Query 023264
Match_columns 285
No_of_seqs 216 out of 1074
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 02:43:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023264.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023264hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK14134 recX recombination re 100.0 1.3E-29 2.8E-34 236.0 12.5 128 140-285 5-134 (283)
2 PRK14135 recX recombination re 99.9 2E-27 4.4E-32 216.0 13.2 128 142-285 3-132 (263)
3 COG2137 OraA Uncharacterized p 99.8 7.9E-20 1.7E-24 160.8 10.0 92 183-285 3-94 (174)
4 PRK00117 recX recombination re 99.7 8.1E-18 1.8E-22 142.7 8.3 78 207-285 8-85 (157)
5 PRK14136 recX recombination re 99.7 2E-17 4.3E-22 156.5 8.4 77 207-285 159-235 (309)
6 PRK14137 recX recombination re 99.7 5.2E-17 1.1E-21 145.0 8.5 74 208-285 38-111 (195)
7 PF02631 RecX: RecX family; I 99.3 1.4E-12 3E-17 106.5 5.0 52 234-285 1-52 (121)
8 PRK14135 recX recombination re 98.0 9.7E-06 2.1E-10 74.1 5.1 78 208-285 106-185 (263)
9 PRK00117 recX recombination re 96.7 0.0084 1.8E-07 50.9 7.7 58 210-272 62-119 (157)
10 PF02631 RecX: RecX family; I 95.4 0.14 3.1E-06 41.7 8.9 60 208-273 26-85 (121)
11 PF07553 Lipoprotein_Ltp: Host 90.9 0.58 1.3E-05 33.7 4.8 42 210-251 4-48 (48)
12 COG2137 OraA Uncharacterized p 90.8 0.92 2E-05 40.5 7.1 90 158-255 66-168 (174)
13 PRK14136 recX recombination re 87.5 2.7 5.8E-05 41.0 8.1 45 224-272 225-269 (309)
14 PF12802 MarR_2: MarR family; 82.1 3.8 8.3E-05 28.8 5.0 41 214-257 8-51 (62)
15 PRK14137 recX recombination re 80.9 4.9 0.00011 36.4 6.3 66 183-254 114-182 (195)
16 PF03551 PadR: Transcriptional 79.9 3.5 7.6E-05 30.8 4.3 42 217-258 2-48 (75)
17 TIGR03882 cyclo_dehyd_2 bacter 79.5 4.3 9.3E-05 36.2 5.5 45 213-259 32-76 (193)
18 PF13463 HTH_27: Winged helix 79.3 2.8 6.2E-05 29.9 3.5 41 214-257 6-48 (68)
19 cd00090 HTH_ARSR Arsenical Res 78.1 8.9 0.00019 26.5 5.8 40 216-258 12-51 (78)
20 smart00418 HTH_ARSR helix_turn 77.9 6.7 0.00015 26.5 5.0 39 217-258 3-41 (66)
21 smart00550 Zalpha Z-DNA-bindin 76.5 10 0.00022 28.4 5.9 43 213-258 8-53 (68)
22 PRK14134 recX recombination re 75.4 11 0.00024 35.7 7.3 65 183-253 137-208 (283)
23 PF13730 HTH_36: Helix-turn-he 75.2 6.2 0.00013 27.5 4.3 29 226-257 27-55 (55)
24 PF01022 HTH_5: Bacterial regu 73.6 13 0.00028 25.5 5.5 43 213-258 4-46 (47)
25 PF08784 RPA_C: Replication pr 73.3 4.2 9.2E-05 32.1 3.4 32 223-257 64-95 (102)
26 PF12840 HTH_20: Helix-turn-he 72.4 15 0.00031 26.4 5.7 45 211-258 10-55 (61)
27 PF01978 TrmB: Sugar-specific 71.9 8.9 0.00019 28.0 4.6 36 219-257 17-52 (68)
28 smart00345 HTH_GNTR helix_turn 69.9 9 0.0002 26.1 4.0 30 226-258 22-51 (60)
29 PF00325 Crp: Bacterial regula 69.8 9.6 0.00021 25.3 3.9 30 225-257 3-32 (32)
30 PF09012 FeoC: FeoC like trans 69.1 10 0.00022 28.1 4.4 37 219-258 8-45 (69)
31 cd07377 WHTH_GntR Winged helix 68.9 9.6 0.00021 26.5 4.1 31 225-258 26-56 (66)
32 PF13412 HTH_24: Winged helix- 66.1 23 0.00049 24.0 5.4 41 214-257 6-47 (48)
33 cd07153 Fur_like Ferric uptake 66.1 17 0.00037 28.7 5.5 37 222-258 14-52 (116)
34 PF01325 Fe_dep_repress: Iron 65.3 19 0.00042 26.4 5.2 43 214-259 10-54 (60)
35 PF04695 Pex14_N: Peroxisomal 64.0 18 0.00038 30.7 5.4 45 211-255 4-51 (136)
36 COG1695 Predicted transcriptio 63.9 9.1 0.0002 31.6 3.6 47 213-259 11-62 (138)
37 smart00346 HTH_ICLR helix_turn 63.5 21 0.00045 26.8 5.3 40 216-258 10-51 (91)
38 PF10390 ELL: RNA polymerase I 61.1 5.1 0.00011 38.1 1.8 52 210-261 197-249 (284)
39 TIGR03433 padR_acidobact trans 61.0 13 0.00027 29.6 3.8 44 215-258 8-56 (100)
40 PF03965 Penicillinase_R: Peni 60.0 13 0.00029 30.0 3.8 36 223-258 16-52 (115)
41 PF01475 FUR: Ferric uptake re 60.0 30 0.00064 27.8 5.9 46 213-258 10-59 (120)
42 TIGR00122 birA_repr_reg BirA b 58.9 31 0.00066 25.2 5.3 39 216-257 5-43 (69)
43 PF09106 SelB-wing_2: Elongati 58.8 7.6 0.00017 28.1 2.0 35 223-257 16-50 (59)
44 TIGR00738 rrf2_super rrf2 fami 58.8 23 0.00049 28.7 5.1 40 216-258 13-56 (132)
45 PF02082 Rrf2: Transcriptional 58.5 42 0.0009 25.5 6.2 31 225-258 26-56 (83)
46 PF08312 cwf21: cwf21 domain; 58.2 13 0.00028 26.6 3.0 27 227-253 13-39 (46)
47 PRK09462 fur ferric uptake reg 57.5 31 0.00067 29.1 5.8 46 213-258 19-69 (148)
48 TIGR02944 suf_reg_Xantho FeS a 57.4 24 0.00052 28.8 5.0 39 217-258 15-56 (130)
49 TIGR02698 CopY_TcrY copper tra 56.9 33 0.00072 28.7 5.8 38 221-258 15-53 (130)
50 COG1846 MarR Transcriptional r 55.6 27 0.00058 26.6 4.7 45 211-258 22-67 (126)
51 PRK03430 hypothetical protein; 55.2 14 0.00031 32.7 3.5 34 226-259 22-55 (157)
52 PF04361 DUF494: Protein of un 53.9 17 0.00037 31.8 3.7 33 226-258 22-54 (155)
53 smart00347 HTH_MARR helix_turn 53.9 35 0.00075 25.3 5.0 42 214-258 13-55 (101)
54 TIGR02787 codY_Gpos GTP-sensin 53.9 70 0.0015 30.6 8.0 48 208-258 165-229 (251)
55 PF14394 DUF4423: Domain of un 53.8 51 0.0011 29.0 6.7 31 226-257 41-71 (171)
56 PF07223 DUF1421: Protein of u 52.8 17 0.00037 36.1 3.9 35 222-256 316-350 (358)
57 PF04433 SWIRM: SWIRM domain; 50.9 87 0.0019 24.0 6.9 49 208-258 34-85 (86)
58 smart00420 HTH_DEOR helix_turn 50.5 34 0.00073 22.5 4.0 33 223-258 13-45 (53)
59 smart00344 HTH_ASNC helix_turn 50.1 45 0.00096 26.0 5.3 39 217-258 9-48 (108)
60 TIGR02010 IscR iron-sulfur clu 49.9 36 0.00077 28.3 4.9 40 216-258 13-56 (135)
61 COG1654 BirA Biotin operon rep 48.1 56 0.0012 25.8 5.4 41 213-256 8-48 (79)
62 PF06180 CbiK: Cobalt chelatas 47.2 20 0.00043 33.9 3.3 39 218-256 33-72 (262)
63 TIGR02719 repress_PhaQ poly-be 47.1 33 0.00071 29.7 4.4 47 212-258 25-74 (138)
64 PRK03573 transcriptional regul 47.0 43 0.00092 27.6 4.9 41 215-258 35-77 (144)
65 TIGR02702 SufR_cyano iron-sulf 45.8 52 0.0011 29.1 5.6 42 214-258 4-46 (203)
66 cd04752 Commd4 COMM_Domain con 45.5 1.1E+02 0.0024 26.9 7.5 69 183-253 20-88 (174)
67 PF03979 Sigma70_r1_1: Sigma-7 44.6 29 0.00064 26.8 3.4 34 223-256 20-53 (82)
68 PF08461 HTH_12: Ribonuclease 44.5 56 0.0012 24.5 4.8 41 222-262 11-53 (66)
69 COG2511 GatE Archaeal Glu-tRNA 44.0 98 0.0021 32.9 7.9 72 178-255 513-585 (631)
70 cd00052 EH Eps15 homology doma 43.6 69 0.0015 22.1 4.9 44 225-268 16-61 (67)
71 PF00392 GntR: Bacterial regul 41.9 44 0.00096 24.0 3.8 31 225-258 25-55 (64)
72 smart00419 HTH_CRP helix_turn_ 41.9 54 0.0012 21.4 4.0 31 225-258 9-39 (48)
73 KOG4796 RNA polymerase II elon 41.7 39 0.00084 35.6 4.6 43 211-253 211-253 (604)
74 PRK11512 DNA-binding transcrip 41.5 61 0.0013 26.8 5.1 41 215-258 44-85 (144)
75 PF05402 PqqD: Coenzyme PQQ sy 41.3 57 0.0012 23.4 4.3 41 216-257 22-67 (68)
76 cd03412 CbiK_N Anaerobic cobal 41.3 26 0.00056 29.1 2.8 35 222-256 36-70 (127)
77 PF13801 Metal_resist: Heavy-m 40.7 1.6E+02 0.0035 22.4 7.5 62 183-256 40-101 (125)
78 PF01988 VIT1: VIT family; In 40.5 78 0.0017 28.4 5.9 36 218-253 73-108 (213)
79 PRK09416 lstR lineage-specific 40.2 65 0.0014 28.0 5.1 49 210-259 42-95 (135)
80 PF03444 HrcA_DNA-bdg: Winged 40.0 56 0.0012 25.9 4.3 35 221-258 20-54 (78)
81 PF01047 MarR: MarR family; I 40.0 98 0.0021 21.4 5.3 34 221-257 14-47 (59)
82 PF07848 PaaX: PaaX-like prote 39.3 50 0.0011 25.2 3.9 35 224-258 20-54 (70)
83 PF01726 LexA_DNA_bind: LexA D 38.6 1.6E+02 0.0035 22.0 6.5 47 210-258 9-57 (65)
84 COG0735 Fur Fe2+/Zn2+ uptake r 37.7 74 0.0016 27.1 5.1 50 213-262 23-76 (145)
85 PF07106 TBPIP: Tat binding pr 36.8 80 0.0017 27.2 5.2 50 214-264 4-55 (169)
86 PRK05638 threonine synthase; V 35.7 64 0.0014 32.1 5.0 47 212-259 372-418 (442)
87 PF13545 HTH_Crp_2: Crp-like h 35.6 62 0.0013 23.4 3.8 32 224-258 28-59 (76)
88 TIGR01884 cas_HTH CRISPR locus 35.1 83 0.0018 27.8 5.2 42 214-258 146-188 (203)
89 TIGR01889 Staph_reg_Sar staphy 34.9 96 0.0021 24.7 5.1 40 216-258 30-74 (109)
90 PRK09834 DNA-binding transcrip 34.6 80 0.0017 29.0 5.2 38 217-257 17-56 (263)
91 PF14748 P5CR_dimer: Pyrroline 33.2 1.7E+02 0.0037 23.6 6.3 65 169-256 25-89 (107)
92 COG2512 Predicted membrane-ass 32.7 52 0.0011 31.1 3.7 41 215-258 199-241 (258)
93 TIGR01610 phage_O_Nterm phage 32.5 76 0.0016 25.0 4.1 34 222-258 45-78 (95)
94 PF13601 HTH_34: Winged helix 32.4 95 0.0021 23.9 4.5 40 216-258 5-45 (80)
95 PF10007 DUF2250: Uncharacteri 32.3 46 0.00099 27.0 2.8 21 238-258 32-52 (92)
96 PRK11639 zinc uptake transcrip 31.4 1.1E+02 0.0023 26.7 5.2 49 214-262 29-81 (169)
97 cd00092 HTH_CRP helix_turn_hel 31.4 89 0.0019 21.8 3.9 33 223-258 24-56 (67)
98 TIGR01446 DnaD_dom DnaD and ph 31.0 2.1E+02 0.0046 20.9 7.0 43 229-272 20-62 (73)
99 PRK10906 DNA-binding transcrip 29.9 1.2E+02 0.0025 28.1 5.4 41 214-257 8-49 (252)
100 PF07261 DnaB_2: Replication i 29.8 1.1E+02 0.0025 22.2 4.4 43 229-272 20-62 (77)
101 PF10905 DUF2695: Protein of u 29.5 88 0.0019 23.1 3.6 29 224-255 15-43 (53)
102 PRK14165 winged helix-turn-hel 29.4 1.4E+02 0.003 27.6 5.7 31 225-258 22-52 (217)
103 PF01638 HxlR: HxlR-like helix 29.2 1.1E+02 0.0025 23.5 4.5 42 215-258 9-50 (90)
104 PF09339 HTH_IclR: IclR helix- 29.1 55 0.0012 22.7 2.5 38 217-257 9-48 (52)
105 PRK15431 ferrous iron transpor 28.7 98 0.0021 24.6 4.0 29 226-257 18-46 (78)
106 PRK12423 LexA repressor; Provi 28.1 2E+02 0.0044 25.5 6.5 43 214-259 13-58 (202)
107 smart00027 EH Eps15 homology d 27.6 1.9E+02 0.004 22.3 5.5 49 224-272 26-76 (96)
108 COG2739 Uncharacterized protei 27.2 2.4E+02 0.0051 23.8 6.1 73 158-253 30-103 (105)
109 cd02432 Nodulin-21_like_1 Nodu 26.1 1.7E+02 0.0038 26.8 5.8 34 222-255 83-116 (218)
110 PF08220 HTH_DeoR: DeoR-like h 26.1 2.3E+02 0.0049 20.2 5.3 33 222-257 12-44 (57)
111 PF07499 RuvA_C: RuvA, C-termi 26.1 2.3E+02 0.0049 19.6 5.6 40 228-271 4-43 (47)
112 PRK04214 rbn ribonuclease BN/u 25.9 82 0.0018 31.2 3.9 34 221-257 307-340 (412)
113 PRK06474 hypothetical protein; 25.8 1.7E+02 0.0037 25.8 5.5 45 212-258 12-58 (178)
114 PF03962 Mnd1: Mnd1 family; I 25.5 79 0.0017 28.3 3.4 40 221-260 8-48 (188)
115 PF08780 NTase_sub_bind: Nucle 25.3 1.3E+02 0.0028 25.1 4.4 54 207-270 34-88 (124)
116 PTZ00431 pyrroline carboxylate 25.0 3.1E+02 0.0067 25.1 7.3 73 161-256 166-241 (260)
117 PF02037 SAP: SAP domain; Int 24.6 1.3E+02 0.0028 19.8 3.4 19 223-241 2-20 (35)
118 TIGR02431 pcaR_pcaU beta-ketoa 24.3 1.8E+02 0.004 26.2 5.6 44 212-258 7-55 (248)
119 COG3682 Predicted transcriptio 24.0 2.6E+02 0.0057 24.0 6.0 38 221-258 17-55 (123)
120 smart00816 Amb_V_allergen Amb 23.9 36 0.00078 24.3 0.7 19 33-51 11-29 (45)
121 TIGR00373 conserved hypothetic 23.8 2.2E+02 0.0048 24.7 5.7 43 213-258 17-59 (158)
122 PHA02554 13 neck protein; Prov 23.7 97 0.0021 30.4 3.8 35 222-256 3-49 (311)
123 PF10557 Cullin_Nedd8: Cullin 23.6 1.1E+02 0.0024 22.7 3.3 36 222-257 20-60 (68)
124 PF06014 DUF910: Bacterial pro 23.6 2.6E+02 0.0057 21.3 5.3 44 224-267 1-53 (62)
125 PF12363 DUF3647: Phage protei 23.5 1.5E+02 0.0031 24.5 4.3 49 207-256 51-103 (113)
126 PRK10947 global DNA-binding tr 23.2 3.3E+02 0.0072 23.5 6.6 57 183-244 19-75 (135)
127 PRK10857 DNA-binding transcrip 23.2 1.7E+02 0.0038 25.5 5.0 32 224-258 25-56 (164)
128 TIGR02337 HpaR homoprotocatech 23.2 1.8E+02 0.0039 23.1 4.8 41 215-258 32-73 (118)
129 TIGR03544 DivI1A_domain DivIVA 23.2 96 0.0021 20.3 2.6 17 237-253 16-32 (34)
130 PRK11050 manganese transport r 22.5 4.8E+02 0.01 22.1 8.4 45 212-259 38-83 (152)
131 PRK12727 flagellar biosynthesi 22.2 6.2E+02 0.013 27.0 9.5 63 183-254 255-321 (559)
132 smart00422 HTH_MERR helix_turn 22.1 86 0.0019 22.3 2.5 20 231-250 50-69 (70)
133 PRK09764 DNA-binding transcrip 22.0 1.3E+02 0.0027 27.1 4.0 33 223-258 28-60 (240)
134 PF09851 SHOCT: Short C-termin 22.0 1.7E+02 0.0037 18.8 3.6 21 246-266 6-26 (31)
135 PF01454 MAGE: MAGE family; I 21.8 92 0.002 27.2 3.0 46 214-259 110-164 (195)
136 PF14338 Mrr_N: Mrr N-terminal 21.8 1.9E+02 0.0041 22.4 4.5 56 212-269 5-66 (92)
137 PF08279 HTH_11: HTH domain; 21.4 2.6E+02 0.0057 19.1 4.8 38 215-255 4-43 (55)
138 COG1762 PtsN Phosphotransferas 21.2 1.9E+02 0.0041 24.1 4.7 27 240-266 20-46 (152)
139 PF15524 Toxin_45: Putative to 21.2 48 0.001 27.0 1.0 30 42-76 14-44 (94)
140 TIGR00112 proC pyrroline-5-car 21.0 4E+02 0.0088 24.2 7.2 75 161-258 153-230 (245)
141 PRK12491 pyrroline-5-carboxyla 20.9 4.2E+02 0.0091 24.6 7.4 65 169-256 184-248 (272)
142 PF11181 YflT: Heat induced st 20.8 1.1E+02 0.0023 24.5 2.9 44 211-257 57-100 (103)
143 PF00216 Bac_DNA_binding: Bact 20.6 1.3E+02 0.0028 22.7 3.3 28 226-253 2-30 (90)
144 COG4187 RocB Arginine degradat 20.4 9.3E+02 0.02 25.5 10.1 116 141-272 278-405 (553)
No 1
>PRK14134 recX recombination regulator RecX; Provisional
Probab=99.96 E-value=1.3e-29 Score=236.03 Aligned_cols=128 Identities=18% Similarity=0.252 Sum_probs=121.0
Q ss_pred cccchhhccCcccccceEEecCCccchhh--hHHHHhcccCCCCcCCCCHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHH
Q 023264 140 FASHKKFQNHNRMTNNNILLDAAKQEFGE--EISCEHGLFEESEVFEEPQEVAEEMKILQQKDFYLQAAKARQDAENLAV 217 (285)
Q Consensus 140 ~~~~~~~k~~~~r~~~NIyiDg~efafsv--dvlik~~L~kG~~~~ELdee~leeI~~~~q~~~~eq~~~~~~kA~~~AL 217 (285)
|..|+.|++++.|| |||||| +|+|+| +++++|+|.+| ++||++++++|. .. +.+.+|++.||
T Consensus 5 ItkIe~qk~~k~R~--~i~ld~-~~af~v~~~~l~~~~L~kG---~eld~e~~~ei~------~~----~~~~~a~~~AL 68 (283)
T PRK14134 5 ITKIEVQKRNKDRV--NVYIDE-EFAFACSAELVYYHNLKKG---KVIDVNSLNDII------KE----DNYIKCKGYAL 68 (283)
T ss_pred EEEEeeecCCCCeE--EEEecC-CeEEEecHHHHHHhCCcCC---CCcCHHHHHHHH------HH----HHHHHHHHHHH
Confidence 45689999999999 999999 999999 99999999999 999999999998 22 46789999999
Q ss_pred HHHhhccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhhhhcCCcchHHHhccC
Q 023264 218 KLLATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLINDSLYAESYSRSRWSSASWGPRRIKQGW 285 (285)
Q Consensus 218 ~lLS~RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLDD~rYAesyVrsr~~~k~kGprrIrqEL 285 (285)
+||++|+||++||++||.++||++++|+.||++|+++|||||.+||++||+++.. ++||++|+++|
T Consensus 69 ~~Ls~r~rSe~Elr~KL~~k~~~~~~Ie~vI~~L~e~~yldD~ryA~~yv~~~~~--~~G~~~I~~eL 134 (283)
T PRK14134 69 KYIEKSYKTEKQIKEKLYLKEYDEDAVNRVIRFLKEYNFIDDDKYCDMYIREKIN--SYGRNKIKYTL 134 (283)
T ss_pred HHhccCcchHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHH--hhhHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999985 79999999987
No 2
>PRK14135 recX recombination regulator RecX; Provisional
Probab=99.95 E-value=2e-27 Score=215.95 Aligned_cols=128 Identities=28% Similarity=0.345 Sum_probs=121.2
Q ss_pred cchhhccCcccccceEEecCCccchhh--hHHHHhcccCCCCcCCCCHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHH
Q 023264 142 SHKKFQNHNRMTNNNILLDAAKQEFGE--EISCEHGLFEESEVFEEPQEVAEEMKILQQKDFYLQAAKARQDAENLAVKL 219 (285)
Q Consensus 142 ~~~~~k~~~~r~~~NIyiDg~efafsv--dvlik~~L~kG~~~~ELdee~leeI~~~~q~~~~eq~~~~~~kA~~~AL~l 219 (285)
-|++|++++.|| |||||| +|+|+| +++++|+|.+| ++||++++++|.. . +...+|+++|++|
T Consensus 3 ~i~~~~~~~~r~--~v~ld~-~~~~~~~~~~~~~~~L~~g---~~l~~~~~~~i~~------~----~~~~~a~~~Al~~ 66 (263)
T PRK14135 3 KITVQKKNKERY--NIFLDE-KYAFSVDEDTLVKFMLKKG---KELDEEDLEEIQY------A----DQVSKGKNLALYY 66 (263)
T ss_pred eeeecccCCceE--EEEEcC-CeEEEeeHHHHHHhcCcCC---CcCCHHHHHHHHH------H----HHHHHHHHHHHHH
Confidence 578999999999 999999 999999 99999999999 9999999999982 2 3568999999999
Q ss_pred HhhccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhhhhcCCcchHHHhccC
Q 023264 220 LATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLINDSLYAESYSRSRWSSASWGPRRIKQGW 285 (285)
Q Consensus 220 LS~RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLDD~rYAesyVrsr~~~k~kGprrIrqEL 285 (285)
|++|+||+.||++||.++|+++++|+.||++|++.|||||.+||+.|++++++.+++||++|+++|
T Consensus 67 L~~r~~s~~el~~kL~~kg~~~~~Ie~vl~~l~~~~~ldD~~~a~~~~~~~~~~~~~g~~~I~~kL 132 (263)
T PRK14135 67 LSYQMRTEKEVRDYLKKHEISEEIISEVIDKLKEEKYIDDKEYAESYVRTNINTGDKGPRVIKQKL 132 (263)
T ss_pred hhhccccHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhccccchHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999987789999999986
