 151 (240)
Q Consensus 78 ~aQ~q~G~Lp~~am~~VA~~----L~lp~~~VyeVA-TFYtmF~~kP~G~~~~~~~~K~~I~VC~~t~C~lrGs~~I-l~ 151 (240)
.+-+-+.+++++-++.|+.. =.+++..+.+|. -||..|.... | ...|+.+. .+
T Consensus 26 ~aa~vlk~L~~~ei~~l~~~m~~l~~v~~~~~~~vl~eF~~~~~~~~-~--------------------~~~g~~~~~~~ 84 (338)
T TIGR00207 26 RSAEVFKHLSQEEIETLSAEIANVTQIDNQQKDDVLEEFEQIAEAQA-Y--------------------INIGGLDYARE 84 (338)
T ss_pred hHHHHHHcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhcC-C--------------------ccCChHHHHHH
Confidence 46667789999988887766 479999999995 8999886542 2 12455554 55
Q ss_pred HHHHHcCceEeecCCCHHhHHHHHHHHhcCCCCCCCCCCCCCCCcC
Q psy8528 152 VIKKKCNMMLERQDLEPKDMEQIIDDLKAGKKPAPGPSGYTSGIGS 197 (240)
Q Consensus 152 ~l~~~LgImv~y~~Ltpe~i~~IL~~lk~g~~p~~gp~g~~~~~~~ 197 (240)
.|++.|| +++.+.||+.+..+....+ +|..++.+.+
T Consensus 85 ~L~~alg---------~~~a~~il~~i~~~~~~~~-~~~~L~~~~~ 120 (338)
T TIGR00207 85 VLEKALG---------EEKAASILNDLTSSLQTAP-GFEFLRKAEP 120 (338)
T ss_pred HHHHhcC---------HHHHHHHHHHHhcccccCc-hhHHHHCCCH
Confidence 6666666 5788888888776543321 4666655544
No 44
>PF04963 Sigma54_CBD: Sigma-54 factor, core binding domain; InterPro: IPR007046 This domain makes a direct interaction with the core RNA polymerase, to form an enhancer dependent holoenzyme []. The centre of this domain contains a very weak similarity to a helix-turn-helix motif, which may represent a DNA binding domain.; GO: 0003677 DNA binding, 0006352 transcription initiation, DNA-dependent; PDB: 2K9L_A 2K9M_A.
Probab=38.90 E-value=3.6 Score=35.71 Aligned_cols=99 Identities=15% Similarity=0.321 Sum_probs=36.1
Q ss_pred HHHcCCCCHHHHHHHHHHcCCChhhHHHHhhhccCCccccCCcccccccccEEEEecCChhhhhcC-HHHHHHHHHHHcC
Q psy8528 80 QRQHGWLPISAMHYVADFLNLPKMRVYEVATFYTMFIRKPIGEERIKSILQYHLNWCTTTPCWLRN-SDAILEVIKKKCN 158 (240)
Q Consensus 80 Q~q~G~Lp~~am~~VA~~L~lp~~~VyeVATFYtmF~~kP~G~~~~~~~~K~~I~VC~~t~C~lrG-s~~Il~~l~~~Lg 158 (240)
-+..||+. ..++.+|+.++++..+|..+...-.. ..|.| +.-.-++=|--.=..-.+ .+.....+++.|.
T Consensus 45 LD~~GyL~-~~~~eia~~l~~~~~~v~~~l~~lQ~--leP~G------igAr~l~EcLllQl~~~~~~~~~~~il~~~l~ 115 (194)
T PF04963_consen 45 LDDDGYLT-ESLEEIAEELGVSEEEVEKALELLQS--LEPAG------IGARDLQECLLLQLERKGPPDLAYRILENHLE 115 (194)
T ss_dssp BTTTSTCS-S-HHHHHHHCTS-HHHHHHHHHHHHT--TSS--------TTTS-TTHHHHHHHHHS-S--TTHHHHHHHHH
T ss_pred CCCCCccC-CCHHHHHHHhCCCHHHHHHHHHHHHc--CCCCc------cCcCCHHHHHHHHHhccCCcHHHHHHHHHHHH
Confidence 35679999 55788999999999999999998764 67777 112223223221111111 1122222233322
Q ss_pred c-------eEe-ecCCCHHhHHHHHHHHhcCCCCCCCC
Q psy8528 159 M-------MLE-RQDLEPKDMEQIIDDLKAGKKPAPGP 188 (240)
Q Consensus 159 I-------mv~-y~~Ltpe~i~~IL~~lk~g~~p~~gp 188 (240)
. .+. --+++.+++.++++.++ .=.|+||-
T Consensus 116 ~l~~~~~~~ia~~l~~s~~~v~~~~~~Ir-~L~P~Pg~ 152 (194)
T PF04963_consen 116 LLANKDYKKIAKKLGISEEEVQEAIELIR-TLNPKPGR 152 (194)
T ss_dssp HHHH----------------------------------
T ss_pred HHHHhhhcccccccccccccccccccccc-cccccccc
Confidence 2 111 33678888888888876 45678875
No 45
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=38.60 E-value=56 Score=26.63 Aligned_cols=49 Identities=12% Similarity=0.175 Sum_probs=31.7
Q ss_pred CHHhHHHHHHHHHhCCCCCCcccHHHHHHHHHHHcCCCCHHHHHHHHHHcCCChhhHHH
Q psy8528 49 TPDNKKRAEAIISIYPVGHERAAVIPLLDLAQRQHGWLPISAMHYVADFLNLPKMRVYE 107 (240)
Q Consensus 49 t~e~~~~i~~il~~Yp~~~~rsalIplL~~aQ~q~G~Lp~~am~~VA~~L~lp~~~Vye 107 (240)
..+..+.+...|.+.|. ..+..+ +|. |+-.-..++||+.||++..-|+.
T Consensus 106 ~~~~~~~l~~~l~~L~~-~~r~i~--~l~-------~~~~~s~~EIA~~lgis~~tV~~ 154 (173)
T PRK12522 106 QKVEAEMIREVIQLLNE-KYKTVL--VLY-------YYEQYSYKEMSEILNIPIGTVKY 154 (173)
T ss_pred HHHHHHHHHHHHHhCCH-HHHHHH--HHH-------HHcCCCHHHHHHHhCCCHHHHHH
Confidence 34556678888888885 222222 122 23334568899999999988874
No 46
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=38.40 E-value=22 Score=29.63 Aligned_cols=45 Identities=20% Similarity=0.230 Sum_probs=32.6
Q ss_pred CcccHHHHHHHHHHHcCCCCHHHHHHHHHHcCCChhhHHHHhhhccCCcccc
Q psy8528 68 ERAAVIPLLDLAQRQHGWLPISAMHYVADFLNLPKMRVYEVATFYTMFIRKP 119 (240)
Q Consensus 68 ~rsalIplL~~aQ~q~G~Lp~~am~~VA~~L~lp~~~VyeVATFYtmF~~kP 119 (240)
.+..++..-..+-.+.|| ..-.|+.||+..|++. .|||.+|..|-
T Consensus 12 ~r~~Il~aa~~lf~~~G~-~~~ti~~Ia~~agvsk------~t~Y~~F~sKe 56 (213)
T PRK09975 12 TRQELIETAIAQFALRGV-SNTTLNDIADAANVTR------GAIYWHFENKT 56 (213)
T ss_pred HHHHHHHHHHHHHHHcCc-ccCCHHHHHHHcCCCH------HHHHHHcCCHH
Confidence 456677777777777885 4556888999999986 47777775443
No 47
>PLN03169 chalcone synthase family protein; Provisional
Probab=37.76 E-value=16 Score=34.80 Aligned_cols=54 Identities=19% Similarity=0.293 Sum_probs=38.6
Q ss_pred cCHHHHHHHHHHHcCc----e------Ee-ecCCCHHhHHHHHHHHhc-CCC--CCCCCCCCCCCCcC
Q psy8528 144 RNSDAILEVIKKKCNM----M------LE-RQDLEPKDMEQIIDDLKA-GKK--PAPGPSGYTSGIGS 197 (240)
Q Consensus 144 rGs~~Il~~l~~~LgI----m------v~-y~~Ltpe~i~~IL~~lk~-g~~--p~~gp~g~~~~~~~ 197 (240)
.|...|++.+.++||+ + +. ||++....+--.|+++.+ |+. ..+|-++.+.|+|+
T Consensus 310 q~n~~il~~v~~~Lgl~~ek~~~s~~~l~~~GNtsSasip~~L~~~~~~~~~~~~~~gd~~ll~afG~ 377 (391)
T PLN03169 310 PGGPAILNRLEKKLKLAPEKLECSRRALMDYGNVSSNTIVYVLEYMREELKKKGEEDEEWGLILAFGP 377 (391)
T ss_pred CCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhCCchHhHHHHHHHHHHHhhcccCCCCCcEEEEEEEcc
Confidence 5678999999999998 2 22 999999999999988764 332 12455555555544
No 48
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=37.37 E-value=66 Score=24.32 Aligned_cols=39 Identities=18% Similarity=0.135 Sum_probs=32.2
Q ss_pred ccHHHHHHHHHHHcC-CCCHHHHHHHHHHcCCChhhHHHH
Q psy8528 70 AAVIPLLDLAQRQHG-WLPISAMHYVADFLNLPKMRVYEV 108 (240)
Q Consensus 70 salIplL~~aQ~q~G-~Lp~~am~~VA~~L~lp~~~VyeV 108 (240)
..+.|+|..+++.-| .=..++.+.||+.++++..+....
T Consensus 4 ~~~~piL~~L~~~g~~~~~~ei~~~v~~~~~ls~e~~~~~ 43 (92)
T PF14338_consen 4 ELMPPILEALKDLGGSASRKEIYERVAERFGLSDEERNER 43 (92)
T ss_pred HHHHHHHHHHHHcCCCcCHHHHHHHHHHHhCCCHHHHHHH
Confidence 567899999999776 566788899999999998876654
No 49
>PF13551 HTH_29: Winged helix-turn helix
Probab=37.19 E-value=1.6e+02 Score=21.84 Aligned_cols=51 Identities=8% Similarity=0.089 Sum_probs=35.3
Q ss_pred CCHHhHHHHHHHHHhCCCCCCcccHHHHHHH-H-HHHcC-CCCHHHHHHHHHHc
Q psy8528 48 FTPDNKKRAEAIISIYPVGHERAAVIPLLDL-A-QRQHG-WLPISAMHYVADFL 98 (240)
Q Consensus 48 ft~e~~~~i~~il~~Yp~~~~rsalIplL~~-a-Q~q~G-~Lp~~am~~VA~~L 98 (240)
++++..+.|.+++...|.........+.|.. + .+++| -+|.+.+..+=..+
T Consensus 58 l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~~~ 111 (112)
T PF13551_consen 58 LSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILKRA 111 (112)
T ss_pred CCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHHHC
Confidence 8999999999999998853222345666655 3 55666 67888777665443
No 50
>PF14261 DUF4351: Domain of unknown function (DUF4351)
Probab=37.17 E-value=27 Score=25.22 Aligned_cols=30 Identities=23% Similarity=0.305 Sum_probs=24.6
Q ss_pred CCcccHHHHHHHHHHHcCCCCHHHHHHHHH
Q psy8528 67 HERAAVIPLLDLAQRQHGWLPISAMHYVAD 96 (240)
Q Consensus 67 ~~rsalIplL~~aQ~q~G~Lp~~am~~VA~ 96 (240)
.+++..--+++.+++.||-||++....|..
T Consensus 4 ~qeg~~~lllRlL~rrFG~lp~~~~~~I~~ 33 (59)
T PF14261_consen 4 RQEGEARLLLRLLTRRFGELPPEIQERIQQ 33 (59)
T ss_pred HHHHHHHHHHHHHHHHcCCCCHHHHHHHHc
Confidence 345667778999999999999999877763
No 51
>COG1212 KdsB CMP-2-keto-3-deoxyoctulosonic acid synthetase [Cell envelope biogenesis, outer membrane]
Probab=36.81 E-value=53 Score=30.49 Aligned_cols=52 Identities=17% Similarity=0.331 Sum_probs=43.2
Q ss_pred cEEEEecCChhhhhcCHHHHHHHHHHH-cC---ceEe-ecC---CCHHhHHHHHHHHhcC
Q psy8528 130 QYHLNWCTTTPCWLRNSDAILEVIKKK-CN---MMLE-RQD---LEPKDMEQIIDDLKAG 181 (240)
Q Consensus 130 K~~I~VC~~t~C~lrGs~~Il~~l~~~-Lg---Imv~-y~~---Ltpe~i~~IL~~lk~g 181 (240)
++...||.|-+-+-.|++.+.+++++. +. ++|| -|| +.|+.+.++++.|++.
T Consensus 61 ~~G~~avmT~~~h~SGTdR~~Ev~~~l~~~~~~iIVNvQGDeP~i~p~~I~~~~~~L~~~ 120 (247)
T COG1212 61 AFGGEAVMTSKDHQSGTDRLAEVVEKLGLPDDEIIVNVQGDEPFIEPEVIRAVAENLENS 120 (247)
T ss_pred HhCCEEEecCCCCCCccHHHHHHHHhcCCCcceEEEEccCCCCCCCHHHHHHHHHHHHhC
Confidence 456889999999999999999999876 44 3788 333 6789999999999976
No 52
>KOG1719|consensus
Probab=36.60 E-value=88 Score=27.74 Aligned_cols=66 Identities=23% Similarity=0.325 Sum_probs=52.9
Q ss_pred CHHhHHHHHHHHHhCCC-----------CCCcccHHHHHHHHHHHcCCCCHHHHHHHHHH---cCCChhhHHHHhhhccC
Q psy8528 49 TPDNKKRAEAIISIYPV-----------GHERAAVIPLLDLAQRQHGWLPISAMHYVADF---LNLPKMRVYEVATFYTM 114 (240)
Q Consensus 49 t~e~~~~i~~il~~Yp~-----------~~~rsalIplL~~aQ~q~G~Lp~~am~~VA~~---L~lp~~~VyeVATFYtm 114 (240)
+.+++.+.=+.|.+|-. |+-||+.+-.-.++|. ++|-|++|.++|++. .-+.+++-.-+--||..
T Consensus 91 s~~~i~~aVeFi~k~asLGktvYVHCKAGRtRSaTvV~cYLmq~-~~wtpe~A~~~vr~iRp~VlL~~~Qw~~l~ef~~~ 169 (183)
T KOG1719|consen 91 SLENIQKAVEFIHKNASLGKTVYVHCKAGRTRSATVVACYLMQH-KNWTPEAAVEHVRKIRPRVLLRPAQWDVLKEFYKQ 169 (183)
T ss_pred CHHHHHHHHHHHHhccccCCeEEEEecCCCccchhhhhhhhhhh-cCCCHHHHHHHHHhcCcceeecHHHHHHHHHHHHH
Confidence 44666666677777743 6789999999999885 689999999999974 56788888888888876
Q ss_pred C
Q psy8528 115 F 115 (240)
Q Consensus 115 F 115 (240)
.
T Consensus 170 ~ 170 (183)
T KOG1719|consen 170 I 170 (183)
T ss_pred H
Confidence 4
No 53
>PLN02192 3-ketoacyl-CoA synthase
Probab=36.19 E-value=22 Score=35.93 Aligned_cols=57 Identities=16% Similarity=0.212 Sum_probs=44.4
Q ss_pred hhhcCHHHHHHHHHHHcCc----------eEe-ecCCCHHhHHHHHHHHhcCCCCCCCCCCCCCCCcC
Q psy8528 141 CWLRNSDAILEVIKKKCNM----------MLE-RQDLEPKDMEQIIDDLKAGKKPAPGPSGYTSGIGS 197 (240)
Q Consensus 141 C~lrGs~~Il~~l~~~LgI----------mv~-y~~Ltpe~i~~IL~~lk~g~~p~~gp~g~~~~~~~ 197 (240)
|--.|+..|++.+++.||+ .+. ||+.....+--.|+.+.+....++|-.+.+.|.|+
T Consensus 403 ~iHqggr~IId~v~k~LgL~~~~~e~sr~tL~rfGNTSSaSI~~aL~~~eakgrik~GDrVl~iaFGs 470 (511)
T PLN02192 403 CIHAGGRAVLDELEKNLQLSDWHMEPSRMTLYRFGNTSSSSLWYELAYSEAKGRIKKGDRTWQIAFGS 470 (511)
T ss_pred eeccCCHHHHHHHHHHcCCCchhhhHHHHHHhHcCChHHhHHHHHHHHHHHcCCCCCCCEEEEEEEcc
Confidence 4558999999999999998 122 99999999998888877655678887665555554
No 54
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=35.84 E-value=36 Score=24.39 Aligned_cols=30 Identities=27% Similarity=0.355 Sum_probs=23.3
Q ss_pred HHHHHHHcCCChhhHHHHhhhccCCccccC
Q psy8528 91 MHYVADFLNLPKMRVYEVATFYTMFIRKPI 120 (240)
Q Consensus 91 m~~VA~~L~lp~~~VyeVATFYtmF~~kP~ 120 (240)
+..||+.||+|..-||.-+.=|..=...|.
