Query 022828
Match_columns 291
No_of_seqs 249 out of 1673
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 06:26:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022828.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022828hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3196 NADH:ubiquinone oxidor 100.0 1.1E-68 2.4E-73 473.7 18.8 214 66-291 20-233 (233)
2 PRK12373 NADH dehydrogenase su 100.0 2.2E-55 4.9E-60 425.8 22.0 194 70-280 5-201 (400)
3 COG1905 NuoE NADH:ubiquinone o 100.0 2E-50 4.3E-55 350.0 15.7 158 83-253 3-160 (160)
4 PRK07571 bidirectional hydroge 100.0 1.5E-48 3.1E-53 341.7 19.1 158 80-250 11-168 (169)
5 PRK05988 formate dehydrogenase 100.0 4.2E-48 9.2E-53 334.6 18.0 152 86-250 4-155 (156)
6 PRK07539 NADH dehydrogenase su 100.0 2E-47 4.3E-52 328.8 17.2 153 85-250 2-154 (154)
7 TIGR01958 nuoE_fam NADH-quinon 100.0 1.1E-46 2.4E-51 322.0 16.3 146 93-249 2-147 (148)
8 PF01257 2Fe-2S_thioredx: Thio 100.0 1.3E-46 2.7E-51 320.7 14.7 145 93-250 1-145 (145)
9 cd03081 TRX_Fd_NuoE_FDH_gamma 99.9 1E-23 2.2E-28 163.2 9.1 80 160-249 1-80 (80)
10 cd03083 TRX_Fd_NuoE_hoxF TRX-l 99.9 1.1E-22 2.5E-27 157.3 9.1 80 160-249 1-80 (80)
11 cd03064 TRX_Fd_NuoE TRX-like [ 99.8 4.3E-21 9.2E-26 147.4 9.5 80 160-249 1-80 (80)
12 cd03082 TRX_Fd_NuoE_W_FDH_beta 99.7 3.9E-18 8.6E-23 130.2 8.1 70 161-248 2-71 (72)
13 cd02980 TRX_Fd_family Thioredo 99.7 1.2E-17 2.7E-22 125.8 8.4 76 161-248 1-76 (77)
14 cd03063 TRX_Fd_FDH_beta TRX-li 99.5 2.8E-14 6.1E-19 114.2 8.5 78 162-251 2-79 (92)
15 cd03062 TRX_Fd_Sucrase TRX-lik 99.4 1.8E-12 3.9E-17 104.0 8.9 80 161-252 2-85 (97)
16 COG3411 Ferredoxin [Energy pro 99.0 4.2E-10 9.1E-15 84.5 5.3 52 199-258 2-54 (64)
17 PF06999 Suc_Fer-like: Sucrase 97.9 4.9E-05 1.1E-09 68.7 9.2 92 154-257 126-224 (230)
18 PF07845 DUF1636: Protein of u 97.9 4.9E-05 1.1E-09 63.5 7.3 79 173-260 18-97 (116)
19 COG5469 Predicted metal-bindin 97.7 0.00021 4.5E-09 61.3 7.9 83 155-248 12-105 (143)
20 PF07293 DUF1450: Protein of u 96.3 0.016 3.5E-07 45.4 6.7 65 162-249 4-71 (78)
21 PRK13669 hypothetical protein; 94.1 0.19 4.1E-06 39.6 6.2 64 162-248 4-70 (78)
22 PF14297 DUF4373: Domain of un 82.1 4.6 9.9E-05 31.4 5.8 67 89-157 10-77 (87)
23 TIGR02435 CobG precorrin-3B sy 81.0 8.5 0.00018 37.9 8.6 86 122-214 266-376 (390)
24 cd00086 homeodomain Homeodomai 78.9 4.1 8.8E-05 28.3 4.2 37 108-145 10-46 (59)
25 PF00046 Homeobox: Homeobox do 78.6 3.4 7.5E-05 28.9 3.8 35 109-144 11-45 (57)
26 PF10820 DUF2543: Protein of u 75.7 2.3 5E-05 33.1 2.3 33 122-154 47-79 (81)
27 smart00389 HOX Homeodomain. DN 72.8 7.4 0.00016 26.9 4.2 37 108-145 10-46 (56)
28 PRK14996 TetR family transcrip 65.8 3.4 7.4E-05 35.5 1.5 45 105-158 9-54 (192)
29 PLN02431 ferredoxin--nitrite r 65.2 36 0.00079 35.7 9.1 52 160-214 465-519 (587)
30 PRK09480 slmA division inhibit 61.8 5.6 0.00012 33.8 2.0 44 105-157 11-55 (194)
31 COG4759 Uncharacterized protei 61.7 21 0.00046 34.8 6.0 79 155-247 126-208 (316)
32 PRK09567 nirA ferredoxin-nitri 58.1 42 0.0009 35.2 8.0 50 161-213 445-497 (593)
33 PRK13504 sulfite reductase sub 57.9 23 0.00049 36.8 6.0 74 137-213 400-485 (569)
34 TIGR02066 dsrB sulfite reducta 56.8 11 0.00023 37.0 3.2 110 84-215 40-159 (341)
35 PRK09566 nirA ferredoxin-nitri 54.8 45 0.00098 34.1 7.5 89 122-213 331-444 (513)
36 TIGR02366 DHAK_reg probable di 54.2 8.9 0.00019 32.3 2.0 40 109-157 8-48 (176)
37 PF13404 HTH_AsnC-type: AsnC-t 52.2 15 0.00033 25.1 2.6 31 110-145 6-36 (42)
38 PF00440 TetR_N: Bacterial reg 50.4 9.8 0.00021 26.0 1.4 36 112-156 5-40 (47)
39 PF01726 LexA_DNA_bind: LexA D 49.4 17 0.00036 27.2 2.6 37 106-145 8-45 (65)
40 PRK13756 tetracycline represso 48.9 15 0.00032 33.0 2.7 43 106-157 6-49 (205)
41 PLN00178 sulfite reductase 48.8 78 0.0017 33.6 8.3 90 122-213 415-534 (623)
42 TIGR03209 P21_Cbot clostridium 47.0 26 0.00056 28.6 3.6 46 88-144 96-141 (142)
43 TIGR01565 homeo_ZF_HD homeobox 45.9 40 0.00088 24.9 4.1 22 122-143 24-49 (58)
44 PF09999 DUF2240: Uncharacteri 45.7 38 0.00083 29.5 4.6 75 66-144 57-141 (144)
45 PRK12529 RNA polymerase sigma 45.6 29 0.00062 29.7 3.8 47 88-145 116-162 (178)
46 PRK09047 RNA polymerase factor 45.3 34 0.00074 28.1 4.2 47 88-145 95-141 (161)
47 COG0155 CysI Sulfite reductase 45.2 88 0.0019 32.5 7.9 87 160-250 376-480 (510)
48 TIGR02374 nitri_red_nirB nitri 44.7 1.9E+02 0.0041 31.3 10.6 140 83-249 563-724 (785)
49 PRK14989 nitrite reductase sub 44.3 2.2E+02 0.0047 31.4 11.0 144 84-250 575-737 (847)
50 PHA01812 hypothetical protein 41.9 12 0.00026 30.7 0.8 44 65-115 5-50 (122)
51 PF04539 Sigma70_r3: Sigma-70 41.0 36 0.00077 25.2 3.3 32 116-150 13-44 (78)
52 PRK00767 transcriptional regul 40.0 20 0.00044 30.4 2.0 44 105-157 10-54 (197)
53 PF13309 HTH_22: HTH domain 39.5 54 0.0012 24.3 4.0 54 91-145 5-61 (64)
54 TIGR03384 betaine_BetI transcr 39.5 22 0.00047 29.9 2.1 43 106-157 10-53 (189)
55 PF08281 Sigma70_r4_2: Sigma-7 38.9 28 0.00061 24.0 2.3 44 91-145 2-45 (54)
56 PRK09642 RNA polymerase sigma 38.4 51 0.0011 27.3 4.2 48 88-146 95-142 (160)
57 COG1309 AcrR Transcriptional r 37.3 21 0.00045 28.2 1.6 29 122-157 29-57 (201)
58 PRK09975 DNA-binding transcrip 36.8 25 0.00054 30.4 2.1 44 106-157 13-56 (213)
59 PF06056 Terminase_5: Putative 36.4 36 0.00079 24.9 2.6 30 128-157 15-44 (58)
60 PRK12536 RNA polymerase sigma 36.1 50 0.0011 28.2 3.9 48 88-146 118-165 (181)
61 PRK12530 RNA polymerase sigma 35.2 54 0.0012 28.4 4.0 45 91-146 126-170 (189)
62 TIGR03613 RutR pyrimidine util 34.9 25 0.00055 30.1 1.9 43 106-157 10-53 (202)
63 PRK10668 DNA-binding transcrip 34.2 29 0.00062 30.1 2.1 43 106-157 13-56 (215)
64 PRK09649 RNA polymerase sigma 34.0 56 0.0012 28.2 3.9 48 88-146 119-166 (185)
65 PRK11640 putative transcriptio 33.5 31 0.00066 30.2 2.2 39 109-156 6-45 (191)
66 PRK12543 RNA polymerase sigma 33.2 65 0.0014 27.4 4.1 50 85-145 103-152 (179)
67 TIGR02983 SigE-fam_strep RNA p 32.9 66 0.0014 26.6 4.0 50 86-146 97-146 (162)
68 PRK12525 RNA polymerase sigma 32.9 61 0.0013 27.3 3.9 47 88-145 107-153 (168)
69 PF12728 HTH_17: Helix-turn-he 32.7 36 0.00079 23.2 2.0 20 129-148 4-23 (51)
70 PF13700 DUF4158: Domain of un 32.5 1E+02 0.0022 26.4 5.2 55 82-142 24-85 (166)
71 smart00027 EH Eps15 homology d 32.5 88 0.0019 24.2 4.4 50 82-147 1-50 (96)
72 TIGR02989 Sig-70_gvs1 RNA poly 32.3 65 0.0014 26.4 3.9 49 87-146 99-147 (159)
73 PRK11202 DNA-binding transcrip 32.1 26 0.00057 30.6 1.5 43 106-157 13-57 (203)
74 PRK07037 extracytoplasmic-func 32.0 63 0.0014 26.7 3.8 47 88-145 98-144 (163)
75 PF14338 Mrr_N: Mrr N-terminal 31.9 75 0.0016 24.7 3.9 39 107-145 4-42 (92)
76 PF13384 HTH_23: Homeodomain-l 31.5 37 0.00081 22.9 1.9 23 128-150 19-41 (50)
77 PRK12523 RNA polymerase sigma 31.2 68 0.0015 27.1 3.9 48 88-146 108-155 (172)
78 TIGR01764 excise DNA binding d 30.5 42 0.00091 21.9 2.0 19 129-147 4-22 (49)
79 TIGR02041 CysI sulfite reducta 30.4 66 0.0014 33.2 4.3 74 137-213 384-468 (541)
80 PRK09645 RNA polymerase sigma 30.3 68 0.0015 26.9 3.7 45 90-145 109-153 (173)
81 PRK12528 RNA polymerase sigma 30.3 73 0.0016 26.4 3.9 46 89-145 103-148 (161)
82 PF14174 YycC: YycC-like prote 30.3 49 0.0011 24.2 2.3 21 124-144 6-26 (53)
83 PF13443 HTH_26: Cro/C1-type H 30.2 35 0.00075 24.1 1.6 24 122-145 36-59 (63)
84 PF13518 HTH_28: Helix-turn-he 29.5 71 0.0015 21.4 3.1 25 128-152 14-38 (52)
85 PRK12534 RNA polymerase sigma 29.2 75 0.0016 27.1 3.8 49 87-146 125-173 (187)
86 TIGR02959 SigZ RNA polymerase 29.2 74 0.0016 27.0 3.8 48 88-146 89-136 (170)
87 PF15508 NAAA-beta: beta subun 29.0 1.8E+02 0.0039 22.9 5.7 44 108-151 48-94 (95)
88 PRK15008 HTH-type transcriptio 28.8 38 0.00082 29.7 2.0 44 106-158 20-64 (212)
89 PF06373 CART: Cocaine and amp 28.8 12 0.00027 29.0 -1.0 26 1-27 44-69 (73)
90 PRK12527 RNA polymerase sigma 28.7 84 0.0018 26.0 4.0 46 89-145 95-140 (159)
91 cd01782 AF6_RA_repeat1 Ubiquit 28.3 78 0.0017 26.6 3.6 58 142-205 19-76 (112)
92 PRK12520 RNA polymerase sigma 28.2 84 0.0018 27.0 4.0 46 90-146 122-167 (191)
93 KOG3769 Ribonuclease III domai 28.2 60 0.0013 31.9 3.3 36 96-139 135-170 (333)
94 PRK12516 RNA polymerase sigma 28.1 79 0.0017 27.5 3.8 47 88-145 105-151 (187)
95 KOG1719 Dual specificity phosp 28.0 1.6E+02 0.0036 26.5 5.7 68 86-155 91-172 (183)
96 COG1595 RpoE DNA-directed RNA 27.9 1E+02 0.0022 26.3 4.5 49 87-146 115-163 (182)
97 PRK12537 RNA polymerase sigma 27.9 79 0.0017 27.0 3.8 45 90-145 124-168 (182)
98 TIGR02943 Sig70_famx1 RNA poly 27.9 86 0.0019 27.1 4.0 47 88-145 120-166 (188)
99 PRK12532 RNA polymerase sigma 27.8 82 0.0018 27.1 3.9 47 89-146 126-172 (195)
100 PF04967 HTH_10: HTH DNA bindi 27.5 74 0.0016 23.1 2.9 33 111-145 7-42 (53)
101 PRK12533 RNA polymerase sigma 27.4 73 0.0016 28.7 3.6 49 87-146 122-170 (216)
102 PF09339 HTH_IclR: IclR helix- 27.4 43 0.00093 23.2 1.7 36 109-148 5-40 (52)
103 PF04214 DUF411: Protein of un 27.0 1.3E+02 0.0028 23.3 4.3 42 180-248 10-51 (70)
104 TIGR03044 PS_II_psb27 photosys 26.3 93 0.002 27.0 3.8 82 65-188 45-126 (135)
105 PRK12512 RNA polymerase sigma 26.2 1.2E+02 0.0027 25.6 4.7 49 87-146 119-167 (184)
106 PRK06759 RNA polymerase factor 25.8 95 0.0021 25.3 3.7 48 88-146 95-142 (154)
107 PF04659 Arch_fla_DE: Archaeal 25.8 1.9E+02 0.0041 23.6 5.4 42 90-137 22-63 (99)
108 PRK12524 RNA polymerase sigma 25.7 91 0.002 27.0 3.8 48 88-146 125-172 (196)
109 PRK12545 RNA polymerase sigma 25.6 91 0.002 27.3 3.8 44 91-145 131-174 (201)
110 PF02796 HTH_7: Helix-turn-hel 25.6 50 0.0011 22.5 1.7 19 128-146 23-41 (45)
111 PF07638 Sigma70_ECF: ECF sigm 25.3 97 0.0021 26.9 3.9 21 122-146 151-171 (185)
112 TIGR02985 Sig70_bacteroi1 RNA 25.2 1E+02 0.0023 24.8 3.9 50 87-147 101-150 (161)
113 PRK06811 RNA polymerase factor 25.2 1E+02 0.0022 26.5 3.9 48 88-146 120-167 (189)
114 PRK09648 RNA polymerase sigma 24.7 1.1E+02 0.0023 26.2 4.0 48 88-146 128-175 (189)
115 PRK12542 RNA polymerase sigma 24.7 1E+02 0.0023 26.2 3.9 46 90-146 113-158 (185)
116 PF09012 FeoC: FeoC like trans 24.6 49 0.0011 24.4 1.6 58 109-176 2-62 (69)
117 TIGR02947 SigH_actino RNA poly 24.5 59 0.0013 28.0 2.4 46 90-146 122-167 (193)
118 PRK12522 RNA polymerase sigma 24.3 1.1E+02 0.0025 25.6 4.0 49 86-145 106-154 (173)
119 KOG3325 Membrane coat complex 24.3 1.3E+02 0.0028 27.0 4.4 65 148-212 67-140 (183)
120 PRK12547 RNA polymerase sigma 24.1 1.1E+02 0.0023 25.7 3.8 46 89-145 102-147 (164)
121 PRK09651 RNA polymerase sigma 24.1 88 0.0019 26.5 3.3 48 88-146 108-155 (172)
122 PRK12514 RNA polymerase sigma 24.1 1.1E+02 0.0024 25.8 3.9 47 88-145 118-164 (179)
123 PRK13919 putative RNA polymera 24.0 1.1E+02 0.0023 26.0 3.9 46 89-145 125-170 (186)
124 PRK09637 RNA polymerase sigma 24.0 1.1E+02 0.0023 26.4 3.8 48 88-146 95-142 (181)
125 TIGR02950 SigM_subfam RNA poly 23.5 69 0.0015 26.1 2.5 47 89-146 95-141 (154)
126 TIGR02999 Sig-70_X6 RNA polyme 22.9 1.3E+02 0.0027 25.4 4.1 44 91-145 123-169 (183)
127 PRK12511 RNA polymerase sigma 22.8 1.1E+02 0.0025 26.4 3.8 47 89-146 101-147 (182)
128 COG2920 DsrC Dissimilatory sul 22.8 1.4E+02 0.003 25.1 4.0 49 125-190 26-79 (111)
129 PF01978 TrmB: Sugar-specific 22.6 69 0.0015 23.2 2.1 23 127-149 23-45 (68)
130 PRK01381 Trp operon repressor; 22.5 2.3E+02 0.0049 23.3 5.2 59 105-188 37-95 (99)
131 PF13744 HTH_37: Helix-turn-he 22.4 98 0.0021 23.5 3.0 36 107-147 17-52 (80)
132 PRK09641 RNA polymerase sigma 22.1 1.5E+02 0.0032 24.9 4.4 45 91-146 128-172 (187)
133 PF10668 Phage_terminase: Phag 22.1 62 0.0013 24.2 1.7 17 129-145 25-41 (60)
134 PRK11924 RNA polymerase sigma 22.1 1.4E+02 0.0031 24.5 4.2 50 87-147 113-162 (179)
135 TIGR03001 Sig-70_gmx1 RNA poly 22.1 1.1E+02 0.0024 28.1 3.8 46 89-145 151-196 (244)
136 PRK09646 RNA polymerase sigma 22.0 1.1E+02 0.0024 26.4 3.6 47 88-145 131-177 (194)
137 PRK09647 RNA polymerase sigma 21.8 1.2E+02 0.0027 26.7 3.9 47 89-146 128-174 (203)
138 COG3531 Predicted protein-disu 21.7 1.1E+02 0.0023 28.5 3.5 53 91-145 91-147 (212)
139 TIGR02952 Sig70_famx2 RNA poly 21.6 1.3E+02 0.0027 24.9 3.7 48 88-146 111-158 (170)
140 PRK12544 RNA polymerase sigma 21.6 1.3E+02 0.0027 26.8 3.9 44 91-145 140-183 (206)
141 TIGR02937 sigma70-ECF RNA poly 21.3 1.5E+02 0.0032 23.1 3.9 49 88-147 99-147 (158)
142 TIGR02948 SigW_bacill RNA poly 21.2 1.3E+02 0.0029 25.2 3.9 46 90-146 127-172 (187)
143 PRK12535 RNA polymerase sigma 21.1 1.3E+02 0.0029 26.3 3.9 47 88-145 122-168 (196)
144 PRK12538 RNA polymerase sigma 21.0 1.1E+02 0.0024 27.8 3.5 48 88-146 160-207 (233)
145 PRK09644 RNA polymerase sigma 20.7 1.6E+02 0.0036 24.4 4.3 48 88-146 97-144 (165)
146 PRK09636 RNA polymerase sigma 20.6 1.6E+02 0.0034 27.5 4.5 47 90-147 106-152 (293)
147 TIGR02435 CobG precorrin-3B sy 20.6 4.7E+02 0.01 25.7 8.0 112 82-214 26-145 (390)
148 PRK09415 RNA polymerase factor 20.4 1.4E+02 0.003 25.4 3.8 48 87-145 115-162 (179)
149 cd02950 TxlA TRX-like protein 20.4 3.7E+02 0.008 22.4 6.3 42 214-258 77-118 (142)
150 PF13936 HTH_38: Helix-turn-he 20.3 70 0.0015 21.8 1.6 21 127-147 21-41 (44)
151 PRK07408 RNA polymerase sigma 20.2 1.4E+02 0.0031 27.4 4.1 51 85-146 189-239 (256)
No 1
>KOG3196 consensus NADH:ubiquinone oxidoreductase, NDUFV2/24 kD subunit [Energy production and conversion]
Probab=100.00 E-value=1.1e-68 Score=473.73 Aligned_cols=214 Identities=58% Similarity=1.004 Sum_probs=210.4
Q ss_pred ccceeccCCCCCCCCCCCCCChhhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhh
Q 022828 66 LELCKHLDSPDNNPDLPWKFSDTNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYE 145 (291)
Q Consensus 66 ~~~~~h~~~~~~~~~~~~~~~~~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~ 145 (291)
+.|++|||||+||++++|+|++||.+++++|++.||..+++++|||+|+++|+|+ ||||..+|++||+.++||+++|||
T Consensus 20 ~~l~~h~dt~en~~~~~feFt~eN~~rvkAIla~YP~~~k~~AliPLLDLAQRQ~-GWlpiSAM~~VA~~~~v~~mrvye 98 (233)
T KOG3196|consen 20 QPLFVHRDTPENNPDLPFEFTPENQKRVKAILAIYPEGHKAGALIPLLDLAQRQH-GWLPISAMNEVAEVLEVPPMRVYE 98 (233)
T ss_pred cccccccCCcccCCCCCcccCHHHHHHHHHHHHHCcccccccchhhhhHHHHHhc-CCcCHHHHHHHHHHHcCChHHHHH
Confidence 8999999999999999999999999999999999999999999999999999998 899999999999999999999999
Q ss_pred hhhhhcccccccCCceEEEEcCCCcccccChHHHHHHHHHHhCCCCCcccCCCcEEEEEecCCCCCCCCCeEEEcccCCC
Q 022828 146 VATFYSMFNRSKVGKYHLLVCGTTPCMVRGSREIEDALLKHLGVKRNEVTKDGLFSVGEMECMGCCVNAPMITVADYSNG 225 (291)
Q Consensus 146 VaTFY~~f~~~P~gK~~I~VC~gtsC~~~Gs~~lleaL~~~Lgi~~Gett~DG~ftL~~v~CLG~C~~aPvV~Vnd~~~G 225 (291)
||+||+||+++|+|||||+||++++|+++|+++|.+++++.||++.|+||+|+.|+|++++|||+|.+||+|.|||
T Consensus 99 vatfYtmf~r~p~gKy~v~VC~ttpC~lrg~d~i~ea~~k~lgi~~Gett~d~~Ftl~e~eClGaCvnaPmi~IND---- 174 (233)
T KOG3196|consen 99 VATFYTMFFRKPVGKYHVQVCTTTPCMLRGSDDILEACKKQLGIKVGETTKDGLFTLEEVECLGACVNAPMIAIND---- 174 (233)
T ss_pred HHHHHHHhhccCCCCceEEEecCcHHhhhccHHHHHHHHHHhCccccccccccceeeecchhhhhhccCceeeecc----
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred CCCccceEecCCChhhHHHHHHHHHcCCCCCCCCCCCCCccCCCCCCCccccCCCCCCCCCCCCCC
Q 022828 226 SEGYTYNYYEDVTPKRVIEIVEMLRRGEKLPPGTQNPKRIKSGPEGGNTTLLSEPKPPPCRDLDAC 291 (291)
Q Consensus 226 ~~g~~~~~Y~~vTpE~V~~ILe~l~~G~~~~~g~~~~~r~~~~p~~g~~~l~~~~~~~~~~~~~~~ 291 (291)
++|+++|++++.+|+++|++|+.|++||++ +|-++||.||+|||.++|+||+|+...+|
T Consensus 175 ------~yyedlt~k~l~eIle~L~~~k~pp~Gprn-gR~a~eP~Gg~tsL~~~P~~PgF~~q~~~ 233 (233)
T KOG3196|consen 175 ------DYYEDLTPKKLVEILEDLKAGKKPPAGPRN-GRFASEPKGGLTSLKEEPKGPGFGLQAAL 233 (233)
T ss_pred ------hhhccCCHHHHHHHHHHHhcCCCCCCCCCC-CccccCCCCCccccccCCCCCCchhcccC
Confidence 899999999999999999999999999999 69999999999999999999999988765
No 2
>PRK12373 NADH dehydrogenase subunit E; Provisional
Probab=100.00 E-value=2.2e-55 Score=425.84 Aligned_cols=194 Identities=43% Similarity=0.764 Sum_probs=185.9
Q ss_pred eccCCCCCCCCCCCCCChhhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhhhhh
Q 022828 70 KHLDSPDNNPDLPWKFSDTNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEVATF 149 (291)
Q Consensus 70 ~h~~~~~~~~~~~~~~~~~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~VaTF 149 (291)
.|.+.|. .|.|+++++++|++||++||.++++++|||+||++|+++ ||||+++|++||+.|+||+++||+|+||
T Consensus 5 ~~~~~p~-----~f~f~~e~~~~i~~ii~~yp~~~~~salIplL~~~Qe~~-GyIp~~ai~~VAe~Lgvp~~~V~eVATF 78 (400)
T PRK12373 5 LHEDQPD-----SFAFTPENAAWAEKQITKYPEGRQASAVIPLLMRAQEQE-GWVTRAAIEKVADMLDMAYIRVLEVATF 78 (400)
T ss_pred ccccCCc-----cccCCHHHHHHHHHHHHHCCCccCHHHHHHHHHHHHHHc-CCCCHHHHHHHHHHhCCCHHHHHHHHHH
Confidence 3666666 899999999999999999997678999999999999986 9999999999999999999999999999
Q ss_pred hcccccccCCc-eEEEEcCCCcccccChHHHHHHHHHHhCCCCCcccCCCcEEEEEecCCCCCCCCCeEEEcccCCCCCC
Q 022828 150 YSMFNRSKVGK-YHLLVCGTTPCMVRGSREIEDALLKHLGVKRNEVTKDGLFSVGEMECMGCCVNAPMITVADYSNGSEG 228 (291)
Q Consensus 150 Y~~f~~~P~gK-~~I~VC~gtsC~~~Gs~~lleaL~~~Lgi~~Gett~DG~ftL~~v~CLG~C~~aPvV~Vnd~~~G~~g 228 (291)
|+||+++|+|| |+|+||++++|+++|+++|+++|+++||++.|+||.||+|+|+++.|||+|++||+|+||+
T Consensus 79 YtmF~~~P~Gk~~~I~VC~~t~C~l~Ga~~ll~~le~~Lgik~GeTT~DG~FTLe~veCLGaC~~APv~~Ind------- 151 (400)
T PRK12373 79 YTQFQLQPVGTRAHIQVCGTTPCMLRGSEALMAVCKSKIHAHPHELNADGTLSWEEVECLGACVNAPMVQIGK------- 151 (400)
T ss_pred hhcccccCCCCceEEEEcCChHHHhCChHHHHHHHHHHhCCCCCCcCCCCeEEEEeeeecCccCCCCeEEECC-------
Confidence 99999999998 9999999999999999999999999999999999999999999999999999999999998
Q ss_pred ccceEecCCChhhHHHHHHHHHcCCCCC--CCCCCCCCccCCCCCCCccccCCC
Q 022828 229 YTYNYYEDVTPKRVIEIVEMLRRGEKLP--PGTQNPKRIKSGPEGGNTTLLSEP 280 (291)
Q Consensus 229 ~~~~~Y~~vTpE~V~~ILe~l~~G~~~~--~g~~~~~r~~~~p~~g~~~l~~~~ 280 (291)
++|++||++++.+||++++.|++++ +|||+ +|..++|.||+|||+++.