No 3
>COG2137 OraA Uncharacterized protein conserved in bacteria [General function prediction only]
Probab=99.81 E-value=7.9e-20 Score=160.84 Aligned_cols=92 Identities=35% Similarity=0.482 Sum_probs=85.7
Q ss_pred CCCCHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCCHHHH
Q 023264 183 FEEPQEVAEEMKILQQKDFYLQAAKARQDAENLAVKLLATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLINDSLY 262 (285)
Q Consensus 183 ~ELdee~leeI~~~~q~~~~eq~~~~~~kA~~~AL~lLS~RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLDD~rY 262 (285)
++++++.+.++. .. +....++++||++|++|+||++||++||+++|+++++|+.||++|.+.|||||.+|
T Consensus 3 ~~~~~~~~~~~~------~~----~~~~~~~~~Al~~Ls~R~rse~ELr~kL~k~~~~~~~Ie~Vi~~l~~~~~ldD~~f 72 (174)
T COG2137 3 KELDDEDLEEIS------RS----DQYAKGLNRALRLLSRRDRSEKELRRKLAKKEFSEEIIEEVIDRLAEEGYLDDTRF 72 (174)
T ss_pred cccchhhhhhhh------hH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHcCcccHHHH
Confidence 888999999887 23 35689999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhhhcCCcchHHHhccC
Q 023264 263 AESYSRSRWSSASWGPRRIKQGW 285 (285)
Q Consensus 263 AesyVrsr~~~k~kGprrIrqEL 285 (285)
|++|++++.+ +++||.+|+|+|
T Consensus 73 Ae~~i~~r~~-~g~G~~rl~qeL 94 (174)
T COG2137 73 AEAYIRSRSR-KGKGPARLKQEL 94 (174)
T ss_pred HHHHHHHHHh-cccChHHHHHHH
Confidence 9999999998 559999999987
No 4
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=99.73 E-value=8.1e-18 Score=142.66 Aligned_cols=78 Identities=41% Similarity=0.692 Sum_probs=74.1
Q ss_pred HHHHHHHHHHHHHHhhccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhhhhcCCcchHHHhccC
Q 023264 207 KARQDAENLAVKLLATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLINDSLYAESYSRSRWSSASWGPRRIKQGW 285 (285)
Q Consensus 207 ~~~~kA~~~AL~lLS~RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLDD~rYAesyVrsr~~~k~kGprrIrqEL 285 (285)
+....|+++|++||++|+||++||++||.++|+++++|+.||++|.+.|||||.+||+.|++++ ..+++|+++|+++|
T Consensus 8 ~~~~~a~~~al~~L~~r~~s~~el~~kL~~kg~~~~~i~~vl~~l~~~~~ldD~~~a~~~~~~~-~~~~~g~~~I~~~L 85 (157)
T PRK00117 8 RMYASARARALRLLARREHSRAELRRKLAAKGFSEEVIEAVLDRLKEEGLLDDERFAESFVRSR-ARKGYGPRRIRQEL 85 (157)
T ss_pred cHHHHHHHHHHHHHccchhHHHHHHHHHHhcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHH-HhCCchHHHHHHHH
Confidence 3568999999999999999999999999999999999999999999999999999999999999 44899999999987
No 5
>PRK14136 recX recombination regulator RecX; Provisional
Probab=99.71 E-value=2e-17 Score=156.47 Aligned_cols=77 Identities=23% Similarity=0.361 Sum_probs=72.7
Q ss_pred HHHHHHHHHHHHHHhhccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhhhhcCCcchHHHhccC
Q 023264 207 KARQDAENLAVKLLATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLINDSLYAESYSRSRWSSASWGPRRIKQGW 285 (285)
Q Consensus 207 ~~~~kA~~~AL~lLS~RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLDD~rYAesyVrsr~~~k~kGprrIrqEL 285 (285)
.....++++||+||++|+||+.||++||+++||++++|+.||++|+++|||||.+||++||+.+.. +|||.+|+++|
T Consensus 159 ~~~~~lk~kAL~lLSrReRSe~ELr~KL~kkG~~ee~IE~VIerLke~gYLDDeRFAesyVr~R~~--kkGp~rIrqEL 235 (309)
T PRK14136 159 RPARSLKGRALGYLSRREYSRAELARKLAPYADESDSVEPLLDALEREGWLSDARFAESLVHRRAS--RVGSARIVSEL 235 (309)
T ss_pred ccHHHHHHHHHHHhhcccccHHHHHHHHHHcCCCHHHHHHHHHHHHHcCCcCHHHHHHHHHHHHhh--chhHHHHHHHH
Confidence 355789999999999999999999999999999999999999999999999999999999998764 69999999987
No 6
>PRK14137 recX recombination regulator RecX; Provisional
Probab=99.69 E-value=5.2e-17 Score=145.01 Aligned_cols=74 Identities=28% Similarity=0.365 Sum_probs=68.9
Q ss_pred HHHHHHHHHHHHHhhccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhhhhcCCcchHHHhccC
Q 023264 208 ARQDAENLAVKLLATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLINDSLYAESYSRSRWSSASWGPRRIKQGW 285 (285)
Q Consensus 208 ~~~kA~~~AL~lLS~RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLDD~rYAesyVrsr~~~k~kGprrIrqEL 285 (285)
...+++++|++||++|+||++||++||.++||++++|+.||++|+++|||||.+||+.|.. .++|||++|+++|
T Consensus 38 ~~~~~~~~Al~~Ls~R~rS~~ELr~KL~~kg~~~e~Ie~vI~rL~e~gyLDD~rfAe~~~~----~k~~Gp~rI~~eL 111 (195)
T PRK14137 38 AREALLAYAFRALAARAMTAAELRAKLERRSEDEALVTEVLERVQELGYQDDAQVARAENS----RRGVGALRVRQTL 111 (195)
T ss_pred HHHHHHHHHHHHHhcchhhHHHHHHHHHhcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHH----hcCchHHHHHHHH
Confidence 3468999999999999999999999999999999999999999999999999999999832 2689999999987
No 7
>PF02631 RecX: RecX family; InterPro: IPR003783 RecX is a putative bacterial regulatory protein []. The gene encoding RecX is found downstream of recA, and it is suggested that the RecX protein might be regulator of RecA activity by interaction with the RecA protein or filament [].; GO: 0006282 regulation of DNA repair; PDB: 3DFG_A 3D5L_B 3C1D_B 3E3V_A.
Probab=99.32 E-value=1.4e-12 Score=106.54 Aligned_cols=52 Identities=46% Similarity=0.684 Sum_probs=45.2
Q ss_pred HhcCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhhhhcCCcchHHHhccC
Q 023264 234 LNGKKFPSHVIEAVITDFQSRGLINDSLYAESYSRSRWSSASWGPRRIKQGW 285 (285)
Q Consensus 234 L~~Kg~~ee~Ie~VIerLee~GyLDD~rYAesyVrsr~~~k~kGprrIrqEL 285 (285)
|.++||++++|+.||++|+++|||||.+||++|++++++.+++||++|+++|
T Consensus 1 L~~kg~~~e~I~~vi~~l~~~gyidD~~ya~~~v~~~~~~~~~G~~~I~~~L 52 (121)
T PF02631_consen 1 LKRKGFSEEAIEEVIDRLKELGYIDDERYAESYVRSRLRRKGKGPRRIRQKL 52 (121)
T ss_dssp HHHTT--HHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHTT--HHHHHHHH
T ss_pred CcccCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHhcccccccHHHHHHHH
Confidence 7889999999999999999999999999999999999988999999999986
No 8
>PRK14135 recX recombination regulator RecX; Provisional
Probab=97.96 E-value=9.7e-06 Score=74.13 Aligned_cols=78 Identities=17% Similarity=0.147 Sum_probs=61.2
Q ss_pred HHHHHHHHHHHHHhhccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCCHHH-HHHHHHHhhhhc-CCcchHHHhccC
Q 023264 208 ARQDAENLAVKLLATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLINDSL-YAESYSRSRWSS-ASWGPRRIKQGW 285 (285)
Q Consensus 208 ~~~kA~~~AL~lLS~RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLDD~r-YAesyVrsr~~~-k~kGprrIrqEL 285 (285)
...-|...+-.++..+.++..+|+++|.++|++++.|+.||+.|.+.+++||.+ +|+.+.+..... ...++.+|.+.|
T Consensus 106 D~~~a~~~~~~~~~~~~~g~~~I~~kL~~kGi~~~~Ie~~l~~l~~~~~~d~a~~~~~k~~~~~~~~~~~~~k~Ki~~~L 185 (263)
T PRK14135 106 DKEYAESYVRTNINTGDKGPRVIKQKLLQKGIEDEIIEEALSEYTEEDQIEVAQKLAEKLLKKYQKLPFKALKQKIIQSL 185 (263)
T ss_pred HHHHHHHHHHHHHhccccchHHHHHHHHHcCCCHHHHHHHHHhCChhhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHH
Confidence 456788888888888889999999999999999999999999999999999974 777766654210 113456666554
No 9
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=96.65 E-value=0.0084 Score=50.95 Aligned_cols=58 Identities=19% Similarity=0.335 Sum_probs=47.3
Q ss_pred HHHHHHHHHHHhhccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhhhh
Q 023264 210 QDAENLAVKLLATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLINDSLYAESYSRSRWS 272 (285)
Q Consensus 210 ~kA~~~AL~lLS~RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLDD~rYAesyVrsr~~ 272 (285)
.-|...+-.. ..+.++...|+++|.++|++.+.|+.+++.+. .|+.+.|...++.+..
T Consensus 62 ~~a~~~~~~~-~~~~~g~~~I~~~L~~kGi~~~~I~~~l~~~~----~d~~e~a~~~~~k~~~ 119 (157)
T PRK00117 62 RFAESFVRSR-ARKGYGPRRIRQELRQKGVDREIIEEALAELD----IDWEELARELARKKFR 119 (157)
T ss_pred HHHHHHHHHH-HhCCchHHHHHHHHHHcCCCHHHHHHHHHHcC----ccHHHHHHHHHHHHcC
Confidence 4444444444 55788999999999999999999999999874 7888889998888765
No 10
>PF02631 RecX: RecX family; InterPro: IPR003783 RecX is a putative bacterial regulatory protein []. The gene encoding RecX is found downstream of recA, and it is suggested that the RecX protein might be regulator of RecA activity by interaction with the RecA protein or filament [].; GO: 0006282 regulation of DNA repair; PDB: 3DFG_A 3D5L_B 3C1D_B 3E3V_A.
Probab=95.38 E-value=0.14 Score=41.72 Aligned_cols=60 Identities=17% Similarity=0.214 Sum_probs=45.3
Q ss_pred HHHHHHHHHHHHHhhccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhhhhc
Q 023264 208 ARQDAENLAVKLLATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLINDSLYAESYSRSRWSS 273 (285)
Q Consensus 208 ~~~kA~~~AL~lLS~RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLDD~rYAesyVrsr~~~ 273 (285)
...-|..++-..+..+.++..-|+++|+++|++++.|+.+++ -+|+...|...++.+...
T Consensus 26 D~~ya~~~v~~~~~~~~~G~~~I~~~L~~kGi~~~~i~~~l~------~~~~~e~a~~~~~kk~~~ 85 (121)
T PF02631_consen 26 DERYAESYVRSRLRRKGKGPRRIRQKLKQKGIDREIIEEALE------EYDEEEEALELAEKKYRR 85 (121)
T ss_dssp HHHHHHHHHHHHHHHTT--HHHHHHHHHHTT--HHHHHHHHT------CS-HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhcccccccHHHHHHHHHHHCCChHHHHHHHH------HhhHHHHHHHHHHHHHhc
Confidence 445677777777878999999999999999999999999998 566666688888887763
No 11
>PF07553 Lipoprotein_Ltp: Host cell surface-exposed lipoprotein; InterPro: IPR011434 This domain is found as 1-3 copies in a small family of proteins of unknown function.
Probab=90.88 E-value=0.58 Score=33.70 Aligned_cols=42 Identities=14% Similarity=0.200 Sum_probs=37.9
Q ss_pred HHHHHHHHHHHhhccccHHHHHHHHhcC---CCCHHHHHHHHHHH
Q 023264 210 QDAENLAVKLLATRAFTAVEMRKKLNGK---KFPSHVIEAVITDF 251 (285)
Q Consensus 210 ~kA~~~AL~lLS~RdrS~~ELr~KL~~K---g~~ee~Ie~VIerL 251 (285)
+.|...|-.|+.....|..+|.+.|... +|++++++.+|+-|
T Consensus 4 ~~Al~~Ak~Y~~~~~~Sk~~l~~QL~se~ge~Ft~e~A~YAv~~l 48 (48)
T PF07553_consen 4 KNALKKAKSYLKTMHMSKQGLYDQLTSEYGEGFTEEEAQYAVDHL 48 (48)
T ss_pred HHHHHHHHHHHHhccCCHHHHHHHHHhhcccCCCHHHHHHHHHcC
Confidence 5688999999999999999999999976 89999999999754
No 12
>COG2137 OraA Uncharacterized protein conserved in bacteria [General function prediction only]
Probab=90.82 E-value=0.92 Score=40.51 Aligned_cols=90 Identities=16% Similarity=0.167 Sum_probs=60.9
Q ss_pred EecCCccchhh-hHHHHhcccCCC-----C--cCCCCHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHhhcc--cc-
Q 023264 158 LLDAAKQEFGE-EISCEHGLFEES-----E--VFEEPQEVAEEMKILQQKDFYLQAAKARQDAENLAVKLLATRA--FT- 226 (285)
Q Consensus 158 yiDg~efafsv-dvlik~~L~kG~-----~--~~ELdee~leeI~~~~q~~~~eq~~~~~~kA~~~AL~lLS~Rd--rS- 226 (285)
|+|++.||-+. ..-+..| +|. + .+-|+++.+++++ ++... .+....|...+...+.+.. ..
T Consensus 66 ~ldD~~fAe~~i~~r~~~g--~G~~rl~qeL~qkGi~~~~Ie~aL--~~~~~----~~~~~~a~~~~~kk~~~~~~~~~~ 137 (174)
T COG2137 66 YLDDTRFAEAYIRSRSRKG--KGPARLKQELKQKGIDDEIIEEAL--ELIDE----EDEQERARKVLRKKFKRENKPPDK 137 (174)
T ss_pred cccHHHHHHHHHHHHHhcc--cChHHHHHHHHHcCCCHHHHHHHH--hccch----HHHHHHHHHHHHHHhCccccCcch
Confidence 48887888665 3333333 332 1 1458999999888 22222 2456777788877776652 33
Q ss_pred --HHHHHHHHhcCCCCHHHHHHHHHHHHHCC
Q 023264 227 --AVEMRKKLNGKKFPSHVIEAVITDFQSRG 255 (285)
Q Consensus 227 --~~ELr~KL~~Kg~~ee~Ie~VIerLee~G 255 (285)
..-+.++|..+||+.++|..++..+.+..
T Consensus 138 ~~k~Ki~r~L~~rGFs~~~i~~~l~~~~~~~ 168 (174)
T COG2137 138 KEKAKIQRFLLRRGFSYEVIKEALNEAEEEE 168 (174)
T ss_pred hHHHHHHHHHHHcCCCHHHHHHHHHHhhhcc
Confidence 45688899999999999999999887654
No 13
>PRK14136 recX recombination regulator RecX; Provisional
Probab=87.51 E-value=2.7 Score=40.95 Aligned_cols=45 Identities=11% Similarity=0.172 Sum_probs=35.2
Q ss_pred cccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhhhh
Q 023264 224 AFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLINDSLYAESYSRSRWS 272 (285)
Q Consensus 224 drS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLDD~rYAesyVrsr~~ 272 (285)
.+...-|+..|++||++++.|+.+|+.+. .|+..-|...++.++.
T Consensus 225 kkGp~rIrqELrQKGId~eLIEqALeeie----EDE~E~A~~L~eKK~~ 269 (309)
T PRK14136 225 RVGSARIVSELKRHAVGDALVESVGAQLR----ETEFERAQAVWRKKFG 269 (309)
T ss_pred chhHHHHHHHHHHcCCCHHHHHHHHHhcc----HhHHHHHHHHHHHHhc
Confidence 37889999999999999999999998653 2555666666666653
No 14
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=82.12 E-value=3.8 Score=28.76 Aligned_cols=41 Identities=17% Similarity=0.397 Sum_probs=34.6
Q ss_pred HHHHHHHhhcc---ccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCC
Q 023264 214 NLAVKLLATRA---FTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLI 257 (285)
Q Consensus 214 ~~AL~lLS~Rd---rS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyL 257 (285)
-.+|.+|...+ -|..||.+.|. ++...+..+|.+|++.|||
T Consensus 8 ~~vL~~l~~~~~~~~t~~~la~~l~---~~~~~vs~~v~~L~~~Glv 51 (62)
T PF12802_consen 8 FRVLMALARHPGEELTQSELAERLG---ISKSTVSRIVKRLEKKGLV 51 (62)
T ss_dssp HHHHHHHHHSTTSGEEHHHHHHHHT---S-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHCCCCCcCHHHHHHHHC---cCHHHHHHHHHHHHHCCCE
Confidence 35677777777 59999999885 8999999999999999998
No 15
>PRK14137 recX recombination regulator RecX; Provisional
Probab=80.90 E-value=4.9 Score=36.38 Aligned_cols=66 Identities=18% Similarity=0.161 Sum_probs=40.1
Q ss_pred CCCCHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHhh---ccccHHHHHHHHhcCCCCHHHHHHHHHHHHHC
Q 023264 183 FEEPQEVAEEMKILQQKDFYLQAAKARQDAENLAVKLLAT---RAFTAVEMRKKLNGKKFPSHVIEAVITDFQSR 254 (285)
Q Consensus 183 ~ELdee~leeI~~~~q~~~~eq~~~~~~kA~~~AL~lLS~---RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~ 254 (285)
.-|+++.+++.. .+.+.. +....|...+-+.+.. ......-+.++|..+||+.++|..||..+.+.
T Consensus 114 KGI~~~lI~~al--~~~d~e----de~e~a~~l~~KK~~~~~~~~~~k~K~~~~L~rRGFs~~~I~~al~~~~~~ 182 (195)
T PRK14137 114 RGVEETLIEETL--AARDPQ----EEQQEARNLLERRWSSFARKRDPRASAYAFLARRGFSGAVIWPAIREVAAL 182 (195)
T ss_pred cCCCHHHHHHHH--HhcCch----hHHHHHHHHHHHhccccCcchhHHHHHHHHHHHCCCCHHHHHHHHHHHHHh
Confidence 447888888766 221111 2233344433333321 11223558889999999999999999988764
No 16
>PF03551 PadR: Transcriptional regulator PadR-like family; InterPro: IPR005149 Phenolic acids, also called substituted hydroxycinnamic acids, are abundant in the plant kingdom because they are involved in the structure of plant cell walls and are present in some vacuoles. In plant-soil ecosystems they are released as free acids by hemicellulases produced by several fungi and bacteria. Of these weak acids, the most abundant are p-coumaric, ferulic, and caffeic acids, considered to be natural toxins that inhibit the growth of microorganisms, especially at low pHs. In spite of this chemical stress, some bacteria can use phenolic acids as a sole source of carbon. For other microorganisms, these compounds induce a specific response by which the organism adapts to its environment. The ubiquitous lactic acid bacterium Lactobacillus plantarum exhibits an inducible phenolic acid decarboxylase (PAD) activity which converts these substrates into less-toxic vinyl phenol derivatives. PadR acts as a repressor of padA gene expression in the phenolic acid stress response [].; PDB: 1XMA_B 2ESH_A 2DQL_B 3L9F_C 3ELK_B 4EJO_B 3L7W_A 3HHH_A 1YG2_A 3F8B_A ....
Probab=79.87 E-value=3.5 Score=30.76 Aligned_cols=42 Identities=19% Similarity=0.426 Sum_probs=36.8
Q ss_pred HHHHhhccccHHHHHHHHhcC-----CCCHHHHHHHHHHHHHCCCCC
Q 023264 217 VKLLATRAFTAVEMRKKLNGK-----KFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 217 L~lLS~RdrS~~ELr~KL~~K-----g~~ee~Ie~VIerLee~GyLD 258 (285)
|.+|+.++.+-.||.+.|.+. ..++..|-.+|.+|++.|||.
T Consensus 2 L~~L~~~~~~Gyei~~~l~~~~~~~~~i~~g~lY~~L~~Le~~gli~ 48 (75)
T PF03551_consen 2 LGLLSEGPMHGYEIKQELEERTGGFWKISPGSLYPALKRLEEEGLIE 48 (75)
T ss_dssp HHHHHHS-EEHHHHHHHHHHCSTTTEETTHHHHHHHHHHHHHTTSEE
T ss_pred hhhhccCCCcHHHHHHHHHHHhCCCcccChhHHHHHHHHHHhCCCEE
Confidence 668888999999999999987 367899999999999999984
No 17
>TIGR03882 cyclo_dehyd_2 bacteriocin biosynthesis cyclodehydratase domain. This model describes a ThiF-like domain of a fusion protein found in clusters associated with the production of TOMMs (thiazole/oxazole-modified microcins), small bacteriocins with characteristic heterocycle modifications. This domain is presumed to act as a cyclodehydratase, as do members of the SagC family modeled by TIGR03603.
