Query 024196
Match_columns 271
No_of_seqs 161 out of 345
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 02:47:00 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024196.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024196hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2829 E2F-like protein [Tran 100.0 5.3E-63 1.1E-67 456.9 21.3 180 92-271 38-218 (326)
2 PF08781 DP: Transcription fac 99.9 1.2E-27 2.6E-32 203.2 11.3 87 185-271 1-87 (142)
3 KOG2577 Transcription factor E 99.9 2.6E-24 5.6E-29 204.4 11.7 146 94-268 67-231 (354)
4 PF02319 E2F_TDP: E2F/DP famil 99.7 1.3E-17 2.7E-22 125.9 4.5 67 96-178 2-71 (71)
5 KOG2578 Transcription factor E 98.9 1.3E-09 2.7E-14 103.6 4.7 71 123-194 30-101 (388)
6 KOG2578 Transcription factor E 95.8 0.0041 9E-08 59.9 1.6 72 98-180 159-239 (388)
7 PF01978 TrmB: Sugar-specific 95.4 0.03 6.4E-07 40.9 4.6 59 98-177 4-63 (68)
8 COG1378 Predicted transcriptio 92.9 0.61 1.3E-05 43.0 8.7 35 148-182 41-76 (247)
9 smart00420 HTH_DEOR helix_turn 90.4 0.83 1.8E-05 30.3 5.0 48 106-174 4-51 (53)
10 COG3355 Predicted transcriptio 89.3 2.6 5.7E-05 35.9 8.3 56 98-174 23-79 (126)
11 PF05402 PqqD: Coenzyme PQQ sy 88.6 0.86 1.9E-05 32.9 4.3 55 99-168 14-68 (68)
12 smart00346 HTH_ICLR helix_turn 86.6 8.4 0.00018 28.7 8.8 45 105-170 8-53 (91)
13 PF13412 HTH_24: Winged helix- 83.4 4.3 9.4E-05 27.5 5.4 44 104-168 5-48 (48)
14 PF09012 FeoC: FeoC like trans 83.1 2 4.4E-05 31.7 4.0 43 106-169 4-46 (69)
15 PF09339 HTH_IclR: IclR helix- 82.6 2.3 5E-05 29.6 3.9 45 105-170 6-51 (52)
16 smart00347 HTH_MARR helix_turn 81.0 20 0.00042 26.4 8.8 52 98-170 6-57 (101)
17 smart00418 HTH_ARSR helix_turn 80.6 3.4 7.3E-05 27.7 4.1 41 107-169 2-42 (66)
18 TIGR02337 HpaR homoprotocatech 78.9 23 0.00049 28.1 9.0 52 98-170 24-75 (118)
19 smart00550 Zalpha Z-DNA-bindin 77.2 7.4 0.00016 28.9 5.3 52 105-177 9-63 (68)
20 PRK10411 DNA-binding transcrip 76.9 22 0.00048 32.4 9.4 53 105-178 7-60 (240)
21 PF08279 HTH_11: HTH domain; 76.6 6.9 0.00015 27.0 4.8 39 106-165 4-43 (55)
22 smart00344 HTH_ASNC helix_turn 74.0 7.5 0.00016 30.1 4.9 45 104-169 5-49 (108)
23 smart00419 HTH_CRP helix_turn_ 73.3 7.6 0.00017 25.4 4.1 26 149-174 20-45 (48)
24 PF12840 HTH_20: Helix-turn-he 72.7 11 0.00023 26.9 5.0 44 105-169 13-56 (61)
25 cd07153 Fur_like Ferric uptake 71.1 11 0.00025 29.5 5.4 48 106-169 5-53 (116)
26 PF01022 HTH_5: Bacterial regu 70.8 10 0.00022 25.9 4.4 41 107-169 7-47 (47)
27 PRK15090 DNA-binding transcrip 70.8 50 0.0011 29.8 10.1 61 97-178 7-70 (257)
28 PF09079 Cdc6_C: CDC6, C termi 69.5 3 6.6E-05 31.6 1.7 21 149-169 37-57 (85)
29 PF01475 FUR: Ferric uptake re 68.5 13 0.00028 29.6 5.2 65 98-178 2-72 (120)
30 PRK09462 fur ferric uptake reg 66.7 16 0.00035 30.5 5.7 56 98-169 11-70 (148)
31 PRK09834 DNA-binding transcrip 66.1 62 0.0013 29.4 9.7 50 105-175 14-66 (263)
32 PRK03947 prefoldin subunit alp 66.0 37 0.00079 28.1 7.6 56 168-223 73-132 (140)
33 cd00090 HTH_ARSR Arsenical Res 66.0 28 0.00061 23.6 6.0 44 104-169 9-52 (78)
34 PF08220 HTH_DeoR: DeoR-like h 66.0 20 0.00043 25.7 5.2 49 105-174 3-51 (57)
35 cd00092 HTH_CRP helix_turn_hel 65.5 15 0.00032 25.7 4.4 40 114-174 23-63 (67)
36 TIGR00293 prefoldin, archaeal 64.8 38 0.00082 27.4 7.3 67 154-220 51-121 (126)
37 PF14338 Mrr_N: Mrr N-terminal 63.4 9.6 0.00021 29.5 3.4 66 105-177 7-79 (92)
38 PF14193 DUF4315: Domain of un 63.3 25 0.00055 27.9 5.8 36 186-221 2-37 (83)
39 TIGR02431 pcaR_pcaU beta-ketoa 62.9 65 0.0014 28.8 9.1 50 105-175 12-62 (248)
40 cd00890 Prefoldin Prefoldin is 61.4 71 0.0015 25.4 8.3 54 169-222 67-124 (129)
41 PF01047 MarR: MarR family; I 60.9 20 0.00044 24.8 4.4 44 105-169 6-49 (59)
42 TIGR01889 Staph_reg_Sar staphy 60.8 65 0.0014 25.5 7.9 74 99-193 22-103 (109)
43 PRK11179 DNA-binding transcrip 60.1 27 0.00058 29.3 5.8 51 98-169 5-55 (153)
44 PRK09802 DNA-binding transcrip 59.6 54 0.0012 30.4 8.2 49 105-174 20-69 (269)
45 COG1522 Lrp Transcriptional re 59.3 21 0.00046 29.0 5.0 50 100-170 6-55 (154)
46 cd08768 Cdc6_C Winged-helix do 59.1 6.3 0.00014 29.5 1.7 21 149-169 44-64 (87)
47 PRK10163 DNA-binding transcrip 58.8 88 0.0019 28.7 9.4 60 98-178 19-82 (271)
48 PRK11169 leucine-responsive tr 58.5 24 0.00051 30.1 5.3 52 97-169 9-60 (164)
49 PRK13777 transcriptional regul 58.0 1.4E+02 0.003 26.6 10.5 75 98-193 41-119 (185)
50 PF12802 MarR_2: MarR family; 57.6 37 0.00079 23.5 5.3 51 99-170 2-54 (62)
51 PF13730 HTH_36: Helix-turn-he 56.8 14 0.0003 25.4 3.0 20 148-167 36-55 (55)
52 PRK10434 srlR DNA-bindng trans 55.3 53 0.0011 30.1 7.3 45 105-170 8-52 (256)
53 PRK13509 transcriptional repre 54.9 76 0.0017 29.0 8.3 44 105-169 8-51 (251)
54 PF13463 HTH_27: Winged helix 54.3 23 0.00051 24.9 3.9 43 106-169 7-50 (68)
55 COG0735 Fur Fe2+/Zn2+ uptake r 53.8 55 0.0012 27.7 6.7 63 98-176 15-82 (145)
56 PF01726 LexA_DNA_bind: LexA D 52.9 42 0.00092 25.0 5.2 39 114-172 23-61 (65)
57 PRK09954 putative kinase; Prov 52.4 28 0.00061 32.7 5.2 46 103-169 4-49 (362)
58 TIGR00589 ogt O-6-methylguanin 52.4 17 0.00038 28.2 3.2 25 102-126 2-29 (80)
59 PF00392 GntR: Bacterial regul 50.6 21 0.00047 25.5 3.2 55 119-173 2-61 (64)
60 PF01035 DNA_binding_1: 6-O-me 50.3 12 0.00026 29.1 2.0 25 102-126 2-29 (85)
61 cd00584 Prefoldin_alpha Prefol 48.0 1.5E+02 0.0032 24.0 8.7 54 169-222 67-124 (129)
62 PF03836 RasGAP_C: RasGAP C-te 46.6 6.5 0.00014 33.1 0.0 26 149-175 4-29 (142)
63 TIGR01884 cas_HTH CRISPR locus 45.9 59 0.0013 28.5 5.9 52 99-171 140-191 (203)
64 PF07106 TBPIP: Tat binding pr 44.4 2E+02 0.0043 24.5 11.3 88 106-212 5-106 (169)
65 cd06445 ATase The DNA repair p 44.3 25 0.00055 26.7 2.9 23 104-126 2-27 (79)
66 PF03979 Sigma70_r1_1: Sigma-7 43.7 42 0.00091 25.7 4.1 43 106-166 11-53 (82)
67 PRK11050 manganese transport r 42.8 92 0.002 26.4 6.4 51 105-176 40-91 (152)
68 PRK11512 DNA-binding transcrip 42.7 1.9E+02 0.0041 23.7 11.3 63 98-181 36-102 (144)
69 TIGR01242 26Sp45 26S proteasom 42.6 87 0.0019 29.8 6.9 40 189-228 3-42 (364)
70 PRK11639 zinc uptake transcrip 42.2 64 0.0014 27.9 5.4 62 98-175 20-86 (169)
71 COG5625 Predicted transcriptio 41.5 57 0.0012 27.4 4.7 48 112-180 32-79 (113)
72 TIGR00122 birA_repr_reg BirA b 41.1 1E+02 0.0022 22.3 5.6 47 106-174 4-51 (69)
73 PF13545 HTH_Crp_2: Crp-like h 40.9 56 0.0012 23.5 4.2 39 116-175 28-66 (76)
74 TIGR00498 lexA SOS regulatory 40.8 46 0.001 28.7 4.4 54 100-174 4-63 (199)
75 PF02996 Prefoldin: Prefoldin 39.8 1.3E+02 0.0028 23.8 6.5 69 156-224 44-116 (120)
76 PRK09039 hypothetical protein; 39.4 83 0.0018 30.5 6.3 76 184-271 143-232 (343)
77 PF13518 HTH_28: Helix-turn-he 39.2 75 0.0016 21.1 4.4 38 106-166 4-41 (52)
78 TIGR02894 DNA_bind_RsfA transc 39.1 1.4E+02 0.0031 26.6 7.1 44 186-229 105-155 (161)
79 COG1510 Predicted transcriptio 38.4 2.2E+02 0.0048 25.8 8.3 36 113-169 38-73 (177)
80 PF13404 HTH_AsnC-type: AsnC-t 38.2 53 0.0011 22.5 3.5 25 102-126 3-27 (42)
81 TIGR03697 NtcA_cyano global ni 38.1 59 0.0013 26.9 4.5 35 143-177 149-183 (193)
82 COG0350 Ada Methylated DNA-pro 37.7 32 0.00069 30.1 2.9 25 102-126 88-115 (168)
83 TIGR02698 CopY_TcrY copper tra 37.4 2.4E+02 0.0052 23.4 11.7 56 105-177 7-64 (130)
84 PRK07037 extracytoplasmic-func 37.4 25 0.00055 28.7 2.1 34 114-164 123-156 (163)
85 PRK11753 DNA-binding transcrip 36.8 56 0.0012 27.6 4.2 33 144-176 175-207 (211)
86 TIGR02716 C20_methyl_CrtF C-20 36.7 58 0.0013 29.9 4.6 49 105-175 13-61 (306)
87 PF06717 DUF1202: Protein of u 36.6 1.4E+02 0.003 29.2 7.1 58 164-223 119-176 (308)
88 PF04703 FaeA: FaeA-like prote 36.6 99 0.0021 23.1 5.0 52 105-177 3-59 (62)
89 PF11594 Med28: Mediator compl 36.6 1.3E+02 0.0027 25.3 6.0 37 188-224 38-74 (106)
90 KOG2264 Exostosin EXT1L [Signa 36.3 95 0.0021 33.3 6.4 38 188-225 110-151 (907)
91 PRK00901 methylated-DNA--prote 36.1 36 0.00079 29.6 3.0 26 101-126 72-100 (155)
92 smart00345 HTH_GNTR helix_turn 35.7 70 0.0015 21.3 3.8 23 148-170 31-53 (60)
93 smart00338 BRLZ basic region l 35.7 1.7E+02 0.0037 21.1 6.2 34 187-220 28-61 (65)
94 PRK10803 tol-pal system protei 35.3 1.2E+02 0.0027 28.1 6.5 44 183-226 59-103 (263)
95 TIGR01610 phage_O_Nterm phage 35.1 1.3E+02 0.0028 23.6 5.7 31 148-179 58-88 (95)
96 PF05732 RepL: Firmicute plasm 34.5 62 0.0013 28.3 4.2 26 148-173 86-111 (165)
97 TIGR02147 Fsuc_second hypothet 34.1 4.1E+02 0.0089 25.1 12.1 60 98-177 114-178 (271)
98 PF08317 Spc7: Spc7 kinetochor 33.7 1.6E+02 0.0035 28.0 7.2 38 186-223 210-247 (325)
99 PF10473 CENP-F_leu_zip: Leuci 33.6 1.5E+02 0.0033 25.6 6.3 40 185-224 73-112 (140)
100 PF14394 DUF4423: Domain of un 33.5 3.3E+02 0.0071 23.8 11.4 26 150-176 54-79 (171)
101 PF01638 HxlR: HxlR-like helix 33.2 69 0.0015 24.5 3.8 44 105-169 8-51 (90)
102 PF12958 DUF3847: Protein of u 32.9 1.9E+02 0.004 23.3 6.3 45 186-230 2-48 (86)
103 PF08317 Spc7: Spc7 kinetochor 32.9 1.3E+02 0.0029 28.5 6.5 81 186-270 231-319 (325)
104 PRK11569 transcriptional repre 32.9 3.9E+02 0.0084 24.5 9.5 46 105-171 31-77 (274)
105 smart00529 HTH_DTXR Helix-turn 32.6 2.1E+02 0.0046 21.4 6.6 23 150-172 12-34 (96)
106 PHA02943 hypothetical protein; 32.5 2E+02 0.0043 25.8 6.9 66 107-194 16-83 (165)
107 PRK13923 putative spore coat p 31.9 1.9E+02 0.0042 25.9 6.9 44 186-229 112-155 (170)
108 PF07544 Med9: RNA polymerase 31.4 1.1E+02 0.0023 23.9 4.6 50 148-213 31-80 (83)
109 TIGR02702 SufR_cyano iron-sulf 31.1 1.1E+02 0.0023 26.9 5.1 45 105-170 4-48 (203)
110 PF02050 FliJ: Flagellar FliJ 31.0 2.3E+02 0.005 21.2 7.4 44 185-228 59-102 (123)
111 PRK10870 transcriptional repre 29.6 3.7E+02 0.008 23.2 10.8 64 98-182 51-120 (176)
112 PF11853 DUF3373: Protein of u 29.5 50 0.0011 34.0 3.1 28 200-227 32-59 (489)
113 smart00787 Spc7 Spc7 kinetocho 29.2 1.6E+02 0.0036 28.3 6.4 38 186-223 205-242 (312)
114 PF10481 CENP-F_N: Cenp-F N-te 29.0 1.3E+02 0.0027 29.4 5.5 37 176-212 8-45 (307)
115 COG3883 Uncharacterized protei 28.7 2.1E+02 0.0046 27.4 6.9 40 188-227 62-102 (265)
116 PRK06798 fliD flagellar cappin 28.4 1.5E+02 0.0032 29.8 6.2 65 148-224 357-422 (440)
117 PF04977 DivIC: Septum formati 28.1 1.9E+02 0.0041 20.9 5.3 26 186-211 25-50 (80)
118 PF08221 HTH_9: RNA polymerase 28.0 1.5E+02 0.0033 21.6 4.8 46 102-168 13-58 (62)
119 PF11315 Med30: Mediator compl 27.7 1.6E+02 0.0034 26.0 5.5 31 185-215 104-134 (150)
120 PF07334 IFP_35_N: Interferon- 27.4 1.4E+02 0.003 23.7 4.6 27 187-213 2-28 (76)
121 PRK06474 hypothetical protein; 27.2 1.4E+02 0.003 26.1 5.1 45 105-169 14-59 (178)
122 PF04568 IATP: Mitochondrial A 27.0 1.9E+02 0.0042 23.7 5.6 9 204-212 88-96 (100)
123 COG1414 IclR Transcriptional r 26.8 1.8E+02 0.0038 26.6 5.9 46 105-171 7-53 (246)
124 PF09766 FimP: Fms-interacting 26.4 1.9E+02 0.0041 28.1 6.4 38 185-222 108-145 (355)
125 PF04545 Sigma70_r4: Sigma-70, 26.4 1.2E+02 0.0025 20.6 3.6 32 114-162 18-49 (50)
126 PF08664 YcbB: YcbB domain; I 26.4 81 0.0018 27.1 3.4 49 118-168 41-89 (134)
127 PF05529 Bap31: B-cell recepto 25.5 1.6E+02 0.0035 25.6 5.2 26 190-215 159-184 (192)
128 PF04182 B-block_TFIIIC: B-blo 25.5 1.5E+02 0.0032 22.2 4.4 19 151-169 32-50 (75)
129 PF01325 Fe_dep_repress: Iron 25.5 2.1E+02 0.0046 20.7 5.1 45 105-170 11-55 (60)
130 PF13601 HTH_34: Winged helix 25.4 74 0.0016 24.3 2.8 45 106-171 4-48 (80)
131 KOG3478 Prefoldin subunit 6, K 24.6 1.5E+02 0.0032 25.3 4.6 24 156-179 37-60 (120)
132 PF04492 Phage_rep_O: Bacterio 24.2 63 0.0014 26.2 2.3 26 149-174 66-91 (100)
133 PRK12423 LexA repressor; Provi 24.1 2E+02 0.0043 25.3 5.6 47 105-172 13-61 (202)
134 TIGR03859 PQQ_PqqD coenzyme PQ 24.0 1.6E+02 0.0034 22.5 4.4 55 98-168 27-81 (81)
135 PF01920 Prefoldin_2: Prefoldi 24.0 3.3E+02 0.0071 20.7 7.0 68 150-219 24-96 (106)
136 PF14817 HAUS5: HAUS augmin-li 24.0 2.3E+02 0.0051 30.1 6.9 48 168-215 53-109 (632)
137 PRK07720 fliJ flagellar biosyn 23.8 3.3E+02 0.0072 22.5 6.6 43 186-228 79-121 (146)
138 KOG1962 B-cell receptor-associ 23.8 2.1E+02 0.0046 26.6 5.9 40 186-225 152-191 (216)
139 PRK10884 SH3 domain-containing 23.4 3.4E+02 0.0074 24.7 7.1 45 184-228 99-144 (206)
140 PRK14127 cell division protein 23.2 2E+02 0.0044 23.9 5.1 51 163-215 8-67 (109)
141 PRK13182 racA polar chromosome 23.0 2.7E+02 0.0058 24.7 6.2 40 185-224 85-124 (175)
142 PF10186 Atg14: UV radiation r 23.0 3.8E+02 0.0082 24.0 7.3 12 148-159 37-48 (302)
143 PRK10906 DNA-binding transcrip 22.9 1.5E+02 0.0032 27.2 4.7 48 105-173 8-56 (252)
144 PF03962 Mnd1: Mnd1 family; I 22.9 4.9E+02 0.011 23.1 7.8 52 154-206 32-90 (188)
145 PRK13922 rod shape-determining 22.8 2.4E+02 0.0051 25.8 6.0 18 186-203 70-87 (276)
146 PF04156 IncA: IncA protein; 22.8 4E+02 0.0087 22.7 7.1 30 198-227 157-186 (191)
147 COG1730 GIM5 Predicted prefold 22.7 5.1E+02 0.011 22.5 8.9 39 185-223 94-132 (145)
148 PF12269 zf-CpG_bind_C: CpG bi 22.7 2.1E+02 0.0046 26.9 5.7 51 175-228 15-65 (236)
149 PRK11402 DNA-binding transcrip 22.6 1.3E+02 0.0028 26.7 4.2 54 116-169 8-65 (241)
150 PF05103 DivIVA: DivIVA protei 22.6 20 0.00043 28.8 -0.9 48 173-220 12-67 (131)
151 PRK10286 O-6-alkylguanine-DNA: 22.4 85 0.0018 27.9 2.9 26 101-126 87-115 (171)
152 smart00787 Spc7 Spc7 kinetocho 22.3 3.3E+02 0.0071 26.3 7.1 42 186-227 226-267 (312)
153 TIGR02338 gimC_beta prefoldin, 22.2 3.1E+02 0.0067 22.0 5.9 65 152-216 31-98 (110)
154 PRK10079 phosphonate metabolis 22.0 1.4E+02 0.003 26.5 4.3 53 117-169 12-67 (241)
155 TIGR02404 trehalos_R_Bsub treh 21.9 1.4E+02 0.003 26.3 4.2 51 119-169 2-56 (233)
156 TIGR02473 flagell_FliJ flagell 21.3 4.1E+02 0.009 21.2 6.6 43 185-227 75-117 (141)
157 PF06163 DUF977: Bacterial pro 21.3 2.6E+02 0.0057 24.1 5.5 50 102-172 12-61 (127)
158 PF10234 Cluap1: Clusterin-ass 21.3 2.4E+02 0.0051 27.0 5.8 22 187-208 185-206 (267)
159 PRK14165 winged helix-turn-hel 21.2 2.4E+02 0.0053 25.8 5.7 39 110-169 15-53 (217)
160 TIGR03338 phnR_burk phosphonat 21.1 5.3E+02 0.011 22.1 7.8 29 147-175 44-73 (212)
161 cd07377 WHTH_GntR Winged helix 20.8 2.1E+02 0.0047 19.3 4.2 23 148-170 36-58 (66)
162 COG1938 Archaeal enzymes of AT 20.8 2.5E+02 0.0055 26.5 5.8 28 186-213 205-232 (244)
163 PRK13918 CRP/FNR family transc 20.6 1.7E+02 0.0037 24.5 4.3 34 144-177 156-189 (202)
164 PRK03887 methylated-DNA--prote 20.5 1.3E+02 0.0028 27.2 3.7 29 98-126 88-120 (175)
165 PRK00888 ftsB cell division pr 20.5 3.5E+02 0.0076 21.9 5.9 42 184-225 33-74 (105)
166 PF10828 DUF2570: Protein of u 20.5 4.6E+02 0.01 21.1 7.1 64 151-225 2-65 (110)
167 PRK11414 colanic acid/biofilm 20.4 5.7E+02 0.012 22.2 8.0 28 148-175 45-73 (221)
168 TIGR02894 DNA_bind_RsfA transc 20.4 3.1E+02 0.0067 24.6 5.9 24 103-126 15-40 (161)
169 PRK09413 IS2 repressor TnpA; R 20.3 4.7E+02 0.01 21.1 11.9 13 114-126 27-39 (121)
170 PF04380 BMFP: Membrane fusoge 20.3 2.3E+02 0.005 21.8 4.6 49 147-213 30-78 (79)
171 PRK05689 fliJ flagellar biosyn 20.1 4.4E+02 0.0094 21.7 6.6 42 186-227 79-120 (147)
No 1
>KOG2829 consensus E2F-like protein [Transcription]
Probab=100.00 E-value=5.3e-63 Score=456.95 Aligned_cols=180 Identities=61% Similarity=0.898 Sum_probs=173.0
Q ss_pred CCCccccccchhHHHHHHHHHhcCCCcHHHHHHHHHHHhcCCCC-CCCCCChhhhccccchhhhhhHHHHhhhccceeec
Q 024196 92 GGDKSGRGLRQFSMKVCEKVESKGRTTYNEVADELVAEFADPSN-SLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKD 170 (271)
Q Consensus 92 ~~~k~~~GLR~fS~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~-~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K~ 170 (271)
.++++|+|||||||+||+||++||.|||+||||+||++|..+++ ....+++++||+|||||||||||||||||+||+|+
T Consensus 38 ks~k~g~gLRhfs~kVCeKve~Kg~TtYneVADelVaef~~~n~~~~i~~n~~~yd~KNIRRRVYDALNVlmAmnIIsKd 117 (326)
T KOG2829|consen 38 KSDKAGGGLRHFSMKVCEKVERKGTTTYNEVADELVAEFAGANNYSHICPNEQEYDQKNIRRRVYDALNVLMAMNIISKD 117 (326)
T ss_pred CCCCCCcchhhhhHHHHHHHHhcCCccHHHHHHHHHHHHhccccccccCccccccchHHHHHHHHHHHHHHHHHHHHhcc
Confidence 36789999999999999999999999999999999999998876 35678899999999999999999999999999999
Q ss_pred CCceEEecCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCcccccEEEEEcCC
Q 024196 171 KKEIQWKGLPRTSLNDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQRNERLYSSGNAPSGGVALPFILVQTRP 250 (271)
Q Consensus 171 Kk~i~W~G~~~~s~~~~~~Lk~E~~~l~e~I~~Kk~~LqEL~~Q~~~lknLI~RNk~l~~~~~~~~~~i~LPFIvV~T~~ 250 (271)
||.|+|+|+|.++.+++++|++|+.+++++|++|+++|+||+.|+++|++||+||+.+++++..|.+.|+||||||+|+|
T Consensus 118 KKEIrW~GLP~~ss~dv~~le~Er~k~~erI~kK~a~lqEl~~q~~~fknLV~RN~~~e~~~~~P~~~i~LPFiiinT~k 197 (326)
T KOG2829|consen 118 KKEIRWIGLPATSSQDVSELEEERKKRMERIKKKAAQLQELIEQVSAFKNLVQRNRHAESQGQPPSENIHLPFIIINTSK 197 (326)
T ss_pred cceeeeeccCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhccCCCCcccccceEEEecCC
Confidence 99999999999999999999999999999999999999999999999999999999999888888888999999999999
Q ss_pred CcEEEEeecCCceEEEEeecC
Q 024196 251 HATVEVEISEDMQLVHFDFNR 271 (271)
Q Consensus 251 ~t~IeceiseD~~~~~F~F~~ 271 (271)
+|+|+|+||||+++|||+||+
T Consensus 198 ~a~IeceiseDks~~~F~Fnk 218 (326)
T KOG2829|consen 198 KAVIECEISEDKSEYLFKFNK 218 (326)
T ss_pred CceEEEEecccceeeeeecCC
Confidence 999999999999999999995
No 2
>PF08781 DP: Transcription factor DP; InterPro: IPR014889 DP forms a heterodimer with E2F and regulates genes involved in cell cycle progression. The transcriptional activity of E2F is inhibited by the retinoblastoma protein which binds to the E2F-DP heterodimer [] and negatively regulates the G1-S transition. ; PDB: 2AZE_A.