T Consensus 152 ---~~y~~LTpe~v~~IL~~l~ag~~~~~~~g~~~-~r~~~~p~~g~t~l~~~~ 201 (400)
T PRK12373 152 ---DYYEDLTPERLEEIIDAFAAGKGPVVKPGPQI-GRYASEPAGGLTSLTEEA 201 (400)
T ss_pred ---EEeCCCCHHHHHHHHHHHhCCCCCCCCCCCCC-CccccCCCCCCcccCCCC
Confidence 8999999999999999999999887 99998 899999999999999854
No 3
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=100.00 E-value=2e-50 Score=350.01 Aligned_cols=158 Identities=42% Similarity=0.798 Sum_probs=152.8
Q ss_pred CCCChhhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhhhhhhcccccccCCceE
Q 022828 83 WKFSDTNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEVATFYSMFNRSKVGKYH 162 (291)
Q Consensus 83 ~~~~~~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~VaTFY~~f~~~P~gK~~ 162 (291)
|.|++++.+.+++++++|| ++|++|||+||++|+++ ||||++++++||+.|+||+++||||+|||+||+++|+|||+
T Consensus 3 ~~~~~~~~~~~~~~i~~yp--~~rsAlip~L~~aQ~~~-G~l~~~ai~~iA~~L~i~~~~v~~VaTFY~~f~~~P~Gr~~ 79 (160)
T COG1905 3 FAFSAENLELIEAIIAKYP--DKRSALIPLLHIAQEQF-GWLPPEAIEEIADMLGIPRARVYGVATFYTQFFLKPVGRHH 79 (160)
T ss_pred cccchhHHHHHHHHHHHCc--cchhHHHHHHHHHHHHh-CCCCHHHHHHHHHHhCCCHHHheeeeeeehhhccCcCCCeE
Confidence 4489999999999999999 48999999999999997 99999999999999999999999999999999999999999
Q ss_pred EEEcCCCcccccChHHHHHHHHHHhCCCCCcccCCCcEEEEEecCCCCCCCCCeEEEcccCCCCCCccceEecCCChhhH
Q 022828 163 LLVCGTTPCMVRGSREIEDALLKHLGVKRNEVTKDGLFSVGEMECMGCCVNAPMITVADYSNGSEGYTYNYYEDVTPKRV 242 (291)
Q Consensus 163 I~VC~gtsC~~~Gs~~lleaL~~~Lgi~~Gett~DG~ftL~~v~CLG~C~~aPvV~Vnd~~~G~~g~~~~~Y~~vTpE~V 242 (291)
|+||++++|+++|+++|+++|+++|++++|+||.||+|+|++++|||+|++||+|+||| ++|+++|||++
T Consensus 80 i~VC~~t~C~l~Gs~~l~~~l~~~lgi~~gett~DG~ftl~~v~ClGaC~~AP~vmind----------~~~~~lt~e~l 149 (160)
T COG1905 80 IRVCTGTACHLKGSEALLKALEKKLGIKPGETTADGKFTLEPVECLGACGQAPVVMIND----------DVYGRLTPEKL 149 (160)
T ss_pred EEEeCCcHHhhcChHHHHHHHHHHhCCCCCCcCCCCeEEEeeeeeecccccCCEEEECC----------chhccCCHHHH
Confidence 99999999999999999999999999999999999999999999999999999999998 79999999999
Q ss_pred HHHHHHHHcCC
Q 022828 243 IEIVEMLRRGE 253 (291)
Q Consensus 243 ~~ILe~l~~G~ 253 (291)
.+||+++++++
T Consensus 150 ~eil~~~~~~~ 160 (160)
T COG1905 150 EEILEKLKAKK 160 (160)
T ss_pred HHHHHHHhcCC
Confidence 99999988653
No 4
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=100.00 E-value=1.5e-48 Score=341.68 Aligned_cols=158 Identities=30% Similarity=0.469 Sum_probs=152.3
Q ss_pred CCCCCCChhhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhhhhhhcccccccCC
Q 022828 80 DLPWKFSDTNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEVATFYSMFNRSKVG 159 (291)
Q Consensus 80 ~~~~~~~~~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~VaTFY~~f~~~P~g 159 (291)
.....++++.++++++||++||. ++++|||+||++|+++ ||||++++++||+.||||+++||||+|||+||+++|+|
T Consensus 11 ~~~~~~~~~~~~~i~~ii~~~~~--~~~~li~~L~~iQ~~~-GyIp~e~~~~iA~~l~v~~a~V~gVatFY~~f~~~P~G 87 (169)
T PRK07571 11 SATHPSGDKRFKVLEATMKRNQY--RQDALIEVLHKAQELF-GYLERDLLLYVARQLKLPLSRVYGVATFYHLFSLKPSG 87 (169)
T ss_pred CccCcCcHHHHHHHHHHHHHcCC--CHHHHHHHHHHHHHHc-CCCCHHHHHHHHHHhCcCHHHHHHHHHHccccCcCCCC
Confidence 44567999999999999999985 7999999999999976 99999999999999999999999999999999999999
Q ss_pred ceEEEEcCCCcccccChHHHHHHHHHHhCCCCCcccCCCcEEEEEecCCCCCCCCCeEEEcccCCCCCCccceEecCCCh
Q 022828 160 KYHLLVCGTTPCMVRGSREIEDALLKHLGVKRNEVTKDGLFSVGEMECMGCCVNAPMITVADYSNGSEGYTYNYYEDVTP 239 (291)
Q Consensus 160 K~~I~VC~gtsC~~~Gs~~lleaL~~~Lgi~~Gett~DG~ftL~~v~CLG~C~~aPvV~Vnd~~~G~~g~~~~~Y~~vTp 239 (291)
||+|+||+|++|+++|+++|+++|+++||++.|++|+||+|+|+.+.|+|+|+.||+|+||+ ++|++||+
T Consensus 88 k~~I~VC~g~aC~~~G~~~ll~~l~~~Lgi~~gett~DG~ftL~~~~ClG~C~~AP~~~Vn~----------~~~~~lt~ 157 (169)
T PRK07571 88 EHTCVVCTGTACYVKGSAAILEDLENELGIKAGETTADGKLSLLTARCLGACGIAPAVVFDG----------KVAGKQTP 157 (169)
T ss_pred CEEEEEcCChHHHHCCcHHHHHHHHHHhCCCCCCcCCCCeEEEEEecccCccCCCCeEEECC----------EEeCCCCH
Confidence 99999999999999999999999999999999999999999999999999999999999997 89999999
Q ss_pred hhHHHHHHHHH
Q 022828 240 KRVIEIVEMLR 250 (291)
Q Consensus 240 E~V~~ILe~l~ 250 (291)
+++++||++++
T Consensus 158 e~v~~il~~~~ 168 (169)
T PRK07571 158 ESVLEKVQGWL 168 (169)
T ss_pred HHHHHHHHHHh
Confidence 99999999885
No 5
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=100.00 E-value=4.2e-48 Score=334.63 Aligned_cols=152 Identities=21% Similarity=0.442 Sum_probs=146.4
Q ss_pred ChhhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhhhhhhcccccccCCceEEEE
Q 022828 86 SDTNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEVATFYSMFNRSKVGKYHLLV 165 (291)
Q Consensus 86 ~~~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~VaTFY~~f~~~P~gK~~I~V 165 (291)
++...+++++|+++|+. ++++|||+||++|+++ ||||+++|++||+.|+||+++||+|+|||+||+++|+|||+|+|
T Consensus 4 ~~~~~~~i~~ii~~y~~--~~~~li~~L~~vQ~~~-G~Ip~e~~~~iA~~l~v~~~~V~~vatFY~~f~~~p~Gk~~I~V 80 (156)
T PRK05988 4 EPWDAARIAAIIAEHKH--LEGALLPILHAIQDEF-GYVPEDAVPVIAEALNLSRAEVHGVITFYHDFRTHPPGRHVLKL 80 (156)
T ss_pred chhHHHHHHHHHHHcCC--CHHHHHHHHHHHHHHc-CCCCHHHHHHHHHHhCCCHHHHHHHHHHhhccCCCCCCCEEEEE
Confidence 45677789999999985 7899999999999986 99999999999999999999999999999999999999999999
Q ss_pred cCCCcccccChHHHHHHHHHHhCCCCCcccCCCcEEEEEecCCCCCCCCCeEEEcccCCCCCCccceEecCCChhhHHHH
Q 022828 166 CGTTPCMVRGSREIEDALLKHLGVKRNEVTKDGLFSVGEMECMGCCVNAPMITVADYSNGSEGYTYNYYEDVTPKRVIEI 245 (291)
Q Consensus 166 C~gtsC~~~Gs~~lleaL~~~Lgi~~Gett~DG~ftL~~v~CLG~C~~aPvV~Vnd~~~G~~g~~~~~Y~~vTpE~V~~I 245 (291)
|+|++|+++|+++|+++|+++||++.|+||+||+|+|+++.|+|+|+.||+|+||+ ++|++||++++++|
T Consensus 81 C~~~~C~~~G~~~ll~~l~~~Lgi~~gett~Dg~ftL~~~~ClG~C~~aP~~~in~----------~~~~~lt~~~~~~i 150 (156)
T PRK05988 81 CRAEACQAMGGDALAAHAKARLGIDFHQTTADGAVTLEPVYCLGLCACSPAAMLDG----------EVHGRLDPQRLDAL 150 (156)
T ss_pred eCCchhhcCCHHHHHHHHHHHhCCCCCCcCCCCeEEEEeeeecCccCCCCeEEECC----------EEeCCCCHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999998 89999999999999
Q ss_pred HHHHH
Q 022828 246 VEMLR 250 (291)
Q Consensus 246 Le~l~ 250 (291)
|++++
T Consensus 151 l~~~~ 155 (156)
T PRK05988 151 LAEAR 155 (156)
T ss_pred HHHhh
Confidence 99876
No 6
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=100.00 E-value=2e-47 Score=328.75 Aligned_cols=153 Identities=42% Similarity=0.780 Sum_probs=147.7
Q ss_pred CChhhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhhhhhhcccccccCCceEEE
Q 022828 85 FSDTNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEVATFYSMFNRSKVGKYHLL 164 (291)
Q Consensus 85 ~~~~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~VaTFY~~f~~~P~gK~~I~ 164 (291)
|+++.++++++|+++|+. ++++|||+||++|+++ ||||+++|++||+.|++|+++||+|+|||+||+++|+|||+|+
T Consensus 2 ~~~~~~~~~~~i~~~~~~--~~~~ll~~L~~vQ~~~-g~ip~~~~~~iA~~l~v~~~~v~~v~tFY~~f~~~p~gk~~I~ 78 (154)
T PRK07539 2 LSAEELAAIEREIAKYPR--PRSAVIPALKIVQEQR-GWVPDEAIEAVADYLGMPAIDVEEVATFYSMIFRQPVGRHVIQ 78 (154)
T ss_pred CCHHHHHHHHHHHHHCCC--CHHHHHHHHHHHHHHh-CCCCHHHHHHHHHHhCcCHHHHHHHHHHHhhhCcCCCCCEEEE
Confidence 778888999999999994 7999999999999985 9999999999999999999999999999999999999999999
Q ss_pred EcCCCcccccChHHHHHHHHHHhCCCCCcccCCCcEEEEEecCCCCCCCCCeEEEcccCCCCCCccceEecCCChhhHHH
Q 022828 165 VCGTTPCMVRGSREIEDALLKHLGVKRNEVTKDGLFSVGEMECMGCCVNAPMITVADYSNGSEGYTYNYYEDVTPKRVIE 244 (291)
Q Consensus 165 VC~gtsC~~~Gs~~lleaL~~~Lgi~~Gett~DG~ftL~~v~CLG~C~~aPvV~Vnd~~~G~~g~~~~~Y~~vTpE~V~~ 244 (291)
||+|++|+++|+++|+++|+++|+++.|++|+||+|+|++++|||.|+.||+|+||+ +||++||++++++
T Consensus 79 VC~g~~C~~~Ga~~l~~~l~~~L~i~~g~tt~dg~~~l~~~~ClG~C~~gPvv~V~~----------~~y~~vt~e~v~~ 148 (154)
T PRK07539 79 VCTSTPCWLRGGEAILAALKKKLGIKPGETTADGRFTLLEVECLGACDNAPVVMIND----------DTYEDLTPEKIDE 148 (154)
T ss_pred EcCCchHHHCCHHHHHHHHHHHhCCCCCCcCCCCeEEEEEccccCccCCCCEEEECC----------EEeCCCCHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999987 8999999999999
Q ss_pred HHHHHH
Q 022828 245 IVEMLR 250 (291)
Q Consensus 245 ILe~l~ 250 (291)
||++++
T Consensus 149 il~~~~ 154 (154)
T PRK07539 149 LLDELK 154 (154)
T ss_pred HHHhcC
Confidence 998763
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=1.1e-46 Score=322.04 Aligned_cols=146 Identities=45% Similarity=0.892 Sum_probs=140.5
Q ss_pred HHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhhhhhhcccccccCCceEEEEcCCCccc
Q 022828 93 VKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEVATFYSMFNRSKVGKYHLLVCGTTPCM 172 (291)
Q Consensus 93 i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~VaTFY~~f~~~P~gK~~I~VC~gtsC~ 172 (291)
+++|+++||.+.++++|||+||++|+++ ||||++++++||+.|+||+++||+|+|||+||+++|+|||+|+||+|++|+
T Consensus 2 ~~~i~~~~~~~~~~~~li~~L~~vQ~~~-G~i~~~~~~~iA~~l~~~~~~v~~v~tFY~~f~~~p~gk~~I~VC~g~~C~ 80 (148)
T TIGR01958 2 IEEIIAKYPDDQKRSAIMPALMIAQEQK-GWVTPEAIAAVAEMLGIPPVWVYEVATFYSMFDTEPVGRYHLQVCTNVPCA 80 (148)
T ss_pred hHHHHHHCCCCCChhHHHHHHHHHHHHh-CCCCHHHHHHHHHHhCcCHHHHHHHHhHHhhcCcCCCCCEEEEEcCCchhh
Confidence 6899999995337899999999999985 999999999999999999999999999999999999999999999999999
Q ss_pred ccChHHHHHHHHHHhCCCCCcccCCCcEEEEEecCCCCCCCCCeEEEcccCCCCCCccceEecCCChhhHHHHHHHH
Q 022828 173 VRGSREIEDALLKHLGVKRNEVTKDGLFSVGEMECMGCCVNAPMITVADYSNGSEGYTYNYYEDVTPKRVIEIVEML 249 (291)
Q Consensus 173 ~~Gs~~lleaL~~~Lgi~~Gett~DG~ftL~~v~CLG~C~~aPvV~Vnd~~~G~~g~~~~~Y~~vTpE~V~~ILe~l 249 (291)
++|+++|+++|+++|+++.|++|+||+|+|+.++|||+|+.||+|+||+ ++|++||++++++||+++
T Consensus 81 ~~Ga~~v~~~l~~~L~i~~g~~t~dg~~~l~~~~ClG~C~~aP~v~V~~----------~~y~~vt~e~v~~il~~~ 147 (148)
T TIGR01958 81 LRGSEALLKYLENKLGIKPGETTPDGRFTLVEVECLGACGNAPVMMIND----------DYYEFLTPEKLDELLERY 147 (148)
T ss_pred hcCHHHHHHHHHHHhCCCCCCCCCCCeEEEEEcCccCccCCCCEEEECC----------EEeCCCCHHHHHHHHHhc
Confidence 9999999999999999999999999999999999999999999999987 899999999999999875
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=1.3e-46 Score=320.71 Aligned_cols=145 Identities=43% Similarity=0.832 Sum_probs=131.4
Q ss_pred HHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhhhhhhcccccccCCceEEEEcCCCccc
Q 022828 93 VKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEVATFYSMFNRSKVGKYHLLVCGTTPCM 172 (291)
Q Consensus 93 i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~VaTFY~~f~~~P~gK~~I~VC~gtsC~ 172 (291)
|++||++||. ++++|||+||++|+++ ||||++++++||+.|+||+++||+|+|||+||+++|.|||+|+||+|++|+
T Consensus 1 i~~i~~~~~~--~~~~ll~~L~~~Q~~~-g~i~~~~~~~iA~~l~i~~~~v~~v~tFY~~f~~~p~gk~~I~VC~g~~C~ 77 (145)
T PF01257_consen 1 IEEIIARYPS--KRSALLPILHEVQEEY-GYIPEEALEEIAEALGIPPAEVYGVATFYSMFRLEPKGKHHIRVCTGTSCH 77 (145)
T ss_dssp -HHHHHTS----GGGGHHHHHHHHHHHH-SS--HHHHHHHHHHHTS-HHHHHHHHHHSSSS-SSS--SEEEEEE-SHHHH
T ss_pred ChHHHHHCCC--CHHHHHHHHHHHHHHc-CCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHcccCCCCCcEEEeCCCchHH
Confidence 6899999995 8999999999999986 999999999999999999999999999999999999999999999999999
Q ss_pred ccChHHHHHHHHHHhCCCCCcccCCCcEEEEEecCCCCCCCCCeEEEcccCCCCCCccceEecCCChhhHHHHHHHHH
Q 022828 173 VRGSREIEDALLKHLGVKRNEVTKDGLFSVGEMECMGCCVNAPMITVADYSNGSEGYTYNYYEDVTPKRVIEIVEMLR 250 (291)
Q Consensus 173 ~~Gs~~lleaL~~~Lgi~~Gett~DG~ftL~~v~CLG~C~~aPvV~Vnd~~~G~~g~~~~~Y~~vTpE~V~~ILe~l~ 250 (291)
++|+++|+++|+++|+++.|+++.||+|+|+.++|+|.|+.||+|+||+ +||++||+|++++||++++
T Consensus 78 ~~Ga~~l~~~l~~~l~i~~g~~~~dg~~~l~~~~ClG~C~~aP~v~V~~----------~~y~~vt~e~v~~il~~lk 145 (145)
T PF01257_consen 78 LRGAEELLEALEEELGIKPGETTEDGKFTLEETGCLGACDQAPVVMVDG----------EWYGNVTPEKVDEILEELK 145 (145)
T ss_dssp TTTHHHHHHHHHHHHCTSCCCCSTTTTEEEEEESSSSSGGGSSEEEECC----------CEEESSSCCHHHHHHHHH-
T ss_pred hCCCHHHHHHHHHHhCCcccccCCCceEEEEECCCccccCCCCEEEECC----------EEECCCCHHHHHHHHHhcC
Confidence 9999999999999999999999999999999999999999999999987 8999999999999999875
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=99.90 E-value=1e-23 Score=163.19 Aligned_cols=80 Identities=21% Similarity=0.477 Sum_probs=77.1
Q ss_pred ceEEEEcCCCcccccChHHHHHHHHHHhCCCCCcccCCCcEEEEEecCCCCCCCCCeEEEcccCCCCCCccceEecCCCh
Q 022828 160 KYHLLVCGTTPCMVRGSREIEDALLKHLGVKRNEVTKDGLFSVGEMECMGCCVNAPMITVADYSNGSEGYTYNYYEDVTP 239 (291)
Q Consensus 160 K~~I~VC~gtsC~~~Gs~~lleaL~~~Lgi~~Gett~DG~ftL~~v~CLG~C~~aPvV~Vnd~~~G~~g~~~~~Y~~vTp 239 (291)
||+|+||+|++|+++|+++|+++|+++|+++.|+++.||+|+|+.++|||.|+.||+|+||+ +||+++|+
T Consensus 1 ~~~i~vC~~~~C~~~G~~~ll~~l~~~l~~~~g~~~~dg~~~l~~~~ClG~C~~gP~~~v~~----------~~~~~~~~ 70 (80)
T cd03081 1 RHVLKLCRAEACQAMGAEALAAHIKARLGIDFHETTADGSVTLEPVYCLGLCACSPAAMIDG----------EVHGRVDP 70 (80)
T ss_pred CeEEEEcCChHHHhCCHHHHHHHHHHHhCCCCCCcCCCCeEEEEEeeecCccCCCCEEEECC----------EEECCCCH
Confidence 68999999999999999999999999999999999999999999999999999999999987 89999999
Q ss_pred hhHHHHHHHH
Q 022828 240 KRVIEIVEML 249 (291)
Q Consensus 240 E~V~~ILe~l 249 (291)
++|++||+++
T Consensus 71 e~i~~il~~~ 80 (80)
T cd03081 71 EKFDALLAEL 80 (80)
T ss_pred HHHHHHHHcC
Confidence 9999999763
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=99.88 E-value=1.1e-22 Score=157.34 Aligned_cols=80 Identities=26% Similarity=0.569 Sum_probs=76.7
Q ss_pred ceEEEEcCCCcccccChHHHHHHHHHHhCCCCCcccCCCcEEEEEecCCCCCCCCCeEEEcccCCCCCCccceEecCCCh
Q 022828 160 KYHLLVCGTTPCMVRGSREIEDALLKHLGVKRNEVTKDGLFSVGEMECMGCCVNAPMITVADYSNGSEGYTYNYYEDVTP 239 (291)
Q Consensus 160 K~~I~VC~gtsC~~~Gs~~lleaL~~~Lgi~~Gett~DG~ftL~~v~CLG~C~~aPvV~Vnd~~~G~~g~~~~~Y~~vTp 239 (291)
||+|+||++++|+++||++++++|+++|+++.|++|.||.|+|++++|+|.|+.||+|+|++ ++|+++|+
T Consensus 1 ~~~i~vC~~~~C~~~Ga~~v~~~l~~~l~~~~~~~t~d~~v~l~~~gClG~C~~~P~v~V~~----------~~y~~v~~ 70 (80)
T cd03083 1 KYRIYLSDSITDRMNGYKAVLDALCRELGIRFGEVDEDGMVGLFFTSCTGLCDQGPALLINN----------RVFTRLTP 70 (80)
T ss_pred CEEEEEcCChHHHhCCHHHHHHHHHHHHCCCCCCcCCCCeEEEEEeceecCcCCCCeEEECC----------EEECCCCH
Confidence 69999999999999999999999999999999999999999999999999999999999976 89999999
Q ss_pred hhHHHHHHHH
Q 022828 240 KRVIEIVEML 249 (291)
Q Consensus 240 E~V~~ILe~l 249 (291)
+++++|++++
T Consensus 71 ~~v~~iv~~~ 80 (80)
T cd03083 71 GRIDQIAELI 80 (80)
T ss_pred HHHHHHHhcC
Confidence 9999999753
No 11
>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=99.85 E-value=4.3e-21 Score=147.44 Aligned_cols=80 Identities=41% Similarity=0.763 Sum_probs=75.8
Q ss_pred ceEEEEcCCCcccccChHHHHHHHHHHhCCCCCcccCCCcEEEEEecCCCCCCCCCeEEEcccCCCCCCccceEecCCCh
Q 022828 160 KYHLLVCGTTPCMVRGSREIEDALLKHLGVKRNEVTKDGLFSVGEMECMGCCVNAPMITVADYSNGSEGYTYNYYEDVTP 239 (291)
Q Consensus 160 K~~I~VC~gtsC~~~Gs~~lleaL~~~Lgi~~Gett~DG~ftL~~v~CLG~C~~aPvV~Vnd~~~G~~g~~~~~Y~~vTp 239 (291)
||+|+||++++|+.+|+++++++|+++++++.++++.|+.|+|++++|||.|+.||+|+|++ .||+++|+
T Consensus 1 ~~~v~vC~~~~C~~~Ga~~~~~~l~~~l~~~~~~~~~~~~v~v~~t~ClG~C~~gP~v~v~g----------~~y~~vt~ 70 (80)
T cd03064 1 KHVIRVCTGTACHLRGAEALLEALEKKLGIKPGETTPDGRFTLEEVECLGACDLAPVMMIND----------DVYGRLTP 70 (80)
T ss_pred CEEEEECCCcHHHhCCHHHHHHHHHHHhCCCCCCcCCCCEEEEEEecCcCcCCCCCEEEECC----------EEECCCCH
Confidence 68999999999999999999999999999888888899999999999999999999999975 89999999
Q ss_pred hhHHHHHHHH
Q 022828 240 KRVIEIVEML 249 (291)
Q Consensus 240 E~V~~ILe~l 249 (291)
+++++|++++
T Consensus 71 ~~i~~i~~~~ 80 (80)
T cd03064 71 EKVDAILEAL 80 (80)
T ss_pred HHHHHHHHhC
Confidence 9999999864
No 12
>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=99.75 E-value=3.9e-18 Score=130.15 Aligned_cols=70 Identities=30% Similarity=0.479 Sum_probs=65.7
Q ss_pred eEEEEcCCCcccccChHHHHHHHHHHhCCCCCcccCCCcEEEEEecCCCCCCCCCeEEEcccCCCCCCccceEecCCChh
Q 022828 161 YHLLVCGTTPCMVRGSREIEDALLKHLGVKRNEVTKDGLFSVGEMECMGCCVNAPMITVADYSNGSEGYTYNYYEDVTPK 240 (291)
Q Consensus 161 ~~I~VC~gtsC~~~Gs~~lleaL~~~Lgi~~Gett~DG~ftL~~v~CLG~C~~aPvV~Vnd~~~G~~g~~~~~Y~~vTpE 240 (291)
++|+||++++|+.+|+++|+++|+++|+++ +|+|..++|||.|+.||+|+||+ ++|+++|++
T Consensus 2 ~~I~vC~~~~C~~~Ga~~l~~~l~~~L~~~--------~v~l~~~~ClG~C~~gP~v~V~~----------~~~~~~t~~ 63 (72)
T cd03082 2 LTVRVCDSLSCAMAGAEELLAALEAGLGPE--------GVRVVRAPCVGRCERAPAALVGQ----------RPVDGATPA 63 (72)
T ss_pred eEEEEcCChHHHHCCHHHHHHHHHHHhCCC--------eEEEEecCcCCccCCCCeEEECC----------EEeCCcCHH
Confidence 689999999999999999999999999753 69999999999999999999998 899999999
Q ss_pred hHHHHHHH
Q 022828 241 RVIEIVEM 248 (291)
Q Consensus 241 ~V~~ILe~ 248 (291)
++++++++
T Consensus 64 ~i~~~~~~ 71 (72)
T cd03082 64 AVAAAVEA 71 (72)
T ss_pred HHHHHHhc
Confidence 99999863
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=99.73 E-value=1.2e-17 Score=125.85 Aligned_cols=76 Identities=43% Similarity=0.787 Sum_probs=68.9
Q ss_pred eEEEEcCCCcccccChHHHHHHHHHHhCCCCCcccCCCcEEEEEecCCCCCCCCCeEEEcccCCCCCCccceEecCCChh
Q 022828 161 YHLLVCGTTPCMVRGSREIEDALLKHLGVKRNEVTKDGLFSVGEMECMGCCVNAPMITVADYSNGSEGYTYNYYEDVTPK 240 (291)
Q Consensus 161 ~~I~VC~gtsC~~~Gs~~lleaL~~~Lgi~~Gett~DG~ftL~~v~CLG~C~~aPvV~Vnd~~~G~~g~~~~~Y~~vTpE 240 (291)
++|+||++++|..+|+++|+++|+++++...+ |+.|++.+++|+|.|..||+|.|++ ++ .||+++|++
T Consensus 1 ~~I~VC~~~~C~~~G~~~l~~~l~~~~~~~~~----~~~v~v~~~~Clg~C~~~P~v~i~~--~~------~~y~~v~~~ 68 (77)
T cd02980 1 HHILVCTGTACGLRGAEELLEALEKELGIRGG----DGRVTVERVGCLGACGLAPVVVVYP--DG------VWYGRVTPE 68 (77)
T ss_pred CEEEEccCCCcccCCHHHHHHHHHHHHhhhcC----CCeEEEEEcCCcCcccCCCEEEEeC--CC------eEEccCCHH
Confidence 57999999999999999999999999986532 6789999999999999999999984 22 899999999
Q ss_pred hHHHHHHH
Q 022828 241 RVIEIVEM 248 (291)
Q Consensus 241 ~V~~ILe~ 248 (291)
++++||++
T Consensus 69 ~~~~il~~ 76 (77)
T cd02980 69 DVEEIVEE 76 (77)
T ss_pred HHHHHHHh
Confidence 99999986
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=99.53 E-value=2.8e-14 Score=114.20 Aligned_cols=78 Identities=17% Similarity=0.261 Sum_probs=67.0
Q ss_pred EEEEcCCCcccccChHHHHHHHHHHhCCCCCcccCCCcEEEEEecCCCCCCCCCeEEEcccCCCCCCccceEecCCChhh
Q 022828 162 HLLVCGTTPCMVRGSREIEDALLKHLGVKRNEVTKDGLFSVGEMECMGCCVNAPMITVADYSNGSEGYTYNYYEDVTPKR 241 (291)
Q Consensus 162 ~I~VC~gtsC~~~Gs~~lleaL~~~Lgi~~Gett~DG~ftL~~v~CLG~C~~aPvV~Vnd~~~G~~g~~~~~Y~~vTpE~ 241 (291)
+|+||++|.|.+.||++++++|++++..+ | . .+.+..+||+|+|+.+|+|.|.+ |+| .++|.+||+++
T Consensus 2 ~I~Vc~gT~ciAaGA~~V~~al~~ei~~~-g-l----~v~v~~tGC~G~C~~ePlV~V~~-p~g-----~v~Y~~V~~ed 69 (92)
T cd03063 2 RIYVPRDAAALALGADEVAEAIEAEAAAR-G-L----AATIVRNGSRGMYWLEPLVEVET-PGG-----RVAYGPVTPAD 69 (92)
T ss_pred EEEEeCChhhhhhCHHHHHHHHHHHHHHc-C-C----eEEEEEecCceecCCCCEEEEEe-CCC-----cEEEEeCCHHH
Confidence 59999999999999999999999999742 2 1 48999999999999999999963 222 28999999999
Q ss_pred HHHHHHHHHc
Q 022828 242 VIEIVEMLRR 251 (291)
Q Consensus 242 V~~ILe~l~~ 251 (291)
+++|++++..
