Query 025511
Match_columns 251
No_of_seqs 105 out of 121
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 06:35:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025511.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025511hhsearch_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 1E-63 2.2E-68 451.2 18.5 176 60-237 118-295 (299)
2 PF09756 DDRGK: DDRGK domain; 100.0 5.8E-64 1.3E-68 434.6 6.3 170 61-231 19-188 (188)
3 smart00088 PINT motif in prote 97.2 0.0017 3.8E-08 48.1 7.2 61 143-203 11-71 (88)
4 smart00753 PAM PCI/PINT associ 97.2 0.0017 3.8E-08 48.1 7.2 61 143-203 11-71 (88)
5 smart00418 HTH_ARSR helix_turn 97.1 0.0035 7.6E-08 41.7 7.5 61 148-209 3-63 (66)
6 PF09012 FeoC: FeoC like trans 96.8 0.002 4.3E-08 47.1 4.3 49 144-192 2-50 (69)
7 PF01399 PCI: PCI domain; Int 96.6 0.012 2.6E-07 43.5 7.1 57 144-200 48-104 (105)
8 PF08220 HTH_DeoR: DeoR-like h 95.9 0.022 4.7E-07 40.6 5.3 53 145-200 3-55 (57)
9 cd00090 HTH_ARSR Arsenical Res 95.7 0.1 2.3E-06 35.2 8.0 56 145-201 10-65 (78)
10 smart00344 HTH_ASNC helix_turn 95.7 0.063 1.4E-06 41.0 7.4 74 145-218 6-91 (108)
11 PRK14165 winged helix-turn-hel 95.6 0.041 8.8E-07 49.5 7.0 58 153-210 18-75 (217)
12 TIGR02337 HpaR homoprotocatech 95.6 0.063 1.4E-06 42.0 7.3 66 146-211 32-100 (118)
13 PF13463 HTH_27: Winged helix 95.5 0.047 1E-06 38.2 5.7 56 147-202 8-67 (68)
14 PRK06266 transcription initiat 95.4 0.096 2.1E-06 45.5 8.5 68 145-212 25-98 (178)
15 smart00347 HTH_MARR helix_turn 95.4 0.12 2.6E-06 37.6 7.6 70 145-214 13-85 (101)
16 PRK03902 manganese transport t 95.3 0.15 3.2E-06 41.5 8.8 70 141-214 7-76 (142)
17 PRK11169 leucine-responsive tr 95.2 0.11 2.5E-06 43.5 7.9 74 145-218 17-104 (164)
18 PF09743 DUF2042: Uncharacteri 94.6 0.15 3.3E-06 47.1 7.8 62 165-227 18-81 (272)
19 cd07377 WHTH_GntR Winged helix 94.4 0.26 5.6E-06 33.6 6.9 42 156-200 25-66 (66)
20 PF06936 Selenoprotein_S: Sele 94.4 0.23 4.9E-06 44.2 8.1 19 34-52 35-53 (190)
21 PRK11179 DNA-binding transcrip 93.9 0.28 6E-06 40.6 7.3 85 145-229 12-109 (153)
22 smart00420 HTH_DEOR helix_turn 93.9 0.2 4.4E-06 32.7 5.2 42 146-187 4-45 (53)
23 TIGR01884 cas_HTH CRISPR locus 93.7 0.2 4.3E-06 43.2 6.3 57 145-202 146-202 (203)
24 COG1522 Lrp Transcriptional re 93.5 0.18 3.9E-06 40.5 5.3 69 146-214 12-93 (154)
25 KOG1144 Translation initiation 93.2 0.69 1.5E-05 49.5 10.3 28 175-202 296-327 (1064)
26 smart00345 HTH_GNTR helix_turn 93.2 0.17 3.8E-06 33.8 4.2 31 158-188 22-52 (60)
27 PF08279 HTH_11: HTH domain; 93.0 0.47 1E-05 32.4 6.1 49 145-195 3-52 (55)
28 PF13412 HTH_24: Winged helix- 93.0 0.33 7.1E-06 32.6 5.2 42 145-186 6-47 (48)
29 COG1349 GlpR Transcriptional r 92.9 0.25 5.4E-06 44.4 5.9 47 143-189 6-52 (253)
30 TIGR01889 Staph_reg_Sar staphy 92.8 0.78 1.7E-05 35.9 7.8 67 147-213 30-103 (109)
31 KOG3654 Uncharacterized CH dom 92.5 0.21 4.6E-06 51.0 5.3 81 45-130 374-463 (708)
32 PLN03083 E3 UFM1-protein ligas 92.0 0.4 8.6E-06 50.7 6.8 62 165-227 21-85 (803)
33 PF13518 HTH_28: Helix-turn-he 91.8 0.4 8.7E-06 31.9 4.5 46 147-195 5-50 (52)
34 PRK11512 DNA-binding transcrip 91.7 1.1 2.4E-05 36.3 7.8 64 147-210 45-111 (144)
35 PRK10434 srlR DNA-bindng trans 91.6 0.4 8.8E-06 43.0 5.7 46 142-187 5-50 (256)
36 smart00346 HTH_ICLR helix_turn 91.1 2 4.4E-05 31.5 8.1 67 145-213 8-75 (91)
37 PF03297 Ribosomal_S25: S25 ri 91.1 0.86 1.9E-05 37.2 6.5 60 141-200 44-103 (105)
38 PRK03573 transcriptional regul 90.8 1.7 3.6E-05 34.9 7.9 65 147-211 36-104 (144)
39 PTZ00266 NIMA-related protein 90.5 1.2 2.7E-05 48.2 8.9 11 52-62 424-434 (1021)
40 PF13551 HTH_29: Winged helix- 90.2 0.84 1.8E-05 34.3 5.4 76 158-234 14-99 (112)
41 PF04703 FaeA: FaeA-like prote 90.2 0.86 1.9E-05 33.9 5.3 51 146-196 4-55 (62)
42 PRK09954 putative kinase; Prov 89.6 1.4 3E-05 40.5 7.4 43 145-187 6-48 (362)
43 PF01978 TrmB: Sugar-specific 89.6 2 4.3E-05 30.7 6.7 57 146-202 12-68 (68)
44 PF01726 LexA_DNA_bind: LexA D 89.4 1.1 2.4E-05 33.1 5.4 46 142-187 10-57 (65)
45 PRK13509 transcriptional repre 89.4 0.97 2.1E-05 40.5 6.1 47 142-188 5-51 (251)
46 KOG1029 Endocytic adaptor prot 89.3 2 4.3E-05 46.2 9.0 37 201-238 471-511 (1118)
47 TIGR00122 birA_repr_reg BirA b 89.1 1.7 3.6E-05 31.3 6.0 42 147-189 5-46 (69)
48 TIGR02702 SufR_cyano iron-sulf 88.9 1.4 3.1E-05 38.0 6.5 59 145-203 4-67 (203)
49 cd04761 HTH_MerR-SF Helix-Turn 88.7 1.3 2.8E-05 29.1 4.9 46 158-208 2-47 (49)
50 TIGR02944 suf_reg_Xantho FeS a 88.2 1 2.2E-05 35.9 4.8 65 148-212 15-81 (130)
51 PF12840 HTH_20: Helix-turn-he 87.9 2.4 5.2E-05 29.9 6.1 47 145-191 13-59 (61)
52 PRK09334 30S ribosomal protein 87.8 2.1 4.5E-05 34.0 6.3 59 141-199 26-84 (86)
53 PRK09802 DNA-binding transcrip 87.6 1.3 2.8E-05 40.3 5.7 47 141-187 16-62 (269)
54 PRK15431 ferrous iron transpor 87.3 2.1 4.6E-05 33.5 6.0 48 143-190 3-50 (78)
55 PF13404 HTH_AsnC-type: AsnC-t 87.2 1.5 3.3E-05 29.9 4.5 36 146-181 7-42 (42)
56 PRK10870 transcriptional repre 86.9 2.4 5.2E-05 36.1 6.6 59 154-212 69-130 (176)
57 TIGR01764 excise DNA binding d 86.8 3.6 7.9E-05 26.4 6.1 45 157-207 2-46 (49)
58 PRK10906 DNA-binding transcrip 86.8 1.8 3.8E-05 39.1 6.0 47 142-188 5-51 (252)
59 PTZ00266 NIMA-related protein 86.8 3 6.5E-05 45.4 8.7 10 61-70 430-439 (1021)
60 PRK13777 transcriptional regul 86.8 3.8 8.3E-05 36.0 7.9 68 146-213 49-119 (185)
61 smart00419 HTH_CRP helix_turn_ 86.7 1.6 3.5E-05 28.2 4.4 31 157-187 9-39 (48)
62 PRK00441 argR arginine repress 85.9 2.2 4.8E-05 36.2 5.8 56 143-203 5-66 (149)
63 PRK10411 DNA-binding transcrip 85.2 3.1 6.8E-05 37.2 6.8 55 143-200 5-59 (240)
64 smart00550 Zalpha Z-DNA-bindin 85.2 3.4 7.3E-05 30.3 5.8 45 145-189 9-55 (68)
65 PRK10681 DNA-binding transcrip 85.2 1.5 3.2E-05 39.3 4.7 47 142-188 7-53 (252)
66 PF08784 RPA_C: Replication pr 85.2 1.9 4.2E-05 33.2 4.8 52 141-192 46-101 (102)
67 PRK04424 fatty acid biosynthes 85.1 1.4 3.1E-05 38.0 4.4 63 142-204 7-97 (185)
68 cd00092 HTH_CRP helix_turn_hel 85.0 2 4.3E-05 29.6 4.4 43 155-200 24-66 (67)
69 PF09012 FeoC: FeoC like trans 84.9 0.68 1.5E-05 33.7 2.0 24 204-227 2-25 (69)
70 COG1339 Transcriptional regula 84.3 2.5 5.4E-05 38.7 5.7 53 157-209 20-72 (214)
71 PRK04172 pheS phenylalanyl-tRN 84.1 7.4 0.00016 38.3 9.4 78 147-225 11-97 (489)
72 PF14947 HTH_45: Winged helix- 84.1 7.5 0.00016 29.0 7.4 64 142-210 6-69 (77)
73 smart00342 HTH_ARAC helix_turn 83.9 2.6 5.7E-05 29.1 4.6 60 157-227 2-61 (84)
74 cd04764 HTH_MlrA-like_sg1 Heli 83.8 6.4 0.00014 27.9 6.7 64 158-227 2-67 (67)
75 PF09743 DUF2042: Uncharacteri 83.5 4.2 9.1E-05 37.7 7.0 81 143-227 56-141 (272)
76 smart00422 HTH_MERR helix_turn 83.3 5.5 0.00012 27.9 6.1 64 158-225 2-66 (70)
77 PRK00215 LexA repressor; Valid 83.1 3.7 8.1E-05 35.0 6.1 48 154-202 21-69 (205)
78 PF13545 HTH_Crp_2: Crp-like h 82.6 4 8.8E-05 29.0 5.3 47 157-206 29-75 (76)
79 PF12419 DUF3670: SNF2 Helicas 82.4 2.3 5.1E-05 35.3 4.5 47 177-225 89-138 (141)
80 smart00529 HTH_DTXR Helix-turn 82.1 5.2 0.00011 29.7 5.9 49 159-210 2-50 (96)
81 TIGR00373 conserved hypothetic 82.0 7.6 0.00017 33.1 7.5 68 147-214 19-89 (158)
82 PRK11886 bifunctional biotin-- 81.6 5.1 0.00011 36.7 6.8 51 144-194 6-56 (319)
83 cd01106 HTH_TipAL-Mta Helix-Tu 81.4 8.2 0.00018 29.9 7.0 63 159-226 3-67 (103)
84 PRK11050 manganese transport r 81.3 13 0.00027 31.1 8.5 64 146-213 41-104 (152)
85 PF12802 MarR_2: MarR family; 81.3 7.7 0.00017 26.5 6.1 46 147-192 10-57 (62)
86 TIGR00498 lexA SOS regulatory 81.2 6 0.00013 33.6 6.6 57 144-201 12-70 (199)
87 PF01710 HTH_Tnp_IS630: Transp 80.4 11 0.00023 30.3 7.5 78 140-226 4-81 (119)
88 COG1846 MarR Transcriptional r 80.3 4.9 0.00011 29.7 5.2 53 160-212 40-95 (126)
89 PF03444 HrcA_DNA-bdg: Winged 80.2 5.3 0.00012 31.3 5.5 57 141-197 7-64 (78)
90 KOG2412 Nuclear-export-signal 79.7 6.6 0.00014 40.5 7.4 34 204-237 409-446 (591)
91 COG3140 Uncharacterized protei 79.6 3.2 6.9E-05 31.2 3.8 32 170-214 13-44 (60)
92 PTZ00121 MAEBL; Provisional 79.5 6.6 0.00014 44.9 7.8 11 168-178 1371-1381(2084)
93 COG0711 AtpF F0F1-type ATP syn 79.5 38 0.00082 28.8 11.2 24 38-62 16-39 (161)
94 TIGR03338 phnR_burk phosphonat 79.5 6 0.00013 33.4 6.1 50 157-207 35-85 (212)
95 PF12728 HTH_17: Helix-turn-he 79.2 9.5 0.00021 25.7 5.9 45 157-207 2-46 (51)
96 KOG1144 Translation initiation 78.7 9.3 0.0002 41.4 8.3 15 56-70 218-232 (1064)
97 PRK03341 arginine repressor; P 78.6 4.5 9.8E-05 35.2 5.2 58 142-204 15-79 (168)
98 CHL00118 atpG ATP synthase CF0 78.5 38 0.00083 28.3 11.2 15 38-52 32-46 (156)
99 PF01325 Fe_dep_repress: Iron 78.2 7.8 0.00017 28.0 5.5 36 152-187 18-53 (60)
100 PRK14474 F0F1 ATP synthase sub 78.0 40 0.00086 30.7 11.2 18 38-55 15-32 (250)
101 PF13601 HTH_34: Winged helix 77.0 27 0.00058 26.5 8.4 67 147-213 5-75 (80)
102 KOG0163 Myosin class VI heavy 76.9 7.8 0.00017 42.0 7.1 13 107-119 967-979 (1259)
103 PF05158 RNA_pol_Rpc34: RNA po 76.7 15 0.00032 34.9 8.4 82 143-227 14-111 (327)
104 PRK15002 redox-sensitivie tran 76.7 13 0.00028 31.8 7.3 69 153-227 8-78 (154)
105 cd04782 HTH_BltR Helix-Turn-He 76.6 9.9 0.00022 29.4 6.1 64 158-226 2-67 (97)
106 cd04783 HTH_MerR1 Helix-Turn-H 76.5 11 0.00024 30.3 6.5 65 158-227 2-68 (126)
107 PF01022 HTH_5: Bacterial regu 76.4 6.6 0.00014 26.5 4.5 41 146-187 6-46 (47)
108 cd04768 HTH_BmrR-like Helix-Tu 76.1 13 0.00027 28.8 6.5 65 158-227 2-68 (96)
109 cd04773 HTH_TioE_rpt2 Second H 76.0 11 0.00024 29.7 6.3 67 158-228 2-69 (108)
110 KOG3634 Troponin [Cytoskeleton 75.8 14 0.00031 36.1 8.1 40 143-183 212-252 (361)
111 PF13411 MerR_1: MerR HTH fami 75.7 20 0.00043 25.1 6.9 64 159-227 3-67 (69)
112 TIGR02787 codY_Gpos GTP-sensin 75.4 7.7 0.00017 36.3 6.0 56 144-199 185-242 (251)
113 PRK11414 colanic acid/biofilm 75.3 15 0.00033 31.4 7.4 63 144-207 17-85 (221)
114 PF00392 GntR: Bacterial regul 74.4 14 0.0003 26.1 5.9 52 145-197 7-64 (64)
115 PHA02943 hypothetical protein; 73.7 33 0.00071 30.5 9.1 70 141-213 10-82 (165)
116 PF14493 HTH_40: Helix-turn-he 73.3 14 0.00029 28.2 6.0 71 155-231 12-82 (91)
117 PRK10141 DNA-binding transcrip 73.2 31 0.00067 28.4 8.4 68 146-213 20-87 (117)
118 cd01105 HTH_GlnR-like Helix-Tu 73.1 12 0.00027 28.5 5.7 70 157-230 2-72 (88)
119 PRK09391 fixK transcriptional 73.1 11 0.00023 32.7 6.0 50 157-208 180-229 (230)
120 PF01402 RHH_1: Ribbon-helix-h 72.9 7.2 0.00016 25.0 3.8 28 197-225 4-31 (39)
121 PRK10512 selenocysteinyl-tRNA- 72.9 26 0.00056 35.9 9.5 78 144-226 495-576 (614)
122 PRK10402 DNA-binding transcrip 72.4 19 0.00041 30.9 7.4 50 158-211 171-221 (226)
123 KOG1029 Endocytic adaptor prot 72.3 15 0.00033 39.8 7.9 12 145-156 429-440 (1118)
124 KOG3054 Uncharacterized conser 71.7 15 0.00032 35.0 7.0 22 204-225 202-223 (299)
125 PF06969 HemN_C: HemN C-termin 71.5 6.3 0.00014 27.8 3.6 53 146-202 10-63 (66)
126 PRK12423 LexA repressor; Provi 71.2 11 0.00024 32.6 5.7 47 141-187 9-57 (202)
127 PRK06231 F0F1 ATP synthase sub 70.8 76 0.0016 28.1 11.2 14 39-52 59-72 (205)
128 PF01047 MarR: MarR family; I 70.7 17 0.00036 24.8 5.4 46 147-192 8-53 (59)
129 PRK11534 DNA-binding transcrip 70.6 13 0.00028 31.9 5.9 50 155-206 30-80 (224)
130 PF13730 HTH_36: Helix-turn-he 70.3 7 0.00015 26.6 3.5 29 158-186 27-55 (55)
131 TIGR02051 MerR Hg(II)-responsi 70.3 19 0.00042 29.0 6.6 63 159-227 2-67 (124)
132 PRK14473 F0F1 ATP synthase sub 69.7 65 0.0014 26.9 11.2 18 38-55 18-35 (164)
133 cd04762 HTH_MerR-trunc Helix-T 69.5 16 0.00036 23.0 4.9 45 158-207 2-46 (49)
134 PF06163 DUF977: Bacterial pro 69.5 10 0.00022 32.3 4.9 80 137-223 7-87 (127)
135 COG4901 Ribosomal protein S25 69.2 15 0.00032 30.6 5.7 61 140-200 43-103 (107)
136 PRK05114 hypothetical protein; 69.1 3.4 7.4E-05 31.1 1.8 32 170-214 13-44 (59)
137 cd00131 PAX Paired Box domain 69.1 21 0.00045 29.3 6.6 94 130-225 9-102 (128)
138 KOG2235 Uncharacterized conser 69.1 8 0.00017 40.8 5.0 60 167-227 23-84 (776)
139 cd04788 HTH_NolA-AlbR Helix-Tu 68.5 26 0.00057 27.0 6.7 65 158-227 2-68 (96)
140 cd04789 HTH_Cfa Helix-Turn-Hel 67.9 27 0.0006 27.3 6.8 64 158-227 3-68 (102)
141 PRK13918 CRP/FNR family transc 67.6 19 0.00041 29.7 6.1 48 157-208 150-198 (202)
142 smart00351 PAX Paired Box doma 67.6 65 0.0014 26.1 9.5 84 139-225 18-102 (125)
143 PF15236 CCDC66: Coiled-coil d 67.6 37 0.0008 29.8 8.1 14 49-62 32-45 (157)
144 PF13994 PgaD: PgaD-like prote 67.6 7.8 0.00017 32.1 3.8 37 157-197 101-137 (138)
145 PF06936 Selenoprotein_S: Sele 66.7 20 0.00044 32.0 6.5 46 77-122 82-127 (190)
146 COG2378 Predicted transcriptio 66.6 31 0.00068 32.2 8.0 70 142-213 8-90 (311)
147 PRK14471 F0F1 ATP synthase sub 66.5 76 0.0016 26.5 10.5 15 39-53 19-33 (164)
148 TIGR02812 fadR_gamma fatty aci 66.1 12 0.00025 32.3 4.8 39 158-197 32-70 (235)
149 COG1802 GntR Transcriptional r 65.9 13 0.00029 32.1 5.1 51 156-207 39-90 (230)
150 PLN02853 Probable phenylalanyl 65.3 45 0.00098 33.9 9.3 78 146-224 7-94 (492)
151 PF03701 UPF0181: Uncharacteri 65.2 4.6 9.9E-05 29.7 1.7 32 170-214 13-44 (51)
152 PF02002 TFIIE_alpha: TFIIE al 65.1 19 0.00041 27.9 5.4 63 147-209 18-86 (105)
153 PRK10219 DNA-binding transcrip 64.9 31 0.00067 26.3 6.5 75 141-226 4-80 (107)
154 TIGR01529 argR_whole arginine 64.7 28 0.0006 29.4 6.6 53 149-204 9-65 (146)
155 PF01710 HTH_Tnp_IS630: Transp 64.7 13 0.00028 29.9 4.4 37 144-180 59-95 (119)
156 COG1497 Predicted transcriptio 64.6 22 0.00047 33.6 6.5 66 153-229 22-87 (260)
157 PF09397 Ftsk_gamma: Ftsk gamm 64.6 24 0.00052 26.5 5.6 52 139-190 3-54 (65)
158 TIGR03697 NtcA_cyano global ni 64.6 21 0.00046 29.0 5.8 46 157-206 144-190 (193)
159 PRK04984 fatty acid metabolism 63.6 11 0.00025 32.4 4.3 52 145-197 14-71 (239)
160 PRK07353 F0F1 ATP synthase sub 63.4 77 0.0017 25.5 10.9 15 38-52 15-29 (140)
161 PF00325 Crp: Bacterial regula 63.3 12 0.00026 24.7 3.3 29 158-186 4-32 (32)
162 TIGR02209 ftsL_broad cell divi 63.3 58 0.0013 24.0 8.0 20 33-52 3-22 (85)
163 PRK14584 hmsS hemin storage sy 63.3 14 0.00031 32.2 4.8 45 153-201 95-139 (153)
164 TIGR03321 alt_F1F0_F0_B altern 63.2 1.1E+02 0.0025 27.4 10.9 16 38-53 15-30 (246)
165 TIGR02297 HpaA 4-hydroxyphenyl 63.2 51 0.0011 28.8 8.2 75 142-227 186-262 (287)
166 PRK13453 F0F1 ATP synthase sub 62.4 98 0.0021 26.3 11.2 13 40-52 30-42 (173)
167 PRK10079 phosphonate metabolis 62.3 11 0.00025 32.8 4.1 63 155-218 34-101 (241)
168 PRK13428 F0F1 ATP synthase sub 62.1 1.1E+02 0.0024 30.2 11.1 17 38-54 11-27 (445)
169 KOG2002 TPR-containing nuclear 62.1 34 0.00073 37.7 8.1 19 14-32 753-771 (1018)
170 TIGR00475 selB selenocysteine- 61.7 37 0.0008 34.4 8.0 74 143-225 476-549 (581)
171 PF08220 HTH_DeoR: DeoR-like h 61.3 8.9 0.00019 27.2 2.7 23 205-227 3-25 (57)
172 PRK10421 DNA-binding transcrip 61.3 15 0.00032 32.2 4.6 42 156-198 26-67 (253)
173 PLN00104 MYST -like histone ac 60.7 31 0.00067 34.8 7.2 57 148-210 365-423 (450)
174 COG1725 Predicted transcriptio 60.7 48 0.001 27.9 7.3 47 153-202 32-78 (125)
175 cd01107 HTH_BmrR Helix-Turn-He 60.7 29 0.00064 27.2 5.8 67 158-228 2-70 (108)
176 PRK11511 DNA-binding transcrip 60.6 78 0.0017 25.4 8.3 70 141-227 8-85 (127)
177 PRK14472 F0F1 ATP synthase sub 60.4 1.1E+02 0.0023 26.0 11.1 11 141-151 160-170 (175)
178 COG3355 Predicted transcriptio 60.2 73 0.0016 27.0 8.3 63 145-207 31-99 (126)
179 PRK11402 DNA-binding transcrip 59.9 14 0.00031 32.1 4.2 43 154-197 31-73 (241)
180 PRK14999 histidine utilization 59.7 29 0.00063 30.3 6.1 70 145-217 19-101 (241)
181 TIGR02844 spore_III_D sporulat 59.7 25 0.00053 27.4 5.0 55 142-212 6-60 (80)
182 TIGR00738 rrf2_super rrf2 fami 59.4 18 0.00038 28.5 4.3 47 154-200 23-69 (132)
183 PF06224 HTH_42: Winged helix 59.1 25 0.00054 31.8 5.8 65 140-204 164-230 (327)
184 KOG2002 TPR-containing nuclear 59.1 63 0.0014 35.7 9.5 6 100-105 861-866 (1018)
185 PF09339 HTH_IclR: IclR helix- 59.1 18 0.00039 24.7 3.8 42 146-187 7-49 (52)
186 KOG3634 Troponin [Cytoskeleton 58.9 36 0.00079 33.4 7.1 21 58-78 91-111 (361)
187 PF07160 DUF1395: Protein of u 58.8 3.2 6.8E-05 37.9 0.0 31 197-229 130-160 (243)
188 cd04777 HTH_MerR-like_sg1 Heli 58.8 46 0.001 25.9 6.5 62 158-226 2-65 (107)
189 COG1422 Predicted membrane pro 58.7 73 0.0016 29.1 8.6 22 39-60 50-71 (201)
190 PRK08475 F0F1 ATP synthase sub 58.7 1.2E+02 0.0025 25.9 11.2 15 39-53 33-47 (167)
191 PRK09990 DNA-binding transcrip 58.6 16 0.00034 31.9 4.3 40 158-198 33-72 (251)
192 PRK09392 ftrB transcriptional 58.2 19 0.0004 30.7 4.6 45 160-209 177-222 (236)
193 PF09202 Rio2_N: Rio2, N-termi 58.2 32 0.00068 26.7 5.4 57 149-208 17-75 (82)
194 KOG4661 Hsp27-ERE-TATA-binding 58.2 55 0.0012 34.8 8.6 12 156-167 737-748 (940)
195 cd01104 HTH_MlrA-CarA Helix-Tu 58.0 46 0.001 23.2 5.9 63 158-224 2-65 (68)
196 cd04770 HTH_HMRTR Helix-Turn-H 57.8 37 0.0008 26.9 5.9 66 158-228 2-69 (123)
197 PRK14585 pgaD putative PGA bio 57.6 13 0.00029 32.0 3.5 45 155-203 88-132 (137)
198 TIGR03337 phnR transcriptional 57.6 34 0.00073 29.2 6.1 52 145-197 8-65 (231)
199 PF08280 HTH_Mga: M protein tr 57.6 33 0.00071 24.4 5.1 37 146-182 9-45 (59)
200 cd04784 HTH_CadR-PbrR Helix-Tu 57.4 47 0.001 26.6 6.5 65 158-227 2-68 (127)
201 TIGR02018 his_ut_repres histid 57.3 25 0.00054 30.4 5.3 61 155-218 24-91 (230)
202 KOG2908 26S proteasome regulat 57.3 20 0.00044 35.4 5.1 48 153-200 291-338 (380)
203 PRK11523 DNA-binding transcrip 57.3 20 0.00043 31.5 4.7 53 144-197 14-72 (253)
204 cd07977 TFIIE_beta_winged_heli 57.2 19 0.00041 27.5 4.0 57 142-201 9-71 (75)
205 PF02082 Rrf2: Transcriptional 56.9 35 0.00076 25.4 5.3 50 147-196 13-65 (83)
206 PF11972 HTH_13: HTH DNA bindi 56.9 21 0.00046 26.3 4.0 48 144-196 1-48 (54)
207 KOG2412 Nuclear-export-signal 56.7 63 0.0014 33.7 8.7 6 145-150 304-309 (591)
208 PLN03238 probable histone acet 56.6 50 0.0011 31.7 7.5 56 149-209 215-271 (290)
209 PRK09464 pdhR transcriptional 56.6 21 0.00045 31.2 4.7 54 143-197 15-74 (254)
210 PF09756 DDRGK: DDRGK domain; 56.5 3.7 7.9E-05 36.6 0.0 25 203-227 100-124 (188)
211 cd04774 HTH_YfmP Helix-Turn-He 56.4 61 0.0013 25.2 6.8 64 158-227 2-68 (96)
212 PF05225 HTH_psq: helix-turn-h 56.3 28 0.00061 23.9 4.4 38 141-179 2-39 (45)
213 PF07789 DUF1627: Protein of u 55.9 18 0.0004 31.8 4.2 43 159-202 9-51 (155)
214 PF02186 TFIIE_beta: TFIIE bet 55.6 42 0.00092 25.1 5.6 54 144-201 7-62 (65)
215 COG1321 TroR Mn-dependent tran 55.5 29 0.00064 29.6 5.3 65 141-208 9-73 (154)
216 PRK10225 DNA-binding transcrip 55.2 21 0.00046 31.2 4.6 39 158-197 35-73 (257)
217 PRK15481 transcriptional regul 54.7 36 0.00077 32.0 6.2 57 141-198 8-70 (431)
218 PF14502 HTH_41: Helix-turn-he 54.5 20 0.00043 25.9 3.5 34 154-187 4-37 (48)
219 PRK10163 DNA-binding transcrip 54.4 1E+02 0.0023 27.7 8.9 89 146-236 29-123 (271)
220 PF08221 HTH_9: RNA polymerase 54.1 11 0.00023 27.5 2.1 24 204-227 15-38 (62)
221 KOG4364 Chromatin assembly fac 54.1 61 0.0013 34.7 8.2 15 141-155 372-386 (811)
222 KOG4404 Tandem pore domain K+ 53.9 33 0.00071 33.7 5.9 53 43-96 13-65 (350)
223 KOG0163 Myosin class VI heavy 53.8 57 0.0012 35.8 8.0 16 97-112 965-980 (1259)
224 TIGR03070 couple_hipB transcri 53.7 54 0.0012 21.5 5.4 52 144-211 3-54 (58)
225 cd01109 HTH_YyaN Helix-Turn-He 53.7 52 0.0011 25.9 6.1 63 158-225 2-66 (113)
226 PRK09764 DNA-binding transcrip 53.6 20 0.00044 31.3 4.1 52 145-197 12-69 (240)
227 PRK13503 transcriptional activ 53.1 29 0.00064 30.0 5.1 76 140-226 169-246 (278)
228 cd04765 HTH_MlrA-like_sg2 Heli 53.1 63 0.0014 25.3 6.5 65 159-228 3-70 (99)
229 PF02731 SKIP_SNW: SKIP/SNW do 52.9 49 0.0011 29.1 6.3 17 53-69 109-125 (158)
230 PF06305 DUF1049: Protein of u 52.7 47 0.001 23.6 5.3 20 37-56 21-40 (68)
231 cd04790 HTH_Cfa-like_unk Helix 52.5 48 0.001 28.4 6.2 66 157-227 2-69 (172)
232 PF13591 MerR_2: MerR HTH fami 52.4 48 0.001 25.3 5.5 53 158-216 2-54 (84)
233 KOG4364 Chromatin assembly fac 52.2 45 0.00097 35.7 6.9 8 207-214 458-465 (811)
234 PRK10857 DNA-binding transcrip 51.9 25 0.00055 30.1 4.4 52 152-203 21-73 (164)
235 cd00592 HTH_MerR-like Helix-Tu 51.8 57 0.0012 24.7 5.9 65 158-227 2-67 (100)
236 PF13442 Cytochrome_CBB3: Cyto 51.7 13 0.00027 26.1 2.1 33 175-211 35-67 (67)
237 PF04760 IF2_N: Translation in 51.7 16 0.00035 25.3 2.6 47 157-212 4-52 (54)
238 KOG3558 Hypoxia-inducible fact 51.5 30 0.00065 36.9 5.6 82 112-202 60-147 (768)
239 TIGR00331 hrcA heat shock gene 51.2 34 0.00073 32.5 5.5 73 142-214 6-97 (337)
240 PRK13460 F0F1 ATP synthase sub 51.2 1.5E+02 0.0033 25.1 11.1 7 44-50 32-38 (173)
241 PRK13749 transcriptional regul 51.2 52 0.0011 27.2 6.0 65 157-226 4-70 (121)
242 PRK11161 fumarate/nitrate redu 51.1 46 0.00099 28.2 5.8 48 157-208 185-233 (235)
243 COG2188 PhnF Transcriptional r 51.1 22 0.00048 31.4 4.0 67 155-224 30-103 (236)
244 smart00531 TFIIE Transcription 51.0 93 0.002 25.9 7.5 67 148-214 7-82 (147)
245 PTZ00326 phenylalanyl-tRNA syn 50.9 1.1E+02 0.0024 31.2 9.3 78 145-224 9-96 (494)
246 PF12793 SgrR_N: Sugar transpo 50.6 22 0.00047 29.0 3.6 69 156-224 19-94 (115)
247 cd04766 HTH_HspR Helix-Turn-He 50.4 86 0.0019 23.7 6.7 65 157-226 2-68 (91)
248 cd04775 HTH_Cfa-like Helix-Tur 50.3 86 0.0019 24.4 6.8 62 158-225 3-66 (102)
249 PF11761 CbiG_mid: Cobalamin b 50.1 23 0.0005 26.0 3.4 36 157-192 2-39 (93)
250 PRK03837 transcriptional regul 50.1 33 0.00071 29.5 4.8 54 143-197 18-77 (241)
251 PF13814 Replic_Relax: Replica 49.8 59 0.0013 26.9 6.2 61 149-209 2-72 (191)
252 PRK15090 DNA-binding transcrip 49.2 1.2E+02 0.0026 26.9 8.3 87 146-234 18-109 (257)
253 smart00862 Trans_reg_C Transcr 49.2 32 0.0007 24.1 3.9 32 194-225 1-33 (78)
254 PF15615 TerB-C: TerB-C domain 48.9 75 0.0016 26.5 6.6 61 145-206 79-142 (144)
255 COG1654 BirA Biotin operon rep 48.7 24 0.00051 27.5 3.4 30 156-185 19-48 (79)
256 PF13412 HTH_24: Winged helix- 48.2 20 0.00043 23.9 2.5 23 205-227 6-28 (48)
257 TIGR02404 trehalos_R_Bsub treh 48.1 21 0.00045 30.9 3.3 52 145-197 7-64 (233)
258 PHA00738 putative HTH transcri 48.0 69 0.0015 26.6 6.2 55 145-201 15-69 (108)
259 PRK13239 alkylmercury lyase; P 48.0 39 0.00084 30.7 5.1 52 141-197 21-72 (206)
260 PRK15431 ferrous iron transpor 47.6 20 0.00044 28.1 2.9 25 204-228 4-28 (78)
261 cd04772 HTH_TioE_rpt1 First He 47.3 85 0.0018 24.4 6.4 61 158-223 2-63 (99)
262 cd01279 HTH_HspR-like Helix-Tu 47.0 1E+02 0.0022 24.0 6.7 63 157-224 2-66 (98)
263 TIGR02325 C_P_lyase_phnF phosp 47.0 37 0.00081 29.1 4.7 52 145-197 15-72 (238)
264 TIGR02054 MerD mercuric resist 46.4 93 0.002 25.6 6.7 68 156-227 3-71 (120)
265 PF01316 Arg_repressor: Argini 46.4 77 0.0017 24.0 5.8 57 144-203 7-67 (70)
266 KOG1363 Predicted regulator of 46.4 79 0.0017 31.9 7.4 7 170-176 406-412 (460)
267 PRK06568 F0F1 ATP synthase sub 46.2 2E+02 0.0042 24.9 11.6 12 41-52 17-28 (154)
268 cd04780 HTH_MerR-like_sg5 Heli 46.1 1E+02 0.0022 24.0 6.6 67 158-228 2-70 (95)
269 PF12514 DUF3718: Protein of u 45.5 18 0.00039 27.2 2.2 23 203-226 46-68 (68)
270 PF05529 Bap31: B-cell recepto 45.4 1.9E+02 0.0042 24.7 10.1 29 38-66 105-133 (192)
271 cd01111 HTH_MerD Helix-Turn-He 45.0 98 0.0021 24.6 6.5 68 158-229 2-70 (107)
272 KOG0686 COP9 signalosome, subu 44.3 39 0.00085 34.2 4.9 46 157-202 366-411 (466)
273 PHA03103 double-strand RNA-bin 44.3 37 0.00081 30.4 4.3 52 138-189 9-60 (183)
274 PF15236 CCDC66: Coiled-coil d 44.0 2.2E+02 0.0049 25.0 9.2 10 175-184 142-151 (157)
275 KOG4661 Hsp27-ERE-TATA-binding 43.8 84 0.0018 33.5 7.3 40 58-97 611-651 (940)
276 PRK10227 DNA-binding transcrip 43.5 89 0.0019 25.9 6.2 65 158-227 2-68 (135)
277 PRK10572 DNA-binding transcrip 43.5 87 0.0019 27.6 6.6 76 141-227 182-259 (290)
278 PRK13461 F0F1 ATP synthase sub 43.2 1.9E+02 0.0042 23.9 11.1 14 39-52 16-29 (159)
279 PF05262 Borrelia_P83: Borreli 43.1 1.3E+02 0.0027 30.8 8.3 25 14-38 81-105 (489)
280 PRK05472 redox-sensing transcr 42.9 54 0.0012 28.4 5.1 42 143-185 17-61 (213)
281 PF04967 HTH_10: HTH DNA bindi 42.9 36 0.00078 24.6 3.3 30 152-181 19-48 (53)
282 PRK12705 hypothetical protein; 42.7 3.5E+02 0.0075 27.8 11.3 54 176-229 220-282 (508)
283 PF03551 PadR: Transcriptional 42.6 64 0.0014 23.4 4.7 43 166-208 27-74 (75)
284 KOG4691 Uncharacterized conser 41.8 1.6E+02 0.0034 27.4 8.0 65 57-122 94-158 (227)
285 PRK14472 F0F1 ATP synthase sub 41.3 2.2E+02 0.0048 24.1 11.9 6 57-62 43-48 (175)
286 PRK13752 putative transcriptio 41.0 1.1E+02 0.0024 25.6 6.5 66 157-227 8-75 (144)
287 PRK11642 exoribonuclease R; Pr 40.6 61 0.0013 34.6 6.0 49 147-197 24-77 (813)
288 TIGR02844 spore_III_D sporulat 40.4 31 0.00067 26.8 2.9 25 203-228 7-31 (80)
289 PF08222 HTH_CodY: CodY helix- 40.3 83 0.0018 24.0 5.0 43 157-203 5-52 (61)
290 PRK12704 phosphodiesterase; Pr 40.3 3.5E+02 0.0077 27.5 11.0 54 177-231 233-296 (520)
291 PLN03239 histone acetyltransfe 40.2 38 0.00083 33.2 4.1 50 155-210 283-333 (351)
292 COG2345 Predicted transcriptio 40.2 57 0.0012 29.9 5.0 47 143-189 12-58 (218)
293 PF05043 Mga: Mga helix-turn-h 40.1 78 0.0017 23.4 4.9 62 143-205 17-78 (87)
294 PRK00082 hrcA heat-inducible t 40.0 55 0.0012 31.1 5.1 78 150-228 19-114 (339)
295 PTZ00064 histone acetyltransfe 40.0 87 0.0019 32.5 6.7 49 157-210 472-520 (552)
296 TIGR02431 pcaR_pcaU beta-ketoa 39.7 69 0.0015 28.1 5.3 86 146-236 13-105 (248)
297 PRK09416 lstR lineage-specific 39.7 82 0.0018 27.0 5.6 60 165-224 72-134 (135)
298 PF00034 Cytochrom_C: Cytochro 39.7 24 0.00051 24.4 2.0 16 198-213 74-89 (91)
299 KOG1497 COP9 signalosome, subu 39.4 49 0.0011 32.8 4.7 50 156-205 317-367 (399)
300 COG1777 Predicted transcriptio 39.3 67 0.0015 29.7 5.3 55 146-201 19-78 (217)
301 cd04767 HTH_HspR-like_MBC Heli 39.1 1.7E+02 0.0036 24.4 7.2 63 157-225 2-66 (120)
302 PRK00135 scpB segregation and 39.1 1.5E+02 0.0033 26.2 7.3 59 154-212 17-81 (188)
303 PRK07352 F0F1 ATP synthase sub 39.1 2.4E+02 0.0052 23.9 10.9 14 39-52 30-43 (174)
304 PLN03083 E3 UFM1-protein ligas 38.9 1.8E+02 0.0039 31.6 9.0 81 143-227 61-145 (803)
305 PRK11569 transcriptional repre 38.5 2.4E+02 0.0053 25.3 8.7 88 146-236 32-126 (274)
306 PF04157 EAP30: EAP30/Vps36 fa 38.5 61 0.0013 28.6 4.8 74 113-186 141-220 (223)
307 TIGR02010 IscR iron-sulfur clu 38.3 71 0.0015 25.9 4.8 52 153-204 22-74 (135)
308 PF15086 UPF0542: Uncharacteri 38.3 1.5E+02 0.0033 23.3 6.3 22 39-60 23-44 (74)
309 PF05584 Sulfolobus_pRN: Sulfo 38.1 92 0.002 24.2 5.1 41 146-187 9-49 (72)
310 cd04785 HTH_CadR-PbrR-like Hel 38.1 1.3E+02 0.0027 24.3 6.2 64 158-226 2-67 (126)
311 TIGR01950 SoxR redox-sensitive 38.1 1.6E+02 0.0035 24.6 7.0 65 158-228 3-69 (142)
312 PRK11753 DNA-binding transcrip 37.2 66 0.0014 26.6 4.6 40 157-200 169-208 (211)
313 PLN03086 PRLI-interacting fact 37.2 70 0.0015 33.2 5.6 20 187-207 141-163 (567)
314 CHL00088 apcB allophycocyanin 37.1 16 0.00035 31.6 0.9 39 191-231 13-53 (161)
315 PF13613 HTH_Tnp_4: Helix-turn 36.9 65 0.0014 22.3 3.8 35 147-181 10-44 (53)
316 PF02841 GBP_C: Guanylate-bind 36.8 3.4E+02 0.0074 24.9 13.4 37 2-38 142-178 (297)
317 PF04157 EAP30: EAP30/Vps36 fa 36.7 58 0.0013 28.7 4.4 112 116-227 62-201 (223)
318 PF09286 Pro-kuma_activ: Pro-k 36.7 2E+02 0.0043 23.3 7.2 59 140-200 25-91 (143)
319 TIGR01144 ATP_synt_b ATP synth 36.6 2.3E+02 0.005 22.9 11.1 17 38-54 5-21 (147)
320 cd04619 CBS_pair_6 The CBS dom 36.5 98 0.0021 22.7 5.0 39 166-206 8-47 (114)
321 KOG1425 Microfibrillar-associa 36.4 1E+02 0.0022 31.0 6.3 23 175-197 304-326 (430)