Probab=99.95 E-value=1.2e-27 Score=203.15 Aligned_cols=87 Identities=54% Similarity=0.748 Sum_probs=78.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCcccccEEEEEcCCCcEEEEeecCCceE
Q 024196 185 NDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQRNERLYSSGNAPSGGVALPFILVQTRPHATVEVEISEDMQL 264 (271)
Q Consensus 185 ~~~~~Lk~E~~~l~e~I~~Kk~~LqEL~~Q~~~lknLI~RNk~l~~~~~~~~~~i~LPFIvV~T~~~t~IeceiseD~~~ 264 (271)
++|++|++|+.+++++|++|+++|+||+.|+++|+|||+||+.++.++..|+++|+||||||+|+++|+|+|+||+|+++
T Consensus 1 q~~~~Le~ek~~~~~rI~~K~~~LqEL~~Q~va~knLv~RN~~~~~~~~~p~~~i~LPFIlV~T~~~a~I~ceiS~D~~~ 80 (142)
T PF08781_consen 1 QECEELEEEKQRRRERIKKKKEQLQELILQQVAFKNLVQRNRQLEQSGNAPSSGIQLPFILVNTSKKAVIECEISEDKSE 80 (142)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSSS--GEEESS-EEEEEESS--EEEEE-TTSSE
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCeeecCEEEEEecCCcEEEEEEcCCccE
Confidence 57999999999999999999999999999999999999999999988888889999999999999999999999999999
Q ss_pred EEEeecC
Q 024196 265 VHFDFNR 271 (271)
Q Consensus 265 ~~F~F~~ 271 (271)
||||||+
T Consensus 81 ~~F~Fn~ 87 (142)
T PF08781_consen 81 YHFDFNS 87 (142)
T ss_dssp EEEEESS
T ss_pred EEEEcCC
Confidence 9999995
No 3
>KOG2577 consensus Transcription factor E2F/dimerization partner (TDP) [Transcription]
Probab=99.91 E-value=2.6e-24 Score=204.41 Aligned_cols=146 Identities=28% Similarity=0.411 Sum_probs=114.3
Q ss_pred CccccccchhHHHHHHHHHh--cCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceee-c
Q 024196 94 DKSGRGLRQFSMKVCEKVES--KGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK-D 170 (271)
Q Consensus 94 ~k~~~GLR~fS~KVcekVk~--kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K-~ 170 (271)
-+..++|-.+++||.+.|++ -|...+|++|..| ++.|||||||||||||||||+| +
T Consensus 67 ~R~d~SLglLTkKFv~Llq~s~dGvldLn~aA~~L---------------------~VqKRRIYDITNVLEGI~LIeKks 125 (354)
T KOG2577|consen 67 TRSDTSLGLLTKKFVDLLQESPDGVLDLNKAAEVL---------------------NVQKRRIYDITNVLEGIGLIEKKS 125 (354)
T ss_pred ccchhhHHHHHHHHHHHHHhCCCceeeHHHHHHHh---------------------ccccceeeehhhhhhcccceeecc
Confidence 34568999999999999999 5799999999999 5779999999999999999999 9
Q ss_pred CCceEEecCCCCC----h-------hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-hcC--CCCCC
Q 024196 171 KKEIQWKGLPRTS----L-------NDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQRNERL-YSS--GNAPS 236 (271)
Q Consensus 171 Kk~i~W~G~~~~s----~-------~~~~~Lk~E~~~l~e~I~~Kk~~LqEL~~Q~~~lknLI~RNk~l-~~~--~~~~~ 236 (271)
||+|+|+|.+.++ . .+++.|+++...|+++|+.+++.|..|++.. .|+.+ |++ ++...
T Consensus 126 KN~IqW~G~~~~~~~~~~e~~~~l~~e~~~L~~~E~~LD~~i~~~q~~L~~lted~--------~n~~laYVT~eDI~~i 197 (354)
T KOG2577|consen 126 KNNIQWIGGDFNSTGGVPERLNGLEAEVEDLSQEEDDLDQLIRDCQQNLRLLTEDV--------ENRRLAYVTYEDIRSI 197 (354)
T ss_pred ccceeeecCCCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcch--------hcccceeeeHHHHhhc
Confidence 9999999988664 1 3344444444555666666666666666555 45554 553 34445
Q ss_pred Cccc-ccEEEEEcCCCcEEEEeec-CCceEEEEe
Q 024196 237 GGVA-LPFILVQTRPHATVEVEIS-EDMQLVHFD 268 (271)
Q Consensus 237 ~~i~-LPFIvV~T~~~t~Ieceis-eD~~~~~F~ 268 (271)
..|+ ..+|+|++|+.|+++|+++ +++..++.+
T Consensus 198 ~~f~~q~vi~vkap~et~levp~~~~~~~~i~L~ 231 (354)
T KOG2577|consen 198 PGFDEQTVIAVKAPPETRLEVPDPDEDRYQIRLK 231 (354)
T ss_pred cccCCceEEEEecCCcceEecccCCCCceEEEec
Confidence 5688 8999999999999999999 777766654
No 4
>PF02319 E2F_TDP: E2F/DP family winged-helix DNA-binding domain; InterPro: IPR003316 The mammalian transcription factor E2F plays an important role in regulating the expression of genes that are required for passage through the cell cycle. Multiple E2F family members have been identified that bind to DNA as heterodimers, interacting with proteins known as DP - the dimerisation partners [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005667 transcription factor complex; PDB: 1CF7_B.
Probab=99.70 E-value=1.3e-17 Score=125.90 Aligned_cols=67 Identities=36% Similarity=0.644 Sum_probs=57.6
Q ss_pred cccccchhHHHHHHHHHh--cCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceee-cCC
Q 024196 96 SGRGLRQFSMKVCEKVES--KGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK-DKK 172 (271)
Q Consensus 96 ~~~GLR~fS~KVcekVk~--kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K-~Kk 172 (271)
..+||..++.++.+.+.. .+.++++++|++|+.+ ..++.|||||||+|||+|+|||+| .|+
T Consensus 2 ~~~sL~~lt~~fi~~~~~~~~~~i~l~~ia~~l~~~----------------~~k~~~RRlYDI~NVLealgli~K~~k~ 65 (71)
T PF02319_consen 2 KEKSLKLLTQRFIQLFESSPDKSISLNEIADKLISE----------------NVKTQRRRLYDIINVLEALGLIEKQSKN 65 (71)
T ss_dssp TTTHHHHHHHHHHHHHHHCCCTEEEHHHHHHHCHHH----------------CCHHHCHHHHHHHHHHHHCTSEEEEETT
T ss_pred CcCCHHHHHHHHHHHHHHCCCCcccHHHHHHHHccc----------------ccccccchhhHHHHHHHHhCceeecCCC
Confidence 458999999996666654 5899999999999887 247899999999999999999999 999
Q ss_pred ceEEec
Q 024196 173 EIQWKG 178 (271)
Q Consensus 173 ~i~W~G 178 (271)
.|+|.|
T Consensus 66 ~~~W~G 71 (71)
T PF02319_consen 66 SYKWIG 71 (71)
T ss_dssp EEEE--
T ss_pred ceEecC
Confidence 999998
No 5
>KOG2578 consensus Transcription factor E2F/dimerization partner (TDP)-like proteins [Transcription]
Probab=98.90 E-value=1.3e-09 Score=103.55 Aligned_cols=71 Identities=24% Similarity=0.427 Sum_probs=55.4
Q ss_pred HHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceee-cCCceEEecCCCCChhHHHHHHHHH
Q 024196 123 ADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK-DKKEIQWKGLPRTSLNDIEELKAER 194 (271)
Q Consensus 123 AdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K-~Kk~i~W~G~~~~s~~~~~~Lk~E~ 194 (271)
+..++-.|..+.....++++.+....+-|||||||.||||+||++.| .||.|+|+|+.... .-+.+|++|-
T Consensus 30 v~nfl~lynr~dvdlvgLddaA~KlgVErRRIYDiVNvlEsig~var~~KnqYsWkGf~aiP-ral~eLqeEg 101 (388)
T KOG2578|consen 30 VQNFLILYNRSDVDLVGLDDAARKLGVERRRIYDIVNVLESIGAVARRGKNQYSWKGFGAIP-RALFELQEEG 101 (388)
T ss_pred HHHHHHHhcCCCcceechhhHHHhcCchHHHHHHHHHHHHHHHHHHhcccCcccccchhhhh-HHHHHHHHHH
Confidence 44444455666666777888888999999999999999999999999 99999999996542 2355666653
No 6
>KOG2578 consensus Transcription factor E2F/dimerization partner (TDP)-like proteins [Transcription]
Probab=95.80 E-value=0.0041 Score=59.95 Aligned_cols=72 Identities=24% Similarity=0.380 Sum_probs=47.5
Q ss_pred cccchhHHHHHHHHHh--cC-CCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceeec----
Q 024196 98 RGLRQFSMKVCEKVES--KG-RTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKD---- 170 (271)
Q Consensus 98 ~GLR~fS~KVcekVk~--kg-~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K~---- 170 (271)
++|-.+...+....-. .- ..|+...|.-|+.+-... ...-.-=||+|||-|||-+|+||+|.
T Consensus 159 kSL~lL~qnFvklflcs~~~~lvslD~Aak~Ll~ds~~~-----------~~mRtkvRRLYDIANVlssm~LIeKtH~l~ 227 (388)
T KOG2578|consen 159 KSLWLLAQNFVKLFLCSDDDILVSLDSAAKALLKDSEDE-----------PPMRTKVRRLYDIANVLSSMNLIEKTHYLF 227 (388)
T ss_pred hHHHHHHHHHHHheeccccceEEeecHHHHHHhcCCCCC-----------ccHHHHHHHHHHHHHHHHHhhhhhhhcccc
Confidence 6788888776554433 22 567766666665432111 11223459999999999999999992
Q ss_pred --CCceEEecCC
Q 024196 171 --KKEIQWKGLP 180 (271)
Q Consensus 171 --Kk~i~W~G~~ 180 (271)
|--++|-|.-
T Consensus 228 trkPafrwlG~~ 239 (388)
T KOG2578|consen 228 TRKPAFRWLGSK 239 (388)
T ss_pred cccchhheeCCC
Confidence 6678998864
No 7
>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=95.41 E-value=0.03 Score=40.89 Aligned_cols=59 Identities=27% Similarity=0.387 Sum_probs=49.2
Q ss_pred cccchhHHHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceee-cCCceEE
Q 024196 98 RGLRQFSMKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK-DKKEIQW 176 (271)
Q Consensus 98 ~GLR~fS~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K-~Kk~i~W 176 (271)
-||...-.+|+..+-..+..|-.|||+.+ ..-+..||++|+-|+..|+|++ .++...|
T Consensus 4 ~gLs~~E~~vy~~Ll~~~~~t~~eIa~~l---------------------~i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y 62 (68)
T PF01978_consen 4 LGLSENEAKVYLALLKNGPATAEEIAEEL---------------------GISRSTVYRALKSLEEKGLVEREEGRPKVY 62 (68)
T ss_dssp HCHHHHHHHHHHHHHHHCHEEHHHHHHHH---------------------TSSHHHHHHHHHHHHHTTSEEEEEECCEEE
T ss_pred CCcCHHHHHHHHHHHHcCCCCHHHHHHHH---------------------CcCHHHHHHHHHHHHHCCCEEEEcCceEEE
Confidence 46666778888888899999999999998 3568999999999999999999 5555555
Q ss_pred e
Q 024196 177 K 177 (271)
Q Consensus 177 ~ 177 (271)
.
T Consensus 63 ~ 63 (68)
T PF01978_consen 63 R 63 (68)
T ss_dssp E
T ss_pred E
Confidence 4
No 8
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=92.94 E-value=0.61 Score=43.04 Aligned_cols=35 Identities=20% Similarity=0.415 Sum_probs=28.9
Q ss_pred ccchhhhhhHHHHhhhccceee-cCCceEEecCCCC
Q 024196 148 KNIRRRVYDALNVLMAMDIISK-DKKEIQWKGLPRT 182 (271)
Q Consensus 148 K~ikRRVYD~lNVL~ai~lI~K-~Kk~i~W~G~~~~ 182 (271)
..-+=||||+|+.|+.-|+|+. .++--.+.-.++.
T Consensus 41 gvP~~kvY~vl~sLe~kG~v~~~~g~P~~y~av~p~ 76 (247)
T COG1378 41 GVPRPKVYDVLRSLEKKGLVEVIEGRPKKYRAVPPE 76 (247)
T ss_pred CCCchhHHHHHHHHHHCCCEEeeCCCCceEEeCCHH
Confidence 4567899999999999999999 7777777766554
No 9
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=90.36 E-value=0.83 Score=30.31 Aligned_cols=48 Identities=17% Similarity=0.255 Sum_probs=39.1
Q ss_pred HHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceeecCCce
Q 024196 106 KVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKDKKEI 174 (271)
Q Consensus 106 KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K~Kk~i 174 (271)
.|++.+..++.++-.++|+.| ..-++.||.++.-|+..|+|.+..+.+
T Consensus 4 ~il~~l~~~~~~s~~~l~~~l---------------------~~s~~tv~~~l~~L~~~g~i~~~~~~~ 51 (53)
T smart00420 4 QILELLAQQGKVSVEELAELL---------------------GVSEMTIRRDLNKLEEQGLLTRVHGGA 51 (53)
T ss_pred HHHHHHHHcCCcCHHHHHHHH---------------------CCCHHHHHHHHHHHHHCCCEEEeecCc
Confidence 467777777889999999887 256788999999999999999855544
No 10
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=89.31 E-value=2.6 Score=35.87 Aligned_cols=56 Identities=25% Similarity=0.478 Sum_probs=45.2
Q ss_pred cccchhHHHHHHHHH-hcCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceeecCCce
Q 024196 98 RGLRQFSMKVCEKVE-SKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKDKKEI 174 (271)
Q Consensus 98 ~GLR~fS~KVcekVk-~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K~Kk~i 174 (271)
-||...=..|..++- +.+..|-.|+|.+| .--|-.||-+++=|+..|||.|.|-.+
T Consensus 23 ~GLs~~Dv~v~~~LL~~~~~~tvdelae~l---------------------nr~rStv~rsl~~L~~~GlV~Rek~~~ 79 (126)
T COG3355 23 YGLSELDVEVYKALLEENGPLTVDELAEIL---------------------NRSRSTVYRSLQNLLEAGLVEREKVNL 79 (126)
T ss_pred hCCcHHHHHHHHHHHhhcCCcCHHHHHHHH---------------------CccHHHHHHHHHHHHHcCCeeeeeecc
Confidence 366666677777776 68888888999998 345789999999999999999976554
No 11
>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=88.63 E-value=0.86 Score=32.88 Aligned_cols=55 Identities=22% Similarity=0.291 Sum_probs=39.3
Q ss_pred ccchhHHHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhcccee
Q 024196 99 GLRQFSMKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIIS 168 (271)
Q Consensus 99 GLR~fS~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~ 168 (271)
.|...+..|++.+ .|..|..|+++.|...|..+ ...++..|...++-|...|||+
T Consensus 14 ~Ln~~a~~Iw~~~--~g~~t~~ei~~~l~~~y~~~-------------~~~~~~dv~~fl~~L~~~glIe 68 (68)
T PF05402_consen 14 TLNETAAFIWELL--DGPRTVEEIVDALAEEYDVD-------------PEEAEEDVEEFLEQLREKGLIE 68 (68)
T ss_dssp ---THHHHHHHH----SSS-HHHHHHHHHHHTT---------------HHHHHHHHHHHHHHHHHTT---
T ss_pred cccHHHHHHHHHc--cCCCCHHHHHHHHHHHcCCC-------------HHHHHHHHHHHHHHHHHCcCcC
Confidence 7888889999999 46789999999999998542 2467999999999999999985
No 12
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=86.56 E-value=8.4 Score=28.69 Aligned_cols=45 Identities=22% Similarity=0.329 Sum_probs=37.8
Q ss_pred HHHHHHHHhc-CCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceeec
Q 024196 105 MKVCEKVESK-GRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKD 170 (271)
Q Consensus 105 ~KVcekVk~k-g~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K~ 170 (271)
..|++.+... +..|..|+|+++ ..-+..||..++.|+..|+|.+.
T Consensus 8 ~~Il~~l~~~~~~~t~~~ia~~l---------------------~i~~~tv~r~l~~L~~~g~l~~~ 53 (91)
T smart00346 8 LAVLRALAEEPGGLTLAELAERL---------------------GLSKSTAHRLLNTLQELGYVEQD 53 (91)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHh---------------------CCCHHHHHHHHHHHHHCCCeeec
Confidence 4577777776 789999999998 24578899999999999999995
No 13
>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=83.39 E-value=4.3 Score=27.46 Aligned_cols=44 Identities=25% Similarity=0.259 Sum_probs=36.8
Q ss_pred HHHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhcccee
Q 024196 104 SMKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIIS 168 (271)
Q Consensus 104 S~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~ 168 (271)
-.+|...+.+++.+|-.|+|+.+ ..-+..|+.+++-|+.-|+|+
T Consensus 5 ~~~Il~~l~~~~~~t~~ela~~~---------------------~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 5 QRKILNYLRENPRITQKELAEKL---------------------GISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHHCTTS-HHHHHHHH---------------------TS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHcCCCCHHHHHHHh---------------------CCCHHHHHHHHHHHHHCcCcC
Confidence 46788899999999999999998 355788999999999999985
No 14
>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=83.07 E-value=2 Score=31.65 Aligned_cols=43 Identities=23% Similarity=0.316 Sum_probs=35.8
Q ss_pred HHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceee
Q 024196 106 KVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (271)
Q Consensus 106 KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K 169 (271)
.|.+.++.++.+|..|+|.+| ..-..-|=+.|.+|+..|.|+|
T Consensus 4 ~i~~~l~~~~~~S~~eLa~~~---------------------~~s~~~ve~mL~~l~~kG~I~~ 46 (69)
T PF09012_consen 4 EIRDYLRERGRVSLAELAREF---------------------GISPEAVEAMLEQLIRKGYIRK 46 (69)
T ss_dssp HHHHHHHHS-SEEHHHHHHHT---------------------T--HHHHHHHHHHHHCCTSCEE
T ss_pred HHHHHHHHcCCcCHHHHHHHH---------------------CcCHHHHHHHHHHHHHCCcEEE
Confidence 567889999999999999998 2445678899999999999999
No 15
>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=82.55 E-value=2.3 Score=29.58 Aligned_cols=45 Identities=22% Similarity=0.347 Sum_probs=34.7
Q ss_pred HHHHHHHHhcC-CCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceeec
Q 024196 105 MKVCEKVESKG-RTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKD 170 (271)
Q Consensus 105 ~KVcekVk~kg-~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K~ 170 (271)
..|.+.+...+ ..+..|+|+.+ ..-|--+|.+++.|+..|+|+|+
T Consensus 6 l~iL~~l~~~~~~~t~~eia~~~---------------------gl~~stv~r~L~tL~~~g~v~~d 51 (52)
T PF09339_consen 6 LRILEALAESGGPLTLSEIARAL---------------------GLPKSTVHRLLQTLVEEGYVERD 51 (52)
T ss_dssp HHHHHCHHCTBSCEEHHHHHHHH---------------------TS-HHHHHHHHHHHHHTTSEEEC
T ss_pred HHHHHHHHcCCCCCCHHHHHHHH---------------------CcCHHHHHHHHHHHHHCcCeecC
Confidence 44556666644 46999999998 24577899999999999999985
No 16
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=80.97 E-value=20 Score=26.39 Aligned_cols=52 Identities=21% Similarity=0.190 Sum_probs=42.4
Q ss_pred cccchhHHHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceeec
Q 024196 98 RGLRQFSMKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKD 170 (271)
Q Consensus 98 ~GLR~fS~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K~ 170 (271)
-||-..-..+...+...+.++..++|+.+ ..-+..|+.+++-|+..|+|++.
T Consensus 6 ~~l~~~~~~il~~l~~~~~~~~~~la~~~---------------------~~s~~~i~~~l~~L~~~g~v~~~ 57 (101)
T smart00347 6 LGLTPTQFLVLRILYEEGPLSVSELAKRL---------------------GVSPSTVTRVLDRLEKKGLIRRL 57 (101)
T ss_pred cCCCHHHHHHHHHHHHcCCcCHHHHHHHH---------------------CCCchhHHHHHHHHHHCCCeEec
Confidence 56777778888889888889999999887 12245689999999999999984
No 17
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=80.55 E-value=3.4 Score=27.72 Aligned_cols=41 Identities=17% Similarity=0.206 Sum_probs=32.6
Q ss_pred HHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceee
Q 024196 107 VCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (271)
Q Consensus 107 VcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K 169 (271)
|.+.+. .+..+..++++.| ..-+..|+++++.|..-|+|..
T Consensus 2 il~~l~-~~~~~~~~i~~~l---------------------~is~~~v~~~l~~L~~~g~i~~ 42 (66)
T smart00418 2 ILKLLA-EGELCVCELAEIL---------------------GLSQSTVSHHLKKLREAGLVES 42 (66)
T ss_pred HHHHhh-cCCccHHHHHHHH---------------------CCCHHHHHHHHHHHHHCCCeee
Confidence 345555 7788999999988 1345679999999999999997
No 18
>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=78.88 E-value=23 Score=28.06 Aligned_cols=52 Identities=13% Similarity=0.268 Sum_probs=39.2
Q ss_pred cccchhHHHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceeec
Q 024196 98 RGLRQFSMKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKD 170 (271)
Q Consensus 98 ~GLR~fS~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K~ 170 (271)
.||-.--..|...+...+.+|.+|+|+.+ ..-+-.|+-+++-|+.-|+|++.
T Consensus 24 ~~lt~~q~~iL~~l~~~~~~t~~ela~~~---------------------~~~~~tvs~~l~~Le~~GlI~r~ 75 (118)
T TIGR02337 24 HGLTEQQWRILRILAEQGSMEFTQLANQA---------------------CILRPSLTGILARLERDGLVTRL 75 (118)
T ss_pred cCCCHHHHHHHHHHHHcCCcCHHHHHHHh---------------------CCCchhHHHHHHHHHHCCCEEec
Confidence 35544445677777778888888888887 23355688999999999999993
No 19
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=77.19 E-value=7.4 Score=28.89 Aligned_cols=52 Identities=25% Similarity=0.294 Sum_probs=41.8
Q ss_pred HHHHHHHHhcCC--CcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceeecC-CceEEe
Q 024196 105 MKVCEKVESKGR--TTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKDK-KEIQWK 177 (271)
Q Consensus 105 ~KVcekVk~kg~--TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K~K-k~i~W~ 177 (271)
.+|++.+...|. .+-.|+|..| ..-++-|.-+|.-|+..|+|.+.. +.=.|.
T Consensus 9 ~~IL~~L~~~g~~~~ta~eLa~~l---------------------gl~~~~v~r~L~~L~~~G~V~~~~~~~~~W~ 63 (68)
T smart00550 9 EKILEFLENSGDETSTALQLAKNL---------------------GLPKKEVNRVLYSLEKKGKVCKQGGTPPLWK 63 (68)
T ss_pred HHHHHHHHHCCCCCcCHHHHHHHH---------------------CCCHHHHHHHHHHHHHCCCEEecCCCCCceE
Confidence 578999999877 9999999998 345678888999999999999933 424664
No 20
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=76.95 E-value=22 Score=32.36 Aligned_cols=53 Identities=13% Similarity=0.139 Sum_probs=40.6
Q ss_pred HHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceee-cCCceEEec
Q 024196 105 MKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK-DKKEIQWKG 178 (271)
Q Consensus 105 ~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K-~Kk~i~W~G 178 (271)
.++.+.+++.+.+++.|+|+.| ..-.+.|..-|+.|+..|+|.+ .+.-+.+.+
T Consensus 7 ~~Il~~l~~~~~~~~~eLa~~l---------------------~VS~~TiRRdL~~L~~~~~l~r~~Gga~~~~~ 60 (240)
T PRK10411 7 QAIVDLLLNHTSLTTEALAEQL---------------------NVSKETIRRDLNELQTQGKILRNHGRAKYIHR 60 (240)
T ss_pred HHHHHHHHHcCCCcHHHHHHHH---------------------CcCHHHHHHHHHHHHHCCCEEEecCeEEEecC
Confidence 3578999999999999999998 1334666667888888898988 565555553
No 21
>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=76.62 E-value=6.9 Score=26.98 Aligned_cols=39 Identities=28% Similarity=0.325 Sum_probs=31.2
Q ss_pred HHHHHH-HhcCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhcc
Q 024196 106 KVCEKV-ESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMD 165 (271)
Q Consensus 106 KVcekV-k~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~ 165 (271)
++...+ +..+.+|..|+|++| ..-+|-||..++.|...+
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 455556 667779999999998 467899999999999988
No 22
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=74.01 E-value=7.5 Score=30.15 Aligned_cols=45 Identities=18% Similarity=0.239 Sum_probs=37.1
Q ss_pred HHHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceee
Q 024196 104 SMKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (271)
Q Consensus 104 S~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K 169 (271)
=.+|...++..+.++++|+|+.+ ..-..-|+..++-|+.-|+|.+
T Consensus 5 D~~il~~L~~~~~~~~~~la~~l---------------------~~s~~tv~~~l~~L~~~g~i~~ 49 (108)
T smart00344 5 DRKILEELQKDARISLAELAKKV---------------------GLSPSTVHNRVKRLEEEGVIKG 49 (108)
T ss_pred HHHHHHHHHHhCCCCHHHHHHHH---------------------CcCHHHHHHHHHHHHHCCCeec
Confidence 36788889999999999999998 1335567778899999999996
No 23
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=73.33 E-value=7.6 Score=25.40 Aligned_cols=26 Identities=27% Similarity=0.286 Sum_probs=21.7
Q ss_pred cchhhhhhHHHHhhhccceeecCCce
Q 024196 149 NIRRRVYDALNVLMAMDIISKDKKEI 174 (271)
Q Consensus 149 ~ikRRVYD~lNVL~ai~lI~K~Kk~i 174 (271)
.-+..|+.+++.|++.|+|++.++.|
T Consensus 20 ~s~~tv~~~l~~L~~~g~l~~~~~~~ 45 (48)
T smart00419 20 LTRETVSRTLKRLEKEGLISREGGRI 45 (48)
T ss_pred CCHHHHHHHHHHHHHCCCEEEeCCEE
Confidence 45778999999999999999866544
No 24
>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=72.70 E-value=11 Score=26.94 Aligned_cols=44 Identities=25% Similarity=0.295 Sum_probs=36.5
Q ss_pred HHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceee
Q 024196 105 MKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (271)
Q Consensus 105 ~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K 169 (271)
.+|+..+...+..|..|+|+.| ..-.-.+|-=+++|+..|||+.