T Consensus 70 v~~Iv~~~~~ 79 (92)
T cd03063 70 VASLLDAGAL 79 (92)
T ss_pred HHHHHHHHhh
Confidence 9999999553
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=99.38 E-value=1.8e-12 Score=104.02 Aligned_cols=80 Identities=28% Similarity=0.355 Sum_probs=66.5
Q ss_pred eEEEEcCC----CcccccChHHHHHHHHHHhCCCCCcccCCCcEEEEEecCCCCCCCCCeEEEcccCCCCCCccceEecC
Q 022828 161 YHLLVCGT----TPCMVRGSREIEDALLKHLGVKRNEVTKDGLFSVGEMECMGCCVNAPMITVADYSNGSEGYTYNYYED 236 (291)
Q Consensus 161 ~~I~VC~g----tsC~~~Gs~~lleaL~~~Lgi~~Gett~DG~ftL~~v~CLG~C~~aPvV~Vnd~~~G~~g~~~~~Y~~ 236 (291)
.+|+||+. ..|...| .+|+++|++++... | .+.+.+..++|||.|..||+|+|.+..+| +||+.
T Consensus 2 ~~ilVCth~rrd~~C~~~g-~~l~~~l~~~l~~~-~----~~~v~v~~~~clG~c~~gp~vvvyP~~~g------~wy~~ 69 (97)
T cd03062 2 PLVLVCTHGKRDKRCGICG-PPLAAELRAELPEH-G----PGGVRVWEVSHVGGHKFAGNVIIYPKGDG------IWYGR 69 (97)
T ss_pred CEEEEeCCCCCCcChhhcC-HHHHHHHHHHHHHh-C----CCceEEEeCCcCCccCcCCEEEEEeCCCe------eEEee
Confidence 58999995 6788888 68999999998633 2 35689999999999999999999431055 99999
Q ss_pred CChhhHHHHHHHHHcC
Q 022828 237 VTPKRVIEIVEMLRRG 252 (291)
Q Consensus 237 vTpE~V~~ILe~l~~G 252 (291)
|||+++++||+++..+
T Consensus 70 v~p~~v~~Iv~~hl~~ 85 (97)
T cd03062 70 VTPEHVPPIVDRLILG 85 (97)
T ss_pred cCHHHHHHHHHHHhcC
Confidence 9999999999986544
No 16
>COG3411 Ferredoxin [Energy production and conversion]
Probab=99.02 E-value=4.2e-10 Score=84.48 Aligned_cols=52 Identities=25% Similarity=0.503 Sum_probs=44.9
Q ss_pred cEEEEEecCCCCCCCCCeEEEcccCCCCCCccceEecCCChhhHHHHHHHH-HcCCCCCCC
Q 022828 199 LFSVGEMECMGCCVNAPMITVADYSNGSEGYTYNYYEDVTPKRVIEIVEML-RRGEKLPPG 258 (291)
Q Consensus 199 ~ftL~~v~CLG~C~~aPvV~Vnd~~~G~~g~~~~~Y~~vTpE~V~~ILe~l-~~G~~~~~g 258 (291)
.+.+..++|||.|..||+|.|.+ +| .||.+||++++++|++++ .+|+++...
T Consensus 2 ~i~~t~tgCl~~C~~gPvl~vYp--eg------vWY~~V~p~~a~rIv~~hl~~Gr~Ve~~ 54 (64)
T COG3411 2 SIRVTRTGCLGVCQDGPVLVVYP--EG------VWYTRVDPEDARRIVQSHLLGGRPVEEL 54 (64)
T ss_pred ceEEeecchhhhhccCCEEEEec--CC------eeEeccCHHHHHHHHHHHHhCCCcchhh
Confidence 57889999999999999999954 66 999999999999999995 567776553
No 17
>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=97.94 E-value=4.9e-05 Score=68.67 Aligned_cols=92 Identities=26% Similarity=0.382 Sum_probs=71.5
Q ss_pred ccccCCceEEEEcCC----CcccccChHHHHHHHHHHhCCCCCcccCCCcEEEEEecCCCCCCCCCeEEEcc--cCCCCC
Q 022828 154 NRSKVGKYHLLVCGT----TPCMVRGSREIEDALLKHLGVKRNEVTKDGLFSVGEMECMGCCVNAPMITVAD--YSNGSE 227 (291)
Q Consensus 154 ~~~P~gK~~I~VC~g----tsC~~~Gs~~lleaL~~~Lgi~~Gett~DG~ftL~~v~CLG~C~~aPvV~Vnd--~~~G~~ 227 (291)
..+...+..|+||+- ..|...| ..|+++|++.+... + . +.. .|-.+..+|.+.-||+|+|.. .++|
T Consensus 126 ~~~~~~~~~iLVCtHg~RD~rCg~~G-p~l~~~l~~~~~~~-~-l--~~~-~V~~iSHiGGHkfAgNvIiy~~~~p~g-- 197 (230)
T PF06999_consen 126 PREPPDKPLILVCTHGKRDKRCGILG-PPLARELEKELRER-G-L--SRD-RVWEISHIGGHKFAGNVIIYSKPKPDG-- 197 (230)
T ss_pred CcccCCCCEEEEcCCCCcCCchhccc-HHHHHHHHHHhhhc-C-C--ccc-eEEEecccccceecCeEEEEecCCCcE--
Confidence 344456789999986 4788876 57999999998633 1 1 111 289999999999999999960 0344
Q ss_pred CccceEecCCChhhHHHHHHH-HHcCCCCCC
Q 022828 228 GYTYNYYEDVTPKRVIEIVEM-LRRGEKLPP 257 (291)
Q Consensus 228 g~~~~~Y~~vTpE~V~~ILe~-l~~G~~~~~ 257 (291)
.||++|+|++++.||++ +.+|+..+.
T Consensus 198 ----~wyGrv~p~~v~~iv~~t~~~g~vi~~ 224 (230)
T PF06999_consen 198 ----IWYGRVTPEDVEGIVDATILDGKVIPE 224 (230)
T ss_pred ----EEEEeeCHHHHHHHHHHHHhCCcCcCc
Confidence 99999999999999999 888887764
No 18
>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=97.87 E-value=4.9e-05 Score=63.49 Aligned_cols=79 Identities=19% Similarity=0.260 Sum_probs=57.8
Q ss_pred ccChHHHHHHHHHHhCCCCCcccCCCcEEEEEecCCCCCCCCCeEEEcccCCCCCCccceEecCCCh-hhHHHHHHHHHc
Q 022828 173 VRGSREIEDALLKHLGVKRNEVTKDGLFSVGEMECMGCCVNAPMITVADYSNGSEGYTYNYYEDVTP-KRVIEIVEMLRR 251 (291)
Q Consensus 173 ~~Gs~~lleaL~~~Lgi~~Gett~DG~ftL~~v~CLG~C~~aPvV~Vnd~~~G~~g~~~~~Y~~vTp-E~V~~ILe~l~~ 251 (291)
.++++.|+++|+..+.-. .....|+|++++||..|+.+=+|.+.. .|+. ..+|++++| ++++.||+-...
T Consensus 18 ~~~G~~L~~aL~~~~~~~----~~~~~v~v~~v~CL~~C~r~CtVA~~~--~gK~---tYlfGdl~p~~~a~~il~~a~~ 88 (116)
T PF07845_consen 18 PRPGAALLDALRAALADA----PLPDGVEVRPVECLSACDRPCTVALQA--PGKW---TYLFGDLDPDEDAEDILAFAAL 88 (116)
T ss_pred CChHHHHHHHHHHHHhcC----CCCCceEEEeccHHhcCCCceEEEEEc--CCCc---EEEEecCCcccCHHHHHHHHHH
Confidence 358899999999998632 122359999999999999999998874 3332 368999999 889999976443
Q ss_pred CCCCCCCCC
Q 022828 252 GEKLPPGTQ 260 (291)
Q Consensus 252 G~~~~~g~~ 260 (291)
--..+.|-.
T Consensus 89 Y~~s~dG~v 97 (116)
T PF07845_consen 89 YAASPDGLV 97 (116)
T ss_pred HHhCCCCcc
Confidence 222344433
No 19
>COG5469 Predicted metal-binding protein [Function unknown]
Probab=97.65 E-value=0.00021 Score=61.31 Aligned_cols=83 Identities=19% Similarity=0.373 Sum_probs=61.6
Q ss_pred cccCCceEEEEcCCCcccc----------cChHHHHHHHHHHhCCCCCcccCCCcEEEEEecCCCCCCCCCeEEEcccCC
Q 022828 155 RSKVGKYHLLVCGTTPCMV----------RGSREIEDALLKHLGVKRNEVTKDGLFSVGEMECMGCCVNAPMITVADYSN 224 (291)
Q Consensus 155 ~~P~gK~~I~VC~gtsC~~----------~Gs~~lleaL~~~Lgi~~Gett~DG~ftL~~v~CLG~C~~aPvV~Vnd~~~ 224 (291)
..+..+|.++||+. |+. .++..|++.|++..... .....|+|+.|+||.+|+.+=+|.+.. +
T Consensus 12 ~~~~~~htlfVCks--C~~~~~~~~~~~p~~G~~Ll~kl~~l~qe~----~~~~e~~I~~VeCl~~C~r~c~vA~~~--~ 83 (143)
T COG5469 12 INGMPKHTLFVCKS--CRDVSQEGKENGPSDGSILLDKLQELAQEW----EIAHEFEIQTVECLAACNRGCVVAFSG--P 83 (143)
T ss_pred ccccCceEEEEecc--ccccccCCccCCCCcHHHHHHHHHHHHhhh----hhhccceeeeeHhhhhcCCCeEEEEec--C
Confidence 34556899999984 432 35778999988765421 122359999999999999999888865 3
Q ss_pred CCCCccceEecCCChhh-HHHHHHH
Q 022828 225 GSEGYTYNYYEDVTPKR-VIEIVEM 248 (291)
Q Consensus 225 G~~g~~~~~Y~~vTpE~-V~~ILe~ 248 (291)
|++ -.+|+++||++ ..+||+-
T Consensus 84 ~k~---sYLFgdL~p~d~a~dLl~~ 105 (143)
T COG5469 84 GKP---SYLFGDLTPDDSASDLLEF 105 (143)
T ss_pred CCc---eEEEccCCccccHHHHHHH
Confidence 433 36899999998 8888875
No 20
>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=96.29 E-value=0.016 Score=45.40 Aligned_cols=65 Identities=18% Similarity=0.331 Sum_probs=48.1
Q ss_pred EEEEcCCCcccccChHHHHHHHHHHhCCCCCcccCCCcEEEEEecCCCCCC---CCCeEEEcccCCCCCCccceEecCCC
Q 022828 162 HLLVCGTTPCMVRGSREIEDALLKHLGVKRNEVTKDGLFSVGEMECMGCCV---NAPMITVADYSNGSEGYTYNYYEDVT 238 (291)
Q Consensus 162 ~I~VC~gtsC~~~Gs~~lleaL~~~Lgi~~Gett~DG~ftL~~v~CLG~C~---~aPvV~Vnd~~~G~~g~~~~~Y~~vT 238 (291)
.|.+|.+- ...|++.+++.|++.- .+.+.+.+|++.|+ ..|-.+||+ ++...-|
T Consensus 4 iVefC~~N--l~~g~~~~~~~Le~~p-----------~~~Vie~gCl~~Cg~C~~~pFAlVnG----------~~V~A~t 60 (78)
T PF07293_consen 4 IVEFCVSN--LASGTDQVYEKLEKDP-----------DIDVIEYGCLSYCGPCAKKPFALVNG----------EIVAAET 60 (78)
T ss_pred eEEEcccC--chhhhHHHHHHHhcCC-----------CccEEEcChhhhCcCCCCCccEEECC----------EEEecCC
Confidence 57888753 5579999888887431 26789999999775 689999987 6777778
Q ss_pred hhhHHHHHHHH
Q 022828 239 PKRVIEIVEML 249 (291)
Q Consensus 239 pE~V~~ILe~l 249 (291)
+|++-+-|.+.
T Consensus 61 ~eeL~~kI~~~ 71 (78)
T PF07293_consen 61 AEELLEKIKEK 71 (78)
T ss_pred HHHHHHHHHHH
Confidence 87765555443
No 21
>PRK13669 hypothetical protein; Provisional
Probab=94.08 E-value=0.19 Score=39.56 Aligned_cols=64 Identities=25% Similarity=0.388 Sum_probs=45.5
Q ss_pred EEEEcCCCcccccChHHHHHHHHHHhCCCCCcccCCCcEEEEEecCCCCCC---CCCeEEEcccCCCCCCccceEecCCC
Q 022828 162 HLLVCGTTPCMVRGSREIEDALLKHLGVKRNEVTKDGLFSVGEMECMGCCV---NAPMITVADYSNGSEGYTYNYYEDVT 238 (291)
Q Consensus 162 ~I~VC~gtsC~~~Gs~~lleaL~~~Lgi~~Gett~DG~ftL~~v~CLG~C~---~aPvV~Vnd~~~G~~g~~~~~Y~~vT 238 (291)
.|.+|.+. ...|++.+++.|++ |..+.|.+.+|++.|+ ..|-.+||+ ++...-|
T Consensus 4 iVEfC~sN--l~~G~~~~~~~Le~-----------dP~~dVie~gCls~CG~C~~~~FAlVng----------~~V~a~t 60 (78)
T PRK13669 4 IVEFCVSN--LASGSQAAFEKLEK-----------DPNLDVLEYGCLGYCGICSEGLFALVNG----------EVVEGET 60 (78)
T ss_pred eeeehhcc--hhhhHHHHHHHHHh-----------CCCceEEEcchhhhCcCcccCceEEECC----------eEeecCC
Confidence 57788865 45688887776632 2347899999998765 689999987 5666778
Q ss_pred hhhHHHHHHH
Q 022828 239 PKRVIEIVEM 248 (291)
Q Consensus 239 pE~V~~ILe~ 248 (291)
+|++.+-|.+
T Consensus 61 ~eeL~~kI~~ 70 (78)
T PRK13669 61 PEELVENIYA 70 (78)
T ss_pred HHHHHHHHHH
Confidence 7775544444
No 22
>PF14297 DUF4373: Domain of unknown function (DUF4373)
Probab=82.14 E-value=4.6 Score=31.42 Aligned_cols=67 Identities=19% Similarity=0.302 Sum_probs=54.6
Q ss_pred hHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCC-CCHHHHHHHHHHhCCCchhhhhhhhhhccccccc
Q 022828 89 NKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGW-LPVSAMNEVAKIIEVAPIRVYEVATFYSMFNRSK 157 (291)
Q Consensus 89 ~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~Gy-Ip~eam~~IAe~L~ip~~~V~~VaTFY~~f~~~P 157 (291)
+-.+++.+.++|..+ .-+..+-+|..+-++. || ++-+.+..+|+.++++...|..|+.=|..|...-
T Consensus 10 ~D~ki~~l~~~~G~~-G~~~y~~ll~~iy~~~-~y~~~~~~~~~~a~~~~~~~~~v~~II~~~~LF~~~~ 77 (87)
T PF14297_consen 10 SDPKIRRLMAEYGCE-GYGIYWYLLEYIYKQG-GYYLWWDKLFLIARKLGVSEEYVEEIINEYGLFDIEE 77 (87)
T ss_pred cCHHHHHHHHHcCCc-hHHHHHHHHHHHHcCC-CeEeeHHHHHHHHHHHCcCHHHHHHHHHHhCCcccCC
Confidence 345788999999863 4567777888887765 55 7777799999999999999999999888888554
No 23
>TIGR02435 CobG precorrin-3B synthase. An iron-sulfur protein. An oxygen atom from dioxygen is incorporated into the macrocycle at C-20. In the aerobic cobalamin biosythesis pathway, four enzymes are involved in the conversion of precorrin-3A to precorrin-6A. The first of the four steps is carried out by EC 1.14.13.83, precorrin-3B synthase (CobG), yielding precorrin-3B as the product. This is followed by three methylation reactions, which introduce a methyl group at C-17 (CobJ; EC 2.1.1.131), C-11 (CobM; EC 2.1.1.133) and C-1 (CobF; EC 2.1.1.152) of the macrocycle, giving rise to precorrin-4, precorrin-5 and precorrin-6A, respectively.
Probab=80.96 E-value=8.5 Score=37.86 Aligned_cols=86 Identities=16% Similarity=0.280 Sum_probs=54.5
Q ss_pred CCCCHHHHHHHHHHh-------------------CCCchhhhhhhhhhccccc--ccCC-ceEEEEcCCC-cccc--cCh
Q 022828 122 GWLPVSAMNEVAKII-------------------EVAPIRVYEVATFYSMFNR--SKVG-KYHLLVCGTT-PCMV--RGS 176 (291)
Q Consensus 122 GyIp~eam~~IAe~L-------------------~ip~~~V~~VaTFY~~f~~--~P~g-K~~I~VC~gt-sC~~--~Gs 176 (291)
|+|+.+.+..||+.. +|+..++.+|...-..+.. .+.+ ...|..|.|. .|.. .-+
T Consensus 266 G~i~~~~l~~la~ia~~~g~~~irlT~~Q~l~i~~i~~~~~~~~~~~l~~~gl~~~~~~~~~~v~aC~G~~~C~~~~~~t 345 (390)
T TIGR02435 266 GQLTAAQLRGLAQLAQALGDGDLRLTPWRALLVLGLPPERADAAQRALAALGLVTSASDPRARIIACTGAPGCASALADT 345 (390)
T ss_pred cccCHHHHHHHHHHHHHhCCCeEEEcCCcceEEcCCCHHHHHHHHHHHHHCCCCcCCCCCeeeEEECCCccccccchhhH
Confidence 566777766666543 4555555555444333222 2322 3458899995 7763 347
Q ss_pred HHHHHHHHHHhCCCCCcccCCCcEEEEEecCCCCCCCC
Q 022828 177 REIEDALLKHLGVKRNEVTKDGLFSVGEMECMGCCVNA 214 (291)
Q Consensus 177 ~~lleaL~~~Lgi~~Gett~DG~ftL~~v~CLG~C~~a 214 (291)
+.+..+|.+.++.. . .++|.-+||-..|...
T Consensus 346 ~~~a~~l~~~~~~~-----~--~~~i~vSGC~n~C~~~ 376 (390)
T TIGR02435 346 RADAEALAAYCEPT-----A--PITVHLSGCAKGCAHP 376 (390)
T ss_pred HHHHHHHHHHhccc-----C--CcEEEEeCCcccccCC
Confidence 77888888877532 1 1899999999999973
No 24
>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=78.89 E-value=4.1 Score=28.27 Aligned_cols=37 Identities=14% Similarity=0.113 Sum_probs=30.5
Q ss_pred cHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhh
Q 022828 108 AVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYE 145 (291)
Q Consensus 108 alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~ 145 (291)
.-+.+|..+-... .|.+.+.+..||+.+||+..+|..
T Consensus 10 ~~~~~Le~~f~~~-~~P~~~~~~~la~~~~l~~~qV~~ 46 (59)
T cd00086 10 EQLEELEKEFEKN-PYPSREEREELAKELGLTERQVKI 46 (59)
T ss_pred HHHHHHHHHHHhC-CCCCHHHHHHHHHHHCcCHHHHHH
Confidence 3566777766665 899999999999999999998754
No 25
>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=78.58 E-value=3.4 Score=28.94 Aligned_cols=35 Identities=17% Similarity=0.174 Sum_probs=27.6
Q ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhh
Q 022828 109 VIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVY 144 (291)
Q Consensus 109 lipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~ 144 (291)
-+.+|...-+.. .|++.+.++.||+.|||+..+|.
T Consensus 11 q~~~L~~~f~~~-~~p~~~~~~~la~~l~l~~~~V~ 45 (57)
T PF00046_consen 11 QLKVLEEYFQEN-PYPSKEEREELAKELGLTERQVK 45 (57)
T ss_dssp HHHHHHHHHHHS-SSCHHHHHHHHHHHHTSSHHHHH
T ss_pred HHHHHHHHHHHh-ccccccccccccccccccccccc
Confidence 345555555554 89999999999999999999874
No 26
>PF10820 DUF2543: Protein of unknown function (DUF2543); InterPro: IPR020251 This entry contains proteins with no known function.
Probab=75.66 E-value=2.3 Score=33.12 Aligned_cols=33 Identities=18% Similarity=0.273 Sum_probs=29.9
Q ss_pred CCCCHHHHHHHHHHhCCCchhhhhhhhhhcccc
Q 022828 122 GWLPVSAMNEVAKIIEVAPIRVYEVATFYSMFN 154 (291)
Q Consensus 122 GyIp~eam~~IAe~L~ip~~~V~~VaTFY~~f~ 154 (291)
.=||++++++.|...||...++.++++|...+-
T Consensus 47 eeIsEeaQ~EMA~eAgi~~~rID~IA~fLNqWG 79 (81)
T PF10820_consen 47 EEISEEAQQEMASEAGIDEQRIDDIANFLNQWG 79 (81)
T ss_pred HhhhHHHHHHHHHHcCCcHHHHHHHHHHHHHhc
Confidence 349999999999999999999999999987653
No 27
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=72.79 E-value=7.4 Score=26.85 Aligned_cols=37 Identities=14% Similarity=0.107 Sum_probs=29.4
Q ss_pred cHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhh
Q 022828 108 AVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYE 145 (291)
Q Consensus 108 alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~ 145 (291)
.-+.+|...-+.. -|.+.+.+..||+.+|++..+|..
T Consensus 10 ~~~~~L~~~f~~~-~~P~~~~~~~la~~~~l~~~qV~~ 46 (56)
T smart00389 10 EQLEELEKEFQKN-PYPSREEREELAAKLGLSERQVKV 46 (56)
T ss_pred HHHHHHHHHHHhC-CCCCHHHHHHHHHHHCcCHHHHHH
Confidence 3567777766555 699999999999999999887643
No 28
>PRK14996 TetR family transcriptional regulator; Provisional
Probab=65.79 E-value=3.4 Score=35.49 Aligned_cols=45 Identities=13% Similarity=0.254 Sum_probs=32.9
Q ss_pred CcccHHH-HHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhhhhhhcccccccC
Q 022828 105 KQSAVIP-LLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEVATFYSMFNRSKV 158 (291)
Q Consensus 105 ~~~alip-iL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~VaTFY~~f~~~P~ 158 (291)
++..||. .++.+.+ + || ..-.|+.||+..||+.. +||++|..+..
T Consensus 9 ~R~~Il~aA~~lf~e-~-G~-~~tSi~~Ia~~aGvsk~------~lY~~F~sK~~ 54 (192)
T PRK14996 9 RREVILQAAMRVALA-E-GF-AAMTVRRIASEAQVAAG------QVHHHFSSAGE 54 (192)
T ss_pred HHHHHHHHHHHHHHh-c-Ch-hhccHHHHHHHhCCCcH------HHHHHcCCHHH
Confidence 4555665 5555554 4 88 67789999999999987 78888876543
No 29
>PLN02431 ferredoxin--nitrite reductase
Probab=65.23 E-value=36 Score=35.74 Aligned_cols=52 Identities=13% Similarity=0.134 Sum_probs=31.3
Q ss_pred ceEEEEcCCC-ccccc--ChHHHHHHHHHHhCCCCCcccCCCcEEEEEecCCCCCCCC
Q 022828 160 KYHLLVCGTT-PCMVR--GSREIEDALLKHLGVKRNEVTKDGLFSVGEMECMGCCVNA 214 (291)
Q Consensus 160 K~~I~VC~gt-sC~~~--Gs~~lleaL~~~Lgi~~Gett~DG~ftL~~v~CLG~C~~a 214 (291)
...|..|+|+ -|... -...+..+|.+.|... ...+..|+|.-+||...|...