322 PHA03033 hypothetical protein; 36.4 50 0.0011 28.6 3.8 44 174-217 45-93 (142)
323 TIGR02277 PaaX_trns_reg phenyl 36.3 1.1E+02 0.0024 28.2 6.4 52 158-209 22-73 (280)
324 PF10543 ORF6N: ORF6N domain; 36.2 64 0.0014 24.8 4.1 55 151-211 7-61 (88)
325 cd04781 HTH_MerR-like_sg6 Heli 36.2 1.5E+02 0.0033 23.6 6.3 65 158-228 2-68 (120)
326 PRK05066 arginine repressor; P 36.2 1.2E+02 0.0027 26.0 6.2 54 147-204 14-73 (156)
327 PRK11014 transcriptional repre 35.8 87 0.0019 25.5 5.0 63 152-215 21-84 (141)
328 TIGR01339 phycocy_beta phycocy 35.3 18 0.00039 31.9 0.9 39 191-231 11-51 (170)
329 KOG2587 RNA polymerase III (C) 35.2 1.7E+02 0.0037 30.5 7.9 73 152-224 30-127 (551)
330 smart00342 HTH_ARAC helix_turn 35.2 93 0.002 21.2 4.4 38 141-179 36-74 (84)
331 cd04763 HTH_MlrA-like Helix-Tu 35.0 1.6E+02 0.0035 20.7 6.1 61 158-224 2-65 (68)
332 COG3064 TolA Membrane protein 34.8 3.1E+02 0.0068 27.3 9.2 8 29-36 7-14 (387)
333 PF13182 DUF4007: Protein of u 34.5 82 0.0018 29.2 5.2 61 141-202 201-274 (286)
334 PF01988 VIT1: VIT family; In 34.1 2.6E+02 0.0055 24.5 8.0 32 121-152 113-144 (213)
335 PRK13502 transcriptional activ 34.0 1.6E+02 0.0034 25.8 6.6 76 141-227 175-252 (282)
336 PF08721 Tn7_Tnp_TnsA_C: TnsA 33.9 93 0.002 22.1 4.4 42 146-187 31-76 (79)
337 PRK12704 phosphodiesterase; Pr 33.9 5.2E+02 0.011 26.3 11.5 11 166-176 148-158 (520)
338 smart00843 Ftsk_gamma This dom 33.8 1.6E+02 0.0035 22.1 5.7 49 140-188 3-51 (63)
339 cd07970 OBF_DNA_ligase_LigC Th 33.7 67 0.0015 26.2 4.0 31 185-215 20-56 (122)
340 cd03174 DRE_TIM_metallolyase D 33.6 82 0.0018 27.2 4.7 73 141-216 114-189 (265)
341 PF01418 HTH_6: Helix-turn-hel 33.5 50 0.0011 24.4 3.0 28 199-227 14-45 (77)
342 PF11932 DUF3450: Protein of u 33.5 3.5E+02 0.0076 24.2 13.9 19 160-178 137-155 (251)
343 PF06757 Ins_allergen_rp: Inse 33.5 28 0.0006 29.8 1.8 82 141-235 5-89 (179)
344 PF10007 DUF2250: Uncharacteri 33.4 59 0.0013 26.0 3.6 52 146-200 11-62 (92)
345 PRK09836 DNA-binding transcrip 33.2 58 0.0013 26.5 3.6 34 193-226 145-179 (227)
346 KOG3878 Protein involved in ma 33.1 1.2E+02 0.0025 30.5 6.1 32 62-94 131-162 (469)
347 PF08448 PAS_4: PAS fold; Int 32.6 55 0.0012 23.0 3.0 25 180-204 1-25 (110)
348 cd07153 Fur_like Ferric uptake 32.2 2.3E+02 0.005 21.6 6.8 52 148-199 7-64 (116)
349 PRK09978 DNA-binding transcrip 32.2 1.2E+02 0.0027 28.3 6.0 75 141-227 141-217 (274)
350 PRK09863 putative frv operon r 32.0 3.3E+02 0.0071 27.2 9.2 35 147-182 9-43 (584)
351 PF01638 HxlR: HxlR-like helix 32.0 1.1E+02 0.0024 23.0 4.8 51 150-201 13-67 (90)
352 KOG3654 Uncharacterized CH dom 31.9 1.8E+02 0.0038 30.7 7.4 36 71-106 406-443 (708)
353 TIGR01610 phage_O_Nterm phage 31.8 1.3E+02 0.0028 23.2 5.2 35 153-187 44-78 (95)
354 COG3343 RpoE DNA-directed RNA 31.8 49 0.0011 29.7 3.1 59 159-230 37-95 (175)
355 PF12324 HTH_15: Helix-turn-he 31.7 1.4E+02 0.0031 23.4 5.3 52 141-197 23-74 (77)
356 PF06163 DUF977: Bacterial pro 31.7 56 0.0012 27.9 3.3 21 205-225 15-35 (127)
357 PLN03086 PRLI-interacting fact 31.6 2.2E+02 0.0048 29.6 8.1 25 193-223 135-159 (567)
358 TIGR02063 RNase_R ribonuclease 31.5 1E+02 0.0022 31.9 5.8 52 146-199 6-63 (709)
359 TIGR03319 YmdA_YtgF conserved 31.4 3.7E+02 0.008 27.3 9.5 52 177-228 227-287 (514)
360 COG2186 FadR Transcriptional r 31.2 51 0.0011 29.4 3.2 58 141-201 13-76 (241)
361 COG5340 Predicted transcriptio 31.2 67 0.0014 30.4 4.0 69 150-220 24-101 (269)
362 PRK09514 zntR zinc-responsive 31.1 2.2E+02 0.0047 23.6 6.7 65 158-227 3-69 (140)
363 PF00486 Trans_reg_C: Transcri 31.1 79 0.0017 22.1 3.6 32 194-225 1-33 (77)
364 PRK05638 threonine synthase; V 31.0 1.6E+02 0.0035 28.5 6.8 64 146-210 375-441 (442)
365 COG3646 Uncharacterized phage- 30.9 58 0.0013 28.9 3.4 53 147-199 3-69 (167)
366 PRK13877 conjugal transfer rel 30.8 74 0.0016 26.3 3.8 30 196-226 14-43 (114)
367 PF07848 PaaX: PaaX-like prote 30.5 1.1E+02 0.0023 23.1 4.3 59 144-202 7-69 (70)
368 KOG2072 Translation initiation 30.4 2E+02 0.0043 31.8 7.7 20 178-197 740-759 (988)
369 TIGR03433 padR_acidobact trans 30.3 1.6E+02 0.0034 22.8 5.4 47 166-212 35-86 (100)
370 TIGR03453 partition_RepA plasm 30.1 1.2E+02 0.0027 28.5 5.7 55 155-213 32-86 (387)
371 TIGR00570 cdk7 CDK-activating 30.0 3.1E+02 0.0067 26.5 8.3 8 48-55 105-112 (309)
372 PF12833 HTH_18: Helix-turn-he 29.9 98 0.0021 22.1 4.0 56 162-227 1-56 (81)
373 cd07972 OBF_DNA_ligase_Arch_Li 29.8 80 0.0017 25.4 3.8 29 187-215 26-62 (122)
374 CHL00019 atpF ATP synthase CF0 29.1 3.7E+02 0.0079 23.0 11.1 78 38-115 34-117 (184)
375 PRK08476 F0F1 ATP synthase sub 29.0 3.3E+02 0.0072 22.5 11.1 15 39-53 18-32 (141)
376 PF03997 VPS28: VPS28 protein; 28.8 1.1E+02 0.0023 27.5 4.7 94 141-241 33-147 (188)
377 KOG1363 Predicted regulator of 28.7 2.3E+02 0.005 28.7 7.5 10 144-153 406-415 (460)
378 cd04613 CBS_pair_SpoIVFB_EriC_ 28.7 96 0.0021 22.1 3.7 38 186-226 26-67 (114)
379 PF13384 HTH_23: Homeodomain-l 28.6 47 0.001 22.0 2.0 33 156-189 17-49 (50)
380 PF04277 OAD_gamma: Oxaloaceta 28.5 86 0.0019 23.1 3.5 30 35-64 3-32 (79)
381 PRK07718 fliL flagellar basal 28.5 35 0.00077 28.4 1.6 48 142-190 88-135 (142)
382 cd04787 HTH_HMRTR_unk Helix-Tu 28.5 2.8E+02 0.0061 22.5 6.8 65 158-227 2-68 (133)
383 PF04679 DNA_ligase_A_C: ATP d 28.5 86 0.0019 23.9 3.6 30 186-215 9-46 (97)
384 COG5301 Phage-related tail fib 28.5 33 0.00072 35.4 1.7 14 187-200 91-104 (587)
385 PF09862 DUF2089: Protein of u 28.3 34 0.00073 28.5 1.4 25 194-218 29-53 (113)
386 cd04615 CBS_pair_2 The CBS dom 28.2 2.3E+02 0.005 20.3 6.7 57 167-225 9-66 (113)
387 TIGR00683 nanA N-acetylneurami 28.1 1.4E+02 0.003 27.4 5.5 53 166-218 16-72 (290)
388 PF14880 COX14: Cytochrome oxi 28.0 1.4E+02 0.003 21.6 4.5 26 33-58 15-40 (59)
389 COG1414 IclR Transcriptional r 27.9 4.4E+02 0.0096 23.6 8.6 88 146-236 8-102 (246)
390 PF04182 B-block_TFIIIC: B-blo 27.9 87 0.0019 23.2 3.4 44 147-190 7-52 (75)
391 PRK09834 DNA-binding transcrip 27.6 4E+02 0.0087 23.8 8.2 86 147-234 16-107 (263)
392 CHL00090 apcD allophycocyanin 27.6 33 0.00072 29.7 1.3 39 191-231 12-52 (161)
393 PRK09174 F0F1 ATP synthase sub 27.5 4.4E+02 0.0096 23.4 11.6 6 57-62 78-83 (204)
394 PRK15466 carboxysome structura 27.5 63 0.0014 28.8 3.0 34 154-187 122-155 (166)
395 TIGR00570 cdk7 CDK-activating 27.4 4.7E+02 0.01 25.3 9.0 11 62-72 126-136 (309)
396 PRK13460 F0F1 ATP synthase sub 27.3 3.8E+02 0.0083 22.6 11.8 14 51-64 35-48 (173)
397 PF14056 DUF4250: Domain of un 27.1 1.7E+02 0.0037 21.6 4.8 38 142-179 6-43 (55)
398 PF00502 Phycobilisome: Phycob 27.1 23 0.00051 29.9 0.3 39 191-231 8-48 (157)
399 COG3753 Uncharacterized protei 26.9 68 0.0015 28.0 3.0 24 158-181 92-115 (143)
400 PRK11517 transcriptional regul 26.7 2.7E+02 0.0058 22.3 6.4 35 192-226 141-176 (223)
401 TIGR00964 secE_bact preprotein 26.7 77 0.0017 22.5 2.9 38 12-49 3-40 (55)
402 COG2207 AraC AraC-type DNA-bin 26.6 2.4E+02 0.0052 20.7 5.7 73 144-227 22-96 (127)
403 PRK06582 coproporphyrinogen II 26.6 1.7E+02 0.0037 28.1 6.0 49 151-204 328-378 (390)
404 PF13904 DUF4207: Domain of un 26.3 3.2E+02 0.007 25.1 7.5 10 114-123 223-232 (264)
405 PF13025 DUF3886: Protein of u 26.3 2.2E+02 0.0048 22.0 5.4 7 58-64 11-17 (70)
406 PF00430 ATP-synt_B: ATP synth 26.1 3.2E+02 0.0068 21.3 9.4 18 38-55 9-26 (132)
407 PF02319 E2F_TDP: E2F/DP famil 26.0 2E+02 0.0043 21.3 5.1 47 142-188 8-61 (71)
408 cd04769 HTH_MerR2 Helix-Turn-H 25.6 3.3E+02 0.0072 21.5 6.6 65 158-228 2-68 (116)
409 PF10107 Endonuc_Holl: Endonuc 25.5 4.8E+02 0.01 23.1 8.9 15 61-75 16-30 (156)
410 PF05732 RepL: Firmicute plasm 25.4 1.2E+02 0.0026 26.1 4.4 45 156-203 75-119 (165)
411 PRK09393 ftrA transcriptional 25.4 1.4E+02 0.003 27.1 5.0 77 140-227 216-294 (322)
412 PF12674 Zn_ribbon_2: Putative 25.2 1.1E+02 0.0024 23.7 3.7 37 192-228 34-72 (81)
413 COG2512 Predicted membrane-ass 24.9 2.5E+02 0.0054 26.1 6.6 57 143-199 196-253 (258)
414 PF13274 DUF4065: Protein of u 24.7 1.1E+02 0.0023 22.8 3.5 82 146-228 9-100 (108)
415 cd04801 CBS_pair_M50_like This 24.5 2.5E+02 0.0055 20.3 5.4 64 166-234 8-74 (114)
416 TIGR01338 phycocy_alpha phycoc 24.3 39 0.00084 29.6 1.1 40 191-232 12-53 (161)
417 CHL00171 cpcB phycocyanin beta 24.3 36 0.00077 29.9 0.9 40 190-231 12-53 (172)
418 COG4741 Predicted secreted end 24.2 5.3E+02 0.012 23.2 10.5 20 58-77 24-43 (175)
419 PF11845 DUF3365: Protein of u 24.0 2.1E+02 0.0046 23.7 5.5 41 176-218 111-157 (188)
420 KOG0687 26S proteasome regulat 24.0 83 0.0018 31.3 3.4 66 151-216 312-378 (393)
421 CHL00089 apcF allophycocyanin 23.9 40 0.00086 29.6 1.1 39 191-231 13-53 (169)
422 CHL00086 apcA allophycocyanin 23.8 40 0.00087 29.2 1.1 39 191-231 12-52 (161)
423 PRK09685 DNA-binding transcrip 23.8 2.5E+02 0.0055 24.7 6.2 74 141-226 196-274 (302)
424 PRK00888 ftsB cell division pr 23.7 3.9E+02 0.0084 21.5 8.0 13 40-52 7-19 (105)
425 TIGR03319 YmdA_YtgF conserved 23.7 7.8E+02 0.017 25.0 10.7 18 161-178 137-154 (514)
426 PRK13500 transcriptional activ 23.4 1.6E+02 0.0034 26.9 4.9 71 141-227 205-282 (312)
427 PF01997 Translin: Translin fa 23.3 70 0.0015 27.9 2.6 54 145-219 80-134 (200)
428 cd01108 HTH_CueR Helix-Turn-He 23.0 3.8E+02 0.0083 21.5 6.6 64 158-226 2-67 (127)
429 smart00434 TOP4c DNA Topoisome 22.9 71 0.0015 31.7 2.8 35 157-193 235-269 (445)
430 TIGR02044 CueR Cu(I)-responsiv 22.8 3.6E+02 0.0078 21.6 6.4 65 158-227 2-68 (127)
431 PHA02679 ORF091 IMV membrane p 22.7 55 0.0012 24.3 1.5 19 38-56 8-26 (53)
432 PF12668 DUF3791: Protein of u 22.7 77 0.0017 22.8 2.3 22 158-179 7-28 (62)
433 KOG0388 SNF2 family DNA-depend 22.3 3.9E+02 0.0085 29.7 8.1 23 14-36 358-380 (1185)
434 PF14163 SieB: Superinfection 22.2 2.4E+02 0.0053 23.2 5.4 26 36-61 34-59 (151)
435 PF01475 FUR: Ferric uptake re 22.1 3.8E+02 0.0083 20.8 6.5 54 147-200 13-72 (120)
436 PRK13696 hypothetical protein; 21.9 1.5E+02 0.0032 22.6 3.7 27 195-224 4-30 (62)
437 PF00584 SecE: SecE/Sec61-gamm 21.8 86 0.0019 22.0 2.3 39 11-49 3-41 (57)
438 PF10183 ESSS: ESSS subunit of 21.7 1.2E+02 0.0027 24.2 3.5 28 41-69 71-98 (105)
439 cd00397 DNA_BRE_C DNA breaking 21.7 3.1E+02 0.0066 20.7 5.6 70 145-215 3-80 (164)
440 PRK13890 conjugal transfer pro 21.7 4.4E+02 0.0095 21.3 6.9 62 143-225 6-67 (120)
441 COG5187 RPN7 26S proteasome re 21.5 1.2E+02 0.0025 30.2 3.8 68 152-219 327-395 (412)
442 TIGR01337 apcB allophycocyanin 21.4 44 0.00096 29.1 0.9 39 191-231 12-52 (167)
443 PRK04280 arginine repressor; P 21.4 2.2E+02 0.0048 24.2 5.1 56 145-204 7-67 (148)
444 PF00126 HTH_1: Bacterial regu 21.4 2.2E+02 0.0047 19.8 4.3 44 158-202 15-58 (60)
445 COG4125 Predicted membrane pro 21.4 92 0.002 27.3 2.8 24 38-61 116-139 (149)
446 PRK13182 racA polar chromosome 21.3 2.7E+02 0.0059 24.5 5.8 61 158-224 2-64 (175)
447 PF10882 bPH_5: Bacterial PH d 21.2 92 0.002 23.5 2.5 21 195-215 80-100 (100)
448 CHL00170 cpcA phycocyanin alph 21.0 49 0.0011 29.0 1.1 39 191-231 13-53 (162)
449 KOG2784 Phenylalanyl-tRNA synt 20.9 2.2E+02 0.0048 28.9 5.7 77 147-226 8-94 (483)
450 PF10771 DUF2582: Protein of u 20.9 2.7E+02 0.0058 21.0 4.9 51 148-198 14-64 (65)
451 cd04624 CBS_pair_11 The CBS do 20.8 2.4E+02 0.0052 20.2 4.6 38 165-205 7-46 (112)
452 PF06269 DUF1029: Protein of u 20.8 63 0.0014 24.0 1.4 19 38-56 8-26 (53)
453 PF06353 DUF1062: Protein of u 20.8 90 0.002 26.7 2.6 32 160-195 107-138 (142)
454 PRK13428 F0F1 ATP synthase sub 20.6 8.3E+02 0.018 24.2 11.5 19 46-64 15-33 (445)
455 PTZ00399 cysteinyl-tRNA-synthe 20.6 2.4E+02 0.0052 29.5 6.1 8 115-122 602-609 (651)
456 PRK11173 two-component respons 20.5 1.8E+02 0.0039 24.0 4.4 35 192-226 154-189 (237)
457 PF14348 DUF4400: Domain of un 20.5 66 0.0014 27.8 1.8 38 16-53 134-171 (198)
458 PF02731 SKIP_SNW: SKIP/SNW do 20.5 4E+02 0.0086 23.6 6.6 25 50-75 103-127 (158)
459 COG3415 Transposase and inacti 20.4 2.8E+02 0.0061 23.7 5.5 66 157-225 22-89 (138)
460 PRK10265 chaperone-modulator p 20.3 1.4E+02 0.003 23.6 3.5 49 157-210 8-56 (101)
461 COG1695 Predicted transcriptio 20.3 3E+02 0.0065 21.9 5.5 49 167-215 41-94 (138)
462 CHL00183 petJ cytochrome c553; 20.3 76 0.0017 24.5 2.0 17 198-214 87-103 (108)
463 PF01853 MOZ_SAS: MOZ/SAS fami 20.1 1.4E+02 0.0031 26.9 3.9 25 156-180 150-174 (188)
464 PF05262 Borrelia_P83: Borreli 20.1 2.8E+02 0.0061 28.4 6.3 15 56-70 199-213 (489)
No 1
>KOG3054 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=1e-63 Score=451.21 Aligned_cols=176 Identities=53% Similarity=0.767 Sum_probs=160.7
Q ss_pred hhhhHHHHHHHHhhhhHHHHHHHHHHchHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHhhhccceeccCCccchhcc
Q 025511 60 MFDLKADEAARESRQSKQDRYTEMRRRKDEERE--ARESALEEEAKAQKAREEEAAAFEFEKWKGEFSIDAEGTTENEVQ 137 (251)
Q Consensus 60 ~~~Reaee~~RE~Rk~~e~~~ee~rrkkeeere--~eE~~~eEeer~~~eeeerrE~EEY~KwK~~f~VEeeG~~~~e~e 137 (251)
-+|||++++.||+|+++++ +++.+||++|+|. +.+++.+|++|++++|+++++|+||+|||++|+|+++|+++. +.
T Consensus 118 r~qRe~E~~eREeRk~ke~-~eE~erKkdEeR~~eEae~k~ee~~RkakEE~arkeheEylkmKaaFsVeeEGtee~-~~ 195 (299)
T KOG3054|consen 118 RAQREAEEAEREERKRKED-YEEAERKKDEERLAEEAELKEEEKERKAKEEEARKEHEEYLKMKAAFSVEEEGTEEV-QG 195 (299)
T ss_pred HHHHHHHHHHHHHHhHHHH-HHHHHHhhhHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHhheeecccccccc-cc
Confidence 4789999999999999999 5555677777764 444466889999999999999999999999999999998884 44
Q ss_pred cCchhHHHHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHhcCCc
Q 025511 138 DGDRDLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRV 217 (251)
Q Consensus 138 e~sq~lL~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~qrGRV 217 (251)
++.++||++||+|||.+|||+|+|||++|||+|||+|||||.|+++|+|||||||||||||||++||.|||+||+|||||
T Consensus 196 eeqdnll~eFv~YIk~nKvV~ledLas~f~Lrtqd~inriq~~l~eg~ltGVmDDRGKfIYIS~eEl~AVAkfIkqrGRV 275 (299)
T KOG3054|consen 196 EEQDNLLSEFVEYIKKNKVVPLEDLASEFGLRTQDSINRIQELLAEGLLTGVMDDRGKFIYISMEELAAVAKFIKQRGRV 275 (299)
T ss_pred chHHHHHHHHHHHHHhcCeeeHHHHHHHhCccHHHHHHHHHHHHHhhhheeeecCCCceEEecHHHHHHHHHHHHHcCce
Confidence 55558999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cHHHHHhhcccccccccccc
Q 025511 218 SISHLASKSNQFIDLETKAQ 237 (251)
Q Consensus 218 SisELa~~sN~lI~L~p~~~ 237 (251)
||++||+.||+||+|.|...
T Consensus 276 SIaelAe~SN~lI~l~~es~ 295 (299)
T KOG3054|consen 276 SIAELAEKSNQLIDLETESP 295 (299)
T ss_pred eHHHHHHhhcchhccccCCC
Confidence 99999999999999987654
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=5.8e-64 Score=434.57 Aligned_cols=170 Identities=52% Similarity=0.833 Sum_probs=47.9
Q ss_pred hhhHHHHHHHHhhhhHHHHHHHHHHchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccceeccCCccchhcccCc
Q 025511 61 FDLKADEAARESRQSKQDRYTEMRRRKDEEREARESALEEEAKAQKAREEEAAAFEFEKWKGEFSIDAEGTTENEVQDGD 140 (251)
Q Consensus 61 ~~Reaee~~RE~Rk~~e~~~ee~rrkkeeere~eE~~~eEeer~~~eeeerrE~EEY~KwK~~f~VEeeG~~~~e~ee~s 140 (251)
.+|||++++|++|++++++++++|+++++++++++++++++++++++++++++++||++||++|+|+++|++.....+.+
T Consensus 19 ~qREaee~~REerkk~ee~~ee~r~k~ee~~~~~E~~~eeee~~~~eE~e~rE~eEy~k~K~~f~veeeG~~~~~~~~~~ 98 (188)
T PF09756_consen 19 AQREAEEAEREERKKKEEEREEERRKKEEEEEEEEEKKEEEERKAKEEKERREQEEYEKWKSAFSVEEEGEDEEEEEEES 98 (188)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHhccccccchhHHHhhHHH
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999985444444
Q ss_pred hhHHHHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHhcCCccHH
Q 025511 141 RDLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRVSIS 220 (251)
Q Consensus 141 q~lL~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~qrGRVSis 220 (251)
++|++||||||.+|||+|+|||++|||+|+|||+||++|+++|+||||||||||||||||+||.+||+||+++|||||+
T Consensus 99 -~lL~~Fi~yIK~~Kvv~ledla~~f~l~t~~~i~ri~~L~~~g~ltGv~DdrGkfIyIs~eE~~~va~fi~~rGRvsi~ 177 (188)
T PF09756_consen 99 -QLLQEFINYIKEHKVVNLEDLAAEFGLRTQDVINRIQELEAEGRLTGVIDDRGKFIYISEEEMEAVAKFIKQRGRVSIS 177 (188)
T ss_dssp --HHHHHHHHHHH-SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE----------------------
T ss_pred -HHHHHHHHHHHHcceeeHHHHHHHcCCCHHHHHHHHHHHHHCCCceeeEcCCCCeEEecHHHHHHHHHHHHHcCCccHH
Confidence 4999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhcccccc
Q 025511 221 HLASKSNQFID 231 (251)
Q Consensus 221 ELa~~sN~lI~ 231 (251)
+||+.||+|||
T Consensus 178 el~~~~N~~i~ 188 (188)
T PF09756_consen 178 ELAQESNRLIN 188 (188)
T ss_dssp -----------
T ss_pred HHHHHHHhhcC
Confidence 99999999996
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=97.21 E-value=0.0017 Score=48.07 Aligned_cols=61 Identities=18% Similarity=0.259 Sum_probs=56.4
Q ss_pred HHHHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHH
Q 025511 143 LLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAE 203 (251)
Q Consensus 143 lL~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EE 203 (251)
....|..|++..+.+.+++||..|+++..++-.-|-++..+|.|.|-||...++++++...
T Consensus 11 ~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~ 71 (88)
T smart00088 11 RLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVD 71 (88)
T ss_pred HHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCc
Confidence 4567889999999999999999999999999999999999999999999999999998653
No 4
>smart00753 PAM PCI/PINT associated module.
Probab=97.21 E-value=0.0017 Score=48.07 Aligned_cols=61 Identities=18% Similarity=0.259 Sum_probs=56.4
Q ss_pred HHHHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHH
Q 025511 143 LLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAE 203 (251)
Q Consensus 143 lL~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EE 203 (251)
....|..|++..+.+.+++||..|+++..++-.-|-++..+|.|.|-||...++++++...
T Consensus 11 ~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~ 71 (88)
T smart00753 11 RLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVD 71 (88)
T ss_pred HHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCc
Confidence 4567889999999999999999999999999999999999999999999999999998653
No 5
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=97.14 E-value=0.0035 Score=41.73 Aligned_cols=61 Identities=10% Similarity=0.224 Sum_probs=52.1
Q ss_pred HHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHH
Q 025511 148 VEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVAD 209 (251)
Q Consensus 148 I~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~ 209 (251)
+.+|. ..-+.+.|+|.++|++...+-..|+.|.+.|-+.-.-+.++++.++|++.+..+..
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 34555 66678999999999999999999999999999998888888899999986665544
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=96.81 E-value=0.002 Score=47.11 Aligned_cols=49 Identities=20% Similarity=0.358 Sum_probs=41.6
Q ss_pred HHHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeC
Q 025511 144 LADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDD 192 (251)
Q Consensus 144 L~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDD 192 (251)
|.+.-+||+.+..+.+.|||.+||++.+.+-.-|..|+..|.|-=+-+.
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 5678899999999999999999999999999999999999999766554
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=96.56 E-value=0.012 Score=43.54 Aligned_cols=57 Identities=16% Similarity=0.244 Sum_probs=50.5
Q ss_pred HHHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEc
Q 025511 144 LADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYIS 200 (251)
Q Consensus 144 L~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS 200 (251)
...+..+++.-+.+.++++|..++++..++-.-|.++..+|.|.|-||..-+.|+++
T Consensus 48 ~~~l~~l~~~y~~i~~~~ia~~l~~~~~~vE~~l~~~I~~~~i~~~ID~~~~~v~~~ 104 (105)
T PF01399_consen 48 RRNLRQLSKPYSSISISEIAKALQLSEEEVESILIDLISNGLIKAKIDQVNGVVVFS 104 (105)
T ss_dssp HHHHHHHHHC-SEEEHHHHHHHHTCCHHHHHHHHHHHHHTTSSEEEEETTTTEEEE-
T ss_pred HHHHHHHHHHhcccchHHHHHHhccchHHHHHHHHHHHHCCCEEEEEECCCCEEEec
Confidence 456777889999999999999999999999999999999999999999987777765
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=95.93 E-value=0.022 Score=40.61 Aligned_cols=53 Identities=19% Similarity=0.350 Sum_probs=44.1
Q ss_pred HHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEc
Q 025511 145 ADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYIS 200 (251)
Q Consensus 145 ~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS 200 (251)
+..++||+.+..+.+.|||.+||++..-+-.=++.|++.|.|. =-+|-.++++
T Consensus 3 ~~Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~i~---r~~GG~~~~~ 55 (57)
T PF08220_consen 3 QQILELLKEKGKVSVKELAEEFGVSEMTIRRDLNKLEKQGLIK---RTHGGAVLND 55 (57)
T ss_pred HHHHHHHHHcCCEEHHHHHHHHCcCHHHHHHHHHHHHHCCCEE---EEcCEEEeCC
Confidence 5678999999999999999999999999999999999999843 2345555443
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=95.74 E-value=0.1 Score=35.24 Aligned_cols=56 Identities=14% Similarity=0.293 Sum_probs=49.8
Q ss_pred HHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcH
Q 025511 145 ADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQ 201 (251)
Q Consensus 145 ~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~ 201 (251)
..++.+|.... +...++|..+|++...+-..++.|.+.|-|...-+.+.++..+|+
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 899999999999999999999999999999998888888888886
No 10
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=95.67 E-value=0.063 Score=41.05 Aligned_cols=74 Identities=22% Similarity=0.423 Sum_probs=58.6
Q ss_pred HHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcce---eeeCC--Cc----e--EEEc-HHHHHHHHHHHH
Q 025511 145 ADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSG---VMDDR--GK----Y--IYIS-QAEMKAVADYIK 212 (251)
Q Consensus 145 ~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTG---ViDDR--GK----F--IYIS-~EEm~aVA~fI~ 212 (251)
...+.++..+.-+...+||..+|++...+.++|+.|++.|.|.| ++|-+ |. + |.++ ++..+.|++.|.
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 35778888888899999999999999999999999999998874 33432 32 2 4555 678899999888
Q ss_pred hcCCcc
Q 025511 213 RQGRVS 218 (251)
Q Consensus 213 qrGRVS 218 (251)
..-.|.
T Consensus 86 ~~p~v~ 91 (108)
T smart00344 86 KLPEVV 91 (108)
T ss_pred CCcceE
Confidence 765554
No 11
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=95.62 E-value=0.041 Score=49.51 Aligned_cols=58 Identities=16% Similarity=0.247 Sum_probs=51.2
Q ss_pred hcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHH
Q 025511 153 KHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADY 210 (251)
Q Consensus 153 ~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~f 210 (251)
..--+...+||.++|++.+-+-.+|+.|++.|-|+-..|.||.+|++|+.-...+.+-
T Consensus 18 ~~~~IS~~eLA~~L~iS~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~LTekG~~ll~~~ 75 (217)
T PRK14165 18 NTVKISSSEFANHTGTSSKTAARILKQLEDEGYITRTIVPRGQLITITEKGLDVLYNE 75 (217)
T ss_pred CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEEcCCceEEEECHHHHHHHHHH
Confidence 3334678999999999999999999999999999999999999999999887775443
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=95.60 E-value=0.063 Score=41.98 Aligned_cols=66 Identities=14% Similarity=0.193 Sum_probs=56.4
Q ss_pred HHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeee---CCCceEEEcHHHHHHHHHHH
Q 025511 146 DFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMD---DRGKYIYISQAEMKAVADYI 211 (251)
Q Consensus 146 ~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViD---DRGKFIYIS~EEm~aVA~fI 211 (251)
..+.+|..+.-+...+||..+|+....+-..|+.|++.|-|+..-| .|-++|++|++-.+.+....
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 3566777888889999999999999999999999999999999885 47789999998777666543
No 13
>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=95.52 E-value=0.047 Score=38.23 Aligned_cols=56 Identities=20% Similarity=0.242 Sum_probs=42.9
Q ss_pred HHHHHH-hcCccchHhHHhHcCCChHHHHHHHHHHHhcCCccee---eeCCCceEEEcHH
Q 025511 147 FVEYIK-KHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGV---MDDRGKYIYISQA 202 (251)
Q Consensus 147 FI~YIK-~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGV---iDDRGKFIYIS~E 202 (251)
-+.+|. ...-..+.+||..++++.+.+..-|+.|.+.|-|.=. -|.|.+++.+||+
T Consensus 8 vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~~~~~d~R~~~~~LT~~ 67 (68)
T PF13463_consen 8 VLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLVEKERDPHDKRSKRYRLTPA 67 (68)
T ss_dssp HHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEESSCTTSEEEEE-HH
T ss_pred HHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecCCCCcCCeeEEEeCCC
Confidence 466777 6777778999999999999999999999999999544 4557789999985
No 14
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=95.42 E-value=0.096 Score=45.53 Aligned_cols=68 Identities=12% Similarity=0.137 Sum_probs=58.7
Q ss_pred HHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcc--eeee-CCCceEE---EcHHHHHHHHHHHH
Q 025511 145 ADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLS--GVMD-DRGKYIY---ISQAEMKAVADYIK 212 (251)
Q Consensus 145 ~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LT--GViD-DRGKFIY---IS~EEm~aVA~fI~ 212 (251)
...++.++.+..+.-+|||...|+++.+|-.-+..|..+|-++ .+-| ++|.|.| ++++++..+-.+-.
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 3467788999999999999999999999999999999999999 5566 6899888 99998877766544
No 15
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=95.36 E-value=0.12 Score=37.57 Aligned_cols=70 Identities=9% Similarity=0.202 Sum_probs=58.1
Q ss_pred HHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeee---CCCceEEEcHHHHHHHHHHHHhc
Q 025511 145 ADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMD---DRGKYIYISQAEMKAVADYIKRQ 214 (251)
Q Consensus 145 ~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViD---DRGKFIYIS~EEm~aVA~fI~qr 214 (251)
...+..|..+.-+...+||..++++..-+-.-|+.|++.|.|+=.-| .|.+|+++|+.-...+.......
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 34567788888899999999999999999999999999999975533 57789999999988877765543
No 16
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=95.33 E-value=0.15 Score=41.52 Aligned_cols=70 Identities=10% Similarity=0.164 Sum_probs=57.1
Q ss_pred hhHHHHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHhc
Q 025511 141 RDLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQ 214 (251)
Q Consensus 141 q~lL~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~qr 214 (251)
++.|..+..++..+..+.+.+||..+|++..-+-..|+.|++.|-|+= .+++.|++|+.-... |..+..+
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 457888888888889999999999999999999999999999987762 266789999997764 4444433
No 17
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=95.17 E-value=0.11 Score=43.46 Aligned_cols=74 Identities=15% Similarity=0.373 Sum_probs=58.2
Q ss_pred HHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcce---eeeCC--Cc----eEEE-----cHHHHHHHHHH
Q 025511 145 ADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSG---VMDDR--GK----YIYI-----SQAEMKAVADY 210 (251)
Q Consensus 145 ~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTG---ViDDR--GK----FIYI-----S~EEm~aVA~f 210 (251)
...++.+..+=-....+||...|++..-|.+||+.|++.|.|.| ++|.+ |. ||-| +++.++.+++.
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 35667777776777899999999999999999999999999865 45643 53 5666 46778889998
Q ss_pred HHhcCCcc
Q 025511 211 IKRQGRVS 218 (251)
Q Consensus 211 I~qrGRVS 218 (251)
+...--|.
