Query 046034
Match_columns 64
No_of_seqs 104 out of 576
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 08:06:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046034.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046034hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3361 Iron binding protein i 99.7 7.9E-17 1.7E-21 109.1 5.2 50 1-50 106-155 (157)
2 PRK11325 scaffold protein; Pro 99.3 3.1E-12 6.8E-17 82.8 5.3 46 2-47 81-126 (127)
3 TIGR01999 iscU FeS cluster ass 99.3 3.9E-12 8.5E-17 81.8 5.0 45 2-46 79-123 (124)
4 TIGR03419 NifU_clost FeS clust 99.2 1.4E-11 3E-16 79.1 4.6 46 2-47 75-121 (121)
5 PF01592 NifU_N: NifU-like N t 99.0 4.7E-10 1E-14 71.9 4.2 45 2-46 79-124 (126)
6 TIGR02000 NifU_proper Fe-S clu 99.0 5.9E-10 1.3E-14 80.9 4.4 47 2-48 80-127 (290)
7 COG0822 IscU NifU homolog invo 98.7 1.3E-08 2.7E-13 68.2 2.8 47 2-48 82-147 (150)
8 cd06664 IscU_like Iron-sulfur 97.8 1.9E-05 4.1E-10 49.7 2.5 37 2-38 76-123 (123)
9 TIGR01994 SUF_scaf_2 SUF syste 92.8 0.15 3.3E-06 33.2 3.2 21 20-40 117-137 (137)
10 PF13075 DUF3939: Protein of u 72.8 6 0.00013 26.9 3.4 47 5-51 38-99 (140)
11 TIGR02947 SigH_actino RNA poly 72.3 13 0.00027 24.2 4.9 39 7-45 146-185 (193)
12 PF00325 Crp: Bacterial regula 70.5 9.8 0.00021 19.6 3.2 27 8-44 2-28 (32)
13 PF14131 DUF4298: Domain of un 69.4 2.7 5.8E-05 25.8 1.1 27 19-45 55-81 (90)
14 TIGR03121 one_C_dehyd_A formyl 67.7 1.6 3.5E-05 34.9 -0.2 26 7-32 207-240 (556)
15 PF08383 Maf_N: Maf N-terminal 65.7 4.8 0.0001 21.6 1.5 16 3-18 17-32 (35)
16 PRK12519 RNA polymerase sigma 64.3 18 0.00039 23.4 4.3 37 7-43 156-193 (194)
17 PF12918 TcdB_N: TcdB toxin N- 62.4 21 0.00045 20.9 4.0 41 8-48 4-45 (66)
18 PF04539 Sigma70_r3: Sigma-70 61.1 4.5 9.7E-05 22.9 0.9 18 9-26 21-38 (78)
19 PRK12512 RNA polymerase sigma 59.6 22 0.00049 22.7 4.1 37 7-49 146-182 (184)
20 PF10470 AKAP7_RIRII_bdg: PKA- 57.7 16 0.00034 21.7 2.8 27 29-55 15-41 (61)
21 PF10668 Phage_terminase: Phag 57.4 6.8 0.00015 22.9 1.2 17 8-24 22-38 (60)
22 PRK11923 algU RNA polymerase s 54.2 27 0.00059 22.5 3.8 38 7-44 153-191 (193)
23 PF06926 Rep_Org_C: Putative r 51.7 31 0.00067 22.1 3.6 37 13-52 25-61 (95)
24 PF12244 DUF3606: Protein of u 48.4 13 0.00029 21.0 1.5 31 15-45 27-57 (57)
25 cd01304 FMDH_A Formylmethanofu 48.2 5.8 0.00012 31.8 -0.1 26 7-32 203-236 (541)
26 PF13735 tRNA_NucTran2_2: tRNA 45.3 15 0.00032 23.1 1.5 19 7-25 103-121 (149)
27 PF04545 Sigma70_r4: Sigma-70, 44.0 48 0.001 17.2 3.3 19 8-26 20-38 (50)
28 PF14791 DNA_pol_B_thumb: DNA 42.8 15 0.00033 21.2 1.2 19 9-27 43-64 (64)
29 PRK12532 RNA polymerase sigma 42.4 68 0.0015 20.7 4.4 37 7-43 151-188 (195)
30 PF06056 Terminase_5: Putative 41.8 22 0.00047 20.2 1.7 15 8-22 13-27 (58)
31 PRK02919 oxaloacetate decarbox 39.7 25 0.00053 21.5 1.8 14 34-47 69-82 (82)
32 TIGR01764 excise DNA binding d 39.6 22 0.00047 17.6 1.4 15 9-23 2-16 (49)
33 cd08804 Death_ank2 Death domai 39.5 84 0.0018 18.7 4.6 43 5-47 12-59 (84)
34 PRK12520 RNA polymerase sigma 39.3 40 0.00088 21.7 2.9 20 7-26 146-165 (191)
35 PF12728 HTH_17: Helix-turn-he 38.6 22 0.00047 18.6 1.3 12 10-21 3-14 (51)
36 PRK12513 RNA polymerase sigma 38.3 70 0.0015 20.6 3.9 20 7-26 154-173 (194)
37 PF10078 DUF2316: Uncharacteri 37.4 30 0.00066 21.6 2.0 25 2-26 17-41 (89)
38 PRK07037 extracytoplasmic-func 37.0 73 0.0016 19.7 3.7 32 7-44 124-155 (163)
39 PRK05803 sporulation sigma fac 36.3 70 0.0015 21.6 3.8 33 8-40 195-228 (233)
40 PRK12522 RNA polymerase sigma 36.0 95 0.0021 19.6 4.2 20 7-26 134-153 (173)
41 TIGR02937 sigma70-ECF RNA poly 35.6 83 0.0018 18.2 3.6 20 7-26 125-144 (158)
42 cd06171 Sigma70_r4 Sigma70, re 35.5 29 0.00062 16.9 1.4 18 7-24 25-42 (55)
43 PRK05602 RNA polymerase sigma 35.4 79 0.0017 20.2 3.8 20 7-26 143-162 (186)
44 PRK09652 RNA polymerase sigma 34.6 91 0.002 19.3 3.9 20 7-26 143-162 (182)
45 KOG0870 DNA polymerase epsilon 34.2 40 0.00086 23.7 2.3 34 8-47 65-99 (172)
46 PRK11924 RNA polymerase sigma 34.2 69 0.0015 19.7 3.3 19 7-25 140-158 (179)
47 PRK06811 RNA polymerase factor 34.1 96 0.0021 20.0 4.1 34 7-46 146-179 (189)
48 PRK10030 hypothetical protein; 33.9 25 0.00054 24.2 1.3 20 20-39 121-140 (197)
49 TIGR02950 SigM_subfam RNA poly 33.1 1E+02 0.0023 18.7 3.9 20 7-26 120-139 (154)
50 PRK12536 RNA polymerase sigma 33.1 98 0.0021 19.8 4.0 19 7-25 144-162 (181)
51 PF11387 DUF2795: Protein of u 32.7 20 0.00043 19.3 0.5 16 11-26 23-39 (44)
52 PF00531 Death: Death domain; 32.4 93 0.002 17.2 3.8 39 7-45 11-53 (83)
53 cd08318 Death_NMPP84 Death dom 32.4 1.1E+02 0.0024 18.1 4.0 42 7-48 17-62 (86)
54 PRK12530 RNA polymerase sigma 32.3 1.1E+02 0.0024 19.8 4.2 20 7-26 149-168 (189)
55 PRK08583 RNA polymerase sigma 32.0 79 0.0017 21.7 3.5 20 7-26 220-239 (257)
56 PRK09645 RNA polymerase sigma 31.9 95 0.0021 19.5 3.7 20 7-26 133-152 (173)
57 PRK12535 RNA polymerase sigma 31.2 78 0.0017 20.9 3.3 38 7-44 148-186 (196)
58 PHA01623 hypothetical protein 31.0 57 0.0012 18.4 2.3 15 32-46 40-54 (56)
59 PRK09647 RNA polymerase sigma 30.9 81 0.0018 21.1 3.4 32 7-44 153-184 (203)
60 cd08311 Death_p75NR Death doma 30.2 91 0.002 18.5 3.2 37 9-45 16-52 (77)
61 PRK08295 RNA polymerase factor 30.1 91 0.002 20.1 3.4 31 7-43 169-199 (208)
62 cd04752 Commd4 COMM_Domain con 29.4 93 0.002 20.8 3.5 17 8-24 59-78 (174)
63 PF08281 Sigma70_r4_2: Sigma-7 29.2 32 0.00069 18.0 1.0 19 7-25 25-43 (54)
64 smart00550 Zalpha Z-DNA-bindin 28.6 43 0.00093 19.0 1.5 15 9-23 23-37 (68)
65 TIGR02984 Sig-70_plancto1 RNA 28.5 1E+02 0.0022 19.4 3.4 19 8-26 156-174 (189)
66 PRK07204 3-oxoacyl-(acyl carri 28.1 87 0.0019 22.0 3.3 18 25-42 50-67 (329)
67 PF07759 DUF1615: Protein of u 28.1 23 0.0005 27.0 0.4 21 12-32 11-35 (319)
68 TIGR03070 couple_hipB transcri 28.1 53 0.0012 16.7 1.7 17 5-21 12-28 (58)
69 PF09339 HTH_IclR: IclR helix- 28.1 23 0.00049 18.9 0.3 18 9-26 19-36 (52)
70 smart00530 HTH_XRE Helix-turn- 28.0 59 0.0013 15.2 1.8 20 5-24 7-26 (56)
71 PF14451 Ub-Mut7C: Mut7-C ubiq 28.0 32 0.00069 20.8 0.9 17 10-26 34-50 (81)
72 TIGR02859 spore_sigH RNA polym 27.8 1.4E+02 0.003 19.0 4.0 17 8-24 165-181 (198)
73 PRK12514 RNA polymerase sigma 27.5 1.6E+02 0.0035 18.6 4.2 19 7-25 144-162 (179)
74 PRK03814 oxaloacetate decarbox 27.3 58 0.0013 20.0 2.0 15 32-46 69-83 (85)
75 PRK12527 RNA polymerase sigma 26.7 1.3E+02 0.0029 18.6 3.6 20 7-26 120-139 (159)
76 PRK14384 hypothetical protein; 26.1 59 0.0013 18.9 1.8 12 26-37 9-20 (56)
77 PRK12531 RNA polymerase sigma 25.7 1.4E+02 0.0031 19.3 3.8 18 8-25 157-174 (194)
78 PF09077 Phage-MuB_C: Mu B tra 25.6 40 0.00086 20.6 1.0 20 2-21 19-39 (78)
79 CHL00203 fabH 3-oxoacyl-acyl-c 25.5 93 0.002 22.0 3.1 17 26-42 50-66 (326)
80 PRK14382 hypothetical protein; 25.5 59 0.0013 19.3 1.8 13 25-37 28-40 (68)
81 PF11212 DUF2999: Protein of u 25.5 31 0.00068 21.5 0.6 16 13-28 34-49 (82)
82 PF04564 U-box: U-box domain; 25.3 76 0.0017 18.1 2.2 16 32-47 57-72 (73)
83 cd08777 Death_RIP1 Death Domai 25.1 1.6E+02 0.0035 17.6 4.5 43 5-47 10-58 (86)
84 PRK09047 RNA polymerase factor 25.1 1.4E+02 0.0031 18.2 3.6 20 7-26 121-140 (161)
85 PHA01976 helix-turn-helix prot 25.1 62 0.0013 17.5 1.7 18 5-22 12-29 (67)
86 PF03131 bZIP_Maf: bZIP Maf tr 24.8 49 0.0011 19.9 1.3 28 1-28 1-29 (92)
87 TIGR00673 cynS cyanate hydrata 24.7 59 0.0013 22.1 1.9 27 5-31 18-44 (150)
88 smart00005 DEATH DEATH domain, 24.5 1.4E+02 0.0031 16.8 3.3 41 8-48 17-62 (88)
89 PF08513 LisH: LisH; InterPro 24.5 82 0.0018 15.1 1.9 15 35-49 3-17 (27)
90 PF01978 TrmB: Sugar-specific 24.5 30 0.00066 19.1 0.4 18 8-25 22-39 (68)
91 TIGR02985 Sig70_bacteroi1 RNA 24.0 1.5E+02 0.0032 17.8 3.4 18 8-25 129-146 (161)
92 PF04967 HTH_10: HTH DNA bindi 23.8 1.3E+02 0.0029 16.8 3.0 19 7-25 22-40 (53)
93 COG1229 FwdA Formylmethanofura 23.6 29 0.00064 28.1 0.2 26 7-32 210-243 (575)
94 PRK09648 RNA polymerase sigma 23.6 1.5E+02 0.0033 18.9 3.6 19 8-26 155-173 (189)
95 TIGR02835 spore_sigmaE RNA pol 23.6 1.4E+02 0.003 20.2 3.6 18 8-25 198-215 (234)
96 PF00666 Cathelicidins: Cathel 23.5 88 0.0019 18.6 2.2 19 32-50 5-23 (67)
97 TIGR02983 SigE-fam_strep RNA p 23.5 1.9E+02 0.0041 17.8 3.9 18 7-24 125-142 (162)
98 TIGR02948 SigW_bacill RNA poly 23.4 1.6E+02 0.0035 18.5 3.6 20 7-26 151-170 (187)
99 PRK12547 RNA polymerase sigma 23.4 1.8E+02 0.0039 18.2 3.9 19 7-25 127-145 (164)
100 PF14106 DUF4279: Domain of un 23.2 44 0.00095 20.1 0.9 19 8-26 5-23 (118)
101 TIGR02846 spore_sigmaK RNA pol 23.1 1.3E+02 0.0029 20.2 3.4 19 8-26 194-212 (227)
102 PRK09642 RNA polymerase sigma 23.1 1.9E+02 0.0042 17.8 4.0 19 7-25 121-139 (160)
103 PRK12543 RNA polymerase sigma 22.9 1.9E+02 0.0041 18.4 3.9 20 7-26 132-151 (179)
104 PRK10046 dpiA two-component re 22.8 77 0.0017 20.8 2.1 24 8-31 177-202 (225)
105 PRK14390 hypothetical protein; 22.8 73 0.0016 18.7 1.8 13 25-37 21-33 (63)
106 PRK12526 RNA polymerase sigma 22.7 1.7E+02 0.0037 19.3 3.8 30 8-43 169-198 (206)
107 TIGR02939 RpoE_Sigma70 RNA pol 22.7 1.6E+02 0.0034 18.6 3.5 20 7-26 153-172 (190)
108 PRK04217 hypothetical protein; 22.7 1.8E+02 0.0039 18.5 3.7 36 7-42 57-93 (110)
109 cd00336 Ribosomal_L22 Ribosoma 22.5 71 0.0015 19.4 1.8 39 10-48 23-62 (105)
110 PRK09641 RNA polymerase sigma 22.5 1.6E+02 0.0034 18.5 3.5 19 7-25 151-169 (187)
111 smart00421 HTH_LUXR helix_turn 22.4 69 0.0015 15.8 1.5 19 7-25 17-35 (58)
112 TIGR01195 oadG_fam sodium pump 22.3 71 0.0015 19.2 1.7 14 33-46 68-81 (82)
113 PRK09640 RNA polymerase sigma 22.3 2E+02 0.0042 18.5 3.9 20 7-26 149-168 (188)
114 PRK11470 hypothetical protein; 22.3 75 0.0016 22.4 2.0 25 20-44 111-135 (200)
115 PRK12533 RNA polymerase sigma 22.1 1.6E+02 0.0035 20.0 3.7 19 7-25 149-167 (216)
116 TIGR03879 near_KaiC_dom probab 22.0 64 0.0014 19.4 1.4 19 7-25 31-49 (73)
117 TIGR03209 P21_Cbot clostridium 22.0 62 0.0013 19.8 1.4 18 7-24 122-139 (142)
118 COG1595 RpoE DNA-directed RNA 22.0 1.8E+02 0.0039 18.6 3.7 32 7-44 142-173 (182)
119 PF07308 DUF1456: Protein of u 22.0 1.4E+02 0.0031 17.4 2.9 20 5-24 10-32 (68)
120 PF06531 DUF1108: Protein of u 22.0 1.2E+02 0.0026 19.1 2.7 24 26-49 52-75 (86)
121 PRK14373 hypothetical protein; 21.8 77 0.0017 19.1 1.8 13 25-37 32-44 (73)
122 PRK12528 RNA polymerase sigma 21.7 1.2E+02 0.0025 18.9 2.7 17 8-24 129-145 (161)
123 PRK10840 transcriptional regul 21.7 1.2E+02 0.0025 19.6 2.7 21 7-27 164-186 (216)
124 PF07022 Phage_CI_repr: Bacter 21.6 26 0.00057 19.7 -0.3 19 4-22 7-26 (66)
125 PRK02866 cyanate hydratase; Va 21.5 75 0.0016 21.5 1.9 27 5-31 15-41 (147)
126 cd00093 HTH_XRE Helix-turn-hel 21.3 95 0.0021 14.5 1.8 20 5-24 9-28 (58)
127 TIGR02999 Sig-70_X6 RNA polyme 21.3 65 0.0014 20.4 1.5 20 7-26 149-168 (183)
128 COG3413 Predicted DNA binding 21.2 1.3E+02 0.0028 20.3 3.0 20 7-26 177-196 (215)
129 PF14813 NADH_B2: NADH dehydro 21.1 45 0.00098 20.1 0.6 9 16-24 61-69 (71)
130 PLN03168 chalcone synthase; Pr 21.0 84 0.0018 23.5 2.2 17 12-28 310-326 (389)
131 PRK12524 RNA polymerase sigma 21.0 1.7E+02 0.0036 19.0 3.4 32 7-44 151-182 (196)
132 TIGR02960 SigX5 RNA polymerase 20.9 2.2E+02 0.0048 19.8 4.2 20 6-25 156-175 (324)
133 PRK09636 RNA polymerase sigma 20.8 3E+02 0.0066 19.2 5.0 21 5-25 128-148 (293)
134 PRK08301 sporulation sigma fac 20.8 1.9E+02 0.004 19.4 3.7 18 8-25 198-215 (234)
135 PRK12539 RNA polymerase sigma 20.7 2.2E+02 0.0047 18.2 3.9 19 7-25 146-164 (184)
136 PRK14375 hypothetical protein; 20.5 85 0.0018 18.8 1.8 13 25-37 22-34 (70)
137 PF08334 T2SG: Type II secreti 20.5 1.7E+02 0.0038 17.6 3.2 24 28-51 14-37 (108)
138 COG0759 Uncharacterized conser 20.5 81 0.0018 20.0 1.7 13 25-37 33-45 (92)
139 PF14698 ASL_C2: Argininosucci 20.3 57 0.0012 18.9 1.0 18 9-26 2-22 (70)
140 PRK12523 RNA polymerase sigma 20.3 2.4E+02 0.0051 17.8 4.0 18 8-25 135-152 (172)
141 PRK09258 3-oxoacyl-(acyl carri 20.3 1.3E+02 0.0029 21.1 3.0 34 12-45 273-311 (338)
142 PRK11753 DNA-binding transcrip 20.2 2E+02 0.0044 18.3 3.7 29 7-45 167-195 (211)
143 cd04761 HTH_MerR-SF Helix-Turn 20.1 73 0.0016 15.9 1.3 13 10-22 2-14 (49)
144 cd04762 HTH_MerR-trunc Helix-T 20.1 77 0.0017 15.3 1.3 11 11-21 3-13 (49)
No 1
>KOG3361 consensus Iron binding protein involved in Fe-S cluster formation [Energy production and conversion]
Probab=99.67 E-value=7.9e-17 Score=109.06 Aligned_cols=50 Identities=62% Similarity=0.819 Sum_probs=46.9
Q ss_pred ChhHHhhcCCHHHHHHhcCCCCchhHHHHHHHHHHHHHHHHHHHhhCCCc
Q 046034 1 MANLRNLSGLSKEIAKHLSLPPVKLHCSMLAEDAIKAAVKDYEAKHTKSS 50 (64)
Q Consensus 1 ~~~~EA~~I~~~dI~e~LgLP~~K~HCA~LA~~ALk~AI~dY~~k~~~~~ 50 (64)
|.++|+++|++.+|+.+|.|||.|+|||+||++|++.||+||+.||...+
T Consensus 106 kt~dea~kIkNteIAKeL~LPPVKLHCSMLAEDAIKaAikdyk~Kq~~~~ 155 (157)
T KOG3361|consen 106 KTLDEALKIKNTEIAKELSLPPVKLHCSMLAEDAIKAAIKDYKEKQNKPN 155 (157)
T ss_pred ccHHHHHhcccHHHHHhccCCchhhhhHHHHHHHHHHHHHHHHHhccCCC
Confidence 56899999999999999999999999999999999999999999987554
No 2
>PRK11325 scaffold protein; Provisional
Probab=99.32 E-value=3.1e-12 Score=82.78 Aligned_cols=46 Identities=52% Similarity=0.807 Sum_probs=43.4
Q ss_pred hhHHhhcCCHHHHHHhcCCCCchhHHHHHHHHHHHHHHHHHHHhhC
Q 046034 2 ANLRNLSGLSKEIAKHLSLPPVKLHCSMLAEDAIKAAVKDYEAKHT 47 (64)
Q Consensus 2 ~~~EA~~I~~~dI~e~LgLP~~K~HCA~LA~~ALk~AI~dY~~k~~ 47 (64)
.++|++.|+.++|.++|||||.|+||+.|+.+||++||.+|+.++.