T Consensus 465 ~r~vvACtG~~~C~~ai~eTk~~A~~L~~~l~~~---~~lp~k~kI~vSGCpn~C~~~ 519 (587)
T PLN02431 465 LKGLVACTGNQFCGQAIIETKARALKVTEELERL---VEVPRPVRMHWTGCPNSCGQV 519 (587)
T ss_pred ccceeECCCccccCccHHHHHHHHHHHHHHHHHh---hcCCCCeEEEEECCccccccc
Confidence 3468999986 45432 2233334444443211 113567999999999999864
No 30
>PRK09480 slmA division inhibitor protein; Provisional
Probab=61.78 E-value=5.6 Score=33.75 Aligned_cols=44 Identities=14% Similarity=0.308 Sum_probs=32.3
Q ss_pred CcccHHHHH-HHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhhhhhhccccccc
Q 022828 105 KQSAVIPLL-DLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEVATFYSMFNRSK 157 (291)
Q Consensus 105 ~~~alipiL-~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~VaTFY~~f~~~P 157 (291)
++..|+... .++-++. | ..-.++.||+..||+.. |||.+|..+.
T Consensus 11 ~r~~Il~aa~~l~~~~~-G--~~~ti~~Ia~~agvs~g------t~Y~~F~~K~ 55 (194)
T PRK09480 11 RREQILQALAQMLESPP-G--ERITTAKLAARVGVSEA------ALYRHFPSKA 55 (194)
T ss_pred HHHHHHHHHHHHHHhcC-C--CccCHHHHHHHhCCCHh------HHHHHCCCHH
Confidence 455566654 3344322 4 88899999999999986 8999998765
No 31
>COG4759 Uncharacterized protein conserved in bacteria containing thioredoxin-like domain [Posttranslational modification, protein turnover, chaperones]
Probab=61.71 E-value=21 Score=34.78 Aligned_cols=79 Identities=18% Similarity=0.224 Sum_probs=60.1
Q ss_pred cccCCceEEEEcCCC----cccccChHHHHHHHHHHhCCCCCcccCCCcEEEEEecCCCCCCCCCeEEEcccCCCCCCcc
Q 022828 155 RSKVGKYHLLVCGTT----PCMVRGSREIEDALLKHLGVKRNEVTKDGLFSVGEMECMGCCVNAPMITVADYSNGSEGYT 230 (291)
Q Consensus 155 ~~P~gK~~I~VC~gt----sC~~~Gs~~lleaL~~~Lgi~~Gett~DG~ftL~~v~CLG~C~~aPvV~Vnd~~~G~~g~~ 230 (291)
..|.-...|.||+-. +|...| .-++++++..++-. ..+.+.|=.+.=+|+=..||.|.- -|.|
T Consensus 126 ~~~~h~RdiLVCTHgn~D~cCarfG-~P~Y~~~r~~~a~l-----~~~~lRvWq~SHfgGHrFAPTlid--lP~G----- 192 (316)
T COG4759 126 IYPQHTRDILVCTHGNVDVCCARFG-YPFYQQLRAQYADL-----NLENLRVWQSSHFGGHRFAPTLID--LPQG----- 192 (316)
T ss_pred cchhhhceEEEecCCChhhhhhhcC-cHHHHHHHHhhhhc-----cccceEEEEecccCccccCchhhc--CCCC-----
Confidence 333344579999974 666555 67999999988633 134588888999999999998754 3455
Q ss_pred ceEecCCChhhHHHHHH
Q 022828 231 YNYYEDVTPKRVIEIVE 247 (291)
Q Consensus 231 ~~~Y~~vTpE~V~~ILe 247 (291)
.+|++++++.++.||.
T Consensus 193 -qyyG~Ld~~~~~~l~~ 208 (316)
T COG4759 193 -QYYGHLDPESLDSLLT 208 (316)
T ss_pred -ceeeecCHHHHHHHHh
Confidence 8999999999999975
No 32
>PRK09567 nirA ferredoxin-nitrite reductase; Reviewed
Probab=58.12 E-value=42 Score=35.21 Aligned_cols=50 Identities=14% Similarity=0.244 Sum_probs=31.7
Q ss_pred eEEEEcCCC-cccccC--hHHHHHHHHHHhCCCCCcccCCCcEEEEEecCCCCCCC
Q 022828 161 YHLLVCGTT-PCMVRG--SREIEDALLKHLGVKRNEVTKDGLFSVGEMECMGCCVN 213 (291)
Q Consensus 161 ~~I~VC~gt-sC~~~G--s~~lleaL~~~Lgi~~Gett~DG~ftL~~v~CLG~C~~ 213 (291)
..+..|+|+ .|.... ++.+...|.+.|.... ..+..|+|.-+||-..|..
T Consensus 445 ~~~vAC~G~~~C~~a~~dT~~~a~~l~~~l~~~~---~l~~~ikI~vSGCpn~Ca~ 497 (593)
T PRK09567 445 AGLVACTGNAGCKFAAADTKGHALAIADYCEPRV---ALDQPVNIHLTGCHHSCAQ 497 (593)
T ss_pred eccEecCCCCCCCccHhhHHHHHHHHHHHHHHhc---CCCCCcEEEEECCCccccc
Confidence 357899996 665433 3444444444443221 2355799999999999985
No 33
>PRK13504 sulfite reductase subunit beta; Provisional
Probab=57.88 E-value=23 Score=36.79 Aligned_cols=74 Identities=12% Similarity=0.220 Sum_probs=43.1
Q ss_pred CCCchhhhhhhhhhccccc--cc--C-CceEEEEcCCC-cccccC--hHH----HHHHHHHHhCCCCCcccCCCcEEEEE
Q 022828 137 EVAPIRVYEVATFYSMFNR--SK--V-GKYHLLVCGTT-PCMVRG--SRE----IEDALLKHLGVKRNEVTKDGLFSVGE 204 (291)
Q Consensus 137 ~ip~~~V~~VaTFY~~f~~--~P--~-gK~~I~VC~gt-sC~~~G--s~~----lleaL~~~Lgi~~Gett~DG~ftL~~ 204 (291)
+|+..++.++...-.-+.. .+ . -...|.-|.|+ -|...- ++. |.+.|++.+.. .+ ..+..|+|.-
T Consensus 400 ~i~~~~~~~l~~~L~~~gl~~~~~~~~~~~~ivAC~G~~~C~~a~~~t~~~a~~l~~~l~~~~~~-~~--l~~~~i~I~v 476 (569)
T PRK13504 400 NVPPSDKAKIEALLREYGLIDGVEESPLRRNSMACVALPTCGLAMAEAERYLPSFIDRIEALLAK-HG--LSDEHIVIRM 476 (569)
T ss_pred CCCHHHHHHHHHHHHhCCCCCCCCCCCceeceeecCCcccccchhhhHHHHHHHHHHHHHHHHhh-cC--CCCCceEEEE
Confidence 6677776665544433222 12 1 14568899995 575433 333 45555555431 11 1146799999
Q ss_pred ecCCCCCCC
Q 022828 205 MECMGCCVN 213 (291)
Q Consensus 205 v~CLG~C~~ 213 (291)
+||...|..
T Consensus 477 SGCpn~Ca~ 485 (569)
T PRK13504 477 TGCPNGCAR 485 (569)
T ss_pred eCCcccccc
Confidence 999999985
No 34
>TIGR02066 dsrB sulfite reductase, dissimilatory-type beta subunit. This model describes the beta subunit of sulfite reductase.
Probab=56.84 E-value=11 Score=36.95 Aligned_cols=110 Identities=12% Similarity=0.116 Sum_probs=67.7
Q ss_pred CCChhhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhC---CCchhhhhhhhhhcccccccCCc
Q 022828 84 KFSDTNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIE---VAPIRVYEVATFYSMFNRSKVGK 160 (291)
Q Consensus 84 ~~~~~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~---ip~~~V~~VaTFY~~f~~~P~gK 160 (291)
.++.+++..|-+|.++|...+ +-+ .-=|....-||+.+-+..|-+.|. ++.. + . -+.-+
T Consensus 40 ~lt~eqLr~LAdiaekyg~g~-----i~l-TtrQnI~l~~I~~edl~~i~~~L~~~Gl~~~---~---~------G~~vr 101 (341)
T TIGR02066 40 LLSVDTLRKLCDIADKYSDGY-----LRW-TIRNNVEFLVSDESKIQPLIDELEEVGFPVG---G---T------GDAVK 101 (341)
T ss_pred ccCHHHHHHHHHHHHHhCCCe-----EEE-eccCCEEEecCCHHHHHHHHHHHHhccCCCC---C---C------CCccc
Confidence 589999999999999997521 111 111222236899999988888773 3221 0 0 01112
Q ss_pred eEEEEcCCC-cccccC--hHHHHH----HHHHHhCCCCCcccCCCcEEEEEecCCCCCCCCC
Q 022828 161 YHLLVCGTT-PCMVRG--SREIED----ALLKHLGVKRNEVTKDGLFSVGEMECMGCCVNAP 215 (291)
Q Consensus 161 ~~I~VC~gt-sC~~~G--s~~lle----aL~~~Lgi~~Gett~DG~ftL~~v~CLG~C~~aP 215 (291)
..|.-|.|. .|...+ +.++.. .|.+.+. . .....+|.+.-+||-..|...-
T Consensus 102 rni~aC~G~~~C~~a~~dt~~l~~~l~~~l~~~~~-~---~~lP~KfKI~vSGC~~~C~~~~ 159 (341)
T TIGR02066 102 GNIVHTQGWLHCHIPAIDASGIVKAVMDELYEYFT-D---HKLPAMVRISLSCCANMCGGVH 159 (341)
T ss_pred cccccCcCCCCCCcchhchHHHHHHHHHHHHHHHh-c---ccccccceeccccccccccchh
Confidence 247889997 586654 444444 4444442 1 1234479999999999998853
No 35
>PRK09566 nirA ferredoxin-nitrite reductase; Reviewed
Probab=54.78 E-value=45 Score=34.11 Aligned_cols=89 Identities=17% Similarity=0.178 Sum_probs=51.6
Q ss_pred CCCCHHHHHHHHHHh-------------------CCCchhhhhhhhh--hcccccccC-CceEEEEcCCC-cccccC--h
Q 022828 122 GWLPVSAMNEVAKII-------------------EVAPIRVYEVATF--YSMFNRSKV-GKYHLLVCGTT-PCMVRG--S 176 (291)
Q Consensus 122 GyIp~eam~~IAe~L-------------------~ip~~~V~~VaTF--Y~~f~~~P~-gK~~I~VC~gt-sC~~~G--s 176 (291)
|.|+.+.+..||+.. +|+..+|.++..- ..-|...|. ....|.-|+|+ -|...- +
T Consensus 331 G~lt~~~l~~la~ia~~yg~g~irlT~~Qni~l~~i~~~~v~~l~~~~~~~~~~~~~~~~~~~~vaC~G~~~C~~a~~dT 410 (513)
T PRK09566 331 GRLYAEDMFELARLAEVYGSGEIRLTVEQNVIIPNIPDENLETFLAEPLLQKFSLEPGPLARGLVSCTGNQYCNFALIET 410 (513)
T ss_pred ccCCHHHHHHHHHHHHHhCCCeEEEcCCCCEEEeCCCHHHHHHHHHHHhhccCCCCCCccccCceeCcCcccccccHhhH
Confidence 567777777666654 5666666666543 222333332 23458899996 565322 3
Q ss_pred HHHHHHHHHHhCCCCCcccCCCcEEEEEecCCCCCCC
Q 022828 177 REIEDALLKHLGVKRNEVTKDGLFSVGEMECMGCCVN 213 (291)
Q Consensus 177 ~~lleaL~~~Lgi~~Gett~DG~ftL~~v~CLG~C~~ 213 (291)
..+...|.++|... ...+..|.|.-+||...|..
T Consensus 411 ~~~a~~l~~~l~~~---~~lp~~~kI~iSGCpn~C~~ 444 (513)
T PRK09566 411 KNRALALAKELDAE---LDLPQPVRIHWTGCPNSCGQ 444 (513)
T ss_pred HHHHHHHHHHHHHh---cCCCCceEEEEECChhhhhc
Confidence 33333344333211 11345789999999999985
No 36
>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=54.18 E-value=8.9 Score=32.33 Aligned_cols=40 Identities=18% Similarity=0.360 Sum_probs=28.1
Q ss_pred HHH-HHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhhhhhhccccccc
Q 022828 109 VIP-LLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEVATFYSMFNRSK 157 (291)
Q Consensus 109 lip-iL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~VaTFY~~f~~~P 157 (291)
+.. ++++++++ | +..=.++.|++..||+.. |||.+|..+.
T Consensus 8 I~~a~~~Ll~~k--~-~~~ITV~~I~~~AgvsR~------TFY~hF~dK~ 48 (176)
T TIGR02366 8 IAKAFKDLMEVQ--A-FSKISVSDIMSTAQIRRQ------TFYNHFQDKY 48 (176)
T ss_pred HHHHHHHHHHHC--C-CccCCHHHHHHHhCCCHH------HHHHHCCCHH
Confidence 444 35555654 3 445567899999999977 8999998654
No 37
>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=52.24 E-value=15 Score=25.11 Aligned_cols=31 Identities=19% Similarity=0.207 Sum_probs=22.1
Q ss_pred HHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhh
Q 022828 110 IPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYE 145 (291)
Q Consensus 110 ipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~ 145 (291)
..||+.+|+. +.....+||+.+|+++..|..
T Consensus 6 ~~Il~~Lq~d-----~r~s~~~la~~lglS~~~v~~ 36 (42)
T PF13404_consen 6 RKILRLLQED-----GRRSYAELAEELGLSESTVRR 36 (42)
T ss_dssp HHHHHHHHH------TTS-HHHHHHHHTS-HHHHHH
T ss_pred HHHHHHHHHc-----CCccHHHHHHHHCcCHHHHHH
Confidence 3578888863 455678899999999998864
No 38
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=50.40 E-value=9.8 Score=25.96 Aligned_cols=36 Identities=22% Similarity=0.479 Sum_probs=24.9
Q ss_pred HHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhhhhhhcccccc
Q 022828 112 LLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEVATFYSMFNRS 156 (291)
Q Consensus 112 iL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~VaTFY~~f~~~ 156 (291)
.++.+.++ || ..-.++.||+.+|++.. +||.+|..+
T Consensus 5 a~~l~~~~--G~-~~~s~~~Ia~~~gvs~~------~~y~~f~~k 40 (47)
T PF00440_consen 5 ALELFAEK--GY-EAVSIRDIARRAGVSKG------SFYRYFPSK 40 (47)
T ss_dssp HHHHHHHH--HT-TTSSHHHHHHHHTSCHH------HHHHHCSSH
T ss_pred HHHHHHHh--CH-HhCCHHHHHHHHccchh------hHHHHcCCH
Confidence 34455543 44 45568899999999976 678787653
No 39
>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=49.45 E-value=17 Score=27.20 Aligned_cols=37 Identities=19% Similarity=0.382 Sum_probs=22.9
Q ss_pred cccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCC-chhhhh
Q 022828 106 QSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVA-PIRVYE 145 (291)
Q Consensus 106 ~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip-~~~V~~ 145 (291)
|..++..+....+.+ ||-| .+.+||+.+|+. ++-|+.
T Consensus 8 Q~~vL~~I~~~~~~~-G~~P--t~rEIa~~~g~~S~~tv~~ 45 (65)
T PF01726_consen 8 QKEVLEFIREYIEEN-GYPP--TVREIAEALGLKSTSTVQR 45 (65)
T ss_dssp HHHHHHHHHHHHHHH-SS-----HHHHHHHHTSSSHHHHHH
T ss_pred HHHHHHHHHHHHHHc-CCCC--CHHHHHHHhCCCChHHHHH
Confidence 445666666655555 7765 788899999986 665543
No 40
>PRK13756 tetracycline repressor protein TetR; Provisional
Probab=48.93 E-value=15 Score=32.99 Aligned_cols=43 Identities=21% Similarity=0.308 Sum_probs=30.5
Q ss_pred cccHHH-HHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhhhhhhccccccc
Q 022828 106 QSAVIP-LLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEVATFYSMFNRSK 157 (291)
Q Consensus 106 ~~alip-iL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~VaTFY~~f~~~P 157 (291)
++.||. .+.++.+ . | +..-.|..||+.+|++++ ++|++|..|.
T Consensus 6 re~Il~aA~~l~~e-~-G-~~~lsmr~lA~~lgv~~~------slY~hf~~K~ 49 (205)
T PRK13756 6 KEKVIDSALELLNE-V-G-IEGLTTRKLAQKLGVEQP------TLYWHVKNKR 49 (205)
T ss_pred HHHHHHHHHHHHHH-c-C-cccCCHHHHHHHhCCCch------HHHHHcCCHH
Confidence 344554 4555543 4 6 677789999999999987 7888886544
No 41
>PLN00178 sulfite reductase
Probab=48.80 E-value=78 Score=33.56 Aligned_cols=90 Identities=14% Similarity=0.228 Sum_probs=50.6
Q ss_pred CCCCHHHHHHHHHHh------------------CCCchhhhhhhhhhcccccc---cCC--ceEEEEcCCC-cccccC--
Q 022828 122 GWLPVSAMNEVAKII------------------EVAPIRVYEVATFYSMFNRS---KVG--KYHLLVCGTT-PCMVRG-- 175 (291)
Q Consensus 122 GyIp~eam~~IAe~L------------------~ip~~~V~~VaTFY~~f~~~---P~g--K~~I~VC~gt-sC~~~G-- 175 (291)
|.|+.+.|..||++. +|++.++.+|...-.-+-.. +.+ ...+.-|.|. -|...-
T Consensus 415 Grit~~~l~~La~iAe~yg~~iRlT~~Qnlil~~I~~~~~~~i~~~L~~~Gl~~~~~~~~~~r~~vAC~G~~~C~lA~~e 494 (623)
T PLN00178 415 GRIKGEAKKALREVIEKYNLPVRLTPNQNLILCDIRPAWKEPITAALAAAGLLEPEEVDPLNRTAMACPALPLCPLAITE 494 (623)
T ss_pred eecCHHHHHHHHHHHHHhCCcEEEeCCCCEEEcCCCHHHHHHHHHHHHhCCCCCCCCCCcceeeeeecCCCCCCcccHHH
Confidence 556667777655553 67777666665443322222 111 2345679994 675432
Q ss_pred hH----HHHHHHHHHhCCCCCcccCCCcEEEEEecCCCCCCC
Q 022828 176 SR----EIEDALLKHLGVKRNEVTKDGLFSVGEMECMGCCVN 213 (291)
Q Consensus 176 s~----~lleaL~~~Lgi~~Gett~DG~ftL~~v~CLG~C~~ 213 (291)
++ .|.+.+++.+. +.+ ...+..|+|.-+||-..|..
T Consensus 495 t~~~a~~l~~~l~~~~~-~~~-l~~~~~i~I~vSGCpNgCar 534 (623)
T PLN00178 495 AERGIPDILKRVRAMFN-KVG-LKYDESVVVRMTGCPNGCAR 534 (623)
T ss_pred HHHHHHHHHHHHHHHHh-hcC-CCCCCceEEEEeCCCccccc
Confidence 33 33444444432 111 11256799999999999985
No 42
>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR. Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.
Probab=46.99 E-value=26 Score=28.59 Aligned_cols=46 Identities=17% Similarity=0.294 Sum_probs=32.0
Q ss_pred hhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhh
Q 022828 88 TNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVY 144 (291)
Q Consensus 88 ~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~ 144 (291)
+....+.++|++.|++ + .-+=.|+..++. ..++||+.||||+..|+
T Consensus 96 ~~~~~l~~~l~~Lp~~--~-r~v~~l~~~~~~--------s~~EIA~~l~is~~tV~ 141 (142)
T TIGR03209 96 DLEFEFNDLISILPNK--Q-KKIIYMKFFEDM--------KEIDIAKKLHISRQSVY 141 (142)
T ss_pred HHHHHHHHHHHhCCHH--H-HHHHHHHHHcCC--------CHHHHHHHHCcCHHhhc
Confidence 3456788999999962 2 234445555532 46899999999998775
No 43
>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=45.94 E-value=40 Score=24.92 Aligned_cols=22 Identities=23% Similarity=0.348 Sum_probs=20.0
Q ss_pred CC----CCHHHHHHHHHHhCCCchhh
Q 022828 122 GW----LPVSAMNEVAKIIEVAPIRV 143 (291)
Q Consensus 122 Gy----Ip~eam~~IAe~L~ip~~~V 143 (291)
|| ++.+..+++|+.|||+...|
T Consensus 24 ~y~~~~~~~~~r~~la~~lgl~~~vv 49 (58)
T TIGR01565 24 GWKLKDKRREEVREFCEEIGVTRKVF 49 (58)
T ss_pred CCCCCCCCHHHHHHHHHHhCCCHHHe
Confidence 88 99999999999999998754
No 44
>PF09999 DUF2240: Uncharacterized protein conserved in archaea (DUF2240); InterPro: IPR018716 This family of various hypothetical archaeal proteins has no known function.
Probab=45.69 E-value=38 Score=29.49 Aligned_cols=75 Identities=19% Similarity=0.213 Sum_probs=47.6
Q ss_pred ccceeccCCCCCCCCCCCCCChh-----hHH----HHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHH-HHHHH
Q 022828 66 LELCKHLDSPDNNPDLPWKFSDT-----NKE----KVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMN-EVAKI 135 (291)
Q Consensus 66 ~~~~~h~~~~~~~~~~~~~~~~~-----~~~----~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~-~IAe~ 135 (291)
+.|....|... -.+|-.|.+. +.. .++.|.++-.- .+..++..+...|+.++|.|+.++.. .+|+.
T Consensus 57 ~~l~~~Fd~~~--v~iP~~FkP~~~~l~e~~~fe~ild~ia~~~g~--~~~evv~~in~~q~~~~~~l~~e~aall~ake 132 (144)
T PF09999_consen 57 GYLVPNFDPSE--VEIPLGFKPDEEILQERDPFERILDYIAAKTGI--EKQEVVAEINELQEELGGLLDPEAAALLYAKE 132 (144)
T ss_pred CEEEEecCccc--cccCCCCCCcHHHHhcccHHHHHHHHHHHhcCC--CHHHHHHHHHHHHHHHhccCCHHHHHHHHHHH
Confidence 34444444433 4556666653 122 34444444543 45668889999999886688888765 56999
Q ss_pred hCCCchhhh
Q 022828 136 IEVAPIRVY 144 (291)
Q Consensus 136 L~ip~~~V~ 144 (291)
.|++.++.+
T Consensus 133 ~Gvdv~~~~ 141 (144)
T PF09999_consen 133 KGVDVSDFA 141 (144)
T ss_pred hCCCHHHHh
Confidence 999887754
No 45
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=45.64 E-value=29 Score=29.75 Aligned_cols=47 Identities=11% Similarity=0.169 Sum_probs=34.2
Q ss_pred hhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhh
Q 022828 88 TNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYE 145 (291)
Q Consensus 88 ~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~ 145 (291)
+....|++.|++-|+ +...+-+|+.++.. ..++||+.||+|+..|..
T Consensus 116 ~~~~~l~~~l~~Lp~---~~R~v~~L~~~~g~--------s~~EIA~~lgis~~tVk~ 162 (178)
T PRK12529 116 ETLHEIDALLDTLRP---RVKQAFLMATLDGM--------KQKDIAQALDIALPTVKK 162 (178)
T ss_pred HHHHHHHHHHHhCCH---HHHHHHHHHHHcCC--------CHHHHHHHHCCCHHHHHH
Confidence 345568899999996 33455566666532 368999999999998765
No 46
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=45.33 E-value=34 Score=28.14 Aligned_cols=47 Identities=15% Similarity=0.133 Sum_probs=33.3
Q ss_pred hhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhh
Q 022828 88 TNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYE 145 (291)
Q Consensus 88 ~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~ 145 (291)
+....+.+.|++.|+. ..-+=.|+.++. + ..++||+.||+|+..|+.
T Consensus 95 ~~~~~l~~~l~~Lp~~---~r~v~~l~~~~g----~----s~~EIA~~lgis~~tV~~ 141 (161)
T PRK09047 95 QVLQLIEEAIQKLPAR---QREAFLLRYWED----M----DVAETAAAMGCSEGSVKT 141 (161)
T ss_pred HHHHHHHHHHHhCCHH---HHHHHHHHHHhc----C----CHHHHHHHHCCCHHHHHH
Confidence 3456688999999962 234445555553 2 378999999999998765
No 47
>COG0155 CysI Sulfite reductase, beta subunit (hemoprotein) [Inorganic ion transport and metabolism]
Probab=45.16 E-value=88 Score=32.51 Aligned_cols=87 Identities=11% Similarity=0.243 Sum_probs=50.0
Q ss_pred ceEEEEcCC-Cccccc--ChHHHHHHHHHHhCCCCCcccCCCcEEEEEecCCCCCCCCC--------------eEEEccc
Q 022828 160 KYHLLVCGT-TPCMVR--GSREIEDALLKHLGVKRNEVTKDGLFSVGEMECMGCCVNAP--------------MITVADY 222 (291)
Q Consensus 160 K~~I~VC~g-tsC~~~--Gs~~lleaL~~~Lgi~~Gett~DG~ftL~~v~CLG~C~~aP--------------vV~Vnd~ 222 (291)
+..+.-|.| ..|.+. -++.++..+.+++.-...+. |-.++|.-+||...|.... .|.+.+.
T Consensus 376 ~~~~~AC~G~p~C~lA~aet~~~a~~i~~~l~~~~~~~--~~~i~i~isGCpn~Ca~~~~a~Igl~G~~~~~y~v~lGG~ 453 (510)
T COG0155 376 RRNSIACVGLPTCALALAETERDAPRIIARLEDLLDKH--GLPITLHISGCPNGCGRPHLAEIGLVGKAKGGYQVYLGGG 453 (510)
T ss_pred hhhcccCCCCCchhhhHhhHHHHHHHHHHHHHhhhccc--CCceeEEeccCcchhcCcccCceeEeeccCcceEEEecCC
Confidence 456899999 678664 34555555555554211110 1158999999999998632 2333221
Q ss_pred CCCCCCccceE-ecCCChhhHHHHHHHHH
Q 022828 223 SNGSEGYTYNY-YEDVTPKRVIEIVEMLR 250 (291)
Q Consensus 223 ~~G~~g~~~~~-Y~~vTpE~V~~ILe~l~ 250 (291)
.++..+ ..+ -++++.+++.+.++.+.
T Consensus 454 ~~~~~~--~~~~~~~~~~~~i~~~~~~l~ 480 (510)
T COG0155 454 ADGTRG--GKLYGENVPAEEILDAIDRLI 480 (510)
T ss_pred CCCCcc--ceeecCCCCHHHHHHHHHHHH
Confidence 111111 134 35689988777776654
No 48
>TIGR02374 nitri_red_nirB nitrite reductase [NAD(P)H], large subunit.