T Consensus 97 l~~~p~V~ 104 (164)
T PRK11169 97 VQKLEEIQ 104 (164)
T ss_pred HhcCccee
Confidence 88775444
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=94.60 E-value=0.15 Score=47.13 Aligned_cols=62 Identities=26% Similarity=0.430 Sum_probs=51.8
Q ss_pred HcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHH-HHHHH-HhcCCccHHHHHhhcc
Q 025511 165 EFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKA-VADYI-KRQGRVSISHLASKSN 227 (251)
Q Consensus 165 ~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~a-VA~fI-~qrGRVSisELa~~sN 227 (251)
-..|+--.||+=|+.|.+.|.|.=|....||- ||||+++.. +.+-| ...||||+.||+..-|
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 34678889999999999999999888889986 899999975 45466 6679999999997654
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=94.43 E-value=0.26 Score=33.62 Aligned_cols=42 Identities=17% Similarity=0.269 Sum_probs=34.5
Q ss_pred ccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEc
Q 025511 156 CIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYIS 200 (251)
Q Consensus 156 VV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS 200 (251)
+....+||.+||++.+-+-..|+.|...|-|+ -.+|+.+++|
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 2457777765
No 20
>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=94.36 E-value=0.23 Score=44.20 Aligned_cols=19 Identities=11% Similarity=0.338 Sum_probs=0.0
Q ss_pred chhHHHHHHHHHhhhhhhh
Q 025511 34 ANSLLLILVCLCTSFLFLL 52 (251)
Q Consensus 34 ~~~~~~~~~~~~~~~~~~~ 52 (251)
.+...++++|++..|+|.-
T Consensus 35 ~yGWyil~~~I~ly~l~qk 53 (190)
T PF06936_consen 35 SYGWYILFGCILLYLLWQK 53 (190)
T ss_dssp -------------------
T ss_pred HhCHHHHHHHHHHHHHHHH
Confidence 3456667777776666543
No 21
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=93.90 E-value=0.28 Score=40.60 Aligned_cols=85 Identities=15% Similarity=0.262 Sum_probs=63.8
Q ss_pred HHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcce---eeeCC--Cc----eEEEc---HHHHHHHHHHHH
Q 025511 145 ADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSG---VMDDR--GK----YIYIS---QAEMKAVADYIK 212 (251)
Q Consensus 145 ~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTG---ViDDR--GK----FIYIS---~EEm~aVA~fI~ 212 (251)
...++.+..+=-.+..+||...|++.+.|-+||+.|+++|.|.| ++|.. |. |+.|+ +..+..++..|.
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 45677788888889999999999999999999999999999974 45642 54 55554 456889999888
Q ss_pred hcCCccH-HHHHhhcccc
Q 025511 213 RQGRVSI-SHLASKSNQF 229 (251)
Q Consensus 213 qrGRVSi-sELa~~sN~l 229 (251)
..-.|.- ...+-..|=+
T Consensus 92 ~~p~V~~~~~~tG~~dl~ 109 (153)
T PRK11179 92 SLDEVVEAYYTTGHYSIF 109 (153)
T ss_pred CCCCEEEEEEcccCCCEE
Confidence 8766653 4444444433
No 22
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=93.86 E-value=0.2 Score=32.68 Aligned_cols=42 Identities=19% Similarity=0.337 Sum_probs=38.2
Q ss_pred HHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcc
Q 025511 146 DFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLS 187 (251)
Q Consensus 146 ~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LT 187 (251)
.+++|+..+.-+.+.+||..||++..-+-..|+.|.+.|.|.
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 578888888889999999999999999999999999998765
No 23
>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=93.72 E-value=0.2 Score=43.21 Aligned_cols=57 Identities=14% Similarity=0.194 Sum_probs=50.1
Q ss_pred HHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHH
Q 025511 145 ADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQA 202 (251)
Q Consensus 145 ~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~E 202 (251)
...+.+|..+.-+.+.+||..+|++..-+-..|+.|++.|-|.-.-+ |++.+++|+.
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 35677888877789999999999999999999999999999987754 9999999973
No 24
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=93.49 E-value=0.18 Score=40.47 Aligned_cols=69 Identities=19% Similarity=0.401 Sum_probs=51.6
Q ss_pred HHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCccee---eeCC--C----ceEEEcHHH----HHHHHHHHH
Q 025511 146 DFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGV---MDDR--G----KYIYISQAE----MKAVADYIK 212 (251)
Q Consensus 146 ~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGV---iDDR--G----KFIYIS~EE----m~aVA~fI~ 212 (251)
.-++.+...-=.++.+||...|++...|.+||+.|++.|-|.|. +|.+ | =||-|+.+. +..++..+.
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 34555655555999999999999999999999999999988775 4421 3 566666655 666666665
Q ss_pred hc
Q 025511 213 RQ 214 (251)
Q Consensus 213 qr 214 (251)
+-
T Consensus 92 ~~ 93 (154)
T COG1522 92 KL 93 (154)
T ss_pred CC
Confidence 43
No 25
>KOG1144 consensus Translation initiation factor 5B (eIF-5B) [Translation, ribosomal structure and biogenesis]
Probab=93.22 E-value=0.69 Score=49.46 Aligned_cols=28 Identities=25% Similarity=0.280 Sum_probs=21.9
Q ss_pred HHHHHHHhcCCcceeeeCCC----ceEEEcHH
Q 025511 175 NRITSLENMGRLSGVMDDRG----KYIYISQA 202 (251)
Q Consensus 175 ~RIq~Lea~G~LTGViDDRG----KFIYIS~E 202 (251)
.+.+.|++.|..-||-|..| ++||....
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 35788999999999997665 79997643
No 26
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=93.20 E-value=0.17 Score=33.82 Aligned_cols=31 Identities=19% Similarity=0.282 Sum_probs=28.5
Q ss_pred chHhHHhHcCCChHHHHHHHHHHHhcCCcce
Q 025511 158 PLEDLAAEFKLRTQECINRITSLENMGRLSG 188 (251)
Q Consensus 158 ~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTG 188 (251)
...+||..||++..-+-..++.|++.|.|+-
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 27
>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=93.00 E-value=0.47 Score=32.43 Aligned_cols=49 Identities=20% Similarity=0.360 Sum_probs=38.7
Q ss_pred HHHHHHH-HhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCc
Q 025511 145 ADFVEYI-KKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGK 195 (251)
Q Consensus 145 ~~FI~YI-K~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGK 195 (251)
...+.++ +.+.-+...+||..||++..-+.+-|+.|.+.| .-|.-.+|+
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 4567777 555569999999999999999999999999999 555556665
No 28
>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=92.95 E-value=0.33 Score=32.61 Aligned_cols=42 Identities=17% Similarity=0.373 Sum_probs=37.2
Q ss_pred HHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCc
Q 025511 145 ADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRL 186 (251)
Q Consensus 145 ~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~L 186 (251)
...++||..+.-+...+||..+|++..-+-..|+.|++.|-|
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 467899999999999999999999999999999999999976
No 29
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=92.86 E-value=0.25 Score=44.45 Aligned_cols=47 Identities=23% Similarity=0.315 Sum_probs=42.3
Q ss_pred HHHHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCccee
Q 025511 143 LLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGV 189 (251)
Q Consensus 143 lL~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGV 189 (251)
..+..+++++.+..|.++|||..||++..-+..=|..|++.|.|..+
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 45778999999999999999999999877777779999999999874
No 30
>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=92.76 E-value=0.78 Score=35.89 Aligned_cols=67 Identities=19% Similarity=0.332 Sum_probs=55.5
Q ss_pred HHHHHH----hcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceee---eCCCceEEEcHHHHHHHHHHHHh
Q 025511 147 FVEYIK----KHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVM---DDRGKYIYISQAEMKAVADYIKR 213 (251)
Q Consensus 147 FI~YIK----~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGVi---DDRGKFIYIS~EEm~aVA~fI~q 213 (251)
++.+|. ...-+...+||..+++...-+-.-|..|++.|-|+=+- |-|-.+||+|+.-...++.....
T Consensus 30 vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~r~~~~~D~R~~~i~lT~~G~~~~~~~~~~ 103 (109)
T TIGR01889 30 ILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLSKKGYLSKERSEDDERKVIISINKEQRSKIESLISE 103 (109)
T ss_pred HHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEeccCCcccCCeEEEEECHHHHHHHHHHHHH
Confidence 466666 34568999999999999999999999999999999554 45899999999998888776543
No 31
>KOG3654 consensus Uncharacterized CH domain protein [Cytoskeleton]
Probab=92.49 E-value=0.21 Score=50.96 Aligned_cols=81 Identities=22% Similarity=0.254 Sum_probs=39.7
Q ss_pred HhhhhhhhhHHhHHhhhhhHHHHHHHHhhhhHHHHHHHHHHchHHHHHHHHHHHHHHH------HHHHHHH-HHHH--HH
Q 025511 45 CTSFLFLLSFSLLFDMFDLKADEAARESRQSKQDRYTEMRRRKDEEREARESALEEEA------KAQKARE-EEAA--AF 115 (251)
Q Consensus 45 ~~~~~~~~~~~~~~~~~~Reaee~~RE~Rk~~e~~~ee~rrkkeeere~eE~~~eEee------r~~~eee-errE--~E 115 (251)
|..|+|-----.--||+++.|..-++..||..+. |++|...+.+.|.+++|+. |..++++ .+|| ..
T Consensus 374 g~gfffkdeqkaedema~kraallekqqrraeea-----r~rkqqleae~e~kreearrkaeeer~~keee~arrefirq 448 (708)
T KOG3654|consen 374 GLGFFFKDEQKAEDEMAQKRAALLEKQQRRAEEA-----RRRKQQLEAEKEQKREEARRKAEEERAPKEEEVARREFIRQ 448 (708)
T ss_pred ceeeeeccccchhHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHhhHhhhcchhhhhhHHHHHHH
Confidence 5566665444444577787776666655554433 2222222222333333333 3333222 2333 26
Q ss_pred HHHhhhccceeccCC
Q 025511 116 EFEKWKGEFSIDAEG 130 (251)
Q Consensus 116 EY~KwK~~f~VEeeG 130 (251)
||..-|..-..|+-|
T Consensus 449 ey~rrkqlklmed~d 463 (708)
T KOG3654|consen 449 EYERRKQLKLMEDLD 463 (708)
T ss_pred HHHHHHHHHHHHhhc
Confidence 788777766555544
No 32
>PLN03083 E3 UFM1-protein ligase 1 homolog; Provisional
Probab=92.01 E-value=0.4 Score=50.74 Aligned_cols=62 Identities=26% Similarity=0.469 Sum_probs=53.5
Q ss_pred HcCCChHHHHHHHHHHHhcCCcc--eeeeCCCceEEEcHHHHH-HHHHHHHhcCCccHHHHHhhcc
Q 025511 165 EFKLRTQECINRITSLENMGRLS--GVMDDRGKYIYISQAEMK-AVADYIKRQGRVSISHLASKSN 227 (251)
Q Consensus 165 ~FgLrTqdvI~RIq~Lea~G~LT--GViDDRGKFIYIS~EEm~-aVA~fI~qrGRVSisELa~~sN 227 (251)
-..|+--.||+-|+.|.+.|.|- =|..-.|| =||||+++. .|.+.|...|||++.||+..-|
T Consensus 21 s~rLSErNcIEiV~KLie~~~ld~dll~T~DGK-EYiT~~qL~~EI~~El~~gGRvnlvdLa~~Ln 85 (803)
T PLN03083 21 SVRLSERNVVELVQKLQELGIIDFDLLHTVSGK-EYITQDQLRNEIEAEIKKLGRVSLVDLADTIG 85 (803)
T ss_pred hhhcchhhHHHHHHHHHHhcccCcceEEecCCc-eeeCHHHHHHHHHHHHHhCCCeeHHHHhhhcC
Confidence 34688889999999999999773 56667899 999999996 5888898899999999998766
No 33
>PF13518 HTH_28: Helix-turn-helix domain
Probab=91.80 E-value=0.4 Score=31.95 Aligned_cols=46 Identities=17% Similarity=0.354 Sum_probs=36.3
Q ss_pred HHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCc
Q 025511 147 FVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGK 195 (251)
Q Consensus 147 FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGK 195 (251)
.|..+.... .+.++|.+||++..-+-.-++...+.| +.|+.+.+|+
T Consensus 5 iv~~~~~g~--s~~~~a~~~gis~~tv~~w~~~y~~~G-~~~l~~~~~r 50 (52)
T PF13518_consen 5 IVELYLEGE--SVREIAREFGISRSTVYRWIKRYREGG-IEGLKPKKRR 50 (52)
T ss_pred HHHHHHcCC--CHHHHHHHHCCCHhHHHHHHHHHHhcC-HHHhccCCCC
Confidence 456666443 999999999998887777788888877 8899987763
No 34
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=91.70 E-value=1.1 Score=36.28 Aligned_cols=64 Identities=13% Similarity=0.190 Sum_probs=54.4
Q ss_pred HHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeee---CCCceEEEcHHHHHHHHHH
Q 025511 147 FVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMD---DRGKYIYISQAEMKAVADY 210 (251)
Q Consensus 147 FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViD---DRGKFIYIS~EEm~aVA~f 210 (251)
++..|..+..+...+||..+|++..-+-.-|+.|++.|-|.=.-| -|.+.||+|++-...+...
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 344565677889999999999999999999999999999998765 4899999999988766553
No 35
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=91.64 E-value=0.4 Score=43.05 Aligned_cols=46 Identities=24% Similarity=0.341 Sum_probs=41.5
Q ss_pred hHHHHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcc
Q 025511 142 DLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLS 187 (251)
Q Consensus 142 ~lL~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LT 187 (251)
+.....+++++.++.|.+.|||..||++..-+...|+.|+++|.|.
T Consensus 5 eR~~~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~Le~~g~l~ 50 (256)
T PRK10434 5 QRQAAILEYLQKQGKTSVEELAQYFDTTGTTIRKDLVILEHAGTVI 50 (256)
T ss_pred HHHHHHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 3457789999999999999999999999999999999999999663
No 36
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=91.14 E-value=2 Score=31.47 Aligned_cols=67 Identities=10% Similarity=0.210 Sum_probs=51.1
Q ss_pred HHHHHHHHhc-CccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHh
Q 025511 145 ADFVEYIKKH-KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKR 213 (251)
Q Consensus 145 ~~FI~YIK~~-KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~q 213 (251)
...+++|..+ .-+.+.|||.++|++..-+-..++.|++.|-|... ..|+..++++.=+.-...++..
T Consensus 8 ~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~--~~~~~y~l~~~~~~~~~~~~~~ 75 (91)
T smart00346 8 LAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQD--GQNGRYRLGPKVLELGQSYLSS 75 (91)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeec--CCCCceeecHHHHHHHHHHHhc
Confidence 4567788776 67999999999999999999999999999999763 2344456777655554555443
No 37
>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=91.06 E-value=0.86 Score=37.23 Aligned_cols=60 Identities=18% Similarity=0.274 Sum_probs=56.8
Q ss_pred hhHHHHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEc
Q 025511 141 RDLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYIS 200 (251)
Q Consensus 141 q~lL~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS 200 (251)
+..++.+...|..-|+|..--||..|+++-.-+-.-|++|+..|.|--|.-.++-.||..
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 667899999999999999999999999999999999999999999999999999999963
No 38
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=90.76 E-value=1.7 Score=34.93 Aligned_cols=65 Identities=15% Similarity=0.163 Sum_probs=52.6
Q ss_pred HHHHHHhc-CccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeee---CCCceEEEcHHHHHHHHHHH
Q 025511 147 FVEYIKKH-KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMD---DRGKYIYISQAEMKAVADYI 211 (251)
Q Consensus 147 FI~YIK~~-KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViD---DRGKFIYIS~EEm~aVA~fI 211 (251)
.+.+|-.. .-....|||..+|++.+-+-.-|..|++.|-|+=+-| -|.++||+|+.-...+....
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 34555443 3456789999999999999999999999999999976 38999999998777666544
No 39
>PTZ00266 NIMA-related protein kinase; Provisional
Probab=90.52 E-value=1.2 Score=48.22 Aligned_cols=11 Identities=9% Similarity=-0.191 Sum_probs=5.2
Q ss_pred hhHHhHHhhhh
Q 025511 52 LSFSLLFDMFD 62 (251)
Q Consensus 52 ~~~~~~~~~~~ 62 (251)
..++..+|.-+
T Consensus 424 g~~g~r~eke~ 434 (1021)
T PTZ00266 424 GHYGGRVDKDH 434 (1021)
T ss_pred CccccccchhH
Confidence 34444555543
No 40
>PF13551 HTH_29: Winged helix-turn helix
Probab=90.25 E-value=0.84 Score=34.26 Aligned_cols=76 Identities=12% Similarity=0.309 Sum_probs=59.9
Q ss_pred chHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeC--C-CceEE-EcHHHHHHHHHHHHhc-----CCccHHHHHhhc-c
Q 025511 158 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDD--R-GKYIY-ISQAEMKAVADYIKRQ-----GRVSISHLASKS-N 227 (251)
Q Consensus 158 ~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDD--R-GKFIY-IS~EEm~aVA~fI~qr-----GRVSisELa~~s-N 227 (251)
...++|..+|++.+-+-+-|+...+.| +.|+.++ + |+.-- +|++..+.|-+++.+. ++.|...|+... .
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 025511 228 QFIDLET 234 (251)
Q Consensus 228 ~lI~L~p 234 (251)
.-..+.+
T Consensus 93 ~~~~~~~ 99 (112)
T PF13551_consen 93 EEFGIDV 99 (112)
T ss_pred hccCccC
Confidence 4433333
No 41
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=90.18 E-value=0.86 Score=33.88 Aligned_cols=51 Identities=24% Similarity=0.351 Sum_probs=41.4
Q ss_pred HHHHHHHh-cCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCce
Q 025511 146 DFVEYIKK-HKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKY 196 (251)
Q Consensus 146 ~FI~YIK~-~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKF 196 (251)
..++||+. +.-+.-.|+|..+|++.-.+..-++.|+.+|.|.=+=--||+=
T Consensus 4 ~Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~~~~~~rG~~ 55 (62)
T PF04703_consen 4 KILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLEKEGKVERSPVRRGKS 55 (62)
T ss_dssp CHHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEES-SSSSS
T ss_pred HHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCCCcc
Confidence 35788888 8889999999999999999999999999999986554456763
No 42
>PRK09954 putative kinase; Provisional
Probab=89.65 E-value=1.4 Score=40.45 Aligned_cols=43 Identities=14% Similarity=0.348 Sum_probs=40.1
Q ss_pred HHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcc
Q 025511 145 ADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLS 187 (251)
Q Consensus 145 ~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LT 187 (251)
...+++|+.+.-+...+||..+|++..-|-.||+.|.+.|.|.
T Consensus 6 ~~il~~l~~~~~~s~~~la~~l~~s~~~v~~~i~~L~~~g~i~ 48 (362)
T PRK09954 6 KEILAILRRNPLIQQNEIADILQISRSRVAAHIMDLMRKGRIK 48 (362)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCcC
Confidence 4588999999999999999999999999999999999999884
No 43
>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=89.55 E-value=2 Score=30.73 Aligned_cols=57 Identities=16% Similarity=0.162 Sum_probs=45.7
Q ss_pred HHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHH
Q 025511 146 DFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQA 202 (251)
Q Consensus 146 ~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~E 202 (251)
....++-.+.-....|||...|++...|-+-++.|...|-+.-.-...-.|-.+.||
T Consensus 12 ~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y~a~~pe 68 (68)
T PF01978_consen 12 KVYLALLKNGPATAEEIAEELGISRSTVYRALKSLEEKGLVEREEGRPKVYRAVPPE 68 (68)
T ss_dssp HHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEEECCEEEEEE-HH
T ss_pred HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcCceEEEEEeCCC
Confidence 455566678888999999999999999999999999999998777554555555554
No 44
>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=89.42 E-value=1.1 Score=33.14 Aligned_cols=46 Identities=22% Similarity=0.400 Sum_probs=36.3
Q ss_pred hHHHHHHHHHHhcCcc-chHhHHhHcCCC-hHHHHHHHHHHHhcCCcc
Q 025511 142 DLLADFVEYIKKHKCI-PLEDLAAEFKLR-TQECINRITSLENMGRLS 187 (251)
Q Consensus 142 ~lL~~FI~YIK~~KVV-~LEDLAa~FgLr-TqdvI~RIq~Lea~G~LT 187 (251)
..|.-..+||..+-+. .+-|||.+||++ |.-|-..++.|+..|.|.
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 3455556688877655 569999999998 888999999999999875
No 45
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=89.40 E-value=0.97 Score=40.51 Aligned_cols=47 Identities=13% Similarity=0.252 Sum_probs=42.2
Q ss_pred hHHHHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcce
Q 025511 142 DLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSG 188 (251)
Q Consensus 142 ~lL~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTG 188 (251)
+.....+++++.++.+.+.|||..||++..-+...|+.|++.|.|..
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 34567889999999999999999999999989899999999999864
No 46
>KOG1029 consensus Endocytic adaptor protein intersectin [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=89.30 E-value=2 Score=46.17 Aligned_cols=37 Identities=14% Similarity=0.161 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHHhcCCccHHH----HHhhcccccccccccch
Q 025511 201 QAEMKAVADYIKRQGRVSISH----LASKSNQFIDLETKAQF 238 (251)
Q Consensus 201 ~EEm~aVA~fI~qrGRVSisE----La~~sN~lI~L~p~~~~ 238 (251)
.++++.|-.++... +-.|++ |-..-|.|+.|.|..+-
T Consensus 471 kt~ie~~~~q~e~~-isei~qlqarikE~q~kl~~l~~Ekq~ 511 (1118)
T KOG1029|consen 471 KTEIEEVTKQRELM-ISEIDQLQARIKELQEKLQKLAPEKQE 511 (1118)
T ss_pred HHHHHHhhhHHHHH-HHHHHHHHHHHHHHHHHHHhhhhHHHH
Confidence 45666666655432 222333 33445678888877664
No 47
>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=89.07 E-value=1.7 Score=31.28 Aligned_cols=42 Identities=12% Similarity=0.128 Sum_probs=34.3
Q ss_pred HHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCccee
Q 025511 147 FVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGV 189 (251)
Q Consensus 147 FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGV 189 (251)
.+..+...... ..+||..||++..-+-.+|+.|++.|-....
T Consensus 5 il~~L~~~~~~-~~eLa~~l~vS~~tv~~~l~~L~~~g~~i~~ 46 (69)
T TIGR00122 5 LLALLADNPFS-GEKLGEALGMSRTAVNKHIQTLREWGVDVLT 46 (69)
T ss_pred HHHHHHcCCcC-HHHHHHHHCCCHHHHHHHHHHHHHCCCeEEe
Confidence 34456666654 9999999999999999999999998875544
No 48
>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=88.95 E-value=1.4 Score=37.95 Aligned_cols=59 Identities=19% Similarity=0.206 Sum_probs=47.3
Q ss_pred HHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeee----CCC-ceEEEcHHH
Q 025511 145 ADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMD----DRG-KYIYISQAE 203 (251)
Q Consensus 145 ~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViD----DRG-KFIYIS~EE 203 (251)
...+.+++.+.-+...+||..+|++..-+-..++.|++.|.|.-..+ +|. +.+++|+.-
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 35678888888899999999999999999999999999999976632 233 345788663
No 49
>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=88.65 E-value=1.3 Score=29.07 Aligned_cols=46 Identities=20% Similarity=0.293 Sum_probs=35.3
Q ss_pred chHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHH
Q 025511 158 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVA 208 (251)
Q Consensus 158 ~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA 208 (251)
.+.++|..+|++.. .|....+.|.|.+.-++.|... .|++++..+.
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 4567789999997666666655 4999988763
No 50
>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=88.21 E-value=1 Score=35.94 Aligned_cols=65 Identities=15% Similarity=0.194 Sum_probs=48.2
Q ss_pred HHHHHh--cCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHH
Q 025511 148 VEYIKK--HKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIK 212 (251)
Q Consensus 148 I~YIK~--~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~ 212 (251)
+.|+-. .+-+.+.+||.++|++..-+-..++.|.+.|-|.++-...|.|-...+-+--.+.+++.
T Consensus 15 l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~~~g~~ggy~l~~~~~~it~~~v~~ 81 (130)
T TIGR02944 15 LTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTSKRGVEGGYTLARAPRDITVADIVK 81 (130)
T ss_pred HHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEecCCCCCChhhcCCccccCHHHHHH
Confidence 445543 35789999999999999999999999999999988766667776665553222444433
No 51
>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=87.88 E-value=2.4 Score=29.91 Aligned_cols=47 Identities=13% Similarity=0.239 Sum_probs=41.3
Q ss_pred HHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeee
Q 025511 145 ADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMD 191 (251)
Q Consensus 145 ~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViD 191 (251)
...+.++....-....+||..+|++.+.+-..++.|+..|-|+.+-+
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 45777888899999999999999999999999999999999987654
No 52
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=87.80 E-value=2.1 Score=34.05 Aligned_cols=59 Identities=24% Similarity=0.345 Sum_probs=55.4
Q ss_pred hhHHHHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEE
Q 025511 141 RDLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYI 199 (251)
Q Consensus 141 q~lL~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYI 199 (251)
+..++.+..-|..-|+|..--||..++++-.-+-.-|++|+..|.|--|.-.++--||.
T Consensus 26 k~t~dkl~kEV~~~K~ITps~lserlkI~~SlAr~~Lr~L~~kG~Ik~V~~~~~q~IYt 84 (86)
T PRK09334 26 EELLKRVAKEVKKEKIVTPYTLASKYGIKISVAKKVLRELEKRGVLVLYSKNRRTPIYV 84 (86)
T ss_pred HHHHHHHHHHhccCcEEcHHHHHHHhcchHHHHHHHHHHHHHCCCEEEEecCCCeEEec
Confidence 56688888899999999999999999999999999999999999999999899999996
No 53
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=87.56 E-value=1.3 Score=40.26 Aligned_cols=47 Identities=17% Similarity=0.297 Sum_probs=42.8
Q ss_pred hhHHHHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcc
Q 025511 141 RDLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLS 187 (251)
Q Consensus 141 q~lL~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LT 187 (251)
.+.+...+++++.++.|.+.|||..||++..-+..-|..|+++|.+.
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 45678899999999999999999999999988888899999999985
No 54
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=87.32 E-value=2.1 Score=33.54 Aligned_cols=48 Identities=10% Similarity=0.156 Sum_probs=43.4
Q ss_pred HHHHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceee
Q 025511 143 LLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVM 190 (251)
Q Consensus 143 lL~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGVi 190 (251)
.|.+.=+||..+.-+.+.+||.+|+++..-|-.=+..|...|++.=|-
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 467788999999999999999999998777777899999999999887
No 55
>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=87.17 E-value=1.5 Score=29.89 Aligned_cols=36 Identities=22% Similarity=0.330 Sum_probs=27.9
Q ss_pred HHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHH
Q 025511 146 DFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLE 181 (251)
Q Consensus 146 ~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Le 181 (251)
..++-+...=-.+..+||...|++...|.+||+.|+
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 355556666668899999999999999999999985
No 56
>PRK10870 transcriptional repressor MprA; Provisional
Probab=86.88 E-value=2.4 Score=36.14 Aligned_cols=59 Identities=10% Similarity=0.144 Sum_probs=50.5
Q ss_pred cCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeee---CCCceEEEcHHHHHHHHHHHH
Q 025511 154 HKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMD---DRGKYIYISQAEMKAVADYIK 212 (251)
Q Consensus 154 ~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViD---DRGKFIYIS~EEm~aVA~fI~ 212 (251)
..-+..-|||..++++.+-+-.-|+.|++.|-|.=.-| -|.++|++|+.-.+.+.....
T Consensus 69 ~~~it~~eLa~~l~l~~~tvsr~v~rLe~kGlV~R~~~~~DrR~~~v~LT~~G~~~~~~i~~ 130 (176)
T PRK10870 69 NHSIQPSELSCALGSSRTNATRIADELEKRGWIERRESDNDRRCLHLQLTEKGHEFLREVLP 130 (176)
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHHHHH
Confidence 45677789999999999999999999999999998866 389999999998877776543
No 57
>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=86.83 E-value=3.6 Score=26.39 Aligned_cols=45 Identities=16% Similarity=0.259 Sum_probs=35.4
Q ss_pred cchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHH
Q 025511 157 IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAV 207 (251)
Q Consensus 157 V~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aV 207 (251)
..+.++|..+|++..- |..|...|.|.++.. |+-.+++.++++..
T Consensus 2 lt~~e~a~~lgis~~t----i~~~~~~g~i~~~~~--g~~~~~~~~~l~~~ 46 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDT----VYRLIHEGELPAYRV--GRHYRIPREDVDEY 46 (49)
T ss_pred CCHHHHHHHHCCCHHH----HHHHHHcCCCCeEEe--CCeEEEeHHHHHHH
Confidence 3578999999997654 556678999999886 66778999887653
No 58
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=86.79 E-value=1.8 Score=39.06 Aligned_cols=47 Identities=15% Similarity=0.304 Sum_probs=40.4
Q ss_pred hHHHHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcce
Q 025511 142 DLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSG 188 (251)
Q Consensus 142 ~lL~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTG 188 (251)
+.....+++++.++.+.+.|||..||++..-+..-+..|+++|.|.-
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 34577899999999999999999999976666666999999999864
No 59
>PTZ00266 NIMA-related protein kinase; Provisional
Probab=86.77 E-value=3 Score=45.41 Aligned_cols=10 Identities=40% Similarity=0.408 Sum_probs=4.2
Q ss_pred hhhHHHHHHH
Q 025511 61 FDLKADEAAR 70 (251)
Q Consensus 61 ~~Reaee~~R 70 (251)
++++..+++|
T Consensus 430 ~eke~~ER~r 439 (1021)
T PTZ00266 430 VDKDHAERAR 439 (1021)
T ss_pred cchhHHHHHH
Confidence 3444444333
No 60
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=86.76 E-value=3.8 Score=35.95 Aligned_cols=68 Identities=16% Similarity=0.177 Sum_probs=56.1
Q ss_pred HHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceee---eCCCceEEEcHHHHHHHHHHHHh
Q 025511 146 DFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVM---DDRGKYIYISQAEMKAVADYIKR 213 (251)
Q Consensus 146 ~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGVi---DDRGKFIYIS~EEm~aVA~fI~q 213 (251)
.++-+|..+.-+...|||...+++.+-+..-|+.|++.|-|.=.. |-|-++||+|+.-...+.+....
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 356677777888999999999998888888899999999999664 44899999999887777665543
No 61
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=86.74 E-value=1.6 Score=28.21 Aligned_cols=31 Identities=19% Similarity=0.328 Sum_probs=28.2
Q ss_pred cchHhHHhHcCCChHHHHHHHHHHHhcCCcc
Q 025511 157 IPLEDLAAEFKLRTQECINRITSLENMGRLS 187 (251)
Q Consensus 157 V~LEDLAa~FgLrTqdvI~RIq~Lea~G~LT 187 (251)
+...|||..+|++.+.+-.-++.|.+.|-|.
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 4568999999999999999999999999886
No 62
>PRK00441 argR arginine repressor; Provisional
Probab=85.89 E-value=2.2 Score=36.24 Aligned_cols=56 Identities=32% Similarity=0.484 Sum_probs=44.4
Q ss_pred HHHHHHHHHHhcCccchHhHHhHc-----CCChHHHHHH-HHHHHhcCCcceeeeCCCceEEEcHHH
Q 025511 143 LLADFVEYIKKHKCIPLEDLAAEF-----KLRTQECINR-ITSLENMGRLSGVMDDRGKYIYISQAE 203 (251)
Q Consensus 143 lL~~FI~YIK~~KVV~LEDLAa~F-----gLrTqdvI~R-Iq~Lea~G~LTGViDDRGKFIYIS~EE 203 (251)
......++|+.+.++..+||+..+ ++ ||.+|.| |++| | |.=|-|..|+|.|.-|.+
T Consensus 5 R~~~I~~ll~~~~~~~q~eL~~~L~~~G~~v-SqaTisRDl~~L---~-lvKv~~~~G~~~Y~l~~~ 66 (149)
T PRK00441 5 RHAKILEIINSKEIETQEELAEELKKMGFDV-TQATVSRDIKEL---K-LIKVLSNDGKYKYATISK 66 (149)
T ss_pred HHHHHHHHHHHcCCCcHHHHHHHHHhcCCCc-CHHHHHHHHHHc---C-cEEeECCCCCEEEEeCcc
Confidence 456678899999999999999995 86 7888887 5555 2 455778999999986554
No 63
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=85.24 E-value=3.1 Score=37.17 Aligned_cols=55 Identities=18% Similarity=0.384 Sum_probs=46.1
Q ss_pred HHHHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEc
Q 025511 143 LLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYIS 200 (251)
Q Consensus 143 lL~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS 200 (251)
.....++|++.++.+...|||..||++..-+-.-|+.|+..|.|.= -.|..+|+.
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 3466789999999999999999999998888889999999988753 467766654
No 64
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=85.21 E-value=3.4 Score=30.34 Aligned_cols=45 Identities=20% Similarity=0.282 Sum_probs=38.3
Q ss_pred HHHHHHHHhcCc--cchHhHHhHcCCChHHHHHHHHHHHhcCCccee
Q 025511 145 ADFVEYIKKHKC--IPLEDLAAEFKLRTQECINRITSLENMGRLSGV 189 (251)
Q Consensus 145 ~~FI~YIK~~KV--V~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGV 189 (251)
...+.+++.+.= +..-|||..+|+++..|-.-+..|++.|.+.-.
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 457788888866 999999999999999777777999999998653
No 65
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=85.21 E-value=1.5 Score=39.30 Aligned_cols=47 Identities=15% Similarity=0.198 Sum_probs=39.5
Q ss_pred hHHHHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcce
Q 025511 142 DLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSG 188 (251)
Q Consensus 142 ~lL~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTG 188 (251)
+..+..++|++.++.|.+.|||..||++..-+..=+..|+..++..|
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 45577899999999999999999999987777777999997776544
No 66
>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=85.15 E-value=1.9 Score=33.22 Aligned_cols=52 Identities=19% Similarity=0.416 Sum_probs=42.5
Q ss_pred hhHHHHHHHHHHhcC----ccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeC
Q 025511 141 RDLLADFVEYIKKHK----CIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDD 192 (251)
Q Consensus 141 q~lL~~FI~YIK~~K----VV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDD 192 (251)
..+-+..++||+... =|.+++||..+++...++.+-|+.|..+|.|-==+||
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 344567888898833 3899999999999999999999999999999887777
No 67
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=85.07 E-value=1.4 Score=38.01 Aligned_cols=63 Identities=19% Similarity=0.165 Sum_probs=51.1
Q ss_pred hHHHHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcc-------------------eeee-----CCCceE
Q 025511 142 DLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLS-------------------GVMD-----DRGKYI 197 (251)
Q Consensus 142 ~lL~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LT-------------------GViD-----DRGKFI 197 (251)
...+..++|+..+..+.+.|||.+||++.+-+..=|+.|.+.|.+. -|+| +-|+++
T Consensus 7 ~R~~~Il~~l~~~~~~~~~~La~~~~vS~~TiRRDl~~L~~~g~~~r~~~~~~~~~~~~~~~~~~~~vD~i~eie~g~~a 86 (185)
T PRK04424 7 ERQKALQELIEENPFITDEELAEKFGVSIQTIRLDRMELGIPELRERIKHVAEKNYDKVKSLPEEEVVGELIDLELGRSA 86 (185)
T ss_pred HHHHHHHHHHHHCCCEEHHHHHHHHCcCHHHHHHHHHHHhcchHHHHHHHHHHHhHHhhhcCCcccceeeEEEecCCcEE
Confidence 3567789999999999999999999998888888899999998763 4444 478754
Q ss_pred ----EEcHHHH
Q 025511 198 ----YISQAEM 204 (251)
Q Consensus 198 ----YIS~EEm 204 (251)
+||.+|+
T Consensus 87 ~~~k~Vt~ne~ 97 (185)
T PRK04424 87 ISILEITEEMV 97 (185)
T ss_pred EEEEecChhhc
Confidence 5688886
No 68
>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=84.99 E-value=2 Score=29.63 Aligned_cols=43 Identities=23% Similarity=0.366 Sum_probs=34.2
Q ss_pred CccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEc
Q 025511 155 KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYIS 200 (251)
Q Consensus 155 KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS 200 (251)
--+...|||..+|++..-+-..|+.|.+.|.|.-. .+|+| .|+
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~~--~~~~~-~l~ 66 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKELEEEGLISRR--GRGKY-RVN 66 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec--CCCeE-EeC
Confidence 45789999999999999999999999999888643 24554 444
No 69
>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=84.88 E-value=0.68 Score=33.73 Aligned_cols=24 Identities=33% Similarity=0.735 Sum_probs=20.4
Q ss_pred HHHHHHHHHhcCCccHHHHHhhcc
Q 025511 204 MKAVADYIKRQGRVSISHLASKSN 227 (251)
Q Consensus 204 m~aVA~fI~qrGRVSisELa~~sN 227 (251)
|.+|-+||+++|+||+.+|+...|
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 357899999999999999999876
No 70
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=84.25 E-value=2.5 Score=38.70 Aligned_cols=53 Identities=19% Similarity=0.410 Sum_probs=48.6
Q ss_pred cchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHH
Q 025511 157 IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVAD 209 (251)
Q Consensus 157 V~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~ 209 (251)
|.+.+||.+.|.+.|-+-..|++|+..|-|+=-+--+|.+|-||+.-++.+-+
T Consensus 20 ~t~~ela~~l~~S~qta~R~l~~le~~~~I~R~~~~~Gq~i~iTekG~~~L~~ 72 (214)
T COG1339 20 VTSSELAKRLGVSSQTAARKLKELEDEGYITRTISKRGQLITITEKGIDLLYK 72 (214)
T ss_pred ccHHHHHHHhCcCcHHHHHHHHhhccCCcEEEEecCCCcEEEehHhHHHHHHH
Confidence 67889999999999999999999999999999999999999999987766544
No 71
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=84.12 E-value=7.4 Score=38.34 Aligned_cols=78 Identities=21% Similarity=0.279 Sum_probs=61.7
Q ss_pred HHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHH---------HHHHHHHhcCCc
Q 025511 147 FVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMK---------AVADYIKRQGRV 217 (251)
Q Consensus 147 FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~---------aVA~fI~qrGRV 217 (251)
.+.+|..+..+...+||...|++.+.+..-|..|++.|-|+= -|.|-+++++|++--. .+.+++...|-+
T Consensus 11 vL~~L~~~~~~s~~eLA~~l~l~~~tVt~~i~~Le~kGlV~~-~~~~~~~i~LTeeG~~~~~~g~pE~rl~~~l~~~~g~ 89 (489)
T PRK04172 11 VLKALKELKEATLEELAEKLGLPPEAVMRAAEWLEEKGLVKV-EERVEEVYVLTEEGKKYAEEGLPERRLLNALKDGGEV 89 (489)
T ss_pred HHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHHHhCCCEEE-EeeeEEEEEECHHHHHHHHhcCHHHHHHHhhHhcCCc
Confidence 455667777889999999999999999999999999998875 4667799999998433 334555566678
Q ss_pred cHHHHHhh
Q 025511 218 SISHLASK 225 (251)
Q Consensus 218 SisELa~~ 225 (251)
++.+|...