T Consensus 16 ~~eIA~~Lg~~~~TV~~W~~r~~W~~~~~~ 45 (58)
T PF06056_consen 16 IKEIAEELGVPRSTVYSWKDRYKWDELLPI 45 (58)
T ss_pred HHHHHHHHCCChHHHHHHHHhhCccccCch
Confidence 567999999999999998887765444443
No 55
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=35.81 E-value=17 Score=24.96 Aligned_cols=24 Identities=17% Similarity=0.260 Sum_probs=16.0
Q ss_pred CCCCHHHHHHHHHHcCCChhhHHH
Q psy8528 84 GWLPISAMHYVADFLNLPKMRVYE 107 (240)
Q Consensus 84 G~Lp~~am~~VA~~L~lp~~~Vye 107 (240)
..++.+.+..||+.||+++.++.+
T Consensus 36 ~~~~~~~l~~ia~~l~~~~~el~~ 59 (63)
T PF13443_consen 36 SNPSLDTLEKIAKALNCSPEELFE 59 (63)
T ss_dssp ----HHHHHHHHHHHT--HHHCTE
T ss_pred ccccHHHHHHHHHHcCCCHHHHhh
Confidence 479999999999999999887654
No 56
>PLN02377 3-ketoacyl-CoA synthase
Probab=35.81 E-value=22 Score=35.75 Aligned_cols=56 Identities=13% Similarity=0.227 Sum_probs=42.1
Q ss_pred hhhcCHHHHHHHHHHHcCc----------eEe-ecCCCHHhHHHHHHHHhcCCCCCCCCCCCCCCCc
Q psy8528 141 CWLRNSDAILEVIKKKCNM----------MLE-RQDLEPKDMEQIIDDLKAGKKPAPGPSGYTSGIG 196 (240)
Q Consensus 141 C~lrGs~~Il~~l~~~LgI----------mv~-y~~Ltpe~i~~IL~~lk~g~~p~~gp~g~~~~~~ 196 (240)
|-=.|+..|++.+++.||+ .+. ||+.+...+--.|+.+.+..+.++|-...+.|+|
T Consensus 399 ~iHqggr~IId~v~k~LgL~~~~~e~sr~tL~r~GNTSSaSI~~aL~~~~~~grik~Gd~VlliaFG 465 (502)
T PLN02377 399 CIHAGGRAVIDELEKNLQLLPVHVEASRMTLHRFGNTSSSSIWYELAYIEAKGRMRKGNRVWQIAFG 465 (502)
T ss_pred EECCCCHHHHHHHHHHcCCCcccchHHHHHHHhcCCchhhHHHHHHHHHHHcCCCCCCCeEEEEEEc
Confidence 3448999999999999998 122 9999999999999888766667777633333333
No 57
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=35.62 E-value=48 Score=24.54 Aligned_cols=37 Identities=16% Similarity=0.288 Sum_probs=28.6
Q ss_pred cccHHHHHHHHHHHcCCCCHHHHHHHHHHcCCChhhHHHHh
Q psy8528 69 RAAVIPLLDLAQRQHGWLPISAMHYVADFLNLPKMRVYEVA 109 (240)
Q Consensus 69 rsalIplL~~aQ~q~G~Lp~~am~~VA~~L~lp~~~VyeVA 109 (240)
++.++-.|..+.++.|| ....+|+.||++.++|..+-
T Consensus 16 k~~l~~~i~~~~~~~~l----tQ~e~A~~lgisq~~vS~l~ 52 (80)
T PF13744_consen 16 KAQLMAAIRELREERGL----TQAELAERLGISQPRVSRLE 52 (80)
T ss_dssp HHHHHHHHHHHHHCCT------HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHHHHHHcCC----CHHHHHHHHCCChhHHHHHH
Confidence 46677778888888887 45678999999999999887
No 58
>PF14756 Pdase_C33_assoc: Peptidase_C33-associated domain
Probab=35.19 E-value=27 Score=29.54 Aligned_cols=106 Identities=23% Similarity=0.241 Sum_probs=68.0
Q ss_pred CccccCCHHhHHHHHHHHHhCCCCCCcccHHHHHHHHHHHcCCCCHHHHHHHHHHcCCChhhHHHHhhhccCCccccCCc
Q psy8528 43 DVKFEFTPDNKKRAEAIISIYPVGHERAAVIPLLDLAQRQHGWLPISAMHYVADFLNLPKMRVYEVATFYTMFIRKPIGE 122 (240)
Q Consensus 43 ~~~f~ft~e~~~~i~~il~~Yp~~~~rsalIplL~~aQ~q~G~Lp~~am~~VA~~L~lp~~~VyeVATFYtmF~~kP~G~ 122 (240)
-.-|-|+|.-++++.+++. .| +.+|| .|+.+++.-++-|.+-|-.|=|--.||-+.--|
T Consensus 6 vev~gfdpacldrla~vmh-lp-----s~~ip--------------aalaems~d~~rp~sp~ttvwtvsqf~arh~gg- 64 (147)
T PF14756_consen 6 VEVSGFDPACLDRLAEVMH-LP-----SSVIP--------------AALAEMSGDPNRPASPVTTVWTVSQFFARHRGG- 64 (147)
T ss_pred eeecCCChHHHHHHHHHhc-Cc-----cchhH--------------HHHHHhcCCCCCCCCcccceeeHHHHHHHhcCC-
Confidence 3457788888887776652 23 55554 456666666777776666665555556667778
Q ss_pred ccccccccEEEEecCChhhhhcCHHHHHHHHHHHcCceEeecCCCHHhHHHHHHHHhcCC
Q psy8528 123 ERIKSILQYHLNWCTTTPCWLRNSDAILEVIKKKCNMMLERQDLEPKDMEQIIDDLKAGK 182 (240)
Q Consensus 123 ~~~~~~~K~~I~VC~~t~C~lrGs~~Il~~l~~~LgImv~y~~Ltpe~i~~IL~~lk~g~ 182 (240)
.|.-|||.+--=.++ ++++.++-..+. -.+.|||.+..-|+.|-.|.
T Consensus 65 -------~hpdq~~lgkiislc---qvie~ccc~qnk---tnr~tpeeva~kidqYlrgA 111 (147)
T PF14756_consen 65 -------EHPDQVCLGKIISLC---QVIEECCCSQNK---TNRATPEEVAAKIDQYLRGA 111 (147)
T ss_pred -------CCcchhHHHHHHHHH---HHHHHHHcccCc---ccCCCHHHHHHHHHHHHhcc
Confidence 899999987532222 333333322221 56899999999888887663
No 59
>PF07845 DUF1636: Protein of unknown function (DUF1636); InterPro: IPR012863 The sequences featured in this family are derived from a number of hypothetical prokaryotic proteins. The region in question is approximately 130 amino acids long.
Probab=35.06 E-value=59 Score=26.59 Aligned_cols=47 Identities=23% Similarity=0.295 Sum_probs=32.9
Q ss_pred hhhcCHHHHHHHHHHHcC-------c-----------------eEe--------ecCCCH-HhHHHHHHHHhcCCCCCCC
Q psy8528 141 CWLRNSDAILEVIKKKCN-------M-----------------MLE--------RQDLEP-KDMEQIIDDLKAGKKPAPG 187 (240)
Q Consensus 141 C~lrGs~~Il~~l~~~Lg-------I-----------------mv~--------y~~Ltp-e~i~~IL~~lk~g~~p~~g 187 (240)
-.-++++.|+++|++.+. + -++ |+||+| ++++.||+-.+.--.-..|
T Consensus 16 ~~~~~G~~L~~aL~~~~~~~~~~~~v~v~~v~CL~~C~r~CtVA~~~~gK~tYlfGdl~p~~~a~~il~~a~~Y~~s~dG 95 (116)
T PF07845_consen 16 DGPRPGAALLDALRAALADAPLPDGVEVRPVECLSACDRPCTVALQAPGKWTYLFGDLDPDEDAEDILAFAALYAASPDG 95 (116)
T ss_pred CCCChHHHHHHHHHHHHhcCCCCCceEEEeccHHhcCCCceEEEEEcCCCcEEEEecCCcccCHHHHHHHHHHHHhCCCC
Confidence 344689999999998732 2 122 999999 9999999866543333333
No 60
>PF05049 IIGP: Interferon-inducible GTPase (IIGP); InterPro: IPR007743 Interferon-inducible GTPase (IIGP) is thought to play a role in in intracellular defence. IIGP is predominantly associated with the Golgi apparatus and also localizes to the endoplasmic reticulum and exerts a distinct role in IFN-induced intracellular membrane trafficking or processing [].; GO: 0005525 GTP binding, 0016817 hydrolase activity, acting on acid anhydrides, 0016020 membrane; PDB: 1TPZ_A 1TQD_A 1TQ6_A 1TQ2_B 1TQ4_A.
Probab=34.94 E-value=68 Score=31.27 Aligned_cols=48 Identities=10% Similarity=0.033 Sum_probs=38.9
Q ss_pred cHHHHHHHHHHHcCCCCHHHHHHHHHHcCCChhhHHHHhhhccCCcccc
Q psy8528 71 AVIPLLDLAQRQHGWLPISAMHYVADFLNLPKMRVYEVATFYTMFIRKP 119 (240)
Q Consensus 71 alIplL~~aQ~q~G~Lp~~am~~VA~~L~lp~~~VyeVATFYtmF~~kP 119 (240)
.|...|...|..|| |.++.++.+|+.+|+|..++..+...-.++....
T Consensus 274 ~L~~~l~~Yr~~FG-LDd~SL~~lA~~~g~~~~~lk~~iksp~~~~~~~ 321 (376)
T PF05049_consen 274 ILEKCLNQYRSSFG-LDDESLQKLAQDTGKPVEELKSIIKSPLLLSLIK 321 (376)
T ss_dssp HHHHHHHHHHHHTT--SHHHHHHHHHHTTS-HHHHHCTSSGGGTTSSBS
T ss_pred HHHHHHHHHHHHhC-CCHHHHHHHHHHhCCCHHHHHHHHcCHhhhhccC
Confidence 46677888888899 9999999999999999999999988776665544
No 61
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=34.80 E-value=33 Score=28.40 Aligned_cols=49 Identities=14% Similarity=0.190 Sum_probs=31.6
Q ss_pred HHhHHHHHHHHHhCCCCCCcccHHHHHHHHHHHcCCCCHHHHHHHHHHcCCChhhHHHH
Q psy8528 50 PDNKKRAEAIISIYPVGHERAAVIPLLDLAQRQHGWLPISAMHYVADFLNLPKMRVYEV 108 (240)
Q Consensus 50 ~e~~~~i~~il~~Yp~~~~rsalIplL~~aQ~q~G~Lp~~am~~VA~~L~lp~~~VyeV 108 (240)
.+..+.+...|.+.|+ .++..++ |.. +-.-..++||+.||++...|+.-
T Consensus 127 ~e~~~~l~~~l~~L~~-~~r~i~~--l~~-------~~g~s~~EIA~~lgis~~tV~~~ 175 (189)
T PRK09648 127 SESSNRMRELLDTLPE-KQREILI--LRV-------VVGLSAEETAEAVGSTPGAVRVA 175 (189)
T ss_pred HHHHHHHHHHHHhCCH-HHHHHHH--HHH-------HcCCCHHHHHHHHCCCHHHHHHH
Confidence 3445668888999985 2333322 221 22234789999999999988754
No 62
>COG1152 CdhA CO dehydrogenase/acetyl-CoA synthase alpha subunit [Energy production and conversion]
Probab=34.68 E-value=71 Score=33.59 Aligned_cols=105 Identities=10% Similarity=0.126 Sum_probs=67.3
Q ss_pred CCccccCCHHhHHHHHHHHHhCCCCCCcccHHHHHHHHHH--HcCCCCHHHHHHHHHHcCCChhhHHHHhhhccCCcccc
Q psy8528 42 LDVKFEFTPDNKKRAEAIISIYPVGHERAAVIPLLDLAQR--QHGWLPISAMHYVADFLNLPKMRVYEVATFYTMFIRKP 119 (240)
Q Consensus 42 ~~~~f~ft~e~~~~i~~il~~Yp~~~~rsalIplL~~aQ~--q~G~Lp~~am~~VA~~L~lp~~~VyeVATFYtmF~~kP 119 (240)
..+-.-++|..+..+++.++.-. .+=..++..+|.-|+ ..+|=|...-.-..+.|+|-.+++--++.| . -|
T Consensus 144 ~~t~~G~kPktlgdle~~l~y~E--eqlt~~ls~~h~gqE~~~~dyeSkAlhaG~~d~l~~EiaDiaqi~a~-~----~p 216 (772)
T COG1152 144 IETVTGIKPKTLGDLEAALEYAE--EQLTQLLSAVHTGQEGSLLDYESKALHAGMIDHLGMEIADIAQIVAY-D----FP 216 (772)
T ss_pred hhhhhCCCccchHHHHHHHHHHH--HHHHHHHHHHhccCcccccchhHHHhhhhhhhHHHHHHHHHHHHHhh-c----CC
Confidence 33445678899999999998764 355667777777773 347777777777788888888888887765 2 36
Q ss_pred CCcccccccc-------c-EEEEecCChhhhhcCHHHHHHHHHH
Q psy8528 120 IGEERIKSIL-------Q-YHLNWCTTTPCWLRNSDAILEVIKK 155 (240)
Q Consensus 120 ~G~~~~~~~~-------K-~~I~VC~~t~C~lrGs~~Il~~l~~ 155 (240)
.||++-|-+- | .-.-+|-|- .+.++..|+++|++
T Consensus 217 k~e~~aPliE~G~g~idksKP~il~iGH--nv~~~~~i~dyleE 258 (772)
T COG1152 217 KGEPDAPLIEIGMGTIDKSKPTILVIGH--NVAPGTYIMDYLEE 258 (772)
T ss_pred CCCCCCceEeecCCccCCCCceEEEecc--ccccchHHHHHHHh
Confidence 6665444110 1 111222221 34577888888884
No 63
>TIGR02366 DHAK_reg probable dihydroxyacetone kinase regulator. The seed alignment for this family was built from a set of closely related uncharacterized proteins associated with operons for the type of bacterial dihydroxyacetone kinase that transfers PEP-derived phosphate from a phosphoprotein, as in phosphotransferase system transport, rather than from ATP. Members have a TetR transcriptional regulator domain (pfam00440) at the N-terminus and sequence homology throughout.
Probab=34.45 E-value=29 Score=28.15 Aligned_cols=42 Identities=12% Similarity=0.164 Sum_probs=26.8
Q ss_pred cHHHHHHHHHHHcCCCCHHHHHHHHHHcCCChhhHHHHhhhccCCcccc
Q psy8528 71 AVIPLLDLAQRQHGWLPISAMHYVADFLNLPKMRVYEVATFYTMFIRKP 119 (240)
Q Consensus 71 alIplL~~aQ~q~G~Lp~~am~~VA~~L~lp~~~VyeVATFYtmF~~kP 119 (240)
.+...+-.+=++.| +..=.+..||+..||+.. |||.+|.-+.
T Consensus 7 ~I~~a~~~Ll~~k~-~~~ITV~~I~~~AgvsR~------TFY~hF~dK~ 48 (176)
T TIGR02366 7 KIAKAFKDLMEVQA-FSKISVSDIMSTAQIRRQ------TFYNHFQDKY 48 (176)
T ss_pred HHHHHHHHHHHHCC-CccCCHHHHHHHhCCCHH------HHHHHCCCHH
Confidence 34444333334555 333446789999999875 8888887654
No 64
>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=34.06 E-value=34 Score=26.98 Aligned_cols=47 Identities=19% Similarity=0.197 Sum_probs=30.8
Q ss_pred hHHHHHHHHHhCCCCCCcccHHHHHHHHHHHcCCCCHHHHHHHHHHcCCChhhHHHH
Q psy8528 52 NKKRAEAIISIYPVGHERAAVIPLLDLAQRQHGWLPISAMHYVADFLNLPKMRVYEV 108 (240)
Q Consensus 52 ~~~~i~~il~~Yp~~~~rsalIplL~~aQ~q~G~Lp~~am~~VA~~L~lp~~~VyeV 108 (240)
..+.+...|.+.|+ ..+.+++- . |+..--.++||+.||+++..|+--
T Consensus 95 ~~~~l~~~l~~L~~-~~r~i~~l--~-------~~~g~s~~eIA~~lgis~~tv~~~ 141 (154)
T TIGR02950 95 EQEEITHHLSRLPE-NYRTVLIL--R-------EFKEFSYKEIAELLNLSLAKVKSN 141 (154)
T ss_pred HHHHHHHHHHhCCH-hheeeeee--h-------hhccCcHHHHHHHHCCCHHHHHHH
Confidence 34567778888875 22332221 1 444556789999999999888754
No 65
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=33.95 E-value=75 Score=25.18 Aligned_cols=47 Identities=17% Similarity=0.062 Sum_probs=31.0
Q ss_pred HhHHHHHHHHHhCCCCCCcccHHHHHHHHHHHcCCCCHHHHHHHHHHcCCChhhHHH
Q psy8528 51 DNKKRAEAIISIYPVGHERAAVIPLLDLAQRQHGWLPISAMHYVADFLNLPKMRVYE 107 (240)
Q Consensus 51 e~~~~i~~il~~Yp~~~~rsalIplL~~aQ~q~G~Lp~~am~~VA~~L~lp~~~Vye 107 (240)
+....+.+.|++.|+ +..-+=.|+.++ |+ ..++||+.||++...|+.
T Consensus 95 ~~~~~l~~~l~~Lp~---~~r~v~~l~~~~---g~----s~~EIA~~lgis~~tV~~ 141 (161)
T PRK09047 95 QVLQLIEEAIQKLPA---RQREAFLLRYWE---DM----DVAETAAAMGCSEGSVKT 141 (161)
T ss_pred HHHHHHHHHHHhCCH---HHHHHHHHHHHh---cC----CHHHHHHHHCCCHHHHHH
Confidence 345668888999985 222223343333 32 268899999999998874
No 66
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. 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 RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=33.95 E-value=57 Score=29.26 Aligned_cols=78 Identities=17% Similarity=0.194 Sum_probs=44.2
Q ss_pred eeeccCCCCCCCCccccCCHHhHHHHHHHHHhCCCC-----C--Ccc---cHHHHHHHHHHHc-CCCCHHHHHHHHHHcC
Q psy8528 31 LFVHRDTKDDNLDVKFEFTPDNKKRAEAIISIYPVG-----H--ERA---AVIPLLDLAQRQH-GWLPISAMHYVADFLN 99 (240)
Q Consensus 31 ~~~h~~t~~~n~~~~f~ft~e~~~~i~~il~~Yp~~-----~--~rs---alIplL~~aQ~q~-G~Lp~~am~~VA~~L~ 99 (240)
|+-+.+.=+. +..|.|+-=..-+|+.-|.+|=.. + .+. .+.--+..+.+.. |+.++...++||+.||
T Consensus 73 l~~a~~~fd~--~~~~~FsTYA~~~Ir~~i~~~l~~~~~~ir~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eiA~~l~ 150 (270)
T TIGR02392 73 LMKAVKRFDP--ERGVRLVSFAVHWIKAEIHEYILRNWRLVKVATTKAQRKLFFNLRKMKKRLQGWLNPEEVEAIAEELG 150 (270)
T ss_pred HHHHHHHhCc--ccCCChHHhhHHHHHHHHHHHHHHcCCceecCchHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHhC
Confidence 4444443333 334566655566666555443100 0 011 1222344444444 7777666899999999
Q ss_pred CChhhHHHHhh
Q psy8528 100 LPKMRVYEVAT 110 (240)
Q Consensus 100 lp~~~VyeVAT 110 (240)
++..+|.++..
T Consensus 151 ~~~~~v~~~~~ 161 (270)
T TIGR02392 151 VSEREVREMES 161 (270)
T ss_pred CCHHHHHHHHH
Confidence 99999999843
No 67
>PLN02854 3-ketoacyl-CoA synthase
Probab=33.79 E-value=26 Score=35.52 Aligned_cols=56 Identities=13% Similarity=0.222 Sum_probs=42.5
Q ss_pred hhhcCHHHHHHHHHHHcCce---E-------e-ecCCCHHhHHHHHHHHhcCCCCCCCCCCCCCCCc
Q psy8528 141 CWLRNSDAILEVIKKKCNMM---L-------E-RQDLEPKDMEQIIDDLKAGKKPAPGPSGYTSGIG 196 (240)
Q Consensus 141 C~lrGs~~Il~~l~~~LgIm---v-------~-y~~Ltpe~i~~IL~~lk~g~~p~~gp~g~~~~~~ 196 (240)
|-=.|+..|++++++.||+- + . ||+.....+--.|+.+.+....++|-..-+.|.|
T Consensus 415 ~iHqggr~IId~v~k~LgL~~~~~e~sr~tL~rfGNTSSASI~~~L~~~~~kGrik~GD~Vl~iaFG 481 (521)
T PLN02854 415 CIHAGGRAVLDELQKNLQLSDWHMEPSRMTLHRFGNTSSSSLWYELAYTEAKGRVSAGDRVWQIAFG 481 (521)
T ss_pred EECCCCHHHHHHHHHHcCCCcccccchHHHhhhcCChHhhHHHHHHHHHHHcCCCCCCCEEEEEEEc
Confidence 34489999999999999981 1 2 9999999999999888765556777644444444
No 68
>PF04472 DUF552: Protein of unknown function (DUF552); InterPro: IPR007561 This entry represents a cell division protein, designated SepF, which is conserved in Gram-positive bacteria. SepF accumulates at the cell division site in an FtsZ-dependent manner and is required for proper septum formation []. Mutants are viable but the formation of the septum is much slower and occurs with a very abnormal morphology. This entry also includes archaeal related proteins of unknown function.; GO: 0000917 barrier septum formation; PDB: 3P04_A.
Probab=33.75 E-value=71 Score=23.38 Aligned_cols=41 Identities=15% Similarity=0.391 Sum_probs=30.7
Q ss_pred hhhhcCHHHHHHHHHHHcCceEeecCCCHHhHHHHHHHHhc
Q psy8528 140 PCWLRNSDAILEVIKKKCNMMLERQDLEPKDMEQIIDDLKA 180 (240)
Q Consensus 140 ~C~lrGs~~Il~~l~~~LgImv~y~~Ltpe~i~~IL~~lk~ 180 (240)
|....-+.++.++|++.--+++|.++|+.+....++|.+..