Probab=44.71 E-value=1.9e+02 Score=31.29 Aligned_cols=140 Identities=13% Similarity=0.138 Sum_probs=86.5
Q ss_pred CCCChhhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhhhhhhcccccccCC--c
Q 022828 83 WKFSDTNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEVATFYSMFNRSKVG--K 160 (291)
Q Consensus 83 ~~~~~~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~VaTFY~~f~~~P~g--K 160 (291)
-.+|++++..|-++.++|...+ +.+ .--|+...-||+.+-+..|-+.|...-.. ...| -
T Consensus 563 G~lt~~ql~~la~ia~~yg~~~-----i~i-T~~Q~i~l~gi~~~~l~~i~~~L~~~gl~-------------~~~g~~~ 623 (785)
T TIGR02374 563 GRTNPEQLRTIANIAEAYSIPY-----VKI-TGGQRLDLFGAKKDDLPNIWKDLKMPGYE-------------HAYGKAL 623 (785)
T ss_pred cccCHHHHHHHHHHHHHhCCCe-----EEE-cCCceEEECCCCHHHHHHHHHHHHhCCCC-------------CCCCCCc
Confidence 3479999999999999997421 111 11233334689999999998888532111 1112 2
Q ss_pred eEEEEcCCC-cccc--cChHHHHHHHHHHhCCCCCcccCCCcEEEEEecCCCCCCCCCe-------------EEEcccCC
Q 022828 161 YHLLVCGTT-PCMV--RGSREIEDALLKHLGVKRNEVTKDGLFSVGEMECMGCCVNAPM-------------ITVADYSN 224 (291)
Q Consensus 161 ~~I~VC~gt-sC~~--~Gs~~lleaL~~~Lgi~~Gett~DG~ftL~~v~CLG~C~~aPv-------------V~Vnd~~~ 224 (291)
..|.-|.|+ -|.. .-+..+...|++.+. +. ....+|.+.-+||...|...-+ |.|.+
T Consensus 624 r~v~aC~G~~~C~~g~~ds~~la~~l~~~~~---~~-~~p~k~ki~vSGC~~~C~~~~~~DiG~i~~~~g~~v~vGG--- 696 (785)
T TIGR02374 624 RTVKTCVGSQWCRYGNQDSVQLAIQLERRYE---GL-RTPHKIKIGVSGCERECAEAAGKDVGVIATEKGWNLYVGG--- 696 (785)
T ss_pred cCcccCCCccccCcchhhHHHHHHHHHHHhc---cc-CCCCceEEEEECCccccchhhhCcEEEEEecCCeEEEECC---
Confidence 357889885 5753 336677778877774 11 1234799999999999985422 22221
Q ss_pred CCCCcc----ceEecCCChhhHHHHHHHH
Q 022828 225 GSEGYT----YNYYEDVTPKRVIEIVEML 249 (291)
Q Consensus 225 G~~g~~----~~~Y~~vTpE~V~~ILe~l 249 (291)
..|.+ ..+...+++|++.++++.+
T Consensus 697 -~~g~~~~~a~~l~~~~~~e~v~~~i~~~ 724 (785)
T TIGR02374 697 -NGGTHPRHGDLLAVDEDEETLIGYIDRF 724 (785)
T ss_pred -cCCCCCcceeeecCCCCHHHHHHHHHHH
Confidence 11111 1334457888888888764
No 49
>PRK14989 nitrite reductase subunit NirD; Provisional
Probab=44.31 E-value=2.2e+02 Score=31.36 Aligned_cols=144 Identities=13% Similarity=0.111 Sum_probs=89.9
Q ss_pred CCChhhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHh---CCCchhhhhhhhhhcccccccCCc
Q 022828 84 KFSDTNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKII---EVAPIRVYEVATFYSMFNRSKVGK 160 (291)
Q Consensus 84 ~~~~~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L---~ip~~~V~~VaTFY~~f~~~P~gK 160 (291)
.+|++++..|-++.++|.. + + -|---|+...-||+.+-+..|-+.| |++....++ ..-
T Consensus 575 ~lt~~ql~~ia~iA~kyg~-~-----~-~iT~~Q~i~L~~i~~~~l~~v~~~L~~~Gl~~~~~~g------------~~v 635 (847)
T PRK14989 575 EITPEGLMAVGRIAREFNL-Y-----T-KITGSQRIGLFGAQKDDLPEIWRQLIEAGFETGHAYA------------KAL 635 (847)
T ss_pred EeCHHHHHHHHHHHHHHCC-c-----E-EEcCCCceEeCCCCHHHHHHHHHHHHHCCCCcCCCCC------------CCc
Confidence 3799999999999999973 1 1 1122343334789999999999887 666542211 112
Q ss_pred eEEEEcCCCc-ccc--cChHHHHHHHHHHhCCCCCcccCCCcEEEEEecCCCCCCCCCeEEEc--cc-------CCCCCC
Q 022828 161 YHLLVCGTTP-CMV--RGSREIEDALLKHLGVKRNEVTKDGLFSVGEMECMGCCVNAPMITVA--DY-------SNGSEG 228 (291)
Q Consensus 161 ~~I~VC~gts-C~~--~Gs~~lleaL~~~Lgi~~Gett~DG~ftL~~v~CLG~C~~aPvV~Vn--d~-------~~G~~g 228 (291)
..|.-|.|+. |.. .-+..+...|++++. +.. ..-+|.+.-+||...|..+-+--|. .. -.|..|
T Consensus 636 r~v~aC~G~~~C~~g~~dt~~la~~l~~~~~---~~~-~P~k~ki~vSGC~~~C~~~~i~DiG~i~~~~G~~v~vGG~~G 711 (847)
T PRK14989 636 RMAKTCVGSTWCRYGVGDSVGLGVELENRYK---GIR-TPHKMKFGVSGCTRECAEAQGKDVGIIATEKGWNLYVCGNGG 711 (847)
T ss_pred CceeeCCCCCccccccccHHHHHHHHHHHhc---cCC-CCCceEEEEeCCcccccccccccEEEEEecCceEEEECCCCC
Confidence 4588999874 632 236677777887763 211 2347999999999999864432110 00 011111
Q ss_pred c----cceEecCCChhhHHHHHHHHH
Q 022828 229 Y----TYNYYEDVTPKRVIEIVEMLR 250 (291)
Q Consensus 229 ~----~~~~Y~~vTpE~V~~ILe~l~ 250 (291)
. ...+...++++++.++++.+.
T Consensus 712 ~~~~~g~~l~~~~~~~~v~~~i~~~l 737 (847)
T PRK14989 712 MKPRHADLLAADLDRETLIKYLDRFM 737 (847)
T ss_pred CCCcceeeecCCCCHHHHHHHHHHHH
Confidence 1 123556789999998887743
No 50
>PHA01812 hypothetical protein
Probab=41.90 E-value=12 Score=30.66 Aligned_cols=44 Identities=18% Similarity=0.314 Sum_probs=33.0
Q ss_pred cccceeccCCCCCCCCCCCCCChhhHHH--HHHHHHhCCCCCCcccHHHHHHH
Q 022828 65 CLELCKHLDSPDNNPDLPWKFSDTNKEK--VKEILSHYPSNYKQSAVIPLLDL 115 (291)
Q Consensus 65 ~~~~~~h~~~~~~~~~~~~~~~~~~~~~--i~~il~~yp~~~~~~alipiL~~ 115 (291)
.|.|+.|+||-. .|+|.+.+++- +.+++++|.- ++..++-.|.-
T Consensus 5 kdilsrhqntla-----rfefeekerefiklselvekygm--kkeyivralft 50 (122)
T PHA01812 5 KDILSRHQNTLA-----RFEFEEKEREFIKLSELVEKYGM--KKEYIVRALFT 50 (122)
T ss_pred HHHHHHhhhhHh-----heeeHHHHHHHHHHHHHHHHhCc--cHHHHHHHHHc
Confidence 478889998876 78998877764 5589999984 66666666643
No 51
>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=40.96 E-value=36 Score=25.19 Aligned_cols=32 Identities=19% Similarity=0.172 Sum_probs=22.7
Q ss_pred HHHhcCCCCCHHHHHHHHHHhCCCchhhhhhhhhh
Q 022828 116 AQQQHGGWLPVSAMNEVAKIIEVAPIRVYEVATFY 150 (291)
Q Consensus 116 ~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~VaTFY 150 (291)
+++++ |. .+..++||+.|||+..+|..+..+-
T Consensus 13 L~~~l-gr--~Pt~eEiA~~lgis~~~v~~~l~~~ 44 (78)
T PF04539_consen 13 LEQEL-GR--EPTDEEIAEELGISVEEVRELLQAS 44 (78)
T ss_dssp HHHHH-SS----BHHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHh-CC--CCCHHHHHHHHcccHHHHHHHHHhC
Confidence 33344 66 4667899999999999999987654
No 52
>PRK00767 transcriptional regulator BetI; Validated
Probab=39.95 E-value=20 Score=30.37 Aligned_cols=44 Identities=16% Similarity=0.249 Sum_probs=30.8
Q ss_pred CcccHHH-HHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhhhhhhccccccc
Q 022828 105 KQSAVIP-LLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEVATFYSMFNRSK 157 (291)
Q Consensus 105 ~~~alip-iL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~VaTFY~~f~~~P 157 (291)
++..+|. .+..+-+ . ||-. -.++.||+..||+.. +||.+|..+.
T Consensus 10 ~r~~Il~aA~~lf~~-~-G~~~-~s~~~Ia~~aGvs~g------slY~~F~~Ke 54 (197)
T PRK00767 10 RRQQLIDATLRAIGE-V-GLLD-ATIAQIARRAGVSTG------IISHYFGGKD 54 (197)
T ss_pred HHHHHHHHHHHHHHH-c-Cccc-CCHHHHHHHhCCCHH------HHHHHhCCHH
Confidence 4455554 4555543 4 7754 789999999999865 7888886544
No 53
>PF13309 HTH_22: HTH domain
Probab=39.54 E-value=54 Score=24.26 Aligned_cols=54 Identities=15% Similarity=0.246 Sum_probs=36.4
Q ss_pred HHHHHHHHhCCCC---CCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhh
Q 022828 91 EKVKEILSHYPSN---YKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYE 145 (291)
Q Consensus 91 ~~i~~il~~yp~~---~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~ 145 (291)
..|++++.++... -.+.-=+.++..++++ +=|.=..++..||+.|||+...||-
T Consensus 5 ~~i~~~~~~~~~~~~~l~~~~k~~iV~~L~~~-G~F~lKgav~~vA~~L~iS~~TVY~ 61 (64)
T PF13309_consen 5 SIIEEVIAEVGKPPSRLSKEEKKEIVRQLYEK-GIFLLKGAVEYVAEKLGISRATVYR 61 (64)
T ss_pred HHHHHHHHHhCCChhhCCHHHHHHHHHHHHHC-CCcccCcHHHHHHHHHCCCHHHHHH
Confidence 3466666665431 1233345666666653 3467789999999999999988774
No 54
>TIGR03384 betaine_BetI transcriptional repressor BetI. BetI is a DNA-binding transcriptional repressor of the bet (betaine) regulon. In sequence, it is related to TetR (pfam00440). Choline, through BetI, induces the expression of the betaine biosynthesis genes betA and betB by derepression. The choline porter gene betT is also part of this regulon in Escherichia coli. Note that a different transcriptional regulator, ArcA, controls the expression of bet regulon genes in response to oxygen, as BetA is an oxygen-dependent enzyme.
Probab=39.45 E-value=22 Score=29.88 Aligned_cols=43 Identities=14% Similarity=0.226 Sum_probs=30.0
Q ss_pred cccHHH-HHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhhhhhhccccccc
Q 022828 106 QSAVIP-LLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEVATFYSMFNRSK 157 (291)
Q Consensus 106 ~~alip-iL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~VaTFY~~f~~~P 157 (291)
+..+|. .+..+.+ + ||= .-.|..||+..||+.. +||++|..+.
T Consensus 10 r~~Il~aA~~lf~~-~-G~~-~~s~~~IA~~agvsk~------~ly~~F~sK~ 53 (189)
T TIGR03384 10 RAELIDATIESIGE-R-GSL-DVTIAQIARRAGVSSG------IISHYFGGKQ 53 (189)
T ss_pred HHHHHHHHHHHHHh-c-Ccc-cCCHHHHHHHhCCCHH------HHHHHcCCHH
Confidence 444555 4455544 4 764 6778999999999976 7888886544
No 55
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=38.89 E-value=28 Score=23.97 Aligned_cols=44 Identities=25% Similarity=0.339 Sum_probs=26.7
Q ss_pred HHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhh
Q 022828 91 EKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYE 145 (291)
Q Consensus 91 ~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~ 145 (291)
+.|.+.|+.-|+ +...+-.|+.++ .-...+||+.+|+++..|+.
T Consensus 2 ~~l~~~l~~L~~---~~r~i~~l~~~~--------g~s~~eIa~~l~~s~~~v~~ 45 (54)
T PF08281_consen 2 EALQQALAQLPE---RQREIFLLRYFQ--------GMSYAEIAEILGISESTVKR 45 (54)
T ss_dssp HHHHHHHHCS-H---HHHHHHHHHHTS-----------HHHHHHHCTS-HHHHHH
T ss_pred HHHHHHHHCCCH---HHHHHHHHHHHH--------CcCHHHHHHHHCcCHHHHHH
Confidence 567788888885 223333444443 23568999999999998764
No 56
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=38.37 E-value=51 Score=27.25 Aligned_cols=48 Identities=17% Similarity=0.161 Sum_probs=32.8
Q ss_pred hhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhh
Q 022828 88 TNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEV 146 (291)
Q Consensus 88 ~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~V 146 (291)
+....+...|++-|++ .+ -+-+|+.++.. ..++||+.||+++..|+.-
T Consensus 95 e~~~~l~~~l~~Lp~~-~r--~v~~l~~~~g~--------s~~EIA~~lgis~~tV~~~ 142 (160)
T PRK09642 95 EQKLLIAQKLRELPEN-YR--DVVLAHYLEEK--------SYQEIALQEKIEVKTVEMK 142 (160)
T ss_pred HHHHHHHHHHHhCCHH-HH--HHHHHHHHhCC--------CHHHHHHHHCCCHHHHHHH
Confidence 3445688899999963 22 34445555432 3679999999999988653
No 57
>COG1309 AcrR Transcriptional regulator [Transcription]
Probab=37.26 E-value=21 Score=28.20 Aligned_cols=29 Identities=28% Similarity=0.510 Sum_probs=22.6
Q ss_pred CCCCHHHHHHHHHHhCCCchhhhhhhhhhccccccc
Q 022828 122 GWLPVSAMNEVAKIIEVAPIRVYEVATFYSMFNRSK 157 (291)
Q Consensus 122 GyIp~eam~~IAe~L~ip~~~V~~VaTFY~~f~~~P 157 (291)
|| ..-.+..||+.+||+.. |||.+|..+.
T Consensus 29 G~-~~~t~~~Ia~~agvs~~------~~Y~~f~~K~ 57 (201)
T COG1309 29 GY-AATTVDEIAKAAGVSKG------TLYRHFPSKE 57 (201)
T ss_pred Cc-CCCCHHHHHHHhCCCcc------hhHHHcCCHH
Confidence 55 34467889999999976 7898888765
No 58
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=36.78 E-value=25 Score=30.42 Aligned_cols=44 Identities=16% Similarity=0.200 Sum_probs=29.4
Q ss_pred cccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhhhhhhccccccc
Q 022828 106 QSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEVATFYSMFNRSK 157 (291)
Q Consensus 106 ~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~VaTFY~~f~~~P 157 (291)
+..|+..-..+-.+. || ..-.|+.||+..||+.. |||.+|..+.
T Consensus 13 r~~Il~aa~~lf~~~-G~-~~~ti~~Ia~~agvsk~------t~Y~~F~sKe 56 (213)
T PRK09975 13 RQELIETAIAQFALR-GV-SNTTLNDIADAANVTRG------AIYWHFENKT 56 (213)
T ss_pred HHHHHHHHHHHHHHc-Cc-ccCCHHHHHHHcCCCHH------HHHHHcCCHH
Confidence 445666333333333 65 55678999999999976 8888887554
No 59
>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=36.45 E-value=36 Score=24.92 Aligned_cols=30 Identities=20% Similarity=0.206 Sum_probs=23.5
Q ss_pred HHHHHHHHhCCCchhhhhhhhhhccccccc
Q 022828 128 AMNEVAKIIEVAPIRVYEVATFYSMFNRSK 157 (291)
Q Consensus 128 am~~IAe~L~ip~~~V~~VaTFY~~f~~~P 157 (291)
.+.+||+.||+|...||.-+.-|..=...|
T Consensus 15 ~~~eIA~~Lg~~~~TV~~W~~r~~W~~~~~ 44 (58)
T PF06056_consen 15 SIKEIAEELGVPRSTVYSWKDRYKWDELLP 44 (58)
T ss_pred CHHHHHHHHCCChHHHHHHHHhhCccccCc
Confidence 467899999999999999887775544443
No 60
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=36.11 E-value=50 Score=28.20 Aligned_cols=48 Identities=10% Similarity=0.136 Sum_probs=33.8
Q ss_pred hhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhh
Q 022828 88 TNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEV 146 (291)
Q Consensus 88 ~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~V 146 (291)
+....+++.|+..|+ +...+=+|+.++.. ..++||+.||||+..|+--
T Consensus 118 ~~~~~l~~~l~~L~~---~~r~v~~l~~~~g~--------s~~EIA~~l~is~~tV~~~ 165 (181)
T PRK12536 118 EARRDLGKLLEQLPD---RQRLPIVHVKLEGL--------SVAETAQLTGLSESAVKVG 165 (181)
T ss_pred HHHHHHHHHHHHCCH---HHHHHHHHHHHcCC--------CHHHHHHHHCCCHHHHHHH
Confidence 455678999999996 33344455555432 4689999999999988653
No 61
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=35.24 E-value=54 Score=28.39 Aligned_cols=45 Identities=11% Similarity=0.186 Sum_probs=32.5
Q ss_pred HHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhh
Q 022828 91 EKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEV 146 (291)
Q Consensus 91 ~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~V 146 (291)
..++..|++-|+ +...+-+|+.++.. ...+||+.||+|+..|+.-
T Consensus 126 ~~l~~~l~~Lp~---~~R~v~~L~~~~g~--------s~~EIA~~lgis~~tVk~~ 170 (189)
T PRK12530 126 LIFEACLNHLPA---QQARVFMMREYLEL--------SSEQICQECDISTSNLHVL 170 (189)
T ss_pred HHHHHHHHhCCH---HHHHHHhHHHHcCC--------CHHHHHHHHCCCHHHHHHH
Confidence 457888999996 33345566666532 3789999999999988653
No 62
>TIGR03613 RutR pyrimidine utilization regulatory protein R. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the TetR family of transcriptional regulators defined by the N-teminal model pfam00440 and the C-terminal model pfam08362 (YcdC-like protein, C-terminal region).
Probab=34.95 E-value=25 Score=30.10 Aligned_cols=43 Identities=16% Similarity=0.371 Sum_probs=30.4
Q ss_pred cccHHH-HHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhhhhhhccccccc
Q 022828 106 QSAVIP-LLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEVATFYSMFNRSK 157 (291)
Q Consensus 106 ~~alip-iL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~VaTFY~~f~~~P 157 (291)
+..|+. .+..+.+ + || ..-.|..||+.+||+.. +||.+|..+.
T Consensus 10 r~~Il~aA~~lf~e-~-G~-~~~s~~~IA~~agvs~~------~lY~hF~sKe 53 (202)
T TIGR03613 10 RKAILSAALDTFSR-F-GF-HGTSLEQIAELAGVSKT------NLLYYFPSKD 53 (202)
T ss_pred HHHHHHHHHHHHHH-h-Cc-ccCCHHHHHHHhCCCHH------HHHHHcCCHH
Confidence 444555 5555554 3 64 55678999999999976 7888887654
No 63
>PRK10668 DNA-binding transcriptional repressor AcrR; Provisional
Probab=34.24 E-value=29 Score=30.13 Aligned_cols=43 Identities=21% Similarity=0.348 Sum_probs=29.7
Q ss_pred cccHHH-HHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhhhhhhccccccc
Q 022828 106 QSAVIP-LLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEVATFYSMFNRSK 157 (291)
Q Consensus 106 ~~alip-iL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~VaTFY~~f~~~P 157 (291)
+..|+. .++.+.+ + || ..-.|..||+..||+.. |||++|..+.
T Consensus 13 R~~Il~AA~~lf~e-~-G~-~~~t~~~Ia~~agvs~~------tlY~~F~sKe 56 (215)
T PRK10668 13 RQHILDAALRLFSQ-Q-GV-SATSLADIAKAAGVTRG------AIYWHFKNKS 56 (215)
T ss_pred HHHHHHHHHHHHHH-c-Cc-ccCCHHHHHHHhCCChH------HHHHHCCCHH
Confidence 444555 4555554 3 66 44568999999999976 8898887543
No 64
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=34.01 E-value=56 Score=28.16 Aligned_cols=48 Identities=8% Similarity=0.070 Sum_probs=33.8
Q ss_pred hhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhh
Q 022828 88 TNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEV 146 (291)
Q Consensus 88 ~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~V 146 (291)
+....+.+.|++-|++ ...+-+|..++. + ..++||+.||+|+..|+.-
T Consensus 119 e~~~~l~~~l~~Lp~~---~r~v~~L~~~~g----~----s~~EIA~~lgis~~tVk~~ 166 (185)
T PRK09649 119 EDLVEVTTMIADLTTD---QREALLLTQLLG----L----SYADAAAVCGCPVGTIRSR 166 (185)
T ss_pred HHHHHHHHHHHhCCHH---HhHHhhhHHHcC----C----CHHHHHHHHCCCHHHHHHH
Confidence 4556788999999962 234445555543 1 3789999999999887654
No 65
>PRK11640 putative transcriptional regulator; Provisional
Probab=33.50 E-value=31 Score=30.20 Aligned_cols=39 Identities=15% Similarity=0.256 Sum_probs=28.4
Q ss_pred HHH-HHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhhhhhhcccccc
Q 022828 109 VIP-LLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEVATFYSMFNRS 156 (291)
Q Consensus 109 lip-iL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~VaTFY~~f~~~ 156 (291)
+|. .++++.+ + || ..-.|+.|++..||+.. |||++|..+
T Consensus 6 il~~A~~lf~~-~-Gy-~~tsi~~I~~~aGv~k~------slY~~F~sK 45 (191)
T PRK11640 6 VLGEALKLLEQ-Q-GL-ANTTLEMLAERVDYPLD------ELQRFWPDR 45 (191)
T ss_pred HHHHHHHHHHH-h-Cc-ccCCHHHHHHHhCcCHH------HHHHHCCCH
Confidence 444 6667765 3 66 44568899999999987 889999543
No 66
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=33.22 E-value=65 Score=27.43 Aligned_cols=50 Identities=14% Similarity=0.295 Sum_probs=34.0
Q ss_pred CChhhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhh
Q 022828 85 FSDTNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYE 145 (291)
Q Consensus 85 ~~~~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~ 145 (291)
...+..+.+...|.+-|+ +...+-+|..++. -..++||+.||||..-|+.
T Consensus 103 ~~~~~~~~l~~~l~~Lp~---~~r~i~~l~~~e~--------~s~~EIA~~lgis~~tV~~ 152 (179)
T PRK12543 103 LSKESNQELIELIHKLPY---KLRQVIILRYLHD--------YSQEEIAQLLQIPIGTVKS 152 (179)
T ss_pred HHHHHHHHHHHHHHhCCH---HHHHHHHHHHHcc--------CCHHHHHHHHCCCHHHHHH
Confidence 345666788899999986 2223334444432 2578999999999887654
No 67
>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=32.89 E-value=66 Score=26.59 Aligned_cols=50 Identities=12% Similarity=0.161 Sum_probs=34.5
Q ss_pred ChhhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhh
Q 022828 86 SDTNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEV 146 (291)
Q Consensus 86 ~~~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~V 146 (291)
..+..+.+...|.+-|. +...+-.|..++. -..++||+.||+|...|+--
T Consensus 97 ~~~~~~~l~~~l~~L~~---~~r~i~~l~~~~g--------~s~~eIA~~lgis~~tV~~~ 146 (162)
T TIGR02983 97 DVALRAALARALRRLPA---RQRAVVVLRYYED--------LSEAQVAEALGISVGTVKSR 146 (162)
T ss_pred hHHHHHHHHHHHHhCCH---HHHHHhhhHHHhc--------CCHHHHHHHhCCCHHHHHHH
Confidence 44566778999999986 2233444444442 24789999999999988653
No 68
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=32.87 E-value=61 Score=27.27 Aligned_cols=47 Identities=11% Similarity=0.156 Sum_probs=32.3
Q ss_pred hhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhh
Q 022828 88 TNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYE 145 (291)
Q Consensus 88 ~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~ 145 (291)
+....+++.|++.|+ +...+-+|...+. + ..++||+.||+|...|..
T Consensus 107 ~~~~~l~~~l~~L~~---~~r~v~~L~~~eg----~----s~~EIA~~l~is~~tV~~ 153 (168)
T PRK12525 107 ETLLAIDRLLDGLSG---KARAAFLMSQLEG----L----TYVEIGERLGVSLSRIHQ 153 (168)
T ss_pred HHHHHHHHHHHhCCH---HHHHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHH
Confidence 334668889999986 2234445554542 2 478999999999987764
No 69
>PF12728 HTH_17: Helix-turn-helix domain
Probab=32.72 E-value=36 Score=23.22 Aligned_cols=20 Identities=20% Similarity=0.398 Sum_probs=16.7
Q ss_pred HHHHHHHhCCCchhhhhhhh
Q 022828 129 MNEVAKIIEVAPIRVYEVAT 148 (291)
Q Consensus 129 m~~IAe~L~ip~~~V~~VaT 148 (291)
.+++|+.|||+...||..+.
T Consensus 4 ~~e~a~~l~is~~tv~~~~~ 23 (51)
T PF12728_consen 4 VKEAAELLGISRSTVYRWIR 23 (51)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46899999999998888763
No 70
>PF13700 DUF4158: Domain of unknown function (DUF4158)
Probab=32.52 E-value=1e+02 Score=26.44 Aligned_cols=55 Identities=18% Similarity=0.233 Sum_probs=36.1
Q ss_pred CCCCChhhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCC-------CCHHHHHHHHHHhCCCchh
Q 022828 82 PWKFSDTNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGW-------LPVSAMNEVAKIIEVAPIR 142 (291)
Q Consensus 82 ~~~~~~~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~Gy-------Ip~eam~~IAe~L~ip~~~ 142 (291)
-|.+++++++.|.. .+-+ ..+=.++-.|--.|. .|+ +|.+.+++||+.|++++..
T Consensus 24 ~ftLs~~d~~~i~~--~r~~--~~rlgfalqL~~fr~--~g~f~~~~~~~p~~~i~~va~ql~~~~~~ 85 (166)
T PF13700_consen 24 YFTLSPEDLELINS--RRGP--ANRLGFALQLGYFRA--LGRFPDDPEDIPKADIEYVAKQLGLPPSD 85 (166)
T ss_pred HhCCCHHHHHHHhc--ccCC--ccchhHHHHHHHHhc--ccccccccccCCHHHHHHHHHHhCCchHH
Confidence 57788887776664 1122 134445555555553 254 6689999999999999864
No 71
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=32.49 E-value=88 Score=24.18 Aligned_cols=50 Identities=16% Similarity=0.232 Sum_probs=34.3
Q ss_pred CCCCChhhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhhh
Q 022828 82 PWKFSDTNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEVA 147 (291)
Q Consensus 82 ~~~~~~~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~Va 147 (291)
+|.+++++.+.++++...+..+ .. |+|+.+-+..+=..++++..+|..+.