T Consensus 90 ~~~el~~~ 97 (489)
T PRK04172 90 SLDELKEA 97 (489)
T ss_pred CHHHHHHh
Confidence 88887764
No 72
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=84.09 E-value=7.5 Score=29.01 Aligned_cols=64 Identities=8% Similarity=0.165 Sum_probs=46.1
Q ss_pred hHHHHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHH
Q 025511 142 DLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADY 210 (251)
Q Consensus 142 ~lL~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~f 210 (251)
+.+.+.+.++. +.-....+|+..-||+..-+...|+.|+..|-|.+ .|+..+|||.-.+.+-.+
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 34566677776 67777899999999999999999999999999944 455558999877766544
No 73
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=83.93 E-value=2.6 Score=29.12 Aligned_cols=60 Identities=13% Similarity=0.273 Sum_probs=42.9
Q ss_pred cchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHhcCCccHHHHHhhcc
Q 025511 157 IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRVSISHLASKSN 227 (251)
Q Consensus 157 V~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~qrGRVSisELa~~sN 227 (251)
+.+++||.++|++..-+-..+...-... . .+ |+...=+..+..+|... .+++.++|..|+
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 3689999999998777666666542111 1 11 35566688899999876 889999998875
No 74
>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=83.84 E-value=6.4 Score=27.89 Aligned_cols=64 Identities=11% Similarity=0.198 Sum_probs=46.3
Q ss_pred chHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHH--HHhcCCccHHHHHhhcc
Q 025511 158 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADY--IKRQGRVSISHLASKSN 227 (251)
Q Consensus 158 ~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~f--I~qrGRVSisELa~~sN 227 (251)
.+.|+|..+|+++.- |...+..|.|.+. .+.|.+=+.|++++..+... .++.| +|+.++....|
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 467899999998764 4466777777753 56677778899998877653 34456 88888877654
No 75
>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=83.49 E-value=4.2 Score=37.74 Aligned_cols=81 Identities=21% Similarity=0.311 Sum_probs=66.8
Q ss_pred HHHHHHHHH-HhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHhc----CCc
Q 025511 143 LLADFVEYI-KKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQ----GRV 217 (251)
Q Consensus 143 lL~~FI~YI-K~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~qr----GRV 217 (251)
+-.+..+.| ...--|++-|||.-.|+....|=++++.+.+++. |++=-.|- .||..=++.+|.-|+.+ |.|
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 445555555 5556899999999999999999899999999887 66666675 68999999999888877 999
Q ss_pred cHHHHHhhcc
Q 025511 218 SISHLASKSN 227 (251)
Q Consensus 218 SisELa~~sN 227 (251)
||++|++.-|
T Consensus 132 si~eLa~~~~ 141 (272)
T PF09743_consen 132 SISELAKQYD 141 (272)
T ss_pred eHHHHHHhcC
Confidence 9999997643
No 76
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=83.34 E-value=5.5 Score=27.88 Aligned_cols=64 Identities=13% Similarity=0.159 Sum_probs=46.1
Q ss_pred chHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHhc-CCccHHHHHhh
Q 025511 158 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQ-GRVSISHLASK 225 (251)
Q Consensus 158 ~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~qr-GRVSisELa~~ 225 (251)
.+.++|..+|++++.+. ..++.|.|.++..+.|.+-|.|++++..+.....-+ --+|++++...
T Consensus 2 s~~eva~~~gvs~~tlr----~~~~~gli~~~~~~~~g~r~y~~~dl~~l~~i~~lr~~g~~~~~i~~~ 66 (70)
T smart00422 2 TIGEVAKLAGVSVRTLR----YYERIGLLPPPIRTEGGYRLYSDEDLERLRFIKRLKELGFSLEEIKEL 66 (70)
T ss_pred CHHHHHHHHCcCHHHHH----HHHHCCCCCCCccCCCCCEecCHHHHHHHHHHHHHHHcCCCHHHHHHH
Confidence 36789999999876644 456799999884444455578999998887666555 34677777654
No 77
>PRK00215 LexA repressor; Validated
Probab=83.09 E-value=3.7 Score=35.01 Aligned_cols=48 Identities=13% Similarity=0.126 Sum_probs=39.3
Q ss_pred cCccchHhHHhHcCC-ChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHH
Q 025511 154 HKCIPLEDLAAEFKL-RTQECINRITSLENMGRLSGVMDDRGKYIYISQA 202 (251)
Q Consensus 154 ~KVV~LEDLAa~FgL-rTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~E 202 (251)
..-..+.|||.++|+ ++.-+-..|+.|++.|.|...-++ ++-+.|+++
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 78
>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=82.62 E-value=4 Score=29.04 Aligned_cols=47 Identities=17% Similarity=0.342 Sum_probs=35.4
Q ss_pred cchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHH
Q 025511 157 IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKA 206 (251)
Q Consensus 157 V~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~a 206 (251)
+..++||...|++.+-+-.-++.|.++|.|. -.+|+++-..++-|.+
T Consensus 29 lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I~---~~~~~i~I~d~~~L~~ 75 (76)
T PF13545_consen 29 LTQEEIADMLGVSRETVSRILKRLKDEGIIE---VKRGKIIILDPERLEE 75 (76)
T ss_dssp SSHHHHHHHHTSCHHHHHHHHHHHHHTTSEE---EETTEEEESSHHHHHH
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE---EcCCEEEECCHHHHhc
Confidence 4679999999999999999999999998766 2445444445555543
No 79
>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=82.37 E-value=2.3 Score=35.26 Aligned_cols=47 Identities=9% Similarity=0.319 Sum_probs=39.3
Q ss_pred HHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHhcC---CccHHHHHhh
Q 025511 177 ITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQG---RVSISHLASK 225 (251)
Q Consensus 177 Iq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~qrG---RVSisELa~~ 225 (251)
+++|.+.+ .|++==||+||++.++++.++.+|+.+.+ ++|..|+.+.
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 48888899999999999999999999976 5999888764
No 80
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=82.08 E-value=5.2 Score=29.73 Aligned_cols=49 Identities=10% Similarity=0.158 Sum_probs=37.7
Q ss_pred hHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHH
Q 025511 159 LEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADY 210 (251)
Q Consensus 159 LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~f 210 (251)
+.+||..+|++..-+-..|+.|++.|-|.= .+++.+++|+.-..-+..+
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 468999999999999999999999865433 3347899999665544433
No 81
>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=81.96 E-value=7.6 Score=33.05 Aligned_cols=68 Identities=18% Similarity=0.229 Sum_probs=49.9
Q ss_pred HHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceee--e-CCCceEEEcHHHHHHHHHHHHhc
Q 025511 147 FVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVM--D-DRGKYIYISQAEMKAVADYIKRQ 214 (251)
Q Consensus 147 FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGVi--D-DRGKFIYIS~EEm~aVA~fI~qr 214 (251)
.++.+-.+..+.-||||...|+++.+|-.-+..|..+|-++-.- | +.|.+-|+=-=....+-+.|+.+
T Consensus 19 Vl~aL~~~~~~tdEeLa~~Lgi~~~~VRk~L~~L~e~~Lv~~~r~r~~~~gw~~Y~w~i~~~~i~d~Ik~~ 89 (158)
T TIGR00373 19 VLFSLGIKGEFTDEEISLELGIKLNEVRKALYALYDAGLADYKRRKDDETGWYEYTWRINYEKALDVLKRK 89 (158)
T ss_pred HHHHHhccCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCceeeeeeecCCCcEEEEEEeCHHHHHHHHHHH
Confidence 45566678899999999999999999999999999999996443 3 45766644111444455555544
No 82
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=81.64 E-value=5.1 Score=36.73 Aligned_cols=51 Identities=16% Similarity=0.215 Sum_probs=42.2
Q ss_pred HHHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCC
Q 025511 144 LADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRG 194 (251)
Q Consensus 144 L~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRG 194 (251)
+.+.+.++....-+...+||..||++..-|-.+|+.|++.|....-...+|
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 457788888888999999999999999999999999999998433333344
No 83
>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=81.38 E-value=8.2 Score=29.91 Aligned_cols=63 Identities=11% Similarity=0.246 Sum_probs=46.9
Q ss_pred hHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHH--HHHHHhcCCccHHHHHhhc
Q 025511 159 LEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAV--ADYIKRQGRVSISHLASKS 226 (251)
Q Consensus 159 LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aV--A~fI~qrGRVSisELa~~s 226 (251)
+.++|..+|+++.- |...+..|.|...-.+.|.|=|.|++++..+ ..+.++.| +|++++...-
T Consensus 3 i~eva~~~gvs~~t----lR~ye~~Gll~~~~~~~~g~R~y~~~di~~l~~i~~lr~~g-~~l~~i~~~~ 67 (103)
T cd01106 3 VGEVAKLTGVSVRT----LHYYDEIGLLKPSRRTENGYRLYTEEDLERLQQILFLKELG-FSLKEIKELL 67 (103)
T ss_pred HHHHHHHHCcCHHH----HHHHHHCCCCCCCccCCCCceeeCHHHHHHHHHHHHHHHcC-CCHHHHHHHH
Confidence 57899999997755 3456779998766556667888999999876 34556666 8988877654
No 84
>PRK11050 manganese transport regulator MntR; Provisional
Probab=81.26 E-value=13 Score=31.11 Aligned_cols=64 Identities=13% Similarity=0.126 Sum_probs=46.5
Q ss_pred HHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHh
Q 025511 146 DFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKR 213 (251)
Q Consensus 146 ~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~q 213 (251)
....++....-+.+.+||..||++..-+-..|+.|++.|.|. ..+++-+++|+.-.. ++..+..
T Consensus 41 ~I~~~l~~~~~~t~~eLA~~l~is~stVsr~l~~Le~~GlI~---r~~~~~v~LT~~G~~-l~~~~~~ 104 (152)
T PRK11050 41 LIADLIAEVGEARQVDIAARLGVSQPTVAKMLKRLARDGLVE---MRPYRGVFLTPEGEK-LAQESRE 104 (152)
T ss_pred HHHHHHHhcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE---EecCCceEECchHHH-HHHHHHH
Confidence 334455565667889999999999999999999999997653 234566899986544 3334443
No 85
>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=81.25 E-value=7.7 Score=26.51 Aligned_cols=46 Identities=15% Similarity=0.239 Sum_probs=38.1
Q ss_pred HHHHHHhcCc--cchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeC
Q 025511 147 FVEYIKKHKC--IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDD 192 (251)
Q Consensus 147 FI~YIK~~KV--V~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDD 192 (251)
.+.+|..+.= +...|||..++++.+-+-.-|+.|++.|-|.=.-|.
T Consensus 10 vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~~~~ 57 (62)
T PF12802_consen 10 VLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKKGLVERERDP 57 (62)
T ss_dssp HHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE-S
T ss_pred HHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCC
Confidence 4556666665 899999999999999999999999999999887774
No 86
>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=81.15 E-value=6 Score=33.61 Aligned_cols=57 Identities=18% Similarity=0.212 Sum_probs=41.8
Q ss_pred HHHHHHHHHhcCc-cchHhHHhHcCCC-hHHHHHHHHHHHhcCCcceeeeCCCceEEEcH
Q 025511 144 LADFVEYIKKHKC-IPLEDLAAEFKLR-TQECINRITSLENMGRLSGVMDDRGKYIYISQ 201 (251)
Q Consensus 144 L~~FI~YIK~~KV-V~LEDLAa~FgLr-TqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~ 201 (251)
|.-..+|+..+.. ..+.+||..+|++ +.-|-.+|+.|++.|-|+.. +.+.+.|.+++
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 3333345544444 5689999999999 89999999999999999886 34444566654
No 87
>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=80.39 E-value=11 Score=30.28 Aligned_cols=78 Identities=19% Similarity=0.341 Sum_probs=58.5
Q ss_pred chhHHHHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHhcCCccH
Q 025511 140 DRDLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRVSI 219 (251)
Q Consensus 140 sq~lL~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~qrGRVSi 219 (251)
|.+|=+..|+|++... ...++|..|+++..-|..-++ -...|.+. --+||.- =| .++.+..+|......++
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 3455677899998877 889999999999888887777 55566552 2345431 22 35678999999999999
Q ss_pred HHHHhhc
Q 025511 220 SHLASKS 226 (251)
Q Consensus 220 sELa~~s 226 (251)
.||+..-
T Consensus 75 ~Ela~~l 81 (119)
T PF01710_consen 75 RELAERL 81 (119)
T ss_pred HHHHHHc
Confidence 9999754
No 88
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=80.30 E-value=4.9 Score=29.70 Aligned_cols=53 Identities=15% Similarity=0.298 Sum_probs=46.6
Q ss_pred HhHHhHcCCChHHHHHHHHHHHhcCCcceeeeC---CCceEEEcHHHHHHHHHHHH
Q 025511 160 EDLAAEFKLRTQECINRITSLENMGRLSGVMDD---RGKYIYISQAEMKAVADYIK 212 (251)
Q Consensus 160 EDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDD---RGKFIYIS~EEm~aVA~fI~ 212 (251)
.+||...+++...+-.-|+.|++.|-|.=..|. |.++|.+|+.--..++....
T Consensus 40 ~~la~~l~i~~~~vt~~l~~Le~~glv~r~~~~~DrR~~~l~lT~~G~~~~~~~~~ 95 (126)
T COG1846 40 KELAERLGLDRSTVTRLLKRLEDKGLIERLRDPEDRRAVLVRLTEKGRELLEQLLP 95 (126)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCeeecCCccccceeeEEECccHHHHHHHhcc
Confidence 999999999999999999999999999988873 78899999987776666554
No 89
>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=80.20 E-value=5.3 Score=31.32 Aligned_cols=57 Identities=25% Similarity=0.385 Sum_probs=49.7
Q ss_pred hhHHHHHHH-HHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceE
Q 025511 141 RDLLADFVE-YIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYI 197 (251)
Q Consensus 141 q~lL~~FI~-YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFI 197 (251)
+..|...|+ |++...=|--..||..++++..-+-|-.++|++.|-|.++=-..|-||
T Consensus 7 ~~IL~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~~Le~lGlve~~p~~s~Gri 64 (78)
T PF03444_consen 7 REILKALVELYIETGEPVGSKTIAEELGRSPATIRNEMADLEELGLVESQPHPSGGRI 64 (78)
T ss_pred HHHHHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHHHHHHHCCCccCCCCCCCCCC
Confidence 456777776 999999999999999999999999999999999999988776666554
No 90
>KOG2412 consensus Nuclear-export-signal (NES)-containing protein/polyadenylated-RNA export factor [RNA processing and modification]
Probab=79.71 E-value=6.6 Score=40.51 Aligned_cols=34 Identities=21% Similarity=0.280 Sum_probs=23.3
Q ss_pred HHHHHHHHHhc----CCccHHHHHhhcccccccccccc
Q 025511 204 MKAVADYIKRQ----GRVSISHLASKSNQFIDLETKAQ 237 (251)
Q Consensus 204 m~aVA~fI~qr----GRVSisELa~~sN~lI~L~p~~~ 237 (251)
+..|+-||... |-+=++.|...|=-+|-.-+..+
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 66667888888887776665544
No 91
>COG3140 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=79.60 E-value=3.2 Score=31.22 Aligned_cols=32 Identities=28% Similarity=0.419 Sum_probs=26.9
Q ss_pred hHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHhc
Q 025511 170 TQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQ 214 (251)
Q Consensus 170 TqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~qr 214 (251)
.|.+|.|||+|.++|.=+| |-+.-||+-|+.+
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 6678888888765
No 92
>PTZ00121 MAEBL; Provisional
Probab=79.50 E-value=6.6 Score=44.93 Aligned_cols=11 Identities=9% Similarity=0.217 Sum_probs=4.4
Q ss_pred CChHHHHHHHH
Q 025511 168 LRTQECINRIT 178 (251)
Q Consensus 168 LrTqdvI~RIq 178 (251)
+++.+.-.++.
T Consensus 1371 ~~~~~~~kk~~ 1381 (2084)
T PTZ00121 1371 KKKEEAKKKAD 1381 (2084)
T ss_pred hhhhHHHHhHH
Confidence 33444444433
No 93
>COG0711 AtpF F0F1-type ATP synthase, subunit b [Energy production and conversion]
Probab=79.48 E-value=38 Score=28.78 Aligned_cols=24 Identities=21% Similarity=0.335 Sum_probs=14.0
Q ss_pred HHHHHHHHhhhhhhhhHHhHHhhhh
Q 025511 38 LLILVCLCTSFLFLLSFSLLFDMFD 62 (251)
Q Consensus 38 ~~~~~~~~~~~~~~~~~~~~~~~~~ 62 (251)
++|++.+|.-|++ |.+..++|--+
T Consensus 16 F~ill~ll~~~~~-~pi~~~l~~R~ 39 (161)
T COG0711 16 FVILLWLLKKFVW-KPILKALDERQ 39 (161)
T ss_pred HHHHHHHHHHHhH-HHHHHHHHHHH
Confidence 3456666766666 55666655433
No 94
>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=79.46 E-value=6 Score=33.45 Aligned_cols=50 Identities=24% Similarity=0.358 Sum_probs=38.8
Q ss_pred cchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceE-EEcHHHHHHH
Q 025511 157 IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYI-YISQAEMKAV 207 (251)
Q Consensus 157 V~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFI-YIS~EEm~aV 207 (251)
++-.+||..||++..-|.+-|+.|+.+|-|. +.--+|-|| .+|++++..+
T Consensus 35 L~e~~La~~lgVSRtpVReAL~~L~~eGlv~-~~~~~G~~V~~~~~~~~~ei 85 (212)
T TIGR03338 35 LNESDIAARLGVSRGPVREAFRALEEAGLVR-NEKNRGVFVREISLAEADEI 85 (212)
T ss_pred ecHHHHHHHhCCChHHHHHHHHHHHHCCCEE-EecCCCeEEecCCHHHHHHH
Confidence 3678999999999999999999999999886 233456665 3566665543
No 95
>PF12728 HTH_17: Helix-turn-helix domain
Probab=79.18 E-value=9.5 Score=25.67 Aligned_cols=45 Identities=9% Similarity=0.209 Sum_probs=36.8
Q ss_pred cchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHH
Q 025511 157 IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAV 207 (251)
Q Consensus 157 V~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aV 207 (251)
..+.|+|..+|++.+- |..+...|.|.++- .|+-++++.+++++.
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 4578999999997765 55677899999995 788899999987764
No 96
>KOG1144 consensus Translation initiation factor 5B (eIF-5B) [Translation, ribosomal structure and biogenesis]
Probab=78.70 E-value=9.3 Score=41.38 Aligned_cols=15 Identities=13% Similarity=0.315 Sum_probs=6.8
Q ss_pred hHHhhhhhHHHHHHH
Q 025511 56 LLFDMFDLKADEAAR 70 (251)
Q Consensus 56 ~~~~~~~Reaee~~R 70 (251)
.+-+|+.+..++.+|
T Consensus 218 ~~qe~La~~qe~eE~ 232 (1064)
T KOG1144|consen 218 AMQEALAKRQEEEER 232 (1064)
T ss_pred HHHHHHHHHHHHHHH
Confidence 344555554444333
No 97
>PRK03341 arginine repressor; Provisional
Probab=78.63 E-value=4.5 Score=35.24 Aligned_cols=58 Identities=21% Similarity=0.324 Sum_probs=45.3
Q ss_pred hHHHHHHHHHHhcCccchHhHHhHc-----CCChHHHHHH-HHHHHhcCCcceeeeCCCce-EEEcHHHH
Q 025511 142 DLLADFVEYIKKHKCIPLEDLAAEF-----KLRTQECINR-ITSLENMGRLSGVMDDRGKY-IYISQAEM 204 (251)
Q Consensus 142 ~lL~~FI~YIK~~KVV~LEDLAa~F-----gLrTqdvI~R-Iq~Lea~G~LTGViDDRGKF-IYIS~EEm 204 (251)
.......+-|+.+++..-+||+..+ ++ ||-+|+| |++|... =|-|..|+| +|.-|.+.
T Consensus 15 ~R~~~I~~li~~~~i~tQ~eL~~~L~~~Gi~v-TQaTiSRDl~eL~~~----Kv~~~~G~~~~Y~lp~~~ 79 (168)
T PRK03341 15 ARQARIVAILSRQSVRSQAELAALLADEGIEV-TQATLSRDLDELGAV----KLRGADGGLGVYVVPEEG 79 (168)
T ss_pred HHHHHHHHHHHHCCCccHHHHHHHHHHcCCcc-cHHHHHHHHHHhcCE----eeecCCCCEEEEEecccc
Confidence 3455667789999999999999998 75 8999998 5555432 388999999 99876643
No 98
>CHL00118 atpG ATP synthase CF0 B' subunit; Validated
Probab=78.45 E-value=38 Score=28.29 Aligned_cols=15 Identities=27% Similarity=0.474 Sum_probs=9.3
Q ss_pred HHHHHHHHhhhhhhh
Q 025511 38 LLILVCLCTSFLFLL 52 (251)
Q Consensus 38 ~~~~~~~~~~~~~~~ 52 (251)
++||+.++.-|+|.|
T Consensus 32 FliL~~lL~k~l~~P 46 (156)
T CHL00118 32 FLLLMVLLNIILYKP 46 (156)
T ss_pred HHHHHHHHHHHHHHH
Confidence 345556666677766
No 99
>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=78.15 E-value=7.8 Score=28.04 Aligned_cols=36 Identities=11% Similarity=0.212 Sum_probs=32.2
Q ss_pred HhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcc
Q 025511 152 KKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLS 187 (251)
Q Consensus 152 K~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LT 187 (251)
.....|...|||..+|++..-|-+-++.|.+.|-+.
T Consensus 18 ~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV~ 53 (60)
T PF01325_consen 18 EEGGPVRTKDIAERLGVSPPTVTEMLKRLAEKGLVE 53 (60)
T ss_dssp HCTSSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred cCCCCccHHHHHHHHCCChHHHHHHHHHHHHCCCEE
Confidence 467899999999999999999999999999999764
No 100
>PRK14474 F0F1 ATP synthase subunit B; Provisional
Probab=78.01 E-value=40 Score=30.75 Aligned_cols=18 Identities=39% Similarity=0.558 Sum_probs=13.1
Q ss_pred HHHHHHHHhhhhhhhhHH
Q 025511 38 LLILVCLCTSFLFLLSFS 55 (251)
Q Consensus 38 ~~~~~~~~~~~~~~~~~~ 55 (251)
++|||.++--|+|.|-..
T Consensus 15 FlILv~lL~~fl~kPi~~ 32 (250)
T PRK14474 15 FLILVYLLRRFLYKPIIQ 32 (250)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 567778888888888443
No 101
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=77.02 E-value=27 Score=26.46 Aligned_cols=67 Identities=13% Similarity=0.263 Sum_probs=51.9
Q ss_pred HHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCc----eEEEcHHHHHHHHHHHHh
Q 025511 147 FVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGK----YIYISQAEMKAVADYIKR 213 (251)
Q Consensus 147 FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGK----FIYIS~EEm~aVA~fI~q 213 (251)
.+.|+....-+...+|....|++...+-.-++.|++.|-|.---.-.|+ ++-||+.--+++..|+..
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 3456667777889999999999999999999999999999865443333 788999999999988763
No 102
>KOG0163 consensus Myosin class VI heavy chain [Cytoskeleton]
Probab=76.89 E-value=7.8 Score=42.01 Aligned_cols=13 Identities=31% Similarity=0.258 Sum_probs=6.3
Q ss_pred HHHHHHHHHHHHh
Q 025511 107 AREEEAAAFEFEK 119 (251)
Q Consensus 107 eeeerrE~EEY~K 119 (251)
+|++++.++||++
T Consensus 967 eEeqr~~qee~e~ 979 (1259)
T KOG0163|consen 967 EEEQRKAQEEEER 979 (1259)
T ss_pred HHHHHHhhhhHHH
Confidence 3444445555554
No 103
>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=76.71 E-value=15 Score=34.94 Aligned_cols=82 Identities=29% Similarity=0.281 Sum_probs=60.5
Q ss_pred HHHHHHHHHHhcCccchHhHHhH-cCCChHHHHHHHHHHHhcCCcceeeeCCCceEEE-------------cHHHHHHHH
Q 025511 143 LLADFVEYIKKHKCIPLEDLAAE-FKLRTQECINRITSLENMGRLSGVMDDRGKYIYI-------------SQAEMKAVA 208 (251)
Q Consensus 143 lL~~FI~YIK~~KVV~LEDLAa~-FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYI-------------S~EEm~aVA 208 (251)
+++.+..+ ...+.+..+||... .++..++.+.-||.|...|.|..+- ..|+.+|- |++|. -|=
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 33444333 44799999999999 6899999999999999999999888 55555554 55666 788
Q ss_pred HHHHhcCCccH--HHHHhhcc
Q 025511 209 DYIKRQGRVSI--SHLASKSN 227 (251)
Q Consensus 209 ~fI~qrGRVSi--sELa~~sN 227 (251)
+.|..-|.--| .+|...+|
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 79988888
No 104
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=76.70 E-value=13 Score=31.80 Aligned_cols=69 Identities=12% Similarity=0.228 Sum_probs=52.1
Q ss_pred hcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHH--HHHHhcCCccHHHHHhhcc
Q 025511 153 KHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVA--DYIKRQGRVSISHLASKSN 227 (251)
Q Consensus 153 ~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA--~fI~qrGRVSisELa~~sN 227 (251)
.+++..+.++|..+|+++. -|.--+..|.|.++-++.|-..| +++.+..+. ...+.-| +|+.++....+
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 46788999999997666665555 888887763 3344556 89988887655
No 105
>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=76.56 E-value=9.9 Score=29.42 Aligned_cols=64 Identities=13% Similarity=0.246 Sum_probs=49.0
Q ss_pred chHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHH--HHHHHhcCCccHHHHHhhc
Q 025511 158 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAV--ADYIKRQGRVSISHLASKS 226 (251)
Q Consensus 158 ~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aV--A~fI~qrGRVSisELa~~s 226 (251)
.+.++|..+|+++.- |.--+..|.|.+...+.|.|=|-|++++..+ ..+.++-| +|++++...-
T Consensus 2 ~i~eva~~~gvs~~t----lR~ye~~Gll~p~~~~~~gyR~Y~~~~~~~l~~I~~lr~~G-~~l~eI~~~l 67 (97)
T cd04782 2 TTGEFAKLCGISKQT----LFHYDKIGLFKPEIVKENGYRYYTLEQFEQLDIILLLKELG-ISLKEIKDYL 67 (97)
T ss_pred CHHHHHHHHCcCHHH----HHHHHHCCCCCCCccCCCCCccCCHHHHHHHHHHHHHHHcC-CCHHHHHHHH
Confidence 367899999997654 5566889999998766677888899997766 45666667 9998887644
No 106
>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=76.50 E-value=11 Score=30.28 Aligned_cols=65 Identities=14% Similarity=0.213 Sum_probs=49.8
Q ss_pred chHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHH--HHHHHhcCCccHHHHHhhcc
Q 025511 158 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAV--ADYIKRQGRVSISHLASKSN 227 (251)
Q Consensus 158 ~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aV--A~fI~qrGRVSisELa~~sN 227 (251)
.+.++|..+|+++.- |.-.+..|-|...-.+.|.|-|-|++.+..+ ..+.++-| +|++++....+
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 367899999997754 4778999999855556778999999998876 34455556 99888776554
No 107
>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=76.40 E-value=6.6 Score=26.52 Aligned_cols=41 Identities=15% Similarity=0.327 Sum_probs=33.9
Q ss_pred HHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcc
Q 025511 146 DFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLS 187 (251)
Q Consensus 146 ~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LT 187 (251)
..+.++.. +-....|||.++|++..-+-.-+..|.+.|-++
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 35667766 667889999999999999999999999999764
No 108
>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=76.13 E-value=13 Score=28.79 Aligned_cols=65 Identities=12% Similarity=0.270 Sum_probs=52.1
Q ss_pred chHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHH--HHHHhcCCccHHHHHhhcc
Q 025511 158 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVA--DYIKRQGRVSISHLASKSN 227 (251)
Q Consensus 158 ~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA--~fI~qrGRVSisELa~~sN 227 (251)
.+.|+|..+|+++. .|.--+..|.|.++-.+.|.|=|-|++++..+. .+.++-| +|++++...-+
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 466778889999998888889999999998875 4566667 99988776544
No 109
>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=75.96 E-value=11 Score=29.74 Aligned_cols=67 Identities=15% Similarity=0.171 Sum_probs=50.7
Q ss_pred chHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHhc-CCccHHHHHhhccc
Q 025511 158 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQ-GRVSISHLASKSNQ 228 (251)
Q Consensus 158 ~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~qr-GRVSisELa~~sN~ 228 (251)
.+.++|..+|+++.- |..-+..|.|.++-++.|.|-|.|++++..+-.-..-+ --+|++++.+..+.
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 467899999997755 44557889999988888899999999998775433333 23788888776654
No 110
>KOG3634 consensus Troponin [Cytoskeleton]
Probab=75.79 E-value=14 Score=36.13 Aligned_cols=40 Identities=25% Similarity=0.362 Sum_probs=24.5
Q ss_pred HHHHHHHHHHhcCccchHhHH-hHcCCChHHHHHHHHHHHhc
Q 025511 143 LLADFVEYIKKHKCIPLEDLA-AEFKLRTQECINRITSLENM 183 (251)
Q Consensus 143 lL~~FI~YIK~~KVV~LEDLA-a~FgLrTqdvI~RIq~Lea~ 183 (251)
....|+.-| .+|+.+++.|- .++.=+.+++-.||-.|+.+
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 455666666 35566655555 55555666777777777655
No 111
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=75.65 E-value=20 Score=25.14 Aligned_cols=64 Identities=14% Similarity=0.253 Sum_probs=45.8
Q ss_pred hHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHhc-CCccHHHHHhhcc
Q 025511 159 LEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQ-GRVSISHLASKSN 227 (251)
Q Consensus 159 LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~qr-GRVSisELa~~sN 227 (251)
+.|+|..+|+++. .|...+..|.|...-+++|. -|-|++.+..+.....-+ --+|+.++.+..+
T Consensus 3 i~eva~~~gvs~~----tlr~y~~~gll~~~~~~~g~-r~y~~~dv~~l~~i~~l~~~G~sl~~I~~~l~ 67 (69)
T PF13411_consen 3 IKEVAKLLGVSPS----TLRYYEREGLLPPPRDENGY-RYYSEEDVERLREIKELRKQGMSLEEIKKLLK 67 (69)
T ss_dssp HHHHHHHTTTTHH----HHHHHHHTTSSTTBESTTSS-EEE-HHHHHHHHHHHHHHHTTTHHHHHHHHH-
T ss_pred HHHHHHHHCcCHH----HHHHHHHhcCcccccccCce-eeccHHHHHHHHHHHHHHHCcCCHHHHHHHHc
Confidence 6799999999764 46677889999998855555 778999998876654433 4577777766543
No 112
>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=75.41 E-value=7.7 Score=36.35 Aligned_cols=56 Identities=16% Similarity=0.289 Sum_probs=43.5
Q ss_pred HHHHHHHHHh-cCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeC-CCceEEE
Q 025511 144 LADFVEYIKK-HKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDD-RGKYIYI 199 (251)
Q Consensus 144 L~~FI~YIK~-~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDD-RGKFIYI 199 (251)
+...+.-+.. .=.++-.+||..+|++..-|.+|++.|++.|-|.+.==- +|.||-.
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 4444555555 257788899999999999999999999999999876523 5888743
No 113
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=75.28 E-value=15 Score=31.44 Aligned_cols=63 Identities=13% Similarity=0.175 Sum_probs=43.3
Q ss_pred HHHHHHHHHhcC-----ccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEE-EcHHHHHHH
Q 025511 144 LADFVEYIKKHK-----CIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIY-ISQAEMKAV 207 (251)
Q Consensus 144 L~~FI~YIK~~K-----VV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIY-IS~EEm~aV 207 (251)
....-+.|.... -++-.+||.+||++..-|.+-|+.|+.+|-|+ +.-.+|-|+- +|.+++..+
T Consensus 17 ~~~l~~~I~~g~l~pG~~L~e~~La~~lgVSRtpVREAL~~L~~eGLV~-~~~~~g~~v~~~~~~~~~ei 85 (221)
T PRK11414 17 ENDLKHQLSIGALKPGARLITKNLAEQLGMSITPVREALLRLVSVNALS-VAPAQAFTVPEVSKRQLDEI 85 (221)
T ss_pred HHHHHHHHHhCCCCCCCccCHHHHHHHHCCCchhHHHHHHHHHHCCCEE-ecCCCceeecCCCHHHHHHH
Confidence 344445554432 23568899999999999999999999999886 3445665542 455555433
No 114
>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=74.38 E-value=14 Score=26.12 Aligned_cols=52 Identities=15% Similarity=0.297 Sum_probs=36.7
Q ss_pred HHHHHHHHhcC-----cc-chHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceE
Q 025511 145 ADFVEYIKKHK-----CI-PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYI 197 (251)
Q Consensus 145 ~~FI~YIK~~K-----VV-~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFI 197 (251)
....+.|.... -+ ...+||..||++..-+.+-+..|.++|.|.- ..-+|-||
T Consensus 7 ~~l~~~I~~g~~~~g~~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~~-~~~~G~~V 64 (64)
T PF00392_consen 7 DQLRQAILSGRLPPGDRLPSERELAERYGVSRTTVREALRRLEAEGLIER-RPGRGTFV 64 (64)
T ss_dssp HHHHHHHHTTSS-TTSBE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE-ETTTEEEE
T ss_pred HHHHHHHHcCCCCCCCEeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEEE-ECCceEEC
Confidence 34455554432 33 7889999999999999999999999998863 34455554
No 115
>PHA02943 hypothetical protein; Provisional
Probab=73.72 E-value=33 Score=30.52 Aligned_cols=70 Identities=11% Similarity=0.189 Sum_probs=57.6
Q ss_pred hhHHHHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCc--eEEEcHHHH-HHHHHHHHh
Q 025511 141 RDLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGK--YIYISQAEM-KAVADYIKR 213 (251)
Q Consensus 141 q~lL~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGK--FIYIS~EEm-~aVA~fI~q 213 (251)
.+-+.++++|| ..=+....++|..+|++...+-.-|.-|+.+|.+.-|= +|+ |-++.++.+ +.|+.|++.
T Consensus 10 ~~R~~eILE~L-k~G~~TtseIAkaLGlS~~qa~~~LyvLErEG~VkrV~--~G~~tyw~l~~day~~~v~~~~Re 82 (165)
T PHA02943 10 HTRMIKTLRLL-ADGCKTTSRIANKLGVSHSMARNALYQLAKEGMVLKVE--IGRAAIWCLDEDAYTNLVFEIKRE 82 (165)
T ss_pred HHHHHHHHHHH-hcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCceEEEe--ecceEEEEEChHHHHHHHHHHHHH
Confidence 45678899999 77788899999999999999999999999999999976 776 455777654 346666654
No 116
>PF14493 HTH_40: Helix-turn-helix domain
Probab=73.30 E-value=14 Score=28.21 Aligned_cols=71 Identities=17% Similarity=0.256 Sum_probs=60.1
Q ss_pred CccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHhcCCccHHHHHhhcccccc
Q 025511 155 KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRVSISHLASKSNQFID 231 (251)
Q Consensus 155 KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~qrGRVSisELa~~sN~lI~ 231 (251)
+=..++++|..-||+..-+.+-+-.+-..|.-..+- .| |++++++.+.+.+.+.|..+++.+-..++.-++
T Consensus 12 ~G~si~eIA~~R~L~~sTI~~HL~~~~~~g~~~~~~----~~--l~~e~~~~I~~~~~~~~~~~lk~i~e~l~~~~s 82 (91)
T PF14493_consen 12 KGLSIEEIAKIRGLKESTIYGHLAELIESGEPLDIE----EL--LSEEEIKQIEDAIEKLGSEKLKPIKEALPGDYS 82 (91)
T ss_pred cCCCHHHHHHHcCCCHHHHHHHHHHHHHhCCCCCHH----Hh--CCHHHHHHHHHHHHHcCcccHHHHHHHCCCCCC
Confidence 446799999999999999999999999999833332 33 899999999999999999888999888886554
No 117
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=73.24 E-value=31 Score=28.37 Aligned_cols=68 Identities=13% Similarity=0.088 Sum_probs=50.9
Q ss_pred HHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHh
Q 025511 146 DFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKR 213 (251)
Q Consensus 146 ~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~q 213 (251)
..+.++....-+.+-|||..||++..-+=.-++-|.+.|-|+.--+-|=.|.++.++--.-++.++..
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 34556766556888999999999888888899999999999998887766777776533334444443
No 118
>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=73.11 E-value=12 Score=28.48 Aligned_cols=70 Identities=11% Similarity=0.108 Sum_probs=52.1
Q ss_pred cchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHhc-CCccHHHHHhhccccc
Q 025511 157 IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQ-GRVSISHLASKSNQFI 230 (251)
Q Consensus 157 V~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~qr-GRVSisELa~~sN~lI 230 (251)
..+.++|..+|+++.- |.-.+..|.|...-++.|-+=|-|++++..+.....-+ .-+|+.++.+.-+...
T Consensus 2 ~ti~evA~~~gvs~~t----LR~ye~~Gll~p~r~~~~g~R~Ys~~dv~~l~~I~~Lr~~G~sl~~i~~~l~~~~ 72 (88)
T cd01105 2 IGIGEVSKLTGVSPRQ----LRYWEEKGLIKSIRSDGGGQRKYSLADVDRLLVIKELLDEGFTLAAAVEKLRRRR 72 (88)
T ss_pred cCHHHHHHHHCcCHHH----HHHHHHCCCCCCCccCCCCceecCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHcc
Confidence 4678999999997754 56678999998766666577788999998775544433 4479988888776444
No 119
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=73.10 E-value=11 Score=32.66 Aligned_cols=50 Identities=10% Similarity=0.244 Sum_probs=34.9
Q ss_pred cchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHH
Q 025511 157 IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVA 208 (251)
Q Consensus 157 V~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA 208 (251)
+...|||...|++.+-+-.-+++|+++|-|. ...+|+++-..++.|.+++
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 3468999999997777766699999998652 2223444444577776665
No 120
>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=72.91 E-value=7.2 Score=25.03 Aligned_cols=28 Identities=21% Similarity=0.246 Sum_probs=25.7
Q ss_pred EEEcHHHHHHHHHHHHhcCCccHHHHHhh
Q 025511 197 IYISQAEMKAVADYIKRQGRVSISHLASK 225 (251)
Q Consensus 197 IYIS~EEm~aVA~fI~qrGRVSisELa~~ 225 (251)
|+++++.++.+-+.-++.| +|.+++.+.
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 999988764
No 121
>PRK10512 selenocysteinyl-tRNA-specific translation factor; Provisional
Probab=72.86 E-value=26 Score=35.91 Aligned_cols=78 Identities=10% Similarity=0.100 Sum_probs=62.3
Q ss_pred HHHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHH----HHHHHHHhcCCccH
Q 025511 144 LADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMK----AVADYIKRQGRVSI 219 (251)
Q Consensus 144 L~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~----aVA~fI~qrGRVSi 219 (251)
.+...++.. -.--.+.||+..+|+...+.-+-+..|...|.|.-|-+ .+|++++-+. .+.++++..|.+++
T Consensus 495 ~~~l~~~~~-~~p~~~~~~~~~l~~~~~~~~~~l~~l~~~g~lv~l~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 569 (614)
T PRK10512 495 WQKAEPLFG-DEPWWVRDLAKETGTDEQAMRLTLRQAAQQGIITAIVK----DRYYRNDRIVQFANMIRELDQECGSTCA 569 (614)
T ss_pred HHHHHHHHh-cCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecC----CEEECHHHHHHHHHHHHHHHhhCCcEeH
Confidence 344444444 45567789999999999999999999999999999976 5899998776 56677777899999
Q ss_pred HHHHhhc
Q 025511 220 SHLASKS 226 (251)
Q Consensus 220 sELa~~s 226 (251)
+++-...