T Consensus 6 p~~~~D~~~i~~~l~~g~~Vivnl~~l~~~~~~Ri~Dfl~G 46 (73)
T PF04472_consen 6 PKSFEDAREIVDALREGKIVIVNLENLDDEEAQRILDFLSG 46 (73)
T ss_dssp -SSGGGHHHHHHHHHTT--EEEE-TTS-HHHHHHHHHHHHH
T ss_pred eCCHHHHHHHHHHHHcCCEEEEECCCCCHHHHHHHHHHHhc
Confidence 44556788899999998777899999999999999998863
No 69
>PF15508 NAAA-beta: beta subunit of N-acylethanolamine-hydrolyzing acid amidase
Probab=33.48 E-value=2e+02 Score=22.05 Aligned_cols=44 Identities=18% Similarity=0.315 Sum_probs=33.0
Q ss_pred ccHHHHHHHHHHHc-CCCCHH---HHHHHHHHcCCChhhHHHHhhhcc
Q psy8528 70 AAVIPLLDLAQRQH-GWLPIS---AMHYVADFLNLPKMRVYEVATFYT 113 (240)
Q Consensus 70 salIplL~~aQ~q~-G~Lp~~---am~~VA~~L~lp~~~VyeVATFYt 113 (240)
+.++++++.+-... +++|.+ -|+-||+.+|+|..+|.-.--||-
T Consensus 47 ~~~~~~v~~~~~~l~~~~~~~~~~EirGIA~~~gi~l~~iv~lN~~yE 94 (95)
T PF15508_consen 47 GKVLDFVDKLLPHLLRYLPQPYAEEIRGIAKAAGIPLGDIVLLNLFYE 94 (95)
T ss_pred hHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCCCHHHHHHHHHHhh
Confidence 35777776666553 677754 567789999999999988888874
No 70
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=33.44 E-value=41 Score=22.10 Aligned_cols=24 Identities=21% Similarity=0.344 Sum_probs=17.2
Q ss_pred HHHHHHHHcCCChhhHHHHhhhcc
Q psy8528 90 AMHYVADFLNLPKMRVYEVATFYT 113 (240)
Q Consensus 90 am~~VA~~L~lp~~~VyeVATFYt 113 (240)
....||+.||++..-|+-...=|.
T Consensus 19 s~~~ia~~lgvs~~Tv~~w~kr~~ 42 (50)
T PF13384_consen 19 SIREIAKRLGVSRSTVYRWIKRYR 42 (50)
T ss_dssp -HHHHHHHHTS-HHHHHHHHT---
T ss_pred CHHHHHHHHCcCHHHHHHHHHHcc
Confidence 467799999999999999887663
No 71
>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=31.42 E-value=42 Score=22.33 Aligned_cols=19 Identities=16% Similarity=0.347 Sum_probs=14.6
Q ss_pred HHHHHHHHcCCChhhHHHH
Q psy8528 90 AMHYVADFLNLPKMRVYEV 108 (240)
Q Consensus 90 am~~VA~~L~lp~~~VyeV 108 (240)
.+..||+.+|++.+-||-+
T Consensus 23 si~~IA~~~gvsr~TvyR~ 41 (45)
T PF02796_consen 23 SIAEIAKQFGVSRSTVYRY 41 (45)
T ss_dssp -HHHHHHHTTS-HHHHHHH
T ss_pred CHHHHHHHHCcCHHHHHHH
Confidence 3678999999999988854
No 72
>KOG2251|consensus
Probab=31.23 E-value=66 Score=29.56 Aligned_cols=42 Identities=26% Similarity=0.249 Sum_probs=30.8
Q ss_pred cccCCHHhHHHHHHHHHhCCCCCCcccHHHHHHHHHHHcCCCCHHHHHHHHHHcCCChhhHH
Q psy8528 45 KFEFTPDNKKRAEAIISIYPVGHERAAVIPLLDLAQRQHGWLPISAMHYVADFLNLPKMRVY 106 (240)
Q Consensus 45 ~f~ft~e~~~~i~~il~~Yp~~~~rsalIplL~~aQ~q~G~Lp~~am~~VA~~L~lp~~~Vy 106 (240)
--.|+-+.++.+++++++- -|=...+.++||..|+||.++|-
T Consensus 41 RTtFtr~QlevLe~LF~kT--------------------qYPDv~~rEelAlklnLpeSrVq 82 (228)
T KOG2251|consen 41 RTTFTRKQLEVLEALFAKT--------------------QYPDVFMREELALKLNLPESRVQ 82 (228)
T ss_pred cceecHHHHHHHHHHHHhh--------------------cCccHHHHHHHHHHhCCchhhhh
Confidence 4456666677777766542 25556788999999999999964
No 73
>PF14842 FliG_N: FliG N-terminal domain; PDB: 3HJL_A 3AJC_A 3USY_B.
Probab=30.56 E-value=57 Score=25.67 Aligned_cols=77 Identities=17% Similarity=0.199 Sum_probs=37.0
Q ss_pred HHHHHcCCCCHHHHHHHHHHc----CCChhhHHHHhh-hcc-CCccccCCcccccccccEEEEecCChhhhhcCHHHHHH
Q psy8528 78 LAQRQHGWLPISAMHYVADFL----NLPKMRVYEVAT-FYT-MFIRKPIGEERIKSILQYHLNWCTTTPCWLRNSDAILE 151 (240)
Q Consensus 78 ~aQ~q~G~Lp~~am~~VA~~L----~lp~~~VyeVAT-FYt-mF~~kP~G~~~~~~~~K~~I~VC~~t~C~lrGs~~Il~ 151 (240)
.+.+-..+++++.++.|+..+ ++++..|.+|.. ||. ++...... .-|-+.+.+
T Consensus 22 ~Aa~vlk~l~~~ei~~i~~~ma~l~~v~~~~~~~Vl~EF~~~~~~~~~~~---------------------~gg~~~~~~ 80 (108)
T PF14842_consen 22 AAAEVLKHLDEEEIERISREMAKLGSVSPEEVEEVLEEFYDEIRAQGGIV---------------------SGGRDFARR 80 (108)
T ss_dssp HHHHHHHHS-HHHHHHHHHHHHT-----HHHHHHHHHHHHHHHHHTT------------------------S-HHHHHHH
T ss_pred HHHHHHccCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHccccc---------------------cChHHHHHH
Confidence 344556788888887766554 688888888875 666 33333322 134455666
Q ss_pred HHHHHcCceEeecCCCHHhHHHHHHHHhcCCCC
Q psy8528 152 VIKKKCNMMLERQDLEPKDMEQIIDDLKAGKKP 184 (240)
Q Consensus 152 ~l~~~LgImv~y~~Ltpe~i~~IL~~lk~g~~p 184 (240)
.|++.|| +++.++|++++......
T Consensus 81 lL~~alg---------~~~a~~il~~~~~~~~~ 104 (108)
T PF14842_consen 81 LLEKALG---------EEKAKEILDRLEQSMES 104 (108)
T ss_dssp -HHHHS------------HHHHH----------
T ss_pred HHHHHCC---------HHHHHHHHHHHhcccCC
Confidence 6888787 57889999988765433
No 74
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=30.54 E-value=1e+02 Score=24.53 Aligned_cols=51 Identities=22% Similarity=0.309 Sum_probs=32.4
Q ss_pred CHHhHHHHHHHHHhCCCCCCcccHHHHHHHHHHHcCCCCHHHHHHHHHHcCCChhhHHHHh
Q psy8528 49 TPDNKKRAEAIISIYPVGHERAAVIPLLDLAQRQHGWLPISAMHYVADFLNLPKMRVYEVA 109 (240)
Q Consensus 49 t~e~~~~i~~il~~Yp~~~~rsalIplL~~aQ~q~G~Lp~~am~~VA~~L~lp~~~VyeVA 109 (240)
..+..+.+...|++.|+ ..+..+ .|.. +..-...+||+.||+++..|+...
T Consensus 112 ~~e~~~~l~~~l~~L~~-~~r~i~--~l~~-------~~~~~~~eIA~~lgis~~tv~~~~ 162 (179)
T PRK11924 112 AKDDLARIDRCLDALPV-KQREVF--LLRY-------VEGLSYREIAEILGVPVGTVKSRL 162 (179)
T ss_pred hHHHHHHHHHHHHhCCH-HHHHHh--hHHH-------HcCCCHHHHHHHHCCCHHHHHHHH
Confidence 34556677888888885 222222 2222 222345789999999999998654
No 75
>PRK10668 DNA-binding transcriptional repressor AcrR; Provisional
Probab=30.36 E-value=38 Score=28.36 Aligned_cols=44 Identities=16% Similarity=0.172 Sum_probs=30.5
Q ss_pred CcccHHHHHHHHHHHcCCCCHHHHHHHHHHcCCChhhHHHHhhhccCCccc
Q psy8528 68 ERAAVIPLLDLAQRQHGWLPISAMHYVADFLNLPKMRVYEVATFYTMFIRK 118 (240)
Q Consensus 68 ~rsalIplL~~aQ~q~G~Lp~~am~~VA~~L~lp~~~VyeVATFYtmF~~k 118 (240)
.+..++..-..+=.+.|| ..-.|+.||+..|++.. |||.+|..|
T Consensus 12 ~R~~Il~AA~~lf~e~G~-~~~t~~~Ia~~agvs~~------tlY~~F~sK 55 (215)
T PRK10668 12 TRQHILDAALRLFSQQGV-SATSLADIAKAAGVTRG------AIYWHFKNK 55 (215)
T ss_pred HHHHHHHHHHHHHHHcCc-ccCCHHHHHHHhCCChH------HHHHHCCCH
Confidence 345566666666677786 34457889999999874 677777543
No 76
>PF07293 DUF1450: Protein of unknown function (DUF1450); InterPro: IPR009910 This entry consists of several hypothetical bacterial proteins of around 80 residues in length representing two families. Members contain four highly conserved cysteine residues and their function is unknown.
Probab=29.74 E-value=58 Score=25.03 Aligned_cols=26 Identities=15% Similarity=0.465 Sum_probs=21.1
Q ss_pred EEEecCChhhhhcCHHHHHHHHHHHcCc
Q psy8528 132 HLNWCTTTPCWLRNSDAILEVIKKKCNM 159 (240)
Q Consensus 132 ~I~VC~~t~C~lrGs~~Il~~l~~~LgI 159 (240)
.|.+|.+- ...|++.+++.|++.-++
T Consensus 4 iVefC~~N--l~~g~~~~~~~Le~~p~~ 29 (78)
T PF07293_consen 4 IVEFCVSN--LASGTDQVYEKLEKDPDI 29 (78)
T ss_pred eEEEcccC--chhhhHHHHHHHhcCCCc
Confidence 68889774 457999999999987665
No 77
>COG2964 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.54 E-value=95 Score=28.37 Aligned_cols=24 Identities=33% Similarity=0.506 Sum_probs=21.0
Q ss_pred C-CCCHHHHHHHHHHcCCChhhHHH
Q psy8528 84 G-WLPISAMHYVADFLNLPKMRVYE 107 (240)
Q Consensus 84 G-~Lp~~am~~VA~~L~lp~~~Vye 107 (240)
| +=-..|+.+||+.|++++.-||-
T Consensus 186 GiF~lK~Ai~~VA~~L~iSr~TVY~ 210 (220)
T COG2964 186 GIFNLKDAINIVADRLGISRHTVYR 210 (220)
T ss_pred CccchhhHHHHHHHHhCCChHHHHH
Confidence 6 55678999999999999999984
No 78
>PF14174 YycC: YycC-like protein
Probab=28.85 E-value=60 Score=23.46 Aligned_cols=21 Identities=10% Similarity=0.153 Sum_probs=18.7
Q ss_pred CCHHHHHHHHHHcCCChhhHH
Q psy8528 86 LPISAMHYVADFLNLPKMRVY 106 (240)
Q Consensus 86 Lp~~am~~VA~~L~lp~~~Vy 106 (240)
||.+....+|+.||+|.-++-
T Consensus 6 IS~eTA~kLs~~L~vPlE~lM 26 (53)
T PF14174_consen 6 ISPETAVKLSKKLGVPLEQLM 26 (53)
T ss_pred cCHHHHHHHHHHHCCcHHHHh
Confidence 789999999999999987764
No 79
>smart00035 CLa CLUSTERIN alpha chain.
Probab=28.84 E-value=25 Score=31.96 Aligned_cols=53 Identities=17% Similarity=0.322 Sum_probs=33.5
Q ss_pred HHHHHHHHhCCCCCCcccHHHHHHHHHHHcCCCCHHHHHHHHHHcCCChhhHHHHhhhcc
Q psy8528 54 KRAEAIISIYPVGHERAAVIPLLDLAQRQHGWLPISAMHYVADFLNLPKMRVYEVATFYT 113 (240)
Q Consensus 54 ~~i~~il~~Yp~~~~rsalIplL~~aQ~q~G~Lp~~am~~VA~~L~lp~~~VyeVATFYt 113 (240)
++.+++|..|. ++-....-+|....+||||++. +|....-+..-+.-|.|-++
T Consensus 112 qqYd~lL~~~q--~~m~nTs~Lle~ln~QFgWVS~-----LAN~t~~~~~~~f~v~tv~~ 164 (216)
T smart00035 112 QQYDQLLQSYQ--KKMLNTSSLLEQLNEQFGWVSQ-----LANLTQGEDQYYLQVTTVPS 164 (216)
T ss_pred HHHHHHHHHHH--HHHHhHHHHHHHHHHHhhHHHH-----HHhcCCCCCCceEEEEEeec
Confidence 44556777775 3566778899999999999765 45444433333344555443
No 80
>PLN02804 chalcone isomerase
Probab=28.64 E-value=66 Score=28.96 Aligned_cols=91 Identities=12% Similarity=0.164 Sum_probs=68.5
Q ss_pred CCCHHHHHHHHHHcCCChhhHHHHhhhccCCccccCCcccccccccEEEEecCChhhhhcCHHHHHHHHHHHcCc---eE
Q psy8528 85 WLPISAMHYVADFLNLPKMRVYEVATFYTMFIRKPIGEERIKSILQYHLNWCTTTPCWLRNSDAILEVIKKKCNM---ML 161 (240)
Q Consensus 85 ~Lp~~am~~VA~~L~lp~~~VyeVATFYtmF~~kP~G~~~~~~~~K~~I~VC~~t~C~lrGs~~Il~~l~~~LgI---mv 161 (240)
|+.+++...+++.-|.|..++.+=..||...-..|+. | .+||+.- --+.|. +.-+.+++.++- -.
T Consensus 47 Yle~~~~~~L~kwkgk~a~EL~~~~~Ff~dlv~~p~e--------k-~~Ri~~i--~~l~g~-qy~~~~ee~~~~rlk~~ 114 (206)
T PLN02804 47 YLEPSVKGHLQSWKGKPGSELAEDDDFFQALIQAPVE--------K-LIRIVVI--KEIKGS-QYGVQLESSVRDRLAED 114 (206)
T ss_pred EecHHHHHHHHHhcCCCHHHHhcCHHHHHHHHcCChh--------h-EEEEEEE--ecCcCc-cHHHHHHHHHHHHHhcC
Confidence 8888999999999999999999999999999999997 4 5666544 234564 444444444433 33
Q ss_pred e-ecCCCHHhHHHHHHHHhcCCCCCCCC
Q psy8528 162 E-RQDLEPKDMEQIIDDLKAGKKPAPGP 188 (240)
Q Consensus 162 ~-y~~Ltpe~i~~IL~~lk~g~~p~~gp 188 (240)
+ |++-+.+-++++.+-. +++..++|.
T Consensus 115 ~~y~d~e~~aL~kf~~~F-k~~~fp~Gs 141 (206)
T PLN02804 115 DKYEEEEEEALEKVVEFF-QSKYFKKNS 141 (206)
T ss_pred CCCcchHHHHHHHHHHHh-CCCcCCCCC
Confidence 3 9998889999998888 566777786
No 81
>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=28.56 E-value=54 Score=23.09 Aligned_cols=22 Identities=18% Similarity=0.280 Sum_probs=18.7
Q ss_pred HHHHHHHHcCCChhhHHHHhhh
Q psy8528 90 AMHYVADFLNLPKMRVYEVATF 111 (240)
Q Consensus 90 am~~VA~~L~lp~~~VyeVATF 111 (240)
....||+.+|+|...||.+...
T Consensus 24 t~~eIa~~l~i~~~~v~~~L~~ 45 (68)
T PF01978_consen 24 TAEEIAEELGISRSTVYRALKS 45 (68)
T ss_dssp EHHHHHHHHTSSHHHHHHHHHH
T ss_pred CHHHHHHHHCcCHHHHHHHHHH
Confidence 3567999999999999998754
No 82
>COG3531 Predicted protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=28.04 E-value=94 Score=28.28 Aligned_cols=36 Identities=19% Similarity=0.270 Sum_probs=30.5
Q ss_pred HHHHHHHHHHc---C--CCCHHHHHHHHHHcCCChhhHHHH
Q psy8528 73 IPLLDLAQRQH---G--WLPISAMHYVADFLNLPKMRVYEV 108 (240)
Q Consensus 73 IplL~~aQ~q~---G--~Lp~~am~~VA~~L~lp~~~VyeV 108 (240)
+++|+.||+.| | -.--+++..||..+||+...+-.+
T Consensus 108 l~ml~aIQrA~YvEGrdi~~t~vl~~laa~~GL~~~~f~~~ 148 (212)
T COG3531 108 LTMLHAIQRAHYVEGRDITQTEVLAELAAAIGLAAEEFDNA 148 (212)
T ss_pred hHHHHHHHHHHHhccccchhhHHHHHHHHHcCCCHHHHHHh
Confidence 89999999986 5 677899999999999998765443
No 83
>COG3343 RpoE DNA-directed RNA polymerase, delta subunit [Transcription]
Probab=27.94 E-value=94 Score=27.53 Aligned_cols=49 Identities=12% Similarity=0.205 Sum_probs=39.1
Q ss_pred cHHHHHHHHHHHcC--CCCHHHHHHHHHHcCCChhhHHH-HhhhccCCcccc
Q psy8528 71 AVIPLLDLAQRQHG--WLPISAMHYVADFLNLPKMRVYE-VATFYTMFIRKP 119 (240)
Q Consensus 71 alIplL~~aQ~q~G--~Lp~~am~~VA~~L~lp~~~Vye-VATFYtmF~~kP 119 (240)
++|.+=|.+-++.| +-=.+.+++|++.+|++..++.. +.-|||-|+.-+
T Consensus 15 s~IevA~~ile~~~~~~~F~dii~EI~~~~~~s~~ei~~~i~~FYTdln~Dg 66 (175)
T COG3343 15 SLIEVAHAILEEKKKPFNFSDIINEIQKLLGVSKEEIRSRIGQFYTDLNIDG 66 (175)
T ss_pred HHHHHHHHHHHHcCCCccHHHHHHHHHHHhCcCHHHHHHHHHHHHHHhccCC
Confidence 56777777777776 44467889999999999999976 667999998876
No 84
>PF13700 DUF4158: Domain of unknown function (DUF4158)
Probab=27.49 E-value=1.5e+02 Score=24.64 Aligned_cols=57 Identities=19% Similarity=0.234 Sum_probs=34.9
Q ss_pred ccccCCHHhHHHHHHHHHhCCCCCCcccHHHHHHHHHHHc------CCCCHHHHHHHHHHcCCChhh
Q psy8528 44 VKFEFTPDNKKRAEAIISIYPVGHERAAVIPLLDLAQRQH------GWLPISAMHYVADFLNLPKMR 104 (240)
Q Consensus 44 ~~f~ft~e~~~~i~~il~~Yp~~~~rsalIplL~~aQ~q~------G~Lp~~am~~VA~~L~lp~~~ 104 (240)
.-|.++++..+.+.. ......+=.++-.|--.|... .=+|.+++++||+.|++++..