T Consensus 81 tl~ea~~i~~~~i~~~lg~p~~r~~CA~la~~al~~a~~~y~~~~~ 126 (127)
T PRK11325 81 TLDEALAIKNTDIAEELALPPVKIHCSILAEDAIKAAIADYKSKQA 126 (127)
T ss_pred CHHHHHhcCHHHHHHHcCCCcccchHHHHHHHHHHHHHHHHHhhcC
Confidence 4789999999999999999999999999999999999999988764
No 3
>TIGR01999 iscU FeS cluster assembly scaffold IscU. This model represents IscU, a homolog of the N-terminal region of NifU, an Fe-S cluster assembly protein found mostly in nitrogen-fixing bacteria. IscU is considered part of the IscSUA-hscAB-fdx system of Fe-S assembly, whereas NifU is found in nitrogenase-containing (nitrogen-fixing) species. A NifU-type protein is also found in Helicobacter and Campylobacter. IscU and NifU are considered scaffold proteins on which Fe-S clusters are assembled before transfer to apoproteins. This model excludes true NifU proteins as in Klebsiella pneumoniae and Anabaena sp. as well as archaeal homologs. It includes largely proteobacterial and eukaryotic forms.
Probab=99.30 E-value=3.9e-12 Score=81.80 Aligned_cols=45 Identities=64% Similarity=0.893 Sum_probs=42.6
Q ss_pred hhHHhhcCCHHHHHHhcCCCCchhHHHHHHHHHHHHHHHHHHHhh
Q 046034 2 ANLRNLSGLSKEIAKHLSLPPVKLHCSMLAEDAIKAAVKDYEAKH 46 (64)
Q Consensus 2 ~~~EA~~I~~~dI~e~LgLP~~K~HCA~LA~~ALk~AI~dY~~k~ 46 (64)
.++|+..|++++|.++|||||.|+||+.|+.+||+.||.+|+.++
T Consensus 79 tl~ea~~i~~~~i~~~lg~p~~r~~CA~l~~~al~~a~~~y~~~~ 123 (124)
T TIGR01999 79 SLEEALKIKNTEIAKELSLPPVKLHCSLLAEDAIKAAIKDYKSKQ 123 (124)
T ss_pred CHHHHHhccHHHHHHHcCCCcccchHHHHHHHHHHHHHHHHHHhc
Confidence 478999999999999999999999999999999999999998765
No 4
>TIGR03419 NifU_clost FeS cluster assembly scaffold protein NifU, Clostridium type. NifU and NifS form a pair of iron-sulfur (FeS) cluster biosynthesis proteins much simpler than the ISC and SUF systems. Members of this protein family are a distinct group of NifU-like proteins, found always to a NifS-like protein and restricted to species that lack a SUF system. Typically, NIF systems service a smaller number of FeS-containing proteins than do ISC or SUF. Members of this particular branch typically are found, almost half the time, near the mnmA gene, involved in the carboxymethylaminomethyl modification of U34 in some tRNAs (see GenProp0704). While other NifU proteins are associated with nitrogen fixation, this family is not.
Probab=99.23 E-value=1.4e-11 Score=79.10 Aligned_cols=46 Identities=43% Similarity=0.687 Sum_probs=42.9
Q ss_pred hhHHhhcCCHHHHHHhc-CCCCchhHHHHHHHHHHHHHHHHHHHhhC
Q 046034 2 ANLRNLSGLSKEIAKHL-SLPPVKLHCSMLAEDAIKAAVKDYEAKHT 47 (64)
Q Consensus 2 ~~~EA~~I~~~dI~e~L-gLP~~K~HCA~LA~~ALk~AI~dY~~k~~ 47 (64)
.++|+..|+.++|.++| ||||.|+||+.|+.+||+.|+.+|+.+++
T Consensus 75 ~l~ea~~i~~~~i~~~l~~l~~~r~~CA~la~~al~~a~~~y~~~~~ 121 (121)
T TIGR03419 75 TLEEAWELTNKAVAEALDGLPPVKMHCSVLAEEAIHKAINDYREKNG 121 (121)
T ss_pred CHHHHHHhhhHHHHHHHcCCCcccCHHHHHHHHHHHHHHHHHHhccC
Confidence 47899999999999999 79999999999999999999999998764
No 5
>PF01592 NifU_N: NifU-like N terminal domain; InterPro: IPR002871 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] []. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins [, ]. It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly []. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA []. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA [], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins []. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen []. This entry represents the N-terminal of NifU and homologous proteins. NifU contains two domains: an N-terminal and a C-terminal domain (IPR001075 from INTERPRO) []. These domains exist either together or on different polypeptides, both domains being found in organisms that do not fix nitrogen (e.g. yeast), so they have a broader significance in the cell than nitrogen fixation. ; GO: 0005506 iron ion binding, 0051536 iron-sulfur cluster binding, 0016226 iron-sulfur cluster assembly; PDB: 3LVL_A 4EB5_C 4EB7_C 1WFZ_A 2Z7E_C 2AZH_A 1XJS_A 1Q48_A 1R9P_A 2KQK_A ....
Probab=99.00 E-value=4.7e-10 Score=71.94 Aligned_cols=45 Identities=44% Similarity=0.705 Sum_probs=41.6
Q ss_pred hhHHhhcCCHHHHHHhc-CCCCchhHHHHHHHHHHHHHHHHHHHhh
Q 046034 2 ANLRNLSGLSKEIAKHL-SLPPVKLHCSMLAEDAIKAAVKDYEAKH 46 (64)
Q Consensus 2 ~~~EA~~I~~~dI~e~L-gLP~~K~HCA~LA~~ALk~AI~dY~~k~ 46 (64)
.++||++|+.++|.++| ++|+++.||+.|+.+||+.||.+|+.++
T Consensus 79 ~l~ea~~i~~~~i~~~l~~~~~~~~~~~~l~~~al~~av~~y~~r~ 124 (126)
T PF01592_consen 79 TLEEALKITAEDIEEALGGLPPERQHCAELADDALKAAVADYPARH 124 (126)
T ss_dssp BHHHHHCHHHHHHHHHHTC-CGTCGHHHHHHHHHHHHHHHHHHHHC
T ss_pred CHHHHHHHHHHHHHHHHhccccCcccHHHHHHHHHHHHHHHHHhhh
Confidence 47899999999999999 7999999999999999999999999875
No 6
>TIGR02000 NifU_proper Fe-S cluster assembly protein NifU. Three different but partially homologous Fe-S cluster assembly systems have been described: Isc, Suf, and Nif. The latter is associated with donation of an Fe-S cluster to nitrogenase in a number of nitrogen-fixing species. NifU, described here, consists of an N-terminal domain (pfam01592) and a C-terminal domain (pfam01106). Homologs with an equivalent domain archictecture from Helicobacter and Campylobacter, however, are excluded from this model by a high trusted cutoff. The model, therefore, is specific for NifU involved in nitrogenase maturation. The related model TIGR01999 homologous to the N-terminus of this model describes IscU from the Isc system as in E. coli, Saccharomyces cerevisiae, and Homo sapiens.
Probab=98.98 E-value=5.9e-10 Score=80.87 Aligned_cols=47 Identities=32% Similarity=0.594 Sum_probs=43.7
Q ss_pred hhHHhhcCCHHHHHHhc-CCCCchhHHHHHHHHHHHHHHHHHHHhhCC
Q 046034 2 ANLRNLSGLSKEIAKHL-SLPPVKLHCSMLAEDAIKAAVKDYEAKHTK 48 (64)
Q Consensus 2 ~~~EA~~I~~~dI~e~L-gLP~~K~HCA~LA~~ALk~AI~dY~~k~~~ 48 (64)
.++||+.|++++|.++| ||||.|+||+.|+.+||+.||.+|+++...
T Consensus 80 tv~ea~~i~~~di~~~L~~lpp~r~~CA~La~~Al~~Al~~y~~kp~~ 127 (290)
T TIGR02000 80 TLDEALKVSNQDIADYLGGLPPEKMHCSVMGQEALEAAIANYRGEPLE 127 (290)
T ss_pred CHHHHHHhhHHHHHHHHcCCChhhchHHHHHHHHHHHHHHHHhcCccc
Confidence 47899999999999999 899999999999999999999999987654
No 7
>COG0822 IscU NifU homolog involved in Fe-S cluster formation [Energy production and conversion]
Probab=98.68 E-value=1.3e-08 Score=68.22 Aligned_cols=47 Identities=43% Similarity=0.644 Sum_probs=43.0
Q ss_pred hhHHhhcCC--HHHHHHhcC-----------------CCCchhHHHHHHHHHHHHHHHHHHHhhCC
Q 046034 2 ANLRNLSGL--SKEIAKHLS-----------------LPPVKLHCSMLAEDAIKAAVKDYEAKHTK 48 (64)
Q Consensus 2 ~~~EA~~I~--~~dI~e~Lg-----------------LP~~K~HCA~LA~~ALk~AI~dY~~k~~~ 48 (64)
.++||++|+ ..++.+.|| +||.|+||++|+.+||+.||.+|..++..
T Consensus 82 ti~EAl~i~~~~~~m~~~~~~~~~~~l~d~~~l~~v~~~p~r~~C~~L~~~al~~ai~~~~~~~~~ 147 (150)
T COG0822 82 TLDEALKITEAFTDMAKELGGDPDDRLGDLVALAGVALPPARIKCSLLAWDALKAAIKDYKGKAEE 147 (150)
T ss_pred CHHHHHHHHHHHHHHHHHcCCCccchhhhhHhhhhhccccccccchhccHHHHHHHHHHhhccccc
Confidence 478999999 999999995 89999999999999999999999988654
No 8
>cd06664 IscU_like Iron-sulfur cluster scaffold-like proteins. IscU_like and NifU_like proteins. IscU and NifU function as a scaffold for the assembly of [2Fe-2S] clusters before they are transferred to apo target proteins. They are highly conserved and play vital roles in the ISC and NIF systems of Fe-S protein maturation. NIF genes participate in nitrogen fixation in several isolated bacterial species. The NifU domain, however, is also found in bacteria that do not fix nitrogen, so it may have wider significance in the cell. Human IscU interacts with frataxin, the Friedreich ataxia gene product, and incorrectly spliced IscU has been shown to disrupt iron homeostasis in skeletal muscle and cause myopathy.
Probab=97.77 E-value=1.9e-05 Score=49.70 Aligned_cols=37 Identities=43% Similarity=0.589 Sum_probs=32.7
Q ss_pred hhHHhhcCCHHHHHHh----------c-CCCCchhHHHHHHHHHHHHH
Q 046034 2 ANLRNLSGLSKEIAKH----------L-SLPPVKLHCSMLAEDAIKAA 38 (64)
Q Consensus 2 ~~~EA~~I~~~dI~e~----------L-gLP~~K~HCA~LA~~ALk~A 38 (64)
.++|+..|+.+.+... + ++||.|+||+.|+.+||+.|
T Consensus 76 ~~~ea~~i~~~~~~~~~~~~~l~~~~~~~~~~~R~~Ca~L~~~Al~~a 123 (123)
T cd06664 76 TLDEALKLLNKDIAMLDGKEELAALAGVGLPPARIHCALLAWKALKAA 123 (123)
T ss_pred cHHHHHHHHHHHHHHhcCchhHHHhcccccCcccchHHHHHHHHHHhC
Confidence 4688999999999887 5 89999999999999999864
No 9
>TIGR01994 SUF_scaf_2 SUF system FeS assembly protein, NifU family. Three iron-sulfur cluster assembly systems are known so far. ISC is broadly distributed while NIF tends to be associated with nitrogenase in nitrogen-fixing bacteria. The most recently described is SUF, believed to be important to maintain the function during aerobic stress of enzymes with labile Fe-S clusters. It is fairly widely distributed. This family represents one of two different proteins proposed to act as a scaffold on which the Fe-S cluster is built and from which it is transferred.
Probab=92.79 E-value=0.15 Score=33.16 Aligned_cols=21 Identities=29% Similarity=0.510 Sum_probs=18.6
Q ss_pred CCCchhHHHHHHHHHHHHHHH
Q 046034 20 LPPVKLHCSMLAEDAIKAAVK 40 (64)
Q Consensus 20 LP~~K~HCA~LA~~ALk~AI~ 40 (64)
-.|.+++|+.|+.+||+.||.
T Consensus 117 ~~p~R~~Ca~L~~~al~~al~ 137 (137)
T TIGR01994 117 KFPARIKCATLAWKALERALA 137 (137)
T ss_pred cCcchHHHHHHHHHHHHHHhC
Confidence 368999999999999999873
No 10
>PF13075 DUF3939: Protein of unknown function (DUF3939)
Probab=72.78 E-value=6 Score=26.90 Aligned_cols=47 Identities=21% Similarity=0.189 Sum_probs=35.8
Q ss_pred HhhcCCHHHHHHhc-CCCCchhHHHHH--------------HHHHHHHHHHHHHHhhCCCcc
Q 046034 5 RNLSGLSKEIAKHL-SLPPVKLHCSML--------------AEDAIKAAVKDYEAKHTKSSA 51 (64)
Q Consensus 5 EA~~I~~~dI~e~L-gLP~~K~HCA~L--------------A~~ALk~AI~dY~~k~~~~~~ 51 (64)
+-..|+.+.+..+| |+|..++.-|-- -.+..|.||+.|..+.+.-+-
T Consensus 38 ~d~~iD~~~L~~yL~g~p~q~FymSkeTyeifeeee~~ip~~iD~VQ~AVD~Y~~e~~~lPi 99 (140)
T PF13075_consen 38 DDQSIDFERLAPYLGGIPDQRFYMSKETYEIFEEEEKDIPKEIDKVQKAVDQYVKETGKLPI 99 (140)
T ss_pred CCceecHHHHhhhcCCCCCcceeeeHHHHHhhhHHHHhCHHHHHHHHHHHHHHHHhcCccCC
Confidence 33578899999999 898887765543 356779999999998776543
No 11
>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=72.32 E-value=13 Score=24.20 Aligned_cols=39 Identities=15% Similarity=0.153 Sum_probs=27.1
Q ss_pred hcCCHHHHHHhcCCCCchhHHHH-HHHHHHHHHHHHHHHh
Q 046034 7 LSGLSKEIAKHLSLPPVKLHCSM-LAEDAIKAAVKDYEAK 45 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K~HCA~-LA~~ALk~AI~dY~~k 45 (64)
.+++.++|++.||+|+..+.--. -|.+.|+..+.++...
T Consensus 146 ~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~~~ 185 (193)
T TIGR02947 146 EGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLVDVAGE 185 (193)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 45788999999999877665432 2566667777666554
No 12
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=70.48 E-value=9.8 Score=19.61 Aligned_cols=27 Identities=22% Similarity=0.316 Sum_probs=16.9
Q ss_pred cCCHHHHHHhcCCCCchhHHHHHHHHHHHHHHHHHHH
Q 046034 8 SGLSKEIAKHLSLPPVKLHCSMLAEDAIKAAVKDYEA 44 (64)
Q Consensus 8 ~I~~~dI~e~LgLP~~K~HCA~LA~~ALk~AI~dY~~ 44 (64)
.++..||+++||+.+ +++-+.+.+++.