T Consensus 570 ~~~r~~~ 576 (614)
T PRK10512 570 ADFRDRL 576 (614)
T ss_pred HHHHHHh
Confidence 8776554
No 122
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=72.45 E-value=19 Score=30.88 Aligned_cols=50 Identities=10% Similarity=0.104 Sum_probs=37.4
Q ss_pred chHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEE-cHHHHHHHHHHH
Q 025511 158 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYI-SQAEMKAVADYI 211 (251)
Q Consensus 158 ~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYI-S~EEm~aVA~fI 211 (251)
.-+|||..+|++.+-+-.-+++|+.+|.|. -.|+-|+| ..+.|.++|.-+
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 468999999997777777799999998764 34555666 466777766554
No 123
>KOG1029 consensus Endocytic adaptor protein intersectin [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=72.32 E-value=15 Score=39.81 Aligned_cols=12 Identities=17% Similarity=0.537 Sum_probs=6.5
Q ss_pred HHHHHHHHhcCc
Q 025511 145 ADFVEYIKKHKC 156 (251)
Q Consensus 145 ~~FI~YIK~~KV 156 (251)
++.|=|.+.+|-
T Consensus 429 qe~iv~~nak~~ 440 (1118)
T KOG1029|consen 429 QEWIVYLNAKKK 440 (1118)
T ss_pred HHHHHHHHHHHH
Confidence 445556665553
No 124
>KOG3054 consensus Uncharacterized conserved protein [Function unknown]
Probab=71.73 E-value=15 Score=34.99 Aligned_cols=22 Identities=32% Similarity=0.578 Sum_probs=16.1
Q ss_pred HHHHHHHHHhcCCccHHHHHhh
Q 025511 204 MKAVADYIKRQGRVSISHLASK 225 (251)
Q Consensus 204 m~aVA~fI~qrGRVSisELa~~ 225 (251)
+....+||++.--|.+.||+..
T Consensus 202 l~eFv~YIk~nKvV~ledLas~ 223 (299)
T KOG3054|consen 202 LSEFVEYIKKNKVVPLEDLASE 223 (299)
T ss_pred HHHHHHHHHhcCeeeHHHHHHH
Confidence 3456678888888888888765
No 125
>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=71.51 E-value=6.3 Score=27.78 Aligned_cols=53 Identities=15% Similarity=0.242 Sum_probs=38.9
Q ss_pred HHHHHHHhcCccchHhHHhHcCCChHHH-HHHHHHHHhcCCcceeeeCCCceEEEcHH
Q 025511 146 DFVEYIKKHKCIPLEDLAAEFKLRTQEC-INRITSLENMGRLSGVMDDRGKYIYISQA 202 (251)
Q Consensus 146 ~FI~YIK~~KVV~LEDLAa~FgLrTqdv-I~RIq~Lea~G~LTGViDDRGKFIYIS~E 202 (251)
..+.=+..+.=|.++++...||.+..+. -+.|+.|.++|.+ .-.|..|++|+.
T Consensus 10 ~i~~~LR~~~Gi~~~~~~~~~g~~~~~~~~~~l~~l~~~Gll----~~~~~~l~lT~~ 63 (66)
T PF06969_consen 10 YIMLGLRCNEGIDLSEFEQRFGIDFAEEFQKELEELQEDGLL----EIDGGRLRLTEK 63 (66)
T ss_dssp HHHHHHHHHSEEEHHHHHHHTT--THHH-HHHHHHHHHTTSE----EE-SSEEEE-TT
T ss_pred HHHHHHHhHCCcCHHHHHHHHCcCHHHHHHHHHHHHHHCCCE----EEeCCEEEECcc
Confidence 3455567788899999999999997777 5569999999655 566788888875
No 126
>PRK12423 LexA repressor; Provisional
Probab=71.20 E-value=11 Score=32.61 Aligned_cols=47 Identities=19% Similarity=0.257 Sum_probs=38.7
Q ss_pred hhHHHHHHHHHHhcCcc-chHhHHhHcCC-ChHHHHHHHHHHHhcCCcc
Q 025511 141 RDLLADFVEYIKKHKCI-PLEDLAAEFKL-RTQECINRITSLENMGRLS 187 (251)
Q Consensus 141 q~lL~~FI~YIK~~KVV-~LEDLAa~FgL-rTqdvI~RIq~Lea~G~LT 187 (251)
+..|+...+||..+.+. ...+||.+||+ ++.-+-..++.|.+.|.|+
T Consensus 9 ~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~~l~~L~~~G~l~ 57 (202)
T PRK12423 9 AAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKHVQALAEAGLIE 57 (202)
T ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEE
Confidence 55677777788888775 78999999996 6666778999999999886
No 127
>PRK06231 F0F1 ATP synthase subunit B; Validated
Probab=70.80 E-value=76 Score=28.10 Aligned_cols=14 Identities=21% Similarity=0.192 Sum_probs=9.4
Q ss_pred HHHHHHHhhhhhhh
Q 025511 39 LILVCLCTSFLFLL 52 (251)
Q Consensus 39 ~~~~~~~~~~~~~~ 52 (251)
+||+.++.-|+|.|
T Consensus 59 lIlv~lL~k~l~kP 72 (205)
T PRK06231 59 SILLLLGIFLFWKP 72 (205)
T ss_pred HHHHHHHHHHHHHH
Confidence 55666667777766
No 128
>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=70.65 E-value=17 Score=24.81 Aligned_cols=46 Identities=17% Similarity=0.247 Sum_probs=38.8
Q ss_pred HHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeC
Q 025511 147 FVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDD 192 (251)
Q Consensus 147 FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDD 192 (251)
++.+|-.+.=+.+.+||..++++..-+-.-|+.|+..|-|.=-.|.
T Consensus 8 iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~~~~ 53 (59)
T PF01047_consen 8 ILRILYENGGITQSELAEKLGISRSTVTRIIKRLEKKGLIERERDP 53 (59)
T ss_dssp HHHHHHHHSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEET
T ss_pred HHHHHHHcCCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEeccCC
Confidence 4566777777999999999999999999999999999999866653
No 129
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=70.55 E-value=13 Score=31.88 Aligned_cols=50 Identities=16% Similarity=0.254 Sum_probs=37.6
Q ss_pred CccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceE-EEcHHHHHH
Q 025511 155 KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYI-YISQAEMKA 206 (251)
Q Consensus 155 KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFI-YIS~EEm~a 206 (251)
|+ +..+||..||++..-|.+-|+.|+.+|-|. +.--+|-|| .+|++++..
T Consensus 30 ~L-~e~eLae~lgVSRtpVREAL~~L~~eGlv~-~~~~~G~~V~~~~~~~~~e 80 (224)
T PRK11534 30 KL-RMSLLTSRYALGVGPLREALSQLVAERLVT-VVNQKGYRVASMSEQELLD 80 (224)
T ss_pred cC-CHHHHHHHHCCChHHHHHHHHHHHHCCCEE-EeCCCceEeCCCCHHHHHH
Confidence 44 468999999999999999999999999886 344566554 235554443
No 130
>PF13730 HTH_36: Helix-turn-helix domain
Probab=70.32 E-value=7 Score=26.55 Aligned_cols=29 Identities=24% Similarity=0.360 Sum_probs=26.6
Q ss_pred chHhHHhHcCCChHHHHHHHHHHHhcCCc
Q 025511 158 PLEDLAAEFKLRTQECINRITSLENMGRL 186 (251)
Q Consensus 158 ~LEDLAa~FgLrTqdvI~RIq~Lea~G~L 186 (251)
..+.||...|++..-|..-|+.|++.|-|
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 131
>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=70.26 E-value=19 Score=29.01 Aligned_cols=63 Identities=19% Similarity=0.277 Sum_probs=48.6
Q ss_pred hHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHH---hcCCccHHHHHhhcc
Q 025511 159 LEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIK---RQGRVSISHLASKSN 227 (251)
Q Consensus 159 LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~---qrGRVSisELa~~sN 227 (251)
+.++|..+|+++.-+ .--+..|-|....++.|.|-|-|++.+..+. ||+ +-| +|++++....+
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 568999999977643 5568999998777778889999999998874 444 445 88888776553
No 132
>PRK14473 F0F1 ATP synthase subunit B; Provisional
Probab=69.70 E-value=65 Score=26.89 Aligned_cols=18 Identities=28% Similarity=0.600 Sum_probs=11.4
Q ss_pred HHHHHHHHhhhhhhhhHH
Q 025511 38 LLILVCLCTSFLFLLSFS 55 (251)
Q Consensus 38 ~~~~~~~~~~~~~~~~~~ 55 (251)
++||+.++.-|+|-|-..
T Consensus 18 flil~~lL~~fl~kpi~~ 35 (164)
T PRK14473 18 FLLLIFLLRTFLYRPVLN 35 (164)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 456666777777776443
No 133
>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=69.54 E-value=16 Score=22.98 Aligned_cols=45 Identities=9% Similarity=0.155 Sum_probs=32.8
Q ss_pred chHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHH
Q 025511 158 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAV 207 (251)
Q Consensus 158 ~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aV 207 (251)
.+.++|..+|++..-+- .+...|.+.+.-.+ |+..+++.+|+..+
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 46899999999776644 45557988876544 45667899888765
No 134
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=69.53 E-value=10 Score=32.32 Aligned_cols=80 Identities=21% Similarity=0.309 Sum_probs=63.8
Q ss_pred ccCchhHHHHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCc-eEEEcHHHHHHHHHHHHhcC
Q 025511 137 QDGDRDLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGK-YIYISQAEMKAVADYIKRQG 215 (251)
Q Consensus 137 ee~sq~lL~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGK-FIYIS~EEm~aVA~fI~qrG 215 (251)
.++...+....|++++.+.-+.+.|++..+|++-.-+-..+.+|.+.|.|.. -|+ =||.|+ .|.-+|.+.+-
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 3456778889999999999999999999999999999999999999999875 465 466776 46667777765
Q ss_pred CccHHHHH
Q 025511 216 RVSISHLA 223 (251)
Q Consensus 216 RVSisELa 223 (251)
.....+|.
T Consensus 80 ~~~~~~~~ 87 (127)
T PF06163_consen 80 KLVDPDLI 87 (127)
T ss_pred hhccchhh
Confidence 55444443
No 135
>COG4901 Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=69.23 E-value=15 Score=30.60 Aligned_cols=61 Identities=20% Similarity=0.288 Sum_probs=55.8
Q ss_pred chhHHHHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEc
Q 025511 140 DRDLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYIS 200 (251)
Q Consensus 140 sq~lL~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS 200 (251)
++++++....-+..-++|..--||..+|++...+-.-+..|+.+|.|.-|.-.|--=||+-
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 4677888888899999999999999999999999999999999999999988888888873
No 136
>PRK05114 hypothetical protein; Provisional
Probab=69.14 E-value=3.4 Score=31.11 Aligned_cols=32 Identities=28% Similarity=0.438 Sum_probs=27.3
Q ss_pred hHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHhc
Q 025511 170 TQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQ 214 (251)
Q Consensus 170 TqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~qr 214 (251)
.|.+++|||+|.++|.=|| +=+.-||+-|+..
T Consensus 13 QQ~AVErIq~LMaqGmSsg-------------EAI~~VA~eiRe~ 44 (59)
T PRK05114 13 QQKAVERIQELMAQGMSSG-------------EAIALVAEELRAN 44 (59)
T ss_pred HHHHHHHHHHHHHccccHH-------------HHHHHHHHHHHHH
Confidence 4789999999999998766 6788889988864
No 137
>cd00131 PAX Paired Box domain
Probab=69.10 E-value=21 Score=29.28 Aligned_cols=94 Identities=10% Similarity=0.043 Sum_probs=64.6
Q ss_pred CccchhcccCchhHHHHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHH
Q 025511 130 GTTENEVQDGDRDLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVAD 209 (251)
Q Consensus 130 G~~~~e~ee~sq~lL~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~ 209 (251)
|....+..--|..+=...|...... ..--++|..||++..-|..=|+...+.|.+...---.++-=-+++.....+-.
T Consensus 9 ~~~~~m~~~lS~d~R~rIv~~~~~G--~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk~~gg~rpr~~~~~~~~~i~~ 86 (128)
T cd00131 9 GGVFVNGRPLPDSIRQRIVELAQSG--IRPCDISRQLRVSHGCVSKILNRYYETGSIRPGAIGGSKPRVATPEVVKKIEI 86 (128)
T ss_pred CccccCCCcCCHHHHHHHHHHHHcC--CCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCCCCCCCCCCcCCHHHHHHHHH
Confidence 3333333334444445566666543 46678999999999888888999999998764322101122457777777888
Q ss_pred HHHhcCCccHHHHHhh
Q 025511 210 YIKRQGRVSISHLASK 225 (251)
Q Consensus 210 fI~qrGRVSisELa~~ 225 (251)
+|..++.+|..||+..
T Consensus 87 ~v~~~p~~Tl~El~~~ 102 (128)
T cd00131 87 YKQENPGMFAWEIRDR 102 (128)
T ss_pred HHHHCCCCCHHHHHHH
Confidence 9999999999999776
No 138
>KOG2235 consensus Uncharacterized conserved protein [Function unknown]
Probab=69.07 E-value=8 Score=40.75 Aligned_cols=60 Identities=30% Similarity=0.465 Sum_probs=50.4
Q ss_pred CCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHH-HHHHHHhcC-CccHHHHHhhcc
Q 025511 167 KLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKA-VADYIKRQG-RVSISHLASKSN 227 (251)
Q Consensus 167 gLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~a-VA~fI~qrG-RVSisELa~~sN 227 (251)
.|+--.||+-+|.|.+.-+|--|..-.||= ||||++++. +-+-+--+| |||+.||+..-|
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 466678999999999999999999999994 999999874 455555555 999999999887
No 139
>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=68.51 E-value=26 Score=27.03 Aligned_cols=65 Identities=17% Similarity=0.300 Sum_probs=49.5
Q ss_pred chHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHH--HHHHhcCCccHHHHHhhcc
Q 025511 158 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVA--DYIKRQGRVSISHLASKSN 227 (251)
Q Consensus 158 ~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA--~fI~qrGRVSisELa~~sN 227 (251)
.+.++|..+|+++.- |.--+..|.|.....+.|.|=|-|++.+..+. ...++-| +|++++...-+
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 467999999997643 56678899998876666777778999998664 3455667 99988887654
No 140
>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=67.85 E-value=27 Score=27.27 Aligned_cols=64 Identities=13% Similarity=0.279 Sum_probs=47.2
Q ss_pred chHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHH--HHHhcCCccHHHHHhhcc
Q 025511 158 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVAD--YIKRQGRVSISHLASKSN 227 (251)
Q Consensus 158 ~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~--fI~qrGRVSisELa~~sN 227 (251)
.+.++|..+|+++.- |.--+..|.|.+.-++ |.|-|-|++.+..+.. +.++-| +|++++....+
T Consensus 3 ~i~eva~~~gvs~~t----lR~ye~~Gll~~~r~~-~g~R~Y~~~~l~~l~~I~~l~~~G-~~l~ei~~~l~ 68 (102)
T cd04789 3 TISELAEKAGISRST----LLYYEKLGLITGTRNA-NGYRLYPDSDLQRLLLIQQLQAGG-LSLKECLACLQ 68 (102)
T ss_pred CHHHHHHHHCcCHHH----HHHHHHCCCCCCCcCC-CCCeeCCHHHHHHHHHHHHHHHCC-CCHHHHHHHHc
Confidence 578999999997654 4577888999986655 6677778988887652 444556 88888776544
No 141
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=67.64 E-value=19 Score=29.69 Aligned_cols=48 Identities=17% Similarity=0.158 Sum_probs=35.6
Q ss_pred cchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEE-cHHHHHHHH
Q 025511 157 IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYI-SQAEMKAVA 208 (251)
Q Consensus 157 V~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYI-S~EEm~aVA 208 (251)
+.-++||...|++.+-+-.-+++|..+|.|. -.|+.|+| .++.+.++|
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 4678999999997777766799999988775 34344666 466776655
No 142
>smart00351 PAX Paired Box domain.
Probab=67.63 E-value=65 Score=26.12 Aligned_cols=84 Identities=12% Similarity=0.068 Sum_probs=61.3
Q ss_pred CchhHHHHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCC-ceEEEcHHHHHHHHHHHHhcCCc
Q 025511 139 GDRDLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRG-KYIYISQAEMKAVADYIKRQGRV 217 (251)
Q Consensus 139 ~sq~lL~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRG-KFIYIS~EEm~aVA~fI~qrGRV 217 (251)
-+.++=..+|.+..... ..-++|..||++..-|..=|+...+.|.+...-- .| +-=-+++.....+..++.+++..
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 34455567777776543 5579999999988888888888888886443211 13 44556777778888899999999
Q ss_pred cHHHHHhh
Q 025511 218 SISHLASK 225 (251)
Q Consensus 218 SisELa~~ 225 (251)
+..+|+..
T Consensus 95 t~~el~~~ 102 (125)
T smart00351 95 FAWEIRDR 102 (125)
T ss_pred CHHHHHHH
Confidence 99888654
No 143
>PF15236 CCDC66: Coiled-coil domain-containing protein 66
Probab=67.60 E-value=37 Score=29.77 Aligned_cols=14 Identities=29% Similarity=0.380 Sum_probs=10.0
Q ss_pred hhhhhHHhHHhhhh
Q 025511 49 LFLLSFSLLFDMFD 62 (251)
Q Consensus 49 ~~~~~~~~~~~~~~ 62 (251)
-|+=++..++|..+
T Consensus 32 s~LR~~tallDpa~ 45 (157)
T PF15236_consen 32 SFLRGMTALLDPAQ 45 (157)
T ss_pred CccccccccCCHHH
Confidence 45667777888877
No 144
>PF13994 PgaD: PgaD-like protein
Probab=67.56 E-value=7.8 Score=32.12 Aligned_cols=37 Identities=30% Similarity=0.459 Sum_probs=33.0
Q ss_pred cchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceE
Q 025511 157 IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYI 197 (251)
Q Consensus 157 V~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFI 197 (251)
+..+|+|+.|+++++. +++|...+.+|==.||.|+=|
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 8999999999998665 789999999999999999744
No 145
>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=66.71 E-value=20 Score=32.01 Aligned_cols=46 Identities=22% Similarity=0.322 Sum_probs=17.1
Q ss_pred HHHHHHHHHchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 025511 77 QDRYTEMRRRKDEEREARESALEEEAKAQKAREEEAAAFEFEKWKG 122 (251)
Q Consensus 77 e~~~ee~rrkkeeere~eE~~~eEeer~~~eeeerrE~EEY~KwK~ 122 (251)
+++.++.|++..|+..++-.+..|+.++.+|++.++.-+.+++|..
T Consensus 82 qEa~eaAR~RmQEE~dakA~~~kEKq~q~EEEKRrqkie~we~~q~ 127 (190)
T PF06936_consen 82 QEAMEAARRRMQEELDAKAEEYKEKQKQEEEEKRRQKIEMWESMQE 127 (190)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333444444444443332222233333333333334466666654
No 146
>COG2378 Predicted transcriptional regulator [Transcription]
Probab=66.55 E-value=31 Score=32.22 Aligned_cols=70 Identities=17% Similarity=0.360 Sum_probs=56.4
Q ss_pred hHHHHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCC-------------ceEEEcHHHHHHHH
Q 025511 142 DLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRG-------------KYIYISQAEMKAVA 208 (251)
Q Consensus 142 ~lL~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRG-------------KFIYIS~EEm~aVA 208 (251)
..|-..|.|+..++.|...+||..|+++..-+-.=|.+|...|.- |-=++| --+-.|++|..+++
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 346778899999999999999999999999999999999999987 222444 23456999999987
Q ss_pred HHHHh
Q 025511 209 DYIKR 213 (251)
Q Consensus 209 ~fI~q 213 (251)
.=++.
T Consensus 86 ~~l~~ 90 (311)
T COG2378 86 LALRA 90 (311)
T ss_pred HHHHH
Confidence 65543
No 147
>PRK14471 F0F1 ATP synthase subunit B; Provisional
Probab=66.49 E-value=76 Score=26.47 Aligned_cols=15 Identities=33% Similarity=0.416 Sum_probs=8.4
Q ss_pred HHHHHHHhhhhhhhh
Q 025511 39 LILVCLCTSFLFLLS 53 (251)
Q Consensus 39 ~~~~~~~~~~~~~~~ 53 (251)
+||+.++.-|+|-|-
T Consensus 19 lil~~ll~~~l~~pi 33 (164)
T PRK14471 19 LILLLLLAKFAWKPI 33 (164)
T ss_pred HHHHHHHHHHhHHHH
Confidence 455555556666553
No 148
>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=66.10 E-value=12 Score=32.34 Aligned_cols=39 Identities=10% Similarity=0.158 Sum_probs=33.1
Q ss_pred chHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceE
Q 025511 158 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYI 197 (251)
Q Consensus 158 ~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFI 197 (251)
.-.+||..||++..-|-+-++.|+.+|-|+ +.--+|-||
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 149
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=65.91 E-value=13 Score=32.09 Aligned_cols=51 Identities=24% Similarity=0.360 Sum_probs=43.2
Q ss_pred ccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEE-EcHHHHHHH
Q 025511 156 CIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIY-ISQAEMKAV 207 (251)
Q Consensus 156 VV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIY-IS~EEm~aV 207 (251)
-+...+||..||++..=|-+-+..|.++|-|+=. -.||-||- +|++++..+
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 3667889999999999999999999999988755 78899885 677777664
No 150
>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain
Probab=65.30 E-value=45 Score=33.94 Aligned_cols=78 Identities=15% Similarity=0.209 Sum_probs=58.6
Q ss_pred HHHHHHHhcC-ccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHH---------HHHHHHHhcC
Q 025511 146 DFVEYIKKHK-CIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMK---------AVADYIKRQG 215 (251)
Q Consensus 146 ~FI~YIK~~K-VV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~---------aVA~fI~qrG 215 (251)
..+.++..+. .+..++||...|++.++++.-+..|++.|.++- ...--++..+|+|--+ .|.++++.+|
T Consensus 7 ~iL~~l~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kg~v~~-~~~~~~~~~LT~eG~~~l~~G~PE~rl~~~l~~~~ 85 (492)
T PLN02853 7 ALLGALSNNEEISDSGQFAASHGLDHNEVVGVIKSLHGFRYVDA-QDIKRETWVLTEEGKKYAAEGSPEVQLFAAVPAEG 85 (492)
T ss_pred HHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHHHhCCCEEE-EEEEEEEEEECHHHHHHHHcCCHHHHHHHHHhhcC
Confidence 3456677766 589999999999999999999999999995543 3344455557776433 3557888888
Q ss_pred CccHHHHHh
Q 025511 216 RVSISHLAS 224 (251)
Q Consensus 216 RVSisELa~ 224 (251)
-++++||..
T Consensus 86 ~~~~~eL~~ 94 (492)
T PLN02853 86 SISKDELQK 94 (492)
T ss_pred CccHHHHHH
Confidence 889888765
No 151
>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=65.18 E-value=4.6 Score=29.66 Aligned_cols=32 Identities=31% Similarity=0.461 Sum_probs=25.5
Q ss_pred hHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHhc
Q 025511 170 TQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQ 214 (251)
Q Consensus 170 TqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~qr 214 (251)
.|.+|+||++|.++|.=+| |=+.-||+-|+..
T Consensus 13 QQ~AvE~Iq~LMaqGmSsg-------------EAI~~VA~~iRe~ 44 (51)
T PF03701_consen 13 QQQAVERIQELMAQGMSSG-------------EAIAIVAQEIREE 44 (51)
T ss_pred HHHHHHHHHHHHHhcccHH-------------HHHHHHHHHHHHH
Confidence 4789999999999998665 6677777777653
No 152
>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=65.13 E-value=19 Score=27.91 Aligned_cols=63 Identities=25% Similarity=0.340 Sum_probs=37.3
Q ss_pred HHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCccee--ee-CCCc---eEEEcHHHHHHHHH
Q 025511 147 FVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGV--MD-DRGK---YIYISQAEMKAVAD 209 (251)
Q Consensus 147 FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGV--iD-DRGK---FIYIS~EEm~aVA~ 209 (251)
.++.+-.+.++.=+|||...|+++.++-.-+..|..+|-++.. -| ++|. |-||..+.+..+-.
T Consensus 18 Il~~L~~~~~l~de~la~~~~l~~~~vRkiL~~L~~~~lv~~~~~~d~~~~~~~~yw~i~~~~~~~~ik 86 (105)
T PF02002_consen 18 ILDALLRKGELTDEDLAKKLGLKPKEVRKILYKLYEDGLVSYRRRKDDERGWTRYYWYIDYDQIIDVIK 86 (105)
T ss_dssp HHHHHHHH--B-HHHHHHTT-S-HHHHHHHHHHHHHHSS-EEEEE--------EEEEE-THHHH-----
T ss_pred HHHHHHHcCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeEEEEEEcCCCcEEEEEEEEcHHHHHHHHH
Confidence 4566667888999999999999999999999999999998655 33 4565 45677766544443
No 153
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=64.90 E-value=31 Score=26.29 Aligned_cols=75 Identities=12% Similarity=0.142 Sum_probs=45.7
Q ss_pred hhHHHHHHHHHHhc--CccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHhcCCcc
Q 025511 141 RDLLADFVEYIKKH--KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRVS 218 (251)
Q Consensus 141 q~lL~~FI~YIK~~--KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~qrGRVS 218 (251)
+..+..++.||..+ +-+.+++||..+|++..-+-.+.+.. +|+- =.=||..-=|+..+.-+.. |..|
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 45688888998754 45899999999999888776666664 2210 0002222223444444433 4566
Q ss_pred HHHHHhhc
Q 025511 219 ISHLASKS 226 (251)
Q Consensus 219 isELa~~s 226 (251)
+.++|..|
T Consensus 73 i~~iA~~~ 80 (107)
T PRK10219 73 IFDIAMDL 80 (107)
T ss_pred HHHHHHHH
Confidence 66666554
No 154
>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=64.71 E-value=28 Score=29.36 Aligned_cols=53 Identities=34% Similarity=0.535 Sum_probs=40.6
Q ss_pred HHHHhcCccchHhHHhHcC---C-ChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHH
Q 025511 149 EYIKKHKCIPLEDLAAEFK---L-RTQECINRITSLENMGRLSGVMDDRGKYIYISQAEM 204 (251)
Q Consensus 149 ~YIK~~KVV~LEDLAa~Fg---L-rTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm 204 (251)
..|..+++..-+||..... . =||.+|.| +|.+.|-+- +.+..|+|.|--|.+.
T Consensus 9 ~Li~~~~i~tqeeL~~~L~~~G~~vsqaTIsR--dL~elglvk-~~~~~g~~~Y~~~~~~ 65 (146)
T TIGR01529 9 EIITEEKISTQEELVALLKAEGIEVTQATVSR--DLRELGAVK-VRDEDGSYVYSLPADG 65 (146)
T ss_pred HHHHcCCCCCHHHHHHHHHHhCCCcCHHHHHH--HHHHcCCEE-EECCCCcEEEeecccc
Confidence 3468888888888776543 1 38999999 888888875 7779999999766544
No 155
>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=64.66 E-value=13 Score=29.85 Aligned_cols=37 Identities=11% Similarity=0.207 Sum_probs=32.5
Q ss_pred HHHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHH
Q 025511 144 LADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSL 180 (251)
Q Consensus 144 L~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~L 180 (251)
.+.|..+|+.+.=..+.|||.+||++.+-+...++.|
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 4668889999999999999999999888888777765
No 156
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=64.63 E-value=22 Score=33.60 Aligned_cols=66 Identities=18% Similarity=0.319 Sum_probs=49.5
Q ss_pred hcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHhcCCccHHHHHhhcccc
Q 025511 153 KHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRVSISHLASKSNQF 229 (251)
Q Consensus 153 ~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~qrGRVSisELa~~sN~l 229 (251)
.+--|..-|+|.+.|++.|-|++-|++|-++|-+.- --||.|. ||.+-.+.+-.. ++||-+.++.+
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 RQPRVKQKEIAKKLGITLQAVSEHIKELVKEGLIEK--EGRGEYE-ITKKGAEWLLEQ--------LSDLRRFSEEV 87 (260)
T ss_pred hCCCCCHHHHHHHcCCCHHHHHHHHHHHHhccceee--cCCeeEE-EehhHHHHHHHH--------HHHHHHHHHHH
Confidence 345678889999999999999999999999875433 2344454 999887766553 45677777766
No 157
>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=64.62 E-value=24 Score=26.54 Aligned_cols=52 Identities=19% Similarity=0.275 Sum_probs=43.5
Q ss_pred CchhHHHHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceee
Q 025511 139 GDRDLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVM 190 (251)
Q Consensus 139 ~sq~lL~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGVi 190 (251)
..+.++.+-++|+...+-+...-|-.+|++--.-+-.-|..|++.|-+++--
T Consensus 3 ~~D~ly~~a~~~V~~~~~~S~S~lQR~~rIGynrAariid~LE~~GiVs~~~ 54 (65)
T PF09397_consen 3 EEDPLYEEAVEFVIEEGKASISLLQRKFRIGYNRAARIIDQLEEEGIVSPAN 54 (65)
T ss_dssp TTSTTHHHHHHHHHHCTCECHHHHHHHHT--HHHHHHHHHHHHHCTSBE---
T ss_pred cccHHHHHHHHHHHHcCCccHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCCC
Confidence 3467889999999999999999999999999999999999999999987753
No 158
>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=64.61 E-value=21 Score=28.96 Aligned_cols=46 Identities=11% Similarity=0.070 Sum_probs=33.3
Q ss_pred cchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEc-HHHHHH
Q 025511 157 IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYIS-QAEMKA 206 (251)
Q Consensus 157 V~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS-~EEm~a 206 (251)
+.-+|||...|++.+-+-.-+++|.++|.|.- +++.|+|. .+.+..
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 45699999999977666666999999987754 34456664 555544
No 159
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=63.65 E-value=11 Score=32.42 Aligned_cols=52 Identities=12% Similarity=0.136 Sum_probs=37.0
Q ss_pred HHHHHHHHhcCc-----c-chHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceE
Q 025511 145 ADFVEYIKKHKC-----I-PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYI 197 (251)
Q Consensus 145 ~~FI~YIK~~KV-----V-~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFI 197 (251)
....+.|..... . .-.+||.+||++..-|-+-++.|+.+|.|.- .--+|-||
T Consensus 14 ~~l~~~I~~g~l~pG~~LPsE~eLae~~gVSRt~VReAL~~L~~eGlv~~-~~g~G~~V 71 (239)
T PRK04984 14 EYIIESIWNNRFPPGSILPAERELSELIGVTRTTLREVLQRLARDGWLTI-QHGKPTKV 71 (239)
T ss_pred HHHHHHHHcCCCCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE-eCCCeeEe
Confidence 334445544443 3 4568999999999999999999999998873 22345444
No 160
>PRK07353 F0F1 ATP synthase subunit B'; Validated
Probab=63.44 E-value=77 Score=25.48 Aligned_cols=15 Identities=7% Similarity=0.388 Sum_probs=10.3
Q ss_pred HHHHHHHHhhhhhhh
Q 025511 38 LLILVCLCTSFLFLL 52 (251)
Q Consensus 38 ~~~~~~~~~~~~~~~ 52 (251)
++||+.++.-|+|-|
T Consensus 15 flil~~ll~~~l~~p 29 (140)
T PRK07353 15 FVLLTFILNALFYKP 29 (140)
T ss_pred HHHHHHHHHHHHHHH
Confidence 456666777777777
No 161
>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=63.34 E-value=12 Score=24.75 Aligned_cols=29 Identities=21% Similarity=0.298 Sum_probs=23.2
Q ss_pred chHhHHhHcCCChHHHHHHHHHHHhcCCc
Q 025511 158 PLEDLAAEFKLRTQECINRITSLENMGRL 186 (251)
Q Consensus 158 ~LEDLAa~FgLrTqdvI~RIq~Lea~G~L 186 (251)
.-.|||...|++.+-|-.-+..|+.+|.|
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 35799999999888777788999999865
No 162
>TIGR02209 ftsL_broad cell division protein FtsL. This model represents FtsL, both forms similar to that in E. coli and similar to that in B. subtilis. FtsL is one of the later proteins active in cell division septum formation. FtsL is small, low in complexity, and highly divergent. The scope of this model is broader than that of the Pfam model pfam04999.3 for FtsL, as this one includes FtsL from Bacillus subtilis and related species.
Probab=63.34 E-value=58 Score=24.02 Aligned_cols=20 Identities=15% Similarity=0.182 Sum_probs=11.1
Q ss_pred cchhHHHHHHHHHhhhhhhh
Q 025511 33 RANSLLLILVCLCTSFLFLL 52 (251)
Q Consensus 33 ~~~~~~~~~~~~~~~~~~~~ 52 (251)
+.|.++++++|+|...++..
T Consensus 3 ~l~~~l~~~v~~~~~~~v~~ 22 (85)
T TIGR02209 3 KLYVLLLLAILVSAISVVSA 22 (85)
T ss_pred hHHHHHHHHHHHHHHHHHHH
Confidence 44666666666665444443
No 163
>PRK14584 hmsS hemin storage system protein; Provisional
Probab=63.26 E-value=14 Score=32.19 Aligned_cols=45 Identities=22% Similarity=0.313 Sum_probs=40.2
Q ss_pred hcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcH
Q 025511 153 KHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQ 201 (251)
Q Consensus 153 ~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~ 201 (251)
....+..+++|..|++.++. +++|...+.+|==.||-|+=|-|..
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 45688999999999998876 5899999999999999999998865
No 164
>TIGR03321 alt_F1F0_F0_B alternate F1F0 ATPase, F0 subunit B. CC and in principle may run in either direction. This model represents the F0 subunit B of this apparent second ATP synthase.
Probab=63.17 E-value=1.1e+02 Score=27.35 Aligned_cols=16 Identities=44% Similarity=0.596 Sum_probs=10.3
Q ss_pred HHHHHHHHhhhhhhhh
Q 025511 38 LLILVCLCTSFLFLLS 53 (251)
Q Consensus 38 ~~~~~~~~~~~~~~~~ 53 (251)
++||+.++.-|+|-|-
T Consensus 15 Flil~~lL~kfl~kPi 30 (246)
T TIGR03321 15 FLILVWLLKRFLYRPI 30 (246)
T ss_pred HHHHHHHHHHHhHHHH
Confidence 4566666777777663
No 165
>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=63.16 E-value=51 Score=28.78 Aligned_cols=75 Identities=13% Similarity=0.142 Sum_probs=51.2
Q ss_pred hHHHHHHHHHHhc--CccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHhcCCccH
Q 025511 142 DLLADFVEYIKKH--KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRVSI 219 (251)
Q Consensus 142 ~lL~~FI~YIK~~--KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~qrGRVSi 219 (251)
.++..+++||..+ .-..++++|.++|+++.-+....++..... . .=||+.-=|......+. ....||
T Consensus 186 ~~~~~~~~~I~~~~~~~~sl~~lA~~~~~S~~~l~r~Fk~~~G~t-~---------~~yi~~~Rl~~A~~lL~-~t~~sI 254 (287)
T TIGR02297 186 YLFNRFNFLIEENYKQHLRLPEYADRLGISESRLNDICRRFSALS-P---------KRLIIERVMQEARRLLL-FTQHSI 254 (287)
T ss_pred HHHHHHHHHHHHhhccCCCHHHHHHHHCCCHHHHHHHHHHHhCCC-H---------HHHHHHHHHHHHHHHHH-cCCCCH
Confidence 4678899999654 567999999999999999888888754211 0 01233333555555454 555799
Q ss_pred HHHHhhcc
Q 025511 220 SHLASKSN 227 (251)
Q Consensus 220 sELa~~sN 227 (251)
+++|..|+
T Consensus 255 ~eIA~~~G 262 (287)
T TIGR02297 255 NQIAYDLG 262 (287)
T ss_pred HHHHHHhC
Confidence 99988774
No 166
>PRK13453 F0F1 ATP synthase subunit B; Provisional
Probab=62.45 E-value=98 Score=26.35 Aligned_cols=13 Identities=23% Similarity=0.381 Sum_probs=5.8
Q ss_pred HHHHHHhhhhhhh
Q 025511 40 ILVCLCTSFLFLL 52 (251)
Q Consensus 40 ~~~~~~~~~~~~~ 52 (251)
||+.++.-|+|-|
T Consensus 30 iL~~lL~~~l~~p 42 (173)
T PRK13453 30 VLLALLKKFAWGP 42 (173)
T ss_pred HHHHHHHHHHHHH
Confidence 3444444444444
No 167
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=62.31 E-value=11 Score=32.77 Aligned_cols=63 Identities=14% Similarity=0.180 Sum_probs=42.1
Q ss_pred CccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcH-----HHHHHHHHHHHhcCCcc
Q 025511 155 KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQ-----AEMKAVADYIKRQGRVS 218 (251)
Q Consensus 155 KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~-----EEm~aVA~fI~qrGRVS 218 (251)
|+=.=.+||.+||++..-+.+-|..|..+|.|.- .--+|.||-=++ ..+..+.+.+...|.-.
T Consensus 34 ~LPsE~eLa~~~~VSR~TVR~Al~~L~~eGli~r-~~G~GtfV~~~~~~~~~~~~~~f~~~~~~~g~~~ 101 (241)
T PRK10079 34 YLPAEQQLAARYEVNRHTLRRAIDQLVEKGWVQR-RQGVGVLVLMRPYDYPLNAQARFSQNLLDQGSHP 101 (241)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE-ecCCEEEEecCccccccccccchHHHHHhcCCCc
Confidence 3344457999999999999999999999999873 233566652111 12344455566666543
No 168
>PRK13428 F0F1 ATP synthase subunit delta; Provisional
Probab=62.14 E-value=1.1e+02 Score=30.19 Aligned_cols=17 Identities=18% Similarity=0.192 Sum_probs=11.2
Q ss_pred HHHHHHHHhhhhhhhhH
Q 025511 38 LLILVCLCTSFLFLLSF 54 (251)
Q Consensus 38 ~~~~~~~~~~~~~~~~~ 54 (251)
++||+.+|--|+|-|-.
T Consensus 11 FlIl~~lL~kfl~~Pi~ 27 (445)
T PRK13428 11 FAVIVFLVWRFVVPPVR 27 (445)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 45666677777777743
No 169
>KOG2002 consensus TPR-containing nuclear phosphoprotein that regulates K(+) uptake [Inorganic ion transport and metabolism]
Probab=62.13 E-value=34 Score=37.67 Aligned_cols=19 Identities=21% Similarity=0.223 Sum_probs=8.2
Q ss_pred hhhHhhhhhcccccccccc
Q 025511 14 IFDIHRVLEGYESSTRKDT 32 (251)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~~ 32 (251)
.|++--|+----.+++++.
