Query 026130
Match_columns 243
No_of_seqs 120 out of 123
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 04:08:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026130.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026130hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3054 Uncharacterized conser 100.0 1.5E-72 3.3E-77 505.4 21.7 227 1-229 64-295 (299)
2 PF09756 DDRGK: DDRGK domain; 100.0 7.4E-69 1.6E-73 465.0 6.3 186 37-223 3-188 (188)
3 smart00088 PINT motif in prote 97.4 0.00062 1.3E-08 50.7 7.2 62 134-195 10-71 (88)
4 smart00753 PAM PCI/PINT associ 97.4 0.00062 1.3E-08 50.7 7.2 62 134-195 10-71 (88)
5 smart00418 HTH_ARSR helix_turn 97.3 0.0019 4E-08 43.4 7.4 61 140-201 3-63 (66)
6 PF09012 FeoC: FeoC like trans 97.0 0.001 2.2E-08 48.6 4.4 49 136-184 2-50 (69)
7 PF01399 PCI: PCI domain; Int 96.9 0.0051 1.1E-07 45.8 7.3 58 135-192 47-104 (105)
8 PF08220 HTH_DeoR: DeoR-like h 96.2 0.018 3.9E-07 40.9 6.1 54 136-192 2-55 (57)
9 cd00090 HTH_ARSR Arsenical Res 96.2 0.034 7.3E-07 38.0 7.3 56 137-193 10-65 (78)
10 PF13463 HTH_27: Winged helix 96.0 0.027 5.9E-07 39.5 6.2 57 138-194 7-67 (68)
11 PRK03902 manganese transport t 96.0 0.054 1.2E-06 44.2 8.9 70 133-206 7-76 (142)
12 TIGR02337 HpaR homoprotocatech 96.0 0.042 9.1E-07 43.1 7.7 66 138-203 32-100 (118)
13 smart00347 HTH_MARR helix_turn 95.9 0.059 1.3E-06 39.4 7.9 70 137-206 13-85 (101)
14 smart00344 HTH_ASNC helix_turn 95.9 0.041 8.8E-07 42.2 7.2 74 137-210 6-91 (108)
15 PRK14165 winged helix-turn-hel 95.9 0.028 6.1E-07 50.4 7.0 59 143-201 16-74 (217)
16 PRK06266 transcription initiat 95.8 0.056 1.2E-06 46.9 8.4 68 137-204 25-98 (178)
17 KOG3054 Uncharacterized conser 95.8 0.099 2.1E-06 48.7 10.2 35 28-62 91-125 (299)
18 PF09743 DUF2042: Uncharacteri 95.4 0.065 1.4E-06 49.5 7.8 62 157-219 18-81 (272)
19 cd07377 WHTH_GntR Winged helix 95.3 0.11 2.3E-06 35.7 6.8 42 148-192 25-66 (66)
20 PRK11169 leucine-responsive tr 94.9 0.16 3.4E-06 42.7 8.1 74 137-210 17-104 (164)
21 smart00420 HTH_DEOR helix_turn 94.7 0.1 2.2E-06 34.2 5.2 42 138-179 4-45 (53)
22 TIGR01884 cas_HTH CRISPR locus 94.6 0.096 2.1E-06 45.2 6.2 57 137-194 146-202 (203)
23 smart00345 HTH_GNTR helix_turn 94.2 0.092 2E-06 35.3 4.2 31 150-180 22-52 (60)
24 TIGR01889 Staph_reg_Sar staphy 94.1 0.33 7.1E-06 38.0 7.7 68 138-205 29-103 (109)
25 PF13412 HTH_24: Winged helix- 93.8 0.19 4.1E-06 33.7 5.1 42 137-178 6-47 (48)
26 PF08279 HTH_11: HTH domain; 93.8 0.36 7.9E-06 33.0 6.6 49 137-187 3-52 (55)
27 PRK11179 DNA-binding transcrip 93.8 0.32 6.9E-06 40.3 7.5 86 137-222 12-110 (153)
28 PF03297 Ribosomal_S25: S25 ri 93.7 0.26 5.6E-06 40.0 6.6 60 133-192 44-103 (105)
29 PLN03083 E3 UFM1-protein ligas 93.6 0.17 3.7E-06 53.3 6.8 63 156-219 20-85 (803)
30 COG1349 GlpR Transcriptional r 93.6 0.16 3.4E-06 45.8 5.8 47 135-181 6-52 (253)
31 PRK11512 DNA-binding transcrip 93.5 0.42 9.2E-06 38.8 7.7 64 139-202 45-111 (144)
32 COG1522 Lrp Transcriptional re 93.3 0.19 4E-06 40.5 5.3 68 138-205 12-92 (154)
33 PRK03573 transcriptional regul 93.1 0.59 1.3E-05 37.7 7.8 65 139-203 36-104 (144)
34 PF13518 HTH_28: Helix-turn-he 93.1 0.23 5.1E-06 33.1 4.6 47 138-187 4-50 (52)
35 PF04703 FaeA: FaeA-like prote 93.0 0.26 5.6E-06 36.4 5.1 52 138-189 4-56 (62)
36 smart00346 HTH_ICLR helix_turn 92.7 0.96 2.1E-05 33.3 8.0 68 136-205 7-75 (91)
37 PF13551 HTH_29: Winged helix- 92.6 0.4 8.6E-06 36.2 5.8 76 150-226 14-99 (112)
38 PTZ00266 NIMA-related protein 92.4 1.1 2.5E-05 48.4 10.9 10 32-41 422-431 (1021)
39 PRK10434 srlR DNA-bindng trans 92.0 0.35 7.7E-06 43.5 5.7 45 135-179 6-50 (256)
40 PF01726 LexA_DNA_bind: LexA D 91.8 0.51 1.1E-05 34.8 5.4 46 134-179 10-57 (65)
41 KOG1144 Translation initiation 91.8 2.2 4.9E-05 45.5 11.8 28 167-194 296-327 (1064)
42 PRK09334 30S ribosomal protein 91.5 0.7 1.5E-05 36.4 6.2 60 132-191 25-84 (86)
43 PRK09954 putative kinase; Prov 91.5 0.74 1.6E-05 42.4 7.4 54 136-189 5-60 (362)
44 PF01978 TrmB: Sugar-specific 91.3 1 2.2E-05 32.2 6.4 58 137-194 11-68 (68)
45 TIGR00122 birA_repr_reg BirA b 91.2 0.84 1.8E-05 32.8 5.9 49 139-191 5-53 (69)
46 TIGR02702 SufR_cyano iron-sulf 91.1 0.75 1.6E-05 39.7 6.6 59 137-195 4-67 (203)
47 PRK13777 transcriptional regul 90.8 1.3 2.8E-05 38.7 7.9 68 138-205 49-119 (185)
48 PRK10870 transcriptional repre 90.7 1.3 2.8E-05 37.7 7.7 58 146-203 69-129 (176)
49 TIGR02944 suf_reg_Xantho FeS a 90.7 0.47 1E-05 37.9 4.7 66 139-204 14-81 (130)
50 PF12840 HTH_20: Helix-turn-he 90.4 1.1 2.4E-05 31.5 5.9 47 137-183 13-59 (61)
51 KOG1029 Endocytic adaptor prot 90.4 1.6 3.5E-05 46.4 9.3 36 193-229 471-510 (1118)
52 PRK13509 transcriptional repre 90.3 0.72 1.6E-05 41.4 6.0 47 134-180 5-51 (251)
53 PF08784 RPA_C: Replication pr 90.3 0.75 1.6E-05 35.5 5.3 52 133-184 46-101 (102)
54 cd04761 HTH_MerR-SF Helix-Turn 90.2 0.95 2.1E-05 29.7 5.1 46 150-200 2-47 (49)
55 TIGR01764 excise DNA binding d 89.8 1.8 3.9E-05 27.9 6.2 45 149-199 2-46 (49)
56 PRK15431 ferrous iron transpor 89.5 1.2 2.6E-05 34.6 5.9 48 135-182 3-50 (78)
57 PF11600 CAF-1_p150: Chromatin 89.5 11 0.00024 33.3 12.7 8 133-140 179-186 (216)
58 PRK00441 argR arginine repress 89.1 1.1 2.3E-05 38.0 5.8 57 134-195 4-66 (149)
59 PRK09802 DNA-binding transcrip 89.0 0.93 2E-05 41.2 5.7 47 133-179 16-62 (269)
60 PF09743 DUF2042: Uncharacteri 88.9 1.5 3.2E-05 40.6 7.0 81 135-219 56-141 (272)
61 PRK10411 DNA-binding transcrip 88.4 1.8 3.8E-05 38.8 7.0 55 135-192 5-59 (240)
62 PF13404 HTH_AsnC-type: AsnC-t 88.2 1.2 2.6E-05 30.1 4.5 36 138-173 7-42 (42)
63 PRK10906 DNA-binding transcrip 88.1 1.3 2.8E-05 39.9 6.0 47 134-180 5-51 (252)
64 smart00550 Zalpha Z-DNA-bindin 88.0 1.9 4.2E-05 31.5 5.9 45 137-181 9-55 (68)
65 PF01710 HTH_Tnp_IS630: Transp 88.0 3.2 6.9E-05 33.3 7.6 78 132-218 4-81 (119)
66 PRK04424 fatty acid biosynthes 88.0 0.83 1.8E-05 39.5 4.5 45 134-178 7-51 (185)
67 PF14947 HTH_45: Winged helix- 87.8 3.6 7.8E-05 30.6 7.3 64 134-202 6-69 (77)
68 PRK10681 DNA-binding transcrip 87.5 0.96 2.1E-05 40.5 4.8 47 134-180 7-53 (252)
69 smart00422 HTH_MERR helix_turn 87.5 2.9 6.2E-05 29.4 6.3 65 150-218 2-67 (70)
70 cd04764 HTH_MlrA-like_sg1 Heli 87.4 3.7 7.9E-05 29.1 6.9 64 150-219 2-67 (67)
71 PRK04172 pheS phenylalanyl-tRN 87.3 3.9 8.4E-05 40.3 9.2 79 138-217 10-97 (489)
72 PF11600 CAF-1_p150: Chromatin 87.1 8.9 0.00019 33.9 10.6 12 109-120 179-190 (216)
73 KOG1029 Endocytic adaptor prot 87.0 5.2 0.00011 42.9 10.3 12 137-148 429-440 (1118)
74 smart00342 HTH_ARAC helix_turn 87.0 1.5 3.2E-05 30.6 4.6 60 149-219 2-61 (84)
75 cd00092 HTH_CRP helix_turn_hel 87.0 1.3 2.9E-05 30.5 4.4 43 147-192 24-66 (67)
76 PF12419 DUF3670: SNF2 Helicas 87.0 1.1 2.3E-05 37.2 4.5 47 169-217 89-138 (141)
77 COG1339 Transcriptional regula 86.8 1.4 2.9E-05 40.0 5.3 54 148-201 19-72 (214)
78 smart00419 HTH_CRP helix_turn_ 86.6 1.8 3.9E-05 28.0 4.6 31 149-179 9-39 (48)
79 PF09012 FeoC: FeoC like trans 86.6 0.49 1.1E-05 34.4 2.0 24 196-219 2-25 (69)
80 PRK11050 manganese transport r 86.5 5.5 0.00012 33.2 8.5 65 136-204 39-103 (152)
81 COG1846 MarR Transcriptional r 86.3 3.8 8.2E-05 30.5 6.8 66 139-204 27-95 (126)
82 PF03444 HrcA_DNA-bdg: Winged 86.0 2.6 5.6E-05 32.8 5.8 58 132-189 6-64 (78)
83 PF12728 HTH_17: Helix-turn-he 85.7 3.8 8.2E-05 27.6 5.9 45 149-199 2-46 (51)
84 cd01106 HTH_TipAL-Mta Helix-Tu 85.5 4.8 0.0001 31.2 7.2 65 150-219 2-68 (103)
85 TIGR00498 lexA SOS regulatory 85.4 3.3 7.1E-05 35.3 6.8 57 136-193 12-70 (199)
86 PF01325 Fe_dep_repress: Iron 85.3 3.1 6.8E-05 30.0 5.6 46 134-179 8-53 (60)
87 PF13545 HTH_Crp_2: Crp-like h 85.2 2.6 5.6E-05 30.1 5.2 48 148-198 28-75 (76)
88 smart00529 HTH_DTXR Helix-turn 84.9 3.5 7.6E-05 30.7 6.0 49 151-202 2-50 (96)
89 PF12802 MarR_2: MarR family; 84.9 4.1 8.9E-05 27.9 5.9 47 138-184 9-57 (62)
90 KOG2235 Uncharacterized conser 84.9 1.8 4E-05 44.9 5.7 60 159-219 23-84 (776)
91 PF06163 DUF977: Bacterial pro 84.9 4.1 8.8E-05 34.4 6.8 80 129-215 7-87 (127)
92 PRK00215 LexA repressor; Valid 84.9 3.3 7.1E-05 35.4 6.5 48 146-194 21-69 (205)
93 PF00392 GntR: Bacterial regul 84.4 4.1 8.8E-05 28.8 5.9 53 136-189 6-64 (64)
94 PHA02943 hypothetical protein; 84.1 9.4 0.0002 33.5 8.9 71 132-205 9-82 (165)
95 PRK15002 redox-sensitivie tran 84.1 5.4 0.00012 34.0 7.4 69 145-219 8-78 (154)
96 cd04768 HTH_BmrR-like Helix-Tu 84.0 5.8 0.00012 30.6 7.0 65 150-219 2-68 (96)
97 PF01047 MarR: MarR family; I 83.9 2.6 5.6E-05 28.9 4.5 47 138-184 7-53 (59)
98 PRK11886 bifunctional biotin-- 83.3 3.3 7.2E-05 38.0 6.3 51 136-186 6-56 (319)
99 cd04773 HTH_TioE_rpt2 Second H 83.3 4.9 0.00011 31.7 6.5 67 150-220 2-69 (108)
100 PF05158 RNA_pol_Rpc34: RNA po 83.2 6.7 0.00015 37.2 8.4 82 135-219 14-111 (327)
101 PF01022 HTH_5: Bacterial regu 83.2 2.9 6.3E-05 28.1 4.5 41 138-179 6-46 (47)
102 cd04782 HTH_BltR Helix-Turn-He 83.1 4.8 0.0001 31.1 6.2 65 150-219 2-68 (97)
103 cd04783 HTH_MerR1 Helix-Turn-H 83.0 5.6 0.00012 32.0 6.8 65 150-219 2-68 (126)
104 TIGR00373 conserved hypothetic 82.6 6 0.00013 33.6 7.1 69 138-206 18-89 (158)
105 PF14493 HTH_40: Helix-turn-he 82.6 5.3 0.00011 30.4 6.2 72 147-224 12-83 (91)
106 PRK03341 arginine repressor; P 82.4 2.9 6.4E-05 36.3 5.3 58 134-196 15-79 (168)
107 cd01105 HTH_GlnR-like Helix-Tu 81.8 5.4 0.00012 30.4 6.0 71 149-223 2-73 (88)
108 PRK10512 selenocysteinyl-tRNA- 81.7 9.6 0.00021 38.9 9.4 80 135-219 494-577 (614)
109 PRK10141 DNA-binding transcrip 81.6 12 0.00025 30.7 8.2 68 138-205 20-87 (117)
110 PF13411 MerR_1: MerR HTH fami 81.6 11 0.00024 26.4 7.2 65 150-219 2-67 (69)
111 TIGR03338 phnR_burk phosphonat 81.3 4.8 0.0001 34.2 6.1 51 148-199 34-85 (212)
112 COG4901 Ribosomal protein S25 81.2 4.8 0.0001 33.1 5.7 61 132-192 43-103 (107)
113 PF13601 HTH_34: Winged helix 81.0 18 0.0004 27.2 8.6 67 139-205 5-75 (80)
114 PRK11414 colanic acid/biofilm 80.6 9 0.00019 32.9 7.7 62 136-198 17-84 (221)
115 TIGR02051 MerR Hg(II)-responsi 79.1 9 0.00019 30.9 6.8 63 151-219 2-67 (124)
116 cd04789 HTH_Cfa Helix-Turn-Hel 78.6 11 0.00024 29.4 6.9 65 149-219 2-68 (102)
117 smart00351 PAX Paired Box doma 78.6 24 0.00051 28.6 9.1 84 131-217 18-102 (125)
118 PRK10219 DNA-binding transcrip 77.9 10 0.00022 29.0 6.5 75 133-218 4-80 (107)
119 PF01710 HTH_Tnp_IS630: Transp 77.9 4.4 9.6E-05 32.4 4.6 37 136-172 59-95 (119)
120 COG1777 Predicted transcriptio 77.8 5.1 0.00011 36.5 5.4 55 138-193 19-78 (217)
121 PF06969 HemN_C: HemN C-termin 77.6 3.9 8.4E-05 28.8 3.8 54 137-194 9-63 (66)
122 PF02186 TFIIE_beta: TFIIE bet 76.9 7.6 0.00016 28.8 5.2 55 136-193 7-62 (65)
123 TIGR02787 codY_Gpos GTP-sensin 76.8 6.8 0.00015 36.4 6.0 56 136-191 185-242 (251)
124 PLN00104 MYST -like histone ac 76.7 9.2 0.0002 38.2 7.3 57 140-202 365-423 (450)
125 PRK10402 DNA-binding transcrip 76.5 13 0.00028 32.0 7.4 50 150-203 171-221 (226)
126 PF02002 TFIIE_alpha: TFIIE al 76.4 6.7 0.00015 30.4 5.1 63 138-200 17-85 (105)
127 KOG3634 Troponin [Cytoskeleton 76.3 30 0.00065 33.7 10.4 40 135-175 212-252 (361)
128 cd04788 HTH_NolA-AlbR Helix-Tu 76.1 15 0.00032 28.4 6.9 65 150-219 2-68 (96)
129 PF01402 RHH_1: Ribbon-helix-h 76.0 5.4 0.00012 25.5 3.8 28 189-217 4-31 (39)
130 PRK12423 LexA repressor; Provi 75.7 7.5 0.00016 33.7 5.8 48 132-179 8-57 (202)
131 PRK09391 fixK transcriptional 75.4 8.3 0.00018 33.4 6.0 50 149-200 180-229 (230)
132 cd00131 PAX Paired Box domain 75.4 13 0.00029 30.4 6.8 85 131-217 18-102 (128)
133 COG1725 Predicted transcriptio 74.9 16 0.00034 30.6 7.2 76 145-223 32-121 (125)
134 TIGR02297 HpaA 4-hydroxyphenyl 74.7 20 0.00044 31.4 8.3 75 134-219 186-262 (287)
135 TIGR01529 argR_whole arginine 74.5 12 0.00027 31.4 6.6 55 139-196 7-65 (146)
136 TIGR02844 spore_III_D sporulat 73.8 9.2 0.0002 29.6 5.2 55 134-204 6-60 (80)
137 KOG0163 Myosin class VI heavy 73.7 21 0.00045 38.7 9.2 21 50-70 922-942 (1259)
138 cd04762 HTH_MerR-trunc Helix-T 73.7 12 0.00026 23.7 5.0 45 150-199 2-46 (49)
139 PRK11534 DNA-binding transcrip 73.6 9.4 0.0002 32.8 5.8 51 146-198 29-80 (224)
140 cd07977 TFIIE_beta_winged_heli 73.5 5.8 0.00013 30.1 4.0 57 134-193 9-71 (75)
141 COG2378 Predicted transcriptio 73.1 19 0.0004 33.7 8.0 70 134-205 8-90 (311)
142 PLN02853 Probable phenylalanyl 72.5 25 0.00054 35.6 9.2 78 138-216 7-94 (492)
143 cd04774 HTH_YfmP Helix-Turn-He 72.5 21 0.00046 27.7 7.0 65 150-220 2-69 (96)
144 KOG3654 Uncharacterized CH dom 72.3 11 0.00025 38.6 6.7 73 37-122 389-463 (708)
145 PRK11511 DNA-binding transcrip 72.1 33 0.00072 27.5 8.3 70 133-219 8-85 (127)
146 TIGR00475 selB selenocysteine- 72.0 17 0.00036 36.9 7.9 74 135-217 476-549 (581)
147 cd04775 HTH_Cfa-like Helix-Tur 71.7 21 0.00046 27.8 6.9 62 150-217 3-66 (102)
148 PF13730 HTH_36: Helix-turn-he 71.4 6.5 0.00014 26.7 3.5 29 150-178 27-55 (55)
149 COG3140 Uncharacterized protei 71.3 3.3 7.2E-05 30.6 2.1 32 162-206 13-44 (60)
150 PF07789 DUF1627: Protein of u 71.0 6.4 0.00014 34.3 4.1 43 151-194 9-51 (155)
151 PTZ00121 MAEBL; Provisional 71.0 22 0.00048 40.7 9.0 10 160-169 1371-1380(2084)
152 cd04777 HTH_MerR-like_sg1 Heli 70.5 20 0.00043 27.9 6.5 62 150-218 2-65 (107)
153 PF09397 Ftsk_gamma: Ftsk gamm 70.4 11 0.00025 28.0 4.9 59 132-190 4-62 (65)
154 COG1802 GntR Transcriptional r 70.3 9.2 0.0002 33.1 5.0 51 148-199 39-90 (230)
155 PRK10079 phosphonate metabolis 70.2 7 0.00015 34.2 4.3 62 148-210 35-101 (241)
156 PRK10163 DNA-binding transcrip 70.2 35 0.00075 30.8 8.9 90 137-228 28-123 (271)
157 COG3355 Predicted transcriptio 70.0 36 0.00078 28.6 8.3 63 136-198 30-98 (126)
158 PRK13918 CRP/FNR family transc 70.0 15 0.00033 30.4 6.1 48 149-200 150-198 (202)
159 cd01107 HTH_BmrR Helix-Turn-He 69.8 17 0.00037 28.5 6.0 67 150-220 2-70 (108)
160 cd04784 HTH_CadR-PbrR Helix-Tu 69.6 22 0.00048 28.5 6.8 65 150-219 2-68 (127)
161 PF09339 HTH_IclR: IclR helix- 69.5 8.9 0.00019 26.2 3.9 42 138-179 7-49 (52)
162 PF02082 Rrf2: Transcriptional 69.4 14 0.00031 27.4 5.3 51 138-188 12-65 (83)
163 PF05672 MAP7: MAP7 (E-MAP-115 68.6 84 0.0018 27.8 11.1 14 12-25 8-21 (171)
164 COG1321 TroR Mn-dependent tran 68.4 13 0.00027 31.7 5.4 64 132-198 8-71 (154)
165 PF06224 HTH_42: Winged helix 68.3 13 0.00029 33.7 5.8 65 132-196 164-230 (327)
166 KOG2908 26S proteasome regulat 67.9 9.9 0.00021 37.2 5.1 48 145-192 291-338 (380)
167 PRK05114 hypothetical protein; 67.6 4 8.6E-05 30.3 1.9 32 162-206 13-44 (59)
168 PF08220 HTH_DeoR: DeoR-like h 67.5 5.7 0.00012 28.0 2.6 23 197-219 3-25 (57)
169 cd04770 HTH_HMRTR Helix-Turn-H 67.5 21 0.00045 28.3 6.1 66 150-220 2-69 (123)
170 COG1497 Predicted transcriptio 67.0 18 0.00039 33.8 6.4 65 145-221 22-87 (260)
171 TIGR02812 fadR_gamma fatty aci 66.9 11 0.00023 32.7 4.8 39 150-189 32-70 (235)
172 PF15615 TerB-C: TerB-C domain 66.9 24 0.00053 29.3 6.7 62 136-198 78-142 (144)
173 PF00325 Crp: Bacterial regula 66.9 9.4 0.0002 24.9 3.3 29 150-178 4-32 (32)
174 KOG1144 Translation initiation 66.6 42 0.00092 36.4 9.7 18 32-49 203-220 (1064)
175 TIGR03697 NtcA_cyano global ni 66.0 18 0.0004 29.5 5.8 46 149-198 144-190 (193)
176 PRK11523 DNA-binding transcrip 66.0 19 0.00042 31.6 6.3 54 135-189 13-72 (253)
177 cd01104 HTH_MlrA-CarA Helix-Tu 65.8 29 0.00062 24.2 6.0 63 150-216 2-65 (68)
178 KOG2412 Nuclear-export-signal 65.6 32 0.0007 35.5 8.4 34 196-229 409-446 (591)
179 PF13994 PgaD: PgaD-like prote 65.5 8 0.00017 32.0 3.5 37 149-189 101-137 (138)
180 PF08280 HTH_Mga: M protein tr 65.5 21 0.00046 25.2 5.3 36 138-173 9-44 (59)
181 PRK14584 hmsS hemin storage sy 65.5 12 0.00025 32.5 4.6 45 145-193 95-139 (153)
182 PRK10857 DNA-binding transcrip 65.3 11 0.00024 32.2 4.5 49 142-190 19-67 (164)
183 PLN03238 probable histone acet 65.2 28 0.00061 33.1 7.4 56 141-201 215-271 (290)
184 KOG4364 Chromatin assembly fac 64.9 54 0.0012 34.8 9.9 15 133-147 372-386 (811)
185 PF07160 DUF1395: Protein of u 64.7 2.1 4.6E-05 38.9 0.0 31 189-221 130-160 (243)
186 PRK04984 fatty acid metabolism 64.7 10 0.00022 32.8 4.2 53 137-192 14-72 (239)
187 PHA00738 putative HTH transcri 64.3 24 0.00051 29.1 5.9 56 137-194 15-70 (108)
188 TIGR03070 couple_hipB transcri 64.3 27 0.00058 23.0 5.4 52 136-203 3-54 (58)
189 PF08222 HTH_CodY: CodY helix- 64.1 17 0.00037 27.2 4.6 43 149-195 5-52 (61)
190 PRK09392 ftrB transcriptional 63.9 12 0.00027 31.9 4.5 46 152-202 177-223 (236)
191 PRK11161 fumarate/nitrate redu 63.7 20 0.00044 30.5 5.8 48 149-200 185-233 (235)
192 cd04765 HTH_MlrA-like_sg2 Heli 63.6 35 0.00077 26.6 6.7 66 150-220 2-70 (99)
193 cd01109 HTH_YyaN Helix-Turn-He 63.5 30 0.00064 27.2 6.3 63 150-217 2-66 (113)
194 PF03701 UPF0181: Uncharacteri 63.5 5.4 0.00012 28.9 1.8 31 162-205 13-43 (51)
195 KOG1497 COP9 signalosome, subu 63.4 12 0.00027 36.5 4.8 50 148-197 317-367 (399)
196 PRK10421 DNA-binding transcrip 63.4 12 0.00026 32.9 4.5 42 148-190 26-67 (253)
197 cd04790 HTH_Cfa-like_unk Helix 63.2 26 0.00057 30.0 6.4 66 149-219 2-69 (172)
198 PRK13749 transcriptional regul 62.3 29 0.00064 28.5 6.2 65 149-218 4-70 (121)
199 PHA03103 double-strand RNA-bin 62.3 16 0.00034 32.5 4.9 52 130-181 9-60 (183)
200 PRK15090 DNA-binding transcrip 62.1 52 0.0011 29.2 8.3 88 137-226 17-109 (257)
201 cd04766 HTH_HspR Helix-Turn-He 62.1 44 0.00095 25.3 6.8 65 149-218 2-68 (91)
202 PRK14585 pgaD putative PGA bio 62.0 9.8 0.00021 32.5 3.5 45 147-195 88-132 (137)
203 PRK09464 pdhR transcriptional 62.0 19 0.00041 31.5 5.5 56 135-193 15-76 (254)
204 smart00531 TFIIE Transcription 61.5 45 0.00097 27.7 7.3 67 140-206 7-82 (147)
205 PRK14999 histidine utilization 61.4 24 0.00053 30.8 6.0 70 137-209 19-101 (241)
206 PRK10572 DNA-binding transcrip 61.1 30 0.00064 30.6 6.6 75 134-219 183-259 (290)
207 PRK09990 DNA-binding transcrip 61.0 13 0.00028 32.5 4.2 54 136-190 13-72 (251)
208 TIGR03337 phnR transcriptional 60.9 26 0.00056 30.0 6.0 54 135-189 6-65 (231)
209 TIGR00738 rrf2_super rrf2 fami 60.9 18 0.00039 28.5 4.6 46 146-191 23-68 (132)
210 PRK03837 transcriptional regul 60.8 31 0.00068 29.7 6.5 54 135-189 18-77 (241)
211 PF05225 HTH_psq: helix-turn-h 60.7 23 0.0005 24.2 4.5 37 134-171 3-39 (45)
212 cd04772 HTH_TioE_rpt1 First He 60.6 42 0.0009 26.1 6.6 61 150-215 2-63 (99)
213 PTZ00326 phenylalanyl-tRNA syn 60.5 58 0.0013 33.0 9.1 79 136-216 8-96 (494)
214 KOG2412 Nuclear-export-signal 60.3 70 0.0015 33.1 9.6 6 137-142 304-309 (591)
215 cd01279 HTH_HspR-like Helix-Tu 60.3 48 0.001 25.7 6.8 63 149-216 2-66 (98)
216 PRK15481 transcriptional regul 59.8 27 0.00058 32.9 6.4 57 133-190 8-70 (431)
217 PF13814 Replic_Relax: Replica 59.4 31 0.00067 28.6 6.0 61 141-201 2-72 (191)
218 PRK13503 transcriptional activ 59.4 19 0.00042 31.3 5.0 76 132-218 169-246 (278)
219 TIGR02054 MerD mercuric resist 59.3 46 0.001 27.2 6.9 68 148-219 3-71 (120)
220 PF01316 Arg_repressor: Argini 59.1 37 0.00081 25.5 5.8 58 135-195 6-67 (70)
221 PF14502 HTH_41: Helix-turn-he 59.0 15 0.00033 26.2 3.5 34 146-179 4-37 (48)
222 PF04760 IF2_N: Translation in 58.9 11 0.00024 26.0 2.8 48 149-204 4-52 (54)
223 KOG4364 Chromatin assembly fac 58.8 69 0.0015 34.1 9.4 10 198-207 457-466 (811)
224 TIGR02018 his_ut_repres histid 58.8 12 0.00025 32.5 3.5 71 137-210 8-91 (230)
225 cd00592 HTH_MerR-like Helix-Tu 58.5 39 0.00084 25.5 6.0 66 150-220 2-68 (100)
226 TIGR00331 hrcA heat shock gene 58.5 23 0.00049 33.6 5.6 73 134-206 6-97 (337)
227 KOG0686 COP9 signalosome, subu 58.3 17 0.00038 36.4 4.9 47 148-194 365-411 (466)
228 PF11972 HTH_13: HTH DNA bindi 57.9 21 0.00045 26.1 4.1 47 137-188 2-48 (54)
229 PRK09764 DNA-binding transcrip 57.7 23 0.00049 31.1 5.2 54 135-189 10-69 (240)
230 PF12793 SgrR_N: Sugar transpo 57.5 14 0.00031 29.9 3.6 69 148-216 19-94 (115)
231 PLN03083 E3 UFM1-protein ligas 57.5 63 0.0014 34.7 9.1 95 115-219 47-145 (803)
232 PF05584 Sulfolobus_pRN: Sulfo 57.5 30 0.00065 26.6 5.1 42 137-179 8-49 (72)
233 PTZ00064 histone acetyltransfe 57.4 32 0.0007 35.2 6.7 70 149-230 472-541 (552)
234 PRK10225 DNA-binding transcrip 57.3 18 0.00039 31.8 4.5 39 150-189 35-73 (257)
235 PF13591 MerR_2: MerR HTH fami 57.2 36 0.00078 25.8 5.6 54 149-208 1-54 (84)
236 smart00862 Trans_reg_C Transcr 57.0 20 0.00043 25.2 3.9 32 186-217 1-33 (78)
237 PF08221 HTH_9: RNA polymerase 56.9 9.2 0.0002 27.7 2.2 23 197-219 16-38 (62)
238 KOG3558 Hypoxia-inducible fact 56.8 21 0.00046 37.7 5.5 88 103-203 59-152 (768)
239 PF09202 Rio2_N: Rio2, N-termi 56.7 36 0.00078 26.2 5.5 62 136-200 12-75 (82)
240 PRK09393 ftrA transcriptional 56.6 39 0.00084 30.7 6.7 77 132-219 216-294 (322)
241 PRK10227 DNA-binding transcrip 56.6 45 0.00098 27.5 6.5 65 150-219 2-68 (135)
242 COG2188 PhnF Transcriptional r 56.1 16 0.00034 32.3 3.9 67 147-216 30-103 (236)
243 PRK11569 transcriptional repre 55.6 87 0.0019 28.2 8.7 88 138-228 32-126 (274)
244 cd01111 HTH_MerD Helix-Turn-He 55.4 56 0.0012 25.9 6.6 68 150-221 2-70 (107)
245 cd04780 HTH_MerR-like_sg5 Heli 55.4 64 0.0014 25.0 6.8 67 150-220 2-70 (95)
246 PRK13239 alkylmercury lyase; P 55.4 26 0.00057 31.6 5.2 52 133-189 21-72 (206)
247 PRK00135 scpB segregation and 55.3 58 0.0013 28.7 7.3 56 149-204 21-81 (188)
248 PRK13752 putative transcriptio 54.6 54 0.0012 27.4 6.7 66 149-219 8-75 (144)
249 TIGR01950 SoxR redox-sensitive 54.5 65 0.0014 26.9 7.1 65 150-220 3-69 (142)
250 PRK15431 ferrous iron transpor 54.4 14 0.0003 28.8 2.8 25 196-220 4-28 (78)
251 PF11761 CbiG_mid: Cobalamin b 54.3 17 0.00036 26.8 3.2 36 149-184 2-39 (93)
252 PF09286 Pro-kuma_activ: Pro-k 53.6 71 0.0015 25.8 7.1 60 132-192 25-91 (143)
253 PF13412 HTH_24: Winged helix- 53.3 14 0.00031 24.4 2.5 22 198-219 7-28 (48)
254 PRK11402 DNA-binding transcrip 52.1 15 0.00032 32.1 3.1 43 146-189 31-73 (241)
255 PF13442 Cytochrome_CBB3: Cyto 51.8 14 0.0003 25.9 2.4 33 167-203 35-67 (67)
256 PLN03239 histone acetyltransfe 51.8 21 0.00047 34.7 4.3 50 147-202 283-333 (351)
257 PF04157 EAP30: EAP30/Vps36 fa 51.7 29 0.00062 30.6 4.9 45 134-178 174-220 (223)
258 TIGR02044 CueR Cu(I)-responsiv 51.7 68 0.0015 25.8 6.7 65 150-219 2-68 (127)
259 TIGR02010 IscR iron-sulfur clu 50.7 34 0.00074 27.7 4.8 52 145-196 22-74 (135)
260 cd03174 DRE_TIM_metallolyase D 50.3 33 0.00071 29.8 5.0 73 133-208 114-189 (265)
261 cd04767 HTH_HspR-like_MBC Heli 50.1 95 0.0021 25.6 7.3 63 149-217 2-66 (120)
262 COG3646 Uncharacterized phage- 49.9 18 0.0004 31.8 3.2 53 139-191 3-69 (167)
263 PRK13502 transcriptional activ 49.7 61 0.0013 28.4 6.6 76 133-219 175-252 (282)
264 PF12514 DUF3718: Protein of u 49.6 14 0.00031 27.5 2.2 24 194-218 45-68 (68)
265 PRK11642 exoribonuclease R; Pr 49.3 38 0.00082 36.0 6.0 49 139-189 24-77 (813)
266 cd04785 HTH_CadR-PbrR-like Hel 49.1 74 0.0016 25.6 6.5 64 150-218 2-67 (126)
267 smart00843 Ftsk_gamma This dom 48.9 72 0.0016 23.8 5.8 50 132-181 3-52 (63)
268 PRK11014 transcriptional repre 48.9 40 0.00087 27.4 5.0 63 144-207 21-84 (141)
269 TIGR02325 C_P_lyase_phnF phosp 48.8 32 0.0007 29.6 4.6 55 135-192 13-73 (238)
270 PRK11753 DNA-binding transcrip 48.6 35 0.00075 28.3 4.7 40 149-192 169-208 (211)
271 KOG2587 RNA polymerase III (C) 47.9 80 0.0017 32.5 7.8 72 145-216 31-127 (551)
272 COG3343 RpoE DNA-directed RNA 47.9 20 0.00043 31.8 3.2 59 151-222 37-95 (175)
273 TIGR02431 pcaR_pcaU beta-ketoa 47.9 42 0.00092 29.5 5.3 85 138-227 13-104 (248)
274 PF04967 HTH_10: HTH DNA bindi 47.7 28 0.00061 24.9 3.4 32 142-173 17-48 (53)
275 TIGR02844 spore_III_D sporulat 47.3 21 0.00045 27.6 2.9 25 195-220 7-31 (80)
276 smart00342 HTH_ARAC helix_turn 46.9 51 0.0011 22.6 4.7 39 133-172 36-75 (84)
277 PF06757 Ins_allergen_rp: Inse 46.8 14 0.00031 31.5 2.1 82 133-227 5-89 (179)
278 PF13613 HTH_Tnp_4: Helix-turn 46.7 37 0.00081 23.4 3.9 36 138-173 9-44 (53)
279 cd04763 HTH_MlrA-like Helix-Tu 46.6 1E+02 0.0022 21.7 6.4 62 150-217 2-66 (68)
280 PF10543 ORF6N: ORF6N domain; 46.6 38 0.00081 26.0 4.2 55 143-203 7-61 (88)
281 TIGR02404 trehalos_R_Bsub treh 46.5 22 0.00048 30.7 3.3 72 137-209 7-90 (233)
282 PRK05472 redox-sensing transcr 46.4 44 0.00094 29.0 5.1 42 135-177 17-61 (213)
283 PRK09416 lstR lineage-specific 46.1 54 0.0012 27.8 5.4 59 158-216 73-134 (135)
284 cd04781 HTH_MerR-like_sg6 Heli 45.8 96 0.0021 24.7 6.6 65 150-220 2-68 (120)
285 PHA03033 hypothetical protein; 45.6 30 0.00065 29.6 3.8 43 166-208 45-92 (142)
286 PRK09978 DNA-binding transcrip 45.6 60 0.0013 30.2 6.1 75 133-219 141-217 (274)
287 PF08721 Tn7_Tnp_TnsA_C: TnsA 45.3 45 0.00098 23.7 4.3 42 138-179 31-76 (79)
288 KOG4661 Hsp27-ERE-TATA-binding 45.2 1.7E+02 0.0036 31.1 9.6 14 146-159 735-748 (940)
289 COG2207 AraC AraC-type DNA-bin 44.7 82 0.0018 23.3 5.8 73 136-219 22-96 (127)
290 PRK10371 DNA-binding transcrip 44.6 75 0.0016 29.0 6.6 76 133-219 190-267 (302)
291 cd07970 OBF_DNA_ligase_LigC Th 44.2 35 0.00076 27.7 3.9 31 177-207 20-56 (122)
292 PF04157 EAP30: EAP30/Vps36 fa 44.2 34 0.00074 30.1 4.2 112 108-219 62-201 (223)
293 PRK05066 arginine repressor; P 44.1 79 0.0017 27.1 6.2 56 137-196 12-73 (156)
294 COG2345 Predicted transcriptio 43.9 46 0.001 30.3 5.0 48 134-181 11-58 (218)
295 cd04619 CBS_pair_6 The CBS dom 43.8 60 0.0013 24.0 4.9 39 158-198 8-47 (114)
296 TIGR01610 phage_O_Nterm phage 43.8 73 0.0016 24.5 5.5 35 145-179 44-78 (95)
297 PRK00082 hrcA heat-inducible t 43.6 46 0.00099 31.6 5.1 82 136-218 12-112 (339)
298 cd07153 Fur_like Ferric uptake 43.6 1.2E+02 0.0026 23.2 6.7 52 140-191 7-64 (116)
299 TIGR02277 PaaX_trns_reg phenyl 43.5 71 0.0015 29.5 6.3 52 150-201 22-73 (280)
300 PF14056 DUF4250: Domain of un 43.5 60 0.0013 23.7 4.6 38 134-171 6-43 (55)
301 cd04615 CBS_pair_2 The CBS dom 43.4 1.2E+02 0.0027 21.8 6.8 57 159-217 9-66 (113)
302 PF03551 PadR: Transcriptional 43.1 52 0.0011 23.8 4.3 43 158-200 27-74 (75)
303 PF06936 Selenoprotein_S: Sele 43.1 2.4E+02 0.0053 25.1 9.3 8 107-114 120-127 (190)
304 PRK09514 zntR zinc-responsive 43.1 1.1E+02 0.0025 25.1 6.9 65 150-219 3-69 (140)
305 PRK09834 DNA-binding transcrip 42.9 1.4E+02 0.0031 26.5 8.0 87 138-226 15-107 (263)
306 PF12324 HTH_15: Helix-turn-he 42.8 80 0.0017 24.6 5.4 52 133-189 23-74 (77)
307 PF12833 HTH_18: Helix-turn-he 42.6 45 0.00097 23.9 3.9 56 154-219 1-56 (81)
308 COG1414 IclR Transcriptional r 41.8 1.9E+02 0.0041 25.9 8.6 88 138-228 8-102 (246)
309 COG5340 Predicted transcriptio 41.7 37 0.00081 31.8 4.1 84 142-228 24-116 (269)
310 PF01638 HxlR: HxlR-like helix 41.6 1.1E+02 0.0023 23.1 6.0 53 140-193 11-67 (90)
311 PRK05638 threonine synthase; V 41.5 87 0.0019 30.4 6.8 64 138-202 375-441 (442)
312 COG1654 BirA Biotin operon rep 41.5 36 0.00079 26.2 3.4 40 146-187 17-56 (79)
313 cd04613 CBS_pair_SpoIVFB_EriC_ 41.5 42 0.00092 24.1 3.7 38 178-218 26-67 (114)
314 PF13182 DUF4007: Protein of u 41.1 55 0.0012 30.3 5.1 60 134-194 202-274 (286)
315 PRK09863 putative frv operon r 40.8 2E+02 0.0044 28.7 9.4 36 138-174 8-43 (584)
316 PF02319 E2F_TDP: E2F/DP famil 40.6 76 0.0017 23.4 4.9 47 134-180 8-61 (71)
317 KOG4661 Hsp27-ERE-TATA-binding 40.4 2E+02 0.0044 30.6 9.3 6 106-111 674-679 (940)
318 PF06991 Prp19_bind: Splicing 40.1 1.3E+02 0.0027 28.3 7.3 37 151-190 142-178 (276)
319 TIGR02698 CopY_TcrY copper tra 39.9 1.9E+02 0.0041 23.6 7.7 58 139-197 9-73 (130)
320 TIGR02063 RNase_R ribonuclease 39.9 61 0.0013 33.5 5.7 52 138-191 6-63 (709)
321 cd04787 HTH_HMRTR_unk Helix-Tu 39.6 1.6E+02 0.0034 23.9 7.1 65 150-219 2-68 (133)
322 KOG2891 Surface glycoprotein [ 39.4 3.5E+02 0.0075 26.4 10.2 7 107-113 397-403 (445)
323 KOG2439 Nuclear architecture r 39.3 32 0.00069 34.5 3.4 89 132-222 80-181 (459)
324 KOG2002 TPR-containing nuclear 39.3 2.1E+02 0.0044 31.8 9.5 20 51-70 823-842 (1018)
325 PF10007 DUF2250: Uncharacteri 39.2 85 0.0018 24.9 5.2 53 137-192 10-62 (92)
326 KOG4557 Origin recognition com 39.1 36 0.00078 31.6 3.5 86 129-219 74-164 (262)
327 PF07848 PaaX: PaaX-like prote 39.1 57 0.0012 24.4 4.1 59 136-194 7-69 (70)
328 PF09862 DUF2089: Protein of u 38.9 18 0.00038 29.9 1.4 25 186-210 29-53 (113)
329 KOG3654 Uncharacterized CH dom 38.8 1.6E+02 0.0035 30.7 8.3 25 76-100 408-432 (708)
330 PF13384 HTH_23: Homeodomain-l 38.8 26 0.00056 23.2 2.0 33 148-181 17-49 (50)
331 COG5301 Phage-related tail fib 37.8 19 0.00041 36.8 1.6 15 178-192 90-104 (587)
332 PF09756 DDRGK: DDRGK domain; 37.7 11 0.00024 33.5 0.0 25 195-219 100-124 (188)
333 PF01997 Translin: Translin fa 37.6 29 0.00062 30.2 2.6 57 137-214 80-137 (200)
334 PRK09510 tolA cell envelope in 37.6 3.5E+02 0.0076 26.7 10.2 7 28-34 51-57 (387)
335 PRK13890 conjugal transfer pro 37.6 1.7E+02 0.0038 23.6 7.0 62 135-217 6-67 (120)
336 TIGR03433 padR_acidobact trans 37.5 94 0.002 24.0 5.2 47 158-204 35-86 (100)
337 PF00034 Cytochrom_C: Cytochro 37.4 27 0.00058 24.2 2.0 16 190-205 74-89 (91)
338 cd07972 OBF_DNA_ligase_Arch_Li 37.2 48 0.001 26.6 3.7 29 179-207 26-62 (122)
339 PRK15466 carboxysome structura 36.8 36 0.00078 30.0 3.0 33 147-179 123-155 (166)
340 PRK09685 DNA-binding transcrip 36.7 1.1E+02 0.0025 27.0 6.3 75 133-219 196-275 (302)
341 PF05043 Mga: Mga helix-turn-h 36.5 1E+02 0.0022 22.7 5.1 63 134-197 16-78 (87)
342 PRK13877 conjugal transfer rel 36.3 53 0.0011 26.9 3.8 30 188-218 14-43 (114)
343 PF00486 Trans_reg_C: Transcri 36.0 56 0.0012 22.9 3.5 32 186-217 1-33 (77)
344 PF04679 DNA_ligase_A_C: ATP d 36.0 50 0.0011 25.2 3.5 30 178-207 9-46 (97)
345 PRK09836 DNA-binding transcrip 35.9 47 0.001 27.2 3.5 59 160-218 103-179 (227)
346 KOG0687 26S proteasome regulat 35.7 39 0.00085 33.2 3.4 67 143-209 312-379 (393)
347 CHL00088 apcB allophycocyanin 35.7 17 0.00037 31.3 0.9 39 183-223 13-53 (161)
348 PRK07718 fliL flagellar basal 35.6 23 0.00051 29.4 1.7 48 134-182 88-135 (142)
349 PF04182 B-block_TFIIIC: B-blo 35.5 51 0.0011 24.3 3.3 45 138-182 6-52 (75)
350 COG5187 RPN7 26S proteasome re 35.2 46 0.001 32.5 3.7 68 144-211 327-395 (412)
351 cd04769 HTH_MerR2 Helix-Turn-H 34.9 2E+02 0.0043 22.7 6.8 65 150-220 2-68 (116)
352 TIGR01339 phycocy_beta phycocy 34.8 18 0.00038 31.7 0.9 40 183-224 11-52 (170)
353 PF08448 PAS_4: PAS fold; Int 34.8 44 0.00096 23.6 2.8 24 172-195 1-24 (110)
354 COG3753 Uncharacterized protei 34.7 41 0.00089 29.0 3.0 24 150-173 92-115 (143)
355 PF02186 TFIIE_beta: TFIIE bet 34.5 39 0.00085 25.0 2.5 31 195-227 6-37 (65)
356 COG2512 Predicted membrane-ass 34.4 1.6E+02 0.0034 27.3 7.0 57 135-191 196-253 (258)
357 PF01475 FUR: Ferric uptake re 33.9 1.7E+02 0.0037 22.7 6.3 55 138-192 12-72 (120)
358 TIGR00683 nanA N-acetylneurami 33.8 1E+02 0.0022 28.2 5.6 53 158-210 16-72 (290)
359 PRK10130 transcriptional regul 33.4 1.3E+02 0.0029 28.5 6.5 78 132-219 238-319 (350)
360 KOG1767 40S ribosomal protein 33.4 53 0.0011 27.2 3.3 59 133-191 45-103 (110)
361 PF06163 DUF977: Bacterial pro 33.0 52 0.0011 27.9 3.3 21 197-217 15-35 (127)
362 PF09628 YvfG: YvfG protein; 32.9 1.2E+02 0.0025 23.1 4.8 41 134-174 7-60 (68)
363 PRK11517 transcriptional regul 32.9 1.8E+02 0.0038 23.5 6.4 59 160-218 102-176 (223)
364 cd04449 DEP_DEPDC5-like DEP (D 32.7 88 0.0019 23.7 4.3 31 160-190 47-81 (83)
365 PRK13182 racA polar chromosome 32.6 1.4E+02 0.003 26.1 6.0 61 150-216 2-64 (175)
366 PF01253 SUI1: Translation ini 32.3 44 0.00095 25.2 2.6 64 146-210 18-81 (83)
367 PF12674 Zn_ribbon_2: Putative 32.0 73 0.0016 24.5 3.8 37 184-220 34-72 (81)
368 COG2186 FadR Transcriptional r 31.7 49 0.0011 29.5 3.1 58 132-193 12-76 (241)
369 COG3415 Transposase and inacti 31.7 1.3E+02 0.0029 25.4 5.6 65 150-217 23-89 (138)
370 KOG2072 Translation initiation 31.6 5.1E+02 0.011 28.6 10.8 6 61-66 795-800 (988)
371 PF05732 RepL: Firmicute plasm 31.3 80 0.0017 27.1 4.3 45 148-195 75-119 (165)
372 cd04801 CBS_pair_M50_like This 31.0 1.5E+02 0.0032 21.6 5.2 64 158-226 8-74 (114)
373 PF00126 HTH_1: Bacterial regu 30.7 1.5E+02 0.0033 20.5 5.0 44 150-194 15-58 (60)
374 TIGR02047 CadR-PbrR Cd(II)/Pb( 30.7 1.5E+02 0.0034 23.9 5.7 65 150-219 2-68 (127)
375 PRK04296 thymidine kinase; Pro 30.6 48 0.001 28.2 2.8 66 136-205 65-138 (190)
376 cd04624 CBS_pair_11 The CBS do 30.6 78 0.0017 22.9 3.6 38 157-197 7-46 (112)
377 KOG1425 Microfibrillar-associa 30.5 2.1E+02 0.0046 28.5 7.4 24 167-190 304-327 (430)
378 cd00569 HTH_Hin_like Helix-tur 30.1 1E+02 0.0022 16.8 3.8 29 137-167 12-40 (42)
379 PRK13696 hypothetical protein; 30.0 85 0.0018 23.5 3.7 27 187-216 4-30 (62)
380 KOG2784 Phenylalanyl-tRNA synt 30.0 1.3E+02 0.0029 30.2 5.9 78 138-218 7-94 (483)
381 cd01108 HTH_CueR Helix-Turn-He 29.4 2.7E+02 0.0059 22.3 6.9 64 150-218 2-67 (127)
382 PF10557 Cullin_Nedd8: Cullin 29.3 1.2E+02 0.0026 22.0 4.4 46 138-183 12-65 (68)
383 PF00532 Peripla_BP_1: Peripla 29.2 62 0.0014 28.9 3.4 86 132-225 134-222 (279)
384 PF04320 DUF469: Protein with 29.2 1.2E+02 0.0026 24.7 4.7 67 129-216 29-98 (101)
385 cd04623 CBS_pair_10 The CBS do 29.2 1.6E+02 0.0035 21.0 5.1 63 158-227 8-75 (113)
386 PRK15121 right oriC-binding tr 29.1 1.9E+02 0.004 26.0 6.4 34 134-167 5-40 (289)
387 COG0640 ArsR Predicted transcr 29.0 2E+02 0.0043 19.8 7.9 61 142-202 33-93 (110)
388 COG3877 Uncharacterized protei 28.9 41 0.00088 28.1 2.0 24 186-209 37-60 (122)
389 PRK13500 transcriptional activ 28.9 1.1E+02 0.0024 27.8 5.0 71 133-219 205-282 (312)
390 cd01188 INT_pAE1 pAE1 and rela 28.8 1.6E+02 0.0035 23.8 5.5 71 136-206 10-89 (188)
391 cd04448 DEP_PIKfyve DEP (Dishe 28.8 1.3E+02 0.0028 22.9 4.6 39 137-185 32-70 (81)
392 PRK08455 fliL flagellar basal 28.8 35 0.00077 29.8 1.7 46 136-182 130-175 (182)
393 TIGR03453 partition_RepA plasm 28.6 1.5E+02 0.0033 27.9 6.1 55 147-205 32-86 (387)
394 PRK04280 arginine repressor; P 28.2 1.4E+02 0.0029 25.4 5.1 58 135-196 5-67 (148)
395 CHL00171 cpcB phycocyanin beta 27.8 27 0.00059 30.5 0.8 41 182-224 12-54 (172)
396 PRK12785 fliL flagellar basal 27.8 35 0.00076 29.2 1.5 47 135-182 113-159 (166)
397 cd01110 HTH_SoxR Helix-Turn-He 27.8 2.8E+02 0.006 22.9 6.8 65 150-220 3-69 (139)
398 PF09507 CDC27: DNA polymerase 27.6 75 0.0016 29.7 3.8 58 147-204 1-81 (430)
399 PRK02363 DNA-directed RNA poly 27.5 1.2E+02 0.0026 25.4 4.6 57 135-197 5-66 (129)
400 PF03979 Sigma70_r1_1: Sigma-7 27.3 1.6E+02 0.0035 22.1 4.9 45 132-176 5-52 (82)
401 cd00397 DNA_BRE_C DNA breaking 27.2 2.8E+02 0.0061 21.0 6.4 71 136-207 2-80 (164)
402 PF10771 DUF2582: Protein of u 27.0 1.6E+02 0.0034 22.0 4.6 51 140-190 14-64 (65)
403 PTZ00068 60S ribosomal protein 27.0 60 0.0013 29.3 2.8 27 145-171 131-157 (202)
404 PLN03086 PRLI-interacting fact 26.9 4.7E+02 0.01 27.2 9.5 20 179-199 141-163 (567)
405 cd01182 INT_REC_C DNA breaking 26.9 2.4E+02 0.0052 20.9 5.8 72 136-207 2-80 (162)
406 CHL00089 apcF allophycocyanin 26.7 32 0.00069 30.0 1.0 39 183-223 13-53 (169)
407 PRK09510 tolA cell envelope in 26.6 6.4E+02 0.014 25.0 10.8 10 172-181 334-343 (387)
408 PF00763 THF_DHG_CYH: Tetrahyd 26.4 82 0.0018 25.2 3.3 25 159-183 69-93 (117)
409 PF10882 bPH_5: Bacterial PH d 26.3 63 0.0014 24.4 2.5 22 186-207 79-100 (100)
410 TIGR00674 dapA dihydrodipicoli 26.3 1.5E+02 0.0032 26.8 5.3 52 158-210 14-69 (285)
411 KOG3977 Troponin I [Cytoskelet 26.2 4E+02 0.0086 24.5 7.8 73 132-210 89-161 (221)
412 TIGR03826 YvyF flagellar opero 26.1 1.6E+02 0.0034 25.0 5.0 43 135-181 31-75 (137)
413 smart00434 TOP4c DNA Topoisome 26.1 57 0.0012 32.2 2.8 36 148-185 234-269 (445)
414 PRK11173 two-component respons 25.7 1.2E+02 0.0026 25.2 4.3 35 184-218 154-189 (237)
415 PF13274 DUF4065: Protein of u 25.6 2.8E+02 0.0061 20.5 6.6 84 136-220 7-100 (108)
416 cd01282 HTH_MerR-like_sg3 Heli 25.6 3.3E+02 0.0071 21.4 6.6 66 150-220 2-68 (112)
417 COG1695 Predicted transcriptio 25.6 1.9E+02 0.0041 23.1 5.3 72 136-207 10-94 (138)
418 TIGR02043 ZntR Zn(II)-responsi 25.6 3.2E+02 0.007 22.1 6.7 66 150-220 3-70 (131)
419 PRK10265 chaperone-modulator p 25.5 99 0.0022 24.3 3.6 51 148-203 7-57 (101)
420 PF09681 Phage_rep_org_N: N-te 25.5 1.5E+02 0.0032 24.5 4.7 42 149-193 54-95 (121)
421 KOG1363 Predicted regulator of 25.5 2.4E+02 0.0053 28.3 7.1 12 160-171 404-415 (460)
422 COG0789 SoxR Predicted transcr 25.5 2.9E+02 0.0063 21.3 6.2 65 150-219 2-68 (124)
423 TIGR01337 apcB allophycocyanin 25.4 32 0.0007 29.8 0.9 39 183-223 12-52 (167)
424 PRK06474 hypothetical protein; 25.3 2.1E+02 0.0045 24.6 5.8 46 138-183 15-62 (178)
425 PF01853 MOZ_SAS: MOZ/SAS fami 25.2 73 0.0016 28.5 3.1 25 148-172 150-174 (188)
426 cd04589 CBS_pair_CAP-ED_DUF294 25.2 1.8E+02 0.0038 21.0 4.7 38 158-198 8-46 (111)
427 cd01187 INT_SG4 INT_SG4, DNA b 25.1 3.6E+02 0.0078 23.4 7.4 75 132-206 103-190 (299)
428 cd08315 Death_TRAILR_DR4_DR5 D 25.1 1.3E+02 0.0029 23.5 4.2 72 133-220 3-76 (96)
429 PF02375 JmjN: jmjN domain; I 25.0 45 0.00099 21.9 1.3 20 136-160 10-29 (34)
430 cd04779 HTH_MerR-like_sg4 Heli 24.6 3.8E+02 0.0082 22.2 7.0 64 150-219 2-67 (134)
431 PF12668 DUF3791: Protein of u 24.6 68 0.0015 23.0 2.3 22 150-171 7-28 (62)
432 cd01193 INT_IntI IntI (E2) int 24.5 2.2E+02 0.0048 23.4 5.7 73 133-206 73-150 (242)
433 PRK06582 coproporphyrinogen II 24.3 2.1E+02 0.0045 27.5 6.2 49 143-196 328-378 (390)
434 COG5027 SAS2 Histone acetyltra 24.3 67 0.0014 31.7 2.8 48 144-197 326-375 (395)
435 PF05262 Borrelia_P83: Borreli 24.3 5E+02 0.011 26.5 9.0 18 185-202 397-414 (489)
436 PF09048 Cro: Cro; InterPro: 24.3 1.5E+02 0.0033 22.1 4.0 46 135-189 5-50 (59)
437 cd01186 INT_SG3_C INT_SG3, DNA 24.1 3.7E+02 0.008 21.9 6.9 71 134-205 10-86 (180)
438 TIGR00635 ruvB Holliday juncti 23.8 1.1E+02 0.0024 27.3 3.9 53 133-188 241-294 (305)
439 smart00437 TOP1Ac Bacterial DN 23.6 2.1E+02 0.0045 26.1 5.8 54 150-206 18-71 (259)
440 smart00545 JmjN Small domain f 23.5 73 0.0016 21.8 2.1 20 136-160 12-31 (42)
441 PF09397 Ftsk_gamma: Ftsk gamm 23.4 91 0.002 23.2 2.8 22 196-217 8-29 (65)
442 PF06353 DUF1062: Protein of u 23.3 74 0.0016 27.1 2.6 30 153-186 108-137 (142)
443 PRK06074 NADH dehydrogenase su 23.3 1.9E+02 0.0041 25.3 5.3 47 160-207 2-49 (189)
444 PF01873 eIF-5_eIF-2B: Domain 23.2 1.5E+02 0.0031 24.6 4.3 58 147-222 33-90 (125)
445 PF02899 Phage_int_SAM_1: Phag 23.1 2.7E+02 0.0059 19.5 6.7 43 128-176 18-60 (84)
446 PF05172 Nup35_RRM: Nup53/35/4 23.1 77 0.0017 25.3 2.5 52 158-209 12-77 (100)
447 PF04282 DUF438: Family of unk 22.9 2.9E+02 0.0064 21.0 5.5 28 191-219 29-56 (71)
448 PRK10296 DNA-binding transcrip 22.9 2.8E+02 0.0061 24.3 6.3 75 134-219 171-248 (278)
449 smart00653 eIF2B_5 domain pres 22.9 1.5E+02 0.0032 24.1 4.2 54 148-204 21-78 (110)
450 PF15236 CCDC66: Coiled-coil d 22.7 5.2E+02 0.011 22.6 10.8 106 5-113 2-109 (157)
451 TIGR01338 phycocy_alpha phycoc 22.7 43 0.00092 29.1 1.1 42 183-226 12-55 (161)
452 cd04612 CBS_pair_SpoIVFB_EriC_ 22.6 2E+02 0.0043 20.5 4.5 21 177-198 25-46 (111)
453 COG1959 Predicted transcriptio 22.5 2.8E+02 0.006 23.2 5.9 46 148-193 25-70 (150)
454 TIGR02719 repress_PhaQ poly-be 22.4 2.5E+02 0.0054 23.7 5.6 48 159-206 54-106 (138)
455 PF13426 PAS_9: PAS domain; PD 22.4 69 0.0015 22.2 2.0 14 181-194 6-19 (104)
456 PF01408 GFO_IDH_MocA: Oxidore 22.4 1.1E+02 0.0025 22.9 3.3 53 154-209 42-115 (120)
457 PF07761 DUF1617: Protein of u 22.3 1.1E+02 0.0023 26.4 3.4 76 148-225 35-111 (143)
458 TIGR01714 phage_rep_org_N phag 22.1 1.9E+02 0.0041 23.9 4.7 41 150-193 53-93 (119)
459 PF03997 VPS28: VPS28 protein; 21.9 1.5E+02 0.0033 26.3 4.4 87 134-227 34-141 (188)
460 CHL00086 apcA allophycocyanin 21.9 45 0.00098 28.8 1.1 39 183-223 12-52 (161)
461 PRK08208 coproporphyrinogen II 21.9 4E+02 0.0086 25.8 7.6 59 134-196 347-405 (430)
462 PF13443 HTH_26: Cro/C1-type H 21.8 2.3E+02 0.0051 19.2 4.6 54 141-214 4-57 (63)
463 PRK13501 transcriptional activ 21.8 3E+02 0.0065 24.4 6.4 75 134-219 176-252 (290)
464 PHA00542 putative Cro-like pro 21.8 3.2E+02 0.007 20.4 5.6 56 138-209 22-77 (82)
465 PRK07726 DNA topoisomerase III 21.7 1.6E+02 0.0034 30.5 5.1 54 153-209 289-343 (658)
466 cd04626 CBS_pair_13 The CBS do 21.6 2.5E+02 0.0054 20.2 4.9 21 178-198 26-47 (111)
467 PF02042 RWP-RK: RWP-RK domain 21.6 1.1E+02 0.0023 22.0 2.8 23 147-169 3-25 (52)
468 COG0329 DapA Dihydrodipicolina 21.6 2.1E+02 0.0046 26.5 5.5 51 159-210 21-75 (299)
469 PRK05660 HemN family oxidoredu 21.5 2.4E+02 0.0052 26.8 5.9 50 143-196 316-365 (378)
470 PRK04158 transcriptional repre 21.5 73 0.0016 29.8 2.4 43 148-194 201-248 (256)
471 COG2524 Predicted transcriptio 21.2 2E+02 0.0043 27.6 5.2 59 132-190 8-67 (294)
472 cd01297 D-aminoacylase D-amino 21.2 1.4E+02 0.003 28.4 4.3 74 135-210 123-215 (415)
473 PTZ00246 proteasome subunit al 21.2 2.9E+02 0.0064 24.5 6.2 49 159-207 182-245 (253)
474 TIGR02661 MauD methylamine deh 21.1 3.4E+02 0.0074 23.0 6.3 49 151-214 135-188 (189)
475 PF10545 MADF_DNA_bdg: Alcohol 21.0 1E+02 0.0022 21.8 2.6 25 150-174 28-54 (85)
476 cd01191 INT_phiCTX_C phiCTX ph 21.0 4.4E+02 0.0095 21.6 6.8 72 136-207 9-95 (196)
477 KOG0352 ATP-dependent DNA heli 20.9 1.9E+02 0.0042 29.8 5.3 51 135-195 73-123 (641)
478 TIGR03879 near_KaiC_dom probab 20.9 66 0.0014 24.6 1.7 34 147-180 31-64 (73)
479 TIGR02675 tape_meas_nterm tape 20.9 1.1E+02 0.0025 22.8 2.9 27 150-180 46-72 (75)
480 KOG2747 Histone acetyltransfer 20.8 1.2E+02 0.0027 30.0 3.9 38 140-177 319-358 (396)
481 KOG2268 Serine/threonine prote 20.8 1.2E+02 0.0026 30.4 3.8 71 132-206 182-275 (465)
482 PF01395 PBP_GOBP: PBP/GOBP fa 20.8 58 0.0013 24.1 1.4 36 179-220 61-97 (121)
483 PRK08898 coproporphyrinogen II 20.7 3.2E+02 0.0069 26.1 6.6 50 143-196 333-382 (394)
484 PF11462 DUF3203: Protein of u 20.6 81 0.0017 24.5 2.1 20 181-200 40-59 (74)
485 PRK09802 DNA-binding transcrip 20.6 87 0.0019 28.5 2.7 27 193-219 16-42 (269)
486 TIGR02681 phage_pRha phage reg 20.5 1.9E+02 0.004 23.3 4.3 27 149-175 14-40 (108)
487 PRK13347 coproporphyrinogen II 20.5 2.7E+02 0.0058 27.2 6.2 53 139-195 372-427 (453)
488 KOG1463 26S proteasome regulat 20.5 1.1E+02 0.0024 30.3 3.5 68 142-209 339-411 (411)
489 smart00857 Resolvase Resolvase 20.4 1.6E+02 0.0035 23.1 3.9 44 133-177 51-96 (148)
490 PF00989 PAS: PAS fold; Inter 20.1 1.1E+02 0.0023 21.6 2.6 20 175-194 10-29 (113)
491 cd08306 Death_FADD Fas-associa 20.0 1.2E+02 0.0027 23.1 3.0 69 137-220 2-71 (86)
No 1
>KOG3054 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=1.5e-72 Score=505.37 Aligned_cols=227 Identities=48% Similarity=0.679 Sum_probs=188.8
Q ss_pred CCCCCCC-CcCCCCCCccccccc--cCCCccccccCCcchhhhhhHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHH
Q 026130 1 MRRRPAA-GASTSSAGAAEVEET--IEGSDDEGVAGGHYEAKASKKKEKRRQEREAAQQADEAARESRQSKQDRYTEMRR 77 (243)
Q Consensus 1 ~r~~~~~-~~~~~~~~~~~~~~~--~~~~~~e~~~~g~~~~kk~~Kk~~kkqerk~qReaee~~REerk~~e~~~ee~rr 77 (243)
|||.|.+ +..+++.+.....++ .+++..+....+...++|+.+|++.||+|++||+++++.||+|+++++ +++..|
T Consensus 64 ~rrd~~~~~~va~~~sd~ee~~~~dg~ee~~e~~~~~~kigkkK~aKleakqerr~qRe~E~~eREeRk~ke~-~eE~er 142 (299)
T KOG3054|consen 64 MRRDPQAASGVASSTSDVEEEGSGDGDEEEPEAGGLQAKIGKKKEAKLEAKQERRAQREAEEAEREERKRKED-YEEAER 142 (299)
T ss_pred cccChhhhccccccccccccccccccccccccccchhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHH-HHHHHH
Confidence 5666633 322333333222222 233333444455555566666777799999999999999999999999 567778
Q ss_pred hhHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHhhhhccceecccccccccccccchhHHHHHHHHHHhcCccchHHHH
Q 026130 78 RKDEEREARE--SALEEEAKAQKAREEEAAAFEFEKWKGEFSIDAEGTTENEVQDGDRDLLADFVEYIKKHKCIPLEDLA 155 (243)
Q Consensus 78 kkeeere~eE--~~~eEeer~~kee~e~rE~eEY~kwK~~f~VEeeG~~~~~~~~~~~~lL~~Fi~yIK~~KvV~LEdLA 155 (243)
++++++...| ++.++.++++++++++++|+||+|||++|+|+++|+++. +.+...|||.+||+|||.+|||+|+|||
T Consensus 143 KkdEeR~~eEae~k~ee~~RkakEE~arkeheEylkmKaaFsVeeEGtee~-~~eeqdnll~eFv~YIk~nKvV~ledLa 221 (299)
T KOG3054|consen 143 KKDEERLAEEAELKEEEKERKAKEEEARKEHEEYLKMKAAFSVEEEGTEEV-QGEEQDNLLSEFVEYIKKNKVVPLEDLA 221 (299)
T ss_pred hhhHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHhheeecccccccc-ccchHHHHHHHHHHHHHhcCeeeHHHHH
Confidence 8888875544 456888999999999999999999999999999999884 4555569999999999999999999999
Q ss_pred HHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhcCCccHHHHHhhcccccccccchh
Q 026130 156 AEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRVSISHLASKSNQFIDLETKAQ 229 (243)
Q Consensus 156 ~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~rGRVSi~eLa~~sN~lI~L~p~~~ 229 (243)
++|||+|||+|||||.|+++|+|||||||||||||||++||.+||+||+|||||||++||+.||+||+|.|...
T Consensus 222 s~f~Lrtqd~inriq~~l~eg~ltGVmDDRGKfIYIS~eEl~AVAkfIkqrGRVSIaelAe~SN~lI~l~~es~ 295 (299)
T KOG3054|consen 222 SEFGLRTQDSINRIQELLAEGLLTGVMDDRGKFIYISMEELAAVAKFIKQRGRVSIAELAEKSNQLIDLETESP 295 (299)
T ss_pred HHhCccHHHHHHHHHHHHHhhhheeeecCCCceEEecHHHHHHHHHHHHHcCceeHHHHHHhhcchhccccCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999987654
No 2
>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues. They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.
Probab=100.00 E-value=7.4e-69 Score=464.97 Aligned_cols=186 Identities=51% Similarity=0.810 Sum_probs=48.0
Q ss_pred hhhhhhHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccc
Q 026130 37 EAKASKKKEKRRQEREAAQQADEAARESRQSKQDRYTEMRRRKDEEREARESALEEEAKAQKAREEEAAAFEFEKWKGEF 116 (243)
Q Consensus 37 ~~kk~~Kk~~kkqerk~qReaee~~REerk~~e~~~ee~rrkkeeere~eE~~~eEeer~~kee~e~rE~eEY~kwK~~f 116 (243)
++.|+++|+++|++|++||+|++++|++|++++++++++++++++++++++++++++++++++++++++++||++||++|
T Consensus 3 igaKK~kKle~Keerk~qREaee~~REerkk~ee~~ee~r~k~ee~~~~~E~~~eeee~~~~eE~e~rE~eEy~k~K~~f 82 (188)
T PF09756_consen 3 IGAKKRKKLEEKEERKAQREAEEAEREERKKKEEEREEERRKKEEEEEEEEEKKEEEERKAKEEKERREQEEYEKWKSAF 82 (188)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHhc
Confidence 34445568889999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eecccccccccccccchhHHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHH
Q 026130 117 SIDAEGTTENEVQDGDRDLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEM 196 (243)
Q Consensus 117 ~VEeeG~~~~~~~~~~~~lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl 196 (243)
+|+++|++.... +...++|++||+|||.+|||+|+|||++|||+|+|||+||++|+++|+|||||||||||||||++||
T Consensus 83 ~veeeG~~~~~~-~~~~~lL~~Fi~yIK~~Kvv~ledla~~f~l~t~~~i~ri~~L~~~g~ltGv~DdrGkfIyIs~eE~ 161 (188)
T PF09756_consen 83 SVEEEGEDEEEE-EEESQLLQEFINYIKEHKVVNLEDLAAEFGLRTQDVINRIQELEAEGRLTGVIDDRGKFIYISEEEM 161 (188)
T ss_dssp ------------------HHHHHHHHHHH-SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE------
T ss_pred cccccchhHHHh-hHHHHHHHHHHHHHHHcceeeHHHHHHHcCCCHHHHHHHHHHHHHCCCceeeEcCCCCeEEecHHHH
Confidence 999999998544 4434499999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhcCCccHHHHHhhcccccc
Q 026130 197 KAVADYIKRQGRVSISHLASKSNQFID 223 (243)
Q Consensus 197 ~aVA~fI~~rGRVSi~eLa~~sN~lI~ 223 (243)
.+||+||+++|||||++||+.||+|||
T Consensus 162 ~~va~fi~~rGRvsi~el~~~~N~~i~ 188 (188)
T PF09756_consen 162 EAVAKFIKQRGRVSISELAQESNRLIN 188 (188)
T ss_dssp ---------------------------
T ss_pred HHHHHHHHHcCCccHHHHHHHHHhhcC
Confidence 999999999999999999999999997
No 3
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=97.45 E-value=0.00062 Score=50.68 Aligned_cols=62 Identities=18% Similarity=0.235 Sum_probs=57.2
Q ss_pred hHHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHH
Q 026130 134 DLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAE 195 (243)
Q Consensus 134 ~lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eE 195 (243)
-.+..|..|++..+.+.+++||..|+++..++..-|-.+..+|.|.|-||...++|+++...
T Consensus 10 ~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~ 71 (88)
T smart00088 10 IRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVD 71 (88)
T ss_pred HHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCc
Confidence 34678899999999999999999999999999999999999999999999999999998653
No 4
>smart00753 PAM PCI/PINT associated module.
Probab=97.45 E-value=0.00062 Score=50.68 Aligned_cols=62 Identities=18% Similarity=0.235 Sum_probs=57.2
Q ss_pred hHHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHH
Q 026130 134 DLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAE 195 (243)
Q Consensus 134 ~lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eE 195 (243)
-.+..|..|++..+.+.+++||..|+++..++..-|-.+..+|.|.|-||...++|+++...
T Consensus 10 ~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~ 71 (88)
T smart00753 10 IRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVD 71 (88)
T ss_pred HHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCc
Confidence 34678899999999999999999999999999999999999999999999999999998653
No 5
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=97.28 E-value=0.0019 Score=43.35 Aligned_cols=61 Identities=10% Similarity=0.224 Sum_probs=52.0
Q ss_pred HHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHH
Q 026130 140 VEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVAD 201 (243)
Q Consensus 140 i~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~ 201 (243)
+.+|. ..-+.+.+|+.+||++...+-..|+.|.+.|.|+-+-+.++.+.++|++.+..+..
T Consensus 3 l~~l~-~~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~~~~~~~~~~~~~~~~~~~~~~ 63 (66)
T smart00418 3 LKLLA-EGELCVCELAEILGLSQSTVSHHLKKLREAGLVESRREGKRVYYSLTDEKVADLLE 63 (66)
T ss_pred HHHhh-cCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeeecCCEEEEEEchHHHHHHHH
Confidence 44555 66788999999999999999999999999999998888888899999976665544
No 6
>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=97.03 E-value=0.001 Score=48.56 Aligned_cols=49 Identities=20% Similarity=0.358 Sum_probs=41.9
Q ss_pred HHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeC
Q 026130 136 LADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDD 184 (243)
Q Consensus 136 L~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDD 184 (243)
|.+..+||+.+.++.+.|||.+||++.+.+-.-|..|...|.|-=+.+.
T Consensus 2 L~~i~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~~~~ 50 (69)
T PF09012_consen 2 LQEIRDYLRERGRVSLAELAREFGISPEAVEAMLEQLIRKGYIRKVDMS 50 (69)
T ss_dssp CHHHHHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEEEEEE
T ss_pred HHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEecCC
Confidence 6788899999999999999999999999999999999999999766554
No 7
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=96.89 E-value=0.0051 Score=45.83 Aligned_cols=58 Identities=16% Similarity=0.227 Sum_probs=51.3
Q ss_pred HHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEc
Q 026130 135 LLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYIS 192 (243)
Q Consensus 135 lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS 192 (243)
.+..|+.+++.-..+.+++||..|+++..+|..-|..|..+|.|.|.||.--+.|+++
T Consensus 47 ~~~~l~~l~~~y~~i~~~~ia~~l~~~~~~vE~~l~~~I~~~~i~~~ID~~~~~v~~~ 104 (105)
T PF01399_consen 47 RRRNLRQLSKPYSSISISEIAKALQLSEEEVESILIDLISNGLIKAKIDQVNGVVVFS 104 (105)
T ss_dssp HHHHHHHHHHC-SEEEHHHHHHHHTCCHHHHHHHHHHHHHTTSSEEEEETTTTEEEE-
T ss_pred HHHHHHHHHHHhcccchHHHHHHhccchHHHHHHHHHHHHCCCEEEEEECCCCEEEec
Confidence 3566777889999999999999999999999999999999999999999988888775
No 8
>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=96.21 E-value=0.018 Score=40.88 Aligned_cols=54 Identities=19% Similarity=0.334 Sum_probs=44.8
Q ss_pred HHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEc
Q 026130 136 LADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYIS 192 (243)
Q Consensus 136 L~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS 192 (243)
....++||+.+..|.+.+||.+||++..-+-.=|+.|+..|.|. =-+|-.++++
T Consensus 2 ~~~Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~i~---r~~GG~~~~~ 55 (57)
T PF08220_consen 2 QQQILELLKEKGKVSVKELAEEFGVSEMTIRRDLNKLEKQGLIK---RTHGGAVLND 55 (57)
T ss_pred HHHHHHHHHHcCCEEHHHHHHHHCcCHHHHHHHHHHHHHCCCEE---EEcCEEEeCC
Confidence 35788999999999999999999999999999999999999843 2355555544
No 9
>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=96.20 E-value=0.034 Score=37.98 Aligned_cols=56 Identities=14% Similarity=0.293 Sum_probs=49.7
Q ss_pred HHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcH
Q 026130 137 ADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQ 193 (243)
Q Consensus 137 ~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~ 193 (243)
..++.||..+. +.+.+||..||++...+-..|..|...|.|...-+.+.++.++|+
T Consensus 10 ~~il~~l~~~~-~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~~~~~~~~~~~~~ 65 (78)
T cd00090 10 LRILRLLLEGP-LTVSELAERLGLSQSTVSRHLKKLEEAGLVESRREGRRVYYSLTD 65 (78)
T ss_pred HHHHHHHHHCC-cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEEEeccEEEEEeCC
Confidence 45677888888 889999999999999999999999999999988888888888886
No 10
>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=96.03 E-value=0.027 Score=39.53 Aligned_cols=57 Identities=19% Similarity=0.243 Sum_probs=43.5
Q ss_pred HHHHHHH-hcCccchHHHHHHcCCChHHHHHHHHHHHhcCCccee---eeCCCCeEEEcHH
Q 026130 138 DFVEYIK-KHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGV---MDDRGKYIYISQA 194 (243)
Q Consensus 138 ~Fi~yIK-~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGV---iDDRGKFIYIS~e 194 (243)
..+.+|. .+.-+.+.+||..++++..-+..-|+.|...|-|.=. .|.|.+++.+||.
T Consensus 7 ~vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~~~~~d~R~~~~~LT~~ 67 (68)
T PF13463_consen 7 QVLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLVEKERDPHDKRSKRYRLTPA 67 (68)
T ss_dssp HHHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEESSCTTSEEEEE-HH
T ss_pred HHHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecCCCCcCCeeEEEeCCC
Confidence 4466777 7777888999999999999999999999999999444 4557789999985
No 11
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=96.03 E-value=0.054 Score=44.17 Aligned_cols=70 Identities=10% Similarity=0.164 Sum_probs=57.7
Q ss_pred hhHHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhc
Q 026130 133 RDLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQ 206 (243)
Q Consensus 133 ~~lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~r 206 (243)
+++|..|..++..+..+.+.+||..+|++..-|...|+.|...|-|+= .+++.|++|+.-... |..|..+
T Consensus 7 edyL~~I~~l~~~~~~~~~~ela~~l~vs~~svs~~l~~L~~~Gli~~---~~~~~i~LT~~G~~~-a~~~~~~ 76 (142)
T PRK03902 7 EDYIEQIYLLIEEKGYARVSDIAEALSVHPSSVTKMVQKLDKDEYLIY---EKYRGLVLTPKGKKI-GKRLVYR 76 (142)
T ss_pred HHHHHHHHHHHhcCCCcCHHHHHHHhCCChhHHHHHHHHHHHCCCEEE---ecCceEEECHHHHHH-HHHHHHH
Confidence 467888888899999999999999999999999999999999987752 266789999997664 4444333
No 12
>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=95.98 E-value=0.042 Score=43.11 Aligned_cols=66 Identities=14% Similarity=0.193 Sum_probs=56.6
Q ss_pred HHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeee---CCCCeEEEcHHHHHHHHHHH
Q 026130 138 DFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMD---DRGKYIYISQAEMKAVADYI 203 (243)
Q Consensus 138 ~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViD---DRGKFIYIS~eEl~aVA~fI 203 (243)
.++.+|..+..+.+.+||..+|+....+-..|+.|++.|.|+..-| .|-++|++|+.-...+....
T Consensus 32 ~iL~~l~~~~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~LT~~G~~~~~~~~ 100 (118)
T TIGR02337 32 RILRILAEQGSMEFTQLANQACILRPSLTGILARLERDGLVTRLKASNDQRRVYISLTPKGQALYASLS 100 (118)
T ss_pred HHHHHHHHcCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhHHHHHHHhh
Confidence 4666777888899999999999999999999999999999999885 47789999998777666543
No 13
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=95.92 E-value=0.059 Score=39.43 Aligned_cols=70 Identities=9% Similarity=0.202 Sum_probs=58.4
Q ss_pred HHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeee---CCCCeEEEcHHHHHHHHHHHHhc
Q 026130 137 ADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMD---DRGKYIYISQAEMKAVADYIKRQ 206 (243)
Q Consensus 137 ~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViD---DRGKFIYIS~eEl~aVA~fI~~r 206 (243)
...+.+|..+.-+...+||..++++..-+-.-|+.|.+.|.|+=.-| .|.+|+++|+.-...+.......