T Consensus 2 ~mtr~diA~~lG~t~----------ETVSR~l~~l~~ 28 (32)
T PF00325_consen 2 PMTRQDIADYLGLTR----------ETVSRILKKLER 28 (32)
T ss_dssp E--HHHHHHHHTS-H----------HHHHHHHHHHHH
T ss_pred CcCHHHHHHHhCCcH----------HHHHHHHHHHHH
Confidence 578999999999874 455555655544
No 13
>PF14131 DUF4298: Domain of unknown function (DUF4298)
Probab=69.43 E-value=2.7 Score=25.79 Aligned_cols=27 Identities=33% Similarity=0.373 Sum_probs=22.5
Q ss_pred CCCCchhHHHHHHHHHHHHHHHHHHHh
Q 046034 19 SLPPVKLHCSMLAEDAIKAAVKDYEAK 45 (64)
Q Consensus 19 gLP~~K~HCA~LA~~ALk~AI~dY~~k 45 (64)
|.-|..+.|++|++++|-.++.++..-
T Consensus 55 g~~~~~~~~gVLSEDaiyn~lgd~~~l 81 (90)
T PF14131_consen 55 GDLPTDGKCGVLSEDAIYNALGDHYEL 81 (90)
T ss_pred CCCCCCcccCccCchHHHHHHHHHHHH
Confidence 655678999999999999999887643
No 14
>TIGR03121 one_C_dehyd_A formylmethanofuran dehydrogenase subunit A. Members of this largely archaeal protein family are subunit A of the formylmethanofuran dehydrogenase. Nomenclature in some bacteria may reflect inclusion of the formyltransferase described by TIGR03119 as part of the complex, and therefore call this protein formyltransferase/hydrolase complex Fhc subunit A. Note that this model does not distinguish tungsten (FwdA) from molybdenum-containing (FmdA) forms of this enzyme; a single gene from this family is expressed constitutively in Methanobacterium thermoautotrophicum, which has both tungsten and molybdenum forms and may work interchangeably.
Probab=67.70 E-value=1.6 Score=34.88 Aligned_cols=26 Identities=35% Similarity=0.629 Sum_probs=20.3
Q ss_pred hcCCHHHHHHhc-------CCC-CchhHHHHHHH
Q 046034 7 LSGLSKEIAKHL-------SLP-PVKLHCSMLAE 32 (64)
Q Consensus 7 ~~I~~~dI~e~L-------gLP-~~K~HCA~LA~ 32 (64)
+.||+.+|+..| ||| +.++||.+|+.
T Consensus 207 ~~vtp~~i~~~l~~~~e~l~lph~~h~H~nnlg~ 240 (556)
T TIGR03121 207 FGITPREIIKGLARANEELGLPHSIHVHCNNLGV 240 (556)
T ss_pred CCCCHHHHHHHHHHHHHhcCCCceEEEecCCCCC
Confidence 467888877655 798 78999999974
No 15
>PF08383 Maf_N: Maf N-terminal region; InterPro: IPR013592 This region is found in various leucine zipper transcription factors of the Maf family. These are implicated in the regulation of insulin gene expression [], in erythroid differentiation [], and in differentiation of the neuroretina [].
Probab=65.71 E-value=4.8 Score=21.59 Aligned_cols=16 Identities=19% Similarity=0.175 Sum_probs=14.1
Q ss_pred hHHhhcCCHHHHHHhc
Q 046034 3 NLRNLSGLSKEIAKHL 18 (64)
Q Consensus 3 ~~EA~~I~~~dI~e~L 18 (64)
+.|++.+|.+|.+|+|
T Consensus 17 ~pe~l~LtpEDAvEaL 32 (35)
T PF08383_consen 17 NPEALGLTPEDAVEAL 32 (35)
T ss_pred ChhhcCCCHHHHHHHH
Confidence 4689999999999988
No 16
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=64.32 E-value=18 Score=23.36 Aligned_cols=37 Identities=19% Similarity=0.156 Sum_probs=25.4
Q ss_pred hcCCHHHHHHhcCCCCchhHHHHH-HHHHHHHHHHHHH
Q 046034 7 LSGLSKEIAKHLSLPPVKLHCSML-AEDAIKAAVKDYE 43 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K~HCA~L-A~~ALk~AI~dY~ 43 (64)
.+++.++|++.||+++.-+.--.- |.+-|+..+.+|.
T Consensus 156 ~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~~~ 193 (194)
T PRK12519 156 EGLSQSEIAKRLGIPLGTVKARARQGLLKLRELLQDLL 193 (194)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHh
Confidence 357889999999998877665433 5556666665553
No 17
>PF12918 TcdB_N: TcdB toxin N-terminal helical domain; InterPro: IPR024772 Toxins A (TcdA) and B (TcdB) of Clostridium difficile belong to the family of clostridial glucosylating toxins. These toxins glucosylate small GTPases of Rho and Ras families, inhibiting the signalling and regulatory functions of these switch proteins. After receptor-binding, the toxins are endocytosed to reach acidic endosomal compartments from where the toxins are translocated into the cytosol []. TcdB has been shown to consist of a N-terminal glucosyltransferase domain (GTD), responsible for the biological effects of the toxin, a cysteine protease domain (CPD), responsible for autocatalytic cleavage, a hydrophobic region (HR), which has been suggested to be involved in toxin translocation, and a C-terminal repetitive domain involved in receptor binding. The pore-forming region of toxin B has been described to be in a region in the middle of the protein, within amino acid residues 830 and 990 []. This entry represents a short helical bundle domain found associated with the catalytic domain of TcdA and TcdB []. It is also found in some other toxins. The function of this domain is unknown, but it may be involved in substrate recognition.; PDB: 2VKH_C 2VL8_A 2VKD_A 2BVL_A 2BVM_A 3SS1_A 3SRZ_A 2VK9_A.
Probab=62.36 E-value=21 Score=20.92 Aligned_cols=41 Identities=15% Similarity=0.110 Sum_probs=30.3
Q ss_pred cCCHHHHHHhc-CCCCchhHHHHHHHHHHHHHHHHHHHhhCC
Q 046034 8 SGLSKEIAKHL-SLPPVKLHCSMLAEDAIKAAVKDYEAKHTK 48 (64)
Q Consensus 8 ~I~~~dI~e~L-gLP~~K~HCA~LA~~ALk~AI~dY~~k~~~ 48 (64)
+++.+.|.+.| +|.+...-=-..-.+=|+.+|..|+.....
T Consensus 4 dl~~~ni~~~l~~l~~~~~~~~~~~l~~lk~~I~~Y~~l~~~ 45 (66)
T PF12918_consen 4 DLTIDNIEEKLFKLTEEQSPKCYELLKKLKKAIDNYNNLYEN 45 (66)
T ss_dssp HHHHHHHHHHHHTTTTS-HHHHHHHHHHHHHHHHHHHHHTTT
T ss_pred HhHHHHHHHHhhccCccccHHHHHHHHHHHHHHHHHHHHhhh
Confidence 45677888998 887665555556678899999999998433
No 18
>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=61.09 E-value=4.5 Score=22.91 Aligned_cols=18 Identities=22% Similarity=0.333 Sum_probs=14.4
Q ss_pred CCHHHHHHhcCCCCchhH
Q 046034 9 GLSKEIAKHLSLPPVKLH 26 (64)
Q Consensus 9 I~~~dI~e~LgLP~~K~H 26 (64)
-|.++|++.||++.++++
T Consensus 21 Pt~eEiA~~lgis~~~v~ 38 (78)
T PF04539_consen 21 PTDEEIAEELGISVEEVR 38 (78)
T ss_dssp -BHHHHHHHHTS-HHHHH
T ss_pred CCHHHHHHHHcccHHHHH
Confidence 478899999999998876
No 19
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=59.60 E-value=22 Score=22.70 Aligned_cols=37 Identities=22% Similarity=0.183 Sum_probs=26.9
Q ss_pred hcCCHHHHHHhcCCCCchhHHHHHHHHHHHHHHHHHHHhhCCC
Q 046034 7 LSGLSKEIAKHLSLPPVKLHCSMLAEDAIKAAVKDYEAKHTKS 49 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K~HCA~LA~~ALk~AI~dY~~k~~~~ 49 (64)
.+++.++|++.||+|...++ ..++.|....+.+-.++
T Consensus 146 ~g~s~~eIA~~l~is~~tV~------~~l~ra~~~Lr~~l~~~ 182 (184)
T PRK12512 146 EGASIKETAAKLSMSEGAVR------VALHRGLAALAAKFRSE 182 (184)
T ss_pred cCCCHHHHHHHhCCCHHHHH------HHHHHHHHHHHHHhhcC
Confidence 46788999999999976553 66777777777665443
No 20
>PF10470 AKAP7_RIRII_bdg: PKA-RI-RII subunit binding domain of A-kinase anchor protein; InterPro: IPR019511 This entry represents the RI-RII subunit-binding domain found at the C-terminal of the cyclic AMP-dependent protein kinase A (PKA) anchor protein, AKAP7. This protein anchors PKA, for its role in regulating PKA-mediated gene transcription in both somatic cells and oocytes, by binding to its regulatory subunits, RI and RII, hence being known as a dual-specific AKAP []. The 25 crucial amino acids of RII-binding domains in general form structurally conserved amphipathic helices with unrelated sequences; hydrophobic amino acid residues form the backbone of the interaction and hydrogen bond- and salt-bridge-forming amino acid residues increase the affinity of the interaction []. The nuclear localisation signal-containing domain is found at the N terminus.
Probab=57.71 E-value=16 Score=21.71 Aligned_cols=27 Identities=22% Similarity=0.373 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHHHHHHhhCCCcccccc
Q 046034 29 MLAEDAIKAAVKDYEAKHTKSSAASEA 55 (64)
Q Consensus 29 ~LA~~ALk~AI~dY~~k~~~~~~~~~~ 55 (64)
.|...|+-+|+..|.....++...+.+
T Consensus 15 rlVenAVlkAvQQy~eEtq~k~~~~~g 41 (61)
T PF10470_consen 15 RLVENAVLKAVQQYLEETQNKEQPGDG 41 (61)
T ss_pred HHHHHHHHHHHHHHHHHHHhhccCCCC
Confidence 467899999999999887655555544
No 21
>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=57.37 E-value=6.8 Score=22.90 Aligned_cols=17 Identities=24% Similarity=0.212 Sum_probs=14.6
Q ss_pred cCCHHHHHHhcCCCCch
Q 046034 8 SGLSKEIAKHLSLPPVK 24 (64)
Q Consensus 8 ~I~~~dI~e~LgLP~~K 24 (64)
.|+..||++.||.++..
T Consensus 22 ~i~lkdIA~~Lgvs~~t 38 (60)
T PF10668_consen 22 KIKLKDIAEKLGVSEST 38 (60)
T ss_pred CccHHHHHHHHCCCHHH
Confidence 58999999999998654
No 22
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=54.25 E-value=27 Score=22.48 Aligned_cols=38 Identities=18% Similarity=0.130 Sum_probs=25.8
Q ss_pred hcCCHHHHHHhcCCCCchhHH-HHHHHHHHHHHHHHHHH
Q 046034 7 LSGLSKEIAKHLSLPPVKLHC-SMLAEDAIKAAVKDYEA 44 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K~HC-A~LA~~ALk~AI~dY~~ 44 (64)
.+.+.++|++.||+++..+.= -.-+...|+..|..|..
T Consensus 153 ~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~~~~ 191 (193)
T PRK11923 153 DGLSYEDIASVMQCPVGTVRSRIFRAREAIDKALQPLLQ 191 (193)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 457788999999998665542 23366677777776654
No 23
>PF06926 Rep_Org_C: Putative replisome organiser protein C-terminus; InterPro: IPR009696 This entry represents the C terminus (approximately 100 residues) of a putative replisome organiser protein in Lactococcus bacteriophages [].
Probab=51.69 E-value=31 Score=22.10 Aligned_cols=37 Identities=11% Similarity=0.303 Sum_probs=28.2
Q ss_pred HHHHhcCCCCchhHHHHHHHHHHHHHHHHHHHhhCCCccc
Q 046034 13 EIAKHLSLPPVKLHCSMLAEDAIKAAVKDYEAKHTKSSAA 52 (64)
Q Consensus 13 dI~e~LgLP~~K~HCA~LA~~ALk~AI~dY~~k~~~~~~~ 52 (64)
...+++.||+....|++.+..=- |..|..+...++.+
T Consensus 25 A~~eFi~L~~~QkeqaViGA~NY---~~~Ykn~~~dD~~~ 61 (95)
T PF06926_consen 25 ALQEFIKLPSEQKEQAVIGAKNY---VQWYKNENPDDNTG 61 (95)
T ss_pred HHHHHHHcCHHHHHHHHHhHHHH---HHHHHHcCCCCCCc
Confidence 44566689999999999887654 88888887766544
No 24
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=48.35 E-value=13 Score=20.98 Aligned_cols=31 Identities=29% Similarity=0.348 Sum_probs=24.7
Q ss_pred HHhcCCCCchhHHHHHHHHHHHHHHHHHHHh
Q 046034 15 AKHLSLPPVKLHCSMLAEDAIKAAVKDYEAK 45 (64)
Q Consensus 15 ~e~LgLP~~K~HCA~LA~~ALk~AI~dY~~k 45 (64)
++.||.+++.+.=++=.+..-..+|..|++|
T Consensus 27 a~~~gvt~~~L~~AV~~vG~~~~~V~~~L~k 57 (57)
T PF12244_consen 27 AKRFGVTEEQLREAVRAVGNSRAAVRAYLGK 57 (57)
T ss_pred HHHHCcCHHHHHHHHHHHCcCHHHHHHHHcC
Confidence 3445899999888888888888888888765
No 25
>cd01304 FMDH_A Formylmethanofuran dehydrogenase (FMDH) subunit A; Methanogenic bacteria and archea derive the energy for autotrophic growth from methanogenesis, the reduction of CO2 with molecular hydrogen as the electron donor. FMDH catalyzes the first step in methanogenesis, the formyl-methanofuran synthesis. In this step, CO2 is bound to methanofuran and subsequently reduced to the formyl state with electrons derived from hydrogen.
Probab=48.16 E-value=5.8 Score=31.77 Aligned_cols=26 Identities=35% Similarity=0.625 Sum_probs=20.3
Q ss_pred hcCCHHHHHHhc-------CCC-CchhHHHHHHH
Q 046034 7 LSGLSKEIAKHL-------SLP-PVKLHCSMLAE 32 (64)
Q Consensus 7 ~~I~~~dI~e~L-------gLP-~~K~HCA~LA~ 32 (64)
+.||+.+|+..| ||| +.++||.+|+.
T Consensus 203 ~~vtp~~ii~~l~~~~~~lg~ph~iH~h~nnlg~ 236 (541)
T cd01304 203 FDITPREILKGLAEANEELGLPHSIHVHCNNLGV 236 (541)
T ss_pred CCCCHHHHHHHHHHHHHhcCCceEEEEccccCCC
Confidence 467888777655 788 89999999964
No 26
>PF13735 tRNA_NucTran2_2: tRNA nucleotidyltransferase domain 2 putative; PDB: 1MIY_A 1MIV_B 1MIW_B.
Probab=45.30 E-value=15 Score=23.09 Aligned_cols=19 Identities=16% Similarity=0.239 Sum_probs=12.7
Q ss_pred hcCCHHHHHHhcCCCCchh
Q 046034 7 LSGLSKEIAKHLSLPPVKL 25 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K~ 25 (64)
+.||..||.+.||++|-+.
T Consensus 103 LaI~G~DLi~~lg~~pGp~ 121 (149)
T PF13735_consen 103 LAINGNDLIEALGIKPGPW 121 (149)
T ss_dssp -SS-HHHHHHHHT--SSCH
T ss_pred CCcCHHHHHHHcCCCCCcH
Confidence 4699999999999976554
No 27
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=43.97 E-value=48 Score=17.23 Aligned_cols=19 Identities=21% Similarity=0.244 Sum_probs=14.6
Q ss_pred cCCHHHHHHhcCCCCchhH
Q 046034 8 SGLSKEIAKHLSLPPVKLH 26 (64)
Q Consensus 8 ~I~~~dI~e~LgLP~~K~H 26 (64)
+.|..+|++.||++...++
T Consensus 20 ~~t~~eIa~~lg~s~~~V~ 38 (50)
T PF04545_consen 20 GLTLEEIAERLGISRSTVR 38 (50)
T ss_dssp T-SHHHHHHHHTSCHHHHH
T ss_pred CCCHHHHHHHHCCcHHHHH
Confidence 5788999999999866654
No 28
>PF14791 DNA_pol_B_thumb: DNA polymerase beta thumb ; PDB: 1HUZ_A 3K75_D 1HUO_A 2BPC_A 1RPL_A 1NOM_A 1ZQX_A 1ZQU_A 1ZQZ_A 1ZQV_A ....
Probab=42.84 E-value=15 Score=21.20 Aligned_cols=19 Identities=26% Similarity=0.303 Sum_probs=13.5
Q ss_pred CCHHHHHHhcCC---CCchhHH
Q 046034 9 GLSKEIAKHLSL---PPVKLHC 27 (64)
Q Consensus 9 I~~~dI~e~LgL---P~~K~HC 27 (64)
-+.+||.+.||| ||+...|
T Consensus 43 ~~E~dif~~Lgl~yipPe~R~~ 64 (64)
T PF14791_consen 43 ESEEDIFDALGLPYIPPELRED 64 (64)
T ss_dssp SSHHHHHHHTTS----GGGCTT
T ss_pred CCHHHHHHHcCCCCCChhhcCC
Confidence 378899999985 5665554
No 29
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=42.36 E-value=68 Score=20.73 Aligned_cols=37 Identities=16% Similarity=0.142 Sum_probs=23.0
Q ss_pred hcCCHHHHHHhcCCCCchhHH-HHHHHHHHHHHHHHHH
Q 046034 7 LSGLSKEIAKHLSLPPVKLHC-SMLAEDAIKAAVKDYE 43 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K~HC-A~LA~~ALk~AI~dY~ 43 (64)
.+++.++|++.||+|+.-+.= -.-|.+.|+..+..+.
T Consensus 151 ~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~ 188 (195)
T PRK12532 151 LGFSSDEIQQMCGISTSNYHTIMHRARESLRQCLQIKW 188 (195)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Confidence 467889999999988655431 1234555555555443
No 30
>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=41.78 E-value=22 Score=20.16 Aligned_cols=15 Identities=40% Similarity=0.450 Sum_probs=12.6
Q ss_pred cCCHHHHHHhcCCCC
Q 046034 8 SGLSKEIAKHLSLPP 22 (64)
Q Consensus 8 ~I~~~dI~e~LgLP~ 22 (64)
..+..+|++.||+|+
T Consensus 13 G~~~~eIA~~Lg~~~ 27 (58)
T PF06056_consen 13 GWSIKEIAEELGVPR 27 (58)
T ss_pred CCCHHHHHHHHCCCh
Confidence 467889999999983
No 31
>PRK02919 oxaloacetate decarboxylase subunit gamma; Provisional
Probab=39.73 E-value=25 Score=21.54 Aligned_cols=14 Identities=21% Similarity=0.237 Sum_probs=12.2
Q ss_pred HHHHHHHHHHHhhC
Q 046034 34 AIKAAVKDYEAKHT 47 (64)
Q Consensus 34 ALk~AI~dY~~k~~ 47 (64)
++.+||..||.+++
T Consensus 69 vIsAAI~~hR~~~~ 82 (82)
T PRK02919 69 VIAAAIHHHRRLNA 82 (82)
T ss_pred HHHHHHHHHHhcCC
Confidence 89999999998753
No 32
>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=39.56 E-value=22 Score=17.62 Aligned_cols=15 Identities=20% Similarity=0.042 Sum_probs=9.0
Q ss_pred CCHHHHHHhcCCCCc
Q 046034 9 GLSKEIAKHLSLPPV 23 (64)
Q Consensus 9 I~~~dI~e~LgLP~~ 23 (64)
+|-+++++.||+++.