Probab=79.49 E-value=4.3 Score=36.23 Aligned_cols=45 Identities=22% Similarity=0.315 Sum_probs=38.2
Q ss_pred HHHHHHHHhhccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCCH
Q 023264 213 ENLAVKLLATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIND 259 (285)
Q Consensus 213 ~~~AL~lLS~RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLDD 259 (285)
+..-+.+|.- .||..|+.+.|.. +++.+.|.++|..|.+.|||=|
T Consensus 32 ~~~L~~lLdG-~rt~~eI~~~l~~-~~p~~~v~~~L~~L~~~G~l~~ 76 (193)
T TIGR03882 32 YCQLAPLLDG-RRTLDEIIAALAG-RFPAEEVLYALDRLERRGYLVE 76 (193)
T ss_pred HHHHHHHHcC-CCCHHHHHHHhhc-cCCHHHHHHHHHHHHHCCCEec
Confidence 3445556665 6999999999998 7999999999999999999944
No 18
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=79.25 E-value=2.8 Score=29.92 Aligned_cols=41 Identities=17% Similarity=0.424 Sum_probs=32.6
Q ss_pred HHHHHHHh--hccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCC
Q 023264 214 NLAVKLLA--TRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLI 257 (285)
Q Consensus 214 ~~AL~lLS--~RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyL 257 (285)
-..|++|+ ....|..+|.+.|. ++...+-.+|.+|.+.|||
T Consensus 6 ~~vL~~l~~~~~~~t~~~l~~~~~---~~~~~vs~~i~~L~~~glv 48 (68)
T PF13463_consen 6 WQVLRALAHSDGPMTQSDLAERLG---ISKSTVSRIIKKLEEKGLV 48 (68)
T ss_dssp HHHHHHHT--TS-BEHHHHHHHTT-----HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHccCCCcCHHHHHHHHC---cCHHHHHHHHHHHHHCCCE
Confidence 34567777 88888899998874 7999999999999999999
No 19
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=78.06 E-value=8.9 Score=26.52 Aligned_cols=40 Identities=18% Similarity=0.420 Sum_probs=33.2
Q ss_pred HHHHHhhccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCC
Q 023264 216 AVKLLATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 216 AL~lLS~RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLD 258 (285)
.+.+|...+.|..|+.+.| |++...|..+|+.|++.|+|.
T Consensus 12 il~~l~~~~~~~~ei~~~~---~i~~~~i~~~l~~L~~~g~i~ 51 (78)
T cd00090 12 ILRLLLEGPLTVSELAERL---GLSQSTVSRHLKKLEEAGLVE 51 (78)
T ss_pred HHHHHHHCCcCHHHHHHHH---CcCHhHHHHHHHHHHHCCCeE
Confidence 3445555558899998877 689999999999999999996
No 20
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=77.88 E-value=6.7 Score=26.48 Aligned_cols=39 Identities=21% Similarity=0.409 Sum_probs=33.2
Q ss_pred HHHHhhccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCC
Q 023264 217 VKLLATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 217 L~lLS~RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLD 258 (285)
+.+|.....|..++.+.| |++...+..+|.+|.+.|+|.
T Consensus 3 l~~l~~~~~~~~~i~~~l---~is~~~v~~~l~~L~~~g~i~ 41 (66)
T smart00418 3 LKLLAEGELCVCELAEIL---GLSQSTVSHHLKKLREAGLVE 41 (66)
T ss_pred HHHhhcCCccHHHHHHHH---CCCHHHHHHHHHHHHHCCCee
Confidence 344556778899999988 589999999999999999996
No 21
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=76.53 E-value=10 Score=28.36 Aligned_cols=43 Identities=21% Similarity=0.421 Sum_probs=36.7
Q ss_pred HHHHHHHHhhc-c--ccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCC
Q 023264 213 ENLAVKLLATR-A--FTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 213 ~~~AL~lLS~R-d--rS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLD 258 (285)
.+..|.+|..+ . .|..||.+.| |++...+..+|..|++.|||.
T Consensus 8 ~~~IL~~L~~~g~~~~ta~eLa~~l---gl~~~~v~r~L~~L~~~G~V~ 53 (68)
T smart00550 8 EEKILEFLENSGDETSTALQLAKNL---GLPKKEVNRVLYSLEKKGKVC 53 (68)
T ss_pred HHHHHHHHHHCCCCCcCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEE
Confidence 46677788876 5 7999999887 689999999999999999984
No 22
>PRK14134 recX recombination regulator RecX; Provisional
Probab=75.37 E-value=11 Score=35.69 Aligned_cols=65 Identities=15% Similarity=0.089 Sum_probs=41.0
Q ss_pred CCCCHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHhhc---ccc----HHHHHHHHhcCCCCHHHHHHHHHHHHH
Q 023264 183 FEEPQEVAEEMKILQQKDFYLQAAKARQDAENLAVKLLATR---AFT----AVEMRKKLNGKKFPSHVIEAVITDFQS 253 (285)
Q Consensus 183 ~ELdee~leeI~~~~q~~~~eq~~~~~~kA~~~AL~lLS~R---drS----~~ELr~KL~~Kg~~ee~Ie~VIerLee 253 (285)
.-|+++.+++.. ++.... +....|...|-+.+..- +.+ .+-|.++|..+||+.++|..||..+..
T Consensus 137 KGI~~~iIe~al--~~~~~e----~e~e~a~~l~~Kk~~~~~~~~~~~~k~k~Kl~~~L~rrGFs~~~I~~vl~~~~~ 208 (283)
T PRK14134 137 KGIKENIIIEKI--NNIDEE----KEKKVAYKLAEKKYKILILSEKNKFKIYKKLGPYLISRGYSSNIAEWILNELIK 208 (283)
T ss_pred CCCCHHHHHHHH--HhCChh----hHHHHHHHHHHHhhcccccccccHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHh
Confidence 457888888776 222211 23344555554444322 222 245778899999999999999999854
No 23
>PF13730 HTH_36: Helix-turn-helix domain
Probab=75.24 E-value=6.2 Score=27.45 Aligned_cols=29 Identities=21% Similarity=0.476 Sum_probs=25.1
Q ss_pred cHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCC
Q 023264 226 TAVEMRKKLNGKKFPSHVIEAVITDFQSRGLI 257 (285)
Q Consensus 226 S~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyL 257 (285)
|...|.+.+ |++...|..+|..|++.|||
T Consensus 27 S~~~la~~~---g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 27 SQETLAKDL---GVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred CHHHHHHHH---CcCHHHHHHHHHHHHHCcCC
Confidence 566666666 78999999999999999997
No 24
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=73.62 E-value=13 Score=25.50 Aligned_cols=43 Identities=19% Similarity=0.373 Sum_probs=37.6
Q ss_pred HHHHHHHHhhccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCC
Q 023264 213 ENLAVKLLATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 213 ~~~AL~lLS~RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLD 258 (285)
+-..+.+|...+.+..||.+.|. .+...|-.=+..|++.|+|.
T Consensus 4 R~~Il~~L~~~~~~~~el~~~l~---~s~~~vs~hL~~L~~~glV~ 46 (47)
T PF01022_consen 4 RLRILKLLSEGPLTVSELAEELG---LSQSTVSHHLKKLREAGLVE 46 (47)
T ss_dssp HHHHHHHHTTSSEEHHHHHHHHT---S-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHhCCCchhhHHHhcc---ccchHHHHHHHHHHHCcCee
Confidence 45678899999999999999985 89999999999999999974
No 25
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=73.30 E-value=4.2 Score=32.12 Aligned_cols=32 Identities=13% Similarity=0.257 Sum_probs=28.3
Q ss_pred ccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCC
Q 023264 223 RAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLI 257 (285)
Q Consensus 223 RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyL 257 (285)
.-.+..+|.++| +++++.|..+|+.|.+.|+|
T Consensus 64 ~Gv~v~~I~~~l---~~~~~~v~~al~~L~~eG~I 95 (102)
T PF08784_consen 64 EGVHVDEIAQQL---GMSENEVRKALDFLSNEGHI 95 (102)
T ss_dssp TTEEHHHHHHHS---TS-HHHHHHHHHHHHHTTSE
T ss_pred CcccHHHHHHHh---CcCHHHHHHHHHHHHhCCeE
Confidence 347889999999 89999999999999999987
No 26
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=72.37 E-value=15 Score=26.43 Aligned_cols=45 Identities=18% Similarity=0.333 Sum_probs=39.0
Q ss_pred HHHHHHHHHH-hhccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCC
Q 023264 211 DAENLAVKLL-ATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 211 kA~~~AL~lL-S~RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLD 258 (285)
...-..|.+| ...+.|..||.+.| |.+...+-.=|..|++.|+|.
T Consensus 10 p~R~~Il~~L~~~~~~t~~ela~~l---~~~~~t~s~hL~~L~~aGli~ 55 (61)
T PF12840_consen 10 PTRLRILRLLASNGPMTVSELAEEL---GISQSTVSYHLKKLEEAGLIE 55 (61)
T ss_dssp HHHHHHHHHHHHCSTBEHHHHHHHH---TS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHH---CCCHHHHHHHHHHHHHCCCeE
Confidence 3456677888 99999999999999 699999999999999999984
No 27
>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=71.95 E-value=8.9 Score=27.95 Aligned_cols=36 Identities=22% Similarity=0.404 Sum_probs=32.9
Q ss_pred HHhhccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCC
Q 023264 219 LLATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLI 257 (285)
Q Consensus 219 lLS~RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyL 257 (285)
+|.....|..||.+.| |++...|..+|..|.+.|||
T Consensus 17 Ll~~~~~t~~eIa~~l---~i~~~~v~~~L~~L~~~GlV 52 (68)
T PF01978_consen 17 LLKNGPATAEEIAEEL---GISRSTVYRALKSLEEKGLV 52 (68)
T ss_dssp HHHHCHEEHHHHHHHH---TSSHHHHHHHHHHHHHTTSE
T ss_pred HHHcCCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCE
Confidence 4589999999999988 58999999999999999997
No 28
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=69.95 E-value=9 Score=26.10 Aligned_cols=30 Identities=13% Similarity=0.407 Sum_probs=27.1
Q ss_pred cHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCC
Q 023264 226 TAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 226 S~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLD 258 (285)
|..||.+.+ |++...|..++..|++.|+|.
T Consensus 22 s~~~la~~~---~vs~~tv~~~l~~L~~~g~i~ 51 (60)
T smart00345 22 SERELAAQL---GVSRTTVREALSRLEAEGLVQ 51 (60)
T ss_pred CHHHHHHHH---CCCHHHHHHHHHHHHHCCCEE
Confidence 788888887 689999999999999999984
No 29
>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=69.81 E-value=9.6 Score=25.32 Aligned_cols=30 Identities=17% Similarity=0.434 Sum_probs=24.4
Q ss_pred ccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCC
Q 023264 225 FTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLI 257 (285)
Q Consensus 225 rS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyL 257 (285)
.|+.|+.++| |.+.+.+-.++.+|++.|+|
T Consensus 3 mtr~diA~~l---G~t~ETVSR~l~~l~~~glI 32 (32)
T PF00325_consen 3 MTRQDIADYL---GLTRETVSRILKKLERQGLI 32 (32)
T ss_dssp --HHHHHHHH---TS-HHHHHHHHHHHHHTTSE
T ss_pred cCHHHHHHHh---CCcHHHHHHHHHHHHHcCCC
Confidence 5778888887 68999999999999999986
No 30
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=69.12 E-value=10 Score=28.08 Aligned_cols=37 Identities=16% Similarity=0.406 Sum_probs=27.8
Q ss_pred HH-hhccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCC
Q 023264 219 LL-ATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 219 lL-S~RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLD 258 (285)
|| .+...|..||...|. .+++.|+..|+.|+..|||-
T Consensus 8 ~l~~~~~~S~~eLa~~~~---~s~~~ve~mL~~l~~kG~I~ 45 (69)
T PF09012_consen 8 YLRERGRVSLAELAREFG---ISPEAVEAMLEQLIRKGYIR 45 (69)
T ss_dssp HHHHS-SEEHHHHHHHTT-----HHHHHHHHHHHHCCTSCE
T ss_pred HHHHcCCcCHHHHHHHHC---cCHHHHHHHHHHHHHCCcEE
Confidence 44 344578888887764 89999999999999999983
No 31
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=68.91 E-value=9.6 Score=26.47 Aligned_cols=31 Identities=13% Similarity=0.383 Sum_probs=27.7
Q ss_pred ccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCC
Q 023264 225 FTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 225 rS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLD 258 (285)
.|..+|.+.+ +.+...+..+|.+|++.|||.
T Consensus 26 ~~~~~la~~~---~is~~~v~~~l~~L~~~G~i~ 56 (66)
T cd07377 26 PSERELAEEL---GVSRTTVREALRELEAEGLVE 56 (66)
T ss_pred CCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEE
Confidence 3588888888 789999999999999999995
No 32
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=66.13 E-value=23 Score=24.03 Aligned_cols=41 Identities=20% Similarity=0.379 Sum_probs=31.5
Q ss_pred HHHHHHHhhcc-ccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCC
Q 023264 214 NLAVKLLATRA-FTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLI 257 (285)
Q Consensus 214 ~~AL~lLS~Rd-rS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyL 257 (285)
...|.+|...+ .|..||.+++ |++...+...|.+|++.|||
T Consensus 6 ~~Il~~l~~~~~~t~~ela~~~---~is~~tv~~~l~~L~~~g~I 47 (48)
T PF13412_consen 6 RKILNYLRENPRITQKELAEKL---GISRSTVNRYLKKLEEKGLI 47 (48)
T ss_dssp HHHHHHHHHCTTS-HHHHHHHH---TS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHcCCCCHHHHHHHh---CCCHHHHHHHHHHHHHCcCc
Confidence 34455665554 7889999887 48999999999999999997
No 33
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=66.11 E-value=17 Score=28.75 Aligned_cols=37 Identities=19% Similarity=0.281 Sum_probs=33.0
Q ss_pred hccccHHHHHHHHhcCC--CCHHHHHHHHHHHHHCCCCC
Q 023264 222 TRAFTAVEMRKKLNGKK--FPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 222 ~RdrS~~ELr~KL~~Kg--~~ee~Ie~VIerLee~GyLD 258 (285)
.+..|..||.+.|++.+ ++...|-.+|+.|.+.|+|.
T Consensus 14 ~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~ 52 (116)
T cd07153 14 DGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVR 52 (116)
T ss_pred CCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEE
Confidence 35689999999999874 68999999999999999985
No 34
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=65.30 E-value=19 Score=26.42 Aligned_cols=43 Identities=12% Similarity=0.265 Sum_probs=33.6
Q ss_pred HHHHHHHh--hccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCCH
Q 023264 214 NLAVKLLA--TRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIND 259 (285)
Q Consensus 214 ~~AL~lLS--~RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLDD 259 (285)
-.|+..|. ...-+..+|.++|. +++..+-+++.+|.+.|||+=
T Consensus 10 L~~Iy~l~~~~~~v~~~~iA~~L~---vs~~tvt~ml~~L~~~GlV~~ 54 (60)
T PF01325_consen 10 LKAIYELSEEGGPVRTKDIAERLG---VSPPTVTEMLKRLAEKGLVEY 54 (60)
T ss_dssp HHHHHHHHHCTSSBBHHHHHHHHT---S-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHcCCCCccHHHHHHHHC---CChHHHHHHHHHHHHCCCEEe
Confidence 34444444 66778899999885 899999999999999999864
No 35
>PF04695 Pex14_N: Peroxisomal membrane anchor protein (Pex14p) conserved region; InterPro: IPR006785 This conserved region defines a group of peroxisomal membrane anchor proteins which bind the PTS1 (peroxisomal targeting signal) receptor and are required for the import of PTS1-containing proteins into peroxisomes. Loss of functional Pex14p results in defects in both the PTS1 and PTS2-dependent import pathways. Deletion analysis of this conserved region implicates it in selective peroxisome degradation. In the majority of members this region is situated at the N terminus of the protein [, ].; GO: 0005777 peroxisome, 0016020 membrane; PDB: 2W85_A 2W84_A 3FF5_B.
Probab=64.01 E-value=18 Score=30.73 Aligned_cols=45 Identities=22% Similarity=0.150 Sum_probs=33.4
Q ss_pred HHHHHHHHHHhh---ccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCC
Q 023264 211 DAENLAVKLLAT---RAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRG 255 (285)
Q Consensus 211 kA~~~AL~lLS~---RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~G 255 (285)
...+.|.++|.. +.-+..+=+..|+.||.++++|++++.+.....
T Consensus 4 ~li~~A~~FL~~p~V~~sp~~~k~~FL~sKGLt~~EI~~al~~a~~~~ 51 (136)
T PF04695_consen 4 DLIEQAVKFLQDPKVRNSPLEKKIAFLESKGLTEEEIDEALGRAGSPP 51 (136)
T ss_dssp HHHHHHHHHHCTTTCCCS-HHHHHHHHHHCT--HHHHHHHHHHHT--S
T ss_pred HHHHHHHHHhCCcccccCCHHHHHHHHHcCCCCHHHHHHHHHhcCCcc
Confidence 346788889864 667788888999999999999999999976654
No 36
>COG1695 Predicted transcriptional regulators [Transcription]
Probab=63.92 E-value=9.1 Score=31.58 Aligned_cols=47 Identities=23% Similarity=0.318 Sum_probs=41.3
Q ss_pred HHHHHHHHhhccccHHHHHHHHhcCCC-----CHHHHHHHHHHHHHCCCCCH
Q 023264 213 ENLAVKLLATRAFTAVEMRKKLNGKKF-----PSHVIEAVITDFQSRGLIND 259 (285)
Q Consensus 213 ~~~AL~lLS~RdrS~~ELr~KL~~Kg~-----~ee~Ie~VIerLee~GyLDD 259 (285)
.-.+|.+|+.++.+-.||.+.+..... ++..|-.+|.+|++.|||+-
T Consensus 11 ~~~iL~~L~~~~~~Gyei~k~~~~~~~~~~~~s~gtiYp~L~~Le~~Gli~~ 62 (138)
T COG1695 11 ELLILSLLSEKPSHGYEIIKELEELSGGLWEPSPGTIYPLLKRLEKEGLIES 62 (138)
T ss_pred HHHHHHHHhcCCchHHHHHHHHHHHcCCCCcCCCCcHHHHHHHHHHCCCeEE
Confidence 356788999999999999999998744 68899999999999999974
No 37
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=63.53 E-value=21 Score=26.79 Aligned_cols=40 Identities=18% Similarity=0.387 Sum_probs=34.2
Q ss_pred HHHHHhhc--cccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCC
Q 023264 216 AVKLLATR--AFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 216 AL~lLS~R--drS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLD 258 (285)
.+.+|+.. ..|..||.+.| |++...+...|..|++.|||.
T Consensus 10 Il~~l~~~~~~~t~~~ia~~l---~i~~~tv~r~l~~L~~~g~l~ 51 (91)
T smart00346 10 VLRALAEEPGGLTLAELAERL---GLSKSTAHRLLNTLQELGYVE 51 (91)
T ss_pred HHHHHHhCCCCcCHHHHHHHh---CCCHHHHHHHHHHHHHCCCee
Confidence 34566654 68999999998 799999999999999999995
No 38
>PF10390 ELL: RNA polymerase II elongation factor ELL ; InterPro: IPR019464 ELL is a family of RNA polymerase II elongation factors. It is bound stably to elongation-associated factors 1 and 2, EAFs, and together these act as a strong regulator of transcription activity. by direct interaction with Pol II. ELL binds to pol II on its own but the affinity is greatly increased by the cooperation of EAF []. Some members carry an occludin domain (IPR010844 from INTERPRO) just downstream. There is no Saccharomyces cerevisiae (Baker's yeast) member. ; GO: 0006368 transcription elongation from RNA polymerase II promoter, 0008023 transcription elongation factor complex; PDB: 2E5N_A 2DOA_A.
Probab=61.06 E-value=5.1 Score=38.12 Aligned_cols=52 Identities=15% Similarity=0.211 Sum_probs=41.2
Q ss_pred HHHHHHHHHHHhhccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCC-HHH
Q 023264 210 QDAENLAVKLLATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN-DSL 261 (285)
Q Consensus 210 ~kA~~~AL~lLS~RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLD-D~r 261 (285)
.-.+++.+++|+-++++..||..+|.+.|..+...+.+=.-|++-+-+| |..
T Consensus 197 rplReRvIHLLALkpykK~ELl~rL~~dg~~~~dk~~l~~iL~~Va~l~~~~~ 249 (284)
T PF10390_consen 197 RPLRERVIHLLALKPYKKPELLLRLQKDGLSPKDKDELDSILQEVANLNKDNS 249 (284)
T ss_dssp S-HHHHHHHHHHHS-EEHHHHHHHHHHH---HHHHHHHHHHHHHCCEEETTTE
T ss_pred ccccccchhhhhcCccccHHHHHHHHhcCCChHHHHHHHHHHHHHhccCcCCe
Confidence 3457899999999999999999999999999998888888888888887 443
No 39
>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family. Members of this protein family are putative transcriptional regulators of the PadR family, as found in species of the Acidobacteria. This family of proteins has expanded greatly in this lineage, and where it regularly is found in the vicinity of a putative transporter protein
Probab=60.99 E-value=13 Score=29.60 Aligned_cols=44 Identities=14% Similarity=0.276 Sum_probs=38.7
Q ss_pred HHHHHHhhccccHHHHHHHHhcC-----CCCHHHHHHHHHHHHHCCCCC
Q 023264 215 LAVKLLATRAFTAVEMRKKLNGK-----KFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 215 ~AL~lLS~RdrS~~ELr~KL~~K-----g~~ee~Ie~VIerLee~GyLD 258 (285)
..|.+|+..+.+=.||.+.|.+. ..++..|-.+|.+|++.|||.
T Consensus 8 ~iL~~L~~~~~~GYei~~~l~~~~~~~~~i~~gtlY~~L~rLe~~GlI~ 56 (100)
T TIGR03433 8 LILKTLSLGPLHGYGIAQRIQQISEDVLQVEEGSLYPALHRLERRGWIA 56 (100)
T ss_pred HHHHHHhcCCCCHHHHHHHHHHHcCCccccCCCcHHHHHHHHHHCCCeE
Confidence 46778888999999999999775 478889999999999999994
No 40
>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea. Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....
Probab=60.02 E-value=13 Score=29.98 Aligned_cols=36 Identities=11% Similarity=0.332 Sum_probs=30.7
Q ss_pred ccccHHHHHHHHhcC-CCCHHHHHHHHHHHHHCCCCC
Q 023264 223 RAFTAVEMRKKLNGK-KFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 223 RdrS~~ELr~KL~~K-g~~ee~Ie~VIerLee~GyLD 258 (285)
-.-|..|+.+.|.+. +.....|..+|.+|.+.|||.
T Consensus 16 ~~~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~ 52 (115)
T PF03965_consen 16 GEATVREIHEALPEERSWAYSTVQTLLNRLVEKGFLT 52 (115)
T ss_dssp SSEEHHHHHHHHCTTSS--HHHHHHHHHHHHHTTSEE
T ss_pred CCCCHHHHHHHHHhccccchhHHHHHHHHHHhCCcee
Confidence 348999999999987 889999999999999999874
No 41
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=59.97 E-value=30 Score=27.82 Aligned_cols=46 Identities=24% Similarity=0.285 Sum_probs=35.0
Q ss_pred HHHHHHHHhh--ccccHHHHHHHHhcCC--CCHHHHHHHHHHHHHCCCCC
Q 023264 213 ENLAVKLLAT--RAFTAVEMRKKLNGKK--FPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 213 ~~~AL~lLS~--RdrS~~ELr~KL~~Kg--~~ee~Ie~VIerLee~GyLD 258 (285)
+...|.+|.. ...|..||.+.|++++ ++...|-.+|+.|.+.|+|.