T Consensus 1 ~~~ls~~~~~~l~~~F~~~D~d---------------~~-G~Is~~el~~~l~~~~~~~~ev~~i~ 50 (96)
T smart00027 1 DWAISPEDKAKYEQIFRSLDKN---------------QD-GTVTGAQAKPILLKSGLPQTLLAKIW 50 (96)
T ss_pred CCCCCHHHHHHHHHHHHHhCCC---------------CC-CeEeHHHHHHHHHHcCCCHHHHHHHH
Confidence 4678888888899888888742 12 67777766666555666666555443
No 72
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=32.34 E-value=65 Score=26.41 Aligned_cols=49 Identities=14% Similarity=0.225 Sum_probs=32.6
Q ss_pred hhhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhh
Q 022828 87 DTNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEV 146 (291)
Q Consensus 87 ~~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~V 146 (291)
++....+.+.+++.|+. +. -+-.|+.++ .-..++||+.||||...|+.-
T Consensus 99 ~~~~~~l~~~i~~L~~~--~r-~v~~l~~~~--------g~~~~eIA~~l~is~~tv~~~ 147 (159)
T TIGR02989 99 EDELQALEGCLEKLPER--QR-ELLQLRYQR--------GVSLTALAEQLGRTVNAVYKA 147 (159)
T ss_pred HHHHHHHHHHHHHCCHH--HH-HHHHHHHhc--------CCCHHHHHHHhCCCHHHHHHH
Confidence 44556788889999862 22 233333333 225789999999999988753
No 73
>PRK11202 DNA-binding transcriptional repressor FabR; Provisional
Probab=32.13 E-value=26 Score=30.62 Aligned_cols=43 Identities=26% Similarity=0.497 Sum_probs=28.5
Q ss_pred cccHHH-HHH-HHHHhcCCCCCHHHHHHHHHHhCCCchhhhhhhhhhccccccc
Q 022828 106 QSAVIP-LLD-LAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEVATFYSMFNRSK 157 (291)
Q Consensus 106 ~~alip-iL~-~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~VaTFY~~f~~~P 157 (291)
+..||. .+. .+.+ + || ..-.|+.||+..||+.. +||++|..+.
T Consensus 13 R~~Il~aA~~~l~~~-~-G~-~~~si~~IA~~Agvs~~------t~Y~hF~sKe 57 (203)
T PRK11202 13 RRALIDAAFSQLSAE-R-SF-SSLSLREVAREAGIAPT------SFYRHFRDMD 57 (203)
T ss_pred HHHHHHHHHHHHHhc-C-Cc-ccCCHHHHHHHhCCCcc------hHHHHCCCHH
Confidence 334554 344 2343 2 55 45678999999999976 8999996543
No 74
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=32.04 E-value=63 Score=26.73 Aligned_cols=47 Identities=17% Similarity=0.204 Sum_probs=31.5
Q ss_pred hhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhh
Q 022828 88 TNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYE 145 (291)
Q Consensus 88 ~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~ 145 (291)
+..+.+.+.|++.|+ +...+-.|..++. -..++||+.||+|...|+.
T Consensus 98 ~~~~~l~~~l~~L~~---~~r~v~~l~~~~~--------~s~~EIA~~lgis~~tV~~ 144 (163)
T PRK07037 98 DTLRHVADALSELPA---RTRYAFEMYRLHG--------ETQKDIARELGVSPTLVNF 144 (163)
T ss_pred HHHHHHHHHHHhCCH---HHHHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHH
Confidence 345667888889986 2223334444432 2478999999999998875
No 75
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=31.89 E-value=75 Score=24.68 Aligned_cols=39 Identities=15% Similarity=0.141 Sum_probs=31.4
Q ss_pred ccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhh
Q 022828 107 SAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYE 145 (291)
Q Consensus 107 ~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~ 145 (291)
..+.|+|..+++..+..-..+..+.|++.++++..+...
T Consensus 4 ~~~~piL~~L~~~g~~~~~~ei~~~v~~~~~ls~e~~~~ 42 (92)
T PF14338_consen 4 ELMPPILEALKDLGGSASRKEIYERVAERFGLSDEERNE 42 (92)
T ss_pred HHHHHHHHHHHHcCCCcCHHHHHHHHHHHhCCCHHHHHH
Confidence 467899999998554566778999999999999886554
No 76
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=31.48 E-value=37 Score=22.94 Aligned_cols=23 Identities=30% Similarity=0.440 Sum_probs=17.2
Q ss_pred HHHHHHHHhCCCchhhhhhhhhh
Q 022828 128 AMNEVAKIIEVAPIRVYEVATFY 150 (291)
Q Consensus 128 am~~IAe~L~ip~~~V~~VaTFY 150 (291)
...+||+.||++...|+-...=|
T Consensus 19 s~~~ia~~lgvs~~Tv~~w~kr~ 41 (50)
T PF13384_consen 19 SIREIAKRLGVSRSTVYRWIKRY 41 (50)
T ss_dssp -HHHHHHHHTS-HHHHHHHHT--
T ss_pred CHHHHHHHHCcCHHHHHHHHHHc
Confidence 56889999999999999887766
No 77
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=31.17 E-value=68 Score=27.07 Aligned_cols=48 Identities=17% Similarity=0.209 Sum_probs=32.9
Q ss_pred hhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhh
Q 022828 88 TNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEV 146 (291)
Q Consensus 88 ~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~V 146 (291)
+....+++.|++.|++ ...+-.|+.++. -..++||+.|||+..-|..-
T Consensus 108 ~~~~~l~~~l~~Lp~~---~r~v~~L~~~~g--------~s~~EIA~~lgis~~tV~~~ 155 (172)
T PRK12523 108 EDLKAIDRLLGKLSSK---ARAAFLYNRLDG--------MGHAEIAERLGVSVSRVRQY 155 (172)
T ss_pred HHHHHHHHHHHhCCHH---HHHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHH
Confidence 3445788999999962 223444554542 24689999999999987653
No 78
>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=30.55 E-value=42 Score=21.86 Aligned_cols=19 Identities=26% Similarity=0.415 Sum_probs=16.1
Q ss_pred HHHHHHHhCCCchhhhhhh
Q 022828 129 MNEVAKIIEVAPIRVYEVA 147 (291)
Q Consensus 129 m~~IAe~L~ip~~~V~~Va 147 (291)
++++|+.|||+...|+..+
T Consensus 4 ~~e~a~~lgis~~ti~~~~ 22 (49)
T TIGR01764 4 VEEAAEYLGVSKDTVYRLI 22 (49)
T ss_pred HHHHHHHHCCCHHHHHHHH
Confidence 5789999999999887766
No 79
>TIGR02041 CysI sulfite reductase (NADPH) hemoprotein, beta-component. In cyanobacteria and plant species, sulfite reductase ferredoxin (EC 1.8.7.1) catalyzes the reduction of sulfite to sulfide.
Probab=30.45 E-value=66 Score=33.25 Aligned_cols=74 Identities=11% Similarity=0.136 Sum_probs=44.0
Q ss_pred CCCchhhhhhhhhhccccccc---C-CceEEEEcCCC-ccccc--ChHHH----HHHHHHHhCCCCCcccCCCcEEEEEe
Q 022828 137 EVAPIRVYEVATFYSMFNRSK---V-GKYHLLVCGTT-PCMVR--GSREI----EDALLKHLGVKRNEVTKDGLFSVGEM 205 (291)
Q Consensus 137 ~ip~~~V~~VaTFY~~f~~~P---~-gK~~I~VC~gt-sC~~~--Gs~~l----leaL~~~Lgi~~Gett~DG~ftL~~v 205 (291)
+|++.++.++.....-+-..+ . ....|.-|.|+ -|... -++.+ .+.|.+.+.. .+. .+..++|.-+
T Consensus 384 ~v~~~~~~~l~~~l~~~gl~~~~~~~~~~~vvAC~G~~~C~~a~~dT~~~a~~l~~~l~~~~~~-~~~--~~~~~~I~iS 460 (541)
T TIGR02041 384 NVPEGGKAKIEALARQYGLIDGKVTALRRNSMACVALPTCPLAMAEAERYLPDFIDKLDNIMEK-HGL--ADEEIVLRMT 460 (541)
T ss_pred CCCHHHHHHHHHHHHHcCCCCCCCCceeeccEECCCccchhhhHHHHHHHHHHHHHHHHHHHHh-cCC--CCCceEEEEe
Confidence 778886666655544333322 1 13458899995 77642 23344 4455555431 121 2456899999
Q ss_pred cCCCCCCC
Q 022828 206 ECMGCCVN 213 (291)
Q Consensus 206 ~CLG~C~~ 213 (291)
||-..|..
T Consensus 461 GCpn~Ca~ 468 (541)
T TIGR02041 461 GCPNGCGR 468 (541)
T ss_pred cCCccccc
Confidence 99999985
No 80
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=30.29 E-value=68 Score=26.87 Aligned_cols=45 Identities=11% Similarity=0.217 Sum_probs=31.5
Q ss_pred HHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhh
Q 022828 90 KEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYE 145 (291)
Q Consensus 90 ~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~ 145 (291)
...+...|++.|+ +...+-+|+.++. + ..++||+.||+|..-|..
T Consensus 109 ~~~l~~~l~~L~~---~~r~vl~L~~~~g----~----s~~EIA~~lgis~~tV~~ 153 (173)
T PRK09645 109 RLLVADALAQLSP---EHRAVLVRSYYRG----W----STAQIAADLGIPEGTVKS 153 (173)
T ss_pred HHHHHHHHHhCCH---HHHHHHHHHHHcC----C----CHHHHHHHHCcCHHHHHH
Confidence 3468889999996 2334445555542 2 378999999999987754
No 81
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=30.28 E-value=73 Score=26.42 Aligned_cols=46 Identities=15% Similarity=0.164 Sum_probs=31.9
Q ss_pred hHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhh
Q 022828 89 NKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYE 145 (291)
Q Consensus 89 ~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~ 145 (291)
....+.+.|.+.|+ +...+-.|+.++.. ..++||+.||+|...|+.
T Consensus 103 ~~~~l~~~l~~L~~---~~r~v~~L~~~~g~--------s~~EIA~~l~is~~tV~~ 148 (161)
T PRK12528 103 TLVELDQLLDGLPP---LVKRAFLLAQVDGL--------GYGEIATELGISLATVKR 148 (161)
T ss_pred HHHHHHHHHHHCCH---HHHHHHHHHHHcCC--------CHHHHHHHHCCCHHHHHH
Confidence 34578888999996 22344455555532 368999999999987654
No 82
>PF14174 YycC: YycC-like protein
Probab=30.25 E-value=49 Score=24.22 Aligned_cols=21 Identities=10% Similarity=0.134 Sum_probs=19.1
Q ss_pred CCHHHHHHHHHHhCCCchhhh
Q 022828 124 LPVSAMNEVAKIIEVAPIRVY 144 (291)
Q Consensus 124 Ip~eam~~IAe~L~ip~~~V~ 144 (291)
||.+....+|+.||||.-++-
T Consensus 6 IS~eTA~kLs~~L~vPlE~lM 26 (53)
T PF14174_consen 6 ISPETAVKLSKKLGVPLEQLM 26 (53)
T ss_pred cCHHHHHHHHHHHCCcHHHHh
Confidence 899999999999999998764
No 83
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=30.18 E-value=35 Score=24.10 Aligned_cols=24 Identities=17% Similarity=0.434 Sum_probs=16.3
Q ss_pred CCCCHHHHHHHHHHhCCCchhhhh
Q 022828 122 GWLPVSAMNEVAKIIEVAPIRVYE 145 (291)
Q Consensus 122 GyIp~eam~~IAe~L~ip~~~V~~ 145 (291)
..++.+.+..||+.|++++.++.+
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 369999999999999999998754
No 84
>PF13518 HTH_28: Helix-turn-helix domain
Probab=29.54 E-value=71 Score=21.39 Aligned_cols=25 Identities=20% Similarity=0.325 Sum_probs=21.6
Q ss_pred HHHHHHHHhCCCchhhhhhhhhhcc
Q 022828 128 AMNEVAKIIEVAPIRVYEVATFYSM 152 (291)
Q Consensus 128 am~~IAe~L~ip~~~V~~VaTFY~~ 152 (291)
.+.+||+.+||+...|+....-|.-
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHHh
Confidence 5677999999999999999888754
No 85
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=29.21 E-value=75 Score=27.06 Aligned_cols=49 Identities=12% Similarity=0.121 Sum_probs=32.7
Q ss_pred hhhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhh
Q 022828 87 DTNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEV 146 (291)
Q Consensus 87 ~~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~V 146 (291)
.+..+.+.+.|+..|+ +...++ .|..++ .-..++||+.|||++..|+--
T Consensus 125 ~e~~~~l~~~l~~L~~--~~r~i~-~l~~~~--------g~s~~eIA~~lgis~~~v~~~ 173 (187)
T PRK12534 125 ASTRRRIDHCLAELEP--PRSELI-RTAFFE--------GITYEELAARTDTPIGTVKSW 173 (187)
T ss_pred HHHHHHHHHHHHhCCH--HHHHHH-HHHHHc--------CCCHHHHHHHhCCChhHHHHH
Confidence 3455688899999986 232232 233333 225789999999999988653
No 86
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=29.17 E-value=74 Score=26.97 Aligned_cols=48 Identities=8% Similarity=0.061 Sum_probs=32.4
Q ss_pred hhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhh
Q 022828 88 TNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEV 146 (291)
Q Consensus 88 ~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~V 146 (291)
+....++..|++.|+ +...+-.|..+|. + .+++||+.||+|+..|+.-
T Consensus 89 e~~~~l~~~l~~L~~---~~r~v~~l~~~~g----~----s~~eIA~~lgis~~tV~~~ 136 (170)
T TIGR02959 89 ELSQCIPPMIKELPD---EYREAIRLTELEG----L----SQQEIAEKLGLSLSGAKSR 136 (170)
T ss_pred HHHHHHHHHHHhCCH---HHHHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHH
Confidence 344567888899985 2234444444443 2 4789999999999887663
No 87
>PF15508 NAAA-beta: beta subunit of N-acylethanolamine-hydrolyzing acid amidase
Probab=29.01 E-value=1.8e+02 Score=22.90 Aligned_cols=44 Identities=18% Similarity=0.274 Sum_probs=31.2
Q ss_pred cHHHHHHHHHHhcCCCCCHH---HHHHHHHHhCCCchhhhhhhhhhc
Q 022828 108 AVIPLLDLAQQQHGGWLPVS---AMNEVAKIIEVAPIRVYEVATFYS 151 (291)
Q Consensus 108 alipiL~~~Q~~~~GyIp~e---am~~IAe~L~ip~~~V~~VaTFY~ 151 (291)
.+++++..+-....+++|.+ -|+-||+.+|||..+|--.--||.
T Consensus 48 ~~~~~v~~~~~~l~~~~~~~~~~EirGIA~~~gi~l~~iv~lN~~yE 94 (95)
T PF15508_consen 48 KVLDFVDKLLPHLLRYLPQPYAEEIRGIAKAAGIPLGDIVLLNLFYE 94 (95)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCCCHHHHHHHHHHhh
Confidence 46666665554433677755 466789999999999887777773
No 88
>PRK15008 HTH-type transcriptional regulator RutR; Provisional
Probab=28.85 E-value=38 Score=29.72 Aligned_cols=44 Identities=18% Similarity=0.365 Sum_probs=30.7
Q ss_pred cccHHH-HHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhhhhhhcccccccC
Q 022828 106 QSAVIP-LLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEVATFYSMFNRSKV 158 (291)
Q Consensus 106 ~~alip-iL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~VaTFY~~f~~~P~ 158 (291)
+..||. .++++-+ + || ..-.|..||+..||+.. +||.+|..+..
T Consensus 20 r~~IL~AA~~lf~e-~-Gy-~~~s~~dIA~~aGvs~g------tiY~hF~sKe~ 64 (212)
T PRK15008 20 KKAILSAALDTFSQ-F-GF-HGTRLEQIAELAGVSKT------NLLYYFPSKEA 64 (212)
T ss_pred HHHHHHHHHHHHHH-h-Cc-ccCCHHHHHHHhCcCHH------HHHHHCCCHHH
Confidence 444555 5555554 3 64 56679999999999976 78888876543
No 89
>PF06373 CART: Cocaine and amphetamine regulated transcript protein (CART); InterPro: IPR009106 The cocaine and amphetamine regulated transcript (CART) is a brain-localised peptide that acts as a satiety factor in appetite regulation. CART was found to inhibit both normal and starvation-induced feeding, and completely blocks the feeding response induced by neuropeptide Y. CART is regulated by leptin in the hypothalamus, and can be transcriptionally induced after cocaine or amphetamine administration []. Posttranslational processing of CART produces an N-terminal CART peptide and a C-terminal CART peptide. The C-terminal CART peptide has been isolated from the hypothalamus, nucleus accumbens, and the anterior pituitary lobe in rats. C-terminal CART is the biologically active part of the molecule affecting food intake. The structure of C-terminal CART consists of a disulphide-bound fold containing a beta-hairpin and two adjacent disulphide bridges [].; GO: 0000186 activation of MAPKK activity, 0001678 cellular glucose homeostasis, 0007186 G-protein coupled receptor protein signaling pathway, 0008343 adult feeding behavior, 0009267 cellular response to starvation, 0032099 negative regulation of appetite, 0005615 extracellular space; PDB: 1HY9_A.
Probab=28.79 E-value=12 Score=28.99 Aligned_cols=26 Identities=42% Similarity=0.733 Sum_probs=12.3
Q ss_pred CccccccccccccccccCCChhHHHHH
Q 022828 1 MCAVRTGEFVSPTGCVCGRGTKSVALL 27 (291)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 27 (291)
.||||.|--+- .=|.|.|||.+-..|
T Consensus 44 ~CAvrkG~RIG-klCdC~rG~~CN~fl 69 (73)
T PF06373_consen 44 QCAVRKGPRIG-KLCDCPRGTSCNFFL 69 (73)
T ss_dssp -SEEE-SSSEE-E--B--TT--B-TTT
T ss_pred hhhhccccccc-cccCCCCCCchhhhH
Confidence 59999997664 349999999764433
No 90
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=28.71 E-value=84 Score=26.00 Aligned_cols=46 Identities=13% Similarity=0.119 Sum_probs=31.2
Q ss_pred hHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhh
Q 022828 89 NKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYE 145 (291)
Q Consensus 89 ~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~ 145 (291)
....++..|.+-|+. ..-+=.|..++. -..++||+.||+|..-|+.
T Consensus 95 ~~~~l~~~l~~L~~~---~r~v~~l~~~~~--------~s~~eIA~~lgis~~tv~~ 140 (159)
T PRK12527 95 RLALLQRALAELPPA---CRDSFLLRKLEG--------LSHQQIAEHLGISRSLVEK 140 (159)
T ss_pred HHHHHHHHHHhCCHH---HHHHHHHHHHcC--------CCHHHHHHHhCCCHHHHHH
Confidence 345688899999862 223334444432 2478999999999987765
No 91
>cd01782 AF6_RA_repeat1 Ubiquitin domain of AT-6, first repeat. The AF-6 protein (also known as afadin and canoe) is a multidomain cell junction protein that contains two N-terminal Ras-associating (RA) domains in addition to FHA (forkhead-associated), DIL (class V myosin homology region), and PDZ domains and a proline-rich region. AF6 acts downstream of the Egfr (Epidermal Growth Factor-receptor)/Ras signalling pathway and provides a link from Egfr to cytoskeletal elements.
Probab=28.35 E-value=78 Score=26.63 Aligned_cols=58 Identities=21% Similarity=0.241 Sum_probs=39.4
Q ss_pred hhhhhhhhhcccccccCCceEEEEcCCCcccccChHHHHHHHHHHhCCCCCcccCCCcEEEEEe
Q 022828 142 RVYEVATFYSMFNRSKVGKYHLLVCGTTPCMVRGSREIEDALLKHLGVKRNEVTKDGLFSVGEM 205 (291)
Q Consensus 142 ~V~~VaTFY~~f~~~P~gK~~I~VC~gtsC~~~Gs~~lleaL~~~Lgi~~Gett~DG~ftL~~v 205 (291)
+.+||.-||-+=.-....-.+|+|+..+.. .+|++.|-++..++..-.+. ++|.|-++
T Consensus 19 ef~gvmrf~~qd~~~k~atK~VrVsS~~tt-----~eVI~~LLeKFk~d~~~~s~-p~FALYev 76 (112)
T cd01782 19 EFHGVMRFYFQDGGEKVATKCIRVSSTATT-----RDVIDTLSEKFRPDMRMLSN-PTYSLYEV 76 (112)
T ss_pred EEeeEEEEEEEcCCCcEEEEEEEEecCCCH-----HHHHHHHHHHhcccccccCC-cceEEEEE
Confidence 568999999666555555567888876554 69999999999865322222 36666443
No 92
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=28.20 E-value=84 Score=26.98 Aligned_cols=46 Identities=7% Similarity=0.175 Sum_probs=32.2
Q ss_pred HHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhh
Q 022828 90 KEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEV 146 (291)
Q Consensus 90 ~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~V 146 (291)
.+.+++.|++.|+. .+ .+-+|..++. -..++||+.||+|..-|+.-
T Consensus 122 ~~~l~~~l~~Lp~~-~r--~v~~l~~~~g--------~s~~EIA~~lgis~~tV~~~ 167 (191)
T PRK12520 122 FEVLQACVDRLPPR-TG--RVFMMREWLE--------LETEEICQELQITATNAWVL 167 (191)
T ss_pred HHHHHHHHHhCCHH-HH--HHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHH
Confidence 45688999999963 22 3335555542 23689999999999987653
No 93
>KOG3769 consensus Ribonuclease III domain proteins [Translation, ribosomal structure and biogenesis]
Probab=28.18 E-value=60 Score=31.86 Aligned_cols=36 Identities=17% Similarity=0.246 Sum_probs=27.5
Q ss_pred HHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCC
Q 022828 96 ILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVA 139 (291)
Q Consensus 96 il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip 139 (291)
|..+||+ -+ =..|+.++. +|++++++..||.++||.
T Consensus 135 l~~kyPr--lP---~E~l~ai~n---~ll~ee~LahiAt~lGie 170 (333)
T KOG3769|consen 135 LKCKYPR--LP---EEGLHAIVN---GLLGEEVLAHIATHLGIE 170 (333)
T ss_pred HHHhccC--Cc---HHHHHHHHH---HhhhHHHHHHHHHHhhHH
Confidence 4567774 12 236788874 799999999999999985
No 94
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=28.06 E-value=79 Score=27.46 Aligned_cols=47 Identities=19% Similarity=0.145 Sum_probs=33.2
Q ss_pred hhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhh
Q 022828 88 TNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYE 145 (291)
Q Consensus 88 ~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~ 145 (291)
+....+...|++-|. +...+=+|+.++.. ..++||+.||+++..|..
T Consensus 105 ~~~~~l~~~L~~Lp~---~~r~i~~L~~~~g~--------s~~EIA~~Lgis~~tVk~ 151 (187)
T PRK12516 105 LDLQDFRAALDQLPD---DQREAIILVGASGF--------AYEEAAEICGCAVGTIKS 151 (187)
T ss_pred HHHHHHHHHHHhCCH---HHHHHHHHHHHcCC--------CHHHHHHHHCCCHHHHHH
Confidence 345678999999996 23345556555532 368999999999987765
No 95
>KOG1719 consensus Dual specificity phosphatase [Defense mechanisms]
Probab=28.00 E-value=1.6e+02 Score=26.53 Aligned_cols=68 Identities=26% Similarity=0.326 Sum_probs=52.8
Q ss_pred ChhhHHHHHHHHHhCCC-----------CCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHh---CCCchhhhhhhhhhc
Q 022828 86 SDTNKEKVKEILSHYPS-----------NYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKII---EVAPIRVYEVATFYS 151 (291)
Q Consensus 86 ~~~~~~~i~~il~~yp~-----------~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L---~ip~~~V~~VaTFY~ 151 (291)
+-+++.+.=+.|.+|.+ +..|++.+-+-.++|. + +|.|++|.++|+++= -+-+++-.-+..||.
T Consensus 91 s~~~i~~aVeFi~k~asLGktvYVHCKAGRtRSaTvV~cYLmq~-~-~wtpe~A~~~vr~iRp~VlL~~~Qw~~l~ef~~ 168 (183)
T KOG1719|consen 91 SLENIQKAVEFIHKNASLGKTVYVHCKAGRTRSATVVACYLMQH-K-NWTPEAAVEHVRKIRPRVLLRPAQWDVLKEFYK 168 (183)
T ss_pred CHHHHHHHHHHHHhccccCCeEEEEecCCCccchhhhhhhhhhh-c-CCCHHHHHHHHHhcCcceeecHHHHHHHHHHHH
Confidence 34666666677888765 3568999999999994 4 999999999999864 477888888888887
Q ss_pred cccc
Q 022828 152 MFNR 155 (291)
Q Consensus 152 ~f~~ 155 (291)
+.-.
T Consensus 169 ~~~~ 172 (183)
T KOG1719|consen 169 QIVA 172 (183)
T ss_pred HHHh
Confidence 6543
No 96
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=27.93 E-value=1e+02 Score=26.34 Aligned_cols=49 Identities=20% Similarity=0.353 Sum_probs=34.8
Q ss_pred hhhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhh
Q 022828 87 DTNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEV 146 (291)
Q Consensus 87 ~~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~V 146 (291)
.+....+.+.|...|+. .+ -+-+|+.++ || ...+||+.||||...|..-
T Consensus 115 ~~~~~~l~~al~~Lp~~-~R--~~~~l~~~~----gl----s~~EIA~~l~i~~~tVks~ 163 (182)
T COG1595 115 EEELERLRRALARLPPR-QR--EAFLLRYLE----GL----SYEEIAEILGISVGTVKSR 163 (182)
T ss_pred HHHHHHHHHHHHhCCHH-Hh--HHhhhHhhc----CC----CHHHHHHHHCCCHHHHHHH
Confidence 56667899999999973 22 333455554 33 3578999999999988764
No 97
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=27.92 E-value=79 Score=26.97 Aligned_cols=45 Identities=13% Similarity=0.078 Sum_probs=31.5
Q ss_pred HHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhh
Q 022828 90 KEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYE 145 (291)
Q Consensus 90 ~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~ 145 (291)
...+.+.|.+-|+ +...+-+|+.++. -..++||+.|||+...|+.