T Consensus 2 lt~~e~a~~lgis~~ 16 (49)
T TIGR01764 2 LTVEEAAEYLGVSKD 16 (49)
T ss_pred CCHHHHHHHHCCCHH
Confidence 355666666666643
No 33
>cd08804 Death_ank2 Death domain of Ankyrin-2. Death Domain (DD) of Ankyrin-2 (ANK-2) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-2, also called ankyrin-B (for broadly expressed), is required for proper function of the Na/Ca ion exchanger-1 in cardiomyocytes, and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. Human ANK-2 is associated with "Ankyrin-B syndrome", an atypical arrythmia disorder with risk of sudden cardiac death. It also plays key roles in the brain and striated muscle. Loss of ANK-2 is associated with significant nervous system defects and sarcomere disorganization. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other
Probab=39.49 E-value=84 Score=18.74 Aligned_cols=43 Identities=19% Similarity=0.233 Sum_probs=32.6
Q ss_pred HhhcCCHHHHHHhcCCCCchhHHHHHH-----HHHHHHHHHHHHHhhC
Q 046034 5 RNLSGLSKEIAKHLSLPPVKLHCSMLA-----EDAIKAAVKDYEAKHT 47 (64)
Q Consensus 5 EA~~I~~~dI~e~LgLP~~K~HCA~LA-----~~ALk~AI~dY~~k~~ 47 (64)
+-+.-+.+.++..||+++..+.+...= .+-....+..|+.+.+
T Consensus 12 ~~LG~dWk~LAr~Lg~se~dI~~i~~~~~~~~~eq~~~mL~~W~~r~g 59 (84)
T cd08804 12 DHLGFSWTELARELDFTEEQIHQIRIENPNSLQDQSHALLKYWLERDG 59 (84)
T ss_pred HHHhhhHHHHHHHcCCCHHHHHHHHHHCcccHHHHHHHHHHHHHHccC
Confidence 445677889999999999999884443 5666777888887765
No 34
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=39.27 E-value=40 Score=21.74 Aligned_cols=20 Identities=20% Similarity=0.267 Sum_probs=14.0
Q ss_pred hcCCHHHHHHhcCCCCchhH
Q 046034 7 LSGLSKEIAKHLSLPPVKLH 26 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K~H 26 (64)
.+.+.++|++.||+|+.-+.
T Consensus 146 ~g~s~~EIA~~lgis~~tV~ 165 (191)
T PRK12520 146 LELETEEICQELQITATNAW 165 (191)
T ss_pred cCCCHHHHHHHHCCCHHHHH
Confidence 35677888888888765544
No 35
>PF12728 HTH_17: Helix-turn-helix domain
Probab=38.56 E-value=22 Score=18.56 Aligned_cols=12 Identities=33% Similarity=0.363 Sum_probs=6.0
Q ss_pred CHHHHHHhcCCC
Q 046034 10 LSKEIAKHLSLP 21 (64)
Q Consensus 10 ~~~dI~e~LgLP 21 (64)
|.+++++.||++
T Consensus 3 t~~e~a~~l~is 14 (51)
T PF12728_consen 3 TVKEAAELLGIS 14 (51)
T ss_pred CHHHHHHHHCcC
Confidence 444555555544
No 36
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=38.27 E-value=70 Score=20.61 Aligned_cols=20 Identities=20% Similarity=0.101 Sum_probs=16.4
Q ss_pred hcCCHHHHHHhcCCCCchhH
Q 046034 7 LSGLSKEIAKHLSLPPVKLH 26 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K~H 26 (64)
.+.+.++|++.||+|+..++
T Consensus 154 ~g~s~~EIA~~lgis~~tV~ 173 (194)
T PRK12513 154 GDLELEEIAELTGVPEETVK 173 (194)
T ss_pred cCCCHHHHHHHHCCCHHHHH
Confidence 35788999999999987664
No 37
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=37.42 E-value=30 Score=21.62 Aligned_cols=25 Identities=28% Similarity=0.252 Sum_probs=20.5
Q ss_pred hhHHhhcCCHHHHHHhcCCCCchhH
Q 046034 2 ANLRNLSGLSKEIAKHLSLPPVKLH 26 (64)
Q Consensus 2 ~~~EA~~I~~~dI~e~LgLP~~K~H 26 (64)
+|-+-..++.++|+..||+.+++++
T Consensus 17 ~nf~~~~ls~~~ia~dL~~s~~~le 41 (89)
T PF10078_consen 17 ANFELSGLSLEQIAADLGTSPEHLE 41 (89)
T ss_pred HHHHHcCCCHHHHHHHhCCCHHHHH
Confidence 3556678899999999999888876
No 38
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=37.05 E-value=73 Score=19.74 Aligned_cols=32 Identities=22% Similarity=0.360 Sum_probs=22.7
Q ss_pred hcCCHHHHHHhcCCCCchhHHHHHHHHHHHHHHHHHHH
Q 046034 7 LSGLSKEIAKHLSLPPVKLHCSMLAEDAIKAAVKDYEA 44 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K~HCA~LA~~ALk~AI~dY~~ 44 (64)
.+.+.++|++.||+|...++. -|+.|+...+.
T Consensus 124 ~~~s~~EIA~~lgis~~tV~~------~l~ra~~~lr~ 155 (163)
T PRK07037 124 HGETQKDIARELGVSPTLVNF------MIRDALVHCRK 155 (163)
T ss_pred cCCCHHHHHHHHCCCHHHHHH------HHHHHHHHHHH
Confidence 467899999999999877663 34555555443
No 39
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=36.35 E-value=70 Score=21.64 Aligned_cols=33 Identities=18% Similarity=0.095 Sum_probs=22.3
Q ss_pred cCCHHHHHHhcCCCCchhHHH-HHHHHHHHHHHH
Q 046034 8 SGLSKEIAKHLSLPPVKLHCS-MLAEDAIKAAVK 40 (64)
Q Consensus 8 ~I~~~dI~e~LgLP~~K~HCA-~LA~~ALk~AI~ 40 (64)
..+.++|++.||+++..+..- .-|.+.|+.-+.
T Consensus 195 ~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~l~ 228 (233)
T PRK05803 195 EKTQREIAKALGISRSYVSRIEKRALKKLFKELY 228 (233)
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 358899999999998877544 345555554443
No 40
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=36.01 E-value=95 Score=19.59 Aligned_cols=20 Identities=20% Similarity=0.180 Sum_probs=14.7
Q ss_pred hcCCHHHHHHhcCCCCchhH
Q 046034 7 LSGLSKEIAKHLSLPPVKLH 26 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K~H 26 (64)
.+.+.++|++.||+++.-+.
T Consensus 134 ~~~s~~EIA~~lgis~~tV~ 153 (173)
T PRK12522 134 EQYSYKEMSEILNIPIGTVK 153 (173)
T ss_pred cCCCHHHHHHHhCCCHHHHH
Confidence 45778889988888865543
No 41
>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=35.58 E-value=83 Score=18.22 Aligned_cols=20 Identities=25% Similarity=0.109 Sum_probs=14.9
Q ss_pred hcCCHHHHHHhcCCCCchhH
Q 046034 7 LSGLSKEIAKHLSLPPVKLH 26 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K~H 26 (64)
.+.+..+|++.||+++..++
T Consensus 125 ~g~s~~eIA~~l~~s~~~v~ 144 (158)
T TIGR02937 125 EGLSYKEIAEILGISVGTVK 144 (158)
T ss_pred cCCCHHHHHHHHCCCHHHHH
Confidence 35788888888888866554
No 42
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=35.51 E-value=29 Score=16.85 Aligned_cols=18 Identities=22% Similarity=0.099 Sum_probs=12.8
Q ss_pred hcCCHHHHHHhcCCCCch
Q 046034 7 LSGLSKEIAKHLSLPPVK 24 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K 24 (64)
.+++..+|++.+|++...
T Consensus 25 ~~~~~~~ia~~~~~s~~~ 42 (55)
T cd06171 25 EGLSYEEIAEILGISRST 42 (55)
T ss_pred cCCCHHHHHHHHCcCHHH
Confidence 357788888888877443
No 43
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=35.38 E-value=79 Score=20.20 Aligned_cols=20 Identities=15% Similarity=-0.002 Sum_probs=15.9
Q ss_pred hcCCHHHHHHhcCCCCchhH
Q 046034 7 LSGLSKEIAKHLSLPPVKLH 26 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K~H 26 (64)
...+.++|++.||+|+..+.
T Consensus 143 ~g~s~~EIA~~lgis~~tV~ 162 (186)
T PRK05602 143 QGLSNIEAAAVMDISVDALE 162 (186)
T ss_pred cCCCHHHHHHHhCcCHHHHH
Confidence 46788999999999876654
No 44
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=34.64 E-value=91 Score=19.25 Aligned_cols=20 Identities=20% Similarity=0.091 Sum_probs=16.0
Q ss_pred hcCCHHHHHHhcCCCCchhH
Q 046034 7 LSGLSKEIAKHLSLPPVKLH 26 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K~H 26 (64)
.+++.++|++.||+|+..+.
T Consensus 143 ~~~s~~eIA~~lgis~~tV~ 162 (182)
T PRK09652 143 EGLSYEEIAEIMGCPIGTVR 162 (182)
T ss_pred cCCCHHHHHHHHCCCHHHHH
Confidence 46788999999999877664
No 45
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=34.24 E-value=40 Score=23.68 Aligned_cols=34 Identities=15% Similarity=0.259 Sum_probs=23.5
Q ss_pred cCCHHHHHHhc-CCCCchhHHHHHHHHHHHHHHHHHHHhhC
Q 046034 8 SGLSKEIAKHL-SLPPVKLHCSMLAEDAIKAAVKDYEAKHT 47 (64)
Q Consensus 8 ~I~~~dI~e~L-gLP~~K~HCA~LA~~ALk~AI~dY~~k~~ 47 (64)
.|+.+||+..| .|.-..+| .-|+.++..|+....
T Consensus 65 t~sadDVl~aL~Eiefs~f~------~plk~~Le~yk~~~k 99 (172)
T KOG0870|consen 65 TISADDVLKALDEIEFSSFV------NPLKSALEAYKKAVK 99 (172)
T ss_pred cccHHHHHHHHHHhchHHHh------hHHHHHHHHHHHHHH
Confidence 58999999999 44333333 457888888876543
No 46
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=34.20 E-value=69 Score=19.74 Aligned_cols=19 Identities=26% Similarity=0.204 Sum_probs=15.0
Q ss_pred hcCCHHHHHHhcCCCCchh
Q 046034 7 LSGLSKEIAKHLSLPPVKL 25 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K~ 25 (64)
..++.++|++.||+++.-+
T Consensus 140 ~~~~~~eIA~~lgis~~tv 158 (179)
T PRK11924 140 EGLSYREIAEILGVPVGTV 158 (179)
T ss_pred cCCCHHHHHHHHCCCHHHH
Confidence 4678899999999986544
No 47
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=34.10 E-value=96 Score=20.04 Aligned_cols=34 Identities=24% Similarity=0.324 Sum_probs=22.4
Q ss_pred hcCCHHHHHHhcCCCCchhHHHHHHHHHHHHHHHHHHHhh
Q 046034 7 LSGLSKEIAKHLSLPPVKLHCSMLAEDAIKAAVKDYEAKH 46 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K~HCA~LA~~ALk~AI~dY~~k~ 46 (64)
.+++.++|++.||++...++ .-|++|...-+...
T Consensus 146 ~g~s~~EIAe~lgis~~~V~------~~l~Ra~~~Lr~~~ 179 (189)
T PRK06811 146 LGEKIEEIAKKLGLTRSAID------NRLSRGRKKLQKNK 179 (189)
T ss_pred ccCCHHHHHHHHCCCHHHHH------HHHHHHHHHHHHcc
Confidence 35788999999999876654 44555555544433
No 48
>PRK10030 hypothetical protein; Provisional
Probab=33.92 E-value=25 Score=24.18 Aligned_cols=20 Identities=20% Similarity=0.272 Sum_probs=17.5
Q ss_pred CCCchhHHHHHHHHHHHHHH
Q 046034 20 LPPVKLHCSMLAEDAIKAAV 39 (64)
Q Consensus 20 LP~~K~HCA~LA~~ALk~AI 39 (64)
+..++++||.|..++.+.|.
T Consensus 121 ~~d~~~YCSELV~~ay~~a~ 140 (197)
T PRK10030 121 WSDDRIYCSELVWKVYQNAL 140 (197)
T ss_pred cCCCcEEeHHHHHHHHHHcc
Confidence 56789999999999998873
No 49
>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=33.14 E-value=1e+02 Score=18.73 Aligned_cols=20 Identities=35% Similarity=0.237 Sum_probs=15.1
Q ss_pred hcCCHHHHHHhcCCCCchhH
Q 046034 7 LSGLSKEIAKHLSLPPVKLH 26 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K~H 26 (64)
.+.+.++|++.||+|+..+.
T Consensus 120 ~g~s~~eIA~~lgis~~tv~ 139 (154)
T TIGR02950 120 KEFSYKEIAELLNLSLAKVK 139 (154)
T ss_pred ccCcHHHHHHHHCCCHHHHH
Confidence 46788899999999855543
No 50
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=33.07 E-value=98 Score=19.79 Aligned_cols=19 Identities=16% Similarity=-0.031 Sum_probs=14.7
Q ss_pred hcCCHHHHHHhcCCCCchh
Q 046034 7 LSGLSKEIAKHLSLPPVKL 25 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K~ 25 (64)
-+.+.++|++.||+|+..+
T Consensus 144 ~g~s~~EIA~~l~is~~tV 162 (181)
T PRK12536 144 EGLSVAETAQLTGLSESAV 162 (181)
T ss_pred cCCCHHHHHHHHCCCHHHH
Confidence 4578889999998886554
No 51
>PF11387 DUF2795: Protein of unknown function (DUF2795); InterPro: IPR021527 This family of proteins has no known function.
Probab=32.65 E-value=20 Score=19.31 Aligned_cols=16 Identities=19% Similarity=0.407 Sum_probs=11.9
Q ss_pred HHHHHHhc-CCCCchhH
Q 046034 11 SKEIAKHL-SLPPVKLH 26 (64)
Q Consensus 11 ~~dI~e~L-gLP~~K~H 26 (64)
.++|++.| +||+..++
T Consensus 23 ~~~vl~~L~~lP~~~Y~ 39 (44)
T PF11387_consen 23 PDDVLDALERLPDREYE 39 (44)
T ss_pred CHHHHHHHHHCCccCCC
Confidence 35788999 89976654
No 52
>PF00531 Death: Death domain; InterPro: IPR000488 The death domain (DD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. DD is related in sequence and structure to the death effector domain (DED, see IPR001875 from INTERPRO) and the caspase recruitment domain (CARD, see IPR001315 from INTERPRO), which work in similar pathways and show similar interaction properties []. DD bind each other forming oligomers. Mammals have numerous and diverse DD-containing proteins []. Within these proteins, the DD domains can be found in combination with other domains, including: CARDs, DEDs, ankyrin repeats (IPR002110 from INTERPRO), caspase-like folds, kinase domains, leucine zippers (IPR002158 from INTERPRO), leucine-rich repeats (LRR) (IPR001611 from INTERPRO), TIR domains (IPR000157 from INTERPRO), and ZU5 domains (IPR000906 from INTERPRO) []. Some DD-containing proteins are involved in the regulation of apoptosis and inflammation through their activation of caspases and NF-kappaB, which typically involves interactions with TNF (tumour necrosis factor) cytokine receptors [, ]. In humans, eight of the over 30 known TNF receptors contain DD in their cytoplasmic tails; several of these TNF receptors use caspase activation as a signalling mechanism. The DD mediates self-association of these receptors, thus giving the signal to downstream events that lead to apoptosis. Other DD-containing proteins, such as ankyrin, MyD88 and pelle, are probably not directly involved in cell death signalling. DD-containing proteins also have links to innate immunity, communicating with Toll family receptors through bipartite adapter proteins such as MyD88 [].; GO: 0005515 protein binding, 0007165 signal transduction; PDB: 3OQ9_L 3EZQ_F 1E41_A 1E3Y_A 2GF5_A 2OF5_L 3EWV_E 3G5B_A 3MOP_L 2A9I_A ....
Probab=32.45 E-value=93 Score=17.18 Aligned_cols=39 Identities=13% Similarity=0.198 Sum_probs=28.0
Q ss_pred hcCCHHHHHHhcCCCCchhHHHHHHH----HHHHHHHHHHHHh
Q 046034 7 LSGLSKEIAKHLSLPPVKLHCSMLAE----DAIKAAVKDYEAK 45 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K~HCA~LA~----~ALk~AI~dY~~k 45 (64)
..-+.+.++..||++...+.....-- +-....+..|+.+
T Consensus 11 ~~~~Wk~La~~Lg~~~~~i~~i~~~~~~~~~~~~~~L~~W~~~ 53 (83)
T PF00531_consen 11 LGSDWKRLARKLGLSESEIENIEEENPDLREQTYEMLQRWRQR 53 (83)
T ss_dssp HSTCHHHHHHHTTS-HHHHHHHHHHSTSHHHHHHHHHHHHHHH
T ss_pred chhhHHHHHHHhCcCHHHHHHHHHhCCChHHHHHHHHHHHHHh
Confidence 34567889999999888877666544 5666777888877
No 53
>cd08318 Death_NMPP84 Death domain of Nuclear Matrix Protein P84. Death domain (DD) found in the Nuclear Matrix Protein P84 (also known as HPR1 or THOC1). HPR1/p84 resides in the nuclear matrix and is part of the THO complex, also called TREX (transcription/export) complex, which functions in mRNP biogenesis at the interface between transcription and export of mRNA from the nucleus. Mice lacking THOC1 have abnormal testis development and are sterile. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=32.36 E-value=1.1e+02 Score=18.12 Aligned_cols=42 Identities=14% Similarity=0.155 Sum_probs=28.9
Q ss_pred hcCCHHHHHHhcCCCCchhHHHHHH----HHHHHHHHHHHHHhhCC
Q 046034 7 LSGLSKEIAKHLSLPPVKLHCSMLA----EDAIKAAVKDYEAKHTK 48 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K~HCA~LA----~~ALk~AI~dY~~k~~~ 48 (64)
+.-+.++++..|||++..+.....- .+....-+..|+.+.+.