T Consensus 10 R~~Il~~l~~~~~~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~ 59 (120)
T PF01475_consen 10 RLAILELLKESPEHLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIR 59 (120)
T ss_dssp HHHHHHHHHHHSSSEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHcCCCCCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEE
Confidence 3444444443 3789999999999875 66789999999999999984
No 42
>TIGR00122 birA_repr_reg BirA biotin operon repressor domain. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.
Probab=58.85 E-value=31 Score=25.22 Aligned_cols=39 Identities=18% Similarity=0.334 Sum_probs=34.3
Q ss_pred HHHHHhhccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCC
Q 023264 216 AVKLLATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLI 257 (285)
Q Consensus 216 AL~lLS~RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyL 257 (285)
.+..|+....|..||.+.| |++...|...+..|++.|+.
T Consensus 5 il~~L~~~~~~~~eLa~~l---~vS~~tv~~~l~~L~~~g~~ 43 (69)
T TIGR00122 5 LLALLADNPFSGEKLGEAL---GMSRTAVNKHIQTLREWGVD 43 (69)
T ss_pred HHHHHHcCCcCHHHHHHHH---CCCHHHHHHHHHHHHHCCCe
Confidence 4556778888999999988 79999999999999999994
No 43
>PF09106 SelB-wing_2: Elongation factor SelB, winged helix ; InterPro: IPR015190 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []. Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 2". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0005525 GTP binding, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2V9V_A 1LVA_A 2PLY_A 2UWM_A.
Probab=58.81 E-value=7.6 Score=28.09 Aligned_cols=35 Identities=17% Similarity=0.429 Sum_probs=29.3
Q ss_pred ccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCC
Q 023264 223 RAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLI 257 (285)
Q Consensus 223 RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyL 257 (285)
...+..||+.+|...++++...+.+|+.|.+.|.|
T Consensus 16 ~G~~keeLrsrl~~~~l~~k~~~~ll~~l~~~g~l 50 (59)
T PF09106_consen 16 PGMPKEELRSRLFKPRLPPKLFNALLEALVAEGRL 50 (59)
T ss_dssp S-EEHHHHHHHCST-TS-HCCHHHHHHHHHHTTSE
T ss_pred cCcCHHHHHHHHhhccCCHHHHHHHHHHHHHCCCe
Confidence 45678999999998789999999999999999976
No 44
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=58.80 E-value=23 Score=28.69 Aligned_cols=40 Identities=18% Similarity=0.330 Sum_probs=32.8
Q ss_pred HHHHHhhc----cccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCC
Q 023264 216 AVKLLATR----AFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 216 AL~lLS~R----drS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLD 258 (285)
++-+|+.. ..|..||.+.| +.+...+..++..|...|||.
T Consensus 13 ~l~~la~~~~~~~~s~~eia~~~---~i~~~~v~~il~~L~~~gli~ 56 (132)
T TIGR00738 13 ALLDLALNPDEGPVSVKEIAERQ---GISRSYLEKILRTLRRAGLVE 56 (132)
T ss_pred HHHHHHhCCCCCcCcHHHHHHHH---CcCHHHHHHHHHHHHHCCcEE
Confidence 44455543 67999998887 489999999999999999995
No 45
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=58.54 E-value=42 Score=25.53 Aligned_cols=31 Identities=16% Similarity=0.447 Sum_probs=27.0
Q ss_pred ccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCC
Q 023264 225 FTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 225 rS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLD 258 (285)
.|..||.+.+ +.++..+..++..|++.|||.
T Consensus 26 ~s~~eiA~~~---~i~~~~l~kil~~L~~~Gli~ 56 (83)
T PF02082_consen 26 VSSKEIAERL---GISPSYLRKILQKLKKAGLIE 56 (83)
T ss_dssp BEHHHHHHHH---TS-HHHHHHHHHHHHHTTSEE
T ss_pred CCHHHHHHHH---CcCHHHHHHHHHHHhhCCeeE
Confidence 6899999976 589999999999999999984
No 46
>PF08312 cwf21: cwf21 domain; InterPro: IPR013170 The cwf21 domain is found in proteins involved in mRNA splicing. Proteins containing this domain have been isolated as a subcomplex of the splicosome in Schizosaccharomyces pombe (Fission yeast) []. In yeast, this domain binds the protein Prp8p [], a large and highly conserved U5 snRNP protein which has been proposed as a protein cofactor at the spliceosomal catalytic centre []. The cwf21 domain is found in, amongst others, the small Cwc21p protein in yeast as well as in the much larger human ortholog SRm300 (serine/arginine repetitive matrix protein). ; PDB: 2E62_A.
Probab=58.21 E-value=13 Score=26.58 Aligned_cols=27 Identities=19% Similarity=0.484 Sum_probs=21.5
Q ss_pred HHHHHHHHhcCCCCHHHHHHHHHHHHH
Q 023264 227 AVEMRKKLNGKKFPSHVIEAVITDFQS 253 (285)
Q Consensus 227 ~~ELr~KL~~Kg~~ee~Ie~VIerLee 253 (285)
..|++++|...|++++.|+.-|+.+..
T Consensus 13 ~~elrd~LEe~g~~~eeIe~kv~~~R~ 39 (46)
T PF08312_consen 13 CLELRDELEEQGYSEEEIEEKVDELRK 39 (46)
T ss_dssp HHHHHHHHHHHT--HHHHHHHHHHHHH
T ss_pred HHHHHHHHHhCCCCHHHHHHHHHHHHH
Confidence 358899999999999999999988764
No 47
>PRK09462 fur ferric uptake regulator; Provisional
Probab=57.47 E-value=31 Score=29.07 Aligned_cols=46 Identities=15% Similarity=0.277 Sum_probs=37.8
Q ss_pred HHHHHHHHhh---ccccHHHHHHHHhcCC--CCHHHHHHHHHHHHHCCCCC
Q 023264 213 ENLAVKLLAT---RAFTAVEMRKKLNGKK--FPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 213 ~~~AL~lLS~---RdrS~~ELr~KL~~Kg--~~ee~Ie~VIerLee~GyLD 258 (285)
+...|.+|.. ..-|..||.++|++.+ ++...|-.+|+.|.+.|+|.
T Consensus 19 R~~Il~~l~~~~~~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~Gli~ 69 (148)
T PRK09462 19 RLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVT 69 (148)
T ss_pred HHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCCEE
Confidence 4555666642 5789999999999875 57899999999999999994
No 48
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=57.38 E-value=24 Score=28.84 Aligned_cols=39 Identities=13% Similarity=0.393 Sum_probs=32.3
Q ss_pred HHHHhhc---cccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCC
Q 023264 217 VKLLATR---AFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 217 L~lLS~R---drS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLD 258 (285)
|.+|+.. ..|..||.++| |+++..+..++..|++.|+|.
T Consensus 15 l~~la~~~~~~~s~~eia~~l---~is~~~v~~~l~~L~~~Gli~ 56 (130)
T TIGR02944 15 LTTLAQNDSQPYSAAEIAEQT---GLNAPTVSKILKQLSLAGIVT 56 (130)
T ss_pred HHHHHhCCCCCccHHHHHHHH---CcCHHHHHHHHHHHHHCCcEE
Confidence 4466654 35899998887 589999999999999999995
No 49
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=56.89 E-value=33 Score=28.75 Aligned_cols=38 Identities=13% Similarity=0.292 Sum_probs=33.0
Q ss_pred hhccccHHHHHHHHhc-CCCCHHHHHHHHHHHHHCCCCC
Q 023264 221 ATRAFTAVEMRKKLNG-KKFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 221 S~RdrS~~ELr~KL~~-Kg~~ee~Ie~VIerLee~GyLD 258 (285)
..-+-|..||.+.|.+ ++.....|..+|.+|.+.|||.
T Consensus 15 ~~~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~KG~v~ 53 (130)
T TIGR02698 15 TLGETTSRDIIRILAEKKDWSDSTIKTLLGRLVDKGCLT 53 (130)
T ss_pred cCCCCCHHHHHHHHhhccCCcHHHHHHHHHHHHHCCcee
Confidence 3456799999999954 5789999999999999999996
No 50
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=55.60 E-value=27 Score=26.64 Aligned_cols=45 Identities=13% Similarity=0.267 Sum_probs=36.7
Q ss_pred HHHHHHHHHHhhccccH-HHHHHHHhcCCCCHHHHHHHHHHHHHCCCCC
Q 023264 211 DAENLAVKLLATRAFTA-VEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 211 kA~~~AL~lLS~RdrS~-~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLD 258 (285)
..--..|..|...+-.. .||.++|. ++...+..+|++|++.|||.
T Consensus 22 ~~q~~~L~~l~~~~~~~~~~la~~l~---i~~~~vt~~l~~Le~~glv~ 67 (126)
T COG1846 22 PPQYQVLLALYEAGGITVKELAERLG---LDRSTVTRLLKRLEDKGLIE 67 (126)
T ss_pred HHHHHHHHHHHHhCCCcHHHHHHHHC---CCHHHHHHHHHHHHHCCCee
Confidence 34456677778777777 88888875 89999999999999999983
No 51
>PRK03430 hypothetical protein; Validated
Probab=55.17 E-value=14 Score=32.66 Aligned_cols=34 Identities=9% Similarity=0.103 Sum_probs=29.8
Q ss_pred cHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCCH
Q 023264 226 TAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIND 259 (285)
Q Consensus 226 S~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLDD 259 (285)
-..+|.++|.+-||+++.|.+++++|+.+.=+.+
T Consensus 22 d~~~L~~~L~~aGF~~~eI~~AL~WLe~L~~~~~ 55 (157)
T PRK03430 22 DQDKLEDDLTDAGFHREDIYNALLWLEKLADLQE 55 (157)
T ss_pred CHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcc
Confidence 3688999999999999999999999999864444
No 52
>PF04361 DUF494: Protein of unknown function (DUF494); InterPro: IPR007456 Members of this family of uncharacterised proteins are often named Smg.
Probab=53.93 E-value=17 Score=31.85 Aligned_cols=33 Identities=9% Similarity=0.212 Sum_probs=29.6
Q ss_pred cHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCC
Q 023264 226 TAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 226 S~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLD 258 (285)
...+|.++|.+-||+++.|.+++++|....-+.
T Consensus 22 d~~~L~~~L~~aGF~~~eI~~Al~WL~~L~~~~ 54 (155)
T PF04361_consen 22 DQDDLTRELSAAGFEDEEINKALDWLEGLAELQ 54 (155)
T ss_pred CHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcc
Confidence 488999999999999999999999999776554
No 53
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=53.93 E-value=35 Score=25.32 Aligned_cols=42 Identities=21% Similarity=0.453 Sum_probs=32.8
Q ss_pred HHHHHHHhh-ccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCC
Q 023264 214 NLAVKLLAT-RAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 214 ~~AL~lLS~-RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLD 258 (285)
-.+|.+|.. ..-|..+|.+.+ +++...|..+|.+|++.|||-
T Consensus 13 ~~il~~l~~~~~~~~~~la~~~---~~s~~~i~~~l~~L~~~g~v~ 55 (101)
T smart00347 13 FLVLRILYEEGPLSVSELAKRL---GVSPSTVTRVLDRLEKKGLIR 55 (101)
T ss_pred HHHHHHHHHcCCcCHHHHHHHH---CCCchhHHHHHHHHHHCCCeE
Confidence 344555543 346888998876 588999999999999999994
No 54
>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY. This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.
Probab=53.85 E-value=70 Score=30.56 Aligned_cols=48 Identities=19% Similarity=0.364 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHHHhhc-----------------cccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCC
Q 023264 208 ARQDAENLAVKLLATR-----------------AFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 208 ~~~kA~~~AL~lLS~R-----------------drS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLD 258 (285)
-.+.+-+.|+.-|||. --|..+|.+++ |.+...|-+++.+|++.|+|.
T Consensus 165 Rkka~Vq~Ai~tLSySEleAv~~IL~~L~~~egrlse~eLAerl---GVSRs~ireAlrkLE~aGvIe 229 (251)
T TIGR02787 165 RKKAAVQMAINTLSYSELEAVEHIFEELDGNEGLLVASKIADRV---GITRSVIVNALRKLESAGVIE 229 (251)
T ss_pred HHHHHHHHHHHhccHhHHHHHHHHHHHhccccccccHHHHHHHH---CCCHHHHHHHHHHHHHCCCEE
Confidence 3456778888888877 22444444443 789999999999999999985
No 55
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=53.76 E-value=51 Score=29.05 Aligned_cols=31 Identities=19% Similarity=0.275 Sum_probs=28.6
Q ss_pred cHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCC
Q 023264 226 TAVEMRKKLNGKKFPSHVIEAVITDFQSRGLI 257 (285)
Q Consensus 226 S~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyL 257 (285)
...+|.++|.- +++.+.+..+|+.|++.|+|
T Consensus 41 d~~~iak~l~p-~is~~ev~~sL~~L~~~gli 71 (171)
T PF14394_consen 41 DPEWIAKRLRP-KISAEEVRDSLEFLEKLGLI 71 (171)
T ss_pred CHHHHHHHhcC-CCCHHHHHHHHHHHHHCCCe
Confidence 68999999974 69999999999999999999
No 56
>PF07223 DUF1421: Protein of unknown function (DUF1421); InterPro: IPR010820 This family represents a conserved region approximately 350 residues long within a number of plant proteins of unknown function.
Probab=52.76 E-value=17 Score=36.15 Aligned_cols=35 Identities=11% Similarity=0.186 Sum_probs=31.7
Q ss_pred hccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCC
Q 023264 222 TRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGL 256 (285)
Q Consensus 222 ~RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~Gy 256 (285)
-+-+...||.+|+..-||..|.|..+|.||+|.|=
T Consensus 316 ~~~~p~ddvidKv~~MGf~rDqV~a~v~rl~E~GQ 350 (358)
T PF07223_consen 316 GNRHPYDDVIDKVASMGFRRDQVRATVRRLTENGQ 350 (358)
T ss_pred cccCcHHHHHHHHHHcCCcHHHHHHHHHHHHhcCC
Confidence 35677889999999999999999999999999883
No 57
>PF04433 SWIRM: SWIRM domain; InterPro: IPR007526 The SWIRM domain is a small alpha-helical domain of about 85 amino acid residues found in eukaryotic chromosomal proteins. It is named after the proteins SWI3, RSC8 and MOIRA in which it was first recognised. This domain is predicted to mediate protein-protein interactions in the assembly of chromatin-protein complexes. The SWIRM domain can be linked to different domains, such as the ZZ-type zinc finger (IPR000433 from INTERPRO), the Myb DNA-binding domain (IPR001005 from INTERPRO), the HORMA domain (IPR003511 from INTERPRO), the amino-oxidase domain, the chromo domain (IPR000953 from INTERPRO), and the JAB1/PAD1 domain.; GO: 0005515 protein binding; PDB: 2Z3Y_A 2UXN_A 2Y48_A 2HKO_A 2XAF_A 2X0L_A 2XAJ_A 2UXX_A 2V1D_A 2L3D_A ....
Probab=50.91 E-value=87 Score=24.02 Aligned_cols=49 Identities=18% Similarity=0.214 Sum_probs=34.3
Q ss_pred HHHHHHHHHHHH--H-hhccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCC
Q 023264 208 ARQDAENLAVKL--L-ATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 208 ~~~kA~~~AL~l--L-S~RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLD 258 (285)
.+-..++..+.. . ..+.-|..+.+.-+. |.+...+..|-+.|+..||||
T Consensus 34 ~Yl~iRn~il~~w~~n~~~~lt~~~~~~~i~--~~d~~~~~ri~~FL~~~G~IN 85 (86)
T PF04433_consen 34 QYLKIRNTILAEWRKNPNKYLTKTDARKLIK--GIDVNKIRRIYDFLERWGLIN 85 (86)
T ss_dssp HHHHHHHHHHHHHHHHTTS---HHHHHHHTT--SSSHHHHHHHHHHHHHTTSSS
T ss_pred HHHHHHHHHHHHHHHCCCCcccHHHHHHHcc--ccCHHHHHHHHHHHHHcCccC
Confidence 445555665554 3 355666777766665 789999999999999999998
No 58
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=50.46 E-value=34 Score=22.55 Aligned_cols=33 Identities=15% Similarity=0.301 Sum_probs=29.1
Q ss_pred ccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCC
Q 023264 223 RAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 223 RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLD 258 (285)
..-|..+|.+.| +++...+...|..|.+.|+|.
T Consensus 13 ~~~s~~~l~~~l---~~s~~tv~~~l~~L~~~g~i~ 45 (53)
T smart00420 13 GKVSVEELAELL---GVSEMTIRRDLNKLEEQGLLT 45 (53)
T ss_pred CCcCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEE
Confidence 456888898888 789999999999999999984
No 59
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=50.09 E-value=45 Score=26.00 Aligned_cols=39 Identities=15% Similarity=0.358 Sum_probs=32.0
Q ss_pred HHHHhhc-cccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCC
Q 023264 217 VKLLATR-AFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 217 L~lLS~R-drS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLD 258 (285)
+.+|... ..|..||.+.| |.++..+-..+.+|++.|+|-
T Consensus 9 l~~L~~~~~~~~~~la~~l---~~s~~tv~~~l~~L~~~g~i~ 48 (108)
T smart00344 9 LEELQKDARISLAELAKKV---GLSPSTVHNRVKRLEEEGVIK 48 (108)
T ss_pred HHHHHHhCCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCee
Confidence 3444443 36888998888 899999999999999999987
No 60
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=49.87 E-value=36 Score=28.29 Aligned_cols=40 Identities=18% Similarity=0.298 Sum_probs=32.3
Q ss_pred HHHHHhh----ccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCC
Q 023264 216 AVKLLAT----RAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 216 AL~lLS~----RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLD 258 (285)
|+-+|+. ...|..||.+.+ +.|+..+++++..|.+.|||.
T Consensus 13 ~l~~La~~~~~~~~s~~~ia~~~---~ip~~~l~kil~~L~~~glv~ 56 (135)
T TIGR02010 13 AMLDLALNAETGPVTLADISERQ---GISLSYLEQLFAKLRKAGLVK 56 (135)
T ss_pred HHHHHHhCCCCCcCcHHHHHHHH---CcCHHHHHHHHHHHHHCCceE
Confidence 4456653 246889998876 589999999999999999996
No 61
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=48.14 E-value=56 Score=25.76 Aligned_cols=41 Identities=15% Similarity=0.212 Sum_probs=35.4
Q ss_pred HHHHHHHHhhccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCC
Q 023264 213 ENLAVKLLATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGL 256 (285)
Q Consensus 213 ~~~AL~lLS~RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~Gy 256 (285)
....+.+++....|=.+|.+.| |++..+|.+.|+.|++.|+
T Consensus 8 ~~~ll~~~~~~~~SGe~La~~L---giSRtaVwK~Iq~Lr~~G~ 48 (79)
T COG1654 8 LLLLLLLLTGNFVSGEKLAEEL---GISRTAVWKHIQQLREEGV 48 (79)
T ss_pred HHHHHHHcCCCcccHHHHHHHH---CccHHHHHHHHHHHHHhCC
Confidence 3456667788889999999887 6999999999999999997
No 62
>PF06180 CbiK: Cobalt chelatase (CbiK); InterPro: IPR010388 This group, typified by Salmonella typhimurium CbiK, contains anaerobic cobalt chelatases that act in the anaerobic cobalamin biosynthesis pathway [, ]. Cobalamin (vitamin B12) can be complexed with metal via ATP-dependent reactions (aerobic pathway) (e.g., in Pseudomonas denitrificans) or via ATP-independent reactions (anaerobic pathway) (e.g., in S. typhimurium) [, ]. The corresponding cobalt chelatases are not homologous. This group belongs to the class of ATP-independent, single-subunit chelatases that also includes distantly related protoporphyrin IX (PPIX) ferrochelatase (HemH) (Class II chelatases) []. The structure of S. typhimurium CbiK shows that it has a remarkably similar topology to Bacillus subtilis ferrochelatase despite only weak sequence conservation []. Both enzymes contain a histidine residue identified as the metal ion ligand, but CbiK contains a second histidine in place of the glutamic acid residue identified as a general base in PPIX ferrochelatase []. Site-directed mutagenesis has confirmed a role for this histidine and a nearby glutamic acid in cobalt binding, modulating metal ion specificity as well as catalytic efficiency []. It should be noted that CysG and Met8p, which are multifunctional proteins associated with siroheme biosynthesis, include chelatase activity and can therefore be considered as the third class of chelatases []. As with the class II chelatases, they do not require ATP for activity. However, they are not structurally similar to HemH or CbiK, and it is likely that they have arisen by the acquisition of a chelatase function within a dehydrogenase catalytic framework [, ].; GO: 0016852 sirohydrochlorin cobaltochelatase activity; PDB: 1QGO_A 2XWP_A 2XVZ_A 2XVX_A 2XVY_A.
Probab=47.18 E-value=20 Score=33.92 Aligned_cols=39 Identities=26% Similarity=0.342 Sum_probs=29.3
Q ss_pred HHHhhccccHHHHHHHHhcC-CCCHHHHHHHHHHHHHCCC
Q 023264 218 KLLATRAFTAVEMRKKLNGK-KFPSHVIEAVITDFQSRGL 256 (285)
Q Consensus 218 ~lLS~RdrS~~ELr~KL~~K-g~~ee~Ie~VIerLee~Gy 256 (285)
.+--++.+|+.=+++||+++ |+.-+...++|++|.+.||
T Consensus 33 ~~~V~~AfTS~~I~~kl~~~~g~~i~~~~eaL~~L~~~G~ 72 (262)
T PF06180_consen 33 DYDVRRAFTSRIIRKKLAERDGIKIDSPEEALAKLADEGY 72 (262)
T ss_dssp TSEEEEEES-HHHHHHHHHCHT-----HHHHHHHHHHCT-
T ss_pred CCcEEEEchHHHHHHHHHhcCCCCcCCHHHHHHHHHHCCC
Confidence 36678999999999999999 8888999999999999987
No 63
>TIGR02719 repress_PhaQ poly-beta-hydroxybutyrate-responsive repressor. Members of this family are transcriptional regulatory proteins found in the vicinity of poly-beta-hydroxybutyrate (PHB) operons in several species of Bacillus. This protein appears to have repressor activity modulated by PHB itself. This protein belongs to the larger PadR family (see pfam03551).