T Consensus 13 ~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~~~~~~~r~~~~~lT~~g~~~~~~~~~~~ 85 (101)
T smart00347 13 FLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRLPSPEDRRSVLVSLTEEGRELIEELLEAR 85 (101)
T ss_pred HHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEecCCCCCCCeEEEEECHhHHHHHHHHHHHH
Confidence 45667788888899999999999999999999999999999975533 47789999999988877765543
No 14
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=95.91 E-value=0.041 Score=42.25 Aligned_cols=74 Identities=22% Similarity=0.423 Sum_probs=59.0
Q ss_pred HHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcce---eeeCC--CC----e--EEEc-HHHHHHHHHHHH
Q 026130 137 ADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSG---VMDDR--GK----Y--IYIS-QAEMKAVADYIK 204 (243)
Q Consensus 137 ~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtG---ViDDR--GK----F--IYIS-~eEl~aVA~fI~ 204 (243)
..++.++..+.-+...+||..+|++..-|..+|+.|.+.|.|.| ++|-+ |. | |.++ ++.+..|++.|.
T Consensus 6 ~~il~~L~~~~~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~~~~~~~~~~~~g~~~~~~v~i~~~~~~~~~~v~~~l~ 85 (108)
T smart00344 6 RKILEELQKDARISLAELAKKVGLSPSTVHNRVKRLEEEGVIKGYTAVINPKKLGLSVTAFVGVDLESPDKLEEFLEKLE 85 (108)
T ss_pred HHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeceEEEeCHHHcCCCEEEEEEEEECChhHHHHHHHHHh
Confidence 46788888888899999999999999999999999999998874 33432 32 2 4555 678899999888
Q ss_pred hcCCcc
Q 026130 205 RQGRVS 210 (243)
Q Consensus 205 ~rGRVS 210 (243)
..-.|+
T Consensus 86 ~~p~v~ 91 (108)
T smart00344 86 KLPEVV 91 (108)
T ss_pred CCcceE
Confidence 765554
No 15
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=95.85 E-value=0.028 Score=50.42 Aligned_cols=59 Identities=15% Similarity=0.280 Sum_probs=51.6
Q ss_pred HHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHH
Q 026130 143 IKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVAD 201 (243)
Q Consensus 143 IK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~ 201 (243)
+...--+...+||.++|++.+-+-.+|+.|+..|-|+-..|.||.+|+||+.-...+.+
T Consensus 16 l~~~~~IS~~eLA~~L~iS~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~LTekG~~ll~~ 74 (217)
T PRK14165 16 VNNTVKISSSEFANHTGTSSKTAARILKQLEDEGYITRTIVPRGQLITITEKGLDVLYN 74 (217)
T ss_pred cCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEEcCCceEEEECHHHHHHHHH
Confidence 33344467899999999999999999999999999999999999999999988776544
No 16
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=95.79 E-value=0.056 Score=46.91 Aligned_cols=68 Identities=12% Similarity=0.137 Sum_probs=58.6
Q ss_pred HHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcc--eeee-CCCCeEE---EcHHHHHHHHHHHH
Q 026130 137 ADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLS--GVMD-DRGKYIY---ISQAEMKAVADYIK 204 (243)
Q Consensus 137 ~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~Lt--GViD-DRGKFIY---IS~eEl~aVA~fI~ 204 (243)
..+++.++.+..+.-+|||..+||++..|-.-+..|..+|.++ .+-| ..|.|.| |+++.+..+-.+-.
T Consensus 25 ~~Vl~~L~~~g~~tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~~~r~r~~~~Gr~~y~w~l~~~~i~d~ik~~~ 98 (178)
T PRK06266 25 FEVLKALIKKGEVTDEEIAEQTGIKLNTVRKILYKLYDARLADYKREKDEETNWYTYTWKPELEKLPEIIKKKK 98 (178)
T ss_pred hHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEeeeeccCCCcEEEEEEeCHHHHHHHHHHHH
Confidence 3567788999999999999999999999999999999999999 5556 6899888 99988777666544
No 17
>KOG3054 consensus Uncharacterized conserved protein [Function unknown]
Probab=95.75 E-value=0.099 Score=48.69 Aligned_cols=35 Identities=29% Similarity=0.404 Sum_probs=26.6
Q ss_pred cccccCCcchhhhhhHHHHHHHHHHHHHHHHHHHH
Q 026130 28 DEGVAGGHYEAKASKKKEKRRQEREAAQQADEAAR 62 (243)
Q Consensus 28 ~e~~~~g~~~~kk~~Kk~~kkqerk~qReaee~~R 62 (243)
++....|...+|-.+||++|.++|.++|.+-+++-
T Consensus 91 ee~~e~~~~~~kigkkK~aKleakqerr~qRe~E~ 125 (299)
T KOG3054|consen 91 EEEPEAGGLQAKIGKKKEAKLEAKQERRAQREAEE 125 (299)
T ss_pred cccccccchhhhhhhHHHHHHHHHHHHHHHHHHHH
Confidence 34466788889999999999998887777655543
No 18
>PF09743 DUF2042: Uncharacterized conserved protein (DUF2042); InterPro: IPR018611 The ubiquitin fold modifier 1 (Ufm1) is the most recently discovered ubiquitin-like modifier whose conjugation (ufmylation) system is conserved in multicellular organisms. Ufm1 is known to covalently attach with cellular protein(s) via a specific E1-activating enzyme (Uba5), an E2-conjugating enzyme (Ufc1), and a E3-ligating enzyme []. This entry represents E3 UFM1-protein ligase 1.
Probab=95.39 E-value=0.065 Score=49.46 Aligned_cols=62 Identities=26% Similarity=0.430 Sum_probs=51.7
Q ss_pred HcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHH-HHHHH-HhcCCccHHHHHhhcc
Q 026130 157 EFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKA-VADYI-KRQGRVSISHLASKSN 219 (243)
Q Consensus 157 ~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~a-VA~fI-~~rGRVSi~eLa~~sN 219 (243)
...|+--.||+-|+.|.+.|.|.=|....||- ||||+++.. |.+-| ...||||+.||+..-|
T Consensus 18 ~~rLSErnciEiv~kL~~~~~ldli~T~dGke-yiT~~~L~~EI~~el~~~gGRv~~~dL~~~Ln 81 (272)
T PF09743_consen 18 SQRLSERNCIEIVNKLIEKKLLDLIHTTDGKE-YITPEQLEKEIKDELYVHGGRVNLVDLAQALN 81 (272)
T ss_pred hhhcchhhHHHHHHHHHHcCCeeEEEECCCCE-EECHHHHHHHHHHHHHHcCCceEHHHHHHhcC
Confidence 34688889999999999999999888889986 899999975 44355 6779999999996544
No 19
>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=95.27 E-value=0.11 Score=35.66 Aligned_cols=42 Identities=17% Similarity=0.269 Sum_probs=34.8
Q ss_pred ccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEc
Q 026130 148 CIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYIS 192 (243)
Q Consensus 148 vV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS 192 (243)
++...+||.+||++..-+-..|+.|...|.|+ -.+|++++||
T Consensus 25 ~~~~~~la~~~~is~~~v~~~l~~L~~~G~i~---~~~~~~~~l~ 66 (66)
T cd07377 25 LPSERELAEELGVSRTTVREALRELEAEGLVE---RRPGRGTFVA 66 (66)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE---ecCCCeEEeC
Confidence 34599999999999999999999999999865 2357777775
No 20
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=94.91 E-value=0.16 Score=42.67 Aligned_cols=74 Identities=15% Similarity=0.373 Sum_probs=58.4
Q ss_pred HHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcce---eeeCC--CC----eEEE-----cHHHHHHHHHH
Q 026130 137 ADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSG---VMDDR--GK----YIYI-----SQAEMKAVADY 202 (243)
Q Consensus 137 ~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtG---ViDDR--GK----FIYI-----S~eEl~aVA~f 202 (243)
...|+.+..+==....+||...||+..-|.+||+.|+..|.|.| ++|.. |. ||.| ++.-+..|+.+
T Consensus 17 ~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~GvI~~~~~~v~p~~lg~~~~a~v~i~~~~~~~~~~~~~~~~ 96 (164)
T PRK11169 17 RNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQGFIQGYTALLNPHYLDASLLVFVEITLNRGAPDVFEQFNAA 96 (164)
T ss_pred HHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEEEECHHHhCCCEEEEEEEEEcCCChHHHHHHHHH
Confidence 46677777777777899999999999999999999999999865 45642 53 6666 46778889998
Q ss_pred HHhcCCcc
Q 026130 203 IKRQGRVS 210 (243)
Q Consensus 203 I~~rGRVS 210 (243)
|...--|.
T Consensus 97 l~~~p~V~ 104 (164)
T PRK11169 97 VQKLEEIQ 104 (164)
T ss_pred HhcCccee
Confidence 88774444
No 21
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=94.68 E-value=0.1 Score=34.18 Aligned_cols=42 Identities=19% Similarity=0.337 Sum_probs=38.2
Q ss_pred HHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcc
Q 026130 138 DFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLS 179 (243)
Q Consensus 138 ~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~Lt 179 (243)
.+++||..+.-+.+.+||..||++..-+-..|+.|...|.|.
T Consensus 4 ~il~~l~~~~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~ 45 (53)
T smart00420 4 QILELLAQQGKVSVEELAELLGVSEMTIRRDLNKLEEQGLLT 45 (53)
T ss_pred HHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 578888888889999999999999999999999999998764
No 22
>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=94.61 E-value=0.096 Score=45.23 Aligned_cols=57 Identities=14% Similarity=0.194 Sum_probs=50.4
Q ss_pred HHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHH
Q 026130 137 ADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQA 194 (243)
Q Consensus 137 ~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~e 194 (243)
...+.||..+.-+.+.+||..+|++..-+-..|+.|++.|.|.-+-+ |++++++|+.
T Consensus 146 ~~IL~~l~~~g~~s~~eia~~l~is~stv~r~L~~Le~~GlI~r~~~-r~~~~~lT~~ 202 (203)
T TIGR01884 146 LKVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLRELEKKGLVEQKGR-KGKRYSLTKL 202 (203)
T ss_pred HHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcC-CccEEEeCCC
Confidence 36677888877789999999999999999999999999999987764 9999999973
No 23
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=94.22 E-value=0.092 Score=35.32 Aligned_cols=31 Identities=19% Similarity=0.282 Sum_probs=28.4
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcce
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSG 180 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtG 180 (243)
...+||..||++..-+-..|+.|...|.|+-
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~L~~~g~i~~ 52 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSRLEAEGLVQR 52 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 6999999999999999999999999998763
No 24
>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=94.08 E-value=0.33 Score=38.02 Aligned_cols=68 Identities=18% Similarity=0.287 Sum_probs=56.0
Q ss_pred HHHHHHH----hcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeee---CCCCeEEEcHHHHHHHHHHHHh
Q 026130 138 DFVEYIK----KHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMD---DRGKYIYISQAEMKAVADYIKR 205 (243)
Q Consensus 138 ~Fi~yIK----~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViD---DRGKFIYIS~eEl~aVA~fI~~ 205 (243)
.++.+|. ...-+.+.+||..+++...-+-.-|..|++.|-|+=+-| -|-.+||+|+.-...+......
T Consensus 29 ~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~r~~~~~D~R~~~i~lT~~G~~~~~~~~~~ 103 (109)
T TIGR01889 29 LILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLSKKGYLSKERSEDDERKVIISINKEQRSKIESLISE 103 (109)
T ss_pred HHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEeccCCcccCCeEEEEECHHHHHHHHHHHHH
Confidence 3456666 345789999999999999999999999999999995544 4899999999988888776543
No 25
>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=93.81 E-value=0.19 Score=33.70 Aligned_cols=42 Identities=17% Similarity=0.373 Sum_probs=37.5
Q ss_pred HHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCc
Q 026130 137 ADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRL 178 (243)
Q Consensus 137 ~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~L 178 (243)
...++||..+--+...+||..+|++..-|-..|+.|...|-|
T Consensus 6 ~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~~~g~I 47 (48)
T PF13412_consen 6 RKILNYLRENPRITQKELAEKLGISRSTVNRYLKKLEEKGLI 47 (48)
T ss_dssp HHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHCcCc
Confidence 577899999999999999999999999999999999999976
No 26
>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=93.77 E-value=0.36 Score=32.97 Aligned_cols=49 Identities=20% Similarity=0.360 Sum_probs=39.1
Q ss_pred HHHHHHH-HhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCC
Q 026130 137 ADFVEYI-KKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGK 187 (243)
Q Consensus 137 ~~Fi~yI-K~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGK 187 (243)
..++.++ ..+.-|...+||..||++..-+.+-|+.|...| .-|.-.+|+
T Consensus 3 ~~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~--~~I~~~~~~ 52 (55)
T PF08279_consen 3 KQILKLLLESKEPITAKELAEELGVSRRTIRRDIKELREWG--IPIESKRGK 52 (55)
T ss_dssp HHHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT---EEEEETTT
T ss_pred HHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC--CeEEeeCCC
Confidence 4677777 555569999999999999999999999999999 555556665
No 27
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=93.76 E-value=0.32 Score=40.29 Aligned_cols=86 Identities=16% Similarity=0.263 Sum_probs=64.6
Q ss_pred HHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcce---eeeC--CCC----eEEEc---HHHHHHHHHHHH
Q 026130 137 ADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSG---VMDD--RGK----YIYIS---QAEMKAVADYIK 204 (243)
Q Consensus 137 ~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtG---ViDD--RGK----FIYIS---~eEl~aVA~fI~ 204 (243)
...++.+..+=-....+||...|++...|-.||+.|+..|.|.| ++|. =|. ||+|+ +..+..|+..|.
T Consensus 12 ~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI~~~~~~v~~~~lg~~~~a~v~v~v~~~~~~~~~~~~l~ 91 (153)
T PRK11179 12 RGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQAGIITGTRVDVNPKQLGYDVCCFIGIILKSAKDYPSALAKLE 91 (153)
T ss_pred HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeEEEEECHHHcCCCEEEEEEEEEcccccHHHHHHHHh
Confidence 46778888888889999999999999999999999999999974 4564 354 55554 456889999888
Q ss_pred hcCCcc-HHHHHhhccccc
Q 026130 205 RQGRVS-ISHLASKSNQFI 222 (243)
Q Consensus 205 ~rGRVS-i~eLa~~sN~lI 222 (243)
..-.|. ...++-..|=++
T Consensus 92 ~~p~V~~~~~~tG~~dl~~ 110 (153)
T PRK11179 92 SLDEVVEAYYTTGHYSIFI 110 (153)
T ss_pred CCCCEEEEEEcccCCCEEE
Confidence 776665 344444444333
No 28
>PF03297 Ribosomal_S25: S25 ribosomal protein; InterPro: IPR004977 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S25 ribosomal protein is a component of the 40S ribosomal subunit.; PDB: 2XZM_8 2XZN_8 3O30_Q 3U5G_Z 3IZB_V 3U5C_Z 3O2Z_Q 3IZ6_V.
Probab=93.69 E-value=0.26 Score=39.98 Aligned_cols=60 Identities=18% Similarity=0.274 Sum_probs=56.7
Q ss_pred hhHHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEc
Q 026130 133 RDLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYIS 192 (243)
Q Consensus 133 ~~lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS 192 (243)
+.+++.++..|..-|+|..--||..|+++-.-+-.-|++|+..|.|--|.-.++-.||..
T Consensus 44 ~~~~~kl~kEV~~~K~ITp~~lserlkI~~SlAr~~Lr~L~~kG~Ik~V~k~~~~~IYtr 103 (105)
T PF03297_consen 44 KETYDKLLKEVPKMKLITPSVLSERLKINGSLARKALRELESKGLIKPVSKHHRQRIYTR 103 (105)
T ss_dssp CHHHHHHHHHCTTSSCECHHHHHHHHCCSCHHHHHHHHHHHHCCSSEEEECCTTCEEEEE
T ss_pred HHHHHHHHHHhccCcEeeHHHHHHhHhhHHHHHHHHHHHHHHCCCEEEEeccCCeEEEec
Confidence 567889999999999999999999999999999999999999999999999999999963
No 29
>PLN03083 E3 UFM1-protein ligase 1 homolog; Provisional
Probab=93.65 E-value=0.17 Score=53.25 Aligned_cols=63 Identities=25% Similarity=0.468 Sum_probs=53.6
Q ss_pred HHcCCChHHHHHHHHHHHhcCCcc--eeeeCCCCeEEEcHHHHH-HHHHHHHhcCCccHHHHHhhcc
Q 026130 156 AEFKLRTQECINRITSLENMGRLS--GVMDDRGKYIYISQAEMK-AVADYIKRQGRVSISHLASKSN 219 (243)
Q Consensus 156 ~~F~lrtqd~I~RIq~Le~~g~Lt--GViDDRGKFIYIS~eEl~-aVA~fI~~rGRVSi~eLa~~sN 219 (243)
.-..|+--.||+-|+.|.+.|.|- =|..-.|| =||||++|. .|.+-|...|||++.+|+..-|
T Consensus 20 ss~rLSErNcIEiV~KLie~~~ld~dll~T~DGK-EYiT~~qL~~EI~~El~~gGRvnlvdLa~~Ln 85 (803)
T PLN03083 20 SSVRLSERNVVELVQKLQELGIIDFDLLHTVSGK-EYITQDQLRNEIEAEIKKLGRVSLVDLADTIG 85 (803)
T ss_pred hhhhcchhhHHHHHHHHHHhcccCcceEEecCCc-eeeCHHHHHHHHHHHHHhCCCeeHHHHhhhcC
Confidence 345788889999999999999773 55666899 999999996 4888898899999999998766
No 30
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=93.64 E-value=0.16 Score=45.83 Aligned_cols=47 Identities=23% Similarity=0.315 Sum_probs=42.6
Q ss_pred HHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCccee
Q 026130 135 LLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGV 181 (243)
Q Consensus 135 lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGV 181 (243)
..+..+++++.+..|.++|||..||++..-+-.=|..|++.|.|..|
T Consensus 6 R~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l~R~ 52 (253)
T COG1349 6 RHQKILELLKEKGKVSVEELAELFGVSEMTIRRDLNELEEQGLLLRV 52 (253)
T ss_pred HHHHHHHHHHHcCcEEHHHHHHHhCCCHHHHHHhHHHHHHCCcEEEE
Confidence 56889999999999999999999999877777779999999999874
No 31
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=93.53 E-value=0.42 Score=38.78 Aligned_cols=64 Identities=13% Similarity=0.190 Sum_probs=54.4
Q ss_pred HHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeee---CCCCeEEEcHHHHHHHHHH
Q 026130 139 FVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMD---DRGKYIYISQAEMKAVADY 202 (243)
Q Consensus 139 Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViD---DRGKFIYIS~eEl~aVA~f 202 (243)
++..|-.+..+..-+||..+|++..-+-.-|..|++.|-|.=+.| -|.++||+|+.-...+...
T Consensus 45 vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~~~~~DrR~~~l~LT~~G~~~~~~~ 111 (144)
T PRK11512 45 VLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTSGAAICEQC 111 (144)
T ss_pred HHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCcccCCeeEeEEChhHHHHHHHH
Confidence 345565677899999999999999999999999999999998765 3899999999888766553
No 32
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=93.32 E-value=0.19 Score=40.54 Aligned_cols=68 Identities=19% Similarity=0.414 Sum_probs=51.5
Q ss_pred HHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCccee---eeCC--C----CeEEEcHHH----HHHHHHHHH
Q 026130 138 DFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGV---MDDR--G----KYIYISQAE----MKAVADYIK 204 (243)
Q Consensus 138 ~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGV---iDDR--G----KFIYIS~eE----l~aVA~fI~ 204 (243)
..++.+...-=..+.+||...||+...|.+||+.|+..|-|.|. +|.+ | =||.|+... +..++..+.
T Consensus 12 ~IL~~L~~d~r~~~~eia~~lglS~~~v~~Ri~~L~~~GiI~~~~~~v~~~~lg~~~~a~v~v~~~~~~~~~~~~~~~~~ 91 (154)
T COG1522 12 RILRLLQEDARISNAELAERVGLSPSTVLRRIKRLEEEGVIKGYTAVLDPEKLGLDLTAFVEVKLERSLEDLEEFAEALA 91 (154)
T ss_pred HHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCceeeEEEEECHHHcCCCEEEEEEEEecCChhHHHHHHHHHh
Confidence 45555655555999999999999999999999999999988775 4421 3 566666665 666666665
Q ss_pred h
Q 026130 205 R 205 (243)
Q Consensus 205 ~ 205 (243)
.
T Consensus 92 ~ 92 (154)
T COG1522 92 K 92 (154)
T ss_pred C
Confidence 4
No 33
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=93.08 E-value=0.59 Score=37.66 Aligned_cols=65 Identities=15% Similarity=0.163 Sum_probs=52.6
Q ss_pred HHHHHHhc-CccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeC---CCCeEEEcHHHHHHHHHHH
Q 026130 139 FVEYIKKH-KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDD---RGKYIYISQAEMKAVADYI 203 (243)
Q Consensus 139 Fi~yIK~~-KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDD---RGKFIYIS~eEl~aVA~fI 203 (243)
++.+|-.. ..+..-+||..+|++.+-+-.-|..|++.|-|+=+-|. |.++||+|+.-...+....
T Consensus 36 vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~~~~ 104 (144)
T PRK03573 36 TLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQTCASDRRAKRIKLTEKAEPLISEVE 104 (144)
T ss_pred HHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeecCCCCcCeeeeEEChHHHHHHHHHH
Confidence 34555543 35667899999999999999999999999999999763 8999999998776665543
No 34
>PF13518 HTH_28: Helix-turn-helix domain
Probab=93.05 E-value=0.23 Score=33.11 Aligned_cols=47 Identities=17% Similarity=0.352 Sum_probs=36.7
Q ss_pred HHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCC
Q 026130 138 DFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGK 187 (243)
Q Consensus 138 ~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGK 187 (243)
..|.++.... .+.++|.+|||+..-|-.-|+.....| +.|+.+.+|+
T Consensus 4 ~iv~~~~~g~--s~~~~a~~~gis~~tv~~w~~~y~~~G-~~~l~~~~~r 50 (52)
T PF13518_consen 4 QIVELYLEGE--SVREIAREFGISRSTVYRWIKRYREGG-IEGLKPKKRR 50 (52)
T ss_pred HHHHHHHcCC--CHHHHHHHHCCCHhHHHHHHHHHHhcC-HHHhccCCCC
Confidence 3566666443 899999999998887777788888877 7899987653
No 35
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=93.00 E-value=0.26 Score=36.40 Aligned_cols=52 Identities=23% Similarity=0.340 Sum_probs=41.5
Q ss_pred HHHHHHHh-cCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeE
Q 026130 138 DFVEYIKK-HKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYI 189 (243)
Q Consensus 138 ~Fi~yIK~-~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFI 189 (243)
..++||+. +.-+.-.|||..|||+.-.+...+..|+.+|.|.=+=--||+=.
T Consensus 4 ~Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~~~~~~rG~~~ 56 (62)
T PF04703_consen 4 KILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLEKEGKVERSPVRRGKST 56 (62)
T ss_dssp CHHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEES-SSSSS-
T ss_pred HHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCCCcce
Confidence 46788888 88899999999999999999999999999999865444567643
No 36
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=92.74 E-value=0.96 Score=33.28 Aligned_cols=68 Identities=10% Similarity=0.186 Sum_probs=51.8
Q ss_pred HHHHHHHHHhc-CccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHh
Q 026130 136 LADFVEYIKKH-KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKR 205 (243)
Q Consensus 136 L~~Fi~yIK~~-KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~ 205 (243)
....++||..+ .-+.+.|||..+|++..-|-..|..|...|.|... ..|...++++.=+.-...|+..
T Consensus 7 ~~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~--~~~~~y~l~~~~~~~~~~~~~~ 75 (91)
T smart00346 7 GLAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQD--GQNGRYRLGPKVLELGQSYLSS 75 (91)
T ss_pred HHHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeec--CCCCceeecHHHHHHHHHHHhc
Confidence 34677888776 67999999999999999999999999999999763 2344456777655555555543
No 37
>PF13551 HTH_29: Winged helix-turn helix
Probab=92.57 E-value=0.4 Score=36.19 Aligned_cols=76 Identities=12% Similarity=0.309 Sum_probs=60.4
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeC--C-CCeEE-EcHHHHHHHHHHHHhc-----CCccHHHHHhhc-c
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDD--R-GKYIY-ISQAEMKAVADYIKRQ-----GRVSISHLASKS-N 219 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDD--R-GKFIY-IS~eEl~aVA~fI~~r-----GRVSi~eLa~~s-N 219 (243)
.+.++|..||++..-|-+-|+.....| +.|+.++ + |+.-- ||++....|-+++.+. ++.|...|+... .
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~~~G-~~~l~~~~~~~g~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~ 92 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYREGG-IEGLLPRKPRGGRPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIE 92 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHccc-HHHHHhccccCCCCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHH
Confidence 689999999999988888888888777 8889984 3 55554 9999999999999987 378888888743 4
Q ss_pred ccccccc
Q 026130 220 QFIDLET 226 (243)
Q Consensus 220 ~lI~L~p 226 (243)
....+.+
T Consensus 93 ~~~~~~~ 99 (112)
T PF13551_consen 93 EEFGIDV 99 (112)
T ss_pred hccCccC
Confidence 4444433
No 38
>PTZ00266 NIMA-related protein kinase; Provisional
Probab=92.39 E-value=1.1 Score=48.41 Aligned_cols=10 Identities=30% Similarity=0.797 Sum_probs=5.0
Q ss_pred cCCcchhhhh
Q 026130 32 AGGHYEAKAS 41 (243)
Q Consensus 32 ~~g~~~~kk~ 41 (243)
..|.++.+..
T Consensus 422 ~~g~~g~r~e 431 (1021)
T PTZ00266 422 VNGHYGGRVD 431 (1021)
T ss_pred ccCccccccc
Confidence 3455555543
No 39
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=91.96 E-value=0.35 Score=43.48 Aligned_cols=45 Identities=24% Similarity=0.342 Sum_probs=41.3
Q ss_pred HHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcc
Q 026130 135 LLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLS 179 (243)
Q Consensus 135 lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~Lt 179 (243)
.....+++|+.++.|.+.|||..||++..-+...|+.|+++|.|.
T Consensus 6 R~~~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~Le~~g~l~ 50 (256)
T PRK10434 6 RQAAILEYLQKQGKTSVEELAQYFDTTGTTIRKDLVILEHAGTVI 50 (256)
T ss_pred HHHHHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 567889999999999999999999999999999999999999653
No 40
>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=91.82 E-value=0.51 Score=34.76 Aligned_cols=46 Identities=22% Similarity=0.400 Sum_probs=36.3
Q ss_pred hHHHHHHHHHHhcCcc-chHHHHHHcCCC-hHHHHHHHHHHHhcCCcc
Q 026130 134 DLLADFVEYIKKHKCI-PLEDLAAEFKLR-TQECINRITSLENMGRLS 179 (243)
Q Consensus 134 ~lL~~Fi~yIK~~KvV-~LEdLA~~F~lr-tqd~I~RIq~Le~~g~Lt 179 (243)
..|.-+.+||..+-+. .+-|||.+||++ |.-|-..|+.|+..|.|.
T Consensus 10 ~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~kG~I~ 57 (65)
T PF01726_consen 10 EVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKALERKGYIR 57 (65)
T ss_dssp HHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCcCcc
Confidence 3455556688877665 568999999998 999999999999999875
No 41
>KOG1144 consensus Translation initiation factor 5B (eIF-5B) [Translation, ribosomal structure and biogenesis]
Probab=91.76 E-value=2.2 Score=45.48 Aligned_cols=28 Identities=25% Similarity=0.280 Sum_probs=22.3
Q ss_pred HHHHHHHhcCCcceeeeCCC----CeEEEcHH
Q 026130 167 NRITSLENMGRLSGVMDDRG----KYIYISQA 194 (243)
Q Consensus 167 ~RIq~Le~~g~LtGViDDRG----KFIYIS~e 194 (243)
.+++.|++.|...||-|..| +|||....
T Consensus 296 a~l~~ll~sg~~~~va~kdg~~kKrpiY~nKK 327 (1064)
T KOG1144|consen 296 AFLKQLLASGGGLPVADKDGDSKKRPIYANKK 327 (1064)
T ss_pred HHHHHHHhcCCCCCCCcccCCcccCccccccc
Confidence 45788999999999997665 89997643
No 42
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=91.53 E-value=0.7 Score=36.42 Aligned_cols=60 Identities=25% Similarity=0.366 Sum_probs=55.7
Q ss_pred chhHHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEE
Q 026130 132 DRDLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYI 191 (243)
Q Consensus 132 ~~~lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYI 191 (243)
...+++.+..-|..-|+|..--||..|+++-.-+-.-|.+|+..|.|.-|.-.++.-||.
T Consensus 25 dk~t~dkl~kEV~~~K~ITps~lserlkI~~SlAr~~Lr~L~~kG~Ik~V~~~~~q~IYt 84 (86)
T PRK09334 25 DEELLKRVAKEVKKEKIVTPYTLASKYGIKISVAKKVLRELEKRGVLVLYSKNRRTPIYV 84 (86)
T ss_pred CHHHHHHHHHHhccCcEEcHHHHHHHhcchHHHHHHHHHHHHHCCCEEEEecCCCeEEec
Confidence 345678888889999999999999999999999999999999999999999999999996
No 43
>PRK09954 putative kinase; Provisional
Probab=91.48 E-value=0.74 Score=42.44 Aligned_cols=54 Identities=15% Similarity=0.330 Sum_probs=44.7
Q ss_pred HHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcc--eeeeCCCCeE
Q 026130 136 LADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLS--GVMDDRGKYI 189 (243)
Q Consensus 136 L~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~Lt--GViDDRGKFI 189 (243)
-..++.+|+.+.-+...+||..+|++..-|-.+|+.|.+.|.|. |.+-+..+||
T Consensus 5 ~~~il~~l~~~~~~s~~~la~~l~~s~~~v~~~i~~L~~~g~i~~~~~~l~~~~~v 60 (362)
T PRK09954 5 EKEILAILRRNPLIQQNEIADILQISRSRVAAHIMDLMRKGRIKGKGYILTEQEYC 60 (362)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCcCCcEEEEcCCccE
Confidence 35688999999999999999999999999999999999999884 3333444444
No 44
>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=91.26 E-value=1 Score=32.23 Aligned_cols=58 Identities=17% Similarity=0.173 Sum_probs=45.9
Q ss_pred HHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHH
Q 026130 137 ADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQA 194 (243)
Q Consensus 137 ~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~e 194 (243)
.....++-.+.-+...|||...|++-..|-+-|+.|...|.|.-+-...-.|-.+.|+
T Consensus 11 ~~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y~a~~pe 68 (68)
T PF01978_consen 11 AKVYLALLKNGPATAEEIAEELGISRSTVYRALKSLEEKGLVEREEGRPKVYRAVPPE 68 (68)
T ss_dssp HHHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEEECCEEEEEE-HH
T ss_pred HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcCceEEEEEeCCC
Confidence 3455566688889999999999999999999999999999998777554445555543
No 45
>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=91.17 E-value=0.84 Score=32.79 Aligned_cols=49 Identities=14% Similarity=0.162 Sum_probs=37.6
Q ss_pred HHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEE
Q 026130 139 FVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYI 191 (243)
Q Consensus 139 Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYI 191 (243)
++..+....+. ..+||..||++..-|-.+|+.|.+.|-....- |++.|+
T Consensus 5 il~~L~~~~~~-~~eLa~~l~vS~~tv~~~l~~L~~~g~~i~~~---~~g~~l 53 (69)
T TIGR00122 5 LLALLADNPFS-GEKLGEALGMSRTAVNKHIQTLREWGVDVLTV---GKGYRL 53 (69)
T ss_pred HHHHHHcCCcC-HHHHHHHHCCCHHHHHHHHHHHHHCCCeEEec---CCceEe
Confidence 44556666655 99999999999999999999999988755443 444444
No 46
>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=91.07 E-value=0.75 Score=39.72 Aligned_cols=59 Identities=19% Similarity=0.206 Sum_probs=47.6
Q ss_pred HHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeee----CCC-CeEEEcHHH
Q 026130 137 ADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMD----DRG-KYIYISQAE 195 (243)
Q Consensus 137 ~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViD----DRG-KFIYIS~eE 195 (243)
...+.+|+.+.-+...+||..+|++..-|-..|+.|+..|.|.-..+ +|. .++++|+.-
T Consensus 4 ~~IL~~L~~~~~~t~~eLA~~lgis~~tV~~~L~~Le~~GlV~r~~~~~~~gRp~~~y~LT~~G 67 (203)
T TIGR02702 4 EDILSYLLKQGQATAAALAEALAISPQAVRRHLKDLETEGLIEYEAVVQGMGRPQYHYQLSRQG 67 (203)
T ss_pred HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEeecccCCCCCceEEEECcch
Confidence 35778888888899999999999999999999999999999976632 233 345888663
No 47
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=90.78 E-value=1.3 Score=38.74 Aligned_cols=68 Identities=16% Similarity=0.177 Sum_probs=56.3
Q ss_pred HHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceee---eCCCCeEEEcHHHHHHHHHHHHh
Q 026130 138 DFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVM---DDRGKYIYISQAEMKAVADYIKR 205 (243)
Q Consensus 138 ~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGVi---DDRGKFIYIS~eEl~aVA~fI~~ 205 (243)
.++-+|..+.-+...|||..+++...-+..-|+.|+..|-|+=.. |-|-++||+|+.-...+...+..
T Consensus 49 ~iL~~L~~~~~itq~eLa~~l~l~~sTvtr~l~rLE~kGlI~R~~~~~DrR~~~I~LTekG~~l~~~l~~~ 119 (185)
T PRK13777 49 HILWIAYHLKGASISEIAKFGVMHVSTAFNFSKKLEERGYLTFSKKEDDKRNTYIELTEKGEELLLETMEE 119 (185)
T ss_pred HHHHHHHhCCCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHHHHHH
Confidence 456677778888999999999998888888999999999999664 34999999999887777665543
No 48
>PRK10870 transcriptional repressor MprA; Provisional
Probab=90.72 E-value=1.3 Score=37.75 Aligned_cols=58 Identities=12% Similarity=0.179 Sum_probs=50.2
Q ss_pred cCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeC---CCCeEEEcHHHHHHHHHHH
Q 026130 146 HKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDD---RGKYIYISQAEMKAVADYI 203 (243)
Q Consensus 146 ~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDD---RGKFIYIS~eEl~aVA~fI 203 (243)
..-+..-|||..++++..-+-.-|..|++.|-|.=.-|. |.++|++|+.-...+...+
T Consensus 69 ~~~it~~eLa~~l~l~~~tvsr~v~rLe~kGlV~R~~~~~DrR~~~v~LT~~G~~~~~~i~ 129 (176)
T PRK10870 69 NHSIQPSELSCALGSSRTNATRIADELEKRGWIERRESDNDRRCLHLQLTEKGHEFLREVL 129 (176)
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHHHH
Confidence 456778899999999999999999999999999987663 8999999998877776654
No 49
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=90.70 E-value=0.47 Score=37.93 Aligned_cols=66 Identities=15% Similarity=0.191 Sum_probs=48.5
Q ss_pred HHHHHHh--cCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHH
Q 026130 139 FVEYIKK--HKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIK 204 (243)
Q Consensus 139 Fi~yIK~--~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~ 204 (243)
++.||-. ..-+.+.+||..+|++..-+-..|+.|...|-|.++-...|.|-...+-+--.+.+++.
T Consensus 14 ~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~~~g~~ggy~l~~~~~~it~~~v~~ 81 (130)
T TIGR02944 14 VLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTSKRGVEGGYTLARAPRDITVADIVK 81 (130)
T ss_pred HHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEecCCCCCChhhcCCccccCHHHHHH
Confidence 3445543 35789999999999999999999999999999988765566676665553222444443
No 50
>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=90.44 E-value=1.1 Score=31.51 Aligned_cols=47 Identities=13% Similarity=0.239 Sum_probs=41.6
Q ss_pred HHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeee
Q 026130 137 ADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMD 183 (243)
Q Consensus 137 ~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViD 183 (243)
..++.+|....-..+.+||..||++.+.+-..|+.|+..|-|+.+-+
T Consensus 13 ~~Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli~~~~~ 59 (61)
T PF12840_consen 13 LRILRLLASNGPMTVSELAEELGISQSTVSYHLKKLEEAGLIEVERE 59 (61)
T ss_dssp HHHHHHHHHCSTBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE
T ss_pred HHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEecc
Confidence 46788888999999999999999999999999999999999987654
No 51
>KOG1029 consensus Endocytic adaptor protein intersectin [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=90.42 E-value=1.6 Score=46.44 Aligned_cols=36 Identities=17% Similarity=0.213 Sum_probs=19.8
Q ss_pred HHHHHHHHHHHHhcCCccHHHH----Hhhcccccccccchh
Q 026130 193 QAEMKAVADYIKRQGRVSISHL----ASKSNQFIDLETKAQ 229 (243)
Q Consensus 193 ~eEl~aVA~fI~~rGRVSi~eL----a~~sN~lI~L~p~~~ 229 (243)
.++++.|-.|+-.. +..|++| -..-|.|+.|.|..+
T Consensus 471 kt~ie~~~~q~e~~-isei~qlqarikE~q~kl~~l~~Ekq 510 (1118)
T KOG1029|consen 471 KTEIEEVTKQRELM-ISEIDQLQARIKELQEKLQKLAPEKQ 510 (1118)
T ss_pred HHHHHHhhhHHHHH-HHHHHHHHHHHHHHHHHHHhhhhHHH
Confidence 45666666665432 1223333 344567888888766
No 52
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=90.32 E-value=0.72 Score=41.39 Aligned_cols=47 Identities=13% Similarity=0.252 Sum_probs=42.4
Q ss_pred hHHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcce
Q 026130 134 DLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSG 180 (243)
Q Consensus 134 ~lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtG 180 (243)
+.+...++||+.++.+.+.+||..||++..-+...|+.|++.|.|..
T Consensus 5 ~R~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le~~g~i~r 51 (251)
T PRK13509 5 QRHQILLELLAQLGFVTVEKVIERLGISPATARRDINKLDESGKLKK 51 (251)
T ss_pred HHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence 34677899999999999999999999999888899999999999854
No 53
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=90.25 E-value=0.75 Score=35.49 Aligned_cols=52 Identities=19% Similarity=0.416 Sum_probs=42.9
Q ss_pred hhHHHHHHHHHHhcC----ccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeC
Q 026130 133 RDLLADFVEYIKKHK----CIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDD 184 (243)
Q Consensus 133 ~~lL~~Fi~yIK~~K----vV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDD 184 (243)
..+-...++||+... =|.+.+|+..|++...+|..-|..|..+|.|.=-|||
T Consensus 46 ~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd 101 (102)
T PF08784_consen 46 SPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNEGHIYSTIDD 101 (102)
T ss_dssp -HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTTSEEESSST
T ss_pred CHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhCCeEecccCC
Confidence 345677888998833 3899999999999999999999999999999888887
No 54
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=90.23 E-value=0.95 Score=29.72 Aligned_cols=46 Identities=20% Similarity=0.293 Sum_probs=35.4
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHH
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVA 200 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA 200 (243)
.+.++|..+|++.. .|..+...|.|.++-++.|... .|++++..+.
T Consensus 2 ~~~e~a~~~gv~~~----tlr~~~~~g~l~~~~~~~~~~~-y~~~~v~~l~ 47 (49)
T cd04761 2 TIGELAKLTGVSPS----TLRYYERIGLLSPARTEGGYRL-YSDADLERLR 47 (49)
T ss_pred cHHHHHHHHCcCHH----HHHHHHHCCCCCCCcCCCCCEE-eCHHHHHHhh
Confidence 46789999999765 4667789999997766666665 4999987763
No 55
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=89.84 E-value=1.8 Score=27.85 Aligned_cols=45 Identities=16% Similarity=0.259 Sum_probs=35.5
Q ss_pred cchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHH
Q 026130 149 IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAV 199 (243)
Q Consensus 149 V~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aV 199 (243)
+.+.++|..||++.. .|..|...|.|.++.. |+-.+|+.+++...
T Consensus 2 lt~~e~a~~lgis~~----ti~~~~~~g~i~~~~~--g~~~~~~~~~l~~~ 46 (49)
T TIGR01764 2 LTVEEAAEYLGVSKD----TVYRLIHEGELPAYRV--GRHYRIPREDVDEY 46 (49)
T ss_pred CCHHHHHHHHCCCHH----HHHHHHHcCCCCeEEe--CCeEEEeHHHHHHH
Confidence 467899999999765 4566778999999886 66778898887653
No 56
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=89.55 E-value=1.2 Score=34.56 Aligned_cols=48 Identities=10% Similarity=0.156 Sum_probs=44.0
Q ss_pred HHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceee
Q 026130 135 LLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVM 182 (243)
Q Consensus 135 lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGVi 182 (243)
.|.+.=+||-.+.-+-+-+||.+|+++..-|-.=+..|...|+|.=|-
T Consensus 3 ~L~qlRd~l~~~gr~s~~~Ls~~~~~p~~~VeaMLe~l~~kGkverv~ 50 (78)
T PRK15431 3 SLIQVRDLLALRGRMEAAQISQTLNTPQPMINAMLQQLESMGKAVRIQ 50 (78)
T ss_pred cHHHHHHHHHHcCcccHHHHHHHHCcCHHHHHHHHHHHHHCCCeEeec
Confidence 477888999999999999999999998877777999999999999887
No 57
>PF11600 CAF-1_p150: Chromatin assembly factor 1 complex p150 subunit, N-terminal; InterPro: IPR021644 P150 is a polypeptide subunit of CAF-1, which functions in depositing newly synthesised and acetylated histones H3/H4 into chromatin during DNA replication and repair [].P150 is the HP1 interaction site of CAF-1 and lies within the N-terminal region of the protein [].
Probab=89.47 E-value=11 Score=33.31 Aligned_cols=8 Identities=13% Similarity=0.418 Sum_probs=3.2
Q ss_pred hhHHHHHH
Q 026130 133 RDLLADFV 140 (243)
Q Consensus 133 ~~lL~~Fi 140 (243)
+..|..|.
T Consensus 179 q~~~~~FF 186 (216)
T PF11600_consen 179 QARITSFF 186 (216)
T ss_pred HHHHHHHh
Confidence 33344443
No 58
>PRK00441 argR arginine repressor; Provisional
Probab=89.14 E-value=1.1 Score=38.04 Aligned_cols=57 Identities=32% Similarity=0.479 Sum_probs=45.1
Q ss_pred hHHHHHHHHHHhcCccchHHHHHHc-----CCChHHHHHH-HHHHHhcCCcceeeeCCCCeEEEcHHH
Q 026130 134 DLLADFVEYIKKHKCIPLEDLAAEF-----KLRTQECINR-ITSLENMGRLSGVMDDRGKYIYISQAE 195 (243)
Q Consensus 134 ~lL~~Fi~yIK~~KvV~LEdLA~~F-----~lrtqd~I~R-Iq~Le~~g~LtGViDDRGKFIYIS~eE 195 (243)
..+..+..+|+.+.++..++|+..| ++ ||.+|.| |.+| | |.=|-|..|+|+|.-|.+
T Consensus 4 ~R~~~I~~ll~~~~~~~q~eL~~~L~~~G~~v-SqaTisRDl~~L---~-lvKv~~~~G~~~Y~l~~~ 66 (149)
T PRK00441 4 SRHAKILEIINSKEIETQEELAEELKKMGFDV-TQATVSRDIKEL---K-LIKVLSNDGKYKYATISK 66 (149)
T ss_pred HHHHHHHHHHHHcCCCcHHHHHHHHHhcCCCc-CHHHHHHHHHHc---C-cEEeECCCCCEEEEeCcc
Confidence 3467788999999999999999995 86 7888887 5555 2 455778999999986554
No 59
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=88.95 E-value=0.93 Score=41.21 Aligned_cols=47 Identities=17% Similarity=0.297 Sum_probs=42.7
Q ss_pred hhHHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcc
Q 026130 133 RDLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLS 179 (243)
Q Consensus 133 ~~lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~Lt 179 (243)
...+...++||+.++.|.+.|||..||++..-+..-|..|++.|.|.
T Consensus 16 ~eR~~~Il~~L~~~~~vtv~eLa~~l~VS~~TIRRDL~~Le~~G~l~ 62 (269)
T PRK09802 16 SERREQIIQRLRQQGSVQVNDLSALYGVSTVTIRNDLAFLEKQGIAV 62 (269)
T ss_pred HHHHHHHHHHHHHcCCEeHHHHHHHHCCCHHHHHHHHHHHHhCCCeE
Confidence 34688999999999999999999999999988888899999999885
No 60
>PF09743 DUF2042: Uncharacterized conserved protein (DUF2042); InterPro: IPR018611 The ubiquitin fold modifier 1 (Ufm1) is the most recently discovered ubiquitin-like modifier whose conjugation (ufmylation) system is conserved in multicellular organisms. Ufm1 is known to covalently attach with cellular protein(s) via a specific E1-activating enzyme (Uba5), an E2-conjugating enzyme (Ufc1), and a E3-ligating enzyme []. This entry represents E3 UFM1-protein ligase 1.
Probab=88.88 E-value=1.5 Score=40.65 Aligned_cols=81 Identities=21% Similarity=0.311 Sum_probs=67.7
Q ss_pred HHHHHHHHH-HhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhc----CCc
Q 026130 135 LLADFVEYI-KKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQ----GRV 209 (243)
Q Consensus 135 lL~~Fi~yI-K~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~r----GRV 209 (243)
+-.+..+.| ...--|+|-||+...|+....|=.++..+..++. |++=-.|- .||..=++.||.-|+.+ |.|
T Consensus 56 L~~EI~~el~~~gGRv~~~dL~~~LnVd~~~ie~~~~~i~~~~~--~~~l~~ge--lit~~Yld~l~~Eine~Lqe~G~v 131 (272)
T PF09743_consen 56 LEKEIKDELYVHGGRVNLVDLAQALNVDLDHIERRAQEIVKSDK--SLQLVQGE--LITDSYLDSLAEEINEKLQESGQV 131 (272)
T ss_pred HHHHHHHHHHHcCCceEHHHHHHhcCcCHHHHHHHHHHHHhCCC--cEEEECCE--EccHHHHHHHHHHHHHHHHHcCeE
Confidence 455666666 5556799999999999999999999999999988 66666775 68999999999888777 999
Q ss_pred cHHHHHhhcc
Q 026130 210 SISHLASKSN 219 (243)
Q Consensus 210 Si~eLa~~sN 219 (243)
||++|+..-|
T Consensus 132 si~eLa~~~~ 141 (272)
T PF09743_consen 132 SISELAKQYD 141 (272)
T ss_pred eHHHHHHhcC
Confidence 9999997644
No 61
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=88.39 E-value=1.8 Score=38.81 Aligned_cols=55 Identities=18% Similarity=0.384 Sum_probs=46.0
Q ss_pred HHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEc
Q 026130 135 LLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYIS 192 (243)
Q Consensus 135 lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS 192 (243)
.....++||+.++.+.+.|||..||++..-+-.-|..|...|.|.= -.|..+|+.
T Consensus 5 R~~~Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~~L~~~~~l~r---~~Gga~~~~ 59 (240)
T PRK10411 5 RQQAIVDLLLNHTSLTTEALAEQLNVSKETIRRDLNELQTQGKILR---NHGRAKYIH 59 (240)
T ss_pred HHHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE---ecCeEEEec
Confidence 4567899999999999999999999999888889999999888753 366666654
No 62
>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=88.20 E-value=1.2 Score=30.11 Aligned_cols=36 Identities=22% Similarity=0.330 Sum_probs=28.3
Q ss_pred HHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHH
Q 026130 138 DFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLE 173 (243)
Q Consensus 138 ~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le 173 (243)
..|+-+...=-.++.+||..+||+...|..||+.|+
T Consensus 7 ~Il~~Lq~d~r~s~~~la~~lglS~~~v~~Ri~rL~ 42 (42)
T PF13404_consen 7 KILRLLQEDGRRSYAELAEELGLSESTVRRRIRRLE 42 (42)
T ss_dssp HHHHHHHH-TTS-HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHcCCccHHHHHHHHCcCHHHHHHHHHHhC
Confidence 456666666678899999999999999999999985
No 63
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=88.09 E-value=1.3 Score=39.94 Aligned_cols=47 Identities=15% Similarity=0.304 Sum_probs=40.6
Q ss_pred hHHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcce
Q 026130 134 DLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSG 180 (243)
Q Consensus 134 ~lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtG 180 (243)
..+...++|++.++.+.+.|||..|+++..-+-.-|..|+++|.|.-
T Consensus 5 ~R~~~Il~~l~~~~~~~~~ela~~l~vS~~TiRRdL~~Le~~g~l~r 51 (252)
T PRK10906 5 QRHDAIIELVKQQGYVSTEELVEHFSVSPQTIRRDLNDLAEQNKILR 51 (252)
T ss_pred HHHHHHHHHHHHcCCEeHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE
Confidence 35678899999999999999999999976665556999999999864
No 64
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=88.05 E-value=1.9 Score=31.50 Aligned_cols=45 Identities=20% Similarity=0.282 Sum_probs=38.7
Q ss_pred HHHHHHHHhcCc--cchHHHHHHcCCChHHHHHHHHHHHhcCCccee
Q 026130 137 ADFVEYIKKHKC--IPLEDLAAEFKLRTQECINRITSLENMGRLSGV 181 (243)
Q Consensus 137 ~~Fi~yIK~~Kv--V~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGV 181 (243)
...+.|++.+.= +.+-+||..+||++..|-.-+..|+..|.|.-.
T Consensus 9 ~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~~ 55 (68)
T smart00550 9 EKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCKQ 55 (68)
T ss_pred HHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence 577888888866 999999999999999777778999999998653
No 65
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=88.03 E-value=3.2 Score=33.28 Aligned_cols=78 Identities=19% Similarity=0.341 Sum_probs=58.6
Q ss_pred chhHHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhcCCccH
Q 026130 132 DRDLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRVSI 211 (243)
Q Consensus 132 ~~~lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~rGRVSi 211 (243)
|.+|=+..|+|+.... ...++|..|+++..-|..-++ -...|.+. --+||-- -| .++.+..||.....+++
T Consensus 4 S~DlR~rVl~~~~~g~--s~~eaa~~F~VS~~Tv~~W~k-~~~~G~~~--~k~r~~~-Ki---d~~~L~~~v~~~pd~tl 74 (119)
T PF01710_consen 4 SLDLRQRVLAYIEKGK--SIREAAKRFGVSRNTVYRWLK-RKETGDLE--PKPRGRK-KI---DRDELKALVEENPDATL 74 (119)
T ss_pred CHHHHHHHHHHHHccc--hHHHHHHHhCcHHHHHHHHHH-hccccccc--ccccccc-cc---cHHHHHHHHHHCCCcCH
Confidence 4456678899998876 788999999999888887777 55566542 2235531 22 36778999999999999
Q ss_pred HHHHhhc
Q 026130 212 SHLASKS 218 (243)
Q Consensus 212 ~eLa~~s 218 (243)
.||+...
T Consensus 75 ~Ela~~l 81 (119)
T PF01710_consen 75 RELAERL 81 (119)
T ss_pred HHHHHHc
Confidence 9999754
No 66
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=87.95 E-value=0.83 Score=39.45 Aligned_cols=45 Identities=20% Similarity=0.115 Sum_probs=40.2
Q ss_pred hHHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCc
Q 026130 134 DLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRL 178 (243)
Q Consensus 134 ~lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~L 178 (243)
...+..++||..+..+.+.|||.+||++..-+..=|..|...|.|
T Consensus 7 ~R~~~Il~~l~~~~~~~~~~La~~~~vS~~TiRRDl~~L~~~g~~ 51 (185)
T PRK04424 7 ERQKALQELIEENPFITDEELAEKFGVSIQTIRLDRMELGIPELR 51 (185)
T ss_pred HHHHHHHHHHHHCCCEEHHHHHHHHCcCHHHHHHHHHHHhcchHH
Confidence 356788999999999999999999999888887789999998876
No 67
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=87.77 E-value=3.6 Score=30.64 Aligned_cols=64 Identities=8% Similarity=0.165 Sum_probs=46.5
Q ss_pred hHHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHH
Q 026130 134 DLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADY 202 (243)
Q Consensus 134 ~lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~f 202 (243)
..+.+.+.++. +......+|+..-||+..-+...|..|+..|-|.+ .|...+||+.-...+-.|
T Consensus 6 ~Ii~~IL~~l~-~~~~~~t~i~~~~~L~~~~~~~yL~~L~~~gLI~~----~~~~Y~lTekG~~~l~~l 69 (77)
T PF14947_consen 6 EIIFDILKILS-KGGAKKTEIMYKANLNYSTLKKYLKELEEKGLIKK----KDGKYRLTEKGKEFLEEL 69 (77)
T ss_dssp HHHHHHHHHH--TT-B-HHHHHTTST--HHHHHHHHHHHHHTTSEEE----ETTEEEE-HHHHHHHHHH
T ss_pred HHHHHHHHHHH-cCCCCHHHHHHHhCcCHHHHHHHHHHHHHCcCeeC----CCCEEEECccHHHHHHHH
Confidence 34567777776 77778899999999999999999999999999844 555668999877665544
No 68
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=87.54 E-value=0.96 Score=40.55 Aligned_cols=47 Identities=15% Similarity=0.198 Sum_probs=39.8
Q ss_pred hHHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcce
Q 026130 134 DLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSG 180 (243)
Q Consensus 134 ~lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtG 180 (243)
+.....++|++.+..|.+.|||..||++..-+..=|..|+..+..+|
T Consensus 7 eR~~~I~~~l~~~~~v~v~eLa~~~~VS~~TIRRDL~~Le~~~~~~g 53 (252)
T PRK10681 7 ERIGQLLQALKRSDKLHLKDAAALLGVSEMTIRRDLNAHSAPVVLLG 53 (252)
T ss_pred HHHHHHHHHHHHcCCCcHHHHHHHhCCCHHHHHHHHHHhhcCeEEEC
Confidence 45678899999999999999999999987766677999997776544
No 69
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=87.46 E-value=2.9 Score=29.38 Aligned_cols=65 Identities=12% Similarity=0.146 Sum_probs=46.5
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhc-CCccHHHHHhhc
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQ-GRVSISHLASKS 218 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~r-GRVSi~eLa~~s 218 (243)
.+.++|..+|+++..+. .++..|.|.++..+.|.+-|.|+.++..+.....-+ --+|+..+....
T Consensus 2 s~~eva~~~gvs~~tlr----~~~~~gli~~~~~~~~g~r~y~~~dl~~l~~i~~lr~~g~~~~~i~~~l 67 (70)
T smart00422 2 TIGEVAKLAGVSVRTLR----YYERIGLLPPPIRTEGGYRLYSDEDLERLRFIKRLKELGFSLEEIKELL 67 (70)
T ss_pred CHHHHHHHHCcCHHHHH----HHHHCCCCCCCccCCCCCEecCHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 36789999999876644 446799999884444445578999998887666555 347777776543
No 70
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=87.36 E-value=3.7 Score=29.12 Aligned_cols=64 Identities=11% Similarity=0.198 Sum_probs=46.1
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHH--HHhcCCccHHHHHhhcc
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADY--IKRQGRVSISHLASKSN 219 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~f--I~~rGRVSi~eLa~~sN 219 (243)
.+.++|..+|+++.- |...+..|.|.+. .+.|.+=|.|++++..+... +++.| +|+.++....|
T Consensus 2 ~i~evA~~~gvs~~t----lR~~~~~g~l~~~-~~~~g~R~y~~~~l~~l~~i~~l~~~g-~~l~~i~~~l~ 67 (67)
T cd04764 2 TIKEVSEIIGVKPHT----LRYYEKEFNLYIP-RTENGRRYYTDEDIELLKKIKTLLEKG-LSIKEIKEILN 67 (67)
T ss_pred CHHHHHHHHCcCHHH----HHHHHHhcCCCCC-CCCCCceeeCHHHHHHHHHHHHHHHCC-CCHHHHHHHhC
Confidence 467899999998874 4456666667744 55677778899998877543 44456 89988887655
No 71
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=87.29 E-value=3.9 Score=40.31 Aligned_cols=79 Identities=20% Similarity=0.277 Sum_probs=61.9
Q ss_pred HHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHH---------HHHHHHHhcCC
Q 026130 138 DFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMK---------AVADYIKRQGR 208 (243)
Q Consensus 138 ~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~---------aVA~fI~~rGR 208 (243)
..+.+|..+..+...+||..+|++...|..-|..|++.|-|+= .|.+-++|++|++=.. .+.+++...|-
T Consensus 10 ~vL~~L~~~~~~s~~eLA~~l~l~~~tVt~~i~~Le~kGlV~~-~~~~~~~i~LTeeG~~~~~~g~pE~rl~~~l~~~~g 88 (489)
T PRK04172 10 KVLKALKELKEATLEELAEKLGLPPEAVMRAAEWLEEKGLVKV-EERVEEVYVLTEEGKKYAEEGLPERRLLNALKDGGE 88 (489)
T ss_pred HHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHHHhCCCEEE-EeeeEEEEEECHHHHHHHHhcCHHHHHHHhhHhcCC
Confidence 3455667777889999999999999999999999999998874 4667799999997332 34455556667
Q ss_pred ccHHHHHhh
Q 026130 209 VSISHLASK 217 (243)
Q Consensus 209 VSi~eLa~~ 217 (243)
+++.+|...
T Consensus 89 ~~~~el~~~ 97 (489)
T PRK04172 89 VSLDELKEA 97 (489)
T ss_pred cCHHHHHHh
Confidence 888887754
No 72
>PF11600 CAF-1_p150: Chromatin assembly factor 1 complex p150 subunit, N-terminal; InterPro: IPR021644 P150 is a polypeptide subunit of CAF-1, which functions in depositing newly synthesised and acetylated histones H3/H4 into chromatin during DNA replication and repair [].P150 is the HP1 interaction site of CAF-1 and lies within the N-terminal region of the protein [].
Probab=87.11 E-value=8.9 Score=33.90 Aligned_cols=12 Identities=8% Similarity=-0.031 Sum_probs=6.4
Q ss_pred Hhhhhccceecc
Q 026130 109 FEKWKGEFSIDA 120 (243)
Q Consensus 109 Y~kwK~~f~VEe 120 (243)
-..+-.+|..-.
T Consensus 179 q~~~~~FF~k~~ 190 (216)
T PF11600_consen 179 QARITSFFKKPK 190 (216)
T ss_pred HHHHHHHhCCCC
Confidence 345566675433
No 73
>KOG1029 consensus Endocytic adaptor protein intersectin [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=87.04 E-value=5.2 Score=42.88 Aligned_cols=12 Identities=17% Similarity=0.537 Sum_probs=7.1
Q ss_pred HHHHHHHHhcCc
Q 026130 137 ADFVEYIKKHKC 148 (243)
Q Consensus 137 ~~Fi~yIK~~Kv 148 (243)
++.|-|.+.+|-
T Consensus 429 qe~iv~~nak~~ 440 (1118)
T KOG1029|consen 429 QEWIVYLNAKKK 440 (1118)
T ss_pred HHHHHHHHHHHH
Confidence 456666666553
No 74
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=87.00 E-value=1.5 Score=30.57 Aligned_cols=60 Identities=13% Similarity=0.273 Sum_probs=43.0
Q ss_pred cchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhcCCccHHHHHhhcc
Q 026130 149 IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRVSISHLASKSN 219 (243)
Q Consensus 149 V~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~rGRVSi~eLa~~sN 219 (243)
+.|.+||..||++..-+...+..+.... + .+ |+...=+..+..+|... .+|+.+|+..|+
T Consensus 2 ~~~~~la~~~~~s~~~l~~~f~~~~~~s-~---~~------~~~~~r~~~a~~~l~~~-~~~~~~ia~~~g 61 (84)
T smart00342 2 LTLEDLAEALGMSPRHLQRLFKKETGTT-P---KQ------YLRDRRLERARRLLRDT-DLSVTEIALRVG 61 (84)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHhCcC-H---HH------HHHHHHHHHHHHHHHcC-CCCHHHHHHHhC
Confidence 4689999999998777666666552211 1 11 35556688899999876 889999998775
No 75
>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=86.99 E-value=1.3 Score=30.54 Aligned_cols=43 Identities=21% Similarity=0.301 Sum_probs=34.2
Q ss_pred CccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEc
Q 026130 147 KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYIS 192 (243)
Q Consensus 147 KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS 192 (243)
--+...+||..+|++..-+-..|+.|...|.|.-+ .+|+ |.|+
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~~--~~~~-~~l~ 66 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKELEEEGLISRR--GRGK-YRVN 66 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec--CCCe-EEeC
Confidence 45789999999999999999999999999887643 2455 4454
No 76
>PF12419 DUF3670: SNF2 Helicase protein ; InterPro: IPR022138 This domain family is found in bacteria, archaea and eukaryotes, and is approximately 140 amino acids in length. The family is found in association with PF00271 from PFAM, PF00176 from PFAM. Most of the proteins in this family are annotated as SNF2 helicases but there is little accompanying literature to confirm this.
Probab=86.98 E-value=1.1 Score=37.21 Aligned_cols=47 Identities=9% Similarity=0.319 Sum_probs=39.5
Q ss_pred HHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhcC---CccHHHHHhh
Q 026130 169 ITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQG---RVSISHLASK 217 (243)
Q Consensus 169 Iq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~rG---RVSi~eLa~~ 217 (243)
+..|.+.+ .|++==||+|||+.++++.++..|+.+.+ .+|+.|+.+.
T Consensus 89 f~~L~~~~--~~LV~~rg~WV~ld~~~l~~~~~~~~~~~~~~~lt~~e~Lr~ 138 (141)
T PF12419_consen 89 FEQLVEQK--RPLVRFRGRWVELDPEELRRALAFLEKAPKGEKLTLAEALRA 138 (141)
T ss_pred HHHHHHcC--CCeEEECCEEEEECHHHHHHHHHHHHhccccCCCCHHHHHHH
Confidence 45566555 58888899999999999999999999976 5999988764
No 77
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=86.81 E-value=1.4 Score=40.02 Aligned_cols=54 Identities=19% Similarity=0.385 Sum_probs=48.9
Q ss_pred ccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHH
Q 026130 148 CIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVAD 201 (243)
Q Consensus 148 vV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~ 201 (243)
-|.+-+||.+.|.+.|-+-..|++|+..|-|+=-+--+|.+|-||+.-++.+-+
T Consensus 19 ~~t~~ela~~l~~S~qta~R~l~~le~~~~I~R~~~~~Gq~i~iTekG~~~L~~ 72 (214)
T COG1339 19 KVTSSELAKRLGVSSQTAARKLKELEDEGYITRTISKRGQLITITEKGIDLLYK 72 (214)
T ss_pred cccHHHHHHHhCcCcHHHHHHHHhhccCCcEEEEecCCCcEEEehHhHHHHHHH
Confidence 367889999999999999999999999999999999999999999987766544
No 78
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=86.60 E-value=1.8 Score=27.99 Aligned_cols=31 Identities=19% Similarity=0.328 Sum_probs=28.2
Q ss_pred cchHHHHHHcCCChHHHHHHHHHHHhcCCcc
Q 026130 149 IPLEDLAAEFKLRTQECINRITSLENMGRLS 179 (243)
Q Consensus 149 V~LEdLA~~F~lrtqd~I~RIq~Le~~g~Lt 179 (243)
+...|||..+|++.+.+-..|..|.+.|.|.
T Consensus 9 ~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~ 39 (48)
T smart00419 9 LTRQEIAELLGLTRETVSRTLKRLEKEGLIS 39 (48)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 4568999999999999999999999999885
No 79
>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=86.59 E-value=0.49 Score=34.40 Aligned_cols=24 Identities=33% Similarity=0.735 Sum_probs=20.4
Q ss_pred HHHHHHHHHhcCCccHHHHHhhcc
Q 026130 196 MKAVADYIKRQGRVSISHLASKSN 219 (243)
Q Consensus 196 l~aVA~fI~~rGRVSi~eLa~~sN 219 (243)
|..|-+||+++|+||+.+|+...|
T Consensus 2 L~~i~~~l~~~~~~S~~eLa~~~~ 25 (69)
T PF09012_consen 2 LQEIRDYLRERGRVSLAELAREFG 25 (69)
T ss_dssp CHHHHHHHHHS-SEEHHHHHHHTT
T ss_pred HHHHHHHHHHcCCcCHHHHHHHHC
Confidence 457899999999999999999876
No 80
>PRK11050 manganese transport regulator MntR; Provisional
Probab=86.49 E-value=5.5 Score=33.21 Aligned_cols=65 Identities=12% Similarity=0.116 Sum_probs=47.1
Q ss_pred HHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHH
Q 026130 136 LADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIK 204 (243)
Q Consensus 136 L~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~ 204 (243)
|..+..+|-..--+.+.+||..||++..-+-..|+.|+..|.|+ -.+++-+++|+.-..- ...+.
T Consensus 39 l~~I~~~l~~~~~~t~~eLA~~l~is~stVsr~l~~Le~~GlI~---r~~~~~v~LT~~G~~l-~~~~~ 103 (152)
T PRK11050 39 VELIADLIAEVGEARQVDIAARLGVSQPTVAKMLKRLARDGLVE---MRPYRGVFLTPEGEKL-AQESR 103 (152)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE---EecCCceEECchHHHH-HHHHH
Confidence 33444456566677899999999999999999999999997553 2345668999865443 33443
No 81
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=86.29 E-value=3.8 Score=30.49 Aligned_cols=66 Identities=14% Similarity=0.244 Sum_probs=51.4
Q ss_pred HHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeC---CCCeEEEcHHHHHHHHHHHH
Q 026130 139 FVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDD---RGKYIYISQAEMKAVADYIK 204 (243)
Q Consensus 139 Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDD---RGKFIYIS~eEl~aVA~fI~ 204 (243)
++.+|...--+...+||..++++..-+-.-|+.|++.|-|.=..|. |.++|++|+.--..+.....
T Consensus 27 ~L~~l~~~~~~~~~~la~~l~i~~~~vt~~l~~Le~~glv~r~~~~~DrR~~~l~lT~~G~~~~~~~~~ 95 (126)
T COG1846 27 VLLALYEAGGITVKELAERLGLDRSTVTRLLKRLEDKGLIERLRDPEDRRAVLVRLTEKGRELLEQLLP 95 (126)
T ss_pred HHHHHHHhCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCeeecCCccccceeeEEECccHHHHHHHhcc
Confidence 3334433333322999999999999999999999999999988873 78899999987776666554
No 82
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=85.98 E-value=2.6 Score=32.75 Aligned_cols=58 Identities=24% Similarity=0.384 Sum_probs=50.5
Q ss_pred chhHHHHHHH-HHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeE
Q 026130 132 DRDLLADFVE-YIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYI 189 (243)
Q Consensus 132 ~~~lL~~Fi~-yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFI 189 (243)
....|...|+ ||+...-|--..||..++++.--|-|-++.|++.|-|.++--..|-||
T Consensus 6 q~~IL~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~~Le~lGlve~~p~~s~Gri 64 (78)
T PF03444_consen 6 QREILKALVELYIETGEPVGSKTIAEELGRSPATIRNEMADLEELGLVESQPHPSGGRI 64 (78)
T ss_pred HHHHHHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHHHHHHHCCCccCCCCCCCCCC
Confidence 3456778887 999999999999999999999999999999999999988876666555
No 83
>PF12728 HTH_17: Helix-turn-helix domain
Probab=85.66 E-value=3.8 Score=27.56 Aligned_cols=45 Identities=9% Similarity=0.209 Sum_probs=36.9
Q ss_pred cchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHH
Q 026130 149 IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAV 199 (243)
Q Consensus 149 V~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aV 199 (243)
..+.|+|..+|++.+- |..|...|.|.++- -|+.+||+..++.+.
T Consensus 2 lt~~e~a~~l~is~~t----v~~~~~~g~i~~~~--~g~~~~~~~~~l~~~ 46 (51)
T PF12728_consen 2 LTVKEAAELLGISRST----VYRWIRQGKIPPFK--IGRKWRIPKSDLDRW 46 (51)
T ss_pred CCHHHHHHHHCcCHHH----HHHHHHcCCCCeEE--eCCEEEEeHHHHHHH
Confidence 4678999999997765 56777899999996 788899999887754
No 84
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=85.51 E-value=4.8 Score=31.20 Aligned_cols=65 Identities=11% Similarity=0.243 Sum_probs=47.8
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHH--HHHHHhcCCccHHHHHhhcc
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAV--ADYIKRQGRVSISHLASKSN 219 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aV--A~fI~~rGRVSi~eLa~~sN 219 (243)
.+.++|..||+++.- |...+..|.|..+-.+.|.|=|.|++++..+ ..+++..| +|++++...-.
T Consensus 2 ti~eva~~~gvs~~t----lR~ye~~Gll~~~~~~~~g~R~y~~~di~~l~~i~~lr~~g-~~l~~i~~~~~ 68 (103)
T cd01106 2 TVGEVAKLTGVSVRT----LHYYDEIGLLKPSRRTENGYRLYTEEDLERLQQILFLKELG-FSLKEIKELLK 68 (103)
T ss_pred CHHHHHHHHCcCHHH----HHHHHHCCCCCCCccCCCCceeeCHHHHHHHHHHHHHHHcC-CCHHHHHHHHH
Confidence 357899999997765 3455678988766556667888999999876 34566666 99988776543
No 85
>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=85.39 E-value=3.3 Score=35.29 Aligned_cols=57 Identities=18% Similarity=0.212 Sum_probs=42.0
Q ss_pred HHHHHHHHHhcCc-cchHHHHHHcCCC-hHHHHHHHHHHHhcCCcceeeeCCCCeEEEcH
Q 026130 136 LADFVEYIKKHKC-IPLEDLAAEFKLR-TQECINRITSLENMGRLSGVMDDRGKYIYISQ 193 (243)
Q Consensus 136 L~~Fi~yIK~~Kv-V~LEdLA~~F~lr-tqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~ 193 (243)
|.-...|+..+.+ ..+.+||..||++ +.-|-.+|+.|++.|-|+.. +.+.+.|.+++
T Consensus 12 L~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~g~i~~~-~~~~~~~~~~~ 70 (199)
T TIGR00498 12 LDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALERKGYIERD-PGKPRAIRILD 70 (199)
T ss_pred HHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHHHCCCEecC-CCCCCeEEeCC
Confidence 3333345554444 6689999999999 99999999999999999886 33444566654
No 86
>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=85.25 E-value=3.1 Score=29.96 Aligned_cols=46 Identities=15% Similarity=0.237 Sum_probs=36.6
Q ss_pred hHHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcc
Q 026130 134 DLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLS 179 (243)
Q Consensus 134 ~lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~Lt 179 (243)
++|............|..-|||..||++..-|-+-|+.|...|-|.
T Consensus 8 ~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV~ 53 (60)
T PF01325_consen 8 DYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLAEKGLVE 53 (60)
T ss_dssp HHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHHHCCCEE
Confidence 3444444444578899999999999999999999999999999764
No 87
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=85.18 E-value=2.6 Score=30.07 Aligned_cols=48 Identities=17% Similarity=0.313 Sum_probs=35.7
Q ss_pred ccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHH
Q 026130 148 CIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKA 198 (243)
Q Consensus 148 vV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~a 198 (243)
-+..++||...|++.+-+-.-|+.|..+|.|. -.+|+++-..++-|.+
T Consensus 28 ~lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I~---~~~~~i~I~d~~~L~~ 75 (76)
T PF13545_consen 28 PLTQEEIADMLGVSRETVSRILKRLKDEGIIE---VKRGKIIILDPERLEE 75 (76)
T ss_dssp ESSHHHHHHHHTSCHHHHHHHHHHHHHTTSEE---EETTEEEESSHHHHHH
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE---EcCCEEEECCHHHHhc
Confidence 35689999999999999999999999998665 2445444445555543
No 88
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=84.95 E-value=3.5 Score=30.70 Aligned_cols=49 Identities=10% Similarity=0.158 Sum_probs=37.5
Q ss_pred hHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHH
Q 026130 151 LEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADY 202 (243)
Q Consensus 151 LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~f 202 (243)
+.+||..||++..-+-..|+.|++.|.|.= .+++++++|+.-..-+..+
T Consensus 2 ~~ela~~l~is~stvs~~l~~L~~~glI~r---~~~~~~~lT~~g~~~~~~~ 50 (96)
T smart00529 2 TSEIAERLNVSPPTVTQMLKKLEKDGLVEY---EPYRGITLTEKGRRLARRL 50 (96)
T ss_pred HHHHHHHhCCChHHHHHHHHHHHHCCCEEE---cCCCceEechhHHHHHHHH
Confidence 468999999999999999999999854433 2447899999665544433
No 89
>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=84.88 E-value=4.1 Score=27.87 Aligned_cols=47 Identities=15% Similarity=0.232 Sum_probs=38.8
Q ss_pred HHHHHHHhcCc--cchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeC
Q 026130 138 DFVEYIKKHKC--IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDD 184 (243)
Q Consensus 138 ~Fi~yIK~~Kv--V~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDD 184 (243)
..+.||..+.= +.+.+||..++++.+-+-.-|+.|++.|-|+=.-|.
T Consensus 9 ~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~~~~ 57 (62)
T PF12802_consen 9 RVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKKGLVERERDP 57 (62)
T ss_dssp HHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE-S
T ss_pred HHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCC
Confidence 45566776666 899999999999999999999999999999877764
No 90
>KOG2235 consensus Uncharacterized conserved protein [Function unknown]
Probab=84.88 E-value=1.8 Score=44.92 Aligned_cols=60 Identities=30% Similarity=0.465 Sum_probs=50.1
Q ss_pred CCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHH-HHHHHHhc-CCccHHHHHhhcc
Q 026130 159 KLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKA-VADYIKRQ-GRVSISHLASKSN 219 (243)
Q Consensus 159 ~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~a-VA~fI~~r-GRVSi~eLa~~sN 219 (243)
.|+--.||.-+|.|.+.-+|--|..-.||= ||||+++.. +-+-|--+ ||||+.||+..-|
T Consensus 23 kLSerNcvEivqkLie~~~ldvvhT~dGke-YIT~~hLe~EI~dEl~v~GgRaslvDla~tln 84 (776)
T KOG2235|consen 23 KLSERNCVEIVQKLIESHRLDVVHTRDGKE-YITPNHLETEIKDELIVAGGRASLVDLAVTLN 84 (776)
T ss_pred HhhhccHHHHHHHHHHhhhcceEEecCCcc-ccCHHHHHHHHHHHHHHhCCcchhHHHHHHhC
Confidence 466678999999999999999999989984 999999975 44455555 5999999999888
No 91
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=84.87 E-value=4.1 Score=34.39 Aligned_cols=80 Identities=21% Similarity=0.309 Sum_probs=64.8
Q ss_pred cccchhHHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCC-eEEEcHHHHHHHHHHHHhcC
Q 026130 129 QDGDRDLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGK-YIYISQAEMKAVADYIKRQG 207 (243)
Q Consensus 129 ~~~~~~lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGK-FIYIS~eEl~aVA~fI~~rG 207 (243)
.++...+....|++++.+.-+.+.||+..+|++-.-+-..+.+|.+.|.|.. -|+ =||.|+ .++-+|.+.+-
T Consensus 7 ~eer~eLk~rIvElVRe~GRiTi~ql~~~TGasR~Tvk~~lreLVa~G~l~~----~G~~GvF~se---qA~~dw~~~~~ 79 (127)
T PF06163_consen 7 PEEREELKARIVELVREHGRITIKQLVAKTGASRNTVKRYLRELVARGDLYR----HGRSGVFPSE---QARKDWDKARK 79 (127)
T ss_pred HHHHHHHHHHHHHHHHHcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCCeEe----CCCccccccH---HHHHHHHHhHH
Confidence 3456778899999999999999999999999999999999999999998875 466 477776 46677777776
Q ss_pred CccHHHHH
Q 026130 208 RVSISHLA 215 (243)
Q Consensus 208 RVSi~eLa 215 (243)
......|.
T Consensus 80 ~~~~~~~~ 87 (127)
T PF06163_consen 80 KLVDPDLI 87 (127)
T ss_pred hhccchhh
Confidence 55544443
No 92
>PRK00215 LexA repressor; Validated
Probab=84.86 E-value=3.3 Score=35.45 Aligned_cols=48 Identities=13% Similarity=0.126 Sum_probs=39.6
Q ss_pred cCccchHHHHHHcCC-ChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHH
Q 026130 146 HKCIPLEDLAAEFKL-RTQECINRITSLENMGRLSGVMDDRGKYIYISQA 194 (243)
Q Consensus 146 ~KvV~LEdLA~~F~l-rtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~e 194 (243)
..-..+.|||.+||+ ++.-+-..|+.|++.|.|+..-++ ++-+.|+++
T Consensus 21 ~~~~s~~ela~~~~~~~~~tv~~~l~~L~~~g~i~~~~~~-~r~~~l~~~ 69 (205)
T PRK00215 21 GYPPSRREIADALGLRSPSAVHEHLKALERKGFIRRDPGR-SRAIEVAAP 69 (205)
T ss_pred CCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEeCCCC-cceEEeccc
Confidence 445679999999999 788888899999999999987655 667777554
No 93
>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=84.44 E-value=4.1 Score=28.84 Aligned_cols=53 Identities=15% Similarity=0.292 Sum_probs=37.5
Q ss_pred HHHHHHHHHhcC-----cc-chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeE
Q 026130 136 LADFVEYIKKHK-----CI-PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYI 189 (243)
Q Consensus 136 L~~Fi~yIK~~K-----vV-~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFI 189 (243)
...+.+.|.... .+ ...+||..||++..-+..-+..|..+|.|+- ..-+|-||
T Consensus 6 ~~~l~~~I~~g~~~~g~~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~~-~~~~G~~V 64 (64)
T PF00392_consen 6 YDQLRQAILSGRLPPGDRLPSERELAERYGVSRTTVREALRRLEAEGLIER-RPGRGTFV 64 (64)
T ss_dssp HHHHHHHHHTTSS-TTSBE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE-ETTTEEEE
T ss_pred HHHHHHHHHcCCCCCCCEeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEEE-ECCceEEC
Confidence 345555555432 33 7889999999999999999999999998863 34455554
No 94
>PHA02943 hypothetical protein; Provisional
Probab=84.15 E-value=9.4 Score=33.51 Aligned_cols=71 Identities=11% Similarity=0.166 Sum_probs=58.4
Q ss_pred chhHHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCe--EEEcHHHH-HHHHHHHHh
Q 026130 132 DRDLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKY--IYISQAEM-KAVADYIKR 205 (243)
Q Consensus 132 ~~~lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKF--IYIS~eEl-~aVA~fI~~ 205 (243)
-.+-+.++++|| ..=+....+||..+|++...+-.-|.-|+.+|.|.-|= +|++ -+|.++.+ +.|+.|++.
T Consensus 9 v~~R~~eILE~L-k~G~~TtseIAkaLGlS~~qa~~~LyvLErEG~VkrV~--~G~~tyw~l~~day~~~v~~~~Re 82 (165)
T PHA02943 9 VHTRMIKTLRLL-ADGCKTTSRIANKLGVSHSMARNALYQLAKEGMVLKVE--IGRAAIWCLDEDAYTNLVFEIKRE 82 (165)
T ss_pred HHHHHHHHHHHH-hcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCceEEEe--ecceEEEEEChHHHHHHHHHHHHH
Confidence 345678999999 77788899999999999999999999999999999976 7764 55777664 456666664
No 95
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=84.08 E-value=5.4 Score=33.97 Aligned_cols=69 Identities=12% Similarity=0.228 Sum_probs=52.2
Q ss_pred hcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHH--HHHHhcCCccHHHHHhhcc
Q 026130 145 KHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVA--DYIKRQGRVSISHLASKSN 219 (243)
Q Consensus 145 ~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA--~fI~~rGRVSi~eLa~~sN 219 (243)
.+++..+.++|..+|+++. .|.--+..|.|.++-++.|-.+| |+..+..|. ..++.-| +|+.++....+
T Consensus 8 ~~~~~~IgevAk~~gvs~~----TlRyYE~~GLi~~~r~~~g~R~Y-~~~~i~~L~~I~~lr~lG-~sL~eIk~ll~ 78 (154)
T PRK15002 8 IKALLTPGEVAKRSGVAVS----ALHFYESKGLITSIRNSGNQRRY-KRDVLRYVAIIKIAQRIG-IPLATIGEAFG 78 (154)
T ss_pred hcccccHHHHHHHHCcCHH----HHHHHHHCCCCCCccCCCCCEEE-CHHHHHHHHHHHHHHHcC-CCHHHHHHHHH
Confidence 3567889999999999764 46778999999997766665555 888887763 3444557 99988887655
No 96
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=84.00 E-value=5.8 Score=30.62 Aligned_cols=65 Identities=12% Similarity=0.270 Sum_probs=52.2
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHH--HHHHhcCCccHHHHHhhcc
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVA--DYIKRQGRVSISHLASKSN 219 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA--~fI~~rGRVSi~eLa~~sN 219 (243)
.+.++|..||+++. .|.--+..|.|.++-.+.|.|=|-|++++..|. .+++.-| +|+.++....+
T Consensus 2 ti~eva~~~gvs~~----tLRyye~~Gll~p~~~~~~gyR~Y~~~~l~~l~~I~~lr~~G-~~l~~I~~~l~ 68 (96)
T cd04768 2 TIGEFAKLAGVSIR----TLRHYDDIGLFKPAKIAENGYRYYSYAQLYQLQFILFLRELG-FSLAEIKELLD 68 (96)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHCCCCCCCccCCCCeeeCCHHHHHHHHHHHHHHHcC-CCHHHHHHHHh
Confidence 46799999999764 466678889999998887889999999998775 4666667 99988876544
No 97
>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=83.92 E-value=2.6 Score=28.87 Aligned_cols=47 Identities=17% Similarity=0.240 Sum_probs=39.5
Q ss_pred HHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeC
Q 026130 138 DFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDD 184 (243)
Q Consensus 138 ~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDD 184 (243)
.++.+|-.+.=+.+.+||..++++..-+-.-|+.|+..|-|.=..|.