T Consensus 23 ~~ftLs~~d~~~i~~----~r~~~~rlgfalqL~~fr~~g~f~~~~~~~p~~~i~~va~ql~~~~~~ 85 (166)
T PF13700_consen 23 RYFTLSPEDLELINS----RRGPANRLGFALQLGYFRALGRFPDDPEDIPKADIEYVAKQLGLPPSD 85 (166)
T ss_pred HHhCCCHHHHHHHhc----ccCCccchhHHHHHHHHhcccccccccccCCHHHHHHHHHHhCCchHH
Confidence 457778877766654 221123444444444444321 147799999999999999754
No 85
>CHL00124 acpP acyl carrier protein; Validated
Probab=26.76 E-value=1.3e+02 Score=21.89 Aligned_cols=50 Identities=18% Similarity=0.163 Sum_probs=27.9
Q ss_pred HHHHHHHHHcCCChhhHHHHhhhccCCccccCCcccccccccEEEEecCChhhhhcCHHHHHHHHHHHcCceEe
Q psy8528 89 SAMHYVADFLNLPKMRVYEVATFYTMFIRKPIGEERIKSILQYHLNWCTTTPCWLRNSDAILEVIKKKCNMMLE 162 (240)
Q Consensus 89 ~am~~VA~~L~lp~~~VyeVATFYtmF~~kP~G~~~~~~~~K~~I~VC~~t~C~lrGs~~Il~~l~~~LgImv~ 162 (240)
...+.+++.+++++..+-.-.+|..-+..-- .+.-+|+..+++++||.+.
T Consensus 9 ~l~~ii~~~~~~~~~~i~~d~~l~~dlg~DS------------------------l~~~eli~~le~~f~i~i~ 58 (82)
T CHL00124 9 KVQSIVAEQLGIEKSEVTLDANFTRDLGADS------------------------LDVVELVMAIEEKFDIEIP 58 (82)
T ss_pred HHHHHHHHHHCCCHHHCCCCcchhhhcCCcH------------------------HHHHHHHHHHHHHHCCccC
Confidence 3445666777776666555555544332222 2345667777777777555
No 86
>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=26.65 E-value=56 Score=20.38 Aligned_cols=20 Identities=10% Similarity=0.117 Sum_probs=16.7
Q ss_pred HHHHHHHcCCChhhHHHHhh
Q psy8528 91 MHYVADFLNLPKMRVYEVAT 110 (240)
Q Consensus 91 m~~VA~~L~lp~~~VyeVAT 110 (240)
+.++|+.||++...|+.-+.
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~ 22 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVK 22 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 57899999999998887654
No 87
>PRK07194 fliG flagellar motor switch protein G; Reviewed
Probab=26.57 E-value=1.5e+02 Score=27.97 Aligned_cols=87 Identities=9% Similarity=0.062 Sum_probs=58.8
Q ss_pred HHHHHcCCCCHHHHHHHHHH----cCCChhhHHHH-hhhccCCccccCCcccccccccEEEEecCChhhhhcCHHH-HHH
Q psy8528 78 LAQRQHGWLPISAMHYVADF----LNLPKMRVYEV-ATFYTMFIRKPIGEERIKSILQYHLNWCTTTPCWLRNSDA-ILE 151 (240)
Q Consensus 78 ~aQ~q~G~Lp~~am~~VA~~----L~lp~~~VyeV-ATFYtmF~~kP~G~~~~~~~~K~~I~VC~~t~C~lrGs~~-Il~ 151 (240)
.+-+-+.+++++-++.|+.. =.+++..+..| .-||..|... .| ...|+.+ +.+
T Consensus 24 ~aa~vl~~L~~~ei~~l~~~m~~l~~v~~~~~~~vl~eF~~~~~~~-~~--------------------~~~g~~~~~~~ 82 (334)
T PRK07194 24 AAAMVMQQLSREEVQRLSQKMARLSGIKVDQARQVLQRFFDDYREQ-SG--------------------INGASRSYLQR 82 (334)
T ss_pred HHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHhc-CC--------------------cccchHHHHHH
Confidence 45667789999988887766 58999999999 5899988533 22 1145555 456
Q ss_pred HHHHHcCceEeecCCCHHhHHHHHHHHhcCCCCCCCCCCCCCCCc
Q psy8528 152 VIKKKCNMMLERQDLEPKDMEQIIDDLKAGKKPAPGPSGYTSGIG 196 (240)
Q Consensus 152 ~l~~~LgImv~y~~Ltpe~i~~IL~~lk~g~~p~~gp~g~~~~~~ 196 (240)
.|++.|| +++...|++.+..+... -||..++.+.
T Consensus 83 ~L~~alg---------~~~a~~il~~i~~~~~~--~~~~~L~~~~ 116 (334)
T PRK07194 83 TLNKALG---------GDIAKSLINSIYGDEIR--HRMQRLQWVD 116 (334)
T ss_pred HHHHHcC---------HHHHHHHHHHHhccccC--chHHHHHCCC
Confidence 6777666 57777888777654432 2555554443
No 88
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=26.32 E-value=1.2e+02 Score=23.47 Aligned_cols=61 Identities=13% Similarity=0.102 Sum_probs=37.4
Q ss_pred CCCccccCCHHhHHHHHHHHHhCCCCCCcccHHH-HHHHHHHHcCCCCHHHHHHHHHHcCCChhhHH
Q psy8528 41 NLDVKFEFTPDNKKRAEAIISIYPVGHERAAVIP-LLDLAQRQHGWLPISAMHYVADFLNLPKMRVY 106 (240)
Q Consensus 41 n~~~~f~ft~e~~~~i~~il~~Yp~~~~rsalIp-lL~~aQ~q~G~Lp~~am~~VA~~L~lp~~~Vy 106 (240)
+....-.|+++..+++.+.+...-. ...+.+.| -|..+.++.|+ + ...+|+.+|+++..|.
T Consensus 35 ~~CGe~~~~~e~~~~~~~~i~~~~~-~~~~~~~~~~i~~~r~~~gl-t---q~~lA~~lg~~~~tis 96 (127)
T TIGR03830 35 PACGEELLDPEESKRNSAALADFYR-KVDGLLTPPEIRRIRKKLGL-S---QREAAELLGGGVNAFS 96 (127)
T ss_pred CCCCCEEEcHHHHHHHHHHHHHHHH-HccCCcCHHHHHHHHHHcCC-C---HHHHHHHhCCCHHHHH
Confidence 3344556788888877776655422 23344444 56667777775 3 3457888888875543
No 89
>PF09999 DUF2240: Uncharacterized protein conserved in archaea (DUF2240); InterPro: IPR018716 This family of various hypothetical archaeal proteins has no known function.
Probab=25.83 E-value=4.1e+02 Score=22.65 Aligned_cols=50 Identities=16% Similarity=0.082 Sum_probs=37.1
Q ss_pred HHHHHHhCCCCCCcccHHHHHHHHHHHcC-CCCHHHHH-HHHHHcCCChhhHHH
Q psy8528 56 AEAIISIYPVGHERAAVIPLLDLAQRQHG-WLPISAMH-YVADFLNLPKMRVYE 107 (240)
Q Consensus 56 i~~il~~Yp~~~~rsalIplL~~aQ~q~G-~Lp~~am~-~VA~~L~lp~~~Vye 107 (240)
++.|.++-. ..+..++..+...|+++| .|+.++.. .+|...|++.++.++
T Consensus 91 ld~ia~~~g--~~~~evv~~in~~q~~~~~~l~~e~aall~ake~Gvdv~~~~~ 142 (144)
T PF09999_consen 91 LDYIAAKTG--IEKQEVVAEINELQEELGGLLDPEAAALLYAKEKGVDVSDFAD 142 (144)
T ss_pred HHHHHHhcC--CCHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHhCCCHHHHhh
Confidence 333444343 577889999999999997 77777655 579999999887654
No 90
>PRK15480 glucose-1-phosphate thymidylyltransferase RfbA; Provisional
Probab=25.52 E-value=55 Score=30.11 Aligned_cols=51 Identities=12% Similarity=0.139 Sum_probs=38.9
Q ss_pred CHHhHHHHHHHHHhCCCCCCcccHHHHHHHHHHHcCCCCHHHHHHHHHHcCCC
Q psy8528 49 TPDNKKRAEAIISIYPVGHERAAVIPLLDLAQRQHGWLPISAMHYVADFLNLP 101 (240)
Q Consensus 49 t~e~~~~i~~il~~Yp~~~~rsalIplL~~aQ~q~G~Lp~~am~~VA~~L~lp 101 (240)
|++.+.++.+.+.... ..++..|..+.++.=..|||+.+.+..+|+.++-+
T Consensus 229 t~~~l~~a~~~~~~~~--~~~g~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~ 279 (292)
T PRK15480 229 THQSLIEASNFIATIE--ERQGLKVSCPEEIAFRKGFIDAEQVKVLAEPLKKN 279 (292)
T ss_pred CHHHHHHHHHHHHHHH--HHCCCEEEChHHHHHHcCCcCHHHHHHHHHHhccC
Confidence 4566777776666554 35666788888888888999999999999988643
No 91
>KOG0372|consensus
Probab=25.41 E-value=1.6e+02 Score=27.90 Aligned_cols=70 Identities=13% Similarity=0.134 Sum_probs=49.4
Q ss_pred CHHHHHHHHHHHcCc-----eEe------ecCCCH--HhHHHHHHHHhcCCCCCCCCCCCCCCCcCcCCCccccccCCCC
Q psy8528 145 NSDAILEVIKKKCNM-----MLE------RQDLEP--KDMEQIIDDLKAGKKPAPGPSGYTSGIGSQSGRFCQAREAYHD 211 (240)
Q Consensus 145 Gs~~Il~~l~~~LgI-----mv~------y~~Ltp--e~i~~IL~~lk~g~~p~~gp~g~~~~~~~~~gr~~~~~e~~~g 211 (240)
|+..+...+.+.+.- +|+ ++.|+| ..+++|..-=|.++.|..|| +-.=. .|.|..+
T Consensus 131 G~~~vWr~c~eiFdyL~l~aiid~kifCVHGGlSP~i~~lDqIr~lDR~~Eiph~g~---------m~Dll--WSDPee~ 199 (303)
T KOG0372|consen 131 GSANVWRYCTEIFDYLSLAAIIDGKIFCVHGGLSPSIQTLDQIRVLDRKQEVPHDGA---------MCDLL--WSDPEEG 199 (303)
T ss_pred CChHHHHHHHHHHHhhhHhheecCcEEEEcCCCCcchhhHHHHHHhhccccCCCCCc---------chhee--ccCcccC
Confidence 677777777776554 565 999999 45677765556788999998 66666 7888776
Q ss_pred CCccCCCCCCCCCCC
Q psy8528 212 MTSLTGEPHGPWDSK 226 (240)
Q Consensus 212 ~t~l~~~~~~~~~~~ 226 (240)
. ...-.|.|.||-.
T Consensus 200 ~-g~~~SPRGaGylF 213 (303)
T KOG0372|consen 200 P-GWGLSPRGAGYLF 213 (303)
T ss_pred C-CcccCCCCccccc
Confidence 5 3444577777543
No 92
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=25.33 E-value=72 Score=21.23 Aligned_cols=21 Identities=14% Similarity=0.088 Sum_probs=14.2
Q ss_pred HHHHHHHHHcCCChhhHHHHh
Q psy8528 89 SAMHYVADFLNLPKMRVYEVA 109 (240)
Q Consensus 89 ~am~~VA~~L~lp~~~VyeVA 109 (240)
-.+.+||+.||++++-|+-..
T Consensus 21 ~s~~~IA~~lg~s~sTV~rel 41 (44)
T PF13936_consen 21 MSIREIAKRLGRSRSTVSREL 41 (44)
T ss_dssp --HHHHHHHTT--HHHHHHHH
T ss_pred CCHHHHHHHHCcCcHHHHHHH
Confidence 356789999999999998653
No 93
>KOG2577|consensus
Probab=25.09 E-value=62 Score=31.51 Aligned_cols=56 Identities=21% Similarity=0.366 Sum_probs=41.2
Q ss_pred HHHHHHHHc-CCCCHHHHHHHHHHcCCChhhHHHHhhhccCCcc-ccCCcccccccccEEEEecCChhh
Q psy8528 75 LLDLAQRQH-GWLPISAMHYVADFLNLPKMRVYEVATFYTMFIR-KPIGEERIKSILQYHLNWCTTTPC 141 (240)
Q Consensus 75 lL~~aQ~q~-G~Lp~~am~~VA~~L~lp~~~VyeVATFYtmF~~-kP~G~~~~~~~~K~~I~VC~~t~C 141 (240)
.++++|+.- |-|. ++++|+.|+|-.-|||.|-.---=..+ +.+- |.+||+=.+-.+
T Consensus 80 Fv~Llq~s~dGvld---Ln~aA~~L~VqKRRIYDITNVLEGI~LIeKks--------KN~IqW~G~~~~ 137 (354)
T KOG2577|consen 80 FVDLLQESPDGVLD---LNKAAEVLNVQKRRIYDITNVLEGIGLIEKKS--------KNNIQWIGGDFN 137 (354)
T ss_pred HHHHHHhCCCceee---HHHHHHHhccccceeeehhhhhhcccceeecc--------ccceeeecCCCc
Confidence 567777775 7775 688999999999999999877665544 3344 788876544444
No 94
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=25.08 E-value=82 Score=31.19 Aligned_cols=127 Identities=17% Similarity=0.263 Sum_probs=70.8
Q ss_pred hHHHHHHHHHhCCCCCCcccHHHHHHHHHHHcCCCCHHHHHHHHHHcCCChhhHHHHhhhccCCccccCCcccccccccE
Q psy8528 52 NKKRAEAIISIYPVGHERAAVIPLLDLAQRQHGWLPISAMHYVADFLNLPKMRVYEVATFYTMFIRKPIGEERIKSILQY 131 (240)
Q Consensus 52 ~~~~i~~il~~Yp~~~~rsalIplL~~aQ~q~G~Lp~~am~~VA~~L~lp~~~VyeVATFYtmF~~kP~G~~~~~~~~K~ 131 (240)
..+.+..-|.-+.-....-.+...|-.--+..||+.. -++.||+.|+++..+|..|...--. .+|.| +.-.
T Consensus 103 L~e~L~~Ql~~~~l~~~~~~ia~~iI~~LD~~GyL~~-~~~eia~~l~~~~~~v~~~l~~lQ~--leP~G------igAr 173 (455)
T PRK05932 103 LQDHLLEQIELTPFSETDRAIATYIIDALDDEGYLTE-DLEEIAESLGVELDEVEAVLKRIQS--FDPAG------VGAR 173 (455)
T ss_pred HHHHHHHHHcccCCCHHHHHHHHHHHHhCCCCCCCCC-CHHHHHHHcCCCHHHHHHHHHHHhc--CCCCc------cCcC
Confidence 3444555555443211222333333333456899985 5778999999999999999988654 68888 1122
Q ss_pred EEEecCChhhhhcC----HHHHHHHHHHHcCceEe--------ecCCCHHhHHHHHHHHhcCCCCCCCC
Q psy8528 132 HLNWCTTTPCWLRN----SDAILEVIKKKCNMMLE--------RQDLEPKDMEQIIDDLKAGKKPAPGP 188 (240)
Q Consensus 132 ~I~VC~~t~C~lrG----s~~Il~~l~~~LgImv~--------y~~Ltpe~i~~IL~~lk~g~~p~~gp 188 (240)
-++=|--.=-.-.+ -......+.+.|..+.+ --+++.+++.++++.++. =.|+||-
T Consensus 174 ~L~ECLllQl~~~~~~~~~~~~~~il~~~le~la~~~~~~ia~~l~is~~~v~~~~~~Ir~-L~P~Pg~ 241 (455)
T PRK05932 174 DLQECLLLQLEQLDDTPRLDEAMEIISDHLDLLARRDFRTLAKKLGVKEEDLQEALDLIRS-LDPKPGA 241 (455)
T ss_pred CHHHHHHHHHhccCCCchHHHHHHHHHHHHHHHHcCCHHHHHHHHCcCHHHHHHHHHHHhC-CCCCCcc
Confidence 22222211111111 01122333333332111 336789999999988875 5688885
No 95
>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=25.06 E-value=45 Score=26.01 Aligned_cols=50 Identities=14% Similarity=0.038 Sum_probs=31.0
Q ss_pred HHhHHHHHHHHHhCCCCCCcccHHHHHHHHHHHcCCCCHHHHHHHHHHcCCChhhHHHHh
Q psy8528 50 PDNKKRAEAIISIYPVGHERAAVIPLLDLAQRQHGWLPISAMHYVADFLNLPKMRVYEVA 109 (240)
Q Consensus 50 ~e~~~~i~~il~~Yp~~~~rsalIplL~~aQ~q~G~Lp~~am~~VA~~L~lp~~~VyeVA 109 (240)
.+....+.+.+...|. +...++- |+.+ .|+ ...+||+.||+++..|+...
T Consensus 101 ~e~~~~l~~~l~~L~~--~~r~il~-l~~~---~~~----~~~eIA~~lgis~~tv~~~~ 150 (161)
T TIGR02985 101 KELQLIIYKAIEKLPE--QCRKIFI-LSRF---EGK----SYKEIAEELGISVKTVEYHI 150 (161)
T ss_pred HHHHHHHHHHHHHCCH--HHHHHHH-HHHH---cCC----CHHHHHHHHCCCHHHHHHHH
Confidence 3445567888888874 2222222 2221 233 45679999999999998754
No 96
>TIGR01207 rmlA glucose-1-phosphate thymidylyltransferase, short form. This model describes a tightly conserved but broadly distributed subfamily (here designated as short form) of known and putative bacterial glucose-1-phosphate thymidylyltransferases. It is well characterized in several species as the first of four enzymes involved in the biosynthesis of dTDP-L-rhamnose, a cell wall constituent and a feedback inhibitor of the enzyme.
Probab=25.02 E-value=72 Score=29.14 Aligned_cols=51 Identities=16% Similarity=0.192 Sum_probs=39.2
Q ss_pred CHHhHHHHHHHHHhCCCCCCcccHHHHHHHHHHHcCCCCHHHHHHHHHHcCCC
Q psy8528 49 TPDNKKRAEAIISIYPVGHERAAVIPLLDLAQRQHGWLPISAMHYVADFLNLP 101 (240)
Q Consensus 49 t~e~~~~i~~il~~Yp~~~~rsalIplL~~aQ~q~G~Lp~~am~~VA~~L~lp 101 (240)
|++.+.++.+.++... .+++..|..+.++-=..|||+.+.+..+|+.+.-+
T Consensus 225 t~~~l~~A~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 275 (286)
T TIGR01207 225 THDSLLEASNFIQTIE--KRQGLKVACPEEIAWRNGWIDDEQLEELARPLAKN 275 (286)
T ss_pred CHHHHHHHHHHHHHHH--HhcCCEEecHHHHHHHcCCCCHHHHHHHHHHhccC
Confidence 4566666666666554 36677888888888888999999999999988643
No 97
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=24.88 E-value=61 Score=26.38 Aligned_cols=45 Identities=18% Similarity=0.307 Sum_probs=29.9
Q ss_pred HHHHHHHHhCCCCCCcccHHHHHHHHHHHcCCCCHHHHHHHHHHcCCChhhHHHH
Q psy8528 54 KRAEAIISIYPVGHERAAVIPLLDLAQRQHGWLPISAMHYVADFLNLPKMRVYEV 108 (240)
Q Consensus 54 ~~i~~il~~Yp~~~~rsalIplL~~aQ~q~G~Lp~~am~~VA~~L~lp~~~VyeV 108 (240)
..+.+.++.-|. ..+..+ .|. |+..-..++||+.||++...|+..