Probab=47.13 E-value=33 Score=29.65 Aligned_cols=47 Identities=9% Similarity=0.064 Sum_probs=40.7
Q ss_pred HHHHHHHHHhhccccHHHHHHHHhcCC---CCHHHHHHHHHHHHHCCCCC
Q 023264 212 AENLAVKLLATRAFTAVEMRKKLNGKK---FPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 212 A~~~AL~lLS~RdrS~~ELr~KL~~Kg---~~ee~Ie~VIerLee~GyLD 258 (285)
..-..|.+|+..+..=.||.+.|.+.| .++..+-.+|.+|++.|||-
T Consensus 25 l~~~IL~~L~~~p~hGYeI~q~l~~~g~~~v~~GtLYp~L~RLE~~GlI~ 74 (138)
T TIGR02719 25 LVPFLLLCLKDWNLHGYKLIQMLMDFGFSSVDQGNVYRTLRKLEKDNLIS 74 (138)
T ss_pred HHHHHHHHHccCCCCHHHHHHHHHHcCCCCCCcChHHHHHHHHHHCCCEE
Confidence 334578889999999999999999875 46788999999999999996
No 64
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=46.97 E-value=43 Score=27.57 Aligned_cols=41 Identities=10% Similarity=0.310 Sum_probs=33.3
Q ss_pred HHHHHHhhc--cccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCC
Q 023264 215 LAVKLLATR--AFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 215 ~AL~lLS~R--drS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLD 258 (285)
.+|..|... ..|..||.+.|. ++...|-.+|++|++.|||-
T Consensus 35 ~vL~~l~~~~~~~t~~eLa~~l~---~~~~tvt~~v~~Le~~GlV~ 77 (144)
T PRK03573 35 VTLHNIHQLPPEQSQIQLAKAIG---IEQPSLVRTLDQLEEKGLIS 77 (144)
T ss_pred HHHHHHHHcCCCCCHHHHHHHhC---CChhhHHHHHHHHHHCCCEe
Confidence 456677653 358889988874 89999999999999999983
No 65
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=45.76 E-value=52 Score=29.08 Aligned_cols=42 Identities=19% Similarity=0.338 Sum_probs=35.1
Q ss_pred HHHHHHH-hhccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCC
Q 023264 214 NLAVKLL-ATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 214 ~~AL~lL-S~RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLD 258 (285)
...|.+| .....|..||.+.| |++...|-..|+.|++.|||.
T Consensus 4 ~~IL~~L~~~~~~t~~eLA~~l---gis~~tV~~~L~~Le~~GlV~ 46 (203)
T TIGR02702 4 EDILSYLLKQGQATAAALAEAL---AISPQAVRRHLKDLETEGLIE 46 (203)
T ss_pred HHHHHHHHHcCCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCeE
Confidence 3445555 45678999999999 799999999999999999994
No 66
>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=45.50 E-value=1.1e+02 Score=26.89 Aligned_cols=69 Identities=9% Similarity=0.034 Sum_probs=46.9
Q ss_pred CCCCHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHHhcCCCCHHHHHHHHHHHHH
Q 023264 183 FEEPQEVAEEMKILQQKDFYLQAAKARQDAENLAVKLLATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQS 253 (285)
Q Consensus 183 ~ELdee~leeI~~~~q~~~~eq~~~~~~kA~~~AL~lLS~RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee 253 (285)
..+|++++..+...-..+. +.-...-.|....+.--++.+-+..++.+-|.+-|+|++.++.+..-+.+
T Consensus 20 ~~~~~~~~~kl~~~~~~~~--~~lk~~va~l~fiL~~A~k~n~~~~~l~~eL~~lglp~e~~~~l~~~~~~ 88 (174)
T cd04752 20 EGIDYEKVLKLTADAKFES--GDVKASIAVLSFILSSAAKYNVDGESLSSELQQLGLPKEHATSLCRSYEE 88 (174)
T ss_pred ccCCHHHHHHHHHHhCCCH--hhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 6688888888873221111 11122333444445555789999999999999999999999988876654
No 67
>PF03979 Sigma70_r1_1: Sigma-70 factor, region 1.1; InterPro: IPR007127 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 [, ]. This entry represents Region 1.1 which modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase [, ]. Region 1.1 is also involved in promoter binding.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2K6X_A.
Probab=44.62 E-value=29 Score=26.76 Aligned_cols=34 Identities=15% Similarity=0.293 Sum_probs=24.2
Q ss_pred ccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCC
Q 023264 223 RAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGL 256 (285)
Q Consensus 223 RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~Gy 256 (285)
.--|..||...|-...++++.|+.++..|.+.|.
T Consensus 20 G~lT~~eI~~~L~~~~~~~e~id~i~~~L~~~gI 53 (82)
T PF03979_consen 20 GYLTYDEINDALPEDDLDPEQIDEIYDTLEDEGI 53 (82)
T ss_dssp SS-BHHHHHHH-S-S---HHHHHHHHHHHHTT--
T ss_pred CcCCHHHHHHHcCccCCCHHHHHHHHHHHHHCCC
Confidence 4478899999999999999999999999999985
No 68
>PF08461 HTH_12: Ribonuclease R winged-helix domain; InterPro: IPR013668 This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaea.
Probab=44.45 E-value=56 Score=24.46 Aligned_cols=41 Identities=7% Similarity=0.131 Sum_probs=34.1
Q ss_pred hccccHHHHHHHHhcCCCC--HHHHHHHHHHHHHCCCCCHHHH
Q 023264 222 TRAFTAVEMRKKLNGKKFP--SHVIEAVITDFQSRGLINDSLY 262 (285)
Q Consensus 222 ~RdrS~~ELr~KL~~Kg~~--ee~Ie~VIerLee~GyLDD~rY 262 (285)
..+-+..+|.+.|...|++ +++|-.-+..|++.||+.=..|
T Consensus 11 ~~P~g~~~l~~~L~~~g~~~se~avRrrLr~me~~Glt~~~g~ 53 (66)
T PF08461_consen 11 DKPLGRKQLAEELKLRGEELSEEAVRRRLRAMERDGLTRKVGR 53 (66)
T ss_pred CCCCCHHHHHHHHHhcChhhhHHHHHHHHHHHHHCCCccccCC
Confidence 3567999999999998876 5999999999999997754333
No 69
>COG2511 GatE Archaeal Glu-tRNAGln amidotransferase subunit E (contains GAD domain) [Translation, ribosomal structure and biogenesis]
Probab=43.98 E-value=98 Score=32.89 Aligned_cols=72 Identities=24% Similarity=0.237 Sum_probs=54.9
Q ss_pred CCCCcCCCCHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHhh-ccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCC
Q 023264 178 EESEVFEEPQEVAEEMKILQQKDFYLQAAKARQDAENLAVKLLAT-RAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRG 255 (285)
Q Consensus 178 kG~~~~ELdee~leeI~~~~q~~~~eq~~~~~~kA~~~AL~lLS~-RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~G 255 (285)
+|++...|+++.+.++.. ... ..+..+.+.+-+|..|+. -..+..|+..+|.=..++++.|+.+|+.+.+.+
T Consensus 513 eg~~i~~l~~~~i~~~~~-----~~~-~g~iake~iee~l~~l~~~p~~~~~e~~~~~gL~~ls~eEve~iI~eii~~~ 585 (631)
T COG2511 513 EGVEIDNLDDEHIEELLR-----LVS-EGKIAKEAIEEILKALAENPGKDAAEIAEKLGLKELSEEEVEKIIDEIIESN 585 (631)
T ss_pred cCCccccCCHHHHHHHHH-----HHh-cccchHHHHHHHHHHHHhCCCCCHHHHHHHhccccCCHHHHHHHHHHHHHhh
Confidence 344445678898888872 111 124557788889999887 667899999999888999999999999998765
No 70
>cd00052 EH Eps15 homology domain; found in proteins implicated in endocytosis, vesicle transport, and signal transduction. The alignment contains a pair of EF-hand motifs, typically one of them is canonical and binds to Ca2+, while the other may not bind to Ca2+. A hydrophobic binding pocket is formed by residues from both EF-hand motifs. The EH domain binds to proteins containing NPF (class I), [WF]W or SWG (class II), or H[TS]F (class III) sequence motifs.
Probab=43.64 E-value=69 Score=22.12 Aligned_cols=44 Identities=16% Similarity=0.222 Sum_probs=35.0
Q ss_pred ccHHHHHHHHhcCCCCHHHHHHHHHHHHH--CCCCCHHHHHHHHHH
Q 023264 225 FTAVEMRKKLNGKKFPSHVIEAVITDFQS--RGLINDSLYAESYSR 268 (285)
Q Consensus 225 rS~~ELr~KL~~Kg~~ee~Ie~VIerLee--~GyLDD~rYAesyVr 268 (285)
-|..|+..-|...|++++.++.++..+.. .|.|+=.+|...+..
T Consensus 16 i~~~el~~~l~~~g~~~~~~~~i~~~~d~~~~g~i~~~ef~~~~~~ 61 (67)
T cd00052 16 ISGDEARPFLGKSGLPRSVLAQIWDLADTDKDGKLDKEEFAIAMHL 61 (67)
T ss_pred CcHHHHHHHHHHcCCCHHHHHHHHHHhcCCCCCcCCHHHHHHHHHH
Confidence 47778888888888999999999988864 588998888766543
No 71
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=41.93 E-value=44 Score=24.05 Aligned_cols=31 Identities=13% Similarity=0.334 Sum_probs=24.7
Q ss_pred ccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCC
Q 023264 225 FTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 225 rS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLD 258 (285)
-|+.+|.+.+ |++...+.+++..|++.|+|.
T Consensus 25 ps~~~la~~~---~vsr~tvr~al~~L~~~g~i~ 55 (64)
T PF00392_consen 25 PSERELAERY---GVSRTTVREALRRLEAEGLIE 55 (64)
T ss_dssp --HHHHHHHH---TS-HHHHHHHHHHHHHTTSEE
T ss_pred CCHHHHHHHh---ccCCcHHHHHHHHHHHCCcEE
Confidence 3888888776 589999999999999999973
No 72
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=41.88 E-value=54 Score=21.41 Aligned_cols=31 Identities=19% Similarity=0.401 Sum_probs=25.8
Q ss_pred ccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCC
Q 023264 225 FTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 225 rS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLD 258 (285)
.|..||.+.| |.+...+..+|..|++.|+|.
T Consensus 9 ~s~~~la~~l---~~s~~tv~~~l~~L~~~g~l~ 39 (48)
T smart00419 9 LTRQEIAELL---GLTRETVSRTLKRLEKEGLIS 39 (48)
T ss_pred cCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEE
Confidence 4666777766 578999999999999999985
No 73
>KOG4796 consensus RNA polymerase II elongation factor [Transcription]
Probab=41.72 E-value=39 Score=35.62 Aligned_cols=43 Identities=19% Similarity=0.308 Sum_probs=38.8
Q ss_pred HHHHHHHHHHhhccccHHHHHHHHhcCCCCHHHHHHHHHHHHH
Q 023264 211 DAENLAVKLLATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQS 253 (285)
Q Consensus 211 kA~~~AL~lLS~RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee 253 (285)
-.+++.++||+-+.|...||..+|+.-|++++.++.+=.-|++
T Consensus 211 ~ir~RviHLlalk~ykk~El~~rLk~dGl~~~e~~~i~~il~~ 253 (604)
T KOG4796|consen 211 PIRDRVIHLLALKAYKKPELLARLKKDGLPQEEKNKIRSILQQ 253 (604)
T ss_pred chHHHHHHHHHhhhcccHHHHHHHhhcCCcHHHHHHHHHHHHh
Confidence 4578999999999999999999999999999998888777776
No 74
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=41.50 E-value=61 Score=26.81 Aligned_cols=41 Identities=15% Similarity=0.276 Sum_probs=32.5
Q ss_pred HHHHHHhhc-cccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCC
Q 023264 215 LAVKLLATR-AFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 215 ~AL~lLS~R-drS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLD 258 (285)
.+|..|... .-|..||.+.| +++...+-.+|++|++.|||-
T Consensus 44 ~vL~~l~~~~~~t~~eLa~~l---~i~~~tvsr~l~~Le~~GlI~ 85 (144)
T PRK11512 44 KVLCSIRCAACITPVELKKVL---SVDLGALTRMLDRLVCKGWVE 85 (144)
T ss_pred HHHHHHHHcCCCCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEE
Confidence 344455443 46889999887 489999999999999999984
No 75
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=41.33 E-value=57 Score=23.45 Aligned_cols=41 Identities=22% Similarity=0.327 Sum_probs=26.0
Q ss_pred HHHHHhhccccHHHHHHHHhcC-CCCHH----HHHHHHHHHHHCCCC
Q 023264 216 AVKLLATRAFTAVEMRKKLNGK-KFPSH----VIEAVITDFQSRGLI 257 (285)
Q Consensus 216 AL~lLS~RdrS~~ELr~KL~~K-g~~ee----~Ie~VIerLee~GyL 257 (285)
.+.+| ...+|..|+.+.|.++ +.+++ .+...|+.|.+.|+|
T Consensus 22 Iw~~~-~g~~t~~ei~~~l~~~y~~~~~~~~~dv~~fl~~L~~~glI 67 (68)
T PF05402_consen 22 IWELL-DGPRTVEEIVDALAEEYDVDPEEAEEDVEEFLEQLREKGLI 67 (68)
T ss_dssp HHHH---SSS-HHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT--
T ss_pred HHHHc-cCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHCcCc
Confidence 34455 5679999999999965 44543 567788888888876
No 76
>cd03412 CbiK_N Anaerobic cobalamin biosynthetic cobalt chelatase (CbiK), N-terminal domain. CbiK is part of the cobalt-early path for cobalamin biosynthesis. It catalyzes the insertion of cobalt into the oxidized form of precorrin-2, factor II (sirohydrochlorin), the second step of the anaerobic branch of vitamin B12 biosynthesis. CbiK belongs to the class II family of chelatases and is a homomeric enzyme that does not require ATP for its enzymatic activity.
Probab=41.30 E-value=26 Score=29.10 Aligned_cols=35 Identities=26% Similarity=0.384 Sum_probs=32.1
Q ss_pred hccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCC
Q 023264 222 TRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGL 256 (285)
Q Consensus 222 ~RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~Gy 256 (285)
+..+|+.=++++|+++|.....+.++|++|.+.||
T Consensus 36 ~~afts~~i~~~l~~~~~~~p~~~eaL~~l~~~G~ 70 (127)
T cd03412 36 RWAFTSRMIRKKLKKRGIEVDTPEEALAKLAADGY 70 (127)
T ss_pred EEEecHHHHHHHHHhcCCCCCCHHHHHHHHHHCCC
Confidence 56789999999999999999999999999999996
No 77
>PF13801 Metal_resist: Heavy-metal resistance; PDB: 3EPV_C 2Y3D_A 2Y3H_D 2Y3G_B 2Y3B_A 2Y39_A 3LAY_H.
Probab=40.74 E-value=1.6e+02 Score=22.40 Aligned_cols=62 Identities=13% Similarity=0.110 Sum_probs=39.9
Q ss_pred CCCCHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCC
Q 023264 183 FEEPQEVAEEMKILQQKDFYLQAAKARQDAENLAVKLLATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGL 256 (285)
Q Consensus 183 ~ELdee~leeI~~~~q~~~~eq~~~~~~kA~~~AL~lLS~RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~Gy 256 (285)
..||+++..+|.. ...........+-..-...+.||..-|..-.++++.|+.+++++.+..-
T Consensus 40 l~Lt~eQ~~~l~~------------~~~~~~~~~~~~r~~~~~~r~~l~~ll~~~~~D~~~i~a~~~~~~~~~~ 101 (125)
T PF13801_consen 40 LNLTPEQQAKLRA------------LMDEFRQEMRALRQELRAARQELRALLAAPPPDEAAIEALLEEIREAQA 101 (125)
T ss_dssp S-TTHHHHHHHHH------------HHHHHHHHHHHHHHHHHHHHHHHHHHHCCSSS-HHHHHHHHHHHHHHHH
T ss_pred cCCCHHHHHHHHH------------HHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHH
Confidence 4678888887761 1122222333333334456778888898889999999999999887643
No 78
>PF01988 VIT1: VIT family; InterPro: IPR008217 Proteins containing this entry have no known function and are predicted to be integral membrane proteins. They include the Ccc1 protein from Saccharomyces cerevisiae (Baker's yeast) (P47818 from SWISSPROT) that may have a role in regulating calcium levels [].
Probab=40.48 E-value=78 Score=28.41 Aligned_cols=36 Identities=11% Similarity=0.112 Sum_probs=30.9
Q ss_pred HHHhhccccHHHHHHHHhcCCCCHHHHHHHHHHHHH
Q 023264 218 KLLATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQS 253 (285)
Q Consensus 218 ~lLS~RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee 253 (285)
.+-...+.-+.||.+.++++|++++.++.+++.|.+
T Consensus 73 e~~~~pe~e~~el~~iy~~~Gl~~~~a~~i~~~l~~ 108 (213)
T PF01988_consen 73 ELENNPEEEKEELVEIYRAKGLSEEDAEEIAEELSK 108 (213)
T ss_pred HHHhChHhHHHHHHHHHHHCCCCHHHHHHHHHHHHh
Confidence 345567778889999999999999999999999866
No 79
>PRK09416 lstR lineage-specific thermal regulator protein; Provisional
Probab=40.19 E-value=65 Score=27.99 Aligned_cols=49 Identities=14% Similarity=0.160 Sum_probs=41.6
Q ss_pred HHHHHHHHHHHhhccccHHHHHHHHhcCC-----CCHHHHHHHHHHHHHCCCCCH
Q 023264 210 QDAENLAVKLLATRAFTAVEMRKKLNGKK-----FPSHVIEAVITDFQSRGLIND 259 (285)
Q Consensus 210 ~kA~~~AL~lLS~RdrS~~ELr~KL~~Kg-----~~ee~Ie~VIerLee~GyLDD 259 (285)
....-..|.+|+.. .+=.+|.+.|.+.+ .++..|-.+|.+|++.|||.-
T Consensus 42 ~~~~l~IL~lL~~~-~yGYeI~k~I~e~~~g~~~~s~GtIYp~L~RLE~~GlI~s 95 (135)
T PRK09416 42 EDILLAILQLLMNE-KTGYELLQLLRQRGILTFEGNEGSLYTLLHRLEQNRFIQS 95 (135)
T ss_pred ccHHHHHHHHHhCC-CCHHHHHHHHHHhcCCcccCCCccHHHHHHHHHHCCCeEE
Confidence 44566788899988 99999999999864 357899999999999999953
No 80
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=39.97 E-value=56 Score=25.94 Aligned_cols=35 Identities=14% Similarity=0.276 Sum_probs=30.2
Q ss_pred hhccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCC
Q 023264 221 ATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 221 S~RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLD 258 (285)
..++-..++|.++| +.++..|...+..|+++|||.
T Consensus 20 ~~~PVgSk~ia~~l---~~s~aTIRN~M~~Le~lGlve 54 (78)
T PF03444_consen 20 TGEPVGSKTIAEEL---GRSPATIRNEMADLEELGLVE 54 (78)
T ss_pred cCCCcCHHHHHHHH---CCChHHHHHHHHHHHHCCCcc
Confidence 35777888888876 578999999999999999996
No 81
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=39.96 E-value=98 Score=21.39 Aligned_cols=34 Identities=24% Similarity=0.474 Sum_probs=28.7
Q ss_pred hhccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCC
Q 023264 221 ATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLI 257 (285)
Q Consensus 221 S~RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyL 257 (285)
...+.|..||.+++. ++...+-.++.+|++.|||
T Consensus 14 ~~~~~~~~~la~~~~---~~~~~~t~~i~~L~~~g~I 47 (59)
T PF01047_consen 14 ENGGITQSELAEKLG---ISRSTVTRIIKRLEKKGLI 47 (59)
T ss_dssp HHSSEEHHHHHHHHT---S-HHHHHHHHHHHHHTTSE
T ss_pred HcCCCCHHHHHHHHC---CChhHHHHHHHHHHHCCCE
Confidence 445678889998885 7999999999999999998
No 82
>PF07848 PaaX: PaaX-like protein; InterPro: IPR012906 This entry describes the N-terminal region of proteins that are similar to, and nclude, the product of the paaX gene of Escherichia coli (P76086 from SWISSPROT). PaaX is a transcriptional regulator that is always found in association with operons believed to be involved in the degradation of phenylacetic acid []. The gene product has been shown to bind to the promoter sites and repress their transcription []. ; PDB: 3KFW_X 3L09_B.
Probab=39.29 E-value=50 Score=25.23 Aligned_cols=35 Identities=9% Similarity=0.178 Sum_probs=29.5
Q ss_pred cccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCC
Q 023264 224 AFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 224 drS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLD 258 (285)
.-+..+|.+-|..-|+++..+-.+|.+|...|+|.
T Consensus 20 ~i~~~~Li~ll~~~Gv~e~avR~alsRl~~~G~L~ 54 (70)
T PF07848_consen 20 WIWVASLIRLLAAFGVSESAVRTALSRLVRRGWLE 54 (70)
T ss_dssp -EEHHHHHHHHCCTT--HHHHHHHHHHHHHTTSEE
T ss_pred ceeHHHHHHHHHHcCCChHHHHHHHHHHHHcCcee
Confidence 34678999999999999999999999999999984
No 83
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=38.57 E-value=1.6e+02 Score=22.00 Aligned_cols=47 Identities=13% Similarity=0.242 Sum_probs=33.8
Q ss_pred HHHHHHHHHHHhh--ccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCC
Q 023264 210 QDAENLAVKLLAT--RAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 210 ~kA~~~AL~lLS~--RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLD 258 (285)
.+.++....++.. .+=|..||.+.|-=+ +...|..-|..|++.|||.
T Consensus 9 ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~--S~~tv~~~L~~Le~kG~I~ 57 (65)
T PF01726_consen 9 KEVLEFIREYIEENGYPPTVREIAEALGLK--STSTVQRHLKALERKGYIR 57 (65)
T ss_dssp HHHHHHHHHHHHHHSS---HHHHHHHHTSS--SHHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHhCCC--ChHHHHHHHHHHHHCcCcc
Confidence 3445555556654 345889999988643 6999999999999999984
No 84
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=37.71 E-value=74 Score=27.14 Aligned_cols=50 Identities=14% Similarity=0.232 Sum_probs=38.8
Q ss_pred HHHHHHHHhhc--cccHHHHHHHHhcC--CCCHHHHHHHHHHHHHCCCCCHHHH
Q 023264 213 ENLAVKLLATR--AFTAVEMRKKLNGK--KFPSHVIEAVITDFQSRGLINDSLY 262 (285)
Q Consensus 213 ~~~AL~lLS~R--drS~~ELr~KL~~K--g~~ee~Ie~VIerLee~GyLDD~rY 262 (285)
+...|.+|... ..|..||.+.|++. +.+...|-.+|+.|++.|+|.--.+
T Consensus 23 R~~vl~~L~~~~~~~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~~~~ 76 (145)
T COG0735 23 RLAVLELLLEADGHLSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHRLEF 76 (145)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCCCEEEEEe
Confidence 34455566532 38999999999985 5778999999999999999965443
No 85
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=36.81 E-value=80 Score=27.19 Aligned_cols=50 Identities=14% Similarity=0.361 Sum_probs=40.4
Q ss_pred HHHHHHH--hhccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCCHHHHHH
Q 023264 214 NLAVKLL--ATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLINDSLYAE 264 (285)
Q Consensus 214 ~~AL~lL--S~RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLDD~rYAe 264 (285)
...+.|| ..||||..+|..-|.. +|+-..+..+|+.|.+.|-|--..|..