T Consensus 7 ~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~~~~ 53 (59)
T PF01047_consen 7 RILRILYENGGITQSELAEKLGISRSTVTRIIKRLEKKGLIERERDP 53 (59)
T ss_dssp HHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEET
T ss_pred HHHHHHHHcCCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEeccCC
Confidence 35566777777999999999999999999999999999998766653
No 98
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=83.27 E-value=3.3 Score=38.02 Aligned_cols=51 Identities=16% Similarity=0.215 Sum_probs=42.5
Q ss_pred HHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCC
Q 026130 136 LADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRG 186 (243)
Q Consensus 136 L~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRG 186 (243)
+...+.+|.....+...+||..||++..-|-.+|+.|...|........+|
T Consensus 6 ~~~il~~L~~~~~~s~~~LA~~lgvsr~tV~~~l~~L~~~G~~i~~~~~~G 56 (319)
T PRK11886 6 MLQLLSLLADGDFHSGEQLGEELGISRAAIWKHIQTLEEWGLDIFSVKGKG 56 (319)
T ss_pred HHHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCceEEecCCe
Confidence 467888888888999999999999999999999999999998443333344
No 99
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=83.26 E-value=4.9 Score=31.71 Aligned_cols=67 Identities=15% Similarity=0.171 Sum_probs=50.7
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhc-CCccHHHHHhhccc
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQ-GRVSISHLASKSNQ 220 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~r-GRVSi~eLa~~sN~ 220 (243)
.+.++|..+|+++.- |...+..|.|..+-++.|.|-|.|+.++..+-....-+ --+|++++....+.
T Consensus 2 ~i~eva~~~gvs~~t----lR~ye~~Gll~p~~~~~~g~R~Y~~~dl~~l~~I~~lr~~G~~l~~I~~~l~~ 69 (108)
T cd04773 2 TIGELAHLLGVPPST----LRHWEKEGLLSPDREPETGYRVYDPSDVRDARLIHLLRRGGYLLEQIATVVEQ 69 (108)
T ss_pred CHHHHHHHHCcCHHH----HHHHHHCCCCCCCcCCCCCceeeCHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
Confidence 467899999997765 44557789999988888899999999998765433333 23798888776654
No 100
>PF05158 RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; InterPro: IPR007832 The family comprises a subunit specific to RNA Pol III, the tRNA specific polymerase. The C34 subunit of Saccharomyces cerevisiae RNA Pol III is part of a subcomplex of three subunits which have no counterpart in the other two nuclear RNA polymerases. This subunit interacts with TFIIIB70 and therefore participates in Pol III recruitment [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2DK8_A 2DK5_A 2YU3_A.
Probab=83.20 E-value=6.7 Score=37.17 Aligned_cols=82 Identities=29% Similarity=0.281 Sum_probs=60.8
Q ss_pred HHHHHHHHHHhcCccchHHHHHH-cCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEE-------------cHHHHHHHH
Q 026130 135 LLADFVEYIKKHKCIPLEDLAAE-FKLRTQECINRITSLENMGRLSGVMDDRGKYIYI-------------SQAEMKAVA 200 (243)
Q Consensus 135 lL~~Fi~yIK~~KvV~LEdLA~~-F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYI-------------S~eEl~aVA 200 (243)
+|+-+..+ -..+.+..+||... .++..++.+.-|+.|+..|.|..+- ..|+.+|- |++|. -|=
T Consensus 14 l~~~~~~~-~~~~~~~~~~L~~~~~~~~~~~~~~~in~Ll~~~~~~~~~-~~~~l~~~~~~~~~a~k~~~l~~~e~-lvy 90 (327)
T PF05158_consen 14 LLELCREN-PSPKGFSQEDLQQLIPGLDLQELVKAINELLSSGLLKLLK-KGGGLSYKAVSEEEAKKLKGLSDEER-LVY 90 (327)
T ss_dssp HHHHHHH----SS-EEHHHHHHH-TTS-HHHHHHHHHHHHHHTSEEEEE--SSSEEEEE--SSS-----SSSCCHH-HHH
T ss_pred HHHHHHHh-cCCCCcCHHHHHhhcCCCCHHHHHHHHHHHHhCCCEEEEE-cCCEEEEEEeCHHHHhhhcCCCHHHH-HHH
Confidence 34444444 44799999999999 6899999999999999999999888 55555554 56666 788
Q ss_pred HHHHhcCCccH--HHHHhhcc
Q 026130 201 DYIKRQGRVSI--SHLASKSN 219 (243)
Q Consensus 201 ~fI~~rGRVSi--~eLa~~sN 219 (243)
+.|..-|.--| .+|...+|
T Consensus 91 ~~I~~ag~~GIw~~~i~~~t~ 111 (327)
T PF05158_consen 91 QLIEEAGNKGIWTKDIKKKTN 111 (327)
T ss_dssp HHHHHHTTT-EEHHHHHHHCT
T ss_pred HHHHHhCCCCCcHHHHHHHcC
Confidence 99999998665 78888887
No 101
>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=83.17 E-value=2.9 Score=28.13 Aligned_cols=41 Identities=15% Similarity=0.327 Sum_probs=34.3
Q ss_pred HHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcc
Q 026130 138 DFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLS 179 (243)
Q Consensus 138 ~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~Lt 179 (243)
..+.+|.. +-..+.|||.+||++..-+-.-+..|...|-|+
T Consensus 6 ~Il~~L~~-~~~~~~el~~~l~~s~~~vs~hL~~L~~~glV~ 46 (47)
T PF01022_consen 6 RILKLLSE-GPLTVSELAEELGLSQSTVSHHLKKLREAGLVE 46 (47)
T ss_dssp HHHHHHTT-SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHh-CCCchhhHHHhccccchHHHHHHHHHHHCcCee
Confidence 46677777 667889999999999999999999999999764
No 102
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=83.09 E-value=4.8 Score=31.13 Aligned_cols=65 Identities=12% Similarity=0.253 Sum_probs=49.4
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHH--HHHHHhcCCccHHHHHhhcc
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAV--ADYIKRQGRVSISHLASKSN 219 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aV--A~fI~~rGRVSi~eLa~~sN 219 (243)
.+-++|..||+++.- |.-.+..|.|.+...+.|.|=|-|++++..+ ..+++.-| +|+.++....+
T Consensus 2 ~i~eva~~~gvs~~t----lR~ye~~Gll~p~~~~~~gyR~Y~~~~~~~l~~I~~lr~~G-~~l~eI~~~l~ 68 (97)
T cd04782 2 TTGEFAKLCGISKQT----LFHYDKIGLFKPEIVKENGYRYYTLEQFEQLDIILLLKELG-ISLKEIKDYLD 68 (97)
T ss_pred CHHHHHHHHCcCHHH----HHHHHHCCCCCCCccCCCCCccCCHHHHHHHHHHHHHHHcC-CCHHHHHHHHh
Confidence 367899999997654 5566789999998766677888899997765 45667777 99988876443
No 103
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=83.02 E-value=5.6 Score=31.98 Aligned_cols=65 Identities=14% Similarity=0.213 Sum_probs=50.0
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHH--HHHHHhcCCccHHHHHhhcc
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAV--ADYIKRQGRVSISHLASKSN 219 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aV--A~fI~~rGRVSi~eLa~~sN 219 (243)
.+-++|..||+++.- |.-.+..|.|.....+.|.|-|-|++.+..| ..+++.-| +|+.++....+
T Consensus 2 ~I~e~a~~~gvs~~t----lR~Ye~~GLl~~~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G-~sL~eI~~~l~ 68 (126)
T cd04783 2 TIGELAKAAGVNVET----IRYYQRRGLLPEPPRPEGGYRRYPEETVTRLRFIKRAQELG-FTLDEIAELLE 68 (126)
T ss_pred CHHHHHHHHCcCHHH----HHHHHHCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcC-CCHHHHHHHHh
Confidence 467899999997754 4677999999855556778999999998875 34556667 99988876554
No 104
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=82.58 E-value=6 Score=33.63 Aligned_cols=69 Identities=17% Similarity=0.207 Sum_probs=51.2
Q ss_pred HHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceee--e-CCCCeEEEcHHHHHHHHHHHHhc
Q 026130 138 DFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVM--D-DRGKYIYISQAEMKAVADYIKRQ 206 (243)
Q Consensus 138 ~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGVi--D-DRGKFIYIS~eEl~aVA~fI~~r 206 (243)
..++.+-.+.++.-+|||...||++.+|-.-+..|..+|.++-.- | +.|.+.|+=-=.+..+-+.|+.+
T Consensus 18 ~Vl~aL~~~~~~tdEeLa~~Lgi~~~~VRk~L~~L~e~~Lv~~~r~r~~~~gw~~Y~w~i~~~~i~d~Ik~~ 89 (158)
T TIGR00373 18 LVLFSLGIKGEFTDEEISLELGIKLNEVRKALYALYDAGLADYKRRKDDETGWYEYTWRINYEKALDVLKRK 89 (158)
T ss_pred HHHHHHhccCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCceeeeeeecCCCcEEEEEEeCHHHHHHHHHHH
Confidence 445556678899999999999999999999999999999996443 3 45766654112555566666655
No 105
>PF14493 HTH_40: Helix-turn-helix domain
Probab=82.57 E-value=5.3 Score=30.42 Aligned_cols=72 Identities=17% Similarity=0.253 Sum_probs=61.4
Q ss_pred CccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhcCCccHHHHHhhccccccc
Q 026130 147 KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRVSISHLASKSNQFIDL 224 (243)
Q Consensus 147 KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~rGRVSi~eLa~~sN~lI~L 224 (243)
+=..|+++|..-||+..-+.+-|-.+...|.-..+- .| |+++.+..+.+.|...|..+++.|-..++.-++.
T Consensus 12 ~G~si~eIA~~R~L~~sTI~~HL~~~~~~g~~~~~~----~~--l~~e~~~~I~~~~~~~~~~~lk~i~e~l~~~~sy 83 (91)
T PF14493_consen 12 KGLSIEEIAKIRGLKESTIYGHLAELIESGEPLDIE----EL--LSEEEIKQIEDAIEKLGSEKLKPIKEALPGDYSY 83 (91)
T ss_pred cCCCHHHHHHHcCCCHHHHHHHHHHHHHhCCCCCHH----Hh--CCHHHHHHHHHHHHHcCcccHHHHHHHCCCCCCH
Confidence 456899999999999999999999999999844443 33 8999999999999999998899999988865543
No 106
>PRK03341 arginine repressor; Provisional
Probab=82.39 E-value=2.9 Score=36.26 Aligned_cols=58 Identities=21% Similarity=0.310 Sum_probs=45.8
Q ss_pred hHHHHHHHHHHhcCccchHHHHHHc-----CCChHHHHHH-HHHHHhcCCcceeeeCCCCe-EEEcHHHH
Q 026130 134 DLLADFVEYIKKHKCIPLEDLAAEF-----KLRTQECINR-ITSLENMGRLSGVMDDRGKY-IYISQAEM 196 (243)
Q Consensus 134 ~lL~~Fi~yIK~~KvV~LEdLA~~F-----~lrtqd~I~R-Iq~Le~~g~LtGViDDRGKF-IYIS~eEl 196 (243)
..+..+...|..+.++.-+||+..+ ++ ||-+|+| |++|.. .=|-|..|+| +|.-|.+.
T Consensus 15 ~R~~~I~~li~~~~i~tQ~eL~~~L~~~Gi~v-TQaTiSRDl~eL~~----~Kv~~~~G~~~~Y~lp~~~ 79 (168)
T PRK03341 15 ARQARIVAILSRQSVRSQAELAALLADEGIEV-TQATLSRDLDELGA----VKLRGADGGLGVYVVPEEG 79 (168)
T ss_pred HHHHHHHHHHHHCCCccHHHHHHHHHHcCCcc-cHHHHHHHHHHhcC----EeeecCCCCEEEEEecccc
Confidence 4566777889999999999999998 75 8999998 555532 3388899999 99876643
No 107
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=81.77 E-value=5.4 Score=30.37 Aligned_cols=71 Identities=11% Similarity=0.093 Sum_probs=52.8
Q ss_pred cchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhc-CCccHHHHHhhcccccc
Q 026130 149 IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQ-GRVSISHLASKSNQFID 223 (243)
Q Consensus 149 V~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~r-GRVSi~eLa~~sN~lI~ 223 (243)
..+.++|..+|+++.- |.-.+..|.|...-++.|-|=|-|++++..+.....-+ .-+|+.++.+.-+....
T Consensus 2 ~ti~evA~~~gvs~~t----LR~ye~~Gll~p~r~~~~g~R~Ys~~dv~~l~~I~~Lr~~G~sl~~i~~~l~~~~~ 73 (88)
T cd01105 2 IGIGEVSKLTGVSPRQ----LRYWEEKGLIKSIRSDGGGQRKYSLADVDRLLVIKELLDEGFTLAAAVEKLRRRRV 73 (88)
T ss_pred cCHHHHHHHHCcCHHH----HHHHHHCCCCCCCccCCCCceecCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHccC
Confidence 4678999999998754 55668899998766666577788999998775544443 44799988887775543
No 108
>PRK10512 selenocysteinyl-tRNA-specific translation factor; Provisional
Probab=81.73 E-value=9.6 Score=38.90 Aligned_cols=80 Identities=11% Similarity=0.116 Sum_probs=63.5
Q ss_pred HHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHH----HHHHHHHhcCCcc
Q 026130 135 LLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMK----AVADYIKRQGRVS 210 (243)
Q Consensus 135 lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~----aVA~fI~~rGRVS 210 (243)
+.+.+..+.. -.--.+.||+..+|+....+.+-+..|...|.|+-|-+ .+|++.+-+. .|..++...|.++
T Consensus 494 ~~~~l~~~~~-~~p~~~~~~~~~l~~~~~~~~~~l~~l~~~g~lv~l~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~ 568 (614)
T PRK10512 494 LWQKAEPLFG-DEPWWVRDLAKETGTDEQAMRLTLRQAAQQGIITAIVK----DRYYRNDRIVQFANMIRELDQECGSTC 568 (614)
T ss_pred HHHHHHHHHh-cCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecC----CEEECHHHHHHHHHHHHHHHhhCCcEe
Confidence 3445555444 45567789999999999999999999999999999976 5899999777 5667777789999
Q ss_pred HHHHHhhcc
Q 026130 211 ISHLASKSN 219 (243)
Q Consensus 211 i~eLa~~sN 219 (243)
++++-...+
T Consensus 569 ~~~~r~~~g 577 (614)
T PRK10512 569 AADFRDRLG 577 (614)
T ss_pred HHHHHHHhC
Confidence 987765543
No 109
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=81.61 E-value=12 Score=30.66 Aligned_cols=68 Identities=13% Similarity=0.088 Sum_probs=51.0
Q ss_pred HHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHh
Q 026130 138 DFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKR 205 (243)
Q Consensus 138 ~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~ 205 (243)
..+.++....-+.+-+||..||++..-+=.-|+-|...|-|+..-+-|=.|.+|.+.-..-++.++..
T Consensus 20 ~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~~L~~AGLV~~~r~Gr~~~Y~l~~~~~~~~~~~~~~ 87 (117)
T PRK10141 20 GIVLLLRESGELCVCDLCTALDQSQPKISRHLALLRESGLLLDRKQGKWVHYRLSPHIPAWAAKIIEQ 87 (117)
T ss_pred HHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEEEcCEEEEEECchHHHHHHHHHHH
Confidence 45566766666888999999999888888899999999999998886666777776533334444443
No 110
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=81.59 E-value=11 Score=26.45 Aligned_cols=65 Identities=14% Similarity=0.249 Sum_probs=46.4
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhc-CCccHHHHHhhcc
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQ-GRVSISHLASKSN 219 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~r-GRVSi~eLa~~sN 219 (243)
.+.|+|..+|+++. .|...+..|.|....+++|. -|.|++.+..+.....-+ --+|+.++.+..+
T Consensus 2 ti~eva~~~gvs~~----tlr~y~~~gll~~~~~~~g~-r~y~~~dv~~l~~i~~l~~~G~sl~~I~~~l~ 67 (69)
T PF13411_consen 2 TIKEVAKLLGVSPS----TLRYYEREGLLPPPRDENGY-RYYSEEDVERLREIKELRKQGMSLEEIKKLLK 67 (69)
T ss_dssp EHHHHHHHTTTTHH----HHHHHHHTTSSTTBESTTSS-EEE-HHHHHHHHHHHHHHHTTTHHHHHHHHH-
T ss_pred cHHHHHHHHCcCHH----HHHHHHHhcCcccccccCce-eeccHHHHHHHHHHHHHHHCcCCHHHHHHHHc
Confidence 36799999999764 46677889999999855555 778999988876654433 4577777776543
No 111
>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=81.33 E-value=4.8 Score=34.15 Aligned_cols=51 Identities=24% Similarity=0.333 Sum_probs=38.9
Q ss_pred ccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeE-EEcHHHHHHH
Q 026130 148 CIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYI-YISQAEMKAV 199 (243)
Q Consensus 148 vV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFI-YIS~eEl~aV 199 (243)
.++-.+||..||++..-|-+-|+.|+.+|-|. +.--+|-|| .+|++++..+
T Consensus 34 ~L~e~~La~~lgVSRtpVReAL~~L~~eGlv~-~~~~~G~~V~~~~~~~~~ei 85 (212)
T TIGR03338 34 KLNESDIAARLGVSRGPVREAFRALEEAGLVR-NEKNRGVFVREISLAEADEI 85 (212)
T ss_pred EecHHHHHHHhCCChHHHHHHHHHHHHCCCEE-EecCCCeEEecCCHHHHHHH
Confidence 33678999999999999999999999999876 233466665 3566665543
No 112
>COG4901 Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=81.19 E-value=4.8 Score=33.08 Aligned_cols=61 Identities=20% Similarity=0.288 Sum_probs=56.2
Q ss_pred chhHHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEc
Q 026130 132 DRDLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYIS 192 (243)
Q Consensus 132 ~~~lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS 192 (243)
.+.+++....-|..-.||..--||..+|++...+-.-|..|+..|.|.-|.-.|-.=||+-
T Consensus 43 dee~~~ki~KEV~~~r~VTpy~la~r~gI~~SvAr~vLR~LeeeGvv~lvsknrR~~IY~~ 103 (107)
T COG4901 43 DEELLDKIRKEVPRERVVTPYVLASRYGINGSVARIVLRHLEEEGVVQLVSKNRRQAIYTR 103 (107)
T ss_pred cHHHHHHHHHhcccceeecHHHHHHHhccchHHHHHHHHHHHhCCceeeeccCccceeeec
Confidence 4567888888899999999999999999999999999999999999999998899999974
No 113
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=80.98 E-value=18 Score=27.24 Aligned_cols=67 Identities=13% Similarity=0.263 Sum_probs=52.1
Q ss_pred HHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCC----eEEEcHHHHHHHHHHHHh
Q 026130 139 FVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGK----YIYISQAEMKAVADYIKR 205 (243)
Q Consensus 139 Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGK----FIYIS~eEl~aVA~fI~~ 205 (243)
.+.|+....-+...+|....|++...+-.-++.|+..|-|.---.--|+ |+-||+.-..++..|+..
T Consensus 5 Il~~L~~~~~~~f~~L~~~l~lt~g~Ls~hL~~Le~~GyV~~~k~~~~~~p~t~~~lT~~Gr~~~~~~~~~ 75 (80)
T PF13601_consen 5 ILALLYANEEATFSELKEELGLTDGNLSKHLKKLEEAGYVEVEKEFEGRRPRTWYSLTDKGREAFERYVAA 75 (80)
T ss_dssp HHHHHHHHSEEEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEE-SSS--EEEEEE-HHHHHHHHHHHHH
T ss_pred HHHHHhhcCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEEEeccCCCCeEEEEECHHHHHHHHHHHHH
Confidence 4566777788899999999999999999999999999999854443333 788999999999888763
No 114
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=80.63 E-value=9 Score=32.92 Aligned_cols=62 Identities=13% Similarity=0.162 Sum_probs=42.9
Q ss_pred HHHHHHHHHhcC-----ccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEE-EcHHHHHH
Q 026130 136 LADFVEYIKKHK-----CIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIY-ISQAEMKA 198 (243)
Q Consensus 136 L~~Fi~yIK~~K-----vV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIY-IS~eEl~a 198 (243)
...+.+.|.... -++..+||..||++-.-|.+-|+.|+..|-|+ +.-.+|-|+- +|..++..
T Consensus 17 ~~~l~~~I~~g~l~pG~~L~e~~La~~lgVSRtpVREAL~~L~~eGLV~-~~~~~g~~v~~~~~~~~~e 84 (221)
T PRK11414 17 ENDLKHQLSIGALKPGARLITKNLAEQLGMSITPVREALLRLVSVNALS-VAPAQAFTVPEVSKRQLDE 84 (221)
T ss_pred HHHHHHHHHhCCCCCCCccCHHHHHHHHCCCchhHHHHHHHHHHCCCEE-ecCCCceeecCCCHHHHHH
Confidence 344445555432 23568899999999999999999999999886 3444665542 45555543
No 115
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator. This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=79.12 E-value=9 Score=30.89 Aligned_cols=63 Identities=19% Similarity=0.277 Sum_probs=48.6
Q ss_pred hHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHH---hcCCccHHHHHhhcc
Q 026130 151 LEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIK---RQGRVSISHLASKSN 219 (243)
Q Consensus 151 LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~---~rGRVSi~eLa~~sN 219 (243)
+-++|..+|+++.-+ .--+..|-|.....+.|.|-|-|++.+..+. ||+ .-| +|+.++....+
T Consensus 2 I~e~a~~~gvs~~tl----R~Ye~~GLl~~~~r~~~g~R~Y~~~~l~~l~-~I~~l~~~G-~sl~eI~~~l~ 67 (124)
T TIGR02051 2 IGELAKAAGVNVETI----RYYERKGLLPEPDRPEGGYRRYPEETVKRLR-FIKRAQELG-FSLEEIGGLLG 67 (124)
T ss_pred HHHHHHHHCcCHHHH----HHHHHCCCCCCCccCCCCCEeECHHHHHHHH-HHHHHHHCC-CCHHHHHHHHh
Confidence 568999999987644 4558899998777777889999999998874 444 445 89888776554
No 116
>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator. Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=78.59 E-value=11 Score=29.43 Aligned_cols=65 Identities=12% Similarity=0.296 Sum_probs=47.7
Q ss_pred cchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHH--HHHHhcCCccHHHHHhhcc
Q 026130 149 IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVA--DYIKRQGRVSISHLASKSN 219 (243)
Q Consensus 149 V~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA--~fI~~rGRVSi~eLa~~sN 219 (243)
..+.++|..+|+++.- |.-.+..|.|.+.-++ |.|-|-|++.+..+. .+.++-| +|++++....+
T Consensus 2 ~~i~eva~~~gvs~~t----lR~ye~~Gll~~~r~~-~g~R~Y~~~~l~~l~~I~~l~~~G-~~l~ei~~~l~ 68 (102)
T cd04789 2 YTISELAEKAGISRST----LLYYEKLGLITGTRNA-NGYRLYPDSDLQRLLLIQQLQAGG-LSLKECLACLQ 68 (102)
T ss_pred CCHHHHHHHHCcCHHH----HHHHHHCCCCCCCcCC-CCCeeCCHHHHHHHHHHHHHHHCC-CCHHHHHHHHc
Confidence 3578999999997654 4577788999986665 667777888888765 2445556 89988776544
No 117
>smart00351 PAX Paired Box domain.
Probab=78.59 E-value=24 Score=28.60 Aligned_cols=84 Identities=12% Similarity=0.068 Sum_probs=61.5
Q ss_pred cchhHHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCC-CeEEEcHHHHHHHHHHHHhcCCc
Q 026130 131 GDRDLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRG-KYIYISQAEMKAVADYIKRQGRV 209 (243)
Q Consensus 131 ~~~~lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRG-KFIYIS~eEl~aVA~fI~~rGRV 209 (243)
-+.++=..||.+..... ..-+||..||++..-|..-|+...+.|.+-..-- .| +-=-+++.....|..++.+++.+
T Consensus 18 ~s~~~R~riv~~~~~G~--s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~~-gg~rp~~~~~~~~~~I~~~~~~~p~~ 94 (125)
T smart00351 18 LPDEERQRIVELAQNGV--RPCDISRQLCVSHGCVSKILGRYYETGSIRPGAI-GGSKPKVATPKVVKKIADYKQENPGI 94 (125)
T ss_pred CCHHHHHHHHHHHHcCC--CHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcCC-CCCCCCccCHHHHHHHHHHHHHCCCC
Confidence 34455567787776443 5579999999998888888898988876443211 13 45556777777888899999999
Q ss_pred cHHHHHhh
Q 026130 210 SISHLASK 217 (243)
Q Consensus 210 Si~eLa~~ 217 (243)
+..+|+..
T Consensus 95 t~~el~~~ 102 (125)
T smart00351 95 FAWEIRDR 102 (125)
T ss_pred CHHHHHHH
Confidence 99888654
No 118
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=77.92 E-value=10 Score=28.97 Aligned_cols=75 Identities=12% Similarity=0.142 Sum_probs=46.0
Q ss_pred hhHHHHHHHHHHhc--CccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhcCCcc
Q 026130 133 RDLLADFVEYIKKH--KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRVS 210 (243)
Q Consensus 133 ~~lL~~Fi~yIK~~--KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~rGRVS 210 (243)
+.++..++.||..+ .-+.+++||..+|++.--+-..++.. +|+- =.=||..-=|...+..|.. |-.|
T Consensus 4 ~~~~~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~f~~~------~g~s----~~~~i~~~Rl~~a~~~L~~-~~~~ 72 (107)
T PRK10219 4 QKIIQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTV------THQT----LGDYIRQRRLLLAAVELRT-TERP 72 (107)
T ss_pred HHHHHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHH------HCcC----HHHHHHHHHHHHHHHHHHc-cCCC
Confidence 45788889998765 45899999999999888777666664 2210 0012223333444444433 5566
Q ss_pred HHHHHhhc
Q 026130 211 ISHLASKS 218 (243)
Q Consensus 211 i~eLa~~s 218 (243)
|.+++..|
T Consensus 73 i~~iA~~~ 80 (107)
T PRK10219 73 IFDIAMDL 80 (107)
T ss_pred HHHHHHHH
Confidence 66666554
No 119
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=77.88 E-value=4.4 Score=32.45 Aligned_cols=37 Identities=11% Similarity=0.207 Sum_probs=33.0
Q ss_pred HHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHH
Q 026130 136 LADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSL 172 (243)
Q Consensus 136 L~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~L 172 (243)
.+.|..+|..+.-..|.+||.+||++.+-+...++.|
T Consensus 59 ~~~L~~~v~~~pd~tl~Ela~~l~Vs~~ti~~~Lkrl 95 (119)
T PF01710_consen 59 RDELKALVEENPDATLRELAERLGVSPSTIWRALKRL 95 (119)
T ss_pred HHHHHHHHHHCCCcCHHHHHHHcCCCHHHHHHHHHHc
Confidence 5678999999999999999999999988888877766
No 120
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=77.83 E-value=5.1 Score=36.51 Aligned_cols=55 Identities=18% Similarity=0.443 Sum_probs=45.0
Q ss_pred HHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeC--CC---CeEEEcH
Q 026130 138 DFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDD--RG---KYIYISQ 193 (243)
Q Consensus 138 ~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDD--RG---KFIYIS~ 193 (243)
+.|+.+-..- +++-+|+...|++.+-|+.-++-|+..|-|+--+|. || ||-+||.
T Consensus 19 ~Il~lLt~~p-~yvsEiS~~lgvsqkAVl~HL~~LE~AGlveS~ie~~~Rg~~rKYY~Is~ 78 (217)
T COG1777 19 RILQLLTRRP-CYVSEISRELGVSQKAVLKHLRILERAGLVESRIEKIPRGRPRKYYMISR 78 (217)
T ss_pred HHHHHHhcCc-hHHHHHHhhcCcCHHHHHHHHHHHHHcCCchhhccccccCCCcceeeccC
Confidence 4455554444 888999999999999999999999999999998887 43 6877763
No 121
>PF06969 HemN_C: HemN C-terminal domain; InterPro: IPR010723 Proteins containing this domain are all oxygen-independent coproporphyrinogen-III oxidases (HemN). This enzyme catalyses the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen-IX [], one of the last steps in haem biosynthesis. The function of this domain is unclear, but comparison to other proteins containing a radical SAM domain suggest it may be a substrate binding domain.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin-containing compound biosynthetic process, 0055114 oxidation-reduction process, 0005737 cytoplasm; PDB: 1OLT_A.
Probab=77.63 E-value=3.9 Score=28.83 Aligned_cols=54 Identities=13% Similarity=0.230 Sum_probs=39.3
Q ss_pred HHHHHHHHhcCccchHHHHHHcCCChHHH-HHHHHHHHhcCCcceeeeCCCCeEEEcHH
Q 026130 137 ADFVEYIKKHKCIPLEDLAAEFKLRTQEC-INRITSLENMGRLSGVMDDRGKYIYISQA 194 (243)
Q Consensus 137 ~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~-I~RIq~Le~~g~LtGViDDRGKFIYIS~e 194 (243)
..+|.=+..+.=|.+.++...||.+..+. ...|+.|.++|. +.-.|.+|++|+.
T Consensus 9 e~i~~~LR~~~Gi~~~~~~~~~g~~~~~~~~~~l~~l~~~Gl----l~~~~~~l~lT~~ 63 (66)
T PF06969_consen 9 EYIMLGLRCNEGIDLSEFEQRFGIDFAEEFQKELEELQEDGL----LEIDGGRLRLTEK 63 (66)
T ss_dssp HHHHHHHHHHSEEEHHHHHHHTT--THHH-HHHHHHHHHTTS----EEE-SSEEEE-TT
T ss_pred HHHHHHHHhHCCcCHHHHHHHHCcCHHHHHHHHHHHHHHCCC----EEEeCCEEEECcc
Confidence 34455577788899999999999997777 556999999954 4666788999875
No 122
>PF02186 TFIIE_beta: TFIIE beta subunit core domain; InterPro: IPR003166 Initiation of eukaryotic mRNA transcription requires melting of promoter DNA with the help of the general transcription factors TFIIE and TFIIH. In higher eukaryotes, the general transcription factor TFIIE consists of two subunits: the large alpha subunit (IPR002853 from INTERPRO) and the small beta (IPR003166 from INTERPRO). TFIIE beta has been found to bind to the region where the promoter starts to open to be single-stranded upon transcription initiation by RNA polymerase II. The approximately 120-residue central core domain of TFIIE beta plays a role in double-stranded DNA binding of TFIIE []. The TFIIE beta central core DNA-binding domain consists of three helices with a beta hairpin at the C terminus, resembling the winged helix proteins. It shows a novel double-stranded DNA-binding activity where the DNA-binding surface locates on the opposite side to the previously reported winged helix motif by forming a positively charged furrow []. This entry represents the beta subunit of the transcription factor TFIIE.; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005673 transcription factor TFIIE complex; PDB: 1D8K_A 1D8J_A.
Probab=76.90 E-value=7.6 Score=28.81 Aligned_cols=55 Identities=24% Similarity=0.344 Sum_probs=33.3
Q ss_pred HHHHHHHHHh-cCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcH
Q 026130 136 LADFVEYIKK-HKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQ 193 (243)
Q Consensus 136 L~~Fi~yIK~-~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~ 193 (243)
|..-|+|||. .+-+.++||..+.++.....+ ++-|....+|. +-.|.|+|.|.++
T Consensus 7 l~~~VeymK~r~~Plt~~eI~d~l~~d~~~~~--~~~Lk~npKI~-~d~~~~~f~fkp~ 62 (65)
T PF02186_consen 7 LAKAVEYMKKRDHPLTLEEILDYLSLDIGKKL--KQWLKNNPKIE-YDPDGNTFSFKPK 62 (65)
T ss_dssp HHHHHHHHHHH-S-B-HHHHHHHHTSSS-HHH--HHHHHH-TTEE-EE-TT-CEEE--T
T ss_pred HHHHHHHHHhcCCCcCHHHHHHHHcCCCCHHH--HHHHHcCCCEE-EecCCCEEEeccC
Confidence 6778999976 578899999999998876543 34455555553 3335569999874
No 123
>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY. This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.
Probab=76.77 E-value=6.8 Score=36.42 Aligned_cols=56 Identities=16% Similarity=0.289 Sum_probs=45.1
Q ss_pred HHHHHHHHHh-cCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeC-CCCeEEE
Q 026130 136 LADFVEYIKK-HKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDD-RGKYIYI 191 (243)
Q Consensus 136 L~~Fi~yIK~-~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDD-RGKFIYI 191 (243)
+...+.-+.. .=.+.-.+||..||++..-|.+||+.|++.|.|.+.=-- +|.||-.
T Consensus 185 v~~IL~~L~~~egrlse~eLAerlGVSRs~ireAlrkLE~aGvIe~r~LG~kGt~V~~ 242 (251)
T TIGR02787 185 VEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRSLGMKGTYIKV 242 (251)
T ss_pred HHHHHHHhccccccccHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCCCCccEeCC
Confidence 4555666666 357788899999999999999999999999999887634 5888744
No 124
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=76.74 E-value=9.2 Score=38.22 Aligned_cols=57 Identities=18% Similarity=0.335 Sum_probs=42.0
Q ss_pred HHHHHhc-CccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCe-EEEcHHHHHHHHHH
Q 026130 140 VEYIKKH-KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKY-IYISQAEMKAVADY 202 (243)
Q Consensus 140 i~yIK~~-KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKF-IYIS~eEl~aVA~f 202 (243)
+.++..+ ..+.|.||+..-||++.|||..++.| |.|. -.+|.| |+|+++-++...+-
T Consensus 365 ~~~L~~~~~~~si~~is~~T~i~~~Dii~tL~~l---~~l~---~~kg~~~i~~~~~~i~~~~~~ 423 (450)
T PLN00104 365 LEILKKHKGNISIKELSDMTAIKAEDIVSTLQSL---NLIQ---YRKGQHVICADPKVLEEHLKA 423 (450)
T ss_pred HHHHHhcCCCccHHHHHHHhCCCHHHHHHHHHHC---CCEE---ecCCcEEEEECHHHHHHHHHH
Confidence 3445544 58999999999999999998776665 5443 246666 88999887766554
No 125
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=76.46 E-value=13 Score=32.00 Aligned_cols=50 Identities=10% Similarity=0.104 Sum_probs=37.5
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEE-cHHHHHHHHHHH
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYI-SQAEMKAVADYI 203 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYI-S~eEl~aVA~fI 203 (243)
..+|||..+|++.+-+-.-+++|..+|.|. -.|+-|+| ....|.++|.-+
T Consensus 171 t~~~lA~~lG~sretvsR~L~~L~~~G~I~----~~~~~i~I~d~~~L~~~~~~~ 221 (226)
T PRK10402 171 KHTQAAEYLGVSYRHLLYVLAQFIQDGYLK----KSKRGYLIKNRKQLSGLALEL 221 (226)
T ss_pred hHHHHHHHHCCcHHHHHHHHHHHHHCCCEE----eeCCEEEEeCHHHHHHHHHHh
Confidence 469999999998887777799999998664 34556676 466666666544
No 126
>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits, TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF []. This entry represents a helix-turn-helix (HTH) domain found in eukaryotic TFIIE-alpha []. It is also found in proteins from archaebacteria that are presumed to be TFIIE-alpha subunits [], the transcriptional regulator SarR, and also DNA-directed RNA polymerase III subunit Rpc3.; PDB: 1VD4_A 1Q1H_A.
Probab=76.39 E-value=6.7 Score=30.40 Aligned_cols=63 Identities=25% Similarity=0.336 Sum_probs=37.4
Q ss_pred HHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCccee--ee-CCCC---eEEEcHHHHHHHH
Q 026130 138 DFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGV--MD-DRGK---YIYISQAEMKAVA 200 (243)
Q Consensus 138 ~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGV--iD-DRGK---FIYIS~eEl~aVA 200 (243)
..++.|-.+.++.=+|||...||++.++-.-+..|..+|-|+.. -| ++|. |-||....+..+-
T Consensus 17 ~Il~~L~~~~~l~de~la~~~~l~~~~vRkiL~~L~~~~lv~~~~~~d~~~~~~~~yw~i~~~~~~~~i 85 (105)
T PF02002_consen 17 RILDALLRKGELTDEDLAKKLGLKPKEVRKILYKLYEDGLVSYRRRKDDERGWTRYYWYIDYDQIIDVI 85 (105)
T ss_dssp HHHHHHHHH--B-HHHHHHTT-S-HHHHHHHHHHHHHHSS-EEEEE--------EEEEE-THHHH----
T ss_pred HHHHHHHHcCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeEEEEEEcCCCcEEEEEEEEcHHHHHHHH
Confidence 45666667889999999999999999999999999999998655 33 4665 4466665554333
No 127
>KOG3634 consensus Troponin [Cytoskeleton]
Probab=76.34 E-value=30 Score=33.70 Aligned_cols=40 Identities=25% Similarity=0.362 Sum_probs=20.3
Q ss_pred HHHHHHHHHHhcCccchHHHH-HHcCCChHHHHHHHHHHHhc
Q 026130 135 LLADFVEYIKKHKCIPLEDLA-AEFKLRTQECINRITSLENM 175 (243)
Q Consensus 135 lL~~Fi~yIK~~KvV~LEdLA-~~F~lrtqd~I~RIq~Le~~ 175 (243)
.-..||.-| .+|+.++..|- ..+.=+.+++-.||-.|+.+
T Consensus 212 akk~~l~ai-Rkk~~~~~~~~e~~LkeKiKELhqrI~kLE~E 252 (361)
T KOG3634|consen 212 AKKKFLLAI-RKKPLNISELPENDLKEKIKELHQRICKLETE 252 (361)
T ss_pred HHHHHHHHH-HhcccccccCCHHHHHHHHHHHHHHHHHHHHh
Confidence 345566665 34555554444 44444455555555555543
No 128
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=76.11 E-value=15 Score=28.35 Aligned_cols=65 Identities=17% Similarity=0.300 Sum_probs=49.6
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHH--HHHHhcCCccHHHHHhhcc
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVA--DYIKRQGRVSISHLASKSN 219 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA--~fI~~rGRVSi~eLa~~sN 219 (243)
.+.++|..||+++.- |.--+..|.|.....+.|.|=|.|++.+..+. .+.++-| +|+.++...-+
T Consensus 2 ~i~eva~~~gvs~~t----lR~ye~~Gll~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G-~~l~eI~~~l~ 68 (96)
T cd04788 2 KIGELARRTGLSVRT----LHHYDHIGLLSPSQRTEGGHRLYDRADIRRLHQIIALRRLG-FSLREIGRALD 68 (96)
T ss_pred CHHHHHHHHCcCHHH----HHHHHHCCCCCCCccCCCCceeeCHHHHHHHHHHHHHHHcC-CCHHHHHHHHh
Confidence 467899999997654 56667899998876666777778999997664 4556667 99988887654
No 129
>PF01402 RHH_1: Ribbon-helix-helix protein, copG family; InterPro: IPR002145 CopG, also known as RepA, is responsible for the regulation of plasmid copy number. It binds to the repAB promoter and controls synthesis of the plasmid replication initiator protein RepB. Many bacterial transcription regulation proteins bind DNA through a 'helix-turn-helix' motif, nevertheless CopG displays a fully defined HTH-motif structure that is involved not in DNA-binding, but in the maintenance of the intrinsic dimeric functional structure and cooperativity [, ].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2BJ3_B 2BJ8_A 2BJ1_A 2BJ9_A 2BJ7_B 1EA4_L 2CPG_C 1B01_B 2BA3_A 2K9I_B ....
Probab=76.01 E-value=5.4 Score=25.51 Aligned_cols=28 Identities=21% Similarity=0.246 Sum_probs=25.8
Q ss_pred EEEcHHHHHHHHHHHHhcCCccHHHHHhh
Q 026130 189 IYISQAEMKAVADYIKRQGRVSISHLASK 217 (243)
Q Consensus 189 IYIS~eEl~aVA~fI~~rGRVSi~eLa~~ 217 (243)
|+|+++.++.+-.+.+..| +|.+++...
T Consensus 4 i~l~~~~~~~l~~~a~~~g-~s~s~~ir~ 31 (39)
T PF01402_consen 4 IRLPDELYERLDELAKELG-RSRSELIRE 31 (39)
T ss_dssp EEEEHHHHHHHHHHHHHHT-SSHHHHHHH
T ss_pred EEeCHHHHHHHHHHHHHHC-cCHHHHHHH
Confidence 7899999999999999999 999998764
No 130
>PRK12423 LexA repressor; Provisional
Probab=75.74 E-value=7.5 Score=33.72 Aligned_cols=48 Identities=19% Similarity=0.250 Sum_probs=39.3
Q ss_pred chhHHHHHHHHHHhcCcc-chHHHHHHcCC-ChHHHHHHHHHHHhcCCcc
Q 026130 132 DRDLLADFVEYIKKHKCI-PLEDLAAEFKL-RTQECINRITSLENMGRLS 179 (243)
Q Consensus 132 ~~~lL~~Fi~yIK~~KvV-~LEdLA~~F~l-rtqd~I~RIq~Le~~g~Lt 179 (243)
.+.+|+-+.+||..+.+. .+.+||.+||+ ++.-+-..|+.|...|.|+
T Consensus 8 q~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~~l~~L~~~G~l~ 57 (202)
T PRK12423 8 RAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKHVQALAEAGLIE 57 (202)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEE
Confidence 355677777789888875 78999999996 6666778999999999886
No 131
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=75.44 E-value=8.3 Score=33.41 Aligned_cols=50 Identities=10% Similarity=0.244 Sum_probs=34.7
Q ss_pred cchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHH
Q 026130 149 IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVA 200 (243)
Q Consensus 149 V~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA 200 (243)
+...+||...|++.+-+-.-++.|..+|-|. +..+|+++-..++-|.+++
T Consensus 180 lt~~~IA~~lGisretlsR~L~~L~~~GlI~--~~~~~~i~I~D~~~L~~l~ 229 (230)
T PRK09391 180 MSRRDIADYLGLTIETVSRALSQLQDRGLIG--LSGARQIELRNRQALRNLD 229 (230)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCcEE--ecCCceEEEcCHHHHHHhh
Confidence 3458999999998877777799999987552 1223444444566776654
No 132
>cd00131 PAX Paired Box domain
Probab=75.39 E-value=13 Score=30.37 Aligned_cols=85 Identities=9% Similarity=0.056 Sum_probs=62.0
Q ss_pred cchhHHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhcCCcc
Q 026130 131 GDRDLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRVS 210 (243)
Q Consensus 131 ~~~~lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~rGRVS 210 (243)
-+..+=...|..+... ...-++|..||++..-|..-|+.....|.+...---..+-=.+++.....+-.||..++.+|
T Consensus 18 lS~d~R~rIv~~~~~G--~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk~~gg~rpr~~~~~~~~~i~~~v~~~p~~T 95 (128)
T cd00131 18 LPDSIRQRIVELAQSG--IRPCDISRQLRVSHGCVSKILNRYYETGSIRPGAIGGSKPRVATPEVVKKIEIYKQENPGMF 95 (128)
T ss_pred CCHHHHHHHHHHHHcC--CCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCCCCCCCCCCcCCHHHHHHHHHHHHHCCCCC
Confidence 3444555666666543 46678999999999989999999999998764322111233457777777888999999999
Q ss_pred HHHHHhh
Q 026130 211 ISHLASK 217 (243)
Q Consensus 211 i~eLa~~ 217 (243)
..+|...
T Consensus 96 l~El~~~ 102 (128)
T cd00131 96 AWEIRDR 102 (128)
T ss_pred HHHHHHH
Confidence 9999776
No 133
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=74.93 E-value=16 Score=30.57 Aligned_cols=76 Identities=14% Similarity=0.295 Sum_probs=54.2
Q ss_pred hcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHH------------HHHHHHHHhc--CCcc
Q 026130 145 KHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEM------------KAVADYIKRQ--GRVS 210 (243)
Q Consensus 145 ~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl------------~aVA~fI~~r--GRVS 210 (243)
..|+-.+-+||.++|+...-|-.--+.|+..|-|. -.||+..|||+... ..+..||..- .=+|
T Consensus 32 GdkLPSvRelA~~~~VNpnTv~raY~eLE~eG~i~---t~rg~G~fV~~~~~~~~~~~~~~~~~~~l~~~I~~~~~~G~s 108 (125)
T COG1725 32 GDKLPSVRELAKDLGVNPNTVQRAYQELEREGIVE---TKRGKGTFVTEDAKEILDQLKRELAEEELEEFIEEAKALGLS 108 (125)
T ss_pred CCCCCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEE---EecCeeEEEcCCchhhHHHHHHHHHHHHHHHHHHHHHHcCCC
Confidence 35777889999999999988888899999999865 46999999996522 2233344332 3466
Q ss_pred HHHHHhhcccccc
Q 026130 211 ISHLASKSNQFID 223 (243)
Q Consensus 211 i~eLa~~sN~lI~ 223 (243)
..++...|-.+++
T Consensus 109 ~eei~~~~~~~~~ 121 (125)
T COG1725 109 LEEILELLKEIYE 121 (125)
T ss_pred HHHHHHHHHHHHh
Confidence 6666666655544
No 134
>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA. This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (pfam02311) and the helix-turn-helix DNA-binding domain (pfam00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway.
Probab=74.67 E-value=20 Score=31.40 Aligned_cols=75 Identities=13% Similarity=0.148 Sum_probs=51.7
Q ss_pred hHHHHHHHHHHhc--CccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhcCCccH
Q 026130 134 DLLADFVEYIKKH--KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRVSI 211 (243)
Q Consensus 134 ~lL~~Fi~yIK~~--KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~rGRVSi 211 (243)
.++..|++||..+ .-..|++||..+||+..-+...++....... .=||+.-=|......+. ....||
T Consensus 186 ~~~~~~~~~I~~~~~~~~sl~~lA~~~~~S~~~l~r~Fk~~~G~t~----------~~yi~~~Rl~~A~~lL~-~t~~sI 254 (287)
T TIGR02297 186 YLFNRFNFLIEENYKQHLRLPEYADRLGISESRLNDICRRFSALSP----------KRLIIERVMQEARRLLL-FTQHSI 254 (287)
T ss_pred HHHHHHHHHHHHhhccCCCHHHHHHHHCCCHHHHHHHHHHHhCCCH----------HHHHHHHHHHHHHHHHH-cCCCCH
Confidence 4678899999755 5679999999999999988888887542210 11333333555555454 556799
Q ss_pred HHHHhhcc
Q 026130 212 SHLASKSN 219 (243)
Q Consensus 212 ~eLa~~sN 219 (243)
+++|..|+
T Consensus 255 ~eIA~~~G 262 (287)
T TIGR02297 255 NQIAYDLG 262 (287)
T ss_pred HHHHHHhC
Confidence 99988774
No 135
>TIGR01529 argR_whole arginine repressor. This model includes most members of the arginine-responsive transcriptional regulator family ArgR. This hexameric protein binds DNA at its amino end to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbor-joining tree, some of these paralogous sequences show long branches and differ significantly in an otherwise well-conserved C-terminal region motif GT[VIL][AC]GDDT. These paralogs are excluded from the seed and score in the gray zone of this model, between trusted and noise cutoffs.
Probab=74.48 E-value=12 Score=31.37 Aligned_cols=55 Identities=33% Similarity=0.478 Sum_probs=41.4
Q ss_pred HHHHHHhcCccchHHHHHHcC----CChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHH
Q 026130 139 FVEYIKKHKCIPLEDLAAEFK----LRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEM 196 (243)
Q Consensus 139 Fi~yIK~~KvV~LEdLA~~F~----lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl 196 (243)
+...|..+.+...+||...+. -=||.+|.| .|...|-+- +.+..|+|.|.-|.+.
T Consensus 7 i~~Li~~~~i~tqeeL~~~L~~~G~~vsqaTIsR--dL~elglvk-~~~~~g~~~Y~~~~~~ 65 (146)
T TIGR01529 7 IKEIITEEKISTQEELVALLKAEGIEVTQATVSR--DLRELGAVK-VRDEDGSYVYSLPADG 65 (146)
T ss_pred HHHHHHcCCCCCHHHHHHHHHHhCCCcCHHHHHH--HHHHcCCEE-EECCCCcEEEeecccc
Confidence 344568888999998776543 138999999 888888875 6779999999766544
No 136
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=73.75 E-value=9.2 Score=29.55 Aligned_cols=55 Identities=11% Similarity=0.230 Sum_probs=40.8
Q ss_pred hHHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHH
Q 026130 134 DLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIK 204 (243)
Q Consensus 134 ~lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~ 204 (243)
..+...++||.. +-+.+.|||..||++. .+|+| .| .|.+-+||++=-..|-..+.
T Consensus 6 ~R~~~I~e~l~~-~~~ti~dvA~~~gvS~-~TVsr--~L------------~~~~~~Vs~~Tr~rV~~aa~ 60 (80)
T TIGR02844 6 ERVLEIGKYIVE-TKATVRETAKVFGVSK-STVHK--DV------------TERLPEINPELAEEVKEVLD 60 (80)
T ss_pred HHHHHHHHHHHH-CCCCHHHHHHHhCCCH-HHHHH--Hh------------cCCCCCCCHHHHHHHHHHHc
Confidence 357889999999 9999999999999954 56666 22 33333588877777766665
No 137
>KOG0163 consensus Myosin class VI heavy chain [Cytoskeleton]
Probab=73.74 E-value=21 Score=38.66 Aligned_cols=21 Identities=24% Similarity=0.347 Sum_probs=10.6
Q ss_pred HHHHHHHHHHHHHHHHhhhHH
Q 026130 50 EREAAQQADEAARESRQSKQD 70 (243)
Q Consensus 50 erk~qReaee~~REerk~~e~ 70 (243)
+-+.+|.-.+...-+|++++.
T Consensus 922 e~er~rk~qE~~E~ER~rrEa 942 (1259)
T KOG0163|consen 922 ELERLRKIQELAEAERKRREA 942 (1259)
T ss_pred HHHHHHHHHHHHHHHHHhhhh
Confidence 334445544555555555554
No 138
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=73.71 E-value=12 Score=23.65 Aligned_cols=45 Identities=9% Similarity=0.155 Sum_probs=32.6
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHH
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAV 199 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aV 199 (243)
.+.++|..||++..-+- .+...|.|.++-.. |...+++..++..+
T Consensus 2 s~~e~a~~lgvs~~tl~----~~~~~g~~~~~~~~-~~~~~~~~~ei~~~ 46 (49)
T cd04762 2 TTKEAAELLGVSPSTLR----RWVKEGKLKAIRTP-GGHRRFPEEDLERL 46 (49)
T ss_pred CHHHHHHHHCcCHHHHH----HHHHcCCCCceeCC-CCceecCHHHHHHH
Confidence 46899999999776544 45567988876544 45667888888765
No 139
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=73.61 E-value=9.4 Score=32.80 Aligned_cols=51 Identities=16% Similarity=0.251 Sum_probs=37.7
Q ss_pred cCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeE-EEcHHHHHH
Q 026130 146 HKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYI-YISQAEMKA 198 (243)
Q Consensus 146 ~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFI-YIS~eEl~a 198 (243)
.++ +..+||..||++..-|.+-|+.|+.+|-|. +.--+|-|| .+|+.++..
T Consensus 29 ~~L-~e~eLae~lgVSRtpVREAL~~L~~eGlv~-~~~~~G~~V~~~~~~~~~e 80 (224)
T PRK11534 29 EKL-RMSLLTSRYALGVGPLREALSQLVAERLVT-VVNQKGYRVASMSEQELLD 80 (224)
T ss_pred CcC-CHHHHHHHHCCChHHHHHHHHHHHHCCCEE-EeCCCceEeCCCCHHHHHH
Confidence 344 458999999999999999999999999886 344566544 235554433
No 140
>cd07977 TFIIE_beta_winged_helix TFIIE_beta_winged_helix domain, located at the central core region of TFIIE beta, with double-stranded DNA binding activity. Transcription Factor IIE (TFIIE) beta winged-helix (or forkhead) domain is located at the central core region of TFIIE beta. The winged-helix is a form of helix-turn-helix (HTH) domain which typically binds DNA with the 3rd helix. The winged-helix domain is distinguished by the presence of a C-terminal beta-strand hairpin unit (the wing) that packs against the cleft of the tri-helical core. Although most winged-helix domains are multi-member families, TFIIE beta winged-helix domain is typically found as a single orthologous group. TFIIE is one of the six eukaryotic general transcription factors (TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH) that are required for transcription initiation of protein-coding genes. TFIIE is a heterotetramer consisting of two copies each of alpha and beta subunits. TFIIE beta contains several functional
Probab=73.54 E-value=5.8 Score=30.07 Aligned_cols=57 Identities=19% Similarity=0.374 Sum_probs=38.6
Q ss_pred hHHHHHHHHHHhcC--ccchHHHHHHcC-CChHHHHHHHHHHHhcCCcc--eeee-CCCCeEEEcH
Q 026130 134 DLLADFVEYIKKHK--CIPLEDLAAEFK-LRTQECINRITSLENMGRLS--GVMD-DRGKYIYISQ 193 (243)
Q Consensus 134 ~lL~~Fi~yIK~~K--vV~LEdLA~~F~-lrtqd~I~RIq~Le~~g~Lt--GViD-DRGKFIYIS~ 193 (243)
.-|..-|+|||.+- -+.|+||..+.+ +... ..+..++..-.+. -.+| ..|+|.|-+.
T Consensus 9 t~l~~aV~ymK~r~~~Plt~~EIl~~ls~~d~~---~~~~~~L~~~~~~~n~~~~~~~~tf~fkP~ 71 (75)
T cd07977 9 TQLAKIVDYMKKRHQHPLTLDEILDYLSLLDIG---PKLKEWLKSEALVNNPKIDPKDGTFSFKPK 71 (75)
T ss_pred hhHHHHHHHHHhcCCCCccHHHHHHHHhccCcc---HHHHHHHHhhhhccCceeccCCCEEEeccC
Confidence 34889999999875 789999999998 5554 4444444433333 2233 4799999763
No 141
>COG2378 Predicted transcriptional regulator [Transcription]
Probab=73.09 E-value=19 Score=33.66 Aligned_cols=70 Identities=17% Similarity=0.360 Sum_probs=56.3
Q ss_pred hHHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCC-------------CeEEEcHHHHHHHH
Q 026130 134 DLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRG-------------KYIYISQAEMKAVA 200 (243)
Q Consensus 134 ~lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRG-------------KFIYIS~eEl~aVA 200 (243)
..|-..|.||..++.|...+||..|+++.--+..=|..|...|.- |--++| -.+-.|++|..+++
T Consensus 8 ~RL~~ii~~L~~~~~vta~~lA~~~~VS~RTi~RDi~~L~~~gvP--I~~e~G~~~gy~~~~~~~L~pl~ft~~E~~Al~ 85 (311)
T COG2378 8 ERLLQIIQILRAKETVTAAELADEFEVSVRTIYRDIATLRAAGVP--IEGERGKGGGYRLRPGFKLPPLMFTEEEAEALL 85 (311)
T ss_pred HHHHHHHHHHHhCccchHHHHHHhcCCCHHHHHHHHHHHHHCCCC--eEeecCCCccEEEccCCCCCcccCCHHHHHHHH
Confidence 347788999999999999999999999999999999999999987 222334 23456899999987
Q ss_pred HHHHh
Q 026130 201 DYIKR 205 (243)
Q Consensus 201 ~fI~~ 205 (243)
.=++.
T Consensus 86 ~~l~~ 90 (311)
T COG2378 86 LALRA 90 (311)
T ss_pred HHHHH
Confidence 65543
No 142
>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain
Probab=72.54 E-value=25 Score=35.62 Aligned_cols=78 Identities=15% Similarity=0.207 Sum_probs=59.1
Q ss_pred HHHHHHHhcC-ccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHH---------HHHHHHHhcC
Q 026130 138 DFVEYIKKHK-CIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMK---------AVADYIKRQG 207 (243)
Q Consensus 138 ~Fi~yIK~~K-vV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~---------aVA~fI~~rG 207 (243)
..+.++..+. ++..++||...|++.+.++.-|..|++.|.++ |..---++..+|++-.. .|.++|...|
T Consensus 7 ~iL~~l~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kg~v~-~~~~~~~~~~LT~eG~~~l~~G~PE~rl~~~l~~~~ 85 (492)
T PLN02853 7 ALLGALSNNEEISDSGQFAASHGLDHNEVVGVIKSLHGFRYVD-AQDIKRETWVLTEEGKKYAAEGSPEVQLFAAVPAEG 85 (492)
T ss_pred HHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHHHhCCCEE-EEEEEEEEEEECHHHHHHHHcCCHHHHHHHHHhhcC
Confidence 4556677766 58999999999999999999999999998544 44444555567776333 3557888888
Q ss_pred CccHHHHHh
Q 026130 208 RVSISHLAS 216 (243)
Q Consensus 208 RVSi~eLa~ 216 (243)
-+++++|..
T Consensus 86 ~~~~~eL~~ 94 (492)
T PLN02853 86 SISKDELQK 94 (492)
T ss_pred CccHHHHHH
Confidence 889988765
No 143
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=72.50 E-value=21 Score=27.70 Aligned_cols=65 Identities=17% Similarity=0.335 Sum_probs=46.6
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHH--HHHh-cCCccHHHHHhhccc
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVAD--YIKR-QGRVSISHLASKSNQ 220 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~--fI~~-rGRVSi~eLa~~sN~ 220 (243)
.+.++|..||+++..+-.. +..|.|..+-++ |.|=|.|+.++..+.. +++. -| +|++++...-|.
T Consensus 2 ~I~e~a~~~gvs~~tLR~y----e~~Gll~p~r~~-~g~R~Y~~~dv~~l~~I~~L~~~~G-~~l~ei~~~l~~ 69 (96)
T cd04774 2 KVDEVAKRLGLTKRTLKYY----EEIGLVSPERSE-GRYRLYSEEDLKRLERILRLREVLG-FSLQEVTHFLER 69 (96)
T ss_pred CHHHHHHHHCcCHHHHHHH----HHCCCCCCCcCC-CCCEEECHHHHHHHHHHHHHHHHcC-CCHHHHHHHHhc
Confidence 4679999999987665444 567999876655 5677779999887766 5666 56 888766654433
No 144
>KOG3654 consensus Uncharacterized CH domain protein [Cytoskeleton]
Probab=72.33 E-value=11 Score=38.64 Aligned_cols=73 Identities=25% Similarity=0.298 Sum_probs=31.4
Q ss_pred hhhhhhHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHhhHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHhhhhc
Q 026130 37 EAKASKKKEKRRQEREAAQQADEAARESRQSKQDRYTEMRRRKDEERE--ARESALEEEAKAQKAREEEAAAFEFEKWKG 114 (243)
Q Consensus 37 ~~kk~~Kk~~kkqerk~qReaee~~REerk~~e~~~ee~rrkkeeere--~eE~~~eEeer~~kee~e~rE~eEY~kwK~ 114 (243)
+++|++..+++. ||.++++ |+++|.+..+...++++-++ ++++...|+++.+++ =-..||..-|.
T Consensus 389 ma~kraallekq-----qrraeea----r~rkqqleae~e~kreearrkaeeer~~keee~arre----firqey~rrkq 455 (708)
T KOG3654|consen 389 MAQKRAALLEKQ-----QRRAEEA----RRRKQQLEAEKEQKREEARRKAEEERAPKEEEVARRE----FIRQEYERRKQ 455 (708)
T ss_pred HHHHHHHHHHHH-----HHHHHHH----HHHHHHHHHHHHHHHHHHHHhhHhhhcchhhhhhHHH----HHHHHHHHHHH
Confidence 566666555433 3444443 44444444444333333332 222333333333331 11356666555
Q ss_pred cceecccc
Q 026130 115 EFSIDAEG 122 (243)
Q Consensus 115 ~f~VEeeG 122 (243)
.-..++-|
T Consensus 456 lklmed~d 463 (708)
T KOG3654|consen 456 LKLMEDLD 463 (708)
T ss_pred HHHHHhhc
Confidence 54444433
No 145
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=72.10 E-value=33 Score=27.47 Aligned_cols=70 Identities=13% Similarity=0.147 Sum_probs=49.2
Q ss_pred hhHHHHHHHHHHhc--CccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHH------HHHHHHHH
Q 026130 133 RDLLADFVEYIKKH--KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEM------KAVADYIK 204 (243)
Q Consensus 133 ~~lL~~Fi~yIK~~--KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl------~aVA~fI~ 204 (243)
...+..+++||..+ .-..|++||.++|++..-+-...+.-.. +|+.++ ...+..|.
T Consensus 8 ~~~i~~~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~~~G----------------~s~~~~l~~~Rl~~A~~~L~ 71 (127)
T PRK11511 8 AITIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETG----------------HSLGQYIRSRKMTEIAQKLK 71 (127)
T ss_pred HHHHHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHC----------------cCHHHHHHHHHHHHHHHHHH
Confidence 45688999999765 3488999999999988877666665432 455555 44555555
Q ss_pred hcCCccHHHHHhhcc
Q 026130 205 RQGRVSISHLASKSN 219 (243)
Q Consensus 205 ~rGRVSi~eLa~~sN 219 (243)
. +..||.+++..|.
T Consensus 72 ~-t~~~i~eIA~~~G 85 (127)
T PRK11511 72 E-SNEPILYLAERYG 85 (127)
T ss_pred c-CCCCHHHHHHHhC
Confidence 4 4578888887764
No 146
>TIGR00475 selB selenocysteine-specific elongation factor SelB. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3-prime or 5-prime non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation. This model describes the elongation factor SelB, a close homolog rf EF-Tu. It may function by replacing EF-Tu. A C-terminal domain not found in EF-Tu is in all SelB sequences in the seed alignment except that from Methanococcus jannaschii. This model does not find an equivalent protein for eukaryotes.
Probab=72.01 E-value=17 Score=36.86 Aligned_cols=74 Identities=12% Similarity=0.180 Sum_probs=62.7
Q ss_pred HHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhcCCccHHHH
Q 026130 135 LLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRVSISHL 214 (243)
Q Consensus 135 lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~rGRVSi~eL 214 (243)
+.+.+..+.. .....+.||+..+|+....+.+.+..|...|.|+-|.+| +|++ ..|..|+...|.+|++++
T Consensus 476 ~~~~i~~~~~-~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~g~~~~~~~~----~~~~----~~~~~~~~~~~~~~~~~~ 546 (581)
T TIGR00475 476 IWQKIKGTFG-TKGAWVREFAEEVNGDEKVMLKRVRKAGHRGGETLIVKD----RLLK----KYINELKEEGGTFNVQQA 546 (581)
T ss_pred HHHHHHHHHh-cCCCCHHHHHhhhCCCHHHHHHHHHHHHhCCCEEEEeCC----eEHH----HHHHHHHhcCCcCcHHHH
Confidence 5666666665 578899999999999999999999999999999999886 4555 899999999999999876
Q ss_pred Hhh
Q 026130 215 ASK 217 (243)
Q Consensus 215 a~~ 217 (243)
-..
T Consensus 547 r~~ 549 (581)
T TIGR00475 547 RDK 549 (581)
T ss_pred HHH
Confidence 554
No 147
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil
Probab=71.75 E-value=21 Score=27.77 Aligned_cols=62 Identities=13% Similarity=0.387 Sum_probs=45.4
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHH--HHHhcCCccHHHHHhh
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVAD--YIKRQGRVSISHLASK 217 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~--fI~~rGRVSi~eLa~~ 217 (243)
.+.++|..||+++.- |.-.+..|-|.- ..+.|.|=|.|++.+..+.. +.++-| +|++++...
T Consensus 3 ~i~eva~~~gvs~~t----LR~ye~~Gll~~-~r~~~g~R~Y~~~dl~~l~~I~~l~~~G-~~l~ei~~~ 66 (102)
T cd04775 3 TIGQMSRKFGVSRST----LLYYESIGLIPS-ARSEANYRLYSEADLSRLEKIVFLQAGG-LPLEEIAGC 66 (102)
T ss_pred CHHHHHHHHCcCHHH----HHHHHHCCCCCC-CCCCCCCeeeCHHHHHHHHHHHHHHHCC-CCHHHHHHH
Confidence 577999999997655 467778898844 44456778889998886653 345556 999988864
No 148
>PF13730 HTH_36: Helix-turn-helix domain
Probab=71.42 E-value=6.5 Score=26.66 Aligned_cols=29 Identities=24% Similarity=0.360 Sum_probs=26.6
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCc
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRL 178 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~L 178 (243)
..+.||..+|++..-|...|+.|+..|-|
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHCcCC
Confidence 47999999999999999999999999865
No 149
>COG3140 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=71.27 E-value=3.3 Score=30.65 Aligned_cols=32 Identities=28% Similarity=0.419 Sum_probs=26.6
Q ss_pred hHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhc
Q 026130 162 TQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQ 206 (243)
Q Consensus 162 tqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~r 206 (243)
.|.+|.|||.|.++|.-+| +=+.-||+-|+.+
T Consensus 13 QQ~AVE~Iq~lMaeGmSsG-------------EAIa~VA~elRe~ 44 (60)
T COG3140 13 QQKAVERIQELMAEGMSSG-------------EAIALVAQELREN 44 (60)
T ss_pred HHHHHHHHHHHHHccccch-------------hHHHHHHHHHHHH
Confidence 4789999999999998777 5677788888764
No 150
>PF07789 DUF1627: Protein of unknown function (DUF1627); InterPro: IPR012432 This is a group of sequences found in hypothetical proteins predicted to be expressed in a number of bacterial species. The region in question is approximately 150 amino acid residues long.
Probab=71.03 E-value=6.4 Score=34.25 Aligned_cols=43 Identities=28% Similarity=0.475 Sum_probs=37.7
Q ss_pred hHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHH
Q 026130 151 LEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQA 194 (243)
Q Consensus 151 LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~e 194 (243)
-++||..||++|--+.+-+.-+-+.|+|.-|. ..|||=|-=|.
T Consensus 9 ~eELA~~FGvttRkvaStLa~~ta~Grl~Rv~-q~gkfRy~iPg 51 (155)
T PF07789_consen 9 AEELAGKFGVTTRKVASTLAMVTATGRLIRVN-QNGKFRYCIPG 51 (155)
T ss_pred HHHHHHHhCcchhhhHHHHHHHHhcceeEEec-CCCceEEeCCC
Confidence 47999999999999999999999999998774 57999997653
No 151
>PTZ00121 MAEBL; Provisional
Probab=70.98 E-value=22 Score=40.72 Aligned_cols=10 Identities=10% Similarity=0.238 Sum_probs=4.0
Q ss_pred CChHHHHHHH
Q 026130 160 LRTQECINRI 169 (243)
Q Consensus 160 lrtqd~I~RI 169 (243)
+++.+.-.+|
T Consensus 1371 ~~~~~~~kk~ 1380 (2084)
T PTZ00121 1371 KKKEEAKKKA 1380 (2084)
T ss_pred hhhhHHHHhH
Confidence 3344443333
No 152
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=70.50 E-value=20 Score=27.94 Aligned_cols=62 Identities=13% Similarity=0.224 Sum_probs=45.7
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHH--HHHHHhcCCccHHHHHhhc
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAV--ADYIKRQGRVSISHLASKS 218 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aV--A~fI~~rGRVSi~eLa~~s 218 (243)
.+-++|..+|+++. .|.--+..|-|... ++.|.+.| ++..+..| ..++++-| +|+.++....
T Consensus 2 ~Ige~a~~~gvs~~----tlRyYe~~GLl~p~-~~~g~r~Y-~~~~~~~l~~I~~lr~~G-~sL~eI~~~l 65 (107)
T cd04777 2 KIGKFAKKNNITID----TVRHYIDLGLLIPE-KKGGQYFF-DEKCQDDLEFILELKGLG-FSLIEIQKIF 65 (107)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHCCCcCCc-cCCCcccc-CHHHHHHHHHHHHHHHCC-CCHHHHHHHH
Confidence 46789999999765 46778899999884 45788877 88887543 34445567 8988887754
No 153
>PF09397 Ftsk_gamma: Ftsk gamma domain; InterPro: IPR018541 This domain directs oriented DNA translocation and forms a winged helix structure []. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding []. ; PDB: 2VE9_B 2VE8_E 2J5O_A 2J5P_A.
Probab=70.45 E-value=11 Score=28.03 Aligned_cols=59 Identities=17% Similarity=0.274 Sum_probs=45.4
Q ss_pred chhHHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEE
Q 026130 132 DRDLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIY 190 (243)
Q Consensus 132 ~~~lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIY 190 (243)
.+.++.+-+.||....-+.+.-|-++|++--.-+-.-|..|+..|.|++--....+=|+
T Consensus 4 ~D~ly~~a~~~V~~~~~~S~S~lQR~~rIGynrAariid~LE~~GiVs~~~~~~~R~Vl 62 (65)
T PF09397_consen 4 EDPLYEEAVEFVIEEGKASISLLQRKFRIGYNRAARIIDQLEEEGIVSPANGSKPREVL 62 (65)
T ss_dssp TSTTHHHHHHHHHHCTCECHHHHHHHHT--HHHHHHHHHHHHHCTSBE---TTSEEEB-
T ss_pred ccHHHHHHHHHHHHcCCccHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCCCCCCCCeec
Confidence 45688999999999999999999999999999999999999999988775433333333
No 154
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=70.28 E-value=9.2 Score=33.14 Aligned_cols=51 Identities=24% Similarity=0.360 Sum_probs=42.8
Q ss_pred ccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEE-EcHHHHHHH
Q 026130 148 CIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIY-ISQAEMKAV 199 (243)
Q Consensus 148 vV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIY-IS~eEl~aV 199 (243)
-+....||..||++..=|-+-|..|..+|-|+=. -.||-||- ||..++..+
T Consensus 39 ~l~e~~La~~~gvSrtPVReAL~rL~~eGlv~~~-p~rG~~V~~~~~~~~~ei 90 (230)
T COG1802 39 RLSEEELAEELGVSRTPVREALRRLEAEGLVEIE-PNRGAFVAPLSLAEAREI 90 (230)
T ss_pred CccHHHHHHHhCCCCccHHHHHHHHHHCCCeEec-CCCCCeeCCCCHHHHHHH
Confidence 3678889999999999999999999999988755 77898875 677776653
No 155
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=70.20 E-value=7 Score=34.18 Aligned_cols=62 Identities=15% Similarity=0.187 Sum_probs=41.8
Q ss_pred ccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEc-----HHHHHHHHHHHHhcCCcc
Q 026130 148 CIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYIS-----QAEMKAVADYIKRQGRVS 210 (243)
Q Consensus 148 vV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS-----~eEl~aVA~fI~~rGRVS 210 (243)
+=.=.+||..||++..-|-.-|..|..+|.|.- .--+|.||--+ ...+..+...+...|...
T Consensus 35 LPsE~eLa~~~~VSR~TVR~Al~~L~~eGli~r-~~G~GtfV~~~~~~~~~~~~~~f~~~~~~~g~~~ 101 (241)
T PRK10079 35 LPAEQQLAARYEVNRHTLRRAIDQLVEKGWVQR-RQGVGVLVLMRPYDYPLNAQARFSQNLLDQGSHP 101 (241)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE-ecCCEEEEecCccccccccccchHHHHHhcCCCc
Confidence 333456999999999999999999999999873 23355555211 122344555666666544
No 156
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=70.16 E-value=35 Score=30.77 Aligned_cols=90 Identities=14% Similarity=0.240 Sum_probs=64.8
Q ss_pred HHHHHHHHh-cCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhcCCcc-----
Q 026130 137 ADFVEYIKK-HKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRVS----- 210 (243)
Q Consensus 137 ~~Fi~yIK~-~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~rGRVS----- 210 (243)
-+.+++|-. ..-+.|.|||...||...-|-.-++.|...|-| .-|+.++.-++++.=+.-=..+.....-+.
T Consensus 28 l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l--~~~~~~~~Y~lG~~l~~Lg~~~~~~~~l~~~a~p~ 105 (271)
T PRK10163 28 IAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQAADFV--YQDSQLGWWHIGLGVFNVGAAYIHNRDVLSVAGPF 105 (271)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCE--EEcCCCCeEEecHHHHHHHHHHHhcCCHHHHHHHH
Confidence 355667754 467889999999999999999999999999998 456665655677765554444444444443
Q ss_pred HHHHHhhcccccccccch
Q 026130 211 ISHLASKSNQFIDLETKA 228 (243)
Q Consensus 211 i~eLa~~sN~lI~L~p~~ 228 (243)
+.+|+..+|.-+.|.--.
T Consensus 106 l~~La~~~getv~l~v~~ 123 (271)
T PRK10163 106 MRRLMLLSGETVNVAIRN 123 (271)
T ss_pred HHHHHHHHCCeEEEEEEE
Confidence 468888888777665543
No 157
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=70.01 E-value=36 Score=28.58 Aligned_cols=63 Identities=16% Similarity=0.308 Sum_probs=46.8
Q ss_pred HHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeee--CCC--CeEE--EcHHHHHH
Q 026130 136 LADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMD--DRG--KYIY--ISQAEMKA 198 (243)
Q Consensus 136 L~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViD--DRG--KFIY--IS~eEl~a 198 (243)
+.-|...+..+.=...++||...|++-.-|=.-+|.|...|.+.=.-+ +.| +||| |.++++..
T Consensus 30 v~v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~~~~Ggy~yiY~~i~~ee~k~ 98 (126)
T COG3355 30 VEVYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVNLKGGGYYYLYKPIDPEEIKK 98 (126)
T ss_pred HHHHHHHHhhcCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeeccCCCceeEEEecCCHHHHHH
Confidence 344444555677788999999999998888889999999998876554 455 5666 55666553
No 158
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=69.98 E-value=15 Score=30.38 Aligned_cols=48 Identities=17% Similarity=0.158 Sum_probs=35.7
Q ss_pred cchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEE-cHHHHHHHH
Q 026130 149 IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYI-SQAEMKAVA 200 (243)
Q Consensus 149 V~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYI-S~eEl~aVA 200 (243)
+..++||...|++.+-+-.-+..|...|.|. -.++.|+| .++.|..+|
T Consensus 150 ~t~~~iA~~lG~tretvsR~l~~l~~~g~I~----~~~~~i~I~d~~~L~~~~ 198 (202)
T PRK13918 150 ATHDELAAAVGSVRETVTKVIGELSREGYIR----SGYGKIQLLDLKGLEELA 198 (202)
T ss_pred CCHHHHHHHhCccHHHHHHHHHHHHHCCCEE----cCCCEEEEECHHHHHHHH
Confidence 4678999999998877777799999987764 34445666 466666655
No 159
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=69.84 E-value=17 Score=28.53 Aligned_cols=67 Identities=12% Similarity=0.179 Sum_probs=49.3
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeC-CCCeEEEcHHHHHHHHHHHHhc-CCccHHHHHhhccc
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDD-RGKYIYISQAEMKAVADYIKRQ-GRVSISHLASKSNQ 220 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDD-RGKFIYIS~eEl~aVA~fI~~r-GRVSi~eLa~~sN~ 220 (243)
.+.++|..||+++.- |.-.+..|.|..+-.+ .+.|=|-|+.++..+.....-+ --+|++++...-+.
T Consensus 2 ~i~eva~~~gis~~t----lR~ye~~GLi~p~~~~~~ngyR~Y~~~~i~~l~~I~~lr~~G~sl~~i~~l~~~ 70 (108)
T cd01107 2 TIGEFAKLSNLSIKA----LRYYDKIGLLKPAYVDPDTGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEILDA 70 (108)
T ss_pred CHHHHHHHHCcCHHH----HHHHHHcCCCCCCcCCCCCCccccCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 467999999997654 5667778999998754 5788888999999885433333 23899888765443
No 160
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=69.58 E-value=22 Score=28.48 Aligned_cols=65 Identities=12% Similarity=0.189 Sum_probs=49.4
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHH--HHHHhcCCccHHHHHhhcc
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVA--DYIKRQGRVSISHLASKSN 219 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA--~fI~~rGRVSi~eLa~~sN 219 (243)
.+.++|..||+++. .|.--+..|.|.....+.|-|=|-|++.+..|. .+.+.-| +|+.++....+
T Consensus 2 ~IgevA~~~gvs~~----tLRyYe~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G-~sL~eI~~~l~ 68 (127)
T cd04784 2 KIGELAKKTGCSVE----TIRYYEKEGLLPAPARSANNYRLYDEEHLERLLFIRRCRSLD-MSLDEIRTLLQ 68 (127)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcC-CCHHHHHHHHH
Confidence 46789999999764 466778899998765556778888999998554 4556667 99988877543
No 161
>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=69.55 E-value=8.9 Score=26.15 Aligned_cols=42 Identities=14% Similarity=0.246 Sum_probs=34.3
Q ss_pred HHHHHHHhcCc-cchHHHHHHcCCChHHHHHHHHHHHhcCCcc
Q 026130 138 DFVEYIKKHKC-IPLEDLAAEFKLRTQECINRITSLENMGRLS 179 (243)
Q Consensus 138 ~Fi~yIK~~Kv-V~LEdLA~~F~lrtqd~I~RIq~Le~~g~Lt 179 (243)
..+++|..+.- +.+.|||...|++..-|-.-++.|...|-|.
T Consensus 7 ~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~ 49 (52)
T PF09339_consen 7 RILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVEEGYVE 49 (52)
T ss_dssp HHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCee
Confidence 45666666555 6999999999999999999999999999763
No 162
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=69.41 E-value=14 Score=27.42 Aligned_cols=51 Identities=16% Similarity=0.332 Sum_probs=37.7
Q ss_pred HHHHHHHhc---CccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCe
Q 026130 138 DFVEYIKKH---KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKY 188 (243)
Q Consensus 138 ~Fi~yIK~~---KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKF 188 (243)
.++-|+..+ +.+.+.+||..+|++..-+..-++.|...|-|...--..|=|
T Consensus 12 ~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~~G~~GGy 65 (83)
T PF02082_consen 12 RILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIESSRGRGGGY 65 (83)
T ss_dssp HHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETSTTSEE
T ss_pred HHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEecCCCCCce
Confidence 344455433 359999999999999999999999999999887665444444
No 163
>PF05672 MAP7: MAP7 (E-MAP-115) family; InterPro: IPR008604 The organisation of microtubules varies with the cell type and is presumably controlled by tissue-specific microtubule-associated proteins (MAPs). The 115 kDa epithelial MAP (E-MAP-115) has been identified as a microtubule-stabilising protein predominantly expressed in cell lines of epithelial origin []. The binding of this microtubule associated protein is nucleotide independent [].
Probab=68.62 E-value=84 Score=27.77 Aligned_cols=14 Identities=21% Similarity=0.200 Sum_probs=6.9
Q ss_pred CCCCccccccccCC
Q 026130 12 SSAGAAEVEETIEG 25 (243)
Q Consensus 12 ~~~~~~~~~~~~~~ 25 (243)
+++++-+.+|+.|.
T Consensus 8 ~~~~~K~saGTtda 21 (171)
T PF05672_consen 8 SPASGKPSAGTTDA 21 (171)
T ss_pred CCCCCCCCCCCCCH
Confidence 44444455555544
No 164
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=68.43 E-value=13 Score=31.69 Aligned_cols=64 Identities=14% Similarity=0.265 Sum_probs=50.3
Q ss_pred chhHHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHH
Q 026130 132 DRDLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKA 198 (243)
Q Consensus 132 ~~~lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~a 198 (243)
..++|....+++...-.+.+-|||..+|++..-|-.-++.|...|.+. .+ .-..|-+|+.-...
T Consensus 8 ~edYL~~Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~--~~-~y~gi~LT~~G~~~ 71 (154)
T COG1321 8 EEDYLETIYELLEEKGFARTKDIAERLKVSPPSVTEMLKRLERLGLVE--YE-PYGGVTLTEKGREK 71 (154)
T ss_pred HHHHHHHHHHHHhccCcccHHHHHHHhCCCcHHHHHHHHHHHHCCCeE--Ee-cCCCeEEChhhHHH
Confidence 456788888888888999999999999999999999999999998764 22 23345577655543
No 165
>PF06224 HTH_42: Winged helix DNA-binding domain; InterPro: IPR009351 This is a family of conserved bacterial proteins with unknown function.