T Consensus 17 iG~~Wk~Lar~LGls~~dI~~i~~~~~~~~eq~~~mL~~W~~r~g~ 62 (86)
T cd08318 17 LGEDWKTLAPHLEMKDKEIRAIESDSEDIKMQAKQLLVAWQDREGS 62 (86)
T ss_pred HhhhHHHHHHHcCCCHHHHHHHHhcCCCHHHHHHHHHHHHHHhcCc
Confidence 4456788888889988877665532 35556667778777653
No 54
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=32.30 E-value=1.1e+02 Score=19.83 Aligned_cols=20 Identities=25% Similarity=0.356 Sum_probs=15.2
Q ss_pred hcCCHHHHHHhcCCCCchhH
Q 046034 7 LSGLSKEIAKHLSLPPVKLH 26 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K~H 26 (64)
.+.+.++|++.||+|+.-+.
T Consensus 149 ~g~s~~EIA~~lgis~~tVk 168 (189)
T PRK12530 149 LELSSEQICQECDISTSNLH 168 (189)
T ss_pred cCCCHHHHHHHHCCCHHHHH
Confidence 46788888888888876554
No 55
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=31.96 E-value=79 Score=21.66 Aligned_cols=20 Identities=15% Similarity=0.194 Sum_probs=15.5
Q ss_pred hcCCHHHHHHhcCCCCchhH
Q 046034 7 LSGLSKEIAKHLSLPPVKLH 26 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K~H 26 (64)
.+++.++|++.||+|+..++
T Consensus 220 ~g~s~~eIA~~l~is~~tV~ 239 (257)
T PRK08583 220 ENLSQKETGERLGISQMHVS 239 (257)
T ss_pred CCCCHHHHHHHHCCCHHHHH
Confidence 35678888888888877765
No 56
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=31.85 E-value=95 Score=19.47 Aligned_cols=20 Identities=20% Similarity=0.248 Sum_probs=15.0
Q ss_pred hcCCHHHHHHhcCCCCchhH
Q 046034 7 LSGLSKEIAKHLSLPPVKLH 26 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K~H 26 (64)
.+.+.++|++.||+|+.-++
T Consensus 133 ~g~s~~EIA~~lgis~~tV~ 152 (173)
T PRK09645 133 RGWSTAQIAADLGIPEGTVK 152 (173)
T ss_pred cCCCHHHHHHHHCcCHHHHH
Confidence 36788889998888865543
No 57
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=31.17 E-value=78 Score=20.92 Aligned_cols=38 Identities=21% Similarity=0.069 Sum_probs=23.0
Q ss_pred hcCCHHHHHHhcCCCCchhHHH-HHHHHHHHHHHHHHHH
Q 046034 7 LSGLSKEIAKHLSLPPVKLHCS-MLAEDAIKAAVKDYEA 44 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K~HCA-~LA~~ALk~AI~dY~~ 44 (64)
.+++.++|++.||+|+.-++=- .-|...|+..+.+|..
T Consensus 148 ~g~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~~~~ 186 (196)
T PRK12535 148 LGYTYEEAAKIADVRVGTIRSRVARARADLIAATATGQA 186 (196)
T ss_pred hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhccccc
Confidence 4678889999998887554422 2244455555555443
No 58
>PHA01623 hypothetical protein
Probab=31.02 E-value=57 Score=18.37 Aligned_cols=15 Identities=40% Similarity=0.632 Sum_probs=12.3
Q ss_pred HHHHHHHHHHHHHhh
Q 046034 32 EDAIKAAVKDYEAKH 46 (64)
Q Consensus 32 ~~ALk~AI~dY~~k~ 46 (64)
-++++.||..|..+.
T Consensus 40 Se~IreAI~~yL~~~ 54 (56)
T PHA01623 40 TQAIEEAIKEYLQKR 54 (56)
T ss_pred HHHHHHHHHHHHHHc
Confidence 478899999998764
No 59
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=30.91 E-value=81 Score=21.07 Aligned_cols=32 Identities=19% Similarity=0.104 Sum_probs=21.0
Q ss_pred hcCCHHHHHHhcCCCCchhHHHHHHHHHHHHHHHHHHH
Q 046034 7 LSGLSKEIAKHLSLPPVKLHCSMLAEDAIKAAVKDYEA 44 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K~HCA~LA~~ALk~AI~dY~~ 44 (64)
.+++.++|++.||+|+.-++ ..|++|....+.
T Consensus 153 ~g~s~~EIA~~Lgis~~tV~------~~l~RArk~Lr~ 184 (203)
T PRK09647 153 EGLSYEEIAATLGVKLGTVR------SRIHRGRQQLRA 184 (203)
T ss_pred cCCCHHHHHHHHCCCHHHHH------HHHHHHHHHHHH
Confidence 46788999999998875543 444555444443
No 60
>cd08311 Death_p75NR Death domain of p75 Neurotophin Receptor. Death Domain (DD) found in p75 neurotrophin receptor (p75NTR, NGFR, TNFRSF16). p75NTR binds members of the neurotrophin (NT) family including nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), and NT3, among others. It contains an NT-binding extracellular region that bears four cysteine-rich repeats, a transmembrane domain, and an intracellular DD. p75NTR plays roles in the immune, vascular, and nervous systems, and has been shown to promote cell death or survival, and to induce neurite outgrowth or collapse depending on its ligands and co-receptors. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptor
Probab=30.21 E-value=91 Score=18.54 Aligned_cols=37 Identities=14% Similarity=0.165 Sum_probs=28.6
Q ss_pred CCHHHHHHhcCCCCchhHHHHHHHHHHHHHHHHHHHh
Q 046034 9 GLSKEIAKHLSLPPVKLHCSMLAEDAIKAAVKDYEAK 45 (64)
Q Consensus 9 I~~~dI~e~LgLP~~K~HCA~LA~~ALk~AI~dY~~k 45 (64)
=+...+++.||+++..+.+..--.+-.+.-+.+|..+
T Consensus 16 ~dW~~LA~~LG~~~~~I~~i~~~~~p~~~lL~~W~~r 52 (77)
T cd08311 16 RDWRSLAGELGYEDEAIDTFGREESPVRTLLADWSAQ 52 (77)
T ss_pred cCHHHHHHHcCCCHHHHHHHHcChhHHHHHHHHHHHC
Confidence 3568899999999988887766566667778888864
No 61
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=30.09 E-value=91 Score=20.13 Aligned_cols=31 Identities=19% Similarity=0.209 Sum_probs=21.5
Q ss_pred hcCCHHHHHHhcCCCCchhHHHHHHHHHHHHHHHHHH
Q 046034 7 LSGLSKEIAKHLSLPPVKLHCSMLAEDAIKAAVKDYE 43 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K~HCA~LA~~ALk~AI~dY~ 43 (64)
.+.+.++|++.||+|+..++ ..|+++....+
T Consensus 169 e~~s~~EIA~~lgis~~tV~------~~l~rar~~Lr 199 (208)
T PRK08295 169 DGKSYQEIAEELNRHVKSID------NALQRVKRKLE 199 (208)
T ss_pred ccCCHHHHHHHHCCCHHHHH------HHHHHHHHHHH
Confidence 36788999999999987765 44555544443
No 62
>cd04752 Commd4 COMM_Domain containing protein 4. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=29.39 E-value=93 Score=20.80 Aligned_cols=17 Identities=18% Similarity=0.274 Sum_probs=13.5
Q ss_pred cCCHHHHHHhc---CCCCch
Q 046034 8 SGLSKEIAKHL---SLPPVK 24 (64)
Q Consensus 8 ~I~~~dI~e~L---gLP~~K 24 (64)
.++.+++.+.| |||+++
T Consensus 59 n~~~~~l~~eL~~lglp~e~ 78 (174)
T cd04752 59 NVDGESLSSELQQLGLPKEH 78 (174)
T ss_pred CCCHHHHHHHHHHcCCCHHH
Confidence 47888888888 899765
No 63
>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=29.15 E-value=32 Score=18.02 Aligned_cols=19 Identities=21% Similarity=0.141 Sum_probs=11.7
Q ss_pred hcCCHHHHHHhcCCCCchh
Q 046034 7 LSGLSKEIAKHLSLPPVKL 25 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K~ 25 (64)
.+.+..+|++.+|+++..+
T Consensus 25 ~g~s~~eIa~~l~~s~~~v 43 (54)
T PF08281_consen 25 QGMSYAEIAEILGISESTV 43 (54)
T ss_dssp S---HHHHHHHCTS-HHHH
T ss_pred HCcCHHHHHHHHCcCHHHH
Confidence 4578899999999886544
No 64
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=28.60 E-value=43 Score=19.02 Aligned_cols=15 Identities=33% Similarity=0.514 Sum_probs=12.7
Q ss_pred CCHHHHHHhcCCCCc
Q 046034 9 GLSKEIAKHLSLPPV 23 (64)
Q Consensus 9 I~~~dI~e~LgLP~~ 23 (64)
++..+|++.||++..
T Consensus 23 ~ta~eLa~~lgl~~~ 37 (68)
T smart00550 23 STALQLAKNLGLPKK 37 (68)
T ss_pred cCHHHHHHHHCCCHH
Confidence 888999999999843
No 65
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=28.52 E-value=1e+02 Score=19.37 Aligned_cols=19 Identities=11% Similarity=0.011 Sum_probs=12.1
Q ss_pred cCCHHHHHHhcCCCCchhH
Q 046034 8 SGLSKEIAKHLSLPPVKLH 26 (64)
Q Consensus 8 ~I~~~dI~e~LgLP~~K~H 26 (64)
+.+.++|++.||+++..++
T Consensus 156 g~s~~eIA~~lgis~~~v~ 174 (189)
T TIGR02984 156 GLSFAEVAERMDRSEGAVS 174 (189)
T ss_pred CCCHHHHHHHHCcCHHHHH
Confidence 4566777777777754443
No 66
>PRK07204 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed
Probab=28.14 E-value=87 Score=21.98 Aligned_cols=18 Identities=33% Similarity=0.351 Sum_probs=15.1
Q ss_pred hHHHHHHHHHHHHHHHHH
Q 046034 25 LHCSMLAEDAIKAAVKDY 42 (64)
Q Consensus 25 ~HCA~LA~~ALk~AI~dY 42 (64)
...+.|+.+|.++|+.+.
T Consensus 50 ~~~~~la~~Aa~~aL~~a 67 (329)
T PRK07204 50 ETSSYMGAEAAKKAVEDA 67 (329)
T ss_pred CCHHHHHHHHHHHHHHHc
Confidence 357889999999999875
No 67
>PF07759 DUF1615: Protein of unknown function (DUF1615); InterPro: IPR011673 This is a family of proteins of unknown function expressed by various bacterial species. Some members of this family (e.g. Q8Z8Z7 from SWISSPROT, Q8ZRF4 from SWISSPROT) are thought to be lipoproteins. Another member of this family (Q93SV8 from SWISSPROT) is thought to be involved in photosynthesis [].
Probab=28.12 E-value=23 Score=26.96 Aligned_cols=21 Identities=33% Similarity=0.730 Sum_probs=15.3
Q ss_pred HHHHHhc---CCCCchhH-HHHHHH
Q 046034 12 KEIAKHL---SLPPVKLH-CSMLAE 32 (64)
Q Consensus 12 ~dI~e~L---gLP~~K~H-CA~LA~ 32 (64)
.||.+.+ |+|+.+-| |++||+
T Consensus 11 ~DI~~af~~~~ip~t~en~CavlAV 35 (319)
T PF07759_consen 11 QDIYTAFEAQGIPPTKENVCAVLAV 35 (319)
T ss_pred HHHHHHHHhcCCCCCcccccceeee
Confidence 4555555 89988766 998886
No 68
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=28.11 E-value=53 Score=16.67 Aligned_cols=17 Identities=12% Similarity=0.135 Sum_probs=13.4
Q ss_pred HhhcCCHHHHHHhcCCC
Q 046034 5 RNLSGLSKEIAKHLSLP 21 (64)
Q Consensus 5 EA~~I~~~dI~e~LgLP 21 (64)
+...++..++++.+|++
T Consensus 12 ~~~gltq~~lA~~~gvs 28 (58)
T TIGR03070 12 KALGLTQADLADLAGVG 28 (58)
T ss_pred HHcCCCHHHHHHHhCCC
Confidence 45678888888888876
No 69
>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=28.10 E-value=23 Score=18.86 Aligned_cols=18 Identities=39% Similarity=0.492 Sum_probs=13.6
Q ss_pred CCHHHHHHhcCCCCchhH
Q 046034 9 GLSKEIAKHLSLPPVKLH 26 (64)
Q Consensus 9 I~~~dI~e~LgLP~~K~H 26 (64)
++-.+|++.+|+|....|
T Consensus 19 ~t~~eia~~~gl~~stv~ 36 (52)
T PF09339_consen 19 LTLSEIARALGLPKSTVH 36 (52)
T ss_dssp EEHHHHHHHHTS-HHHHH
T ss_pred CCHHHHHHHHCcCHHHHH
Confidence 578899999999966555
No 70
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=28.02 E-value=59 Score=15.16 Aligned_cols=20 Identities=15% Similarity=0.180 Sum_probs=14.2
Q ss_pred HhhcCCHHHHHHhcCCCCch
Q 046034 5 RNLSGLSKEIAKHLSLPPVK 24 (64)
Q Consensus 5 EA~~I~~~dI~e~LgLP~~K 24 (64)
+...++..++++.+|+++..
T Consensus 7 ~~~~~s~~~la~~~~i~~~~ 26 (56)
T smart00530 7 EEKGLTQEELAEKLGVSRST 26 (56)
T ss_pred HHcCCCHHHHHHHhCCCHHH
Confidence 44567888888888877544
No 71
>PF14451 Ub-Mut7C: Mut7-C ubiquitin
Probab=27.98 E-value=32 Score=20.78 Aligned_cols=17 Identities=18% Similarity=0.417 Sum_probs=13.3
Q ss_pred CHHHHHHhcCCCCchhH
Q 046034 10 LSKEIAKHLSLPPVKLH 26 (64)
Q Consensus 10 ~~~dI~e~LgLP~~K~H 26 (64)
|=+|++|.||+|...++
T Consensus 34 tvkd~IEsLGVP~tEV~ 50 (81)
T PF14451_consen 34 TVKDVIESLGVPHTEVG 50 (81)
T ss_pred cHHHHHHHcCCChHHeE
Confidence 56899999999976543
No 72
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=27.84 E-value=1.4e+02 Score=19.03 Aligned_cols=17 Identities=24% Similarity=0.053 Sum_probs=11.9
Q ss_pred cCCHHHHHHhcCCCCch
Q 046034 8 SGLSKEIAKHLSLPPVK 24 (64)
Q Consensus 8 ~I~~~dI~e~LgLP~~K 24 (64)
+.+.++|++.||+|...
T Consensus 165 ~~s~~eIA~~l~~s~~t 181 (198)
T TIGR02859 165 GKSYQEIACDLNRHVKS 181 (198)
T ss_pred CCCHHHHHHHHCCCHHH
Confidence 56777888888877443
No 73
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=27.52 E-value=1.6e+02 Score=18.59 Aligned_cols=19 Identities=21% Similarity=0.167 Sum_probs=14.4
Q ss_pred hcCCHHHHHHhcCCCCchh
Q 046034 7 LSGLSKEIAKHLSLPPVKL 25 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K~ 25 (64)
.+.+.++|++.||+|+.-+
T Consensus 144 ~g~s~~eIA~~lgis~~tV 162 (179)
T PRK12514 144 EGLSYKELAERHDVPLNTM 162 (179)
T ss_pred cCCCHHHHHHHHCCChHHH
Confidence 3567888888888887665
No 74
>PRK03814 oxaloacetate decarboxylase subunit gamma; Provisional
Probab=27.28 E-value=58 Score=19.98 Aligned_cols=15 Identities=40% Similarity=0.341 Sum_probs=12.7
Q ss_pred HHHHHHHHHHHHHhh
Q 046034 32 EDAIKAAVKDYEAKH 46 (64)
Q Consensus 32 ~~ALk~AI~dY~~k~ 46 (64)
.-|+.+||..||.++
T Consensus 69 vAAI~AAV~q~R~~~ 83 (85)
T PRK03814 69 VAAISAAVHQHRASK 83 (85)
T ss_pred HHHHHHHHHHHHhhc
Confidence 459999999998875
No 75
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=26.69 E-value=1.3e+02 Score=18.59 Aligned_cols=20 Identities=20% Similarity=0.227 Sum_probs=14.6
Q ss_pred hcCCHHHHHHhcCCCCchhH
Q 046034 7 LSGLSKEIAKHLSLPPVKLH 26 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K~H 26 (64)
-+++.++|++.||+|..-++
T Consensus 120 ~~~s~~eIA~~lgis~~tv~ 139 (159)
T PRK12527 120 EGLSHQQIAEHLGISRSLVE 139 (159)
T ss_pred cCCCHHHHHHHhCCCHHHHH
Confidence 45788899999988865443
No 76
>PRK14384 hypothetical protein; Provisional
Probab=26.12 E-value=59 Score=18.85 Aligned_cols=12 Identities=50% Similarity=0.733 Sum_probs=9.9
Q ss_pred HHHHHHHHHHHH
Q 046034 26 HCSMLAEDAIKA 37 (64)
Q Consensus 26 HCA~LA~~ALk~ 37 (64)
-||.++.+||+.