T Consensus 128 ~~l~~~l~~L~~-~~r~il--~l~-------~~~~~s~~eIA~~lgis~~~v~~~ 172 (187)
T PRK09641 128 ETIQEAILQLPE-KYRTVI--VLK-------YIEDLSLKEISEILDLPVGTVKTR 172 (187)
T ss_pred HHHHHHHHhCCH-HHHHHh--hhH-------HhhCCCHHHHHHHHCCCHHHHHHH
Confidence 457777888874 233333 333 334456788999999999888754
No 98
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=24.73 E-value=1.3e+02 Score=23.03 Aligned_cols=34 Identities=12% Similarity=0.049 Sum_probs=26.6
Q ss_pred cHHHHHHHHHHHcCCCCHHHHHHHHHHcCCChhhHHHHh
Q psy8528 71 AVIPLLDLAQRQHGWLPISAMHYVADFLNLPKMRVYEVA 109 (240)
Q Consensus 71 alIplL~~aQ~q~G~Lp~~am~~VA~~L~lp~~~VyeVA 109 (240)
-+..|+..+++ |-++ +..||+.+|++.+.|.-+.
T Consensus 7 R~~~I~e~l~~--~~~t---i~dvA~~~gvS~~TVsr~L 40 (80)
T TIGR02844 7 RVLEIGKYIVE--TKAT---VRETAKVFGVSKSTVHKDV 40 (80)
T ss_pred HHHHHHHHHHH--CCCC---HHHHHHHhCCCHHHHHHHh
Confidence 45567777777 7665 7889999999999988755
No 99
>PF14779 BBS1: Ciliary BBSome complex subunit 1
Probab=24.60 E-value=1.2e+02 Score=28.25 Aligned_cols=99 Identities=14% Similarity=0.199 Sum_probs=67.2
Q ss_pred cccccCcceeeccCCCCCCCCccccCCHHhHHHHH-HHHHhCCCCC-CcccHHHHHHHHHHH-cCCCCHHHHHHHHHHcC
Q psy8528 23 TQRLNHDALFVHRDTKDDNLDVKFEFTPDNKKRAE-AIISIYPVGH-ERAAVIPLLDLAQRQ-HGWLPISAMHYVADFLN 99 (240)
Q Consensus 23 ~~~~~~~~~~~h~~t~~~n~~~~f~ft~e~~~~i~-~il~~Yp~~~-~rsalIplL~~aQ~q-~G~Lp~~am~~VA~~L~ 99 (240)
-+......+++.|+ ..+--+|.+++-.....| ++-.++..+. +...+...|..+++. +-.|+...++.+ .
T Consensus 83 iAVA~G~~vyiYkN---lkP~yKftlP~~~~~~~E~eiW~~~~~~~i~~~~l~~~L~~lr~~~~~~LS~rSl~~L----~ 155 (257)
T PF14779_consen 83 IAVAAGPSVYIYKN---LKPFYKFTLPPLEINPLEQEIWQQLREGKIDPETLKEMLESLRDIAGVKLSPRSLRFL----Q 155 (257)
T ss_pred EEEEeCCEEEEEec---ccceeeecCCCCCCCHHHHHHHHhcccCCCCHHHHHHHHHHHhhccCCccCHHHHHHH----C
Confidence 34445667899988 677677766655444443 3556665432 467888899998886 458999888866 4
Q ss_pred CChhhHHHHhhhccCCccccCCcccccccccEEEEecCCh
Q psy8528 100 LPKMRVYEVATFYTMFIRKPIGEERIKSILQYHLNWCTTT 139 (240)
Q Consensus 100 lp~~~VyeVATFYtmF~~kP~G~~~~~~~~K~~I~VC~~t 139 (240)
+++ .+-..|-..+...|.. +-.+-.|.++
T Consensus 156 l~~---ee~~~fi~~~k~~pl~--------~~t~ITcm~t 184 (257)
T PF14779_consen 156 LDP---EEREAFIERYKDSPLK--------RQTVITCMAT 184 (257)
T ss_pred CCH---HHHHHHHHHHhcCCcc--------cCceeEEeee
Confidence 455 4555666777888887 7677788765
No 100
>PF11165 DUF2949: Protein of unknown function (DUF2949); InterPro: IPR021336 This family of proteins with unknown function appear to be restricted to Cyanobacteria.
Probab=24.51 E-value=88 Score=22.92 Aligned_cols=34 Identities=18% Similarity=0.339 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHcCc--------------------eEe--ecCCCHHhHHHHHHHHh
Q psy8528 146 SDAILEVIKKKCNM--------------------MLE--RQDLEPKDMEQIIDDLK 179 (240)
Q Consensus 146 s~~Il~~l~~~LgI--------------------mv~--y~~Ltpe~i~~IL~~lk 179 (240)
+.+++..|.+++++ ||= ||=+|-+.+++|+|-+.
T Consensus 2 ~~~l~~fL~~el~ls~~~i~lalr~~~~~~~pLPmiLWqyGLItL~QL~~i~DWl~ 57 (58)
T PF11165_consen 2 STQLIRFLQEELGLSEASIALALRQQEQDQGPLPMILWQYGLITLEQLDQIFDWLE 57 (58)
T ss_pred cHHHHHHHHHHcCCCHHHHHHHHHhHhccCCCcchHHHHhccccHHHHHHHHHHHh
Confidence 46788999999998 433 99999999999998764
No 101
>PRK05883 acyl carrier protein; Validated
Probab=24.50 E-value=1.1e+02 Score=23.56 Aligned_cols=68 Identities=16% Similarity=0.081 Sum_probs=45.9
Q ss_pred CHHHHHHHHHHcCCChhhHHHHhhhccCCccccCCcccccccccEEEEecCChhhhhcCHHHHHHHHHHHcCceEe----
Q psy8528 87 PISAMHYVADFLNLPKMRVYEVATFYTMFIRKPIGEERIKSILQYHLNWCTTTPCWLRNSDAILEVIKKKCNMMLE---- 162 (240)
Q Consensus 87 p~~am~~VA~~L~lp~~~VyeVATFYtmF~~kP~G~~~~~~~~K~~I~VC~~t~C~lrGs~~Il~~l~~~LgImv~---- 162 (240)
-....+.||+.|++++.+|-.-++|+.-+..--.. --+++-.+++++||.+.
T Consensus 16 ~~~l~~iia~~l~v~~~~I~~d~~l~~dlg~DSL~------------------------~v~lv~~lE~~fgI~i~~ee~ 71 (91)
T PRK05883 16 SATLLSILRDDLNVDLTRVTPDARLVDDVGLDSVA------------------------FAVGMVAIEERLGVALSEEDL 71 (91)
T ss_pred HHHHHHHHHHHhCCChhhCCCCCchhhccCCChHH------------------------HHHHHHHHHHHHCCCcCHHHH
Confidence 34567788999999998888777776555443322 23566689999998666
Q ss_pred ecCCCHHhHHHHHHHH
Q psy8528 163 RQDLEPKDMEQIIDDL 178 (240)
Q Consensus 163 y~~Ltpe~i~~IL~~l 178 (240)
.+--|..++.+.|+..
T Consensus 72 ~~~~TV~dl~~~v~~~ 87 (91)
T PRK05883 72 LSCDTVGDLEAAIAAK 87 (91)
T ss_pred HhCCCHHHHHHHHHHH
Confidence 4445666666666553
No 102
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=24.48 E-value=71 Score=26.52 Aligned_cols=47 Identities=17% Similarity=0.285 Sum_probs=30.7
Q ss_pred HhHHHHHHHHHhCCCCCCcccHHHHHHHHHHHcCCCCHHHHHHHHHHcCCChhhHHH
Q psy8528 51 DNKKRAEAIISIYPVGHERAAVIPLLDLAQRQHGWLPISAMHYVADFLNLPKMRVYE 107 (240)
Q Consensus 51 e~~~~i~~il~~Yp~~~~rsalIplL~~aQ~q~G~Lp~~am~~VA~~L~lp~~~Vye 107 (240)
+..+.++..|++.|+ ..+..+. | -|+-.-..++||+.||++...|+.
T Consensus 128 ~~~~~l~~~l~~L~~-~~r~i~~--l-------~~~~g~s~~EIA~~lgis~~tV~~ 174 (194)
T PRK12513 128 RDRRRLQAALETLPD-EQREVFL--L-------REHGDLELEEIAELTGVPEETVKS 174 (194)
T ss_pred HHHHHHHHHHHhCCH-hHhhhee--e-------ehccCCCHHHHHHHHCCCHHHHHH
Confidence 344567788888885 2222222 1 134445678899999999999974
No 103
>PLN02326 3-oxoacyl-[acyl-carrier-protein] synthase III
Probab=24.25 E-value=66 Score=30.28 Aligned_cols=52 Identities=13% Similarity=0.283 Sum_probs=38.5
Q ss_pred CHHHHHHHHHHHcCc----eE---e-ecCCCHHhHHHHHHHHhcCCCCCCCCCCCCCCCc
Q psy8528 145 NSDAILEVIKKKCNM----ML---E-RQDLEPKDMEQIIDDLKAGKKPAPGPSGYTSGIG 196 (240)
Q Consensus 145 Gs~~Il~~l~~~LgI----mv---~-y~~Ltpe~i~~IL~~lk~g~~p~~gp~g~~~~~~ 196 (240)
++..+++.+.++||+ +. . |+++...++--.|+++.+....++|-...+.|+|
T Consensus 308 ~n~~~~~~~~~~Lgl~~ek~~~~l~~~GNt~sAsi~~~L~~~~~~g~~~~Gd~vll~~~G 367 (379)
T PLN02326 308 ANQRIIDAVAQRLGIPPEKVISNLANYGNTSAASIPLALDEAVRSGKVKKGDVIATAGFG 367 (379)
T ss_pred CCHHHHHHHHHHcCCCHHHeeecHhhcCcHHHHHHHHHHHHHHHcCCCCCCCEEEEEEEC
Confidence 457889999999998 22 2 9999999999999888765567777544444433
No 104
>KOG0183|consensus
Probab=24.25 E-value=94 Score=28.75 Aligned_cols=56 Identities=16% Similarity=0.376 Sum_probs=43.7
Q ss_pred CCccccCCcccccccccEEEEecCChhhhhcCHHHHHHHHHHHcCc-------------------------------eEe
Q psy8528 114 MFIRKPIGEERIKSILQYHLNWCTTTPCWLRNSDAILEVIKKKCNM-------------------------------MLE 162 (240)
Q Consensus 114 mF~~kP~G~~~~~~~~K~~I~VC~~t~C~lrGs~~Il~~l~~~LgI-------------------------------mv~ 162 (240)
.|.++|.| -|+-+.|+.+ -++|..+-+.|++..+- ++.
T Consensus 145 lyqtePsG--------~f~ewka~ai---Gr~sk~VrEflEK~y~e~~~~~~~~~ikL~ir~LleVvqs~~~nie~aVm~ 213 (249)
T KOG0183|consen 145 LYQTEPSG--------IFSEWKANAI---GRSSKTVREFLEKNYKEEAIATEGETIKLAIRALLEVVQSGGKNIEVAVMK 213 (249)
T ss_pred eEeeCCCc--------chhhhhcccc---ccccHHHHHHHHHhcccccccccccHHHHHHHHHHHHhhcCCCeeEEEEEe
Confidence 48889999 8999999987 58899999999995543 222
Q ss_pred ----ecCCCHHhHHHHHHHHhc
Q psy8528 163 ----RQDLEPKDMEQIIDDLKA 180 (240)
Q Consensus 163 ----y~~Ltpe~i~~IL~~lk~ 180 (240)
..-|+.+.++.++..+.+
T Consensus 214 ~~~~~~~l~~~~I~~~v~~ie~ 235 (249)
T KOG0183|consen 214 RRKDLKMLESEEIDDIVKEIEQ 235 (249)
T ss_pred cCCceeecCHHHHHHHHHHHHH
Confidence 556888888888876653
No 105
>COG5469 Predicted metal-binding protein [Function unknown]
Probab=24.24 E-value=2.2e+02 Score=24.49 Aligned_cols=46 Identities=17% Similarity=0.414 Sum_probs=31.9
Q ss_pred cEEEEecCChhhhh----------cCHHHHHHHHHHH---------cCc-------------eEe----------ecCCC
Q psy8528 130 QYHLNWCTTTPCWL----------RNSDAILEVIKKK---------CNM-------------MLE----------RQDLE 167 (240)
Q Consensus 130 K~~I~VC~~t~C~l----------rGs~~Il~~l~~~---------LgI-------------mv~----------y~~Lt 167 (240)
||++-||++ |+- .++..|++.|.+. +.| +|- ++|||
T Consensus 17 ~htlfVCks--C~~~~~~~~~~~p~~G~~Ll~kl~~l~qe~~~~~e~~I~~VeCl~~C~r~c~vA~~~~~k~sYLFgdL~ 94 (143)
T COG5469 17 KHTLFVCKS--CRDVSQEGKENGPSDGSILLDKLQELAQEWEIAHEFEIQTVECLAACNRGCVVAFSGPGKPSYLFGDLT 94 (143)
T ss_pred ceEEEEecc--ccccccCCccCCCCcHHHHHHHHHHHHhhhhhhccceeeeeHhhhhcCCCeEEEEecCCCceEEEccCC
Confidence 899999975 532 3567788877633 223 222 89999
Q ss_pred HHh-HHHHHHH
Q psy8528 168 PKD-MEQIIDD 177 (240)
Q Consensus 168 pe~-i~~IL~~ 177 (240)
|++ ..+||+-
T Consensus 95 p~d~a~dLl~~ 105 (143)
T COG5469 95 PDDSASDLLEF 105 (143)
T ss_pred ccccHHHHHHH
Confidence 988 7778764
No 106
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=24.19 E-value=92 Score=28.37 Aligned_cols=69 Identities=20% Similarity=0.246 Sum_probs=40.9
Q ss_pred CccccCCHHhHHHHHHHHHhCCCCC-------Cc---ccHHHHHHHHHHHcCCCCHHHHHHHHHHcCCChhhHHHHhhh
Q psy8528 43 DVKFEFTPDNKKRAEAIISIYPVGH-------ER---AAVIPLLDLAQRQHGWLPISAMHYVADFLNLPKMRVYEVATF 111 (240)
Q Consensus 43 ~~~f~ft~e~~~~i~~il~~Yp~~~-------~r---salIplL~~aQ~q~G~Lp~~am~~VA~~L~lp~~~VyeVATF 111 (240)
...|.|+-=..-+|+.-|.+|=... .+ ..+.--+..+.++.|+..++...+||+.||++..+|.++...
T Consensus 96 ~~~~~FstYA~~~Ir~~i~~~l~~~~~~vr~p~~~~~~~~~~~~~~~~~~l~~~~~~t~~eiA~~l~~~~~~v~~~~~~ 174 (284)
T PRK06596 96 EVGVRLVSFAVHWIKAEIHEYILRNWRIVKVATTKAQRKLFFNLRKAKKRLGWLNPEEVEMVAEELGVSEEEVREMESR 174 (284)
T ss_pred ccCCCHHHHHHHHHHHHHHHHHHHcCCeeeccchHHHHHHHHHHHHHHHHhccCCCCCHHHHHHHhCcCHHHHHHHHHH
Confidence 3445666555566665554441100 00 112223444445556666667899999999999999988543
No 107
>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=24.13 E-value=76 Score=21.04 Aligned_cols=23 Identities=13% Similarity=0.216 Sum_probs=17.7
Q ss_pred CCHHHHHHHHHHcCCChhhHHHH
Q psy8528 86 LPISAMHYVADFLNLPKMRVYEV 108 (240)
Q Consensus 86 Lp~~am~~VA~~L~lp~~~VyeV 108 (240)
.-.-.+.+||+.||++...|...
T Consensus 18 ~~~~t~~eIa~~lg~s~~~V~~~ 40 (50)
T PF04545_consen 18 FEGLTLEEIAERLGISRSTVRRI 40 (50)
T ss_dssp TST-SHHHHHHHHTSCHHHHHHH
T ss_pred cCCCCHHHHHHHHCCcHHHHHHH
Confidence 44445789999999999998754
No 108
>PF05379 Peptidase_C23: Carlavirus endopeptidase ; InterPro: IPR008041 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to the MEROPS peptidase family C23 (clan CA). The type example is Carlavirus (apple stem pitting virus) endopeptidase, this thought to play a role in the post-translational cleavage of the high molecular weight primary translation products of the virus.; GO: 0003968 RNA-directed RNA polymerase activity, 0016817 hydrolase activity, acting on acid anhydrides
Probab=23.85 E-value=75 Score=24.72 Aligned_cols=21 Identities=19% Similarity=0.243 Sum_probs=18.9
Q ss_pred HHHHHHHHcCCChhhHHHHhh
Q psy8528 90 AMHYVADFLNLPKMRVYEVAT 110 (240)
Q Consensus 90 am~~VA~~L~lp~~~VyeVAT 110 (240)
++.+||+.|+-++.+|+.|..
T Consensus 6 vi~AiA~aL~R~~~dVl~Vl~ 26 (89)
T PF05379_consen 6 VIRAIAEALGRREQDVLAVLS 26 (89)
T ss_pred hhHHHHHHhCCCHHHHHHHHH
Confidence 578899999999999999975
No 109
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=23.80 E-value=93 Score=24.81 Aligned_cols=45 Identities=16% Similarity=0.209 Sum_probs=32.9
Q ss_pred HHHHHHHHHHcCCCCHHHHHHHHHHcCCChhhHHH----------HhhhccCCccccCC
Q psy8528 73 IPLLDLAQRQHGWLPISAMHYVADFLNLPKMRVYE----------VATFYTMFIRKPIG 121 (240)
Q Consensus 73 IplL~~aQ~q~G~Lp~~am~~VA~~L~lp~~~Vye----------VATFYtmF~~kP~G 121 (240)
+-+|..+|+... .-+..+|+.+|+++..|.. +-.|....+....|
T Consensus 11 ~~IL~~L~~d~r----~~~~eia~~lglS~~~v~~Ri~~L~~~GiI~~~~~~v~~~~lg 65 (154)
T COG1522 11 RRILRLLQEDAR----ISNAELAERVGLSPSTVLRRIKRLEEEGVIKGYTAVLDPEKLG 65 (154)
T ss_pred HHHHHHHHHhCC----CCHHHHHHHHCCCHHHHHHHHHHHHHCCceeeEEEEECHHHcC
Confidence 357788887766 4467899999999999876 33466666766677
No 110
>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=23.75 E-value=1.4e+02 Score=20.19 Aligned_cols=23 Identities=22% Similarity=0.241 Sum_probs=18.5
Q ss_pred HHHHHHHHHcCCChhhHHHHhhh
Q psy8528 89 SAMHYVADFLNLPKMRVYEVATF 111 (240)
Q Consensus 89 ~am~~VA~~L~lp~~~VyeVATF 111 (240)
-.+..+|+.+|++...|.....-
T Consensus 26 ~s~~ela~~~g~s~~tv~r~l~~ 48 (67)
T cd00092 26 LTRQEIADYLGLTRETVSRTLKE 48 (67)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHH
Confidence 35778999999999999876643
No 111
>PF13518 HTH_28: Helix-turn-helix domain
Probab=23.63 E-value=80 Score=20.55 Aligned_cols=25 Identities=16% Similarity=0.259 Sum_probs=21.2
Q ss_pred HHHHHHHHcCCChhhHHHHhhhccC
Q psy8528 90 AMHYVADFLNLPKMRVYEVATFYTM 114 (240)
Q Consensus 90 am~~VA~~L~lp~~~VyeVATFYtm 114 (240)
.+..+|+.+||+...|+....-|.-
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHHh
Confidence 4566999999999999998887755
No 112
>PF00390 malic: Malic enzyme, N-terminal domain; InterPro: IPR012301 Malic enzymes (malate oxidoreductases) catalyse the oxidative decarboxylation of malate to form pyruvate [], a reaction important in a number of metabolic pathways - e.g. carbon dioxide released from the reaction may be used in sugar production during the Calvin cycle of photosynthesis []. There are 3 forms of the enzyme []: an NAD-dependent form that decarboxylates oxaloacetate; an NAD-dependent form that does not decarboxylate oxalo-acetate; and an NADPH-dependent form []. Other proteins known to be similar to malic enzymes are the Escherichia coli scfA protein; an enzyme from Zea mays (Maize), formerly thought to be cinnamyl-alcohol dehydrogenase []; and the hypothetical Saccharomyces cerevisiae protein YKL029c. Studies on the duck liver malic enzyme reveals that it can be alkylated by bromopyruvate, resulting in the loss of oxidative decarboxylation and the subsequent enhancement of pyruvate reductase activity []. The alkylated form is able to bind NADPH but not L-malate, indicating impaired substrate-or divalent metal ion-binding in the active site []. Sequence analysis has highlighted a cysteine residue as the point of alkylation, suggesting that it may play an important role in the activity of the enzyme [], although it is absent in the sequences from some species. There are three well conserved regions in the enzyme sequences. Two of them seem to be involved in the binding NAD or NADP. The significance of the third one, located in the central part of the enzymes, is not yet known.; GO: 0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor, 0055114 oxidation-reduction process; PDB: 2DVM_B 1WW8_A 2HAE_B 1VL6_A 1PJ2_A 1PJL_B 1GZ3_A 1PJ4_A 1PJ3_C 1EFL_A ....