Probab=68.29 E-value=13 Score=33.68 Aligned_cols=65 Identities=23% Similarity=0.294 Sum_probs=55.6
Q ss_pred chhHHHHHH-HHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCC-eEEEcHHHH
Q 026130 132 DRDLLADFV-EYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGK-YIYISQAEM 196 (243)
Q Consensus 132 ~~~lL~~Fi-~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGK-FIYIS~eEl 196 (243)
....+...+ .|+..+=.+.+.|+|--+||+..++-.-++.|.+.|.|..|..++|+ +.|+.++.+
T Consensus 164 ~~ea~~~Lv~Ryl~~~GPat~~d~a~w~gl~~~~~r~~l~~l~~~~~L~~v~~~~G~~~~~~~~~~~ 230 (327)
T PF06224_consen 164 REEALAELVRRYLRAYGPATLADFAWWSGLPKTQARRALAQLVEEGELVEVEVEGGKEPLYDLPEDL 230 (327)
T ss_pred HHHHHHHHHHHHHHHcCCccHHHHHHHhccCHHHHHHHHHhhccCCcEEEEEEcCcceeEEechhhh
Confidence 334455554 49999999999999999999999999999999999999999999777 588888765
No 166
>KOG2908 consensus 26S proteasome regulatory complex, subunit RPN9/PSMD13 [Posttranslational modification, protein turnover, chaperones]
Probab=67.86 E-value=9.9 Score=37.18 Aligned_cols=48 Identities=17% Similarity=0.364 Sum_probs=45.4
Q ss_pred hcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEc
Q 026130 145 KHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYIS 192 (243)
Q Consensus 145 ~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS 192 (243)
..+-|.++++|..-.|+..+|.--|-.=..-|-|+|.||+=+.-+|+|
T Consensus 291 ~~R~lsf~~Ia~~tkip~~eVE~LVMKAlslgLikG~Idqv~~~v~~s 338 (380)
T KOG2908|consen 291 NERTLSFKEIAEATKIPNKEVELLVMKALSLGLIKGSIDQVEGVVYMS 338 (380)
T ss_pred hhccccHHHHHHHhCCCHHHHHHHHHHHHhccceeeeecccccEEEEe
Confidence 568899999999999999999999999999999999999999999997
No 167
>PRK05114 hypothetical protein; Provisional
Probab=67.62 E-value=4 Score=30.33 Aligned_cols=32 Identities=28% Similarity=0.438 Sum_probs=27.1
Q ss_pred hHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhc
Q 026130 162 TQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQ 206 (243)
Q Consensus 162 tqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~r 206 (243)
.|.++.|||.|.+.|.=|| +=+.-||+-|+..
T Consensus 13 QQ~AVErIq~LMaqGmSsg-------------EAI~~VA~eiRe~ 44 (59)
T PRK05114 13 QQKAVERIQELMAQGMSSG-------------EAIALVAEELRAN 44 (59)
T ss_pred HHHHHHHHHHHHHccccHH-------------HHHHHHHHHHHHH
Confidence 4789999999999998776 6678888888864
No 168
>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=67.54 E-value=5.7 Score=28.02 Aligned_cols=23 Identities=26% Similarity=0.547 Sum_probs=20.2
Q ss_pred HHHHHHHHhcCCccHHHHHhhcc
Q 026130 197 KAVADYIKRQGRVSISHLASKSN 219 (243)
Q Consensus 197 ~aVA~fI~~rGRVSi~eLa~~sN 219 (243)
..+-+||+++|.||+.+|++..|
T Consensus 3 ~~Il~~l~~~~~~s~~ela~~~~ 25 (57)
T PF08220_consen 3 QQILELLKEKGKVSVKELAEEFG 25 (57)
T ss_pred HHHHHHHHHcCCEEHHHHHHHHC
Confidence 56889999999999999998754
No 169
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=67.45 E-value=21 Score=28.32 Aligned_cols=66 Identities=15% Similarity=0.202 Sum_probs=51.1
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHH--HHHhcCCccHHHHHhhccc
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVAD--YIKRQGRVSISHLASKSNQ 220 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~--fI~~rGRVSi~eLa~~sN~ 220 (243)
.+.++|..||+++.- |.-.+..|-|..+.-+.|.|=|-|++.+..+.. +.+.-| +|+.++....+.
T Consensus 2 ~I~eva~~~gvs~~t----LRyYe~~GLl~p~~r~~~gyR~Y~~~~i~~l~~I~~lr~~G-~sl~eI~~~l~~ 69 (123)
T cd04770 2 KIGELAKAAGVSPDT----IRYYERIGLLPPPQRSENGYRLYGEADLARLRFIRRAQALG-FSLAEIRELLSL 69 (123)
T ss_pred CHHHHHHHHCcCHHH----HHHHHHCCCCCCCCCCCCCCccCCHHHHHHHHHHHHHHHCC-CCHHHHHHHHHh
Confidence 467899999997753 456899999997665678899999999987653 455556 999888776653
No 170
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=67.01 E-value=18 Score=33.82 Aligned_cols=65 Identities=15% Similarity=0.258 Sum_probs=49.5
Q ss_pred hcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCC-eEEEcHHHHHHHHHHHHhcCCccHHHHHhhcccc
Q 026130 145 KHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGK-YIYISQAEMKAVADYIKRQGRVSISHLASKSNQF 221 (243)
Q Consensus 145 ~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGK-FIYIS~eEl~aVA~fI~~rGRVSi~eLa~~sN~l 221 (243)
.+--|..-|+|.++|++.|-|++.|+.|..+|- ++..|. +--||.+-.+.+-.. +++|-.+++.+
T Consensus 22 ~qp~v~q~eIA~~lgiT~QaVsehiK~Lv~eG~----i~~~gR~~Y~iTkkG~e~l~~~--------~~dlr~f~~ev 87 (260)
T COG1497 22 RQPRVKQKEIAKKLGITLQAVSEHIKELVKEGL----IEKEGRGEYEITKKGAEWLLEQ--------LSDLRRFSEEV 87 (260)
T ss_pred hCCCCCHHHHHHHcCCCHHHHHHHHHHHHhccc----eeecCCeeEEEehhHHHHHHHH--------HHHHHHHHHHH
Confidence 346678899999999999999999999999865 455555 334898877666543 46777777766
No 171
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR. Members of this family are FadR, a transcriptional regulator of fatty acid metabolism, including both biosynthesis and beta-oxidation. It is found exclusively in a subset of Gammaproteobacteria, with strictly one copy per genome. It has an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR from this family heterologously expressed in Escherichia coli show differences in regulatory response and fatty acid binding profiles. The family is nevertheless designated equivalog, as all member proteins have at least nominally the same function.
Probab=66.95 E-value=11 Score=32.69 Aligned_cols=39 Identities=10% Similarity=0.158 Sum_probs=33.0
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeE
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYI 189 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFI 189 (243)
.-.+||..||++..-|-.-|+.|+..|-|+ +.--+|-||
T Consensus 32 sE~~La~~lgVSRtpVREAL~~Le~eGlV~-~~~~~G~~V 70 (235)
T TIGR02812 32 AERELSELIGVTRTTLREVLQRLARDGWLT-IQHGKPTKV 70 (235)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHCCCEE-EeCCCccEe
Confidence 567899999999999999999999999887 444567665
No 172
>PF15615 TerB-C: TerB-C domain
Probab=66.95 E-value=24 Score=29.33 Aligned_cols=62 Identities=16% Similarity=0.119 Sum_probs=50.3
Q ss_pred HHHHHHHHHhcCcc---chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHH
Q 026130 136 LADFVEYIKKHKCI---PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKA 198 (243)
Q Consensus 136 L~~Fi~yIK~~KvV---~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~a 198 (243)
...|+..+..+.-+ -++++|..+||-+.-+|+.|++..-+--=.-||+. |-.|||.++=+..
T Consensus 78 ~~~lL~~Ll~~~~w~r~e~~~~a~~~glm~~~~ie~INE~afd~~gd~vie~-~d~i~I~~dy~e~ 142 (144)
T PF15615_consen 78 HSALLRALLSRESWSREELEDIARDHGLMPDGAIESINEKAFDYFGDPVIEG-DDPIEINEDYREE 142 (144)
T ss_pred HHHHHHHHHhCCCccHHHHHHHHHHcCCCHHHHHHHHHHHHHHhcCCeeEeC-CCCceEcHHHHHh
Confidence 56777877777665 45689999999999999999998877666678888 9999998875443
No 173
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=66.86 E-value=9.4 Score=24.89 Aligned_cols=29 Identities=21% Similarity=0.298 Sum_probs=23.4
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCc
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRL 178 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~L 178 (243)
.-.|||...|++.+-|-.-+..|..+|.|
T Consensus 4 tr~diA~~lG~t~ETVSR~l~~l~~~glI 32 (32)
T PF00325_consen 4 TRQDIADYLGLTRETVSRILKKLERQGLI 32 (32)
T ss_dssp -HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred CHHHHHHHhCCcHHHHHHHHHHHHHcCCC
Confidence 35799999999888888888999999865
No 174
>KOG1144 consensus Translation initiation factor 5B (eIF-5B) [Translation, ribosomal structure and biogenesis]
Probab=66.60 E-value=42 Score=36.38 Aligned_cols=18 Identities=28% Similarity=0.224 Sum_probs=8.4
Q ss_pred cCCcchhhhhhHHHHHHH
Q 026130 32 AGGHYEAKASKKKEKRRQ 49 (243)
Q Consensus 32 ~~g~~~~kk~~Kk~~kkq 49 (243)
+.|+...++..|=....|
T Consensus 203 ak~Kk~~kk~~Kgv~~~q 220 (1064)
T KOG1144|consen 203 AKGKKAEKKKPKGVRAMQ 220 (1064)
T ss_pred hhhcccccccchhHHHHH
Confidence 445555555544433333
No 175
>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=66.03 E-value=18 Score=29.49 Aligned_cols=46 Identities=11% Similarity=0.070 Sum_probs=33.6
Q ss_pred cchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEc-HHHHHH
Q 026130 149 IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYIS-QAEMKA 198 (243)
Q Consensus 149 V~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS-~eEl~a 198 (243)
+.-+|||...|++.+-+-.-|+.|..+|.|.- +++.|+|. .+.|..
T Consensus 144 ~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~----~~~~i~I~d~~~L~~ 190 (193)
T TIGR03697 144 LSHQAIAEAIGSTRVTITRLLGDLRKKKLISI----HKKKITVHDPIALGQ 190 (193)
T ss_pred CCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEe----cCCEEEEeCHHHHHH
Confidence 46799999999977776667999999987654 44556664 555544
No 176
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=66.00 E-value=19 Score=31.58 Aligned_cols=54 Identities=22% Similarity=0.169 Sum_probs=40.6
Q ss_pred HHHHHHHHHHhcCc------cchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeE
Q 026130 135 LLADFVEYIKKHKC------IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYI 189 (243)
Q Consensus 135 lL~~Fi~yIK~~Kv------V~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFI 189 (243)
....+.+.|....+ ..-.+||..||++..-|..-|+.|+..|-|+ +.--+|-||
T Consensus 13 v~~~l~~~I~~g~l~pG~~LpsE~eLae~~gVSRtpVREAL~~L~~eGlV~-~~~~~G~~V 72 (253)
T PRK11523 13 LAAELKERIEQGVYLVGDKLPAERFIADEKNVSRTVVREAIIMLEVEGYVE-VRKGSGIHV 72 (253)
T ss_pred HHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE-EecCCeeEE
Confidence 34455556655543 3456899999999999999999999999887 333477777
No 177
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=65.83 E-value=29 Score=24.18 Aligned_cols=63 Identities=16% Similarity=0.062 Sum_probs=41.7
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhc-CCccHHHHHh
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQ-GRVSISHLAS 216 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~r-GRVSi~eLa~ 216 (243)
.+.++|..+|+++.-+-.-++. .|.+...-++ |.+-+.|++++..+-.....+ --+|+.++.+
T Consensus 2 s~~eva~~~gvs~~tlr~w~~~---~g~~~~~r~~-~~~r~yt~~~v~~l~~i~~l~~~g~~l~~i~~ 65 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAWERR---YGLPAPQRTD-GGHRLYSEADVARLRLIRRLTSEGVRISQAAA 65 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHh---CCCCCCCcCC-CCCeecCHHHHHHHHHHHHHHHCCCCHHHHHH
Confidence 4678999999987776655543 2544444444 566778999988776554443 4577777654
No 178
>KOG2412 consensus Nuclear-export-signal (NES)-containing protein/polyadenylated-RNA export factor [RNA processing and modification]
Probab=65.56 E-value=32 Score=35.46 Aligned_cols=34 Identities=21% Similarity=0.280 Sum_probs=24.7
Q ss_pred HHHHHHHHHhc----CCccHHHHHhhcccccccccchh
Q 026130 196 MKAVADYIKRQ----GRVSISHLASKSNQFIDLETKAQ 229 (243)
Q Consensus 196 l~aVA~fI~~r----GRVSi~eLa~~sN~lI~L~p~~~ 229 (243)
+..|+-||... |-|=++.|...|=-+|-..+...
T Consensus 409 la~V~l~i~~q~Pdv~dlllA~l~KkCP~~VPf~~~~~ 446 (591)
T KOG2412|consen 409 LAKVILYIWSQFPDVGDLLLARLHKKCPYVVPFHIVNS 446 (591)
T ss_pred HHHHHHHHHHhCchHHHHHHHHHHhcCCccccccccCc
Confidence 45677777654 66667888888888877666554
No 179
>PF13994 PgaD: PgaD-like protein
Probab=65.54 E-value=8 Score=31.99 Aligned_cols=37 Identities=30% Similarity=0.459 Sum_probs=33.1
Q ss_pred cchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeE
Q 026130 149 IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYI 189 (243)
Q Consensus 149 V~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFI 189 (243)
|..+|||..|+++++. |++|.....+|==.||.|+=|
T Consensus 101 ~~~~elA~~f~l~~~~----l~~lr~~k~~~V~~d~~G~I~ 137 (138)
T PF13994_consen 101 VSDEELARSFGLSPEQ----LQQLRQAKVLTVHHDDHGRII 137 (138)
T ss_pred CCHHHHHHHcCCCHHH----HHHHHhCCeEEEEeCCCCCcC
Confidence 8999999999998655 789999999999999999754
No 180
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=65.51 E-value=21 Score=25.19 Aligned_cols=36 Identities=28% Similarity=0.473 Sum_probs=31.4
Q ss_pred HHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHH
Q 026130 138 DFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLE 173 (243)
Q Consensus 138 ~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le 173 (243)
..++|+-.++-+.+.+||..+|++.--+.+.|..|.
T Consensus 9 ~Ll~~L~~~~~~~~~ela~~l~~S~rti~~~i~~L~ 44 (59)
T PF08280_consen 9 KLLELLLKNKWITLKELAKKLNISERTIKNDINELN 44 (59)
T ss_dssp HHHHHHHHHTSBBHHHHHHHCTS-HHHHHHHHHHHH
T ss_pred HHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHHHHHH
Confidence 567777679999999999999999999999999987
No 181
>PRK14584 hmsS hemin storage system protein; Provisional
Probab=65.50 E-value=12 Score=32.50 Aligned_cols=45 Identities=22% Similarity=0.313 Sum_probs=40.2
Q ss_pred hcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcH
Q 026130 145 KHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQ 193 (243)
Q Consensus 145 ~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~ 193 (243)
....+..+++|..|++.++. |++|...+.+|==+||-|+-|-|..
T Consensus 95 ~~~~l~~dElA~sF~l~~e~----i~qLr~~kiltVh~De~G~Ii~V~~ 139 (153)
T PRK14584 95 HRPDLDDDELASSFALSPEL----IAQLKSGSCLTLYNDEHGHIIDVKE 139 (153)
T ss_pred CCCCCChHHHHHHcCCCHHH----HHHHHhCCeEEEEECCCCCEEEeec
Confidence 44689999999999998876 5899999999999999999999865
No 182
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=65.29 E-value=11 Score=32.15 Aligned_cols=49 Identities=18% Similarity=0.253 Sum_probs=42.4
Q ss_pred HHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEE
Q 026130 142 YIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIY 190 (243)
Q Consensus 142 yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIY 190 (243)
|-.....|.+.+||..+|++..-+..-++.|...|-|..+-...|-|.-
T Consensus 19 ~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s~rG~~GGy~L 67 (164)
T PRK10857 19 LNSEAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSVRGPGGGYLL 67 (164)
T ss_pred hCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCCCCCCCeec
Confidence 3345578999999999999999999999999999999987777777765
No 183
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=65.24 E-value=28 Score=33.08 Aligned_cols=56 Identities=13% Similarity=0.200 Sum_probs=41.3
Q ss_pred HHHHh-cCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHH
Q 026130 141 EYIKK-HKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVAD 201 (243)
Q Consensus 141 ~yIK~-~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~ 201 (243)
.++.. .+.+.+.|||..-|+++.|||..++. .|.| ..-..+-+|+|+++.++..-+
T Consensus 215 ~~L~~~~~~isi~~is~~T~i~~~Dii~tL~~---l~~l--~~~~g~~~i~~~~~~~~~~~~ 271 (290)
T PLN03238 215 EQLRDVKGDVSIKDLSLATGIRGEDIVSTLQS---LNLI--KYWKGQHVIHVDQRVLDEHWA 271 (290)
T ss_pred HHHHhcCCCccHHHHHHHhCCCHHHHHHHHHH---CCcE--EEECCcEEEEeCHHHHHHHHH
Confidence 34444 57899999999999999999877664 5655 345567788899887666443
No 184
>KOG4364 consensus Chromatin assembly factor-I [Chromatin structure and dynamics]
Probab=64.92 E-value=54 Score=34.81 Aligned_cols=15 Identities=13% Similarity=0.233 Sum_probs=9.4
Q ss_pred hhHHHHHHHHHHhcC
Q 026130 133 RDLLADFVEYIKKHK 147 (243)
Q Consensus 133 ~~lL~~Fi~yIK~~K 147 (243)
.+.+..|+.-|+..+
T Consensus 372 ~aei~Kffqk~~~k~ 386 (811)
T KOG4364|consen 372 EAEIGKFFQKIDNKF 386 (811)
T ss_pred HHHHHhhhccccccc
Confidence 345777777775544
No 185
>PF07160 DUF1395: Protein of unknown function (DUF1395); InterPro: IPR009829 This family consists of several hypothetical eukaryotic proteins of around 250 residues in length. The function of this family is unknown.; PDB: 4AJ5_G.
Probab=64.73 E-value=2.1 Score=38.92 Aligned_cols=31 Identities=19% Similarity=0.617 Sum_probs=0.0
Q ss_pred EEEcHHHHHHHHHHHHhcCCccHHHHHhhcccc
Q 026130 189 IYISQAEMKAVADYIKRQGRVSISHLASKSNQF 221 (243)
Q Consensus 189 IYIS~eEl~aVA~fI~~rGRVSi~eLa~~sN~l 221 (243)
=|||.+|++.|=+|++ ||+|+..|-.+.+.+
T Consensus 130 ~~IT~eEF~sIPkYMr--GRLTleqlN~~i~ei 160 (243)
T PF07160_consen 130 WFITVEEFDSIPKYMR--GRLTLEQLNAAIDEI 160 (243)
T ss_dssp ---------------------------------
T ss_pred ccccHHHHhcchHHHH--hhccHHHHHHHHHHH
Confidence 3899999999999997 999988776666543
No 186
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=64.69 E-value=10 Score=32.84 Aligned_cols=53 Identities=15% Similarity=0.182 Sum_probs=37.7
Q ss_pred HHHHHHHHhcCc-----c-chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEc
Q 026130 137 ADFVEYIKKHKC-----I-PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYIS 192 (243)
Q Consensus 137 ~~Fi~yIK~~Kv-----V-~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS 192 (243)
..+.+.|....+ + .-.+||..||++..-|-.-|..|+.+|.|.- -.|+-.||+
T Consensus 14 ~~l~~~I~~g~l~pG~~LPsE~eLae~~gVSRt~VReAL~~L~~eGlv~~---~~g~G~~V~ 72 (239)
T PRK04984 14 EYIIESIWNNRFPPGSILPAERELSELIGVTRTTLREVLQRLARDGWLTI---QHGKPTKVN 72 (239)
T ss_pred HHHHHHHHcCCCCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE---eCCCeeEeC
Confidence 344445554443 3 4568999999999999999999999998873 234444454
No 187
>PHA00738 putative HTH transcription regulator
Probab=64.30 E-value=24 Score=29.08 Aligned_cols=56 Identities=13% Similarity=0.237 Sum_probs=44.2
Q ss_pred HHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHH
Q 026130 137 ADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQA 194 (243)
Q Consensus 137 ~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~e 194 (243)
...+.+|....-+.+.+|+..|+|+..-+-.-|+-|...|-|+-- ..|+++|.+-.
T Consensus 15 r~IL~lL~~~e~~~V~eLae~l~lSQptVS~HLKvLreAGLV~sr--K~Gr~vyY~Ln 70 (108)
T PHA00738 15 RKILELIAENYILSASLISHTLLLSYTTVLRHLKILNEQGYIELY--KEGRTLYAKIR 70 (108)
T ss_pred HHHHHHHHHcCCccHHHHHHhhCCCHHHHHHHHHHHHHCCceEEE--EECCEEEEEEC
Confidence 467778888767888999999999888888889999998877543 36777777643
No 188
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=64.29 E-value=27 Score=22.95 Aligned_cols=52 Identities=19% Similarity=0.181 Sum_probs=36.4
Q ss_pred HHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHH
Q 026130 136 LADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYI 203 (243)
Q Consensus 136 L~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI 203 (243)
+..+|..+...+-+...+||...|++ +.+|.++. +|+. .+|.+.+..+|+++
T Consensus 3 ~~~~l~~~r~~~gltq~~lA~~~gvs-~~~vs~~e--------------~g~~-~~~~~~~~~i~~~l 54 (58)
T TIGR03070 3 IGMLVRARRKALGLTQADLADLAGVG-LRFIRDVE--------------NGKP-TVRLDKVLRVLDAL 54 (58)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhCCC-HHHHHHHH--------------CCCC-CCCHHHHHHHHHHc
Confidence 34556666666677789999999995 55666664 4442 46888888888775
No 189
>PF08222 HTH_CodY: CodY helix-turn-helix domain; InterPro: IPR013198 This family consists of the C-terminal helix-turn-helix domain found in several bacterial GTP-sensing transcriptional pleiotropic repressor CodY proteins. CodY has been found to repress the dipeptide transport operon (dpp) of Bacillus subtilis in nutrient-rich conditions []. The CodY protein also has a repressor effect on many genes in Lactococcus lactis during growth in milk [].; PDB: 2B0L_C.
Probab=64.08 E-value=17 Score=27.18 Aligned_cols=43 Identities=21% Similarity=0.425 Sum_probs=30.1
Q ss_pred cchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeC-----CCCeEEEcHHH
Q 026130 149 IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDD-----RGKYIYISQAE 195 (243)
Q Consensus 149 V~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDD-----RGKFIYIS~eE 195 (243)
++-..+|-.+|+....++|-+..|+..| ||+. .|.||.|--..
T Consensus 5 lvas~iAd~~GiTRSvIVNALRKleSaG----vIesrSlGmKGT~ikvlN~~ 52 (61)
T PF08222_consen 5 LVASKIADRVGITRSVIVNALRKLESAG----VIESRSLGMKGTYIKVLNDY 52 (61)
T ss_dssp E-HHHHHHHHT--HHHHHHHHHHHHHTT----SEEEEETTSS-EEEEE--TH
T ss_pred ehHHHHHHHhCccHHHHHHHHHHHHhcC----ceeecccCCCceeeeeecHH
Confidence 4456789999999999999999999976 5554 49999886544
No 190
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=63.94 E-value=12 Score=31.94 Aligned_cols=46 Identities=17% Similarity=0.223 Sum_probs=32.5
Q ss_pred HHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEc-HHHHHHHHHH
Q 026130 152 EDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYIS-QAEMKAVADY 202 (243)
Q Consensus 152 EdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS-~eEl~aVA~f 202 (243)
.|||..+|++.+-+-.-++.|...| | ++ .+ +.|.|. .+-|..++.+
T Consensus 177 ~~iA~~lG~tretvsR~l~~L~~~g-l--~~-~~-~~i~I~d~~~L~~~~~~ 223 (236)
T PRK09392 177 RVLASYLGMTPENLSRAFAALASHG-V--HV-DG-SAVTITDPAGLARFAKP 223 (236)
T ss_pred HHHHHHhCCChhHHHHHHHHHHhCC-e--Ee-eC-CEEEEcCHHHHHHhhcc
Confidence 7899999997766555589999999 5 33 34 456664 6666665543
No 191
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=63.65 E-value=20 Score=30.49 Aligned_cols=48 Identities=19% Similarity=0.339 Sum_probs=35.5
Q ss_pred cchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEc-HHHHHHHH
Q 026130 149 IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYIS-QAEMKAVA 200 (243)
Q Consensus 149 V~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS-~eEl~aVA 200 (243)
+...+||...|++.+-+-.-++.|.++|. |.-.|++|+|. ...|..+|
T Consensus 185 lt~~~iA~~lG~sr~tvsR~l~~l~~~g~----I~~~~~~i~i~d~~~L~~~~ 233 (235)
T PRK11161 185 MTRGDIGNYLGLTVETISRLLGRFQKSGM----LAVKGKYITIENNDALAQLA 233 (235)
T ss_pred ccHHHHHHHhCCcHHHHHHHHHHHHHCCC----EEecCCEEEEcCHHHHHHHh
Confidence 45689999999977766666899999865 55666677775 66666554
No 192
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=63.57 E-value=35 Score=26.63 Aligned_cols=66 Identities=11% Similarity=0.104 Sum_probs=45.9
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhc-CCcceeeeCCCCeEEEcHHHHHHHHHHHH--hcCCccHHHHHhhccc
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENM-GRLSGVMDDRGKYIYISQAEMKAVADYIK--RQGRVSISHLASKSNQ 220 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~-g~LtGViDDRGKFIYIS~eEl~aVA~fI~--~rGRVSi~eLa~~sN~ 220 (243)
.+.++|..+|+++.- |...+.. |.| ++.-+.|.|=|.|++++..+..... +..-+||+++...-|.
T Consensus 2 ti~EvA~~~gVs~~t----LR~ye~~~gli-~p~r~~~g~R~Yt~~di~~l~~I~~llr~~G~~l~~i~~~l~~ 70 (99)
T cd04765 2 SIGEVAEILGLPPHV----LRYWETEFPQL-KPVKRAGGRRYYRPKDVELLLLIKHLLYEKGYTIEGAKQALKE 70 (99)
T ss_pred CHHHHHHHHCcCHHH----HHHHHHHcCCC-CCcCCCCCCeeeCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence 356899999997654 4455666 544 4444556688899999998865543 2345999888876654
No 193
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=63.55 E-value=30 Score=27.19 Aligned_cols=63 Identities=16% Similarity=0.292 Sum_probs=46.0
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHH--HHHHhcCCccHHHHHhh
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVA--DYIKRQGRVSISHLASK 217 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA--~fI~~rGRVSi~eLa~~ 217 (243)
.+.++|..||+++.- |.-.+..|.|..+-.+.|-|=|-|++++..+. .+.++-| +|+.++...
T Consensus 2 ~i~e~a~~~gvs~~t----lr~ye~~gll~~~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G-~sL~eI~~~ 66 (113)
T cd01109 2 TIKEVAEKTGLSADT----LRYYEKEGLLPPVKRDENGIRDFTEEDLEWLEFIKCLRNTG-MSIKDIKEY 66 (113)
T ss_pred CHHHHHHHHCcCHHH----HHHHHHCCCCCCCCcCCCCCccCCHHHHHHHHHHHHHHHcC-CCHHHHHHH
Confidence 367899999997655 44557789886655555667788999998874 3455567 998887654
No 194
>PF03701 UPF0181: Uncharacterised protein family (UPF0181); InterPro: IPR005371 This family contains small proteins of about 50 amino acids of unknown function. The family includes YoaH P76260 from SWISSPROT.
Probab=63.49 E-value=5.4 Score=28.89 Aligned_cols=31 Identities=32% Similarity=0.458 Sum_probs=24.8
Q ss_pred hHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHh
Q 026130 162 TQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKR 205 (243)
Q Consensus 162 tqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~ 205 (243)
.|.+|+||+.|.+.|.=+| +=+.-||+-|+.
T Consensus 13 QQ~AvE~Iq~LMaqGmSsg-------------EAI~~VA~~iRe 43 (51)
T PF03701_consen 13 QQQAVERIQELMAQGMSSG-------------EAIAIVAQEIRE 43 (51)
T ss_pred HHHHHHHHHHHHHhcccHH-------------HHHHHHHHHHHH
Confidence 4789999999999998665 556777777765
No 195
>KOG1497 consensus COP9 signalosome, subunit CSN4 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=63.45 E-value=12 Score=36.54 Aligned_cols=50 Identities=20% Similarity=0.325 Sum_probs=42.0
Q ss_pred ccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEc-HHHHH
Q 026130 148 CIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYIS-QAEMK 197 (243)
Q Consensus 148 vV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS-~eEl~ 197 (243)
++..+.|+.+|++++.-+-.-.-++.-+|++.|-||.=.-+|+.- .++|.
T Consensus 317 nisf~~Lg~ll~i~~ekaekiaa~MI~qeRmng~IDQ~egiihFe~~e~l~ 367 (399)
T KOG1497|consen 317 NISFEELGALLKIDAEKAEKIAAQMITQERMNGSIDQIEGIIHFEDREELP 367 (399)
T ss_pred hccHHHHHHHhCCCHHHHHHHHHHHHhHHHhccchHhhcceEeecchhhhh
Confidence 567889999999999999888999999999999999865666554 46663
No 196
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=63.39 E-value=12 Score=32.86 Aligned_cols=42 Identities=17% Similarity=0.183 Sum_probs=34.0
Q ss_pred ccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEE
Q 026130 148 CIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIY 190 (243)
Q Consensus 148 vV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIY 190 (243)
+..-.+||..||++-.-|-.-|+.|+.+|.|+ +.--+|-||-
T Consensus 26 LpsE~eLae~~gVSRtpVREAL~~Le~~GlV~-~~~~~G~~V~ 67 (253)
T PRK10421 26 LPAERQLAMQLGVSRNSLREALAKLVSEGVLL-SRRGGGTFIR 67 (253)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE-EeCCCeEEEe
Confidence 33567999999999999999999999999987 3334666653
No 197
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain
Probab=63.24 E-value=26 Score=29.96 Aligned_cols=66 Identities=20% Similarity=0.333 Sum_probs=49.3
Q ss_pred cchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHh-c-CCccHHHHHhhcc
Q 026130 149 IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKR-Q-GRVSISHLASKSN 219 (243)
Q Consensus 149 V~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~-r-GRVSi~eLa~~sN 219 (243)
..+.+||..||+++.- |.-.+..|-|.....+.|.|=|-|++++..| .+|+. + .-+|+.++....+
T Consensus 2 ~~I~evA~~~gvs~~t----LRyYe~~GLl~p~~r~~~gyR~Y~~~dl~rL-~~I~~lr~~G~sL~eI~~ll~ 69 (172)
T cd04790 2 LTISQLARQFGLSRST----LLYYERIGLLSPSARSESNYRLYGERDLERL-EQICAYRSAGVSLEDIRSLLQ 69 (172)
T ss_pred CCHHHHHHHHCcCHHH----HHHHHHCCCCCCCccCCCCCccCCHHHHHHH-HHHHHHHHcCCCHHHHHHHHh
Confidence 3578999999998765 4556778999987777778888899998887 33332 2 4488888777554
No 198
>PRK13749 transcriptional regulator MerD; Provisional
Probab=62.28 E-value=29 Score=28.54 Aligned_cols=65 Identities=15% Similarity=0.234 Sum_probs=51.6
Q ss_pred cchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHh--cCCccHHHHHhhc
Q 026130 149 IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKR--QGRVSISHLASKS 218 (243)
Q Consensus 149 V~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~--rGRVSi~eLa~~s 218 (243)
..+.+||..+|+++. -|.-.+..|-|.++-.+.|.|=|-|+..+..+ .||+. .==+|+.++....
T Consensus 4 ~tIgelA~~~gvS~~----tiR~YE~~GLl~p~~r~~~gyR~Y~~~~l~rL-~~I~~~r~~G~sL~eI~~ll 70 (121)
T PRK13749 4 YTVSRLALDAGVSVH----IVRDYLLRGLLRPVACTTGGYGLFDDAALQRL-CFVRAAFEAGIGLDALARLC 70 (121)
T ss_pred CcHHHHHHHHCCCHH----HHHHHHHCCCCCCCCcCCCCCccCCHHHHHHH-HHHHHHHHcCCCHHHHHHHH
Confidence 467899999999865 46778899999998777799999999999998 56653 4457877776543
No 199
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=62.26 E-value=16 Score=32.51 Aligned_cols=52 Identities=12% Similarity=0.124 Sum_probs=45.7
Q ss_pred ccchhHHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCccee
Q 026130 130 DGDRDLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGV 181 (243)
Q Consensus 130 ~~~~~lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGV 181 (243)
...-+|+..+|+++..+.-+.-=+||.++||...+|=.-+=.|+..|.|..+
T Consensus 9 ~~~~~lv~~~~~~l~~~~~~~a~~i~~~l~~~k~~vNr~LY~l~~~~~v~~~ 60 (183)
T PHA03103 9 VDIYELVKKEVKNLGLGEGITAIEISRKLNIEKSEVNKQLYKLQREGMVYMS 60 (183)
T ss_pred HHHHHHHHHHHHHhccCCCccHHHHHHHhCCCHHHHHHHHHHHHhcCceecC
Confidence 3456789999999999999999999999999998865568899999999776
No 200
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=62.13 E-value=52 Score=29.17 Aligned_cols=88 Identities=9% Similarity=0.222 Sum_probs=62.8
Q ss_pred HHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhcCCcc-----H
Q 026130 137 ADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRVS-----I 211 (243)
Q Consensus 137 ~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~rGRVS-----i 211 (243)
-..++++-.+.-+.|.|||.+.||+..-|-.-++.|...|-|.=. ++.|+| ++++.=+.--..|+....-+. +
T Consensus 17 l~IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~~~-~~~~~Y-~lG~~~~~lg~~~~~~~~l~~~a~p~l 94 (257)
T PRK15090 17 FGILQALGEEREIGITELSQRVMMSKSTVYRFLQTMKTLGYVAQE-GESEKY-SLTLKLFELGAKALQNVDLIRSADIQM 94 (257)
T ss_pred HHHHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEc-CCCCcE-EecHHHHHHHHHHHhhCcHHHHHHHHH
Confidence 345566666677899999999999999999999999999987532 345665 477775555555665554333 3
Q ss_pred HHHHhhccccccccc
Q 026130 212 SHLASKSNQFIDLET 226 (243)
Q Consensus 212 ~eLa~~sN~lI~L~p 226 (243)
.+|+..+|.-+.|.-
T Consensus 95 ~~La~~~~etv~L~v 109 (257)
T PRK15090 95 REISRLTKETIHLGA 109 (257)
T ss_pred HHHHHHhCCeEEEEE
Confidence 677777777655543
No 201
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=62.10 E-value=44 Score=25.26 Aligned_cols=65 Identities=14% Similarity=0.086 Sum_probs=46.4
Q ss_pred cchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhc--CCccHHHHHhhc
Q 026130 149 IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQ--GRVSISHLASKS 218 (243)
Q Consensus 149 V~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~r--GRVSi~eLa~~s 218 (243)
..+.++|..+|+++.- |...+..|.|...-+ .|.|-|.|+.++..+..-..-+ --+|++++...-
T Consensus 2 ~~i~e~A~~~gvs~~t----Lr~ye~~Gli~p~r~-~~g~R~y~~~dv~~l~~i~~L~~d~g~~l~~i~~~l 68 (91)
T cd04766 2 YVISVAAELSGMHPQT----LRLYERLGLLSPSRT-DGGTRRYSERDIERLRRIQRLTQELGVNLAGVKRIL 68 (91)
T ss_pred cCHHHHHHHHCcCHHH----HHHHHHCCCcCCCcC-CCCCeeECHHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 4578999999998765 445577899987654 4568889999998876554322 348887665543
No 202
>PRK14585 pgaD putative PGA biosynthesis protein; Provisional
Probab=62.04 E-value=9.8 Score=32.53 Aligned_cols=45 Identities=11% Similarity=0.163 Sum_probs=39.9
Q ss_pred CccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHH
Q 026130 147 KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAE 195 (243)
Q Consensus 147 KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eE 195 (243)
..+..++||+.||++++. +++|...+.+|==+||-|.-+.|+-|-
T Consensus 88 ~~~~~~eLA~Sf~is~el----~~qL~~~~~lTvh~D~~G~i~~v~~~~ 132 (137)
T PRK14585 88 YQYTPQEYAESLAIPDEL----YQQLQKSHRMSVHFTSQGQIKMVVSEK 132 (137)
T ss_pred CCCChHHHHHHcCCCHHH----HHHHhcCCeEEEEEcCCCCchhhhHHH
Confidence 678889999999998864 789999999999999999999887664
No 203
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=61.99 E-value=19 Score=31.50 Aligned_cols=56 Identities=20% Similarity=0.237 Sum_probs=40.2
Q ss_pred HHHHHHHHHHhcC------ccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcH
Q 026130 135 LLADFVEYIKKHK------CIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQ 193 (243)
Q Consensus 135 lL~~Fi~yIK~~K------vV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~ 193 (243)
....+.+.|-... +..-.+||..||++..-|.+-|+.|+.+|-|+-+ .|+-.||++
T Consensus 15 v~~~l~~~I~~g~l~pG~~LpsE~eLa~~lgVSRtpVREAL~~L~~eGlv~~~---~~~G~~V~~ 76 (254)
T PRK09464 15 IEQQLEFLILEGTLRPGEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRR---QGGGTFVQS 76 (254)
T ss_pred HHHHHHHHHHcCCCCCCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe---cCceeEEec
Confidence 3445555555443 3357789999999999999999999999988743 344445544
No 204
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=61.48 E-value=45 Score=27.74 Aligned_cols=67 Identities=19% Similarity=0.299 Sum_probs=48.3
Q ss_pred HHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCC--ccee--eeCCCC-----eEEEcHHHHHHHHHHHHhc
Q 026130 140 VEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGR--LSGV--MDDRGK-----YIYISQAEMKAVADYIKRQ 206 (243)
Q Consensus 140 i~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~--LtGV--iDDRGK-----FIYIS~eEl~aVA~fI~~r 206 (243)
++.+-.+.++.=+|||...||++.+|-.-+..|..++. .... .|..++ |-||....+-.|.+|-..+
T Consensus 7 ~d~L~~~~~~~dedLa~~l~i~~n~vRkiL~~L~ed~~~~~~~~~e~~~~~~~~~~~yw~i~y~~~~~vik~r~~~ 82 (147)
T smart00531 7 LDALMRNGCVTEEDLAELLGIKQKQLRKILYLLYDEKLIKIDYKREKDPETKTWYRYYWYINYDTLLDVVKYKLDK 82 (147)
T ss_pred hHHHHhcCCcCHHHHHHHhCCCHHHHHHHHHHHHhhhcchhheeeeeCCCCceEEEEEEEecHHHHHHHHHHHHHH
Confidence 44455678999999999999999999999999999555 3333 454444 4468877776666654433
No 205
>PRK14999 histidine utilization repressor; Provisional
Probab=61.43 E-value=24 Score=30.81 Aligned_cols=70 Identities=16% Similarity=0.282 Sum_probs=45.9
Q ss_pred HHHHHHHHhc------CccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcH-------HHHHHHHHHH
Q 026130 137 ADFVEYIKKH------KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQ-------AEMKAVADYI 203 (243)
Q Consensus 137 ~~Fi~yIK~~------KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~-------eEl~aVA~fI 203 (243)
..+.+.|... |+=.-.+||..||++..-|..-|..|..+|.|.-+= -+|.|| ++ ..+..+...+
T Consensus 19 ~~i~~~I~~g~~~~G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~~-GkGTfV--~~~~~~~~~~~~~~~~~~~ 95 (241)
T PRK14999 19 QDICKKIAGGVWQPHDRIPSEAELVAQYGFSRMTINRALRELTDEGWLVRLQ-GVGTFV--AEPKGQSALFEVRSIAEEI 95 (241)
T ss_pred HHHHHHHHcCCCCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec-CcEEEE--CCCCccccHHHHHHHHHHH
Confidence 4455556543 344567899999999999999999999999875321 145554 32 2244455555
Q ss_pred HhcCCc
Q 026130 204 KRQGRV 209 (243)
Q Consensus 204 ~~rGRV 209 (243)
...|..
T Consensus 96 ~~~g~~ 101 (241)
T PRK14999 96 AARRHQ 101 (241)
T ss_pred HHcCCC
Confidence 555643
No 206
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=61.11 E-value=30 Score=30.64 Aligned_cols=75 Identities=11% Similarity=0.201 Sum_probs=54.5
Q ss_pred hHHHHHHHHHHhc--CccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhcCCccH
Q 026130 134 DLLADFVEYIKKH--KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRVSI 211 (243)
Q Consensus 134 ~lL~~Fi~yIK~~--KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~rGRVSi 211 (243)
..+..+++||-.+ .-+.|++||.++|++..-+....+.-..... .+ ||..-=|......+.. +..||
T Consensus 183 ~~i~~~~~~i~~~~~~~isl~~lA~~~~lS~~~l~r~Fk~~~G~tp----~~------~l~~~Rl~~A~~lL~~-t~~sI 251 (290)
T PRK10572 183 PRVREACQYISDHLASEFDIESVAQHVCLSPSRLAHLFRQQLGISV----LR------WREDQRISRAKLLLQT-TRMPI 251 (290)
T ss_pred HHHHHHHHHHHhcccCCCCHHHHHHHHCCCHHHHHHHHHHHHCcCH----HH------HHHHHHHHHHHHHHHc-CCCCH
Confidence 4688999999554 4688999999999998776666665432221 11 6666667777776654 77999
Q ss_pred HHHHhhcc
Q 026130 212 SHLASKSN 219 (243)
Q Consensus 212 ~eLa~~sN 219 (243)
+++|..|.
T Consensus 252 ~eIA~~~G 259 (290)
T PRK10572 252 ATIGRNVG 259 (290)
T ss_pred HHHHHHhC
Confidence 99998764
No 207
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=60.98 E-value=13 Score=32.52 Aligned_cols=54 Identities=13% Similarity=0.206 Sum_probs=39.3
Q ss_pred HHHHHHHHHhcCc-----c-chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEE
Q 026130 136 LADFVEYIKKHKC-----I-PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIY 190 (243)
Q Consensus 136 L~~Fi~yIK~~Kv-----V-~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIY 190 (243)
...+.+.|....+ + .-.+||..||++..-|-+-|+.|+.+|-|.-+ --+|-||-
T Consensus 13 ~~~i~~~I~~g~l~pG~~LPsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~-~~~G~~V~ 72 (251)
T PRK09990 13 AERIERLIVDGVLKVGQALPSERRLCEKLGFSRSALREGLTVLRGRGIIETA-QGRGSFVA 72 (251)
T ss_pred HHHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe-CCCeeEEe
Confidence 3444445544332 3 45699999999999999999999999988733 34677664
No 208
>TIGR03337 phnR transcriptional regulator protein. 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 Salmonella, Vibrio Aeromonas hydrophila, Hahella chejuensis and Psychromonas ingrahamii.
Probab=60.91 E-value=26 Score=30.01 Aligned_cols=54 Identities=19% Similarity=0.210 Sum_probs=41.2
Q ss_pred HHHHHHHHHHhc------CccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeE
Q 026130 135 LLADFVEYIKKH------KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYI 189 (243)
Q Consensus 135 lL~~Fi~yIK~~------KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFI 189 (243)
+-..|.+.|... ++-.-.+||..||++.--+..+|..|..+|.|..+- -+|.||
T Consensus 6 i~~~l~~~I~~g~~~~g~~lPsE~eLa~~~~Vsr~Tvr~Al~~L~~eGli~~~~-g~Gt~V 65 (231)
T TIGR03337 6 IKDHLSYQIRAGALLPGDKLPSERDLGERFNTTRVTIREALQQLEAEGLIYRED-RRGWFV 65 (231)
T ss_pred HHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCeEEEeC-CCEEEE
Confidence 345677777653 344567899999999999999999999999987642 256665
No 209
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=60.89 E-value=18 Score=28.53 Aligned_cols=46 Identities=13% Similarity=0.194 Sum_probs=38.9
Q ss_pred cCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEE
Q 026130 146 HKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYI 191 (243)
Q Consensus 146 ~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYI 191 (243)
...+.+.+||..+|++..-+-+-++.|...|-|..+-...|-|..-
T Consensus 23 ~~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~~~g~~ggy~l~ 68 (132)
T TIGR00738 23 EGPVSVKEIAERQGISRSYLEKILRTLRRAGLVESVRGPGGGYRLA 68 (132)
T ss_pred CCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEeccCCCCCccCC
Confidence 3489999999999999999999999999999987655556666653
No 210
>PRK03837 transcriptional regulator NanR; Provisional
Probab=60.83 E-value=31 Score=29.70 Aligned_cols=54 Identities=11% Similarity=0.158 Sum_probs=40.0
Q ss_pred HHHHHHHHHHhcCc-----c-chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeE
Q 026130 135 LLADFVEYIKKHKC-----I-PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYI 189 (243)
Q Consensus 135 lL~~Fi~yIK~~Kv-----V-~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFI 189 (243)
....+.+.|-...+ + ...+||..||++..-|-+-|..|+..|-|+-+ --+|-||
T Consensus 18 v~~~l~~~I~~g~l~pG~~Lp~E~~Lae~~gVSRt~VREAL~~L~~eGlv~~~-~~~G~~V 77 (241)
T PRK03837 18 VEERLEQMIRSGEFGPGDQLPSERELMAFFGVGRPAVREALQALKRKGLVQIS-HGERARV 77 (241)
T ss_pred HHHHHHHHHHhCCCCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe-cCCceeE
Confidence 44555556655544 3 56799999999999999999999999998763 2344443
No 211
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=60.66 E-value=23 Score=24.16 Aligned_cols=37 Identities=16% Similarity=0.286 Sum_probs=28.8
Q ss_pred hHHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHH
Q 026130 134 DLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITS 171 (243)
Q Consensus 134 ~lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~ 171 (243)
+.|+.=|++|+..+ +.+-..|..||++..-+.+|+.-
T Consensus 3 e~l~~Ai~~v~~g~-~S~r~AA~~ygVp~sTL~~r~~g 39 (45)
T PF05225_consen 3 EDLQKAIEAVKNGK-MSIRKAAKKYGVPRSTLRRRLRG 39 (45)
T ss_dssp HHHHHHHHHHHTTS-S-HHHHHHHHT--HHHHHHHHHH
T ss_pred HHHHHHHHHHHhCC-CCHHHHHHHHCcCHHHHHHHHcC
Confidence 45778889999999 89999999999999888887753
No 212
>cd04772 HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.
Probab=60.60 E-value=42 Score=26.08 Aligned_cols=61 Identities=15% Similarity=0.159 Sum_probs=45.0
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhc-CCccHHHHH
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQ-GRVSISHLA 215 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~r-GRVSi~eLa 215 (243)
.+.++|..||+++.- |.-.+..|.|..+..+.|-|=|.|++++..+ .||+.- =-++++++.
T Consensus 2 ~i~e~A~~~gvs~~t----lR~Ye~~Gll~~~~r~~~g~R~Y~~~~v~~l-~~I~~l~~g~~l~~i~ 63 (99)
T cd04772 2 RTVDLARAIGLSPQT----VRNYESLGLIPPAERTANGYRIYTDKHIAAL-RAYRALLPGYGYRVAQ 63 (99)
T ss_pred CHHHHHHHHCcCHHH----HHHHHHcCCCCCCCcCCCCCeecCHHHHHHH-HHHHHHhhCCCHHHHH
Confidence 367899999998754 4566889999987666666888999999887 556543 145566553
No 213
>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional
Probab=60.53 E-value=58 Score=33.02 Aligned_cols=79 Identities=14% Similarity=0.184 Sum_probs=57.8
Q ss_pred HHHHHHHHHh-cCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHH---------HHHHHHh
Q 026130 136 LADFVEYIKK-HKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKA---------VADYIKR 205 (243)
Q Consensus 136 L~~Fi~yIK~-~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~a---------VA~fI~~ 205 (243)
-..++.++.. ...+..++||..+|++.+.++.-|..|++.|.|+ |....-+++-+|++-... |.++|..
T Consensus 8 e~~iL~~l~~~~~~~~~~~la~~~~~~~~~v~~~~~~L~~kg~v~-~~~~~~~~~~LT~eG~~~~~~G~PE~rl~~~l~~ 86 (494)
T PTZ00326 8 ENTILSKLESENEIVNSLALAESLNIDHQKVVGAIKSLESANYIT-TEMKKSNTWTLTEEGEDYLKNGSPEYRLWQKLKE 86 (494)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHHHhCCCEE-EEEEEEEEEEECHHHHHHHHcCCHHHHHHHHhhh
Confidence 3466677777 6788999999999999999999999999998444 444445555677764332 4457777
Q ss_pred cCCccHHHHHh
Q 026130 206 QGRVSISHLAS 216 (243)
Q Consensus 206 rGRVSi~eLa~ 216 (243)
.| +++.+|..
T Consensus 87 ~~-~~~~~l~~ 96 (494)
T PTZ00326 87 GG-ISKADDAK 96 (494)
T ss_pred cC-CCHHHHHh
Confidence 66 46667654
No 214
>KOG2412 consensus Nuclear-export-signal (NES)-containing protein/polyadenylated-RNA export factor [RNA processing and modification]
Probab=60.32 E-value=70 Score=33.13 Aligned_cols=6 Identities=17% Similarity=0.013 Sum_probs=2.5
Q ss_pred HHHHHH
Q 026130 137 ADFVEY 142 (243)
Q Consensus 137 ~~Fi~y 142 (243)
+-|-+|
T Consensus 304 ~m~w~~ 309 (591)
T KOG2412|consen 304 QMFWNS 309 (591)
T ss_pred HhhhhH
Confidence 344443
No 215
>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator HspR and related proteins, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=60.32 E-value=48 Score=25.70 Aligned_cols=63 Identities=11% Similarity=0.146 Sum_probs=45.5
Q ss_pred cchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhc--CCccHHHHHh
Q 026130 149 IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQ--GRVSISHLAS 216 (243)
Q Consensus 149 V~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~r--GRVSi~eLa~ 216 (243)
..+.++|..+|+++.-+. ..+..|.|..+- +.|.+-|.|+.++..|-....-+ .=+|+.++..
T Consensus 2 ~~i~eva~~~gVs~~tLR----~ye~~Gli~p~r-~~~g~R~Ys~~dv~~l~~I~~L~~~~G~~l~~i~~ 66 (98)
T cd01279 2 YPISVAAELLGIHPQTLR----VYDRLGLVSPAR-TNGGGRRYSNNDLELLRQVQRLSQDEGFNLAGIKR 66 (98)
T ss_pred cCHHHHHHHHCcCHHHHH----HHHHCCCCCCCc-CCCCCeeECHHHHHHHHHHHHHHHHCCCCHHHHHH
Confidence 467899999999876544 446789888754 45677788999999887755433 4688766553
No 216
>PRK15481 transcriptional regulatory protein PtsJ; Provisional
Probab=59.84 E-value=27 Score=32.92 Aligned_cols=57 Identities=16% Similarity=0.278 Sum_probs=43.7
Q ss_pred hhHHHHHHHHHHh------cCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEE
Q 026130 133 RDLLADFVEYIKK------HKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIY 190 (243)
Q Consensus 133 ~~lL~~Fi~yIK~------~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIY 190 (243)
+.+.+.+...|.. .|+-..-+||.+||++..-|..-+..|+++|.|+. .--+|.||.
T Consensus 8 ~~~~~~i~~~i~~g~l~~g~~lps~r~la~~~~vsr~tv~~a~~~L~~~g~i~~-~~~~G~~v~ 70 (431)
T PRK15481 8 NEIFDSIRQLIQAGRLRPGDSLPPVRELASELGVNRNTVAAAYKRLVTAGLAQS-QGRNGTVIR 70 (431)
T ss_pred HHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE-eCCCceEEc
Confidence 3445556666654 44556789999999999999999999999998874 334787774
No 217
>PF13814 Replic_Relax: Replication-relaxation
Probab=59.38 E-value=31 Score=28.63 Aligned_cols=61 Identities=16% Similarity=0.379 Sum_probs=50.1
Q ss_pred HHHHhcCccchHHHHHHcCCChH---HHHHHHHHHHhcCCcceeeeC------CCCeE-EEcHHHHHHHHH
Q 026130 141 EYIKKHKCIPLEDLAAEFKLRTQ---ECINRITSLENMGRLSGVMDD------RGKYI-YISQAEMKAVAD 201 (243)
Q Consensus 141 ~yIK~~KvV~LEdLA~~F~lrtq---d~I~RIq~Le~~g~LtGViDD------RGKFI-YIS~eEl~aVA~ 201 (243)
.+|-.++++..+.|+.-|+.... -|-.|++.|...|-|.-+-.- .+.+| |+|+.-...|+.
T Consensus 2 ~~L~~~r~lt~~Qi~~l~~~~~~~~~~~~rrL~~L~~~glv~~~~~~~~~~~g~~~~vy~Lt~~G~~~l~~ 72 (191)
T PF13814_consen 2 RLLARHRFLTTDQIARLLFPSSKSERTARRRLKRLRELGLVDRFRRRVGARGGSQPYVYYLTPAGARLLAD 72 (191)
T ss_pred hhHHHhcCcCHHHHHHHHcCCCcchHHHHHHHHHHhhCCcEEeecccccccCCCcceEEEECHHHHHHHHh
Confidence 45778999999999999999997 688999999999988777653 34566 789988877763
No 218
>PRK13503 transcriptional activator RhaS; Provisional
Probab=59.36 E-value=19 Score=31.29 Aligned_cols=76 Identities=14% Similarity=0.325 Sum_probs=51.8
Q ss_pred chhHHHHHHHHHHhc--CccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhcCCc
Q 026130 132 DRDLLADFVEYIKKH--KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRV 209 (243)
Q Consensus 132 ~~~lL~~Fi~yIK~~--KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~rGRV 209 (243)
....+..+++||..+ +-+.|+|||..|||+..-+....+.---... .=||..-=|......| ..+..
T Consensus 169 ~~~~i~~~~~~I~~~~~~~~tl~~lA~~~~lS~~~l~r~Fk~~~G~S~----------~~yi~~~Rl~~A~~LL-~~~~~ 237 (278)
T PRK13503 169 SDARLNQLLAWLEDHFAEEVNWEALADQFSLSLRTLHRQLKQQTGLTP----------QRYLNRLRLLKARHLL-RHSDA 237 (278)
T ss_pred cHHHHHHHHHHHHHhhcCCCCHHHHHHHHCCCHHHHHHHHHHHhCcCH----------HHHHHHHHHHHHHHHH-HcCCC
Confidence 345699999999877 6788999999999999888877775322110 1133444444444444 44667
Q ss_pred cHHHHHhhc
Q 026130 210 SISHLASKS 218 (243)
Q Consensus 210 Si~eLa~~s 218 (243)
||++++..|
T Consensus 238 sI~eIA~~~ 246 (278)
T PRK13503 238 SVTDIAYRC 246 (278)
T ss_pred CHHHHHHHh
Confidence 888888776
No 219
>TIGR02054 MerD mercuric resistence transcriptional repressor protein MerD. This model represents a transcriptional repressor protein of the MerR family (pfam00376) whose expression is regulated by the mercury-sensitive transcriptional activator, MerR. MerD has been shown to repress the transcription of the mer operon.
Probab=59.32 E-value=46 Score=27.20 Aligned_cols=68 Identities=13% Similarity=0.129 Sum_probs=52.8
Q ss_pred ccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHH-hcCCccHHHHHhhcc
Q 026130 148 CIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIK-RQGRVSISHLASKSN 219 (243)
Q Consensus 148 vV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~-~rGRVSi~eLa~~sN 219 (243)
...+.+||..+|+++. -|.--+..|-|..+-.+.|-|=|-|++.+..+..-.. +..-+|+.++...++
T Consensus 3 ~~tI~elA~~~gvs~~----tlR~Ye~~GLL~p~~r~~~gyR~Y~~~~l~rL~~I~~lr~~G~~L~eI~~ll~ 71 (120)
T TIGR02054 3 AYTISRLAEDAGVSVH----VVRDYLLRGLLHPVRRTTSGYGIFDDASLQRLRFVRAAFEAGIGLGELARLCR 71 (120)
T ss_pred CCcHHHHHHHHCcCHH----HHHHHHHCCCCCCCccCCCCCeeCCHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 3568899999999764 4667788899998866667799999999998754444 347799998886554
No 220
>PF01316 Arg_repressor: Arginine repressor, DNA binding domain; InterPro: IPR020900 The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia (Giardia intestinalis) []. The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 10% of total cell protein []. Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR []. This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine []. The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography []. The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006525 arginine metabolic process; PDB: 1AOY_A 3V4G_A 3LAJ_D 3FHZ_A 3LAP_B 3ERE_D 2P5L_C 1F9N_D 2P5K_A 1B4A_A ....
Probab=59.06 E-value=37 Score=25.53 Aligned_cols=58 Identities=31% Similarity=0.436 Sum_probs=35.3
Q ss_pred HHHHHHHHHHhcCccchHHHHHHc---CCC-hHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHH
Q 026130 135 LLADFVEYIKKHKCIPLEDLAAEF---KLR-TQECINRITSLENMGRLSGVMDDRGKYIYISQAE 195 (243)
Q Consensus 135 lL~~Fi~yIK~~KvV~LEdLA~~F---~lr-tqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eE 195 (243)
.+..+...|+.+.|..=+||...+ |+. ||-+|+| +|-..| ++=|-|..|+|+|.-|++
T Consensus 6 R~~~I~~li~~~~i~sQ~eL~~~L~~~Gi~vTQaTiSR--DLkeL~-~vKv~~~~g~~~Y~l~~~ 67 (70)
T PF01316_consen 6 RQELIKELISEHEISSQEELVELLEEEGIEVTQATISR--DLKELG-AVKVPDGNGKYRYVLPEE 67 (70)
T ss_dssp HHHHHHHHHHHS---SHHHHHHHHHHTT-T--HHHHHH--HHHHHT--EEEECTTSSEEEE-TTS
T ss_pred HHHHHHHHHHHCCcCCHHHHHHHHHHcCCCcchhHHHH--HHHHcC-cEEeeCCCCCEEEEecCc
Confidence 345666678888888777765432 333 7888887 344444 455889999999997764
No 221
>PF14502 HTH_41: Helix-turn-helix domain
Probab=59.02 E-value=15 Score=26.20 Aligned_cols=34 Identities=15% Similarity=0.288 Sum_probs=30.7
Q ss_pred cCccchHHHHHHcCCChHHHHHHHHHHHhcCCcc
Q 026130 146 HKCIPLEDLAAEFKLRTQECINRITSLENMGRLS 179 (243)
Q Consensus 146 ~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~Lt 179 (243)
.++-.+.+++..|+++.--+=+-|+.|+++|.|+
T Consensus 4 dRi~tI~e~~~~~~vs~GtiQ~Alk~Le~~gaI~ 37 (48)
T PF14502_consen 4 DRIPTISEYSEKFGVSRGTIQNALKFLEENGAIK 37 (48)
T ss_pred cccCCHHHHHHHhCcchhHHHHHHHHHHHCCcEE
Confidence 4577899999999999999999999999999885
No 222
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=58.92 E-value=11 Score=25.99 Aligned_cols=48 Identities=23% Similarity=0.396 Sum_probs=28.9
Q ss_pred cchHHHHHHcCCChHHHHHHH-HHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHH
Q 026130 149 IPLEDLAAEFKLRTQECINRI-TSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIK 204 (243)
Q Consensus 149 V~LEdLA~~F~lrtqd~I~RI-q~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~ 204 (243)
+-+.|||..+|+++.++|..+ +++ |+..-. --=.|++++...|+..+.
T Consensus 4 i~V~elAk~l~v~~~~ii~~l~~~~-------Gi~~~~-~~~~ld~e~~~~i~~~~~ 52 (54)
T PF04760_consen 4 IRVSELAKELGVPSKEIIKKLFKEL-------GIMVKS-INSSLDEEEAELIAEEFG 52 (54)
T ss_dssp E-TTHHHHHHSSSHHHHHHHH-HHH-------TS---S-SSS-EETTGGGHHHHHH-
T ss_pred eEHHHHHHHHCcCHHHHHHHHHHhC-------CcCcCC-CCCcCCHHHHHHHHHHhC
Confidence 457899999999999999888 545 333110 011256666666666543
No 223
>KOG4364 consensus Chromatin assembly factor-I [Chromatin structure and dynamics]
Probab=58.82 E-value=69 Score=34.10 Aligned_cols=10 Identities=20% Similarity=0.102 Sum_probs=4.7
Q ss_pred HHHHHHHhcC
Q 026130 198 AVADYIKRQG 207 (243)
Q Consensus 198 aVA~fI~~rG 207 (243)
.+|+|+..-|
T Consensus 457 ~~adf~~sa~ 466 (811)
T KOG4364|consen 457 EEADFDGSAC 466 (811)
T ss_pred eecccccccc
Confidence 3455554433
No 224
>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial. This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.
Probab=58.77 E-value=12 Score=32.50 Aligned_cols=71 Identities=20% Similarity=0.340 Sum_probs=46.5
Q ss_pred HHHHHHHHhc------CccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcH-------HHHHHHHHHH
Q 026130 137 ADFVEYIKKH------KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQ-------AEMKAVADYI 203 (243)
Q Consensus 137 ~~Fi~yIK~~------KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~-------eEl~aVA~fI 203 (243)
..+.+.|... |+=.-.+||..||++..-|..-|..|..+|.|.-+ --+|.|| ++ ..+..+...+
T Consensus 8 ~~l~~~I~~g~~~~g~~LPsE~eLa~~~~VSR~TVR~Al~~L~~eGli~r~-~G~GtfV--~~~~~~~~~~~~~~~~~~~ 84 (230)
T TIGR02018 8 QDILERIRSGEWPPGHRIPSEHELVAQYGCSRMTVNRALRELTDAGLLERR-QGVGTFV--AEPKAQSALLEIRNIADEI 84 (230)
T ss_pred HHHHHHHHhCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe-cCCEEEE--ccCcccchhhcchhHHHHH
Confidence 3444555543 44455689999999999999999999999987643 2256565 32 1234445556
Q ss_pred HhcCCcc
Q 026130 204 KRQGRVS 210 (243)
Q Consensus 204 ~~rGRVS 210 (243)
...|.-.
T Consensus 85 ~~~g~~~ 91 (230)
T TIGR02018 85 VARGHRY 91 (230)
T ss_pred HhcCCCc
Confidence 6666543
No 225
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=58.54 E-value=39 Score=25.55 Aligned_cols=66 Identities=11% Similarity=0.125 Sum_probs=47.3
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhc-CCccHHHHHhhccc
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQ-GRVSISHLASKSNQ 220 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~r-GRVSi~eLa~~sN~ 220 (243)
.+.++|..+|+++.-+. .....|.|.++.+..|.+ |.|+.++..+.....-+ .-+|+.++......
T Consensus 2 ~~~eva~~~gi~~~tlr----~~~~~Gll~~~~~~~g~r-~y~~~dv~~l~~i~~l~~~g~~~~~i~~~l~~ 68 (100)
T cd00592 2 TIGEVAKLLGVSVRTLR----YYEEKGLLPPERSENGYR-LYSEEDLERLRLIRRLRELGLSLKEIRELLDA 68 (100)
T ss_pred CHHHHHHHHCcCHHHHH----HHHHCCCcCCCcCCCCCc-ccCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 36789999999765543 456689998766665555 57999998776665554 57888888876543
No 226
>TIGR00331 hrcA heat shock gene repressor HrcA. In Bacillus subtilis, hrcA is the first gene of the dnaK operon and so is itself a heat shock gene.
Probab=58.45 E-value=23 Score=33.59 Aligned_cols=73 Identities=21% Similarity=0.367 Sum_probs=55.3
Q ss_pred hHHHHHHH-HHHhcCccchHHHHHH--cCCChHHHHHHHHHHHhcCCcc----eee---eCCC------Ce---EEEcHH
Q 026130 134 DLLADFVE-YIKKHKCIPLEDLAAE--FKLRTQECINRITSLENMGRLS----GVM---DDRG------KY---IYISQA 194 (243)
Q Consensus 134 ~lL~~Fi~-yIK~~KvV~LEdLA~~--F~lrtqd~I~RIq~Le~~g~Lt----GVi---DDRG------KF---IYIS~e 194 (243)
..|...|+ ||....-|...+||.. ||++..-+-+-+..|++.|.|. |.. -+.| .| -.++.+
T Consensus 6 ~il~aIV~~~l~~~~pv~s~~l~~~~~~~vS~aTiR~d~~~Le~~G~l~~~h~sagript~kGYR~yv~~~~~~~~~~~~ 85 (337)
T TIGR00331 6 KILKAIVEEYIKTGQPVGSKTLLEKYNLGLSSATIRNDMADLEDLGFIEKPHTSSGRIPTDKGYRYYVDHLLKVDSLTEE 85 (337)
T ss_pred HHHHHHHHHHHhcCCCcCHHHHHhhcCCCCChHHHHHHHHHHHHCCCccCCCCCCCcCcChhHHHHHHHHhcccCCCCHH
Confidence 45555555 9999999999999999 9999888899999999999983 211 0110 11 136788
Q ss_pred HHHHHHHHHHhc
Q 026130 195 EMKAVADYIKRQ 206 (243)
Q Consensus 195 El~aVA~fI~~r 206 (243)
+...++.++..+
T Consensus 86 ~k~~i~~~~~~~ 97 (337)
T TIGR00331 86 EKRRIQNQFLQR 97 (337)
T ss_pred HHHHHHHHHhhc
Confidence 999999988765
No 227
>KOG0686 consensus COP9 signalosome, subunit CSN1 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=58.33 E-value=17 Score=36.37 Aligned_cols=47 Identities=21% Similarity=0.347 Sum_probs=42.6
Q ss_pred ccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHH
Q 026130 148 CIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQA 194 (243)
Q Consensus 148 vV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~e 194 (243)
-+.+--+|..||++...+-+.+.+|..+|.|.|=||---|-+||-+.
T Consensus 365 s~~m~~mA~af~~sv~~le~~l~~LI~~~~i~~rIDs~~ki~~~~~~ 411 (466)
T KOG0686|consen 365 SADMSKMAEAFNTSVAILESELLELILEGKISGRIDSHNKILYARDA 411 (466)
T ss_pred cchHHHHHHHhcccHHHHHHHHHHHHHccchheeeccccceeeeccc
Confidence 34566799999999999999999999999999999999999999765
No 228
>PF11972 HTH_13: HTH DNA binding domain; InterPro: IPR021068 The proteins in this entry have not been characterised. They contain a C-terminal helix-turn-helix DNA binding domain.
Probab=57.85 E-value=21 Score=26.05 Aligned_cols=47 Identities=19% Similarity=0.373 Sum_probs=40.5
Q ss_pred HHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCe
Q 026130 137 ADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKY 188 (243)
Q Consensus 137 ~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKF 188 (243)
-.+|+.+..+-||..--+|.+.|++++-+.+-|.+|-. --+|| ||.|
T Consensus 2 p~Lidll~~~P~Vsa~mva~~L~vT~~~A~~li~eLg~-rEiTG----r~R~ 48 (54)
T PF11972_consen 2 PRLIDLLLSRPLVSAPMVAKELGVTPQAAQRLIAELGL-REITG----RGRY 48 (54)
T ss_pred HHHHHHHHhCccccHHHHHHHhCCCHHHHHHHHHHhhc-eeecC----Cccc
Confidence 47899999999999999999999999999999999877 55565 5555
No 229
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=57.66 E-value=23 Score=31.05 Aligned_cols=54 Identities=17% Similarity=0.227 Sum_probs=40.6
Q ss_pred HHHHHHHHHHhc------CccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeE
Q 026130 135 LLADFVEYIKKH------KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYI 189 (243)
Q Consensus 135 lL~~Fi~yIK~~------KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFI 189 (243)
.-..+.+.|... |+=.-.+||..||++..-|..-|..|..+|.|.-+- -+|.||
T Consensus 10 i~~~L~~~I~~g~~~~G~~LPsE~eL~~~~~VSR~TvR~Al~~L~~eGli~r~~-G~GtfV 69 (240)
T PRK09764 10 IADRIREQIARGELKPGDALPTESALQTEFGVSRVTVRQALRQLVEQQILESIQ-GSGTYV 69 (240)
T ss_pred HHHHHHHHHHcCCCCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec-CceeEE
Confidence 345566667654 444567899999999999999999999999987542 246665
No 230
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=57.55 E-value=14 Score=29.92 Aligned_cols=69 Identities=17% Similarity=0.238 Sum_probs=52.5
Q ss_pred ccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeee-CCCCe----EEEcHHH-HHHHHHHHHhcCCccH-HHHHh
Q 026130 148 CIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMD-DRGKY----IYISQAE-MKAVADYIKRQGRVSI-SHLAS 216 (243)
Q Consensus 148 vV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViD-DRGKF----IYIS~eE-l~aVA~fI~~rGRVSi-~eLa~ 216 (243)
-|.|.+||..|.+++-.+-..|+.|.+.|-|+=.=- -||+. +.+++++ +..++.-+-..|.+.- ..|+.
T Consensus 19 ~vtl~elA~~l~cS~Rn~r~lLkkm~~~gWi~W~pg~GRG~~S~L~~l~~~~~~~~~~~~~~l~~g~~~~a~~ll~ 94 (115)
T PF12793_consen 19 EVTLDELAELLFCSRRNARTLLKKMQEEGWITWQPGRGRGNRSQLTFLKSPEELLEQQAEELLEQGKYEQALQLLD 94 (115)
T ss_pred ceeHHHHHHHhCCCHHHHHHHHHHHHHCCCeeeeCCCCCCCCCeeEEeeCHHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence 478999999999999999999999999988752221 26663 3345554 5677888888899885 46665
No 231
>PLN03083 E3 UFM1-protein ligase 1 homolog; Provisional
Probab=57.51 E-value=63 Score=34.70 Aligned_cols=95 Identities=20% Similarity=0.243 Sum_probs=71.2
Q ss_pred cceecccccccccccccchhHHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHH
Q 026130 115 EFSIDAEGTTENEVQDGDRDLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQA 194 (243)
Q Consensus 115 ~f~VEeeG~~~~~~~~~~~~lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~e 194 (243)
.|+++...+.- . ..|-.+..+.|...--|+|-|||.-.|+....|-.+++.+...+ -|++=-.|- -||+.
T Consensus 47 l~T~DGKEYiT---~---~qL~~EI~~El~~gGRvnlvdLa~~LnVD~~hiEr~~~~iv~~d--~~~~l~~Ge--Lit~~ 116 (803)
T PLN03083 47 LHTVSGKEYIT---Q---DQLRNEIEAEIKKLGRVSLVDLADTIGVDLYHVERQAQQVVSDD--PGLMLVQGE--IISQS 116 (803)
T ss_pred EEecCCceeeC---H---HHHHHHHHHHHHhCCCeeHHHHhhhcCCCHHHHHHHHHHHhcCC--CceEEecCE--ecchH
Confidence 45665554442 2 22445666777777889999999999999999999999998887 455555564 47888
Q ss_pred HHHHHHHHHH----hcCCccHHHHHhhcc
Q 026130 195 EMKAVADYIK----RQGRVSISHLASKSN 219 (243)
Q Consensus 195 El~aVA~fI~----~rGRVSi~eLa~~sN 219 (243)
=|+.||.-|+ +.|.|||+||++.-|
T Consensus 117 Yld~iaeEIne~LqE~G~isI~eLa~~~~ 145 (803)
T PLN03083 117 YWDSIAEEINERLQECSQIALAELARQLQ 145 (803)
T ss_pred HHHHHHHHHHHHHHHcCcChHHHHHHhcC
Confidence 8888777765 569999999998654
No 232
>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=57.45 E-value=30 Score=26.58 Aligned_cols=42 Identities=17% Similarity=0.351 Sum_probs=36.0
Q ss_pred HHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcc
Q 026130 137 ADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLS 179 (243)
Q Consensus 137 ~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~Lt 179 (243)
+.++.++..+ ++.|++|-..+|++-..+.=.+..|.+.|-|+
T Consensus 8 ~~IL~~ls~~-c~TLeeL~ekTgi~k~~LlV~LsrL~k~GiI~ 49 (72)
T PF05584_consen 8 QKILIILSKR-CCTLEELEEKTGISKNTLLVYLSRLAKRGIIE 49 (72)
T ss_pred HHHHHHHHhc-cCCHHHHHHHHCCCHHHHHHHHHHHHHCCCee
Confidence 3455555555 99999999999999999999999999999876
No 233
>PTZ00064 histone acetyltransferase; Provisional
Probab=57.44 E-value=32 Score=35.22 Aligned_cols=70 Identities=13% Similarity=0.324 Sum_probs=47.1
Q ss_pred cchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhcCCccHHHHHhhcccccccccch
Q 026130 149 IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRVSISHLASKSNQFIDLETKA 228 (243)
Q Consensus 149 V~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~rGRVSi~eLa~~sN~lI~L~p~~ 228 (243)
+.|.||+..-||++.|||.-++.| |.|.=+ ..+-+|+++++-++....-..++| +.| --+.+.|.|..
T Consensus 472 iSI~dIS~~TgI~~eDII~TLq~L---~llky~--kgq~~I~~~~~~ie~~~~~~~k~~-~~i------d~~~L~W~Py~ 539 (552)
T PTZ00064 472 KFIDNVVRSTGIRREDVIRILEEN---GIMRNI--KDQHYIFCNQEFLKGIVKRSGRPG-ITL------IDKYFNWVPFS 539 (552)
T ss_pred ccHHHHHHHhCCCHHHHHHHHHHC---CcEEEe--CCCEEEEECHHHHHHHHHHhcCCC-cee------chhHceecCCC
Confidence 789999999999999998877765 655522 236778999998877655432222 222 12356777765
Q ss_pred hh
Q 026130 229 QF 230 (243)
Q Consensus 229 ~~ 230 (243)
..
T Consensus 540 ~~ 541 (552)
T PTZ00064 540 RA 541 (552)
T ss_pred CC
Confidence 54
No 234
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=57.26 E-value=18 Score=31.82 Aligned_cols=39 Identities=21% Similarity=0.325 Sum_probs=32.5
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeE
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYI 189 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFI 189 (243)
.-.+||..||++..-|-+-|+.|+..|-|. +.--+|-||
T Consensus 35 sE~eLa~~~gVSRtpVREAL~~L~~eGlV~-~~~~~G~~V 73 (257)
T PRK10225 35 PEREIAEMLDVTRTVVREALIMLEIKGLVE-VRRGAGIYV 73 (257)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHCCCEE-EecCCEEEE
Confidence 466899999999999999999999999887 333466665
No 235
>PF13591 MerR_2: MerR HTH family regulatory protein
Probab=57.24 E-value=36 Score=25.81 Aligned_cols=54 Identities=13% Similarity=0.233 Sum_probs=44.0
Q ss_pred cchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhcCC
Q 026130 149 IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGR 208 (243)
Q Consensus 149 V~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~rGR 208 (243)
+.+++++..+|+.+.. |..|...|-|....++.+-| ++...+..+..+++-+--
T Consensus 1 is~~e~~~~~~i~~~~----l~~lve~Gli~p~~~~~~~~--f~~~~l~rl~~~~rL~~D 54 (84)
T PF13591_consen 1 ISLEEFCEACGIEPEF----LRELVEEGLIEPEGEEEEWY--FSEEDLARLRRIRRLHRD 54 (84)
T ss_pred CCHHHHHHHHCcCHHH----HHHHHHCCCeeecCCCCeee--ECHHHHHHHHHHHHHHHH
Confidence 3578999999998765 66788999999988886555 899999999988876643
No 236
>smart00862 Trans_reg_C Transcriptional regulatory protein, C terminal. This domain is almost always found associated with the response regulator receiver domain. It may play a role in DNA binding.
Probab=57.05 E-value=20 Score=25.16 Aligned_cols=32 Identities=25% Similarity=0.398 Sum_probs=27.7
Q ss_pred CCeEEEcHHHHHHHHHHHHhcCC-ccHHHHHhh
Q 026130 186 GKYIYISQAEMKAVADYIKRQGR-VSISHLASK 217 (243)
Q Consensus 186 GKFIYIS~eEl~aVA~fI~~rGR-VSi~eLa~~ 217 (243)
|+-|.+|+.|+.-++-|+...|+ ||..+|...
T Consensus 1 ~~~v~Lt~~e~~lL~~L~~~~~~~vs~~~l~~~ 33 (78)
T smart00862 1 GEPIKLTPKEFRLLELLLRNPGRVVSREELLEA 33 (78)
T ss_pred CCeEecCHHHHHHHHHHHhCCCCccCHHHHHHH
Confidence 56789999999999999999997 777888764
No 237
>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=56.94 E-value=9.2 Score=27.68 Aligned_cols=23 Identities=13% Similarity=0.459 Sum_probs=20.5
Q ss_pred HHHHHHHHhcCCccHHHHHhhcc
Q 026130 197 KAVADYIKRQGRVSISHLASKSN 219 (243)
Q Consensus 197 ~aVA~fI~~rGRVSi~eLa~~sN 219 (243)
..|+.++-++||.|+.+|++.+|
T Consensus 16 ~~V~~~Ll~~G~ltl~~i~~~t~ 38 (62)
T PF08221_consen 16 AKVGEVLLSRGRLTLREIVRRTG 38 (62)
T ss_dssp HHHHHHHHHC-SEEHHHHHHHHT
T ss_pred HHHHHHHHHcCCcCHHHHHHHhC
Confidence 57899999999999999999988
No 238
>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]
Probab=56.84 E-value=21 Score=37.74 Aligned_cols=88 Identities=17% Similarity=0.262 Sum_probs=56.2
Q ss_pred HHHHHHHhhhhccceecccccccccccccchhHHHHHHHHHHhcCccchHHH---HHHcCCC---hHHHHHHHHHHHhcC
Q 026130 103 EAAAFEFEKWKGEFSIDAEGTTENEVQDGDRDLLADFVEYIKKHKCIPLEDL---AAEFKLR---TQECINRITSLENMG 176 (243)
Q Consensus 103 ~rE~eEY~kwK~~f~VEeeG~~~~~~~~~~~~lL~~Fi~yIK~~KvV~LEdL---A~~F~lr---tqd~I~RIq~Le~~g 176 (243)
-||.++|-.++-..-+.+.-.. .-+.-+++.==|.|++.+|....-|. ...-... +.++| |++-+
T Consensus 59 sKEn~~FyeLa~~lPlp~aiss----hLDkaSimRLtISyLRlrk~a~~g~~p~~e~~~~~~e~~l~~~i-----LqsLD 129 (768)
T KOG3558|consen 59 SKENEEFYELAKLLPLPAAISS----HLDKASIMRLTISYLRLRKFAGAGDPPRAEGEPENLEQHLGDHI-----LQSLD 129 (768)
T ss_pred ccchHHHHHHHHhCCCcchhhh----hhhhHHHHHHHHHHHHHHHHhhcCCcccccCCCcchhhhhhhhH-----Hhhcc
Confidence 3677888888888777663322 23355677778999999998766554 2211111 12222 44445
Q ss_pred CcceeeeCCCCeEEEcHHHHHHHHHHH
Q 026130 177 RLSGVMDDRGKYIYISQAEMKAVADYI 203 (243)
Q Consensus 177 ~LtGViDDRGKFIYIS~eEl~aVA~fI 203 (243)
-..=|+++.|+|||||+. |+.|+
T Consensus 130 GFVm~l~~dG~~lYiSEt----VS~yL 152 (768)
T KOG3558|consen 130 GFVMALTQDGDFLYISET----VSIYL 152 (768)
T ss_pred ceEEEEccCCCEEEEech----hHhhh
Confidence 566688999999999975 55554
No 239
>PF09202 Rio2_N: Rio2, N-terminal; InterPro: IPR015285 This N-terminal domain is found in RIO2 kinases, and is structurally homologous to the winged helix (wHTH) domain. It adopts a structure consisting of four alpha helices followed by two beta strands and a fifth alpha helix. The domain confers DNA binding properties to the protein, as per other winged helix domains []. ; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1TQP_A 1ZAR_A 1TQI_A 1ZAO_A 1TQM_A.
Probab=56.68 E-value=36 Score=26.25 Aligned_cols=62 Identities=21% Similarity=0.226 Sum_probs=43.8
Q ss_pred HHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCe--EEEcHHHHHHHH
Q 026130 136 LADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKY--IYISQAEMKAVA 200 (243)
Q Consensus 136 L~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKF--IYIS~eEl~aVA 200 (243)
|...-.-.+.+.+|+++.|+..-||+...+-.+|+.|...+.|.- +.++| --+|-.-++.+|
T Consensus 12 L~aiE~gmk~hE~VP~~~I~~~s~l~~~~~~~~L~~L~~~kLv~~---~~~~Y~GYrLT~~GYD~LA 75 (82)
T PF09202_consen 12 LRAIEMGMKNHEWVPLELIEKISGLSEGEVEKRLKRLVKLKLVSR---RNKPYDGYRLTFLGYDYLA 75 (82)
T ss_dssp HHHHHTTTTT-SSEEHHHHHHHHT--HHHHHHHHHHHHHTTSEEE---E-SSS-EEEE-HHHHHHHH
T ss_pred HHHHHHcccCCccCCHHHHHHHhCcCHHHHHHHHHHHHhcCCccc---cCCCcceEEEeecchhHHH
Confidence 333334468999999999999999999999999999999999987 44444 235555555554
No 240
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=56.57 E-value=39 Score=30.72 Aligned_cols=77 Identities=16% Similarity=0.358 Sum_probs=52.1
Q ss_pred chhHHHHHHHHHHhc--CccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhcCCc
Q 026130 132 DRDLLADFVEYIKKH--KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRV 209 (243)
Q Consensus 132 ~~~lL~~Fi~yIK~~--KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~rGRV 209 (243)
....+..+++||..+ .-+.|++||.++|++..-+-.+.+........ =||..-=|......|.. +..