T Consensus 13 ~~Il~~L~~~~~~t~~ela~~l---------------------~~~~~t~s~hL~~L~~aGli~~ 56 (61)
T PF12840_consen 13 LRILRLLASNGPMTVSELAEEL---------------------GISQSTVSYHLKKLEEAGLIEV 56 (61)
T ss_dssp HHHHHHHHHCSTBEHHHHHHHH---------------------TS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHhcCCCCCHHHHHHHH---------------------CCCHHHHHHHHHHHHHCCCeEE
Confidence 5677788889999999999998 1334568999999999999987
No 25
>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=71.11 E-value=11 Score=29.47 Aligned_cols=48 Identities=19% Similarity=0.241 Sum_probs=35.8
Q ss_pred HHHHHHHh-cCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceee
Q 024196 106 KVCEKVES-KGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (271)
Q Consensus 106 KVcekVk~-kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K 169 (271)
.|.+.+.+ .+..|-.||.+.|-.+.. .--+--||-+|+.|+..|+|.|
T Consensus 5 ~Il~~l~~~~~~~sa~ei~~~l~~~~~----------------~i~~~TVYR~L~~L~~~Gli~~ 53 (116)
T cd07153 5 AILEVLLESDGHLTAEEIYERLRKKGP----------------SISLATVYRTLELLEEAGLVRE 53 (116)
T ss_pred HHHHHHHhCCCCCCHHHHHHHHHhcCC----------------CCCHHHHHHHHHHHHhCCCEEE
Confidence 46677766 566888888888754311 1335689999999999999999
No 26
>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=70.82 E-value=10 Score=25.92 Aligned_cols=41 Identities=24% Similarity=0.311 Sum_probs=31.5
Q ss_pred HHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceee
Q 024196 107 VCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (271)
Q Consensus 107 VcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K 169 (271)
+...+.. |..+..|+|+.+ +.-+--|+--|+.|+..|+|+|
T Consensus 7 Il~~L~~-~~~~~~el~~~l---------------------~~s~~~vs~hL~~L~~~glV~~ 47 (47)
T PF01022_consen 7 ILKLLSE-GPLTVSELAEEL---------------------GLSQSTVSHHLKKLREAGLVEK 47 (47)
T ss_dssp HHHHHTT-SSEEHHHHHHHH---------------------TS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHh-CCCchhhHHHhc---------------------cccchHHHHHHHHHHHCcCeeC
Confidence 4444544 888999999998 3456678888999999999986
No 27
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=70.81 E-value=50 Score=29.80 Aligned_cols=61 Identities=8% Similarity=0.158 Sum_probs=44.0
Q ss_pred ccccchhH--HHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceeec-CCc
Q 024196 97 GRGLRQFS--MKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKD-KKE 173 (271)
Q Consensus 97 ~~GLR~fS--~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K~-Kk~ 173 (271)
..++.-+. ..|.+.+...+..+..|+|+.+ .--|=.+|.+|+.|+..|+++++ .+.
T Consensus 7 ~~~v~sl~r~l~IL~~l~~~~~l~l~eia~~l---------------------gl~kstv~Rll~tL~~~G~l~~~~~~~ 65 (257)
T PRK15090 7 PDSVSSVLKVFGILQALGEEREIGITELSQRV---------------------MMSKSTVYRFLQTMKTLGYVAQEGESE 65 (257)
T ss_pred ccccHHHHHHHHHHHHhhcCCCCCHHHHHHHH---------------------CcCHHHHHHHHHHHHHCCCEEEcCCCC
Confidence 34555554 5577777666778999999998 24467899999999999999993 333
Q ss_pred eEEec
Q 024196 174 IQWKG 178 (271)
Q Consensus 174 i~W~G 178 (271)
-...|
T Consensus 66 ~Y~lG 70 (257)
T PRK15090 66 KYSLT 70 (257)
T ss_pred cEEec
Confidence 33344
No 28
>PF09079 Cdc6_C: CDC6, C terminal ; InterPro: IPR015163 The C-terminal domain of CDC6 assumes a winged helix fold, with a five alpha-helical bundle (alpha15-alpha19) structure, backed on one side by three beta strands (beta6-beta8). It has been shown that this domain acts as a DNA-localisation factor, however its exact function is, as yet, unknown. Putative functions include: (1) mediation of protein-protein interactions and (2) regulation of nucleotide binding and hydrolysis. Mutagenesis studies have shown that this domain is essential for appropriate Cdc6 activity []. ; PDB: 2QBY_A 2V1U_A 1W5T_A 1W5S_B 1FNN_B.
Probab=69.53 E-value=3 Score=31.59 Aligned_cols=21 Identities=29% Similarity=0.284 Sum_probs=18.0
Q ss_pred cchhhhhhHHHHhhhccceee
Q 024196 149 NIRRRVYDALNVLMAMDIISK 169 (271)
Q Consensus 149 ~ikRRVYD~lNVL~ai~lI~K 169 (271)
.-.||+||+++-|+.+|||+-
T Consensus 37 ls~~r~~~~l~eL~~~gli~~ 57 (85)
T PF09079_consen 37 LSYRRFSDYLSELEMLGLIES 57 (85)
T ss_dssp --HHHHHHHHHHHHHTTSEEE
T ss_pred CCHHHHHHHHHHHHhCCCeEE
Confidence 457999999999999999986
No 29
>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=68.54 E-value=13 Score=29.64 Aligned_cols=65 Identities=23% Similarity=0.289 Sum_probs=43.6
Q ss_pred cccchhH--HHHHHHHHh-cCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceee---cC
Q 024196 98 RGLRQFS--MKVCEKVES-KGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK---DK 171 (271)
Q Consensus 98 ~GLR~fS--~KVcekVk~-kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K---~K 171 (271)
.|||.-. ..|.+.+.+ .+..|-.||.+.|-.+. ...-+=-||.+|+.|+..|||.| ..
T Consensus 2 ~glr~T~~R~~Il~~l~~~~~~~ta~ei~~~l~~~~----------------~~is~~TVYR~L~~L~e~Gli~~~~~~~ 65 (120)
T PF01475_consen 2 AGLRLTPQRLAILELLKESPEHLTAEEIYDKLRKKG----------------PRISLATVYRTLDLLEEAGLIRKIEFGD 65 (120)
T ss_dssp TTHHHHHHHHHHHHHHHHHSSSEEHHHHHHHHHHTT----------------TT--HHHHHHHHHHHHHTTSEEEEEETT
T ss_pred CCCCCCHHHHHHHHHHHcCCCCCCHHHHHHHhhhcc----------------CCcCHHHHHHHHHHHHHCCeEEEEEcCC
Confidence 4566544 347777777 45888888888885331 12335579999999999999999 33
Q ss_pred CceEEec
Q 024196 172 KEIQWKG 178 (271)
Q Consensus 172 k~i~W~G 178 (271)
+...+..
T Consensus 66 ~~~~Y~~ 72 (120)
T PF01475_consen 66 GESRYEL 72 (120)
T ss_dssp SEEEEEE
T ss_pred CcceEee
Confidence 4444443
No 30
>PRK09462 fur ferric uptake regulator; Provisional
Probab=66.67 E-value=16 Score=30.47 Aligned_cols=56 Identities=18% Similarity=0.244 Sum_probs=41.8
Q ss_pred cccchhH--HHHHHHHHh--cCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceee
Q 024196 98 RGLRQFS--MKVCEKVES--KGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (271)
Q Consensus 98 ~GLR~fS--~KVcekVk~--kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K 169 (271)
.|||.-. ..|.+.+.+ .+..|-.||.+.|..+.. ..-+=-||.+|+.|+..|||.+
T Consensus 11 ~glr~T~qR~~Il~~l~~~~~~h~sa~eI~~~l~~~~~----------------~i~~aTVYR~L~~L~e~Gli~~ 70 (148)
T PRK09462 11 AGLKVTLPRLKILEVLQEPDNHHVSAEDLYKRLIDMGE----------------EIGLATVYRVLNQFDDAGIVTR 70 (148)
T ss_pred cCCCCCHHHHHHHHHHHhCCCCCCCHHHHHHHHHhhCC----------------CCCHHHHHHHHHHHHHCCCEEE
Confidence 4676555 458888886 368888888888854421 1235679999999999999998
No 31
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=66.09 E-value=62 Score=29.40 Aligned_cols=50 Identities=16% Similarity=0.168 Sum_probs=38.4
Q ss_pred HHHHHHHHhc-CCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceeec--CCceE
Q 024196 105 MKVCEKVESK-GRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKD--KKEIQ 175 (271)
Q Consensus 105 ~KVcekVk~k-g~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K~--Kk~i~ 175 (271)
..|.+.+-.. +..+..|+|+.+ ..-|-.+|.+|+-|+..|+|+++ .+.|.
T Consensus 14 l~iL~~l~~~~~~ls~~eia~~l---------------------gl~kstv~RlL~tL~~~g~v~~~~~~~~Y~ 66 (263)
T PRK09834 14 LMVLRALNRLDGGATVGLLAELT---------------------GLHRTTVRRLLETLQEEGYVRRSASDDSFR 66 (263)
T ss_pred HHHHHHHHhcCCCCCHHHHHHHH---------------------CcCHHHHHHHHHHHHHCCCEEEecCCCcEE
Confidence 5566777554 458999999998 24467899999999999999993 55555
No 32
>PRK03947 prefoldin subunit alpha; Reviewed
Probab=66.04 E-value=37 Score=28.10 Aligned_cols=56 Identities=25% Similarity=0.225 Sum_probs=35.0
Q ss_pred eecCCceEEecCCCC----ChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024196 168 SKDKKEIQWKGLPRT----SLNDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQ 223 (271)
Q Consensus 168 ~K~Kk~i~W~G~~~~----s~~~~~~Lk~E~~~l~e~I~~Kk~~LqEL~~Q~~~lknLI~ 223 (271)
....+-+-|.|.+-. ....++.|+..+..+.+.++...+.|.++..+...+...+.
T Consensus 73 ~~~~kV~v~lG~g~~vE~~~~eA~~~l~~~~~~l~~~~~~l~~~l~~~~~~~~~~~~~l~ 132 (140)
T PRK03947 73 KDKDKVIVSLGAGYSAEKDLDEAIEILDKRKEELEKALEKLEEALQKLASRIAQLAQELQ 132 (140)
T ss_pred cCCCeEEEEcCCCEEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345677888887532 23445556666666666777777777777666655555444
No 33
>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=66.02 E-value=28 Score=23.63 Aligned_cols=44 Identities=16% Similarity=0.183 Sum_probs=34.3
Q ss_pred HHHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceee
Q 024196 104 SMKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (271)
Q Consensus 104 S~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K 169 (271)
...|...+...+ .++.|+|+.+ ..-+..|+-+++.|+..|+|.+
T Consensus 9 ~~~il~~l~~~~-~~~~ei~~~~---------------------~i~~~~i~~~l~~L~~~g~i~~ 52 (78)
T cd00090 9 RLRILRLLLEGP-LTVSELAERL---------------------GLSQSTVSRHLKKLEEAGLVES 52 (78)
T ss_pred HHHHHHHHHHCC-cCHHHHHHHH---------------------CcCHhHHHHHHHHHHHCCCeEE
Confidence 456777776666 8899998887 1235668889999999999998
No 34
>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=66.02 E-value=20 Score=25.67 Aligned_cols=49 Identities=29% Similarity=0.444 Sum_probs=36.0
Q ss_pred HHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceeecCCce
Q 024196 105 MKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKDKKEI 174 (271)
Q Consensus 105 ~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K~Kk~i 174 (271)
.++.+.|++++..+..|+|+.| .....++|| =||.|+.-|+|.|....+
T Consensus 3 ~~Il~~l~~~~~~s~~ela~~~-----------------~VS~~TiRR----Dl~~L~~~g~i~r~~GG~ 51 (57)
T PF08220_consen 3 QQILELLKEKGKVSVKELAEEF-----------------GVSEMTIRR----DLNKLEKQGLIKRTHGGA 51 (57)
T ss_pred HHHHHHHHHcCCEEHHHHHHHH-----------------CcCHHHHHH----HHHHHHHCCCEEEEcCEE
Confidence 3577899999999999999998 011235554 467899999999854443
No 35
>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=65.47 E-value=15 Score=25.69 Aligned_cols=40 Identities=28% Similarity=0.219 Sum_probs=31.9
Q ss_pred cCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceeecC-Cce
Q 024196 114 KGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKDK-KEI 174 (271)
Q Consensus 114 kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K~K-k~i 174 (271)
.+..+..|+|+.+ ..-+..|+.+++.|+.-|+|++.. +.|
T Consensus 23 ~~~~s~~ela~~~---------------------g~s~~tv~r~l~~L~~~g~i~~~~~~~~ 63 (67)
T cd00092 23 QLPLTRQEIADYL---------------------GLTRETVSRTLKELEEEGLISRRGRGKY 63 (67)
T ss_pred cCCcCHHHHHHHH---------------------CCCHHHHHHHHHHHHHCCCEEecCCCeE
Confidence 4567888888887 355788999999999999999955 444
No 36
>TIGR00293 prefoldin, archaeal alpha subunit/eukaryotic subunit 5. This model finds a set of small proteins from the Archaea and from Aquifex aeolicus that may represent two orthologous groups. The proteins are predicted to be mostly coiled coil, and may hit large numbers of proteins that contain coiled coil regions.
Probab=64.84 E-value=38 Score=27.37 Aligned_cols=67 Identities=21% Similarity=0.094 Sum_probs=40.5
Q ss_pred hhhHHHHhhhccceeecCCceEEecCCCC----ChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024196 154 VYDALNVLMAMDIISKDKKEIQWKGLPRT----SLNDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQN 220 (271)
Q Consensus 154 VYD~lNVL~ai~lI~K~Kk~i~W~G~~~~----s~~~~~~Lk~E~~~l~e~I~~Kk~~LqEL~~Q~~~lkn 220 (271)
++-+..-+..=+-|...++-+-|.|.+-. ....++.|+..+..+.+.+++..+.+.++..+...+..
T Consensus 51 lv~lg~~~~v~~~v~~~~~v~v~iG~g~~vE~~~~eA~~~l~~~~~~l~~~~~~l~~~l~~l~~~~~~i~~ 121 (126)
T TIGR00293 51 LVPVGAGSFVKAKVKDTDKVLVSIGSGYYVEKDAEEAIEFLKKRIEELEKAIEKLQEALAELASRAQQLEQ 121 (126)
T ss_pred EEEcCCCeEEEEEeCCCCEEEEEcCCCEEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33344434444445556788899997633 23445556666666677777777777777766655543
No 37
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=63.41 E-value=9.6 Score=29.53 Aligned_cols=66 Identities=15% Similarity=0.341 Sum_probs=46.3
Q ss_pred HHHHHHHHh-cCCCcHHHHHHHHHHHhcCCCCCCCCCChhh----hccc--cchhhhhhHHHHhhhccceeecCCceEEe
Q 024196 105 MKVCEKVES-KGRTTYNEVADELVAEFADPSNSLATPDQQQ----YDEK--NIRRRVYDALNVLMAMDIISKDKKEIQWK 177 (271)
Q Consensus 105 ~KVcekVk~-kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~----~d~K--~ikRRVYD~lNVL~ai~lI~K~Kk~i~W~ 177 (271)
.-|.+-+.. ++..+..||.+.|...+.-.. ++.. .... ..+.||.=++.-|...|+|++.+.. .|.
T Consensus 7 ~piL~~L~~~g~~~~~~ei~~~v~~~~~ls~------e~~~~~~~sg~~~~~~~~ri~Wa~~~L~~aGli~~~~rG-~~~ 79 (92)
T PF14338_consen 7 PPILEALKDLGGSASRKEIYERVAERFGLSD------EERNERLPSGQGYSRFKNRIRWARSYLKKAGLIERPKRG-IWR 79 (92)
T ss_pred HHHHHHHHHcCCCcCHHHHHHHHHHHhCCCH------HHHHHHcccCCcchhHHHhHHHHHHHHHHCCCccCCCCC-ceE
Confidence 346677778 899999999999987664211 1111 1112 5799999999999999999994433 443
No 38
>PF14193 DUF4315: Domain of unknown function (DUF4315)
Probab=63.34 E-value=25 Score=27.89 Aligned_cols=36 Identities=33% Similarity=0.421 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024196 186 DIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNL 221 (271)
Q Consensus 186 ~~~~Lk~E~~~l~e~I~~Kk~~LqEL~~Q~~~lknL 221 (271)
.++++..++.+-+++|...+.+|.+|..|+.-..|+
T Consensus 2 KleKi~~eieK~k~Kiae~Q~rlK~Le~qk~E~EN~ 37 (83)
T PF14193_consen 2 KLEKIRAEIEKTKEKIAELQARLKELEAQKTEAENL 37 (83)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 467888888888888888888898888888766554
No 39
>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=62.90 E-value=65 Score=28.81 Aligned_cols=50 Identities=20% Similarity=0.238 Sum_probs=39.0
Q ss_pred HHHHHHHHh-cCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceeecCCceE
Q 024196 105 MKVCEKVES-KGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKDKKEIQ 175 (271)
Q Consensus 105 ~KVcekVk~-kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K~Kk~i~ 175 (271)
..|.+.+.. ....+..|+|+++ .--|=.+|.+|+-|+..|+++++.+.|.
T Consensus 12 l~IL~~l~~~~~~~~l~eia~~l---------------------glpksT~~RlL~tL~~~G~l~~~~~~Y~ 62 (248)
T TIGR02431 12 LAVIEAFGAERPRLTLTDVAEAT---------------------GLTRAAARRFLLTLVELGYVTSDGRLFW 62 (248)
T ss_pred HHHHHHHhcCCCCCCHHHHHHHH---------------------CcCHHHHHHHHHHHHHCCCEEeCCCEEE
Confidence 456666654 6678999999998 2457789999999999999999655544
No 40
>cd00890 Prefoldin Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.
Probab=61.44 E-value=71 Score=25.36 Aligned_cols=54 Identities=31% Similarity=0.270 Sum_probs=30.8
Q ss_pred ecCCceEEecCCCCC----hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024196 169 KDKKEIQWKGLPRTS----LNDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLI 222 (271)
Q Consensus 169 K~Kk~i~W~G~~~~s----~~~~~~Lk~E~~~l~e~I~~Kk~~LqEL~~Q~~~lknLI 222 (271)
...+-+.|+|.+... ..-.+.|+..+..+..+++...+.+.++..+...++.-+
T Consensus 67 ~~~~v~v~iG~~~~ve~~~~eA~~~l~~r~~~l~~~~~~l~~~~~~~~~~~~~l~~~l 124 (129)
T cd00890 67 DDDKVLVDLGTGVYVEKSLEEAIEFLKKRLETLEKQIEKLEKQLEKLQDQITELQEEL 124 (129)
T ss_pred CCCEEEEEecCCEEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456678899865332 223344555555555566666666666666665555444
No 41
>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=60.91 E-value=20 Score=24.76 Aligned_cols=44 Identities=20% Similarity=0.284 Sum_probs=36.2
Q ss_pred HHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceee
Q 024196 105 MKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (271)
Q Consensus 105 ~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K 169 (271)
..|...+.+.+.++..|+|+.+ ..-+-.+-.+++-|+.-|+|+|
T Consensus 6 ~~iL~~l~~~~~~~~~~la~~~---------------------~~~~~~~t~~i~~L~~~g~I~r 49 (59)
T PF01047_consen 6 FRILRILYENGGITQSELAEKL---------------------GISRSTVTRIIKRLEKKGLIER 49 (59)
T ss_dssp HHHHHHHHHHSSEEHHHHHHHH---------------------TS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHcCCCCHHHHHHHH---------------------CCChhHHHHHHHHHHHCCCEEe
Confidence 3466778888889999999998 2446678889999999999998
No 42
>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=60.79 E-value=65 Score=25.46 Aligned_cols=74 Identities=18% Similarity=0.209 Sum_probs=48.8
Q ss_pred ccchhHHHHHHHHH----hcCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceee----c
Q 024196 99 GLRQFSMKVCEKVE----SKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK----D 170 (271)
Q Consensus 99 GLR~fS~KVcekVk----~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K----~ 170 (271)
||..--..|+..+. ..+.++-.|+|+.+ ..-+-.|-=+++-|+.-|+|.| .
T Consensus 22 ~ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l---------------------~~~~stvs~~i~~Le~kg~I~r~~~~~ 80 (109)
T TIGR01889 22 NLSLEELLILYYLGKLENNEGKLTLKEIIKEI---------------------LIKQSALVKIIKKLSKKGYLSKERSED 80 (109)
T ss_pred CCCHHHHHHHHHHHhhhccCCcCcHHHHHHHH---------------------CCCHHHHHHHHHHHHHCCCEeccCCcc
Confidence 55444455666666 45778888888887 2335567778999999999998 3
Q ss_pred CCceEEecCCCCChhHHHHHHHH
Q 024196 171 KKEIQWKGLPRTSLNDIEELKAE 193 (271)
Q Consensus 171 Kk~i~W~G~~~~s~~~~~~Lk~E 193 (271)
.++..+.-+.......++++..+
T Consensus 81 D~R~~~i~lT~~G~~~~~~~~~~ 103 (109)
T TIGR01889 81 DERKVIISINKEQRSKIESLISE 103 (109)
T ss_pred cCCeEEEEECHHHHHHHHHHHHH
Confidence 46777776644434344444433
No 43
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=60.12 E-value=27 Score=29.34 Aligned_cols=51 Identities=20% Similarity=0.290 Sum_probs=39.9
Q ss_pred cccchhHHHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceee
Q 024196 98 RGLRQFSMKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (271)
Q Consensus 98 ~GLR~fS~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K 169 (271)
..|-.+=.++.+.++..++++|.|+|++| . -.+..++|| ++=|+.-|+|.+
T Consensus 5 ~~lD~~D~~Il~~Lq~d~R~s~~eiA~~l----------g-------lS~~tV~~R----i~rL~~~GvI~~ 55 (153)
T PRK11179 5 YQIDNLDRGILEALMENARTPYAELAKQF----------G-------VSPGTIHVR----VEKMKQAGIITG 55 (153)
T ss_pred cccCHHHHHHHHHHHHcCCCCHHHHHHHH----------C-------cCHHHHHHH----HHHHHHCCCeee
Confidence 34677788999999999999999999998 0 112355665 577899999986
No 44
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=59.63 E-value=54 Score=30.35 Aligned_cols=49 Identities=14% Similarity=0.236 Sum_probs=36.1
Q ss_pred HHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceee-cCCce
Q 024196 105 MKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK-DKKEI 174 (271)
Q Consensus 105 ~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K-~Kk~i 174 (271)
.++.+.+++++..+..|+|+.| ...+.++|| =|..|+..|++.| .+.-+
T Consensus 20 ~~Il~~L~~~~~vtv~eLa~~l-----------------~VS~~TIRR----DL~~Le~~G~l~r~~GGa~ 69 (269)
T PRK09802 20 EQIIQRLRQQGSVQVNDLSALY-----------------GVSTVTIRN----DLAFLEKQGIAVRAYGGAL 69 (269)
T ss_pred HHHHHHHHHcCCEeHHHHHHHH-----------------CCCHHHHHH----HHHHHHhCCCeEEEeCCEE
Confidence 5577999999999999999998 011235555 4567899999999 54443
No 45
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=59.26 E-value=21 Score=29.04 Aligned_cols=50 Identities=14% Similarity=0.193 Sum_probs=37.8
Q ss_pred cchhHHHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceeec
Q 024196 100 LRQFSMKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKD 170 (271)
Q Consensus 100 LR~fS~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K~ 170 (271)
|-.+=.++.+.++..++++|.|+|+.| ..-...|..-+.-|+.-|+|.+-
T Consensus 6 lD~~D~~IL~~L~~d~r~~~~eia~~l---------------------glS~~~v~~Ri~~L~~~GiI~~~ 55 (154)
T COG1522 6 LDDIDRRILRLLQEDARISNAELAERV---------------------GLSPSTVLRRIKRLEEEGVIKGY 55 (154)
T ss_pred ccHHHHHHHHHHHHhCCCCHHHHHHHH---------------------CCCHHHHHHHHHHHHHCCceeeE
Confidence 445567899999999999999999998 12233344445679999999984
No 46
>cd08768 Cdc6_C Winged-helix domain of essential DNA replication protein Cell division control protein (Cdc6), which mediates DNA binding. This model characterizes the winged-helix, C-terminal domain of the Cell division control protein (Cdc6_C). Cdc6 (also known as Cell division cycle 6 or Cdc18) functions as a regulator at the early stages of DNA replication, by helping to recruit and load the Minichromosome Maintenance Complex (MCM) onto DNA and may have additional roles in the control of mitotic entry. Precise duplication of chromosomal DNA is required for genomic stability during replication. Cdc6 has an essential role in DNA replication and irregular expression of Cdc6 may lead to genomic instability. Cdc6 over-expression is observed in many cancerous lesions. DNA replication begins when an origin recognition complex (ORC) binds to a replication origin site on the chromatin. Studies indicate that Cdc6 interacts with ORC through the Orc1 subunit, and that this association increases
Probab=59.10 E-value=6.3 Score=29.46 Aligned_cols=21 Identities=24% Similarity=0.400 Sum_probs=18.9
Q ss_pred cchhhhhhHHHHhhhccceee
Q 024196 149 NIRRRVYDALNVLMAMDIISK 169 (271)
Q Consensus 149 ~ikRRVYD~lNVL~ai~lI~K 169 (271)
--.||++|++|-|+..|||+-
T Consensus 44 l~~~~~~~~l~~L~~~gli~~ 64 (87)
T cd08768 44 LTQRRISDLLSELEMLGLLET 64 (87)
T ss_pred CcHHHHHHHHHHHHHcCCeEE
Confidence 446999999999999999985
No 47
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=58.77 E-value=88 Score=28.67 Aligned_cols=60 Identities=18% Similarity=0.313 Sum_probs=42.2
Q ss_pred cccchhH--HHHHHHHHh-cCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceeec-CCc
Q 024196 98 RGLRQFS--MKVCEKVES-KGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKD-KKE 173 (271)
Q Consensus 98 ~GLR~fS--~KVcekVk~-kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K~-Kk~ 173 (271)
.|+.-+. ..|.+.+.. .+..+..|+|+++ .--|=.+|.+|+.|+..|+++++ ...
T Consensus 19 ~~~~sl~r~l~IL~~~~~~~~~~tl~eIa~~l---------------------glpkStv~RlL~tL~~~G~l~~~~~~~ 77 (271)
T PRK10163 19 KGAQALERGIAILQYLEKSGGSSSVSDISLNL---------------------DLPLSTTFRLLKVLQAADFVYQDSQLG 77 (271)
T ss_pred ccchHHHHHHHHHHHHHhCCCCcCHHHHHHHH---------------------CcCHHHHHHHHHHHHHCCCEEEcCCCC
Confidence 3444443 456666655 3568899999998 24577899999999999999994 333
Q ss_pred eEEec
Q 024196 174 IQWKG 178 (271)
Q Consensus 174 i~W~G 178 (271)
-.+.|
T Consensus 78 ~Y~lG 82 (271)
T PRK10163 78 WWHIG 82 (271)
T ss_pred eEEec
Confidence 33344
No 48
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=58.50 E-value=24 Score=30.08 Aligned_cols=52 Identities=15% Similarity=0.264 Sum_probs=41.1
Q ss_pred ccccchhHHHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceee
Q 024196 97 GRGLRQFSMKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (271)
Q Consensus 97 ~~GLR~fS~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K 169 (271)
...|-.+=.++...++..++++|.|+|+.+ .. ....++|| ++=|+.-|+|++
T Consensus 9 ~~~lD~~D~~IL~~Lq~d~R~s~~eiA~~l----------gl-------S~~tv~~R----i~rL~~~GvI~~ 60 (164)
T PRK11169 9 GKDLDRIDRNILNELQKDGRISNVELSKRV----------GL-------SPTPCLER----VRRLERQGFIQG 60 (164)
T ss_pred hhhHHHHHHHHHHHhccCCCCCHHHHHHHH----------Cc-------CHHHHHHH----HHHHHHCCCeEE
Confidence 466888889999999999999999999998 01 12345555 578999999986
No 49
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=58.03 E-value=1.4e+02 Score=26.63 Aligned_cols=75 Identities=13% Similarity=0.005 Sum_probs=49.2
Q ss_pred cccchhHHHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceee----cCCc
Q 024196 98 RGLRQFSMKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK----DKKE 173 (271)
Q Consensus 98 ~GLR~fS~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K----~Kk~ 173 (271)
-||..--..|...+...+.+|-.|+|+.+.. -+-.|--+++-|+.-|+|+| ..++
T Consensus 41 ~gLt~~q~~iL~~L~~~~~itq~eLa~~l~l---------------------~~sTvtr~l~rLE~kGlI~R~~~~~DrR 99 (185)
T PRK13777 41 YDLNINEHHILWIAYHLKGASISEIAKFGVM---------------------HVSTAFNFSKKLEERGYLTFSKKEDDKR 99 (185)
T ss_pred CCCCHHHHHHHHHHHhCCCcCHHHHHHHHCC---------------------CHhhHHHHHHHHHHCCCEEecCCCCCCC
Confidence 5666666677778877778888888886521 11235558889999999998 3577
Q ss_pred eEEecCCCCChhHHHHHHHH
Q 024196 174 IQWKGLPRTSLNDIEELKAE 193 (271)
Q Consensus 174 i~W~G~~~~s~~~~~~Lk~E 193 (271)
.++.-+......-.+++...