T Consensus 4 ~~Il~y~~~qNRPys~~di~~nL~~-~~~K~~v~k~Ld~L~~~g~i~~K~~GK 55 (169)
T PF07106_consen 4 DAILEYMKEQNRPYSAQDIFDNLHN-KVGKTAVQKALDSLVEEGKIVEKEYGK 55 (169)
T ss_pred HHHHHHHHHcCCCCcHHHHHHHHHh-hccHHHHHHHHHHHHhCCCeeeeeecc
Confidence 3444444 4699999999999997 799999999999999999886555443
No 86
>PRK05638 threonine synthase; Validated
Probab=35.65 E-value=64 Score=32.14 Aligned_cols=47 Identities=21% Similarity=0.338 Sum_probs=41.9
Q ss_pred HHHHHHHHHhhccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCCH
Q 023264 212 AENLAVKLLATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIND 259 (285)
Q Consensus 212 A~~~AL~lLS~RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLDD 259 (285)
..-..|.+|+..+.+-.||.+.|.. ..+...|-..|.+|++.|+|.-
T Consensus 372 ~r~~IL~~L~~~~~~~~el~~~l~~-~~s~~~v~~hL~~Le~~GLV~~ 418 (442)
T PRK05638 372 TKLEILKILSEREMYGYEIWKALGK-PLKYQAVYQHIKELEELGLIEE 418 (442)
T ss_pred hHHHHHHHHhhCCccHHHHHHHHcc-cCCcchHHHHHHHHHHCCCEEE
Confidence 3667889999999999999999984 5789999999999999999964
No 87
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=35.59 E-value=62 Score=23.45 Aligned_cols=32 Identities=16% Similarity=0.397 Sum_probs=27.8
Q ss_pred cccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCC
Q 023264 224 AFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 224 drS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLD 258 (285)
+.|..+|.+.+ |.+.+.+..++.+|++.|+|+
T Consensus 28 ~lt~~~iA~~~---g~sr~tv~r~l~~l~~~g~I~ 59 (76)
T PF13545_consen 28 PLTQEEIADML---GVSRETVSRILKRLKDEGIIE 59 (76)
T ss_dssp ESSHHHHHHHH---TSCHHHHHHHHHHHHHTTSEE
T ss_pred cCCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEE
Confidence 45788888877 689999999999999999985
No 88
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.
Probab=35.11 E-value=83 Score=27.81 Aligned_cols=42 Identities=17% Similarity=0.275 Sum_probs=35.0
Q ss_pred HHHHHHHhh-ccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCC
Q 023264 214 NLAVKLLAT-RAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 214 ~~AL~lLS~-RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLD 258 (285)
...|.+|.. ...|..|+.+.| |.++..+...|..|++.|||.
T Consensus 146 ~~IL~~l~~~g~~s~~eia~~l---~is~stv~r~L~~Le~~GlI~ 188 (203)
T TIGR01884 146 LKVLEVLKAEGEKSVKNIAKKL---GKSLSTISRHLRELEKKGLVE 188 (203)
T ss_pred HHHHHHHHHcCCcCHHHHHHHH---CcCHHHHHHHHHHHHHCCCEE
Confidence 355667766 456999999988 689999999999999999984
No 89
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=34.86 E-value=96 Score=24.68 Aligned_cols=40 Identities=15% Similarity=0.301 Sum_probs=32.5
Q ss_pred HHHHHh----h-ccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCC
Q 023264 216 AVKLLA----T-RAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 216 AL~lLS----~-RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLD 258 (285)
.|.+|. . ...|..||...|. ++...|-.+|++|++.|||-
T Consensus 30 vL~~l~~~~~~~~~~t~~eL~~~l~---~~~stvs~~i~~Le~kg~I~ 74 (109)
T TIGR01889 30 ILYYLGKLENNEGKLTLKEIIKEIL---IKQSALVKIIKKLSKKGYLS 74 (109)
T ss_pred HHHHHHhhhccCCcCcHHHHHHHHC---CCHHHHHHHHHHHHHCCCEe
Confidence 455555 2 3588999998875 78999999999999999984
No 90
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=34.58 E-value=80 Score=28.95 Aligned_cols=38 Identities=11% Similarity=0.186 Sum_probs=32.2
Q ss_pred HHHHhhc--cccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCC
Q 023264 217 VKLLATR--AFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLI 257 (285)
Q Consensus 217 L~lLS~R--drS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyL 257 (285)
|.+|+.. ..|..||.+.| |++...+-.+|..|++.|||
T Consensus 17 L~~l~~~~~~ls~~eia~~l---gl~kstv~RlL~tL~~~g~v 56 (263)
T PRK09834 17 LRALNRLDGGATVGLLAELT---GLHRTTVRRLLETLQEEGYV 56 (263)
T ss_pred HHHHHhcCCCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCE
Confidence 3445543 36999999998 89999999999999999999
No 91
>PF14748 P5CR_dimer: Pyrroline-5-carboxylate reductase dimerisation; PDB: 2RCY_D 3TRI_A 2IZZ_B 2GR9_B 2GRA_B 2GER_C 1YQG_A 2AG8_A 3GT0_A 2AMF_E ....
Probab=33.16 E-value=1.7e+02 Score=23.56 Aligned_cols=65 Identities=20% Similarity=0.206 Sum_probs=44.0
Q ss_pred hHHHHhcccCCCCcCCCCHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHHhcCCCCHHHHHHHH
Q 023264 169 EISCEHGLFEESEVFEEPQEVAEEMKILQQKDFYLQAAKARQDAENLAVKLLATRAFTAVEMRKKLNGKKFPSHVIEAVI 248 (285)
Q Consensus 169 dvlik~~L~kG~~~~ELdee~leeI~~~~q~~~~eq~~~~~~kA~~~AL~lLS~RdrS~~ELr~KL~~Kg~~ee~Ie~VI 248 (285)
+-+++.++..| |+.++-.+|. .....-+..+|....++..+|+++....| ..-.+.|
T Consensus 25 eal~~a~v~~G-----l~~~~A~~lv---------------~~t~~G~a~ll~~~~~~~~~l~~~v~tPg---G~T~~gl 81 (107)
T PF14748_consen 25 EALADAAVAQG-----LPREEARKLV---------------AQTFIGAAKLLEESGRSPAELRDEVTTPG---GTTIAGL 81 (107)
T ss_dssp HHHHHHHHHTT-------HHHHHHHH---------------HHHHHHHHHHHHHCSS-HHHHHHHHS-TT---SHHHHHH
T ss_pred HHHHHHHHHcC-----CCHHHHHHHH---------------HHHHHHHHHHHHccCCCHHHHhhhccCCC---CcHHHHH
Confidence 88888888888 4555555444 44566677788888999999999998643 3445566
Q ss_pred HHHHHCCC
Q 023264 249 TDFQSRGL 256 (285)
Q Consensus 249 erLee~Gy 256 (285)
..|++.|+
T Consensus 82 ~~L~~~~~ 89 (107)
T PF14748_consen 82 EVLEKGGL 89 (107)
T ss_dssp HHHHHTTH
T ss_pred HHHHHCCH
Confidence 66666664
No 92
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=32.74 E-value=52 Score=31.14 Aligned_cols=41 Identities=24% Similarity=0.521 Sum_probs=32.4
Q ss_pred HHHHHHhhcc--ccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCC
Q 023264 215 LAVKLLATRA--FTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 215 ~AL~lLS~Rd--rS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLD 258 (285)
.+|.+|..+. -+..||+++| |+|...+-.+|.+|+++|||.
T Consensus 199 ~il~~i~~~GGri~Q~eL~r~l---glsktTvsR~L~~LEk~GlIe 241 (258)
T COG2512 199 EILDLIRERGGRITQAELRRAL---GLSKTTVSRILRRLEKRGLIE 241 (258)
T ss_pred HHHHHHHHhCCEEeHHHHHHhh---CCChHHHHHHHHHHHhCCceE
Confidence 3444555444 4778888876 799999999999999999984
No 93
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=32.48 E-value=76 Score=25.03 Aligned_cols=34 Identities=15% Similarity=0.173 Sum_probs=28.3
Q ss_pred hccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCC
Q 023264 222 TRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 222 ~RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLD 258 (285)
.-..|..||...+ |.+.+.+..+|..|++.|||-
T Consensus 45 ~~~is~~eLa~~~---g~sr~tVsr~L~~Le~~GlI~ 78 (95)
T TIGR01610 45 QDRVTATVIAELT---GLSRTHVSDAIKSLARRRIIF 78 (95)
T ss_pred CCccCHHHHHHHH---CcCHHHHHHHHHHHHHCCCee
Confidence 3456778887765 679999999999999999984
No 94
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=32.39 E-value=95 Score=23.90 Aligned_cols=40 Identities=15% Similarity=0.298 Sum_probs=31.3
Q ss_pred HHHHHhh-ccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCC
Q 023264 216 AVKLLAT-RAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 216 AL~lLS~-RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLD 258 (285)
.+.+|.. ..-+-.||++.| |.++..+..-+..|++.|||.
T Consensus 5 Il~~L~~~~~~~f~~L~~~l---~lt~g~Ls~hL~~Le~~GyV~ 45 (80)
T PF13601_consen 5 ILALLYANEEATFSELKEEL---GLTDGNLSKHLKKLEEAGYVE 45 (80)
T ss_dssp HHHHHHHHSEEEHHHHHHHT---T--HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHhhcCCCCHHHHHHHh---CcCHHHHHHHHHHHHHCCCEE
Confidence 3445555 778888998887 589999999999999999995
No 95
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=32.34 E-value=46 Score=27.00 Aligned_cols=21 Identities=19% Similarity=0.501 Sum_probs=20.0
Q ss_pred CCCHHHHHHHHHHHHHCCCCC
Q 023264 238 KFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 238 g~~ee~Ie~VIerLee~GyLD 258 (285)
+++.+.|..++++|++.|+|.
T Consensus 32 ~~~~~~v~~~l~~Le~~GLle 52 (92)
T PF10007_consen 32 KIPLEEVREALEKLEEMGLLE 52 (92)
T ss_pred CCCHHHHHHHHHHHHHCCCeE
Confidence 899999999999999999994
No 96
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=31.41 E-value=1.1e+02 Score=26.70 Aligned_cols=49 Identities=10% Similarity=0.154 Sum_probs=38.3
Q ss_pred HHHHHHHh--hccccHHHHHHHHhcCC--CCHHHHHHHHHHHHHCCCCCHHHH
Q 023264 214 NLAVKLLA--TRAFTAVEMRKKLNGKK--FPSHVIEAVITDFQSRGLINDSLY 262 (285)
Q Consensus 214 ~~AL~lLS--~RdrS~~ELr~KL~~Kg--~~ee~Ie~VIerLee~GyLDD~rY 262 (285)
...|.+|. .+.-|..||.++|.+.+ ++...|-.+|+.|.+.|+|.--..
T Consensus 29 ~~IL~~l~~~~~hlSa~eI~~~L~~~~~~is~aTVYRtL~~L~e~Glv~~~~~ 81 (169)
T PRK11639 29 LEVLRLMSLQPGAISAYDLLDLLREAEPQAKPPTVYRALDFLLEQGFVHKVES 81 (169)
T ss_pred HHHHHHHHhcCCCCCHHHHHHHHHhhCCCCCcchHHHHHHHHHHCCCEEEEec
Confidence 34444443 35789999999999885 678899999999999999965443
No 97
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=31.38 E-value=89 Score=21.80 Aligned_cols=33 Identities=18% Similarity=0.382 Sum_probs=28.4
Q ss_pred ccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCC
Q 023264 223 RAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 223 RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLD 258 (285)
-.-|..||.+.+ |++...+..+|..|++.|||.
T Consensus 24 ~~~s~~ela~~~---g~s~~tv~r~l~~L~~~g~i~ 56 (67)
T cd00092 24 LPLTRQEIADYL---GLTRETVSRTLKELEEEGLIS 56 (67)
T ss_pred CCcCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEE
Confidence 456888888876 589999999999999999985
No 98
>TIGR01446 DnaD_dom DnaD and phage-associated domain. This model represents the conserved domain of DnaD, part of Bacillus subtilis replication restart primosome, and of a number of phage-associated proteins. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria.
Probab=30.96 E-value=2.1e+02 Score=20.86 Aligned_cols=43 Identities=12% Similarity=0.122 Sum_probs=33.9
Q ss_pred HHHHHHhcCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhhhh
Q 023264 229 EMRKKLNGKKFPSHVIEAVITDFQSRGLINDSLYAESYSRSRWS 272 (285)
Q Consensus 229 ELr~KL~~Kg~~ee~Ie~VIerLee~GyLDD~rYAesyVrsr~~ 272 (285)
.|...+.+.|++++.|..+++++...|-.+ -.|.+.-+++...
T Consensus 20 ~i~~~~~~~~~~~evI~~ai~~a~~~~~~~-~~Yi~~Il~~W~~ 62 (73)
T TIGR01446 20 DLKYWLDEFGNSPELIKEALKEAVSNNKAN-YKYIDAILNNWKN 62 (73)
T ss_pred HHHHHHHHhCCCHHHHHHHHHHHHHcCCCC-HHHHHHHHHHHHH
Confidence 344555677999999999999998877666 5788888888765
No 99
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=29.88 E-value=1.2e+02 Score=28.13 Aligned_cols=41 Identities=12% Similarity=0.305 Sum_probs=34.1
Q ss_pred HHHHHHHhhcc-ccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCC
Q 023264 214 NLAVKLLATRA-FTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLI 257 (285)
Q Consensus 214 ~~AL~lLS~Rd-rS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyL 257 (285)
+..+.+|..+. -|..||.+.| +.++..|-.-|..|++.|+|
T Consensus 8 ~~Il~~l~~~~~~~~~ela~~l---~vS~~TiRRdL~~Le~~g~l 49 (252)
T PRK10906 8 DAIIELVKQQGYVSTEELVEHF---SVSPQTIRRDLNDLAEQNKI 49 (252)
T ss_pred HHHHHHHHHcCCEeHHHHHHHh---CCCHHHHHHHHHHHHHCCCE
Confidence 44555665554 7999999988 79999999999999999997
No 100
>PF07261 DnaB_2: Replication initiation and membrane attachment; InterPro: IPR006343 This entry represents a domain found in several bacterial replication initiation and membrane attachment proteins, DnaB and DnaD. The DnaD protein is a component of the PriA primosome. The PriA primosome functions to recruit the replication fork helicase onto the DNA []. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria []. The DnaB protein is essential for both replication initiation and membrane attachment of the origin region of the chromosome and Plasmid pUB110 in Bacillus subtilis. It is known that there are two different classes (DnaBI and DnaBII) in the DnaB mutants; DnaBI is essential for both chromosome and pUB110 replication, whereas DnaBII is necessary only for chromosome replication []. This domain tends to be found towards the C terminus of DnaB and DnaD proteins and is alpha helical in nature.; PDB: 2I5U_A 2ZC2_A.
Probab=29.79 E-value=1.1e+02 Score=22.21 Aligned_cols=43 Identities=14% Similarity=0.115 Sum_probs=31.4
Q ss_pred HHHHHHhcCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhhhh
Q 023264 229 EMRKKLNGKKFPSHVIEAVITDFQSRGLINDSLYAESYSRSRWS 272 (285)
Q Consensus 229 ELr~KL~~Kg~~ee~Ie~VIerLee~GyLDD~rYAesyVrsr~~ 272 (285)
.|...+.+.+++++.|..+++++...|=.+ ..|...-+++...
T Consensus 20 ~l~~~~~~~~~~~~~v~~ai~~~~~~~~~~-~~Yi~~Il~~W~~ 62 (77)
T PF07261_consen 20 KLEKWIDDYGFSPEVVNEAIEYALENNKRS-FNYIEKILNNWKQ 62 (77)
T ss_dssp HHHHHHCCCHHHHHHHHHHHHHHHHCT--S-HHHHHHHHHHHHH
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHHHcCCCC-HHHHHHHHHHHHH
Confidence 344455556899999999999999877777 8888887777754
No 101
>PF10905 DUF2695: Protein of unknown function (DUF2695); InterPro: IPR024248 This bacterial family of proteins has no known function.
Probab=29.49 E-value=88 Score=23.09 Aligned_cols=29 Identities=21% Similarity=0.217 Sum_probs=22.9
Q ss_pred cccHHHHHHHHhcCCCCHHHHHHHHHHHHHCC
Q 023264 224 AFTAVEMRKKLNGKKFPSHVIEAVITDFQSRG 255 (285)
Q Consensus 224 drS~~ELr~KL~~Kg~~ee~Ie~VIerLee~G 255 (285)
++|-+--++.|.+++++. +.|+++|++.|
T Consensus 15 dHtlr~t~~fl~~~~~~~---~~vl~~l~~nG 43 (53)
T PF10905_consen 15 DHTLRLTRQFLRQRQLDW---EDVLEWLRENG 43 (53)
T ss_pred CCcHHHHHHHHHHcCCCH---HHHHHHHHHcC
Confidence 577777788888888877 77888888776
No 102
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=29.36 E-value=1.4e+02 Score=27.63 Aligned_cols=31 Identities=13% Similarity=0.307 Sum_probs=28.8
Q ss_pred ccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCC
Q 023264 225 FTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 225 rS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLD 258 (285)
-|..||.+.| +++...+...|.+|++.|||.
T Consensus 22 IS~~eLA~~L---~iS~~Tvsr~Lk~LEe~GlI~ 52 (217)
T PRK14165 22 ISSSEFANHT---GTSSKTAARILKQLEDEGYIT 52 (217)
T ss_pred cCHHHHHHHH---CcCHHHHHHHHHHHHHCCCEE
Confidence 6899999999 689999999999999999993
No 103
>PF01638 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002577 The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure. The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde []. The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH []. The crystal structure of ytfH resembles the DNA-binding domains of winged helix proteins, containing a three helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-H2-B1-H3-H4-B2-B3-H5-H6. This topology corresponds with that of the marR-type DNA-binding domain, wherein helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. ; PDB: 2F2E_B 3DF8_A 1Z7U_B 1YYV_A 4A5M_D 4A5N_B 2FSW_A 2HZT_D.
Probab=29.18 E-value=1.1e+02 Score=23.52 Aligned_cols=42 Identities=17% Similarity=0.406 Sum_probs=35.7
Q ss_pred HHHHHHhhccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCC
Q 023264 215 LAVKLLATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 215 ~AL~lLS~RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLD 258 (285)
..|..|...+..-.||.+.|. |+++.+....+..|++.|+|.
T Consensus 9 ~IL~~l~~g~~rf~el~~~l~--~is~~~L~~~L~~L~~~GLv~ 50 (90)
T PF01638_consen 9 LILRALFQGPMRFSELQRRLP--GISPKVLSQRLKELEEAGLVE 50 (90)
T ss_dssp HHHHHHTTSSEEHHHHHHHST--TS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHhCCCcHHHHHHhcc--hhHHHHHHHHHHHHHHcchhh
Confidence 346677778999999999985 899999999999999999994
No 104
>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=29.09 E-value=55 Score=22.71 Aligned_cols=38 Identities=18% Similarity=0.370 Sum_probs=29.9
Q ss_pred HHHHhhccc--cHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCC
Q 023264 217 VKLLATRAF--TAVEMRKKLNGKKFPSHVIEAVITDFQSRGLI 257 (285)
Q Consensus 217 L~lLS~Rdr--S~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyL 257 (285)
|.+|+.... |-.||.+.+ |++...+..++..|.+.|||
T Consensus 9 L~~l~~~~~~~t~~eia~~~---gl~~stv~r~L~tL~~~g~v 48 (52)
T PF09339_consen 9 LEALAESGGPLTLSEIARAL---GLPKSTVHRLLQTLVEEGYV 48 (52)
T ss_dssp HHCHHCTBSCEEHHHHHHHH---TS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHcCCCCCCHHHHHHHH---CcCHHHHHHHHHHHHHCcCe
Confidence 444554444 788888887 59999999999999999998
No 105
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=28.72 E-value=98 Score=24.60 Aligned_cols=29 Identities=28% Similarity=0.488 Sum_probs=22.5
Q ss_pred cHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCC
Q 023264 226 TAVEMRKKLNGKKFPSHVIEAVITDFQSRGLI 257 (285)
Q Consensus 226 S~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyL 257 (285)
+..+|...|. .|++.|+..+++|+..|-|
T Consensus 18 s~~~Ls~~~~---~p~~~VeaMLe~l~~kGkv 46 (78)
T PRK15431 18 EAAQISQTLN---TPQPMINAMLQQLESMGKA 46 (78)
T ss_pred cHHHHHHHHC---cCHHHHHHHHHHHHHCCCe
Confidence 4445555554 7999999999999999865
No 106
>PRK12423 LexA repressor; Provisional
Probab=28.09 E-value=2e+02 Score=25.48 Aligned_cols=43 Identities=16% Similarity=0.246 Sum_probs=32.1
Q ss_pred HHHHHHHhhcc--ccHHHHHHHHhcCCC-CHHHHHHHHHHHHHCCCCCH
Q 023264 214 NLAVKLLATRA--FTAVEMRKKLNGKKF-PSHVIEAVITDFQSRGLIND 259 (285)
Q Consensus 214 ~~AL~lLS~Rd--rS~~ELr~KL~~Kg~-~ee~Ie~VIerLee~GyLDD 259 (285)
+....++.... -|..||.+.| |+ +...|.+.|..|++.|||.-
T Consensus 13 ~~l~~~i~~~g~~Ps~~eia~~~---g~~s~~~v~~~l~~L~~~G~l~~ 58 (202)
T PRK12423 13 AFIRERIAQAGQPPSLAEIAQAF---GFASRSVARKHVQALAEAGLIEV 58 (202)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHh---CCCChHHHHHHHHHHHHCCCEEe
Confidence 33333444443 4999999877 64 78899999999999999963
No 107
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=27.60 E-value=1.9e+02 Score=22.30 Aligned_cols=49 Identities=10% Similarity=0.135 Sum_probs=39.2
Q ss_pred cccHHHHHHHHhcCCCCHHHHHHHHHHHH--HCCCCCHHHHHHHHHHhhhh
Q 023264 224 AFTAVEMRKKLNGKKFPSHVIEAVITDFQ--SRGLINDSLYAESYSRSRWS 272 (285)
Q Consensus 224 drS~~ELr~KL~~Kg~~ee~Ie~VIerLe--e~GyLDD~rYAesyVrsr~~ 272 (285)
--|..||+.-|+..|++++.++.++..+- ..|+||=.+|-..+..-...
T Consensus 26 ~Is~~el~~~l~~~~~~~~ev~~i~~~~d~~~~g~I~~~eF~~~~~~~~~~ 76 (96)
T smart00027 26 TVTGAQAKPILLKSGLPQTLLAKIWNLADIDNDGELDKDEFALAMHLIYRK 76 (96)
T ss_pred eEeHHHHHHHHHHcCCCHHHHHHHHHHhcCCCCCCcCHHHHHHHHHHHHHH
Confidence 46888999999989999999999888664 46899999998766655543
No 108
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.19 E-value=2.4e+02 Score=23.76 Aligned_cols=73 Identities=16% Similarity=0.183 Sum_probs=47.3
Q ss_pred EecCCccchhh-hHHHHhcccCCCCcCCCCHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHHhc
Q 023264 158 LLDAAKQEFGE-EISCEHGLFEESEVFEEPQEVAEEMKILQQKDFYLQAAKARQDAENLAVKLLATRAFTAVEMRKKLNG 236 (285)
Q Consensus 158 yiDg~efafsv-dvlik~~L~kG~~~~ELdee~leeI~~~~q~~~~eq~~~~~~kA~~~AL~lLS~RdrS~~ELr~KL~~ 236 (285)
|+|+ +|. ++...+++.+- +....|+ .++ ..-..|+..|.+++... -+.||.++|++
T Consensus 30 y~dD----lSl~EIAee~~VSRq--------AIyDnIK------r~~----~~L~~YE~KL~l~~k~~-~R~el~d~lk~ 86 (105)
T COG2739 30 YLDD----LSLSEIAEEFNVSRQ--------AIYDNIK------RTE----KILEDYEEKLKLYEKYK-IRKELYDKLKE 86 (105)
T ss_pred HHhh----ccHHHHHHHhCccHH--------HHHHHHH------HHH----HHHHHHHHHHHHHHHHH-HHHHHHHHHHH
Confidence 3566 777 77777777644 4455555 221 23456777888887664 78888898887
Q ss_pred CCCCHHHHHHHHHHHHH
Q 023264 237 KKFPSHVIEAVITDFQS 253 (285)
Q Consensus 237 Kg~~ee~Ie~VIerLee 253 (285)
+=-.++.+.+.+..|..