T Consensus 216 ~~~~~~~~~~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~~~g~s~~----------~~~~~~Rl~~A~~lL~~-~~~ 284 (322)
T PRK09393 216 ESDRLGPLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAATGMTPA----------EWLLRERLARARDLLES-SAL 284 (322)
T ss_pred chHHHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHH----------HHHHHHHHHHHHHHHHc-CCC
Confidence 445789999999886 46889999999999998888888775431110 13333334444444444 567
Q ss_pred cHHHHHhhcc
Q 026130 210 SISHLASKSN 219 (243)
Q Consensus 210 Si~eLa~~sN 219 (243)
||++++..|.
T Consensus 285 ~i~~IA~~~G 294 (322)
T PRK09393 285 SIDQIAERAG 294 (322)
T ss_pred CHHHHHHHhC
Confidence 8888877663
No 241
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=56.56 E-value=45 Score=27.52 Aligned_cols=65 Identities=17% Similarity=0.223 Sum_probs=51.9
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHH--HHHhcCCccHHHHHhhcc
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVAD--YIKRQGRVSISHLASKSN 219 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~--fI~~rGRVSi~eLa~~sN 219 (243)
.+-+||..+|+++. .|.--+..|-|..+-.+.|-|=|-|++.+..|.. +.++-| +|+.++....+
T Consensus 2 ~Ige~a~~~gvs~~----tlRyYE~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G-~sl~eI~~~l~ 68 (135)
T PRK10227 2 NISDVAKITGLTSK----AIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVG-FNLEESGELVN 68 (135)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHCCCCCCcccCCCCcccCCHHHHHHHHHHHHHHHCC-CCHHHHHHHHH
Confidence 46799999999765 4677899999998888788899999999988764 344557 99988877654
No 242
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=56.06 E-value=16 Score=32.34 Aligned_cols=67 Identities=19% Similarity=0.301 Sum_probs=49.1
Q ss_pred CccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcH-------HHHHHHHHHHHhcCCccHHHHHh
Q 026130 147 KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQ-------AEMKAVADYIKRQGRVSISHLAS 216 (243)
Q Consensus 147 KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~-------eEl~aVA~fI~~rGRVSi~eLa~ 216 (243)
++=.=.+||..||++.--|..-|..|..+|.|.= -+|+=.||++ .++..+.+.+..+|.-..+.+..
T Consensus 30 ~LPsE~eLa~~f~VSR~TvRkAL~~L~~eGli~r---~~G~GtfV~~~~~~~~~~~~~~f~e~~~~~g~~~~~~vl~ 103 (236)
T COG2188 30 KLPSERELAEQFGVSRMTVRKALDELVEEGLIVR---RQGKGTFVASPKEQSPLLELTSFSEELKSQGLEPTTEVLS 103 (236)
T ss_pred CCCCHHHHHHHHCCcHHHHHHHHHHHHHCCcEEE---EecCeeEEcCccccccccccccHHHHHHhCCCCCceEEEE
Confidence 3444457999999999999999999999998753 2444444544 36777888888888875555444
No 243
>PRK11569 transcriptional repressor IclR; Provisional
Probab=55.65 E-value=87 Score=28.21 Aligned_cols=88 Identities=15% Similarity=0.302 Sum_probs=61.2
Q ss_pred HHHHHHHh-cCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCC-CCeEEEcHHHHHHHHHHHHhcCCc-----c
Q 026130 138 DFVEYIKK-HKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDR-GKYIYISQAEMKAVADYIKRQGRV-----S 210 (243)
Q Consensus 138 ~Fi~yIK~-~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDR-GKFIYIS~eEl~aVA~fI~~rGRV-----S 210 (243)
..++++.. +.-+.|.|||...||...-|-.-++.|...|-|. -|++ |+| .+++.=+.--..|.....-+ -
T Consensus 32 ~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~~G~l~--~~~~~~~Y-~lG~~l~~Lg~~~~~~~~l~~~a~p~ 108 (274)
T PRK11569 32 KLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQQGFVR--QVGELGHW-AIGAHAFIVGSSFLQSRNLLAIVHPI 108 (274)
T ss_pred HHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE--EcCCCCeE-ecCHHHHHHHHHHHhhCcHHHHHHHH
Confidence 45666654 5678999999999999999999999999999995 5654 554 46655444333444333222 2
Q ss_pred HHHHHhhcccccccccch
Q 026130 211 ISHLASKSNQFIDLETKA 228 (243)
Q Consensus 211 i~eLa~~sN~lI~L~p~~ 228 (243)
+.+|+..+|.-+.|.--.
T Consensus 109 l~~La~~~getv~L~v~~ 126 (274)
T PRK11569 109 LRNLMEDSGETVNLAVLD 126 (274)
T ss_pred HHHHHHHHCCeEEEEEEe
Confidence 468888888777665543
No 244
>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator. Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs,
Probab=55.38 E-value=56 Score=25.88 Aligned_cols=68 Identities=13% Similarity=0.160 Sum_probs=51.6
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhc-CCccHHHHHhhcccc
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQ-GRVSISHLASKSNQF 221 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~r-GRVSi~eLa~~sN~l 221 (243)
.+.++|..+|+++.- |.-.+..|-|..+-.+.|.|=|.|++.+..+..-..-+ .=+|+.++....+-+
T Consensus 2 ~Ige~A~~~gvs~~t----lR~ye~~GLl~p~~r~~~g~R~Y~~~~l~~l~~I~~lr~~G~~l~~I~~~l~~~ 70 (107)
T cd01111 2 SISQLALDAGVSVHI----VRDYLLRGLLHPVARTEGGYGLFDDCALQRLRFVRAAFEAGIGLDELARLCRAL 70 (107)
T ss_pred CHHHHHHHHCcCHHH----HHHHHHCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 357899999998654 67778889999987777889999999998875433322 457888888776543
No 245
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=55.36 E-value=64 Score=24.99 Aligned_cols=67 Identities=13% Similarity=0.074 Sum_probs=49.4
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHh--cCCccHHHHHhhccc
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKR--QGRVSISHLASKSNQ 220 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~--rGRVSi~eLa~~sN~ 220 (243)
.+.+||..+|+++. .|...+..|.|...-.+.+.|=|-|+..+..+-.-..- ..-+|+.++...-+.
T Consensus 2 ~I~eva~~~gvs~~----tlR~Ye~~GLl~p~~r~~~g~r~Y~~~dv~~l~~I~~L~~~~G~~l~~I~~~l~~ 70 (95)
T cd04780 2 RMSELSKRSGVSVA----TIKYYLREGLLPEGRRLAPNQAEYSEAHVERLRLIRALQQEGGLPISQIKEVLDA 70 (95)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHCCCCCCCcCCCCCCeecCHHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 36799999999876 46677789999997665555556699999887654333 368999888875554
No 246
>PRK13239 alkylmercury lyase; Provisional
Probab=55.36 E-value=26 Score=31.55 Aligned_cols=52 Identities=19% Similarity=0.325 Sum_probs=40.9
Q ss_pred hhHHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeE
Q 026130 133 RDLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYI 189 (243)
Q Consensus 133 ~~lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFI 189 (243)
..++...+..+-.-+-|.+.+||..+|.+.+.+-..++.|- .+ ++|+.|.-|
T Consensus 21 ~~~~~~llr~la~G~pvt~~~lA~~~~~~~~~v~~~L~~l~---~~--~~d~~g~iv 72 (206)
T PRK13239 21 ATLLVPLLRLLAKGRPVSVTTLAAALGWPVEEVEAVLEAMP---DT--EYDEDGRII 72 (206)
T ss_pred hHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhCC---Ce--EECCCCCEE
Confidence 45666777777799999999999999999999998888863 22 677776643
No 247
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=55.33 E-value=58 Score=28.69 Aligned_cols=56 Identities=20% Similarity=0.303 Sum_probs=42.3
Q ss_pred cchHHHHHHcCCChHHHHHHHHHHHhc----CCcceeeeCCCCeEEEcHHHHHH-HHHHHH
Q 026130 149 IPLEDLAAEFKLRTQECINRITSLENM----GRLSGVMDDRGKYIYISQAEMKA-VADYIK 204 (243)
Q Consensus 149 V~LEdLA~~F~lrtqd~I~RIq~Le~~----g~LtGViDDRGKFIYIS~eEl~a-VA~fI~ 204 (243)
|.+.+||.-||+...+|.+-|..|... |+=.=|.---|+|.+.|.-++.. |.+|+.
T Consensus 21 ls~~~La~~l~~~~~~v~~~l~~L~~~y~~~~~gi~i~~~~~~y~l~tk~e~~~~v~~~~~ 81 (188)
T PRK00135 21 LSLEQLAEILELEPTEVQQLLEELQEKYEGDDRGLKLIEFNDVYKLVTKEENADYLQKLVK 81 (188)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHhhCCCCEEEEEECCEEEEEEcHHHHHHHHHHhc
Confidence 899999999999999998888888554 44344555678898888888764 444543
No 248
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=54.59 E-value=54 Score=27.41 Aligned_cols=66 Identities=17% Similarity=0.192 Sum_probs=52.7
Q ss_pred cchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHH--HHHHhcCCccHHHHHhhcc
Q 026130 149 IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVA--DYIKRQGRVSISHLASKSN 219 (243)
Q Consensus 149 V~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA--~fI~~rGRVSi~eLa~~sN 219 (243)
..+.++|..+|+++. .|.--+..|-|....++.|.|=|-|++.+..|. .+.++-| +|+.++....+
T Consensus 8 ~~IgevAk~~Gvs~~----TLRyYE~~GLl~p~~r~~~gyR~Y~~~~l~rl~~I~~lr~~G-~sL~eI~~ll~ 75 (144)
T PRK13752 8 LTIGVFAKAAGVNVE----TIRFYQRKGLLPEPDKPYGSIRRYGEADVTRVRFVKSAQRLG-FSLDEIAELLR 75 (144)
T ss_pred ccHHHHHHHHCcCHH----HHHHHHHCCCCCCCccCCCCCeecCHHHHHHHHHHHHHHHcC-CCHHHHHHHHh
Confidence 678999999999754 467778899999877777889999999998764 4555667 79988887654
No 249
>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR. SoxR is a MerR-family homodimeric transcription factor with a 2Fe-2S cluster in each monomer. The motif CIGCGCxxxxxC is conserved. Oxidation of the iron-sulfur cluster activates SoxR. The physiological role in E. coli is response to oxidative stress. It is activated by superoxide, singlet oxygen, nitric oxide (NO), and hydrogen peroxide. In E. coli, SoxR increases expression of transcription factor SoxS; different downstream targets may exist in other species.
Probab=54.52 E-value=65 Score=26.88 Aligned_cols=65 Identities=11% Similarity=0.196 Sum_probs=47.1
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHH--HHHHHhcCCccHHHHHhhccc
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAV--ADYIKRQGRVSISHLASKSNQ 220 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aV--A~fI~~rGRVSi~eLa~~sN~ 220 (243)
.+.+||..+|+++. -|.--+..|.|..+-++.| |=|-|++.+..| ....+.-| +|+.++....+.
T Consensus 3 ~IgevA~~~Gvs~~----tLRyYE~~GLl~~~r~~~g-~R~Y~~~di~~l~~I~~lr~~G-~sL~eI~~~l~~ 69 (142)
T TIGR01950 3 TVGELAKRSGVAVS----ALHFYESKGLITSIRNSGN-QRRYKRDVLRRVAVIKAAQRVG-IPLATIGEALAV 69 (142)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHCCCCCCccCCCC-CEEECHHHHHHHHHHHHHHHcC-CCHHHHHHHHHh
Confidence 57899999999754 4667788899998555444 556678887654 34556667 998888876654
No 250
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=54.38 E-value=14 Score=28.80 Aligned_cols=25 Identities=20% Similarity=0.404 Sum_probs=21.8
Q ss_pred HHHHHHHHHhcCCccHHHHHhhccc
Q 026130 196 MKAVADYIKRQGRVSISHLASKSNQ 220 (243)
Q Consensus 196 l~aVA~fI~~rGRVSi~eLa~~sN~ 220 (243)
|-.|-+||..+||+|.++|+...|-
T Consensus 4 L~qlRd~l~~~gr~s~~~Ls~~~~~ 28 (78)
T PRK15431 4 LIQVRDLLALRGRMEAAQISQTLNT 28 (78)
T ss_pred HHHHHHHHHHcCcccHHHHHHHHCc
Confidence 4578899999999999999987763
No 251
>PF11761 CbiG_mid: Cobalamin biosynthesis central region; InterPro: IPR021745 Members of this family are involved in cobalamin synthesis. The gene encoded by P72862 from SWISSPROT has been designated cbiH but in fact represents a fusion between cbiH and cbiG. As other multi-functional proteins involved in cobalamin biosynthesis catalyse adjacent steps in the pathway, including CysG, CobL (CbiET), CobIJ and CobA-HemD, it is therefore possible that CbiG catalyses a reaction step adjacent to CbiH. In the anaerobic pathway such a step could be the formation of a gamma lactone, which is thought to help to mediate the anaerobic ring contraction process [].
Probab=54.29 E-value=17 Score=26.80 Aligned_cols=36 Identities=22% Similarity=0.324 Sum_probs=32.5
Q ss_pred cchHHHHHHcCCCh--HHHHHHHHHHHhcCCcceeeeC
Q 026130 149 IPLEDLAAEFKLRT--QECINRITSLENMGRLSGVMDD 184 (243)
Q Consensus 149 V~LEdLA~~F~lrt--qd~I~RIq~Le~~g~LtGViDD 184 (243)
.-|+-||..+|+.. -+.+.+|..++-+|.-.||++|
T Consensus 2 ~AvD~la~~~g~~i~~~~~~k~vsaalv~g~~V~~~~~ 39 (93)
T PF11761_consen 2 PAVDLLARELGWRIENREAVKRVSAALVNGEPVALYQD 39 (93)
T ss_pred CCcchhhhhCCCEEcCHHHHHHHHHHHHCCCEEEEEEe
Confidence 45788999999987 4789999999999999999999
No 252
>PF09286 Pro-kuma_activ: Pro-kumamolisin, activation domain ; InterPro: IPR015366 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain is found at the N terminus of peptidases belonging to MEROPS peptidase family S53 (sedolisin, clan SB). The domain adopts a ferredoxin-like fold, with an alpha+beta sandwich. Cleavage of the domain results in activation of the peptidase []. ; GO: 0008236 serine-type peptidase activity; PDB: 1T1E_A 3EDY_A 3EE6_A.
Probab=53.64 E-value=71 Score=25.82 Aligned_cols=60 Identities=23% Similarity=0.350 Sum_probs=38.6
Q ss_pred chhHHHHHHHHHHh------cCccchHHHHHHcCCChHHHHHHHHH-HHhcCCcceeeeCCCCeEEEc
Q 026130 132 DRDLLADFVEYIKK------HKCIPLEDLAAEFKLRTQECINRITS-LENMGRLSGVMDDRGKYIYIS 192 (243)
Q Consensus 132 ~~~lL~~Fi~yIK~------~KvV~LEdLA~~F~lrtqd~I~RIq~-Le~~g~LtGViDDRGKFIYIS 192 (243)
+.+.|..++.-|-. +|.+..++++..|+-+ .+.|+.|.. |...|.-...+...|-||.++
T Consensus 25 n~~~L~~~l~~vsdP~s~~Ygk~Lt~~e~~~~~~p~-~~~v~~V~~wL~~~G~~~~~~~~~~~~i~~~ 91 (143)
T PF09286_consen 25 NLDALEQYLAEVSDPGSPNYGKYLTPEEFAALFAPS-PEDVAAVKSWLKSHGLTVVEVSANGDWITVS 91 (143)
T ss_dssp THHHHHHHHHHHHTTTSTTTT----HHHHHHHHS---HHHHHHHHHHHHHCT-EEEEEETTTTEEEEE
T ss_pred CHHHHHHHHHhCcCCCCcccccCCCHHHHHHHHCCC-HHHHHHHHHHHHHcCCceeEEeCCCCEEEEE
Confidence 44567888877755 7999999999999985 455555555 777774333458899999875
No 253
>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=53.28 E-value=14 Score=24.42 Aligned_cols=22 Identities=23% Similarity=0.493 Sum_probs=18.8
Q ss_pred HHHHHHHhcCCccHHHHHhhcc
Q 026130 198 AVADYIKRQGRVSISHLASKSN 219 (243)
Q Consensus 198 aVA~fI~~rGRVSi~eLa~~sN 219 (243)
.|-.+|...|++|+++|+..+|
T Consensus 7 ~Il~~l~~~~~~t~~ela~~~~ 28 (48)
T PF13412_consen 7 KILNYLRENPRITQKELAEKLG 28 (48)
T ss_dssp HHHHHHHHCTTS-HHHHHHHHT
T ss_pred HHHHHHHHcCCCCHHHHHHHhC
Confidence 4568999999999999999988
No 254
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=52.09 E-value=15 Score=32.12 Aligned_cols=43 Identities=14% Similarity=0.275 Sum_probs=34.6
Q ss_pred cCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeE
Q 026130 146 HKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYI 189 (243)
Q Consensus 146 ~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFI 189 (243)
.|+=.-.+||..||++..-|..-|..|..+|.|.-. --+|.||
T Consensus 31 ~kLPsE~eLa~~~~VSR~TvR~Al~~L~~eGli~r~-~G~GTfV 73 (241)
T PRK11402 31 QQIPTENELCTQYNVSRITIRKAISDLVADGVLIRW-QGKGTFV 73 (241)
T ss_pred CcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe-cCceeEE
Confidence 366667789999999999999999999999998744 2245555
No 255
>PF13442 Cytochrome_CBB3: Cytochrome C oxidase, cbb3-type, subunit III ; PDB: 1KB0_A 2DGE_D 2CE1_A 2CE0_A 2V07_A 1W2L_A 2ZOO_A 2ZBO_G 1DVV_A 2EXV_A ....
Probab=51.79 E-value=14 Score=25.86 Aligned_cols=33 Identities=33% Similarity=0.513 Sum_probs=24.6
Q ss_pred HHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHH
Q 026130 167 NRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYI 203 (243)
Q Consensus 167 ~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI 203 (243)
..|......|. |.|-.-+. .+|++|+.+|+.||
T Consensus 35 ~~l~~~i~~g~--~~Mp~~~~--~ls~~e~~~l~~yi 67 (67)
T PF13442_consen 35 EELYNIIRNGR--GGMPPFGG--QLSDEEIEALAAYI 67 (67)
T ss_dssp HHHHHHHHHTB--TTBSCTTT--TSTHHHHHHHHHHH
T ss_pred HHHHHHHHhCc--CCCCCCCC--CCCHHHHHHHHHHC
Confidence 44445555555 67777666 89999999999998
No 256
>PLN03239 histone acetyltransferase; Provisional
Probab=51.78 E-value=21 Score=34.66 Aligned_cols=50 Identities=16% Similarity=0.304 Sum_probs=38.5
Q ss_pred CccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCe-EEEcHHHHHHHHHH
Q 026130 147 KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKY-IYISQAEMKAVADY 202 (243)
Q Consensus 147 KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKF-IYIS~eEl~aVA~f 202 (243)
..+.|+|||..-|+++.|||..++. .|.|. ...|.| |+|++.-++...+-
T Consensus 283 ~~~si~dis~~Tgi~~~DIi~tL~~---l~~l~---~~~g~~~i~~~~~~l~~~~~~ 333 (351)
T PLN03239 283 SSLSIMDIAKKTSIMAEDIVFALNQ---LGILK---FINGIYFIAAEKGLLEELAEK 333 (351)
T ss_pred CCccHHHHHHHhCCCHHHHHHHHHH---CCcEE---EECCeEEEEeCHHHHHHHHHH
Confidence 4689999999999999999876554 56663 235555 88999988887664
No 257
>PF04157 EAP30: EAP30/Vps36 family; InterPro: IPR007286 EAP30 is a subunit of the ELL complex. The ELL is an 80kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity. ; PDB: 2ZME_A 3CUQ_A 1W7P_D 1U5T_B.
Probab=51.70 E-value=29 Score=30.62 Aligned_cols=45 Identities=16% Similarity=0.219 Sum_probs=40.4
Q ss_pred hHHHHHHHHH--HhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCc
Q 026130 134 DLLADFVEYI--KKHKCIPLEDLAAEFKLRTQECINRITSLENMGRL 178 (243)
Q Consensus 134 ~lL~~Fi~yI--K~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~L 178 (243)
......+.++ ....-|...+||.+||++..-+...|..|+..|.|
T Consensus 174 ~~~~~il~~~~~~~~g~vt~~~l~~~~~ws~~~a~~~L~~~~~~G~l 220 (223)
T PF04157_consen 174 KDQSRILELAEEENGGGVTASELAEKLGWSVERAKEALEELEREGLL 220 (223)
T ss_dssp HHHHHHHHHH--TTTSEEEHHHHHHHHTB-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHHHhhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCE
Confidence 4567888899 88999999999999999999999999999999986
No 258
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator. This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.
Probab=51.69 E-value=68 Score=25.77 Aligned_cols=65 Identities=17% Similarity=0.212 Sum_probs=49.2
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHH--HHHhcCCccHHHHHhhcc
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVAD--YIKRQGRVSISHLASKSN 219 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~--fI~~rGRVSi~eLa~~sN 219 (243)
.+-++|..+|+++. .|.--+..|-|...-.+.|-|=|-|++.+..|.. +.++-| +|+.++....+
T Consensus 2 ~I~e~a~~~gvs~~----tlRyYe~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G-~sL~eI~~~l~ 68 (127)
T TIGR02044 2 NIGQVAKLTGLSSK----MIRYYEEKGLIPPPLRSEGGYRTYTQQHLDELRLISRARQVG-FSLEECKELLN 68 (127)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHCC-CCHHHHHHHHH
Confidence 46789999999764 4667889999998766666688889999988763 345556 78888876544
No 259
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=50.70 E-value=34 Score=27.69 Aligned_cols=52 Identities=13% Similarity=0.175 Sum_probs=41.8
Q ss_pred hcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEc-HHHH
Q 026130 145 KHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYIS-QAEM 196 (243)
Q Consensus 145 ~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS-~eEl 196 (243)
..+.+.+.+||..++++..-+-.-++.|...|-|..+-...|-|---. ++++
T Consensus 22 ~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s~~G~~Ggy~l~~~~~~I 74 (135)
T TIGR02010 22 ETGPVTLADISERQGISLSYLEQLFAKLRKAGLVKSVRGPGGGYQLGRPAEDI 74 (135)
T ss_pred CCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEeCCCCCEeccCCHHHC
Confidence 456899999999999999999999999999999987656666665433 4443
No 260
>cd03174 DRE_TIM_metallolyase DRE-TIM metallolyase superfamily. The DRE-TIM metallolyase superfamily includes 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC. These members all share a conserved triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices. The domain has a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel. In addition, the catalytic site includes three invariant residues - an aspartate (D), an arginine (R), and a glutamate (E) - which is the basis for the domain name "DRE-TIM".
Probab=50.32 E-value=33 Score=29.78 Aligned_cols=73 Identities=14% Similarity=0.131 Sum_probs=58.7
Q ss_pred hhHHHHHHHHHHhcCccchHHHHHHcC--CChHHHHHHHHHHHhcCC-cceeeeCCCCeEEEcHHHHHHHHHHHHhcCC
Q 026130 133 RDLLADFVEYIKKHKCIPLEDLAAEFK--LRTQECINRITSLENMGR-LSGVMDDRGKYIYISQAEMKAVADYIKRQGR 208 (243)
Q Consensus 133 ~~lL~~Fi~yIK~~KvV~LEdLA~~F~--lrtqd~I~RIq~Le~~g~-LtGViDDRGKFIYIS~eEl~aVA~fI~~rGR 208 (243)
-..+..+|.|++...+-+.=.+..-|+ .....+.+.++.+.+.|. ...+.|.-| +.||+++..+..+|+++..
T Consensus 114 ~~~~~~~i~~a~~~G~~v~~~~~~~~~~~~~~~~l~~~~~~~~~~g~~~i~l~Dt~G---~~~P~~v~~li~~l~~~~~ 189 (265)
T cd03174 114 LENAEEAIEAAKEAGLEVEGSLEDAFGCKTDPEYVLEVAKALEEAGADEISLKDTVG---LATPEEVAELVKALREALP 189 (265)
T ss_pred HHHHHHHHHHHHHCCCeEEEEEEeecCCCCCHHHHHHHHHHHHHcCCCEEEechhcC---CcCHHHHHHHHHHHHHhCC
Confidence 345667788888887766666666778 899999999999999885 566778877 5999999999999998754
No 261
>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators. Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind spe
Probab=50.12 E-value=95 Score=25.63 Aligned_cols=63 Identities=14% Similarity=0.162 Sum_probs=48.0
Q ss_pred cchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhc--CCccHHHHHhh
Q 026130 149 IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQ--GRVSISHLASK 217 (243)
Q Consensus 149 V~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~r--GRVSi~eLa~~ 217 (243)
..+.++|..+|+++.- |.-.+..|.|.+. . +|.+-|-|++++..+..-..-+ .-+++.++...
T Consensus 2 ysI~eVA~~~GVs~~T----LR~wE~~GLl~p~-r-~~G~R~Ys~~dv~rL~~I~~L~~e~G~~l~eI~~~ 66 (120)
T cd04767 2 YPIGVVAELLNIHPET----LRIWERHGLIKPA-R-RNGQRLYSNNDLKRLRFIKKLINEKGLNIAGVKQI 66 (120)
T ss_pred CCHHHHHHHHCcCHHH----HHHHHHCCCCCCc-C-CCCcEEECHHHHHHHHHHHHHHHHcCCCHHHHHHH
Confidence 4678999999998764 4467778999885 3 5788889999998876554443 67888887764
No 262
>COG3646 Uncharacterized phage-encoded protein [Function unknown]
Probab=49.90 E-value=18 Score=31.77 Aligned_cols=53 Identities=17% Similarity=0.161 Sum_probs=43.1
Q ss_pred HHHHHHhcC--ccchHHHHHHcCCChHHHHHHHHHHHhcCC------------cceeeeCCCCeEEE
Q 026130 139 FVEYIKKHK--CIPLEDLAAEFKLRTQECINRITSLENMGR------------LSGVMDDRGKYIYI 191 (243)
Q Consensus 139 Fi~yIK~~K--vV~LEdLA~~F~lrtqd~I~RIq~Le~~g~------------LtGViDDRGKFIYI 191 (243)
++.+|..++ ++.--.+|--||-+..+++.-|..|-.++. =++-++-.|+++|.
T Consensus 3 ~l~vi~~N~~i~t~S~~IAe~~gkrH~~ilrsIe~~~~~~~~n~~~~~l~ff~es~y~~~~gkk~~~ 69 (167)
T COG3646 3 NLAVIDSNKLIVTNSREIAEMVGKRHDNILRSIENLKRDFDQNEKLGSLEFFIESLYLRGQGKKVKM 69 (167)
T ss_pred hHHHhhcCCceeecHHHHHHHHhhhhhhHHHHHHHHHhhhccCcchhhhhhhhhhchhcccCceehh
Confidence 678899999 888889999999999999999999998882 13345556777764
No 263
>PRK13502 transcriptional activator RhaR; Provisional
Probab=49.70 E-value=61 Score=28.45 Aligned_cols=76 Identities=11% Similarity=0.162 Sum_probs=50.0
Q ss_pred hhHHHHHHHHHHhc--CccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhcCCcc
Q 026130 133 RDLLADFVEYIKKH--KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRVS 210 (243)
Q Consensus 133 ~~lL~~Fi~yIK~~--KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~rGRVS 210 (243)
..++..+++||..+ .-+.+++||..||++..-+...++.-...... =||..-=|......| ..+..|
T Consensus 175 ~~~~~~~~~~I~~~~~~~~~~~~lA~~~~iS~~~L~r~fk~~~G~t~~----------~yi~~~Rl~~A~~lL-~~t~~s 243 (282)
T PRK13502 175 ETLLDKLITALANSLECPFALDAFCQQEQCSERVLRQQFRAQTGMTIN----------QYLRQVRICHAQYLL-QHSPLM 243 (282)
T ss_pred HHHHHHHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHH----------HHHHHHHHHHHHHHH-HcCCCC
Confidence 34688999998654 23678999999999988777666653221110 034444455444444 457889
Q ss_pred HHHHHhhcc
Q 026130 211 ISHLASKSN 219 (243)
Q Consensus 211 i~eLa~~sN 219 (243)
|+++|..|.
T Consensus 244 I~eIA~~~G 252 (282)
T PRK13502 244 ISEISMQCG 252 (282)
T ss_pred HHHHHHHcC
Confidence 999998875
No 264
>PF12514 DUF3718: Protein of unknown function (DUF3718); InterPro: IPR022193 This entry is represented by Bacteriophage Aaphi23, Orf19. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This domain family is found in bacteria and viruses, and is approximately 70 amino acids in length. There is a single completely conserved residue C that may be functionally important.
Probab=49.58 E-value=14 Score=27.52 Aligned_cols=24 Identities=29% Similarity=0.398 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHhcCCccHHHHHhhc
Q 026130 194 AEMKAVADYIKRQGRVSISHLASKS 218 (243)
Q Consensus 194 eEl~aVA~fI~~rGRVSi~eLa~~s 218 (243)
.....++.|| -.|+|||++|+.++
T Consensus 45 ~~A~kt~~~l-~~~~~~~~dla~~~ 68 (68)
T PF12514_consen 45 YGANKTAEFL-AVKRVSIKDLAAAE 68 (68)
T ss_pred cCHHHHHHHH-hcCCccHHHHhhcC
Confidence 3467899999 88999999998753
No 265
>PRK11642 exoribonuclease R; Provisional
Probab=49.32 E-value=38 Score=36.04 Aligned_cols=49 Identities=27% Similarity=0.409 Sum_probs=37.3
Q ss_pred HHHHHHh-cCccchHHHHHHcCCCh----HHHHHHHHHHHhcCCcceeeeCCCCeE
Q 026130 139 FVEYIKK-HKCIPLEDLAAEFKLRT----QECINRITSLENMGRLSGVMDDRGKYI 189 (243)
Q Consensus 139 Fi~yIK~-~KvV~LEdLA~~F~lrt----qd~I~RIq~Le~~g~LtGViDDRGKFI 189 (243)
.++|+.. .+-+.+.+||..|||+. +.+...|..|+..|.|. .+.+|+|.
T Consensus 24 Il~~l~~~~~~~~~~~L~~~l~l~~~~~~~~l~~~L~~L~~~g~l~--~~~~~~~~ 77 (813)
T PRK11642 24 ILEHLTKREKPASREELAVELNIEGEEQLEALRRRLRAMERDGQLV--FTRRQCYA 77 (813)
T ss_pred HHHHHHhcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHHHHCCCEE--EcCCceEe
Confidence 4555554 68999999999999975 34778999999999885 45555553
No 266
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=49.14 E-value=74 Score=25.58 Aligned_cols=64 Identities=17% Similarity=0.267 Sum_probs=49.4
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHH--HHHHhcCCccHHHHHhhc
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVA--DYIKRQGRVSISHLASKS 218 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA--~fI~~rGRVSi~eLa~~s 218 (243)
.+.++|..||+++. -|.--+..|-|.....+.|.|=|-|++.+..+. .+++.-| +|++++...-
T Consensus 2 ~I~e~a~~~gvs~~----tlR~Ye~~Gll~~~~r~~~g~R~Y~~~~l~~l~~I~~lr~~G-~sL~eI~~~l 67 (126)
T cd04785 2 SIGELARRTGVNVE----TIRYYESIGLLPEPARTAGGYRLYGAAHVERLRFIRRARDLG-FSLEEIRALL 67 (126)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHCCCCCCCCcCCCCccccCHHHHHHHHHHHHHHHCC-CCHHHHHHHH
Confidence 46789999999765 456788999999877777888889999988764 3455556 8988877653
No 267
>smart00843 Ftsk_gamma This domain directs oriented DNA translocation and forms a winged helix structure. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding.
Probab=48.90 E-value=72 Score=23.78 Aligned_cols=50 Identities=16% Similarity=0.228 Sum_probs=44.9
Q ss_pred chhHHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCccee
Q 026130 132 DRDLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGV 181 (243)
Q Consensus 132 ~~~lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGV 181 (243)
.+.++.+-++||...+-+...-|=++|++--.-+-.-|..|+..|-|+.-
T Consensus 3 ~D~ly~~a~~~V~~~~~~S~S~lQR~~~IGynrAariid~lE~~GiV~p~ 52 (63)
T smart00843 3 EDELYDEAVELVIETQKASTSLLQRRLRIGYNRAARLIDQLEEEGIVGPA 52 (63)
T ss_pred ccHHHHHHHHHHHHhCCCChHHHHHHHhcchhHHHHHHHHHHHCcCCCCC
Confidence 35688999999999999999999999999999999999999999988763
No 268
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=48.89 E-value=40 Score=27.40 Aligned_cols=63 Identities=10% Similarity=0.263 Sum_probs=46.7
Q ss_pred HhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCe-EEEcHHHHHHHHHHHHhcC
Q 026130 144 KKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKY-IYISQAEMKAVADYIKRQG 207 (243)
Q Consensus 144 K~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKF-IYIS~eEl~aVA~fI~~rG 207 (243)
.....+...+||..||++..=+..-++.|...|-|..+---.|-| +--.++++ .|.+.+.--+
T Consensus 21 ~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~~G~~GG~~l~~~~~~i-tl~dI~~aiE 84 (141)
T PRK11014 21 PEGRMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVRGKNGGIRLGKPASTI-RIGDVVRELE 84 (141)
T ss_pred CCCCccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEecCCCCCeeecCCHHHC-CHHHHHHHHc
Confidence 344678899999999999999999999999999887765555556 44455553 4555555444
No 269
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
Probab=48.83 E-value=32 Score=29.57 Aligned_cols=55 Identities=16% Similarity=0.209 Sum_probs=40.4
Q ss_pred HHHHHHHHHHhc------CccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEc
Q 026130 135 LLADFVEYIKKH------KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYIS 192 (243)
Q Consensus 135 lL~~Fi~yIK~~------KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS 192 (243)
.-..+.+.|... |+=.-.+||..||++..-|..-|..|..+|.|.-+ +|+=.||+
T Consensus 13 i~~~l~~~I~~g~~~~G~~LPsE~eLa~~~~VSR~TvR~Al~~L~~eGli~r~---~G~GtfV~ 73 (238)
T TIGR02325 13 IADKIEQEIAAGHLRAGDYLPAEMQLAERFGVNRHTVRRAIAALVERGLLRAE---QGRGTFVA 73 (238)
T ss_pred HHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe---cCCEEEEC
Confidence 345566666554 45556689999999999999999999999988755 44444444
No 270
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=48.57 E-value=35 Score=28.33 Aligned_cols=40 Identities=20% Similarity=0.243 Sum_probs=28.8
Q ss_pred cchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEc
Q 026130 149 IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYIS 192 (243)
Q Consensus 149 V~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS 192 (243)
+...+||..+|++.+-+-.-++.|.++|.|. -.|+.|.|.
T Consensus 169 ~t~~~lA~~lG~tr~tvsR~l~~l~~~gii~----~~~~~i~i~ 208 (211)
T PRK11753 169 ITRQEIGRIVGCSREMVGRVLKMLEDQGLIS----AHGKTIVVY 208 (211)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE----ecCCEEEEe
Confidence 5568999999996665555588999998653 345556654
No 271
>KOG2587 consensus RNA polymerase III (C) subunit [Transcription]
Probab=47.91 E-value=80 Score=32.50 Aligned_cols=72 Identities=18% Similarity=0.321 Sum_probs=59.6
Q ss_pred hcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCC---------------------CeEEEcHHHHH----HH
Q 026130 145 KHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRG---------------------KYIYISQAEMK----AV 199 (243)
Q Consensus 145 ~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRG---------------------KFIYIS~eEl~----aV 199 (243)
......+.=++..=|++..-|-.-+=.|...|.++=+.+.++ ||+||+.+++. +|
T Consensus 31 ~G~lss~~~~~~~t~i~~~kVk~aL~sLiQh~~V~y~~~~~~~g~vt~Y~~~~~ei~hilry~r~~~i~~~~~~q~~~sI 110 (551)
T KOG2587|consen 31 TGRLSSLRVIAKDTGISLDKVKKALVSLIQHNCVSYQVHTRNSGKVTTYEAQCSEILHILRYPRYIYITKTLYSQTAESI 110 (551)
T ss_pred cCCcchhHHHHhhcCCChHHHHHHHHHHHHhcceEEEEecCCCCceEEEEehhhHHHHHHhcccceeeHHHHhhhHHHHH
Confidence 333334667888889999999999999999999999888775 99999999985 56
Q ss_pred HHHHHhcCCccHHHHHh
Q 026130 200 ADYIKRQGRVSISHLAS 216 (243)
Q Consensus 200 A~fI~~rGRVSi~eLa~ 216 (243)
++++-..||.++++..+
T Consensus 111 v~~Lls~GrLTv~e~i~ 127 (551)
T KOG2587|consen 111 VEELLSNGRLTVSEVIK 127 (551)
T ss_pred HHHHHhcCceeHHHHHH
Confidence 77888999999988754
No 272
>COG3343 RpoE DNA-directed RNA polymerase, delta subunit [Transcription]
Probab=47.89 E-value=20 Score=31.83 Aligned_cols=59 Identities=8% Similarity=0.232 Sum_probs=44.0
Q ss_pred hHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhcCCccHHHHHhhccccc
Q 026130 151 LEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRVSISHLASKSNQFI 222 (243)
Q Consensus 151 LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~rGRVSi~eLa~~sN~lI 222 (243)
+.+++.+||++-+++-+||-.|=-+ +.-.|.|||+....|. .|-..++-++-..++.++
T Consensus 37 i~EI~~~~~~s~~ei~~~i~~FYTd------ln~DgrFi~LGdn~Wg-------LRswy~~Deideei~~~~ 95 (175)
T COG3343 37 INEIQKLLGVSKEEIRSRIGQFYTD------LNIDGRFISLGDNKWG-------LRSWYPLDEIDEEIQAMT 95 (175)
T ss_pred HHHHHHHhCcCHHHHHHHHHHHHHH------hccCCceeeccccccc-------hhhccchhHHHHHHhhhh
Confidence 4557899999999999999776543 3457999999998774 456667777766666544
No 273
>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=47.85 E-value=42 Score=29.48 Aligned_cols=85 Identities=11% Similarity=0.190 Sum_probs=59.1
Q ss_pred HHHHHHHh-cCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhcCCc------c
Q 026130 138 DFVEYIKK-HKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRV------S 210 (243)
Q Consensus 138 ~Fi~yIK~-~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~rGRV------S 210 (243)
..+++|-. ..-+.+.|||...||+..-|-.-++.|...|-|.- | .|+| .+++. +-.++.-+..+..+ -
T Consensus 13 ~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~~G~l~~--~-~~~Y-~lG~~-~~~lg~~~~~~~~l~~~a~p~ 87 (248)
T TIGR02431 13 AVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVELGYVTS--D-GRLF-WLTPR-VLRLGYAYLSSAPLPKVAQPL 87 (248)
T ss_pred HHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe--C-CCEE-EecHH-HHHHHHHHHhcCchHHHHHHH
Confidence 45666654 56789999999999999999999999999999963 4 4665 36665 44444332222222 3
Q ss_pred HHHHHhhcccccccccc
Q 026130 211 ISHLASKSNQFIDLETK 227 (243)
Q Consensus 211 i~eLa~~sN~lI~L~p~ 227 (243)
+.+|+..+|.-+.|.--
T Consensus 88 l~~L~~~~g~tv~L~v~ 104 (248)
T TIGR02431 88 LERLSAQTHESCSVAVL 104 (248)
T ss_pred HHHHHHHHCCeEEEEEE
Confidence 46888888776666543
No 274
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=47.67 E-value=28 Score=24.92 Aligned_cols=32 Identities=25% Similarity=0.414 Sum_probs=25.2
Q ss_pred HHHhcCccchHHHHHHcCCChHHHHHHHHHHH
Q 026130 142 YIKKHKCIPLEDLAAEFKLRTQECINRITSLE 173 (243)
Q Consensus 142 yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le 173 (243)
|.-.-+=+.+.|||..||++.+-+-.+|..-+
T Consensus 17 Yfd~PR~~tl~elA~~lgis~st~~~~LRrae 48 (53)
T PF04967_consen 17 YFDVPRRITLEELAEELGISKSTVSEHLRRAE 48 (53)
T ss_pred CCCCCCcCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 33445668899999999999999988886543
No 275
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=47.28 E-value=21 Score=27.57 Aligned_cols=25 Identities=12% Similarity=0.223 Sum_probs=21.7
Q ss_pred HHHHHHHHHHhcCCccHHHHHhhccc
Q 026130 195 EMKAVADYIKRQGRVSISHLASKSNQ 220 (243)
Q Consensus 195 El~aVA~fI~~rGRVSi~eLa~~sN~ 220 (243)
=...+..+|.. |+|+|.+|+..+|-
T Consensus 7 R~~~I~e~l~~-~~~ti~dvA~~~gv 31 (80)
T TIGR02844 7 RVLEIGKYIVE-TKATVRETAKVFGV 31 (80)
T ss_pred HHHHHHHHHHH-CCCCHHHHHHHhCC
Confidence 46788999999 99999999998763
No 276
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=46.93 E-value=51 Score=22.58 Aligned_cols=39 Identities=8% Similarity=0.106 Sum_probs=29.8
Q ss_pred hhHHHHHHHHHHhcCccchHHHHHHcCC-ChHHHHHHHHHH
Q 026130 133 RDLLADFVEYIKKHKCIPLEDLAAEFKL-RTQECINRITSL 172 (243)
Q Consensus 133 ~~lL~~Fi~yIK~~KvV~LEdLA~~F~l-rtqd~I~RIq~L 172 (243)
...+...+.||..+ -..|.+||..+|+ +..-.....+..
T Consensus 36 ~~r~~~a~~~l~~~-~~~~~~ia~~~g~~s~~~f~r~Fk~~ 75 (84)
T smart00342 36 DRRLERARRLLRDT-DLSVTEIALRVGFSSQSYFSRAFKKL 75 (84)
T ss_pred HHHHHHHHHHHHcC-CCCHHHHHHHhCCCChHHHHHHHHHH
Confidence 34578889999887 6889999999999 666665555443
No 277
>PF06757 Ins_allergen_rp: Insect allergen related repeat, nitrile-specifier detoxification; InterPro: IPR010629 This entry represents several insect specific allergen repeats. These repeats are commonly found in various proteins from cockroaches, fruit flies and mosquitos. It has been suggested that the repeat sequences have evolved by duplication of an ancestral amino acid domain, which may have arisen from the mitochondrial energy transfer proteins []. This family exemplifies a case of novel gene evolution. The case in point is the arms-race between plants and their infective insective herbivores in the area of the glucosinolate-myrosinase system. Brassicas have developed the glucosinolate-myrosinase system as chemical defence mechanism against the insects, and consequently the insects have adapted to produce a detoxifying molecule, nitrile-specifier protein (NSP). NSP is present in the Pieris rapae (Cabbage white butterfly). NSP is structurally different from and has no amino acid homology to any known detoxifying enzymes, and it appears to have arisen by a process of domain and gene duplication of a sequence of unknown function that is widespread in insect species and referred to as insect-allergen-repeat protein. Thus this family is found either as a single domain or as a multiple repeat-domain [].
Probab=46.81 E-value=14 Score=31.52 Aligned_cols=82 Identities=18% Similarity=0.345 Sum_probs=52.9
Q ss_pred hhHHHHHHHHHHhcCccchHHHHHHc---CCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhcCCc
Q 026130 133 RDLLADFVEYIKKHKCIPLEDLAAEF---KLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRV 209 (243)
Q Consensus 133 ~~lL~~Fi~yIK~~KvV~LEdLA~~F---~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~rGRV 209 (243)
++-+++|++.|-..+ +.+|..++ .-..+.+++.++.-.-...+..+ .+..|+..+-+|+...| |
T Consensus 5 ~~d~~dfl~lIp~~~---i~~i~~~Y~~~D~efq~~~~yl~s~~f~~l~~~l---------~~~pE~~~l~~yL~~~g-l 71 (179)
T PF06757_consen 5 QEDFQDFLDLIPMEE---IQDIVQRYYLEDAEFQAAVRYLNSSEFKQLWQQL---------EALPEVKALLDYLESAG-L 71 (179)
T ss_pred HHHHHHHHHhcCHHH---HHHHHHHHHHcCHHHHHHHHHHcChHHHHHHHHH---------HcCHHHHHHHHHHHHCC-C
Confidence 345788888887766 34444444 33445555555444322222222 45678899999999887 7
Q ss_pred cHHHHHhhcccccccccc
Q 026130 210 SISHLASKSNQFIDLETK 227 (243)
Q Consensus 210 Si~eLa~~sN~lI~L~p~ 227 (243)
.+..+...-|.+|.+.|.
T Consensus 72 dv~~~i~~i~~~l~~~~~ 89 (179)
T PF06757_consen 72 DVYYYINQINDLLGLPPL 89 (179)
T ss_pred CHHHHHHHHHHHHcCCcC
Confidence 888888888888887765
No 278
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=46.74 E-value=37 Score=23.42 Aligned_cols=36 Identities=11% Similarity=0.121 Sum_probs=28.1
Q ss_pred HHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHH
Q 026130 138 DFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLE 173 (243)
Q Consensus 138 ~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le 173 (243)
=|+-..+.+.-+...+||..||++..-|-+.+..+.
T Consensus 9 lll~L~~LR~~~~~~~La~~FgIs~stvsri~~~~~ 44 (53)
T PF13613_consen 9 LLLTLMYLRLNLTFQDLAYRFGISQSTVSRIFHEWI 44 (53)
T ss_pred HHHHHHHHHcCCcHhHHhhheeecHHHHHHHHHHHH
Confidence 355567788889999999999998877776666543
No 279
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=46.60 E-value=1e+02 Score=21.73 Aligned_cols=62 Identities=15% Similarity=0.192 Sum_probs=40.8
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhc-CCcceeeeCCCCeEEEcHHHHHHHHHH--HHhcCCccHHHHHhh
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENM-GRLSGVMDDRGKYIYISQAEMKAVADY--IKRQGRVSISHLASK 217 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~-g~LtGViDDRGKFIYIS~eEl~aVA~f--I~~rGRVSi~eLa~~ 217 (243)
.+.++|..+|+++.-+ ...+.. |.+...-++ |-+-|.|..++..+..- +++ .-+||.++...
T Consensus 2 ~i~e~A~~~gVs~~tl----r~ye~~~gl~~~~r~~-~g~R~yt~~di~~l~~i~~l~~-~g~~l~~i~~~ 66 (68)
T cd04763 2 TIGEVALLTGIKPHVL----RAWEREFGLLKPQRSD-GGHRLFNDADIDRILEIKRWID-NGVQVSKVKKL 66 (68)
T ss_pred CHHHHHHHHCcCHHHH----HHHHHhcCCCCCCcCC-CCCcccCHHHHHHHHHHHHHHH-cCCCHHHHHHH
Confidence 4678999999987654 455665 655555444 55567899998876542 223 55777777653
No 280
>PF10543 ORF6N: ORF6N domain; InterPro: IPR018873 This entry represents an N-terminal DNA-binding domain found in a wide range of proteins from bacterial and eukaryotic DNA viruses and there bacterial homologues, they include the poxvirus D6R/N1R and baculoviral Bro protein families. The KilA-N domain is considered to be homologous to the fungal DNA-binding APSES domain. Both the KilA-N and APSES domains share a common fold with the nucleic acid-binding modules of the LAGLIDADG nucleases and the amino-terminal domains of the tRNA endonuclease []. This entry represents the amino-terminal domain of the Enterobacteria phage P22 antirepressor ((P03037 from SWISSPROT) []. It is found associated with IPR018876 from INTERPRO.
Probab=46.59 E-value=38 Score=25.99 Aligned_cols=55 Identities=15% Similarity=0.264 Sum_probs=39.7
Q ss_pred HHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHH
Q 026130 143 IKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYI 203 (243)
Q Consensus 143 IK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI 203 (243)
++..+||...|||.-||..+-.+-..++.=.. =+.+..-|+.++.+|+..+..-+
T Consensus 7 ~rg~rV~t~~~lA~~yg~~~~~i~~~~~rN~~------rF~eg~~~f~L~~~e~~~~~~~~ 61 (88)
T PF10543_consen 7 YRGQRVMTDEDLAELYGVETKTINRNFKRNKD------RFIEGKDYFQLTGEELKELKSQL 61 (88)
T ss_pred EcCEEEEEHHHHHHHhCcCHHHHHHHHHHHHH------hCCCCCcEEEecchhhhhhhhhh
Confidence 35678999999999999987666555554322 13445568889999999876543
No 281
>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=46.52 E-value=22 Score=30.75 Aligned_cols=72 Identities=10% Similarity=0.177 Sum_probs=47.4
Q ss_pred HHHHHHHHh------cCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEc------HHHHHHHHHHHH
Q 026130 137 ADFVEYIKK------HKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYIS------QAEMKAVADYIK 204 (243)
Q Consensus 137 ~~Fi~yIK~------~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS------~eEl~aVA~fI~ 204 (243)
..+.+.|.. .|+=.-.+||.+||++..-|..-|+.|..+|.|.-+ --+|.||-=. ..-+..+...+.
T Consensus 7 ~~l~~~I~~g~~~~G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~-~G~GTfV~~~~~~~~~~~~~~~f~~~~~ 85 (233)
T TIGR02404 7 QDLEQKITHGQYKEGDYLPSEHELMDQYGASRETVRKALNLLTEAGYIQKI-QGKGSIVLNRKQIEFPISGITSFKELNE 85 (233)
T ss_pred HHHHHHHHhCCCCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe-CCceEEEecCcccccccccchhHHHHHH
Confidence 455666654 344556789999999999999999999999988643 1256665211 112344555555
Q ss_pred hcCCc
Q 026130 205 RQGRV 209 (243)
Q Consensus 205 ~rGRV 209 (243)
..|..
T Consensus 86 ~~g~~ 90 (233)
T TIGR02404 86 TLGLD 90 (233)
T ss_pred hcCCC
Confidence 56653
No 282
>PRK05472 redox-sensing transcriptional repressor Rex; Provisional
Probab=46.41 E-value=44 Score=28.98 Aligned_cols=42 Identities=14% Similarity=0.371 Sum_probs=35.5
Q ss_pred HHHHHHHHHHhcC--ccchHHHHHHcCCChHHHHHH-HHHHHhcCC
Q 026130 135 LLADFVEYIKKHK--CIPLEDLAAEFKLRTQECINR-ITSLENMGR 177 (243)
Q Consensus 135 lL~~Fi~yIK~~K--vV~LEdLA~~F~lrtqd~I~R-Iq~Le~~g~ 177 (243)
.....+.++..+. .|...+||..||+++. +|.| |..|...|.
T Consensus 17 ~~~~il~~l~~~~~~~vs~~~L~~~~~v~~~-tirrDl~~l~~~G~ 61 (213)
T PRK05472 17 LYYRYLKELKEEGVERVSSKELAEALGVDSA-QIRKDLSYFGEFGK 61 (213)
T ss_pred HHHHHHHHHHHcCCcEEeHHHHHHHhCcCHH-HHHHHHHHHHhcCC
Confidence 4567888999998 9999999999999886 6665 899988774
No 283
>PRK09416 lstR lineage-specific thermal regulator protein; Provisional
Probab=46.11 E-value=54 Score=27.85 Aligned_cols=59 Identities=19% Similarity=0.231 Sum_probs=46.2
Q ss_pred cCCChHHHHHHHHHHHhcCCcceeeeCCC-CeEEEcHHHHHHHHHHHH--hcCCccHHHHHh
Q 026130 158 FKLRTQECINRITSLENMGRLSGVMDDRG-KYIYISQAEMKAVADYIK--RQGRVSISHLAS 216 (243)
Q Consensus 158 F~lrtqd~I~RIq~Le~~g~LtGViDDRG-KFIYIS~eEl~aVA~fI~--~rGRVSi~eLa~ 216 (243)
|.++..-+---+..|+.+|.|+...+.++ ||-.||+.-...+..|+. +.-|..|..|++
T Consensus 73 ~~~s~GtIYp~L~RLE~~GlI~s~~~~~~RK~Y~ITe~Gre~L~e~~~~~~~~~~~~~~l~~ 134 (135)
T PRK09416 73 FEGNEGSLYTLLHRLEQNRFIQSSWDHEGAKYYQLTDKGNKMLRKAEKNATKARFILKGLVQ 134 (135)
T ss_pred ccCCCccHHHHHHHHHHCCCeEEeecCCCceEEEECHHHHHHHHHHHhCHHHhHHHHHHHhc
Confidence 55667777788999999999999776655 787799999999999988 445555555554
No 284
>cd04781 HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, an
Probab=45.84 E-value=96 Score=24.66 Aligned_cols=65 Identities=12% Similarity=0.170 Sum_probs=49.2
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhc--CCccHHHHHhhccc
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQ--GRVSISHLASKSNQ 220 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~r--GRVSi~eLa~~sN~ 220 (243)
.+.++|..+|+++.- |.--+..|.|..+-.+ |.|=|-|++.+..+- ||+.- --+|+.++....|.
T Consensus 2 ~IgevA~~~gvs~~t----lRyYe~~GLl~p~~~~-~gyR~Y~~~~l~~l~-~I~~lr~~G~~L~eI~~~l~~ 68 (120)
T cd04781 2 DIAEVARQSGLPAST----LRYYEEKGLIASIGRR-GLRRQYDPQVLDRLA-LIALGRAAGFSLDEIQAMLSH 68 (120)
T ss_pred CHHHHHHHHCcCHHH----HHHHHHCCCCCCCcCC-CCceecCHHHHHHHH-HHHHHHHcCCCHHHHHHHHhc
Confidence 467999999997644 5666778999998765 789999999998875 44321 35799998886654
No 285
>PHA03033 hypothetical protein; Provisional
Probab=45.62 E-value=30 Score=29.62 Aligned_cols=43 Identities=23% Similarity=0.305 Sum_probs=34.3
Q ss_pred HHHHHHHHhcCCcce---eeeCCCCeEE--EcHHHHHHHHHHHHhcCC
Q 026130 166 INRITSLENMGRLSG---VMDDRGKYIY--ISQAEMKAVADYIKRQGR 208 (243)
Q Consensus 166 I~RIq~Le~~g~LtG---ViDDRGKFIY--IS~eEl~aVA~fI~~rGR 208 (243)
-+.|.+|.++..-+| |+-+.|+||| ||.+=++.+.+-|+-+--
T Consensus 45 yg~V~eLk~Qkk~~GeVAvLk~d~RyIYYLITKdyie~~v~~~ni~r~ 92 (142)
T PHA03033 45 YNSIKELKKQKKKKGEVAYIYKNNKYIIYIIIADYIEDIVDDINILRA 92 (142)
T ss_pred hCCHHHHHhhccCCCeEEEEecCCEEEEEEEeHHHHHHHHHHHHHHHH
Confidence 556999999999998 5668999999 888888887777765433
No 286
>PRK09978 DNA-binding transcriptional regulator GadX; Provisional
Probab=45.59 E-value=60 Score=30.24 Aligned_cols=75 Identities=12% Similarity=0.155 Sum_probs=54.4
Q ss_pred hhHHHHHHHHHHhc--CccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhcCCcc
Q 026130 133 RDLLADFVEYIKKH--KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRVS 210 (243)
Q Consensus 133 ~~lL~~Fi~yIK~~--KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~rGRVS 210 (243)
...+..+++||..+ .-+.|++||.++||+..-.....+. .| +.+ .=||..-=|...+..|.. +..|
T Consensus 141 ~~~~~~v~~yI~~~~~~~lsl~~lA~~~g~S~~~L~R~Fk~---~G--~S~------~~yl~~~Rl~~A~~LL~~-t~~s 208 (274)
T PRK09978 141 PNMRTRVCTVINNNIAHEWTLARIASELLMSPSLLKKKLRE---EE--TSY------SQLLTECRMQRALQLIVI-HGFS 208 (274)
T ss_pred HHHHHHHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHh---cC--CCH------HHHHHHHHHHHHHHHHHc-CCCC
Confidence 35678899999775 5679999999999999887777764 24 111 125666667777777764 5689
Q ss_pred HHHHHhhcc
Q 026130 211 ISHLASKSN 219 (243)
Q Consensus 211 i~eLa~~sN 219 (243)
|+++|..|.
T Consensus 209 I~eIA~~~G 217 (274)
T PRK09978 209 IKRVAVSCG 217 (274)
T ss_pred HHHHHHHhC
Confidence 999888764
No 287
>PF08721 Tn7_Tnp_TnsA_C: TnsA endonuclease C terminal; InterPro: IPR014832 The Tn7 transposase is composed of proteins TnsA and TnsB. DNA breakage at the 5'-end of the transposon is carried out by TnsA, and breakage and joining at the 3'-end is carried out by TnsB. The C-terminal domain of TnsA binds DNA. ; PDB: 1F1Z_B 1T0F_B.
Probab=45.30 E-value=45 Score=23.72 Aligned_cols=42 Identities=19% Similarity=0.329 Sum_probs=36.0
Q ss_pred HHHHHHHhcCccchHHHHHHc----CCChHHHHHHHHHHHhcCCcc
Q 026130 138 DFVEYIKKHKCIPLEDLAAEF----KLRTQECINRITSLENMGRLS 179 (243)
Q Consensus 138 ~Fi~yIK~~KvV~LEdLA~~F----~lrtqd~I~RIq~Le~~g~Lt 179 (243)
.|+.++..+.-..|.+|+.+| ++.....+.-|..|.+.+.|.
T Consensus 31 ~i~~~l~~~~~~tl~~l~~~~d~~~~l~~g~~L~~l~~LiA~k~i~ 76 (79)
T PF08721_consen 31 LILARLRKNPTMTLRDLCKELDKDYELEPGTALPLLRHLIATKRIK 76 (79)
T ss_dssp HHHHHHHHTTTSBHHHHHHHHHHHCT--TTHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHcCCCCHHHHHHHHHHhcCCCcCChHHHHHHHHhCChhc
Confidence 688888888889999999888 999999999999999998774
No 288
>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]
Probab=45.21 E-value=1.7e+02 Score=31.13 Aligned_cols=14 Identities=21% Similarity=0.463 Sum_probs=8.1
Q ss_pred cCccchHHHHHHcC
Q 026130 146 HKCIPLEDLAAEFK 159 (243)
Q Consensus 146 ~KvV~LEdLA~~F~ 159 (243)
+.+-+|++-.+.|+
T Consensus 735 kr~a~~drY~sdf~ 748 (940)
T KOG4661|consen 735 KRKAVLDRYSSDFK 748 (940)
T ss_pred hhhhHhhhhhcccc
Confidence 33455666666665
No 289
>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]
Probab=44.67 E-value=82 Score=23.29 Aligned_cols=73 Identities=22% Similarity=0.327 Sum_probs=49.0
Q ss_pred HHHHHHHHHhcCc--cchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhcCCccHHH
Q 026130 136 LADFVEYIKKHKC--IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRVSISH 213 (243)
Q Consensus 136 L~~Fi~yIK~~Kv--V~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~rGRVSi~e 213 (243)
+..++.||..+-. +.|++||..+|++..-+-.++......... .||..-=|.. |..+-..|.-+|++
T Consensus 22 ~~~~~~~i~~~~~~~~~l~~la~~~g~S~~~l~r~f~~~~g~s~~----------~~~~~~Rl~~-A~~lL~~~~~~i~~ 90 (127)
T COG2207 22 LARALDYIEENLAEPLTLEDLARRLGMSRRTLSRLFKKETGTSPS----------QYLRQLRLEE-ARRLLRSTDLSITE 90 (127)
T ss_pred HHHHHHHHHHHhcCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCHH----------HHHHHHHHHH-HHHHHHcCCCCHHH
Confidence 3388888887444 679999999999998888887765433222 3444444444 44445556668888
Q ss_pred HHhhcc
Q 026130 214 LASKSN 219 (243)
Q Consensus 214 La~~sN 219 (243)
+|-.|.
T Consensus 91 iA~~~G 96 (127)
T COG2207 91 IALRLG 96 (127)
T ss_pred HHHHhC
Confidence 887664
No 290
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=44.60 E-value=75 Score=28.95 Aligned_cols=76 Identities=14% Similarity=0.279 Sum_probs=51.4
Q ss_pred hhHHHHHHHHHHhc--CccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhcCCcc
Q 026130 133 RDLLADFVEYIKKH--KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRVS 210 (243)
Q Consensus 133 ~~lL~~Fi~yIK~~--KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~rGRVS 210 (243)
...+...+.||..+ .-+.|.+||.++|++.--+-...+.- +|+- =.=||..-=+...+..|. .|..|
T Consensus 190 ~~~i~~~~~~i~~~~~~~~tl~~lA~~~~~S~~~l~r~Fk~~------~G~t----~~~~l~~~Rl~~A~~lL~-~~~~s 258 (302)
T PRK10371 190 QFYVSQMLGFIAENYDQALTINDVAEHVKLNANYAMGIFQRV------MQLT----MKQYITAMRINHVRALLS-DTDKS 258 (302)
T ss_pred HHHHHHHHHHHHHhhcCCCCHHHHHHHHCcCHHHHHHHHHHH------hCCC----HHHHHHHHHHHHHHHHHh-cCCCC
Confidence 34688999999887 67999999999999988777666653 2310 011344444444444444 46788
Q ss_pred HHHHHhhcc
Q 026130 211 ISHLASKSN 219 (243)
Q Consensus 211 i~eLa~~sN 219 (243)
|+++|..|.
T Consensus 259 i~eIA~~~G 267 (302)
T PRK10371 259 ILDIALTAG 267 (302)
T ss_pred HHHHHHHcC
Confidence 888887664
No 291
>cd07970 OBF_DNA_ligase_LigC The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase LigC is a DNA-binding module that is part of the catalytic core unit. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of Mycobacterium tuberculosis LigC and similar ba
Probab=44.20 E-value=35 Score=27.71 Aligned_cols=31 Identities=26% Similarity=0.440 Sum_probs=26.4
Q ss_pred CcceeeeCCCCeEEE------cHHHHHHHHHHHHhcC
Q 026130 177 RLSGVMDDRGKYIYI------SQAEMKAVADYIKRQG 207 (243)
Q Consensus 177 ~LtGViDDRGKFIYI------S~eEl~aVA~fI~~rG 207 (243)
-|.|+.|+.|+|+|| |+.++.++.++++...
T Consensus 20 LlLg~~~~~g~l~yvG~vtGf~~~~~~~L~~~l~~l~ 56 (122)
T cd07970 20 LLLGLYDDGGRLRHVGRTSPLAAAERRELAELLEPAR 56 (122)
T ss_pred EEEEEECCCCCEEEEEEECCCCHHHHHHHHHHHHHhh
Confidence 467899998999997 8999999999888764
No 292
>PF04157 EAP30: EAP30/Vps36 family; InterPro: IPR007286 EAP30 is a subunit of the ELL complex. The ELL is an 80kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity. ; PDB: 2ZME_A 3CUQ_A 1W7P_D 1U5T_B.
Probab=44.19 E-value=34 Score=30.14 Aligned_cols=112 Identities=20% Similarity=0.243 Sum_probs=72.1
Q ss_pred HHhhhhccceeccccccc------ccccccchhHHHHHHHHHH----hcC-ccchHHHHHHc--------CCChHHHHHH
Q 026130 108 EFEKWKGEFSIDAEGTTE------NEVQDGDRDLLADFVEYIK----KHK-CIPLEDLAAEF--------KLRTQECINR 168 (243)
Q Consensus 108 EY~kwK~~f~VEeeG~~~------~~~~~~~~~lL~~Fi~yIK----~~K-vV~LEdLA~~F--------~lrtqd~I~R 168 (243)
.|..|-..++|+.--... ....+-..+|-..++.++- .+- ++.|.||=..| -++++|+..-
T Consensus 62 ~f~~~~~~lGvdp~~s~~~~s~~l~~~~~f~~ELa~qi~e~c~~~~~~~GGii~L~dl~~~~nr~R~g~~lISp~Di~~A 141 (223)
T PF04157_consen 62 QFQSMCASLGVDPLASSKFWSESLKGSGDFYYELAVQIAEVCLATRSKNGGIISLSDLYCRYNRARGGSELISPEDILRA 141 (223)
T ss_dssp HHHHHHHHHT--CHCCTTCCCCCCSCHHHHHHHHHHHHHHHHHHHCCTTTSEEEHHHHHHHHHHCTTTSST--HHHHHHH
T ss_pred HHHHHHHHcCCCcccchhhhhhccccchhHHHHHHHHHHHHHHHHHhcCCCEEEHHHHHHHHHHhcccCCCcCHHHHHHH
Confidence 667777777776321111 0111223444444555442 233 89999976665 3689999999
Q ss_pred HHHHHhcCCcceeeeCC-CCeEEEcH--HHH----HHHHHHH--HhcCCccHHHHHhhcc
Q 026130 169 ITSLENMGRLSGVMDDR-GKYIYISQ--AEM----KAVADYI--KRQGRVSISHLASKSN 219 (243)
Q Consensus 169 Iq~Le~~g~LtGViDDR-GKFIYIS~--eEl----~aVA~fI--~~rGRVSi~eLa~~sN 219 (243)
|+.|...|.=..|+.=. |+.+-.|. .++ ..|-.++ ...|.||..+|+...|
T Consensus 142 ~~~l~~lg~g~~l~~~~sg~~vv~s~~~~e~~~~~~~il~~~~~~~~g~vt~~~l~~~~~ 201 (223)
T PF04157_consen 142 CKLLEVLGLGFRLRKFGSGVKVVQSVPYSELSKDQSRILELAEEENGGGVTASELAEKLG 201 (223)
T ss_dssp HHHHCCCTSSEEEEEETTTEEEEECST-CHH-HHHHHHHHHH--TTTSEEEHHHHHHHHT
T ss_pred HHHHHHcCCCeEEEEeCCCcEEEEeCCchhhhHHHHHHHHHHHhhcCCCCCHHHHHHHhC
Confidence 99999999777777644 65554444 477 7788888 8889999999999877
No 293
>PRK05066 arginine repressor; Provisional
Probab=44.07 E-value=79 Score=27.09 Aligned_cols=56 Identities=20% Similarity=0.315 Sum_probs=40.8
Q ss_pred HHHHHHHHhcCccchHHHHH---HcCCC--hHHHHHH-HHHHHhcCCcceeeeCCCCeEEEcHHHH
Q 026130 137 ADFVEYIKKHKCIPLEDLAA---EFKLR--TQECINR-ITSLENMGRLSGVMDDRGKYIYISQAEM 196 (243)
Q Consensus 137 ~~Fi~yIK~~KvV~LEdLA~---~F~lr--tqd~I~R-Iq~Le~~g~LtGViDDRGKFIYIS~eEl 196 (243)
.....-|..++|-.=+||.. .-|+. ||-+|+| |++| | |.=|-+..|+|+|.-|.+.
T Consensus 12 ~~I~~iI~~~~I~tQeeL~~~L~~~Gi~~vTQATiSRDikeL---~-lvKv~~~~G~~~Y~l~~~~ 73 (156)
T PRK05066 12 KAFKALLKEEKFGSQGEIVTALQEQGFDNINQSKVSRMLTKF---G-AVRTRNAKMEMVYCLPAEL 73 (156)
T ss_pred HHHHHHHhhCCCCCHHHHHHHHHHCCCCeecHHHHHHHHHHc---C-CEEeeCCCCCEEEEeCCCC
Confidence 33445678888888777665 34888 8999998 5554 4 4448899999999876643
No 294
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=43.91 E-value=46 Score=30.25 Aligned_cols=48 Identities=19% Similarity=0.255 Sum_probs=42.8
Q ss_pred hHHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCccee
Q 026130 134 DLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGV 181 (243)
Q Consensus 134 ~lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGV 181 (243)
..=+..+-++|.+.=+.+.|||..+||++.-|..-++.|+++|-+.=.
T Consensus 11 ~tr~~il~lL~~~g~~sa~elA~~Lgis~~avR~HL~~Le~~Glv~~~ 58 (218)
T COG2345 11 STRERILELLKKSGPVSADELAEELGISPMAVRRHLDDLEAEGLVEVE 58 (218)
T ss_pred cHHHHHHHHHhccCCccHHHHHHHhCCCHHHHHHHHHHHHhCcceeee
Confidence 344677888999999999999999999999999999999999977665
No 295
>cd04619 CBS_pair_6 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic genera
Probab=43.79 E-value=60 Score=23.96 Aligned_cols=39 Identities=18% Similarity=0.161 Sum_probs=26.4
Q ss_pred cCCChHHHHHHHHHHHhcCCcceeeeCCCCeE-EEcHHHHHH
Q 026130 158 FKLRTQECINRITSLENMGRLSGVMDDRGKYI-YISQAEMKA 198 (243)
Q Consensus 158 F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFI-YIS~eEl~a 198 (243)
.+.+..++++++. ...-....|+|+.|+|+ +||...+..
T Consensus 8 ~~~~l~~a~~~~~--~~~~~~~~Vvd~~g~~~G~vt~~dl~~ 47 (114)
T cd04619 8 VNATLQRAAKILG--EPGIDLVVVCDPHGKLAGVLTKTDVVR 47 (114)
T ss_pred CCCcHHHHHHHHH--hcCCCEEEEECCCCCEEEEEehHHHHH
Confidence 3556666766652 22234567889999998 788888764
No 296
>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=43.75 E-value=73 Score=24.53 Aligned_cols=35 Identities=17% Similarity=0.098 Sum_probs=28.7
Q ss_pred hcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcc
Q 026130 145 KHKCIPLEDLAAEFKLRTQECINRITSLENMGRLS 179 (243)
Q Consensus 145 ~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~Lt 179 (243)
...-+.-.+||...|++.+-|-.-|..|+..|.|.
T Consensus 44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~ 78 (95)
T TIGR01610 44 KQDRVTATVIAELTGLSRTHVSDAIKSLARRRIIF 78 (95)
T ss_pred cCCccCHHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence 45666788999999997775555599999999987
No 297
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=43.58 E-value=46 Score=31.57 Aligned_cols=82 Identities=22% Similarity=0.392 Sum_probs=57.7
Q ss_pred HHHHHH-HHHhcCccchHHHHHH--cCCChHHHHHHHHHHHhcCCcceeeeCCC----------------CeEEEcHHHH
Q 026130 136 LADFVE-YIKKHKCIPLEDLAAE--FKLRTQECINRITSLENMGRLSGVMDDRG----------------KYIYISQAEM 196 (243)
Q Consensus 136 L~~Fi~-yIK~~KvV~LEdLA~~--F~lrtqd~I~RIq~Le~~g~LtGViDDRG----------------KFIYIS~eEl 196 (243)
|...|+ ||+...-|...+||.. ||+++.-+.+-+..|++.|-|.=+----| ++-.+++++.
T Consensus 12 l~~IV~~yi~~~~pv~s~~l~~~~~l~~S~aTIR~dm~~Le~~G~l~~~h~sagrIPT~kGYR~YVd~L~~~~~~~~~~~ 91 (339)
T PRK00082 12 LRAIVEDYIATGEPVGSKTLSKRYGLGVSSATIRNDMADLEELGLLEKPHTSSGRIPTDKGYRYFVDHLLEVKPLSEEER 91 (339)
T ss_pred HHHHHHHHHhcCCCcCHHHHHHHhCCCCChHHHHHHHHHHHhCCCcCCCcCCCCCCcCHHHHHHHHHHhCCCCCCCHHHH
Confidence 444443 8999999999999966 99999999999999999998763211111 1114678888
Q ss_pred HHHHHHHHhcCCccHHHHHhhc
Q 026130 197 KAVADYIKRQGRVSISHLASKS 218 (243)
Q Consensus 197 ~aVA~fI~~rGRVSi~eLa~~s 218 (243)
..+...+.++. .++.++.+.+
T Consensus 92 ~~i~~~~~~~~-~~~~~~l~~a 112 (339)
T PRK00082 92 RAIEKFLDERG-VSLEDVLQEA 112 (339)
T ss_pred HHHHHHHHhcc-CCHHHHHHHH
Confidence 88887665542 4666555443
No 298
>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=43.56 E-value=1.2e+02 Score=23.24 Aligned_cols=52 Identities=15% Similarity=0.236 Sum_probs=41.3
Q ss_pred HHHHHh-cCccchHHHHHHc-----CCChHHHHHHHHHHHhcCCcceeeeCCCCeEEE
Q 026130 140 VEYIKK-HKCIPLEDLAAEF-----KLRTQECINRITSLENMGRLSGVMDDRGKYIYI 191 (243)
Q Consensus 140 i~yIK~-~KvV~LEdLA~~F-----~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYI 191 (243)
++++.. ..-+..+||...+ +++..-|-+-|+.|.+.|.|.=|-.+.|.+.|-
T Consensus 7 l~~l~~~~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~~~~~~~~~y~ 64 (116)
T cd07153 7 LEVLLESDGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREIELGDGKARYE 64 (116)
T ss_pred HHHHHhCCCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEEEeCCCceEEE
Confidence 444444 4567788887776 688888888999999999999998888888884
No 299
>TIGR02277 PaaX_trns_reg phenylacetic acid degradation operon negative regulatory protein PaaX. This transcriptional regulator is always found in association with operons believed to be involved in the degradation of phenylacetic acid. The gene product has been shown to bind to the promoter sites and repress their transcription.
Probab=43.55 E-value=71 Score=29.47 Aligned_cols=52 Identities=13% Similarity=0.204 Sum_probs=44.1
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHH
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVAD 201 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~ 201 (243)
.|=.|...||++..-+---+..|.++|.|+..-..|.+|-+||+.=...+..
T Consensus 22 ~Li~l~~~~gi~~~~vr~al~RL~~~G~l~~~~~grr~~Y~LT~~g~~~l~~ 73 (280)
T TIGR02277 22 SLIEFLAGLGINERLVRTAVSRLVAQGWLQSERKGRRSFYSLTDKGRRRFAA 73 (280)
T ss_pred HHHHHHHhcCCCcchHHHHHHHHHHCCCEEeeecCCCCEEEECHHHHHHHHH
Confidence 4556889999999999999999999999999877777999999987554443
No 300
>PF14056 DUF4250: Domain of unknown function (DUF4250)
Probab=43.48 E-value=60 Score=23.66 Aligned_cols=38 Identities=16% Similarity=0.392 Sum_probs=32.5
Q ss_pred hHHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHH
Q 026130 134 DLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITS 171 (243)
Q Consensus 134 ~lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~ 171 (243)
..|-.|||---.--+-.|++|+..|++..++++.++..
T Consensus 6 ~mLlS~VN~kLRD~~~sLd~Lc~~~~id~~~l~~kL~~ 43 (55)
T PF14056_consen 6 NMLLSIVNMKLRDEYSSLDELCYDYDIDKEELEEKLAS 43 (55)
T ss_pred HHHHHHHHHHHHhccCCHHHHHHHhCCCHHHHHHHHHH
Confidence 46778888766667889999999999999999998865
No 301
>cd04615 CBS_pair_2 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic genera
Probab=43.37 E-value=1.2e+02 Score=21.81 Aligned_cols=57 Identities=11% Similarity=0.159 Sum_probs=31.3
Q ss_pred CCChHHHHHHHHHHHhcCCcceeeeCCCCeE-EEcHHHHHHHHHHHHhcCCccHHHHHhh
Q 026130 159 KLRTQECINRITSLENMGRLSGVMDDRGKYI-YISQAEMKAVADYIKRQGRVSISHLASK 217 (243)
Q Consensus 159 ~lrtqd~I~RIq~Le~~g~LtGViDDRGKFI-YIS~eEl~aVA~fI~~rGRVSi~eLa~~ 217 (243)
+.+..+++.++. ........|+|+.|+|+ |||...+.....=-......++.++...
T Consensus 9 ~~~~~~~~~~~~--~~~~~~~~vvd~~~~~~G~v~~~dl~~~~~~~~~~~~~~i~~~~~~ 66 (113)
T cd04615 9 NTDIARAVAEMY--TSGSRALPVVDDKKRLVGIITRYDVLSYALESEELKDAKVREVMNS 66 (113)
T ss_pred CCcHHHHHHHHH--HcCCceEeEEcCCCCEEEEEEHHHHHHhhhhhhhhcCCcHHHhccC
Confidence 344555665542 22223456888889998 7898888653110111133456666643
No 302
>PF03551 PadR: Transcriptional regulator PadR-like family; InterPro: IPR005149 Phenolic acids, also called substituted hydroxycinnamic acids, are abundant in the plant kingdom because they are involved in the structure of plant cell walls and are present in some vacuoles. In plant-soil ecosystems they are released as free acids by hemicellulases produced by several fungi and bacteria. Of these weak acids, the most abundant are p-coumaric, ferulic, and caffeic acids, considered to be natural toxins that inhibit the growth of microorganisms, especially at low pHs. In spite of this chemical stress, some bacteria can use phenolic acids as a sole source of carbon. For other microorganisms, these compounds induce a specific response by which the organism adapts to its environment. The ubiquitous lactic acid bacterium Lactobacillus plantarum exhibits an inducible phenolic acid decarboxylase (PAD) activity which converts these substrates into less-toxic vinyl phenol derivatives. PadR acts as a repressor of padA gene expression in the phenolic acid stress response [].; PDB: 1XMA_B 2ESH_A 2DQL_B 3L9F_C 3ELK_B 4EJO_B 3L7W_A 3HHH_A 1YG2_A 3F8B_A ....
Probab=43.13 E-value=52 Score=23.78 Aligned_cols=43 Identities=16% Similarity=0.294 Sum_probs=36.3
Q ss_pred cCCChHHHHHHHHHHHhcCCcceeeeC-----CCCeEEEcHHHHHHHH
Q 026130 158 FKLRTQECINRITSLENMGRLSGVMDD-----RGKYIYISQAEMKAVA 200 (243)
Q Consensus 158 F~lrtqd~I~RIq~Le~~g~LtGViDD-----RGKFIYIS~eEl~aVA 200 (243)
|.++..-+-..|..|+..|.|++...+ +-||-.||+.=...+.
T Consensus 27 ~~i~~g~lY~~L~~Le~~gli~~~~~~~~~~~~rk~Y~iT~~G~~~l~ 74 (75)
T PF03551_consen 27 WKISPGSLYPALKRLEEEGLIESRWEEEGNGRPRKYYRITEKGREELR 74 (75)
T ss_dssp EETTHHHHHHHHHHHHHTTSEEEEEEEETTSSEEEEEEESHHHHHHHH
T ss_pred cccChhHHHHHHHHHHhCCCEEEeeeccCCCCCCEEEEECHHHHHHhc
Confidence 778899999999999999999999998 4567779988766553
No 303
>PF06936 Selenoprotein_S: Selenoprotein S (SelS); InterPro: IPR009703 This family consists of several mammalian selenoprotein S (SelS) sequences. SelS is a plasma membrane protein and is present in a variety of tissues and cell types. These proteins are involved in the degradation process of misfolded endoplasmic reticulum (ER) luminal proteins which participate in the transfer of misfolded proteins from the ER to the cytosol, where they are destroyed by the proteasome in a ubiquitin-dependent manner []. They probably serve as a linker between DER1, which mediates the retro-translocation of misfolded proteins into the cytosol, and the ATPase complex VCP, which mediates the translocation and ubiquitination.; GO: 0008430 selenium binding, 0006886 intracellular protein transport, 0030176 integral to endoplasmic reticulum membrane; PDB: 2Q2F_A.
Probab=43.08 E-value=2.4e+02 Score=25.09 Aligned_cols=8 Identities=13% Similarity=0.048 Sum_probs=2.6
Q ss_pred HHHhhhhc
Q 026130 107 FEFEKWKG 114 (243)
Q Consensus 107 eEY~kwK~ 114 (243)
+.++.|..