T Consensus 100 ~~~I~LTekG~~l~~~l~~~ 119 (185)
T PRK13777 100 NTYIELTEKGEELLLETMEE 119 (185)
T ss_pred eeEEEECHHHHHHHHHHHHH
Confidence 88776544333333444333
No 50
>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=57.64 E-value=37 Score=23.46 Aligned_cols=51 Identities=18% Similarity=0.235 Sum_probs=38.6
Q ss_pred ccchhHHHHHHHHHhcCC--CcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceeec
Q 024196 99 GLRQFSMKVCEKVESKGR--TTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKD 170 (271)
Q Consensus 99 GLR~fS~KVcekVk~kg~--TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K~ 170 (271)
||-.--..|.-.|...+. +|-.|+|+.+ ..-+-.|--+++-|+..|+|+|.
T Consensus 2 glt~~q~~vL~~l~~~~~~~~t~~~la~~l---------------------~~~~~~vs~~v~~L~~~Glv~r~ 54 (62)
T PF12802_consen 2 GLTPSQFRVLMALARHPGEELTQSELAERL---------------------GISKSTVSRIVKRLEKKGLVERE 54 (62)
T ss_dssp TSTHHHHHHHHHHHHSTTSGEEHHHHHHHH---------------------TS-HHHHHHHHHHHHHTTSEEEE
T ss_pred ccCHHHHHHHHHHHHCCCCCcCHHHHHHHH---------------------CcCHHHHHHHHHHHHHCCCEEEe
Confidence 344444567777777776 8999999998 24466788899999999999983
No 51
>PF13730 HTH_36: Helix-turn-helix domain
Probab=56.79 E-value=14 Score=25.45 Aligned_cols=20 Identities=30% Similarity=0.287 Sum_probs=17.5
Q ss_pred ccchhhhhhHHHHhhhccce
Q 024196 148 KNIRRRVYDALNVLMAMDII 167 (271)
Q Consensus 148 K~ikRRVYD~lNVL~ai~lI 167 (271)
+.-++.|+.+++.|+..|+|
T Consensus 36 g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 36 GVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred CcCHHHHHHHHHHHHHCcCC
Confidence 34599999999999999987
No 52
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=55.35 E-value=53 Score=30.07 Aligned_cols=45 Identities=20% Similarity=0.350 Sum_probs=36.3
Q ss_pred HHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceeec
Q 024196 105 MKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKD 170 (271)
Q Consensus 105 ~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K~ 170 (271)
.++.+.+++++..+.+|+|+.| ....-++||. |+.|+.-|+|.|.
T Consensus 8 ~~Il~~L~~~~~v~v~eLa~~l-----------------~VS~~TIRRD----L~~Le~~g~l~r~ 52 (256)
T PRK10434 8 AAILEYLQKQGKTSVEELAQYF-----------------DTTGTTIRKD----LVILEHAGTVIRT 52 (256)
T ss_pred HHHHHHHHHcCCEEHHHHHHHH-----------------CCCHHHHHHH----HHHHHHCCCEEEE
Confidence 4678999999999999999998 1123477776 6889999999993
No 53
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=54.93 E-value=76 Score=28.96 Aligned_cols=44 Identities=18% Similarity=0.109 Sum_probs=34.0
Q ss_pred HHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceee
Q 024196 105 MKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (271)
Q Consensus 105 ~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K 169 (271)
.++.+.+++++..+-.|+|+.| ......|+--|+.|+..|+|.|
T Consensus 8 ~~Il~~l~~~~~~~~~ela~~l---------------------~vS~~TirRdL~~Le~~g~i~r 51 (251)
T PRK13509 8 QILLELLAQLGFVTVEKVIERL---------------------GISPATARRDINKLDESGKLKK 51 (251)
T ss_pred HHHHHHHHHcCCcCHHHHHHHH---------------------CcCHHHHHHHHHHHHHCCCEEE
Confidence 4578999999999999999998 1223333334788999999999
No 54
>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=54.34 E-value=23 Score=24.86 Aligned_cols=43 Identities=21% Similarity=0.293 Sum_probs=31.9
Q ss_pred HHHHHHH-hcCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceee
Q 024196 106 KVCEKVE-SKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (271)
Q Consensus 106 KVcekVk-~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K 169 (271)
.|...|. +.+..+..++|+.+ ..-+--|.++++-|+..|+|+|
T Consensus 7 ~vL~~l~~~~~~~t~~~l~~~~---------------------~~~~~~vs~~i~~L~~~glv~~ 50 (68)
T PF13463_consen 7 QVLRALAHSDGPMTQSDLAERL---------------------GISKSTVSRIIKKLEEKGLVEK 50 (68)
T ss_dssp HHHHHHT--TS-BEHHHHHHHT---------------------T--HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHccCCCcCHHHHHHHH---------------------CcCHHHHHHHHHHHHHCCCEEe
Confidence 3445555 78888889999987 2346778999999999999988
No 55
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=53.83 E-value=55 Score=27.69 Aligned_cols=63 Identities=22% Similarity=0.233 Sum_probs=43.1
Q ss_pred cccchhH--HHHHHHHHhc-CCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceee--cCC
Q 024196 98 RGLRQFS--MKVCEKVESK-GRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK--DKK 172 (271)
Q Consensus 98 ~GLR~fS--~KVcekVk~k-g~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K--~Kk 172 (271)
.|||.-. ..|.+.+.+. +..|-.||-++|..++.. .-.--||.+|+.|...|||.+ ..+
T Consensus 15 ~glr~T~qR~~vl~~L~~~~~~~sAeei~~~l~~~~p~----------------islaTVYr~L~~l~e~Glv~~~~~~~ 78 (145)
T COG0735 15 AGLRLTPQRLAVLELLLEADGHLSAEELYEELREEGPG----------------ISLATVYRTLKLLEEAGLVHRLEFEG 78 (145)
T ss_pred cCCCcCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCC----------------CCHhHHHHHHHHHHHCCCEEEEEeCC
Confidence 5666655 4588888864 557776777777543221 114579999999999999999 445
Q ss_pred ceEE
Q 024196 173 EIQW 176 (271)
Q Consensus 173 ~i~W 176 (271)
...|
T Consensus 79 ~~~~ 82 (145)
T COG0735 79 GKTR 82 (145)
T ss_pred CEEE
Confidence 4444
No 56
>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=52.91 E-value=42 Score=25.00 Aligned_cols=39 Identities=23% Similarity=0.196 Sum_probs=28.4
Q ss_pred cCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceeecCC
Q 024196 114 KGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKDKK 172 (271)
Q Consensus 114 kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K~Kk 172 (271)
+-.-|+.|||+.| . -.-..-|++.|..|+.-|+|.+..+
T Consensus 23 G~~Pt~rEIa~~~---------g-----------~~S~~tv~~~L~~Le~kG~I~r~~~ 61 (65)
T PF01726_consen 23 GYPPTVREIAEAL---------G-----------LKSTSTVQRHLKALERKGYIRRDPG 61 (65)
T ss_dssp SS---HHHHHHHH---------T-----------SSSHHHHHHHHHHHHHTTSEEEGCC
T ss_pred CCCCCHHHHHHHh---------C-----------CCChHHHHHHHHHHHHCcCccCCCC
Confidence 4578999999998 0 0235789999999999999999543
No 57
>PRK09954 putative kinase; Provisional
Probab=52.43 E-value=28 Score=32.68 Aligned_cols=46 Identities=24% Similarity=0.167 Sum_probs=39.1
Q ss_pred hHHHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceee
Q 024196 103 FSMKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (271)
Q Consensus 103 fS~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K 169 (271)
.-.+|++.+++.+.+++.|+|+.| ..-|..|+..++=|+.-|+|.+
T Consensus 4 ~~~~il~~l~~~~~~s~~~la~~l---------------------~~s~~~v~~~i~~L~~~g~i~~ 49 (362)
T PRK09954 4 REKEILAILRRNPLIQQNEIADIL---------------------QISRSRVAAHIMDLMRKGRIKG 49 (362)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHH---------------------CCCHHHHHHHHHHHHHCCCcCC
Confidence 446789999999999999999999 3568888888898888888864
No 58
>TIGR00589 ogt O-6-methylguanine DNA methyltransferase. All proteins in this family for which functions are known are involved alkyl-DNA transferases which remove alkyl groups from DNA as part of alkylation DNA repair. Some of the proteins in this family are also transcription regulators and have a distinct transcription regulatory domain. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=52.37 E-value=17 Score=28.19 Aligned_cols=25 Identities=16% Similarity=0.436 Sum_probs=21.4
Q ss_pred hhHHHHHHHHHh---cCCCcHHHHHHHH
Q 024196 102 QFSMKVCEKVES---KGRTTYNEVADEL 126 (271)
Q Consensus 102 ~fS~KVcekVk~---kg~TTYnEVAdeL 126 (271)
.|..+|.+.|.+ ...+||.+||..+
T Consensus 2 ~f~~~V~~~l~~IP~G~v~TYg~iA~~~ 29 (80)
T TIGR00589 2 PFQQRVWQALRTIPYGETKSYGQLAARI 29 (80)
T ss_pred hHHHHHHHHHhCCCCCCcCCHHHHHHHh
Confidence 377888888887 7899999999986
No 59
>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=50.56 E-value=21 Score=25.52 Aligned_cols=55 Identities=18% Similarity=0.178 Sum_probs=34.4
Q ss_pred HHHHHHHHHHHhcCCCCCCC----CCChhhhccccchhhhhhHHHHhhhccceee-cCCc
Q 024196 119 YNEVADELVAEFADPSNSLA----TPDQQQYDEKNIRRRVYDALNVLMAMDIISK-DKKE 173 (271)
Q Consensus 119 YnEVAdeLV~e~~~~~~~~~----~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K-~Kk~ 173 (271)
|.+|++.|...+....-..+ +..+-+...+.-+.-|..+++.|++.|+|++ .++.
T Consensus 2 ~~~i~~~l~~~I~~g~~~~g~~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~~~~~~G 61 (64)
T PF00392_consen 2 YEQIYDQLRQAILSGRLPPGDRLPSERELAERYGVSRTTVREALRRLEAEGLIERRPGRG 61 (64)
T ss_dssp HHHHHHHHHHHHHTTSS-TTSBE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTTE
T ss_pred HHHHHHHHHHHHHcCCCCCCCEeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEEEECCce
Confidence 66677777766654221111 1122344456778899999999999999998 4443
No 60
>PF01035 DNA_binding_1: 6-O-methylguanine DNA methyltransferase, DNA binding domain; InterPro: IPR014048 Synonym(s): 6-O-methylguanine-DNA methyltransferase, O-6-methylguanine-DNA-alkyltransferase This entry represents the DNA binding region of 6-O-methylguanine-DNA methyltransferases. The repair of DNA containing O6-alkylated guanine is carried out by DNA-[protein]-cysteine S-methyltransferase (2.1.1.63 from EC). The major mutagenic and carcinogenic effect of methylating agents in DNA is the formation of O6-alkylguanine. The alkyl group at the O-6 position is transferred to a cysteine residue in the enzyme []. This is a suicide reaction since the enzyme is irreversibly inactivated and the methylated protein accumulates as a dead-end product. Most, but not all of the methyltransferases are also able to repair O-4-methylthymine. DNA-[protein]-cysteine S-methyltransferases are widely distributed and are found in various prokaryotic and eukaryotic sources [].; GO: 0003824 catalytic activity, 0006281 DNA repair; PDB: 1SFE_A 1T39_B 1T38_A 1EH7_A 1EH6_A 1YFH_C 1EH8_A 1QNT_A 2KIM_A 2KIF_A ....
Probab=50.31 E-value=12 Score=29.06 Aligned_cols=25 Identities=40% Similarity=0.489 Sum_probs=20.6
Q ss_pred hhHHHHHHHHHh---cCCCcHHHHHHHH
Q 024196 102 QFSMKVCEKVES---KGRTTYNEVADEL 126 (271)
Q Consensus 102 ~fS~KVcekVk~---kg~TTYnEVAdeL 126 (271)
.|..+|.+.|.+ ...+||.+||..+
T Consensus 2 ~f~~~V~~~v~~IP~G~v~TYg~iA~~~ 29 (85)
T PF01035_consen 2 PFQRRVWEAVRQIPYGKVTTYGEIARLL 29 (85)
T ss_dssp HHHHHHHHHHTTS-TT-BEEHHHHHHHT
T ss_pred hHHHHHHHHHHcCCCCceEeHHHHHHHH
Confidence 367888888888 7899999999987
No 61
>cd00584 Prefoldin_alpha Prefoldin alpha subunit; Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.
Probab=47.99 E-value=1.5e+02 Score=24.01 Aligned_cols=54 Identities=26% Similarity=0.178 Sum_probs=28.8
Q ss_pred ecCCceEEecCCCCC----hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024196 169 KDKKEIQWKGLPRTS----LNDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLI 222 (271)
Q Consensus 169 K~Kk~i~W~G~~~~s----~~~~~~Lk~E~~~l~e~I~~Kk~~LqEL~~Q~~~lknLI 222 (271)
..++-+-|.|.+-.. ....+-++..+..+++.+++..+.+..+..+...+..-+
T Consensus 67 ~~~~v~v~iG~g~~vE~~~~eA~~~l~~r~~~l~~~~~~l~~~l~~l~~~~~~~~~~l 124 (129)
T cd00584 67 DTDKVLVDLGTGYYVEKDLEEAIEFLDKKIEELTKQIEKLQKELAKLKDQINTLEAEL 124 (129)
T ss_pred CCCEEEEEcCCCEEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 346667888875332 223344455555555555555555555555554444333
No 62
>PF03836 RasGAP_C: RasGAP C-terminus; InterPro: IPR000593 Ras GTPase-activating protein (rasGAP) is a major contributor to the down-regulation of ras by facilitating GTP hydrolysis of activated ras. In addition, GAP participates in the down-stream effector system of the ras signalling pathway. Abnormal signal transduction involving activated ras genes plays a major role in the development of a variety of tumours. Depending on the precise genetic alteration, its location within the gene and the effects it exerts on protein function, rasGAP can theoretically function as either an oncogene or as a tumour suppressor gene [].; GO: 0005099 Ras GTPase activator activity, 0007264 small GTPase mediated signal transduction, 0005622 intracellular; PDB: 3ISU_A 3IEZ_A 4EZA_B 1X0H_A.
Probab=46.56 E-value=6.5 Score=33.14 Aligned_cols=26 Identities=19% Similarity=0.544 Sum_probs=0.0
Q ss_pred cchhhhhhHHHHhhhccceeecCCceE
Q 024196 149 NIRRRVYDALNVLMAMDIISKDKKEIQ 175 (271)
Q Consensus 149 ~ikRRVYD~lNVL~ai~lI~K~Kk~i~ 175 (271)
..|+++-+-+..||.+|+|.++ |.++
T Consensus 4 ~lk~~~l~~l~~LE~~G~v~~~-n~yQ 29 (142)
T PF03836_consen 4 ELKKKILENLKELESLGIVSRS-NNYQ 29 (142)
T ss_dssp ---------------------------
T ss_pred HHHHHHHHHHHHHHHCCCCCCc-ccHH
Confidence 4678899999999999999998 6666
No 63
>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=45.92 E-value=59 Score=28.51 Aligned_cols=52 Identities=19% Similarity=0.314 Sum_probs=40.1
Q ss_pred ccchhHHHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceeecC
Q 024196 99 GLRQFSMKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKDK 171 (271)
Q Consensus 99 GLR~fS~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K~K 171 (271)
+|-.--.+|...+...+..+.+|+|+.+ ..-+-.++-.++-|+..|+|++.+
T Consensus 140 ~ls~~~~~IL~~l~~~g~~s~~eia~~l---------------------~is~stv~r~L~~Le~~GlI~r~~ 191 (203)
T TIGR01884 140 GLSREELKVLEVLKAEGEKSVKNIAKKL---------------------GKSLSTISRHLRELEKKGLVEQKG 191 (203)
T ss_pred CCCHHHHHHHHHHHHcCCcCHHHHHHHH---------------------CcCHHHHHHHHHHHHHCCCEEEEc
Confidence 3444446788888888889999999998 123456888899999999999954
No 64
>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=44.42 E-value=2e+02 Score=24.51 Aligned_cols=88 Identities=24% Similarity=0.321 Sum_probs=47.2
Q ss_pred HHHHHHHh-cCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhcc-ceee-cCC-ceEEe---c
Q 024196 106 KVCEKVES-KGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMD-IISK-DKK-EIQWK---G 178 (271)
Q Consensus 106 KVcekVk~-kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~-lI~K-~Kk-~i~W~---G 178 (271)
.|.+-+++ +.+-+.++|.+.|=..|. |=-|==+|.-|..-| |+.| -+| .|.|. .
T Consensus 5 ~Il~y~~~qNRPys~~di~~nL~~~~~-------------------K~~v~k~Ld~L~~~g~i~~K~~GKqkiY~~~Q~~ 65 (169)
T PF07106_consen 5 AILEYMKEQNRPYSAQDIFDNLHNKVG-------------------KTAVQKALDSLVEEGKIVEKEYGKQKIYFANQDE 65 (169)
T ss_pred HHHHHHHHcCCCCcHHHHHHHHHhhcc-------------------HHHHHHHHHHHHhCCCeeeeeecceEEEeeCccc
Confidence 35555555 788899999999843322 333444566666555 4567 444 45553 2
Q ss_pred CCCCChh-------HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024196 179 LPRTSLN-------DIEELKAERLGLRNRIEKKTAYLQELE 212 (271)
Q Consensus 179 ~~~~s~~-------~~~~Lk~E~~~l~e~I~~Kk~~LqEL~ 212 (271)
++..+.. ++..|++++..+...++.....|..|.
T Consensus 66 ~~~~s~eel~~ld~ei~~L~~el~~l~~~~k~l~~eL~~L~ 106 (169)
T PF07106_consen 66 LEVPSPEELAELDAEIKELREELAELKKEVKSLEAELASLS 106 (169)
T ss_pred cCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 2322222 344555555555555555555554443
No 65
>cd06445 ATase The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases are specific for repair of guanines with O6-alkyl adducts, however human ATase is not limited to O6-methylguanine, repairing many other adducts at the O6-position of guanine as well. ATase is widely distributed among species. Most ATases have N- and C-terminal domains. The C-terminal domain contains the conserved active-site cysteine motif (PCHR), the O6-alkylguanine binding channel, and the helix-turn-helix (HTH) DNA-binding motif. The active site is located near the recognition helix of the HTH motif. While the C-terminal domain of ATase contains residues that are necessary for DNA binding and alkyl transfer, the function of the N-terminal domain is still unknown. Removal of the N-terminal domain abolishes the activity of
Probab=44.33 E-value=25 Score=26.69 Aligned_cols=23 Identities=26% Similarity=0.323 Sum_probs=18.1
Q ss_pred HHHHHHHHHh---cCCCcHHHHHHHH
Q 024196 104 SMKVCEKVES---KGRTTYNEVADEL 126 (271)
Q Consensus 104 S~KVcekVk~---kg~TTYnEVAdeL 126 (271)
-.+|.+.|.+ ...+||.+||+.+
T Consensus 2 ~~~V~~~v~~IP~G~v~TYg~iA~~~ 27 (79)
T cd06445 2 QRRVWEALRQIPYGEVTTYGQIAKLA 27 (79)
T ss_pred HHHHHHHHhcCCCCCcCcHHHHHHHH
Confidence 3456666664 8899999999998
No 66
>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=43.68 E-value=42 Score=25.72 Aligned_cols=43 Identities=28% Similarity=0.364 Sum_probs=25.3
Q ss_pred HHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccc
Q 024196 106 KVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDI 166 (271)
Q Consensus 106 KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~l 166 (271)
++..+-+.+|..||.||.+.|-.. ..--..|.+++..|+..||
T Consensus 11 ~Li~~gK~~G~lT~~eI~~~L~~~------------------~~~~e~id~i~~~L~~~gI 53 (82)
T PF03979_consen 11 KLIEKGKKKGYLTYDEINDALPED------------------DLDPEQIDEIYDTLEDEGI 53 (82)
T ss_dssp HHHHHHHHHSS-BHHHHHHH-S-S---------------------HHHHHHHHHHHHTT--
T ss_pred HHHHHHhhcCcCCHHHHHHHcCcc------------------CCCHHHHHHHHHHHHHCCC
Confidence 355667789999999999998211 0112457777777776554
No 67
>PRK11050 manganese transport regulator MntR; Provisional
Probab=42.84 E-value=92 Score=26.35 Aligned_cols=51 Identities=12% Similarity=0.133 Sum_probs=38.7
Q ss_pred HHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceee-cCCceEE
Q 024196 105 MKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK-DKKEIQW 176 (271)
Q Consensus 105 ~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K-~Kk~i~W 176 (271)
..++..+...+..+.+|+|+.| ..-+-.|..+++-|+..|+|.+ ..+.+.+
T Consensus 40 ~~I~~~l~~~~~~t~~eLA~~l---------------------~is~stVsr~l~~Le~~GlI~r~~~~~v~L 91 (152)
T PRK11050 40 ELIADLIAEVGEARQVDIAARL---------------------GVSQPTVAKMLKRLARDGLVEMRPYRGVFL 91 (152)
T ss_pred HHHHHHHHhcCCCCHHHHHHHH---------------------CCCHHHHHHHHHHHHHCCCEEEecCCceEE
Confidence 4455677777888999999998 2446678899999999999998 4344443
No 68
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=42.75 E-value=1.9e+02 Score=23.69 Aligned_cols=63 Identities=14% Similarity=0.027 Sum_probs=46.4
Q ss_pred cccchhHHHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceeec----CCc
Q 024196 98 RGLRQFSMKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKD----KKE 173 (271)
Q Consensus 98 ~GLR~fS~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K~----Kk~ 173 (271)
-||..--..|...+...+.+|-.|+|+.+ ..-+-.|--+++-|+.-|+|+|. .++
T Consensus 36 ~glt~~q~~vL~~l~~~~~~t~~eLa~~l---------------------~i~~~tvsr~l~~Le~~GlI~R~~~~~DrR 94 (144)
T PRK11512 36 LDITAAQFKVLCSIRCAACITPVELKKVL---------------------SVDLGALTRMLDRLVCKGWVERLPNPNDKR 94 (144)
T ss_pred cCCCHHHHHHHHHHHHcCCCCHHHHHHHH---------------------CCCHHHHHHHHHHHHHCCCEEeccCcccCC
Confidence 46666666777777777888899999988 13355677889999999999992 457
Q ss_pred eEEecCCC
Q 024196 174 IQWKGLPR 181 (271)
Q Consensus 174 i~W~G~~~ 181 (271)
..+.-+..
T Consensus 95 ~~~l~LT~ 102 (144)
T PRK11512 95 GVLVKLTT 102 (144)
T ss_pred eeEeEECh
Confidence 77765543
No 69
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=42.59 E-value=87 Score=29.75 Aligned_cols=40 Identities=20% Similarity=0.139 Sum_probs=25.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024196 189 ELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQRNERL 228 (271)
Q Consensus 189 ~Lk~E~~~l~e~I~~Kk~~LqEL~~Q~~~lknLI~RNk~l 228 (271)
+|+.+.+.|+++++..+..+.++..+...++..+++++..
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 42 (364)
T TIGR01242 3 ELDVRIRKLEDEKRSLEKEKIRLERELERLRSEIERLRSP 42 (364)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 4555566666666666666666766666677777666654
No 70
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=42.20 E-value=64 Score=27.91 Aligned_cols=62 Identities=19% Similarity=0.257 Sum_probs=41.9
Q ss_pred cccchhH--HHHHHHHHh-cCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceee--cCC
Q 024196 98 RGLRQFS--MKVCEKVES-KGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK--DKK 172 (271)
Q Consensus 98 ~GLR~fS--~KVcekVk~-kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K--~Kk 172 (271)
.|||.-. ..|.+.+.+ .+..|-.||.+.|.++.. ..-+=-||..|+.|+..|||.+ ..+
T Consensus 20 ~GlR~T~qR~~IL~~l~~~~~hlSa~eI~~~L~~~~~----------------~is~aTVYRtL~~L~e~Glv~~~~~~~ 83 (169)
T PRK11639 20 RNVRLTPQRLEVLRLMSLQPGAISAYDLLDLLREAEP----------------QAKPPTVYRALDFLLEQGFVHKVESTN 83 (169)
T ss_pred cCCCCCHHHHHHHHHHHhcCCCCCHHHHHHHHHhhCC----------------CCCcchHHHHHHHHHHCCCEEEEecCC
Confidence 4666555 346777765 457777777777754421 1224579999999999999999 344
Q ss_pred ceE
Q 024196 173 EIQ 175 (271)
Q Consensus 173 ~i~ 175 (271)
.+.