T Consensus 87 ~~~~~~~l~~~l~~l~~ 103 (105)
T COG2739 87 LITDPEELREILEDLDN 103 (105)
T ss_pred HcCCHHHHHHHHHHhHc
Confidence 74444477777776653
No 109
>cd02432 Nodulin-21_like_1 Nodulin-21 and CCC1-related protein family. Nodulin-21_like_1: This is a family of proteins closely related to nodulin-21, a plant nodule-specific protein that may be involved in symbiotic nitrogen fixation. This family is also related to CCC1, a yeast vacuole transmembrane protein that functions as an iron and manganese transporter.
Probab=26.11 E-value=1.7e+02 Score=26.77 Aligned_cols=34 Identities=6% Similarity=0.140 Sum_probs=28.6
Q ss_pred hccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCC
Q 023264 222 TRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRG 255 (285)
Q Consensus 222 ~RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~G 255 (285)
..+...+||.+.+..+|++++.++.+.+++....
T Consensus 83 ~p~~e~~el~~~~~~~G~~~~~a~~~a~~l~~~~ 116 (218)
T cd02432 83 DPEAELEELADIYEERGLSPELARQVADELMAKD 116 (218)
T ss_pred CcHHHHHHHHHHHHHcCCCHHHHHHHHHHHhhcC
Confidence 3455668999999999999999999999998754
No 110
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=26.07 E-value=2.3e+02 Score=20.24 Aligned_cols=33 Identities=15% Similarity=0.323 Sum_probs=28.6
Q ss_pred hccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCC
Q 023264 222 TRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLI 257 (285)
Q Consensus 222 ~RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyL 257 (285)
...-|..||.+.| ++++..|..=+..|++.|+|
T Consensus 12 ~~~~s~~ela~~~---~VS~~TiRRDl~~L~~~g~i 44 (57)
T PF08220_consen 12 KGKVSVKELAEEF---GVSEMTIRRDLNKLEKQGLI 44 (57)
T ss_pred cCCEEHHHHHHHH---CcCHHHHHHHHHHHHHCCCE
Confidence 4566888888887 79999999999999999986
No 111
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.
Probab=26.05 E-value=2.3e+02 Score=19.62 Aligned_cols=40 Identities=5% Similarity=0.097 Sum_probs=28.2
Q ss_pred HHHHHHHhcCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhhh
Q 023264 228 VEMRKKLNGKKFPSHVIEAVITDFQSRGLINDSLYAESYSRSRW 271 (285)
Q Consensus 228 ~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLDD~rYAesyVrsr~ 271 (285)
.|+..-|...||++..|..++..+....-++ .+.+++.-+
T Consensus 4 ~d~~~AL~~LGy~~~e~~~av~~~~~~~~~~----~e~~ik~aL 43 (47)
T PF07499_consen 4 EDALEALISLGYSKAEAQKAVSKLLEKPGMD----VEELIKQAL 43 (47)
T ss_dssp HHHHHHHHHTTS-HHHHHHHHHHHHHSTTS-----HHHHHHHHH
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHhhcCCCCC----HHHHHHHHH
Confidence 5677788889999999999999998744444 444555544
No 112
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=25.88 E-value=82 Score=31.17 Aligned_cols=34 Identities=15% Similarity=0.277 Sum_probs=30.4
Q ss_pred hhccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCC
Q 023264 221 ATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLI 257 (285)
Q Consensus 221 S~RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyL 257 (285)
..++.|..||.+.|. .+++.++++++.|++.|+|
T Consensus 307 ~g~~~t~~~La~~l~---~~~~~v~~iL~~L~~agLI 340 (412)
T PRK04214 307 HGKALDVDEIRRLEP---MGYDELGELLCELARIGLL 340 (412)
T ss_pred cCCCCCHHHHHHHhC---CCHHHHHHHHHHHHhCCCe
Confidence 345789999998886 8999999999999999999
No 113
>PRK06474 hypothetical protein; Provisional
Probab=25.82 E-value=1.7e+02 Score=25.76 Aligned_cols=45 Identities=16% Similarity=0.300 Sum_probs=37.8
Q ss_pred HHHHHHHHHhhcc--ccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCC
Q 023264 212 AENLAVKLLATRA--FTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 212 A~~~AL~lLS~Rd--rS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLD 258 (285)
.....+.+|.... .|..||.+.|. +.+...|-..|..|++.|+|.
T Consensus 12 ~R~~Il~~L~~~~~~~ta~el~~~l~--~is~aTvYrhL~~L~e~GLI~ 58 (178)
T PRK06474 12 VRMKICQVLMRNKEGLTPLELVKILK--DVPQATLYRHLQTMVDSGILH 58 (178)
T ss_pred HHHHHHHHHHhCCCCCCHHHHHHHhc--CCCHHHHHHHHHHHHHCCCEE
Confidence 3456677776654 79999999996 689999999999999999997
No 114
>PF03962 Mnd1: Mnd1 family; InterPro: IPR005647 This family of proteins includes meiotic nuclear division protein 1 (MND1) from Saccharomyces cerevisiae (Baker's yeast). The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair [].
Probab=25.55 E-value=79 Score=28.33 Aligned_cols=40 Identities=20% Similarity=0.275 Sum_probs=34.5
Q ss_pred hhccccHHHHHHHHhc-CCCCHHHHHHHHHHHHHCCCCCHH
Q 023264 221 ATRAFTAVEMRKKLNG-KKFPSHVIEAVITDFQSRGLINDS 260 (285)
Q Consensus 221 S~RdrS~~ELr~KL~~-Kg~~ee~Ie~VIerLee~GyLDD~ 260 (285)
+.--||-+||...+-+ +|+.+..|.++|.-|.+-|+|+=.
T Consensus 8 ~~~~y~lKELEK~~pK~~gI~~~~VKdvlq~LvDDglV~~E 48 (188)
T PF03962_consen 8 SKDFYTLKELEKLAPKEKGIVSMSVKDVLQSLVDDGLVHVE 48 (188)
T ss_pred cCCcccHHHHHHHcccccCCchhhHHHHHHHHhccccchhh
Confidence 4456889999998887 799999999999999999998643
No 115
>PF08780 NTase_sub_bind: Nucleotidyltransferase substrate binding protein like; InterPro: IPR010235 The member of this family from Haemophilus influenzae, HI0074, has been shown by crystal structure to resemble nucleotidyltransferase substrate binding proteins []. It forms a complex with HI0073 (P43933 from SWISSPROT), encoded by the adjacent gene, which contains a nucleotidyltransferase nucleotide binding domain (IPR002934 from INTERPRO). Double- and single-stranded DNA binding assays showed no evidence of DNA binding to HI0074 or to HI0073/HI0074 complex despite the suggestive shape of the putative binding cleft formed by the HI0074 dimer []. ; PDB: 1WWP_A 1JOG_A 1WTY_C 2YWA_B.
Probab=25.28 E-value=1.3e+02 Score=25.05 Aligned_cols=54 Identities=19% Similarity=0.118 Sum_probs=39.8
Q ss_pred HHHHHHHHHHHHHHhhccccHHHHHHHHhcCCC-CHHHHHHHHHHHHHCCCCCHHHHHHHHHHhh
Q 023264 207 KARQDAENLAVKLLATRAFTAVEMRKKLNGKKF-PSHVIEAVITDFQSRGLINDSLYAESYSRSR 270 (285)
Q Consensus 207 ~~~~kA~~~AL~lLS~RdrS~~ELr~KL~~Kg~-~ee~Ie~VIerLee~GyLDD~rYAesyVrsr 270 (285)
..+.-+++.|.+. |+++|...|+ +.-.-..++...-+.|+|+|..---.++..|
T Consensus 34 qrFE~t~ElaWK~----------lK~~L~~~G~~~~~spr~~~r~A~~~glI~d~e~Wl~m~~~R 88 (124)
T PF08780_consen 34 QRFEFTFELAWKT----------LKDYLEYEGISECNSPRDVFREAFKAGLIDDGEIWLDMLEDR 88 (124)
T ss_dssp HHHHHHHHHHHHH----------HHHHHHHCTSSCCTSHHHHHHHHHHTTSSSHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHH----------HHHHHHHhCCcccCCHHHHHHHHHHcCCCCCHHHHHHHHHHh
Confidence 3456667777665 4678888888 4444588999999999999987766666655
No 116
>PTZ00431 pyrroline carboxylate reductase; Provisional
Probab=24.98 E-value=3.1e+02 Score=25.06 Aligned_cols=73 Identities=5% Similarity=0.079 Sum_probs=47.1
Q ss_pred CCccchh--h-hHHHHhcccCCCCcCCCCHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHHhcC
Q 023264 161 AAKQEFG--E-EISCEHGLFEESEVFEEPQEVAEEMKILQQKDFYLQAAKARQDAENLAVKLLATRAFTAVEMRKKLNGK 237 (285)
Q Consensus 161 g~efafs--v-dvlik~~L~kG~~~~ELdee~leeI~~~~q~~~~eq~~~~~~kA~~~AL~lLS~RdrS~~ELr~KL~~K 237 (285)
|+-.||- + +-+++.+++.| +|.++-.+|. .+...=+..+|.....+..+|+++....
T Consensus 166 gsgPA~~~~~~~al~~~~v~~G-----l~~~~a~~l~---------------~~~~~G~a~ll~~~~~~~~~l~~~v~sp 225 (260)
T PTZ00431 166 GCGPAYVFLFIESLIDAGVKNG-----LNRDVSKNLV---------------LQTILGSVHMVKASDQPVQQLKDDVCSP 225 (260)
T ss_pred CCHHHHHHHHHHHHHHHHHHcC-----CCHHHHHHHH---------------HHHHHHHHHHHHhcCCCHHHHHHhCCCC
Confidence 5434443 3 88888888877 4655555444 3344555567778889999999987765
Q ss_pred CCCHHHHHHHHHHHHHCCC
Q 023264 238 KFPSHVIEAVITDFQSRGL 256 (285)
Q Consensus 238 g~~ee~Ie~VIerLee~Gy 256 (285)
| ..-.+.|..|++.|+
T Consensus 226 g---G~T~~gl~~le~~g~ 241 (260)
T PTZ00431 226 G---GITIVGLYTLEKHAF 241 (260)
T ss_pred C---hHHHHHHHHHHHCCh
Confidence 3 334455666666655
No 117
>PF02037 SAP: SAP domain; InterPro: IPR003034 The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA binding domain found in diverse nuclear proteins involved in chromosomal organisation [], including in apoptosis []. In yeast, SAP is found in the most distal N-terminal region of E3 SUMO-protein ligase SIZ1, where it is involved in nuclear localization [].; GO: 0003676 nucleic acid binding; PDB: 2RNN_A 1JEQ_A 2KW9_A 2KVU_A 2DO1_A 1ZBU_B 1ZBH_A 2DO5_A 2RNO_A 1H1J_S ....
Probab=24.60 E-value=1.3e+02 Score=19.78 Aligned_cols=19 Identities=16% Similarity=0.441 Sum_probs=14.9
Q ss_pred ccccHHHHHHHHhcCCCCH
Q 023264 223 RAFTAVEMRKKLNGKKFPS 241 (285)
Q Consensus 223 RdrS~~ELr~KL~~Kg~~e 241 (285)
...|..||++.|++.|.+.
T Consensus 2 ~~l~v~eLk~~l~~~gL~~ 20 (35)
T PF02037_consen 2 SKLTVAELKEELKERGLST 20 (35)
T ss_dssp TTSHHHHHHHHHHHTTS-S
T ss_pred CcCcHHHHHHHHHHCCCCC
Confidence 3467899999999998874
No 118
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=24.34 E-value=1.8e+02 Score=26.16 Aligned_cols=44 Identities=5% Similarity=0.131 Sum_probs=34.7
Q ss_pred HHHHHHHHH---h--hccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCC
Q 023264 212 AENLAVKLL---A--TRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 212 A~~~AL~lL---S--~RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLD 258 (285)
+.++|+..| + .+..|-.||.+.| |++...+...+.-|++.|||.
T Consensus 7 sl~ral~IL~~l~~~~~~~~l~eia~~l---glpksT~~RlL~tL~~~G~l~ 55 (248)
T TIGR02431 7 SLARGLAVIEAFGAERPRLTLTDVAEAT---GLTRAAARRFLLTLVELGYVT 55 (248)
T ss_pred HHHHHHHHHHHHhcCCCCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCEE
Confidence 345555544 4 3567888988876 699999999999999999995
No 119
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=23.98 E-value=2.6e+02 Score=23.97 Aligned_cols=38 Identities=13% Similarity=0.341 Sum_probs=32.5
Q ss_pred hhccccHHHHHHHHhcC-CCCHHHHHHHHHHHHHCCCCC
Q 023264 221 ATRAFTAVEMRKKLNGK-KFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 221 S~RdrS~~ELr~KL~~K-g~~ee~Ie~VIerLee~GyLD 258 (285)
+..+-|..|+...|... +.+...|.-+|.+|...|+|.
T Consensus 17 ~~~~~t~~eI~~~l~~~~ews~sTV~TLl~RL~KKg~l~ 55 (123)
T COG3682 17 SRGPATVREIIEELPADREWSYSTVKTLLNRLVKKGLLT 55 (123)
T ss_pred HcCCccHHHHHHHHhhcccccHHHHHHHHHHHHhccchh
Confidence 34488999999998865 788899999999999999984
No 120
>smart00816 Amb_V_allergen Amb V Allergen. Amb V is an Ambrosia sp (ragweed) pollen allergen. Amb t V has been shown to contain a C-terminal helix as the major T cell epitope. Free sulphhydryl groups also play a major role in the T cell recognition of cross-reactivity T cell epitopes within these related allergens.
Probab=23.94 E-value=36 Score=24.28 Aligned_cols=19 Identities=42% Similarity=0.719 Sum_probs=17.2
Q ss_pred eeecCCCccCccceeeecC
Q 023264 33 SCVKGRDYSSSFPVRYVPK 51 (285)
Q Consensus 33 ~c~~~r~~~~s~~~~y~p~ 51 (285)
.|-+-|.|++|-|=||-|-
T Consensus 11 ~CGekr~YCcSdpGrYCpw 29 (45)
T smart00816 11 NCGEKRKYCCSDPGRYCPW 29 (45)
T ss_pred cccccCccccCCCcccCCc
Confidence 5889999999999999885
No 121
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=23.80 E-value=2.2e+02 Score=24.73 Aligned_cols=43 Identities=16% Similarity=0.186 Sum_probs=36.7
Q ss_pred HHHHHHHHhhccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCC
Q 023264 213 ENLAVKLLATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 213 ~~~AL~lLS~RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLD 258 (285)
....-.++.+...|..||...| |++...|..++..|.+.|++.
T Consensus 17 v~Vl~aL~~~~~~tdEeLa~~L---gi~~~~VRk~L~~L~e~~Lv~ 59 (158)
T TIGR00373 17 GLVLFSLGIKGEFTDEEISLEL---GIKLNEVRKALYALYDAGLAD 59 (158)
T ss_pred HHHHHHHhccCCCCHHHHHHHH---CCCHHHHHHHHHHHHHCCCce
Confidence 3444446668899999999999 799999999999999999985
No 122
>PHA02554 13 neck protein; Provisional
Probab=23.73 E-value=97 Score=30.45 Aligned_cols=35 Identities=9% Similarity=0.082 Sum_probs=26.3
Q ss_pred hccccHHHHHHHHh-cCCCC-------H----HHHHHHHHHHHHCCC
Q 023264 222 TRAFTAVEMRKKLN-GKKFP-------S----HVIEAVITDFQSRGL 256 (285)
Q Consensus 222 ~RdrS~~ELr~KL~-~Kg~~-------e----e~Ie~VIerLee~Gy 256 (285)
++..+.+||.++.. +.|.| + +.|+.+|+...|+||
T Consensus 3 ~~~~sp~eLkD~iLRrLGAPii~Ievt~dQi~D~I~rALely~EYH~ 49 (311)
T PHA02554 3 YNPNNPRELKDYILRRLGAPIINVEVTEDQIYDCIQRALELYGEYHY 49 (311)
T ss_pred CCCCCHHHHHHHHHHhcCCCeeEeecCHHHHHHHHHHHHHHHHHHhc
Confidence 47789999999855 44654 3 567888888888887
No 123
>PF10557 Cullin_Nedd8: Cullin protein neddylation domain; InterPro: IPR019559 This is the neddylation site of cullin proteins, which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae (Baker's yeast), and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue []. ; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_B 1U6G_A 3O6B_J 3O2P_E 4A0K_A 2HYE_C ....
Probab=23.60 E-value=1.1e+02 Score=22.72 Aligned_cols=36 Identities=11% Similarity=0.078 Sum_probs=23.5
Q ss_pred hccccHHHHHHHHhc-----CCCCHHHHHHHHHHHHHCCCC
Q 023264 222 TRAFTAVEMRKKLNG-----KKFPSHVIEAVITDFQSRGLI 257 (285)
Q Consensus 222 ~RdrS~~ELr~KL~~-----Kg~~ee~Ie~VIerLee~GyL 257 (285)
.+..+..+|.....+ -..+...|...|+.|.+.+||
T Consensus 20 ~k~~~~~~L~~~v~~~l~~~f~~~~~~ik~~Ie~LIekeyi 60 (68)
T PF10557_consen 20 EKKLSHDELINEVIEELKKRFPPSVSDIKKRIESLIEKEYI 60 (68)
T ss_dssp SSEEEHHHHHHHHHHHTTTTS---HHHHHHHHHHHHHTTSE
T ss_pred cCceeHHHHHHHHHHHhcCCcCCCHHHHHHHHHHHHHhhhh
Confidence 344555555554332 234567899999999999998
No 124
>PF06014 DUF910: Bacterial protein of unknown function (DUF910); InterPro: IPR009256 This family consists of several short bacterial proteins of unknown function.; PDB: 2NN4_A.
Probab=23.57 E-value=2.6e+02 Score=21.33 Aligned_cols=44 Identities=16% Similarity=0.218 Sum_probs=32.7
Q ss_pred cccHHHHHHHHhcCCC---------CHHHHHHHHHHHHHCCCCCHHHHHHHHH
Q 023264 224 AFTAVEMRKKLNGKKF---------PSHVIEAVITDFQSRGLINDSLYAESYS 267 (285)
Q Consensus 224 drS~~ELr~KL~~Kg~---------~ee~Ie~VIerLee~GyLDD~rYAesyV 267 (285)
+.|-.+|.+-|++.|+ +-+.++.=|..|-+.|+||-..|..+..
T Consensus 1 MktlyDVqQLLK~fG~~IY~gdr~~DielM~~El~~Ly~~~lidk~~y~~A~l 53 (62)
T PF06014_consen 1 MKTLYDVQQLLKKFGIIIYVGDRLWDIELMEIELKELYKSGLIDKKEYLTAKL 53 (62)
T ss_dssp --SHHHHHHHHHTTS-----S-HHHHHHHHHHHHHHHHHTTSS-HHHHHHHHH
T ss_pred CCcHHHHHHHHHHCCEEEEeCChHHHHHHHHHHHHHHHHcCCCCHHHHHHHHH
Confidence 3577788899998875 4466777889999999999999977643
No 125
>PF12363 DUF3647: Phage protein ; InterPro: IPR024410 Proteins in this entry are frequently annotated as phage proteins, however there is little accompanying literature to back this up or to describe the nature of these phage proteins.
Probab=23.52 E-value=1.5e+02 Score=24.46 Aligned_cols=49 Identities=12% Similarity=0.152 Sum_probs=38.9
Q ss_pred HHHHHHHHHHHHHHhhccccHHHHHHHHhc----CCCCHHHHHHHHHHHHHCCC
Q 023264 207 KARQDAENLAVKLLATRAFTAVEMRKKLNG----KKFPSHVIEAVITDFQSRGL 256 (285)
Q Consensus 207 ~~~~kA~~~AL~lLS~RdrS~~ELr~KL~~----Kg~~ee~Ie~VIerLee~Gy 256 (285)
.....+...|+.....++ |..|+...|.+ .+-.++..+.|++.|...++
T Consensus 51 ~al~d~i~~a~~~~~~~~-s~~eIe~~ie~~~e~~~~~~~l~~~vl~el~~s~~ 103 (113)
T PF12363_consen 51 VALADIIYAATAHEKKRP-SREEIEDYIEDIIEDEDDIEELFDEVLKELKKSNF 103 (113)
T ss_pred HHHHHHHHHHhcccCCCC-CHHHHHHHHHHHHhcchhHHHHHHHHHHHHHhChh
Confidence 456778888888888898 99999999995 23356678888888887765
No 126
>PRK10947 global DNA-binding transcriptional dual regulator H-NS; Provisional
Probab=23.24 E-value=3.3e+02 Score=23.47 Aligned_cols=57 Identities=19% Similarity=0.198 Sum_probs=36.6
Q ss_pred CCCCHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHHhcCCCCHHHH
Q 023264 183 FEEPQEVAEEMKILQQKDFYLQAAKARQDAENLAVKLLATRAFTAVEMRKKLNGKKFPSHVI 244 (285)
Q Consensus 183 ~ELdee~leeI~~~~q~~~~eq~~~~~~kA~~~AL~lLS~RdrS~~ELr~KL~~Kg~~ee~I 244 (285)
.|+|-++++++. +... ............+..-..-+..--.+++..|...|++.+.+
T Consensus 19 re~~~e~Lee~~--ekl~---~vv~er~ee~~~~~~~~~er~~kl~~~r~~m~~~Gis~~eL 75 (135)
T PRK10947 19 RECTLETLEEML--EKLE---VVVNERREEESAAAAEVEERTRKLQQYREMLIADGIDPNEL 75 (135)
T ss_pred HHCCHHHHHHHH--HHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHH
Confidence 677888888877 2222 12223333344444555556667788999999999998877
No 127
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=23.22 E-value=1.7e+02 Score=25.50 Aligned_cols=32 Identities=9% Similarity=0.338 Sum_probs=28.4
Q ss_pred cccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCC
Q 023264 224 AFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 224 drS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLD 258 (285)
..|..||.+.+ +.|...+++++..|...|+|.