T Consensus 120 e~we~~q~ 127 (190)
T PF06936_consen 120 EMWESMQE 127 (190)
T ss_dssp HHHHH---
T ss_pred HHHHHHHH
Confidence 45555543
No 304
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=43.06 E-value=1.1e+02 Score=25.14 Aligned_cols=65 Identities=11% Similarity=0.194 Sum_probs=49.3
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHH--HHHhcCCccHHHHHhhcc
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVAD--YIKRQGRVSISHLASKSN 219 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~--fI~~rGRVSi~eLa~~sN 219 (243)
.+-++|..+|+++.- |.--+..|.|.....+.|.|=|-|++.+..|.. +.+.- -+|+.++....+
T Consensus 3 ~I~e~a~~~gvs~~t----lR~Ye~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~-G~sL~eI~~~l~ 69 (140)
T PRK09514 3 RIGELAKLAEVTPDT----LRFYEKQGLMDPEVRTEGGYRLYTEQDLQRLRFIRRAKQL-GFTLEEIRELLS 69 (140)
T ss_pred cHHHHHHHHCcCHHH----HHHHHHCCCCCCcccCCCCCeeeCHHHHHHHHHHHHHHHc-CCCHHHHHHHHH
Confidence 578999999997654 555688899998877777788899999987753 33444 468888887654
No 305
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=42.93 E-value=1.4e+02 Score=26.54 Aligned_cols=87 Identities=11% Similarity=0.069 Sum_probs=57.5
Q ss_pred HHHHHHHhcC-ccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhcCCc-----cH
Q 026130 138 DFVEYIKKHK-CIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRV-----SI 211 (243)
Q Consensus 138 ~Fi~yIK~~K-vV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~rGRV-----Si 211 (243)
..+++|..+. -+.+.|||..+|+...-+-.-|+.|...|-|.=.-+ .|+| ++++.=+.--..+.....-+ .+
T Consensus 15 ~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~~~g~v~~~~~-~~~Y-~Lg~~~~~l~~~~~~~~~l~~~a~p~l 92 (263)
T PRK09834 15 MVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQEEGYVRRSAS-DDSF-RLTLKVRQLSEGFRDEQWISALAAPLL 92 (263)
T ss_pred HHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecC-CCcE-EEcHHHHHHHHhhhccccHHHHHHHHH
Confidence 3455565544 488999999999999999999999999999874333 3444 56765443333333322222 24
Q ss_pred HHHHhhccccccccc
Q 026130 212 SHLASKSNQFIDLET 226 (243)
Q Consensus 212 ~eLa~~sN~lI~L~p 226 (243)
.+|+..++..+.|.-
T Consensus 93 ~~La~~t~etv~L~v 107 (263)
T PRK09834 93 GDLLRRVVWPTDLTT 107 (263)
T ss_pred HHHHHHhCCceeEEE
Confidence 677777777666653
No 306
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=42.83 E-value=80 Score=24.57 Aligned_cols=52 Identities=21% Similarity=0.348 Sum_probs=36.8
Q ss_pred hhHHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeE
Q 026130 133 RDLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYI 189 (243)
Q Consensus 133 ~~lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFI 189 (243)
-.++.-.+..+-.-.=|..++||...|.+.++|...+..+- .=..|+.|+-|
T Consensus 23 ~~L~r~LLr~LA~G~PVt~~~LA~a~g~~~e~v~~~L~~~p-----~tEyD~~GrIV 74 (77)
T PF12324_consen 23 AWLLRPLLRLLAKGQPVTVEQLAAALGWPVEEVRAALAAMP-----DTEYDDQGRIV 74 (77)
T ss_dssp HHHHHHHHHHHTTTS-B-HHHHHHHHT--HHHHHHHHHH-T-----TSEEETTSEEE
T ss_pred HHHHHHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHhCC-----CceEcCCCCee
Confidence 44667777888899999999999999999999988877663 23567777655
No 307
>PF12833 HTH_18: Helix-turn-helix domain; PDB: 2K9S_A 3LSG_C 3OIO_A 1D5Y_B 3GBG_A 3OOU_A 1BL0_A 1XS9_A 3MN2_B 3MKL_B ....
Probab=42.60 E-value=45 Score=23.87 Aligned_cols=56 Identities=14% Similarity=0.258 Sum_probs=32.4
Q ss_pred HHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhcCCccHHHHHhhcc
Q 026130 154 LAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRVSISHLASKSN 219 (243)
Q Consensus 154 LA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~rGRVSi~eLa~~sN 219 (243)
||..+|++...+-..++....... .=||..-=|..+...|.+.+..||.+++..|.
T Consensus 1 lA~~~~~s~~~l~~~f~~~~g~s~----------~~~~~~~R~~~a~~~L~~~~~~~i~~ia~~~G 56 (81)
T PF12833_consen 1 LADELGMSERYLSRIFKKETGMSF----------KQYLRELRLQRAKELLRQNTDLSIAEIAEECG 56 (81)
T ss_dssp HHHHCTS-HHHHHHHHHHHHSS-H----------HHHHHHHHHHHHHHHHHHHTT--HHHHHHHTT
T ss_pred ChHHhCcCHHHHHHHHHHHHCcCH----------HHHHHHHHHHHHHHHHHHhhcccHHHHHHHcC
Confidence 566777776666666665443221 12455555677777776667788888877664
No 308
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=41.83 E-value=1.9e+02 Score=25.91 Aligned_cols=88 Identities=17% Similarity=0.297 Sum_probs=67.6
Q ss_pred HHHHHHHhcCc-cchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeC-CCCeEEEcHHHHHHHHHHHHhcCCccH----
Q 026130 138 DFVEYIKKHKC-IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDD-RGKYIYISQAEMKAVADYIKRQGRVSI---- 211 (243)
Q Consensus 138 ~Fi~yIK~~Kv-V~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDD-RGKFIYIS~eEl~aVA~fI~~rGRVSi---- 211 (243)
.+++++....- +.+.+||..+||+..-+-.-++.|...|-+. -|+ .|+| ++++.=+.-=+.|+....=+++
T Consensus 8 ~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL~~~G~v~--~d~~~g~Y-~Lg~~~~~lg~~~l~~~~l~~~a~p~ 84 (246)
T COG1414 8 AILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTLVELGYVE--QDPEDGRY-RLGPRLLELGAAALSSLDLVSLARPL 84 (246)
T ss_pred HHHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEE--EcCCCCcE-eehHHHHHHHHHHHhcCCHHHHhHHH
Confidence 45666665555 6899999999999999999999999999875 566 4555 6999888777777777655553
Q ss_pred -HHHHhhcccccccccch
Q 026130 212 -SHLASKSNQFIDLETKA 228 (243)
Q Consensus 212 -~eLa~~sN~lI~L~p~~ 228 (243)
.+|+...+...+|.--+
T Consensus 85 l~~L~~~tgetv~L~v~d 102 (246)
T COG1414 85 LEELAEETGETVHLSVLD 102 (246)
T ss_pred HHHHHHHhCCcEEEEEEe
Confidence 57888888777776544
No 309
>COG5340 Predicted transcriptional regulator [Transcription]
Probab=41.70 E-value=37 Score=31.75 Aligned_cols=84 Identities=20% Similarity=0.343 Sum_probs=59.2
Q ss_pred HHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEc-----HHHHHH----HHHHHHhcCCccHH
Q 026130 142 YIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYIS-----QAEMKA----VADYIKRQGRVSIS 212 (243)
Q Consensus 142 yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS-----~eEl~a----VA~fI~~rGRVSi~ 212 (243)
-++.||++.+.|+|.-.|++..-+..-.-.|++-|.|--|. ||+|.-|- ...+.. ++...-..|-|+..
T Consensus 24 aae~hkiiTirdvae~~ev~~n~lr~lasrLekkG~LeRi~--rG~YlI~~lpage~~~~t~he~~~~S~~~~~gyIay~ 101 (269)
T COG5340 24 AAEGHKIITIRDVAETLEVAPNTLRELASRLEKKGWLERIL--RGRYLIIPLPAGEEAVYTTHEYLIASHVAEPGYIAYY 101 (269)
T ss_pred HHHhCceEEeHHhhhhccCCHHHHHHHHhhhhhcchhhhhc--CccEEEeecCCCcccceeehhHHHHHHHcccchhhHH
Confidence 47899999999999999999999999999999999886653 78887653 112222 56667777887764
Q ss_pred HHHhhcccccccccch
Q 026130 213 HLASKSNQFIDLETKA 228 (243)
Q Consensus 213 eLa~~sN~lI~L~p~~ 228 (243)
.-.+. ..|+.-.|..
T Consensus 102 SAL~l-~~ltE~~Pst 116 (269)
T COG5340 102 SALSL-HGLTEQVPST 116 (269)
T ss_pred HHHHh-hcchhcCCce
Confidence 32222 2344444443
No 310
>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=41.64 E-value=1.1e+02 Score=23.09 Aligned_cols=53 Identities=11% Similarity=0.229 Sum_probs=39.1
Q ss_pred HHHHHhcCccchHHHHHHc-CCChHHHHHHHHHHHhcCCcceeeeCC-C-CeEE-EcH
Q 026130 140 VEYIKKHKCIPLEDLAAEF-KLRTQECINRITSLENMGRLSGVMDDR-G-KYIY-ISQ 193 (243)
Q Consensus 140 i~yIK~~KvV~LEdLA~~F-~lrtqd~I~RIq~Le~~g~LtGViDDR-G-KFIY-IS~ 193 (243)
+..|.. ...-..||.... |+++..+-+|++.|++.|-|+=+.... + ++.| +|+
T Consensus 11 L~~l~~-g~~rf~el~~~l~~is~~~L~~~L~~L~~~GLv~r~~~~~~p~~v~Y~LT~ 67 (90)
T PF01638_consen 11 LRALFQ-GPMRFSELQRRLPGISPKVLSQRLKELEEAGLVERRVYPEVPPRVEYSLTE 67 (90)
T ss_dssp HHHHTT-SSEEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSSSEEEEEE-H
T ss_pred HHHHHh-CCCcHHHHHHhcchhHHHHHHHHHHHHHHcchhhcccccCCCCCCccCCCc
Confidence 334444 677889999999 999999999999999999998877652 2 3444 555
No 311
>PRK05638 threonine synthase; Validated
Probab=41.53 E-value=87 Score=30.39 Aligned_cols=64 Identities=13% Similarity=0.254 Sum_probs=47.7
Q ss_pred HHHHHHHhcCccchHHHHHHcC--CChHHHHHHHHHHHhcCCcceeeeC-CCCeEEEcHHHHHHHHHH
Q 026130 138 DFVEYIKKHKCIPLEDLAAEFK--LRTQECINRITSLENMGRLSGVMDD-RGKYIYISQAEMKAVADY 202 (243)
Q Consensus 138 ~Fi~yIK~~KvV~LEdLA~~F~--lrtqd~I~RIq~Le~~g~LtGViDD-RGKFIYIS~eEl~aVA~f 202 (243)
..+.+|+.+ -...-+|+..|+ ++..-+-..|+.|++.|.|+....+ |-+|-+||+.-...+..|
T Consensus 375 ~IL~~L~~~-~~~~~el~~~l~~~~s~~~v~~hL~~Le~~GLV~~~~~~g~~~~Y~Lt~~g~~~l~~~ 441 (442)
T PRK05638 375 EILKILSER-EMYGYEIWKALGKPLKYQAVYQHIKELEELGLIEEAYRKGRRVYYKLTEKGRRLLENL 441 (442)
T ss_pred HHHHHHhhC-CccHHHHHHHHcccCCcchHHHHHHHHHHCCCEEEeecCCCcEEEEECcHHHHHHHhc
Confidence 445566655 578999999998 8888888899999999999875333 444555888777666544
No 312
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=41.50 E-value=36 Score=26.24 Aligned_cols=40 Identities=25% Similarity=0.302 Sum_probs=32.1
Q ss_pred cCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCC
Q 026130 146 HKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGK 187 (243)
Q Consensus 146 ~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGK 187 (243)
.-.|.-++||...|++-..|-..|+.|...|-= |.-.++|
T Consensus 17 ~~~~SGe~La~~LgiSRtaVwK~Iq~Lr~~G~~--I~s~~~k 56 (79)
T COG1654 17 GNFVSGEKLAEELGISRTAVWKHIQQLREEGVD--IESVRGK 56 (79)
T ss_pred CCcccHHHHHHHHCccHHHHHHHHHHHHHhCCc--eEecCCC
Confidence 336888999999999999999999999999853 3334443
No 313
>cd04613 CBS_pair_SpoIVFB_EriC_assoc2 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with either the SpoIVFB domain (sporulation protein, stage IV cell wall formation, F locus, promoter-distal B) or the chloride channel protein EriC. SpoIVFB is one of 4 proteins involved in endospore formation; the others are SpoIVFA (sporulation protein, stage IV cell wall formation, F locus, promoter-proximal A), BofA (bypass-of-forespore A ), and SpoIVB (sporulation protein, stage IV cell wall formation, B locus). SpoIVFB is negatively regulated by SpoIVFA and BofA and activated by SpoIVB. It is thought that SpoIVFB, SpoIVFA, and BofA are located in the mother-cell membrane that surrounds the forespore and that SpoIVB is secreted from the forespore into the space between the two where it activates SpoIVFB. EriC is involved in inorganic ion transport and metabolism. CBS is a small domain originally identified in cystathionine beta-synthase a
Probab=41.49 E-value=42 Score=24.12 Aligned_cols=38 Identities=21% Similarity=0.329 Sum_probs=24.7
Q ss_pred cceeeeCCCCeE-EEcHHHHHHHHHHHHhc---CCccHHHHHhhc
Q 026130 178 LSGVMDDRGKYI-YISQAEMKAVADYIKRQ---GRVSISHLASKS 218 (243)
Q Consensus 178 LtGViDDRGKFI-YIS~eEl~aVA~fI~~r---GRVSi~eLa~~s 218 (243)
...|+|+.|+|+ |||...+.. ++.+. +.+++.+++...
T Consensus 26 ~~~v~~~~~~~~G~v~~~~l~~---~~~~~~~~~~~~v~~~~~~~ 67 (114)
T cd04613 26 NFPVVDDDGRLVGIVSLDDIRE---ILFDPSLYDLVVASDIMTKP 67 (114)
T ss_pred ceeEECCCCCEEEEEEHHHHHH---HHhcccccccEEHHHhccCC
Confidence 467889999998 899888764 33322 225566666443
No 314
>PF13182 DUF4007: Protein of unknown function (DUF4007)
Probab=41.12 E-value=55 Score=30.33 Aligned_cols=60 Identities=23% Similarity=0.463 Sum_probs=48.6
Q ss_pred hHHHHHHHHH----HhcCccchHHHH-------HHcCCChHHHHHHHHHHHhc-CCcceeeeCCC-CeEEEcHH
Q 026130 134 DLLADFVEYI----KKHKCIPLEDLA-------AEFKLRTQECINRITSLENM-GRLSGVMDDRG-KYIYISQA 194 (243)
Q Consensus 134 ~lL~~Fi~yI----K~~KvV~LEdLA-------~~F~lrtqd~I~RIq~Le~~-g~LtGViDDRG-KFIYIS~e 194 (243)
-++-..++|. ...+.+.|++|+ .-|+|+...++++|..|... |.|+ |.|.-| .=||+.+.
T Consensus 202 i~~YaL~~~~~~~~~~~~sis~~~L~~~~~sPGriF~L~~~~l~~~L~~l~~~~g~i~-~~~TaGl~qv~~~~~ 274 (286)
T PF13182_consen 202 IFLYALLDFAERESPGRNSISFDELLNEPGSPGRIFKLDEESLAERLEQLEEIYGFIS-WSDTAGLDQVYLKDE 274 (286)
T ss_pred HHHHHHHHHHHHhCCCCcEEEHHHHhcCCCCcceEeccCHHHHHHHHHHHHhhcCcEE-EEEcCCCeEEEeccc
Confidence 3455666666 578899999985 67999999999999999999 6665 888888 78888774
No 315
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=40.85 E-value=2e+02 Score=28.72 Aligned_cols=36 Identities=11% Similarity=0.219 Sum_probs=28.5
Q ss_pred HHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHh
Q 026130 138 DFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLEN 174 (243)
Q Consensus 138 ~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~ 174 (243)
..++++. ..-+...+||..||+++.-+.+-|+.|..
T Consensus 8 ~iL~~L~-~~~~t~~~LA~~l~VS~RTIr~dI~~in~ 43 (584)
T PRK09863 8 KIVDLLE-QQDRSGGELAQQLGVSRRTIVRDIAYINF 43 (584)
T ss_pred HHHHHHH-cCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3445554 46789999999999999999998887743
No 316
>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=40.58 E-value=76 Score=23.37 Aligned_cols=47 Identities=26% Similarity=0.458 Sum_probs=32.8
Q ss_pred hHHHHHHHHHHh--cCccchHHHHHHc---CCChH--HHHHHHHHHHhcCCcce
Q 026130 134 DLLADFVEYIKK--HKCIPLEDLAAEF---KLRTQ--ECINRITSLENMGRLSG 180 (243)
Q Consensus 134 ~lL~~Fi~yIK~--~KvV~LEdLA~~F---~lrtq--d~I~RIq~Le~~g~LtG 180 (243)
.+-+.||.++.. .+.+.|.++|..| +.+|+ =+-|-++=|++-|-|+=
T Consensus 8 ~lt~~fi~~~~~~~~~~i~l~~ia~~l~~~~~k~~~RRlYDI~NVLealgli~K 61 (71)
T PF02319_consen 8 LLTQRFIQLFESSPDKSISLNEIADKLISENVKTQRRRLYDIINVLEALGLIEK 61 (71)
T ss_dssp HHHHHHHHHHHHCCCTEEEHHHHHHHCHHHCCHHHCHHHHHHHHHHHHCTSEEE
T ss_pred HHHHHHHHHHHHCCCCcccHHHHHHHHcccccccccchhhHHHHHHHHhCceee
Confidence 345789998874 6899999999999 99444 33444555666665543
No 317
>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]
Probab=40.42 E-value=2e+02 Score=30.55 Aligned_cols=6 Identities=33% Similarity=0.451 Sum_probs=2.3
Q ss_pred HHHHhh
Q 026130 106 AFEFEK 111 (243)
Q Consensus 106 ~eEY~k 111 (243)
..|...
T Consensus 674 RLEreR 679 (940)
T KOG4661|consen 674 RLERER 679 (940)
T ss_pred HHHHHH
Confidence 333333
No 318
>PF06991 Prp19_bind: Splicing factor, Prp19-binding domain; InterPro: IPR009730 This entry represents the C terminus (approximately 300 residues) of eukaryotic micro-fibrillar-associated protein 1, which is a component of elastin-associated microfibrils in the extracellular matrix [].
Probab=40.14 E-value=1.3e+02 Score=28.33 Aligned_cols=37 Identities=11% Similarity=0.140 Sum_probs=20.6
Q ss_pred hHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEE
Q 026130 151 LEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIY 190 (243)
Q Consensus 151 LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIY 190 (243)
.+++-+.-+|+..+- +..+...+....=--.+|||-|
T Consensus 142 keEiERrR~mteEEr---~~ed~~~~k~~~~~~~k~k~~f 178 (276)
T PF06991_consen 142 KEEIERRRNMTEEER---RAEDRENPKQIENKKEKGKMKF 178 (276)
T ss_pred HHHHHHHHhcCHHHH---HHHHHhhhhhhhccccccchhh
Confidence 466777777766543 4455555544333335677644
No 319
>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=39.93 E-value=1.9e+02 Score=23.56 Aligned_cols=58 Identities=21% Similarity=0.241 Sum_probs=39.8
Q ss_pred HHHHHHhcCccchHH----HHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEE---EcHHHHH
Q 026130 139 FVEYIKKHKCIPLED----LAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIY---ISQAEMK 197 (243)
Q Consensus 139 Fi~yIK~~KvV~LEd----LA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIY---IS~eEl~ 197 (243)
+.+.|-.+.-+...+ |+..+|++..-+..-|..|..-|-|.=.-+.| .|+| ||++++.
T Consensus 9 VM~vlW~~~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~KG~v~~~k~gr-~~~Y~p~vs~ee~~ 73 (130)
T TIGR02698 9 VMRVVWTLGETTSRDIIRILAEKKDWSDSTIKTLLGRLVDKGCLTTEKEGR-KFIYTALVSEDEAV 73 (130)
T ss_pred HHHHHHcCCCCCHHHHHHHHhhccCCcHHHHHHHHHHHHHCCceeeecCCC-cEEEEecCCHHHHH
Confidence 445554444556667 44445888888888999999999886444444 5666 7899984
No 320
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=39.91 E-value=61 Score=33.52 Aligned_cols=52 Identities=33% Similarity=0.519 Sum_probs=40.0
Q ss_pred HHHHHHH--hcCccchHHHHHHcCCCh----HHHHHHHHHHHhcCCcceeeeCCCCeEEE
Q 026130 138 DFVEYIK--KHKCIPLEDLAAEFKLRT----QECINRITSLENMGRLSGVMDDRGKYIYI 191 (243)
Q Consensus 138 ~Fi~yIK--~~KvV~LEdLA~~F~lrt----qd~I~RIq~Le~~g~LtGViDDRGKFIYI 191 (243)
..++|++ ..+-+.+.+|+..||++. ..+...|..|...|.|. .+.+|+|...
T Consensus 6 ~il~~l~~~~~~~~~~~~l~~~l~~~~~~~~~~l~~~l~~l~~~g~l~--~~~~~~~~~~ 63 (709)
T TIGR02063 6 LILEFLKSKKGKPISLKELAKAFHLKGADEKKALRKRLRALEDDGLVK--KNRRGLYALP 63 (709)
T ss_pred HHHHHHHhCCCCCCCHHHHHHHhCCCChHHHHHHHHHHHHHHHCCCEE--EcCCceEecC
Confidence 4677777 458899999999999974 34788999999999985 4555666443
No 321
>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules, such as, metal ions, drugs, and organic substrates. This subgroup lacks one of the c
Probab=39.63 E-value=1.6e+02 Score=23.89 Aligned_cols=65 Identities=14% Similarity=0.213 Sum_probs=48.0
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHH--HHHHhcCCccHHHHHhhcc
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVA--DYIKRQGRVSISHLASKSN 219 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA--~fI~~rGRVSi~eLa~~sN 219 (243)
.+-++|..+|+++.- |.--+..|-|...-++.|.|=|-|++.+..|. .+.+.-| +|+.++...-+
T Consensus 2 ~IgE~A~~~gvs~~T----LRyYE~~GLl~p~r~~~~gyR~Y~~~~~~~l~~I~~lr~~G-~sL~eI~~~l~ 68 (133)
T cd04787 2 KVKELANAAGVTPDT----VRFYTRIGLLRPTRDPVNGYRLYSEKDLSRLRFILSARQLG-FSLKDIKEILS 68 (133)
T ss_pred CHHHHHHHHCcCHHH----HHHHHHCCCCCCCcCCCCCeeeCCHHHHHHHHHHHHHHHcC-CCHHHHHHHHh
Confidence 467899999997763 45568999999987765777788888888763 3445556 89888766443
No 322
>KOG2891 consensus Surface glycoprotein [General function prediction only]
Probab=39.37 E-value=3.5e+02 Score=26.45 Aligned_cols=7 Identities=57% Similarity=0.273 Sum_probs=2.7
Q ss_pred HHHhhhh
Q 026130 107 FEFEKWK 113 (243)
Q Consensus 107 eEY~kwK 113 (243)
.+-.|++
T Consensus 397 keeeklk 403 (445)
T KOG2891|consen 397 KEEEKLK 403 (445)
T ss_pred hHHHHHH
Confidence 3333443
No 323
>KOG2439 consensus Nuclear architecture related protein [Nuclear structure]
Probab=39.28 E-value=32 Score=34.49 Aligned_cols=89 Identities=21% Similarity=0.287 Sum_probs=57.8
Q ss_pred chhHHHHHHHHHHhcC-----ccchH-----HHHHHcCCChHHHHHHHHHHHhcCCcceeeeCC--CCeEE-EcHHHHHH
Q 026130 132 DRDLLADFVEYIKKHK-----CIPLE-----DLAAEFKLRTQECINRITSLENMGRLSGVMDDR--GKYIY-ISQAEMKA 198 (243)
Q Consensus 132 ~~~lL~~Fi~yIK~~K-----vV~LE-----dLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDR--GKFIY-IS~eEl~a 198 (243)
++.....|..-+-.+| ||.+- -||+.|||+++++--+|-.+...=-+.=|+|.- -.|+| -|.+|+-
T Consensus 80 s~Qs~~~~~k~l~~~k~~~~lvvsvSPQ~~~slAa~~gls~~e~~~~L~~F~kklgvhyv~DT~~sR~~sl~es~~Efv- 158 (459)
T KOG2439|consen 80 SEQSHKEFLKVLQKSKQQKVLVVSVSPQSRASLAAKYGLSLREAALRLTSFFKKLGVHYVVDTSFSRDFSLSESYEEFV- 158 (459)
T ss_pred hhhhHHHHHHhhhhccccceEEEecChhHHHHHHHHhCCCHHHHHHHHHHHHHhcCeeEEeehHHHHHHHHHHHHHHHH-
Confidence 3445677877777777 44443 599999999999999999988887788888862 22332 2344432
Q ss_pred HHHHHHhcCCccHHHHHhhccccc
Q 026130 199 VADYIKRQGRVSISHLASKSNQFI 222 (243)
Q Consensus 199 VA~fI~~rGRVSi~eLa~~sN~lI 222 (243)
++|=.+.|-=+..=|.++|+=+|
T Consensus 159 -~~~r~~~~~~~~PlLsSaCPG~v 181 (459)
T KOG2439|consen 159 -ARYRQHSEEERTPLLSSACPGWV 181 (459)
T ss_pred -HHhhcccccccccchhhcCCcee
Confidence 23333333333355888888444
No 324
>KOG2002 consensus TPR-containing nuclear phosphoprotein that regulates K(+) uptake [Inorganic ion transport and metabolism]
Probab=39.25 E-value=2.1e+02 Score=31.77 Aligned_cols=20 Identities=40% Similarity=0.499 Sum_probs=8.6
Q ss_pred HHHHHHHHHHHHHHHhhhHH
Q 026130 51 REAAQQADEAARESRQSKQD 70 (243)
Q Consensus 51 rk~qReaee~~REerk~~e~ 70 (243)
..-..+|++...++|+.+++
T Consensus 823 ~~~~~~Aq~e~e~er~~kq~ 842 (1018)
T KOG2002|consen 823 LEHVAQAQEEDEEERRAKQE 842 (1018)
T ss_pred HHHHHHHhHHHHHHHHHHHH
Confidence 33334444444444444443
No 325
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=39.22 E-value=85 Score=24.91 Aligned_cols=53 Identities=28% Similarity=0.301 Sum_probs=41.7
Q ss_pred HHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEc
Q 026130 137 ADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYIS 192 (243)
Q Consensus 137 ~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS 192 (243)
-..+.|++..-+=.---+|..++++.++|...+..|+..|-|.=|- |+.|.=|
T Consensus 10 ~~IL~hl~~~~~Dy~k~ia~~l~~~~~~v~~~l~~Le~~GLler~~---g~~iK~~ 62 (92)
T PF10007_consen 10 LKILQHLKKAGPDYAKSIARRLKIPLEEVREALEKLEEMGLLERVE---GKTIKRS 62 (92)
T ss_pred HHHHHHHHHHCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEec---Ccccchh
Confidence 4556666666666666689999999999999999999999887664 7766554
No 326
>KOG4557 consensus Origin recognition complex, subunit 6 [Replication, recombination and repair]
Probab=39.09 E-value=36 Score=31.65 Aligned_cols=86 Identities=19% Similarity=0.191 Sum_probs=56.2
Q ss_pred cccchhHHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhc--CCcceeeeCCCCeEEEcHHHHHHHHHHHH--
Q 026130 129 QDGDRDLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENM--GRLSGVMDDRGKYIYISQAEMKAVADYIK-- 204 (243)
Q Consensus 129 ~~~~~~lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~--g~LtGViDDRGKFIYIS~eEl~aVA~fI~-- 204 (243)
....++-+..|-+.|-.++-..+.|||++||+ -+||+-.+.++.. |+|-.--|-. .-.|.--+.+.|-|.-
T Consensus 74 k~~Y~~~~~sfe~llgln~~~~VrdlaVQfgc--~evi~~a~~vl~syk~~lpaT~~~~---~D~SrP~ft~aA~~~ack 148 (262)
T KOG4557|consen 74 KKAYSRSFNSFENLLGLNIKLNVRDLAVQFGC--VEVIKSAQNVLSSYKERLPATRRAN---ADFSRPVFTAAAFYLACK 148 (262)
T ss_pred HHHHHHHHHHHHHHhcchhhcCHHHHHHHHhH--HHHHHHHHHHHHHHHhcCchhhhcC---CcccchHHHHHHHHHHHH
Confidence 34567778899999999999999999999998 5677777776643 2221111100 1134445566666653
Q ss_pred -hcCCccHHHHHhhcc
Q 026130 205 -RQGRVSISHLASKSN 219 (243)
Q Consensus 205 -~rGRVSi~eLa~~sN 219 (243)
.+=.|+..-|...||
T Consensus 149 ~lKlKVdK~kli~~sg 164 (262)
T KOG4557|consen 149 KLKLKVDKLKLIEVSG 164 (262)
T ss_pred HHHHhhhHhhcccccC
Confidence 335677777777776
No 327
>PF07848 PaaX: PaaX-like protein; InterPro: IPR012906 This entry describes the N-terminal region of proteins that are similar to, and nclude, the product of the paaX gene of Escherichia coli (P76086 from SWISSPROT). PaaX is a transcriptional regulator that is always found in association with operons believed to be involved in the degradation of phenylacetic acid []. The gene product has been shown to bind to the promoter sites and repress their transcription []. ; PDB: 3KFW_X 3L09_B.
Probab=39.05 E-value=57 Score=24.36 Aligned_cols=59 Identities=17% Similarity=0.273 Sum_probs=43.5
Q ss_pred HHHHHHHHHhcC----ccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHH
Q 026130 136 LADFVEYIKKHK----CIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQA 194 (243)
Q Consensus 136 L~~Fi~yIK~~K----vV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~e 194 (243)
++-|-+|+..+- +-.|=+|...||++.+-+-.-|-.|-++|.|...-+.|--|-.+|+.
T Consensus 7 ~tl~Gdy~~~~g~~i~~~~Li~ll~~~Gv~e~avR~alsRl~~~G~L~~~r~Gr~~~Y~Lt~~ 69 (70)
T PF07848_consen 7 VTLLGDYLRPRGGWIWVASLIRLLAAFGVSESAVRTALSRLVRRGWLESERRGRRSYYRLTER 69 (70)
T ss_dssp HHHHHHHCCTTTS-EEHHHHHHHHCCTT--HHHHHHHHHHHHHTTSEEEECCCTEEEEEE-HH
T ss_pred HHHHHHHhccCCCceeHHHHHHHHHHcCCChHHHHHHHHHHHHcCceeeeecCccceEeeCCC
Confidence 444556664432 44567799999999999999999999999999988888777777763
No 328
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=38.90 E-value=18 Score=29.89 Aligned_cols=25 Identities=16% Similarity=0.364 Sum_probs=22.8
Q ss_pred CCeEEEcHHHHHHHHHHHHhcCCcc
Q 026130 186 GKYIYISQAEMKAVADYIKRQGRVS 210 (243)
Q Consensus 186 GKFIYIS~eEl~aVA~fI~~rGRVS 210 (243)
++|-|+|++++.=|-.||+.+|.+.
T Consensus 29 ~~~~~L~~E~~~Fi~~Fi~~rGnlK 53 (113)
T PF09862_consen 29 PWFARLSPEQLEFIKLFIKNRGNLK 53 (113)
T ss_pred chhhcCCHHHHHHHHHHHHhcCCHH
Confidence 7899999999999999999999653
No 329
>KOG3654 consensus Uncharacterized CH domain protein [Cytoskeleton]
Probab=38.85 E-value=1.6e+02 Score=30.67 Aligned_cols=25 Identities=28% Similarity=0.424 Sum_probs=11.9
Q ss_pred HHhhHHHHHHHHHHHHHHHHHHHHH
Q 026130 76 RRRKDEEREARESALEEEAKAQKAR 100 (243)
Q Consensus 76 rrkkeeere~eE~~~eEeer~~kee 100 (243)
|+++.-.+.+.|.+++|..+++.++
T Consensus 408 r~rkqqleae~e~kreearrkaeee 432 (708)
T KOG3654|consen 408 RRRKQQLEAEKEQKREEARRKAEEE 432 (708)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhHhh
Confidence 3444444444555555554444444
No 330
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=38.78 E-value=26 Score=23.17 Aligned_cols=33 Identities=15% Similarity=0.310 Sum_probs=16.8
Q ss_pred ccchHHHHHHcCCChHHHHHHHHHHHhcCCccee
Q 026130 148 CIPLEDLAAEFKLRTQECINRITSLENMGRLSGV 181 (243)
Q Consensus 148 vV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGV 181 (243)
=....++|..||++..-|-+-++.....| +.|+
T Consensus 17 G~s~~~ia~~lgvs~~Tv~~w~kr~~~~G-~~gL 49 (50)
T PF13384_consen 17 GWSIREIAKRLGVSRSTVYRWIKRYREEG-LEGL 49 (50)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHT-----------
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHccccc-cccc
Confidence 56778999999998877777777777666 6654
No 331
>COG5301 Phage-related tail fibre protein [General function prediction only]
Probab=37.77 E-value=19 Score=36.83 Aligned_cols=15 Identities=33% Similarity=0.565 Sum_probs=13.6
Q ss_pred cceeeeCCCCeEEEc
Q 026130 178 LSGVMDDRGKYIYIS 192 (243)
Q Consensus 178 LtGViDDRGKFIYIS 192 (243)
-.||||+.|+||||+
T Consensus 90 EvGlfDadG~liavg 104 (587)
T COG5301 90 EVGLFDADGKLIAVG 104 (587)
T ss_pred EeeeecCCCCEEEEc
Confidence 469999999999996
No 332
>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues. They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.
Probab=37.65 E-value=11 Score=33.46 Aligned_cols=25 Identities=24% Similarity=0.408 Sum_probs=16.7
Q ss_pred HHHHHHHHHHhcCCccHHHHHhhcc
Q 026130 195 EMKAVADYIKRQGRVSISHLASKSN 219 (243)
Q Consensus 195 El~aVA~fI~~rGRVSi~eLa~~sN 219 (243)
-|..+.+||+.+--|.+.+||...|
T Consensus 100 lL~~Fi~yIK~~Kvv~ledla~~f~ 124 (188)
T PF09756_consen 100 LLQEFINYIKEHKVVNLEDLAAEFG 124 (188)
T ss_dssp HHHHHHHHHHH-SEE-HHHHHHHH-
T ss_pred HHHHHHHHHHHcceeeHHHHHHHcC
Confidence 3677788888888888888887654
No 333
>PF01997 Translin: Translin family; InterPro: IPR002848 Translins are DNA-binding proteins that specifically recognise consensus sequences at the breakpoint junctions in chromosomal translocations, mostly involving immunoglobulin (Ig)/T-cell receptor gene segments. They seem to recognise single-stranded DNA ends generated by staggered breaks occuring at recombination hot spots []. Translin folds into an alpha-alpha superhelix, consisting of two curved layers of alpha/alpha topology [, ].; GO: 0043565 sequence-specific DNA binding; PDB: 3QB5_K 3PJA_L 1J1J_D 3RIU_C 3AXJ_B 4DG7_C 2QVA_C 2QRX_A 1KEY_C.
Probab=37.63 E-value=29 Score=30.22 Aligned_cols=57 Identities=12% Similarity=0.271 Sum_probs=36.4
Q ss_pred HHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHH-HHHHHHHHhcCCccHHHH
Q 026130 137 ADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEM-KAVADYIKRQGRVSISHL 214 (243)
Q Consensus 137 ~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl-~aVA~fI~~rGRVSi~eL 214 (243)
..|..|++...++.+++|...+++.+.. -..++|+++++ -.|++++-.--|.+|..+
T Consensus 80 ~~f~~~l~~~~L~t~~ev~~~l~~~~~~---------------------~~~~~v~~~dYL~Gl~DltGEL~R~ai~~v 137 (200)
T PF01997_consen 80 ISFYHYLETGRLLTPEEVGEILGFSEDD---------------------EDRFHVTPEDYLLGLADLTGELMRYAINSV 137 (200)
T ss_dssp HHHHHHHHHSSS--HHHHHHHCTCBSST---------------------SCSSB--HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHcCCCCCCHHHHHHHHhhcccc---------------------ccceecCHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4577799999999999999999987655 45566777664 456666555444444433
No 334
>PRK09510 tolA cell envelope integrity inner membrane protein TolA; Provisional
Probab=37.62 E-value=3.5e+02 Score=26.74 Aligned_cols=7 Identities=14% Similarity=0.079 Sum_probs=2.9
Q ss_pred cccccCC
Q 026130 28 DEGVAGG 34 (243)
Q Consensus 28 ~e~~~~g 34 (243)
+=+|.|+
T Consensus 51 ~AVmvD~ 57 (387)
T PRK09510 51 DAVMVDP 57 (387)
T ss_pred cceecCh
Confidence 3334444
No 335
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=37.60 E-value=1.7e+02 Score=23.58 Aligned_cols=62 Identities=16% Similarity=0.293 Sum_probs=43.1
Q ss_pred HHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhcCCccHHHH
Q 026130 135 LLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRVSISHL 214 (243)
Q Consensus 135 lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~rGRVSi~eL 214 (243)
++..+...+..+. +..++||...|++ +..|.+|. +|+. .+|.+-+.++|+++ .|++..|
T Consensus 6 ~~~~l~~ll~~~G-lsq~eLA~~~Gis-~~~is~iE--------------~g~~-~ps~~~l~kIa~aL----~v~~~~L 64 (120)
T PRK13890 6 FFTNVLRLLDERH-MTKKELSERSGVS-ISFLSDLT--------------TGKA-NPSLKVMEAIADAL----ETPLPLL 64 (120)
T ss_pred HHHHHHHHHHHcC-CCHHHHHHHHCcC-HHHHHHHH--------------cCCC-CCCHHHHHHHHHHH----CCCHHHH
Confidence 4555555565444 4688999999985 55666554 4555 68999999999988 4666666
Q ss_pred Hhh
Q 026130 215 ASK 217 (243)
Q Consensus 215 a~~ 217 (243)
...
T Consensus 65 ~~~ 67 (120)
T PRK13890 65 LES 67 (120)
T ss_pred hcc
Confidence 544
No 336
>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family. Members of this protein family are putative transcriptional regulators of the PadR family, as found in species of the Acidobacteria. This family of proteins has expanded greatly in this lineage, and where it regularly is found in the vicinity of a putative transporter protein
Probab=37.49 E-value=94 Score=23.96 Aligned_cols=47 Identities=17% Similarity=0.272 Sum_probs=36.9
Q ss_pred cCCChHHHHHHHHHHHhcCCccee--eeC---CCCeEEEcHHHHHHHHHHHH
Q 026130 158 FKLRTQECINRITSLENMGRLSGV--MDD---RGKYIYISQAEMKAVADYIK 204 (243)
Q Consensus 158 F~lrtqd~I~RIq~Le~~g~LtGV--iDD---RGKFIYIS~eEl~aVA~fI~ 204 (243)
+.++..-+-.-|..|+.+|-|+.. .++ +=|+.+||+.=-..+...+.
T Consensus 35 ~~i~~gtlY~~L~rLe~~GlI~~~~~~~~~~~~rk~y~iT~~Gr~~l~~~~~ 86 (100)
T TIGR03433 35 LQVEEGSLYPALHRLERRGWIAAEWGESENNRRAKFYRLTAAGRKQLAAETE 86 (100)
T ss_pred cccCCCcHHHHHHHHHHCCCeEEEeeecCCCCCceEEEECHHHHHHHHHHHH
Confidence 467777788899999999999995 332 34899999998777776654
No 337
>PF00034 Cytochrom_C: Cytochrome c; InterPro: IPR003088 Cytochromes c (cytC) can be defined as electron-transfer proteins having one or several haem c groups, bound to the protein by one or, more generally, two thioether bonds involving sulphydryl groups of cysteine residues. The fifth haem iron ligand is always provided by a histidine residue. CytC possess a wide range of properties and function in a large number of different redox processes. Ambler [] recognised four classes of cytC. Class I includes the low-spin soluble cytC of mitochondria and bacteria, with the haem-attachment site towards the N terminus, and the sixth ligand provided by a methionine residue about 40 residues further on towards the C terminus. On the basis of sequence similarity, class I cytC were further subdivided into five classes, IA to IE. Class IB includes the eukaryotic mitochondrial cytC and prokaryotic 'short' cyt c2 exemplified by Rhodopila globiformis cyt c2; class IA includes 'long' cyt c2, such as Rhodospirillum rubrum cyt c2 and Aquaspirillum itersonii cyt c-550, which have several extra loops by comparison with class IB cytC.; GO: 0005506 iron ion binding, 0009055 electron carrier activity, 0020037 heme binding; PDB: 1YNR_B 2AI5_A 1AYG_A 3O5C_C 1YEA_A 3CXH_W 1YTC_A 1YEB_A 2YBB_Y 2B4Z_A ....
Probab=37.40 E-value=27 Score=24.18 Aligned_cols=16 Identities=25% Similarity=0.576 Sum_probs=14.4
Q ss_pred EEcHHHHHHHHHHHHh
Q 026130 190 YISQAEMKAVADYIKR 205 (243)
Q Consensus 190 YIS~eEl~aVA~fI~~ 205 (243)
-+|++|+.+|+.||++
T Consensus 74 ~ls~~e~~~l~ayl~s 89 (91)
T PF00034_consen 74 ILSDEEIADLAAYLRS 89 (91)
T ss_dssp TSSHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHH
Confidence 4899999999999986
No 338
>cd07972 OBF_DNA_ligase_Arch_LigB The Oligonucleotide/oligosaccharide binding (OB)-fold domain of archaeal and bacterial ATP-dependent DNA ligases is a DNA-binding module that is part of the catalytic core unit. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of Pyrococcus furiosus DN
Probab=37.23 E-value=48 Score=26.59 Aligned_cols=29 Identities=14% Similarity=0.368 Sum_probs=24.5
Q ss_pred ceeeeCC-CCeEEE-------cHHHHHHHHHHHHhcC
Q 026130 179 SGVMDDR-GKYIYI-------SQAEMKAVADYIKRQG 207 (243)
Q Consensus 179 tGViDDR-GKFIYI-------S~eEl~aVA~fI~~rG 207 (243)
-||.|+. |+|+|| |++++..+.++++...
T Consensus 26 lg~~d~~~g~l~~vg~vgtG~~~~~~~~l~~~l~~~~ 62 (122)
T cd07972 26 LAVRDEETGELVPVGKVATGLTDEELEELTERLRELI 62 (122)
T ss_pred EEEEcCCCCeEEEEEEEccCCCHHHHHHHHHHhhhhh
Confidence 5899887 899995 7899999999988754
No 339
>PRK15466 carboxysome structural protein EutK; Provisional
Probab=36.81 E-value=36 Score=30.01 Aligned_cols=33 Identities=21% Similarity=0.309 Sum_probs=29.4
Q ss_pred CccchHHHHHHcCCChHHHHHHHHHHHhcCCcc
Q 026130 147 KCIPLEDLAAEFKLRTQECINRITSLENMGRLS 179 (243)
Q Consensus 147 KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~Lt 179 (243)
.=...-++|+|||++.....+-+..|..+|.|-
T Consensus 123 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 155 (166)
T PRK15466 123 QGMTAGEVAAHFGWPLEKARNALEQLFSAGTLR 155 (166)
T ss_pred ccccHHHHHHHhCCcHHHHHHHHHHHHhccchh
Confidence 346678999999999999999999999999874
No 340
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=36.65 E-value=1.1e+02 Score=26.98 Aligned_cols=75 Identities=17% Similarity=0.243 Sum_probs=54.4
Q ss_pred hhHHHHHHHHHHhc--Cc-cchHHHHHHcCCChHHHHHHHHHHHhcCC-cceeeeCCCCeEEEcHHHHHHHHHHHHhc-C
Q 026130 133 RDLLADFVEYIKKH--KC-IPLEDLAAEFKLRTQECINRITSLENMGR-LSGVMDDRGKYIYISQAEMKAVADYIKRQ-G 207 (243)
Q Consensus 133 ~~lL~~Fi~yIK~~--Kv-V~LEdLA~~F~lrtqd~I~RIq~Le~~g~-LtGViDDRGKFIYIS~eEl~aVA~fI~~r-G 207 (243)
...|..+++||-.+ .- +.+++||..+||+.--+..-.+. .|. +.. ||..-=|......|... .
T Consensus 196 ~~~l~~~~~~I~~~l~~~~ls~~~lA~~~giS~r~L~r~Fk~---~G~T~~~---------yi~~~RL~~A~~lL~~~~~ 263 (302)
T PRK09685 196 ERQFQKVVALIDQSIQEEILRPEWIAGELGISVRSLYRLFAE---QGLVVAQ---------YIRNRRLDRCADDLRPAAD 263 (302)
T ss_pred HHHHHHHHHHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHHH---cCCCHHH---------HHHHHHHHHHHHHhhhhcc
Confidence 45688999999887 22 78999999999997666555543 232 222 67788888888888332 3
Q ss_pred CccHHHHHhhcc
Q 026130 208 RVSISHLASKSN 219 (243)
Q Consensus 208 RVSi~eLa~~sN 219 (243)
..||+++|..|.
T Consensus 264 ~~sI~eIA~~~G 275 (302)
T PRK09685 264 DEKITSIAYKWG 275 (302)
T ss_pred CCCHHHHHHHhC
Confidence 579999998773
No 341
>PF05043 Mga: Mga helix-turn-helix domain; InterPro: IPR007737 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions []. The family also contains VirR like proteins which match only at the C terminus of the alignment.; PDB: 3SQN_A.
Probab=36.51 E-value=1e+02 Score=22.71 Aligned_cols=63 Identities=17% Similarity=0.213 Sum_probs=40.6
Q ss_pred hHHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHH
Q 026130 134 DLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMK 197 (243)
Q Consensus 134 ~lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~ 197 (243)
+..-.++.++-.++.+.+++||..++++..-+...|+.|...=.-.|+-= .++-++|+=.|..
T Consensus 16 s~~~~ll~~ll~~~~~s~~~la~~~~iS~sti~~~i~~l~~~l~~~~l~i-~~~~~~l~G~E~~ 78 (87)
T PF05043_consen 16 SLNYQLLKLLLNNEYVSIEDLAEELFISRSTIYRDIKKLNKYLKKYGLKI-SKKGYRLEGDESN 78 (87)
T ss_dssp SHHHHHHHHHHH-SEEEHHHHHHHHT--HHHHHHHHHHHHHHHHCCT-EE--SSEEEEES-HHH
T ss_pred hHHHHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCeEE-eCCCeEEEeCHHH
Confidence 34456777777999999999999999999988887766654333344433 6666777666654
No 342
>PRK13877 conjugal transfer relaxosome component TraJ; Provisional
Probab=36.28 E-value=53 Score=26.93 Aligned_cols=30 Identities=10% Similarity=0.107 Sum_probs=26.0
Q ss_pred eEEEcHHHHHHHHHHHHhcCCccHHHHHhhc
Q 026130 188 YIYISQAEMKAVADYIKRQGRVSISHLASKS 218 (243)
Q Consensus 188 FIYIS~eEl~aVA~fI~~rGRVSi~eLa~~s 218 (243)
.+|+||+|+..|-.=-.+-|- |++++.+.|
T Consensus 14 ~vrvt~eE~~~I~~kA~~AGl-S~SeYLR~~ 43 (114)
T PRK13877 14 RVPVLPDEKAEIEANAAAAGL-SVARYLRDV 43 (114)
T ss_pred EEEeCHHHHHHHHHHHHHhCC-CHHHHHHHH
Confidence 578899999999999999998 988887765
No 343
>PF00486 Trans_reg_C: Transcriptional regulatory protein, C terminal; InterPro: IPR001867 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. This entry represents a domain that is almost always found associated with the response regulator receiver domain (see IPR001789 from INTERPRO). It may play a role in DNA binding [].; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0000160 two-component signal transduction system (phosphorelay), 0006355 regulation of transcription, DNA-dependent; PDB: 2K4J_A 2JPB_A 1ODD_A 1OPC_A 1KGS_A 2PMU_E 2JZY_A 1GXP_B 1QQI_A 2Z33_A ....
Probab=36.04 E-value=56 Score=22.89 Aligned_cols=32 Identities=22% Similarity=0.396 Sum_probs=27.8
Q ss_pred CCeEEEcHHHHHHHHHHHHhcCC-ccHHHHHhh
Q 026130 186 GKYIYISQAEMKAVADYIKRQGR-VSISHLASK 217 (243)
Q Consensus 186 GKFIYIS~eEl~aVA~fI~~rGR-VSi~eLa~~ 217 (243)
|+=|-+|+.|+.-++-|+...|+ ||..+|...
T Consensus 1 G~~v~Lt~~e~~lL~~L~~~~~~~vs~~~l~~~ 33 (77)
T PF00486_consen 1 GQPVKLTPKEFRLLELLLRNPGRVVSREELIEA 33 (77)
T ss_dssp TEEEESSHHHHHHHHHHHHTTTSEEEHHHHHHH
T ss_pred CcEEecCHHHHHHHHHHHhCCCCCCCHHHhCCh
Confidence 56688999999999999999999 588888874
No 344
>PF04679 DNA_ligase_A_C: ATP dependent DNA ligase C terminal region ; InterPro: IPR012309 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalysing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase, one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC), the latter being restricted to eubacteria. Eukaryotic, archaebacterial, viral and some eubacterial DNA ligases are ATP-dependent. The first step in the ligation reaction is the formation of a covalent enzyme-AMP complex. The co-factor ATP is cleaved to pyrophosphate and AMP, with the AMP being covalently joined to a highly conserved lysine residue in the active site of the ligase. The activated AMP residue is then transferred to the 5'phosphate of the nick, before the nick is sealed by phosphodiester-bond formation and AMP elimination [,]. Vertebrate cells encode three well-characterised DNA ligases (DNA ligases I, III and IV), all of which are related in structure and sequence. With the exception of the atypically small PBCV-1 viral enzyme, two regions of primary sequence are common to all members of the family. The catalytic region comprises six conserved sequence motifs (I, III, IIIa, IV, V-VI), motif I includes the lysine residue that is adenylated in the first step of the ligation reaction. The function of the second, less well-conserved region is unknown. When folded, each protein comprises of two distinct sub-domains: a large amino-terminal sub-domain ('domain 1') and a smaller carboxy-terminal sub-domain ('domain 2'). The ATP-binding site of the enzyme lies in the cleft between the two sub-domains. Domain 1 consists of two antiparallel beta sheets flanked by alpha helices, whereas domain 2 consists of a five-stranded beta barrel and a single alpha helix, which form the oligonucleotide-binding fold [, ]. This region is found in many but not all ATP-dependent DNA ligase enzymes (6.5.1.1 from EC). It is thought to constitute part of the catalytic core of ATP dependent DNA ligase []. ; GO: 0003910 DNA ligase (ATP) activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 3RR5_A 2CFM_A 1X9N_A 1VS0_B 3GDE_A 2HIX_A 2HIV_A 3L2P_A 4EQ5_A.
Probab=36.00 E-value=50 Score=25.18 Aligned_cols=30 Identities=27% Similarity=0.562 Sum_probs=23.3
Q ss_pred cceeeeCC-CCeEEE-------cHHHHHHHHHHHHhcC
Q 026130 178 LSGVMDDR-GKYIYI-------SQAEMKAVADYIKRQG 207 (243)
Q Consensus 178 LtGViDDR-GKFIYI-------S~eEl~aVA~fI~~rG 207 (243)
|-|+.|+. |+|+|| |.+++..+-..+....
T Consensus 9 llg~~d~~~~~l~~vg~vgtG~~~~~~~~l~~~l~~~~ 46 (97)
T PF04679_consen 9 LLGVYDPDSGRLVYVGKVGTGFSDEELRELRERLEPLW 46 (97)
T ss_dssp EEEEEETTTTEEEEEEEE-SS--HHHHHHHHHHHGGGE
T ss_pred EEEEEcCCCCcEEEEEEECCCCCHHHHHHHHHHhhCcc
Confidence 67999997 999997 6778877777776544
No 345
>PRK09836 DNA-binding transcriptional activator CusR; Provisional
Probab=35.89 E-value=47 Score=27.22 Aligned_cols=59 Identities=24% Similarity=0.414 Sum_probs=44.0
Q ss_pred CChHHHHHHHHHHHhcCC--c-------cee-ee-------CCCCeEEEcHHHHHHHHHHHHhcCCc-cHHHHHhhc
Q 026130 160 LRTQECINRITSLENMGR--L-------SGV-MD-------DRGKYIYISQAEMKAVADYIKRQGRV-SISHLASKS 218 (243)
Q Consensus 160 lrtqd~I~RIq~Le~~g~--L-------tGV-iD-------DRGKFIYIS~eEl~aVA~fI~~rGRV-Si~eLa~~s 218 (243)
+...++..+|..+...+. . .++ +| .+|+-|.+|+.|+.-+.-|+...|+| |..+|....
T Consensus 103 ~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Lt~~E~~ll~~l~~~~g~~~sr~~l~~~~ 179 (227)
T PRK09836 103 FAFAELLARVRTLLRRGAAVIIESQFQVADLMVDLVSRKVTRSGTRITLTSKEFTLLEFFLRHQGEVLPRSLIASQV 179 (227)
T ss_pred CCHHHHHHHHHHHHhcccccCCCCcEEEcCEEEEcccCEEEECCEEEecCHHHHHHHHHHHhCCCeeEcHHHHHHHH
Confidence 356788888888775432 1 111 12 35889999999999999999999995 788888875
No 346
>KOG0687 consensus 26S proteasome regulatory complex, subunit RPN7/PSMD6 [Posttranslational modification, protein turnover, chaperones]
Probab=35.70 E-value=39 Score=33.20 Aligned_cols=67 Identities=18% Similarity=0.250 Sum_probs=48.5
Q ss_pred HHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEE-cHHHHHHHHHHHHhcCCc
Q 026130 143 IKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYI-SQAEMKAVADYIKRQGRV 209 (243)
Q Consensus 143 IK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYI-S~eEl~aVA~fI~~rGRV 209 (243)
+..-|.+.|+-.|..||+++.=+=+-+-.+.+.|+|.-+||-=+--|.. +|++-++.-+-.-..|-+
T Consensus 312 LESYrsl~l~~MA~aFgVSVefiDreL~rFI~~grL~ckIDrVnGVVEtNrpD~KN~qyq~vikqGd~ 379 (393)
T KOG0687|consen 312 LESYRSLTLESMAKAFGVSVEFIDRELGRFIAAGRLHCKIDRVNGVVETNRPDEKNAQYQAVIKQGDL 379 (393)
T ss_pred HHHHHHHHHHHHHHHhCchHHHHHhHHHHhhccCceeeeeecccceeecCCccccchHHHHHHhhhHH
Confidence 4567889999999999998876666799999999999999975445544 355555444443344543
No 347
>CHL00088 apcB allophycocyanin beta subunit
Probab=35.69 E-value=17 Score=31.34 Aligned_cols=39 Identities=23% Similarity=0.472 Sum_probs=30.6
Q ss_pred eCCCCeEEEcHHHHHHHHHHHHhc-CCccHH-HHHhhcccccc
Q 026130 183 DDRGKYIYISQAEMKAVADYIKRQ-GRVSIS-HLASKSNQFID 223 (243)
Q Consensus 183 DDRGKFIYIS~eEl~aVA~fI~~r-GRVSi~-eLa~~sN~lI~ 223 (243)
|++|+| +|..||+.|..|+++- =|+++. -|..+++.||+
T Consensus 13 D~~gRy--ls~~eL~~l~~~~~~~~~Rl~aa~~L~~na~~Iv~ 53 (161)
T CHL00088 13 DVQGKY--LDDNSVEKLRSYFQTGELRVRAAATIAANAATIIK 53 (161)
T ss_pred HhcCCC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHH
Confidence 678886 7999999999999875 577764 47777776664
No 348
>PRK07718 fliL flagellar basal body-associated protein FliL; Reviewed
Probab=35.61 E-value=23 Score=29.41 Aligned_cols=48 Identities=13% Similarity=0.156 Sum_probs=39.2
Q ss_pred hHHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceee
Q 026130 134 DLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVM 182 (243)
Q Consensus 134 ~lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGVi 182 (243)
..-+.++.|+...+.-.|......-.| -+++.++|+.+...|.+.+|.
T Consensus 88 ~Ird~ii~~L~~~~~~~l~~~~G~~~L-r~el~~~in~~l~~g~V~~Vy 135 (142)
T PRK07718 88 QVKNIIIEELADMNAEDFKGKKGLEAL-KEQLKEKINNLMQEGKVEKVY 135 (142)
T ss_pred hhHHHHHHHHHcCCHHHhcChhHHHHH-HHHHHHHHHHhhccCceEEEE
Confidence 456789999999998877777777777 578999999999999888763
No 349
>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=35.50 E-value=51 Score=24.34 Aligned_cols=45 Identities=20% Similarity=0.291 Sum_probs=35.9
Q ss_pred HHHHHHHhcC--ccchHHHHHHcCCChHHHHHHHHHHHhcCCcceee
Q 026130 138 DFVEYIKKHK--CIPLEDLAAEFKLRTQECINRITSLENMGRLSGVM 182 (243)
Q Consensus 138 ~Fi~yIK~~K--vV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGVi 182 (243)
.++.+|-.++ =+.--||+..||+..-.+-.+++.|+..|-|+..-
T Consensus 6 ~~Le~I~rsR~~Gi~q~~L~~~~~~D~r~i~~~~k~L~~~gLI~k~~ 52 (75)
T PF04182_consen 6 CLLERIARSRYNGITQSDLSKLLGIDPRSIFYRLKKLEKKGLIVKQS 52 (75)
T ss_pred HHHHHHHhcCCCCEehhHHHHHhCCCchHHHHHHHHHHHCCCEEEEE
Confidence 4555565443 25667999999999999999999999999998754
No 350
>COG5187 RPN7 26S proteasome regulatory complex component, contains PCI domain [Posttranslational modification, protein turnover, chaperones]
Probab=35.23 E-value=46 Score=32.54 Aligned_cols=68 Identities=19% Similarity=0.230 Sum_probs=49.1
Q ss_pred HhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeC-CCCeEEEcHHHHHHHHHHHHhcCCccH
Q 026130 144 KKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDD-RGKYIYISQAEMKAVADYIKRQGRVSI 211 (243)
Q Consensus 144 K~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDD-RGKFIYIS~eEl~aVA~fI~~rGRVSi 211 (243)
.+-+...|+-.|+.||+++.=+=+-+-+..-+|+|.-|||- .|=---=+|+|-++=-+-+-..|-+=+
T Consensus 327 ESYr~lsl~sMA~tFgVSV~yvdrDLg~FIp~~~LncvIDRvnGvVetnrpdekn~qy~~vVkqGd~ll 395 (412)
T COG5187 327 ESYRLLSLESMAQTFGVSVEYVDRDLGEFIPEGRLNCVIDRVNGVVETNRPDEKNQQYSSVVKQGDDLL 395 (412)
T ss_pred HHHHHhhHHHHHHHhCccHHHHhhhHHhhCCCCceeeeeecccceEeccCcchhhhhHHHHHhcchHHH
Confidence 45567889999999999998888889999999999999997 454434456664443333334454433
No 351
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=34.91 E-value=2e+02 Score=22.69 Aligned_cols=65 Identities=12% Similarity=0.122 Sum_probs=48.4
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHH--HHHhcCCccHHHHHhhccc
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVAD--YIKRQGRVSISHLASKSNQ 220 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~--fI~~rGRVSi~eLa~~sN~ 220 (243)
.+.++|..+|+++.- |.--+..|-|+.+-++. .|=|-|+..+..+.. +++. -=+|++++....+.
T Consensus 2 ~ige~a~~~gvs~~t----LryYe~~GLi~p~~~~~-~yR~Y~~~d~~~l~~I~~lr~-~G~sl~eI~~~l~~ 68 (116)
T cd04769 2 YIGELAQQTGVTIKA----IRLYEEKGLLPSPKRSG-NYRVYDAQHVECLRFIKEARQ-LGFTLAELKAIFAG 68 (116)
T ss_pred CHHHHHHHHCcCHHH----HHHHHHCCCCCCCCCCC-CceeeCHHHHHHHHHHHHHHH-cCCCHHHHHHHHhc
Confidence 467899999997654 56678889999987665 678889999888643 4444 44888888776554
No 352
>TIGR01339 phycocy_beta phycocyanin, beta subunit. This model excludes the closely related phycoerythrocyanin beta subunit.
Probab=34.82 E-value=18 Score=31.73 Aligned_cols=40 Identities=18% Similarity=0.444 Sum_probs=32.2
Q ss_pred eCCCCeEEEcHHHHHHHHHHHHh-cCCccHH-HHHhhccccccc
Q 026130 183 DDRGKYIYISQAEMKAVADYIKR-QGRVSIS-HLASKSNQFIDL 224 (243)
Q Consensus 183 DDRGKFIYIS~eEl~aVA~fI~~-rGRVSi~-eLa~~sN~lI~L 224 (243)
|..|+| +|..||++|..|++. .-|+.+. -|..+++.||+=
T Consensus 11 D~~gRy--l~~~eL~~l~~~~~~~~~Rl~aa~~L~~na~~IV~~ 52 (170)
T TIGR01339 11 DARGEF--ISSSQIDALSKLVADGNKRSDAVSRITNNASTIVTN 52 (170)
T ss_pred HhccCC--CCHHHHHHHHHHHHhhHHHHHHHHHHHHhHHHHHHH
Confidence 668886 799999999999998 5678875 577777777653
No 353
>PF08448 PAS_4: PAS fold; InterPro: IPR013656 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []. The PAS fold appears in archaea, eubacteria and eukarya. ; PDB: 3K3D_A 3K3C_B 3KX0_X 3FC7_B 3LUQ_D 3MXQ_A 3BWL_C 3FG8_A.
Probab=34.76 E-value=44 Score=23.59 Aligned_cols=24 Identities=29% Similarity=0.379 Sum_probs=18.6
Q ss_pred HHhcCCcceeeeCCCCeEEEcHHH
Q 026130 172 LENMGRLSGVMDDRGKYIYISQAE 195 (243)
Q Consensus 172 Le~~g~LtGViDDRGKFIYIS~eE 195 (243)
|........|+|..|+|+|+.+.=
T Consensus 1 l~~~p~~i~v~D~~~~i~~~N~~~ 24 (110)
T PF08448_consen 1 LDSSPDGIFVIDPDGRIVYANQAA 24 (110)
T ss_dssp HHHCSSEEEEEETTSBEEEE-HHH
T ss_pred CCCCCceeEEECCCCEEEEEHHHH
Confidence 445666788999999999999873
No 354
>COG3753 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.69 E-value=41 Score=28.96 Aligned_cols=24 Identities=25% Similarity=0.320 Sum_probs=21.0
Q ss_pred chHHHHHHcCCChHHHHHHHHHHH
Q 026130 150 PLEDLAAEFKLRTQECINRITSLE 173 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le 173 (243)
.|.+||.++||.+++++++|-+.+
T Consensus 92 ~l~~la~~~Gld~~El~~~Ls~~L 115 (143)
T COG3753 92 TLSQLAQKTGLDEQELLKQLSEQL 115 (143)
T ss_pred HHHHHHHHhCCCHHHHHHHHHHHh
Confidence 578899999999999999987653
No 355
>PF02186 TFIIE_beta: TFIIE beta subunit core domain; InterPro: IPR003166 Initiation of eukaryotic mRNA transcription requires melting of promoter DNA with the help of the general transcription factors TFIIE and TFIIH. In higher eukaryotes, the general transcription factor TFIIE consists of two subunits: the large alpha subunit (IPR002853 from INTERPRO) and the small beta (IPR003166 from INTERPRO). TFIIE beta has been found to bind to the region where the promoter starts to open to be single-stranded upon transcription initiation by RNA polymerase II. The approximately 120-residue central core domain of TFIIE beta plays a role in double-stranded DNA binding of TFIIE []. The TFIIE beta central core DNA-binding domain consists of three helices with a beta hairpin at the C terminus, resembling the winged helix proteins. It shows a novel double-stranded DNA-binding activity where the DNA-binding surface locates on the opposite side to the previously reported winged helix motif by forming a positively charged furrow []. This entry represents the beta subunit of the transcription factor TFIIE.; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005673 transcription factor TFIIE complex; PDB: 1D8K_A 1D8J_A.
Probab=34.51 E-value=39 Score=25.02 Aligned_cols=31 Identities=13% Similarity=0.434 Sum_probs=23.4
Q ss_pred HHHHHHHHHHhc-CCccHHHHHhhcccccccccc
Q 026130 195 EMKAVADYIKRQ-GRVSISHLASKSNQFIDLETK 227 (243)
Q Consensus 195 El~aVA~fI~~r-GRVSi~eLa~~sN~lI~L~p~ 227 (243)
-|..+..||+++ +-||+.||...+| +++++.
T Consensus 6 ql~~~VeymK~r~~Plt~~eI~d~l~--~d~~~~ 37 (65)
T PF02186_consen 6 QLAKAVEYMKKRDHPLTLEEILDYLS--LDIGKK 37 (65)
T ss_dssp HHHHHHHHHHHH-S-B-HHHHHHHHT--SSS-HH
T ss_pred HHHHHHHHHHhcCCCcCHHHHHHHHc--CCCCHH
Confidence 467889999999 5689999999999 776654
No 356
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=34.36 E-value=1.6e+02 Score=27.30 Aligned_cols=57 Identities=14% Similarity=0.205 Sum_probs=45.8
Q ss_pred HHHHHHHHHHhcCc-cchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEE
Q 026130 135 LLADFVEYIKKHKC-IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYI 191 (243)
Q Consensus 135 lL~~Fi~yIK~~Kv-V~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYI 191 (243)
..++.|+||+.|-= |.-.||....|++-.-+-.+|++|++.|-|==.=-.|+.+|-+
T Consensus 196 ~e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LEk~GlIe~~K~G~~n~V~l 253 (258)
T COG2512 196 DEKEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLEKRGLIEKEKKGRTNIVEL 253 (258)
T ss_pred HHHHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHHHHHhCCceEEEEeCCeeEEEE
Confidence 46899999998874 8999999999999999999999999998765444444544443
No 357
>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=33.86 E-value=1.7e+02 Score=22.72 Aligned_cols=55 Identities=15% Similarity=0.274 Sum_probs=38.8
Q ss_pred HHHHHHHhc-CccchHHHHHHc-----CCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEc
Q 026130 138 DFVEYIKKH-KCIPLEDLAAEF-----KLRTQECINRITSLENMGRLSGVMDDRGKYIYIS 192 (243)
Q Consensus 138 ~Fi~yIK~~-KvV~LEdLA~~F-----~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS 192 (243)
..+++|..+ .-+..++|-..+ +++..-|-+-|..|.+.|.|.-|..+.|...|-.
T Consensus 12 ~Il~~l~~~~~~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~~~~~~~~~~Y~~ 72 (120)
T PF01475_consen 12 AILELLKESPEHLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRKIEFGDGESRYEL 72 (120)
T ss_dssp HHHHHHHHHSSSEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEETTSEEEEEE
T ss_pred HHHHHHHcCCCCCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEEEEcCCCcceEee
Confidence 455666554 466667765544 6777778888999999999999998877666643
No 358
>TIGR00683 nanA N-acetylneuraminate lyase. N-acetylneuraminate lyase is also known as N-acetylneuraminic acid aldolase, sialic acid aldolase, or sialate lyase. It is an intracellular enzyme. The structure of this homotetrameric enzyme related to dihydrodipicolinate synthase is known. In Clostridium tertium, the enzyme appears to be in an operon with a secreted sialidase that releases sialic acid from host sialoglycoconjugates. In several E. coli strains, however, this enzyme is responsible for N-acetyl-D-neuraminic acid synthesis for capsule production by condensing N-acetyl-D-mannosamine and pyruvate.
Probab=33.82 E-value=1e+02 Score=28.23 Aligned_cols=53 Identities=13% Similarity=0.164 Sum_probs=43.0
Q ss_pred cCCChHHHHHHHHHHHhcCCcceeee--CCCCeEEEcHHHHHHHHHHHHhc--CCcc
Q 026130 158 FKLRTQECINRITSLENMGRLSGVMD--DRGKYIYISQAEMKAVADYIKRQ--GRVS 210 (243)
Q Consensus 158 F~lrtqd~I~RIq~Le~~g~LtGViD--DRGKFIYIS~eEl~aVA~fI~~r--GRVS 210 (243)
..+.......-|+.|...|.++||+= .-|-|.++|.+|...|....... |||.
T Consensus 16 g~iD~~~~~~~i~~~i~~G~v~gi~~~GstGE~~~Lt~eEr~~~~~~~~~~~~~~~p 72 (290)
T TIGR00683 16 GTINEKGLRQIIRHNIDKMKVDGLYVGGSTGENFMLSTEEKKEIFRIAKDEAKDQIA 72 (290)
T ss_pred CCcCHHHHHHHHHHHHhCCCcCEEEECCcccccccCCHHHHHHHHHHHHHHhCCCCc
Confidence 46777778888999999998999765 47999999999999998877654 6654
No 359
>PRK10130 transcriptional regulator EutR; Provisional
Probab=33.42 E-value=1.3e+02 Score=28.51 Aligned_cols=78 Identities=15% Similarity=0.260 Sum_probs=56.4
Q ss_pred chhHHHHHHHHHHhc--CccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHh--cC
Q 026130 132 DRDLLADFVEYIKKH--KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKR--QG 207 (243)
Q Consensus 132 ~~~lL~~Fi~yIK~~--KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~--rG 207 (243)
...++..+++||..+ .-+.+.|||.++|++.--+....++....... =||..-=|+.+...+.. .+
T Consensus 238 ~~~~v~~~~~~i~~~~~~~ltv~~lA~~~gvS~r~L~r~Fk~~~G~sp~----------~ylr~~RL~~ar~lL~~~~~~ 307 (350)
T PRK10130 238 YRRLLSRAREYVLENMSEPVTVLDLCNQLHVSRRTLQNAFHAILGIGPN----------AWLKRIRLNAVRRELISPWSQ 307 (350)
T ss_pred hHHHHHHHHHHHHhhhcCCCCHHHHHHHHCCCHHHHHHHHHHHHCcCHH----------HHHHHHHHHHHHHHHhccCCC
Confidence 356788889999765 44899999999999998887777765433322 25555566777777766 35
Q ss_pred CccHHHHHhhcc
Q 026130 208 RVSISHLASKSN 219 (243)
Q Consensus 208 RVSi~eLa~~sN 219 (243)
..||+++|..|.
T Consensus 308 ~~sI~eIA~~~G 319 (350)
T PRK10130 308 STTVKDAAMQWG 319 (350)
T ss_pred CCCHHHHHHHhC
Confidence 678888887664
No 360
>KOG1767 consensus 40S ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=33.36 E-value=53 Score=27.20 Aligned_cols=59 Identities=19% Similarity=0.243 Sum_probs=49.9
Q ss_pred hhHHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEE
Q 026130 133 RDLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYI 191 (243)
Q Consensus 133 ~~lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYI 191 (243)
+.++..+..-+-.-|+|...=|+..++|+-.-+-.-|++|...|.|--|.--++.-||-
T Consensus 45 qatydkl~kevp~~k~it~svl~dRlkIngsLAr~alr~L~~kG~Ik~Vs~h~~q~IYT 103 (110)
T KOG1767|consen 45 QATYDKLLKEVPKYKLITPSVLSDRLKINGSLARAALRELSNKGVIKQVSKHSKQVIYT 103 (110)
T ss_pred HHHHHHHHHhcccceeecHHHhhhhhhhchHHHHHHHHHHHhcchHHHHhhcchheeec
Confidence 34445555555667889999999999999999999999999999999999999999984
No 361
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=33.02 E-value=52 Score=27.86 Aligned_cols=21 Identities=24% Similarity=0.665 Sum_probs=17.8
Q ss_pred HHHHHHHHhcCCccHHHHHhh
Q 026130 197 KAVADYIKRQGRVSISHLASK 217 (243)
Q Consensus 197 ~aVA~fI~~rGRVSi~eLa~~ 217 (243)
..|-.|++++||+++.+|+..
T Consensus 15 ~rIvElVRe~GRiTi~ql~~~ 35 (127)
T PF06163_consen 15 ARIVELVREHGRITIKQLVAK 35 (127)
T ss_pred HHHHHHHHHcCCccHHHHHHH
Confidence 457789999999999998764
No 362
>PF09628 YvfG: YvfG protein; InterPro: IPR018590 Yvfg is a hypothetical protein of 71 residues expressed in some bacteria. The monomer consists of two parallel alpha helices, and the protein crystallises as a homo-dimer. ; PDB: 2GSV_A 2JS1_B.
Probab=32.95 E-value=1.2e+02 Score=23.09 Aligned_cols=41 Identities=15% Similarity=0.276 Sum_probs=26.5
Q ss_pred hHHHHHHHHHHhcCc-------------cchHHHHHHcCCChHHHHHHHHHHHh
Q 026130 134 DLLADFVEYIKKHKC-------------IPLEDLAAEFKLRTQECINRITSLEN 174 (243)
Q Consensus 134 ~lL~~Fi~yIK~~Kv-------------V~LEdLA~~F~lrtqd~I~RIq~Le~ 174 (243)
-|+..|-.||..+-- ++..-|-..-=.+..++|.||+.|.+
T Consensus 7 ~~~~N~~q~i~~N~~~~~ki~AmNaYYr~Vv~tlvqDqltKNa~vl~RiqHLdE 60 (68)
T PF09628_consen 7 YFMENFKQHIQMNQNYEDKIHAMNAYYRSVVSTLVQDQLTKNAVVLKRIQHLDE 60 (68)
T ss_dssp HHHHHHHHHHHC-SS-S-CCHHHHHHHHHHHHHHHHHSSS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhCccHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence 466777777765432 33344555555678999999999975
No 363
>PRK11517 transcriptional regulatory protein YedW; Provisional
Probab=32.94 E-value=1.8e+02 Score=23.51 Aligned_cols=59 Identities=15% Similarity=0.195 Sum_probs=42.7
Q ss_pred CChHHHHHHHHHHHhcCC-----cc-e---------eeeCCCCeEEEcHHHHHHHHHHHHhcCCc-cHHHHHhhc
Q 026130 160 LRTQECINRITSLENMGR-----LS-G---------VMDDRGKYIYISQAEMKAVADYIKRQGRV-SISHLASKS 218 (243)
Q Consensus 160 lrtqd~I~RIq~Le~~g~-----Lt-G---------ViDDRGKFIYIS~eEl~aVA~fI~~rGRV-Si~eLa~~s 218 (243)
+...++..+|..+..... +. | .+...|+.|-+|+.|+.-+.-++...|+| |-.+|....
T Consensus 102 ~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Lt~~E~~il~~l~~~~g~~~s~~~i~~~~ 176 (223)
T PRK11517 102 FSFSELLARVRAQLRQHHALNSTLEISGLRMDSVSQSVSRDNISITLTRKEFQLLWLLASRAGEIIPRTVIASEI 176 (223)
T ss_pred CCHHHHHHHHHHHHccccCcCCeEEECCEEEEcCCCEEEECCEEEeCCHHHHHHHHHHHhCCCccCCHHHHHHHh
Confidence 456788888888765332 11 1 12235899999999999999999999985 667777763
No 364
>cd04449 DEP_DEPDC5-like DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in DEPDC5-like proteins. DEPDC5, in human also known as KIAA0645, is a DEP domain containing protein of unknown function.
Probab=32.71 E-value=88 Score=23.69 Aligned_cols=31 Identities=26% Similarity=0.325 Sum_probs=26.0
Q ss_pred CChHHHHHHHHHHHhcCCcceeeeC----CCCeEE
Q 026130 160 LRTQECINRITSLENMGRLSGVMDD----RGKYIY 190 (243)
Q Consensus 160 lrtqd~I~RIq~Le~~g~LtGViDD----RGKFIY 190 (243)
.+-.++|.-.|.|+..|-|.-|.++ .|.|.|
T Consensus 47 ~~r~eAv~lgq~Ll~~g~I~hv~~~~~F~d~~~~Y 81 (83)
T cd04449 47 DTREEAVELGQELMNEGLIEHVSGRHPFLDGFYFY 81 (83)
T ss_pred CCHHHHHHHHHHHHHCCCEEecCCCCCccCCCEeE
Confidence 4567999999999999999999986 466666
No 365
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=32.65 E-value=1.4e+02 Score=26.11 Aligned_cols=61 Identities=11% Similarity=0.268 Sum_probs=40.4
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHh-c-CCccHHHHHh
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKR-Q-GRVSISHLAS 216 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~-r-GRVSi~eLa~ 216 (243)
.+.++|..+|+++.-+.... ..|.|...-|..|.++| |++++. .-.||+. + -=+||.++..
T Consensus 2 ti~evA~~lGVS~~TLRrw~----k~g~L~~~R~~~G~R~y-~~~dl~-~L~~I~~l~~~Gm~i~~i~~ 64 (175)
T PRK13182 2 KTPFVAKKLGVSPKTVQRWV----KQLNLPCEKNEYGHYIF-TEEDLQ-LLEYVKSQIEEGQNMQDTQK 64 (175)
T ss_pred CHHHHHHHHCcCHHHHHHHH----HcCCCCCCcCCCCCEEE-CHHHHH-HHHHHHHHHHcCCCHHHHHH
Confidence 46789999999876554444 46778755556776664 888885 4455542 2 3477777755
No 366
>PF01253 SUI1: Translation initiation factor SUI1; InterPro: IPR001950 In Saccharomyces cerevisiae (Baker's yeast), SUI1 is a translation initiation factor that functions in concert with eIF-2 and the initiator tRNA-Met in directing the ribosome to the proper start site of translation []. SUI1 is a protein of 108 residues. Close homologs of SUI1 have been found [] in mammals, insects and plants. SUI1 is also evolutionary related to hypothetical proteins from Escherichia coli (yciH), Haemophilus influenzae (HI1225) and Methanococcus vannielii.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2OGH_A 1D1R_A 2IF1_A 2XZN_F 2XZM_F.
Probab=32.30 E-value=44 Score=25.18 Aligned_cols=64 Identities=14% Similarity=0.169 Sum_probs=46.3
Q ss_pred cCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhcCCcc
Q 026130 146 HKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRVS 210 (243)
Q Consensus 146 ~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~rGRVS 210 (243)
+.|..+.-|. .|++...++..-++...+-|.-..-....|.-|-|-=+....|++|+..+|-+.
T Consensus 18 K~vT~V~gl~-~~~~d~~~lak~lkk~~ac~~sv~~~~~k~~~I~iQGd~~~~i~~~L~~~~~~~ 81 (83)
T PF01253_consen 18 KFVTIVSGLE-LFGIDLKELAKELKKKFACGGSVTKDPGKGEEIQIQGDHRDEIKDLLVEKGGIP 81 (83)
T ss_dssp EEEEEEES---STTSHHHHHHHHHHHHHTS-EEEEE-TTTSSEEEEESS-HHHHHHHHHHHCSSE
T ss_pred eEEEEEECCc-ccccCHHHHHHHHHHhccCceEEeecCCCCCEEEECCcHHHHHHHHHHHhCCCC
Confidence 3344555555 699999999999999999884433333357889999999999999999998664
No 367
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=32.03 E-value=73 Score=24.52 Aligned_cols=37 Identities=11% Similarity=0.197 Sum_probs=28.5
Q ss_pred CCCCeEE-EcHHHHH-HHHHHHHhcCCccHHHHHhhccc
Q 026130 184 DRGKYIY-ISQAEMK-AVADYIKRQGRVSISHLASKSNQ 220 (243)
Q Consensus 184 DRGKFIY-IS~eEl~-aVA~fI~~rGRVSi~eLa~~sN~ 220 (243)
+.|.|++ +|-+||- .++.||.+.|.++-.++...-..
T Consensus 34 ~~G~Ft~~~t~eemie~~~~~~~~~~~~~~~~a~~~~~~ 72 (81)
T PF12674_consen 34 QNGEFTQDITMEEMIEFCVPFMDEFNGMTPEEARKMMPR 72 (81)
T ss_pred cCCceeecCCHHHHHHHHHHHHHHhCCCCHHHHHHHHHH
Confidence 4799999 9999875 56789999998777666655433
No 368
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=31.69 E-value=49 Score=29.53 Aligned_cols=58 Identities=14% Similarity=0.205 Sum_probs=43.6
Q ss_pred chhHHHHHHHHHHhcCcc------chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeC-CCCeEEEcH
Q 026130 132 DRDLLADFVEYIKKHKCI------PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDD-RGKYIYISQ 193 (243)
Q Consensus 132 ~~~lL~~Fi~yIK~~KvV------~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDD-RGKFIYIS~ 193 (243)
.+..+..+..+|-...+- .=-+||..||++-..+-.-|+.|+..|.| +- .|.=+||.+
T Consensus 12 ~~~v~~~i~~~I~~g~~~~G~~LP~EreLae~fgVSR~~vREAl~~L~a~Glv----e~r~G~Gt~V~~ 76 (241)
T COG2186 12 ADEVAEQIGALIVSGELPPGDRLPSERELAERFGVSRTVVREALKRLEAKGLV----EIRQGSGTFVRP 76 (241)
T ss_pred HHHHHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCcHHHHHHHHHHHHCCCe----eecCCCceEecC
Confidence 345567777788766554 35579999999999999999999998765 43 466666654
No 369
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=31.68 E-value=1.3e+02 Score=25.40 Aligned_cols=65 Identities=9% Similarity=0.227 Sum_probs=55.9
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeC--CCCeEEEcHHHHHHHHHHHHhcCCccHHHHHhh
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDD--RGKYIYISQAEMKAVADYIKRQGRVSISHLASK 217 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDD--RGKFIYIS~eEl~aVA~fI~~rGRVSi~eLa~~ 217 (243)
...++|..||++..-+++=|+.....|.+ ...- .|+==.+|.++++-+..++..+- .++.+++..