T Consensus 84 ~~~ 86 (169)
T PRK11639 84 SYV 86 (169)
T ss_pred cEE
Confidence 443
No 71
>COG5625 Predicted transcription regulator containing HTH domain [Transcription]
Probab=41.49 E-value=57 Score=27.44 Aligned_cols=48 Identities=23% Similarity=0.326 Sum_probs=35.1
Q ss_pred HhcCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceeecCCceEEecCC
Q 024196 112 ESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKDKKEIQWKGLP 180 (271)
Q Consensus 112 k~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K~Kk~i~W~G~~ 180 (271)
+..+.+--.|++.+|. -..|-|.|++-||.--|++.++==.=-|.|.-
T Consensus 32 e~~~~mri~ei~rEl~---------------------is~rtvr~~v~~l~rrGll~relvqkgWvGYi 79 (113)
T COG5625 32 EKGRGMRIREIQRELG---------------------ISERTVRAAVAVLLRRGLLARELVQKGWVGYI 79 (113)
T ss_pred HhcCCchHHHHHHHHh---------------------HHHHHHHHHHHHHHHhhHHHHHHHhccceeeE
Confidence 3444588888888882 34789999999999888888743333488863
No 72
>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=41.07 E-value=1e+02 Score=22.25 Aligned_cols=47 Identities=11% Similarity=0.070 Sum_probs=33.4
Q ss_pred HHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccce-eecCCce
Q 024196 106 KVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDII-SKDKKEI 174 (271)
Q Consensus 106 KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI-~K~Kk~i 174 (271)
++.+.+.. +.++.+|+|+.+ ..-++-|+..+..|++.|+. ...++.+
T Consensus 4 ~il~~L~~-~~~~~~eLa~~l---------------------~vS~~tv~~~l~~L~~~g~~i~~~~~g~ 51 (69)
T TIGR00122 4 RLLALLAD-NPFSGEKLGEAL---------------------GMSRTAVNKHIQTLREWGVDVLTVGKGY 51 (69)
T ss_pred HHHHHHHc-CCcCHHHHHHHH---------------------CCCHHHHHHHHHHHHHCCCeEEecCCce
Confidence 45556554 456699999988 36678999999999998883 3344444
No 73
>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=40.86 E-value=56 Score=23.49 Aligned_cols=39 Identities=31% Similarity=0.263 Sum_probs=33.0
Q ss_pred CCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceeecCCceE
Q 024196 116 RTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKDKKEIQ 175 (271)
Q Consensus 116 ~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K~Kk~i~ 175 (271)
..|..++|+.+ ..-++.|--+++-|+.-|+|+..++.|.
T Consensus 28 ~lt~~~iA~~~---------------------g~sr~tv~r~l~~l~~~g~I~~~~~~i~ 66 (76)
T PF13545_consen 28 PLTQEEIADML---------------------GVSRETVSRILKRLKDEGIIEVKRGKII 66 (76)
T ss_dssp ESSHHHHHHHH---------------------TSCHHHHHHHHHHHHHTTSEEEETTEEE
T ss_pred cCCHHHHHHHH---------------------CCCHHHHHHHHHHHHHCCCEEEcCCEEE
Confidence 45788888887 3678899999999999999999877665
No 74
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=40.79 E-value=46 Score=28.74 Aligned_cols=54 Identities=15% Similarity=0.114 Sum_probs=37.8
Q ss_pred cchhHHHHHHHHHh-----cCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhcccc-chhhhhhHHHHhhhccceeecCCc
Q 024196 100 LRQFSMKVCEKVES-----KGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKN-IRRRVYDALNVLMAMDIISKDKKE 173 (271)
Q Consensus 100 LR~fS~KVcekVk~-----kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~-ikRRVYD~lNVL~ai~lI~K~Kk~ 173 (271)
|--.-.+|.+.+.+ .-..|..|+|+.+ .. -+--|+..|..|+..|+|++..+.
T Consensus 4 lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~---------------------~~~s~~tv~~~l~~L~~~g~i~~~~~~ 62 (199)
T TIGR00498 4 LTARQQEVLDLIRAHIESTGYPPSIREIARAV---------------------GLRSPSAAEEHLKALERKGYIERDPGK 62 (199)
T ss_pred cCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHh---------------------CCCChHHHHHHHHHHHHCCCEecCCCC
Confidence 33334556666664 2247788999988 12 256789999999999999996555
Q ss_pred e
Q 024196 174 I 174 (271)
Q Consensus 174 i 174 (271)
+
T Consensus 63 ~ 63 (199)
T TIGR00498 63 P 63 (199)
T ss_pred C
Confidence 4
No 75
>PF02996 Prefoldin: Prefoldin subunit; InterPro: IPR004127 This entry comprises of several prefoldin subunits. Prefoldin (PFD) is a chaperone that interacts exclusively with type II chaperonins, hetero-oligomers lacking an obligate co-chaperonin that are found only in eukaryotes (chaperonin-containing T-complex polypeptide-1 (CCT)) and archaea. Eukaryotic PFD is a multi-subunit complex containing six polypeptides in the molecular mass range of 14-23 kDa. In archaea, on the other hand, PFD is composed of two types of subunits, two alpha and four beta. The six subunits associate to form two back-to-back up-and-down eight-stranded barrels, from which hang six coiled coils. Each subunit contributes one (beta subunits) or two (alpha subunits) beta hairpin turns to the barrels. The coiled coils are formed by the N and C termini of an individual subunit. Overall, this unique arrangement resembles a jellyfish. The eukaryotic PFD hexamer is composed of six different subunits; however, these can be grouped into two alpha-like (PFD3 and -5) and four beta-like (PFD1, -2, -4, and -6) subunits based on amino acid sequence similarity with their archaeal counterparts. Eukaryotic PFD has a six-legged structure similar to that seen in the archaeal homologue [, ]. This family contains the archaeal alpha subunit, eukaryotic prefoldin subunits 3 and 5 and the UXT (ubiquitously expressed transcript) family. Eukaryotic PFD has been shown to bind both actin and tubulin co-translationally. The chaperone then delivers the target protein to CCT, interacting with the chaperonin through the tips of the coiled coils. No authentic target proteins of any archaeal PFD have been identified, to date.; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0016272 prefoldin complex; PDB: 1FXK_C 2ZDI_C.
Probab=39.80 E-value=1.3e+02 Score=23.77 Aligned_cols=69 Identities=23% Similarity=0.158 Sum_probs=42.1
Q ss_pred hHHHHhhhccceeecCCceEEecCCCCC----hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024196 156 DALNVLMAMDIISKDKKEIQWKGLPRTS----LNDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQR 224 (271)
Q Consensus 156 D~lNVL~ai~lI~K~Kk~i~W~G~~~~s----~~~~~~Lk~E~~~l~e~I~~Kk~~LqEL~~Q~~~lknLI~R 224 (271)
++-..+..-|-|....+-+-|.|.+-.. ..-++-|+..+..+++.++.....+.++..+...+...+++
T Consensus 44 plg~~~~v~g~i~~~~~vlV~lG~~~~vE~s~~eA~~~l~~r~~~l~~~~~~l~~~~~~~~~~~~~~~~~l~~ 116 (120)
T PF02996_consen 44 PLGSGVFVPGKIPDTDKVLVSLGAGYYVEMSLEEAIEFLKKRIKELEEQLEKLEKELAELQAQIEQLEQTLQQ 116 (120)
T ss_dssp EECTTEEEEEE-SSTTEEEEEEETTEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHH
T ss_pred cCCCCeEEEEEeCCCCEEEEEeeCCeEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4444444555566677788888865322 23444556666666667777777777777777666666654
No 76
>PRK09039 hypothetical protein; Validated
Probab=39.45 E-value=83 Score=30.46 Aligned_cols=76 Identities=16% Similarity=0.196 Sum_probs=0.0
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHhhcCCCCCCCcccccEE-----EEEcCCCcE
Q 024196 184 LNDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQ-----RNERLYSSGNAPSGGVALPFI-----LVQTRPHAT 253 (271)
Q Consensus 184 ~~~~~~Lk~E~~~l~e~I~~Kk~~LqEL~~Q~~~lknLI~-----RNk~l~~~~~~~~~~i~LPFI-----vV~T~~~t~ 253 (271)
.++++.|+.++..++..|..-+++..+...+...++.-++ +++.+. .+.-=|+ +..+++.-.
T Consensus 143 ~~qI~aLr~Qla~le~~L~~ae~~~~~~~~~i~~L~~~L~~a~~~~~~~l~--------~~~~~~~~~l~~~~~~~~~ir 214 (343)
T PRK09039 143 NQQIAALRRQLAALEAALDASEKRDRESQAKIADLGRRLNVALAQRVQELN--------RYRSEFFGRLREILGDREGIR 214 (343)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------HhHHHHHHHHHHHhCCCCCcE
Q ss_pred EEEeecCC----ceEEEEeecC
Q 024196 254 VEVEISED----MQLVHFDFNR 271 (271)
Q Consensus 254 IeceiseD----~~~~~F~F~~ 271 (271)
|+ .| ...++|+|+|
T Consensus 215 i~----g~~~~~~~~vlF~~gs 232 (343)
T PRK09039 215 IV----GDRFVFQSEVLFPTGS 232 (343)
T ss_pred EE----CCEEEecCCceeCCCC
No 77
>PF13518 HTH_28: Helix-turn-helix domain
Probab=39.17 E-value=75 Score=21.12 Aligned_cols=38 Identities=24% Similarity=0.273 Sum_probs=27.9
Q ss_pred HHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccc
Q 024196 106 KVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDI 166 (271)
Q Consensus 106 KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~l 166 (271)
+|++.+.+ |. |+.++|.++ ..-+..||.++.-...-|+
T Consensus 4 ~iv~~~~~-g~-s~~~~a~~~---------------------gis~~tv~~w~~~y~~~G~ 41 (52)
T PF13518_consen 4 QIVELYLE-GE-SVREIAREF---------------------GISRSTVYRWIKRYREGGI 41 (52)
T ss_pred HHHHHHHc-CC-CHHHHHHHH---------------------CCCHhHHHHHHHHHHhcCH
Confidence 46677774 44 999999998 2346788888888887663
No 78
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=39.11 E-value=1.4e+02 Score=26.65 Aligned_cols=44 Identities=27% Similarity=0.437 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 024196 186 DIEELKAERLGLRNRI-------EKKTAYLQELEDQFVGLQNLIQRNERLY 229 (271)
Q Consensus 186 ~~~~Lk~E~~~l~e~I-------~~Kk~~LqEL~~Q~~~lknLI~RNk~l~ 229 (271)
+.+.|+.|...|.+++ +...+.+..+...+.+|-.+|+|=+.+.
T Consensus 105 e~~~l~~e~~~l~~~~e~Le~e~~~L~~~~~~~~eDY~~L~~Im~RARkl~ 155 (161)
T TIGR02894 105 ENERLKNQNESLQKRNEELEKELEKLRQRLSTIEEDYQTLIDIMDRARKLA 155 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4444555554444444 4444444455677788888888877764
No 79
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=38.38 E-value=2.2e+02 Score=25.84 Aligned_cols=36 Identities=25% Similarity=0.326 Sum_probs=29.0
Q ss_pred hcCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceee
Q 024196 113 SKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (271)
Q Consensus 113 ~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K 169 (271)
+.+.+|..|++..+ +--|-+|-=++-+|++.+|+.|
T Consensus 38 s~~Pmtl~Ei~E~l---------------------g~Sks~vS~~lkkL~~~~lV~~ 73 (177)
T COG1510 38 SRKPLTLDEIAEAL---------------------GMSKSNVSMGLKKLQDWNLVKK 73 (177)
T ss_pred cCCCccHHHHHHHH---------------------CCCcchHHHHHHHHHhcchHHh
Confidence 36677777777776 4557788889999999999998
No 80
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=38.19 E-value=53 Score=22.47 Aligned_cols=25 Identities=32% Similarity=0.640 Sum_probs=20.1
Q ss_pred hhHHHHHHHHHhcCCCcHHHHHHHH
Q 024196 102 QFSMKVCEKVESKGRTTYNEVADEL 126 (271)
Q Consensus 102 ~fS~KVcekVk~kg~TTYnEVAdeL 126 (271)
.+-.++...++..++++|.++|.++
T Consensus 3 ~~D~~Il~~Lq~d~r~s~~~la~~l 27 (42)
T PF13404_consen 3 ELDRKILRLLQEDGRRSYAELAEEL 27 (42)
T ss_dssp HHHHHHHHHHHH-TTS-HHHHHHHH
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHH
Confidence 3557888999999999999999998
No 81
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=38.07 E-value=59 Score=26.95 Aligned_cols=35 Identities=23% Similarity=0.126 Sum_probs=29.0
Q ss_pred hhhccccchhhhhhHHHHhhhccceeecCCceEEe
Q 024196 143 QQYDEKNIRRRVYDALNVLMAMDIISKDKKEIQWK 177 (271)
Q Consensus 143 ~~~d~K~ikRRVYD~lNVL~ai~lI~K~Kk~i~W~ 177 (271)
-+.-....|..|.-+++-|..-|+|+..+++|...
T Consensus 149 iA~~lG~tretvsR~l~~l~~~g~I~~~~~~i~I~ 183 (193)
T TIGR03697 149 IAEAIGSTRVTITRLLGDLRKKKLISIHKKKITVH 183 (193)
T ss_pred HHHHhCCcHHHHHHHHHHHHHCCCEEecCCEEEEe
Confidence 34444677899999999999999999988888854
No 82
>COG0350 Ada Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]
Probab=37.66 E-value=32 Score=30.12 Aligned_cols=25 Identities=28% Similarity=0.445 Sum_probs=22.9
Q ss_pred hhHHHHHHHHHh---cCCCcHHHHHHHH
Q 024196 102 QFSMKVCEKVES---KGRTTYNEVADEL 126 (271)
Q Consensus 102 ~fS~KVcekVk~---kg~TTYnEVAdeL 126 (271)
.|-.+|.+.+.+ ..++||.|+|..|
T Consensus 88 ~Fq~~Vw~aL~~IP~Get~TY~eiA~~i 115 (168)
T COG0350 88 GFQGRVWQALREIPYGETVTYGEIARRL 115 (168)
T ss_pred hHHHHHHHHHhcCCCCCcEeHHHHHHHh
Confidence 688999999988 7799999999998
No 83
>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=37.43 E-value=2.4e+02 Score=23.39 Aligned_cols=56 Identities=14% Similarity=0.163 Sum_probs=39.2
Q ss_pred HHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceee--cCCceEEe
Q 024196 105 MKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK--DKKEIQWK 177 (271)
Q Consensus 105 ~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K--~Kk~i~W~ 177 (271)
..|++.+=..+..|-.||.+.|-... .--+-.|+=+|+.|+.-|+|++ .+..+.|.
T Consensus 7 ~~VM~vlW~~~~~t~~eI~~~l~~~~-----------------~~~~tTv~T~L~rL~~KG~v~~~k~gr~~~Y~ 64 (130)
T TIGR02698 7 WEVMRVVWTLGETTSRDIIRILAEKK-----------------DWSDSTIKTLLGRLVDKGCLTTEKEGRKFIYT 64 (130)
T ss_pred HHHHHHHHcCCCCCHHHHHHHHhhcc-----------------CCcHHHHHHHHHHHHHCCceeeecCCCcEEEE
Confidence 34677776788888889888872210 1224578889999999999996 45555554
No 84
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=37.40 E-value=25 Score=28.66 Aligned_cols=34 Identities=21% Similarity=0.097 Sum_probs=26.8
Q ss_pred cCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhc
Q 024196 114 KGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAM 164 (271)
Q Consensus 114 kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai 164 (271)
-...+|.|||++| .....++++++|.++..|...
T Consensus 123 ~~~~s~~EIA~~l-----------------gis~~tV~~~l~ra~~~lr~~ 156 (163)
T PRK07037 123 LHGETQKDIAREL-----------------GVSPTLVNFMIRDALVHCRKC 156 (163)
T ss_pred HcCCCHHHHHHHH-----------------CCCHHHHHHHHHHHHHHHHHH
Confidence 3567899999998 123479999999999999863
No 85
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=36.85 E-value=56 Score=27.56 Aligned_cols=33 Identities=24% Similarity=0.078 Sum_probs=27.2
Q ss_pred hhccccchhhhhhHHHHhhhccceeecCCceEE
Q 024196 144 QYDEKNIRRRVYDALNVLMAMDIISKDKKEIQW 176 (271)
Q Consensus 144 ~~d~K~ikRRVYD~lNVL~ai~lI~K~Kk~i~W 176 (271)
+.-....|+.|.-+++-|+.-|+|+..++.|.-
T Consensus 175 A~~lG~tr~tvsR~l~~l~~~gii~~~~~~i~i 207 (211)
T PRK11753 175 GRIVGCSREMVGRVLKMLEDQGLISAHGKTIVV 207 (211)
T ss_pred HHHhCCCHHHHHHHHHHHHHCCCEEecCCEEEE
Confidence 334456788899999999999999998888764
No 86
>TIGR02716 C20_methyl_CrtF C-20 methyltransferase BchU. Members of this protein family are the S-adenosylmethionine-depenedent C-20 methyltransferase BchU, part of the pathway of bacteriochlorophyll c production in photosynthetic green sulfur bacteria. The position modified by this enzyme represents the difference between bacteriochlorophylls c and d; strains lacking this protein can only produced bacteriochlorophyll d.
Probab=36.69 E-value=58 Score=29.94 Aligned_cols=49 Identities=14% Similarity=0.253 Sum_probs=36.5
Q ss_pred HHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceeecCCceE
Q 024196 105 MKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKDKKEIQ 175 (271)
Q Consensus 105 ~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K~Kk~i~ 175 (271)
..|.+.+.+ +..|-.|+|..+ +.-.|.++-.|..|.++|++++....|.
T Consensus 13 Lglfd~L~~-gp~t~~eLA~~~---------------------~~~~~~~~~lL~~L~~lgll~~~~~~y~ 61 (306)
T TIGR02716 13 LDLFSHMAE-GPKDLATLAADT---------------------GSVPPRLEMLLETLRQMRVINLEDGKWS 61 (306)
T ss_pred cCcHHHHhc-CCCCHHHHHHHc---------------------CCChHHHHHHHHHHHhCCCeEecCCcEe
Confidence 345666754 677888888876 2345789999999999999999655443
No 87
>PF06717 DUF1202: Protein of unknown function (DUF1202); InterPro: IPR009592 This family consists of several hypothetical bacterial proteins of around 335 residues in length. Members of this family are found exclusively in Escherichia coli and Salmonella species and are often referred to as YggM proteins. The function of this family is unknown.
Probab=36.61 E-value=1.4e+02 Score=29.18 Aligned_cols=58 Identities=16% Similarity=0.173 Sum_probs=42.1
Q ss_pred ccceeecCCceEEecCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024196 164 MDIISKDKKEIQWKGLPRTSLNDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQ 223 (271)
Q Consensus 164 i~lI~K~Kk~i~W~G~~~~s~~~~~~Lk~E~~~l~e~I~~Kk~~LqEL~~Q~~~lknLI~ 223 (271)
+..|....|-+.|.+-. ...++..++.+....+..|...+.++.+|..+.++++.-|.
T Consensus 119 v~~i~tn~KYLIvn~~~--F~~rf~~Ied~~~~kK~~I~~L~~qisaLdkqi~ai~Kkid 176 (308)
T PF06717_consen 119 VPDIKTNDKYLIVNDQD--FNYRFNQIEDEYNRKKNKIPGLNKQISALDKQIVAINKKID 176 (308)
T ss_pred CCccccCCcEEEecchh--HHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence 55677766888888653 33567777777777777888888888888887777766554
No 88
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=36.57 E-value=99 Score=23.14 Aligned_cols=52 Identities=21% Similarity=0.248 Sum_probs=36.8
Q ss_pred HHHHHHHHh-cCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceee----cCCceEEe
Q 024196 105 MKVCEKVES-KGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK----DKKEIQWK 177 (271)
Q Consensus 105 ~KVcekVk~-kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K----~Kk~i~W~ 177 (271)
-+|.+-++. .+..+-.|||+.+ .--+..+-=+|+.|+.-|.|++ .++...|.
T Consensus 3 e~Il~~i~~~~~p~~T~eiA~~~---------------------gls~~~aR~yL~~Le~eG~V~~~~~~rG~~~~W~ 59 (62)
T PF04703_consen 3 EKILEYIKEQNGPLKTREIADAL---------------------GLSIYQARYYLEKLEKEGKVERSPVRRGKSTYWR 59 (62)
T ss_dssp HCHHHHHHHHTS-EEHHHHHHHH---------------------TS-HHHHHHHHHHHHHCTSEEEES-SSSSS-EEE
T ss_pred HHHHHHHHHcCCCCCHHHHHHHh---------------------CCCHHHHHHHHHHHHHCCCEEEecCCCCcceeee
Confidence 356777777 8888999999998 1234445567999999999997 24455786
No 89
>PF11594 Med28: Mediator complex subunit 28; InterPro: IPR021640 Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species [],[]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function []. Subunit Med28 of the Mediator may function as a scaffolding protein within Mediator by maintaining the stability of a submodule within the head module, and components of this submodule act together in a gene-regulatory programme to suppress smooth muscle cell differentiation. Thus, mammalian Mediator subunit Med28 functions as a repressor of smooth muscle-cell differentiation, which could have implications for disorders associated with abnormalities in smooth muscle cell growth and differentiation, including atherosclerosis, asthma, hypertension, and smooth muscle tumours [].
Probab=36.57 E-value=1.3e+02 Score=25.26 Aligned_cols=37 Identities=22% Similarity=0.295 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024196 188 EELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQR 224 (271)
Q Consensus 188 ~~Lk~E~~~l~e~I~~Kk~~LqEL~~Q~~~lknLI~R 224 (271)
..|++|...|++.+..|.+.++.+......+++|+..
T Consensus 38 ~~lkEEi~eLK~ElqRKe~Ll~Kh~~kI~~w~~lL~d 74 (106)
T PF11594_consen 38 QVLKEEINELKEELQRKEQLLQKHYEKIDYWEKLLSD 74 (106)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3577778888888888888888888888888888763
No 90
>KOG2264 consensus Exostosin EXT1L [Signal transduction mechanisms]
Probab=36.30 E-value=95 Score=33.33 Aligned_cols=38 Identities=26% Similarity=0.297 Sum_probs=16.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHH
Q 024196 188 EELKAERLGLRNRIEKKTAYLQELE----DQFVGLQNLIQRN 225 (271)
Q Consensus 188 ~~Lk~E~~~l~e~I~~Kk~~LqEL~----~Q~~~lknLI~RN 225 (271)
+++....+.++..|.+++..|..|. +-+.+++.|+++|
T Consensus 110 ~~~n~kiEelk~~i~~~q~eL~~Lk~~ieqaq~~~~El~~~n 151 (907)
T KOG2264|consen 110 EEINTKIEELKRLIPQKQLELSALKGEIEQAQRQLEELRETN 151 (907)
T ss_pred HHHHHHHHHHHHHHHHhHHHHHHHHhHHHHHHHHHHHHHhhc
Confidence 3333333344444444444443322 2333555555555
No 91
>PRK00901 methylated-DNA--protein-cysteine methyltransferase; Provisional
Probab=36.11 E-value=36 Score=29.55 Aligned_cols=26 Identities=23% Similarity=0.451 Sum_probs=23.2
Q ss_pred chhHHHHHHHHHh---cCCCcHHHHHHHH
Q 024196 101 RQFSMKVCEKVES---KGRTTYNEVADEL 126 (271)
Q Consensus 101 R~fS~KVcekVk~---kg~TTYnEVAdeL 126 (271)
--|..+|++.+.+ ..++||.|||..|
T Consensus 72 t~fq~~Vw~~l~~Ip~G~t~tY~~lA~~~ 100 (155)
T PRK00901 72 TEFQKKVWKALQEIPYGETRSYKEIAVNI 100 (155)
T ss_pred ChHHHHHHHHHccCCCCCcCCHHHHHHHH
Confidence 3799999999988 7899999999997
No 92
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=35.72 E-value=70 Score=21.34 Aligned_cols=23 Identities=26% Similarity=0.289 Sum_probs=19.2
Q ss_pred ccchhhhhhHHHHhhhccceeec
Q 024196 148 KNIRRRVYDALNVLMAMDIISKD 170 (271)
Q Consensus 148 K~ikRRVYD~lNVL~ai~lI~K~ 170 (271)
..-+--|..+++.|+.-|+|.+.
T Consensus 31 ~vs~~tv~~~l~~L~~~g~i~~~ 53 (60)
T smart00345 31 GVSRTTVREALSRLEAEGLVQRR 53 (60)
T ss_pred CCCHHHHHHHHHHHHHCCCEEEe
Confidence 34567889999999999999883
No 93
>smart00338 BRLZ basic region leucin zipper.
Probab=35.71 E-value=1.7e+02 Score=21.15 Aligned_cols=34 Identities=24% Similarity=0.298 Sum_probs=16.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024196 187 IEELKAERLGLRNRIEKKTAYLQELEDQFVGLQN 220 (271)
Q Consensus 187 ~~~Lk~E~~~l~e~I~~Kk~~LqEL~~Q~~~lkn 220 (271)
++.|+.+...|..........+..|..+...|++
T Consensus 28 ~~~Le~~~~~L~~en~~L~~~~~~l~~e~~~lk~ 61 (65)
T smart00338 28 IEELERKVEQLEAENERLKKEIERLRRELEKLKS 61 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445555555544444444455555544444443
No 94
>PRK10803 tol-pal system protein YbgF; Provisional
Probab=35.29 E-value=1.2e+02 Score=28.09 Aligned_cols=44 Identities=9% Similarity=0.129 Sum_probs=31.8
Q ss_pred ChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHH
Q 024196 183 SLNDIEELKAERLGLRNRIEKKTAYLQELEDQFVG-LQNLIQRNE 226 (271)
Q Consensus 183 s~~~~~~Lk~E~~~l~e~I~~Kk~~LqEL~~Q~~~-lknLI~RNk 226 (271)
..++++.|+.|+.+|+.+|++..-+|+++.+++.. +..|=.|-+
T Consensus 59 l~~ql~~lq~ev~~LrG~~E~~~~~l~~~~~rq~~~y~dld~r~~ 103 (263)
T PRK10803 59 LQQQLSDNQSDIDSLRGQIQENQYQLNQVVERQKQIYLQIDSLSS 103 (263)
T ss_pred HHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 35778889999999999999888888888875543 334433443
No 95
>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=35.11 E-value=1.3e+02 Score=23.56 Aligned_cols=31 Identities=26% Similarity=0.258 Sum_probs=24.1
Q ss_pred ccchhhhhhHHHHhhhccceeecCCceEEecC
Q 024196 148 KNIRRRVYDALNVLMAMDIISKDKKEIQWKGL 179 (271)
Q Consensus 148 K~ikRRVYD~lNVL~ai~lI~K~Kk~i~W~G~ 179 (271)
...|.-|..+|+-|+..|+|.+..+ ..|.|.
T Consensus 58 g~sr~tVsr~L~~Le~~GlI~r~~~-~~~~~~ 88 (95)
T TIGR01610 58 GLSRTHVSDAIKSLARRRIIFRQGM-MGIVGV 88 (95)
T ss_pred CcCHHHHHHHHHHHHHCCCeeeecC-Cceeec
Confidence 4668889999999999999998542 444454
No 96
>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This entry consists of proteins thought to be involved in plasmid replication. ; GO: 0006260 DNA replication, 0006276 plasmid maintenance
Probab=34.53 E-value=62 Score=28.27 Aligned_cols=26 Identities=23% Similarity=0.184 Sum_probs=21.7
Q ss_pred ccchhhhhhHHHHhhhccceeecCCc
Q 024196 148 KNIRRRVYDALNVLMAMDIISKDKKE 173 (271)
Q Consensus 148 K~ikRRVYD~lNVL~ai~lI~K~Kk~ 173 (271)
..-++-|+.++..|+..++|.|.++.
T Consensus 86 ~iS~~Tv~r~ik~L~e~~iI~k~~~G 111 (165)
T PF05732_consen 86 GISKPTVSRAIKELEEKNIIKKIRNG 111 (165)
T ss_pred CCCHHHHHHHHHHHHhCCcEEEccCC
Confidence 35588899999999999999995533
No 97
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147. This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.