T Consensus 25 ~vs~~eIA~~~---~ip~~~l~kIl~~L~~aGLv~ 56 (164)
T PRK10857 25 PVPLADISERQ---GISLSYLEQLFSRLRKNGLVS 56 (164)
T ss_pred cCcHHHHHHHH---CcCHHHHHHHHHHHHHCCCEE
Confidence 46888888776 599999999999999999986
No 128
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=23.22 E-value=1.8e+02 Score=23.07 Aligned_cols=41 Identities=10% Similarity=0.289 Sum_probs=31.8
Q ss_pred HHHHHHhh-ccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCC
Q 023264 215 LAVKLLAT-RAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 215 ~AL~lLS~-RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLD 258 (285)
.+|..|.. ...|..||.+.| +.+...+-.+|++|++.|||-
T Consensus 32 ~iL~~l~~~~~~t~~ela~~~---~~~~~tvs~~l~~Le~~GlI~ 73 (118)
T TIGR02337 32 RILRILAEQGSMEFTQLANQA---CILRPSLTGILARLERDGLVT 73 (118)
T ss_pred HHHHHHHHcCCcCHHHHHHHh---CCCchhHHHHHHHHHHCCCEE
Confidence 35555543 456788888876 478889999999999999995
No 129
>TIGR03544 DivI1A_domain DivIVA domain. This model describes a domain found in Bacillus subtilis cell division initiation protein DivIVA, and homologs, toward the N-terminus. It is also found as a repeated domain in certain other proteins, including family TIGR03543.
Probab=23.19 E-value=96 Score=20.29 Aligned_cols=17 Identities=6% Similarity=0.307 Sum_probs=15.4
Q ss_pred CCCCHHHHHHHHHHHHH
Q 023264 237 KKFPSHVIEAVITDFQS 253 (285)
Q Consensus 237 Kg~~ee~Ie~VIerLee 253 (285)
+||.++.++..|+++.+
T Consensus 16 rGY~~~eVD~fLd~v~~ 32 (34)
T TIGR03544 16 RGYDAAEVDAFLDRVAD 32 (34)
T ss_pred CCCCHHHHHHHHHHHHH
Confidence 69999999999999875
No 130
>PRK11050 manganese transport regulator MntR; Provisional
Probab=22.48 E-value=4.8e+02 Score=22.13 Aligned_cols=45 Identities=16% Similarity=0.287 Sum_probs=35.2
Q ss_pred HHHHHHHHHhh-ccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCCH
Q 023264 212 AENLAVKLLAT-RAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIND 259 (285)
Q Consensus 212 A~~~AL~lLS~-RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLDD 259 (285)
.....+.++.. -..|..||.+.| +++...|...|.+|++.|||.-
T Consensus 38 ~l~~I~~~l~~~~~~t~~eLA~~l---~is~stVsr~l~~Le~~GlI~r 83 (152)
T PRK11050 38 YVELIADLIAEVGEARQVDIAARL---GVSQPTVAKMLKRLARDGLVEM 83 (152)
T ss_pred HHHHHHHHHHhcCCCCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEEE
Confidence 33444445543 457889999988 5999999999999999999964
No 131
>PRK12727 flagellar biosynthesis regulator FlhF; Provisional
Probab=22.24 E-value=6.2e+02 Score=26.96 Aligned_cols=63 Identities=6% Similarity=0.061 Sum_probs=42.4
Q ss_pred CCCCHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHH----hhccccHHHHHHHHhcCCCCHHHHHHHHHHHHHC
Q 023264 183 FEEPQEVAEEMKILQQKDFYLQAAKARQDAENLAVKLL----ATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSR 254 (285)
Q Consensus 183 ~ELdee~leeI~~~~q~~~~eq~~~~~~kA~~~AL~lL----S~RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~ 254 (285)
...+++++.++. +|. ...+...+.=+.-| ..+.-...+|.++|.+.|++++.+..+++++.+.
T Consensus 255 ~~~~~~~l~~m~--~El-------~~lR~lle~q~~~l~~~~~~~~P~~~~l~~~L~~~Gvs~~la~~L~~~l~~~ 321 (559)
T PRK12727 255 APQNDEELKQLR--GEL-------ALMRQMIEREMNRLTDERLRGSPVRAQALELMDDYGFDAGLTRDVAMQIPAD 321 (559)
T ss_pred CCCCHHHHHHHH--HHH-------HHHHHHHHHHHHhhhhhhhccChHHHHHHHHHHHCCCCHHHHHHHHHhhhcc
Confidence 455677777776 211 12333444333333 3445567888999999999999999999999764
No 132
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=22.10 E-value=86 Score=22.30 Aligned_cols=20 Identities=20% Similarity=0.232 Sum_probs=15.4
Q ss_pred HHHHhcCCCCHHHHHHHHHH
Q 023264 231 RKKLNGKKFPSHVIEAVITD 250 (285)
Q Consensus 231 r~KL~~Kg~~ee~Ie~VIer 250 (285)
...|++.|++.+.|..+++-
T Consensus 50 i~~lr~~g~~~~~i~~~l~l 69 (70)
T smart00422 50 IKRLKELGFSLEEIKELLEL 69 (70)
T ss_pred HHHHHHcCCCHHHHHHHHhc
Confidence 44567789999999988863
No 133
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=22.03 E-value=1.3e+02 Score=27.12 Aligned_cols=33 Identities=3% Similarity=0.157 Sum_probs=28.5
Q ss_pred ccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCC
Q 023264 223 RAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 223 RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLD 258 (285)
+--|+.||.+.+ |++...|-++|+.|+..|+|-
T Consensus 28 ~LPsE~eL~~~~---~VSR~TvR~Al~~L~~eGli~ 60 (240)
T PRK09764 28 ALPTESALQTEF---GVSRVTVRQALRQLVEQQILE 60 (240)
T ss_pred cCCCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEE
Confidence 455889988876 799999999999999999874
No 134
>PF09851 SHOCT: Short C-terminal domain; InterPro: IPR018649 This family of hypothetical prokaryotic proteins has no known function.
Probab=22.00 E-value=1.7e+02 Score=18.84 Aligned_cols=21 Identities=14% Similarity=0.377 Sum_probs=17.5
Q ss_pred HHHHHHHHCCCCCHHHHHHHH
Q 023264 246 AVITDFQSRGLINDSLYAESY 266 (285)
Q Consensus 246 ~VIerLee~GyLDD~rYAesy 266 (285)
..+..|.+.|.|++..|.+.-
T Consensus 6 ~~L~~l~~~G~IseeEy~~~k 26 (31)
T PF09851_consen 6 EKLKELYDKGEISEEEYEQKK 26 (31)
T ss_pred HHHHHHHHcCCCCHHHHHHHH
Confidence 467888999999999998754
No 135
>PF01454 MAGE: MAGE family; InterPro: IPR002190 The first mammalian members of the MAGE (melanoma-associated antigen) gene family were originally described as completely silent in normal adult tissues, with the exception of male germ cells and, for some of them, placenta. By contrast, these genes were expressed in various kinds of tumors. However, other members of the family were recently found to be expressed in normal cells, indicating that the family is larger and more disparate than initially expected. MAGE-like genes have also been identified in non-mammalian species, including Drosophila melanogaster (Fruit fly) and Danio rerio (Zebrafish). Although no MAGE homologous sequences have been identified in Caenorhabditis elegans, Saccharomyces cerevisiae (Baker's yeast) or Schizosaccharomyces pombe (Fission yeast), MAGE sequences have been found in several vegetal species, including Arabidopsis thaliana (Mouse-ear cress) []. The only region of homology shared by all of the members of the family is a stretch of about 200 amino acids which has been named the MAGE conserved domain. The MAGE conserved domain is usually located close to the C-terminal, although it can also be found in a more central position in some proteins. The MAGE conserved domain is generally present as a single copy but it is duplicated in some proteins. It has been proposed that the MAGE conserved domain of MAGE-D proteins might interact with p75 neurotrophin or related receptors [].; PDB: 3NW0_B 2WA0_A 1I4F_C.
Probab=21.84 E-value=92 Score=27.17 Aligned_cols=46 Identities=15% Similarity=0.257 Sum_probs=34.6
Q ss_pred HHHHHHHhhccccHHHHHHHHhcCCCCH-------H-HHHHHH-HHHHHCCCCCH
Q 023264 214 NLAVKLLATRAFTAVEMRKKLNGKKFPS-------H-VIEAVI-TDFQSRGLIND 259 (285)
Q Consensus 214 ~~AL~lLS~RdrS~~ELr~KL~~Kg~~e-------e-~Ie~VI-erLee~GyLDD 259 (285)
=.|+=+++-..-++.+|.+.|++-|+++ . .+.++| +.|...+||.-
T Consensus 110 IL~lI~~~g~~i~E~~L~~~L~~lgi~~~~~~~~~g~~~~~~i~~~~vkq~YL~~ 164 (195)
T PF01454_consen 110 ILSLIFMSGNSISEDDLWKFLRRLGIDEDEKHPILGMDIKKLILKEFVKQGYLVR 164 (195)
T ss_dssp HHHHHHHCTT-EEHHHHHHHHHHTT--TTS-BTTTB--HHHHHHCHHHHCTSE-E
T ss_pred HHHHHHhcCCccCHHHHHHHHHhcCCCccccCccCCCCHHHHHHHHHHHhcCHHh
Confidence 4566788889999999999999999873 2 677777 99999999944
No 136
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=21.75 E-value=1.9e+02 Score=22.42 Aligned_cols=56 Identities=11% Similarity=0.148 Sum_probs=33.7
Q ss_pred HHHHHHHHHhh--ccccHHHHHHHHhcC-CCCHHHHHHHHHHHHHC---CCCCHHHHHHHHHHh
Q 023264 212 AENLAVKLLAT--RAFTAVEMRKKLNGK-KFPSHVIEAVITDFQSR---GLINDSLYAESYSRS 269 (285)
Q Consensus 212 A~~~AL~lLS~--RdrS~~ELr~KL~~K-g~~ee~Ie~VIerLee~---GyLDD~rYAesyVrs 269 (285)
.+.-.|..|+- ...+..|+.+.+.+. ++++++.+..+. ... -|-|.-++|.++...
T Consensus 5 ~~~piL~~L~~~g~~~~~~ei~~~v~~~~~ls~e~~~~~~~--sg~~~~~~~~ri~Wa~~~L~~ 66 (92)
T PF14338_consen 5 LMPPILEALKDLGGSASRKEIYERVAERFGLSDEERNERLP--SGQGYSRFKNRIRWARSYLKK 66 (92)
T ss_pred HHHHHHHHHHHcCCCcCHHHHHHHHHHHhCCCHHHHHHHcc--cCCcchhHHHhHHHHHHHHHH
Confidence 34556666666 778888888888765 566664443332 121 245666666666543
No 137
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=21.45 E-value=2.6e+02 Score=19.07 Aligned_cols=38 Identities=26% Similarity=0.420 Sum_probs=29.6
Q ss_pred HHHHHH-hhc-cccHHHHHHHHhcCCCCHHHHHHHHHHHHHCC
Q 023264 215 LAVKLL-ATR-AFTAVEMRKKLNGKKFPSHVIEAVITDFQSRG 255 (285)
Q Consensus 215 ~AL~lL-S~R-drS~~ELr~KL~~Kg~~ee~Ie~VIerLee~G 255 (285)
..+.+| ... ..|..||.+.| +++...|..-|+.|++.|
T Consensus 4 ~il~~L~~~~~~it~~eLa~~l---~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 4 QILKLLLESKEPITAKELAEEL---GVSRRTIRRDIKELREWG 43 (55)
T ss_dssp HHHHHHHHTTTSBEHHHHHHHC---TS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHcCCCcCHHHHHHHh---CCCHHHHHHHHHHHHHCC
Confidence 344555 444 48999999987 589999999999999988
No 138
>COG1762 PtsN Phosphotransferase system mannitol/fructose-specific IIA domain (Ntr-type) [Carbohydrate transport and metabolism / Signal transduction mechanisms]
Probab=21.22 E-value=1.9e+02 Score=24.13 Aligned_cols=27 Identities=22% Similarity=0.380 Sum_probs=21.4
Q ss_pred CHHHHHHHHHHHHHCCCCCHHHHHHHH
Q 023264 240 PSHVIEAVITDFQSRGLINDSLYAESY 266 (285)
Q Consensus 240 ~ee~Ie~VIerLee~GyLDD~rYAesy 266 (285)
-+++|+.+.+.|.+.|++++..|.+..
T Consensus 20 k~e~i~~~~~~L~~~g~i~~~~~~~~i 46 (152)
T COG1762 20 KEEAIEELAEPLLEAGYITDEYFFEAI 46 (152)
T ss_pred HHHHHHHHHHHHHHcCCCCHHHHHHHH
Confidence 367899999999999999994444443
No 139
>PF15524 Toxin_45: Putative toxin 45
Probab=21.18 E-value=48 Score=26.99 Aligned_cols=30 Identities=30% Similarity=0.486 Sum_probs=21.0
Q ss_pred CccceeeecCCccccccccCCCcc-ccccccccccC
Q 023264 42 SSFPVRYVPKKSVKIKESENSVPV-KGLERNELRKQ 76 (285)
Q Consensus 42 ~s~~~~y~p~~s~k~~~~~~s~~~-~~~~~~~~~~~ 76 (285)
-++++||||-|-+|- |-|+ ++-.++-++|+
T Consensus 14 ~~G~iRyiPp~~y~~-----s~~Lprgp~nGyvDkF 44 (94)
T PF15524_consen 14 NQGRIRYIPPKNYKA-----SRPLPRGPNNGYVDKF 44 (94)
T ss_pred CCCceeecCcccccc-----cCccCCCCCCcchhcc
Confidence 589999999998876 4455 55555555544
No 140
>TIGR00112 proC pyrroline-5-carboxylate reductase. This enzyme catalyzes the final step in proline biosynthesis. Among the four paralogs in Bacillus subtilis (proG, proH, proI, and comER), ComER is the most divergent and does not prevent proline auxotrophy from mutation of the other three. It is excluded from the seed and scores between the trusted and noise cutoffs.
Probab=20.98 E-value=4e+02 Score=24.17 Aligned_cols=75 Identities=16% Similarity=0.193 Sum_probs=49.8
Q ss_pred CCccch--hh-hHHHHhcccCCCCcCCCCHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHHhcC
Q 023264 161 AAKQEF--GE-EISCEHGLFEESEVFEEPQEVAEEMKILQQKDFYLQAAKARQDAENLAVKLLATRAFTAVEMRKKLNGK 237 (285)
Q Consensus 161 g~efaf--sv-dvlik~~L~kG~~~~ELdee~leeI~~~~q~~~~eq~~~~~~kA~~~AL~lLS~RdrS~~ELr~KL~~K 237 (285)
|+-.|| .+ +-+.+.++..| ++.++-.++. .....-+..+|.....+..||+++....
T Consensus 153 gsgPA~~~~~~~al~~~~v~~G-----l~~~~A~~lv---------------~~~~~G~a~l~~~~~~~~~~l~~~v~sp 212 (245)
T TIGR00112 153 GSGPAYVFLFIEALADAGVKQG-----LPRELALELA---------------AQTVKGAAKLLEESGEHPALLKDQVTSP 212 (245)
T ss_pred cCcHHHHHHHHHHHHHHHHHcC-----CCHHHHHHHH---------------HHHHHHHHHHHHhcCCCHHHHHHcCCCC
Confidence 444444 33 88888888888 4655555544 3445556667767788999999998755
Q ss_pred CCCHHHHHHHHHHHHHCCCCC
Q 023264 238 KFPSHVIEAVITDFQSRGLIN 258 (285)
Q Consensus 238 g~~ee~Ie~VIerLee~GyLD 258 (285)
| ..-++.|+.|++.|+-+
T Consensus 213 g---GtT~~gl~~Le~~~~~~ 230 (245)
T TIGR00112 213 G---GTTIAGLAVLEEKGVRG 230 (245)
T ss_pred c---HHHHHHHHHHHHCChHH
Confidence 3 45566677777776643
No 141
>PRK12491 pyrroline-5-carboxylate reductase; Reviewed
Probab=20.88 E-value=4.2e+02 Score=24.64 Aligned_cols=65 Identities=12% Similarity=0.197 Sum_probs=43.9
Q ss_pred hHHHHhcccCCCCcCCCCHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHHhcCCCCHHHHHHHH
Q 023264 169 EISCEHGLFEESEVFEEPQEVAEEMKILQQKDFYLQAAKARQDAENLAVKLLATRAFTAVEMRKKLNGKKFPSHVIEAVI 248 (285)
Q Consensus 169 dvlik~~L~kG~~~~ELdee~leeI~~~~q~~~~eq~~~~~~kA~~~AL~lLS~RdrS~~ELr~KL~~Kg~~ee~Ie~VI 248 (285)
+-+++.++..| +|.++-.++. .+...=+..+|.....+..||+++....| ..-.+.|
T Consensus 184 eal~~a~v~~G-----l~~~~A~~l~---------------~~t~~G~a~ll~~~~~~p~~l~~~V~sPG---GtT~~gl 240 (272)
T PRK12491 184 EAMADAAVLGG-----MPRKQAYKFA---------------AQAVLGSAKMVLETGIHPGELKDMVCSPG---GTTIEAV 240 (272)
T ss_pred HHHHHHHHHcC-----CCHHHHHHHH---------------HHHHHHHHHHHHhcCCCHHHHHHhCCCCc---hHHHHHH
Confidence 88888888877 5666555554 23344455667778899999999987654 3444556
Q ss_pred HHHHHCCC
Q 023264 249 TDFQSRGL 256 (285)
Q Consensus 249 erLee~Gy 256 (285)
..|++.|+
T Consensus 241 ~~le~~~~ 248 (272)
T PRK12491 241 ATLEEKGL 248 (272)
T ss_pred HHHHHCCh
Confidence 66666555
No 142
>PF11181 YflT: Heat induced stress protein YflT
Probab=20.82 E-value=1.1e+02 Score=24.47 Aligned_cols=44 Identities=11% Similarity=0.124 Sum_probs=33.6
Q ss_pred HHHHHHHHHHhhccccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCC
Q 023264 211 DAENLAVKLLATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLI 257 (285)
Q Consensus 211 kA~~~AL~lLS~RdrS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyL 257 (285)
.-.+...++++ -...+++.+|.+.|++++.++.--+.|.+-++|
T Consensus 57 ~~~d~~~~~f~---~~~d~~~~~l~~lGl~~~ea~~y~~~l~~Gkiv 100 (103)
T PF11181_consen 57 SFWDKIKNFFT---SGGDELRSKLESLGLSEDEAERYEEELDQGKIV 100 (103)
T ss_pred cHHHHHHHhcc---CCcHHHHHHHHHcCCCHHHHHHHHHHHHCCCEE
Confidence 34555566665 234689999999999999999998888876653
No 143
>PF00216 Bac_DNA_binding: Bacterial DNA-binding protein; InterPro: IPR000119 Bacteria synthesise a set of small, usually basic proteins of about 90 residues that bind DNA and are known as histone-like proteins [, ]. Examples include the HU protein in Escherichia coli is a dimer of closely related alpha and beta chains and in other bacteria can be a dimer of identical chains. HU-type proteins have been found in a variety of eubacteria, cyanobacteria and archaebacteria, and are also encoded in the chloroplast genome of some algae []. The integration host factor (IHF), a dimer of closely related chains which seem to function in genetic recombination as well as in translational and transcriptional control [] is found in enterobacteria and viral proteins include the African Swine fever virus protein A104R (or LMW5-AR) []. The exact function of these proteins is not yet clear but they are capable of wrapping DNA and stabilising it from denaturation under extreme environmental conditions. The structure is known for one of these proteins []. The protein exists as a dimer and two "beta-arms" function as the non-specific binding site for bacterial DNA. ; GO: 0003677 DNA binding; PDB: 3C4I_B 2O97_A 1MUL_A 1P78_A 1P51_C 1P71_B 2HT0_A 1OWG_A 2IIF_A 1OUZ_A ....
Probab=20.64 E-value=1.3e+02 Score=22.67 Aligned_cols=28 Identities=25% Similarity=0.349 Sum_probs=22.4
Q ss_pred cHHHHHHHHhcC-CCCHHHHHHHHHHHHH
Q 023264 226 TAVEMRKKLNGK-KFPSHVIEAVITDFQS 253 (285)
Q Consensus 226 S~~ELr~KL~~K-g~~ee~Ie~VIerLee 253 (285)
|..||.+.+.++ +++...+..+|+.|.+
T Consensus 2 tk~eli~~ia~~~~~s~~~v~~vl~~~~~ 30 (90)
T PF00216_consen 2 TKKELIKRIAEKTGLSKKDVEAVLDALFD 30 (90)
T ss_dssp BHHHHHHHHHHHHTSSHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHhcCCCHHHHHHHHHHHHH
Confidence 567888888776 8999999999887764
No 144
>COG4187 RocB Arginine degradation protein (predicted deacylase) [Amino acid transport and metabolism]
Probab=20.38 E-value=9.3e+02 Score=25.50 Aligned_cols=116 Identities=7% Similarity=-0.080 Sum_probs=67.5
Q ss_pred ccchhhccCcccccceEEecCCccchhhhHHHHhcccCCCCcCCCCHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHH
Q 023264 141 ASHKKFQNHNRMTNNNILLDAAKQEFGEEISCEHGLFEESEVFEEPQEVAEEMKILQQKDFYLQAAKARQDAENLAVKLL 220 (285)
Q Consensus 141 ~~~~~~k~~~~r~~~NIyiDg~efafsvdvlik~~L~kG~~~~ELdee~leeI~~~~q~~~~eq~~~~~~kA~~~AL~lL 220 (285)
+.|..||..++-| ||=-=. .++..+..++ +..+..++-+..++.-..+++ +.++....++-.|.
T Consensus 278 Ps~L~qkDlKe~Y--~VqTp~-~a~~~fN~l~----------h~~ta~~~~d~l~~~a~~A~~---e~i~~~~~~~~~y~ 341 (553)
T COG4187 278 PSCLEQKDLKESY--NVQTPE-RAWLYFNWLY----------HSRTAKELFDRLKEEAETAAE---EAIETLRDRYEEYG 341 (553)
T ss_pred cHhhhhhhhhhhc--cccCcc-hhhhhheehh----------hcCCHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHH
Confidence 4588888888877 654433 2221112221 334445554444212111222 23333333333333
Q ss_pred hhc------------cccHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhhhh
Q 023264 221 ATR------------AFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLINDSLYAESYSRSRWS 272 (285)
Q Consensus 221 S~R------------drS~~ELr~KL~~Kg~~ee~Ie~VIerLee~GyLDD~rYAesyVrsr~~ 272 (285)
... -.|-.||-.+++..|-....+...-..+...|+||++.++-..+.-.+.
T Consensus 342 k~~n~~~~~l~~~~~Vlt~~ell~raR~~g~~d~~~~~~e~~f~~~~~ld~r~~s~~~~~~L~~ 405 (553)
T COG4187 342 KLVNRPAGPLPAKPRVLTFQELLERARVRGHIDAEYAEKEYEFAQNGELDLRLRSTQLTEWLVG 405 (553)
T ss_pred HHhcCCCCCCCCCceEEEHHHHHHHHHhcCCCCHHHHHHHHHhhhCcccCchHHHHHHHHHHHh
Confidence 332 4678899999999985555666677788999999999999887776554
Done!