T Consensus 23 S~re~Ak~~gvs~sTvy~wv~r~~e~G~~--l~~~~~~GrP~kl~~~q~~~l~e~~~~k~-wTl~~~~~~ 89 (138)
T COG3415 23 SCREAAKRFGVSISTVYRWVRRYRETGLD--LPPKPRKGRPRKLSEEQLEILLERLREKD-WTLKELVEE 89 (138)
T ss_pred cHHHHHHHhCccHHHHHHHHHHhcccccc--ccCccCCCCCcccCHHHHHHHHHHHhccc-chHHHHHHH
Confidence 45789999999999999999999999998 4554 78888999999999999999888 877776543
No 370
>KOG2072 consensus Translation initiation factor 3, subunit a (eIF-3a) [Translation, ribosomal structure and biogenesis]
Probab=31.64 E-value=5.1e+02 Score=28.63 Aligned_cols=6 Identities=33% Similarity=0.390 Sum_probs=2.3
Q ss_pred HHHHHh
Q 026130 61 ARESRQ 66 (243)
Q Consensus 61 ~REerk 66 (243)
..++||
T Consensus 795 R~eerk 800 (988)
T KOG2072|consen 795 RIEERK 800 (988)
T ss_pred HHHHHH
Confidence 333333
No 371
>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=31.33 E-value=80 Score=27.11 Aligned_cols=45 Identities=16% Similarity=0.282 Sum_probs=35.7
Q ss_pred ccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHH
Q 026130 148 CIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAE 195 (243)
Q Consensus 148 vV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eE 195 (243)
++...+||..+|++.+-+..-|+.|+..|-|.=+ ..|-| +|.|.-
T Consensus 75 ~~t~~~ia~~l~iS~~Tv~r~ik~L~e~~iI~k~--~~G~Y-~iNP~~ 119 (165)
T PF05732_consen 75 VATQKEIAEKLGISKPTVSRAIKELEEKNIIKKI--RNGAY-MINPNF 119 (165)
T ss_pred EeeHHHHHHHhCCCHHHHHHHHHHHHhCCcEEEc--cCCeE-EECcHH
Confidence 3456779999999999999999999999988654 34644 577763
No 372
>cd04801 CBS_pair_M50_like This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the metalloprotease peptidase M50. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.
Probab=31.03 E-value=1.5e+02 Score=21.56 Aligned_cols=64 Identities=17% Similarity=0.342 Sum_probs=33.7
Q ss_pred cCCChHHHHHHHHHHHhcC--CcceeeeCCCCeE-EEcHHHHHHHHHHHHhcCCccHHHHHhhccccccccc
Q 026130 158 FKLRTQECINRITSLENMG--RLSGVMDDRGKYI-YISQAEMKAVADYIKRQGRVSISHLASKSNQFIDLET 226 (243)
Q Consensus 158 F~lrtqd~I~RIq~Le~~g--~LtGViDDRGKFI-YIS~eEl~aVA~fI~~rGRVSi~eLa~~sN~lI~L~p 226 (243)
.+.+..++++.+. ..+ ...-|+|+.|+|+ +||...+-... .......+++++......++.+.|
T Consensus 8 ~~~~l~~~~~~~~---~~~~~~~~~V~d~~~~~~G~v~~~dl~~~~--~~~~~~~~v~~~~~~~~~~~~v~~ 74 (114)
T cd04801 8 AHLTLREFVREYV---LGSNQRRFVVVDNEGRYVGIISLADLRAIP--TSQWAQTTVIQVMTPAAKLVTVLS 74 (114)
T ss_pred CCCCHHHHHHHHh---ccCCceeEEEEcCCCcEEEEEEHHHHHHHH--HhhccccchhhhhcccccceEECC
Confidence 3455556665442 222 2345679899998 67888765432 122234456666554333333333
No 373
>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI [, , , , ]. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....
Probab=30.74 E-value=1.5e+02 Score=20.49 Aligned_cols=44 Identities=16% Similarity=0.301 Sum_probs=31.6
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHH
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQA 194 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~e 194 (243)
.+...|..+|++..-+-..|+.|+..=-.. +++-.|+-+.+|+.
T Consensus 15 s~~~AA~~l~is~~~vs~~i~~LE~~lg~~-Lf~r~~~~~~lT~~ 58 (60)
T PF00126_consen 15 SISAAAEELGISQSAVSRQIKQLEEELGVP-LFERSGRGLRLTEA 58 (60)
T ss_dssp SHHHHHHHCTSSHHHHHHHHHHHHHHHTS--SEEECSSSEEE-HH
T ss_pred CHHHHHHHhhccchHHHHHHHHHHHHhCCe-EEEECCCCeeEChh
Confidence 778899999999999999999999753322 44444444666653
No 374
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=30.68 E-value=1.5e+02 Score=23.86 Aligned_cols=65 Identities=14% Similarity=0.169 Sum_probs=47.6
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHH--HHHhcCCccHHHHHhhcc
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVAD--YIKRQGRVSISHLASKSN 219 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~--fI~~rGRVSi~eLa~~sN 219 (243)
.+.++|..+|+++. .|.--+..|.|.....+.|.|=|-|++.+..|.. +.+.-| +|+.++....+
T Consensus 2 ~I~e~a~~~gvs~~----tlR~Ye~~GLl~~~~r~~~gyR~Y~~~~l~~l~~I~~lr~lG-~sL~eI~~~l~ 68 (127)
T TIGR02047 2 KIGELAQKTGVSVE----TIRFYEKQGLLPPPARTDNNYRVYTVGHVERLAFIRNCRTLD-MSLAEIRQLLR 68 (127)
T ss_pred cHHHHHHHHCcCHH----HHHHHHHCCCCCCCCcCCCCCCcCCHHHHHHHHHHHHHHHcC-CCHHHHHHHHH
Confidence 46799999999875 3566678899987666667788889999887754 344434 78887776543
No 375
>PRK04296 thymidine kinase; Provisional
Probab=30.61 E-value=48 Score=28.19 Aligned_cols=66 Identities=23% Similarity=0.464 Sum_probs=40.4
Q ss_pred HHHHHHHHHh----cCccchHHHHHHcCCChHHHHHHHHHHHhcC---CcceeeeC-CCCeEEEcHHHHHHHHHHHHh
Q 026130 136 LADFVEYIKK----HKCIPLEDLAAEFKLRTQECINRITSLENMG---RLSGVMDD-RGKYIYISQAEMKAVADYIKR 205 (243)
Q Consensus 136 L~~Fi~yIK~----~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g---~LtGViDD-RGKFIYIS~eEl~aVA~fI~~ 205 (243)
..+++.+++. ..||+|+++ +| |...+++.-++.|...| -+||..-| +|++ |.+...|-.+|+.|..
T Consensus 65 ~~~~~~~~~~~~~~~dvviIDEa--q~-l~~~~v~~l~~~l~~~g~~vi~tgl~~~~~~~~-f~~~~~L~~~aD~V~~ 138 (190)
T PRK04296 65 DTDIFELIEEEGEKIDCVLIDEA--QF-LDKEQVVQLAEVLDDLGIPVICYGLDTDFRGEP-FEGSPYLLALADKVTE 138 (190)
T ss_pred hHHHHHHHHhhCCCCCEEEEEcc--cc-CCHHHHHHHHHHHHHcCCeEEEEecCcccccCc-CchHHHHHHhcCeEEE
Confidence 3455555543 247888887 44 55555777777777777 45565544 6764 5666677777766543
No 376
>cd04624 CBS_pair_11 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic gener
Probab=30.57 E-value=78 Score=22.86 Aligned_cols=38 Identities=11% Similarity=0.140 Sum_probs=25.3
Q ss_pred HcCCChHHHHHHHHHHHhcC-CcceeeeCCCCeE-EEcHHHHH
Q 026130 157 EFKLRTQECINRITSLENMG-RLSGVMDDRGKYI-YISQAEMK 197 (243)
Q Consensus 157 ~F~lrtqd~I~RIq~Le~~g-~LtGViDDRGKFI-YIS~eEl~ 197 (243)
..+.+..++++.+. ..+ ....|+|+.|+|+ +||...+-
T Consensus 7 ~~~~~~~~~~~~~~---~~~~~~~~v~d~~~~~~G~v~~~~l~ 46 (112)
T cd04624 7 DPDTSIREAAKLMA---EENVGSVVVVDPDERPIGIVTERDIV 46 (112)
T ss_pred CCCCcHHHHHHHHH---HcCCCEEEEECCCCCEEEEeeHHHHH
Confidence 34556677776652 233 3456788889998 78888873
No 377
>KOG1425 consensus Microfibrillar-associated protein MFAP1 [Cytoskeleton]
Probab=30.51 E-value=2.1e+02 Score=28.51 Aligned_cols=24 Identities=25% Similarity=0.430 Sum_probs=14.3
Q ss_pred HHHHHHHhcCCcceeeeCCCCeEE
Q 026130 167 NRITSLENMGRLSGVMDDRGKYIY 190 (243)
Q Consensus 167 ~RIq~Le~~g~LtGViDDRGKFIY 190 (243)
.|.+.|.+++.++----+.|||=|
T Consensus 304 ERr~~lrknpkv~tnk~~KgkykF 327 (430)
T KOG1425|consen 304 ERRAELRKNPKVSTNKAKKGKYKF 327 (430)
T ss_pred HHHHHHhhCcccccccccchhHHH
Confidence 366777777766544445566543
No 378
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=30.13 E-value=1e+02 Score=16.84 Aligned_cols=29 Identities=3% Similarity=0.084 Sum_probs=19.0
Q ss_pred HHHHHHHHhcCccchHHHHHHcCCChHHHHH
Q 026130 137 ADFVEYIKKHKCIPLEDLAAEFKLRTQECIN 167 (243)
Q Consensus 137 ~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~ 167 (243)
..++.++... ..+.++|..||++..-+.+
T Consensus 12 ~~i~~~~~~~--~s~~~ia~~~~is~~tv~~ 40 (42)
T cd00569 12 EEARRLLAAG--ESVAEIARRLGVSRSTLYR 40 (42)
T ss_pred HHHHHHHHcC--CCHHHHHHHHCCCHHHHHH
Confidence 3444444433 2788999999997766544
No 379
>PRK13696 hypothetical protein; Provisional
Probab=30.00 E-value=85 Score=23.52 Aligned_cols=27 Identities=26% Similarity=0.261 Sum_probs=23.5
Q ss_pred CeEEEcHHHHHHHHHHHHhcCCccHHHHHh
Q 026130 187 KYIYISQAEMKAVADYIKRQGRVSISHLAS 216 (243)
Q Consensus 187 KFIYIS~eEl~aVA~fI~~rGRVSi~eLa~ 216 (243)
|=|-||++.+..+. ..+|..|.||+..
T Consensus 4 K~ItI~dd~Y~~L~---~kk~~~SFSevi~ 30 (62)
T PRK13696 4 KTITISDDVYEKLL---EIKGDKSFSEVIR 30 (62)
T ss_pred ceEEeCHHHHHHHH---HHhCCCCHHHHHH
Confidence 67999999999999 6678899998875
No 380
>KOG2784 consensus Phenylalanyl-tRNA synthetase, beta subunit [Translation, ribosomal structure and biogenesis]
Probab=29.97 E-value=1.3e+02 Score=30.17 Aligned_cols=78 Identities=27% Similarity=0.380 Sum_probs=57.0
Q ss_pred HHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHH----------HHHHhcC
Q 026130 138 DFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVA----------DYIKRQG 207 (243)
Q Consensus 138 ~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA----------~fI~~rG 207 (243)
..+.++...-=+.--+||+.|+.-.|.++.-|++|.+-|.|+ | -+.-.++|+=-.|=..|| .+|-.-|
T Consensus 7 ~iL~~L~~~de~~s~~l~a~~~~~h~~~v~al~SL~a~~~i~-~-~~~~~~~~~LT~EG~~i~~eGS~E~~v~~~i~~~g 84 (483)
T KOG2784|consen 7 KILEKLQESDEVDSSDLAAPFNEDHQQVVGALKSLQAGGVIE-V-KDVETKTYELTAEGEEIAREGSHEALVFESIPEEG 84 (483)
T ss_pred HHHHHHHhccCCChhhhcCchhhhhHHHHHHHHHHhhcCceE-E-EeeeeEEEeeChhHHHHHhcCCcceeeeeccCccc
Confidence 445566655558888999999999999999999999954443 2 245566665544545544 4777888
Q ss_pred CccHHHHHhhc
Q 026130 208 RVSISHLASKS 218 (243)
Q Consensus 208 RVSi~eLa~~s 218 (243)
++|.+|....
T Consensus 85 -l~~~el~~k~ 94 (483)
T KOG2784|consen 85 -LAIAELMKKL 94 (483)
T ss_pred -cCHHHHHhhh
Confidence 9999998776
No 381
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements
Probab=29.35 E-value=2.7e+02 Score=22.31 Aligned_cols=64 Identities=14% Similarity=0.190 Sum_probs=46.6
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHH--HHHHhcCCccHHHHHhhc
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVA--DYIKRQGRVSISHLASKS 218 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA--~fI~~rGRVSi~eLa~~s 218 (243)
.+.++|..||+++. .|.--+..|.|.....+.|.|=|-|++++..|. .+.+.-| +|+.++...-
T Consensus 2 ~I~e~a~~~gvs~~----tlRyYe~~GLl~~~~r~~~g~R~Y~~~~~~~l~~I~~lr~~G-~sL~eI~~~l 67 (127)
T cd01108 2 NIGEAAKLTGLSAK----MIRYYEEIGLIPPPSRSDNGYRVYNQRDIEELRFIRRARDLG-FSLEEIRELL 67 (127)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHCCCCCCCCcCCCCceecCHHHHHHHHHHHHHHHcC-CCHHHHHHHH
Confidence 46789999999764 356678889998665555667788999988764 3445556 7988887643
No 382
>PF10557 Cullin_Nedd8: Cullin protein neddylation domain; InterPro: IPR019559 This is the neddylation site of cullin proteins, which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae (Baker's yeast), and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue []. ; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_B 1U6G_A 3O6B_J 3O2P_E 4A0K_A 2HYE_C ....
Probab=29.33 E-value=1.2e+02 Score=21.98 Aligned_cols=46 Identities=22% Similarity=0.272 Sum_probs=32.4
Q ss_pred HHHHHHHhcCccchHH--------HHHHcCCChHHHHHHHHHHHhcCCcceeee
Q 026130 138 DFVEYIKKHKCIPLED--------LAAEFKLRTQECINRITSLENMGRLSGVMD 183 (243)
Q Consensus 138 ~Fi~yIK~~KvV~LEd--------LA~~F~lrtqd~I~RIq~Le~~g~LtGViD 183 (243)
..|.-+|.+|.+...+ |...|.+++.++-.+|..|...|-|.=--|
T Consensus 12 aIVrimK~~k~~~~~~L~~~v~~~l~~~f~~~~~~ik~~Ie~LIekeyi~Rd~~ 65 (68)
T PF10557_consen 12 AIVRIMKQEKKLSHDELINEVIEELKKRFPPSVSDIKKRIESLIEKEYIERDED 65 (68)
T ss_dssp HHHHHHHHSSEEEHHHHHHHHHHHTTTTS---HHHHHHHHHHHHHTTSEEEESS
T ss_pred heehhhhhcCceeHHHHHHHHHHHhcCCcCCCHHHHHHHHHHHHHhhhhhcCCC
Confidence 3455678888777666 455899999999999999999987754333
No 383
>PF00532 Peripla_BP_1: Periplasmic binding proteins and sugar binding domain of LacI family; InterPro: IPR001761 This family includes the periplasmic binding proteins, and the LacI family transcriptional regulators. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The LacI family of proteins consist of transcriptional regulators related to the lac repressor. In this case, generally the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain (lacI) [, ].; PDB: 1BAP_A 7ABP_A 6ABP_A 1ABF_A 5ABP_A 2WRZ_B 9ABP_A 1APB_A 1ABE_A 8ABP_A ....
Probab=29.18 E-value=62 Score=28.89 Aligned_cols=86 Identities=14% Similarity=0.202 Sum_probs=58.5
Q ss_pred chhHHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcC-CcceeeeCCCCeEEEcHHHHHHH-HHHHHhcCCc
Q 026130 132 DRDLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMG-RLSGVMDDRGKYIYISQAEMKAV-ADYIKRQGRV 209 (243)
Q Consensus 132 ~~~lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g-~LtGViDDRGKFIYIS~eEl~aV-A~fI~~rGRV 209 (243)
....++=|.++++.+-+-+-+.+-.......++..+-+++|++.+ .|++ |+-+-+.|..- .++++.+||+
T Consensus 134 ~~~R~~Gy~~Al~~~Gl~~~~~~i~~~~~~~~~g~~~~~~ll~~~p~ida--------i~~~nd~~A~ga~~~l~~~gr~ 205 (279)
T PF00532_consen 134 SRERLQGYRDALKEAGLPIDEEWIFEGDFDYESGYEAARELLESHPDIDA--------IFCANDMMAIGAIRALRERGRL 205 (279)
T ss_dssp HHHHHHHHHHHHHHTTSCEEEEEEEESSSSHHHHHHHHHHHHHTSTT-SE--------EEESSHHHHHHHHHHHHHTT-T
T ss_pred HHHHHHHHHHHHHHcCCCCCcccccccCCCHHHHHHHHHHHHhhCCCCEE--------EEEeCHHHHHHHHHHHHHcCCc
Confidence 455678899999998773334433445567788888999999988 4444 45555555544 5999999998
Q ss_pred cHH-HHHhhcccccccc
Q 026130 210 SIS-HLASKSNQFIDLE 225 (243)
Q Consensus 210 Si~-eLa~~sN~lI~L~ 225 (243)
++. ++...++.++.++
T Consensus 206 ~ip~di~~~~~~v~g~d 222 (279)
T PF00532_consen 206 KIPEDIVSGFDSVVGFD 222 (279)
T ss_dssp CTTTEEEECSCCCGGHH
T ss_pred ccChhheeeeccchhhc
Confidence 884 6656666666554
No 384
>PF04320 DUF469: Protein with unknown function (DUF469); InterPro: IPR007416 This entry represents a family of uncharacterised proteins which are predicted to function as phosphotransferases.
Probab=29.18 E-value=1.2e+02 Score=24.66 Aligned_cols=67 Identities=16% Similarity=0.230 Sum_probs=50.5
Q ss_pred cccchhHHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhcCC
Q 026130 129 QDGDRDLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGR 208 (243)
Q Consensus 129 ~~~~~~lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~rGR 208 (243)
.+....+|.+||+||..+.++.-- .- ...+-|++=-. +|--.|++.-.+|..|++.++-
T Consensus 29 ~e~~D~~~D~fId~Ie~~gL~~~G--------gg------------~~~~eG~vc~~-~~gs~tee~R~~v~~WL~~~~e 87 (101)
T PF04320_consen 29 EEQIDAFVDAFIDVIEPNGLAFGG--------GG------------YEQWEGFVCLQ-RYGSCTEEDRAAVEAWLKARPE 87 (101)
T ss_pred HHHHHHHHHHHHHHHHhCCCEEec--------CC------------ccCEeEEEEec-cCCCCCHHHHHHHHHHHHhCCC
Confidence 456788999999999999876432 10 12456777666 7778999999999999999996
Q ss_pred cc---HHHHHh
Q 026130 209 VS---ISHLAS 216 (243)
Q Consensus 209 VS---i~eLa~ 216 (243)
|+ +++|+-
T Consensus 88 v~~v~vs~L~D 98 (101)
T PF04320_consen 88 VSDVEVSELVD 98 (101)
T ss_pred cceEEecceee
Confidence 55 566653
No 385
>cd04623 CBS_pair_10 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic gener
Probab=29.15 E-value=1.6e+02 Score=20.97 Aligned_cols=63 Identities=14% Similarity=0.245 Sum_probs=34.2
Q ss_pred cCCChHHHHHHHHHHHhcCCcceeeeCCCCeE-EEcHHHHHHHHHHHHhcC----CccHHHHHhhcccccccccc
Q 026130 158 FKLRTQECINRITSLENMGRLSGVMDDRGKYI-YISQAEMKAVADYIKRQG----RVSISHLASKSNQFIDLETK 227 (243)
Q Consensus 158 F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFI-YIS~eEl~aVA~fI~~rG----RVSi~eLa~~sN~lI~L~p~ 227 (243)
.+.+..++++.+.. ..-....|+|+.|+|+ +||...+.. ++...+ ..++.+++.. .++.+.+.
T Consensus 8 ~~~~~~~~~~~~~~--~~~~~~~V~~~~~~~~Giv~~~~l~~---~~~~~~~~~~~~~~~~~~~~--~~~~v~~~ 75 (113)
T cd04623 8 PDATVAEAAKLMAE--KNIGAVVVVDDGGRLVGIFSERDIVR---KVALRGASALDTPVSEIMTR--NVITVTPD 75 (113)
T ss_pred CCCcHHHHHHHHHH--cCCCeEEEECCCCCEEEEEehHHHHH---HHhhcCCCccccCHHHhcCC--CcEEECCC
Confidence 34555666655421 1223557788889998 678887753 222223 2356666543 34444443
No 386
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=29.10 E-value=1.9e+02 Score=26.02 Aligned_cols=34 Identities=15% Similarity=0.328 Sum_probs=25.3
Q ss_pred hHHHHHHHHHHhc--CccchHHHHHHcCCChHHHHH
Q 026130 134 DLLADFVEYIKKH--KCIPLEDLAAEFKLRTQECIN 167 (243)
Q Consensus 134 ~lL~~Fi~yIK~~--KvV~LEdLA~~F~lrtqd~I~ 167 (243)
..+...+.||..+ .-..|++||..+|++.--.-.
T Consensus 5 ~~i~~~~~~i~~~~~~~~~l~~lA~~~~~S~~~l~r 40 (289)
T PRK15121 5 GIIRDLLIWLEGHLDQPLSLDNVAAKAGYSKWHLQR 40 (289)
T ss_pred HHHHHHHHHHHhcccCCCCHHHHHHHHCcCHHHHHH
Confidence 4688899999855 447899999988777654433
No 387
>COG0640 ArsR Predicted transcriptional regulators [Transcription]
Probab=28.95 E-value=2e+02 Score=19.84 Aligned_cols=61 Identities=10% Similarity=0.190 Sum_probs=46.1
Q ss_pred HHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHH
Q 026130 142 YIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADY 202 (243)
Q Consensus 142 yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~f 202 (243)
.+....-+...+|+..++++-.-+-.-+..|...|-+.-..+.+..|..++...+..+..+
T Consensus 33 ~l~~~~~~~~~~l~~~~~~~~~~v~~hL~~L~~~glv~~~~~~~~~~~~l~~~~~~~~~~~ 93 (110)
T COG0640 33 LLAEGGELTVGELAEALGLSQSTVSHHLKVLREAGLVELRREGRLRLYRLADEKVAELLEL 93 (110)
T ss_pred HHHhcCCccHHHHHHHHCCChhHHHHHHHHHHHCCCeEEEecccEEEEecCcHHHHHHHHH
Confidence 3333333558899999999999999999999999999998888887777666664444443
No 388
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.94 E-value=41 Score=28.12 Aligned_cols=24 Identities=17% Similarity=0.548 Sum_probs=22.0
Q ss_pred CCeEEEcHHHHHHHHHHHHhcCCc
Q 026130 186 GKYIYISQAEMKAVADYIKRQGRV 209 (243)
Q Consensus 186 GKFIYIS~eEl~aVA~fI~~rGRV 209 (243)
.+|=|+|+++|.=|--||+-||-+
T Consensus 37 s~F~~Lt~d~LeFv~lf~r~RGnl 60 (122)
T COG3877 37 SKFEYLTSDQLEFVELFLRCRGNL 60 (122)
T ss_pred ccccccCHhHhHHHHHHHHHccCH
Confidence 578999999999999999999964
No 389
>PRK13500 transcriptional activator RhaR; Provisional
Probab=28.85 E-value=1.1e+02 Score=27.84 Aligned_cols=71 Identities=14% Similarity=0.271 Sum_probs=50.8
Q ss_pred hhHHHHHHHHHHhc--CccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHH-----HHHHHHHh
Q 026130 133 RDLLADFVEYIKKH--KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMK-----AVADYIKR 205 (243)
Q Consensus 133 ~~lL~~Fi~yIK~~--KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~-----aVA~fI~~ 205 (243)
...+..+++||..+ .-+.|++||..||++..-+-..++.-- | .|+-++- .-|..+-.
T Consensus 205 ~~~l~~i~~yI~~~~~e~isl~~lA~~~~iS~~~L~r~FK~~t------G----------~T~~~yi~~~RL~~A~~LL~ 268 (312)
T PRK13500 205 ETLLDKLITRLAASLKSPFALDKFCDEASCSERVLRQQFRQQT------G----------MTINQYLRQVRVCHAQYLLQ 268 (312)
T ss_pred HHHHHHHHHHHHHcccCCCCHHHHHHHHCcCHHHHHHHHHHHH------C----------cCHHHHHHHHHHHHHHHHHH
Confidence 45789999999885 458999999999999887777666532 2 3343332 23444555
Q ss_pred cCCccHHHHHhhcc
Q 026130 206 QGRVSISHLASKSN 219 (243)
Q Consensus 206 rGRVSi~eLa~~sN 219 (243)
.+..||+++|..|.
T Consensus 269 ~t~~sI~eIA~~~G 282 (312)
T PRK13500 269 HSRLLISDISTECG 282 (312)
T ss_pred cCCCCHHHHHHHhC
Confidence 67899999998774
No 390
>cd01188 INT_pAE1 pAE1 and related integrases, DNA breaking-rejoining enzymes, integrase/recombinases, C-terminal domain. This CD includes various bacterial integrases, including the predicted integrase of the deletion-prone region of plasmid pAE1 of Alcaligenes eutrophus H1.
Probab=28.77 E-value=1.6e+02 Score=23.78 Aligned_cols=71 Identities=17% Similarity=0.225 Sum_probs=44.0
Q ss_pred HHHHHHHHHhcC-----ccchHHHHHHcCCChHHHHH-HHHHHHhcCCcceeeeCCC---CeEEEcHHHHHHHHHHHHhc
Q 026130 136 LADFVEYIKKHK-----CIPLEDLAAEFKLRTQECIN-RITSLENMGRLSGVMDDRG---KYIYISQAEMKAVADYIKRQ 206 (243)
Q Consensus 136 L~~Fi~yIK~~K-----vV~LEdLA~~F~lrtqd~I~-RIq~Le~~g~LtGViDDRG---KFIYIS~eEl~aVA~fI~~r 206 (243)
+..|++++.... ...+=-|+...||+..+++. ++.++.-.+...-|.+..| ..|+|++.=...+-.||...
T Consensus 10 ~~~l~~~~~~~~~~~~~~~~~~~l~~~tGlR~~El~~l~~~di~~~~~~i~i~~~K~~~~r~vpl~~~~~~~l~~~~~~~ 89 (188)
T cd01188 10 VERLLASCDRSTPVGRRDYAILLLLARLGLRAGEVAALRLDDIDWRTGTIRVRQGKGGRVTRLPLPAEVGAALADYLRDG 89 (188)
T ss_pred HHHHHhccccCCchhHhHHHHHHHHHHHCCCHHHHHhCcccccCCCCCeEEEEeCCCCcceEEeCCHHHHHHHHHHHHhc
Confidence 556666554221 11233467779999999987 5666654443344443322 38999998777887887653
No 391
>cd04448 DEP_PIKfyve DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in fungal RhoGEF (GDP/GTP exchange factor) PIKfyve-like proteins. PIKfyve contains N-terminal Fyve finger and DEP domains, a central chaperonin-like domain and a C-terminal PIPK (phosphatidylinositol phosphate kinase) domain. PIKfyve-like proteins are important phosphatidylinositol (3)-monophosphate (PtdIns(3)P)-5-kinases, producing PtdIns(3,5)P2, which plays a major role in multivesicular body (MVB) sorting and control of retrograde traffic from the vacuole back to the endosome and/or Golgi. PIKfyve itself has been shown to be play a role in regulating early-endosome-to-trans-Golgi network (TGN) retrograde trafficking.
Probab=28.76 E-value=1.3e+02 Score=22.88 Aligned_cols=39 Identities=18% Similarity=0.256 Sum_probs=31.3
Q ss_pred HHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCC
Q 026130 137 ADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDR 185 (243)
Q Consensus 137 ~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDR 185 (243)
+++|+|+-.+.- ..+-.+++.--|.|+..|-|.-|.|+.
T Consensus 32 selVdWL~~~~~----------~~~R~eAv~~gq~Ll~~g~i~hV~~~~ 70 (81)
T cd04448 32 KELVNWLIRQGK----------AATRVQAIAIGQALLDAGWIECVSDDD 70 (81)
T ss_pred HHHHHHHHHcCC----------CCCHHHHHHHHHHHHHCCCEEecCCCC
Confidence 578888765521 266789999999999999999999973
No 392
>PRK08455 fliL flagellar basal body-associated protein FliL; Reviewed
Probab=28.76 E-value=35 Score=29.78 Aligned_cols=46 Identities=9% Similarity=0.143 Sum_probs=34.3
Q ss_pred HHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceee
Q 026130 136 LADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVM 182 (243)
Q Consensus 136 L~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGVi 182 (243)
-+.+|.|+..+.+--|......-.| -+++++||+.+...|.|..|+
T Consensus 130 RD~ii~~Ls~kt~~dL~t~~Gk~~L-k~ei~~~iN~~L~~g~V~~Vy 175 (182)
T PRK08455 130 RDIIIRILSSKTVEEVSTNKGKERL-KDEIVGKLNEFLIDGFIKNVF 175 (182)
T ss_pred HHHHHHHHHcCCHHHhcCHHHHHHH-HHHHHHHHHHHhccCceeEEE
Confidence 4667777777766666666666666 578999999999998887763
No 393
>TIGR03453 partition_RepA plasmid partitioning protein RepA. Members of this family are the RepA (or ParA) protein involved in replicon partitioning. All known examples occur in bacterial species with two or more replicons, on a plasmid or the smaller chromosome. Note that an apparent exception may be seen as a pseudomolecule from assembly of an incompletely sequenced genome. Members of this family belong to a larger family that also includes the enzyme cobyrinic acid a,c-diamide synthase, but assignment of that name to members of this family would be in error.
Probab=28.64 E-value=1.5e+02 Score=27.94 Aligned_cols=55 Identities=5% Similarity=0.018 Sum_probs=44.8
Q ss_pred CccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHh
Q 026130 147 KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKR 205 (243)
Q Consensus 147 KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~ 205 (243)
....+-++|..+|+++. + |..++..|.+.++..+-|.+-+-|.+++..+...+..
T Consensus 32 ~~~~i~eva~~~gv~~~-t---lr~~e~~~~~~~~~r~~~g~r~yt~~di~~l~~~~~~ 86 (387)
T TIGR03453 32 RKFTSGEVAKLLGVSDS-Y---LRQLSLEGKGPEPETLSNGRRSYTLEQINELRRHLAQ 86 (387)
T ss_pred ccCCHHHHHHHHCcCHH-H---HHHHHHcCCCCCCCcCCCCceeeCHHHHHHHHHHHHh
Confidence 45789999999999553 3 3447999999988777777889999999999887754
No 394
>PRK04280 arginine repressor; Provisional
Probab=28.22 E-value=1.4e+02 Score=25.36 Aligned_cols=58 Identities=24% Similarity=0.308 Sum_probs=41.6
Q ss_pred HHHHHHHHHHhcCccchHHHHHHc---CCC-hHHHHHH-HHHHHhcCCcceeeeCCCCeEEEcHHHH
Q 026130 135 LLADFVEYIKKHKCIPLEDLAAEF---KLR-TQECINR-ITSLENMGRLSGVMDDRGKYIYISQAEM 196 (243)
Q Consensus 135 lL~~Fi~yIK~~KvV~LEdLA~~F---~lr-tqd~I~R-Iq~Le~~g~LtGViDDRGKFIYIS~eEl 196 (243)
.+..+...|+.+.|-.=+||+..+ |+. ||-+|+| |++| | |.=|-+..|+|.|.-|.+.
T Consensus 5 R~~~I~~iI~~~~I~tQeeL~~~L~~~Gi~vTQATiSRDikeL---~-lvKv~~~~G~~~Y~lp~~~ 67 (148)
T PRK04280 5 RHIKIREIITNNEIETQDELVDRLREEGFNVTQATVSRDIKEL---H-LVKVPLPDGRYKYSLPADQ 67 (148)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHHHcCCCeehHHHHHHHHHc---C-CEEeecCCCcEEEeecccc
Confidence 345566678888888888876642 443 6999998 5554 4 3448889999999987754
No 395
>CHL00171 cpcB phycocyanin beta subunit; Reviewed
Probab=27.79 E-value=27 Score=30.50 Aligned_cols=41 Identities=15% Similarity=0.428 Sum_probs=30.4
Q ss_pred eeCCCCeEEEcHHHHHHHHHHHHhc-CCccHH-HHHhhccccccc
Q 026130 182 MDDRGKYIYISQAEMKAVADYIKRQ-GRVSIS-HLASKSNQFIDL 224 (243)
Q Consensus 182 iDDRGKFIYIS~eEl~aVA~fI~~r-GRVSi~-eLa~~sN~lI~L 224 (243)
-|..|+| +|..||+.|..|+..- =|+++. -|..+++.||+=
T Consensus 12 AD~~gRy--ls~~EL~~l~~~~~~~~~Rl~aa~~L~~na~~IV~~ 54 (172)
T CHL00171 12 ADARGEF--LSNTQLDALSKMVAEGNKRLDAVNKINANASTIVTN 54 (172)
T ss_pred HhhccCC--CCHHHHHHHHHHHHhHHHHHHHHHHHHHhHHHHHHH
Confidence 3667886 7999999999999875 466653 477777776653
No 396
>PRK12785 fliL flagellar basal body-associated protein FliL; Reviewed
Probab=27.78 E-value=35 Score=29.15 Aligned_cols=47 Identities=19% Similarity=0.361 Sum_probs=33.8
Q ss_pred HHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceee
Q 026130 135 LLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVM 182 (243)
Q Consensus 135 lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGVi 182 (243)
.-+.|+.|+.....-.|...+..-.| -+++.++|+.....|.|++|+
T Consensus 113 Ird~i~~~Ls~~~~~~L~~~~Gk~~L-r~ei~~~in~~l~~~~V~~Vl 159 (166)
T PRK12785 113 VTDAFQTYLRELRPSDLNGSAGLFRL-KEELLRRVNVALAPAQVNAVL 159 (166)
T ss_pred HHHHHHHHHHhCCHHHhcChHHHHHH-HHHHHHHHHhhcCCCceeEEE
Confidence 34567777777766555555555556 578899999998888888874
No 397
>cd01110 HTH_SoxR Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator. Helix-turn-helix (HTH) transcriptional regulator SoxR. The global regulator, SoxR, up-regulates gene expression of another transcription activator, SoxS, which directly stimulates the oxidative stress regulon genes in E. coli. The soxRS response renders the bacterial cell resistant to superoxide-generating agents, macrophage-generated nitric oxide, organic solvents, and antibiotics. The SoxR proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the unusually long spacer between the -35 and -10 promoter elements. They also harbor a regulatory C-terminal domain containing an iron-sulfur center.
Probab=27.76 E-value=2.8e+02 Score=22.87 Aligned_cols=65 Identities=14% Similarity=0.214 Sum_probs=47.2
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHH--HHHhcCCccHHHHHhhccc
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVAD--YIKRQGRVSISHLASKSNQ 220 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~--fI~~rGRVSi~eLa~~sN~ 220 (243)
.+.++|..+|+++.- |.--+..|.|..+-+. |.|=|.|++.+..+.. +.+.-| +|+.++....+.
T Consensus 3 ~I~EvA~~~Gvs~~t----LRyYE~~GLl~p~r~~-~g~R~Y~~~dl~~l~~I~~lr~~G-~sl~eI~~~l~~ 69 (139)
T cd01110 3 SVGEVAKRSGVAVSA----LHFYEQKGLIASWRNA-GNQRRYPRDVLRRIAFIKVAQRLG-LSLAEIAEALAT 69 (139)
T ss_pred CHHHHHHHHCcCHHH----HHHHHHCCCCCCCcCC-CCCeEECHHHHHHHHHHHHHHHcC-CCHHHHHHHHHH
Confidence 467999999997654 5566778999986554 5577789988877643 344456 899888876553
No 398
>PF09507 CDC27: DNA polymerase subunit Cdc27; InterPro: IPR019038 This protein forms the C subunit of DNA polymerase delta. It carries the essential residues for binding to the Pol1 subunit of polymerase alpha, from residues 293-332, which are characterised by the motif D--G--VT, referred to as the DPIM motif. The first 160 residues of the protein form the minimal domain for binding to the B subunit, Cdc1, of polymerase delta, the final 10 C-terminal residues, 362-372, being the DNA sliding clamp, PCNA, binding motif. ; GO: 0006260 DNA replication, 0005634 nucleus; PDB: 1U76_B 3E0J_B.
Probab=27.58 E-value=75 Score=29.74 Aligned_cols=58 Identities=14% Similarity=0.302 Sum_probs=42.6
Q ss_pred CccchHHHHHHcCCChHHHHHHHHHHHhcC------------CcceeeeCCCC-----------eEEEcHHHHHHHHHHH
Q 026130 147 KCIPLEDLAAEFKLRTQECINRITSLENMG------------RLSGVMDDRGK-----------YIYISQAEMKAVADYI 203 (243)
Q Consensus 147 KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g------------~LtGViDDRGK-----------FIYIS~eEl~aVA~fI 203 (243)
|||..-=|+..|+|....+-.-|.+..... .|+|+..+.|- ++-++.+.|..+-.-.
T Consensus 1 k~VTYk~LSr~l~ihvn~AK~~L~ef~~~~~~k~~~~l~atYlvsG~~k~~~~~~~~~~~~~~~v~Lv~e~~Le~~k~~f 80 (430)
T PF09507_consen 1 KVVTYKWLSRELGIHVNQAKQMLYEFHEKQNAKKPGSLHATYLVSGWLKDNGEPSHNDEEMDYSVILVREEDLEEAKAKF 80 (430)
T ss_dssp --EEHHHHHHHHT--HHHHHHHHHHHHHHHHHHHS-S-EEEEEEEEEEESSSSEEEE-------EEEEETTTHHHHHHH-
T ss_pred CeeeHHHHHHHhCCCHHHHHHHHHHHHHhccccCCCceEEEEEEEEEeCCCCCccccccccceeEEEeeHHHHHHHHHhc
Confidence 678888899999999998888776655443 48999999885 8889999998876554
Q ss_pred H
Q 026130 204 K 204 (243)
Q Consensus 204 ~ 204 (243)
.
T Consensus 81 ~ 81 (430)
T PF09507_consen 81 E 81 (430)
T ss_dssp S
T ss_pred c
Confidence 4
No 399
>PRK02363 DNA-directed RNA polymerase subunit delta; Reviewed
Probab=27.49 E-value=1.2e+02 Score=25.38 Aligned_cols=57 Identities=16% Similarity=0.255 Sum_probs=39.3
Q ss_pred HHHHHHHHHHhc-CccchHH----HHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHH
Q 026130 135 LLADFVEYIKKH-KCIPLED----LAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMK 197 (243)
Q Consensus 135 lL~~Fi~yIK~~-KvV~LEd----LA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~ 197 (243)
++.-...+++.+ +-+++.+ ++..+|++.+++.++|-+|-.. |.-.|+|||+....|.
T Consensus 5 ~idvAy~iL~~~~~~m~f~dL~~ev~~~~~~s~e~~~~~iaq~Ytd------Ln~DGRFi~lG~n~Wg 66 (129)
T PRK02363 5 LIEVAYEILKEKKEPMSFYDLVNEIQKYLGKSDEEIRERIAQFYTD------LNLDGRFISLGDNKWG 66 (129)
T ss_pred HHHHHHHHHHHcCCcccHHHHHHHHHHHhCCCHHHHHHHHHHHHHH------HhccCCeeEcCCCcee
Confidence 344444555554 5665555 6668999999999999887654 3446899999876653
No 400
>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=27.34 E-value=1.6e+02 Score=22.08 Aligned_cols=45 Identities=16% Similarity=0.279 Sum_probs=27.5
Q ss_pred chhHHHHHHHHHHhcCccchHHHHHHcC---CChHHHHHHHHHHHhcC
Q 026130 132 DRDLLADFVEYIKKHKCIPLEDLAAEFK---LRTQECINRITSLENMG 176 (243)
Q Consensus 132 ~~~lL~~Fi~yIK~~KvV~LEdLA~~F~---lrtqd~I~RIq~Le~~g 176 (243)
....|..||..=|.+.+|..++|...|. +.+..+=+-+..|...|
T Consensus 5 ~~~~i~~Li~~gK~~G~lT~~eI~~~L~~~~~~~e~id~i~~~L~~~g 52 (82)
T PF03979_consen 5 YEEAIKKLIEKGKKKGYLTYDEINDALPEDDLDPEQIDEIYDTLEDEG 52 (82)
T ss_dssp HHHHHHHHHHHHHHHSS-BHHHHHHH-S-S---HHHHHHHHHHHHTT-
T ss_pred hHHHHHHHHHHHhhcCcCCHHHHHHHcCccCCCHHHHHHHHHHHHHCC
Confidence 3456788999999999999999888876 44433333444444444
No 401
>cd00397 DNA_BRE_C DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site residues. The best-studied members of this diverse superfamily include human topoisomerase I, the bacteriophage lambda integrase, the bacteriophage P1 Cre recombinase, the yeast Flp recombinase and the bacterial XerD/C recombinases. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. The enzymes differ in that topoisomerases cleave and then rejoin the same 5' and 3' termini, whereas a site-specific recombinase transfers a 5' hydroxyl gener
Probab=27.22 E-value=2.8e+02 Score=21.03 Aligned_cols=71 Identities=14% Similarity=0.217 Sum_probs=46.6
Q ss_pred HHHHHHHHHh---cCccchHHHHHHcCCChHHHHH-HHHHHHhcCCcceeeeC----CCCeEEEcHHHHHHHHHHHHhcC
Q 026130 136 LADFVEYIKK---HKCIPLEDLAAEFKLRTQECIN-RITSLENMGRLSGVMDD----RGKYIYISQAEMKAVADYIKRQG 207 (243)
Q Consensus 136 L~~Fi~yIK~---~KvV~LEdLA~~F~lrtqd~I~-RIq~Le~~g~LtGViDD----RGKFIYIS~eEl~aVA~fI~~rG 207 (243)
+..|++++.. ...-.+=.|+...|+|..+++. ...++...+... .+.. ...+|+|+++=...+..++...+
T Consensus 2 ~~~l~~~~~~~~~~~~~~~~~l~~~tG~R~~Ei~~l~~~~~~~~~~~~-~i~~~K~~~~~~i~i~~~~~~~l~~~~~~~~ 80 (164)
T cd00397 2 IERLLAAAEASTPERLYLALLLLLATGLRISELCALRWSDIDLDKRVI-HITGTKTKKERTVPLSEEALKLLKEYLKKRR 80 (164)
T ss_pred HHHHHHHhhhccccHHHHHHHHHHHhCCCHHHHhCCchhhhccccCEE-EEecCCCCCeeEEecCHHHHHHHHHHHHHhc
Confidence 3456666665 5555666688889999999987 355555443221 2222 23689999988888888877653
No 402
>PF10771 DUF2582: Protein of unknown function (DUF2582); InterPro: IPR019707 This entry represents conserved proteins found in bacteria and archaea. The function is not known. ; PDB: 2L02_B 2L01_A.
Probab=27.04 E-value=1.6e+02 Score=22.02 Aligned_cols=51 Identities=12% Similarity=0.103 Sum_probs=41.7
Q ss_pred HHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEE
Q 026130 140 VEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIY 190 (243)
Q Consensus 140 i~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIY 190 (243)
-+++..++-..+.+|+..-|++..++.--|==|-.+|.|.-...++--||+
T Consensus 14 w~~L~~~~~~s~~el~k~~~l~~~~~~~AiGWLarE~KI~~~~~~~~~~v~ 64 (65)
T PF10771_consen 14 WQLLNENGEWSVSELKKATGLSDKEVYLAIGWLARENKIEFEEKNGELYVS 64 (65)
T ss_dssp HHHHCCSSSEEHHHHHHHCT-SCHHHHHHHHHHHCTTSEEEEEETTEEEEE
T ss_pred HHHHhhCCCcCHHHHHHHhCcCHHHHHHHHHHHhccCceeEEeeCCEEEEE
Confidence 456667888999999999999999999999999999999766555555554
No 403
>PTZ00068 60S ribosomal protein L13a; Provisional
Probab=26.96 E-value=60 Score=29.33 Aligned_cols=27 Identities=15% Similarity=0.299 Sum_probs=24.4
Q ss_pred hcCccchHHHHHHcCCChHHHHHHHHH
Q 026130 145 KHKCIPLEDLAAEFKLRTQECINRITS 171 (243)
Q Consensus 145 ~~KvV~LEdLA~~F~lrtqd~I~RIq~ 171 (243)
.+|.|.|.+||.++|-+-+++|..+.+
T Consensus 131 ~~ky~~lg~ls~~vGwky~~vv~~le~ 157 (202)
T PTZ00068 131 ERPYTVLGDLSAHVGWKYADVVAKLEE 157 (202)
T ss_pred CCceeeHHHHHHHhCccHHHHHHHHHH
Confidence 478999999999999999999998754
No 404
>PLN03086 PRLI-interacting factor K; Provisional
Probab=26.94 E-value=4.7e+02 Score=27.20 Aligned_cols=20 Identities=20% Similarity=0.426 Sum_probs=10.7
Q ss_pred ceeee---CCCCeEEEcHHHHHHH
Q 026130 179 SGVMD---DRGKYIYISQAEMKAV 199 (243)
Q Consensus 179 tGViD---DRGKFIYIS~eEl~aV 199 (243)
.||++ +-| +||+++-=|..+
T Consensus 141 ~GVlEF~A~EG-~v~lP~wm~~~L 163 (567)
T PLN03086 141 SGVLEFTAEEG-SVGLPPHVWSNL 163 (567)
T ss_pred EEEEEEEcCCC-eEEcCHHHHhhc
Confidence 35555 334 366666555555
No 405
>cd01182 INT_REC_C DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family include the bacteriophage lambda integrase, the bacteriophage P1 Cre recombinase, the yeast Flp recombinase and the bacterial XerD/C recombinases. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many intergrase/recombinases also have N-terminal domains, which show little sequence or structure similarity.
Probab=26.88 E-value=2.4e+02 Score=20.91 Aligned_cols=72 Identities=17% Similarity=0.163 Sum_probs=45.2
Q ss_pred HHHHHHHHHh---cCccchHHHHHHcCCChHHHHH-HHHHHHhcCCcceeeeCCC---CeEEEcHHHHHHHHHHHHhcC
Q 026130 136 LADFVEYIKK---HKCIPLEDLAAEFKLRTQECIN-RITSLENMGRLSGVMDDRG---KYIYISQAEMKAVADYIKRQG 207 (243)
Q Consensus 136 L~~Fi~yIK~---~KvV~LEdLA~~F~lrtqd~I~-RIq~Le~~g~LtGViDDRG---KFIYIS~eEl~aVA~fI~~rG 207 (243)
+..|++.+.. .....+=-|+..+|+|..++.. ...++...+...=|..-.| ..|+|++.-+..+..|+...+
T Consensus 2 ~~~l~~~~~~~~~~~~~~~~~l~~~~G~R~~ei~~l~~~~v~~~~~~~~i~~~K~~~~~~~~i~~~~~~~l~~~~~~~~ 80 (162)
T cd01182 2 LKKLLAALKKDTAPRDRALILLLLYTGLRVSELLALRWSDIDLDKGTITVRRTKTGKERTVPLSPELAELLREYLELRR 80 (162)
T ss_pred HHHHHHHhcccccHHHHHHHHHHHHhCCCHHHHhhhehhcccCcCCEEEEEecCCCCceEEecCHHHHHHHHHHHHHhc
Confidence 3455666654 4444555688889999999887 3345554442222222133 589999887788888887754
No 406
>CHL00089 apcF allophycocyanin beta 18 subunit
Probab=26.65 E-value=32 Score=30.04 Aligned_cols=39 Identities=21% Similarity=0.493 Sum_probs=29.6
Q ss_pred eCCCCeEEEcHHHHHHHHHHHHhc-CCccHH-HHHhhcccccc
Q 026130 183 DDRGKYIYISQAEMKAVADYIKRQ-GRVSIS-HLASKSNQFID 223 (243)
Q Consensus 183 DDRGKFIYIS~eEl~aVA~fI~~r-GRVSi~-eLa~~sN~lI~ 223 (243)
|+.|+| +|..||+.+..|+..- =|+++. -|..+++.||+
T Consensus 13 D~~gRY--ls~~eL~~l~~~~~~~~~Rl~aa~~L~~na~~IV~ 53 (169)
T CHL00089 13 DLTGKY--LDKNAITQLNSYFSSASDRIKIVEIINAQASNIIK 53 (169)
T ss_pred hccCCC--CCHHHHHHHHHHHHhHHHHHHHHHHHHHhHHHHHH
Confidence 778886 7999999999999875 567764 46666666554
No 407
>PRK09510 tolA cell envelope integrity inner membrane protein TolA; Provisional
Probab=26.61 E-value=6.4e+02 Score=24.96 Aligned_cols=10 Identities=30% Similarity=0.388 Sum_probs=4.5
Q ss_pred HHhcCCccee
Q 026130 172 LENMGRLSGV 181 (243)
Q Consensus 172 Le~~g~LtGV 181 (243)
|..+|+|++|
T Consensus 334 LapDG~V~sV 343 (387)
T PRK09510 334 LAPDGTLLDI 343 (387)
T ss_pred EcCCCcEEee
Confidence 3344444444
No 408
>PF00763 THF_DHG_CYH: Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; InterPro: IPR020630 Enzymes that participate in the transfer of one-carbon units require the coenzyme tetrahydrofolate (THF). Various reactions generate one-carbon derivatives of THF, which can be interconverted between different oxidation states by methylene-THF dehydrogenase (1.5.1.5 from EC), methenyl-THF cyclohydrolase (3.5.4.9 from EC) and formyl-THF synthetase (6.3.4.3 from EC) [, ]. The dehydrogenase and cyclohydrolase activities are expressed by a variety of multifunctional enzymes, including the tri-functional eukaryotic C1-tetrahydrofolate synthase []; a bifunctional eukaryotic mitochondrial protein; and the bifunctional Escherichia coli folD protein [, ]. Methylene-tetrahydrofolate dehydrogenase and methenyltetrahydrofolate cyclo-hydrolase share an overlapping active site [], and as such are usually located together in proteins, acting in tandem on the carbon-nitrogen bonds of substrates other than peptide bonds. This entry represents the N-terminal catalytic domain of these enzymes. ; GO: 0003824 catalytic activity, 0004488 methylenetetrahydrofolate dehydrogenase (NADP+) activity, 0009396 folic acid-containing compound biosynthetic process, 0055114 oxidation-reduction process; PDB: 2C2X_B 2C2Y_A 1EDZ_A 1EE9_A 4A26_B 3NGL_C 3NGX_A 1B0A_A 1DIA_A 1A4I_B ....
Probab=26.40 E-value=82 Score=25.21 Aligned_cols=25 Identities=16% Similarity=0.328 Sum_probs=20.7
Q ss_pred CCChHHHHHHHHHHHhcCCcceeee
Q 026130 159 KLRTQECINRITSLENMGRLSGVMD 183 (243)
Q Consensus 159 ~lrtqd~I~RIq~Le~~g~LtGViD 183 (243)
..+++++++.|..|-.+..++|||=
T Consensus 69 ~~~~~el~~~i~~lN~D~~V~GIlv 93 (117)
T PF00763_consen 69 DISEEELLELIEKLNEDPSVHGILV 93 (117)
T ss_dssp TSSHHHHHHHHHHHHH-TT-SEEEE
T ss_pred CcCHHHHHHHHHHHhCCCCCCEEEE
Confidence 4578999999999999999999984
No 409
>PF10882 bPH_5: Bacterial PH domain; InterPro: IPR020482 This entry contains membrane proteins with no known function.
Probab=26.31 E-value=63 Score=24.40 Aligned_cols=22 Identities=18% Similarity=0.268 Sum_probs=18.6
Q ss_pred CCeEEEcHHHHHHHHHHHHhcC
Q 026130 186 GKYIYISQAEMKAVADYIKRQG 207 (243)
Q Consensus 186 GKFIYIS~eEl~aVA~fI~~rG 207 (243)
.+-++|||+..+.+.+.|++|.
T Consensus 79 ~~~y~isp~~~~~fi~~l~~r~ 100 (100)
T PF10882_consen 79 DKTYVISPEDPEEFIEALKKRA 100 (100)
T ss_pred CceEEEcCCCHHHHHHHHHhcC
Confidence 3667799999999999999874
No 410
>TIGR00674 dapA dihydrodipicolinate synthase. Dihydrodipicolinate synthase is a homotetrameric enzyme of lysine biosynthesis. E. coli has several paralogs closely related to dihydrodipicoline synthase (DapA), as well as the more distant N-acetylneuraminate lyase. In Pyrococcus horikoshii, the bidirectional best hit with E. coli is to an uncharacterized paralog of DapA, not DapA itself, and it is omitted from the seed. The putative members from the Chlamydias (pathogens with a parasitic metabolism) are easily the most divergent members of the multiple alignment.
Probab=26.26 E-value=1.5e+02 Score=26.81 Aligned_cols=52 Identities=19% Similarity=0.192 Sum_probs=40.3
Q ss_pred cCCChHHHHHHHHHHHhcCCcceeee--CCCCeEEEcHHHHHHHHHHHHhc--CCcc
Q 026130 158 FKLRTQECINRITSLENMGRLSGVMD--DRGKYIYISQAEMKAVADYIKRQ--GRVS 210 (243)
Q Consensus 158 F~lrtqd~I~RIq~Le~~g~LtGViD--DRGKFIYIS~eEl~aVA~fI~~r--GRVS 210 (243)
..+..+-+..-|..|.+.| +.||+= .-|-|.++|.+|...|.+...+. |||.
T Consensus 14 g~iD~~~~~~~i~~l~~~G-v~Gi~~~GstGE~~~Ls~~Er~~~~~~~~~~~~~~~~ 69 (285)
T TIGR00674 14 GSVDFAALEKLIDFQIENG-TDAIVVVGTTGESPTLSHEEHKKVIEFVVDLVNGRVP 69 (285)
T ss_pred CCcCHHHHHHHHHHHHHcC-CCEEEECccCcccccCCHHHHHHHHHHHHHHhCCCCe
Confidence 4566777777888888765 888764 57999999999999998876654 7763
No 411
>KOG3977 consensus Troponin I [Cytoskeleton]
Probab=26.16 E-value=4e+02 Score=24.49 Aligned_cols=73 Identities=23% Similarity=0.270 Sum_probs=47.4
Q ss_pred chhHHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhcCCcc
Q 026130 132 DRDLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRVS 210 (243)
Q Consensus 132 ~~~lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~rGRVS 210 (243)
.+.+|+++.+-|- .+|+.|++=-=..+..++...--|++|- .-|+|=||||+-=|---...-++-..+-|-.|
T Consensus 89 d~g~Lq~ly~~l~-arv~~leEEkYDi~~~v~qt~~EIndLt-----ikvnDLRGKFvkPtLkkVsks~~kf~ka~~~~ 161 (221)
T KOG3977|consen 89 DRGLLQDLYRELH-ARVDALEEEKYDIEAKVTQTETEINDLT-----IKVNDLRGKFVKPTLKKVSKSADKFLKALLGS 161 (221)
T ss_pred chHHHHHHHHHHH-HHHHHHHHhhcchhheeehhhhhHHHHH-----HHHHHhcccccCccHHHHHhhhHHHHHHhhcc
Confidence 3455888888774 5677777754445555666666777775 35889999999877555444444444444444
No 412
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=26.07 E-value=1.6e+02 Score=25.01 Aligned_cols=43 Identities=16% Similarity=0.283 Sum_probs=33.6
Q ss_pred HHHHHHHHHHhcCc--cchHHHHHHcCCChHHHHHHHHHHHhcCCccee
Q 026130 135 LLADFVEYIKKHKC--IPLEDLAAEFKLRTQECINRITSLENMGRLSGV 181 (243)
Q Consensus 135 lL~~Fi~yIK~~Kv--V~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGV 181 (243)
.....-+||..+.- ..+.+||.+.|++... |..+..+|+|.=+
T Consensus 31 ~f~kV~~yLr~~p~~~ati~eV~e~tgVs~~~----I~~~IreGRL~~~ 75 (137)
T TIGR03826 31 EFEKVYKFLRKHENRQATVSEIVEETGVSEKL----ILKFIREGRLQLK 75 (137)
T ss_pred HHHHHHHHHHHCCCCCCCHHHHHHHHCcCHHH----HHHHHHcCCeecc
Confidence 34566789999977 9999999999998765 5666777887643
No 413
>smart00434 TOP4c DNA Topoisomerase IV. Bacterial DNA topoisomerase IV, GyrA, ParC
Probab=26.07 E-value=57 Score=32.24 Aligned_cols=36 Identities=22% Similarity=0.513 Sum_probs=29.5
Q ss_pred ccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCC
Q 026130 148 CIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDR 185 (243)
Q Consensus 148 vV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDR 185 (243)
-+++.+|- +|+.|+..+..|.+|...|.|.||+|.+
T Consensus 234 ~ivItElP--~~~~~~~~~e~I~~lv~~~ki~~i~~~~ 269 (445)
T smart00434 234 TIVITELP--YQVNKAKLIEKIAELVKDKKIEGIIDVR 269 (445)
T ss_pred eEEEEeCC--CcccHHHHHHHHHHHHhcCCCCcceehh
Confidence 34455554 6889999999999999999999999864
No 414
>PRK11173 two-component response regulator; Provisional
Probab=25.68 E-value=1.2e+02 Score=25.23 Aligned_cols=35 Identities=20% Similarity=0.410 Sum_probs=29.6
Q ss_pred CCCCeEEEcHHHHHHHHHHHHhcCCc-cHHHHHhhc
Q 026130 184 DRGKYIYISQAEMKAVADYIKRQGRV-SISHLASKS 218 (243)
Q Consensus 184 DRGKFIYIS~eEl~aVA~fI~~rGRV-Si~eLa~~s 218 (243)
-.|+-|.+|+.|+.-+.-|+...|+| |..+|....
T Consensus 154 ~~~~~~~Lt~~E~~ll~~l~~~~g~v~sr~~l~~~v 189 (237)
T PRK11173 154 PDGEQYKLPRSEFRAMLHFCENPGKIQSRAELLKKM 189 (237)
T ss_pred cCCeEEeCCHHHHHHHHHHHhCCCccCcHHHHHHHh
Confidence 47899999999999999999999998 556776543
No 415
>PF13274 DUF4065: Protein of unknown function (DUF4065)
Probab=25.63 E-value=2.8e+02 Score=20.53 Aligned_cols=84 Identities=15% Similarity=0.071 Sum_probs=55.8
Q ss_pred HHHHHHHHHhcC-ccchHHHHHHcCCChHHHHHHHHHHHhcCCcc---------eeeeCCCCeEEEcHHHHHHHHHHHHh
Q 026130 136 LADFVEYIKKHK-CIPLEDLAAEFKLRTQECINRITSLENMGRLS---------GVMDDRGKYIYISQAEMKAVADYIKR 205 (243)
Q Consensus 136 L~~Fi~yIK~~K-vV~LEdLA~~F~lrtqd~I~RIq~Le~~g~Lt---------GViDDRGKFIYIS~eEl~aVA~fI~~ 205 (243)
+.++..+.+..+ ++...=.|-.+|==..++.+.++.+...+... +..+ ...+.++|+++...|-.-|+.
T Consensus 7 ~a~~~~~~~~g~~l~~~~~~a~~yGPv~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~i~~V~~~ 85 (108)
T PF13274_consen 7 FADGYYLKKYGKPLFGDDFEAWKYGPVPSDVYDDLKNNGEISIEEFETTYEPIIKYKD-KFDLEELSEEEKEIIDEVINK 85 (108)
T ss_pred HHHHHHHHHhCCCCccchhhhhcCCCcCHHHHHHHHccCCcccccccccccccccccc-ccccccCCHHHHHHHHHHHHH
Confidence 344444555443 44444477788877777766666543332211 1111 146679999999999999999
Q ss_pred cCCccHHHHHhhccc
Q 026130 206 QGRVSISHLASKSNQ 220 (243)
Q Consensus 206 rGRVSi~eLa~~sN~ 220 (243)
-|..|-.+|...|+.
T Consensus 86 ~~~~s~~~L~~~sH~ 100 (108)
T PF13274_consen 86 YGDKSAWELSELSHK 100 (108)
T ss_pred HcCCCHHHHHHHHcC
Confidence 999999999998873
No 416
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=25.62 E-value=3.3e+02 Score=21.41 Aligned_cols=66 Identities=14% Similarity=0.133 Sum_probs=47.9
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhc-CCccHHHHHhhccc
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQ-GRVSISHLASKSNQ 220 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~r-GRVSi~eLa~~sN~ 220 (243)
.+.++|..||+++.- |.--+..|.|...-+ .|.|=|-|++.+..+-....-+ --+|+.++....+.
T Consensus 2 ~i~eva~~~gvs~~t----lR~Ye~~GLl~p~r~-~~g~R~Y~~~~~~~l~~I~~lr~~G~sl~eI~~~l~~ 68 (112)
T cd01282 2 RIGELAARTGVSVRS----LRYYEEQGLLVPERS-ANGYRDYDEAAVDRVRQIRRLLAAGLTLEEIREFLPC 68 (112)
T ss_pred CHHHHHHHHCCCHHH----HHHHHHCCCCCCCcC-CCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 467899999998754 455567799998654 5668888999988776444433 34999888876554
No 417
>COG1695 Predicted transcriptional regulators [Transcription]
Probab=25.62 E-value=1.9e+02 Score=23.08 Aligned_cols=72 Identities=15% Similarity=0.202 Sum_probs=49.9
Q ss_pred HHHHHHHHHhcCccchHHHHHHc--------CCChHHHHHHHHHHHhcCCcceeeeCC-C----CeEEEcHHHHHHHHHH
Q 026130 136 LADFVEYIKKHKCIPLEDLAAEF--------KLRTQECINRITSLENMGRLSGVMDDR-G----KYIYISQAEMKAVADY 202 (243)
Q Consensus 136 L~~Fi~yIK~~KvV~LEdLA~~F--------~lrtqd~I~RIq~Le~~g~LtGViDDR-G----KFIYIS~eEl~aVA~f 202 (243)
|.-.|-+|-..+=.+--+|...+ .++..-+---|..|+++|-|++...+. | ||--||+.-...++.+
T Consensus 10 l~~~iL~~L~~~~~~Gyei~k~~~~~~~~~~~~s~gtiYp~L~~Le~~Gli~~~~~~~~~g~~rk~Y~lTe~G~~~l~~~ 89 (138)
T COG1695 10 LELLILSLLSEKPSHGYEIIKELEELSGGLWEPSPGTIYPLLKRLEKEGLIESRWEESGGGPPRKYYRLTEKGKEELAEL 89 (138)
T ss_pred HHHHHHHHHhcCCchHHHHHHHHHHHcCCCCcCCCCcHHHHHHHHHHCCCeEEEecccCCCCCceEEEECHHHHHHHHHH
Confidence 44444444444444444443332 356667777899999999999997765 4 8999999999999988
Q ss_pred HHhcC
Q 026130 203 IKRQG 207 (243)
Q Consensus 203 I~~rG 207 (243)
.+.-+
T Consensus 90 ~~~~~ 94 (138)
T COG1695 90 REEWG 94 (138)
T ss_pred HHHHH
Confidence 75543
No 418
>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator. This model represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=25.59 E-value=3.2e+02 Score=22.11 Aligned_cols=66 Identities=12% Similarity=0.150 Sum_probs=48.7
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHH--HHHhcCCccHHHHHhhccc
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVAD--YIKRQGRVSISHLASKSNQ 220 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~--fI~~rGRVSi~eLa~~sN~ 220 (243)
.+.++|..+|+++.- |.--+..|-|.....+.|-|=|-|++.+..|.. +++.-| +|+.++....+.
T Consensus 3 ~I~e~a~~~gvs~~t----lR~Ye~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G-~sl~eI~~~l~~ 70 (131)
T TIGR02043 3 QIGELAKLCGVTSDT----LRFYEKNGLIKPAGRTDSGYRLYTDEDQKRLRFILKAKELG-FTLDEIKELLSI 70 (131)
T ss_pred CHHHHHHHHCcCHHH----HHHHHHCCCCCCCCcCCCCceecCHHHHHHHHHHHHHHHcC-CCHHHHHHHHHh
Confidence 477999999998763 455667799998766667788889999887753 334444 788888776653
No 419
>PRK10265 chaperone-modulator protein CbpM; Provisional
Probab=25.52 E-value=99 Score=24.29 Aligned_cols=51 Identities=6% Similarity=0.176 Sum_probs=36.5
Q ss_pred ccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHH
Q 026130 148 CIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYI 203 (243)
Q Consensus 148 vV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI 203 (243)
.+.+++|+...|+..+. |.+|...|-|....++.|.|.|-+ ..+..+-..+
T Consensus 7 ~lt~~Elc~~~gi~~~~----l~eLve~GlIep~~~~~~~~~F~~-~~l~r~~~a~ 57 (101)
T PRK10265 7 TFTITEFCLHTGVSEEE----LNEIVGLGVIEPREIQETTWVFDD-HAAIVVQRAV 57 (101)
T ss_pred EeeHHHHHHHHCcCHHH----HHHHHHCCCeecCCCCcccceECH-HHHHHHHHHH
Confidence 36789999999997765 567888898888777778888755 3344433333
No 420
>PF09681 Phage_rep_org_N: N-terminal phage replisome organiser (Phage_rep_org_N); InterPro: IPR010056 This entry is represented by the N-terminal domain of Bacteriophage A500, Gp45. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. The proteins in this entry contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The low-complexity region is adjacent to this N-terminal domain.
Probab=25.49 E-value=1.5e+02 Score=24.46 Aligned_cols=42 Identities=24% Similarity=0.328 Sum_probs=34.1
Q ss_pred cchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcH
Q 026130 149 IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQ 193 (243)
Q Consensus 149 V~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~ 193 (243)
...+.||..|+-++..|.--|+-|..-|.|.. ++. ..|||+.
T Consensus 54 y~~e~LA~~~~~~~~~V~~AL~~f~k~glIe~--~ed-~~i~i~~ 95 (121)
T PF09681_consen 54 YTAEMLALEFDRPVDTVRLALAVFQKLGLIEI--DED-GVIYIPN 95 (121)
T ss_pred CcHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE--ecC-CeEEeec
Confidence 45678999999999999999999999999976 333 5666665
No 421
>KOG1363 consensus Predicted regulator of the ubiquitin pathway (contains UAS and UBX domains) [Signal transduction mechanisms]
Probab=25.48 E-value=2.4e+02 Score=28.35 Aligned_cols=12 Identities=17% Similarity=0.027 Sum_probs=5.3
Q ss_pred CChHHHHHHHHH
Q 026130 160 LRTQECINRITS 171 (243)
Q Consensus 160 lrtqd~I~RIq~ 171 (243)
.++|++++.|-.
T Consensus 404 ~~~q~l~~~v~~ 415 (460)
T KOG1363|consen 404 DKLQILYDYVDS 415 (460)
T ss_pred cchhHHHHHHHh
Confidence 344444444433
No 422
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=25.45 E-value=2.9e+02 Score=21.26 Aligned_cols=65 Identities=18% Similarity=0.264 Sum_probs=47.8
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhcC--CccHHHHHhhcc
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQG--RVSISHLASKSN 219 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~rG--RVSi~eLa~~sN 219 (243)
.+-++|..+|+++ ..|.--+..|.|.....+.|.|=|-|+..+.. -.||+.-- -||++++-...+
T Consensus 2 ~I~eva~~~gvs~----~tLRyYE~~GLl~p~~~~~~gyR~Ys~~dl~~-l~~I~~~r~~G~~L~~I~~~l~ 68 (124)
T COG0789 2 TIGEVAKLTGVSV----RTLRFYERKGLLSPERRDEGGYRYYTPEDLEL-LQIIKTLRELGFSLAEIKELLD 68 (124)
T ss_pred cHHHHHHHhCCCH----HHHHHHHHcCCCCCcccCCCCceecCHHHHHH-HHHHHHHHHcCCCHHHHHHHHh
Confidence 4578999999975 45788999999999998888888889988544 44554321 478776665443
No 423
>TIGR01337 apcB allophycocyanin, beta subunit. The alpha and beta subunits of allophycocyanin form heterodimers, six of which associate into larger aggregates as part of the phycobilisome, a light-harvesting complex of phycobiliproteins and linker proteins. This model describes allophycocyanin beta subunit. Other, homologous phyobiliproteins include allophycocyanin alpha chain and the phycocyanin and phycoerythrin alpha and beta chains.
Probab=25.35 E-value=32 Score=29.78 Aligned_cols=39 Identities=21% Similarity=0.392 Sum_probs=29.2
Q ss_pred eCCCCeEEEcHHHHHHHHHHHHhc-CCccHH-HHHhhcccccc
Q 026130 183 DDRGKYIYISQAEMKAVADYIKRQ-GRVSIS-HLASKSNQFID 223 (243)
Q Consensus 183 DDRGKFIYIS~eEl~aVA~fI~~r-GRVSi~-eLa~~sN~lI~ 223 (243)
|++|+| +|..||+.|-.|+..- =||++. -|..+++.||+
T Consensus 12 D~~gRY--ls~~eL~~l~~~~~~~~~Rl~aa~~l~~na~~Iv~ 52 (167)
T TIGR01337 12 DLTGKY--LDDNAVTKLKGYFQTGELRLRAAAIINANSATIIK 52 (167)
T ss_pred HhcCCC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHH
Confidence 678886 7999999999999854 466654 46666666654
No 424
>PRK06474 hypothetical protein; Provisional
Probab=25.31 E-value=2.1e+02 Score=24.61 Aligned_cols=46 Identities=11% Similarity=0.192 Sum_probs=33.8
Q ss_pred HHHHHHHhcCc-cchHHHHHHc-CCChHHHHHHHHHHHhcCCcceeee
Q 026130 138 DFVEYIKKHKC-IPLEDLAAEF-KLRTQECINRITSLENMGRLSGVMD 183 (243)
Q Consensus 138 ~Fi~yIK~~Kv-V~LEdLA~~F-~lrtqd~I~RIq~Le~~g~LtGViD 183 (243)
..+.++..+.- ....+|+..+ +++..-+-.-|+.|...|.|.-+-.
T Consensus 15 ~Il~~L~~~~~~~ta~el~~~l~~is~aTvYrhL~~L~e~GLI~~~~~ 62 (178)
T PRK06474 15 KICQVLMRNKEGLTPLELVKILKDVPQATLYRHLQTMVDSGILHVVKE 62 (178)
T ss_pred HHHHHHHhCCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEEeec
Confidence 45667766654 8899999999 5554445557899999998886554
No 425
>PF01853 MOZ_SAS: MOZ/SAS family; InterPro: IPR002717 Moz is a monocytic leukemia Zn_finger protein and the SAS protein from Saccharomyces cerevisiae (Baker's yeast) is involved in silencing the Hmr locus. These proteins were reported to be homologous to acetyltransferases [] but this similarity is not supported by standard sequence analysis.; GO: 0016747 transferase activity, transferring acyl groups other than amino-acyl groups, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3TO6_A 1MJA_A 1MJ9_A 3TO7_A 3TO9_A 1MJB_A 1FY7_A 2OZU_A 2RC4_A 2OU2_A ....
Probab=25.21 E-value=73 Score=28.48 Aligned_cols=25 Identities=24% Similarity=0.531 Sum_probs=21.0
Q ss_pred ccchHHHHHHcCCChHHHHHHHHHH
Q 026130 148 CIPLEDLAAEFKLRTQECINRITSL 172 (243)
Q Consensus 148 vV~LEdLA~~F~lrtqd~I~RIq~L 172 (243)
.+.++||+..-|++..|||..++.|
T Consensus 150 ~isi~~is~~Tgi~~~DIi~tL~~l 174 (188)
T PF01853_consen 150 SISIKDISQETGIRPEDIISTLQQL 174 (188)
T ss_dssp -EEHHHHHHHH-BTHHHHHHHHHHT
T ss_pred eEEHHHHHHHHCCCHHHHHHHHHHC
Confidence 5899999999999999999887765
No 426
>cd04589 CBS_pair_CAP-ED_DUF294_assoc_bac This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the bacterial CAP_ED (cAMP receptor protein effector domain) family of transcription factors and the DUF294 domain. Members of CAP_ED, include CAP which binds cAMP, FNR (fumarate and nitrate reductase) which uses an iron-sulfur cluster to sense oxygen, and CooA a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. DUF294 is a putative nucleotidyltransferase with a conserved DxD motif. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or
Probab=25.18 E-value=1.8e+02 Score=20.97 Aligned_cols=38 Identities=8% Similarity=0.089 Sum_probs=22.9
Q ss_pred cCCChHHHHHHHHHHHhcCCcceeeeCCCCeE-EEcHHHHHH
Q 026130 158 FKLRTQECINRITSLENMGRLSGVMDDRGKYI-YISQAEMKA 198 (243)
Q Consensus 158 F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFI-YIS~eEl~a 198 (243)
.+.+..++++.+. ........|+|+ |+|+ +||...+..
T Consensus 8 ~~~~~~~~~~~~~--~~~~~~~~V~d~-~~~~G~v~~~~l~~ 46 (111)
T cd04589 8 ASTSIRDAARLMR--EHGADALLVRDG-DPRLGIVTRTDLLD 46 (111)
T ss_pred CCCcHHHHHHHHH--HcCCCEEEEecC-CeEEEEEEHHHHHH
Confidence 3455666666552 222235566677 8888 688777653
No 427
>cd01187 INT_SG4 INT_SG4, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 4, N- and C-terminal domains. The CD contains mainly predicted bacterial integrase/recombinases for which not much biochemical characterization is available.
Probab=25.12 E-value=3.6e+02 Score=23.36 Aligned_cols=75 Identities=17% Similarity=0.227 Sum_probs=51.5
Q ss_pred chhHHHHHHHHHHhcC---------ccchHHHHHHcCCChHHHHH-HHHHHHhcCCcceeeeCCC---CeEEEcHHHHHH
Q 026130 132 DRDLLADFVEYIKKHK---------CIPLEDLAAEFKLRTQECIN-RITSLENMGRLSGVMDDRG---KYIYISQAEMKA 198 (243)
Q Consensus 132 ~~~lL~~Fi~yIK~~K---------vV~LEdLA~~F~lrtqd~I~-RIq~Le~~g~LtGViDDRG---KFIYIS~eEl~a 198 (243)
+..-+..|++++.... .-.+=.|+...|++..+++. +.+++.-++...=|-...| .+|+|+++=+..
T Consensus 103 t~~e~~~l~~~~~~~~~~~~~~~~~~~~~i~ll~~tGlR~~E~~~L~~~did~~~~~i~i~~~K~~~~r~vpl~~~l~~~ 182 (299)
T cd01187 103 TDEEIQRLLAAALQLPPTSGLRPWTYRTLFGLLAVTGLRLGEALRLRLSDVDLDSGILTVRDSKFGKSRLVPLHASTRAA 182 (299)
T ss_pred CHHHHHHHHHHHHhCCCCCCchhhHHHHHHHHHHHhCCcHHHHHhCcHHhcCCCCCeEEEEecCCCCccEEeCCHHHHHH
Confidence 3444788888886422 22455688899999999998 6777754433222332322 489999999999
Q ss_pred HHHHHHhc
Q 026130 199 VADYIKRQ 206 (243)
Q Consensus 199 VA~fI~~r 206 (243)
+..|+..+
T Consensus 183 l~~~~~~~ 190 (299)
T cd01187 183 LRDYLARR 190 (299)
T ss_pred HHHHHHHH
Confidence 99888654
No 428
>cd08315 Death_TRAILR_DR4_DR5 Death domain of Tumor necrosis factor-Related Apoptosis-Inducing Ligand Receptors. Death Domain (DD) found in Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL) Receptors. In mammals, this family includes TRAILR1 (also called DR4 or TNFRSF10A) and TRAILR2 (also called DR5, TNFRSF10B, or KILLER). They function as receptors for the cytokine TRAIL and are involved in apoptosis signaling pathways. TRAIL preferentially induces apoptosis in cancer cells while exhibiting little toxicity in normal cells. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=25.07 E-value=1.3e+02 Score=23.51 Aligned_cols=72 Identities=13% Similarity=0.205 Sum_probs=47.8
Q ss_pred hhHHHHHHHHHHhc-CccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhcCCcc-
Q 026130 133 RDLLADFVEYIKKH-KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRVS- 210 (243)
Q Consensus 133 ~~lL~~Fi~yIK~~-KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~rGRVS- 210 (243)
++.|..+.++|-.. -+-...+||+++|| ++.-|+.|..= .++. .+.=++-+-.|-++.|+=-
T Consensus 3 ~~~l~~~f~~i~~~V~~~~Wk~laR~LGL-se~~I~~i~~~-----------~~~~----~eq~~qmL~~W~~~~G~~At 66 (96)
T cd08315 3 QETLRRSFDHFIKEVPFDSWNRLMRQLGL-SENEIDVAKAN-----------ERVT----REQLYQMLLTWVNKTGRKAS 66 (96)
T ss_pred HhHHHHHHHHHHHHCCHHHHHHHHHHcCC-CHHHHHHHHHH-----------CCCC----HHHHHHHHHHHHHhhCCCcH
Confidence 45678888887432 22357789999999 56667777642 2331 4555777888888888743
Q ss_pred HHHHHhhccc
Q 026130 211 ISHLASKSNQ 220 (243)
Q Consensus 211 i~eLa~~sN~ 220 (243)
+..|.++...
T Consensus 67 ~~~L~~aL~~ 76 (96)
T cd08315 67 VNTLLDALEA 76 (96)
T ss_pred HHHHHHHHHH
Confidence 4667665444
No 429
>PF02375 JmjN: jmjN domain; InterPro: IPR003349 Jumonji protein is required for neural tube formation in mice [].There is evidence of domain swapping within the jumonji family of transcription factors []. This domain is often associated with JmjC (see IPR003347 from INTERPRO).; PDB: 2XML_A 2W2I_C 3DXT_A 3DXU_A 2OX0_B 2OQ6_B 2WWJ_A 2Q8D_A 3PDQ_A 2YBK_A ....
Probab=24.96 E-value=45 Score=21.94 Aligned_cols=20 Identities=20% Similarity=0.504 Sum_probs=14.7
Q ss_pred HHHHHHHHHhcCccchHHHHHHcCC
Q 026130 136 LADFVEYIKKHKCIPLEDLAAEFKL 160 (243)
Q Consensus 136 L~~Fi~yIK~~KvV~LEdLA~~F~l 160 (243)
..+|+.||.. ++.+|.+||+
T Consensus 10 F~dp~~yi~~-----i~~~g~~~Gi 29 (34)
T PF02375_consen 10 FKDPIKYISS-----IEPEGEKYGI 29 (34)
T ss_dssp HS-HHHHHHH-----HHHTTGGGSE
T ss_pred HhCHHHHHHH-----HHHHHHHCCE
Confidence 4688888876 7778888886
No 430
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=24.58 E-value=3.8e+02 Score=22.19 Aligned_cols=64 Identities=19% Similarity=0.337 Sum_probs=43.7
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHH--HHHHhcCCccHHHHHhhcc
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVA--DYIKRQGRVSISHLASKSN 219 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA--~fI~~rGRVSi~eLa~~sN 219 (243)
.+.++|..||+++.- |.--+..|.|...-++ |.|-|.|+..+..+. .+.+. --+|++++.....
T Consensus 2 ~I~e~a~~~gvs~~T----LR~Ye~~GLl~p~r~~-~g~R~Y~~~~l~~l~~I~~lr~-~G~sL~eI~~~l~ 67 (134)
T cd04779 2 RIGQLAHLAGVSKRT----IDYYTNLGLLTPERSD-SNYRYYDETALDRLQLIEHLKG-QRLSLAEIKDQLE 67 (134)
T ss_pred CHHHHHHHHCcCHHH----HHHHHHCCCCCCccCC-CCCeeECHHHHHHHHHHHHHHH-CCCCHHHHHHHHH
Confidence 367899999997763 4445688999976555 458888888877653 33333 4578777665543
No 431
>PF12668 DUF3791: Protein of unknown function (DUF3791); InterPro: IPR024269 This entry represents proteins of unknown function.
Probab=24.57 E-value=68 Score=22.97 Aligned_cols=22 Identities=18% Similarity=0.357 Sum_probs=19.8
Q ss_pred chHHHHHHcCCChHHHHHHHHH
Q 026130 150 PLEDLAAEFKLRTQECINRITS 171 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~ 171 (243)
.++.+|..+|++..++.+++..
T Consensus 7 ~Ie~~A~~~~~s~~ea~~~~~~ 28 (62)
T PF12668_consen 7 CIEEFAKKLNISGEEAYNYFKR 28 (62)
T ss_pred HHHHHHHHHCcCHHHHHHHHHH
Confidence 5899999999999999998774
No 432
>cd01193 INT_IntI IntI (E2) integrases, site-specific tyrosine recombinases, DNA breaking-rejoining enzymes, N- and C-terminal domains. This CD includes integrases which are components of multiresistant integrons and mediate recombination between a proximal attI site and a secondary target called the attC (or 59-base element) present on various mobile gene cassettes. Integron-integrases are present in many natural occurring mobile elements, including transposons and conjugative plasmids. Vibrio, Shewanella, Xanthomonas and Pseudomonas species harbor chromosomal super-integrons. All integron-integrases carry large inserts unlike the TnpF ermF-like proteins also seen in this group.