T Consensus 9 TCS~Ya~~Ai~~ 20 (56)
T PRK14384 9 SCSCYAETALKR 20 (56)
T ss_pred cHHHHHHHHHHH
Confidence 599999999853
No 77
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=25.71 E-value=1.4e+02 Score=19.30 Aligned_cols=18 Identities=11% Similarity=0.207 Sum_probs=12.5
Q ss_pred cCCHHHHHHhcCCCCchh
Q 046034 8 SGLSKEIAKHLSLPPVKL 25 (64)
Q Consensus 8 ~I~~~dI~e~LgLP~~K~ 25 (64)
+++.++|++.||+|..-+
T Consensus 157 g~s~~EIA~~lgis~~tV 174 (194)
T PRK12531 157 ELPHQQVAEMFDIPLGTV 174 (194)
T ss_pred CCCHHHHHHHhCcCHHHH
Confidence 567778888887775443
No 78
>PF09077 Phage-MuB_C: Mu B transposition protein, C terminal ; InterPro: IPR009084 Bacteriophage Mu can integrate into the host bacterial genome and replicate via transposition. Mu requires the activity of four proteins for DNA transposition. Two of these proteins are the phage-encoded A and B transposition proteins, while the other two are host-specified accessory factors HU and IHF. These four proteins can form nucleoprotein complexes (transposomes), which enable strand transfer. The stable protein-DNA intermediate is subsequently disassembled prior to DNA replication by host proteins. The Mu B transposition protein is an ATP-dependent, DNA-binding protein required for target capture and immunity, as well as for activating transpososome function []. The C-terminal domain of the B transposition protein is believed to be involved in both DNA-binding and protein-protein contacts with the Mu A transposition protein. The structure of the C-terminal domain consists of four helices in an irregular array [].; GO: 0003677 DNA binding, 0006313 transposition, DNA-mediated; PDB: 1F6V_A.
Probab=25.58 E-value=40 Score=20.57 Aligned_cols=20 Identities=30% Similarity=0.157 Sum_probs=17.2
Q ss_pred hhHHhhcCCHHHHHHhc-CCC
Q 046034 2 ANLRNLSGLSKEIAKHL-SLP 21 (64)
Q Consensus 2 ~~~EA~~I~~~dI~e~L-gLP 21 (64)
|+.+||.|++++...+| ++-
T Consensus 19 Ai~~AWgI~d~~~~~~l~~I~ 39 (78)
T PF09077_consen 19 AIAKAWGITDKEERKLLQSIA 39 (78)
T ss_dssp HHHHSSSSSSSHHHHHHHTTS
T ss_pred HHHHHhCCCCHHHHHHHHHHc
Confidence 67899999999999999 554
No 79
>CHL00203 fabH 3-oxoacyl-acyl-carrier-protein synthase 3; Provisional
Probab=25.55 E-value=93 Score=21.96 Aligned_cols=17 Identities=24% Similarity=0.247 Sum_probs=14.9
Q ss_pred HHHHHHHHHHHHHHHHH
Q 046034 26 HCSMLAEDAIKAAVKDY 42 (64)
Q Consensus 26 HCA~LA~~ALk~AI~dY 42 (64)
..+.|+..|+++|+.+.
T Consensus 50 ~~~~la~~A~~~aL~~a 66 (326)
T CHL00203 50 SLTKLAAEAANKALDKA 66 (326)
T ss_pred CHHHHHHHHHHHHHHHc
Confidence 46899999999999885
No 80
>PRK14382 hypothetical protein; Provisional
Probab=25.52 E-value=59 Score=19.30 Aligned_cols=13 Identities=31% Similarity=0.312 Sum_probs=10.6
Q ss_pred hHHHHHHHHHHHH
Q 046034 25 LHCSMLAEDAIKA 37 (64)
Q Consensus 25 ~HCA~LA~~ALk~ 37 (64)
--||.++.+|++.
T Consensus 28 PTCS~Ya~~Ai~~ 40 (68)
T PRK14382 28 PTCSTYAILSIEK 40 (68)
T ss_pred cCHHHHHHHHHHH
Confidence 4599999999853
No 81
>PF11212 DUF2999: Protein of unknown function (DUF2999); InterPro: IPR021376 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=25.49 E-value=31 Score=21.46 Aligned_cols=16 Identities=25% Similarity=0.374 Sum_probs=11.6
Q ss_pred HHHHhcCCCCchhHHH
Q 046034 13 EIAKHLSLPPVKLHCS 28 (64)
Q Consensus 13 dI~e~LgLP~~K~HCA 28 (64)
.++..||+|++|+.--
T Consensus 34 a~i~qLGip~eKLQ~l 49 (82)
T PF11212_consen 34 ATIQQLGIPQEKLQQL 49 (82)
T ss_pred HHHHHcCCCHHHHHHH
Confidence 3455679999998743
No 82
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=25.26 E-value=76 Score=18.11 Aligned_cols=16 Identities=25% Similarity=0.532 Sum_probs=12.9
Q ss_pred HHHHHHHHHHHHHhhC
Q 046034 32 EDAIKAAVKDYEAKHT 47 (64)
Q Consensus 32 ~~ALk~AI~dY~~k~~ 47 (64)
-.+||.+|..|..++.
T Consensus 57 n~~Lk~~I~~~~~~~~ 72 (73)
T PF04564_consen 57 NRALKSAIEEWCAENK 72 (73)
T ss_dssp -HHHHHHHHHHHHHCT
T ss_pred CHHHHHHHHHHHHHcc
Confidence 4689999999998864
No 83
>cd08777 Death_RIP1 Death Domain of Receptor-Interacting Protein 1. Death domain (DD) found in Receptor-Interacting Protein 1 (RIP1) and related proteins. RIP kinases serve as essential sensors of cellular stress. Vertebrates contain several types containing a homologous N-terminal kinase domain and varying C-terminal domains. RIP1 harbors a C-terminal DD, which binds death receptors (DRs) including TNF receptor 1, Fas, TNF-related apoptosis-inducing ligand receptor 1 (TRAILR1), and TRAILR2. It also interacts with other DD-containing adaptor proteins such as TRADD and FADD. RIP1 plays a crucial role in determining a cell's fate, between survival or death, following exposure to stress signals. It is important in the signaling of NF-kappaB and MAPKs, and it links DR-associated signaling to reactive oxygen species (ROS) production. Abnormal RIP1 function may result in ROS accumulation affecting inflammatory responses, innate immunity, stress responses, and cell survival. In general, DDs ar
Probab=25.09 E-value=1.6e+02 Score=17.62 Aligned_cols=43 Identities=14% Similarity=0.203 Sum_probs=31.1
Q ss_pred HhhcCCHHHHHHhcCCCCchhHHHHHH------HHHHHHHHHHHHHhhC
Q 046034 5 RNLSGLSKEIAKHLSLPPVKLHCSMLA------EDAIKAAVKDYEAKHT 47 (64)
Q Consensus 5 EA~~I~~~dI~e~LgLP~~K~HCA~LA------~~ALk~AI~dY~~k~~ 47 (64)
+-+.=+++.++..||+++..+....-- .+..+..+..|+.+.+
T Consensus 10 ~~lG~~Wk~lar~LG~s~~eI~~ie~~~~r~~~~eq~~~mL~~W~~r~g 58 (86)
T cd08777 10 ENLGKKWKRCARKLGFTESEIEEIDHDYERDGLKEKVHQMLHKWKMKEG 58 (86)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHhcccCCHHHHHHHHHHHHHHccC
Confidence 344557889999999999888776533 3456777778877654
No 84
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=25.08 E-value=1.4e+02 Score=18.22 Aligned_cols=20 Identities=10% Similarity=-0.100 Sum_probs=14.3
Q ss_pred hcCCHHHHHHhcCCCCchhH
Q 046034 7 LSGLSKEIAKHLSLPPVKLH 26 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K~H 26 (64)
.+++.++|++.||+|+..++
T Consensus 121 ~g~s~~EIA~~lgis~~tV~ 140 (161)
T PRK09047 121 EDMDVAETAAAMGCSEGSVK 140 (161)
T ss_pred hcCCHHHHHHHHCCCHHHHH
Confidence 45778888888888765543
No 85
>PHA01976 helix-turn-helix protein
Probab=25.06 E-value=62 Score=17.47 Aligned_cols=18 Identities=6% Similarity=0.060 Sum_probs=13.4
Q ss_pred HhhcCCHHHHHHhcCCCC
Q 046034 5 RNLSGLSKEIAKHLSLPP 22 (64)
Q Consensus 5 EA~~I~~~dI~e~LgLP~ 22 (64)
+...|+-.++++.+|+++
T Consensus 12 ~~~glt~~~lA~~~gvs~ 29 (67)
T PHA01976 12 NARAWSAPELSRRAGVRH 29 (67)
T ss_pred HHcCCCHHHHHHHhCCCH
Confidence 456788888888887773
No 86
>PF03131 bZIP_Maf: bZIP Maf transcription factor; InterPro: IPR004826 There are several different types of Maf transcription factors with different roles in the cell. MafG and MafH are small Mafs which lack a putative transactivation domain. They behave as transcriptional repressors when they dimerize among themselves. However they also serve as transcriptional activators by dimerizing with other (usually larger) basic-zipper proteins and recruiting them to specific DNA-binding sites. Maf transcription factors contain a conserved basic region leucine zipper (bZIP) domain, which mediates their dimerization and DNA binding property. Neural retina-specific leucine zipper proteins also belong to this family. Together with the basic region, the Maf extended homology region (EHR), conserved only within the Maf family, defines the DNA binding specific to Mafs. This structure enables Mafs to make a broader area of contact with DNA and to recognise longer DNA sequences. In particular, the two residues at the beginning of helix H2 are positioned to recognise the flanking region []. Small Maf proteins heterodimerize with Fos and may act as competitive repressors of the NF2-E2 transcription factor. In mouse, Maf1 may play an early role in axial patterning. Defects in these proteins are a cause of autosomal dominant retinitis pigmentosa. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2KZ5_A 3A5T_A 1K1V_A 1SKN_P 2WT7_B 2WTY_B.
Probab=24.84 E-value=49 Score=19.94 Aligned_cols=28 Identities=14% Similarity=0.112 Sum_probs=20.3
Q ss_pred ChhHHhhcCCHHHHHHhc-CCCCchhHHH
Q 046034 1 MANLRNLSGLSKEIAKHL-SLPPVKLHCS 28 (64)
Q Consensus 1 ~~~~EA~~I~~~dI~e~L-gLP~~K~HCA 28 (64)
+.+++...|+-.+.-..| |||++.+.-.
T Consensus 1 ~s~eeL~~m~v~efn~~L~~lt~~q~~~l 29 (92)
T PF03131_consen 1 FSDEELVSMSVREFNRLLRGLTEEQIAEL 29 (92)
T ss_dssp --HHHHHHS-HHHHHHHCTTS-HHHHHHH
T ss_pred CCHHHHhhCCHHHHHHHHHcCCHHHHHHH
Confidence 356888999999999999 9998886643
No 87
>TIGR00673 cynS cyanate hydratase. Alternate names include cyanate lyase, cyanase and cyanate hydrolase.
Probab=24.66 E-value=59 Score=22.10 Aligned_cols=27 Identities=19% Similarity=0.191 Sum_probs=20.6
Q ss_pred HhhcCCHHHHHHhcCCCCchhHHHHHH
Q 046034 5 RNLSGLSKEIAKHLSLPPVKLHCSMLA 31 (64)
Q Consensus 5 EA~~I~~~dI~e~LgLP~~K~HCA~LA 31 (64)
...++|.++|++.+|++++-..=+.|+
T Consensus 18 ~~KGLTwe~IAe~iG~sevwvaaa~lG 44 (150)
T TIGR00673 18 KKKGLTFADIADGLGLAEVFVAAALYG 44 (150)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHhC
Confidence 467899999999999887665555554
No 88
>smart00005 DEATH DEATH domain, found in proteins involved in cell death (apoptosis). Alpha-helical domain present in a variety of proteins with apoptotic functions. Some (but not all) of these domains form homotypic and heterotypic dimers.
Probab=24.55 E-value=1.4e+02 Score=16.79 Aligned_cols=41 Identities=15% Similarity=0.158 Sum_probs=29.1
Q ss_pred cCCHHHHHHhcCCCCchhHHHHHHH-----HHHHHHHHHHHHhhCC
Q 046034 8 SGLSKEIAKHLSLPPVKLHCSMLAE-----DAIKAAVKDYEAKHTK 48 (64)
Q Consensus 8 ~I~~~dI~e~LgLP~~K~HCA~LA~-----~ALk~AI~dY~~k~~~ 48 (64)
.-+...++..||++...+.+...-. +-...-+..|+.+.+.
T Consensus 17 g~~W~~la~~Lg~~~~~i~~i~~~~~~~~~~~~~~lL~~W~~~~g~ 62 (88)
T smart00005 17 GLDWRELARKLGLSEADIDQIRTEAPRDLAEQSVQLLRLWEQREGK 62 (88)
T ss_pred chHHHHHHHHcCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHccch
Confidence 4467788999999877776655554 4666777788777653
No 89
>PF08513 LisH: LisH; InterPro: IPR013720 The LisH motif is found in a large number of eukaryotic proteins, from metazoa, fungi and plants that have a wide range of functions. The recently solved structure of the LisH domain in the N-terminal region of LIS1 depicted it as a novel dimerization motif, and that other structural elements are likely to play an important role in dimerisation [, , ]. The LisH (lis homology) domain mediates protein dimerisation and tetramerisation. The LisH domain is found in Sif2, a component of the Set3 complex which is responsible for repressing meiotic genes. It has been shown that the LisH domain helps mediate interaction with components of the Set3 complex []. ; PDB: 2XTE_L 2XTC_B 2XTD_A 1UUJ_B.
Probab=24.54 E-value=82 Score=15.08 Aligned_cols=15 Identities=13% Similarity=0.275 Sum_probs=11.1
Q ss_pred HHHHHHHHHHhhCCC
Q 046034 35 IKAAVKDYEAKHTKS 49 (64)
Q Consensus 35 Lk~AI~dY~~k~~~~ 49 (64)
|...|.+|..+.+-.
T Consensus 3 Ln~lI~~YL~~~Gy~ 17 (27)
T PF08513_consen 3 LNQLIYDYLVENGYK 17 (27)
T ss_dssp HHHHHHHHHHHCT-H
T ss_pred HHHHHHHHHHHCCcH
Confidence 677899999887643
No 90
>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=24.45 E-value=30 Score=19.09 Aligned_cols=18 Identities=22% Similarity=0.392 Sum_probs=14.3
Q ss_pred cCCHHHHHHhcCCCCchh
Q 046034 8 SGLSKEIAKHLSLPPVKL 25 (64)
Q Consensus 8 ~I~~~dI~e~LgLP~~K~ 25 (64)
..|..+|++.+|+|..++
T Consensus 22 ~~t~~eIa~~l~i~~~~v 39 (68)
T PF01978_consen 22 PATAEEIAEELGISRSTV 39 (68)
T ss_dssp HEEHHHHHHHHTSSHHHH
T ss_pred CCCHHHHHHHHCcCHHHH
Confidence 467889999999995554
No 91
>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=23.97 E-value=1.5e+02 Score=17.83 Aligned_cols=18 Identities=28% Similarity=0.300 Sum_probs=12.4
Q ss_pred cCCHHHHHHhcCCCCchh
Q 046034 8 SGLSKEIAKHLSLPPVKL 25 (64)
Q Consensus 8 ~I~~~dI~e~LgLP~~K~ 25 (64)
.++..+|++.||+|+.-+
T Consensus 129 ~~~~~eIA~~lgis~~tv 146 (161)
T TIGR02985 129 GKSYKEIAEELGISVKTV 146 (161)
T ss_pred CCCHHHHHHHHCCCHHHH
Confidence 567777887777775543
No 92
>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=23.84 E-value=1.3e+02 Score=16.76 Aligned_cols=19 Identities=16% Similarity=0.163 Sum_probs=14.7
Q ss_pred hcCCHHHHHHhcCCCCchh
Q 046034 7 LSGLSKEIAKHLSLPPVKL 25 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K~ 25 (64)
..++-++|++.||+++.-+
T Consensus 22 R~~tl~elA~~lgis~st~ 40 (53)
T PF04967_consen 22 RRITLEELAEELGISKSTV 40 (53)
T ss_pred CcCCHHHHHHHhCCCHHHH
Confidence 3678899999999885443
No 93
>COG1229 FwdA Formylmethanofuran dehydrogenase subunit A [Energy production and conversion]
Probab=23.63 E-value=29 Score=28.06 Aligned_cols=26 Identities=35% Similarity=0.687 Sum_probs=19.4
Q ss_pred hcCCHHHHH-------HhcCCC-CchhHHHHHHH
Q 046034 7 LSGLSKEIA-------KHLSLP-PVKLHCSMLAE 32 (64)
Q Consensus 7 ~~I~~~dI~-------e~LgLP-~~K~HCA~LA~ 32 (64)
++||+.+|+ |.|||| .-++||-.|+.
T Consensus 210 FdiTP~EIi~glaevnE~L~lphsIHlH~N~LG~ 243 (575)
T COG1229 210 FDITPREIIKGLAEVNERLGLPHSIHLHCNNLGH 243 (575)
T ss_pred cccCHHHHHHHHHHHHHhhCCCcceEeccccCCC
Confidence 467777765 455899 77999999874
No 94
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=23.61 E-value=1.5e+02 Score=18.91 Aligned_cols=19 Identities=16% Similarity=0.151 Sum_probs=13.9
Q ss_pred cCCHHHHHHhcCCCCchhH
Q 046034 8 SGLSKEIAKHLSLPPVKLH 26 (64)
Q Consensus 8 ~I~~~dI~e~LgLP~~K~H 26 (64)
+.+.++|++.||+|+..+.
T Consensus 155 g~s~~EIA~~lgis~~tV~ 173 (189)
T PRK09648 155 GLSAEETAEAVGSTPGAVR 173 (189)
T ss_pred CCCHHHHHHHHCCCHHHHH
Confidence 5677888888888865544
No 95
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.
Probab=23.58 E-value=1.4e+02 Score=20.21 Aligned_cols=18 Identities=22% Similarity=0.309 Sum_probs=14.6
Q ss_pred cCCHHHHHHhcCCCCchh
Q 046034 8 SGLSKEIAKHLSLPPVKL 25 (64)
Q Consensus 8 ~I~~~dI~e~LgLP~~K~ 25 (64)
+.+.++|++.||+|+..+
T Consensus 198 g~s~~EIA~~Lgis~~tV 215 (234)
T TIGR02835 198 EKTQKEVADMLGISQSYI 215 (234)
T ss_pred CCCHHHHHHHHCCCHHHH
Confidence 478889999999887765
No 96
>PF00666 Cathelicidins: Cathelicidin; InterPro: IPR001894 The precursor sequences of a number of antimicrobial peptides secreted by neutrophils (polymorphonuclear leukocytes) upon activation have been found to be evolutionarily related and are collectively known as cathelicidins []. Structurally, these proteins consist of three domains: a signal sequence, a conserved region of about 100 residues that contains four cysteines involved in two disulphide bonds, and a highly divergent C-terminal section of variable size. It is in this C-terminal section that the antibacterial peptides are found; they are proteolytically processed from their precursor by enzymes such as elastase. This structure is shown in the following schematic representation: +---+--------------------------------+--------------------+ |Sig| Propeptide C C C C | Antibacterial pep. | +---+----------------|--|--|--|------+--------------------+ | | | | +--+ +--+ 'C': conserved cysteine involved in a disulphide bond. ; GO: 0006952 defense response, 0005576 extracellular region; PDB: 1KWI_A 1PFP_A 1LXE_A 1N5P_A 1N5H_A.