Probab=34.08 E-value=4.1e+02 Score=25.11 Aligned_cols=60 Identities=15% Similarity=0.185 Sum_probs=36.0
Q ss_pred cccchhHHHHHHHHHh-----cCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceeecCC
Q 024196 98 RGLRQFSMKVCEKVES-----KGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKDKK 172 (271)
Q Consensus 98 ~GLR~fS~KVcekVk~-----kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K~Kk 172 (271)
.-+.+|+.=.+-.|++ .+..+..++|+.|.- +.-=..|=|+|..|+.+|||+|+++
T Consensus 114 ~~~~y~~~W~~~virel~~~~~~~~~~~~ia~~l~p-------------------~is~~ev~~sL~~L~~~glikk~~~ 174 (271)
T TIGR02147 114 DQFEYYRHWYNSVIRELLGVMPFADDPEELAKRCFP-------------------KISAEQVKESLDLLERLGLIKKNED 174 (271)
T ss_pred HHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHhCC-------------------CCCHHHHHHHHHHHHHCCCeeECCC
Confidence 4466666555555555 233355555555510 1123456799999999999999554
Q ss_pred ceEEe
Q 024196 173 EIQWK 177 (271)
Q Consensus 173 ~i~W~ 177 (271)
. .|.
T Consensus 175 g-~y~ 178 (271)
T TIGR02147 175 G-FYK 178 (271)
T ss_pred C-cEE
Confidence 3 554
No 98
>PF08317 Spc7: Spc7 kinetochore protein; InterPro: IPR013253 This entry consists of cell division proteins which are required for kinetochore-spindle association [].
Probab=33.66 E-value=1.6e+02 Score=27.99 Aligned_cols=38 Identities=29% Similarity=0.455 Sum_probs=20.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024196 186 DIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQ 223 (271)
Q Consensus 186 ~~~~Lk~E~~~l~e~I~~Kk~~LqEL~~Q~~~lknLI~ 223 (271)
++..|+.++..++..|..+++.|.+|..+...++.-|+
T Consensus 210 eL~~lr~eL~~~~~~i~~~k~~l~el~~el~~l~~~i~ 247 (325)
T PF08317_consen 210 ELEALRQELAEQKEEIEAKKKELAELQEELEELEEKIE 247 (325)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455555555555566555555555555554444443
No 99
>PF10473 CENP-F_leu_zip: Leucine-rich repeats of kinetochore protein Cenp-F/LEK1; InterPro: IPR019513 Cenp-F, a centromeric kinetochore, microtubule-binding protein consisting of two 1,600-amino acid-long coils, is essential for the full functioning of the mitotic checkpoint pathway [, ]. There are several leucine-rich repeats along the sequence of LEK1 that are considered to be zippers, though they do not appear to be binding DNA directly in this instance []. ; GO: 0008134 transcription factor binding, 0042803 protein homodimerization activity, 0045502 dynein binding
Probab=33.56 E-value=1.5e+02 Score=25.65 Aligned_cols=40 Identities=30% Similarity=0.487 Sum_probs=30.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024196 185 NDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQR 224 (271)
Q Consensus 185 ~~~~~Lk~E~~~l~e~I~~Kk~~LqEL~~Q~~~lknLI~R 224 (271)
.++..|..|+..|...+++++.+..+|..-...+.++|+.
T Consensus 73 ~EL~~l~sEk~~L~k~lq~~q~kv~eLE~~~~~~~~~l~~ 112 (140)
T PF10473_consen 73 LELDTLRSEKENLDKELQKKQEKVSELESLNSSLENLLQE 112 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Confidence 3555666677777777888888888888888888888874
No 100
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=33.47 E-value=3.3e+02 Score=23.79 Aligned_cols=26 Identities=27% Similarity=0.394 Sum_probs=20.3
Q ss_pred chhhhhhHHHHhhhccceeecCCceEE
Q 024196 150 IRRRVYDALNVLMAMDIISKDKKEIQW 176 (271)
Q Consensus 150 ikRRVYD~lNVL~ai~lI~K~Kk~i~W 176 (271)
.-..|=++|+.|+.+|+|+|+++ -.|
T Consensus 54 s~~ev~~sL~~L~~~gli~k~~~-g~y 79 (171)
T PF14394_consen 54 SAEEVRDSLEFLEKLGLIKKDGD-GKY 79 (171)
T ss_pred CHHHHHHHHHHHHHCCCeEECCC-CcE
Confidence 34567799999999999999665 344
No 101
>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=33.17 E-value=69 Score=24.54 Aligned_cols=44 Identities=14% Similarity=0.271 Sum_probs=32.8
Q ss_pred HHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceee
Q 024196 105 MKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (271)
Q Consensus 105 ~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K 169 (271)
..|..-+.. |.+.|+|+.+.| + ..-.+-+.+-|.-|++.|||+|
T Consensus 8 ~~IL~~l~~-g~~rf~el~~~l------~--------------~is~~~L~~~L~~L~~~GLv~r 51 (90)
T PF01638_consen 8 LLILRALFQ-GPMRFSELQRRL------P--------------GISPKVLSQRLKELEEAGLVER 51 (90)
T ss_dssp HHHHHHHTT-SSEEHHHHHHHS------T--------------TS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHh-CCCcHHHHHHhc------c--------------hhHHHHHHHHHHHHHHcchhhc
Confidence 344455544 899999988887 0 1335677899999999999999
No 102
>PF12958 DUF3847: Protein of unknown function (DUF3847); InterPro: IPR024215 This entry represents a family of uncharacterised proteins that were found by clustering human gut metagenomic sequences [].
Probab=32.95 E-value=1.9e+02 Score=23.26 Aligned_cols=45 Identities=27% Similarity=0.381 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHhhc
Q 024196 186 DIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQN--LIQRNERLYS 230 (271)
Q Consensus 186 ~~~~Lk~E~~~l~e~I~~Kk~~LqEL~~Q~~~lkn--LI~RNk~l~~ 230 (271)
.+++|++|....++.|++....++.|..+...+.+ =-+||.++..
T Consensus 2 ~Le~l~~e~e~~~~kl~q~e~~~k~L~nr~k~l~k~eRK~RtHRLi~ 48 (86)
T PF12958_consen 2 TLEELQAEIEKAEKKLEQAEHKIKQLENRKKKLEKKERKERTHRLIE 48 (86)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 36778888887777777777777777766644421 1236666543
No 103
>PF08317 Spc7: Spc7 kinetochore protein; InterPro: IPR013253 This entry consists of cell division proteins which are required for kinetochore-spindle association [].
Probab=32.90 E-value=1.3e+02 Score=28.55 Aligned_cols=81 Identities=19% Similarity=0.239 Sum_probs=39.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcC-------CCCCCCccc-ccEEEEEcCCCcEEEEe
Q 024196 186 DIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQRNERLYSS-------GNAPSGGVA-LPFILVQTRPHATVEVE 257 (271)
Q Consensus 186 ~~~~Lk~E~~~l~e~I~~Kk~~LqEL~~Q~~~lknLI~RNk~l~~~-------~~~~~~~i~-LPFIvV~T~~~t~Iece 257 (271)
++.+|+.++..+.+.|+...++.+++..+...++..++.++..... ...-.+.++ .-|+-+. ++.+.+.
T Consensus 231 ~l~el~~el~~l~~~i~~~~~~k~~l~~eI~e~~~~~~~~r~~t~~Ev~~Lk~~~~~Le~~~gw~~~~~~---~~~l~~~ 307 (325)
T PF08317_consen 231 ELAELQEELEELEEKIEELEEQKQELLAEIAEAEKIREECRGWTRSEVKRLKAKVDALEKLTGWKIVSIS---GSTLEFR 307 (325)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHCcEEEEEe---CCeEEEE
Confidence 3345555555555566666666666666666666555544332100 000001112 3333333 4567666
Q ss_pred ecCCceEEEEeec
Q 024196 258 ISEDMQLVHFDFN 270 (271)
Q Consensus 258 iseD~~~~~F~F~ 270 (271)
...+ ..+.|+|-
T Consensus 308 ~~~~-i~~~fd~~ 319 (325)
T PF08317_consen 308 YKDE-IELSFDFF 319 (325)
T ss_pred EcCE-EEEEEecc
Confidence 6655 77777763
No 104
>PRK11569 transcriptional repressor IclR; Provisional
Probab=32.88 E-value=3.9e+02 Score=24.45 Aligned_cols=46 Identities=13% Similarity=0.171 Sum_probs=36.4
Q ss_pred HHHHHHHHh-cCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceeecC
Q 024196 105 MKVCEKVES-KGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKDK 171 (271)
Q Consensus 105 ~KVcekVk~-kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K~K 171 (271)
..|.+.+.+ .+..+..|+|+.+ .--|=.+|-+|+-|+..|+++++.
T Consensus 31 l~IL~~l~~~~~~~~lseia~~l---------------------glpksTv~RlL~tL~~~G~l~~~~ 77 (274)
T PRK11569 31 LKLLEWIAESNGSVALTELAQQA---------------------GLPNSTTHRLLTTMQQQGFVRQVG 77 (274)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHH---------------------CcCHHHHHHHHHHHHHCCCEEEcC
Confidence 445566654 5678999999998 244778999999999999999953
No 105
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=32.62 E-value=2.1e+02 Score=21.36 Aligned_cols=23 Identities=13% Similarity=0.056 Sum_probs=19.0
Q ss_pred chhhhhhHHHHhhhccceeecCC
Q 024196 150 IRRRVYDALNVLMAMDIISKDKK 172 (271)
Q Consensus 150 ikRRVYD~lNVL~ai~lI~K~Kk 172 (271)
-+=.|+.++.-|+.-|+|.+..+
T Consensus 12 s~stvs~~l~~L~~~glI~r~~~ 34 (96)
T smart00529 12 SPPTVTQMLKKLEKDGLVEYEPY 34 (96)
T ss_pred ChHHHHHHHHHHHHCCCEEEcCC
Confidence 35578889999999999999554
No 106
>PHA02943 hypothetical protein; Provisional
Probab=32.47 E-value=2e+02 Score=25.85 Aligned_cols=66 Identities=20% Similarity=0.148 Sum_probs=43.0
Q ss_pred HHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceee--cCCceEEecCCCCCh
Q 024196 107 VCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK--DKKEIQWKGLPRTSL 184 (271)
Q Consensus 107 VcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K--~Kk~i~W~G~~~~s~ 184 (271)
|.|.+ ..|-+|-.|||+.| ..---.+..+|=|||--|.|.+ -++.=-|.=.+....
T Consensus 16 ILE~L-k~G~~TtseIAkaL---------------------GlS~~qa~~~LyvLErEG~VkrV~~G~~tyw~l~~day~ 73 (165)
T PHA02943 16 TLRLL-ADGCKTTSRIANKL---------------------GVSHSMARNALYQLAKEGMVLKVEIGRAAIWCLDEDAYT 73 (165)
T ss_pred HHHHH-hcCCccHHHHHHHH---------------------CCCHHHHHHHHHHHHHcCceEEEeecceEEEEEChHHHH
Confidence 55556 57777778999998 2334568889999999999999 455556764432222
Q ss_pred hHHHHHHHHH
Q 024196 185 NDIEELKAER 194 (271)
Q Consensus 185 ~~~~~Lk~E~ 194 (271)
+-+.....|+
T Consensus 74 ~~v~~~~Rel 83 (165)
T PHA02943 74 NLVFEIKREL 83 (165)
T ss_pred HHHHHHHHHH
Confidence 3334444444
No 107
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=31.88 E-value=1.9e+02 Score=25.91 Aligned_cols=44 Identities=20% Similarity=0.246 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 024196 186 DIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQRNERLY 229 (271)
Q Consensus 186 ~~~~Lk~E~~~l~e~I~~Kk~~LqEL~~Q~~~lknLI~RNk~l~ 229 (271)
++.+|+.+...|...++..++...-...++..|.++++|++.+.
T Consensus 112 e~~kl~~~~e~L~~e~~~L~~~~~~~~eDy~~Li~Im~rark~~ 155 (170)
T PRK13923 112 QIGKLQEEEEKLSWENQTLKQELAITEEDYRALIVIMNRARRMA 155 (170)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence 44555555555555555555555556678889999999999873
No 108
>PF07544 Med9: RNA polymerase II transcription mediator complex subunit 9; InterPro: IPR011425 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This entry represents subunit Med9 of the Mediator complex. Subunit Med9 is part of the middle module of the Mediator complex []; this associates with the core polymerase subunits to form the RNA polymerase II holoenzyme. Med9 alternatively known as the chromosome segregation protein, CSE2 (P33308 from SWISSPROT) is required, along with CSE1 (P33307 from SWISSPROT) for accurate mitotic chromosome segregation in Saccharomyces cerevisiae (Baker's yeast) [].; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=31.43 E-value=1.1e+02 Score=23.85 Aligned_cols=50 Identities=22% Similarity=0.340 Sum_probs=29.6
Q ss_pred ccchhhhhhHHHHhhhccceeecCCceEEecCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024196 148 KNIRRRVYDALNVLMAMDIISKDKKEIQWKGLPRTSLNDIEELKAERLGLRNRIEKKTAYLQELED 213 (271)
Q Consensus 148 K~ikRRVYD~lNVL~ai~lI~K~Kk~i~W~G~~~~s~~~~~~Lk~E~~~l~e~I~~Kk~~LqEL~~ 213 (271)
..+|-|+==+-+++.++.=|+ ..+++.++++..|+++|+.|++.|.++-.
T Consensus 31 ~~lk~Klq~ar~~i~~lpgi~----------------~s~eeq~~~i~~Le~~i~~k~~~L~~~~~ 80 (83)
T PF07544_consen 31 GSLKHKLQKARAAIRELPGID----------------RSVEEQEEEIEELEEQIRKKREVLQKFKE 80 (83)
T ss_pred HHHHHHHHHHHHHHHhCCCcc----------------CCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 356666666666666553221 12455566666777777777777766643
No 109
>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=31.11 E-value=1.1e+02 Score=26.89 Aligned_cols=45 Identities=18% Similarity=0.181 Sum_probs=35.6
Q ss_pred HHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceeec
Q 024196 105 MKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKD 170 (271)
Q Consensus 105 ~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K~ 170 (271)
.+|...+...+..|..|+|+.| ..-+--|.-.|+.|+.-|+|++.
T Consensus 4 ~~IL~~L~~~~~~t~~eLA~~l---------------------gis~~tV~~~L~~Le~~GlV~r~ 48 (203)
T TIGR02702 4 EDILSYLLKQGQATAAALAEAL---------------------AISPQAVRRHLKDLETEGLIEYE 48 (203)
T ss_pred HHHHHHHHHcCCCCHHHHHHHH---------------------CcCHHHHHHHHHHHHHCCCeEEe
Confidence 4677888888889999999998 12234566788999999999984
No 110
>PF02050 FliJ: Flagellar FliJ protein; InterPro: IPR012823 Many flagellar proteins are exported by a flagellum-specific export pathway. Attempts have been made to characterise the apparatus responsible for this process, by designing assays to screen for mutants with export defects []. Experiments involving filament removal from temperature-sensitive flagellar mutants of Salmonella typhimurium have shown that, while most mutants were able to regrow filaments, flhA, fliH, fliI and fliN mutants showed no or greatly reduced regrowth. This suggests that the corresponding gene products are involved in the process of flagellum-specific export. The sequences of fliH, fliI and the adjacent gene, fliJ, have been deduced. FliJ was shown to encode a protein of molecular mass 17,302 Da []. It is a membrane-associated protein that affects chemotactic events, mutations in FliJ result in failure to respond to chemotactic stimuli.; GO: 0003774 motor activity, 0001539 ciliary or flagellar motility, 0006935 chemotaxis, 0009288 bacterial-type flagellum, 0016020 membrane, 0044461 bacterial-type flagellum part; PDB: 3AJW_A.
Probab=31.01 E-value=2.3e+02 Score=21.25 Aligned_cols=44 Identities=23% Similarity=0.256 Sum_probs=34.3
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024196 185 NDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQRNERL 228 (271)
Q Consensus 185 ~~~~~Lk~E~~~l~e~I~~Kk~~LqEL~~Q~~~lknLI~RNk~l 228 (271)
..+..++.++..++..+..+...|.+.......+..|.+|-...
T Consensus 59 ~~i~~~~~~~~~~~~~~~~~r~~l~~a~~~~k~~e~L~e~~~~~ 102 (123)
T PF02050_consen 59 QAIQQQQQELERLEQEVEQAREELQEARRERKKLEKLKERRREE 102 (123)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35666777777778888888888888888888888888866543
No 111
>PRK10870 transcriptional repressor MprA; Provisional
Probab=29.60 E-value=3.7e+02 Score=23.20 Aligned_cols=64 Identities=14% Similarity=0.127 Sum_probs=39.1
Q ss_pred cccchhHHHHHHHHHh--cCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceee----cC
Q 024196 98 RGLRQFSMKVCEKVES--KGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK----DK 171 (271)
Q Consensus 98 ~GLR~fS~KVcekVk~--kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K----~K 171 (271)
.||-.--..|.-.+.. .+.+|-.|+|+.+ ..-+=.|--+++-|+.-|+|+| ..
T Consensus 51 ~gLt~~q~~iL~~L~~~~~~~it~~eLa~~l---------------------~l~~~tvsr~v~rLe~kGlV~R~~~~~D 109 (176)
T PRK10870 51 QGINETLFMALITLESQENHSIQPSELSCAL---------------------GSSRTNATRIADELEKRGWIERRESDND 109 (176)
T ss_pred CCCCHHHHHHHHHHhcCCCCCcCHHHHHHHH---------------------CCCHHHHHHHHHHHHHCCCEEecCCCCC
Confidence 3444433444444443 3445556666665 2334566778899999999999 34
Q ss_pred CceEEecCCCC
Q 024196 172 KEIQWKGLPRT 182 (271)
Q Consensus 172 k~i~W~G~~~~ 182 (271)
++..+.-+...
T Consensus 110 rR~~~v~LT~~ 120 (176)
T PRK10870 110 RRCLHLQLTEK 120 (176)
T ss_pred CCeeEEEECHH
Confidence 57777765443
No 112
>PF11853 DUF3373: Protein of unknown function (DUF3373); InterPro: IPR021803 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 472 to 574 amino acids in length.
Probab=29.48 E-value=50 Score=34.02 Aligned_cols=28 Identities=29% Similarity=0.392 Sum_probs=17.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024196 200 RIEKKTAYLQELEDQFVGLQNLIQRNER 227 (271)
Q Consensus 200 ~I~~Kk~~LqEL~~Q~~~lknLI~RNk~ 227 (271)
+|++.+++|++|.+|+..++.-|.+++.
T Consensus 32 kie~L~kql~~Lk~q~~~l~~~v~k~e~ 59 (489)
T PF11853_consen 32 KIEALKKQLEELKAQQDDLNDRVDKVEK 59 (489)
T ss_pred HHHHHHHHHHHHHHhhcccccccchhhH
Confidence 4555566666666666666666666554
No 113
>smart00787 Spc7 Spc7 kinetochore protein. This domain is found in cell division proteins which are required for kinetochore-spindle association.
Probab=29.18 E-value=1.6e+02 Score=28.30 Aligned_cols=38 Identities=26% Similarity=0.362 Sum_probs=20.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024196 186 DIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQ 223 (271)
Q Consensus 186 ~~~~Lk~E~~~l~e~I~~Kk~~LqEL~~Q~~~lknLI~ 223 (271)
++..+++++..+...|..++..+.++..+...+..-|+
T Consensus 205 eL~~lk~~l~~~~~ei~~~~~~l~e~~~~l~~l~~~I~ 242 (312)
T smart00787 205 ELDRAKEKLKKLLQEIMIKVKKLEELEEELQELESKIE 242 (312)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44455555555555555555556665555555555554
No 114
>PF10481 CENP-F_N: Cenp-F N-terminal domain; InterPro: IPR018463 Mitosin or centromere-associated protein-F (Cenp-F) is found bound across the centromere as one of the proteins of the outer layer of the kinetochore []. Most of the kinetochore/centromere functions appear to depend upon binding of the C-terminal part of the molecule, whereas the N-terminal part, here, may be a cytoplasmic player in controlling the function of microtubules and dynein [].
Probab=29.00 E-value=1.3e+02 Score=29.41 Aligned_cols=37 Identities=32% Similarity=0.623 Sum_probs=27.7
Q ss_pred E-ecCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024196 176 W-KGLPRTSLNDIEELKAERLGLRNRIEKKTAYLQELE 212 (271)
Q Consensus 176 W-~G~~~~s~~~~~~Lk~E~~~l~e~I~~Kk~~LqEL~ 212 (271)
| .|+|....+.|++|+..+++|+..-.+++-+|..|.
T Consensus 8 WKeGL~~~aLqKIqelE~QldkLkKE~qQrQfQleSlE 45 (307)
T PF10481_consen 8 WKEGLPTRALQKIQELEQQLDKLKKERQQRQFQLESLE 45 (307)
T ss_pred HhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHH
Confidence 5 489988899999999988888666566666655444
No 115
>COG3883 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.71 E-value=2.1e+02 Score=27.36 Aligned_cols=40 Identities=25% Similarity=0.491 Sum_probs=18.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHH
Q 024196 188 EELKAERLGLRNRIEKKTAYLQELEDQFVGLQ-NLIQRNER 227 (271)
Q Consensus 188 ~~Lk~E~~~l~e~I~~Kk~~LqEL~~Q~~~lk-nLI~RNk~ 227 (271)
+++..+...++++|.+-+..+.+|..++..++ ++.+||+-
T Consensus 62 ~~~~~k~~~~~~~i~~~~~eik~l~~eI~~~~~~I~~r~~~ 102 (265)
T COG3883 62 EEIQSKIDELQKEIDQSKAEIKKLQKEIAELKENIVERQEL 102 (265)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33333334444444444455555555555444 33345543
No 116
>PRK06798 fliD flagellar capping protein; Validated
Probab=28.41 E-value=1.5e+02 Score=29.77 Aligned_cols=65 Identities=14% Similarity=0.297 Sum_probs=30.7
Q ss_pred ccchhhhhhHHHHhhh-ccceeecCCceEEecCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024196 148 KNIRRRVYDALNVLMA-MDIISKDKKEIQWKGLPRTSLNDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQR 224 (271)
Q Consensus 148 K~ikRRVYD~lNVL~a-i~lI~K~Kk~i~W~G~~~~s~~~~~~Lk~E~~~l~e~I~~Kk~~LqEL~~Q~~~lknLI~R 224 (271)
..+-.|+||+++=+.+ -|+|....+ ....+++.|..+++++++++++++ +.|..|+.++..+|.+
T Consensus 357 ~Gia~~l~~~l~~~~~~~G~i~~r~~---------~l~~~i~~l~~~~~~~e~rl~~~e---~~l~~qf~ale~~ms~ 422 (440)
T PRK06798 357 NGLGKEMEKSLDKIFGDEGIIGERSK---------SIDNRVSKLDLKITDIDTQNKQKQ---DNIVDKYQKLESTLAA 422 (440)
T ss_pred CcHHHHHHHHHHhhhCCCceeehhhh---------HHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHH
Confidence 3566777777765442 112211110 112344445544444444443332 3455677777666654
No 117
>PF04977 DivIC: Septum formation initiator; InterPro: IPR007060 DivIC, from the spore-forming, Gram-positive bacterium Bacillus subtilis, is necessary for both vegetative and sporulation septum formation []. These proteins are mainly composed of an N-terminal coiled-coil. DivIB, DivIC and FtsL inter-depend on each other for stabilisation and localisation. The latter two form a heterodimer. DivIC is always centre cell but the other two associate with it during septation [].; GO: 0007049 cell cycle
Probab=28.12 E-value=1.9e+02 Score=20.92 Aligned_cols=26 Identities=27% Similarity=0.349 Sum_probs=11.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024196 186 DIEELKAERLGLRNRIEKKTAYLQEL 211 (271)
Q Consensus 186 ~~~~Lk~E~~~l~e~I~~Kk~~LqEL 211 (271)
++..|+.+...+++++++.++++..|
T Consensus 25 ei~~l~~~i~~l~~e~~~L~~ei~~l 50 (80)
T PF04977_consen 25 EIAELQKEIEELKKENEELKEEIERL 50 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 33444444444444444444444444
No 118
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and 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 []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=28.01 E-value=1.5e+02 Score=21.64 Aligned_cols=46 Identities=28% Similarity=0.363 Sum_probs=35.0
Q ss_pred hhHHHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhcccee
Q 024196 102 QFSMKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIIS 168 (271)
Q Consensus 102 ~fS~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~ 168 (271)
....+|++.+-++|+.|..+++... +--.+.|-.+|=||+-.+++.
T Consensus 13 ~~~~~V~~~Ll~~G~ltl~~i~~~t---------------------~l~~~~Vk~~L~~LiQh~~v~ 58 (62)
T PF08221_consen 13 EIVAKVGEVLLSRGRLTLREIVRRT---------------------GLSPKQVKKALVVLIQHNLVQ 58 (62)
T ss_dssp HHHHHHHHHHHHC-SEEHHHHHHHH---------------------T--HHHHHHHHHHHHHTTSEE
T ss_pred hHHHHHHHHHHHcCCcCHHHHHHHh---------------------CCCHHHHHHHHHHHHHcCCee
Confidence 3567899999999999999888765 234678889999999888764
No 119
>PF11315 Med30: Mediator complex subunit 30; InterPro: IPR021019 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Med30 is a metazoan-specific subunit of Mediator [], having no homologues in yeasts.
Probab=27.73 E-value=1.6e+02 Score=25.95 Aligned_cols=31 Identities=29% Similarity=0.458 Sum_probs=26.8
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024196 185 NDIEELKAERLGLRNRIEKKTAYLQELEDQF 215 (271)
Q Consensus 185 ~~~~~Lk~E~~~l~e~I~~Kk~~LqEL~~Q~ 215 (271)
.+...+.+|+..+.+++..|.++|.++++|.
T Consensus 104 ~~~~~~~~er~el~e~v~~KN~qLk~iid~l 134 (150)
T PF11315_consen 104 EEYRQLLEERKELIEQVKQKNQQLKEIIDQL 134 (150)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3566788899999999999999999999885
No 120
>PF07334 IFP_35_N: Interferon-induced 35 kDa protein (IFP 35) N-terminus; InterPro: IPR009938 This entry represents the N terminus of interferon-induced 35 kDa protein (IFP 35) (approximately 80 residues long), which contains a leucine zipper motif in an alpha helical configuration []. This group of proteins also includes N-myc-interactor (Nmi), a homologous interferon-induced protein.
Probab=27.40 E-value=1.4e+02 Score=23.65 Aligned_cols=27 Identities=33% Similarity=0.430 Sum_probs=19.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024196 187 IEELKAERLGLRNRIEKKTAYLQELED 213 (271)
Q Consensus 187 ~~~Lk~E~~~l~e~I~~Kk~~LqEL~~ 213 (271)
+.+|.+|-.+|+.+|++.+..|+++..