T Consensus 753 ~FN~a~v~kkla~s~lr~~ 771 (1018)
T KOG2002|consen 753 KFNLALVLKKLAESILRLE 771 (1018)
T ss_pred HhHHHHHHHHHHHHHHhcc
Confidence 4444444444444444333
No 170
>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=61.73 E-value=37 Score=34.43 Aligned_cols=74 Identities=12% Similarity=0.180 Sum_probs=62.3
Q ss_pred HHHHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHhcCCccHHHH
Q 025511 143 LLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRVSISHL 222 (251)
Q Consensus 143 lL~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~qrGRVSisEL 222 (251)
+.+......+ .....+.|++..+|++...+.+.+..|...|.++-|.+| +|.+ +.|.+++...|.+|++++
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 5566666555 578889999999999999999999999999999999886 3555 899999999999999876
Q ss_pred Hhh
Q 025511 223 ASK 225 (251)
Q Consensus 223 a~~ 225 (251)
-..
T Consensus 547 r~~ 549 (581)
T TIGR00475 547 RDK 549 (581)
T ss_pred HHH
Confidence 554
No 171
>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=61.32 E-value=8.9 Score=27.18 Aligned_cols=23 Identities=26% Similarity=0.547 Sum_probs=20.2
Q ss_pred HHHHHHHHhcCCccHHHHHhhcc
Q 025511 205 KAVADYIKRQGRVSISHLASKSN 227 (251)
Q Consensus 205 ~aVA~fI~qrGRVSisELa~~sN 227 (251)
..+-++|+++|.||+.+|++.-|
T Consensus 3 ~~Il~~l~~~~~~s~~ela~~~~ 25 (57)
T PF08220_consen 3 QQILELLKEKGKVSVKELAEEFG 25 (57)
T ss_pred HHHHHHHHHcCCEEHHHHHHHHC
Confidence 56889999999999999998754
No 172
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=61.29 E-value=15 Score=32.24 Aligned_cols=42 Identities=17% Similarity=0.183 Sum_probs=34.0
Q ss_pred ccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEE
Q 025511 156 CIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIY 198 (251)
Q Consensus 156 VV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIY 198 (251)
+..-.+||..||++-.-|.+-|+.|+.+|-|+ +.--+|-||-
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 33467999999999999999999999999987 3334676653
No 173
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=60.72 E-value=31 Score=34.77 Aligned_cols=57 Identities=18% Similarity=0.335 Sum_probs=41.6
Q ss_pred HHHHHhc-CccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCce-EEEcHHHHHHHHHH
Q 025511 148 VEYIKKH-KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKY-IYISQAEMKAVADY 210 (251)
Q Consensus 148 I~YIK~~-KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKF-IYIS~EEm~aVA~f 210 (251)
++++..+ ..+.++||+..-|+++.|+|.-++.| |.|. --+|.| |+|+++-++...+-
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 3344444 58999999999999999998766554 5553 245666 88999888776554
No 174
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=60.72 E-value=48 Score=27.93 Aligned_cols=47 Identities=19% Similarity=0.335 Sum_probs=40.8
Q ss_pred hcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHH
Q 025511 153 KHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQA 202 (251)
Q Consensus 153 ~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~E 202 (251)
.-|+-.+-+||.+.|+.+.-|-.--+.|+.+|-|. -.||+-.|||+.
T Consensus 32 GdkLPSvRelA~~~~VNpnTv~raY~eLE~eG~i~---t~rg~G~fV~~~ 78 (125)
T COG1725 32 GDKLPSVRELAKDLGVNPNTVQRAYQELEREGIVE---TKRGKGTFVTED 78 (125)
T ss_pred CCCCCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEE---EecCeeEEEcCC
Confidence 35778889999999999988888899999999865 569999999965
No 175
>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=60.68 E-value=29 Score=27.24 Aligned_cols=67 Identities=12% Similarity=0.179 Sum_probs=49.5
Q ss_pred chHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeC-CCceEEEcHHHHHHHHHHHHhc-CCccHHHHHhhccc
Q 025511 158 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDD-RGKYIYISQAEMKAVADYIKRQ-GRVSISHLASKSNQ 228 (251)
Q Consensus 158 ~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDD-RGKFIYIS~EEm~aVA~fI~qr-GRVSisELa~~sN~ 228 (251)
.+.|+|..+|+++.- |.--+..|.|.+.-.+ .+.|=|-|++++..+.....-+ --+|++++...-+.
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 6677888999997754 5788888999999886443333 23898888765443
No 176
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=60.57 E-value=78 Score=25.37 Aligned_cols=70 Identities=13% Similarity=0.147 Sum_probs=49.2
Q ss_pred hhHHHHHHHHHHhc--CccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHH------HHHHHHHH
Q 025511 141 RDLLADFVEYIKKH--KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEM------KAVADYIK 212 (251)
Q Consensus 141 q~lL~~FI~YIK~~--KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm------~aVA~fI~ 212 (251)
...+..+++||..+ .-..+++||.++|+++.-+-...+.-.. +|+.++ ...+..+.
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 45678899999765 3488999999999988877666665322 556555 44555555
Q ss_pred hcCCccHHHHHhhcc
Q 025511 213 RQGRVSISHLASKSN 227 (251)
Q Consensus 213 qrGRVSisELa~~sN 227 (251)
. +..++++++..|.
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 177
>PRK14472 F0F1 ATP synthase subunit B; Provisional
Probab=60.38 E-value=1.1e+02 Score=26.03 Aligned_cols=11 Identities=0% Similarity=0.407 Sum_probs=5.0
Q ss_pred hhHHHHHHHHH
Q 025511 141 RDLLADFVEYI 151 (251)
Q Consensus 141 q~lL~~FI~YI 151 (251)
+.++..||+-+
T Consensus 160 ~~li~~~i~~l 170 (175)
T PRK14472 160 KKVVDSMIQDL 170 (175)
T ss_pred HHHHHHHHHHh
Confidence 34444554444
No 178
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=60.16 E-value=73 Score=26.98 Aligned_cols=63 Identities=16% Similarity=0.289 Sum_probs=46.7
Q ss_pred HHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeee--CCC--ceEE--EcHHHHHHH
Q 025511 145 ADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMD--DRG--KYIY--ISQAEMKAV 207 (251)
Q Consensus 145 ~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViD--DRG--KFIY--IS~EEm~aV 207 (251)
..|...+..+.=...+|||...|++-.-|=.-+|.|..-|.+.=.-+ +.| +||| |.++|+...
T Consensus 31 ~v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~~~~Ggy~yiY~~i~~ee~k~~ 99 (126)
T COG3355 31 EVYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVNLKGGGYYYLYKPIDPEEIKKK 99 (126)
T ss_pred HHHHHHHhhcCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeeccCCCceeEEEecCCHHHHHHH
Confidence 33444455677788999999999998888889999999998876555 455 5566 556666543
No 179
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=59.89 E-value=14 Score=32.10 Aligned_cols=43 Identities=14% Similarity=0.275 Sum_probs=34.9
Q ss_pred cCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceE
Q 025511 154 HKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYI 197 (251)
Q Consensus 154 ~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFI 197 (251)
.|+=.-.+||..||++..-+..-|..|..+|.|.-. --+|.||
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 366677789999999999999999999999998744 2245555
No 180
>PRK14999 histidine utilization repressor; Provisional
Probab=59.74 E-value=29 Score=30.26 Aligned_cols=70 Identities=16% Similarity=0.291 Sum_probs=45.5
Q ss_pred HHHHHHHHhc------CccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcH-------HHHHHHHHHH
Q 025511 145 ADFVEYIKKH------KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQ-------AEMKAVADYI 211 (251)
Q Consensus 145 ~~FI~YIK~~------KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~-------EEm~aVA~fI 211 (251)
....+.|... |+=.=.+||.+||++..-|.+-|..|..+|.|.-+ --+|.|| ++ ..+......+
T Consensus 19 ~~i~~~I~~g~~~~G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~-~GkGTfV--~~~~~~~~~~~~~~~~~~~ 95 (241)
T PRK14999 19 QDICKKIAGGVWQPHDRIPSEAELVAQYGFSRMTINRALRELTDEGWLVRL-QGVGTFV--AEPKGQSALFEVRSIAEEI 95 (241)
T ss_pred HHHHHHHHcCCCCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe-cCcEEEE--CCCCccccHHHHHHHHHHH
Confidence 3444555543 44456789999999999999999999999987532 1245554 32 1234444555
Q ss_pred HhcCCc
Q 025511 212 KRQGRV 217 (251)
Q Consensus 212 ~qrGRV 217 (251)
...|..
T Consensus 96 ~~~g~~ 101 (241)
T PRK14999 96 AARRHQ 101 (241)
T ss_pred HHcCCC
Confidence 555543
No 181
>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=59.70 E-value=25 Score=27.41 Aligned_cols=55 Identities=11% Similarity=0.238 Sum_probs=40.1
Q ss_pred hHHHHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHH
Q 025511 142 DLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIK 212 (251)
Q Consensus 142 ~lL~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~ 212 (251)
..+...++||.. +-+.+.|||..||++ ..+|+| .| .|.+=+||++=-..|-..+.
T Consensus 6 ~R~~~I~e~l~~-~~~ti~dvA~~~gvS-~~TVsr--~L------------~~~~~~Vs~~Tr~rV~~aa~ 60 (80)
T TIGR02844 6 ERVLEIGKYIVE-TKATVRETAKVFGVS-KSTVHK--DV------------TERLPEINPELAEEVKEVLD 60 (80)
T ss_pred HHHHHHHHHHHH-CCCCHHHHHHHhCCC-HHHHHH--Hh------------cCCCCCCCHHHHHHHHHHHc
Confidence 356778999999 999999999999995 456666 22 23323588877777666665
No 182
>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=59.38 E-value=18 Score=28.52 Aligned_cols=47 Identities=13% Similarity=0.188 Sum_probs=39.3
Q ss_pred cCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEc
Q 025511 154 HKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYIS 200 (251)
Q Consensus 154 ~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS 200 (251)
++.+...+||..+|++..-+-+-++.|...|-|...-...|-|.--.
T Consensus 23 ~~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~~~g~~ggy~l~~ 69 (132)
T TIGR00738 23 EGPVSVKEIAERQGISRSYLEKILRTLRRAGLVESVRGPGGGYRLAR 69 (132)
T ss_pred CCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEeccCCCCCccCCC
Confidence 34899999999999999999999999999999877555666666533
No 183
>PF06224 HTH_42: Winged helix DNA-binding domain; InterPro: IPR009351 This is a family of conserved bacterial proteins with unknown function.
Probab=59.10 E-value=25 Score=31.80 Aligned_cols=65 Identities=23% Similarity=0.294 Sum_probs=55.5
Q ss_pred chhHHHHHH-HHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCc-eEEEcHHHH
Q 025511 140 DRDLLADFV-EYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGK-YIYISQAEM 204 (251)
Q Consensus 140 sq~lL~~FI-~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGK-FIYIS~EEm 204 (251)
.+..+...+ .|+...=.+.+.|+|--+|++..++-.-++.|.+.|.|..|-.++|+ ..|+.++..
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 344455554 49999999999999999999999999999999999999999999777 588888755
No 184
>KOG2002 consensus TPR-containing nuclear phosphoprotein that regulates K(+) uptake [Inorganic ion transport and metabolism]
Probab=59.07 E-value=63 Score=35.70 Aligned_cols=6 Identities=67% Similarity=0.794 Sum_probs=2.2
Q ss_pred HHHHHH
Q 025511 100 EEAKAQ 105 (251)
Q Consensus 100 Eeer~~ 105 (251)
||++.+
T Consensus 861 eee~~~ 866 (1018)
T KOG2002|consen 861 EEEKAR 866 (1018)
T ss_pred HHHHHH
Confidence 333333
No 185
>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=59.05 E-value=18 Score=24.74 Aligned_cols=42 Identities=14% Similarity=0.246 Sum_probs=33.7
Q ss_pred HHHHHHHhcCc-cchHhHHhHcCCChHHHHHHHHHHHhcCCcc
Q 025511 146 DFVEYIKKHKC-IPLEDLAAEFKLRTQECINRITSLENMGRLS 187 (251)
Q Consensus 146 ~FI~YIK~~KV-V~LEDLAa~FgLrTqdvI~RIq~Lea~G~LT 187 (251)
..++++..+.- +.+.|||.+.|++..-+-.-++.|.+.|-+.
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 34566655554 6899999999999999999999999999763
No 186
>KOG3634 consensus Troponin [Cytoskeleton]
Probab=58.92 E-value=36 Score=33.44 Aligned_cols=21 Identities=24% Similarity=0.403 Sum_probs=10.4
Q ss_pred HhhhhhHHHHHHHHhhhhHHH
Q 025511 58 FDMFDLKADEAARESRQSKQD 78 (251)
Q Consensus 58 ~~~~~Reaee~~RE~Rk~~e~ 78 (251)
+|.++|+.++.+-..=+.+++
T Consensus 91 ~~~~~rer~E~eL~eLkekq~ 111 (361)
T KOG3634|consen 91 FDRIEREREEKELKELKEKQE 111 (361)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 566666655544433333433
No 187
>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=58.85 E-value=3.2 Score=37.91 Aligned_cols=31 Identities=19% Similarity=0.617 Sum_probs=0.0
Q ss_pred EEEcHHHHHHHHHHHHhcCCccHHHHHhhcccc
Q 025511 197 IYISQAEMKAVADYIKRQGRVSISHLASKSNQF 229 (251)
Q Consensus 197 IYIS~EEm~aVA~fI~qrGRVSisELa~~sN~l 229 (251)
=|||.+|+++|-+|++ ||+|...|-.+.+.+
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 3799999999999997 999988776666543
No 188
>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=58.77 E-value=46 Score=25.90 Aligned_cols=62 Identities=13% Similarity=0.229 Sum_probs=45.7
Q ss_pred chHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHH--HHHHhcCCccHHHHHhhc
Q 025511 158 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVA--DYIKRQGRVSISHLASKS 226 (251)
Q Consensus 158 ~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA--~fI~qrGRVSisELa~~s 226 (251)
.+.++|..+|+++. -|.--++.|-|... ++.|.+.| +++.+..+. ...++-| +|++++....
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 36789999999764 47788999999884 56788877 888885442 3445557 8888887754
No 189
>COG1422 Predicted membrane protein [Function unknown]
Probab=58.74 E-value=73 Score=29.11 Aligned_cols=22 Identities=18% Similarity=0.368 Sum_probs=12.7
Q ss_pred HHHHHHHhhhhhhhhHHhHHhh
Q 025511 39 LILVCLCTSFLFLLSFSLLFDM 60 (251)
Q Consensus 39 ~~~~~~~~~~~~~~~~~~~~~~ 60 (251)
+++....|++.+++.-..++|.
T Consensus 50 ilV~avi~gl~~~i~~~~liD~ 71 (201)
T COG1422 50 ILVAAVITGLYITILQKLLIDQ 71 (201)
T ss_pred HHHHHHHHHHHHHHHHHHhccH
Confidence 3334455666666666666663
No 190
>PRK08475 F0F1 ATP synthase subunit B; Validated
Probab=58.66 E-value=1.2e+02 Score=25.94 Aligned_cols=15 Identities=27% Similarity=0.098 Sum_probs=7.4
Q ss_pred HHHHHHHhhhhhhhh
Q 025511 39 LILVCLCTSFLFLLS 53 (251)
Q Consensus 39 ~~~~~~~~~~~~~~~ 53 (251)
+||+.++.-|+|-|-
T Consensus 33 lil~~lL~~fl~kPi 47 (167)
T PRK08475 33 LIFVGILWYFAAKPL 47 (167)
T ss_pred HHHHHHHHHHHHHHH
Confidence 444555555555443
No 191
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=58.63 E-value=16 Score=31.88 Aligned_cols=40 Identities=15% Similarity=0.286 Sum_probs=33.5
Q ss_pred chHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEE
Q 025511 158 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIY 198 (251)
Q Consensus 158 ~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIY 198 (251)
.-.+||..||++..-|.+-|+.|+.+|-|.-. --+|-||-
T Consensus 33 sE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~-~~~G~~V~ 72 (251)
T PRK09990 33 SERRLCEKLGFSRSALREGLTVLRGRGIIETA-QGRGSFVA 72 (251)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe-CCCeeEEe
Confidence 45699999999999999999999999988733 34677765
No 192
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=58.23 E-value=19 Score=30.73 Aligned_cols=45 Identities=18% Similarity=0.254 Sum_probs=31.8
Q ss_pred HhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEc-HHHHHHHHH
Q 025511 160 EDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYIS-QAEMKAVAD 209 (251)
Q Consensus 160 EDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS-~EEm~aVA~ 209 (251)
.|||...|++.+-+-.-+++|...| | .. .+| .|.|. .+.+..+|.
T Consensus 177 ~~iA~~lG~tretvsR~l~~L~~~g-l--~~-~~~-~i~I~d~~~L~~~~~ 222 (236)
T PRK09392 177 RVLASYLGMTPENLSRAFAALASHG-V--HV-DGS-AVTITDPAGLARFAK 222 (236)
T ss_pred HHHHHHhCCChhHHHHHHHHHHhCC-e--Ee-eCC-EEEEcCHHHHHHhhc
Confidence 6899999996666555589999999 5 33 344 56664 666666554
No 193
>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=58.21 E-value=32 Score=26.74 Aligned_cols=57 Identities=21% Similarity=0.233 Sum_probs=42.2
Q ss_pred HHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCce--EEEcHHHHHHHH
Q 025511 149 EYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKY--IYISQAEMKAVA 208 (251)
Q Consensus 149 ~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKF--IYIS~EEm~aVA 208 (251)
.-.|.+..||++.++..-|++...+-.+|+.|...|.|.- +.++| --+|-.-++.+|
T Consensus 17 ~gmk~hE~VP~~~I~~~s~l~~~~~~~~L~~L~~~kLv~~---~~~~Y~GYrLT~~GYD~LA 75 (82)
T PF09202_consen 17 MGMKNHEWVPLELIEKISGLSEGEVEKRLKRLVKLKLVSR---RNKPYDGYRLTFLGYDYLA 75 (82)
T ss_dssp TTTTT-SSEEHHHHHHHHT--HHHHHHHHHHHHHTTSEEE---E-SSS-EEEE-HHHHHHHH
T ss_pred HcccCCccCCHHHHHHHhCcCHHHHHHHHHHHHhcCCccc---cCCCcceEEEeecchhHHH
Confidence 3458899999999999999999999999999999999987 44444 346666666555
No 194
>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]
Probab=58.17 E-value=55 Score=34.80 Aligned_cols=12 Identities=25% Similarity=0.448 Sum_probs=6.4
Q ss_pred ccchHhHHhHcC
Q 025511 156 CIPLEDLAAEFK 167 (251)
Q Consensus 156 VV~LEDLAa~Fg 167 (251)
+-++++-.+.|+
T Consensus 737 ~a~~drY~sdf~ 748 (940)
T KOG4661|consen 737 KAVLDRYSSDFK 748 (940)
T ss_pred hhHhhhhhcccc
Confidence 444555555554
No 195
>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=57.98 E-value=46 Score=23.16 Aligned_cols=63 Identities=16% Similarity=0.062 Sum_probs=41.2
Q ss_pred chHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHhc-CCccHHHHHh
Q 025511 158 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQ-GRVSISHLAS 224 (251)
Q Consensus 158 ~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~qr-GRVSisELa~ 224 (251)
.+.|+|..+|+++.-+-.-.+. .|.+...-++ |.+-+.|++++..+.....-+ --+|+.++.+
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 4678999999977766655432 2544444444 566778999988776555443 4577777654
No 196
>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=57.77 E-value=37 Score=26.90 Aligned_cols=66 Identities=15% Similarity=0.202 Sum_probs=50.9
Q ss_pred chHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHH--HHHhcCCccHHHHHhhccc
Q 025511 158 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVAD--YIKRQGRVSISHLASKSNQ 228 (251)
Q Consensus 158 ~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~--fI~qrGRVSisELa~~sN~ 228 (251)
.+.++|..||+++.- |.--++.|-|..+--+.|.|=|-|++.+..+.. +.++-| +|++++....+.
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 367899999997653 457899999997666678899999999987754 445556 999888776553
No 197
>PRK14585 pgaD putative PGA biosynthesis protein; Provisional
Probab=57.64 E-value=13 Score=32.05 Aligned_cols=45 Identities=11% Similarity=0.163 Sum_probs=39.4
Q ss_pred CccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHH
Q 025511 155 KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAE 203 (251)
Q Consensus 155 KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EE 203 (251)
+.+..+|||+.||++++. +++|...+.+|==+||.|.-+.|..|-
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 567778999999998865 789999999999999999999887664
No 198
>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=57.61 E-value=34 Score=29.21 Aligned_cols=52 Identities=19% Similarity=0.213 Sum_probs=40.0
Q ss_pred HHHHHHHHhc------CccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceE
Q 025511 145 ADFVEYIKKH------KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYI 197 (251)
Q Consensus 145 ~~FI~YIK~~------KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFI 197 (251)
..|.+.|... |+-.-.+||..||++..-+..+|..|..+|.|..+- -+|.||
T Consensus 8 ~~l~~~I~~g~~~~g~~lPsE~eLa~~~~Vsr~Tvr~Al~~L~~eGli~~~~-g~Gt~V 65 (231)
T TIGR03337 8 DHLSYQIRAGALLPGDKLPSERDLGERFNTTRVTIREALQQLEAEGLIYRED-RRGWFV 65 (231)
T ss_pred HHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCeEEEeC-CCEEEE
Confidence 4566667553 344567899999999999999999999999987642 256665
No 199
>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=57.58 E-value=33 Score=24.37 Aligned_cols=37 Identities=27% Similarity=0.468 Sum_probs=31.6
Q ss_pred HHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHh
Q 025511 146 DFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLEN 182 (251)
Q Consensus 146 ~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea 182 (251)
..++++-.++-+.+.+||..+|++.--+.+.|..|..
T Consensus 9 ~Ll~~L~~~~~~~~~ela~~l~~S~rti~~~i~~L~~ 45 (59)
T PF08280_consen 9 KLLELLLKNKWITLKELAKKLNISERTIKNDINELNE 45 (59)
T ss_dssp HHHHHHHHHTSBBHHHHHHHCTS-HHHHHHHHHHHHT
T ss_pred HHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4677776799999999999999999999999999873
No 200
>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=57.38 E-value=47 Score=26.64 Aligned_cols=65 Identities=12% Similarity=0.189 Sum_probs=49.3
Q ss_pred chHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHH--HHHHhcCCccHHHHHhhcc
Q 025511 158 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVA--DYIKRQGRVSISHLASKSN 227 (251)
Q Consensus 158 ~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA--~fI~qrGRVSisELa~~sN 227 (251)
.+.++|..+|+++. -|.--+..|-|...-.+.|.|=|-|++.+..+. ...++-| +|+.++....+
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 46799999999764 467788999998765556778888999998654 4456667 99888776543
No 201
>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=57.34 E-value=25 Score=30.37 Aligned_cols=61 Identities=18% Similarity=0.316 Sum_probs=41.6
Q ss_pred CccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcH-------HHHHHHHHHHHhcCCcc
Q 025511 155 KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQ-------AEMKAVADYIKRQGRVS 218 (251)
Q Consensus 155 KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~-------EEm~aVA~fI~qrGRVS 218 (251)
|+=.-.+||..||++..-|.+-|+.|..+|.|.-+ --+|.|| ++ ..+..+..-+...|.-.
T Consensus 24 ~LPsE~eLa~~~~VSR~TVR~Al~~L~~eGli~r~-~G~GtfV--~~~~~~~~~~~~~~~~~~~~~~g~~~ 91 (230)
T TIGR02018 24 RIPSEHELVAQYGCSRMTVNRALRELTDAGLLERR-QGVGTFV--AEPKAQSALLEIRNIADEIVARGHRY 91 (230)
T ss_pred cCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe-cCCEEEE--ccCcccchhhcchhHHHHHHhcCCCc
Confidence 44455689999999999999999999999987643 2356665 32 12334444455566443
No 202
>KOG2908 consensus 26S proteasome regulatory complex, subunit RPN9/PSMD13 [Posttranslational modification, protein turnover, chaperones]
Probab=57.32 E-value=20 Score=35.39 Aligned_cols=48 Identities=17% Similarity=0.364 Sum_probs=45.2
Q ss_pred hcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEc
Q 025511 153 KHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYIS 200 (251)
Q Consensus 153 ~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS 200 (251)
..+-|.++++|..-.++..+|.=-|-.=..-|-|+|.||+=+.-+|+|
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 567899999999999999999999999999999999999999999997
No 203
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=57.28 E-value=20 Score=31.47 Aligned_cols=53 Identities=21% Similarity=0.140 Sum_probs=40.0
Q ss_pred HHHHHHHHHhcC------ccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceE
Q 025511 144 LADFVEYIKKHK------CIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYI 197 (251)
Q Consensus 144 L~~FI~YIK~~K------VV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFI 197 (251)
.+.+.+.|.... +..-.+||..||++..-|.+-|+.|+.+|-|+ +.--+|-||
T Consensus 14 ~~~l~~~I~~g~l~pG~~LpsE~eLae~~gVSRtpVREAL~~L~~eGlV~-~~~~~G~~V 72 (253)
T PRK11523 14 AAELKERIEQGVYLVGDKLPAERFIADEKNVSRTVVREAIIMLEVEGYVE-VRKGSGIHV 72 (253)
T ss_pred HHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE-EecCCeeEE
Confidence 444555555543 33456899999999999999999999999887 334577777
No 204
>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=57.20 E-value=19 Score=27.47 Aligned_cols=57 Identities=18% Similarity=0.341 Sum_probs=38.1
Q ss_pred hHHHHHHHHHHhcC--ccchHhHHhHcC-CChHHHHHHHHHHHhcCCcc---eeeeCCCceEEEcH
Q 025511 142 DLLADFVEYIKKHK--CIPLEDLAAEFK-LRTQECINRITSLENMGRLS---GVMDDRGKYIYISQ 201 (251)
Q Consensus 142 ~lL~~FI~YIK~~K--VV~LEDLAa~Fg-LrTqdvI~RIq~Lea~G~LT---GViDDRGKFIYIS~ 201 (251)
.-|..-|+|+|.+- -+.++||..+.+ +... ..+..++..-.+. -..-..|+|.|-++
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 34788899999875 789999999999 6555 4443444333332 22235799999753
No 205
>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=56.88 E-value=35 Score=25.38 Aligned_cols=50 Identities=14% Similarity=0.292 Sum_probs=37.0
Q ss_pred HHHHHHh---cCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCce
Q 025511 147 FVEYIKK---HKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKY 196 (251)
Q Consensus 147 FI~YIK~---~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKF 196 (251)
++-|+.. .+.+...+||...|+++.-+-.-++.|...|-|...--..|=|
T Consensus 13 ~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~~G~~GGy 65 (83)
T PF02082_consen 13 ILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIESSRGRGGGY 65 (83)
T ss_dssp HHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETSTTSEE
T ss_pred HHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEecCCCCCce
Confidence 3444543 3349999999999999999999999999999887665444444
No 206
>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=56.87 E-value=21 Score=26.34 Aligned_cols=48 Identities=21% Similarity=0.393 Sum_probs=41.0
Q ss_pred HHHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCce
Q 025511 144 LADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKY 196 (251)
Q Consensus 144 L~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKF 196 (251)
|-++++.+..+-+|..--+|.+.|++++-+.+-|.+|-. --+|| ||.|
T Consensus 1 lp~Lidll~~~P~Vsa~mva~~L~vT~~~A~~li~eLg~-rEiTG----r~R~ 48 (54)
T PF11972_consen 1 LPRLIDLLLSRPLVSAPMVAKELGVTPQAAQRLIAELGL-REITG----RGRY 48 (54)
T ss_pred CHHHHHHHHhCccccHHHHHHHhCCCHHHHHHHHHHhhc-eeecC----Cccc
Confidence 346899999999999999999999999999999999877 55665 5554
No 207
>KOG2412 consensus Nuclear-export-signal (NES)-containing protein/polyadenylated-RNA export factor [RNA processing and modification]
Probab=56.74 E-value=63 Score=33.68 Aligned_cols=6 Identities=17% Similarity=0.013 Sum_probs=2.9
Q ss_pred HHHHHH
Q 025511 145 ADFVEY 150 (251)
Q Consensus 145 ~~FI~Y 150 (251)
.-|-+|
T Consensus 304 ~m~w~~ 309 (591)
T KOG2412|consen 304 QMFWNS 309 (591)
T ss_pred HhhhhH
Confidence 445554
No 208
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=56.63 E-value=50 Score=31.65 Aligned_cols=56 Identities=11% Similarity=0.192 Sum_probs=41.5
Q ss_pred HHHHh-cCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHH
Q 025511 149 EYIKK-HKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVAD 209 (251)
Q Consensus 149 ~YIK~-~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~ 209 (251)
+++.. .+.+.++|||..-|+++.|+|.-++ ..|.| ..-+.+-+|+++++.++..-+
T Consensus 215 ~~L~~~~~~isi~~is~~T~i~~~Dii~tL~---~l~~l--~~~~g~~~i~~~~~~~~~~~~ 271 (290)
T PLN03238 215 EQLRDVKGDVSIKDLSLATGIRGEDIVSTLQ---SLNLI--KYWKGQHVIHVDQRVLDEHWA 271 (290)
T ss_pred HHHHhcCCCccHHHHHHHhCCCHHHHHHHHH---HCCcE--EEECCcEEEEeCHHHHHHHHH
Confidence 33443 5789999999999999999987665 55666 345667788899987766544
No 209
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=56.58 E-value=21 Score=31.21 Aligned_cols=54 Identities=20% Similarity=0.270 Sum_probs=38.8
Q ss_pred HHHHHHHHHHhcC------ccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceE
Q 025511 143 LLADFVEYIKKHK------CIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYI 197 (251)
Q Consensus 143 lL~~FI~YIK~~K------VV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFI 197 (251)
....+-+.|.... +-.-.+||..||++..-|.+-++.|+.+|-|+-+ --+|-||
T Consensus 15 v~~~l~~~I~~g~l~pG~~LpsE~eLa~~lgVSRtpVREAL~~L~~eGlv~~~-~~~G~~V 74 (254)
T PRK09464 15 IEQQLEFLILEGTLRPGEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRR-QGGGTFV 74 (254)
T ss_pred HHHHHHHHHHcCCCCCCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe-cCceeEE
Confidence 3444555554443 3357789999999999999999999999988743 2344444
No 210
>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=56.50 E-value=3.7 Score=36.59 Aligned_cols=25 Identities=24% Similarity=0.408 Sum_probs=17.9
Q ss_pred HHHHHHHHHHhcCCccHHHHHhhcc
Q 025511 203 EMKAVADYIKRQGRVSISHLASKSN 227 (251)
Q Consensus 203 Em~aVA~fI~qrGRVSisELa~~sN 227 (251)
-+....+||+.+--|.+.|||...|
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 4778888899888888888887654
No 211
>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=56.44 E-value=61 Score=25.23 Aligned_cols=64 Identities=17% Similarity=0.342 Sum_probs=45.9
Q ss_pred chHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHH--HHHh-cCCccHHHHHhhcc
Q 025511 158 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVAD--YIKR-QGRVSISHLASKSN 227 (251)
Q Consensus 158 ~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~--fI~q-rGRVSisELa~~sN 227 (251)
.+.++|..+|+++..+-- -+..|.|..+-++ |.|=+-+++++..+.. +.++ -| +|++++...-+
T Consensus 2 ~I~e~a~~~gvs~~tLR~----ye~~Gll~p~r~~-~g~R~Y~~~dv~~l~~I~~L~~~~G-~~l~ei~~~l~ 68 (96)
T cd04774 2 KVDEVAKRLGLTKRTLKY----YEEIGLVSPERSE-GRYRLYSEEDLKRLERILRLREVLG-FSLQEVTHFLE 68 (96)
T ss_pred CHHHHHHHHCcCHHHHHH----HHHCCCCCCCcCC-CCCEEECHHHHHHHHHHHHHHHHcC-CCHHHHHHHHh
Confidence 467999999997765443 3667999876654 5677779999888766 5555 55 88877665443
No 212
>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=56.27 E-value=28 Score=23.92 Aligned_cols=38 Identities=16% Similarity=0.282 Sum_probs=29.2
Q ss_pred hhHHHHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHH
Q 025511 141 RDLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITS 179 (251)
Q Consensus 141 q~lL~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~ 179 (251)
++.|+.=|+.|+..+ +.+-..|..||++..-+.+|++-
T Consensus 2 ee~l~~Ai~~v~~g~-~S~r~AA~~ygVp~sTL~~r~~g 39 (45)
T PF05225_consen 2 EEDLQKAIEAVKNGK-MSIRKAAKKYGVPRSTLRRRLRG 39 (45)
T ss_dssp HHHHHHHHHHHHTTS-S-HHHHHHHHT--HHHHHHHHHH
T ss_pred HHHHHHHHHHHHhCC-CCHHHHHHHHCcCHHHHHHHHcC
Confidence 345777889999999 99999999999999888887753
No 213
>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=55.93 E-value=18 Score=31.79 Aligned_cols=43 Identities=28% Similarity=0.475 Sum_probs=37.3
Q ss_pred hHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHH
Q 025511 159 LEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQA 202 (251)
Q Consensus 159 LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~E 202 (251)
-++||..||.+|--+.+-+.-+-+.|+|.-|- ..|||=|-=|.
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 47999999999999999999999999998764 57999997653
No 214
>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=55.62 E-value=42 Score=25.05 Aligned_cols=54 Identities=26% Similarity=0.407 Sum_probs=33.8
Q ss_pred HHHHHHHHHh-cCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeee-CCCceEEEcH
Q 025511 144 LADFVEYIKK-HKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMD-DRGKYIYISQ 201 (251)
Q Consensus 144 L~~FI~YIK~-~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViD-DRGKFIYIS~ 201 (251)
|..-|+|||. .+-+.++||..+.++.....+ ++-|....+|. .| |.|+|.|.++
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 6677899975 478899999999998877643 34555666663 45 4569999874
No 215
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=55.47 E-value=29 Score=29.56 Aligned_cols=65 Identities=14% Similarity=0.258 Sum_probs=49.7
Q ss_pred hhHHHHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHH
Q 025511 141 RDLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVA 208 (251)
Q Consensus 141 q~lL~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA 208 (251)
++.|....+++..+..+...|||...|+++.-|-+-++.|...|-+. .+.+ +.|-+|+.--...-
T Consensus 9 edYL~~Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~--~~~y-~gi~LT~~G~~~a~ 73 (154)
T COG1321 9 EDYLETIYELLEEKGFARTKDIAERLKVSPPSVTEMLKRLERLGLVE--YEPY-GGVTLTEKGREKAK 73 (154)
T ss_pred HHHHHHHHHHHhccCcccHHHHHHHhCCCcHHHHHHHHHHHHCCCeE--EecC-CCeEEChhhHHHHH
Confidence 45677777778888899999999999999999999999999998764 2233 33557766554333
No 216
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=55.22 E-value=21 Score=31.25 Aligned_cols=39 Identities=21% Similarity=0.325 Sum_probs=32.6
Q ss_pred chHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceE
Q 025511 158 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYI 197 (251)
Q Consensus 158 ~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFI 197 (251)
.-.+||..||++..-|-+-|+.|+++|-|. +.--+|-||
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 333466666
No 217
>PRK15481 transcriptional regulatory protein PtsJ; Provisional
Probab=54.68 E-value=36 Score=31.98 Aligned_cols=57 Identities=16% Similarity=0.278 Sum_probs=43.6
Q ss_pred hhHHHHHHHHHHh------cCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEE
Q 025511 141 RDLLADFVEYIKK------HKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIY 198 (251)
Q Consensus 141 q~lL~~FI~YIK~------~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIY 198 (251)
+...+.+.+.|.. .|+-..-+||.+||++..-|.+-+..|+++|-|+. .--+|.||.
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 3444555566654 45556789999999999999999999999998875 334787774
No 218
>PF14502 HTH_41: Helix-turn-helix domain
Probab=54.53 E-value=20 Score=25.93 Aligned_cols=34 Identities=15% Similarity=0.288 Sum_probs=30.6
Q ss_pred cCccchHhHHhHcCCChHHHHHHHHHHHhcCCcc
Q 025511 154 HKCIPLEDLAAEFKLRTQECINRITSLENMGRLS 187 (251)
Q Consensus 154 ~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LT 187 (251)
.++-.++|+|.+|+++.--+=+-|+.|+++|.|+
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 3567899999999999999999999999999885
No 219
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=54.44 E-value=1e+02 Score=27.70 Aligned_cols=89 Identities=15% Similarity=0.246 Sum_probs=63.8
Q ss_pred HHHHHHHh-cCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHhcCCcc-----H
Q 025511 146 DFVEYIKK-HKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRVS-----I 219 (251)
Q Consensus 146 ~FI~YIK~-~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~qrGRVS-----i 219 (251)
+.++++-. .+-+.+.|||.+.|++..-+-.-++.|...|-| .-|++++.-++++.=+.-=..+.....-+. +
T Consensus 29 ~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l--~~~~~~~~Y~lG~~l~~Lg~~~~~~~~l~~~a~p~l 106 (271)
T PRK10163 29 AILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQAADFV--YQDSQLGWWHIGLGVFNVGAAYIHNRDVLSVAGPFM 106 (271)
T ss_pred HHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCE--EEcCCCCeEEecHHHHHHHHHHHhcCCHHHHHHHHH
Confidence 45566654 467889999999999999999999999999998 456655555677765543334444444433 4
Q ss_pred HHHHhhccccccccccc
Q 025511 220 SHLASKSNQFIDLETKA 236 (251)
Q Consensus 220 sELa~~sN~lI~L~p~~ 236 (251)
.+|+..++.-+.|.--.