Probab=23.51 E-value=88 Score=18.60 Aligned_cols=19 Identities=26% Similarity=0.345 Sum_probs=14.4
Q ss_pred HHHHHHHHHHHHHhhCCCc
Q 046034 32 EDAIKAAVKDYEAKHTKSS 50 (64)
Q Consensus 32 ~~ALk~AI~dY~~k~~~~~ 50 (64)
.+|+..||..|-.++...+
T Consensus 5 ~eav~~Av~~yN~~s~~~n 23 (67)
T PF00666_consen 5 EEAVLRAVDFYNQGSSGEN 23 (67)
T ss_dssp HHHHHHHHHHHHHCS-SSE
T ss_pred HHHHHHHHHHHhcCCCccC
Confidence 4789999999988866543
No 97
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=23.45 E-value=1.9e+02 Score=17.80 Aligned_cols=18 Identities=11% Similarity=0.025 Sum_probs=13.0
Q ss_pred hcCCHHHHHHhcCCCCch
Q 046034 7 LSGLSKEIAKHLSLPPVK 24 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K 24 (64)
.+.+.++|++.||+|..-
T Consensus 125 ~g~s~~eIA~~lgis~~t 142 (162)
T TIGR02983 125 EDLSEAQVAEALGISVGT 142 (162)
T ss_pred hcCCHHHHHHHhCCCHHH
Confidence 357788888888887544
No 98
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=23.40 E-value=1.6e+02 Score=18.50 Aligned_cols=20 Identities=30% Similarity=0.227 Sum_probs=13.9
Q ss_pred hcCCHHHHHHhcCCCCchhH
Q 046034 7 LSGLSKEIAKHLSLPPVKLH 26 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K~H 26 (64)
.+.+.++|++.||+++..+.
T Consensus 151 ~g~s~~eIA~~lgis~~~v~ 170 (187)
T TIGR02948 151 EDLSLKEISEILDLPVGTVK 170 (187)
T ss_pred cCCCHHHHHHHHCCCHHHHH
Confidence 35677888888888765543
No 99
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=23.35 E-value=1.8e+02 Score=18.22 Aligned_cols=19 Identities=5% Similarity=-0.216 Sum_probs=13.6
Q ss_pred hcCCHHHHHHhcCCCCchh
Q 046034 7 LSGLSKEIAKHLSLPPVKL 25 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K~ 25 (64)
.+++.++|++.||+|+.-+
T Consensus 127 ~g~s~~eIA~~lgis~~tV 145 (164)
T PRK12547 127 SGFSYEDAAAICGCAVGTI 145 (164)
T ss_pred cCCCHHHHHHHhCCCHHHH
Confidence 4577888888888876443
No 100
>PF14106 DUF4279: Domain of unknown function (DUF4279)
Probab=23.25 E-value=44 Score=20.09 Aligned_cols=19 Identities=21% Similarity=0.258 Sum_probs=15.0
Q ss_pred cCCHHHHHHhcCCCCchhH
Q 046034 8 SGLSKEIAKHLSLPPVKLH 26 (64)
Q Consensus 8 ~I~~~dI~e~LgLP~~K~H 26 (64)
.++.++|.+.||+.|.+.+
T Consensus 5 ~~~p~eiT~~Lgi~Pt~~~ 23 (118)
T PF14106_consen 5 DFDPDEITRLLGIEPTETW 23 (118)
T ss_pred CCCHHHHHHHHCCCceEEE
Confidence 4677888888888888766
No 101
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.
Probab=23.14 E-value=1.3e+02 Score=20.22 Aligned_cols=19 Identities=26% Similarity=0.291 Sum_probs=15.9
Q ss_pred cCCHHHHHHhcCCCCchhH
Q 046034 8 SGLSKEIAKHLSLPPVKLH 26 (64)
Q Consensus 8 ~I~~~dI~e~LgLP~~K~H 26 (64)
+++.++|++.||+|+..+.
T Consensus 194 ~~S~~EIAe~lgis~~tV~ 212 (227)
T TIGR02846 194 RKTQREIAKILGISRSYVS 212 (227)
T ss_pred CcCHHHHHHHHCCCHHHHH
Confidence 4689999999999988773
No 102
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=23.10 E-value=1.9e+02 Score=17.77 Aligned_cols=19 Identities=16% Similarity=0.018 Sum_probs=14.0
Q ss_pred hcCCHHHHHHhcCCCCchh
Q 046034 7 LSGLSKEIAKHLSLPPVKL 25 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K~ 25 (64)
.+++.++|++.||+|+.-+
T Consensus 121 ~g~s~~EIA~~lgis~~tV 139 (160)
T PRK09642 121 EEKSYQEIALQEKIEVKTV 139 (160)
T ss_pred hCCCHHHHHHHHCCCHHHH
Confidence 4577888888888886554
No 103
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=22.86 E-value=1.9e+02 Score=18.39 Aligned_cols=20 Identities=25% Similarity=0.247 Sum_probs=15.4
Q ss_pred hcCCHHHHHHhcCCCCchhH
Q 046034 7 LSGLSKEIAKHLSLPPVKLH 26 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K~H 26 (64)
.+++.++|++.||+|...++
T Consensus 132 e~~s~~EIA~~lgis~~tV~ 151 (179)
T PRK12543 132 HDYSQEEIAQLLQIPIGTVK 151 (179)
T ss_pred ccCCHHHHHHHHCCCHHHHH
Confidence 45788899999999866554
No 104
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=22.77 E-value=77 Score=20.84 Aligned_cols=24 Identities=13% Similarity=0.162 Sum_probs=17.7
Q ss_pred cCCHHHHHHhcCCCC--chhHHHHHH
Q 046034 8 SGLSKEIAKHLSLPP--VKLHCSMLA 31 (64)
Q Consensus 8 ~I~~~dI~e~LgLP~--~K~HCA~LA 31 (64)
..++++|++.||+.+ .+.|=+.|.
T Consensus 177 g~s~~eIa~~l~iS~~Tv~~~~~~~~ 202 (225)
T PRK10046 177 QHTAETVAQALTISRTTARRYLEYCA 202 (225)
T ss_pred CcCHHHHHHHhCccHHHHHHHHHHHH
Confidence 368999999999987 566654443
No 105
>PRK14390 hypothetical protein; Provisional
Probab=22.76 E-value=73 Score=18.74 Aligned_cols=13 Identities=31% Similarity=0.417 Sum_probs=10.4
Q ss_pred hHHHHHHHHHHHH
Q 046034 25 LHCSMLAEDAIKA 37 (64)
Q Consensus 25 ~HCA~LA~~ALk~ 37 (64)
--||.+|.+|++.
T Consensus 21 PTCS~Ya~~Ai~~ 33 (63)
T PRK14390 21 PSCSSYGYEAITR 33 (63)
T ss_pred ccHHHHHHHHHHH
Confidence 3599999999853
No 106
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=22.70 E-value=1.7e+02 Score=19.30 Aligned_cols=30 Identities=13% Similarity=0.293 Sum_probs=18.7
Q ss_pred cCCHHHHHHhcCCCCchhHHHHHHHHHHHHHHHHHH
Q 046034 8 SGLSKEIAKHLSLPPVKLHCSMLAEDAIKAAVKDYE 43 (64)
Q Consensus 8 ~I~~~dI~e~LgLP~~K~HCA~LA~~ALk~AI~dY~ 43 (64)
+++.++|++.||+++..+ ...|++|+..-+
T Consensus 169 g~s~~EIA~~lgis~~tV------~~~l~Ra~~~Lr 198 (206)
T PRK12526 169 ELSQEQLAQQLNVPLGTV------KSRLRLALAKLK 198 (206)
T ss_pred CCCHHHHHHHHCCCHHHH------HHHHHHHHHHHH
Confidence 577888888888875544 344455554443
No 107
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=22.68 E-value=1.6e+02 Score=18.58 Aligned_cols=20 Identities=15% Similarity=0.115 Sum_probs=14.9
Q ss_pred hcCCHHHHHHhcCCCCchhH
Q 046034 7 LSGLSKEIAKHLSLPPVKLH 26 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K~H 26 (64)
.+.+.++|++.||+++..+.
T Consensus 153 ~~~s~~EIA~~lgis~~tv~ 172 (190)
T TIGR02939 153 EGLSYEDIARIMDCPVGTVR 172 (190)
T ss_pred cCCCHHHHHHHHCcCHHHHH
Confidence 45778899999988865543
No 108
>PRK04217 hypothetical protein; Provisional
Probab=22.65 E-value=1.8e+02 Score=18.53 Aligned_cols=36 Identities=8% Similarity=0.025 Sum_probs=24.8
Q ss_pred hcCCHHHHHHhcCCCCchhHHH-HHHHHHHHHHHHHH
Q 046034 7 LSGLSKEIAKHLSLPPVKLHCS-MLAEDAIKAAVKDY 42 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K~HCA-~LA~~ALk~AI~dY 42 (64)
..++.++|++.||++..-++-. .-+.+.|+..+...
T Consensus 57 eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre~L~~~ 93 (110)
T PRK04217 57 EGLTQEEAGKRMGVSRGTVWRALTSARKKVAQMLVEG 93 (110)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhc
Confidence 3578999999999997776644 33555565555443
No 109
>cd00336 Ribosomal_L22 Ribosomal protein L22/L17e. L22 (L17 in eukaryotes) is a core protein of the large ribosomal subunit. It is the only ribosomal protein that interacts with all six domains of 23S rRNA, and is one of the proteins important for directing the proper folding and stabilizing the conformation of 23S rRNA. L22 is the largest protein contributor to the surface of the polypeptide exit channel, the tunnel through which the polypeptide product passes. L22 is also one of six proteins located at the putative translocon binding site on the exterior surface of the ribosome.
Probab=22.54 E-value=71 Score=19.44 Aligned_cols=39 Identities=15% Similarity=0.115 Sum_probs=26.0
Q ss_pred CHHHHHHhc-CCCCchhHHHHHHHHHHHHHHHHHHHhhCC
Q 046034 10 LSKEIAKHL-SLPPVKLHCSMLAEDAIKAAVKDYEAKHTK 48 (64)
Q Consensus 10 ~~~dI~e~L-gLP~~K~HCA~LA~~ALk~AI~dY~~k~~~ 48 (64)
.+..+-+++ -|.-....++.+-.++|+.|+.++..+...
T Consensus 23 rg~~v~~A~~~L~~~~kk~a~~i~k~l~sa~~nA~~~~~~ 62 (105)
T cd00336 23 RGMSVDEALAQLEFVPKKAAKIILKLLKSAEANAENNGLD 62 (105)
T ss_pred cCCcHHHHHHHHHhCCHHHHHHHHHHHHHHHHhHHHcCCC
Confidence 333344444 233334677899999999999999876554
No 110
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=22.45 E-value=1.6e+02 Score=18.52 Aligned_cols=19 Identities=32% Similarity=0.228 Sum_probs=13.6
Q ss_pred hcCCHHHHHHhcCCCCchh
Q 046034 7 LSGLSKEIAKHLSLPPVKL 25 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K~ 25 (64)
.+.+.++|++.||+++..+
T Consensus 151 ~~~s~~eIA~~lgis~~~v 169 (187)
T PRK09641 151 EDLSLKEISEILDLPVGTV 169 (187)
T ss_pred hCCCHHHHHHHHCCCHHHH
Confidence 3567788888888886554
No 111
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=22.36 E-value=69 Score=15.85 Aligned_cols=19 Identities=26% Similarity=0.267 Sum_probs=13.7
Q ss_pred hcCCHHHHHHhcCCCCchh
Q 046034 7 LSGLSKEIAKHLSLPPVKL 25 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K~ 25 (64)
-..+..+|++.||+++..+
T Consensus 17 ~g~s~~eia~~l~is~~tv 35 (58)
T smart00421 17 EGLTNKEIAERLGISEKTV 35 (58)
T ss_pred cCCCHHHHHHHHCCCHHHH
Confidence 3578888998888775443
No 112
>TIGR01195 oadG_fam sodium pump decarboxylases, gamma subunit. Most sequences scoring between the noise and trusted cutoffs are eukaryotic sodium channel proteins.
Probab=22.31 E-value=71 Score=19.22 Aligned_cols=14 Identities=43% Similarity=0.347 Sum_probs=12.0
Q ss_pred HHHHHHHHHHHHhh
Q 046034 33 DAIKAAVKDYEAKH 46 (64)
Q Consensus 33 ~ALk~AI~dY~~k~ 46 (64)
-++-.||..|+.++
T Consensus 68 AaIsAAI~~~r~~~ 81 (82)
T TIGR01195 68 AAIAAAVHEHLRKT 81 (82)
T ss_pred HHHHHHHHHHHHcc
Confidence 49999999998875
No 113
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=22.28 E-value=2e+02 Score=18.49 Aligned_cols=20 Identities=15% Similarity=-0.027 Sum_probs=14.6
Q ss_pred hcCCHHHHHHhcCCCCchhH
Q 046034 7 LSGLSKEIAKHLSLPPVKLH 26 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K~H 26 (64)
.+.+.++|++.||+|..-+.
T Consensus 149 ~g~s~~EIA~~lgis~~tV~ 168 (188)
T PRK09640 149 AELEFQEIADIMHMGLSATK 168 (188)
T ss_pred cCCCHHHHHHHHCCCHHHHH
Confidence 35788899998888865443
No 114
>PRK11470 hypothetical protein; Provisional
Probab=22.26 E-value=75 Score=22.36 Aligned_cols=25 Identities=20% Similarity=0.134 Sum_probs=20.5
Q ss_pred CCCchhHHHHHHHHHHHHHHHHHHH
Q 046034 20 LPPVKLHCSMLAEDAIKAAVKDYEA 44 (64)
Q Consensus 20 LP~~K~HCA~LA~~ALk~AI~dY~~ 44 (64)
+-..++.||.|..++.+.|..-...
T Consensus 111 ~~d~~~YCSElV~~~y~~a~~i~vg 135 (200)
T PRK11470 111 YESSRQFCSKFVFDIYKEALCIPVG 135 (200)
T ss_pred CCCCceehHHHHHHHHHHhhCCccc
Confidence 5678999999999999999854443
No 115
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=22.13 E-value=1.6e+02 Score=19.98 Aligned_cols=19 Identities=21% Similarity=0.104 Sum_probs=15.2
Q ss_pred hcCCHHHHHHhcCCCCchh
Q 046034 7 LSGLSKEIAKHLSLPPVKL 25 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K~ 25 (64)
..++.++|++.||+|+.-+
T Consensus 149 eg~s~~EIAe~LgiS~~tV 167 (216)
T PRK12533 149 EDMSYREIAAIADVPVGTV 167 (216)
T ss_pred cCCCHHHHHHHHCCCHHHH
Confidence 4678999999999886554
No 116
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=22.03 E-value=64 Score=19.39 Aligned_cols=19 Identities=21% Similarity=0.209 Sum_probs=14.9
Q ss_pred hcCCHHHHHHhcCCCCchh
Q 046034 7 LSGLSKEIAKHLSLPPVKL 25 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K~ 25 (64)
..++..+|++.||+++..+
T Consensus 31 eGlS~kEIAe~LGIS~~TV 49 (73)
T TIGR03879 31 AGKTASEIAEELGRTEQTV 49 (73)
T ss_pred cCCCHHHHHHHHCcCHHHH
Confidence 4678899999999886543
No 117
>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=22.02 E-value=62 Score=19.78 Aligned_cols=18 Identities=22% Similarity=0.147 Sum_probs=13.6
Q ss_pred hcCCHHHHHHhcCCCCch
Q 046034 7 LSGLSKEIAKHLSLPPVK 24 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K 24 (64)
.+++.++|++.||+|+.-
T Consensus 122 ~~~s~~EIA~~l~is~~t 139 (142)
T TIGR03209 122 EDMKEIDIAKKLHISRQS 139 (142)
T ss_pred cCCCHHHHHHHHCcCHHh
Confidence 357888999998888643
No 118
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=22.02 E-value=1.8e+02 Score=18.61 Aligned_cols=32 Identities=19% Similarity=0.123 Sum_probs=20.1
Q ss_pred hcCCHHHHHHhcCCCCchhHHHHHHHHHHHHHHHHHHH
Q 046034 7 LSGLSKEIAKHLSLPPVKLHCSMLAEDAIKAAVKDYEA 44 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K~HCA~LA~~ALk~AI~dY~~ 44 (64)
.+++..+|++.||+|...++ ..|+.|...-+.
T Consensus 142 ~gls~~EIA~~l~i~~~tVk------s~l~ra~~~l~~ 173 (182)
T COG1595 142 EGLSYEEIAEILGISVGTVK------SRLHRARKKLRE 173 (182)
T ss_pred cCCCHHHHHHHHCCCHHHHH------HHHHHHHHHHHH
Confidence 46788888888888855543 445555544433
No 119
>PF07308 DUF1456: Protein of unknown function (DUF1456); InterPro: IPR009921 This domain occurs in several hypothetical bacterial proteins of around 150 residues in length. The function of this domain is unknown.
Probab=21.99 E-value=1.4e+02 Score=17.41 Aligned_cols=20 Identities=10% Similarity=0.079 Sum_probs=13.9
Q ss_pred HhhcCCHHHHHHhc---CCCCch
Q 046034 5 RNLSGLSKEIAKHL---SLPPVK 24 (64)
Q Consensus 5 EA~~I~~~dI~e~L---gLP~~K 24 (64)
-|++|++++|++.+ |.+-.+
T Consensus 10 yal~l~d~~m~~if~l~~~~vs~ 32 (68)
T PF07308_consen 10 YALDLKDDDMIEIFALAGFEVSK 32 (68)
T ss_pred HHHcCChHHHHHHHHHcCCccCH
Confidence 47788888888887 444433
No 120
>PF06531 DUF1108: Protein of unknown function (DUF1108); InterPro: IPR009494 This entry is represented by Bacteriophage 92, Orf49. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several bacterial proteins from Staphylococcus aureus as well as a number of phage proteins. The function of this family is unknown.