Probab=24.50 E-value=2.2e+02 Score=23.42 Aligned_cols=73 Identities=19% Similarity=0.373 Sum_probs=51.5
Q ss_pred hhHHHHHHHHHHhcCccchHHHHHHcCCChHHHHH-HHHHHHhc-CCcceeee---CCCCeEEEcHHHHHHHHHHHHhc
Q 026130 133 RDLLADFVEYIKKHKCIPLEDLAAEFKLRTQECIN-RITSLENM-GRLSGVMD---DRGKYIYISQAEMKAVADYIKRQ 206 (243)
Q Consensus 133 ~~lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~-RIq~Le~~-g~LtGViD---DRGKFIYIS~eEl~aVA~fI~~r 206 (243)
.+-+..+++++.......+=-|+...|+|..+++. ++.++.-+ +.|+ |-. .+...|+|++.-...|..|+...
T Consensus 73 ~ee~~~l~~~~~~~~~~~~~~l~~~tG~R~~E~~~L~~~di~~~~~~~~-i~~~K~~~~~~ipl~~~~~~~l~~~~~~~ 150 (242)
T cd01193 73 PEEVRRLLGALTGLKHRLILSLLYGCGLRLSECLRLRVKDIDFDRGQIR-VRQGKGGKDRYVMLPEALLELLRAYWKRA 150 (242)
T ss_pred HHHHHHHHHhccchhHHHHHHHHHHcCCcHHHHhcCCHHHcCCCCCeEE-EEeCCCCCceEEeccHHHHHHHHHHHHHH
Confidence 34477788887765666777788899999999998 56665433 3332 221 24568899999999998888765
No 433
>PRK06582 coproporphyrinogen III oxidase; Provisional
Probab=24.35 E-value=2.1e+02 Score=27.53 Aligned_cols=49 Identities=14% Similarity=0.361 Sum_probs=37.5
Q ss_pred HHhcCccchHHHHHHcCCChHHHH--HHHHHHHhcCCcceeeeCCCCeEEEcHHHH
Q 026130 143 IKKHKCIPLEDLAAEFKLRTQECI--NRITSLENMGRLSGVMDDRGKYIYISQAEM 196 (243)
Q Consensus 143 IK~~KvV~LEdLA~~F~lrtqd~I--~RIq~Le~~g~LtGViDDRGKFIYIS~eEl 196 (243)
+..+.=|.+.++...||+...... ..|+.|...|.|.- + ..|++|+.-+
T Consensus 328 LR~~~Gl~~~~~~~~~g~~~~~~~~~~~l~~l~~~gll~~--~---~~l~lT~~G~ 378 (390)
T PRK06582 328 LRLSKGINISTLEQKLNTKLENILDMNNLKHYQALDLIRL--D---ENIYLTDKGL 378 (390)
T ss_pred HHhhCCCCHHHHHHHHCcCHHHhhhHHHHHHHHHCCCEEE--C---CEEEECcchh
Confidence 455666788889999999877754 78999999998772 3 3399998644
No 434
>COG5027 SAS2 Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=24.32 E-value=67 Score=31.73 Aligned_cols=48 Identities=21% Similarity=0.458 Sum_probs=33.3
Q ss_pred HhcCccc-hHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEE-EcHHHHH
Q 026130 144 KKHKCIP-LEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIY-ISQAEMK 197 (243)
Q Consensus 144 K~~KvV~-LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIY-IS~eEl~ 197 (243)
+-.+-.. |+|||..-||++.|||--++.|--.+. ..|+||+ |+...++
T Consensus 326 k~~~~~~~I~~Is~~TgM~~dDVI~tLe~L~il~~------~~~~yI~~l~~~~l~ 375 (395)
T COG5027 326 KMDKEITDINEISKETGMSTDDVIHTLEALNILRE------YKGQYIISLNSDKLH 375 (395)
T ss_pred hcCcccccHHHHHhhhCCchhhHHHHHHHhccchh------hCceEEEEeccchhh
Confidence 4444444 999999999999999998888744333 2677876 3443333
No 435
>PF05262 Borrelia_P83: Borrelia P83/100 protein; InterPro: IPR007926 This family consists of several Borrelia P83/P100 antigen proteins.
Probab=24.30 E-value=5e+02 Score=26.50 Aligned_cols=18 Identities=28% Similarity=0.569 Sum_probs=11.7
Q ss_pred CCCeEEEcHHHHHHHHHH
Q 026130 185 RGKYIYISQAEMKAVADY 202 (243)
Q Consensus 185 RGKFIYIS~eEl~aVA~f 202 (243)
||+=||+-+.-+-+||-+
T Consensus 397 r~r~~~~~~~~~vaI~g~ 414 (489)
T PF05262_consen 397 RGRTFYEREDDLVAIAGC 414 (489)
T ss_pred ccceeEEcCCCEEEEecc
Confidence 566677777766666644
No 436
>PF09048 Cro: Cro; InterPro: IPR000655 Bacteriophage lambda encodes two repressors: the Cro repressor that acts to turn off early gene transcription during the lytic cycle, and the lambda or cI repressor that is required to maintain lysogenic growth. Together the Cro and cI repressors form a helix-turn-helix (HTH) superfamily. The lambda Cro repressor binds to DNA as a highly flexible dimer. The crystal structure of the lambda Cro repressor [] reveals a HTH DNA-binding protein with an alpha/beta fold that differs from other Cro family members, possibly by an evolutionary fold change []. Most Cro proteins, such as Enterobacteria phage P22 Cro and Bacteriophage 434 Cro, have an all-alpha structure that is thought to be ancestral to lambda Cro, where the fourth and fifth helices are replaced by a beta-sheet, possibly as a result of secondary structure switching rather than by nonhomologous replacement []. This entry represents the lambda-type Cro repressor with an alpha/beta topology.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 5CRO_A 2ECS_A 2OVG_A 6CRO_A 1D1L_A 2ORC_A 1D1M_B 3ORC_A 1ORC_A 2A63_A ....
Probab=24.27 E-value=1.5e+02 Score=22.09 Aligned_cols=46 Identities=20% Similarity=0.190 Sum_probs=32.2
Q ss_pred HHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeE
Q 026130 135 LLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYI 189 (243)
Q Consensus 135 lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFI 189 (243)
.|.+|+.-+-+. .+|..||+ ||-+|+ +.|.+...|.=.+.+.|.|.
T Consensus 5 ~L~eyv~~~GQ~------kaA~~lGV-~Q~AIs--KAlr~gR~I~v~~~~dGs~~ 50 (59)
T PF09048_consen 5 TLAEYVKEHGQA------KAARALGV-TQSAIS--KALRAGRNIFVTIMPDGSVE 50 (59)
T ss_dssp EHHHHHHHHHHH------HHHHHHTS--HHHHH--HHHHCT-EEEEEEETTSEEE
T ss_pred eHHHHHHHhChH------HHHHHcCC-cHHHHH--HHHHcCCcEEEEEcCCCeEE
Confidence 467777766654 47999999 777876 45677777777778888764
No 437
>cd01186 INT_SG3_C INT_SG3, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 3, catalytic domain. The CD contains various predicted bacterial and phage integrase/recombinase sequences for which not much experimental characterization is available.
Probab=24.07 E-value=3.7e+02 Score=21.87 Aligned_cols=71 Identities=20% Similarity=0.371 Sum_probs=51.6
Q ss_pred hHHHHHHHHHHhc--CccchHHHHHHcCCChHHHHH-HHHHHHhcCCcceeee---CCCCeEEEcHHHHHHHHHHHHh
Q 026130 134 DLLADFVEYIKKH--KCIPLEDLAAEFKLRTQECIN-RITSLENMGRLSGVMD---DRGKYIYISQAEMKAVADYIKR 205 (243)
Q Consensus 134 ~lL~~Fi~yIK~~--KvV~LEdLA~~F~lrtqd~I~-RIq~Le~~g~LtGViD---DRGKFIYIS~eEl~aVA~fI~~ 205 (243)
.-|..|+.+|+.+ ....+=-|+...|++..|++. +..++...+.|+ |.+ .....|.|++.=+..|..|+..
T Consensus 10 ~e~~~l~~~~~~~~~~~~~~~~l~~~tGlR~~El~~l~~~di~~~~~i~-i~~~K~~~~r~vpl~~~l~~~l~~~~~~ 86 (180)
T cd01186 10 EQIKAIKDYLKNHSERNYLLFLIGINTGLRISDILALKVKDVRGDERIS-IKEKKTGKRKRIYLNPILKEELLYYIKD 86 (180)
T ss_pred HHHHHHHHHHhcCCchhHHHHHHHHHhhhHHHHHHhcCHHHhCCCCceE-EEEecCCceEEEEECHHHHHHHHHHHHh
Confidence 3477888888754 455666799999999999998 677775554331 222 1245899999999999999875
No 438
>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=23.80 E-value=1.1e+02 Score=27.27 Aligned_cols=53 Identities=25% Similarity=0.310 Sum_probs=41.7
Q ss_pred hhHHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHH-HHHhcCCcceeeeCCCCe
Q 026130 133 RDLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRIT-SLENMGRLSGVMDDRGKY 188 (243)
Q Consensus 133 ~~lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq-~Le~~g~LtGViDDRGKF 188 (243)
..+|..|+..+...- +.+.++|..+|.++..+..-+. .|...|.|. =..+|.+
T Consensus 241 ~~~L~al~~~~~~~~-~~~~~ia~~lg~~~~~~~~~~e~~Li~~~li~--~~~~g~~ 294 (305)
T TIGR00635 241 RKLLSVLIEQFQGGP-VGLKTLAAALGEDADTIEDVYEPYLLQIGFLQ--RTPRGRI 294 (305)
T ss_pred HHHHHHHHHHhCCCc-ccHHHHHHHhCCCcchHHHhhhHHHHHcCCcc--cCCchhh
Confidence 336777877776654 6699999999999999988888 699999984 4456664
No 439
>smart00437 TOP1Ac Bacterial DNA topoisomerase I DNA-binding domain. Bacterial DNA topoisomerase I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase alpha subunit
Probab=23.58 E-value=2.1e+02 Score=26.11 Aligned_cols=54 Identities=11% Similarity=0.214 Sum_probs=43.0
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhc
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQ 206 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~r 206 (243)
+..+.+..||++.+.+.+-.|.|=..|-||-==-|- =|||++....+..+|...
T Consensus 18 Lq~~a~~~~g~sa~~tl~iaQ~LYe~g~iTYPRTds---~~l~~~~~~~~~~~l~~~ 71 (259)
T smart00437 18 LQQEASRKLGFSAKKTMQIAQKLYEKGLITYPRTDS---TRLSEEAVLEARNYISKH 71 (259)
T ss_pred HHHHHHHhcCCCHHHHHHHHHHHHhCCeeEecCCCC---CcCCHHHHHHHHHHHHHh
Confidence 345678899999999999999999987666543333 379999988888888775
No 440
>smart00545 JmjN Small domain found in the jumonji family of transcription factors. To date, this domain always co-occurs with the JmjC domain (although the reverse is not true).
Probab=23.47 E-value=73 Score=21.85 Aligned_cols=20 Identities=25% Similarity=0.512 Sum_probs=15.4
Q ss_pred HHHHHHHHHhcCccchHHHHHHcCC
Q 026130 136 LADFVEYIKKHKCIPLEDLAAEFKL 160 (243)
Q Consensus 136 L~~Fi~yIK~~KvV~LEdLA~~F~l 160 (243)
.++|+.||.. ++++|..||+
T Consensus 12 F~Dp~~yi~~-----i~~~~~~yGi 31 (42)
T smart00545 12 FKDPLAYISK-----IRPQAEKYGI 31 (42)
T ss_pred HHCHHHHHHH-----HHHHHhhCCE
Confidence 4688888876 6667888886
No 441
>PF09397 Ftsk_gamma: Ftsk gamma domain; InterPro: IPR018541 This domain directs oriented DNA translocation and forms a winged helix structure []. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding []. ; PDB: 2VE9_B 2VE8_E 2J5O_A 2J5P_A.
Probab=23.40 E-value=91 Score=23.23 Aligned_cols=22 Identities=27% Similarity=0.528 Sum_probs=19.6
Q ss_pred HHHHHHHHHhcCCccHHHHHhh
Q 026130 196 MKAVADYIKRQGRVSISHLASK 217 (243)
Q Consensus 196 l~aVA~fI~~rGRVSi~eLa~~ 217 (243)
|..+..||.+.|++|++-|-+.
T Consensus 8 y~~a~~~V~~~~~~S~S~lQR~ 29 (65)
T PF09397_consen 8 YEEAVEFVIEEGKASISLLQRK 29 (65)
T ss_dssp HHHHHHHHHHCTCECHHHHHHH
T ss_pred HHHHHHHHHHcCCccHHHHHHH
Confidence 6789999999999999988765
No 442
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=23.30 E-value=74 Score=27.09 Aligned_cols=30 Identities=23% Similarity=0.255 Sum_probs=24.5
Q ss_pred HHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCC
Q 026130 153 DLAAEFKLRTQECINRITSLENMGRLSGVMDDRG 186 (243)
Q Consensus 153 dLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRG 186 (243)
=||..|||+.. +|+.|.+.|.|+|+.+-.|
T Consensus 108 lLa~~L~lSrs----~l~~l~~~G~I~~~~~~~~ 137 (142)
T PF06353_consen 108 LLARQLGLSRS----RLKRLIEQGLIRSDPDKSK 137 (142)
T ss_pred HHHHHhCcCHH----HHHHHHHCCCEEecCccch
Confidence 38889999864 6899999999999877544
No 443
>PRK06074 NADH dehydrogenase subunit C; Provisional
Probab=23.26 E-value=1.9e+02 Score=25.31 Aligned_cols=47 Identities=6% Similarity=0.109 Sum_probs=34.4
Q ss_pred CChHHHHHHHHHHHhcCCcceee-eCCCCeEEEcHHHHHHHHHHHHhcC
Q 026130 160 LRTQECINRITSLENMGRLSGVM-DDRGKYIYISQAEMKAVADYIKRQG 207 (243)
Q Consensus 160 lrtqd~I~RIq~Le~~g~LtGVi-DDRGKFIYIS~eEl~aVA~fI~~rG 207 (243)
++++++++.|+.-.. +.+..+. -.+=-+|.|+.+.+..|+.+++..|
T Consensus 2 ~~~~~~~~~l~~~f~-~~~~~~~~~~~~~~~~v~~~~l~~v~~~L~~~~ 49 (189)
T PRK06074 2 EKLEELVAKLLEKLP-DAIGKVTVAFGELTLKVPAEKILEVLTFLRDDP 49 (189)
T ss_pred CcHHHHHHHHHHHcc-ccEEEEEEeCCeEEEEEcHHHHHHHHHHHHhCc
Confidence 577888888886443 3444442 2344678999999999999999875
No 444
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=23.21 E-value=1.5e+02 Score=24.64 Aligned_cols=58 Identities=19% Similarity=0.452 Sum_probs=41.8
Q ss_pred CccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhcCCccHHHHHhhccccc
Q 026130 147 KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRVSISHLASKSNQFI 222 (243)
Q Consensus 147 KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~rGRVSi~eLa~~sN~lI 222 (243)
-++++.|+|..++=.++.+..-|. -+-|+ .|-+|+.|++|. +|+++...|...-+++|
T Consensus 33 vi~Nf~dI~~~L~R~p~~~~ky~~--~ELgt-~~~id~~~~lii---------------~G~~~~~~i~~~L~~fI 90 (125)
T PF01873_consen 33 VIVNFVDICKALNRDPEHVLKYFG--KELGT-QGSIDGKGRLII---------------NGRFSSKQIQDLLDKFI 90 (125)
T ss_dssp EETTHHHHHHHHTSSHHHHHHHHH--HHSSS-EEEEETTTEEEE---------------ESSSSCCHHHHHHHHHH
T ss_pred eeecHHHHHHHHCCCHHHHHHHHH--HHHCC-ceEECCCCEEEE---------------EEecCHHHHHHHHHHHH
Confidence 367899999999999999987763 23444 477788899996 57777666555544444
No 445
>PF02899 Phage_int_SAM_1: Phage integrase, N-terminal SAM-like domain; InterPro: IPR004107 Proteins containing this domain cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment [, ]. The phage integrase N-terminal SAM-like domain is almost always found with the signature that defines the phage integrase family (see IPR002104 from INTERPRO).; GO: 0003677 DNA binding, 0015074 DNA integration; PDB: 1Z1G_B 1Z19_A 1Z1B_A 2OXO_A 1P7D_B 3NRW_A 1A0P_A.
Probab=23.08 E-value=2.7e+02 Score=19.46 Aligned_cols=43 Identities=21% Similarity=0.366 Sum_probs=32.3
Q ss_pred ccccchhHHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcC
Q 026130 128 VQDGDRDLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMG 176 (243)
Q Consensus 128 ~~~~~~~lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g 176 (243)
+-......|..|+.|...+.+..+.+| ++.++..-|..|...|
T Consensus 18 T~~~Y~~~l~~f~~~~~~~~~~~~~~i------~~~~v~~f~~~~~~~~ 60 (84)
T PF02899_consen 18 TIRSYRRDLRRFIRWLEEHGIIDWEDI------TEEDVRDFLEYLAKEG 60 (84)
T ss_dssp HHHHHHHHHHHHHHHHHHTTS-CGGG--------HHHHHHHHHHHHCTT
T ss_pred HHHHHHHHHHHHHHhhhhhhhhhhhhh------hhHHHHHHHHHHHccC
Confidence 444566779999999998888888877 6788888888888776
No 446
>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []. This family also includes Q05166 from SWISSPROT a suppressor of thermosensitive mutations in the DNA polymerase delta gene, Pol III []. The conserved central region appears to be distantly related to the RNA-binding region RNP-1 (RNA recognition motif, IPR000504 from INTERPRO), suggesting an RNA binding function for this protein.; PDB: 1WWH_C 3P3D_A.
Probab=23.07 E-value=77 Score=25.32 Aligned_cols=52 Identities=12% Similarity=0.284 Sum_probs=40.6
Q ss_pred cCCChHHHHHHHHHHHhcCCcceee--------------eCCCCeEEEcHHHHHHHHHHHHhcCCc
Q 026130 158 FKLRTQECINRITSLENMGRLSGVM--------------DDRGKYIYISQAEMKAVADYIKRQGRV 209 (243)
Q Consensus 158 F~lrtqd~I~RIq~Le~~g~LtGVi--------------DDRGKFIYIS~eEl~aVA~fI~~rGRV 209 (243)
||.++...-.-|+.+..-|.|.=.. -..|.+|+|+=..-....+-+++.|+|
T Consensus 12 FGfp~~~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~NG~i 77 (100)
T PF05172_consen 12 FGFPPSASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQKNGTI 77 (100)
T ss_dssp E---GGGHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTTTTEE
T ss_pred EccCHHHHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHhCCeE
Confidence 7888888888899999999987664 468999999988888888889999987
No 447
>PF04282 DUF438: Family of unknown function (DUF438); InterPro: IPR007380 This is a a group of uncharacterised proteins.
Probab=22.91 E-value=2.9e+02 Score=20.99 Aligned_cols=28 Identities=14% Similarity=0.385 Sum_probs=22.0
Q ss_pred EcHHHHHHHHHHHHhcCCccHHHHHhhcc
Q 026130 191 ISQAEMKAVADYIKRQGRVSISHLASKSN 219 (243)
Q Consensus 191 IS~eEl~aVA~fI~~rGRVSi~eLa~~sN 219 (243)
||+.|+..+-+-+-+-| +++.++.+.||
T Consensus 29 Vs~~EI~~~Eq~Li~eG-~~~eeiq~LCd 56 (71)
T PF04282_consen 29 VSASEISAAEQELIQEG-MPVEEIQKLCD 56 (71)
T ss_pred CCHHHHHHHHHHHHHcC-CCHHHHHHHhH
Confidence 77888888777777777 88888887776
No 448
>PRK10296 DNA-binding transcriptional regulator ChbR; Provisional
Probab=22.91 E-value=2.8e+02 Score=24.27 Aligned_cols=75 Identities=11% Similarity=0.067 Sum_probs=44.3
Q ss_pred hHHHHHHHHHHhc---CccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhcCCcc
Q 026130 134 DLLADFVEYIKKH---KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRVS 210 (243)
Q Consensus 134 ~lL~~Fi~yIK~~---KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~rGRVS 210 (243)
..+...++||-.+ ....|.+||..||++..-+-..++..--... .=||..-=|......+ ..+..|
T Consensus 171 ~~~~~~i~~i~~~~~~~~~~l~~lA~~~~~s~~~l~r~fk~~~G~t~----------~~yi~~~Rl~~A~~lL-~~t~~s 239 (278)
T PRK10296 171 QWLKATVEKMHDKEQFSESALENMVRLSGKSQEYLTRATRRYYGKTP----------MQIINEIRINFAKKQL-EMTNYS 239 (278)
T ss_pred HHHHHHHHHHHhccccChhhHHHHHHHhCCCHHHHHHHHHHHHCcCH----------HHHHHHHHHHHHHHHH-HcCCCC
Confidence 3567888888655 2347999999999987666666655322111 0123333333333333 346678
Q ss_pred HHHHHhhcc
Q 026130 211 ISHLASKSN 219 (243)
Q Consensus 211 i~eLa~~sN 219 (243)
|+++|..|.
T Consensus 240 I~eIA~~~G 248 (278)
T PRK10296 240 VTDIAFEAG 248 (278)
T ss_pred HHHHHHHhC
Confidence 888887663
No 449
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=22.90 E-value=1.5e+02 Score=24.10 Aligned_cols=54 Identities=17% Similarity=0.348 Sum_probs=36.5
Q ss_pred ccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEE---EcHHHHHHH-HHHHH
Q 026130 148 CIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIY---ISQAEMKAV-ADYIK 204 (243)
Q Consensus 148 vV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIY---IS~eEl~aV-A~fI~ 204 (243)
++++.|+|..++=..+.+..-+ ..+=-..|-+|..|++|. +|+..++.+ -.||.
T Consensus 21 i~Nf~~I~~~L~R~p~hv~kyl---~~ELgt~g~id~~~rlii~G~~~~~~i~~~l~~yI~ 78 (110)
T smart00653 21 IVNFADIAKALNRPPDHVLKFL---LAELGTQGSIDGKGRLIVNGRFTPKKLQDLLRRYIK 78 (110)
T ss_pred EEcHHHHHHHHCCCHHHHHHHH---HHHhCCceeECCCCeEEEEEeeCHHHHHHHHHHHHH
Confidence 6789999999999999887554 444445677777788886 344444432 24443
No 450
>PF15236 CCDC66: Coiled-coil domain-containing protein 66
Probab=22.75 E-value=5.2e+02 Score=22.55 Aligned_cols=106 Identities=25% Similarity=0.327 Sum_probs=0.0
Q ss_pred CCCCcCCCCCCcccc-ccccCCCccccccCCcchhhhhhHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHhhHHHH
Q 026130 5 PAAGASTSSAGAAEV-EETIEGSDDEGVAGGHYEAKASKKKEKRRQEREAAQQADEAARESRQSKQDRYTEMRRRKDEER 83 (243)
Q Consensus 5 ~~~~~~~~~~~~~~~-~~~~~~~~~e~~~~g~~~~kk~~Kk~~kkqerk~qReaee~~REerk~~e~~~ee~rrkkeeer 83 (243)
|..++.+++++.... .++.+-+........+.-+--..---+-..+|..+|.. .-+.+.-...+-++.++++..++
T Consensus 2 ~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~s~LR~~tallDpa~~eEre~rR~k---q~E~q~ai~~QieEk~r~k~~E~ 78 (157)
T PF15236_consen 2 PTPGSQSSPSEDENLGKASRVTSMQSSSKTSFLRGMTALLDPAQIEERERRRQK---QLEHQRAIKQQIEEKRRQKQEEE 78 (157)
T ss_pred CCCccCCCCCchhhhcccccccccccccccCccccccccCCHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHH
Q ss_pred HHHH-HHHHHHHHHHHHHHHHHHHHHHhhhh
Q 026130 84 EARE-SALEEEAKAQKAREEEAAAFEFEKWK 113 (243)
Q Consensus 84 e~eE-~~~eEeer~~kee~e~rE~eEY~kwK 113 (243)
+..- ....|+.+.+++...-+..-|++..+
T Consensus 79 err~~EE~~EE~Rl~rere~~q~~~E~E~~~ 109 (157)
T PF15236_consen 79 ERRRREEEEEEERLAREREELQRQFEEEQRK 109 (157)
T ss_pred HHHHHHhHHHHHHHHHHHHHHHHHHHHHHHH
No 451
>TIGR01338 phycocy_alpha phycocyanin, alpha subunit. This model excludes the closely related phycoerythrocyanin alpha subunit.
Probab=22.69 E-value=43 Score=29.11 Aligned_cols=42 Identities=19% Similarity=0.457 Sum_probs=31.9
Q ss_pred eCCCCeEEEcHHHHHHHHHHHHhc-CCccH-HHHHhhccccccccc
Q 026130 183 DDRGKYIYISQAEMKAVADYIKRQ-GRVSI-SHLASKSNQFIDLET 226 (243)
Q Consensus 183 DDRGKFIYIS~eEl~aVA~fI~~r-GRVSi-~eLa~~sN~lI~L~p 226 (243)
|++|+| +|..||++|..|+.+- =|+.+ .-|+.+++.||+-..
T Consensus 12 D~qgRy--ls~~eL~~l~~~~~~g~~RL~aa~~Lt~na~~IV~~Aa 55 (161)
T TIGR01338 12 DSQGRF--LSNGELQSIFGRFQRATASLEAAKSLTSNAQRLISGAA 55 (161)
T ss_pred HhccCC--CCHHHHHHHHHHHHchHHHHHHHHHHHhhHHHHHHHHH
Confidence 778987 6899999999999864 56665 467777777776443
No 452
>cd04612 CBS_pair_SpoIVFB_EriC_assoc This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with either the SpoIVFB domain (sporulation protein, stage IV cell wall formation, F locus, promoter-distal B) or the chloride channel protein EriC. SpoIVFB is one of 4 proteins involved in endospore formation; the others are SpoIVFA (sporulation protein, stage IV cell wall formation, F locus, promoter-proximal A), BofA (bypass-of-forespore A ), and SpoIVB (sporulation protein, stage IV cell wall formation, B locus). SpoIVFB is negatively regulated by SpoIVFA and BofA and activated by SpoIVB. It is thought that SpoIVFB, SpoIVFA, and BofA are located in the mother-cell membrane that surrounds the forespore and that SpoIVB is secreted from the forespore into the space between the two where it activates SpoIVFB. EriC is involved in inorganic ion transport and metabolism. CBS is a small domain originally identified in cystathionine beta-synthase an
Probab=22.58 E-value=2e+02 Score=20.46 Aligned_cols=21 Identities=29% Similarity=0.566 Sum_probs=15.4
Q ss_pred CcceeeeCCCCeE-EEcHHHHHH
Q 026130 177 RLSGVMDDRGKYI-YISQAEMKA 198 (243)
Q Consensus 177 ~LtGViDDRGKFI-YIS~eEl~a 198 (243)
....|+|+ |+|+ +||..++..
T Consensus 25 ~~~~v~~~-~~~~G~v~~~dl~~ 46 (111)
T cd04612 25 RGYPVVDD-GRLVGIVTLADIRR 46 (111)
T ss_pred CcceEeeC-CeEEEEEEHHHHHH
Confidence 35567788 9988 788888754
No 453
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=22.50 E-value=2.8e+02 Score=23.24 Aligned_cols=46 Identities=13% Similarity=0.175 Sum_probs=41.3
Q ss_pred ccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcH
Q 026130 148 CIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQ 193 (243)
Q Consensus 148 vV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~ 193 (243)
.|.+.+||...|++..-+..-+..|-..|-|..+-=-.|=|.-.-|
T Consensus 25 ~~s~~~IA~~~~is~~~L~kil~~L~kaGlV~S~rG~~GGy~Lar~ 70 (150)
T COG1959 25 PVSSAEIAERQGISPSYLEKILSKLRKAGLVKSVRGKGGGYRLARP 70 (150)
T ss_pred cccHHHHHHHhCcCHHHHHHHHHHHHHcCCEEeecCCCCCccCCCC
Confidence 7889999999999999999999999999999999888777775443
No 454
>TIGR02719 repress_PhaQ poly-beta-hydroxybutyrate-responsive repressor. Members of this family are transcriptional regulatory proteins found in the vicinity of poly-beta-hydroxybutyrate (PHB) operons in several species of Bacillus. This protein appears to have repressor activity modulated by PHB itself. This protein belongs to the larger PadR family (see pfam03551).
Probab=22.40 E-value=2.5e+02 Score=23.71 Aligned_cols=48 Identities=13% Similarity=0.154 Sum_probs=36.0
Q ss_pred CCChHHHHHHHHHHHhcCCcceeeeC--CC---CeEEEcHHHHHHHHHHHHhc
Q 026130 159 KLRTQECINRITSLENMGRLSGVMDD--RG---KYIYISQAEMKAVADYIKRQ 206 (243)
Q Consensus 159 ~lrtqd~I~RIq~Le~~g~LtGViDD--RG---KFIYIS~eEl~aVA~fI~~r 206 (243)
.++.--+---|..|+.+|-|+...+. .| ||..||+.-...+..++..-
T Consensus 54 ~v~~GtLYp~L~RLE~~GlI~~~~~~~~~gp~RK~Y~LTe~Gr~~L~~~~~~w 106 (138)
T TIGR02719 54 SVDQGNVYRTLRKLEKDNLISSQWDTSAEGPAKRIYSLTDAGEQYLSMCANSF 106 (138)
T ss_pred CCCcChHHHHHHHHHHCCCEEEEeeecCCCCCcEEEEECHHHHHHHHHHHHHH
Confidence 56666777789999999999875432 22 45559999988888887643
No 455
>PF13426 PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_B 3P7N_B 1LL8_A 3MJQ_A 3BWL_A 4EET_B 4EEP_A ....
Probab=22.40 E-value=69 Score=22.22 Aligned_cols=14 Identities=29% Similarity=0.833 Sum_probs=11.6
Q ss_pred eeeCCCCeEEEcHH
Q 026130 181 VMDDRGKYIYISQA 194 (243)
Q Consensus 181 ViDDRGKFIYIS~e 194 (243)
++|..|+++|+++.
T Consensus 6 i~d~~g~i~~~N~~ 19 (104)
T PF13426_consen 6 ILDPDGRILYVNPA 19 (104)
T ss_dssp EEETTSBEEEE-HH
T ss_pred EECCcCcEEehhHH
Confidence 68999999999984
No 456
>PF01408 GFO_IDH_MocA: Oxidoreductase family, NAD-binding Rossmann fold; InterPro: IPR000683 This group of enzymes utilise NADP or NAD, and is known as the GFO/IDH/MOCA family in UniProtKB/Swiss-Prot. GFO is a glucose--fructose oxidoreductase, which converts D-glucose and D-fructose into D-gluconolactone and D-glucitol in the sorbitol-gluconate pathway. MOCA is a rhizopine catabolism protein which may catalyse the NADH-dependent dehydrogenase reaction involved in rhizopine catabolism. Other proteins belonging to this family include Gal80, a negative regulator for the expression of lactose and galactose metabolic genes; and several hypothetical proteins from yeast, Escherichia coli and Bacillus subtilis. The oxidoreductase, N-terminal domain is almost always associated with the oxidoreductase, C-terminal domain (see IPR004104 from INTERPRO).; GO: 0016491 oxidoreductase activity; PDB: 1LC0_A 1LC3_A 1GCU_A 3IP3_E 3CEA_C 3EVN_A 3NTQ_A 3NTR_B 3NT5_A 3MZ0_A ....
Probab=22.35 E-value=1.1e+02 Score=22.94 Aligned_cols=53 Identities=15% Similarity=0.285 Sum_probs=40.5
Q ss_pred HHHHcCCChHHHHHHHHHHHhcCCcceeee---------------CCCCeEEE------cHHHHHHHHHHHHhcCCc
Q 026130 154 LAAEFKLRTQECINRITSLENMGRLSGVMD---------------DRGKYIYI------SQAEMKAVADYIKRQGRV 209 (243)
Q Consensus 154 LA~~F~lrtqd~I~RIq~Le~~g~LtGViD---------------DRGKFIYI------S~eEl~aVA~fI~~rGRV 209 (243)
++..||++ +..-+.+|..+..+..|+- ++|+.||+ |.+++..+.+..++.|.+
T Consensus 42 ~~~~~~~~---~~~~~~~ll~~~~~D~V~I~tp~~~h~~~~~~~l~~g~~v~~EKP~~~~~~~~~~l~~~a~~~~~~ 115 (120)
T PF01408_consen 42 FAEKYGIP---VYTDLEELLADEDVDAVIIATPPSSHAEIAKKALEAGKHVLVEKPLALTLEEAEELVEAAKEKGVK 115 (120)
T ss_dssp HHHHTTSE---EESSHHHHHHHTTESEEEEESSGGGHHHHHHHHHHTTSEEEEESSSSSSHHHHHHHHHHHHHHTSC
T ss_pred HHHHhccc---chhHHHHHHHhhcCCEEEEecCCcchHHHHHHHHHcCCEEEEEcCCcCCHHHHHHHHHHHHHhCCE
Confidence 46677776 5555788888777777764 36888887 789999999988888865
No 457
>PF07761 DUF1617: Protein of unknown function (DUF1617); InterPro: IPR011675 This entry is represented by Bacteriophage phi3396 (Streptococcus phage phi3396), Orf51 (Orf: phi3396_51). The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry is found in a family of hypothetical bacterial and bacteriophage proteins. The region represented by this entry is approximately 150 residues long and is highly conserved throughout the family.
Probab=22.26 E-value=1.1e+02 Score=26.41 Aligned_cols=76 Identities=17% Similarity=0.177 Sum_probs=51.8
Q ss_pred ccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhcCCccH-HHHHhhcccccccc
Q 026130 148 CIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRVSI-SHLASKSNQFIDLE 225 (243)
Q Consensus 148 vV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~rGRVSi-~eLa~~sN~lI~L~ 225 (243)
+-.|++.=.+|+=.-+++|+.--.+-.+|. -|+||.|.|++=.|.-+...-.....-+---+ =++...++++++|-
T Consensus 35 i~~v~~k~~ey~kDe~dLi~~ya~kDedG~--~v~dd~gn~~L~Dp~~~~e~n~~~~eL~~e~i~I~g~eY~~~~~dl~ 111 (143)
T PF07761_consen 35 IKLVEEKIKEYAKDEYDLISQYALKDEDGK--FVIDDDGNFKLADPDKLAEFNKERDELLEEEIEIDGPEYSKHFKDLL 111 (143)
T ss_pred HHHHHHHHHHHhhhHHHHHHHHHhcCcCCC--EeecCCCceecCChhhHHHHHHHHHHHhcCceeeeccchhhhHHHHH
Confidence 345778888999999999999999999998 58899999988666655433333333322222 24555666666553
No 458
>TIGR01714 phage_rep_org_N phage replisome organizer, putative, N-terminal region. This model represents the N-terminal domain of a small family of phage proteins. The protein contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The region covered by this model is N-terminal to the low-complexity region.
Probab=22.09 E-value=1.9e+02 Score=23.95 Aligned_cols=41 Identities=22% Similarity=0.358 Sum_probs=34.1
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcH
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQ 193 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~ 193 (243)
..+.||..|+-++..|.--|+-|..-|.|.=. |.| .|||+.
T Consensus 53 ~~e~LA~~~~~~~~~V~~Al~~f~k~glIe~~--d~g-~i~i~~ 93 (119)
T TIGR01714 53 NAEMLATMFNRNVGDIRITLQTLESLGLIEKK--NNG-DIFLEN 93 (119)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe--cCC-cEEehh
Confidence 45679999999999999999999999998633 445 688876
No 459
>PF03997 VPS28: VPS28 protein; InterPro: IPR007143 The Endosomal Sorting Complex Required for Transport (ESCRT) complexes form the machinery driving protein sorting from endosomes to lysosomes. ESCRT complexes are central to receptor down-regulation, lysosome biogenesis, and budding of HIV. Yeast ESCRT-I consists of three protein subunits, VPS23, VPS28, and VPS37. In humans, ESCRT-I comprises TSG101, VPS28, and one of four potential human VPS37 homologues. The main role of ESCRT-I is to recognise ubiquitinated cargo via the UEV domain of the VPS23/TSG101 subunit. The assembly of the ESCRT-I complex is directed by the C-terminal steadiness box (SB) of VPS23, the N-terminal half of VPS28, and the C-terminal half of VPS37. The structure is primarily composed of three long, parallel helical hairpins, each corresponding to a different subunit. The additional domains and motifs extending beyond the core serve as gripping tools for ESCRT-I critical functions [, ].; PDB: 2J9W_B 2J9U_C 2G3K_A 2F66_E 2F6M_D 2J9V_A 2CAZ_E 2P22_B.
Probab=21.95 E-value=1.5e+02 Score=26.29 Aligned_cols=87 Identities=21% Similarity=0.384 Sum_probs=53.1
Q ss_pred hHHHHHHHHHHhcCc---cchHHHHHHcCCChHHHHHHHHHHHhcCCcceeee------CCCCeEEEcHHHHHHHHHHHH
Q 026130 134 DLLADFVEYIKKHKC---IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMD------DRGKYIYISQAEMKAVADYIK 204 (243)
Q Consensus 134 ~lL~~Fi~yIK~~Kv---V~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViD------DRGKFIYIS~eEl~aVA~fI~ 204 (243)
-||..|-.+++.-++ ..|++....|+|.-.-+++||+ .|.-.-|-+ +.|. .+.-=.+.+..||-
T Consensus 34 kLl~Qyk~~~~~~~~~~~~~le~F~~~y~l~cp~A~~Rl~----~G~P~Tie~~~~~~~~~~~---~ak~Vae~t~~FIT 106 (188)
T PF03997_consen 34 KLLNQYKTILKQLKDDEFPDLEEFMKKYNLDCPAALERLR----EGVPATIEHRISSSSDKGN---SAKLVAEATQNFIT 106 (188)
T ss_dssp HHHHHHHHHHTSTTHHHHHHHHHHHHHTTS-HHHHHHHHH----CTSS--------------C---HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcccccCCCHHHHHHHhcccCChHHHHHH----cCCCCchhhhcccccCCch---HHHHHHHHhChhhh
Confidence 367777777776655 6789999999999999999997 777766655 3322 23334566667772
Q ss_pred ----------hcCCcc--HHHHHhhcccccccccc
Q 026130 205 ----------RQGRVS--ISHLASKSNQFIDLETK 227 (243)
Q Consensus 205 ----------~rGRVS--i~eLa~~sN~lI~L~p~ 227 (243)
-.+-+. ++||...-|++-.+.|.
T Consensus 107 ~mDaLKLn~~a~DqLhPlL~dL~~slnr~~~~~~d 141 (188)
T PF03997_consen 107 LMDALKLNYRAKDQLHPLLSDLMQSLNRVTDLPPD 141 (188)
T ss_dssp HHHHHHTT--BHHHHHHHHHHHHHHHHHCTTS-TT
T ss_pred hhHHHhccchhHhhHhhHHHHHHHHHhccCCCCCC
Confidence 222222 46778888887665543
No 460
>CHL00086 apcA allophycocyanin alpha subunit
Probab=21.90 E-value=45 Score=28.78 Aligned_cols=39 Identities=18% Similarity=0.483 Sum_probs=29.8
Q ss_pred eCCCCeEEEcHHHHHHHHHHHHhc-CCccHH-HHHhhcccccc
Q 026130 183 DDRGKYIYISQAEMKAVADYIKRQ-GRVSIS-HLASKSNQFID 223 (243)
Q Consensus 183 DDRGKFIYIS~eEl~aVA~fI~~r-GRVSi~-eLa~~sN~lI~ 223 (243)
|..|+| +|..||+.|..|+..- =|+++. -|..+++.||+
T Consensus 12 D~~gRy--ls~~eL~~l~~~~~~~~~Rl~aa~~l~~na~~IV~ 52 (161)
T CHL00086 12 DAEARY--LSPGELDRIKSFVLSGQRRLRIAQILTDNRERIVK 52 (161)
T ss_pred HhccCC--CCHHHHHHHHHHHHhhHHHHHHHHHHHHhHHHHHH
Confidence 567886 7999999999999876 377764 46666666654
No 461
>PRK08208 coproporphyrinogen III oxidase; Validated
Probab=21.89 E-value=4e+02 Score=25.77 Aligned_cols=59 Identities=12% Similarity=0.157 Sum_probs=43.6
Q ss_pred hHHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHH
Q 026130 134 DLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEM 196 (243)
Q Consensus 134 ~lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl 196 (243)
.++..++.-+....-|.+..+...||....+....|+.|.+.|.|+ ..|.+|.+|+.=+
T Consensus 347 ~~~~~~~~~Lr~~~gl~~~~~~~~~g~~~~~~~~~l~~l~~~gll~----~~~~~l~lT~~G~ 405 (430)
T PRK08208 347 MKRRFIIKSLLQAQGLDLADYRQRFGSDPLRDFPELELLIDRGWLE----QNGGRLRLTEEGL 405 (430)
T ss_pred HHHHHHHHHHHHhCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE----EECCEEEECcchh
Confidence 3455556666777788889999999988777777889999987544 4566788888644
No 462
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=21.84 E-value=2.3e+02 Score=19.21 Aligned_cols=54 Identities=24% Similarity=0.290 Sum_probs=30.4
Q ss_pred HHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhcCCccHHHH
Q 026130 141 EYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRVSISHL 214 (243)
Q Consensus 141 ~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~rGRVSi~eL 214 (243)
.+++.+.+ ...+||..-|++.+ ++++|- . |+.=.+|.+.+.+||.|+. |++.+|
T Consensus 4 ~~m~~~~i-t~~~La~~~gis~~-tl~~~~---~-----------~~~~~~~~~~l~~ia~~l~----~~~~el 57 (63)
T PF13443_consen 4 ELMAERGI-TQKDLARKTGISRS-TLSRIL---N-----------GKPSNPSLDTLEKIAKALN----CSPEEL 57 (63)
T ss_dssp HHHHHTT---HHHHHHHHT--HH-HHHHHH---T-----------TT-----HHHHHHHHHHHT------HHHC
T ss_pred HHHHHcCC-CHHHHHHHHCcCHH-HHHHHH---h-----------cccccccHHHHHHHHHHcC----CCHHHH
Confidence 45666776 88999999999654 444442 1 3333688999999999985 455554
No 463
>PRK13501 transcriptional activator RhaR; Provisional
Probab=21.80 E-value=3e+02 Score=24.37 Aligned_cols=75 Identities=15% Similarity=0.210 Sum_probs=45.7
Q ss_pred hHHHHHHHHHHhc--CccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhcCCccH
Q 026130 134 DLLADFVEYIKKH--KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRVSI 211 (243)
Q Consensus 134 ~lL~~Fi~yIK~~--KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~rGRVSi 211 (243)
..+..+++||..+ .-..|.+||..+|++..-+-..++.- ||+.= .=||..-=|.. |..+-..+..||
T Consensus 176 ~~~~~i~~~I~~~~~e~~sl~~lA~~~~lS~~~l~r~Fk~~------~G~T~----~qyi~~~Ri~~-A~~LL~~t~~sI 244 (290)
T PRK13501 176 EQLDLIMSALQQSLGAYFDMADFCHKNQLVERSLKQLFRQQ------TGMSI----SHYLRQIRLCH-AKCLLRGSEHRI 244 (290)
T ss_pred HHHHHHHHHHHHhhccCCCHHHHHHHHCcCHHHHHHHHHHH------HCcCH----HHHHHHHHHHH-HHHHHHcCCCCH
Confidence 3567788888643 33579999999999888776666643 22100 00233333333 334445577788
Q ss_pred HHHHhhcc
Q 026130 212 SHLASKSN 219 (243)
Q Consensus 212 ~eLa~~sN 219 (243)
+++|..|.
T Consensus 245 ~eIA~~~G 252 (290)
T PRK13501 245 SDIAARCG 252 (290)
T ss_pred HHHHHHhC
Confidence 88888764
No 464
>PHA00542 putative Cro-like protein
Probab=21.78 E-value=3.2e+02 Score=20.42 Aligned_cols=56 Identities=14% Similarity=0.141 Sum_probs=40.2
Q ss_pred HHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhcCCc
Q 026130 138 DFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRV 209 (243)
Q Consensus 138 ~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~rGRV 209 (243)
.++.++..+. +...+||..+|+ ++..|.+|. +|+.-+.+.+.+.++|.++..-+--
T Consensus 22 ~l~~~l~~~g-lTq~elA~~lgI-s~~tIsr~e--------------~g~~~~p~~~~l~ki~~~~~~~~~~ 77 (82)
T PHA00542 22 ELVCALIRAG-WSQEQIADATDV-SQPTICRIY--------------SGRHKDPRYSVVEKLRHLVLNLDDF 77 (82)
T ss_pred HHHHHHHHCC-CCHHHHHHHHCc-CHHHHHHHH--------------cCCCCCCCHHHHHHHHHHHHHhchh
Confidence 4455555555 578889999999 555666664 3554468999999999999876543
No 465
>PRK07726 DNA topoisomerase III; Provisional
Probab=21.70 E-value=1.6e+02 Score=30.52 Aligned_cols=54 Identities=17% Similarity=0.266 Sum_probs=42.9
Q ss_pred HHHHHcCCChHHHHHHHHHHHhc-CCcceeeeCCCCeEEEcHHHHHHHHHHHHhcCCc
Q 026130 153 DLAAEFKLRTQECINRITSLENM-GRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRV 209 (243)
Q Consensus 153 dLA~~F~lrtqd~I~RIq~Le~~-g~LtGViDDRGKFIYIS~eEl~aVA~fI~~rGRV 209 (243)
+.+..||++.+.+.+-.|.|=.. |-||=-=-|- =|||++.+..+..+|+..+.+
T Consensus 289 ~a~~~~g~s~~~tl~iaQ~LYE~~glITYPRTds---~~ls~~~~~~~~~~l~~l~~~ 343 (658)
T PRK07726 289 DANKRFGLSAKETLDIAQSLYETHKLITYPRTDS---RYLPEDMVATLPEVLNAISKV 343 (658)
T ss_pred HHHHhcCCCHHHHHHHHHHHHHhcCEEEecCCCC---ccCCHHHHHHHHHHHHHHhcc
Confidence 46788999999999999999997 6666443332 289999999999999887643
No 466
>cd04626 CBS_pair_13 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic gener
Probab=21.63 E-value=2.5e+02 Score=20.19 Aligned_cols=21 Identities=14% Similarity=0.078 Sum_probs=15.1
Q ss_pred cceeeeCCCCeE-EEcHHHHHH
Q 026130 178 LSGVMDDRGKYI-YISQAEMKA 198 (243)
Q Consensus 178 LtGViDDRGKFI-YIS~eEl~a 198 (243)
...|.|+.|+|+ |||...+..
T Consensus 26 ~~~v~d~~~~~~G~v~~~dl~~ 47 (111)
T cd04626 26 EIIVKDNEEKLKGVVTFTDILD 47 (111)
T ss_pred eEEEEcCCCCEEEEEehHHhHH
Confidence 446678888888 788777654
No 467
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=21.59 E-value=1.1e+02 Score=22.03 Aligned_cols=23 Identities=35% Similarity=0.574 Sum_probs=16.8
Q ss_pred CccchHHHHHHcCCChHHHHHHH
Q 026130 147 KCIPLEDLAAEFKLRTQECINRI 169 (243)
Q Consensus 147 KvV~LEdLA~~F~lrtqd~I~RI 169 (243)
+-+.++||+..|.|+..++-..+
T Consensus 3 ~~lt~~~L~~~fhlp~~eAA~~L 25 (52)
T PF02042_consen 3 KSLTLEDLSQYFHLPIKEAAKEL 25 (52)
T ss_pred CccCHHHHHHHhCCCHHHHHHHh
Confidence 34667888888888888777654
No 468
>COG0329 DapA Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]
Probab=21.56 E-value=2.1e+02 Score=26.51 Aligned_cols=51 Identities=20% Similarity=0.252 Sum_probs=42.1
Q ss_pred CCChHHHHHHHHHHHhcCCcceeeeC--CCCeEEEcHHHHHHHHHHHHhc--CCcc
Q 026130 159 KLRTQECINRITSLENMGRLSGVMDD--RGKYIYISQAEMKAVADYIKRQ--GRVS 210 (243)
Q Consensus 159 ~lrtqd~I~RIq~Le~~g~LtGViDD--RGKFIYIS~eEl~aVA~fI~~r--GRVS 210 (243)
.+..+-...-|..|...| +.||+=- -|-|.++|.+|-..|..+...- |||.
T Consensus 21 ~vD~~a~~~lv~~li~~G-v~gi~~~GttGE~~~Ls~eEr~~v~~~~v~~~~grvp 75 (299)
T COG0329 21 SVDEEALRRLVEFLIAAG-VDGLVVLGTTGESPTLTLEERKEVLEAVVEAVGGRVP 75 (299)
T ss_pred CcCHHHHHHHHHHHHHcC-CCEEEECCCCccchhcCHHHHHHHHHHHHHHHCCCCc
Confidence 355666677788899999 8998874 7999999999999999988875 7864
No 469
>PRK05660 HemN family oxidoreductase; Provisional
Probab=21.50 E-value=2.4e+02 Score=26.78 Aligned_cols=50 Identities=14% Similarity=0.119 Sum_probs=37.9
Q ss_pred HHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHH
Q 026130 143 IKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEM 196 (243)
Q Consensus 143 IK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl 196 (243)
+....=|.+..+...||+...+....|+.|.+.|.|+ ..|..|.+|+.=+
T Consensus 316 Lr~~~G~~~~~~~~~~g~~~~~~~~~l~~l~~~gl~~----~~~~~~~lt~~G~ 365 (378)
T PRK05660 316 FRLLEAAPRADFEAYTGLPESVIRPQLDEALAQGYLT----ETADHWQITEHGK 365 (378)
T ss_pred chhccCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE----EeCCEEEECcchh
Confidence 3445556788888999998888888999999998755 2355788998744
No 470
>PRK04158 transcriptional repressor CodY; Validated
Probab=21.50 E-value=73 Score=29.81 Aligned_cols=43 Identities=23% Similarity=0.450 Sum_probs=34.8
Q ss_pred ccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCC-----CCeEEEcHH
Q 026130 148 CIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDR-----GKYIYISQA 194 (243)
Q Consensus 148 vV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDR-----GKFIYIS~e 194 (243)
+++-.-+|-.+|++-..+||-+..|+.. |||.-| |.||-|--+
T Consensus 201 ~lvASkiADrvgITRSVIVNALRK~ESA----GvIESrSlGMKGTyikvln~ 248 (256)
T PRK04158 201 LLVASKIADRVGITRSVIVNALRKLESA----GVIESRSLGMKGTYIKVLND 248 (256)
T ss_pred eEEeeecccccCCchhhhhhhhhhhhcc----cceeeccCCCCceeEEEecH
Confidence 3444458999999999999999999996 577765 999988543
No 471
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=21.24 E-value=2e+02 Score=27.58 Aligned_cols=59 Identities=24% Similarity=0.442 Sum_probs=52.7
Q ss_pred chhHHHHHHH-HHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEE
Q 026130 132 DRDLLADFVE-YIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIY 190 (243)
Q Consensus 132 ~~~lL~~Fi~-yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIY 190 (243)
..+.|+.+|+ |=+.+.-|--+++|...|-..--+.|-+|.|-+.|.+-||--..|=|+=
T Consensus 8 QkeIL~aLi~LY~~~~r~IKgeeIA~~l~rnpGTVRNqmq~LkaLgLVegvpGPkGGY~P 67 (294)
T COG2524 8 QKEILQALINLYRRKKRPIKGEEIAEVLNRNPGTVRNQMQSLKALGLVEGVPGPKGGYKP 67 (294)
T ss_pred HHHHHHHHHHHHHhcCCCcchHHHHHHHccCcchHHHHHHHHHhcCccccccCCCCCccc
Confidence 3456888888 6677778888999999999999999999999999999999999999974
No 472
>cd01297 D-aminoacylase D-aminoacylases (N-acyl-D-Amino acid amidohydrolases) catalyze the hydrolysis of N-acyl-D-amino acids to produce the corresponding D-amino acids, which are used as intermediates in the synthesis of pesticides, bioactive peptides, and antibiotics.
Probab=21.24 E-value=1.4e+02 Score=28.37 Aligned_cols=74 Identities=24% Similarity=0.416 Sum_probs=47.4
Q ss_pred HHHHHHHHHHhcC-ccchHHHHHHcCCC-----------hHHHHHHHHHHH----hcCCcceeeeCCCCe---EEEcHHH
Q 026130 135 LLADFVEYIKKHK-CIPLEDLAAEFKLR-----------TQECINRITSLE----NMGRLSGVMDDRGKY---IYISQAE 195 (243)
Q Consensus 135 lL~~Fi~yIK~~K-vV~LEdLA~~F~lr-----------tqd~I~RIq~Le----~~g~LtGViDDRGKF---IYIS~eE 195 (243)
.+..+.+++..+. .|.+--+.-|..|+ |...+..+..|. ..| ..|+-+. +-| .|++..+
T Consensus 123 ~~~~~~~~~~~~~~~~~~~~~~~h~~l~~~~~g~~~~~~~~~~~~~~~~l~~~al~~G-a~g~~~~-~~y~~~~~~~~~~ 200 (415)
T cd01297 123 TFAEYLDALEARPPAVNVAALVGHAALRRAVMGLDAREATEEELAKMRELLREALEAG-ALGISTG-LAYAPRLYAGTAE 200 (415)
T ss_pred CHHHHHHHHHhcCCCcCeeeccCcHHHHHHHhCcCCCCCCHHHHHHHHHHHHHHHHCC-CeEEEcc-cccCCcccCCHHH
Confidence 4566777775554 34333222444444 446688888885 445 4555543 233 4799999
Q ss_pred HHHHHHHHHhcCCcc
Q 026130 196 MKAVADYIKRQGRVS 210 (243)
Q Consensus 196 l~aVA~fI~~rGRVS 210 (243)
|..+.++++..|.+=
T Consensus 201 l~~~~~~a~~~g~~v 215 (415)
T cd01297 201 LVALARVAARYGGVY 215 (415)
T ss_pred HHHHHHHHHHcCCEE
Confidence 999999999998864
No 473
>PTZ00246 proteasome subunit alpha; Provisional
Probab=21.20 E-value=2.9e+02 Score=24.54 Aligned_cols=49 Identities=10% Similarity=0.127 Sum_probs=32.5
Q ss_pred CCChHHHHHH----HHHHHhcCCc------ceeeeCCC-----CeEEEcHHHHHHHHHHHHhcC
Q 026130 159 KLRTQECINR----ITSLENMGRL------SGVMDDRG-----KYIYISQAEMKAVADYIKRQG 207 (243)
Q Consensus 159 ~lrtqd~I~R----Iq~Le~~g~L------tGViDDRG-----KFIYIS~eEl~aVA~fI~~rG 207 (243)
+|+.+++++- |..+...+.+ .+||+..| .|..+|++|++.+-.-|...+
T Consensus 182 ~ms~eeai~l~~~al~~~~~~d~~s~~~vev~ii~~~~~~~~~~~~~l~~~ei~~~l~~~~~~~ 245 (253)
T PTZ00246 182 DLTLEQGLLLAAKVLTKSMDSTSPKADKIEVGILSHGETDGEPIQKMLSEKEIAELLKKVTQEY 245 (253)
T ss_pred CCCHHHHHHHHHHHHHHHHhccCCCCCcEEEEEEecCCcCCCCCeEECCHHHHHHHHHHHhhhh
Confidence 4566666663 4445444444 56898654 499999999998877765443
No 474
>TIGR02661 MauD methylamine dehydrogenase accessory protein MauD. This protein, MauD, appears critical to proper formation of the small subunit of methylamine dehydrogenase, which has both an unusual tryptophan tryptophylquinone cofactor and multiple disulfide bonds. MauD shares sequence similarity, including a CPxC motif, with a number of thiol:disulfide interchange proteins. In MauD mutants, the small subunit apparently does not form properly and is rapidly degraded.
Probab=21.12 E-value=3.4e+02 Score=22.95 Aligned_cols=49 Identities=18% Similarity=0.299 Sum_probs=30.1
Q ss_pred hHHHHHHcCCChHHHHHHHHHHHhcCCcceee-eCCCCeEEEc----HHHHHHHHHHHHhcCCccHHHH
Q 026130 151 LEDLAAEFKLRTQECINRITSLENMGRLSGVM-DDRGKYIYIS----QAEMKAVADYIKRQGRVSISHL 214 (243)
Q Consensus 151 LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGVi-DDRGKFIYIS----~eEl~aVA~fI~~rGRVSi~eL 214 (243)
-.+++..||+ .+.-++++ |..|+.+|.. .+.++.+...+ +.|-.|+.++
T Consensus 135 ~~~i~~~y~v--------------~~~P~~~lID~~G~I~~~g~~~~~~~le~ll~~l-~~~~~~~~~~ 188 (189)
T TIGR02661 135 SAEIGMAFQV--------------GKIPYGVLLDQDGKIRAKGLTNTREHLESLLEAD-REGFASLQQY 188 (189)
T ss_pred hhHHHHhccC--------------CccceEEEECCCCeEEEccCCCCHHHHHHHHHHH-HcCcchhhhc
Confidence 4466677765 33445555 7789988863 35666666555 4566666543
No 475
>PF10545 MADF_DNA_bdg: Alcohol dehydrogenase transcription factor Myb/SANT-like; InterPro: IPR006578 The MADF (myb/SANT-like domain in Adf-1) domain is an approximately 80-amino-acid module that directs sequence specific DNA binding to a site consisting of multiple tri-nucleotide repeats. The MADF domain is found in one or more copies in eukaryotic and viral proteins and is often associated with the BESS domain []. MADF is related to the Myb DNA-binding domain (IPR001005 from INTERPRO). The retroviral oncogene v-myb, and its cellular counterpart c-myb, are nuclear DNA-binding proteins that specifically recognise the sequence YAAC(G/T)G. It is likely that the MADF domain is more closely related to the myb/SANT domain than it is to other HTH domains. Some proteins known to contain a MADF domain are listed below: Drosophila Adf-1, a transcription factor first identified on the basis of its interaction with the alcohol dehydrogenase promoter but that binds the promoters of a diverse group of genes []. Drosophila Dorsal-interacting protein 3 (Dip3), which functions both as an activator to bind DNA in a sequence specific manner and a coactivator to stimulate synergistic activation by Dorsal and Twist []. Drosophila Stonewall (Stwl), a putative transcription factor required for maintenance of female germline stem cells as well as oocyte differentiation.
Probab=21.02 E-value=1e+02 Score=21.77 Aligned_cols=25 Identities=20% Similarity=0.523 Sum_probs=21.0
Q ss_pred chHHHHHHcC--CChHHHHHHHHHHHh
Q 026130 150 PLEDLAAEFK--LRTQECINRITSLEN 174 (243)
Q Consensus 150 ~LEdLA~~F~--lrtqd~I~RIq~Le~ 174 (243)
...+||..|| +++.+|..+++.|..
T Consensus 28 aw~~Ia~~l~~~~~~~~~~~~w~~Lr~ 54 (85)
T PF10545_consen 28 AWQEIARELGKEFSVDDCKKRWKNLRD 54 (85)
T ss_pred HHHHHHHHHccchhHHHHHHHHHHHHH
Confidence 4567899999 899999999998864
No 476
>cd01191 INT_phiCTX_C phiCTX phage and phage-related integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes various phage and bacterial integrases, including those similar to phage integrases: Bordetella and Pseudomonas phiCTX; E. coli Rac, Qin, and Shiga toxin 2 933W; and Salmonella typhimurium LT2 Gifsy-2 and Fels-1; and a putative pore-forming cytotoxin integrase from Vibrio parahaemolyticus O3:K6.
Probab=20.97 E-value=4.4e+02 Score=21.62 Aligned_cols=72 Identities=15% Similarity=0.099 Sum_probs=47.6
Q ss_pred HHHHHHHHHh-cCccchHHHHHHcCCChHHHHH-HHHHHHhcCCcceeee-------------CCCCeEEEcHHHHHHHH
Q 026130 136 LADFVEYIKK-HKCIPLEDLAAEFKLRTQECIN-RITSLENMGRLSGVMD-------------DRGKYIYISQAEMKAVA 200 (243)
Q Consensus 136 L~~Fi~yIK~-~KvV~LEdLA~~F~lrtqd~I~-RIq~Le~~g~LtGViD-------------DRGKFIYIS~eEl~aVA 200 (243)
+..|++++.. ...-.+=-|+...||+..+++. ++.++.-.+...-|.. .+...|+|++.-+..+.
T Consensus 9 ~~~ll~~~~~~~~~~~~~~l~~~tGlR~~E~~~L~~~did~~~~~~~i~~~~~~~~~~~~kt~~~~r~vpl~~~~~~~l~ 88 (196)
T cd01191 9 FAALIEAARVCQQEQNLWEFAVFTGLRPSELIALAWEDVDLERGTVYVRRALVRGIFKVPKTKAGTRDVDLNPPALAALK 88 (196)
T ss_pred HHHHHHHhhhCcchhHHHHHHHHHCCCHHHHHhCcHHhcCccCCeEEEEeeeecccccCCCcCCCeEEEeCCHHHHHHHH
Confidence 5566666653 3344556688999999999999 7777754433322221 14457999999888888
Q ss_pred HHHHhcC
Q 026130 201 DYIKRQG 207 (243)
Q Consensus 201 ~fI~~rG 207 (243)
.++...+
T Consensus 89 ~~~~~~~ 95 (196)
T cd01191 89 EQAKLTR 95 (196)
T ss_pred HHHHHhh
Confidence 7765443
No 477
>KOG0352 consensus ATP-dependent DNA helicase [Replication, recombination and repair]
Probab=20.91 E-value=1.9e+02 Score=29.80 Aligned_cols=51 Identities=29% Similarity=0.378 Sum_probs=37.8
Q ss_pred HHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHH
Q 026130 135 LLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAE 195 (243)
Q Consensus 135 lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eE 195 (243)
|+++=|++++.-|| +.+-|-+ .|+|++--.-|-+|.+..+- =||+|||||-
T Consensus 73 LIkDQiDHL~~LKV-p~~SLNS--KlSt~ER~ri~~DL~~ekp~-------~K~LYITPE~ 123 (641)
T KOG0352|consen 73 LIKDQIDHLKRLKV-PCESLNS--KLSTVERSRIMGDLAKEKPT-------IKMLYITPEG 123 (641)
T ss_pred HHHHHHHHHHhcCC-chhHhcc--hhhHHHHHHHHHHHHhcCCc-------eeEEEEchhh
Confidence 45666777777775 4555544 57899888889999988764 4899999974
No 478
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=20.90 E-value=66 Score=24.61 Aligned_cols=34 Identities=18% Similarity=0.170 Sum_probs=29.2
Q ss_pred CccchHHHHHHcCCChHHHHHHHHHHHhcCCcce
Q 026130 147 KCIPLEDLAAEFKLRTQECINRITSLENMGRLSG 180 (243)
Q Consensus 147 KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtG 180 (243)
.=....+||..+|++..-|-++|..+...|.|.-
T Consensus 31 eGlS~kEIAe~LGIS~~TVk~~l~~~~~~~~~~~ 64 (73)
T TIGR03879 31 AGKTASEIAEELGRTEQTVRNHLKGETKAGGLVK 64 (73)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhcCcccchHHH
Confidence 3357789999999999999999999999888753
No 479
>TIGR02675 tape_meas_nterm tape measure domain. Proteins containing this domain are strictly bacterial, including bacteriophage and prophage regions of bacterial genomes. Most members are 800 to 1800 amino acids long, making them among the longest predicted proteins of their respective phage genomes, where they are encoded in tail protein regions. This roughly 80-residue domain described here usually begins between residue 100 and 250. Many members are known or predicted to act as phage tail tape measure proteins, a minor tail component that regulates tail length.
Probab=20.88 E-value=1.1e+02 Score=22.79 Aligned_cols=27 Identities=22% Similarity=0.398 Sum_probs=22.5
Q ss_pred chHHHHHHcCCChHHHHHHHHHHHhcCCcce
Q 026130 150 PLEDLAAEFKLRTQECINRITSLENMGRLSG 180 (243)
Q Consensus 150 ~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtG 180 (243)
++.-||..||+++.+ +++|..+|.||.
T Consensus 46 ~~~~lAk~~G~t~~~----l~~~~~~Gkit~ 72 (75)
T TIGR02675 46 ALQALAKAMGVTRGE----LRKMLSDGKLTA 72 (75)
T ss_pred HHHHHHHHhCCCHHH----HHHHHHCCCCcc
Confidence 677899999998765 589999999983
No 480
>KOG2747 consensus Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=20.84 E-value=1.2e+02 Score=30.03 Aligned_cols=38 Identities=24% Similarity=0.514 Sum_probs=28.7
Q ss_pred HHHHHhcC--ccchHHHHHHcCCChHHHHHHHHHHHhcCC
Q 026130 140 VEYIKKHK--CIPLEDLAAEFKLRTQECINRITSLENMGR 177 (243)
Q Consensus 140 i~yIK~~K--vV~LEdLA~~F~lrtqd~I~RIq~Le~~g~ 177 (243)
+.++..++ -|.+.|||..-||++.|||..++.|---+-
T Consensus 319 l~~L~~~~~~~isI~~iS~~Tgi~~~DIisTL~~L~m~~y 358 (396)
T KOG2747|consen 319 LELLRKHRGEHISIKEISKETGIRPDDIISTLQSLNMIKY 358 (396)
T ss_pred HHHHHhcCCCcccHHHHHHhhCCCHHHHHHHHHhhCCccc
Confidence 34444433 388999999999999999999998844333
No 481
>KOG2268 consensus Serine/threonine protein kinase [Signal transduction mechanisms; General function prediction only]
Probab=20.83 E-value=1.2e+02 Score=30.45 Aligned_cols=71 Identities=15% Similarity=0.353 Sum_probs=58.4
Q ss_pred chhHHHHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcce-------eeeCCCCeEEEcH-----------
Q 026130 132 DRDLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSG-------VMDDRGKYIYISQ----------- 193 (243)
Q Consensus 132 ~~~lL~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtG-------ViDDRGKFIYIS~----------- 193 (243)
.+-.+.+||++.-..+|-.+.|...-| ++++.-|-.|-..|.|.| +++|.|+++.|.=
T Consensus 182 RH~Vvmelv~g~Pl~~v~~v~d~~~ly----~~lm~~Iv~la~~GlIHgDFNEFNimv~dd~~i~vIDFPQmvS~sh~nA 257 (465)
T KOG2268|consen 182 RHCVVMELVDGYPLRQVRHVEDPPTLY----DDLMGLIVRLANHGLIHGDFNEFNIMVKDDDKIVVIDFPQMVSTSHPNA 257 (465)
T ss_pred ceeeHHHhhcccceeeeeecCChHHHH----HHHHHHHHHHHHcCceecccchheeEEecCCCEEEeechHhhccCCCcc
Confidence 455689999999999999999988776 579999999999999999 5678999988753
Q ss_pred -----HHHHHHHHHHHhc
Q 026130 194 -----AEMKAVADYIKRQ 206 (243)
Q Consensus 194 -----eEl~aVA~fI~~r 206 (243)
-.++.|-.|.+++
T Consensus 258 ~~YFdRDv~Ci~~fFrKk 275 (465)
T KOG2268|consen 258 EYYFDRDVECIRAFFRKK 275 (465)
T ss_pred ceeecccHHHHHHHHHHh
Confidence 3456777777776
No 482
>PF01395 PBP_GOBP: PBP/GOBP family; InterPro: IPR006170 The olfactory receptors of terrestrial animals exist in an aqueous environment, yet detect odorants that are primarily hydrophobic. The aqueous solubility of hydrophobic odorants is thought to be greatly enhanced via odorant binding proteins which exist in the extracellular fluid surrounding the odorant receptors []. This family is composed of pheromone binding proteins (PBP), which are male-specific and associate with pheromone-sensitive neurons and general-odorant binding proteins (GOBP). ; GO: 0005549 odorant binding; PDB: 2KPH_A 3NHT_A 3NHI_A 3NGV_A 3K1E_B 3DZT_A 3DYE_A 3DXL_A 3DY9_A 3BJH_A ....
Probab=20.78 E-value=58 Score=24.15 Aligned_cols=36 Identities=25% Similarity=0.541 Sum_probs=26.4
Q ss_pred ceeeeCCCCeEEEcHHHHHHHHHHHHhcCC-ccHHHHHhhccc
Q 026130 179 SGVMDDRGKYIYISQAEMKAVADYIKRQGR-VSISHLASKSNQ 220 (243)
Q Consensus 179 tGViDDRGKFIYIS~eEl~aVA~fI~~rGR-VSi~eLa~~sN~ 220 (243)
.|+||+.|+| .+..+..++...+. -.+..++..|+.
T Consensus 61 ~g~~~~~g~~------~~~~~~~~~~~~~~~~~~~~~~~~C~~ 97 (121)
T PF01395_consen 61 LGLMDDDGKF------DVDKIREQLKKYTDDDEVKKIIEKCNA 97 (121)
T ss_dssp TTSBETTSEB------BHHHHHHHHHHTTHGHHHHHHHHHHHH
T ss_pred hhhhhccCcc------cHHHHHHHHhhcccHHHHHHHHHhCCC
Confidence 6899999999 45556666665554 446788888886
No 483
>PRK08898 coproporphyrinogen III oxidase; Provisional
Probab=20.70 E-value=3.2e+02 Score=26.12 Aligned_cols=50 Identities=12% Similarity=0.092 Sum_probs=35.6
Q ss_pred HHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHH
Q 026130 143 IKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEM 196 (243)
Q Consensus 143 IK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl 196 (243)
+....-|.+..+...||.....+...|+.|.+.|.|+ ..|..|.+|+.-+
T Consensus 333 LR~~~Gld~~~f~~~~g~~~~~~~~~l~~l~~~gll~----~~~~~~~LT~~G~ 382 (394)
T PRK08898 333 LRLTDGVPAHLFQERTGLPLAAIEPQLAAAEQRGLLE----RDHTRIRPTPLGQ 382 (394)
T ss_pred HHHhCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE----EECCEEEEChhHh
Confidence 3444556666777888887777777888999987655 3456788998644
No 484
>PF11462 DUF3203: Protein of unknown function (DUF3203); InterPro: IPR021564 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria. ; PDB: 1YWY_A.
Probab=20.63 E-value=81 Score=24.49 Aligned_cols=20 Identities=40% Similarity=0.650 Sum_probs=11.9
Q ss_pred eeeCCCCeEEEcHHHHHHHH
Q 026130 181 VMDDRGKYIYISQAEMKAVA 200 (243)
Q Consensus 181 ViDDRGKFIYIS~eEl~aVA 200 (243)
|+.=.|+=||||+.|-+++.
T Consensus 40 v~~l~g~Ri~ItEaEAdaLt 59 (74)
T PF11462_consen 40 VVELDGERIYITEAEADALT 59 (74)
T ss_dssp EEEETT--EE--HHHHHHHH
T ss_pred EEEEcCcEEecCHHHhhhee
Confidence 34446999999999988874
No 485
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=20.58 E-value=87 Score=28.51 Aligned_cols=27 Identities=15% Similarity=0.347 Sum_probs=23.3
Q ss_pred HHHHHHHHHHHHhcCCccHHHHHhhcc
Q 026130 193 QAEMKAVADYIKRQGRVSISHLASKSN 219 (243)
Q Consensus 193 ~eEl~aVA~fI~~rGRVSi~eLa~~sN 219 (243)
.+=+..+-++|+++|+|++.+|++..|
T Consensus 16 ~eR~~~Il~~L~~~~~vtv~eLa~~l~ 42 (269)
T PRK09802 16 SERREQIIQRLRQQGSVQVNDLSALYG 42 (269)
T ss_pred HHHHHHHHHHHHHcCCEeHHHHHHHHC
Confidence 456788999999999999999998664
No 486
>TIGR02681 phage_pRha phage regulatory protein, rha family. Members of this protein family are found in temperate phage and bacterial prophage regions. Members include the product of the rha gene of the lambdoid phage phi-80, a late operon gene. The presence of this gene interferes with infection of bacterial strains that lack integration host factor (IHF), which regulates the rha gene. It is suggested that pRha is a phage regulatory protein.
Probab=20.54 E-value=1.9e+02 Score=23.29 Aligned_cols=27 Identities=22% Similarity=0.129 Sum_probs=23.5
Q ss_pred cchHHHHHHcCCChHHHHHHHHHHHhc
Q 026130 149 IPLEDLAAEFKLRTQECINRITSLENM 175 (243)
Q Consensus 149 V~LEdLA~~F~lrtqd~I~RIq~Le~~ 175 (243)
+.--++|..||-+..+|+..|..|...
T Consensus 14 ttS~~IAe~fgK~H~~VlR~Ir~l~~~ 40 (108)
T TIGR02681 14 TDSLTMAQMFGKRHDNVIRDIKVLLIE 40 (108)
T ss_pred EeHHHHHHHHCcchHHHHHHHHHHHhh
Confidence 456689999999999999999999653
No 487
>PRK13347 coproporphyrinogen III oxidase; Provisional
Probab=20.54 E-value=2.7e+02 Score=27.16 Aligned_cols=53 Identities=17% Similarity=0.186 Sum_probs=36.8
Q ss_pred HHHHHHhcCccchHHHHHHcCCChHH---HHHHHHHHHhcCCcceeeeCCCCeEEEcHHH
Q 026130 139 FVEYIKKHKCIPLEDLAAEFKLRTQE---CINRITSLENMGRLSGVMDDRGKYIYISQAE 195 (243)
Q Consensus 139 Fi~yIK~~KvV~LEdLA~~F~lrtqd---~I~RIq~Le~~g~LtGViDDRGKFIYIS~eE 195 (243)
++.-+..+..|.+..+...||+.... ....|+.|...|.|. ..|..|.+|+.-
T Consensus 372 ~~~~L~~~~~ld~~~~~~~~g~~~~~~~~~~~~l~~l~~~gl~~----~~~~~~~lT~~G 427 (453)
T PRK13347 372 IIETLMCNFPVDLAAIAARHGFFARYFLDELARLEPLAADGLVT----IDGGGIRVTPEG 427 (453)
T ss_pred HHHHHHhhCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCEE----EECCEEEECcch
Confidence 44445556667778888889987543 356788999987644 345689999863
No 488
>KOG1463 consensus 26S proteasome regulatory complex, subunit RPN6/PSMD11 [Posttranslational modification, protein turnover, chaperones]
Probab=20.45 E-value=1.1e+02 Score=30.34 Aligned_cols=68 Identities=13% Similarity=0.248 Sum_probs=52.0
Q ss_pred HHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcH-----HHHHHHHHHHHhcCCc
Q 026130 142 YIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQ-----AEMKAVADYIKRQGRV 209 (243)
Q Consensus 142 yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~-----eEl~aVA~fI~~rGRV 209 (243)
-|.---+|-+..+|.-.||.++.|-..|-++.-+..+.|++|..+-.++|=+ .-+.+.-.-|..-|.|
T Consensus 339 iIEPyS~Vei~hIA~~IGl~~~~VEkKLsqMILDKkf~G~LDQg~g~Liv~~e~~~d~~y~~aLetI~~m~kV 411 (411)
T KOG1463|consen 339 IIEPYSRVEISHIAEVIGLDVPQVEKKLSQMILDKKFYGTLDQGEGCLIVFEEPPADNTYDAALETIQNMGKV 411 (411)
T ss_pred HcCchhhhhHHHHHHHHCCCcHHHHHHHHHHHHHHHhhcccccCCCeEEEeCCCCcchHHHHHHHHHHhccCC
Confidence 3444457889999999999999999999999999999999999777666643 2344455555554443
No 489
>smart00857 Resolvase Resolvase, N terminal domain. The N-terminal domain of the resolvase family contains the active site and the dimer interface. The extended arm at the C-terminus of this domain connects to the C-terminal helix-turn-helix domain of resolvase.
Probab=20.40 E-value=1.6e+02 Score=23.12 Aligned_cols=44 Identities=14% Similarity=0.157 Sum_probs=38.0
Q ss_pred hhHHHHHHHHHHhcC--ccchHHHHHHcCCChHHHHHHHHHHHhcCC
Q 026130 133 RDLLADFVEYIKKHK--CIPLEDLAAEFKLRTQECINRITSLENMGR 177 (243)
Q Consensus 133 ~~lL~~Fi~yIK~~K--vV~LEdLA~~F~lrtqd~I~RIq~Le~~g~ 177 (243)
..-|..++++|+..+ +|++.++.+-+- .+.+++.-|..|...|.
T Consensus 51 Rp~l~~ll~~~~~g~~~~ivv~~~~Rl~R-~~~~~~~~~~~l~~~gi 96 (148)
T smart00857 51 RPGLQRLLADLRAGDIDVLVVYKLDRLGR-SLRDLLALLELLEKKGV 96 (148)
T ss_pred CHHHHHHHHHHHcCCCCEEEEeccchhhC-cHHHHHHHHHHHHHCCC
Confidence 556899999999999 999999887665 68899999999999984
No 490
>PF00989 PAS: PAS fold; InterPro: IPR013767 PAS domains are involved in many signalling proteins where they are used as a signal sensor domain []. PAS domains appear in archaea, bacteria and eukaryotes. Several PAS-domain proteins are known to detect their signal by way of an associated cofactor. Haeme, flavin, and a 4-hydroxycinnamyl chromophore are used in different proteins. The PAS domain was named after three proteins that it occurs in: Per- period circadian protein Arnt- Ah receptor nuclear translocator protein Sim- single-minded protein. PAS domains are often associated with PAC domains IPR001610 from INTERPRO. It appears that these domains are directly linked, and that together they form the conserved 3D PAS fold. The division between the PAS and PAC domains is caused by major differences in sequences in the region connecting these two motifs []. In human PAS kinase, this region has been shown to be very flexible, and adopts different conformations depending on the bound ligand []. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels [].; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 2GJ3_A 4F3L_B 1XFN_A 1OTD_A 2PYR_A 1KOU_A 1XFQ_A 2ZOI_A 2ZOH_A 1OTA_A ....
Probab=20.15 E-value=1.1e+02 Score=21.64 Aligned_cols=20 Identities=30% Similarity=0.444 Sum_probs=15.2
Q ss_pred cCCcceeeeCCCCeEEEcHH
Q 026130 175 MGRLSGVMDDRGKYIYISQA 194 (243)
Q Consensus 175 ~g~LtGViDDRGKFIYIS~e 194 (243)
...-.=|+|..|+++|+++.
T Consensus 10 ~~~~i~~~d~~g~I~~~N~a 29 (113)
T PF00989_consen 10 SPDGIFVIDEDGRILYVNQA 29 (113)
T ss_dssp SSSEEEEEETTSBEEEECHH
T ss_pred CCceEEEEeCcCeEEEECHH
Confidence 34444568899999999975
No 491
>cd08306 Death_FADD Fas-associated Death Domain protein-protein interaction domain. Death domain (DD) found in FAS-associated via death domain (FADD). FADD is a component of the death-inducing signaling complex (DISC) and serves as an adaptor in the signaling pathway of death receptor proteins. It modulates apoptosis as well as non-apoptotic processes such as cell cycle progression, survival, innate immune signaling, and hematopoiesis. FADD contains an N-terminal DED and a C-terminal DD. Its DD interacts with the DD of the activated death receptor, FAS, and its DED recruits the initiator caspases, caspase-8 and -10, to the DISC complex via a homotypic interaction with the N-terminal DED of the caspase. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain),
Probab=20.04 E-value=1.2e+02 Score=23.07 Aligned_cols=69 Identities=12% Similarity=0.147 Sum_probs=44.7
Q ss_pred HHHHHHHHhcCccchHHHHHHcCCChHHHHHHHHHHHhcCCcceeeeCCCCeEEEcHHHHHHHHHHHHhcCC-ccHHHHH
Q 026130 137 ADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGR-VSISHLA 215 (243)
Q Consensus 137 ~~Fi~yIK~~KvV~LEdLA~~F~lrtqd~I~RIq~Le~~g~LtGViDDRGKFIYIS~eEl~aVA~fI~~rGR-VSi~eLa 215 (243)
..++++|..+=-----.||.++|++.. -|+.|.. |-++ .+.+.=+.-+-.|..+.|. -++..|.
T Consensus 2 ~~~f~~i~~~lG~~Wk~laR~LGlse~-~Id~i~~-----------~~~~---~~~eq~~~mL~~W~~~~g~~At~~~L~ 66 (86)
T cd08306 2 NAAFDVICENVGRDWRKLARKLGLSET-KIESIEE-----------AHPR---NLREQVRQSLREWKKIKKKEAKVADLI 66 (86)
T ss_pred hHHHHHHHHHHhhhHHHHHHHcCCCHH-HHHHHHH-----------HCCC---CHHHHHHHHHHHHHHhHCcchHHHHHH
Confidence 466777777766677889999999554 4666654 2222 1445566777778888873 3345666
Q ss_pred hhccc
Q 026130 216 SKSNQ 220 (243)
Q Consensus 216 ~~sN~ 220 (243)
++.+.
T Consensus 67 ~aL~~ 71 (86)
T cd08306 67 KALRD 71 (86)
T ss_pred HHHHH
Confidence 65554
Done!