T Consensus 2 i~ei~eEn~~Lk~eiqkle~ELq~~~~ 28 (76)
T PF07334_consen 2 IHEIQEENARLKEEIQKLEAELQQNKR 28 (76)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 456777888888888877777766543
No 121
>PRK06474 hypothetical protein; Provisional
Probab=27.21 E-value=1.4e+02 Score=26.14 Aligned_cols=45 Identities=20% Similarity=0.296 Sum_probs=35.0
Q ss_pred HHHHHHHHhcCC-CcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceee
Q 024196 105 MKVCEKVESKGR-TTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (271)
Q Consensus 105 ~KVcekVk~kg~-TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K 169 (271)
++|++.+...+. .|-.||++.|- ..-+-.||-.|++|+..|||++
T Consensus 14 ~~Il~~L~~~~~~~ta~el~~~l~--------------------~is~aTvYrhL~~L~e~GLI~~ 59 (178)
T PRK06474 14 MKICQVLMRNKEGLTPLELVKILK--------------------DVPQATLYRHLQTMVDSGILHV 59 (178)
T ss_pred HHHHHHHHhCCCCCCHHHHHHHhc--------------------CCCHHHHHHHHHHHHHCCCEEE
Confidence 557777777654 88889988861 1235579999999999999998
No 122
>PF04568 IATP: Mitochondrial ATPase inhibitor, IATP; InterPro: IPR007648 ATP synthase inhibitor prevents the enzyme from switching to ATP hydrolysis during collapse of the electrochemical gradient, for example during oxygen deprivation [] ATP synthase inhibitor forms a one to one complex with the F1 ATPase, possibly by binding at the alpha-beta interface. It is thought to inhibit ATP synthesis by preventing the release of ATP []. The minimum inhibitory region for bovine inhibitor (P01096 from SWISSPROT) is from residues 39 to 72 []. The inhibitor has two oligomeric states, dimer (the active state) and tetramer. At low pH , the inhibitor forms a dimer via antiparallel coiled coil interactions between the C-terminal regions of two monomers. At high pH, the inhibitor forms tetramers and higher oligomers by coiled coil interactions involving the N terminus and inhibitory region, thus preventing the inhibitory activity []. ; GO: 0004857 enzyme inhibitor activity, 0045980 negative regulation of nucleotide metabolic process, 0005739 mitochondrion; PDB: 1GMJ_B 1OHH_H 1HF9_B 2V7Q_J.
Probab=26.99 E-value=1.9e+02 Score=23.72 Aligned_cols=9 Identities=33% Similarity=0.453 Sum_probs=3.8
Q ss_pred HHHHHHHHH
Q 024196 204 KTAYLQELE 212 (271)
Q Consensus 204 Kk~~LqEL~ 212 (271)
.+++|.+|.
T Consensus 88 ~~k~i~~le 96 (100)
T PF04568_consen 88 HRKEIDELE 96 (100)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHH
Confidence 444444443
No 123
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=26.78 E-value=1.8e+02 Score=26.59 Aligned_cols=46 Identities=15% Similarity=0.251 Sum_probs=35.6
Q ss_pred HHHHHHHHhcCC-CcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceeecC
Q 024196 105 MKVCEKVESKGR-TTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKDK 171 (271)
Q Consensus 105 ~KVcekVk~kg~-TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K~K 171 (271)
..|.+.+..... .+..|+|+.+ .--|=.+|-.|+.|+..|+++++.
T Consensus 7 l~iL~~l~~~~~~l~l~ela~~~---------------------glpksT~~RlL~tL~~~G~v~~d~ 53 (246)
T COG1414 7 LAILDLLAEGPGGLSLAELAERL---------------------GLPKSTVHRLLQTLVELGYVEQDP 53 (246)
T ss_pred HHHHHHHHhCCCCCCHHHHHHHh---------------------CcCHHHHHHHHHHHHHCCCEEEcC
Confidence 445666666444 4799999987 244678999999999999999955
No 124
>PF09766 FimP: Fms-interacting protein; InterPro: IPR019163 This entry represents Thoc5 which is one of the subunits of the THO complex, which additionally contains: HPR1, Thoc2, Thoc6 and Thoc7. The evolutionarily conserved multisubunit THO complex, which is recruited to actively transcribed genes is required for the efficient expression of genes that have internal tandem repeats. It is suggested that the THO complex functions to rectify aberrant structures that arise during transcription [, ] and is required for cell proliferation and for proper export of heat-shock mRNAs under heat stress []. This entry also identifies the crucial 144 N-terminal residues of the FmiP protein, which is essential for the binding of the protein to the cytoplasmic domain of activated Fms-molecules in M-CSF induced haematopoietic differentiation of macrophages. The C terminus contains a putative nuclear localisation sequence and a leucine zipper which suggest further, as yet unknown, nuclear functions. The level of FMIP expression might form a threshold that determines whether cells differentiate into macrophages or into granulocytes [].
Probab=26.44 E-value=1.9e+02 Score=28.14 Aligned_cols=38 Identities=24% Similarity=0.406 Sum_probs=25.3
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024196 185 NDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLI 222 (271)
Q Consensus 185 ~~~~~Lk~E~~~l~e~I~~Kk~~LqEL~~Q~~~lknLI 222 (271)
.++++|+.++..+.+.|+.|++.|..|..+...|..-.
T Consensus 108 ~~~~el~~~k~~l~~~~~~k~~~L~~l~~~L~~l~~a~ 145 (355)
T PF09766_consen 108 EQLKELEQRKKKLQQENKKKKKFLDSLPPQLKSLKKAA 145 (355)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Confidence 34556666666677777788888887777666555443
No 125
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=26.44 E-value=1.2e+02 Score=20.58 Aligned_cols=32 Identities=28% Similarity=0.317 Sum_probs=23.8
Q ss_pred cCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhh
Q 024196 114 KGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLM 162 (271)
Q Consensus 114 kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ 162 (271)
....||.|||+.| ......++++..-+++-|.
T Consensus 18 ~~~~t~~eIa~~l-----------------g~s~~~V~~~~~~al~kLR 49 (50)
T PF04545_consen 18 FEGLTLEEIAERL-----------------GISRSTVRRILKRALKKLR 49 (50)
T ss_dssp TST-SHHHHHHHH-----------------TSCHHHHHHHHHHHHHHHH
T ss_pred cCCCCHHHHHHHH-----------------CCcHHHHHHHHHHHHHHhc
Confidence 5667899999998 1234688888888888764
No 126
>PF08664 YcbB: YcbB domain; InterPro: IPR013972 YcbB is a DNA-binding protein [].
Probab=26.40 E-value=81 Score=27.14 Aligned_cols=49 Identities=20% Similarity=0.314 Sum_probs=30.7
Q ss_pred cHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhcccee
Q 024196 118 TYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIIS 168 (271)
Q Consensus 118 TYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~ 168 (271)
+.+++..++.......+. .-..+...-++.|||.|+-+++-|-.+|+..
T Consensus 41 ~Lk~~f~~~~~~~~~~~~--~~~~e~Ka~EQRIRRai~~al~nlAsLGl~D 89 (134)
T PF08664_consen 41 SLKEIFEELAQKKLASDE--EIEKEKKAIEQRIRRAIKQALTNLASLGLED 89 (134)
T ss_pred cHHHHHHHHHHhhccchh--hhhHHHHHHHHHHHHHHHHHHHHHHHhCCcc
Confidence 446666666544311000 0112345567889999999999999998753
No 127
>PF05529 Bap31: B-cell receptor-associated protein 31-like ; InterPro: IPR008417 Bap31 is a polytopic integral protein of the endoplasmic reticulum membrane and a substrate of caspase-8. Bap31 is cleaved within its cytosolic domain, generating pro-apoptotic p20 Bap31 [].; GO: 0006886 intracellular protein transport, 0005783 endoplasmic reticulum, 0016021 integral to membrane
Probab=25.53 E-value=1.6e+02 Score=25.58 Aligned_cols=26 Identities=31% Similarity=0.373 Sum_probs=12.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024196 190 LKAERLGLRNRIEKKTAYLQELEDQF 215 (271)
Q Consensus 190 Lk~E~~~l~e~I~~Kk~~LqEL~~Q~ 215 (271)
+++|.++++++|++++..+..|.+|.
T Consensus 159 ~~~ei~~lk~el~~~~~~~~~LkkQ~ 184 (192)
T PF05529_consen 159 LSEEIEKLKKELEKKEKEIEALKKQS 184 (192)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444444444444444444444444
No 128
>PF04182 B-block_TFIIIC: B-block binding subunit of TFIIIC; InterPro: IPR007309 Yeast transcription factor IIIC (TFIIIC) is a multisubunit protein complex that interacts with two control elements of class III promoters called the A and B blocks. This family represents the subunit within TFIIIC involved in B-block binding []. Although defined as a yeast protein, it is also found in a number of other organisms.
Probab=25.52 E-value=1.5e+02 Score=22.22 Aligned_cols=19 Identities=26% Similarity=0.366 Sum_probs=17.1
Q ss_pred hhhhhhHHHHhhhccceee
Q 024196 151 RRRVYDALNVLMAMDIISK 169 (271)
Q Consensus 151 kRRVYD~lNVL~ai~lI~K 169 (271)
-|-++=.+++|+..|||.|
T Consensus 32 ~r~i~~~~k~L~~~gLI~k 50 (75)
T PF04182_consen 32 PRSIFYRLKKLEKKGLIVK 50 (75)
T ss_pred chHHHHHHHHHHHCCCEEE
Confidence 4678889999999999998
No 129
>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=25.46 E-value=2.1e+02 Score=20.74 Aligned_cols=45 Identities=18% Similarity=0.236 Sum_probs=36.4
Q ss_pred HHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceeec
Q 024196 105 MKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKD 170 (271)
Q Consensus 105 ~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K~ 170 (271)
..+.+.-+.++.++-++||..| ..-+=-|.+.++=|..-|+|..+
T Consensus 11 ~~Iy~l~~~~~~v~~~~iA~~L---------------------~vs~~tvt~ml~~L~~~GlV~~~ 55 (60)
T PF01325_consen 11 KAIYELSEEGGPVRTKDIAERL---------------------GVSPPTVTEMLKRLAEKGLVEYE 55 (60)
T ss_dssp HHHHHHHHCTSSBBHHHHHHHH---------------------TS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHcCCCCccHHHHHHHH---------------------CCChHHHHHHHHHHHHCCCEEec
Confidence 3456666788999999999998 34566799999999999999884
No 130
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=25.39 E-value=74 Score=24.33 Aligned_cols=45 Identities=16% Similarity=0.219 Sum_probs=34.9
Q ss_pred HHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceeecC
Q 024196 106 KVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKDK 171 (271)
Q Consensus 106 KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K~K 171 (271)
.+|..+...+.++|.|+.+.| ..-+=.++=-++.|+..|+|+..|
T Consensus 4 ~Il~~L~~~~~~~f~~L~~~l---------------------~lt~g~Ls~hL~~Le~~GyV~~~k 48 (80)
T PF13601_consen 4 AILALLYANEEATFSELKEEL---------------------GLTDGNLSKHLKKLEEAGYVEVEK 48 (80)
T ss_dssp HHHHHHHHHSEEEHHHHHHHT---------------------T--HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHhhcCCCCHHHHHHHh---------------------CcCHHHHHHHHHHHHHCCCEEEEE
Confidence 467777888999999999988 123445677899999999999843
No 131
>KOG3478 consensus Prefoldin subunit 6, KE2 family [Posttranslational modification, protein turnover, chaperones]
Probab=24.55 E-value=1.5e+02 Score=25.30 Aligned_cols=24 Identities=21% Similarity=0.327 Sum_probs=20.2
Q ss_pred hHHHHhhhccceeecCCceEEecC
Q 024196 156 DALNVLMAMDIISKDKKEIQWKGL 179 (271)
Q Consensus 156 D~lNVL~ai~lI~K~Kk~i~W~G~ 179 (271)
.-.+||+.+++++-+.|.|+-+|-
T Consensus 37 Enk~V~~Eldlle~d~~VYKliGp 60 (120)
T KOG3478|consen 37 ENKIVLEELDLLEEDSNVYKLIGP 60 (120)
T ss_pred hhHHHHHHHHHhcccchHHHHhcc
Confidence 345899999999999999998884
No 132
>PF04492 Phage_rep_O: Bacteriophage replication protein O ; InterPro: IPR006497 This entry is represented by the N-terminal domain of Bacteriophage lambda, GpO. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0006260 DNA replication
Probab=24.18 E-value=63 Score=26.22 Aligned_cols=26 Identities=38% Similarity=0.437 Sum_probs=21.9
Q ss_pred cchhhhhhHHHHhhhccceeecCCce
Q 024196 149 NIRRRVYDALNVLMAMDIISKDKKEI 174 (271)
Q Consensus 149 ~ikRRVYD~lNVL~ai~lI~K~Kk~i 174 (271)
.-+..|.+++|.|+.+++|.++++.+
T Consensus 66 ~~~~~V~~al~~Li~~~vI~~~g~~~ 91 (100)
T PF04492_consen 66 LSRDHVSKALNELIRRGVIIRDGKRI 91 (100)
T ss_pred cCHHHHHHHHHHHHHCCCEEeCCcEE
Confidence 44789999999999999998877544
No 133
>PRK12423 LexA repressor; Provisional
Probab=24.15 E-value=2e+02 Score=25.30 Aligned_cols=47 Identities=15% Similarity=0.217 Sum_probs=33.1
Q ss_pred HHHHHHHHhcC-CCcHHHHHHHHHHHhcCCCCCCCCCChhhhccc-cchhhhhhHHHHhhhccceeecCC
Q 024196 105 MKVCEKVESKG-RTTYNEVADELVAEFADPSNSLATPDQQQYDEK-NIRRRVYDALNVLMAMDIISKDKK 172 (271)
Q Consensus 105 ~KVcekVk~kg-~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K-~ikRRVYD~lNVL~ai~lI~K~Kk 172 (271)
..+++.+.+.+ .-|+.|+|+.| . .-+--|+..|.+|+..|+|++..+
T Consensus 13 ~~l~~~i~~~g~~Ps~~eia~~~---------------------g~~s~~~v~~~l~~L~~~G~l~~~~~ 61 (202)
T PRK12423 13 AFIRERIAQAGQPPSLAEIAQAF---------------------GFASRSVARKHVQALAEAGLIEVVPN 61 (202)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHh---------------------CCCChHHHHHHHHHHHHCCCEEecCC
Confidence 34445555555 35899999887 1 123457899999999999998443
No 134
>TIGR03859 PQQ_PqqD coenzyme PQQ biosynthesis protein PqqD. This model identifies PqqD, a protein involved in the final steps of the biosynthesis of pyrroloquinoline quinone, coenzyme PQQ.
Probab=24.03 E-value=1.6e+02 Score=22.53 Aligned_cols=55 Identities=20% Similarity=0.266 Sum_probs=41.5
Q ss_pred cccchhHHHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhcccee
Q 024196 98 RGLRQFSMKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIIS 168 (271)
Q Consensus 98 ~GLR~fS~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~ 168 (271)
-+|--....|.+.+.. ..|-.|+++.|..+|.. . ..+..+|-.-++-|..-|+|+
T Consensus 27 ~~Ln~~g~~Iw~lldg--~~tv~eI~~~L~~~Y~~-~-------------e~~~~dV~~fL~~L~~~gli~ 81 (81)
T TIGR03859 27 VKLNDSAGEILELCDG--KRSLAEIIQELAQRFPA-A-------------EEIEDDVIAFLAVARAKHWLE 81 (81)
T ss_pred eeeChHHHHHHHHccC--CCcHHHHHHHHHHHcCC-h-------------hhHHHHHHHHHHHHHHCcCcC
Confidence 5677777888888854 55888999999998865 2 356677778888887778774
No 135
>PF01920 Prefoldin_2: Prefoldin subunit; InterPro: IPR002777 Prefoldin (PFD) is a chaperone that interacts exclusively with type II chaperonins, hetero-oligomers lacking an obligate co-chaperonin that are found only in eukaryotes (chaperonin-containing T-complex polypeptide-1 (CCT)) and archaea. Eukaryotic PFD is a multi-subunit complex containing six polypeptides in the molecular mass range of 14-23 kDa. In archaea, on the other hand, PFD is composed of two types of subunits, two alpha and four beta. The six subunits associate to form two back-to-back up-and-down eight-stranded barrels, from which hang six coiled coils. Each subunit contributes one (beta subunits) or two (alpha subunits) beta hairpin turns to the barrels. The coiled coils are formed by the N and C termini of an individual subunit. Overall, this unique arrangement resembles a jellyfish. The eukaryotic PFD hexamer is composed of six different subunits; however, these can be grouped into two alpha-like (PFD3 and -5) and four beta-like (PFD1, -2, -4, and -6) subunits based on amino acid sequence similarity with their archaeal counterparts. Eukaryotic PFD has a six-legged structure similar to that seen in the archaeal homologue [, ]. This family contains the archaeal beta subunit, eukaryotic prefoldin subunits 1, 2, 4 and 6. Eukaryotic PFD has been shown to bind both actin and tubulin co-translationally. The chaperone then delivers the target protein to CCT, interacting with the chaperonin through the tips of the coiled coils. No authentic target proteins of any archaeal PFD have been identified, to date.; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0016272 prefoldin complex; PDB: 2ZDI_B 3AEI_B 2ZQM_A 1FXK_A.
Probab=23.98 E-value=3.3e+02 Score=20.71 Aligned_cols=68 Identities=22% Similarity=0.288 Sum_probs=36.1
Q ss_pred chhhhhhHHHHhhhccceeecCCceEEecCCCCC-----hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024196 150 IRRRVYDALNVLMAMDIISKDKKEIQWKGLPRTS-----LNDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQ 219 (271)
Q Consensus 150 ikRRVYD~lNVL~ai~lI~K~Kk~i~W~G~~~~s-----~~~~~~Lk~E~~~l~e~I~~Kk~~LqEL~~Q~~~lk 219 (271)
+.+.+..+--|+..+..+.-+ ...|..++... ..-.+.|+.....+...|......+..+..+...++
T Consensus 24 l~~~~~~~~~~~~eL~~l~~~--~~~y~~vG~~fv~~~~~~~~~~L~~~~~~~~~~i~~l~~~~~~l~~~l~~~~ 96 (106)
T PF01920_consen 24 LERQLRELELTLEELEKLDDD--RKVYKSVGKMFVKQDKEEAIEELEERIEKLEKEIKKLEKQLKYLEKKLKELK 96 (106)
T ss_dssp HHHHHHHHHHHHHHHHTSSTT---EEEEEETTEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHhCCCc--chhHHHHhHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334444444455555455444 55665554321 233455666666666677766666666666554443
No 136
>PF14817 HAUS5: HAUS augmin-like complex subunit 5
Probab=23.97 E-value=2.3e+02 Score=30.11 Aligned_cols=48 Identities=21% Similarity=0.305 Sum_probs=29.3
Q ss_pred eecCCceEEecCCCCC---------hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024196 168 SKDKKEIQWKGLPRTS---------LNDIEELKAERLGLRNRIEKKTAYLQELEDQF 215 (271)
Q Consensus 168 ~K~Kk~i~W~G~~~~s---------~~~~~~Lk~E~~~l~e~I~~Kk~~LqEL~~Q~ 215 (271)
+|-++.|.|.|..... ..+-.+|++++++|+..|......|..+..+.
T Consensus 53 ~~iRgNl~~~~~~~~~~~~~~~e~~~~~r~~L~~everLraei~~l~~~I~~~e~e~ 109 (632)
T PF14817_consen 53 RKIRGNLLWYGHQQSKERKKSRENEARRRRELEKEVERLRAEIQELDKEIESREREV 109 (632)
T ss_pred HHHHcceeeccccccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3447789998875432 23455666777777777666666655444433
No 137
>PRK07720 fliJ flagellar biosynthesis chaperone; Validated
Probab=23.83 E-value=3.3e+02 Score=22.48 Aligned_cols=43 Identities=12% Similarity=0.246 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024196 186 DIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQRNERL 228 (271)
Q Consensus 186 ~~~~Lk~E~~~l~e~I~~Kk~~LqEL~~Q~~~lknLI~RNk~l 228 (271)
.+...+..+..++..++.++..+.+-......|..|++|-...
T Consensus 79 ~i~~q~~~v~~~~~~ve~~r~~~~ea~~~~k~~ekLker~~~~ 121 (146)
T PRK07720 79 TIDHYQLLVMQAREQMNRKQQDLTEKNIEVKKYEKMKEKKQEM 121 (146)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445555566677788888888999888999999999876543
No 138
>KOG1962 consensus B-cell receptor-associated protein and related proteins [Defense mechanisms]
Probab=23.81 E-value=2.1e+02 Score=26.59 Aligned_cols=40 Identities=23% Similarity=0.279 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024196 186 DIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQRN 225 (271)
Q Consensus 186 ~~~~Lk~E~~~l~e~I~~Kk~~LqEL~~Q~~~lknLI~RN 225 (271)
+...++++..+|+++++.+...|..+..+..+++.-.+.+
T Consensus 152 ~~~~~~~~~~kL~~el~~~~~~Le~~~~~~~al~Kq~e~~ 191 (216)
T KOG1962|consen 152 ENDKLKADLEKLETELEKKQKKLEKAQKKVDALKKQSEGL 191 (216)
T ss_pred hHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 4455666666677777777777766666666555544433
No 139
>PRK10884 SH3 domain-containing protein; Provisional
Probab=23.45 E-value=3.4e+02 Score=24.68 Aligned_cols=45 Identities=24% Similarity=0.284 Sum_probs=0.0
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHh
Q 024196 184 LNDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQN-LIQRNERL 228 (271)
Q Consensus 184 ~~~~~~Lk~E~~~l~e~I~~Kk~~LqEL~~Q~~~lkn-LI~RNk~l 228 (271)
.+++++|++++..+++...+-...+++-..+....-+ |-++|+++
T Consensus 99 e~el~~l~~~l~~~~~~~~~~~~~l~~~~~~~~~~~~~L~~~n~~L 144 (206)
T PRK10884 99 ENQVKTLTDKLNNIDNTWNQRTAEMQQKVAQSDSVINGLKEENQKL 144 (206)
T ss_pred HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
No 140
>PRK14127 cell division protein GpsB; Provisional
Probab=23.22 E-value=2e+02 Score=23.91 Aligned_cols=51 Identities=25% Similarity=0.346 Sum_probs=30.9
Q ss_pred hccceee-cCCceEEecCCCCC--------hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024196 163 AMDIISK-DKKEIQWKGLPRTS--------LNDIEELKAERLGLRNRIEKKTAYLQELEDQF 215 (271)
Q Consensus 163 ai~lI~K-~Kk~i~W~G~~~~s--------~~~~~~Lk~E~~~l~e~I~~Kk~~LqEL~~Q~ 215 (271)
.+.|..| =+.. ++|++..- ..+++.|..|...|++++...++.|.++..+.
T Consensus 8 p~DI~~KeF~~~--~RGYd~~EVD~FLd~V~~dye~l~~e~~~Lk~e~~~l~~~l~e~~~~~ 67 (109)
T PRK14127 8 PKDILEKEFKTS--MRGYDQDEVDKFLDDVIKDYEAFQKEIEELQQENARLKAQVDELTKQV 67 (109)
T ss_pred HHHHhhCccCCC--CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3445556 3332 56876542 34556666777777777777777776666655
No 141
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=23.00 E-value=2.7e+02 Score=24.74 Aligned_cols=40 Identities=30% Similarity=0.377 Sum_probs=26.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024196 185 NDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQR 224 (271)
Q Consensus 185 ~~~~~Lk~E~~~l~e~I~~Kk~~LqEL~~Q~~~lknLI~R 224 (271)
..++.|++.+..+.++|.+.++.|..+....+.++=|-.|
T Consensus 85 ~R~~lLe~~~~~l~~ri~eLe~~l~~kad~vvsYqll~hr 124 (175)
T PRK13182 85 VDFEQLEAQLNTITRRLDELERQLQQKADDVVSYQLLQHR 124 (175)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHhH
Confidence 4556677777777777777777776666666655555444
No 142
>PF10186 Atg14: UV radiation resistance protein and autophagy-related subunit 14; InterPro: IPR018791 Class III phosphatidylinositol 3-kinase (PI3-kinase) regulates multiple membrane trafficking. In yeast, two distinct PI3-kinase complexes are known: complex I (Vps34, Vps15, Vps30/Atg6, and Atg14) is involved in autophagy, and complex II (Vps34, Vps15, Vps30/Atg6, and Vps38) functions in the vacuolar protein sorting pathway. In mammals, the counterparts of Vps34, Vps15, and Vps30/Atg6 are Vps34, p150, and Beclin 1, respectively. Mammalian UV irradiation resistance-associated gene (UVRAG) has been identified as identical to yeast Vps38 []. The Atg14 (autophagy-related protein 14) proteins are hydrophilic proteins and have a coiled-coil motif at the N terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole []. This entry represents Atg14 and UVRAG, which bind Beclin 1 to forms two distinct PI3-kinase complexes. This entry also includes Bakor (beclin-1-associated autophagy-related key regulator), also known as autophagy-related protein 14-like protein, which share sequence similarity to the yeast Atg14 protein []. Barkor positively regulates autophagy through its interaction with Beclin-1, with decreased levels of autophagosome formation observed when Barkor expression is eliminated []. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. ; GO: 0010508 positive regulation of autophagy
Probab=22.97 E-value=3.8e+02 Score=23.98 Aligned_cols=12 Identities=33% Similarity=0.728 Sum_probs=7.4
Q ss_pred ccchhhhhhHHH
Q 024196 148 KNIRRRVYDALN 159 (271)
Q Consensus 148 K~ikRRVYD~lN 159 (271)
..++++|=+++.
T Consensus 37 ~~l~~~i~~~l~ 48 (302)
T PF10186_consen 37 EELRRRIEEILE 48 (302)
T ss_pred HHHHHHHHHHHH
Confidence 456666666665
No 143
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=22.94 E-value=1.5e+02 Score=27.22 Aligned_cols=48 Identities=25% Similarity=0.339 Sum_probs=36.2
Q ss_pred HHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceee-cCCc
Q 024196 105 MKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK-DKKE 173 (271)
Q Consensus 105 ~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K-~Kk~ 173 (271)
.++.+.+++++..+..|+|+.| . ..+.++|| -|..|+.-|+|.| -+.-
T Consensus 8 ~~Il~~l~~~~~~~~~ela~~l-------~----------vS~~TiRR----dL~~Le~~g~l~r~~GGa 56 (252)
T PRK10906 8 DAIIELVKQQGYVSTEELVEHF-------S----------VSPQTIRR----DLNDLAEQNKILRHHGGA 56 (252)
T ss_pred HHHHHHHHHcCCEeHHHHHHHh-------C----------CCHHHHHH----HHHHHHHCCCEEEecCCE
Confidence 4578999999999999999988 0 11235554 4888999999999 4444
No 144
>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=22.87 E-value=4.9e+02 Score=23.15 Aligned_cols=52 Identities=25% Similarity=0.449 Sum_probs=28.3
Q ss_pred hhhHHHHhhhccceeec---CCceEEecCCCCC----hhHHHHHHHHHHHHHHHHHHHHH
Q 024196 154 VYDALNVLMAMDIISKD---KKEIQWKGLPRTS----LNDIEELKAERLGLRNRIEKKTA 206 (271)
Q Consensus 154 VYD~lNVL~ai~lI~K~---Kk~i~W~G~~~~s----~~~~~~Lk~E~~~l~e~I~~Kk~ 206 (271)
|=|++.-|..=|+|.-+ --.+.|. +|... ...++.|++++..++..|...+.