T Consensus 124 ~~~l~~~l~~L~~---~~r~i~~l~~~~~--------~s~~eIA~~lgis~~tV~~ 168 (182)
T PRK12537 124 SGKIHRCLEQLEP---ARRNCILHAYVDG--------CSHAEIAQRLGAPLGTVKA 168 (182)
T ss_pred HHHHHHHHHhCCH---HHHHHHHHHHHcC--------CCHHHHHHHHCCChhhHHH
Confidence 4568888999986 2234445554442 2578999999999988764
No 98
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=27.88 E-value=86 Score=27.12 Aligned_cols=47 Identities=15% Similarity=0.160 Sum_probs=32.1
Q ss_pred hhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhh
Q 022828 88 TNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYE 145 (291)
Q Consensus 88 ~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~ 145 (291)
+....+.++|.+.|+. ..-+=+|..++. -..++||+.||+|..-|+-
T Consensus 120 e~~~~l~~~l~~L~~~---~r~v~~l~~~~g--------~s~~EIA~~lgis~~tvk~ 166 (188)
T TIGR02943 120 EFWEVFEACLYHLPEQ---TARVFMMREVLG--------FESDEICQELEISTSNCHV 166 (188)
T ss_pred HHHHHHHHHHHhCCHH---HHHHHHHHHHhC--------CCHHHHHHHhCCCHHHHHH
Confidence 4446788899999962 223444544443 2468999999999997754
No 99
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=27.82 E-value=82 Score=27.12 Aligned_cols=47 Identities=11% Similarity=0.183 Sum_probs=31.7
Q ss_pred hHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhh
Q 022828 89 NKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEV 146 (291)
Q Consensus 89 ~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~V 146 (291)
....+.+.|.+.|.. .+ .+=+|+.++. + ..++||+.||+|+..|+.-
T Consensus 126 ~~~~l~~~l~~L~~~-~r--~i~~L~~~~g----~----s~~EIA~~lgis~~tVk~~ 172 (195)
T PRK12532 126 FQKILQSCLYNLPEN-TA--RVFTLKEILG----F----SSDEIQQMCGISTSNYHTI 172 (195)
T ss_pred HHHHHHHHHHhCCHH-HH--HHhhhHHHhC----C----CHHHHHHHHCCCHHHHHHH
Confidence 335578889999862 22 3334555542 2 3689999999999887653
No 100
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=27.51 E-value=74 Score=23.08 Aligned_cols=33 Identities=21% Similarity=0.316 Sum_probs=23.9
Q ss_pred HHHHHHHHhcCCCCC---HHHHHHHHHHhCCCchhhhh
Q 022828 111 PLLDLAQQQHGGWLP---VSAMNEVAKIIEVAPIRVYE 145 (291)
Q Consensus 111 piL~~~Q~~~~GyIp---~eam~~IAe~L~ip~~~V~~ 145 (291)
.+|..+-+ .||.. .-.+..||+.|||+.+-+.+
T Consensus 7 e~L~~A~~--~GYfd~PR~~tl~elA~~lgis~st~~~ 42 (53)
T PF04967_consen 7 EILKAAYE--LGYFDVPRRITLEELAEELGISKSTVSE 42 (53)
T ss_pred HHHHHHHH--cCCCCCCCcCCHHHHHHHhCCCHHHHHH
Confidence 35555554 37755 45799999999999987654
No 101
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=27.45 E-value=73 Score=28.68 Aligned_cols=49 Identities=18% Similarity=0.196 Sum_probs=33.6
Q ss_pred hhhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhh
Q 022828 87 DTNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEV 146 (291)
Q Consensus 87 ~~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~V 146 (291)
.+....+.+.|++.|.. ...+=+|+.++. -..++||+.|||++..|+.-
T Consensus 122 ~e~~~~l~~al~~Lp~~---~R~v~~L~y~eg--------~s~~EIAe~LgiS~~tVk~~ 170 (216)
T PRK12533 122 AEDVRLVNAALAKLPVE---YREVLVLRELED--------MSYREIAAIADVPVGTVMSR 170 (216)
T ss_pred HHHHHHHHHHHHcCCHH---HHhHhhhHHhcC--------CCHHHHHHHHCCCHHHHHHH
Confidence 35556788999999862 223444554442 24789999999999987653
No 102
>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=27.40 E-value=43 Score=23.22 Aligned_cols=36 Identities=14% Similarity=0.260 Sum_probs=25.2
Q ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhhhh
Q 022828 109 VIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEVAT 148 (291)
Q Consensus 109 lipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~VaT 148 (291)
.+.||+.+-++. +- -.+.+||+.+|+|.+.||-+..
T Consensus 5 al~iL~~l~~~~-~~---~t~~eia~~~gl~~stv~r~L~ 40 (52)
T PF09339_consen 5 ALRILEALAESG-GP---LTLSEIARALGLPKSTVHRLLQ 40 (52)
T ss_dssp HHHHHHCHHCTB-SC---EEHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHHcCC-CC---CCHHHHHHHHCcCHHHHHHHHH
Confidence 456677666544 22 2688999999999999987654
No 103
>PF04214 DUF411: Protein of unknown function, DUF; InterPro: IPR007332 The function of the members of this bacterial protein family is unknown. Some members may be involved in conferring cation resistance.
Probab=27.02 E-value=1.3e+02 Score=23.32 Aligned_cols=42 Identities=19% Similarity=0.340 Sum_probs=30.7
Q ss_pred HHHHHHHhCCCCCcccCCCcEEEEEecCCCCCCCCCeEEEcccCCCCCCccceEecCCChhhHHHHHHH
Q 022828 180 EDALLKHLGVKRNEVTKDGLFSVGEMECMGCCVNAPMITVADYSNGSEGYTYNYYEDVTPKRVIEIVEM 248 (291)
Q Consensus 180 leaL~~~Lgi~~Gett~DG~ftL~~v~CLG~C~~aPvV~Vnd~~~G~~g~~~~~Y~~vTpE~V~~ILe~ 248 (291)
+..+++++|+... |..|.. ..|++| .+=++|-.++|.++|++
T Consensus 10 l~~ik~~~gVP~~---------------l~SCHT---a~v~gy---------~iEGHVPa~~I~~lL~e 51 (70)
T PF04214_consen 10 LSAIKQRLGVPPE---------------LASCHT---AVVGGY---------VIEGHVPADDIKRLLAE 51 (70)
T ss_pred hHHHHHHhCCCch---------------hccccE---EEECCE---------EEEccCCHHHHHHHHhc
Confidence 5668888887532 456766 566663 77789999999999864
No 104
>TIGR03044 PS_II_psb27 photosystem II protein Psb27. Members of this family are the Psb27 protein of the cyanobacterial photosynthetic supracomplex, photosystem II. Although most protein components of both cyanobacterial and chloroplast versions of photosystem II are closely related and described together by single model families, this family is strictly bacterial. Some uncharacterized proteins with highly divergent sequences, from Arabidopsis, score between trusted and noise cutoffs for this model but are not at this time assigned as functionally equivalent photosystem II proteins.
Probab=26.26 E-value=93 Score=27.00 Aligned_cols=82 Identities=17% Similarity=0.349 Sum_probs=50.8
Q ss_pred cccceeccCCCCCCCCCCCCCChhhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhh
Q 022828 65 CLELCKHLDSPDNNPDLPWKFSDTNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVY 144 (291)
Q Consensus 65 ~~~~~~h~~~~~~~~~~~~~~~~~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~ 144 (291)
.+.|..-.+-|.+.+.. -+.-.+.++.|.+++++|.++ ++- .|--|-..|+ .-+.
T Consensus 45 i~tlr~~i~lpkd~p~~-~~a~~~ar~~indyvsrYRr~-~~v-------------~g~~SFttm~----------TALN 99 (135)
T TIGR03044 45 IQTLREAIDLPDDDPNK-SEAQAEARQLINDYISRYRRR-PRV-------------NGLSSFTTMQ----------TALN 99 (135)
T ss_pred HHHHHHHHcCCCCCccH-HHHHHHHHHHHHHHHHHhcCC-CCc-------------CCcccHHHHH----------HHHH
Confidence 35555555666655553 334457778899999999863 221 1333444444 2355
Q ss_pred hhhhhhcccccccCCceEEEEcCCCcccccChHHHHHHHHHHhC
Q 022828 145 EVATFYSMFNRSKVGKYHLLVCGTTPCMVRGSREIEDALLKHLG 188 (291)
Q Consensus 145 ~VaTFY~~f~~~P~gK~~I~VC~gtsC~~~Gs~~lleaL~~~Lg 188 (291)
.++.||+.|-..|.. +++.+.|.++++
T Consensus 100 sLAGHY~sy~~rPlP-----------------eklk~Rl~~El~ 126 (135)
T TIGR03044 100 SLAGHYKSYANRPLP-----------------EKLKERLEKELK 126 (135)
T ss_pred HHHHHhccCCCCCCC-----------------HHHHHHHHHHHH
Confidence 688999999888876 456666666654
No 105
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=26.23 E-value=1.2e+02 Score=25.60 Aligned_cols=49 Identities=12% Similarity=0.056 Sum_probs=32.7
Q ss_pred hhhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhh
Q 022828 87 DTNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEV 146 (291)
Q Consensus 87 ~~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~V 146 (291)
....+.+.++|++.|+. ..-+=.|..++. -..++||+.||+|...|+.-
T Consensus 119 ~~~~~~l~~~l~~L~~~---~r~v~~l~~~~g--------~s~~eIA~~l~is~~tV~~~ 167 (184)
T PRK12512 119 TLPAGDVGRHLETLPPR---QRDVVQSISVEG--------ASIKETAAKLSMSEGAVRVA 167 (184)
T ss_pred HHHHHHHHHHHHhCCHH---HHHHHHHHHHcC--------CCHHHHHHHhCCCHHHHHHH
Confidence 34557789999999862 222333333332 24789999999999887653
No 106
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=25.84 E-value=95 Score=25.33 Aligned_cols=48 Identities=23% Similarity=0.225 Sum_probs=32.1
Q ss_pred hhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhh
Q 022828 88 TNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEV 146 (291)
Q Consensus 88 ~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~V 146 (291)
+....+.+.+++-|+. + ..+-.|..++ | -...+||+.||+|...|+..
T Consensus 95 ~~~~~l~~~l~~L~~~--~-r~ii~l~~~~----~----~s~~EIA~~l~is~~tV~~~ 142 (154)
T PRK06759 95 DVEMKVKDFMSVLDEK--E-KYIIFERFFV----G----KTMGEIALETEMTYYQVRWI 142 (154)
T ss_pred HHHHHHHHHHHhCCHH--H-HHHHHHHHhc----C----CCHHHHHHHHCCCHHHHHHH
Confidence 4457788999999862 2 2222233332 2 34899999999999988754
No 107
>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=25.83 E-value=1.9e+02 Score=23.63 Aligned_cols=42 Identities=14% Similarity=0.264 Sum_probs=33.5
Q ss_pred HHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhC
Q 022828 90 KEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIE 137 (291)
Q Consensus 90 ~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ 137 (291)
.+.++=++++... .++..+|.-=.+ . ||||+++..++=+.+.
T Consensus 22 ~eWLefLve~~G~----~~~~~~L~YY~~-i-gWISe~V~~~L~~~~~ 63 (99)
T PF04659_consen 22 FEWLEFLVERVGH----NNAADALDYYES-I-GWISEEVREQLLKYLK 63 (99)
T ss_pred HHHHHHHHHHccc----ccHHHHHHHHHH-c-CCcCHHHHHHHHHHHh
Confidence 4677888888873 468889987775 3 9999999999877774
No 108
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=25.66 E-value=91 Score=27.00 Aligned_cols=48 Identities=15% Similarity=0.207 Sum_probs=32.4
Q ss_pred hhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhh
Q 022828 88 TNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEV 146 (291)
Q Consensus 88 ~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~V 146 (291)
+..+.+...|+..|+ +.--+=+|+.++. -..++||+.||||+..|+.-
T Consensus 125 ~~~~~l~~~l~~L~~---~~r~i~~L~~~~g--------~s~~eIA~~lgis~~tV~~~ 172 (196)
T PRK12524 125 DRMRALDAALAALPE---RQRQAVVLRHIEG--------LSNPEIAEVMEIGVEAVESL 172 (196)
T ss_pred HHHHHHHHHHHhCCH---HHHHHHHHHHHcC--------CCHHHHHHHHCcCHHHHHHH
Confidence 445668888999985 2223334444432 24789999999999987654
No 109
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=25.62 E-value=91 Score=27.29 Aligned_cols=44 Identities=7% Similarity=0.135 Sum_probs=30.9
Q ss_pred HHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhh
Q 022828 91 EKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYE 145 (291)
Q Consensus 91 ~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~ 145 (291)
..+.+.|.+-|+. ...+=+|+..+.. ..++||+.||+|+..|+.
T Consensus 131 ~~l~~~L~~Lp~~---~r~v~~L~~~eg~--------s~~EIA~~lgis~~tVk~ 174 (201)
T PRK12545 131 TLFETCLDHLPEQ---IGRVFMMREFLDF--------EIDDICTELTLTANHCSV 174 (201)
T ss_pred HHHHHHHHhCCHH---HHHHHHHHHHcCC--------CHHHHHHHHCcCHHHHHH
Confidence 3577889999962 2344455555532 478999999999987765
No 110
>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=25.56 E-value=50 Score=22.48 Aligned_cols=19 Identities=32% Similarity=0.457 Sum_probs=13.8
Q ss_pred HHHHHHHHhCCCchhhhhh
Q 022828 128 AMNEVAKIIEVAPIRVYEV 146 (291)
Q Consensus 128 am~~IAe~L~ip~~~V~~V 146 (291)
.+..||+.+||+.+.||-+
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 4789999999998866643
No 111
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=25.32 E-value=97 Score=26.94 Aligned_cols=21 Identities=19% Similarity=0.327 Sum_probs=17.8
Q ss_pred CCCCHHHHHHHHHHhCCCchhhhhh
Q 022828 122 GWLPVSAMNEVAKIIEVAPIRVYEV 146 (291)
Q Consensus 122 GyIp~eam~~IAe~L~ip~~~V~~V 146 (291)
|| ..++||+.|||++..|+--
T Consensus 151 Gl----s~~EIA~~lgiS~~tV~r~ 171 (185)
T PF07638_consen 151 GL----SVEEIAERLGISERTVRRR 171 (185)
T ss_pred CC----CHHHHHHHHCcCHHHHHHH
Confidence 77 6789999999999988754
No 112
>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=25.19 E-value=1e+02 Score=24.80 Aligned_cols=50 Identities=12% Similarity=0.118 Sum_probs=31.6
Q ss_pred hhhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhhh
Q 022828 87 DTNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEVA 147 (291)
Q Consensus 87 ~~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~Va 147 (291)
.+....+.+.+.+.|.. ...++- |..++ |+ .+.+||+.||+++..|+...
T Consensus 101 ~e~~~~l~~~l~~L~~~--~r~il~-l~~~~----~~----~~~eIA~~lgis~~tv~~~~ 150 (161)
T TIGR02985 101 KELQLIIYKAIEKLPEQ--CRKIFI-LSRFE----GK----SYKEIAEELGISVKTVEYHI 150 (161)
T ss_pred HHHHHHHHHHHHHCCHH--HHHHHH-HHHHc----CC----CHHHHHHHHCCCHHHHHHHH
Confidence 34445688888888752 222222 22232 22 46789999999999987654
No 113
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=25.18 E-value=1e+02 Score=26.53 Aligned_cols=48 Identities=15% Similarity=0.191 Sum_probs=32.5
Q ss_pred hhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhh
Q 022828 88 TNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEV 146 (291)
Q Consensus 88 ~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~V 146 (291)
+....+.+.|++.|+ +...+-.|..++. -..++||+.||++...|+.-
T Consensus 120 e~~~~l~~~l~~L~~---~~r~i~~l~~~~g--------~s~~EIAe~lgis~~~V~~~ 167 (189)
T PRK06811 120 ENKEEILKLINDLEK---LDREIFIRRYLLG--------EKIEEIAKKLGLTRSAIDNR 167 (189)
T ss_pred HHHHHHHHHHHhCCH---HHHHHHHHHHHcc--------CCHHHHHHHHCCCHHHHHHH
Confidence 344568888999985 2233444444432 35789999999999988764
No 114
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=24.71 E-value=1.1e+02 Score=26.24 Aligned_cols=48 Identities=19% Similarity=0.308 Sum_probs=31.7
Q ss_pred hhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhh
Q 022828 88 TNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEV 146 (291)
Q Consensus 88 ~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~V 146 (291)
+..+.+...|.+.|+. .+ -+-.|..++ .-..++||+.||++...|+.-
T Consensus 128 e~~~~l~~~l~~L~~~-~r--~i~~l~~~~--------g~s~~EIA~~lgis~~tV~~~ 175 (189)
T PRK09648 128 ESSNRMRELLDTLPEK-QR--EILILRVVV--------GLSAEETAEAVGSTPGAVRVA 175 (189)
T ss_pred HHHHHHHHHHHhCCHH-HH--HHHHHHHHc--------CCCHHHHHHHHCCCHHHHHHH
Confidence 3445688899999962 22 222333332 235899999999999887654
No 115
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=24.70 E-value=1e+02 Score=26.24 Aligned_cols=46 Identities=7% Similarity=0.165 Sum_probs=31.8
Q ss_pred HHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhh
Q 022828 90 KEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEV 146 (291)
Q Consensus 90 ~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~V 146 (291)
...+.++|.+-|+. ..-+-+|..++. -..++||+.||+++..|+.-
T Consensus 113 ~~~l~~~l~~L~~~---~r~i~~l~~~~g--------~s~~EIA~~lgis~~tVk~~ 158 (185)
T PRK12542 113 EVQIDTLLKELNES---NRQVFKYKVFYN--------LTYQEISSVMGITEANVRKQ 158 (185)
T ss_pred HHHHHHHHHhCCHH---HHHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHH
Confidence 35688999999963 223334544442 24789999999999988763
No 116
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=24.57 E-value=49 Score=24.38 Aligned_cols=58 Identities=17% Similarity=0.328 Sum_probs=34.5
Q ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhhhhhhcccccccCCceE---EEEcCCCcccccCh
Q 022828 109 VIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEVATFYSMFNRSKVGKYH---LLVCGTTPCMVRGS 176 (291)
Q Consensus 109 lipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~VaTFY~~f~~~P~gK~~---I~VC~gtsC~~~Gs 176 (291)
|..|++.+++ . |.+| +..||++|++++..|..+..+. ...|+.. ..-|.+.+|..++.
T Consensus 2 L~~i~~~l~~-~-~~~S---~~eLa~~~~~s~~~ve~mL~~l-----~~kG~I~~~~~~~~~~~~C~~C~~ 62 (69)
T PF09012_consen 2 LQEIRDYLRE-R-GRVS---LAELAREFGISPEAVEAMLEQL-----IRKGYIRKVDMSSCCGGSCSSCGP 62 (69)
T ss_dssp CHHHHHHHHH-S--SEE---HHHHHHHTT--HHHHHHHHHHH-----HCCTSCEEEEEE--SSSSSSS-SS
T ss_pred HHHHHHHHHH-c-CCcC---HHHHHHHHCcCHHHHHHHHHHH-----HHCCcEEEecCCCCCCCCCCCCCC
Confidence 4556666664 3 6666 5789999999999999998876 4555432 22232456655553
No 117
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=24.50 E-value=59 Score=27.98 Aligned_cols=46 Identities=20% Similarity=0.202 Sum_probs=32.1
Q ss_pred HHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhh
Q 022828 90 KEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEV 146 (291)
Q Consensus 90 ~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~V 146 (291)
...+.+.|++.|++ .+ .+-+|+.++. -..++||+.||+|+..|..-
T Consensus 122 ~~~l~~~l~~Lp~~-~r--~i~~L~~~~g--------~s~~EIA~~lgis~~tVk~~ 167 (193)
T TIGR02947 122 DQDIKDALQGLPEE-FR--QAVYLADVEG--------FAYKEIAEIMGTPIGTVMSR 167 (193)
T ss_pred HHHHHHHHHhCCHH-Hh--hheeehhhcC--------CCHHHHHHHHCCCHHHHHHH
Confidence 46788999999963 22 2333444442 24789999999999988764
No 118
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=24.27 E-value=1.1e+02 Score=25.62 Aligned_cols=49 Identities=14% Similarity=0.221 Sum_probs=33.3
Q ss_pred ChhhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhh
Q 022828 86 SDTNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYE 145 (291)
Q Consensus 86 ~~~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~ 145 (291)
..+..+.+...|.+.|+. .+ -+-+|..++. -..++||+.||++...|+.
T Consensus 106 ~~~~~~~l~~~l~~L~~~-~r--~i~~l~~~~~--------~s~~EIA~~lgis~~tV~~ 154 (173)
T PRK12522 106 QKVEAEMIREVIQLLNEK-YK--TVLVLYYYEQ--------YSYKEMSEILNIPIGTVKY 154 (173)
T ss_pred HHHHHHHHHHHHHhCCHH-HH--HHHHHHHHcC--------CCHHHHHHHhCCCHHHHHH
Confidence 345567788999999963 12 2333444443 3478999999999988765
No 119
>KOG3325 consensus Membrane coat complex Retromer, subunit VPS29/PEP11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=24.25 E-value=1.3e+02 Score=26.99 Aligned_cols=65 Identities=20% Similarity=0.285 Sum_probs=53.0
Q ss_pred hhhcccccccCCceEEEEcCCCcccccChHHHHHHHHHHhCCC---CCc------ccCCCcEEEEEecCCCCCC
Q 022828 148 TFYSMFNRSKVGKYHLLVCGTTPCMVRGSREIEDALLKHLGVK---RNE------VTKDGLFSVGEMECMGCCV 212 (291)
Q Consensus 148 TFY~~f~~~P~gK~~I~VC~gtsC~~~Gs~~lleaL~~~Lgi~---~Ge------tt~DG~ftL~~v~CLG~C~ 212 (291)
.=|++-..--.|.++|-+|.|--=.-.|..+-+..|++.|+++ .|. .+.+|+|-+.+-.|-|+-+
T Consensus 67 ~~yP~~kvvtvGqfkIG~chGhqViP~gd~~sL~~LaRqldvDILl~G~Th~f~Aye~eg~ffvnPGSaTGAfn 140 (183)
T KOG3325|consen 67 LKYPENKVVTVGQFKIGLCHGHQVIPWGDPESLALLARQLDVDILLTGHTHKFEAYEHEGKFFVNPGSATGAFN 140 (183)
T ss_pred ccCCccceEEeccEEEEeecCcEeecCCCHHHHHHHHHhcCCcEEEeCCceeEEEEEeCCcEEeCCCcccCCCc
Confidence 4577777777899999999998888899999999999999864 232 2368899999888888765
No 120
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=24.11 E-value=1.1e+02 Score=25.72 Aligned_cols=46 Identities=15% Similarity=0.113 Sum_probs=32.2
Q ss_pred hHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhh
Q 022828 89 NKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYE 145 (291)
Q Consensus 89 ~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~ 145 (291)
..+.++..|++.|+ +..-+-+|+.++. + ..++||+.||+++..|+.
T Consensus 102 ~~~~l~~~l~~L~~---~~r~v~~l~~~~g----~----s~~eIA~~lgis~~tV~~ 147 (164)
T PRK12547 102 DLQDFKKALNLLSA---DQREAIILIGASG----F----SYEDAAAICGCAVGTIKS 147 (164)
T ss_pred HHHHHHHHHHhCCH---HHHHHHHHHHHcC----C----CHHHHHHHhCCCHHHHHH
Confidence 44678899999996 2234445555542 1 378999999999987765
No 121
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=24.10 E-value=88 Score=26.48 Aligned_cols=48 Identities=15% Similarity=0.111 Sum_probs=32.0
Q ss_pred hhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhh
Q 022828 88 TNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEV 146 (291)
Q Consensus 88 ~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~V 146 (291)
+..+.+.+.|++.|+. .+ -+-+|+.++ .-..++||+.||++...|+.-
T Consensus 108 e~~~~l~~~l~~L~~~-~r--~i~~l~~~~--------g~s~~EIA~~lgis~~tV~~~ 155 (172)
T PRK09651 108 ETLQLLDSMLDGLNGK-TR--EAFLLSQLD--------GLTYSEIAHKLGVSVSSVKKY 155 (172)
T ss_pred HHHHHHHHHHHhCCHH-Hh--HHhhhhhcc--------CCCHHHHHHHhCCCHHHHHHH
Confidence 4456788899999963 22 222344333 234789999999999887653
No 122
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=24.09 E-value=1.1e+02 Score=25.84 Aligned_cols=47 Identities=13% Similarity=0.156 Sum_probs=30.9
Q ss_pred hhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhh
Q 022828 88 TNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYE 145 (291)
Q Consensus 88 ~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~ 145 (291)
+....++..|.+-|+. . ..+-+|..++ | -..++||+.||++...|+.
T Consensus 118 ~~~~~l~~~l~~L~~~--~-r~i~~l~~~~----g----~s~~eIA~~lgis~~tV~~ 164 (179)
T PRK12514 118 DEGQRIDACLEELEKD--R-AAAVRRAYLE----G----LSYKELAERHDVPLNTMRT 164 (179)
T ss_pred HHHHHHHHHHHhCCHH--H-HHHHHHHHHc----C----CCHHHHHHHHCCChHHHHH
Confidence 3445688889998852 2 2333333332 2 2478999999999998854
No 123
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=23.99 E-value=1.1e+02 Score=25.99 Aligned_cols=46 Identities=9% Similarity=0.082 Sum_probs=31.3
Q ss_pred hHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhh
Q 022828 89 NKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYE 145 (291)
Q Consensus 89 ~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~ 145 (291)
..+.+.+.|.+-|+ +...+-+|..++. -..++||+.||++...|+.
T Consensus 125 ~~~~l~~~l~~L~~---~~r~vl~l~~~~~--------~s~~eIA~~lgis~~~V~~ 170 (186)
T PRK13919 125 DRTRLGRALKALSP---EERRVIEVLYYQG--------YTHREAAQLLGLPLGTLKT 170 (186)
T ss_pred HHHHHHHHHHhCCH---HHHHHHHHHHHcC--------CCHHHHHHHHCcCHHHHHH
Confidence 34568899999985 2233444444432 2478999999999988764
No 124
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=23.96 E-value=1.1e+02 Score=26.44 Aligned_cols=48 Identities=10% Similarity=0.051 Sum_probs=32.1
Q ss_pred hhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhh
Q 022828 88 TNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEV 146 (291)
Q Consensus 88 ~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~V 146 (291)
+....+..++++.|+ +...+=.|..+|. -.+++||+.||++...|+.-
T Consensus 95 e~~~~l~~~l~~L~~---~~r~i~~l~~~~g--------~~~~EIA~~lgis~~tV~~~ 142 (181)
T PRK09637 95 ELAPCLRPFIDALPE---KYAEALRLTELEG--------LSQKEIAEKLGLSLSGAKSR 142 (181)
T ss_pred HHHHHHHHHHHhCCH---HHHHHHHHHHhcC--------CCHHHHHHHhCCCHHHHHHH
Confidence 444568888899985 2233334444442 35789999999999876653
No 125
>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=23.47 E-value=69 Score=26.09 Aligned_cols=47 Identities=19% Similarity=0.349 Sum_probs=30.7
Q ss_pred hHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhh
Q 022828 89 NKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEV 146 (291)
Q Consensus 89 ~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~V 146 (291)
..+.+.+.|.+.|+. .+..+ +|. |+..-..++||+.||+|+..|+.-
T Consensus 95 ~~~~l~~~l~~L~~~-~r~i~--~l~--------~~~g~s~~eIA~~lgis~~tv~~~ 141 (154)
T TIGR02950 95 EQEEITHHLSRLPEN-YRTVL--ILR--------EFKEFSYKEIAELLNLSLAKVKSN 141 (154)
T ss_pred HHHHHHHHHHhCCHh-heeee--eeh--------hhccCcHHHHHHHHCCCHHHHHHH
Confidence 345688888888863 22211 122 333446799999999999887654
No 126
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=22.94 E-value=1.3e+02 Score=25.43 Aligned_cols=44 Identities=16% Similarity=0.210 Sum_probs=28.0
Q ss_pred HHHHHHH---HhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhh
Q 022828 91 EKVKEIL---SHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYE 145 (291)
Q Consensus 91 ~~i~~il---~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~ 145 (291)
..+++++ ++.|+ +.-.+=+|+.++.. ..++||+.||||+..|+.