T Consensus 107 ~~La~~~getv~l~v~~ 123 (271)
T PRK10163 107 RRLMLLSGETVNVAIRN 123 (271)
T ss_pred HHHHHHHCCeEEEEEEE
Confidence 68888888877766543
No 220
>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=54.14 E-value=11 Score=27.52 Aligned_cols=24 Identities=13% Similarity=0.462 Sum_probs=20.9
Q ss_pred HHHHHHHHHhcCCccHHHHHhhcc
Q 025511 204 MKAVADYIKRQGRVSISHLASKSN 227 (251)
Q Consensus 204 m~aVA~fI~qrGRVSisELa~~sN 227 (251)
-.+|+.++-++||.|+.+|++.++
T Consensus 15 ~~~V~~~Ll~~G~ltl~~i~~~t~ 38 (62)
T PF08221_consen 15 VAKVGEVLLSRGRLTLREIVRRTG 38 (62)
T ss_dssp HHHHHHHHHHC-SEEHHHHHHHHT
T ss_pred HHHHHHHHHHcCCcCHHHHHHHhC
Confidence 357899999999999999999988
No 221
>KOG4364 consensus Chromatin assembly factor-I [Chromatin structure and dynamics]
Probab=54.12 E-value=61 Score=34.75 Aligned_cols=15 Identities=13% Similarity=0.233 Sum_probs=9.4
Q ss_pred hhHHHHHHHHHHhcC
Q 025511 141 RDLLADFVEYIKKHK 155 (251)
Q Consensus 141 q~lL~~FI~YIK~~K 155 (251)
.+.+..|..-|+..+
T Consensus 372 ~aei~Kffqk~~~k~ 386 (811)
T KOG4364|consen 372 EAEIGKFFQKIDNKF 386 (811)
T ss_pred HHHHHhhhccccccc
Confidence 345677777665554
No 222
>KOG4404 consensus Tandem pore domain K+ channel TASK3/THIK-1 [Inorganic ion transport and metabolism]
Probab=53.95 E-value=33 Score=33.65 Aligned_cols=53 Identities=21% Similarity=0.369 Sum_probs=35.3
Q ss_pred HHHhhhhhhhhHHhHHhhhhhHHHHHHHHhhhhHHHHHHHHHHchHHHHHHHHH
Q 025511 43 CLCTSFLFLLSFSLLFDMFDLKADEAARESRQSKQDRYTEMRRRKDEEREARES 96 (251)
Q Consensus 43 ~~~~~~~~~~~~~~~~~~~~Reaee~~RE~Rk~~e~~~ee~rrkkeeere~eE~ 96 (251)
|+|| |++++-=|..||-++-|.|..+|+.-............--++.-++-|+
T Consensus 13 ivct-~tYLLvGAaVFdaLEse~E~~~r~~l~~~~~~~~~kyn~s~~d~r~~er 65 (350)
T KOG4404|consen 13 IVCT-FTYLLVGAAVFDALESENEARERERLERRLANLKRKYNLSEEDYRELER 65 (350)
T ss_pred HHHH-HHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHHhhCCCHHHHHHHHH
Confidence 4444 6778888999999999988777776555555554444444555555544
No 223
>KOG0163 consensus Myosin class VI heavy chain [Cytoskeleton]
Probab=53.81 E-value=57 Score=35.82 Aligned_cols=16 Identities=31% Similarity=0.418 Sum_probs=7.7
Q ss_pred HHHHHHHHHHHHHHHH
Q 025511 97 ALEEEAKAQKAREEEA 112 (251)
Q Consensus 97 ~~eEeer~~~eeeerr 112 (251)
+.+|++++++++.+++
T Consensus 965 K~eEeqr~~qee~e~~ 980 (1259)
T KOG0163|consen 965 KAEEEQRKAQEEEERR 980 (1259)
T ss_pred HHHHHHHHhhhhHHHH
Confidence 3445555555544444
No 224
>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=53.74 E-value=54 Score=21.46 Aligned_cols=52 Identities=19% Similarity=0.181 Sum_probs=36.1
Q ss_pred HHHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHH
Q 025511 144 LADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYI 211 (251)
Q Consensus 144 L~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI 211 (251)
+.+.|..+...+=....|||...|++ +..|.++. +|+. .++.+.+..+|+++
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 34455656666677789999999994 56666665 4442 46888888888765
No 225
>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=53.70 E-value=52 Score=25.86 Aligned_cols=63 Identities=16% Similarity=0.292 Sum_probs=46.1
Q ss_pred chHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHH--HHHHhcCCccHHHHHhh
Q 025511 158 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVA--DYIKRQGRVSISHLASK 225 (251)
Q Consensus 158 ~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA--~fI~qrGRVSisELa~~ 225 (251)
.+.++|..+|+++.- |.-.+..|.|..+-.+.|-|=|-|++++..+. .+.++-| +|+.++...
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 367999999997654 45567889986655555667788999999875 3445557 898887654
No 226
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=53.60 E-value=20 Score=31.32 Aligned_cols=52 Identities=17% Similarity=0.225 Sum_probs=39.5
Q ss_pred HHHHHHHHhc------CccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceE
Q 025511 145 ADFVEYIKKH------KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYI 197 (251)
Q Consensus 145 ~~FI~YIK~~------KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFI 197 (251)
..+.+.|... |+=.-.+||.+||++..-+.+-|+.|..+|.|.-+= -+|.||
T Consensus 12 ~~L~~~I~~g~~~~G~~LPsE~eL~~~~~VSR~TvR~Al~~L~~eGli~r~~-G~GtfV 69 (240)
T PRK09764 12 DRIREQIARGELKPGDALPTESALQTEFGVSRVTVRQALRQLVEQQILESIQ-GSGTYV 69 (240)
T ss_pred HHHHHHHHcCCCCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec-CceeEE
Confidence 4455666554 444567899999999999999999999999987542 246665
No 227
>PRK13503 transcriptional activator RhaS; Provisional
Probab=53.13 E-value=29 Score=30.02 Aligned_cols=76 Identities=16% Similarity=0.351 Sum_probs=51.1
Q ss_pred chhHHHHHHHHHHhc--CccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHhcCCc
Q 025511 140 DRDLLADFVEYIKKH--KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRV 217 (251)
Q Consensus 140 sq~lL~~FI~YIK~~--KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~qrGRV 217 (251)
....+..+++||..+ +-+.|+|+|.++|++..-+....+.-- |.- =.=||..-=|...+..+ ..+..
T Consensus 169 ~~~~i~~~~~~I~~~~~~~~tl~~lA~~~~lS~~~l~r~Fk~~~------G~S----~~~yi~~~Rl~~A~~LL-~~~~~ 237 (278)
T PRK13503 169 SDARLNQLLAWLEDHFAEEVNWEALADQFSLSLRTLHRQLKQQT------GLT----PQRYLNRLRLLKARHLL-RHSDA 237 (278)
T ss_pred cHHHHHHHHHHHHHhhcCCCCHHHHHHHHCCCHHHHHHHHHHHh------CcC----HHHHHHHHHHHHHHHHH-HcCCC
Confidence 345699999999877 678899999999999988887777532 210 01133333344444444 34667
Q ss_pred cHHHHHhhc
Q 025511 218 SISHLASKS 226 (251)
Q Consensus 218 SisELa~~s 226 (251)
||+++|..|
T Consensus 238 sI~eIA~~~ 246 (278)
T PRK13503 238 SVTDIAYRC 246 (278)
T ss_pred CHHHHHHHh
Confidence 888888776
No 228
>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=53.08 E-value=63 Score=25.33 Aligned_cols=65 Identities=11% Similarity=0.104 Sum_probs=45.9
Q ss_pred hHhHHhHcCCChHHHHHHHHHHHhc-CCcceeeeCCCceEEEcHHHHHHHHHHHH--hcCCccHHHHHhhccc
Q 025511 159 LEDLAAEFKLRTQECINRITSLENM-GRLSGVMDDRGKYIYISQAEMKAVADYIK--RQGRVSISHLASKSNQ 228 (251)
Q Consensus 159 LEDLAa~FgLrTqdvI~RIq~Lea~-G~LTGViDDRGKFIYIS~EEm~aVA~fI~--qrGRVSisELa~~sN~ 228 (251)
+.++|..+|+++.- |...+.. |.+ ++.-+.|.+=|-|++++..+..... +..-+|++++...-|.
T Consensus 3 i~EvA~~~gVs~~t----LR~ye~~~gli-~p~r~~~g~R~Yt~~di~~l~~I~~llr~~G~~l~~i~~~l~~ 70 (99)
T cd04765 3 IGEVAEILGLPPHV----LRYWETEFPQL-KPVKRAGGRRYYRPKDVELLLLIKHLLYEKGYTIEGAKQALKE 70 (99)
T ss_pred HHHHHHHHCcCHHH----HHHHHHHcCCC-CCcCCCCCCeeeCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence 56899999997654 4455666 545 4444556688899999998866543 3345999888876664
No 229
>PF02731 SKIP_SNW: SKIP/SNW domain; InterPro: IPR004015 SKIP (SKI-interacting protein) is an essential spliceosomal component and transcriptional coregulator, which may provide regulatory coupling of transcription initiation and splicing []. SKIP was identified in a yeast 2-hybrid screen, where it was shown to interact with both the cellular and viral forms of SKI through the highly conserved region on SKIP known as the SNW domain []. SKIP is now known to interact with a number of other proteins as well. SKIP potentiates the activity of important transcription factors, such as vitamin D receptor, CBF1 (RBP-Jkappa), Smad2/3, and MyoD. It works with Ski in overcoming pRb-mediated cell cycle arrest, and it is targeted by the viral transactivators EBNA2 and E7 []. This entry represents the SNW domain.; GO: 0000398 nuclear mRNA splicing, via spliceosome, 0005681 spliceosomal complex
Probab=52.94 E-value=49 Score=29.10 Aligned_cols=17 Identities=29% Similarity=0.221 Sum_probs=10.7
Q ss_pred hHHhHHhhhhhHHHHHH
Q 025511 53 SFSLLFDMFDLKADEAA 69 (251)
Q Consensus 53 ~~~~~~~~~~Reaee~~ 69 (251)
.||.+++.++++|.++.
T Consensus 109 ~LseAL~~Ad~~aReev 125 (158)
T PF02731_consen 109 KLSEALYIADRKAREEV 125 (158)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 45677777777764443
No 230
>PF06305 DUF1049: Protein of unknown function (DUF1049); InterPro: IPR010445 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=52.72 E-value=47 Score=23.56 Aligned_cols=20 Identities=35% Similarity=0.326 Sum_probs=10.4
Q ss_pred HHHHHHHHHhhhhhhhhHHh
Q 025511 37 LLLILVCLCTSFLFLLSFSL 56 (251)
Q Consensus 37 ~~~~~~~~~~~~~~~~~~~~ 56 (251)
.++|++|+...++....++.
T Consensus 21 ~l~il~~f~~G~llg~l~~~ 40 (68)
T PF06305_consen 21 GLLILIAFLLGALLGWLLSL 40 (68)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 34555666655555444333
No 231
>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=52.46 E-value=48 Score=28.44 Aligned_cols=66 Identities=20% Similarity=0.333 Sum_probs=49.6
Q ss_pred cchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHh-c-CCccHHHHHhhcc
Q 025511 157 IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKR-Q-GRVSISHLASKSN 227 (251)
Q Consensus 157 V~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~q-r-GRVSisELa~~sN 227 (251)
..+.++|..+|+++.- |.-.+..|-|.....+.|.|=|-|++++..+ .+|+. + .-+|++++....+
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 3578999999998754 5566789999987777788888899998888 33332 2 4488888777554
No 232
>PF13591 MerR_2: MerR HTH family regulatory protein
Probab=52.40 E-value=48 Score=25.26 Aligned_cols=53 Identities=11% Similarity=0.213 Sum_probs=43.7
Q ss_pred chHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHhcCC
Q 025511 158 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGR 216 (251)
Q Consensus 158 ~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~qrGR 216 (251)
.+++++..+|+.+.. |..|.+.|-|....++.+.| ++.+++..+...++-+--
T Consensus 2 s~~e~~~~~~i~~~~----l~~lve~Gli~p~~~~~~~~--f~~~~l~rl~~~~rL~~D 54 (84)
T PF13591_consen 2 SLEEFCEACGIEPEF----LRELVEEGLIEPEGEEEEWY--FSEEDLARLRRIRRLHRD 54 (84)
T ss_pred CHHHHHHHHCcCHHH----HHHHHHCCCeeecCCCCeee--ECHHHHHHHHHHHHHHHH
Confidence 578999999998765 66888999999988886655 899999999988876543
No 233
>KOG4364 consensus Chromatin assembly factor-I [Chromatin structure and dynamics]
Probab=52.18 E-value=45 Score=35.70 Aligned_cols=8 Identities=25% Similarity=0.210 Sum_probs=3.6
Q ss_pred HHHHHHhc
Q 025511 207 VADYIKRQ 214 (251)
Q Consensus 207 VA~fI~qr 214 (251)
+|+|+..-
T Consensus 458 ~adf~~sa 465 (811)
T KOG4364|consen 458 EADFDGSA 465 (811)
T ss_pred eccccccc
Confidence 44444433
No 234
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=51.90 E-value=25 Score=30.08 Aligned_cols=52 Identities=17% Similarity=0.253 Sum_probs=43.7
Q ss_pred HhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEE-EcHHH
Q 025511 152 KKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIY-ISQAE 203 (251)
Q Consensus 152 K~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIY-IS~EE 203 (251)
...+.|.+++||..+|++..-+-.-++.|...|-|..+-...|-|.- -.|++
T Consensus 21 ~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s~rG~~GGy~Lar~p~~ 73 (164)
T PRK10857 21 SEAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSVRGPGGGYLLGKDASS 73 (164)
T ss_pred CCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCCCCCCCeeccCCHHH
Confidence 44568999999999999999999999999999999987778887765 33344
No 235
>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=51.83 E-value=57 Score=24.66 Aligned_cols=65 Identities=11% Similarity=0.139 Sum_probs=46.8
Q ss_pred chHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHhc-CCccHHHHHhhcc
Q 025511 158 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQ-GRVSISHLASKSN 227 (251)
Q Consensus 158 ~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~qr-GRVSisELa~~sN 227 (251)
.+.++|..+|++++-+ ...+..|.|.+..+..|.+ +.|++++..+.....-+ .-+|+.++.....
T Consensus 2 ~~~eva~~~gi~~~tl----r~~~~~Gll~~~~~~~g~r-~y~~~dv~~l~~i~~l~~~g~~~~~i~~~l~ 67 (100)
T cd00592 2 TIGEVAKLLGVSVRTL----RYYEEKGLLPPERSENGYR-LYSEEDLERLRLIRRLRELGLSLKEIRELLD 67 (100)
T ss_pred CHHHHHHHHCcCHHHH----HHHHHCCCcCCCcCCCCCc-ccCHHHHHHHHHHHHHHHcCCCHHHHHHHHh
Confidence 3578999999976543 4456789998766655554 57999998776665554 5788888877654
No 236
>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=51.73 E-value=13 Score=26.13 Aligned_cols=33 Identities=33% Similarity=0.513 Sum_probs=25.3
Q ss_pred HHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHH
Q 025511 175 NRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYI 211 (251)
Q Consensus 175 ~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI 211 (251)
..|......|. |.|-.-+. -+|++|+.+|+.||
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 44555555665 67877776 89999999999997
No 237
>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=51.71 E-value=16 Score=25.31 Aligned_cols=47 Identities=21% Similarity=0.392 Sum_probs=28.9
Q ss_pred cchHhHHhHcCCChHHHHHHH-HHHHhc-CCcceeeeCCCceEEEcHHHHHHHHHHHH
Q 025511 157 IPLEDLAAEFKLRTQECINRI-TSLENM-GRLSGVMDDRGKYIYISQAEMKAVADYIK 212 (251)
Q Consensus 157 V~LEDLAa~FgLrTqdvI~RI-q~Lea~-G~LTGViDDRGKFIYIS~EEm~aVA~fI~ 212 (251)
+-+.|||.++|+++.++|..+ +++=-. -..+-. |++++...|+....
T Consensus 4 i~V~elAk~l~v~~~~ii~~l~~~~Gi~~~~~~~~---------ld~e~~~~i~~~~~ 52 (54)
T PF04760_consen 4 IRVSELAKELGVPSKEIIKKLFKELGIMVKSINSS---------LDEEEAELIAEEFG 52 (54)
T ss_dssp E-TTHHHHHHSSSHHHHHHHH-HHHTS---SSSS----------EETTGGGHHHHHH-
T ss_pred eEHHHHHHHHCcCHHHHHHHHHHhCCcCcCCCCCc---------CCHHHHHHHHHHhC
Confidence 356799999999999999888 545221 122222 55666666665543
No 238
>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]
Probab=51.50 E-value=30 Score=36.91 Aligned_cols=82 Identities=16% Similarity=0.234 Sum_probs=52.7
Q ss_pred HHHHHHHhhhccceeccCCccchhcccCchhHHHHHHHHHHhcCccchHhH---HhHcCCC---hHHHHHHHHHHHhcCC
Q 025511 112 AAAFEFEKWKGEFSIDAEGTTENEVQDGDRDLLADFVEYIKKHKCIPLEDL---AAEFKLR---TQECINRITSLENMGR 185 (251)
Q Consensus 112 rE~EEY~KwK~~f~VEeeG~~~~e~ee~sq~lL~~FI~YIK~~KVV~LEDL---Aa~FgLr---TqdvI~RIq~Lea~G~ 185 (251)
||.+||-.++...-+.+.-.. .-+.-+.+.==|.|++.+|..-.-|. ...-... +.++| |++-+-
T Consensus 60 KEn~~FyeLa~~lPlp~aiss----hLDkaSimRLtISyLRlrk~a~~g~~p~~e~~~~~~e~~l~~~i-----LqsLDG 130 (768)
T KOG3558|consen 60 KENEEFYELAKLLPLPAAISS----HLDKASIMRLTISYLRLRKFAGAGDPPRAEGEPENLEQHLGDHI-----LQSLDG 130 (768)
T ss_pred cchHHHHHHHHhCCCcchhhh----hhhhHHHHHHHHHHHHHHHHhhcCCcccccCCCcchhhhhhhhH-----Hhhccc
Confidence 567888888887777643322 23445677778999999997655544 2211111 12222 445555
Q ss_pred cceeeeCCCceEEEcHH
Q 025511 186 LSGVMDDRGKYIYISQA 202 (251)
Q Consensus 186 LTGViDDRGKFIYIS~E 202 (251)
..=|+++.|+|||||+.
T Consensus 131 FVm~l~~dG~~lYiSEt 147 (768)
T KOG3558|consen 131 FVMALTQDGDFLYISET 147 (768)
T ss_pred eEEEEccCCCEEEEech
Confidence 66688999999999975
No 239
>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=51.22 E-value=34 Score=32.46 Aligned_cols=73 Identities=21% Similarity=0.367 Sum_probs=54.9
Q ss_pred hHHHHHHH-HHHhcCccchHhHHhH--cCCChHHHHHHHHHHHhcCCcc----eee---eCCC------ce---EEEcHH
Q 025511 142 DLLADFVE-YIKKHKCIPLEDLAAE--FKLRTQECINRITSLENMGRLS----GVM---DDRG------KY---IYISQA 202 (251)
Q Consensus 142 ~lL~~FI~-YIK~~KVV~LEDLAa~--FgLrTqdvI~RIq~Lea~G~LT----GVi---DDRG------KF---IYIS~E 202 (251)
..|..-|+ |++..+-|...+||.. +|++..-+-+=+.+|++.|.|. |.. -+.| .| -.++++
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 34555554 8999999999999999 9999888899999999999983 211 0110 11 136788
Q ss_pred HHHHHHHHHHhc
Q 025511 203 EMKAVADYIKRQ 214 (251)
Q Consensus 203 Em~aVA~fI~qr 214 (251)
+-.++++.+.++
T Consensus 86 ~k~~i~~~~~~~ 97 (337)
T TIGR00331 86 EKRRIQNQFLQR 97 (337)
T ss_pred HHHHHHHHHhhc
Confidence 999999988775
No 240
>PRK13460 F0F1 ATP synthase subunit B; Provisional
Probab=51.17 E-value=1.5e+02 Score=25.07 Aligned_cols=7 Identities=14% Similarity=0.472 Sum_probs=2.7
Q ss_pred HHhhhhh
Q 025511 44 LCTSFLF 50 (251)
Q Consensus 44 ~~~~~~~ 50 (251)
++.-|+|
T Consensus 32 iL~~~~~ 38 (173)
T PRK13460 32 VLKKFAW 38 (173)
T ss_pred HHHHHhH
Confidence 3333333
No 241
>PRK13749 transcriptional regulator MerD; Provisional
Probab=51.15 E-value=52 Score=27.24 Aligned_cols=65 Identities=15% Similarity=0.233 Sum_probs=51.5
Q ss_pred cchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHh--cCCccHHHHHhhc
Q 025511 157 IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKR--QGRVSISHLASKS 226 (251)
Q Consensus 157 V~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~q--rGRVSisELa~~s 226 (251)
..+.++|..+|+++.- |.--++.|-|.++-.|.|.|=|-|++.+..+ .||+. .-=+|+.++....
T Consensus 4 ~tIgelA~~~gvS~~t----iR~YE~~GLl~p~~r~~~gyR~Y~~~~l~rL-~~I~~~r~~G~sL~eI~~ll 70 (121)
T PRK13749 4 YTVSRLALDAGVSVHI----VRDYLLRGLLRPVACTTGGYGLFDDAALQRL-CFVRAAFEAGIGLDALARLC 70 (121)
T ss_pred CcHHHHHHHHCCCHHH----HHHHHHCCCCCCCCcCCCCCccCCHHHHHHH-HHHHHHHHcCCCHHHHHHHH
Confidence 4578999999998654 6788999999998777799999999999998 56653 4457777766543
No 242
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=51.09 E-value=46 Score=28.25 Aligned_cols=48 Identities=21% Similarity=0.347 Sum_probs=35.2
Q ss_pred cchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEc-HHHHHHHH
Q 025511 157 IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYIS-QAEMKAVA 208 (251)
Q Consensus 157 V~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS-~EEm~aVA 208 (251)
+..++||...|++.+.+-.-++.|.++|.| .-.|+.|.|. .+.+.++|
T Consensus 185 lt~~~iA~~lG~sr~tvsR~l~~l~~~g~I----~~~~~~i~i~d~~~L~~~~ 233 (235)
T PRK11161 185 MTRGDIGNYLGLTVETISRLLGRFQKSGML----AVKGKYITIENNDALAQLA 233 (235)
T ss_pred ccHHHHHHHhCCcHHHHHHHHHHHHHCCCE----EecCCEEEEcCHHHHHHHh
Confidence 457899999999766665568899998755 4555677775 66666655
No 243
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=51.05 E-value=22 Score=31.39 Aligned_cols=67 Identities=19% Similarity=0.301 Sum_probs=48.7
Q ss_pred CccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcH-------HHHHHHHHHHHhcCCccHHHHHh
Q 025511 155 KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQ-------AEMKAVADYIKRQGRVSISHLAS 224 (251)
Q Consensus 155 KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~-------EEm~aVA~fI~qrGRVSisELa~ 224 (251)
|+=.=.+||.+||++.--|..-|+.|.++|.|.= -||+=.||++ .++..+.+-+..+|.-..+++..
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 3444467999999999999999999999998753 3444444444 35777788888888775554443
No 244
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=50.99 E-value=93 Score=25.91 Aligned_cols=67 Identities=19% Similarity=0.299 Sum_probs=48.7
Q ss_pred HHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCC--ccee--eeCCCc-----eEEEcHHHHHHHHHHHHhc
Q 025511 148 VEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGR--LSGV--MDDRGK-----YIYISQAEMKAVADYIKRQ 214 (251)
Q Consensus 148 I~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~--LTGV--iDDRGK-----FIYIS~EEm~aVA~fI~qr 214 (251)
++.+-.+.++.=+|||...|+++.++-.-+..|..++. .... .|..++ |-||....+-.|.+|=..+
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 44555678899999999999999999999999999555 3333 454444 4468877777666664443
No 245
>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional
Probab=50.87 E-value=1.1e+02 Score=31.18 Aligned_cols=78 Identities=14% Similarity=0.198 Sum_probs=56.8
Q ss_pred HHHHHHHHh-cCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHH---------HHHHHHhc
Q 025511 145 ADFVEYIKK-HKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKA---------VADYIKRQ 214 (251)
Q Consensus 145 ~~FI~YIK~-~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~a---------VA~fI~qr 214 (251)
...+.++.. ...+..++||...|++.++++.-+..|++.|.++ |-...-+..-+|+|--+. |.+++...
T Consensus 9 ~~iL~~l~~~~~~~~~~~la~~~~~~~~~v~~~~~~L~~kg~v~-~~~~~~~~~~LT~eG~~~~~~G~PE~rl~~~l~~~ 87 (494)
T PTZ00326 9 NTILSKLESENEIVNSLALAESLNIDHQKVVGAIKSLESANYIT-TEMKKSNTWTLTEEGEDYLKNGSPEYRLWQKLKEG 87 (494)
T ss_pred HHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHHHhCCCEE-EEEEEEEEEEECHHHHHHHHcCCHHHHHHHHhhhc
Confidence 456677777 6788999999999999999999999999998554 444444555577764332 44577776
Q ss_pred CCccHHHHHh
Q 025511 215 GRVSISHLAS 224 (251)
Q Consensus 215 GRVSisELa~ 224 (251)
| +++.+|.+
T Consensus 88 ~-~~~~~l~~ 96 (494)
T PTZ00326 88 G-ISKADDAK 96 (494)
T ss_pred C-CCHHHHHh
Confidence 6 45666654
No 246
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=50.62 E-value=22 Score=29.00 Aligned_cols=69 Identities=17% Similarity=0.238 Sum_probs=52.8
Q ss_pred ccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeee-CCCce----EEEcHHH-HHHHHHHHHhcCCccH-HHHHh
Q 025511 156 CIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMD-DRGKY----IYISQAE-MKAVADYIKRQGRVSI-SHLAS 224 (251)
Q Consensus 156 VV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViD-DRGKF----IYIS~EE-m~aVA~fI~qrGRVSi-sELa~ 224 (251)
-|.|+|||..|.+++-.+-.-|+.|.+.|-|+=.=- -||+- +.+++++ +...|.-.-..|.+.- .+|+.
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 378999999999999999999999999999863222 36764 3345554 5677888888899885 46665
No 247
>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=50.41 E-value=86 Score=23.73 Aligned_cols=65 Identities=14% Similarity=0.086 Sum_probs=46.5
Q ss_pred cchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHhc--CCccHHHHHhhc
Q 025511 157 IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQ--GRVSISHLASKS 226 (251)
Q Consensus 157 V~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~qr--GRVSisELa~~s 226 (251)
..+.++|..+|+++.- |...+..|.|...-+ .|.|-|.|+.++..+..-..-+ .-+|++++...-
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 3578999999997765 455677899997644 4568889999998876554322 348887665543
No 248
>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=50.33 E-value=86 Score=24.40 Aligned_cols=62 Identities=13% Similarity=0.387 Sum_probs=45.6
Q ss_pred chHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHH--HHHhcCCccHHHHHhh
Q 025511 158 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVAD--YIKRQGRVSISHLASK 225 (251)
Q Consensus 158 ~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~--fI~qrGRVSisELa~~ 225 (251)
.+.++|..+|+++.- |.-.+..|-|.. ..+.|.|=|-|++.+..+.. +.++-| +|++++...
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 567999999997654 477888899944 44556778889998887654 334556 999888864
No 249
>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=50.12 E-value=23 Score=26.01 Aligned_cols=36 Identities=22% Similarity=0.324 Sum_probs=32.6
Q ss_pred cchHhHHhHcCCCh--HHHHHHHHHHHhcCCcceeeeC
Q 025511 157 IPLEDLAAEFKLRT--QECINRITSLENMGRLSGVMDD 192 (251)
Q Consensus 157 V~LEDLAa~FgLrT--qdvI~RIq~Lea~G~LTGViDD 192 (251)
..++-+|.++|++. -+.+.+|....-+|.-.|+.+|
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 250
>PRK03837 transcriptional regulator NanR; Provisional
Probab=50.05 E-value=33 Score=29.49 Aligned_cols=54 Identities=11% Similarity=0.158 Sum_probs=39.8
Q ss_pred HHHHHHHHHHhcCc-----c-chHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceE
Q 025511 143 LLADFVEYIKKHKC-----I-PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYI 197 (251)
Q Consensus 143 lL~~FI~YIK~~KV-----V-~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFI 197 (251)
....+.+.|..... . ...+||..||++..-|.+-|+.|+.+|-|+-. --+|-||
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 34455555655543 3 56799999999999999999999999998863 3345443
No 251
>PF13814 Replic_Relax: Replication-relaxation
Probab=49.83 E-value=59 Score=26.89 Aligned_cols=61 Identities=16% Similarity=0.379 Sum_probs=50.0
Q ss_pred HHHHhcCccchHhHHhHcCCChH---HHHHHHHHHHhcCCcceeeeC------CCceE-EEcHHHHHHHHH
Q 025511 149 EYIKKHKCIPLEDLAAEFKLRTQ---ECINRITSLENMGRLSGVMDD------RGKYI-YISQAEMKAVAD 209 (251)
Q Consensus 149 ~YIK~~KVV~LEDLAa~FgLrTq---dvI~RIq~Lea~G~LTGViDD------RGKFI-YIS~EEm~aVA~ 209 (251)
..|-.++++.-+.|+.-++.+.. -|-.|++.|...|-|.-+-.. .+.+| |+|+.-.+.++.
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 35778899999999999999987 688999999999988777664 34466 789998877763
No 252
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=49.24 E-value=1.2e+02 Score=26.87 Aligned_cols=87 Identities=9% Similarity=0.233 Sum_probs=62.5
Q ss_pred HHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHhcCCcc-----HH
Q 025511 146 DFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRVS-----IS 220 (251)
Q Consensus 146 ~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~qrGRVS-----is 220 (251)
..++++-.++-+.+.|||.+.||+..-|-.-++.|...|-|.=. ++.|+| ++++.=+.--..+.....-+. +.
T Consensus 18 ~IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~~~-~~~~~Y-~lG~~~~~lg~~~~~~~~l~~~a~p~l~ 95 (257)
T PRK15090 18 GILQALGEEREIGITELSQRVMMSKSTVYRFLQTMKTLGYVAQE-GESEKY-SLTLKLFELGAKALQNVDLIRSADIQMR 95 (257)
T ss_pred HHHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEc-CCCCcE-EecHHHHHHHHHHHhhCcHHHHHHHHHH
Confidence 45556656677899999999999999999999999999997532 345665 477775555555655554333 36
Q ss_pred HHHhhccccccccc
Q 025511 221 HLASKSNQFIDLET 234 (251)
Q Consensus 221 ELa~~sN~lI~L~p 234 (251)
+|+..++.-..|.-
T Consensus 96 ~La~~~~etv~L~v 109 (257)
T PRK15090 96 EISRLTKETIHLGA 109 (257)
T ss_pred HHHHHhCCeEEEEE
Confidence 78888777666554
No 253
>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=49.21 E-value=32 Score=24.06 Aligned_cols=32 Identities=25% Similarity=0.398 Sum_probs=27.5
Q ss_pred CceEEEcHHHHHHHHHHHHhcCC-ccHHHHHhh
Q 025511 194 GKYIYISQAEMKAVADYIKRQGR-VSISHLASK 225 (251)
Q Consensus 194 GKFIYIS~EEm~aVA~fI~qrGR-VSisELa~~ 225 (251)
|+-|.+|+.|+.-++-++..+|+ ||..+|...
T Consensus 1 ~~~v~Lt~~e~~lL~~L~~~~~~~vs~~~l~~~ 33 (78)
T smart00862 1 GEPIKLTPKEFRLLELLLRNPGRVVSREELLEA 33 (78)
T ss_pred CCeEecCHHHHHHHHHHHhCCCCccCHHHHHHH
Confidence 56688999999999999999997 777888774
No 254
>PF15615 TerB-C: TerB-C domain
Probab=48.87 E-value=75 Score=26.48 Aligned_cols=61 Identities=16% Similarity=0.132 Sum_probs=48.6
Q ss_pred HHHHHHHHhcCcc---chHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHH
Q 025511 145 ADFVEYIKKHKCI---PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKA 206 (251)
Q Consensus 145 ~~FI~YIK~~KVV---~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~a 206 (251)
..|+..+..+.-. -++++|...|+-+.-+|+.|++..-+--=.-||+. |-.|+|.++=.+.
T Consensus 79 ~~lL~~Ll~~~~w~r~e~~~~a~~~glm~~~~ie~INE~afd~~gd~vie~-~d~i~I~~dy~e~ 142 (144)
T PF15615_consen 79 SALLRALLSRESWSREELEDIARDHGLMPDGAIESINEKAFDYFGDPVIEG-DDPIEINEDYREE 142 (144)
T ss_pred HHHHHHHHhCCCccHHHHHHHHHHcCCCHHHHHHHHHHHHHHhcCCeeEeC-CCCceEcHHHHHh
Confidence 4677777777665 45689999999999999999998777666678888 8999998875443
No 255
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=48.69 E-value=24 Score=27.49 Aligned_cols=30 Identities=23% Similarity=0.306 Sum_probs=28.1
Q ss_pred ccchHhHHhHcCCChHHHHHHHHHHHhcCC
Q 025511 156 CIPLEDLAAEFKLRTQECINRITSLENMGR 185 (251)
Q Consensus 156 VV~LEDLAa~FgLrTqdvI~RIq~Lea~G~ 185 (251)
-+.-++||...|++-..|-..||.|.+.|-
T Consensus 19 ~~SGe~La~~LgiSRtaVwK~Iq~Lr~~G~ 48 (79)
T COG1654 19 FVSGEKLAEELGISRTAVWKHIQQLREEGV 48 (79)
T ss_pred cccHHHHHHHHCccHHHHHHHHHHHHHhCC
Confidence 578899999999999999999999999985
No 256
>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=48.18 E-value=20 Score=23.86 Aligned_cols=23 Identities=22% Similarity=0.511 Sum_probs=19.2
Q ss_pred HHHHHHHHhcCCccHHHHHhhcc
Q 025511 205 KAVADYIKRQGRVSISHLASKSN 227 (251)
Q Consensus 205 ~aVA~fI~qrGRVSisELa~~sN 227 (251)
..|-.+|.+.|++|.++|++.+|
T Consensus 6 ~~Il~~l~~~~~~t~~ela~~~~ 28 (48)
T PF13412_consen 6 RKILNYLRENPRITQKELAEKLG 28 (48)
T ss_dssp HHHHHHHHHCTTS-HHHHHHHHT
T ss_pred HHHHHHHHHcCCCCHHHHHHHhC
Confidence 35668999999999999999988
No 257
>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=48.07 E-value=21 Score=30.85 Aligned_cols=52 Identities=12% Similarity=0.247 Sum_probs=39.2
Q ss_pred HHHHHHHHh------cCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceE
Q 025511 145 ADFVEYIKK------HKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYI 197 (251)
Q Consensus 145 ~~FI~YIK~------~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFI 197 (251)
..+.+.|.. .|+=.-.+||.+||++..-|.+-|+.|.++|.|.-+ --+|.||
T Consensus 7 ~~l~~~I~~g~~~~G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~-~G~GTfV 64 (233)
T TIGR02404 7 QDLEQKITHGQYKEGDYLPSEHELMDQYGASRETVRKALNLLTEAGYIQKI-QGKGSIV 64 (233)
T ss_pred HHHHHHHHhCCCCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe-CCceEEE
Confidence 445556654 345566789999999999999999999999988643 2256665
No 258
>PHA00738 putative HTH transcription regulator
Probab=48.03 E-value=69 Score=26.64 Aligned_cols=55 Identities=13% Similarity=0.245 Sum_probs=43.2
Q ss_pred HHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcH
Q 025511 145 ADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQ 201 (251)
Q Consensus 145 ~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~ 201 (251)
...+.++....-+...|||..|+|+.+-+-.-++-|...|-|+-- -+|+++|.+-
T Consensus 15 r~IL~lL~~~e~~~V~eLae~l~lSQptVS~HLKvLreAGLV~sr--K~Gr~vyY~L 69 (108)
T PHA00738 15 RKILELIAENYILSASLISHTLLLSYTTVLRHLKILNEQGYIELY--KEGRTLYAKI 69 (108)
T ss_pred HHHHHHHHHcCCccHHHHHHhhCCCHHHHHHHHHHHHHCCceEEE--EECCEEEEEE
Confidence 456777887767888999999999888888889999998877643 3577777653
No 259
>PRK13239 alkylmercury lyase; Provisional
Probab=47.98 E-value=39 Score=30.67 Aligned_cols=52 Identities=19% Similarity=0.325 Sum_probs=40.8
Q ss_pred hhHHHHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceE
Q 025511 141 RDLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYI 197 (251)
Q Consensus 141 q~lL~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFI 197 (251)
..++......+-.-+-|.+++||..+|.+.+.+-.++++|- .+ ++|+.|+-|
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 45666666667799999999999999999999998888863 22 677777653
No 260
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=47.56 E-value=20 Score=28.14 Aligned_cols=25 Identities=20% Similarity=0.404 Sum_probs=21.7
Q ss_pred HHHHHHHHHhcCCccHHHHHhhccc
Q 025511 204 MKAVADYIKRQGRVSISHLASKSNQ 228 (251)
Q Consensus 204 m~aVA~fI~qrGRVSisELa~~sN~ 228 (251)
+-+|-+||..+||+|.++|+...|-
T Consensus 4 L~qlRd~l~~~gr~s~~~Ls~~~~~ 28 (78)
T PRK15431 4 LIQVRDLLALRGRMEAAQISQTLNT 28 (78)
T ss_pred HHHHHHHHHHcCcccHHHHHHHHCc
Confidence 4578999999999999999987663
No 261
>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=47.33 E-value=85 Score=24.44 Aligned_cols=61 Identities=15% Similarity=0.159 Sum_probs=44.9
Q ss_pred chHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHhc-CCccHHHHH
Q 025511 158 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQ-GRVSISHLA 223 (251)
Q Consensus 158 ~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~qr-GRVSisELa 223 (251)
.+.|+|..+|+++.- |.-.+..|.|..+-.+.+-|=|-|++++..+ .||+.- =-++++++.
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 367999999997754 4567899999987666666888999999887 555543 135565543
No 262
>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=47.02 E-value=1e+02 Score=24.00 Aligned_cols=63 Identities=11% Similarity=0.146 Sum_probs=45.4
Q ss_pred cchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHhc--CCccHHHHHh
Q 025511 157 IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQ--GRVSISHLAS 224 (251)
Q Consensus 157 V~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~qr--GRVSisELa~ 224 (251)
..+.++|..+|+++.-+. ..+..|.|..+- +.|.+=|.|+.++..+..-..-+ .=+|++++..
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 367899999999876544 447799888854 45677788999999887755433 4678766553
No 263
>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=46.96 E-value=37 Score=29.08 Aligned_cols=52 Identities=19% Similarity=0.243 Sum_probs=38.8
Q ss_pred HHHHHHHHhc------CccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceE
Q 025511 145 ADFVEYIKKH------KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYI 197 (251)
Q Consensus 145 ~~FI~YIK~~------KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFI 197 (251)
..+.+.|... |+=.=.+||.+||++..-|.+-|+.|..+|.|.-+ --+|.||
T Consensus 15 ~~l~~~I~~g~~~~G~~LPsE~eLa~~~~VSR~TvR~Al~~L~~eGli~r~-~G~GtfV 72 (238)
T TIGR02325 15 DKIEQEIAAGHLRAGDYLPAEMQLAERFGVNRHTVRRAIAALVERGLLRAE-QGRGTFV 72 (238)
T ss_pred HHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe-cCCEEEE
Confidence 4455556543 45556689999999999999999999999998765 1245554
No 264
>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=46.40 E-value=93 Score=25.59 Aligned_cols=68 Identities=13% Similarity=0.129 Sum_probs=53.0
Q ss_pred ccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHH-hcCCccHHHHHhhcc
Q 025511 156 CIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIK-RQGRVSISHLASKSN 227 (251)
Q Consensus 156 VV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~-qrGRVSisELa~~sN 227 (251)
...+.+||..+|+++. -|.--+..|-|...-.+.|-|=+-|++.+..+..-.. +..-+|+.++....+
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 4677888899998866667799999999998765444 347789988886554
No 265
>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=46.38 E-value=77 Score=24.03 Aligned_cols=57 Identities=32% Similarity=0.460 Sum_probs=34.3
Q ss_pred HHHHHHHHHhcCccchHhHHhHc---CCC-hHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHH
Q 025511 144 LADFVEYIKKHKCIPLEDLAAEF---KLR-TQECINRITSLENMGRLSGVMDDRGKYIYISQAE 203 (251)
Q Consensus 144 L~~FI~YIK~~KVV~LEDLAa~F---gLr-TqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EE 203 (251)
+..+..-|+.+.|..=+||...+ |+. ||-+|+| +|.+.|. +=|-|..|+|+|.-|++
T Consensus 7 ~~~I~~li~~~~i~sQ~eL~~~L~~~Gi~vTQaTiSR--DLkeL~~-vKv~~~~g~~~Y~l~~~ 67 (70)
T PF01316_consen 7 QELIKELISEHEISSQEELVELLEEEGIEVTQATISR--DLKELGA-VKVPDGNGKYRYVLPEE 67 (70)
T ss_dssp HHHHHHHHHHS---SHHHHHHHHHHTT-T--HHHHHH--HHHHHT--EEEECTTSSEEEE-TTS
T ss_pred HHHHHHHHHHCCcCCHHHHHHHHHHcCCCcchhHHHH--HHHHcCc-EEeeCCCCCEEEEecCc
Confidence 34455667888887777765432 333 7888987 4445554 45889999999998765
No 266
>KOG1363 consensus Predicted regulator of the ubiquitin pathway (contains UAS and UBX domains) [Signal transduction mechanisms]
Probab=46.37 E-value=79 Score=31.87 Aligned_cols=7 Identities=14% Similarity=-0.145 Sum_probs=2.7
Q ss_pred hHHHHHH
Q 025511 170 TQECINR 176 (251)
Q Consensus 170 TqdvI~R 176 (251)
+|++++.