T Consensus 32 VKdvlq~LvDDglV~~EKiGssn~YWs-Fps~~~~~~~~~~~~l~~~~~~~~~~i~~l~~ 90 (188)
T PF03962_consen 32 VKDVLQSLVDDGLVHVEKIGSSNYYWS-FPSQAKQKRQNKLEKLQKEIEELEKKIEELEE 90 (188)
T ss_pred HHHHHHHHhccccchhhhccCeeEEEe-cChHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44666666666777653 3578887 44332 23455555555544444443333
No 145
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=22.82 E-value=2.4e+02 Score=25.83 Aligned_cols=18 Identities=17% Similarity=0.338 Sum_probs=8.1
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 024196 186 DIEELKAERLGLRNRIEK 203 (271)
Q Consensus 186 ~~~~Lk~E~~~l~e~I~~ 203 (271)
...+|.+|-..|++++.+
T Consensus 70 ~~~~l~~en~~L~~e~~~ 87 (276)
T PRK13922 70 SLFDLREENEELKKELLE 87 (276)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 344455554444444333
No 146
>PF04156 IncA: IncA protein; InterPro: IPR007285 Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion. The inclusion is nonfusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA (Inclusion membrane protein A), is functionally associated with the homotypic fusion of inclusions [].
Probab=22.80 E-value=4e+02 Score=22.75 Aligned_cols=30 Identities=20% Similarity=0.385 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024196 198 RNRIEKKTAYLQELEDQFVGLQNLIQRNER 227 (271)
Q Consensus 198 ~e~I~~Kk~~LqEL~~Q~~~lknLI~RNk~ 227 (271)
++.++.+..++.++......+.+.+..++.
T Consensus 157 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~ 186 (191)
T PF04156_consen 157 REEVQELRSQLERLQENLQQLEEKIQELQE 186 (191)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344455555555555555455555554444
No 147
>COG1730 GIM5 Predicted prefoldin, molecular chaperone implicated in de novo protein folding [Posttranslational modification, protein turnover, chaperones]
Probab=22.74 E-value=5.1e+02 Score=22.52 Aligned_cols=39 Identities=33% Similarity=0.290 Sum_probs=30.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024196 185 NDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQ 223 (271)
Q Consensus 185 ~~~~~Lk~E~~~l~e~I~~Kk~~LqEL~~Q~~~lknLI~ 223 (271)
.-++.|+..+..|+..+++..+.|++|......+...++
T Consensus 94 eAie~l~k~~~~l~~~~~~l~~~l~~l~~~~~~l~~~~q 132 (145)
T COG1730 94 EAIEFLKKRIEELEKAIEKLQQALAELAQRIEQLEQEAQ 132 (145)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 457778888888888888888888888887766665554
No 148
>PF12269 zf-CpG_bind_C: CpG binding protein zinc finger C terminal domain; InterPro: IPR022056 This domain family is found in eukaryotes, and is approximately 240 amino acids in length. This domain is the zinc finger domain of a CpG binding DNA methyltransferase protein. It contains a CxxC motif which forms the zinc finger and binds to DNA.
Probab=22.74 E-value=2.1e+02 Score=26.92 Aligned_cols=51 Identities=25% Similarity=0.416 Sum_probs=32.9
Q ss_pred EEecCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024196 175 QWKGLPRTSLNDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQRNERL 228 (271)
Q Consensus 175 ~W~G~~~~s~~~~~~Lk~E~~~l~e~I~~Kk~~LqEL~~Q~~~lknLI~RNk~l 228 (271)
.|...|..+.. .-+..++.++++...-+..|++|+.++..|..+|.|=+..
T Consensus 15 Ew~~~p~~A~E---~~r~~Le~Ir~kq~~v~~~l~eLe~~~~el~~~i~~~k~~ 65 (236)
T PF12269_consen 15 EWQLSPCVAEE---QNRKLLEEIRKKQQKVRNRLQELEKRFKELEAIIARAKQF 65 (236)
T ss_pred HhcCCCchhhh---hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 37666554321 1223333445555566778899999999999999887765
No 149
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=22.65 E-value=1.3e+02 Score=26.65 Aligned_cols=54 Identities=17% Similarity=0.238 Sum_probs=38.5
Q ss_pred CCcHHHHHHHHHHHhcCCC----CCCCCCChhhhccccchhhhhhHHHHhhhccceee
Q 024196 116 RTTYNEVADELVAEFADPS----NSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (271)
Q Consensus 116 ~TTYnEVAdeLV~e~~~~~----~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K 169 (271)
..-|.+|++.|...+.... ...-+..+-+.....-|=-|-.||+.|..-|+|.|
T Consensus 8 ~p~y~qI~~~i~~~I~~G~~~~g~kLPsE~eLa~~~~VSR~TvR~Al~~L~~eGli~r 65 (241)
T PRK11402 8 QLLYATVRQRLLDDIAQGVYQAGQQIPTENELCTQYNVSRITIRKAISDLVADGVLIR 65 (241)
T ss_pred CcHHHHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 3568899999988775421 12222223445556778899999999999999999
No 150
>PF05103 DivIVA: DivIVA protein; InterPro: IPR007793 The Bacillus subtilis divIVA1 mutation causes misplacement of the septum during cell division, resulting in the formation of small, circular, anucleate minicells []. Inactivation of divIVA produces a minicell phenotype, whereas overproduction of DivIVA results in a filamentation phenotype []. These proteins appear to contain coiled-coils.; PDB: 2WUK_C 2WUJ_A.
Probab=22.61 E-value=20 Score=28.82 Aligned_cols=48 Identities=27% Similarity=0.420 Sum_probs=18.4
Q ss_pred ceEEecCCCCCh--------hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024196 173 EIQWKGLPRTSL--------NDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQN 220 (271)
Q Consensus 173 ~i~W~G~~~~s~--------~~~~~Lk~E~~~l~e~I~~Kk~~LqEL~~Q~~~lkn 220 (271)
...|.|+++.-+ .++..|..+...|..++......|.++......+++
T Consensus 12 ~~~~rGYd~~eVD~fl~~l~~~~~~l~~e~~~L~~~~~~l~~~l~~~~~~~~~l~~ 67 (131)
T PF05103_consen 12 KKSMRGYDPDEVDDFLDELAEELERLQRENAELKEEIEELQAQLEELREEEESLQR 67 (131)
T ss_dssp -EEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCT-------------
T ss_pred CCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhHHHHHHH
Confidence 356778876532 234455555555555555555555555444444443
No 151
>PRK10286 O-6-alkylguanine-DNA:cysteine-protein methyltransferase; Provisional
Probab=22.39 E-value=85 Score=27.90 Aligned_cols=26 Identities=19% Similarity=0.408 Sum_probs=22.9
Q ss_pred chhHHHHHHHHHh---cCCCcHHHHHHHH
Q 024196 101 RQFSMKVCEKVES---KGRTTYNEVADEL 126 (271)
Q Consensus 101 R~fS~KVcekVk~---kg~TTYnEVAdeL 126 (271)
-.|..+|.+.|.+ ..++||.|+|..+
T Consensus 87 t~fq~~V~~~l~~IP~G~~~tYg~iA~~~ 115 (171)
T PRK10286 87 TPFQREVWQTLRTIPCGQVMHYGQLAEQL 115 (171)
T ss_pred CHHHHHHHHHHHcCCCCCcEeHHHHHHHh
Confidence 3688999999988 7799999999987
No 152
>smart00787 Spc7 Spc7 kinetochore protein. This domain is found in cell division proteins which are required for kinetochore-spindle association.
Probab=22.31 E-value=3.3e+02 Score=26.29 Aligned_cols=42 Identities=24% Similarity=0.321 Sum_probs=24.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024196 186 DIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQRNER 227 (271)
Q Consensus 186 ~~~~Lk~E~~~l~e~I~~Kk~~LqEL~~Q~~~lknLI~RNk~ 227 (271)
++++++.++..+...|+...++..++..+....+..++.++.
T Consensus 226 ~l~e~~~~l~~l~~~I~~~~~~k~e~~~~I~~ae~~~~~~r~ 267 (312)
T smart00787 226 KLEELEEELQELESKIEDLTNKKSELNTEIAEAEKKLEQCRG 267 (312)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 344555555555566666666666666666666666655543
No 153
>TIGR02338 gimC_beta prefoldin, beta subunit, archaeal. Chaperonins are cytosolic, ATP-dependent molecular chaperones, with a conserved toroidal architecture, that assist in the folding of nascent and/or denatured polypeptide chains. The group I chaperonin system consists of GroEL and GroES, and is found (usually) in bacteria and organelles of bacterial origin. The group II chaperonin system, called the thermosome in Archaea and TRiC or CCT in the Eukaryota, is structurally similar but only distantly related. Prefoldin, also called GimC, is a complex in Archaea and Eukaryota, that works with group II chaperonins. Members of this protein family are the archaeal clade of the beta class of prefoldin subunit. Closely related, but outside the scope of this family are the eukaryotic beta-class prefoldin subunits, Gim-1,3,4 and 6. The alpha class prefoldin subunits are more distantly related.
Probab=22.20 E-value=3.1e+02 Score=21.98 Aligned_cols=65 Identities=18% Similarity=0.216 Sum_probs=30.9
Q ss_pred hhhhhHHHHhhhccceeecCCceEEecCC---CCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024196 152 RRVYDALNVLMAMDIISKDKKEIQWKGLP---RTSLNDIEELKAERLGLRNRIEKKTAYLQELEDQFV 216 (271)
Q Consensus 152 RRVYD~lNVL~ai~lI~K~Kk~i~W~G~~---~~s~~~~~~Lk~E~~~l~e~I~~Kk~~LqEL~~Q~~ 216 (271)
+.+=..-.|+..+.-+.-+.+-|+-+|-- .....-+..|+.....++..|+...+++..|..+..
T Consensus 31 ~~~~E~~~v~~eL~~l~~d~~vyk~VG~vlv~~~~~e~~~~l~~r~e~ie~~i~~lek~~~~l~~~l~ 98 (110)
T TIGR02338 31 AQLKEAEKALEELERLPDDTPVYKSVGNLLVKTDKEEAIQELKEKKETLELRVKTLQRQEERLREQLK 98 (110)
T ss_pred HHHHHHHHHHHHHHcCCCcchhHHHhchhhheecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33334556666666666566666655531 111112234444444555555554444444444443
No 154
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=22.03 E-value=1.4e+02 Score=26.53 Aligned_cols=53 Identities=21% Similarity=0.282 Sum_probs=37.3
Q ss_pred CcHHHHHHHHHHHhcCC---CCCCCCCChhhhccccchhhhhhHHHHhhhccceee
Q 024196 117 TTYNEVADELVAEFADP---SNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (271)
Q Consensus 117 TTYnEVAdeLV~e~~~~---~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K 169 (271)
.-|.+|++.|...+... ....-+..+-+.....-|=-|-.|++.|+.-|+|.+
T Consensus 12 p~Y~qi~~~L~~~I~~~~~~G~~LPsE~eLa~~~~VSR~TVR~Al~~L~~eGli~r 67 (241)
T PRK10079 12 TRYQEIAAKLEQELRQHYRCGDYLPAEQQLAARYEVNRHTLRRAIDQLVEKGWVQR 67 (241)
T ss_pred CHHHHHHHHHHHHHhcccCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 44899999998877531 111111123444556778899999999999999999
No 155
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=21.88 E-value=1.4e+02 Score=26.29 Aligned_cols=51 Identities=22% Similarity=0.292 Sum_probs=35.7
Q ss_pred HHHHHHHHHHHhcCCC----CCCCCCChhhhccccchhhhhhHHHHhhhccceee
Q 024196 119 YNEVADELVAEFADPS----NSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (271)
Q Consensus 119 YnEVAdeLV~e~~~~~----~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K 169 (271)
|.+|++.|...+.... ...-+..+-+.....-|=-|-.||+.|+.-|+|.|
T Consensus 2 y~qi~~~l~~~I~~g~~~~G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~eGli~r 56 (233)
T TIGR02404 2 YEQIYQDLEQKITHGQYKEGDYLPSEHELMDQYGASRETVRKALNLLTEAGYIQK 56 (233)
T ss_pred HHHHHHHHHHHHHhCCCCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 7788888887775321 11112223444556778889999999999999999
No 156
>TIGR02473 flagell_FliJ flagellar export protein FliJ. Members of this family are the FliJ protein found, in nearly every case, in the midst of other flagellar biosynthesis genes in bacgterial genomes. Typically the fliJ gene is found adjacent to the gene for the flagellum-specific ATPase FliI. Sequence scoring in the gray zone between trusted and noise cutoffs include both probable FliJ proteins and components of bacterial type III secretion systems.
Probab=21.34 E-value=4.1e+02 Score=21.19 Aligned_cols=43 Identities=21% Similarity=0.333 Sum_probs=31.8
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024196 185 NDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQRNER 227 (271)
Q Consensus 185 ~~~~~Lk~E~~~l~e~I~~Kk~~LqEL~~Q~~~lknLI~RNk~ 227 (271)
..+...+..+..+...++.++..|.+-......+..|.+|-..
T Consensus 75 ~~i~~q~~~l~~~~~~~e~~r~~l~~a~~~~k~lekL~ek~~~ 117 (141)
T TIGR02473 75 QRIQQQQQELALLQQEVEAKRERLLEARRELKALEKLKEKKQK 117 (141)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455556666677777888888888888888888888886544
No 157
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=21.31 E-value=2.6e+02 Score=24.08 Aligned_cols=50 Identities=20% Similarity=0.285 Sum_probs=39.2
Q ss_pred hhHHHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceeecCC
Q 024196 102 QFSMKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKDKK 172 (271)
Q Consensus 102 ~fS~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K~Kk 172 (271)
.++.+|.|.|++.|+.|..+++.++ ..-|--+=..++.|.+-|-|-+.+.
T Consensus 12 eLk~rIvElVRe~GRiTi~ql~~~T---------------------GasR~Tvk~~lreLVa~G~l~~~G~ 61 (127)
T PF06163_consen 12 ELKARIVELVREHGRITIKQLVAKT---------------------GASRNTVKRYLRELVARGDLYRHGR 61 (127)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHH---------------------CCCHHHHHHHHHHHHHcCCeEeCCC
Confidence 5778899999999999999988876 1234445567888899988888655
No 158
>PF10234 Cluap1: Clusterin-associated protein-1; InterPro: IPR019366 This protein of 413 amino acids contains a central coiled-coil domain, possibly the region that binds to clusterin. Cluap1 expression is highest in the nucleus and gradually increases during late S to G2/M phases of the cell cycle and returns to the basal level in the G0/G1 phases. In addition, it is upregulated in colon cancer tissues compared to corresponding non-cancerous mucosa. It thus plays a crucial role in the life of the cell [].
Probab=21.28 E-value=2.4e+02 Score=27.00 Aligned_cols=22 Identities=32% Similarity=0.510 Sum_probs=10.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 024196 187 IEELKAERLGLRNRIEKKTAYL 208 (271)
Q Consensus 187 ~~~Lk~E~~~l~e~I~~Kk~~L 208 (271)
+..|..+...|+..|++|+..|
T Consensus 185 l~~l~~de~~Le~KIekkk~EL 206 (267)
T PF10234_consen 185 LNNLASDEANLEAKIEKKKQEL 206 (267)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444445555555555444
No 159
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=21.21 E-value=2.4e+02 Score=25.84 Aligned_cols=39 Identities=15% Similarity=0.164 Sum_probs=31.1
Q ss_pred HHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCChhhhccccchhhhhhHHHHhhhccceee
Q 024196 110 KVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (271)
Q Consensus 110 kVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~d~K~ikRRVYD~lNVL~ai~lI~K 169 (271)
.+.+....|..|+|+.| ..-+..+.-++.-|+.-|+|+|
T Consensus 15 ~l~~~~~IS~~eLA~~L---------------------~iS~~Tvsr~Lk~LEe~GlI~R 53 (217)
T PRK14165 15 AVNNTVKISSSEFANHT---------------------GTSSKTAARILKQLEDEGYITR 53 (217)
T ss_pred ccCCCCCcCHHHHHHHH---------------------CcCHHHHHHHHHHHHHCCCEEE
Confidence 34445568899999998 2456788889999999999999
No 160
>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Probab=21.10 E-value=5.3e+02 Score=22.05 Aligned_cols=29 Identities=14% Similarity=0.181 Sum_probs=22.3
Q ss_pred cccchhhhhhHHHHhhhccceee-cCCceE
Q 024196 147 EKNIRRRVYDALNVLMAMDIISK-DKKEIQ 175 (271)
Q Consensus 147 ~K~ikRRVYD~lNVL~ai~lI~K-~Kk~i~ 175 (271)
...-|=-|=+||..|++.|||+. .++.+.
T Consensus 44 lgVSRtpVReAL~~L~~eGlv~~~~~~G~~ 73 (212)
T TIGR03338 44 LGVSRGPVREAFRALEEAGLVRNEKNRGVF 73 (212)
T ss_pred hCCChHHHHHHHHHHHHCCCEEEecCCCeE
Confidence 35667778899999999999998 444443
No 161
>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=20.84 E-value=2.1e+02 Score=19.29 Aligned_cols=23 Identities=26% Similarity=0.281 Sum_probs=19.6
Q ss_pred ccchhhhhhHHHHhhhccceeec
Q 024196 148 KNIRRRVYDALNVLMAMDIISKD 170 (271)
Q Consensus 148 K~ikRRVYD~lNVL~ai~lI~K~ 170 (271)
..-+-.|..+++-|+..|+|++.
T Consensus 36 ~is~~~v~~~l~~L~~~G~i~~~ 58 (66)
T cd07377 36 GVSRTTVREALRELEAEGLVERR 58 (66)
T ss_pred CCCHHHHHHHHHHHHHCCCEEec
Confidence 44577899999999999999984
No 162
>COG1938 Archaeal enzymes of ATP-grasp superfamily [General function prediction only]
Probab=20.76 E-value=2.5e+02 Score=26.53 Aligned_cols=28 Identities=25% Similarity=0.413 Sum_probs=21.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024196 186 DIEELKAERLGLRNRIEKKTAYLQELED 213 (271)
Q Consensus 186 ~~~~Lk~E~~~l~e~I~~Kk~~LqEL~~ 213 (271)
+.+.|.+|.+.++++|++..+++++...
T Consensus 205 ~td~L~keAe~i~~~lekl~eq~~~~~~ 232 (244)
T COG1938 205 DTDKLEKEAEEIEEQLEKLAEQLEKEEE 232 (244)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3568888888888888888888776653
No 163
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=20.62 E-value=1.7e+02 Score=24.50 Aligned_cols=34 Identities=18% Similarity=0.119 Sum_probs=27.4
Q ss_pred hhccccchhhhhhHHHHhhhccceeecCCceEEe
Q 024196 144 QYDEKNIRRRVYDALNVLMAMDIISKDKKEIQWK 177 (271)
Q Consensus 144 ~~d~K~ikRRVYD~lNVL~ai~lI~K~Kk~i~W~ 177 (271)
+.-....|..|--+++-|+.-|+|+..++.|...
T Consensus 156 A~~lG~tretvsR~l~~l~~~g~I~~~~~~i~I~ 189 (202)
T PRK13918 156 AAAVGSVRETVTKVIGELSREGYIRSGYGKIQLL 189 (202)
T ss_pred HHHhCccHHHHHHHHHHHHHCCCEEcCCCEEEEE
Confidence 3334566788999999999999999988888864
No 164
>PRK03887 methylated-DNA--protein-cysteine methyltransferase; Provisional
Probab=20.54 E-value=1.3e+02 Score=27.15 Aligned_cols=29 Identities=38% Similarity=0.494 Sum_probs=23.5
Q ss_pred cccchhHHHHHHH-HHh---cCCCcHHHHHHHH
Q 024196 98 RGLRQFSMKVCEK-VES---KGRTTYNEVADEL 126 (271)
Q Consensus 98 ~GLR~fS~KVcek-Vk~---kg~TTYnEVAdeL 126 (271)
.|+--|..+|.+. ++. ..++||.++|..+
T Consensus 88 ~g~T~Fq~rV~~~Lv~~IP~G~v~TYgqIA~~~ 120 (175)
T PRK03887 88 EGLTPFERKVYEWLTKNVKRGEVITYGELAKAL 120 (175)
T ss_pred CCCCHHHHHHHHHHHHhCCCCCCCcHHHHHHHH
Confidence 4667899999994 433 8899999999987
No 165
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=20.50 E-value=3.5e+02 Score=21.94 Aligned_cols=42 Identities=10% Similarity=0.165 Sum_probs=0.0
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024196 184 LNDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQRN 225 (271)
Q Consensus 184 ~~~~~~Lk~E~~~l~e~I~~Kk~~LqEL~~Q~~~lknLI~RN 225 (271)
.++++.++++..+++++....+.++..|......+..+..++
T Consensus 33 ~~q~~~~~~e~~~l~~~n~~L~~eI~~L~~~~dyiEe~AR~~ 74 (105)
T PRK00888 33 NDQVAAQQQTNAKLKARNDQLFAEIDDLKGGQEAIEERARNE 74 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhCcHHHHHHHHHHH
No 166
>PF10828 DUF2570: Protein of unknown function (DUF2570); InterPro: IPR022538 This entry is represented by Bacteriophage IME08, pseT.3. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a family of proteins with unknown function.
Probab=20.47 E-value=4.6e+02 Score=21.14 Aligned_cols=64 Identities=23% Similarity=0.361 Sum_probs=38.4
Q ss_pred hhhhhhHHHHhhhccceeecCCceEEecCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024196 151 RRRVYDALNVLMAMDIISKDKKEIQWKGLPRTSLNDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQRN 225 (271)
Q Consensus 151 kRRVYD~lNVL~ai~lI~K~Kk~i~W~G~~~~s~~~~~~Lk~E~~~l~e~I~~Kk~~LqEL~~Q~~~lknLI~RN 225 (271)
+|.+|-++-|| .++|. ..-|. ....++.|+.+...+.+.|++...-.++|..+...-+.++..+
T Consensus 2 ~~~~~~~l~~l-vl~L~-----~~l~~-----qs~~i~~L~a~n~~q~~tI~qq~~~~~~L~~~~~~~r~~~~~~ 65 (110)
T PF10828_consen 2 KKYIYIALAVL-VLGLG-----GWLWY-----QSQRIDRLRAENKAQAQTIQQQEDANQELKAQLQQNRQAVEEQ 65 (110)
T ss_pred hHHHHHHHHHH-HHHHH-----HHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56777777555 44433 11221 1246788888877777777777776777666555555555543
No 167
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=20.41 E-value=5.7e+02 Score=22.17 Aligned_cols=28 Identities=18% Similarity=0.139 Sum_probs=21.7
Q ss_pred ccchhhhhhHHHHhhhccceee-cCCceE
Q 024196 148 KNIRRRVYDALNVLMAMDIISK-DKKEIQ 175 (271)
Q Consensus 148 K~ikRRVYD~lNVL~ai~lI~K-~Kk~i~ 175 (271)
..-|=-|=+||..|++.|||+. .+..+.
T Consensus 45 gVSRtpVREAL~~L~~eGLV~~~~~~g~~ 73 (221)
T PRK11414 45 GMSITPVREALLRLVSVNALSVAPAQAFT 73 (221)
T ss_pred CCCchhHHHHHHHHHHCCCEEecCCCcee
Confidence 4567778899999999999998 444443
No 168
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=20.40 E-value=3.1e+02 Score=24.55 Aligned_cols=24 Identities=17% Similarity=0.365 Sum_probs=13.5
Q ss_pred hHHHHHHHHHhcCC--CcHHHHHHHH
Q 024196 103 FSMKVCEKVESKGR--TTYNEVADEL 126 (271)
Q Consensus 103 fS~KVcekVk~kg~--TTYnEVAdeL 126 (271)
++--|..-|+++++ --|.||++.|
T Consensus 15 LAEtVLrhIReG~TQL~AFeEvg~~L 40 (161)
T TIGR02894 15 LAETVLRHIREGSTQLSAFEEVGRAL 40 (161)
T ss_pred HHHHHHHHHhcchHHHHHHHHHHHHH
Confidence 34445555555442 2367777777
No 169
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=20.35 E-value=4.7e+02 Score=21.14 Aligned_cols=13 Identities=23% Similarity=0.074 Sum_probs=10.4
Q ss_pred cCCCcHHHHHHHH
Q 024196 114 KGRTTYNEVADEL 126 (271)
Q Consensus 114 kg~TTYnEVAdeL 126 (271)
....|+.+||.++
T Consensus 27 ~~g~sv~evA~e~ 39 (121)
T PRK09413 27 EPGMTVSLVARQH 39 (121)
T ss_pred cCCCCHHHHHHHH
Confidence 3456899999998
No 170
>PF04380 BMFP: Membrane fusogenic activity; InterPro: IPR007475 BMFP consists of two structural domains, a coiled-coil C-terminal domain via which the protein self-associates as a trimer, and an N-terminal domain disordered at neutral pH but adopting an amphipathic alpha-helical structure in the presence of phospholipid vesicles, high ionic strength, acidic pH or SDS. BMFP interacts with phospholipid vesicles though the predicted amphipathic alpha-helix induced in the N-terminal half of the protein and promotes aggregation and fusion of vesicles in vitro.
Probab=20.27 E-value=2.3e+02 Score=21.82 Aligned_cols=49 Identities=35% Similarity=0.502 Sum_probs=33.1
Q ss_pred cccchhhhhhHHHHhhhccceeecCCceEEecCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024196 147 EKNIRRRVYDALNVLMAMDIISKDKKEIQWKGLPRTSLNDIEELKAERLGLRNRIEKKTAYLQELED 213 (271)
Q Consensus 147 ~K~ikRRVYD~lNVL~ai~lI~K~Kk~i~W~G~~~~s~~~~~~Lk~E~~~l~e~I~~Kk~~LqEL~~ 213 (271)
++++|-++-.+ |..++|++| .+.+.+++.+.+.+++|+....+|.+|..
T Consensus 30 e~~~r~~l~~~---l~kldlVtR---------------EEFd~q~~~L~~~r~kl~~LEarl~~LE~ 78 (79)
T PF04380_consen 30 EKNIRARLQSA---LSKLDLVTR---------------EEFDAQKAVLARTREKLEALEARLAALEA 78 (79)
T ss_pred HHHHHHHHHHH---HHHCCCCcH---------------HHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 35666665443 445566544 56777778888888888888888887764
No 171
>PRK05689 fliJ flagellar biosynthesis chaperone; Validated
Probab=20.15 E-value=4.4e+02 Score=21.69 Aligned_cols=42 Identities=17% Similarity=0.333 Sum_probs=31.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024196 186 DIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQRNER 227 (271)
Q Consensus 186 ~~~~Lk~E~~~l~e~I~~Kk~~LqEL~~Q~~~lknLI~RNk~ 227 (271)
.|...+..+..+...++.++..+.+-.....+|..|++|-..
T Consensus 79 ~I~~q~~~v~~~~~~ve~~r~~~~~a~~~~k~lEkL~ek~~~ 120 (147)
T PRK05689 79 AITQQRQQLTQWTQKVDNARKYWQEKKQRLEALETLQERYQT 120 (147)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444555566677777888888888888888899999886654
Done!