Probab=23.42 E-value=88 Score=27.67 Aligned_cols=34 Identities=18% Similarity=0.433 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHcCc--eEeecCCCHHhHHHHHHHHh
Q psy8528 146 SDAILEVIKKKCNM--MLERQDLEPKDMEQIIDDLK 179 (240)
Q Consensus 146 s~~Il~~l~~~LgI--mv~y~~Ltpe~i~~IL~~lk 179 (240)
-+++++++++..|- +||+||...+..-.||+++|
T Consensus 147 vdefv~av~~~~gp~~~IqfEDf~~~nAf~iL~kYr 182 (182)
T PF00390_consen 147 VDEFVEAVKRRFGPNALIQFEDFSNPNAFRILDKYR 182 (182)
T ss_dssp HHHHHHHHHHHHGCTSEEEE-S--CCHHHHHHHHHT
T ss_pred HHHHHHHHHHHhCCCeEEEEecCCChhHHHHHHhcC
Confidence 36888889999865 89999999999999999885
No 113
>KOG2914|consensus
Probab=23.33 E-value=1.8e+02 Score=26.26 Aligned_cols=79 Identities=13% Similarity=0.107 Sum_probs=58.5
Q ss_pred HHHHHHHHHhCCCCCCcccHHHHHHHHHHHcCCCCHHHHHHHHHHcCCChhhHHHHhhhccCCccccCCcccccccccEE
Q psy8528 53 KKRAEAIISIYPVGHERAAVIPLLDLAQRQHGWLPISAMHYVADFLNLPKMRVYEVATFYTMFIRKPIGEERIKSILQYH 132 (240)
Q Consensus 53 ~~~i~~il~~Yp~~~~rsalIplL~~aQ~q~G~Lp~~am~~VA~~L~lp~~~VyeVATFYtmF~~kP~G~~~~~~~~K~~ 132 (240)
.+..+.++.+|.. .++. +.-++..|+-+.++++.+.+.++.|.+.=+=..-+|.++......
T Consensus 29 ~~~~~~~~~~ygk------~~~~-~~~~~~mG~~~~eaa~~~~~~~~dp~s~ee~~~e~~~~~~~~~~~----------- 90 (222)
T KOG2914|consen 29 TEAWQELLDRYGK------PYPW-DVKVKSMGKRTSEAARLFVKKLPDPVSREEFNKEEEEILDRLFMN----------- 90 (222)
T ss_pred HHHHHHHHHHcCC------CChH-HHHHHHcCCCHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHhccc-----------
Confidence 3457789999973 1222 122336799999999999999999988877777888887766543
Q ss_pred EEecCChhhhhcCHHHHHHHHHHH
Q psy8528 133 LNWCTTTPCWLRNSDAILEVIKKK 156 (240)
Q Consensus 133 I~VC~~t~C~lrGs~~Il~~l~~~ 156 (240)
++-+.|+++++.+|...
T Consensus 91 -------~~~~PGa~kLv~~L~~~ 107 (222)
T KOG2914|consen 91 -------SILMPGAEKLVNHLKNN 107 (222)
T ss_pred -------cccCCcHHHHHHHHHhC
Confidence 23345999999999875
No 114
>PRK09566 nirA ferredoxin-nitrite reductase; Reviewed
Probab=23.31 E-value=3.6e+02 Score=26.78 Aligned_cols=79 Identities=19% Similarity=0.249 Sum_probs=49.5
Q ss_pred CChhhHHHHhhhccCCcccc-CCcccccccccEEEEecCChhhhhcCHHHH--HHHHHHHcC-c---------eEeecCC
Q psy8528 100 LPKMRVYEVATFYTMFIRKP-IGEERIKSILQYHLNWCTTTPCWLRNSDAI--LEVIKKKCN-M---------MLERQDL 166 (240)
Q Consensus 100 lp~~~VyeVATFYtmF~~kP-~G~~~~~~~~K~~I~VC~~t~C~lrGs~~I--l~~l~~~Lg-I---------mv~y~~L 166 (240)
|++.+...--.+|-.|..++ .| .|.++|.. |.-.--++++ +..+-+++| . -||...+
T Consensus 42 ~~~~d~~~~~~~~G~~~~~~~~g--------~fmvRvri--p~G~lt~~Qlr~la~ia~~yg~~g~i~lTtRQniql~~i 111 (513)
T PRK09566 42 MDETDLELRLKWLGMFWRPVTPG--------KFMLRLRV--PNGILTSEQLRVLASIVQRYGDDGSADITTRQNLQLRGI 111 (513)
T ss_pred CCHHHHhhhheeeEEeeEcCCCC--------eEEEEecc--CCccCCHHHHHHHHHHHHHhCCCCeEEEEcccceeecCC
Confidence 45555555566777775533 46 78888875 4434444443 445666666 2 3448899
Q ss_pred CHHhHHHHHHHHhcCCCCCCCC
Q psy8528 167 EPKDMEQIIDDLKAGKKPAPGP 188 (240)
Q Consensus 167 tpe~i~~IL~~lk~g~~p~~gp 188 (240)
..+++.+|+++|.+-.-...++
T Consensus 112 ~~~dl~~i~~~L~~~GL~~~~~ 133 (513)
T PRK09566 112 LLEDLPEILNRLKAVGLTSVQS 133 (513)
T ss_pred cHHHHHHHHHHHHHcCCCchhc
Confidence 9999999999997533333344
No 115
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=23.30 E-value=1.2e+02 Score=25.00 Aligned_cols=49 Identities=18% Similarity=0.291 Sum_probs=33.9
Q ss_pred HHhHHHHHHHHHhCCCCCCcccHHHHHHHHHHHcCCCCHHHHHHHHHHcCCChhhHHHH
Q psy8528 50 PDNKKRAEAIISIYPVGHERAAVIPLLDLAQRQHGWLPISAMHYVADFLNLPKMRVYEV 108 (240)
Q Consensus 50 ~e~~~~i~~il~~Yp~~~~rsalIplL~~aQ~q~G~Lp~~am~~VA~~L~lp~~~VyeV 108 (240)
.+....+.+.|...|+ .++.+++ |+.+ .|| ...+||+.||+|...|..-
T Consensus 115 ~~~~~~l~~al~~Lp~-~~R~~~~--l~~~---~gl----s~~EIA~~l~i~~~tVks~ 163 (182)
T COG1595 115 EEELERLRRALARLPP-RQREAFL--LRYL---EGL----SYEEIAEILGISVGTVKSR 163 (182)
T ss_pred HHHHHHHHHHHHhCCH-HHhHHhh--hHhh---cCC----CHHHHHHHHCCCHHHHHHH
Confidence 5667889999999996 3444433 2222 354 3467999999999998754
No 116
>PLN03171 chalcone synthase-like protein; Provisional
Probab=23.29 E-value=44 Score=32.10 Aligned_cols=44 Identities=20% Similarity=0.310 Sum_probs=34.5
Q ss_pred cCHHHHHHHHHHHcCc----e------Ee-ecCCCHHhHHHHHHHHh-cCC-CCCCC
Q psy8528 144 RNSDAILEVIKKKCNM----M------LE-RQDLEPKDMEQIIDDLK-AGK-KPAPG 187 (240)
Q Consensus 144 rGs~~Il~~l~~~LgI----m------v~-y~~Ltpe~i~~IL~~lk-~g~-~p~~g 187 (240)
.|+..|++.+.++||+ + ++ |+++...++--.|+++. .|+ ..++|
T Consensus 314 q~~~~il~~v~~~Lgl~~ek~~~s~~~l~~yGNtssaSip~~L~~~~~~~~~~~~~G 370 (399)
T PLN03171 314 PGSSAILDQVDAALGLEPEKLAASRRVLSDYGNMFGATVIFALDELRRQMEEAAAAG 370 (399)
T ss_pred CCcHHHHHHHHHHcCCCHHHhHHHHHHHHHhCcchhhhHHHHHHHHHhhHhhcCCCC
Confidence 5677999999999999 3 23 99999999998888765 443 34666
No 117
>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=23.27 E-value=85 Score=17.15 Aligned_cols=19 Identities=16% Similarity=0.314 Sum_probs=15.2
Q ss_pred HHHHHHHHcCCChhhHHHH
Q psy8528 90 AMHYVADFLNLPKMRVYEV 108 (240)
Q Consensus 90 am~~VA~~L~lp~~~VyeV 108 (240)
.+..||+.++++..-||..
T Consensus 23 s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 23 SVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CHHHHHHHHCCCHHHHHHh
Confidence 5678889999998888754
No 118
>PF06569 DUF1128: Protein of unknown function (DUF1128); InterPro: IPR009507 This family consists of several short, hypothetical bacterial proteins of unknown function.
Probab=23.24 E-value=70 Score=24.42 Aligned_cols=33 Identities=33% Similarity=0.648 Sum_probs=22.4
Q ss_pred HHHHHHHHHHcCc------------------------eEe-ecCCCHHhHHHHHHHHh
Q psy8528 147 DAILEVIKKKCNM------------------------MLE-RQDLEPKDMEQIIDDLK 179 (240)
Q Consensus 147 ~~Il~~l~~~LgI------------------------mv~-y~~Ltpe~i~~IL~~lk 179 (240)
+.+++.++++|.+ ||. -..++|..+.+|.++|.
T Consensus 10 ~~MIe~Ik~KL~mvN~~~i~~~~f~~~~yedl~diy~~V~~K~~fS~sEm~aI~~ELG 67 (71)
T PF06569_consen 10 EYMIEEIKQKLNMVNAGAIKPEDFSEEKYEDLKDIYEMVMSKDSFSPSEMQAIAEELG 67 (71)
T ss_pred HHHHHHHHHHHHHhhHHhCCHHhCChhhHHHHHHHHHHHHhccCCCHHHHHHHHHHHH
Confidence 3488999999996 222 45666777777776664
No 119
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=23.10 E-value=1.6e+02 Score=19.19 Aligned_cols=28 Identities=18% Similarity=0.285 Sum_probs=17.8
Q ss_pred HHHHHHHcCCCCHHHHHHHHHHcCCChhhHHH
Q psy8528 76 LDLAQRQHGWLPISAMHYVADFLNLPKMRVYE 107 (240)
Q Consensus 76 L~~aQ~q~G~Lp~~am~~VA~~L~lp~~~Vye 107 (240)
|..+-+.+||= +..+|+.|||++..+|.
T Consensus 10 i~~aL~~~~gn----~~~aA~~Lgisr~tL~~ 37 (42)
T PF02954_consen 10 IRQALERCGGN----VSKAARLLGISRRTLYR 37 (42)
T ss_dssp HHHHHHHTTT-----HHHHHHHHTS-HHHHHH
T ss_pred HHHHHHHhCCC----HHHHHHHHCCCHHHHHH
Confidence 33444445442 46899999999988875
No 120
>PF04659 Arch_fla_DE: Archaeal flagella protein ; InterPro: IPR006752 Archaeal flagella are unique motility structures, and the absence of bacterial structural motility genes in the complete genome sequences of flagellated archaeal species has always suggested that archaeal flagellar biogenesis is likely mediated by novel components. FlaD and FlaE, are present in the cell as membrane-associated proteins but are not major components of isolated flagellar filaments. Interestingly, flaD was found to encode two proteins, each translated from a separate ribosome binding site. This group of sequences contain the archaeal flaD and flaE proteins. The conserved region that defines these sequences is found in the N-teminal region of flaE but towards the C-terminal region of flaD [].; GO: 0001539 ciliary or flagellar motility
Probab=23.08 E-value=2.5e+02 Score=22.45 Aligned_cols=45 Identities=13% Similarity=0.149 Sum_probs=33.5
Q ss_pred HhHHHHHHHHHhCCCCCCcccHHHHHHHHHHHcCCCCHHHHHHHHHHcCC
Q psy8528 51 DNKKRAEAIISIYPVGHERAAVIPLLDLAQRQHGWLPISAMHYVADFLNL 100 (240)
Q Consensus 51 e~~~~i~~il~~Yp~~~~rsalIplL~~aQ~q~G~Lp~~am~~VA~~L~l 100 (240)
-..++++-++++.. ...+.-+|+-- +.-|||++++..++=+++.-
T Consensus 20 ~~~eWLefLve~~G----~~~~~~~L~YY-~~igWISe~V~~~L~~~~~G 64 (99)
T PF04659_consen 20 VVFEWLEFLVERVG----HNNAADALDYY-ESIGWISEEVREQLLKYLKG 64 (99)
T ss_pred HHHHHHHHHHHHcc----cccHHHHHHHH-HHcCCcCHHHHHHHHHHHhC
Confidence 34689999999996 35566666543 34699999999988777653
No 121
>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=23.06 E-value=1.1e+02 Score=24.37 Aligned_cols=50 Identities=14% Similarity=0.100 Sum_probs=33.0
Q ss_pred CHHhHHHHHHHHHhCCCCCCcccHHHHHHHHHHHcCCCCHHHHHHHHHHcCCChhhHHHH
Q psy8528 49 TPDNKKRAEAIISIYPVGHERAAVIPLLDLAQRQHGWLPISAMHYVADFLNLPKMRVYEV 108 (240)
Q Consensus 49 t~e~~~~i~~il~~Yp~~~~rsalIplL~~aQ~q~G~Lp~~am~~VA~~L~lp~~~VyeV 108 (240)
..+..+.+...|.+-|+ +...+=.|..++ | -..++||+.||++...|+--
T Consensus 97 ~~~~~~~l~~~l~~L~~---~~r~i~~l~~~~---g----~s~~eIA~~lgis~~tV~~~ 146 (162)
T TIGR02983 97 DVALRAALARALRRLPA---RQRAVVVLRYYE---D----LSEAQVAEALGISVGTVKSR 146 (162)
T ss_pred hHHHHHHHHHHHHhCCH---HHHHHhhhHHHh---c----CCHHHHHHHhCCCHHHHHHH
Confidence 45566778888998884 233333333332 2 34678999999999988753
No 122
>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=23.05 E-value=81 Score=21.24 Aligned_cols=36 Identities=25% Similarity=0.343 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHHcCCChhhHHHHhh
Q psy8528 72 VIPLLDLAQRQHGWLPISAMHYVADFLNLPKMRVYEVAT 110 (240)
Q Consensus 72 lIplL~~aQ~q~G~Lp~~am~~VA~~L~lp~~~VyeVAT 110 (240)
.+.+|..+-++.+-+ .+..||+.+|+|.+-||-+..
T Consensus 5 al~iL~~l~~~~~~~---t~~eia~~~gl~~stv~r~L~ 40 (52)
T PF09339_consen 5 ALRILEALAESGGPL---TLSEIARALGLPKSTVHRLLQ 40 (52)
T ss_dssp HHHHHHCHHCTBSCE---EHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHHcCCCCC---CHHHHHHHHCcCHHHHHHHHH
Confidence 345666666665543 567899999999999998754
No 123
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=22.96 E-value=1e+02 Score=20.28 Aligned_cols=22 Identities=9% Similarity=0.081 Sum_probs=17.1
Q ss_pred cCCCCHHHHHHHHHHcCCChhh
Q psy8528 83 HGWLPISAMHYVADFLNLPKMR 104 (240)
Q Consensus 83 ~G~Lp~~am~~VA~~L~lp~~~ 104 (240)
...++.+.+..+|+.||+++..
T Consensus 33 ~~~~~~~~~~~ia~~l~~~~~~ 54 (55)
T PF01381_consen 33 KRNPSLDTLKKIAKALGVSPEY 54 (55)
T ss_dssp SSTSBHHHHHHHHHHHTSEHHH
T ss_pred CCCCCHHHHHHHHHHHCCCHHH
Confidence 4578888888888888887754
No 124
>COG4227 Antirestriction protein [DNA replication, recombination, and repair]
Probab=22.87 E-value=1.1e+02 Score=29.21 Aligned_cols=47 Identities=26% Similarity=0.309 Sum_probs=34.7
Q ss_pred HHhHHHHHHHHhcCCCCCCCCCCC--CCCCcCcCCCcccc-ccCCCCCCccC
Q psy8528 168 PKDMEQIIDDLKAGKKPAPGPSGY--TSGIGSQSGRFCQA-REAYHDMTSLT 216 (240)
Q Consensus 168 pe~i~~IL~~lk~g~~p~~gp~g~--~~~~~~~~gr~~~~-~e~~~g~t~l~ 216 (240)
.+=.+.||++|++|..|=.-|||. ++|=+...-|. + -.++.|+..|.