T Consensus 123 ~~l~~~~~~l~~Lp~---~~r~v~~l~~~~g~--------s~~EIA~~lgis~~tVk~ 169 (183)
T TIGR02999 123 LDLDDALDKLAQVDP---RQAEVVELRFFAGL--------TVEEIAELLGVSVRTVER 169 (183)
T ss_pred HHHHHHHHHhhcCCH---HHHHHHHHHHHcCC--------CHHHHHHHhCCCHHHHHH
Confidence 3455554 44885 22344455555532 468999999999998765
No 127
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=22.80 E-value=1.1e+02 Score=26.39 Aligned_cols=47 Identities=9% Similarity=0.118 Sum_probs=32.1
Q ss_pred hHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhh
Q 022828 89 NKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEV 146 (291)
Q Consensus 89 ~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~V 146 (291)
....+.+.|.+.|+. ..-+=.|+.++. -..++||+.||||+..|+.-
T Consensus 101 ~~~~l~~~l~~Lp~~---~R~v~~L~~~eg--------~s~~EIA~~lgis~~tV~~~ 147 (182)
T PRK12511 101 RLAQIRDAFFDLPEE---QRAALHLVAIEG--------LSYQEAAAVLGIPIGTLMSR 147 (182)
T ss_pred HHHHHHHHHHhCCHH---HHHHHHHHHHcC--------CCHHHHHHHhCcCHHHHHHH
Confidence 445688899999962 223444544442 24789999999999877653
No 128
>COG2920 DsrC Dissimilatory sulfite reductase (desulfoviridin), gamma subunit [Inorganic ion transport and metabolism]
Probab=22.76 E-value=1.4e+02 Score=25.06 Aligned_cols=49 Identities=24% Similarity=0.274 Sum_probs=37.8
Q ss_pred CHHHHHHHHHHhCCCchh-----hhhhhhhhcccccccCCceEEEEcCCCcccccChHHHHHHHHHHhCCC
Q 022828 125 PVSAMNEVAKIIEVAPIR-----VYEVATFYSMFNRSKVGKYHLLVCGTTPCMVRGSREIEDALLKHLGVK 190 (291)
Q Consensus 125 p~eam~~IAe~L~ip~~~-----V~~VaTFY~~f~~~P~gK~~I~VC~gtsC~~~Gs~~lleaL~~~Lgi~ 190 (291)
++++.+.||+..++..++ |+=|-.||.-|++.|.-| -|.+++.+++|..
T Consensus 26 ~E~vAe~lA~~e~i~LT~eHWevv~fvR~fy~ef~tsPaiR-----------------MLvK~~~~~~g~~ 79 (111)
T COG2920 26 SEKVAEALAEREGIELTEEHWEVVRFVREFYEEFNTSPAIR-----------------MLVKAMAKKLGEE 79 (111)
T ss_pred CHHHHHHHHHHhccCccHHHHHHHHHHHHHHHHHCCCchHH-----------------HHHHHHHHHhCcc
Confidence 677888888888887665 456778999999998754 4777888888754
No 129
>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=22.63 E-value=69 Score=23.18 Aligned_cols=23 Identities=17% Similarity=0.300 Sum_probs=19.0
Q ss_pred HHHHHHHHHhCCCchhhhhhhhh
Q 022828 127 SAMNEVAKIIEVAPIRVYEVATF 149 (291)
Q Consensus 127 eam~~IAe~L~ip~~~V~~VaTF 149 (291)
.....||+.+|+|.+.||.+...
T Consensus 23 ~t~~eIa~~l~i~~~~v~~~L~~ 45 (68)
T PF01978_consen 23 ATAEEIAEELGISRSTVYRALKS 45 (68)
T ss_dssp EEHHHHHHHHTSSHHHHHHHHHH
T ss_pred CCHHHHHHHHCcCHHHHHHHHHH
Confidence 34678999999999999987654
No 130
>PRK01381 Trp operon repressor; Provisional
Probab=22.54 E-value=2.3e+02 Score=23.35 Aligned_cols=59 Identities=14% Similarity=0.156 Sum_probs=40.0
Q ss_pred CcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhhhhhhcccccccCCceEEEEcCCCcccccChHHHHHHHH
Q 022828 105 KQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEVATFYSMFNRSKVGKYHLLVCGTTPCMVRGSREIEDALL 184 (291)
Q Consensus 105 ~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~VaTFY~~f~~~P~gK~~I~VC~gtsC~~~Gs~~lleaL~ 184 (291)
.+.+|.--++.++....|=. ...+||+.|||+.+ .|-.|+.|....+.+..+.|+
T Consensus 37 Er~al~~R~~I~~~L~~g~~---sQREIa~~lGvSia----------------------TITRgsn~Lk~~~~~~k~~l~ 91 (99)
T PRK01381 37 EREALGTRVRIVEELLRGEL---SQREIKQELGVGIA----------------------TITRGSNSLKTAPPEFKEWLE 91 (99)
T ss_pred HHHHHHHHHHHHHHHHcCCc---CHHHHHHHhCCcee----------------------eehhhHHHhccCCHHHHHHHH
Confidence 34455555555554322322 46788999999888 455667777778888889998
Q ss_pred HHhC
Q 022828 185 KHLG 188 (291)
Q Consensus 185 ~~Lg 188 (291)
+.|.
T Consensus 92 ~~l~ 95 (99)
T PRK01381 92 QQLL 95 (99)
T ss_pred HHhc
Confidence 8885
No 131
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=22.43 E-value=98 Score=23.48 Aligned_cols=36 Identities=14% Similarity=0.297 Sum_probs=24.8
Q ss_pred ccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhhh
Q 022828 107 SAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEVA 147 (291)
Q Consensus 107 ~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~Va 147 (291)
+.++-.|..+.++. || .+..+|+.+|++.++|..+.
T Consensus 17 ~~l~~~i~~~~~~~-~l----tQ~e~A~~lgisq~~vS~l~ 52 (80)
T PF13744_consen 17 AQLMAAIRELREER-GL----TQAELAERLGISQPRVSRLE 52 (80)
T ss_dssp HHHHHHHHHHHHCC-T------HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHHHHHc-CC----CHHHHHHHHCCChhHHHHHH
Confidence 34566666666654 65 46789999999999998876
No 132
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=22.12 E-value=1.5e+02 Score=24.94 Aligned_cols=45 Identities=16% Similarity=0.294 Sum_probs=30.1
Q ss_pred HHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhh
Q 022828 91 EKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEV 146 (291)
Q Consensus 91 ~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~V 146 (291)
..+.+.+++.|.. .+ .+=+|..+ ..-..++||+.|||+...|+..
T Consensus 128 ~~l~~~l~~L~~~-~r--~il~l~~~--------~~~s~~eIA~~lgis~~~v~~~ 172 (187)
T PRK09641 128 ETIQEAILQLPEK-YR--TVIVLKYI--------EDLSLKEISEILDLPVGTVKTR 172 (187)
T ss_pred HHHHHHHHhCCHH-HH--HHhhhHHh--------hCCCHHHHHHHHCCCHHHHHHH
Confidence 4588888888862 22 22234433 3345789999999999887654
No 133
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=22.09 E-value=62 Score=24.24 Aligned_cols=17 Identities=12% Similarity=0.343 Sum_probs=14.9
Q ss_pred HHHHHHHhCCCchhhhh
Q 022828 129 MNEVAKIIEVAPIRVYE 145 (291)
Q Consensus 129 m~~IAe~L~ip~~~V~~ 145 (291)
+..||+.|||++..|..
T Consensus 25 lkdIA~~Lgvs~~tIr~ 41 (60)
T PF10668_consen 25 LKDIAEKLGVSESTIRK 41 (60)
T ss_pred HHHHHHHHCCCHHHHHH
Confidence 67899999999998864
No 134
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=22.08 E-value=1.4e+02 Score=24.51 Aligned_cols=50 Identities=18% Similarity=0.234 Sum_probs=32.3
Q ss_pred hhhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhhh
Q 022828 87 DTNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEVA 147 (291)
Q Consensus 87 ~~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~Va 147 (291)
.+....+.+.|++.|+. .+ -+-.|..++ .-...+||+.||+++..|+...
T Consensus 113 ~e~~~~l~~~l~~L~~~-~r--~i~~l~~~~--------~~~~~eIA~~lgis~~tv~~~~ 162 (179)
T PRK11924 113 KDDLARIDRCLDALPVK-QR--EVFLLRYVE--------GLSYREIAEILGVPVGTVKSRL 162 (179)
T ss_pred HHHHHHHHHHHHhCCHH-HH--HHhhHHHHc--------CCCHHHHHHHHCCCHHHHHHHH
Confidence 34556788888988862 12 222233232 2346899999999999887654
No 135
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=22.07 E-value=1.1e+02 Score=28.11 Aligned_cols=46 Identities=13% Similarity=0.222 Sum_probs=32.6
Q ss_pred hHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhh
Q 022828 89 NKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYE 145 (291)
Q Consensus 89 ~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~ 145 (291)
..+.|++.|++-|++ ..-+-+|+.++.. ..++||+.|||+...|+.
T Consensus 151 ~~~~l~~aL~~Lp~~---~R~v~~L~~~eg~--------S~~EIA~~Lgis~~TVk~ 196 (244)
T TIGR03001 151 FRQALREALAALSER---ERHLLRLHFVDGL--------SMDRIGAMYQVHRSTVSR 196 (244)
T ss_pred HHHHHHHHHHhCCHH---HHHHHHHHHHcCC--------CHHHHHHHHCcCHHHHHH
Confidence 345688999999962 2344455555431 378999999999998765
No 136
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=22.02 E-value=1.1e+02 Score=26.41 Aligned_cols=47 Identities=21% Similarity=0.200 Sum_probs=32.0
Q ss_pred hhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhh
Q 022828 88 TNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYE 145 (291)
Q Consensus 88 ~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~ 145 (291)
+..+.+...|++.|+ +...+-+|..++ | -..++||+.||++...|..
T Consensus 131 ~~~~~l~~~l~~L~~---~~r~vl~l~~~~----~----~s~~EIA~~Lgis~~tVk~ 177 (194)
T PRK09646 131 LERERVRDCLDALTD---TQRESVTLAYYG----G----LTYREVAERLAVPLGTVKT 177 (194)
T ss_pred hHHHHHHHHHHhCCH---HHHHHHHHHHHc----C----CCHHHHHHHhCCChHhHHH
Confidence 445678888999986 222333455443 2 2468999999999998754
No 137
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=21.77 E-value=1.2e+02 Score=26.73 Aligned_cols=47 Identities=15% Similarity=0.094 Sum_probs=31.0
Q ss_pred hHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhh
Q 022828 89 NKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEV 146 (291)
Q Consensus 89 ~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~V 146 (291)
..+.+...|++-|++ + .-+-+|..++. + ..++||+.|||++.-|+.-
T Consensus 128 ~~~~l~~~L~~L~~~--~-r~v~~L~~~~g----~----s~~EIA~~Lgis~~tV~~~ 174 (203)
T PRK09647 128 LDPDLQAALDSLPPE--F-RAAVVLCDIEG----L----SYEEIAATLGVKLGTVRSR 174 (203)
T ss_pred HHHHHHHHHHhCCHH--H-HHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHH
Confidence 345678888999862 2 23334444442 2 4689999999999877653
No 138
>COG3531 Predicted protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=21.73 E-value=1.1e+02 Score=28.51 Aligned_cols=53 Identities=19% Similarity=0.233 Sum_probs=36.1
Q ss_pred HHHHHHHHhCCCCCCcccHHHHHHHHHHhcC--C--CCCHHHHHHHHHHhCCCchhhhh
Q 022828 91 EKVKEILSHYPSNYKQSAVIPLLDLAQQQHG--G--WLPVSAMNEVAKIIEVAPIRVYE 145 (291)
Q Consensus 91 ~~i~~il~~yp~~~~~~alipiL~~~Q~~~~--G--yIp~eam~~IAe~L~ip~~~V~~ 145 (291)
..+..|++---.+ +++. +++|+.||+.+| | -...+++..||..+|++...+..
T Consensus 91 pa~~ai~aA~~l~-~r~~-l~ml~aIQrA~YvEGrdi~~t~vl~~laa~~GL~~~~f~~ 147 (212)
T COG3531 91 PACRAILAARLLD-GRGR-LTMLHAIQRAHYVEGRDITQTEVLAELAAAIGLAAEEFDN 147 (212)
T ss_pred HHHHHHHHHHHhC-cccc-hHHHHHHHHHHHhccccchhhHHHHHHHHHcCCCHHHHHH
Confidence 3455555433221 2322 899999999874 2 24679999999999999886544
No 139
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=21.62 E-value=1.3e+02 Score=24.91 Aligned_cols=48 Identities=21% Similarity=0.192 Sum_probs=31.6
Q ss_pred hhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhh
Q 022828 88 TNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEV 146 (291)
Q Consensus 88 ~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~V 146 (291)
+..+.+.+.|.+-|+ +...+-.|..++ .-...+||+.|||+...|+..
T Consensus 111 ~~~~~l~~~l~~L~~---~~r~vl~l~~~~--------g~s~~eIA~~l~is~~tv~~~ 158 (170)
T TIGR02952 111 EANEKLLKALKILTP---KQQHVIALRFGQ--------NLPIAEVARILGKTEGAVKIL 158 (170)
T ss_pred HHHHHHHHHHHhCCH---HHHHHHHHHHhc--------CCCHHHHHHHHCCCHHHHHHH
Confidence 344568888888885 222333333333 235789999999999988754
No 140
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=21.59 E-value=1.3e+02 Score=26.75 Aligned_cols=44 Identities=11% Similarity=0.169 Sum_probs=31.5
Q ss_pred HHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhh
Q 022828 91 EKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYE 145 (291)
Q Consensus 91 ~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~ 145 (291)
..+++.|.+-|+ +...+-+|+.++.. ...+||+.||++...|+.
T Consensus 140 ~~l~~~L~~L~~---~~r~v~~L~~~~g~--------s~~EIAe~lgis~~tV~~ 183 (206)
T PRK12544 140 RIFEACLDGLPA---KYARVFMMREFIEL--------ETNEICHAVDLSVSNLNV 183 (206)
T ss_pred HHHHHHHHhCCH---HHHHHHHHHHHcCC--------CHHHHHHHHCcCHHHHHH
Confidence 456778999986 33345566666532 368999999999987765
No 141
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=21.29 E-value=1.5e+02 Score=23.05 Aligned_cols=49 Identities=22% Similarity=0.414 Sum_probs=31.2
Q ss_pred hhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhhh
Q 022828 88 TNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEVA 147 (291)
Q Consensus 88 ~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~Va 147 (291)
+....+.+.|+..|+. +..+| .++.++ |+ .+.+||+.+|+++..|+...
T Consensus 99 ~~~~~l~~~l~~L~~~--~~~ii-~~~~~~----g~----s~~eIA~~l~~s~~~v~~~~ 147 (158)
T TIGR02937 99 EEREALREALEKLPER--EREVL-VLRYLE----GL----SYKEIAEILGISVGTVKRRL 147 (158)
T ss_pred HHHHHHHHHHHhCCHH--HHHHH-hhHHhc----CC----CHHHHHHHHCCCHHHHHHHH
Confidence 4445677888888752 22232 222222 33 67799999999999887643
No 142
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=21.19 E-value=1.3e+02 Score=25.23 Aligned_cols=46 Identities=15% Similarity=0.333 Sum_probs=30.0
Q ss_pred HHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhh
Q 022828 90 KEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEV 146 (291)
Q Consensus 90 ~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~V 146 (291)
.+.+..+|++.|+. .+. ++ .|..++ .-..++||+.||+++..|+--
T Consensus 127 ~~~l~~~l~~L~~~-~r~-v~-~l~~~~--------g~s~~eIA~~lgis~~~v~~~ 172 (187)
T TIGR02948 127 RDTIQQEIQALPPK-YRM-VI-VLKYME--------DLSLKEISEILDLPVGTVKTR 172 (187)
T ss_pred HHHHHHHHHhCCHH-HhH-Hh-hhHHhc--------CCCHHHHHHHHCCCHHHHHHH
Confidence 45588888999863 222 22 333332 235789999999999887653
No 143
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=21.07 E-value=1.3e+02 Score=26.28 Aligned_cols=47 Identities=17% Similarity=0.195 Sum_probs=32.6
Q ss_pred hhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhh
Q 022828 88 TNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYE 145 (291)
Q Consensus 88 ~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~ 145 (291)
+....+.++|++.|+ +..-+-+|..++.. ..++||+.||+++.-|+.
T Consensus 122 ~~~~~l~~~l~~Lp~---~~r~v~~l~~~~g~--------s~~EIAe~lgis~~tV~~ 168 (196)
T PRK12535 122 SEWIDVRTLIDALPP---ERREALILTQVLGY--------TYEEAAKIADVRVGTIRS 168 (196)
T ss_pred HHHHHHHHHHHcCCH---HHHHHhhhHHHhCC--------CHHHHHHHhCCCHHHHHH
Confidence 344578899999986 22344445555431 368999999999987765
No 144
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=21.04 E-value=1.1e+02 Score=27.78 Aligned_cols=48 Identities=10% Similarity=0.286 Sum_probs=32.2
Q ss_pred hhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhh
Q 022828 88 TNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEV 146 (291)
Q Consensus 88 ~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~V 146 (291)
+..+.+.+.|++.|.. .+ .+-+|..++. -..++||+.||++...|..-
T Consensus 160 e~~~~l~~~L~~Lp~~-~R--~v~~L~~~eg--------~s~~EIA~~Lgis~~tVk~~ 207 (233)
T PRK12538 160 ELSDLLEAAMQRLPEQ-QR--IAVILSYHEN--------MSNGEIAEVMDTTVAAVESL 207 (233)
T ss_pred HHHHHHHHHHHhCCHH-HH--HHhhhHHhcC--------CCHHHHHHHHCcCHHHHHHH
Confidence 3345688899999862 22 3334544442 24789999999999988653
No 145
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=20.73 E-value=1.6e+02 Score=24.44 Aligned_cols=48 Identities=19% Similarity=0.170 Sum_probs=31.9
Q ss_pred hhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhh
Q 022828 88 TNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEV 146 (291)
Q Consensus 88 ~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~V 146 (291)
+....+..++...|+. ...+=+|..++. -...+||+.||++...|+..
T Consensus 97 ~~~~~l~~~l~~L~~~---~r~v~~l~~~~g--------~s~~eIA~~lgis~~tv~~~ 144 (165)
T PRK09644 97 NSYEKLIQIIHTLPVI---EAQAILLCDVHE--------LTYEEAASVLDLKLNTYKSH 144 (165)
T ss_pred HHHHHHHHHHHhCCHH---HHHHHHhHHHhc--------CCHHHHHHHHCCCHHHHHHH
Confidence 4446788888888863 223334444442 24689999999999987653
No 146
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=20.62 E-value=1.6e+02 Score=27.47 Aligned_cols=47 Identities=15% Similarity=0.108 Sum_probs=34.2
Q ss_pred HHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhhh
Q 022828 90 KEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEVA 147 (291)
Q Consensus 90 ~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~Va 147 (291)
...+...|++.|++ ...+=+|+.+++. ..++||+.||+++.-|+...
T Consensus 106 ~~~l~~~l~~L~~~---~R~v~~L~~~~g~--------s~~EIA~~lg~s~~tVk~~l 152 (293)
T PRK09636 106 SLALMLALERLSPL---ERAAFLLHDVFGV--------PFDEIASTLGRSPAACRQLA 152 (293)
T ss_pred HHHHHHHHHhCCHH---HHHHHHHHHHhCC--------CHHHHHHHHCCCHHHHHHHH
Confidence 34578889999962 3345567766642 36899999999999887654
No 147
>TIGR02435 CobG precorrin-3B synthase. An iron-sulfur protein. An oxygen atom from dioxygen is incorporated into the macrocycle at C-20. In the aerobic cobalamin biosythesis pathway, four enzymes are involved in the conversion of precorrin-3A to precorrin-6A. The first of the four steps is carried out by EC 1.14.13.83, precorrin-3B synthase (CobG), yielding precorrin-3B as the product. This is followed by three methylation reactions, which introduce a methyl group at C-17 (CobJ; EC 2.1.1.131), C-11 (CobM; EC 2.1.1.133) and C-1 (CobF; EC 2.1.1.152) of the macrocycle, giving rise to precorrin-4, precorrin-5 and precorrin-6A, respectively.
Probab=20.55 E-value=4.7e+02 Score=25.71 Aligned_cols=112 Identities=9% Similarity=0.005 Sum_probs=70.2
Q ss_pred CCCCChhhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHh---CCCchhhhhhhhhhcccccccC
Q 022828 82 PWKFSDTNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKII---EVAPIRVYEVATFYSMFNRSKV 158 (291)
Q Consensus 82 ~~~~~~~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L---~ip~~~V~~VaTFY~~f~~~P~ 158 (291)
.-.++.+++..|.+|.++|... ..=+---+.+| .-||+.+ +..+.+.| |++... +.
T Consensus 26 ~G~lt~~ql~~la~ia~~yg~g---~i~lTtRQniq---l~gv~~~-~~~l~~~l~~~GL~~~~--------------~~ 84 (390)
T TIGR02435 26 GGRLTPAQAIGLADLAERLGNG---IIEVTARGNLQ---LRGLTAD-HDALSQALLAAGLGAAG--------------AA 84 (390)
T ss_pred CCccCHHHHHHHHHHHHHhCCC---eEEEEccccce---ecccCcc-HHHHHHHHHHCCCCCcc--------------cc
Confidence 3458999999999999999852 11122223344 3689999 77766555 443321 12
Q ss_pred C--ceEEEEcCCCccc---ccChHHHHHHHHHHhCCCCCcccCCCcEEEEEecCCCCCCCC
Q 022828 159 G--KYHLLVCGTTPCM---VRGSREIEDALLKHLGVKRNEVTKDGLFSVGEMECMGCCVNA 214 (291)
Q Consensus 159 g--K~~I~VC~gtsC~---~~Gs~~lleaL~~~Lgi~~Gett~DG~ftL~~v~CLG~C~~a 214 (291)
| -..|..|-.+.|. ..-...+.++|.+.+...........+|.+.-++|-..|...
T Consensus 85 g~~~Rnv~~cp~~g~~~~~~~dt~~la~~l~~~l~~~~~~~~LPrKfki~vsgc~~~c~~~ 145 (390)
T TIGR02435 85 ADDIRNIEVSPLAGIDPGEIADTRPLAAELRAALENERALLELPPKFSVAIDGGGRLVLLG 145 (390)
T ss_pred CCcccccccCccccCCCccccchHHHHHHHHHHHhcChhhhcCCCceEEEEECCCccccCC
Confidence 2 2346677665443 234667888888877432212234568999999999888754
No 148
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=20.45 E-value=1.4e+02 Score=25.44 Aligned_cols=48 Identities=15% Similarity=0.215 Sum_probs=32.9
Q ss_pred hhhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhh
Q 022828 87 DTNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYE 145 (291)
Q Consensus 87 ~~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~ 145 (291)
.+....+...|.+.|. +...+-+|+.++. -..++||+.||||...|..
T Consensus 115 ~e~~~~l~~~l~~L~~---~~r~v~~l~~~~g--------~s~~EIA~~l~is~~tv~~ 162 (179)
T PRK09415 115 NAEDERLASAVMSLPI---KYREVIYLFYYEE--------LSIKEIAEVTGVNENTVKT 162 (179)
T ss_pred HHHHHHHHHHHHhCCH---HHhhHhHhHHhcC--------CCHHHHHHHHCCCHHHHHH
Confidence 3455678888999985 2234445555542 2468999999999987754
No 149
>cd02950 TxlA TRX-like protein A (TxlA) family; TxlA was originally isolated from the cyanobacterium Synechococcus. It is found only in oxygenic photosynthetic organisms. TRX is a small enzyme that participate in redox reactions, via the reversible oxidation of an active site dithiol present in a CXXC motif. Disruption of the txlA gene suggests that the protein is involved in the redox regulation of the structure and function of photosynthetic apparatus. The plant homolog (designated as HCF164) is localized in the chloroplast and is involved in the assembly of the cytochrome b6f complex, which takes a central position in photosynthetic electron transport.
Probab=20.37 E-value=3.7e+02 Score=22.41 Aligned_cols=42 Identities=21% Similarity=0.258 Sum_probs=26.9
Q ss_pred CCeEEEcccCCCCCCccceEecCCChhhHHHHHHHHHcCCCCCCC
Q 022828 214 APMITVADYSNGSEGYTYNYYEDVTPKRVIEIVEMLRRGEKLPPG 258 (291)
Q Consensus 214 aPvV~Vnd~~~G~~g~~~~~Y~~vTpE~V~~ILe~l~~G~~~~~g 258 (291)
=|.+++.+ ++|.. -..+.+..+.+.+.++|+++.+|.+++.+
T Consensus 77 iPt~v~~~-~~G~~--v~~~~G~~~~~~l~~~l~~l~~~~~~~~~ 118 (142)
T cd02950 77 IPHFVFLD-REGNE--EGQSIGLQPKQVLAQNLDALVAGEPLPYA 118 (142)
T ss_pred CCEEEEEC-CCCCE--EEEEeCCCCHHHHHHHHHHHHcCCCCCcc
Confidence 47776653 23321 01345667788899999998888765554
No 150
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=20.26 E-value=70 Score=21.75 Aligned_cols=21 Identities=19% Similarity=0.151 Sum_probs=14.1
Q ss_pred HHHHHHHHHhCCCchhhhhhh
Q 022828 127 SAMNEVAKIIEVAPIRVYEVA 147 (291)
Q Consensus 127 eam~~IAe~L~ip~~~V~~Va 147 (291)
..+.+||+.||++++-|+-.+
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 357889999999999887543
No 151
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=20.15 E-value=1.4e+02 Score=27.39 Aligned_cols=51 Identities=10% Similarity=0.219 Sum_probs=34.1
Q ss_pred CChhhHHHHHHHHHhCCCCCCcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCchhhhhh
Q 022828 85 FSDTNKEKVKEILSHYPSNYKQSAVIPLLDLAQQQHGGWLPVSAMNEVAKIIEVAPIRVYEV 146 (291)
Q Consensus 85 ~~~~~~~~i~~il~~yp~~~~~~alipiL~~~Q~~~~GyIp~eam~~IAe~L~ip~~~V~~V 146 (291)
...+....+...|.+.|+ +...+-.|+.. ..-.+.+||+.||++...|...
T Consensus 189 ~~~~~~~~l~~~l~~L~~---~~r~vl~l~y~--------~~~s~~eIA~~lgvs~~~V~~~ 239 (256)
T PRK07408 189 LAQEDRIRLQQALAQLEE---RTREVLEFVFL--------HDLTQKEAAERLGISPVTVSRR 239 (256)
T ss_pred hhHHHHHHHHHHHHcCCH---HHHHHHHHHHH--------CCCCHHHHHHHHCcCHHHHHHH
Confidence 344556778899999985 22223233322 2336899999999999998764
Done!