Probab=21.98 E-value=1.2e+02 Score=19.09 Aligned_cols=24 Identities=21% Similarity=0.267 Sum_probs=19.2
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCC
Q 046034 26 HCSMLAEDAIKAAVKDYEAKHTKS 49 (64)
Q Consensus 26 HCA~LA~~ALk~AI~dY~~k~~~~ 49 (64)
.=-..|.+.|++||.+|-..+.++
T Consensus 52 sdl~~A~d~i~~aiyewIE~nTDE 75 (86)
T PF06531_consen 52 SDLYIAMDIINQAIYEWIEENTDE 75 (86)
T ss_pred HHHHHHHHHHHHHHHHHHHhCcch
Confidence 334578999999999999887654
No 121
>PRK14373 hypothetical protein; Provisional
Probab=21.81 E-value=77 Score=19.13 Aligned_cols=13 Identities=38% Similarity=0.554 Sum_probs=10.5
Q ss_pred hHHHHHHHHHHHH
Q 046034 25 LHCSMLAEDAIKA 37 (64)
Q Consensus 25 ~HCA~LA~~ALk~ 37 (64)
--||.++.+|++.
T Consensus 32 PTCS~Ya~~Ai~~ 44 (73)
T PRK14373 32 PTCSQYAVEAVKK 44 (73)
T ss_pred cCHHHHHHHHHHH
Confidence 3599999999853
No 122
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=21.72 E-value=1.2e+02 Score=18.90 Aligned_cols=17 Identities=24% Similarity=0.092 Sum_probs=10.2
Q ss_pred cCCHHHHHHhcCCCCch
Q 046034 8 SGLSKEIAKHLSLPPVK 24 (64)
Q Consensus 8 ~I~~~dI~e~LgLP~~K 24 (64)
+++.++|++.||+|...
T Consensus 129 g~s~~EIA~~l~is~~t 145 (161)
T PRK12528 129 GLGYGEIATELGISLAT 145 (161)
T ss_pred CCCHHHHHHHHCCCHHH
Confidence 45666666666666433
No 123
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=21.66 E-value=1.2e+02 Score=19.63 Aligned_cols=21 Identities=29% Similarity=0.150 Sum_probs=15.5
Q ss_pred hcCCHHHHHHhcCCCC--chhHH
Q 046034 7 LSGLSKEIAKHLSLPP--VKLHC 27 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~--~K~HC 27 (64)
.+.++++|++.|++.+ .+-|-
T Consensus 164 ~G~s~~eIA~~l~iS~~TV~~h~ 186 (216)
T PRK10840 164 EGFLVTEIAKKLNRSIKTISSQK 186 (216)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHH
Confidence 4688999999998875 44443
No 124
>PF07022 Phage_CI_repr: Bacteriophage CI repressor helix-turn-helix domain; InterPro: IPR010744 This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic [].; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2FJR_B.
Probab=21.62 E-value=26 Score=19.71 Aligned_cols=19 Identities=26% Similarity=0.305 Sum_probs=10.8
Q ss_pred HHhhcCCHH-HHHHhcCCCC
Q 046034 4 LRNLSGLSK-EIAKHLSLPP 22 (64)
Q Consensus 4 ~EA~~I~~~-dI~e~LgLP~ 22 (64)
.+++.++.+ ++++.||+++
T Consensus 7 ~~~~g~~~~~~lA~~lgis~ 26 (66)
T PF07022_consen 7 KEALGVKSDKELAERLGISK 26 (66)
T ss_dssp HHHHT-SSCHHHHCCTT--H
T ss_pred HHHhCCCCHHHHHHHhCcCH
Confidence 456666664 8888888773
No 125
>PRK02866 cyanate hydratase; Validated
Probab=21.51 E-value=75 Score=21.50 Aligned_cols=27 Identities=19% Similarity=0.241 Sum_probs=20.8
Q ss_pred HhhcCCHHHHHHhcCCCCchhHHHHHH
Q 046034 5 RNLSGLSKEIAKHLSLPPVKLHCSMLA 31 (64)
Q Consensus 5 EA~~I~~~dI~e~LgLP~~K~HCA~LA 31 (64)
...++|.++|++.+|++++-..=+.++
T Consensus 15 ~~kGLTw~~IA~~iG~S~v~vaaa~lG 41 (147)
T PRK02866 15 KEKGLTWADIAEAIGLSEVWVTAALLG 41 (147)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHhC
Confidence 456799999999999887766655555
No 126
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=21.30 E-value=95 Score=14.51 Aligned_cols=20 Identities=15% Similarity=0.219 Sum_probs=13.4
Q ss_pred HhhcCCHHHHHHhcCCCCch
Q 046034 5 RNLSGLSKEIAKHLSLPPVK 24 (64)
Q Consensus 5 EA~~I~~~dI~e~LgLP~~K 24 (64)
+...++..+++..+|+++..
T Consensus 9 ~~~~~s~~~~a~~~~~~~~~ 28 (58)
T cd00093 9 KEKGLTQEELAEKLGVSRST 28 (58)
T ss_pred HHcCCCHHHHHHHHCCCHHH
Confidence 34567777888877776543
No 127
>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=21.29 E-value=65 Score=20.37 Aligned_cols=20 Identities=20% Similarity=0.137 Sum_probs=15.6
Q ss_pred hcCCHHHHHHhcCCCCchhH
Q 046034 7 LSGLSKEIAKHLSLPPVKLH 26 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K~H 26 (64)
-+++.++|++.||+|+.-+.
T Consensus 149 ~g~s~~EIA~~lgis~~tVk 168 (183)
T TIGR02999 149 AGLTVEEIAELLGVSVRTVE 168 (183)
T ss_pred cCCCHHHHHHHhCCCHHHHH
Confidence 35789999999999965543
No 128
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=21.25 E-value=1.3e+02 Score=20.34 Aligned_cols=20 Identities=25% Similarity=0.247 Sum_probs=16.4
Q ss_pred hcCCHHHHHHhcCCCCchhH
Q 046034 7 LSGLSKEIAKHLSLPPVKLH 26 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K~H 26 (64)
..++-+||++.||+.+.-++
T Consensus 177 R~~~l~dLA~~lGISkst~~ 196 (215)
T COG3413 177 RRVSLKDLAKELGISKSTLS 196 (215)
T ss_pred ccCCHHHHHHHhCCCHHHHH
Confidence 46788999999999877665
No 129
>PF14813 NADH_B2: NADH dehydrogenase 1 beta subcomplex subunit 2
Probab=21.06 E-value=45 Score=20.12 Aligned_cols=9 Identities=33% Similarity=0.800 Sum_probs=6.4
Q ss_pred HhcCCCCch
Q 046034 16 KHLSLPPVK 24 (64)
Q Consensus 16 e~LgLP~~K 24 (64)
|+||+||+.
T Consensus 61 eELGIppdd 69 (71)
T PF14813_consen 61 EELGIPPDD 69 (71)
T ss_pred hhcCCCCCC
Confidence 567888763
No 130
>PLN03168 chalcone synthase; Provisional
Probab=21.01 E-value=84 Score=23.48 Aligned_cols=17 Identities=24% Similarity=0.346 Sum_probs=13.2
Q ss_pred HHHHHhcCCCCchhHHH
Q 046034 12 KEIAKHLSLPPVKLHCS 28 (64)
Q Consensus 12 ~dI~e~LgLP~~K~HCA 28 (64)
+.|.+.||||++|+..|
T Consensus 310 ~~v~~~Lgl~~ek~~~s 326 (389)
T PLN03168 310 DQVEAKLKLTKDKMQGS 326 (389)
T ss_pred HHHHHHcCCCHHHHHHH
Confidence 34566679999999876
No 131
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=20.96 E-value=1.7e+02 Score=19.01 Aligned_cols=32 Identities=13% Similarity=0.046 Sum_probs=21.4
Q ss_pred hcCCHHHHHHhcCCCCchhHHHHHHHHHHHHHHHHHHH
Q 046034 7 LSGLSKEIAKHLSLPPVKLHCSMLAEDAIKAAVKDYEA 44 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K~HCA~LA~~ALk~AI~dY~~ 44 (64)
.+++.++|++.||+|+.-+. .-|++|....+.
T Consensus 151 ~g~s~~eIA~~lgis~~tV~------~~l~Ra~~~Lr~ 182 (196)
T PRK12524 151 EGLSNPEIAEVMEIGVEAVE------SLTARGKRALAA 182 (196)
T ss_pred cCCCHHHHHHHHCcCHHHHH------HHHHHHHHHHHH
Confidence 45788999999999875543 455555555443
No 132
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=20.91 E-value=2.2e+02 Score=19.84 Aligned_cols=20 Identities=20% Similarity=0.119 Sum_probs=14.0
Q ss_pred hhcCCHHHHHHhcCCCCchh
Q 046034 6 NLSGLSKEIAKHLSLPPVKL 25 (64)
Q Consensus 6 A~~I~~~dI~e~LgLP~~K~ 25 (64)
..+++.++|++.||+|+.-+
T Consensus 156 ~~g~s~~EIA~~lgis~~tV 175 (324)
T TIGR02960 156 VLGWRAAETAELLGTSTASV 175 (324)
T ss_pred HhCCCHHHHHHHHCCCHHHH
Confidence 34677788888888876543
No 133
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=20.84 E-value=3e+02 Score=19.18 Aligned_cols=21 Identities=24% Similarity=0.164 Sum_probs=15.6
Q ss_pred HhhcCCHHHHHHhcCCCCchh
Q 046034 5 RNLSGLSKEIAKHLSLPPVKL 25 (64)
Q Consensus 5 EA~~I~~~dI~e~LgLP~~K~ 25 (64)
...+.+.++|++.||+|+..+
T Consensus 128 ~~~g~s~~EIA~~lg~s~~tV 148 (293)
T PRK09636 128 DVFGVPFDEIASTLGRSPAAC 148 (293)
T ss_pred HHhCCCHHHHHHHHCCCHHHH
Confidence 345778889999888886543
No 134
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=20.75 E-value=1.9e+02 Score=19.40 Aligned_cols=18 Identities=22% Similarity=0.309 Sum_probs=13.7
Q ss_pred cCCHHHHHHhcCCCCchh
Q 046034 8 SGLSKEIAKHLSLPPVKL 25 (64)
Q Consensus 8 ~I~~~dI~e~LgLP~~K~ 25 (64)
+++.++|++.||+|+..+
T Consensus 198 g~s~~EIA~~lgis~~tV 215 (234)
T PRK08301 198 EKTQKEVADMLGISQSYI 215 (234)
T ss_pred CCCHHHHHHHHCCCHHHH
Confidence 567888888888886654
No 135
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=20.71 E-value=2.2e+02 Score=18.21 Aligned_cols=19 Identities=11% Similarity=-0.050 Sum_probs=13.5
Q ss_pred hcCCHHHHHHhcCCCCchh
Q 046034 7 LSGLSKEIAKHLSLPPVKL 25 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K~ 25 (64)
.+++.++|++.||+|...+
T Consensus 146 ~g~s~~eIA~~lgis~~tV 164 (184)
T PRK12539 146 EGLSVAEAATRSGMSESAV 164 (184)
T ss_pred cCCcHHHHHHHHCcCHHHH
Confidence 3577788888888875543
No 136
>PRK14375 hypothetical protein; Provisional
Probab=20.54 E-value=85 Score=18.84 Aligned_cols=13 Identities=38% Similarity=0.524 Sum_probs=10.4
Q ss_pred hHHHHHHHHHHHH
Q 046034 25 LHCSMLAEDAIKA 37 (64)
Q Consensus 25 ~HCA~LA~~ALk~ 37 (64)
--||.++.+|++.
T Consensus 22 PTCS~Ya~~Ai~~ 34 (70)
T PRK14375 22 PTCSEYALEALKT 34 (70)
T ss_pred cCHHHHHHHHHHH
Confidence 4599999999853
No 137
>PF08334 T2SG: Type II secretion system (T2SS), protein G; InterPro: IPR013545 The general secretion pathway, or type II pullulanase-like machinery, is responsible for the transport of proteins from the periplasm across the outer membrane in Gram-negative bacteria [, ]. This entry includes protein G (e.g. P45773 from SWISSPROT, Q00514 from SWISSPROT) involved in this pathway. The PulG protein (P15746 from SWISSPROT) is thought to be anchored in the inner membrane with its C terminus directed towards the periplasm []. Together with other members of the secretion machinery, it is thought to assemble into a pilus-like structure that may function as a dynamic mechanism to push secreted proteins out of the cell. The polypeptide is organised into a long N-terminal alpha-helix followed by a loop region that separates it from a C-terminal anti-parallel beta-sheet []. ; PDB: 1T92_A 3G20_B 3GN9_B 2KEP_A 3FU1_B.
Probab=20.52 E-value=1.7e+02 Score=17.57 Aligned_cols=24 Identities=17% Similarity=0.178 Sum_probs=17.2
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCcc
Q 046034 28 SMLAEDAIKAAVKDYEAKHTKSSA 51 (64)
Q Consensus 28 A~LA~~ALk~AI~dY~~k~~~~~~ 51 (64)
+.--...|+.||..|+.+.+.=+.
T Consensus 14 a~~~l~~i~~Ale~Y~~d~G~yP~ 37 (108)
T PF08334_consen 14 AKADLRTIKTALEMYYLDNGRYPS 37 (108)
T ss_dssp HHHHHHHHHHHHHHHHHHHSS---
T ss_pred HHHHHHHHHHHHHHHHHhhCCCcC
Confidence 444578899999999998877655
No 138
>COG0759 Uncharacterized conserved protein [Function unknown]
Probab=20.52 E-value=81 Score=19.97 Aligned_cols=13 Identities=38% Similarity=0.501 Sum_probs=10.6
Q ss_pred hHHHHHHHHHHHH
Q 046034 25 LHCSMLAEDAIKA 37 (64)
Q Consensus 25 ~HCA~LA~~ALk~ 37 (64)
--||.+|.+||+.
T Consensus 33 PTCS~Ya~eAi~~ 45 (92)
T COG0759 33 PTCSEYAIEALKK 45 (92)
T ss_pred ccHHHHHHHHHHH
Confidence 4599999999853
No 139
>PF14698 ASL_C2: Argininosuccinate lyase C-terminal; PDB: 1XWO_A 2E9F_A 1TJW_C 1TJU_A 1DCN_B 1K7W_B 1HY1_C 1TJV_B 1AUW_A 1U15_B ....
Probab=20.31 E-value=57 Score=18.87 Aligned_cols=18 Identities=22% Similarity=0.399 Sum_probs=11.7
Q ss_pred CCHHHHHHhc---CCCCchhH
Q 046034 9 GLSKEIAKHL---SLPPVKLH 26 (64)
Q Consensus 9 I~~~dI~e~L---gLP~~K~H 26 (64)
++..|++++| |+|=-.-|
T Consensus 2 ~~ATdlAD~LVr~GipFR~AH 22 (70)
T PF14698_consen 2 STATDLADYLVRKGIPFREAH 22 (70)
T ss_dssp GGHHHHHHHHHHTTS-HHHHH
T ss_pred ccHHHHHHHHHHcCCCHHHHH
Confidence 3567899999 89844444
No 140
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=20.30 E-value=2.4e+02 Score=17.77 Aligned_cols=18 Identities=22% Similarity=0.224 Sum_probs=11.8
Q ss_pred cCCHHHHHHhcCCCCchh
Q 046034 8 SGLSKEIAKHLSLPPVKL 25 (64)
Q Consensus 8 ~I~~~dI~e~LgLP~~K~ 25 (64)
+++.++|++.||+|+.-+
T Consensus 135 g~s~~EIA~~lgis~~tV 152 (172)
T PRK12523 135 GMGHAEIAERLGVSVSRV 152 (172)
T ss_pred CCCHHHHHHHHCCCHHHH
Confidence 466777777777775443
No 141
>PRK09258 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed
Probab=20.25 E-value=1.3e+02 Score=21.07 Aligned_cols=34 Identities=15% Similarity=0.244 Sum_probs=22.9
Q ss_pred HHHHHhcCCCCchhH-----HHHHHHHHHHHHHHHHHHh
Q 046034 12 KEIAKHLSLPPVKLH-----CSMLAEDAIKAAVKDYEAK 45 (64)
Q Consensus 12 ~dI~e~LgLP~~K~H-----CA~LA~~ALk~AI~dY~~k 45 (64)
+.|.+.||||++|+. +-+++--.+=-++.++..+
T Consensus 273 ~~~~~~lgl~~~k~~~~~~~~GN~~sas~~~~L~~~~~~ 311 (338)
T PRK09258 273 RAILKALGIDPEKVFTTFPTLGNMGPASLPITLAMAAEE 311 (338)
T ss_pred HHHHHHhCCCHHHceehHhhhCCcHHhHHHHHHHHHHHh
Confidence 457777899999987 5555555555666666544
No 142
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=20.23 E-value=2e+02 Score=18.34 Aligned_cols=29 Identities=14% Similarity=0.203 Sum_probs=20.3
Q ss_pred hcCCHHHHHHhcCCCCchhHHHHHHHHHHHHHHHHHHHh
Q 046034 7 LSGLSKEIAKHLSLPPVKLHCSMLAEDAIKAAVKDYEAK 45 (64)
Q Consensus 7 ~~I~~~dI~e~LgLP~~K~HCA~LA~~ALk~AI~dY~~k 45 (64)
..++.++|+++||+.+ .++.+.+++.+.+
T Consensus 167 ~~~t~~~lA~~lG~tr----------~tvsR~l~~l~~~ 195 (211)
T PRK11753 167 IKITRQEIGRIVGCSR----------EMVGRVLKMLEDQ 195 (211)
T ss_pred cCCCHHHHHHHhCCCH----------HHHHHHHHHHHHC
Confidence 3688899999999884 4455566655544
No 143
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=20.11 E-value=73 Score=15.92 Aligned_cols=13 Identities=31% Similarity=0.381 Sum_probs=7.1
Q ss_pred CHHHHHHhcCCCC
Q 046034 10 LSKEIAKHLSLPP 22 (64)
Q Consensus 10 ~~~dI~e~LgLP~ 22 (64)
+-.++++.||+++
T Consensus 2 ~~~e~a~~~gv~~ 14 (49)
T cd04761 2 TIGELAKLTGVSP 14 (49)
T ss_pred cHHHHHHHHCcCH
Confidence 3455666566663
No 144
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=20.09 E-value=77 Score=15.30 Aligned_cols=11 Identities=36% Similarity=0.480 Sum_probs=5.6
Q ss_pred HHHHHHhcCCC
Q 046034 11 SKEIAKHLSLP 21 (64)
Q Consensus 11 ~~dI~e~LgLP 21 (64)
-.++++.||++
T Consensus 3 ~~e~a~~lgvs 13 (49)
T cd04762 3 TKEAAELLGVS 13 (49)
T ss_pred HHHHHHHHCcC
Confidence 34555555554
Done!