T Consensus 14 ~~ItdRIiadLekG~~PWvkPW~~an~~~~~~lPln~--ntg~~YsGiNvLl 63 (316)
T COG4227 14 AEITDRIIADLEKGVRPWVKPWSAANTTGRITLPLNH--NTGRAYSGINVLL 63 (316)
T ss_pred HHHHHHHHHHHhcCcccccCCCccccCCCccccccCc--ccCCcccCchhee
Confidence 455679999999999998899988 44444444455 4 66788987774
No 125
>PRK01530 hypothetical protein; Reviewed
Probab=22.78 E-value=1.7e+02 Score=23.72 Aligned_cols=35 Identities=11% Similarity=0.302 Sum_probs=29.6
Q ss_pred CHHHHHHHHHHHcCc----------------eEeecCCCHHhHHHHHHHHh
Q psy8528 145 NSDAILEVIKKKCNM----------------MLERQDLEPKDMEQIIDDLK 179 (240)
Q Consensus 145 Gs~~Il~~l~~~LgI----------------mv~y~~Ltpe~i~~IL~~lk 179 (240)
--++|++.|.+.||+ .|...+++++.+..+|..++
T Consensus 54 AN~ali~~LAk~l~v~ks~I~IvsG~tSR~K~i~I~g~~~~~l~~~l~~~~ 104 (105)
T PRK01530 54 ANEEIINYLAKEWKLSRSNIEIIKGHTHSLKTILIKNINEDYLNLIINSYI 104 (105)
T ss_pred HHHHHHHHHHHHhCCChhhEEEEecCCCCceEEEEeCCCHHHHHHHHHhhc
Confidence 368999999999998 33388999999999998764
No 126
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.68 E-value=77 Score=26.32 Aligned_cols=34 Identities=18% Similarity=0.336 Sum_probs=25.7
Q ss_pred HHHHHHHcCc--------------eEeecCCCHHhHHH----HHHHHhcCCC
Q psy8528 150 LEVIKKKCNM--------------MLERQDLEPKDMEQ----IIDDLKAGKK 183 (240)
Q Consensus 150 l~~l~~~LgI--------------mv~y~~Ltpe~i~~----IL~~lk~g~~ 183 (240)
++.+++.||+ -++|+...+.+.+. |++.+++|+.
T Consensus 60 lKEvEr~lg~sYptvR~kld~vlramgy~p~~e~~~~i~~~~i~~qle~Gei 111 (122)
T COG3877 60 LKEVERELGISYPTVRTKLDEVLRAMGYNPDSENSVNIGKKKIIDQLEKGEI 111 (122)
T ss_pred HHHHHHHHCCccHHHHHHHHHHHHHcCCCCCCCChhhhhHHHHHHHHHcCCC
Confidence 5667888888 34488877766665 9999999974
No 127
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=22.58 E-value=65 Score=32.33 Aligned_cols=127 Identities=13% Similarity=0.183 Sum_probs=72.3
Q ss_pred hHHHHHHHHHhCCCCCCcccHHHHHHHHHHHcCCCCHHHHHHHHHH----cCCChhhHHHHhhhccCCccccCCcccccc
Q psy8528 52 NKKRAEAIISIYPVGHERAAVIPLLDLAQRQHGWLPISAMHYVADF----LNLPKMRVYEVATFYTMFIRKPIGEERIKS 127 (240)
Q Consensus 52 ~~~~i~~il~~Yp~~~~rsalIplL~~aQ~q~G~Lp~~am~~VA~~----L~lp~~~VyeVATFYtmF~~kP~G~~~~~~ 127 (240)
..+.+..-|.-++-....-.+...|=..-+..|||..+ ++.||+. |+++..+|..|...-.. ..|.|
T Consensus 125 L~~~L~~Ql~~~~~~~~~~~ia~~lI~~LD~~GyL~~~-~~eia~~~~~~l~~~~~~ve~vL~~iQ~--leP~G------ 195 (481)
T PRK12469 125 LHEHLHDALRLYFLTERDREIARTIIDALDDDGYLRQD-LSELAEAADPELGLSEQELEVALRLVQS--LDPPG------ 195 (481)
T ss_pred HHHHHHHHHhccCCCHHHHHHHHHHHhhCCCCCCCCCC-HHHHHhccccccCCCHHHHHHHHHHHhc--CCCCc------
Confidence 34556666655443212223333333344567999964 5779998 99999999999998765 56777
Q ss_pred cccEEEEecCChhhhhcCH--HH---HHHHHHHHcCceEe--------ecCCCHHhHHHHHHHHhcCCCCCCCC
Q psy8528 128 ILQYHLNWCTTTPCWLRNS--DA---ILEVIKKKCNMMLE--------RQDLEPKDMEQIIDDLKAGKKPAPGP 188 (240)
Q Consensus 128 ~~K~~I~VC~~t~C~lrGs--~~---Il~~l~~~LgImv~--------y~~Ltpe~i~~IL~~lk~g~~p~~gp 188 (240)
+.-..++=|--.=..-.+. .. ++..|.+.|..+.. --+++.+++.+.++.++. -.|+||-
T Consensus 196 VgARdL~ECL~lQL~~~~~~~~~~~~a~~il~~~le~La~~~~~~i~~~l~~~~~~l~~a~~~Ir~-L~P~Pg~ 268 (481)
T PRK12469 196 VAARDLSECLLLQLDALPADTPALEEAKEIARHHLERLARRETAEIQRRIGCDQETLREACALVRR-LDPRPGN 268 (481)
T ss_pred cCcCCHHHHHHHHHHhccCCCchHHHHHHHHHHHHHHHHccCHHHHHHHhCcCHHHHHHHHHHHhC-CCCCCcc
Confidence 1123333333221111111 10 22333344432111 347889999999988874 5688885
No 128
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=22.53 E-value=1.4e+02 Score=21.23 Aligned_cols=35 Identities=14% Similarity=0.113 Sum_probs=24.5
Q ss_pred HHHHHHHHHHcCCCCHHHHHHHHHHcCCChhhHHHHhh
Q psy8528 73 IPLLDLAQRQHGWLPISAMHYVADFLNLPKMRVYEVAT 110 (240)
Q Consensus 73 IplL~~aQ~q~G~Lp~~am~~VA~~L~lp~~~VyeVAT 110 (240)
|-.++.+++..+.+.. ..||+.||++++-|.+...
T Consensus 10 L~~Iy~l~~~~~~v~~---~~iA~~L~vs~~tvt~ml~ 44 (60)
T PF01325_consen 10 LKAIYELSEEGGPVRT---KDIAERLGVSPPTVTEMLK 44 (60)
T ss_dssp HHHHHHHHHCTSSBBH---HHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHcCCCCccH---HHHHHHHCCChHHHHHHHH
Confidence 3445555666677765 4689999999999988754
No 129
>PRK05350 acyl carrier protein; Provisional
Probab=22.49 E-value=1.6e+02 Score=21.61 Aligned_cols=65 Identities=9% Similarity=0.168 Sum_probs=35.1
Q ss_pred HHHHHHHHcCCChhhHHHHhhhccCCccccCCcccccccccEEEEecCChhhhhcCHHHHHHHHHHHcCceEe----ecC
Q psy8528 90 AMHYVADFLNLPKMRVYEVATFYTMFIRKPIGEERIKSILQYHLNWCTTTPCWLRNSDAILEVIKKKCNMMLE----RQD 165 (240)
Q Consensus 90 am~~VA~~L~lp~~~VyeVATFYtmF~~kP~G~~~~~~~~K~~I~VC~~t~C~lrGs~~Il~~l~~~LgImv~----y~~ 165 (240)
..+.|++.+++++.++-.-.+|+.-+..--. .--+++-++++++||-+. .+-
T Consensus 11 v~~ii~~~~~~~~~~i~~d~~l~~dlg~DSl------------------------d~veli~~lE~~fgI~i~~~~~~~~ 66 (82)
T PRK05350 11 LRAILVELFEIDPEDITPEANLYEDLDLDSI------------------------DAVDLVVHLQKLTGKKIKPEEFKSV 66 (82)
T ss_pred HHHHHHHHhCCCHHHCCCCccchhhcCCCHH------------------------HHHHHHHHHHHHHCCccCHHHHhhc
Confidence 4455666667777666666665544332222 234566667777776554 223
Q ss_pred CCHHhHHHHHHHH
Q psy8528 166 LEPKDMEQIIDDL 178 (240)
Q Consensus 166 Ltpe~i~~IL~~l 178 (240)
-|..++.+.+.++
T Consensus 67 ~Tv~dlv~~v~~~ 79 (82)
T PRK05350 67 RTVQDVVDAVERL 79 (82)
T ss_pred CcHHHHHHHHHHH
Confidence 3445555554443
No 130
>PRK12423 LexA repressor; Provisional
Probab=22.40 E-value=82 Score=27.24 Aligned_cols=51 Identities=14% Similarity=0.131 Sum_probs=28.9
Q ss_pred cccHHHHHHHHHHHcCCCCHHHHHHHHHHcCC-ChhhHHH---HhhhccCCccccCC
Q psy8528 69 RAAVIPLLDLAQRQHGWLPISAMHYVADFLNL-PKMRVYE---VATFYTMFIRKPIG 121 (240)
Q Consensus 69 rsalIplL~~aQ~q~G~Lp~~am~~VA~~L~l-p~~~Vye---VATFYtmF~~kP~G 121 (240)
|..++..|....+..||- ..+.+||+.||+ +++-|++ +...--+..+.|.+
T Consensus 8 q~~il~~l~~~i~~~g~~--Ps~~eia~~~g~~s~~~v~~~l~~L~~~G~l~~~~~~ 62 (202)
T PRK12423 8 RAAILAFIRERIAQAGQP--PSLAEIAQAFGFASRSVARKHVQALAEAGLIEVVPNQ 62 (202)
T ss_pred HHHHHHHHHHHHHHcCCC--CCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEecCCC
Confidence 455666666666666766 366777777774 6655543 33333344554443
No 131
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=22.24 E-value=2.1e+02 Score=21.43 Aligned_cols=49 Identities=16% Similarity=0.213 Sum_probs=30.9
Q ss_pred ccCCHHhHHHHHHHHHhCCCCCCcccHHHHHHHHHHHcCCCCHHHHHHHHHHcCCChhhHHHHh
Q psy8528 46 FEFTPDNKKRAEAIISIYPVGHERAAVIPLLDLAQRQHGWLPISAMHYVADFLNLPKMRVYEVA 109 (240)
Q Consensus 46 f~ft~e~~~~i~~il~~Yp~~~~rsalIplL~~aQ~q~G~Lp~~am~~VA~~L~lp~~~VyeVA 109 (240)
..++++..+.++++...+-.+ ..|+|+.+-+..+=..++++..+|..+.
T Consensus 2 ~~ls~~~~~~l~~~F~~~D~d---------------~~G~Is~~el~~~l~~~~~~~~ev~~i~ 50 (96)
T smart00027 2 WAISPEDKAKYEQIFRSLDKN---------------QDGTVTGAQAKPILLKSGLPQTLLAKIW 50 (96)
T ss_pred CCCCHHHHHHHHHHHHHhCCC---------------CCCeEeHHHHHHHHHHcCCCHHHHHHHH
Confidence 356777778888877777531 2456666666665555676666655543
No 132
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=22.18 E-value=78 Score=26.04 Aligned_cols=95 Identities=6% Similarity=0.042 Sum_probs=57.5
Q ss_pred HHHHHHHHHHcCCCCHHHHHHHHHHcCCChhhHH---------HHhhhc-cCCccccCCcccccccccEEEEecCChhhh
Q psy8528 73 IPLLDLAQRQHGWLPISAMHYVADFLNLPKMRVY---------EVATFY-TMFIRKPIGEERIKSILQYHLNWCTTTPCW 142 (240)
Q Consensus 73 IplL~~aQ~q~G~Lp~~am~~VA~~L~lp~~~Vy---------eVATFY-tmF~~kP~G~~~~~~~~K~~I~VC~~t~C~ 142 (240)
..||..+|+. +......||+.||+++..|. ||+..| ...+....| . .+..--...|.
T Consensus 12 ~~Il~~Lq~d----~R~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI~~~~~~v~~~~lg--------~-~~~a~v~v~v~ 78 (153)
T PRK11179 12 RGILEALMEN----ARTPYAELAKQFGVSPGTIHVRVEKMKQAGIITGTRVDVNPKQLG--------Y-DVCCFIGIILK 78 (153)
T ss_pred HHHHHHHHHc----CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeEEEEECHHHcC--------C-CEEEEEEEEEc
Confidence 4567777765 44556789999999999886 577744 578888888 2 22222222221
Q ss_pred -hcCHHHHHHHHHHHcCc------------eEeecCCCHHhHHHHH-HHHhc
Q psy8528 143 -LRNSDAILEVIKKKCNM------------MLERQDLEPKDMEQII-DDLKA 180 (240)
Q Consensus 143 -lrGs~~Il~~l~~~LgI------------mv~y~~Ltpe~i~~IL-~~lk~ 180 (240)
-...+++.+.|.+.=++ ++...--+.+.+.+++ +.+..
T Consensus 79 ~~~~~~~~~~~l~~~p~V~~~~~~tG~~dl~~~v~~~d~~~l~~~~~~~l~~ 130 (153)
T PRK11179 79 SAKDYPSALAKLESLDEVVEAYYTTGHYSIFIKVMCRSIDALQHVLINKIQT 130 (153)
T ss_pred ccccHHHHHHHHhCCCCEEEEEEcccCCCEEEEEEECCHHHHHHHHHHHhhc
Confidence 23356777777766565 2222223556777776 45543
No 133
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=22.18 E-value=90 Score=22.85 Aligned_cols=33 Identities=24% Similarity=0.255 Sum_probs=22.6
Q ss_pred HHHHHHHHcCCCCHHHHHHHHHHcCCChhhHHHHhh
Q psy8528 75 LLDLAQRQHGWLPISAMHYVADFLNLPKMRVYEVAT 110 (240)
Q Consensus 75 lL~~aQ~q~G~Lp~~am~~VA~~L~lp~~~VyeVAT 110 (240)
||.-+++++++++-. .||+.+||+...|.-...
T Consensus 5 Il~~i~~~~~p~~T~---eiA~~~gls~~~aR~yL~ 37 (62)
T PF04703_consen 5 ILEYIKEQNGPLKTR---EIADALGLSIYQARYYLE 37 (62)
T ss_dssp HHHHHHHHTS-EEHH---HHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHcCCCCCHH---HHHHHhCCCHHHHHHHHH
Confidence 456667778877654 799999999988765433
No 134
>PHA01083 hypothetical protein
Probab=21.98 E-value=1.2e+02 Score=26.14 Aligned_cols=20 Identities=5% Similarity=0.107 Sum_probs=14.0
Q ss_pred CCCHHHHHHHHHHcCCChhh
Q psy8528 85 WLPISAMHYVADFLNLPKMR 104 (240)
Q Consensus 85 ~Lp~~am~~VA~~L~lp~~~ 104 (240)
|+|++.+..+||.+|+.+.+
T Consensus 43 ~i~de~A~~LAe~aGiDp~e 62 (149)
T PHA01083 43 YISDEEAIFLAESAGIDPEI 62 (149)
T ss_pred CCCHHHHHHHHHHhCCCHHH
Confidence 67777777777777777653
No 135
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=21.72 E-value=1.6e+02 Score=25.69 Aligned_cols=51 Identities=16% Similarity=0.248 Sum_probs=32.9
Q ss_pred CCHHhHHHHHHHHHhCCCCCCcccHHHHHHHHHHHcCCCCHHHHHHHHHHcCCChhhHHHH
Q psy8528 48 FTPDNKKRAEAIISIYPVGHERAAVIPLLDLAQRQHGWLPISAMHYVADFLNLPKMRVYEV 108 (240)
Q Consensus 48 ft~e~~~~i~~il~~Yp~~~~rsalIplL~~aQ~q~G~Lp~~am~~VA~~L~lp~~~VyeV 108 (240)
+..+....+...|.+.|+ ..+. +=+|+.++ | -..++||+.||+++.-|+--
T Consensus 120 ~~~e~~~~l~~al~~Lp~-~~R~--v~~L~y~e---g----~s~~EIAe~LgiS~~tVk~~ 170 (216)
T PRK12533 120 LRAEDVRLVNAALAKLPV-EYRE--VLVLRELE---D----MSYREIAAIADVPVGTVMSR 170 (216)
T ss_pred HHHHHHHHHHHHHHcCCH-HHHh--HhhhHHhc---C----CCHHHHHHHHCCCHHHHHHH
Confidence 344556778888998884 2222 22333332 2 24678999999999998643
No 136
>PRK06840 hypothetical protein; Validated
Probab=21.40 E-value=99 Score=28.17 Aligned_cols=53 Identities=9% Similarity=-0.061 Sum_probs=38.1
Q ss_pred CHHHHHHHHHHHcCc----eEe---ecCCCHHhHHHHHHHHhcCCCCCCCCCCCCCCCcC
Q psy8528 145 NSDAILEVIKKKCNM----MLE---RQDLEPKDMEQIIDDLKAGKKPAPGPSGYTSGIGS 197 (240)
Q Consensus 145 Gs~~Il~~l~~~LgI----mv~---y~~Ltpe~i~~IL~~lk~g~~p~~gp~g~~~~~~~ 197 (240)
++..+++.+.++||+ ++. |+++...++--.|.++.+..+.++|-...+.|+|+
T Consensus 265 ~~~~~~~~~~~~Lgl~~~~~~~~~~~Gn~~sas~~~~L~~~~~~~~~~~Gd~ill~~~G~ 324 (339)
T PRK06840 265 MKRSAHIALLEGLGLTEEQAIYLDEYGHLGQLDQILSLHLALEQGKLKDGDLVVLVSAGT 324 (339)
T ss_pred cCHHHHHHHHHHcCCCHHHeEeHHhccchhhhhHHHHHHHHHHcCCCCCCCEEEEEEEeh
Confidence 457788888999998 333 99999988888787765444467787666655554
No 137
>cd08789 CARD_IPS-1_RIG-I Caspase activation and recruitment domains (CARDs) found in IPS-1 and RIG-I-like RNA helicases. Caspase activation and recruitment domains (CARDs) found in IPS-1 (Interferon beta promoter stimulator protein 1) and Retinoic acid Inducible Gene I (RIG-I)-like DEAD box helicases. RIG-I-like helicases and IPS-1 play important roles in the induction of interferons in response to viral infection. They are crucial in triggering innate immunity and in developing adaptive immunity against viral pathogens. RIG-I-like helicases, including MDA5 and RIG-I, contain two N-terminal CARD domains and a C-terminal DEAD box RNA helicase domain. They are cytoplasmic RNA helicases that play an important role in host antiviral response by sensing incoming viral RNA. Upon activation, the signal is transferred to downstream pathways via the adaptor molecule IPS-1 (MAVS, VISA, CARDIF), leading to the induction of type I interferons. MDA5 and RIG-I associate with IPS-1 through a CARD-CAR
Probab=21.40 E-value=75 Score=24.32 Aligned_cols=39 Identities=28% Similarity=0.342 Sum_probs=31.3
Q ss_pred cCCHHhHHHHHHHHHhCCCCCCcccHHHHHHHHHHHcCCCCH
Q psy8528 47 EFTPDNKKRAEAIISIYPVGHERAAVIPLLDLAQRQHGWLPI 88 (240)
Q Consensus 47 ~ft~e~~~~i~~il~~Yp~~~~rsalIplL~~aQ~q~G~Lp~ 88 (240)
-|+++..++|++...... ..++.--+|+.+.+.-||.+.
T Consensus 29 ~Lt~~d~e~I~a~~~~~G---~~~aa~~Ll~~L~r~~~Wf~~ 67 (84)
T cd08789 29 CLTAEDKERIQAAENNSG---NIKAAWTLLDTLVRRDNWLEP 67 (84)
T ss_pred cCCHHHHHHHHHHHhcCC---hHHHHHHHHHHHhccCChHHH
Confidence 689999998888866664 578888888888877799764
No 138
>PRK09567 nirA ferredoxin-nitrite reductase; Reviewed
Probab=21.17 E-value=4.3e+02 Score=26.97 Aligned_cols=82 Identities=15% Similarity=0.133 Sum_probs=51.4
Q ss_pred CChhhHHHHhhhccCCccccCCcccccccccEEEEecCChhhhhcCHHH--HHHHHHHHcCc---------eEeecCCCH
Q psy8528 100 LPKMRVYEVATFYTMFIRKPIGEERIKSILQYHLNWCTTTPCWLRNSDA--ILEVIKKKCNM---------MLERQDLEP 168 (240)
Q Consensus 100 lp~~~VyeVATFYtmF~~kP~G~~~~~~~~K~~I~VC~~t~C~lrGs~~--Il~~l~~~LgI---------mv~y~~Ltp 168 (240)
++..+......||-+|+..|.+ ..+-++| -.|+-..-+++ .++.+.+++|- -||+..+..
T Consensus 93 ~~~~~~~~~~k~~G~y~~~~~~-------~~fM~Rv--ripgG~lt~~Q~~~la~ia~~yg~g~~~lTTRq~iQlhgI~~ 163 (593)
T PRK09567 93 FPKPADNFRWKYHGLFYVAPAQ-------DSYMCRL--RIPNGILTHWQFAGLADLADRHGGGYSHVTTRANLQLREIPP 163 (593)
T ss_pred CCChhhhhhhccceEEEEcccC-------CeEEEEE--EeCCeecCHHHHHHHHHHHHHHCCCeEEEeccccEEeccCCH
Confidence 3434444467788888887752 0454444 22444444443 34556677764 466899999
Q ss_pred HhHHHHHHHHhcCCCCCCCCCC
Q psy8528 169 KDMEQIIDDLKAGKKPAPGPSG 190 (240)
Q Consensus 169 e~i~~IL~~lk~g~~p~~gp~g 190 (240)
+++.+|++.|.+-.-...+.+|
T Consensus 164 ~d~~~i~~~l~~~GL~t~~a~g 185 (593)
T PRK09567 164 EHAVPVLEGLVDLGLTARGSGA 185 (593)
T ss_pred HHHHHHHHHHHHCCCCCCCCCC
Confidence 9999999999864444445544
No 139
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=21.15 E-value=1.2e+02 Score=20.94 Aligned_cols=18 Identities=22% Similarity=0.255 Sum_probs=8.2
Q ss_pred HHHHHHHcCCChhhHHHH
Q psy8528 91 MHYVADFLNLPKMRVYEV 108 (240)
Q Consensus 91 m~~VA~~L~lp~~~VyeV 108 (240)
...+|+.+|++.+.|..+
T Consensus 17 ~~~lA~~~g~s~s~v~~i 34 (64)
T PF13560_consen 17 QAQLADRLGVSQSTVSRI 34 (64)
T ss_dssp HHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHH
Confidence 344555555555544443
No 140
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=21.04 E-value=1.4e+02 Score=24.55 Aligned_cols=48 Identities=15% Similarity=0.169 Sum_probs=32.4
Q ss_pred HhHHHHHHHHHhCCCCCCcccHHHHHHHHHHHcCCCCHHHHHHHHHHcCCChhhHHHH
Q psy8528 51 DNKKRAEAIISIYPVGHERAAVIPLLDLAQRQHGWLPISAMHYVADFLNLPKMRVYEV 108 (240)
Q Consensus 51 e~~~~i~~il~~Yp~~~~rsalIplL~~aQ~q~G~Lp~~am~~VA~~L~lp~~~VyeV 108 (240)
+....++..|++-|+ +...+=.|+.+ .|+ ..++||+.||+|..-|+.-
T Consensus 116 ~~~~~l~~~l~~Lp~---~~R~v~~L~~~---~g~----s~~EIA~~lgis~~tVk~~ 163 (178)
T PRK12529 116 ETLHEIDALLDTLRP---RVKQAFLMATL---DGM----KQKDIAQALDIALPTVKKY 163 (178)
T ss_pred HHHHHHHHHHHhCCH---HHHHHHHHHHH---cCC----CHHHHHHHHCCCHHHHHHH
Confidence 445678889999995 33333344443 232 3578999999999988753
No 141
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=21.00 E-value=1.4e+02 Score=23.83 Aligned_cols=49 Identities=14% Similarity=0.301 Sum_probs=31.4
Q ss_pred HHhHHHHHHHHHhCCCCCCcccHHHHHHHHHHHcCCCCHHHHHHHHHHcCCChhhHHHHh
Q psy8528 50 PDNKKRAEAIISIYPVGHERAAVIPLLDLAQRQHGWLPISAMHYVADFLNLPKMRVYEVA 109 (240)
Q Consensus 50 ~e~~~~i~~il~~Yp~~~~rsalIplL~~aQ~q~G~Lp~~am~~VA~~L~lp~~~VyeVA 109 (240)
.+....+.+.|.+-|+ ..+.. =.|+. .|+ ...+||+.||++...|+--.
T Consensus 100 ~~~~~~l~~~l~~L~~-~~r~i--l~l~~----~g~----s~~eIA~~lgis~~tV~~~i 148 (166)
T PRK09639 100 KEEITKVQEVLAKMTE-RDRTV--LLLRF----SGY----SYKEIAEALGIKESSVGTTL 148 (166)
T ss_pred HHHHHHHHHHHHcCCH-HHHHH--HHHHH----cCC----CHHHHHHHHCCCHHHHHHHH
Confidence 3455567788888884 22222 22222 344 46789999999999987654
No 142
>PRK11202 DNA-binding transcriptional repressor FabR; Provisional
Probab=20.99 E-value=50 Score=27.91 Aligned_cols=31 Identities=16% Similarity=0.277 Sum_probs=22.6
Q ss_pred HHcCCCCHHHHHHHHHHcCCChhhHHHHhhhccCCccc
Q psy8528 81 RQHGWLPISAMHYVADFLNLPKMRVYEVATFYTMFIRK 118 (240)
Q Consensus 81 ~q~G~Lp~~am~~VA~~L~lp~~~VyeVATFYtmF~~k 118 (240)
.++|| ..-.|+.||+..|+++ .|||.+|..|
T Consensus 26 ~~~G~-~~~si~~IA~~Agvs~------~t~Y~hF~sK 56 (203)
T PRK11202 26 AERSF-SSLSLREVAREAGIAP------TSFYRHFRDM 56 (203)
T ss_pred hcCCc-ccCCHHHHHHHhCCCc------chHHHHCCCH
Confidence 34564 4456788999999987 5788888543
No 143
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=20.90 E-value=2.1e+02 Score=23.71 Aligned_cols=59 Identities=17% Similarity=0.118 Sum_probs=38.7
Q ss_pred HHHHHHHHHhCCC--CCCcccHHHHHHHHHHHcCCCCHHHHHHHHHH--cCCChhhHHHHhhhccC
Q psy8528 53 KKRAEAIISIYPV--GHERAAVIPLLDLAQRQHGWLPISAMHYVADF--LNLPKMRVYEVATFYTM 114 (240)
Q Consensus 53 ~~~i~~il~~Yp~--~~~rsalIplL~~aQ~q~G~Lp~~am~~VA~~--L~lp~~~VyeVATFYtm 114 (240)
.+.+.+.+++-.- -.+|-+| |..+++..++++.+.+...... -+++++.||-+..|+.-
T Consensus 5 ~~~~~~~lk~~glr~T~qR~~v---l~~L~~~~~~~sAeei~~~l~~~~p~islaTVYr~L~~l~e 67 (145)
T COG0735 5 LEDAIERLKEAGLRLTPQRLAV---LELLLEADGHLSAEELYEELREEGPGISLATVYRTLKLLEE 67 (145)
T ss_pred HHHHHHHHHHcCCCcCHHHHHH---HHHHHhcCCCCCHHHHHHHHHHhCCCCCHhHHHHHHHHHHH
Confidence 4455566655432 2355555 4555666778998888766654 67889999998877543
No 144
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=20.84 E-value=85 Score=25.83 Aligned_cols=49 Identities=14% Similarity=0.156 Sum_probs=32.2
Q ss_pred HHhHHHHHHHHHhCCCCCCcccHHHHHHHHHHHcCCCCHHHHHHHHHHcCCChhhHHHH
Q psy8528 50 PDNKKRAEAIISIYPVGHERAAVIPLLDLAQRQHGWLPISAMHYVADFLNLPKMRVYEV 108 (240)
Q Consensus 50 ~e~~~~i~~il~~Yp~~~~rsalIplL~~aQ~q~G~Lp~~am~~VA~~L~lp~~~VyeV 108 (240)
.+..+.++..|+..|+ +...++-+ .. ..| -..++||+.||++...|+--
T Consensus 125 ~e~~~~l~~~l~~L~~--~~r~i~~l-~~---~~g----~s~~eIA~~lgis~~~v~~~ 173 (187)
T PRK12534 125 ASTRRRIDHCLAELEP--PRSELIRT-AF---FEG----ITYEELAARTDTPIGTVKSW 173 (187)
T ss_pred HHHHHHHHHHHHhCCH--HHHHHHHH-HH---HcC----CCHHHHHHHhCCChhHHHHH
Confidence 4556778889999984 33333322 22 123 34678999999999988753
No 145
>smart00803 TAF TATA box binding protein associated factor. TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.
Probab=20.79 E-value=94 Score=22.71 Aligned_cols=18 Identities=33% Similarity=0.676 Sum_probs=12.6
Q ss_pred CCCCHHHHHHHHHHcCCC
Q psy8528 84 GWLPISAMHYVADFLNLP 101 (240)
Q Consensus 84 G~Lp~~am~~VA~~L~lp 101 (240)
+|+|.+.+..+|+..|+.
T Consensus 1 ~~~p~~~i~ria~~~Gi~ 18 (65)
T smart00803 1 SWLPKETIKDVAESLGIG 18 (65)
T ss_pred CCCCHHHHHHHHHHCCCc
Confidence 467777777777777766
No 146
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=20.76 E-value=86 Score=19.96 Aligned_cols=20 Identities=15% Similarity=0.111 Sum_probs=16.2
Q ss_pred HHHHHHHHcCCChhhHHHHh
Q psy8528 90 AMHYVADFLNLPKMRVYEVA 109 (240)
Q Consensus 90 am~~VA~~L~lp~~~VyeVA 109 (240)
...+||+.|+++...|+...
T Consensus 20 s~~eia~~l~is~~tv~~~~ 39 (58)
T smart00421 20 TNKEIAERLGISEKTVKTHL 39 (58)
T ss_pred CHHHHHHHHCCCHHHHHHHH
Confidence 55789999999999887653
No 147
>CHL00203 fabH 3-oxoacyl-acyl-carrier-protein synthase 3; Provisional
Probab=20.68 E-value=50 Score=30.04 Aligned_cols=53 Identities=25% Similarity=0.384 Sum_probs=37.1
Q ss_pred cCHHHHHHHHHHHcCc----eE---e-ecCCCHHhHHHHHHHHhcCCCCCCCCCCCCCCCc
Q psy8528 144 RNSDAILEVIKKKCNM----ML---E-RQDLEPKDMEQIIDDLKAGKKPAPGPSGYTSGIG 196 (240)
Q Consensus 144 rGs~~Il~~l~~~LgI----mv---~-y~~Ltpe~i~~IL~~lk~g~~p~~gp~g~~~~~~ 196 (240)
.++..+++.+.+.||+ +. . |+++...++--.|+++.+....++|-...+.|+|
T Consensus 253 q~~~~~~~~~~~~lgl~~~k~~~~l~~~Gn~~sasi~~~L~~~~~~g~~~~Gd~vll~~~G 313 (326)
T CHL00203 253 QANKRILEAIANRLSVPNSKMITNLEKYGNTSAASIPLALDEAIQNNKIQPGQIIVLSGFG 313 (326)
T ss_pred CCCHHHHHHHHHHhCCCHHHhhhHHHhhCcHHHHHHHHHHHHHHHhCCCCCCCEEEEEEEc
Confidence 3457788888889998 22 2 9999999988888877554456777644444433
No 148
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=20.62 E-value=1e+02 Score=30.26 Aligned_cols=126 Identities=14% Similarity=0.225 Sum_probs=69.7
Q ss_pred HHHHHHHHHhCCCCCCcccHHHHHHHHHHHcCCCCHHHHHHHHHHcCCChhhHHHHhhhccCCccccCCcccccccccEE
Q psy8528 53 KKRAEAIISIYPVGHERAAVIPLLDLAQRQHGWLPISAMHYVADFLNLPKMRVYEVATFYTMFIRKPIGEERIKSILQYH 132 (240)
Q Consensus 53 ~~~i~~il~~Yp~~~~rsalIplL~~aQ~q~G~Lp~~am~~VA~~L~lp~~~VyeVATFYtmF~~kP~G~~~~~~~~K~~ 132 (240)
.+.+..-|.-..-....-.+...|=.--+..||+.. .++.||+.++++..+|..+...-- +..|.| +.-..
T Consensus 79 ~e~L~~Ql~~~~~~~~~~~ia~~iI~~LD~~GyL~~-~~~eia~~l~~~~~~ve~~l~~iq--~leP~G------IgAr~ 149 (429)
T TIGR02395 79 FEHLLEQLDLQLFTERDRKIALYIIDNLDEDGYLEI-DLEEIADELEVSEEEVEKVLELIQ--RLDPAG------VGARD 149 (429)
T ss_pred HHHHHHHHhccCCCHHHHHHHHHHHHhCCCCCCCCC-CHHHHHHHcCCCHHHHHHHHHHHh--cCCCCc------cCcCC
Confidence 344555554443211222333333333466899995 567799999999999999999865 467888 11223
Q ss_pred EEecCChhhhhcCH---HHHHHHHHHHcCceE--------eecCCCHHhHHHHHHHHhcCCCCCCCC
Q psy8528 133 LNWCTTTPCWLRNS---DAILEVIKKKCNMML--------ERQDLEPKDMEQIIDDLKAGKKPAPGP 188 (240)
Q Consensus 133 I~VC~~t~C~lrGs---~~Il~~l~~~LgImv--------~y~~Ltpe~i~~IL~~lk~g~~p~~gp 188 (240)
++=|--.=..-.+. ......+++.|.... .--+++.+++.++++.++. =.|+||-
T Consensus 150 L~EcLllQl~~~~~~~~~~a~~il~~~le~l~~~~~~~i~~~l~is~~~v~~~~~~I~~-L~P~Pg~ 215 (429)
T TIGR02395 150 LQECLLLQLERLDIDDPELAYNILLEHLELLAEKDFRRLAKKLGLSEEELKEALDLIKS-LSPKPGK 215 (429)
T ss_pred HHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHhccHHHHHHHHCcCHHHHHHHHHHHhC-CCCCCcc
Confidence 33332211111110 011122333332211 1336788999999988875 4688886
No 149
>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein. gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module.
Probab=20.55 E-value=2.3e+02 Score=21.89 Aligned_cols=45 Identities=16% Similarity=0.185 Sum_probs=34.4
Q ss_pred HHHHHHHHhCCCCCCcccHHHHHHHHHHHcCCCCHHHHHHHHHHcCCChhhHHHH
Q psy8528 54 KRAEAIISIYPVGHERAAVIPLLDLAQRQHGWLPISAMHYVADFLNLPKMRVYEV 108 (240)
Q Consensus 54 ~~i~~il~~Yp~~~~rsalIplL~~aQ~q~G~Lp~~am~~VA~~L~lp~~~VyeV 108 (240)
.-+++.++. .++..+...|..+-++.|| + .+|+..||++..++.+
T Consensus 19 ~~l~~~le~----~~~~~~~~~l~~~r~~~gl-S-----qLAe~~GIs~stLs~i 63 (89)
T TIGR02684 19 EYLAQALED----GDPAYIAHALGYIARARGM-T-----QLARKTGLSRESLYKA 63 (89)
T ss_pred HHHHHHHHc----CCHHHHHHHHHHHHHHCCh-H-----HHHHHHCCCHHHHHHH
Confidence 346666665 3567788888899888996 3 3999999999988765
No 150
>PRK09325 coenzyme F420-reducing hydrogenase subunit beta; Validated
Probab=20.53 E-value=70 Score=29.31 Aligned_cols=40 Identities=15% Similarity=0.371 Sum_probs=26.7
Q ss_pred ChhhhhcCHHHHHH------HHHHHcCceEe---ecCCCHHhHHHHHHH
Q psy8528 138 TTPCWLRNSDAILE------VIKKKCNMMLE---RQDLEPKDMEQIIDD 177 (240)
Q Consensus 138 ~t~C~lrGs~~Il~------~l~~~LgImv~---y~~Ltpe~i~~IL~~ 177 (240)
++||+++|-.++.. .+.+.+.++|. .+..+++.+.+.|+.
T Consensus 101 GtPCqI~alr~l~~~~~~~~~~~d~l~~~Igl~C~g~~~~~~~~~~l~~ 149 (282)
T PRK09325 101 GTPCQIQAVRKAQLYPVGMRHVPDKIALIVGIFCMENFPYEGLKTIVED 149 (282)
T ss_pred ccChHHHHHHHHHhccccccccccceeEEEcccCCCCCCHHHHHHHHHH
Confidence 67888888777752 23344444455 777788888777776
No 151
>cd00831 CHS_like Chalcone and stilbene synthases; plant-specific polyketide synthases (PKS) and related enzymes, also called type III PKSs. PKS generate an array of different products, dependent on the nature of the starter molecule. They share a common chemical strategy, after the starter molecule is loaded onto the active site cysteine, a carboxylative condensation reation extends the polyketide chain. Plant-specific PKS are dimeric iterative PKSs, using coenzyme A esters to deliver substrate to the active site, but they differ in the choice of starter molecule and the number of condensation reactions.
Probab=20.41 E-value=59 Score=30.03 Aligned_cols=53 Identities=13% Similarity=0.273 Sum_probs=37.8
Q ss_pred cCHHHHHHHHHHHcCc----eE----e---ecCCCHHhHHHHHHHHhcCCCCCCCCCCCCCCCc
Q psy8528 144 RNSDAILEVIKKKCNM----ML----E---RQDLEPKDMEQIIDDLKAGKKPAPGPSGYTSGIG 196 (240)
Q Consensus 144 rGs~~Il~~l~~~LgI----mv----~---y~~Ltpe~i~~IL~~lk~g~~p~~gp~g~~~~~~ 196 (240)
.|+..+++.+.++||+ +. + ||++...++--.|+.+.+....++|-...+.|.|
T Consensus 288 ~~~~~i~~~v~~~lgl~~~~~~~s~~~l~~~GN~~sasi~~~L~~~~~~g~~~~Gd~vll~~~G 351 (361)
T cd00831 288 PGGRAVLDAVEKALGLSPEDLEASRMVLRRYGNMSSSSVLYVLAYMEAKGRVKRGDRGLLIAFG 351 (361)
T ss_pred CCChHHHHHHHHHcCCCHHHHHHHHHHHHHhCCchhccHHHHHHHHHHhCCCCCCCEEEEEEEc
Confidence 4678899999999998 21 2 9999999998888776654455666544443333
No 152
>PRK14996 TetR family transcriptional regulator; Provisional
Probab=20.09 E-value=1.1e+02 Score=25.27 Aligned_cols=44 Identities=9% Similarity=0.087 Sum_probs=32.4
Q ss_pred CcccHHHHHHHHHHHcCCCCHHHHHHHHHHcCCChhhHHHHhhhccCCccc
Q psy8528 68 ERAAVIPLLDLAQRQHGWLPISAMHYVADFLNLPKMRVYEVATFYTMFIRK 118 (240)
Q Consensus 68 ~rsalIplL~~aQ~q~G~Lp~~am~~VA~~L~lp~~~VyeVATFYtmF~~k 118 (240)
+|..+|..-..+=.++|| ..-.|+.||+..|++.. +||.+|..|
T Consensus 9 ~R~~Il~aA~~lf~e~G~-~~tSi~~Ia~~aGvsk~------~lY~~F~sK 52 (192)
T PRK14996 9 RREVILQAAMRVALAEGF-AAMTVRRIASEAQVAAG------QVHHHFSSA 52 (192)
T ss_pred HHHHHHHHHHHHHHhcCh-hhccHHHHHHHhCCCcH------HHHHHcCCH
Confidence 456677666666667897 66789999999999986 556666544
Done!