T Consensus 406 ~q~l~~~ 412 (460)
T KOG1363|consen 406 LQILYDY 412 (460)
T ss_pred hhHHHHH
Confidence 3343333
No 267
>PRK06568 F0F1 ATP synthase subunit B; Validated
Probab=46.23 E-value=2e+02 Score=24.90 Aligned_cols=12 Identities=17% Similarity=-0.161 Sum_probs=4.8
Q ss_pred HHHHHhhhhhhh
Q 025511 41 LVCLCTSFLFLL 52 (251)
Q Consensus 41 ~~~~~~~~~~~~ 52 (251)
|+.+..-|+|-|
T Consensus 17 ll~ll~kfawkP 28 (154)
T PRK06568 17 FVYLIYRPAKKA 28 (154)
T ss_pred HHHHHHHHhHHH
Confidence 333333444444
No 268
>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=46.09 E-value=1e+02 Score=23.96 Aligned_cols=67 Identities=13% Similarity=0.074 Sum_probs=49.6
Q ss_pred chHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHh--cCCccHHHHHhhccc
Q 025511 158 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKR--QGRVSISHLASKSNQ 228 (251)
Q Consensus 158 ~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~q--rGRVSisELa~~sN~ 228 (251)
.+.++|..+|+++. .|...+..|.|...-.+.+.|=|-|++++..+-.-..- ..-+|+.++...-+.
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 36799999999776 46677889999997665555556699999987654333 368999888876554
No 269
>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=45.45 E-value=18 Score=27.19 Aligned_cols=23 Identities=30% Similarity=0.447 Sum_probs=19.4
Q ss_pred HHHHHHHHHHhcCCccHHHHHhhc
Q 025511 203 EMKAVADYIKRQGRVSISHLASKS 226 (251)
Q Consensus 203 Em~aVA~fI~qrGRVSisELa~~s 226 (251)
....++.|| -.|+||++||+.++
T Consensus 46 ~A~kt~~~l-~~~~~~~~dla~~~ 68 (68)
T PF12514_consen 46 GANKTAEFL-AVKRVSIKDLAAAE 68 (68)
T ss_pred CHHHHHHHH-hcCCccHHHHhhcC
Confidence 467889999 88999999998753
No 270
>PF05529 Bap31: B-cell receptor-associated protein 31-like ; InterPro: IPR008417 Bap31 is a polytopic integral protein of the endoplasmic reticulum membrane and a substrate of caspase-8. Bap31 is cleaved within its cytosolic domain, generating pro-apoptotic p20 Bap31 [].; GO: 0006886 intracellular protein transport, 0005783 endoplasmic reticulum, 0016021 integral to membrane
Probab=45.44 E-value=1.9e+02 Score=24.66 Aligned_cols=29 Identities=17% Similarity=0.220 Sum_probs=18.1
Q ss_pred HHHHHHHHhhhhhhhhHHhHHhhhhhHHH
Q 025511 38 LLILVCLCTSFLFLLSFSLLFDMFDLKAD 66 (251)
Q Consensus 38 ~~~~~~~~~~~~~~~~~~~~~~~~~Reae 66 (251)
.+...+|+.+|+..-.++.+.+++.-++.
T Consensus 105 YIsGf~LfL~l~I~r~~~li~~l~~~~~~ 133 (192)
T PF05529_consen 105 YISGFALFLSLVIRRVHSLIKELIKLEEK 133 (192)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455666666666667777777666643
No 271
>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=44.98 E-value=98 Score=24.58 Aligned_cols=68 Identities=13% Similarity=0.160 Sum_probs=51.8
Q ss_pred chHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHhc-CCccHHHHHhhcccc
Q 025511 158 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQ-GRVSISHLASKSNQF 229 (251)
Q Consensus 158 ~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~qr-GRVSisELa~~sN~l 229 (251)
.+.|+|..+|++++- |.--+..|-|..+-.+.|.|=|.|++.+..+..--.-+ .=+|++++.+..+-+
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 67788899999987777889999999999876433322 457888888776543
No 272
>KOG0686 consensus COP9 signalosome, subunit CSN1 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=44.32 E-value=39 Score=34.24 Aligned_cols=46 Identities=22% Similarity=0.354 Sum_probs=42.2
Q ss_pred cchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHH
Q 025511 157 IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQA 202 (251)
Q Consensus 157 V~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~E 202 (251)
+.+.-+|..||++....=+.+.+|..+|.|+|=||---|-+|+-+.
T Consensus 366 ~~m~~mA~af~~sv~~le~~l~~LI~~~~i~~rIDs~~ki~~~~~~ 411 (466)
T KOG0686|consen 366 ADMSKMAEAFNTSVAILESELLELILEGKISGRIDSHNKILYARDA 411 (466)
T ss_pred chHHHHHHHhcccHHHHHHHHHHHHHccchheeeccccceeeeccc
Confidence 4466799999999999999999999999999999999999999765
No 273
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=44.29 E-value=37 Score=30.36 Aligned_cols=52 Identities=12% Similarity=0.124 Sum_probs=45.6
Q ss_pred cCchhHHHHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCccee
Q 025511 138 DGDRDLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGV 189 (251)
Q Consensus 138 e~sq~lL~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGV 189 (251)
.+.-+++.++|+++..++-+.--+||.++|+...++=.-+=.|+..|.+..+
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 3456789999999999999999999999999998855568899999999776
No 274
>PF15236 CCDC66: Coiled-coil domain-containing protein 66
Probab=44.03 E-value=2.2e+02 Score=24.97 Aligned_cols=10 Identities=50% Similarity=0.763 Sum_probs=4.8
Q ss_pred HHHHHHHhcC
Q 025511 175 NRITSLENMG 184 (251)
Q Consensus 175 ~RIq~Lea~G 184 (251)
.||..|...|
T Consensus 142 ~R~r~l~~~~ 151 (157)
T PF15236_consen 142 QRIRELEQKG 151 (157)
T ss_pred HHHHHHHhhc
Confidence 4455554444
No 275
>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]
Probab=43.78 E-value=84 Score=33.52 Aligned_cols=40 Identities=33% Similarity=0.403 Sum_probs=16.4
Q ss_pred HhhhhhHHHHHHHHhhhh-HHHHHHHHHHchHHHHHHHHHH
Q 025511 58 FDMFDLKADEAARESRQS-KQDRYTEMRRRKDEEREARESA 97 (251)
Q Consensus 58 ~~~~~Reaee~~RE~Rk~-~e~~~ee~rrkkeeere~eE~~ 97 (251)
||....+...+++++|++ .++...++|++..-+|++.++.
T Consensus 611 fdk~kE~Rr~Re~eer~RirE~rerEqR~~a~~ERee~eRl 651 (940)
T KOG4661|consen 611 FDKRKEERRRREAEERQRIREEREREQRRKAAVEREELERL 651 (940)
T ss_pred HHhhhhHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344443433333444333 3333334444444444444443
No 276
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=43.50 E-value=89 Score=25.90 Aligned_cols=65 Identities=17% Similarity=0.223 Sum_probs=51.9
Q ss_pred chHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHH--HHHhcCCccHHHHHhhcc
Q 025511 158 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVAD--YIKRQGRVSISHLASKSN 227 (251)
Q Consensus 158 ~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~--fI~qrGRVSisELa~~sN 227 (251)
.+.++|..+|+++. -|.--+..|-|...-.+.|-|=|-|++.+..+.. ..++-| +|+.++.+..+
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 46799999999764 4677899999998888888899999999998764 334556 89988877654
No 277
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=43.49 E-value=87 Score=27.60 Aligned_cols=76 Identities=11% Similarity=0.188 Sum_probs=53.9
Q ss_pred hhHHHHHHHHHHhc--CccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHhcCCcc
Q 025511 141 RDLLADFVEYIKKH--KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRVS 218 (251)
Q Consensus 141 q~lL~~FI~YIK~~--KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~qrGRVS 218 (251)
...+..+++||..+ .-..+++||+++|++..-+....++--...- . =||..-=|......+.. +..|
T Consensus 182 ~~~i~~~~~~i~~~~~~~isl~~lA~~~~lS~~~l~r~Fk~~~G~tp----~------~~l~~~Rl~~A~~lL~~-t~~s 250 (290)
T PRK10572 182 DPRVREACQYISDHLASEFDIESVAQHVCLSPSRLAHLFRQQLGISV----L------RWREDQRISRAKLLLQT-TRMP 250 (290)
T ss_pred cHHHHHHHHHHHhcccCCCCHHHHHHHHCCCHHHHHHHHHHHHCcCH----H------HHHHHHHHHHHHHHHHc-CCCC
Confidence 34688899999554 4788999999999998777666665422111 1 15666667776766654 7799
Q ss_pred HHHHHhhcc
Q 025511 219 ISHLASKSN 227 (251)
Q Consensus 219 isELa~~sN 227 (251)
|+++|..|.
T Consensus 251 I~eIA~~~G 259 (290)
T PRK10572 251 IATIGRNVG 259 (290)
T ss_pred HHHHHHHhC
Confidence 999998764
No 278
>PRK13461 F0F1 ATP synthase subunit B; Provisional
Probab=43.16 E-value=1.9e+02 Score=23.94 Aligned_cols=14 Identities=29% Similarity=0.529 Sum_probs=7.3
Q ss_pred HHHHHHHhhhhhhh
Q 025511 39 LILVCLCTSFLFLL 52 (251)
Q Consensus 39 ~~~~~~~~~~~~~~ 52 (251)
+||+.++.-|+|-|
T Consensus 16 ~il~~iL~~f~~kp 29 (159)
T PRK13461 16 IILLLILKHFFFDK 29 (159)
T ss_pred HHHHHHHHHHhHHH
Confidence 44445555555555
No 279
>PF05262 Borrelia_P83: Borrelia P83/100 protein; InterPro: IPR007926 This family consists of several Borrelia P83/P100 antigen proteins.
Probab=43.07 E-value=1.3e+02 Score=30.80 Aligned_cols=25 Identities=16% Similarity=0.339 Sum_probs=12.3
Q ss_pred hhhHhhhhhcccccccccccchhHH
Q 025511 14 IFDIHRVLEGYESSTRKDTRANSLL 38 (251)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~~~~~~~~ 38 (251)
|-.|.|+|-||-+..-.-...++-+
T Consensus 81 I~nlrrIiagyl~~aygY~~~~a~~ 105 (489)
T PF05262_consen 81 INNLRRIIAGYLEAAYGYSDEDAET 105 (489)
T ss_pred HHHHHHHHHHHHHHhcCCChhhHHH
Confidence 4455566666555444433444433
No 280
>PRK05472 redox-sensing transcriptional repressor Rex; Provisional
Probab=42.92 E-value=54 Score=28.39 Aligned_cols=42 Identities=14% Similarity=0.371 Sum_probs=35.0
Q ss_pred HHHHHHHHHHhcC--ccchHhHHhHcCCChHHHHHH-HHHHHhcCC
Q 025511 143 LLADFVEYIKKHK--CIPLEDLAAEFKLRTQECINR-ITSLENMGR 185 (251)
Q Consensus 143 lL~~FI~YIK~~K--VV~LEDLAa~FgLrTqdvI~R-Iq~Lea~G~ 185 (251)
.-...+++++.++ .|...+||..||+++. +|.| +..|...|.
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 3456788899998 9999999999999886 6665 999988874
No 281
>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=42.89 E-value=36 Score=24.61 Aligned_cols=30 Identities=23% Similarity=0.344 Sum_probs=24.2
Q ss_pred HhcCccchHhHHhHcCCChHHHHHHHHHHH
Q 025511 152 KKHKCIPLEDLAAEFKLRTQECINRITSLE 181 (251)
Q Consensus 152 K~~KVV~LEDLAa~FgLrTqdvI~RIq~Le 181 (251)
-.-+=+.+.|||.++|++.+-+-.+|..=+
T Consensus 19 d~PR~~tl~elA~~lgis~st~~~~LRrae 48 (53)
T PF04967_consen 19 DVPRRITLEELAEELGISKSTVSEHLRRAE 48 (53)
T ss_pred CCCCcCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 344567899999999999999988887543
No 282
>PRK12705 hypothetical protein; Provisional
Probab=42.71 E-value=3.5e+02 Score=27.76 Aligned_cols=54 Identities=20% Similarity=0.338 Sum_probs=33.7
Q ss_pred HHHHHHhcCCcceeeeCCCceEEEcHHH--HHHHHHH----HHhcCCccH---HHHHhhcccc
Q 025511 176 RITSLENMGRLSGVMDDRGKYIYISQAE--MKAVADY----IKRQGRVSI---SHLASKSNQF 229 (251)
Q Consensus 176 RIq~Lea~G~LTGViDDRGKFIYIS~EE--m~aVA~f----I~qrGRVSi---sELa~~sN~l 229 (251)
-|..|+.-.-+.=+|||--+-|-||--. -..+|.+ +-.-||++. .++++..|+.
T Consensus 220 Nir~~E~~tGvdliiddtp~~V~ls~fdp~rreia~~~l~~Li~dgri~p~rIeevv~~~~~~ 282 (508)
T PRK12705 220 NIRAFEGLTGVDLIIDDTPEAVVISSFNPIRREIARLTLEKLLADGRIHPARIEEYVQKANEE 282 (508)
T ss_pred hHHHHHHhhCCceEecCCccchhhcccCccchHHHHHHHHHHHhcCCCChHHHHHHHHHHHHH
Confidence 4788888877777899987776665311 1223322 334588874 5666666664
No 283
>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=42.55 E-value=64 Score=23.37 Aligned_cols=43 Identities=16% Similarity=0.294 Sum_probs=36.7
Q ss_pred cCCChHHHHHHHHHHHhcCCcceeeeC-----CCceEEEcHHHHHHHH
Q 025511 166 FKLRTQECINRITSLENMGRLSGVMDD-----RGKYIYISQAEMKAVA 208 (251)
Q Consensus 166 FgLrTqdvI~RIq~Lea~G~LTGViDD-----RGKFIYIS~EEm~aVA 208 (251)
+.++..-+=..++.|++.|-|++..++ +-|+-.||+.-.+++.
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 678899999999999999999999998 4667779998776654
No 284
>KOG4691 consensus Uncharacterized conserved protein [Function unknown]
Probab=41.77 E-value=1.6e+02 Score=27.36 Aligned_cols=65 Identities=31% Similarity=0.286 Sum_probs=31.2
Q ss_pred HHhhhhhHHHHHHHHhhhhHHHHHHHHHHchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 025511 57 LFDMFDLKADEAARESRQSKQDRYTEMRRRKDEEREARESALEEEAKAQKAREEEAAAFEFEKWKG 122 (251)
Q Consensus 57 ~~~~~~Reaee~~RE~Rk~~e~~~ee~rrkkeeere~eE~~~eEeer~~~eeeerrE~EEY~KwK~ 122 (251)
.-+.+.+-++..+-|.+.-+.....+- +...+.|.+...+.++|....-.++-+++.++-..||.
T Consensus 94 ~g~~ie~~~e~eaaE~~el~a~N~a~N-~~~~~~R~~Rla~~~~E~~~~i~ee~~~~~e~~~a~k~ 158 (227)
T KOG4691|consen 94 AGVLIERKAEKEAAEHRELMAWNQAEN-RRLHELRIARLAQEEREQEQRIAEEQARKAEEVQAWKQ 158 (227)
T ss_pred chhHHHhhhhhHHHHHHHHHHHhHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345555555555555554443332222 22233333333333344444445555566667677764
No 285
>PRK14472 F0F1 ATP synthase subunit B; Provisional
Probab=41.32 E-value=2.2e+02 Score=24.09 Aligned_cols=6 Identities=0% Similarity=0.517 Sum_probs=2.5
Q ss_pred HHhhhh
Q 025511 57 LFDMFD 62 (251)
Q Consensus 57 ~~~~~~ 62 (251)
+..+++
T Consensus 43 i~~~l~ 48 (175)
T PRK14472 43 ILSALE 48 (175)
T ss_pred HHHHHH
Confidence 444443
No 286
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=40.99 E-value=1.1e+02 Score=25.64 Aligned_cols=66 Identities=17% Similarity=0.192 Sum_probs=52.7
Q ss_pred cchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHH--HHHHhcCCccHHHHHhhcc
Q 025511 157 IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVA--DYIKRQGRVSISHLASKSN 227 (251)
Q Consensus 157 V~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA--~fI~qrGRVSisELa~~sN 227 (251)
..+.++|..+|+++. -|.--+..|-|....++.|.|=|-|++.+..+. ...++-| +|++++....+
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 578999999999653 467788999999877888889999999998764 4455557 79988887653
No 287
>PRK11642 exoribonuclease R; Provisional
Probab=40.61 E-value=61 Score=34.58 Aligned_cols=49 Identities=27% Similarity=0.409 Sum_probs=37.4
Q ss_pred HHHHHHh-cCccchHhHHhHcCCCh----HHHHHHHHHHHhcCCcceeeeCCCceE
Q 025511 147 FVEYIKK-HKCIPLEDLAAEFKLRT----QECINRITSLENMGRLSGVMDDRGKYI 197 (251)
Q Consensus 147 FI~YIK~-~KVV~LEDLAa~FgLrT----qdvI~RIq~Lea~G~LTGViDDRGKFI 197 (251)
.++|+.. .+-+.+.+||..||++. +....+|..|+.+|.|. .+.+|+|.
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 34778999999999985 45555553
No 288
>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=40.41 E-value=31 Score=26.85 Aligned_cols=25 Identities=12% Similarity=0.223 Sum_probs=21.7
Q ss_pred HHHHHHHHHHhcCCccHHHHHhhccc
Q 025511 203 EMKAVADYIKRQGRVSISHLASKSNQ 228 (251)
Q Consensus 203 Em~aVA~fI~qrGRVSisELa~~sN~ 228 (251)
=...+.++|.. |++++.++++.++-
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 289
>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=40.32 E-value=83 Score=23.96 Aligned_cols=43 Identities=21% Similarity=0.425 Sum_probs=30.0
Q ss_pred cchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeC-----CCceEEEcHHH
Q 025511 157 IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDD-----RGKYIYISQAE 203 (251)
Q Consensus 157 V~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDD-----RGKFIYIS~EE 203 (251)
++-..+|-++|+....++|-++.|+.-| ||+. .|.||.|-.+.
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 3445789999999999999999999976 5555 49999876544
No 290
>PRK12704 phosphodiesterase; Provisional
Probab=40.26 E-value=3.5e+02 Score=27.45 Aligned_cols=54 Identities=22% Similarity=0.433 Sum_probs=33.4
Q ss_pred HHHHHhcCCcceeeeCCCceEEEcH-HHH------HHHHHHHHhcCCcc---HHHHHhhcccccc
Q 025511 177 ITSLENMGRLSGVMDDRGKYIYISQ-AEM------KAVADYIKRQGRVS---ISHLASKSNQFID 231 (251)
Q Consensus 177 Iq~Lea~G~LTGViDDRGKFIYIS~-EEm------~aVA~fI~qrGRVS---isELa~~sN~lI~ 231 (251)
|..|+.---+.=+|||--..|.||- .-+ .++-. +-..||+. |.+++..++.-++
T Consensus 233 ir~~e~~tgvd~iiddtp~~v~ls~~~~~rre~a~~~l~~-l~~dg~i~P~~iee~~~~~~~~~~ 296 (520)
T PRK12704 233 IRALETLTGVDLIIDDTPEAVILSGFDPIRREIARLALEK-LVQDGRIHPARIEEMVEKARKEVD 296 (520)
T ss_pred HHHHHHHhCCeEEEcCCCCeEEEecCChhhHHHHHHHHHH-HHhcCCcCCCCHHHHHHHHHHHHH
Confidence 5666654444446999999999985 111 12222 23468886 5788887776554
No 291
>PLN03239 histone acetyltransferase; Provisional
Probab=40.25 E-value=38 Score=33.19 Aligned_cols=50 Identities=16% Similarity=0.310 Sum_probs=38.6
Q ss_pred CccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCce-EEEcHHHHHHHHHH
Q 025511 155 KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKY-IYISQAEMKAVADY 210 (251)
Q Consensus 155 KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKF-IYIS~EEm~aVA~f 210 (251)
..+.++|||..-|++++|+|.-+ +..|.|. ..+|.| |+|+++-++..++-
T Consensus 283 ~~~si~dis~~Tgi~~~DIi~tL---~~l~~l~---~~~g~~~i~~~~~~l~~~~~~ 333 (351)
T PLN03239 283 SSLSIMDIAKKTSIMAEDIVFAL---NQLGILK---FINGIYFIAAEKGLLEELAEK 333 (351)
T ss_pred CCccHHHHHHHhCCCHHHHHHHH---HHCCcEE---EECCeEEEEeCHHHHHHHHHH
Confidence 47899999999999999997655 5556664 234555 88999999887664
No 292
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=40.19 E-value=57 Score=29.86 Aligned_cols=47 Identities=19% Similarity=0.257 Sum_probs=42.0
Q ss_pred HHHHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCccee
Q 025511 143 LLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGV 189 (251)
Q Consensus 143 lL~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGV 189 (251)
.=+..+-++|.+.=+.+.|||...|+++.-|..-++.|+++|-+.=.
T Consensus 12 tr~~il~lL~~~g~~sa~elA~~Lgis~~avR~HL~~Le~~Glv~~~ 58 (218)
T COG2345 12 TRERILELLKKSGPVSADELAEELGISPMAVRRHLDDLEAEGLVEVE 58 (218)
T ss_pred HHHHHHHHHhccCCccHHHHHHHhCCCHHHHHHHHHHHHhCcceeee
Confidence 34567788999999999999999999999999999999999977665
No 293
>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=40.06 E-value=78 Score=23.36 Aligned_cols=62 Identities=18% Similarity=0.214 Sum_probs=37.4
Q ss_pred HHHHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHH
Q 025511 143 LLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMK 205 (251)
Q Consensus 143 lL~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~ 205 (251)
..-.++.++-.++-+.++++|..++++..-+.+.|+.|...=.-.|+-= +++-++|+=+|.+
T Consensus 17 ~~~~ll~~ll~~~~~s~~~la~~~~iS~sti~~~i~~l~~~l~~~~l~i-~~~~~~l~G~E~~ 78 (87)
T PF05043_consen 17 LNYQLLKLLLNNEYVSIEDLAEELFISRSTIYRDIKKLNKYLKKYGLKI-SKKGYRLEGDESN 78 (87)
T ss_dssp HHHHHHHHHHH-SEEEHHHHHHHHT--HHHHHHHHHHHHHHHHCCT-EE--SSEEEEES-HHH
T ss_pred HHHHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCeEE-eCCCeEEEeCHHH
Confidence 3345677777999999999999999999988876666554322223222 5555666555543
No 294
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=40.01 E-value=55 Score=31.07 Aligned_cols=78 Identities=22% Similarity=0.405 Sum_probs=55.7
Q ss_pred HHHhcCccchHhHHhH--cCCChHHHHHHHHHHHhcCCcceeee-------CCC---------ceEEEcHHHHHHHHHHH
Q 025511 150 YIKKHKCIPLEDLAAE--FKLRTQECINRITSLENMGRLSGVMD-------DRG---------KYIYISQAEMKAVADYI 211 (251)
Q Consensus 150 YIK~~KVV~LEDLAa~--FgLrTqdvI~RIq~Lea~G~LTGViD-------DRG---------KFIYIS~EEm~aVA~fI 211 (251)
||+...-|...+||.. ||+++.-+.+-+.+|++.|-|.=.-- |.| +.=.+++++...+.+.+
T Consensus 19 yi~~~~pv~s~~l~~~~~l~~S~aTIR~dm~~Le~~G~l~~~h~sagrIPT~kGYR~YVd~L~~~~~~~~~~~~~i~~~~ 98 (339)
T PRK00082 19 YIATGEPVGSKTLSKRYGLGVSSATIRNDMADLEELGLLEKPHTSSGRIPTDKGYRYFVDHLLEVKPLSEEERRAIEKFL 98 (339)
T ss_pred HHhcCCCcCHHHHHHHhCCCCChHHHHHHHHHHHhCCCcCCCcCCCCCCcCHHHHHHHHHHhCCCCCCCHHHHHHHHHHH
Confidence 8999999999999966 99999999999999999998763211 111 11136788888888766
Q ss_pred HhcCCccHHHHHhhccc
Q 025511 212 KRQGRVSISHLASKSNQ 228 (251)
Q Consensus 212 ~qrGRVSisELa~~sN~ 228 (251)
.++. -++.++.+.+-+
T Consensus 99 ~~~~-~~~~~~l~~aa~ 114 (339)
T PRK00082 99 DERG-VSLEDVLQEAAQ 114 (339)
T ss_pred Hhcc-CCHHHHHHHHHH
Confidence 5542 456555544333
No 295
>PTZ00064 histone acetyltransferase; Provisional
Probab=39.98 E-value=87 Score=32.49 Aligned_cols=49 Identities=14% Similarity=0.325 Sum_probs=38.1
Q ss_pred cchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHH
Q 025511 157 IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADY 210 (251)
Q Consensus 157 V~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~f 210 (251)
+.+.||+..-|+++.|+|.-++.| |.|.=+ ..+.+|+++++-++...+-
T Consensus 472 iSI~dIS~~TgI~~eDII~TLq~L---~llky~--kgq~~I~~~~~~ie~~~~~ 520 (552)
T PTZ00064 472 KFIDNVVRSTGIRREDVIRILEEN---GIMRNI--KDQHYIFCNQEFLKGIVKR 520 (552)
T ss_pred ccHHHHHHHhCCCHHHHHHHHHHC---CcEEEe--CCCEEEEECHHHHHHHHHH
Confidence 789999999999999998776655 655532 2367889999988876554
No 296
>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=39.74 E-value=69 Score=28.11 Aligned_cols=86 Identities=10% Similarity=0.164 Sum_probs=59.8
Q ss_pred HHHHHHHh-cCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHhcCCc------c
Q 025511 146 DFVEYIKK-HKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRV------S 218 (251)
Q Consensus 146 ~FI~YIK~-~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~qrGRV------S 218 (251)
+.++++.. ..-+.+.|||...||+..-+-.-++.|...|-|.- | .|+|- +++. +-.++.-...+..+ -
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-GRLFW-LTPR-VLRLGYAYLSSAPLPKVAQPL 87 (248)
T ss_pred HHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe--C-CCEEE-ecHH-HHHHHHHHHhcCchHHHHHHH
Confidence 45566654 56788999999999999999999999999999974 4 46653 6665 44444433333222 3
Q ss_pred HHHHHhhccccccccccc
Q 025511 219 ISHLASKSNQFIDLETKA 236 (251)
Q Consensus 219 isELa~~sN~lI~L~p~~ 236 (251)
+.+|+..++.-..|.--.
T Consensus 88 l~~L~~~~g~tv~L~v~~ 105 (248)
T TIGR02431 88 LERLSAQTHESCSVAVLD 105 (248)
T ss_pred HHHHHHHHCCeEEEEEEe
Confidence 468888888766665533
No 297
>PRK09416 lstR lineage-specific thermal regulator protein; Provisional
Probab=39.72 E-value=82 Score=26.97 Aligned_cols=60 Identities=18% Similarity=0.226 Sum_probs=47.1
Q ss_pred HcCCChHHHHHHHHHHHhcCCcceeeeCCC-ceEEEcHHHHHHHHHHHH--hcCCccHHHHHh
Q 025511 165 EFKLRTQECINRITSLENMGRLSGVMDDRG-KYIYISQAEMKAVADYIK--RQGRVSISHLAS 224 (251)
Q Consensus 165 ~FgLrTqdvI~RIq~Lea~G~LTGViDDRG-KFIYIS~EEm~aVA~fI~--qrGRVSisELa~ 224 (251)
.|.++..-+---++.|+++|-|+.-.+.++ ||-.||+.-.+.+..+.. +.-|-.|.+|.+
T Consensus 72 ~~~~s~GtIYp~L~RLE~~GlI~s~~~~~~RK~Y~ITe~Gre~L~e~~~~~~~~~~~~~~l~~ 134 (135)
T PRK09416 72 TFEGNEGSLYTLLHRLEQNRFIQSSWDHEGAKYYQLTDKGNKMLRKAEKNATKARFILKGLVQ 134 (135)
T ss_pred cccCCCccHHHHHHHHHHCCCeEEeecCCCceEEEECHHHHHHHHHHHhCHHHhHHHHHHHhc
Confidence 356677778888999999999999876655 787899999999999988 445555566554
No 298
>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=39.69 E-value=24 Score=24.35 Aligned_cols=16 Identities=25% Similarity=0.576 Sum_probs=14.3
Q ss_pred EEcHHHHHHHHHHHHh
Q 025511 198 YISQAEMKAVADYIKR 213 (251)
Q Consensus 198 YIS~EEm~aVA~fI~q 213 (251)
-+|++|+.+|+.||++
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 299
>KOG1497 consensus COP9 signalosome, subunit CSN4 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=39.36 E-value=49 Score=32.82 Aligned_cols=50 Identities=20% Similarity=0.321 Sum_probs=42.0
Q ss_pred ccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcH-HHHH
Q 025511 156 CIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQ-AEMK 205 (251)
Q Consensus 156 VV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~-EEm~ 205 (251)
++..++|+++|++++.-+=.-.-++..+||+.|-||.-.-+|+.-+ ++|.
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 5678999999999999888888899999999999998766776554 5663
No 300
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=39.28 E-value=67 Score=29.71 Aligned_cols=55 Identities=18% Similarity=0.428 Sum_probs=43.9
Q ss_pred HHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeC--CC---ceEEEcH
Q 025511 146 DFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDD--RG---KYIYISQ 201 (251)
Q Consensus 146 ~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDD--RG---KFIYIS~ 201 (251)
+.++.+-.+ =...-+++...|++.+-|++-++-|+..|-++--+|. || ||-+||.
T Consensus 19 ~Il~lLt~~-p~yvsEiS~~lgvsqkAVl~HL~~LE~AGlveS~ie~~~Rg~~rKYY~Is~ 78 (217)
T COG1777 19 RILQLLTRR-PCYVSEISRELGVSQKAVLKHLRILERAGLVESRIEKIPRGRPRKYYMISR 78 (217)
T ss_pred HHHHHHhcC-chHHHHHHhhcCcCHHHHHHHHHHHHHcCCchhhccccccCCCcceeeccC
Confidence 344444333 3788899999999999999999999999999998886 43 6887763
No 301
>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=39.13 E-value=1.7e+02 Score=24.39 Aligned_cols=63 Identities=14% Similarity=0.162 Sum_probs=48.0
Q ss_pred cchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHhc--CCccHHHHHhh
Q 025511 157 IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQ--GRVSISHLASK 225 (251)
Q Consensus 157 V~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~qr--GRVSisELa~~ 225 (251)
..+.++|..+|+++.- |.-.+..|.|.+. . +|.+-|-|++++..+..-..-+ .-++++++...
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 3578999999998764 4467778999885 3 5888889999998876554443 67888887764
No 302
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=39.11 E-value=1.5e+02 Score=26.22 Aligned_cols=59 Identities=19% Similarity=0.270 Sum_probs=43.1
Q ss_pred cCc-cchHhHHhHcCCChHHHHHHHHHHHhc----CCcceeeeCCCceEEEcHHHHHH-HHHHHH
Q 025511 154 HKC-IPLEDLAAEFKLRTQECINRITSLENM----GRLSGVMDDRGKYIYISQAEMKA-VADYIK 212 (251)
Q Consensus 154 ~KV-V~LEDLAa~FgLrTqdvI~RIq~Lea~----G~LTGViDDRGKFIYIS~EEm~a-VA~fI~ 212 (251)
..- |.+.+||.-+|+...++.+-|.+|.+. |+=.=|.---|+|.+.|..++.. |.+|..
T Consensus 17 g~pgls~~~La~~l~~~~~~v~~~l~~L~~~y~~~~~gi~i~~~~~~y~l~tk~e~~~~v~~~~~ 81 (188)
T PRK00135 17 GEEGLSLEQLAEILELEPTEVQQLLEELQEKYEGDDRGLKLIEFNDVYKLVTKEENADYLQKLVK 81 (188)
T ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhhCCCCEEEEEECCEEEEEEcHHHHHHHHHHhc
Confidence 344 899999999999998888888888553 44334455678898888877764 444443
No 303
>PRK07352 F0F1 ATP synthase subunit B; Validated
Probab=39.10 E-value=2.4e+02 Score=23.86 Aligned_cols=14 Identities=21% Similarity=0.036 Sum_probs=8.0
Q ss_pred HHHHHHHhhhhhhh
Q 025511 39 LILVCLCTSFLFLL 52 (251)
Q Consensus 39 ~~~~~~~~~~~~~~ 52 (251)
+||+.+..-|+|-|
T Consensus 30 lIl~~lL~~fl~kp 43 (174)
T PRK07352 30 AIVIGLLYYFGRGF 43 (174)
T ss_pred HHHHHHHHHHhHHH
Confidence 44555555566666
No 304
>PLN03083 E3 UFM1-protein ligase 1 homolog; Provisional
Probab=38.89 E-value=1.8e+02 Score=31.57 Aligned_cols=81 Identities=22% Similarity=0.269 Sum_probs=63.9
Q ss_pred HHHHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHH----hcCCcc
Q 025511 143 LLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIK----RQGRVS 218 (251)
Q Consensus 143 lL~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~----qrGRVS 218 (251)
+-.+..+.|...--|++-|||.-.|+....|-.+++.+...+ -|++=-.|- -||+.=++.||.-|+ +.|.||
T Consensus 61 L~~EI~~El~~gGRvnlvdLa~~LnVD~~hiEr~~~~iv~~d--~~~~l~~Ge--Lit~~Yld~iaeEIne~LqE~G~is 136 (803)
T PLN03083 61 LRNEIEAEIKKLGRVSLVDLADTIGVDLYHVERQAQQVVSDD--PGLMLVQGE--IISQSYWDSIAEEINERLQECSQIA 136 (803)
T ss_pred HHHHHHHHHHhCCCeeHHHHhhhcCCCHHHHHHHHHHHhcCC--CceEEecCE--ecchHHHHHHHHHHHHHHHHcCcCh
Confidence 335566667677889999999999999999999999998886 444445553 478888888888765 559999
Q ss_pred HHHHHhhcc
Q 025511 219 ISHLASKSN 227 (251)
Q Consensus 219 isELa~~sN 227 (251)
|+||++.-|
T Consensus 137 I~eLa~~~~ 145 (803)
T PLN03083 137 LAELARQLQ 145 (803)
T ss_pred HHHHHHhcC
Confidence 999998644
No 305
>PRK11569 transcriptional repressor IclR; Provisional
Probab=38.53 E-value=2.4e+02 Score=25.35 Aligned_cols=88 Identities=15% Similarity=0.288 Sum_probs=61.0
Q ss_pred HHHHHHHh-cCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCC-CceEEEcHHHHHHHHHHHHhcCC-----cc
Q 025511 146 DFVEYIKK-HKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDR-GKYIYISQAEMKAVADYIKRQGR-----VS 218 (251)
Q Consensus 146 ~FI~YIK~-~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDR-GKFIYIS~EEm~aVA~fI~qrGR-----VS 218 (251)
+.++++.. ..-+.+.|||...|++..-+-.-++.|...|-|. -|++ |+| .+++.=+.-=..|..+..- =-
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 44566654 5678999999999999999999999999999995 5654 555 4666544333334333322 22
Q ss_pred HHHHHhhccccccccccc
Q 025511 219 ISHLASKSNQFIDLETKA 236 (251)
Q Consensus 219 isELa~~sN~lI~L~p~~ 236 (251)
+.+|+..+|.-..|.--.
T Consensus 109 l~~La~~~getv~L~v~~ 126 (274)
T PRK11569 109 LRNLMEDSGETVNLAVLD 126 (274)
T ss_pred HHHHHHHHCCeEEEEEEe
Confidence 468888888877766543
No 306
>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=38.50 E-value=61 Score=28.59 Aligned_cols=74 Identities=15% Similarity=0.111 Sum_probs=50.6
Q ss_pred HHHHHHhhhccceeccCC--ccchhccc--CchhHHHHHHHHH--HhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCc
Q 025511 113 AAFEFEKWKGEFSIDAEG--TTENEVQD--GDRDLLADFVEYI--KKHKCIPLEDLAAEFKLRTQECINRITSLENMGRL 186 (251)
Q Consensus 113 E~EEY~KwK~~f~VEeeG--~~~~e~ee--~sq~lL~~FI~YI--K~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~L 186 (251)
.=+-+..+-.-|.+-.=| ..--..-. +........+.++ ....-|...+||.++|.+..-+.+.|..|+.+|.+
T Consensus 141 A~~~l~~lg~g~~l~~~~sg~~vv~s~~~~e~~~~~~~il~~~~~~~~g~vt~~~l~~~~~ws~~~a~~~L~~~~~~G~l 220 (223)
T PF04157_consen 141 ACKLLEVLGLGFRLRKFGSGVKVVQSVPYSELSKDQSRILELAEEENGGGVTASELAEKLGWSVERAKEALEELEREGLL 220 (223)
T ss_dssp HHHHHCCCTSSEEEEEETTTEEEEECST-CHH-HHHHHHHHHH--TTTSEEEHHHHHHHHTB-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHcCCCeEEEEeCCCcEEEEeCCchhhhHHHHHHHHHHHhhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCE
Confidence 345556666556554333 11111111 1124457788889 88999999999999999999999999999999976
No 307
>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=38.31 E-value=71 Score=25.88 Aligned_cols=52 Identities=13% Similarity=0.175 Sum_probs=42.0
Q ss_pred hcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEc-HHHH
Q 025511 153 KHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYIS-QAEM 204 (251)
Q Consensus 153 ~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS-~EEm 204 (251)
..+.+...+||...+++..-+-.-++.|...|-|..+-...|-|---. |+++
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 456899999999999999999999999999999987666666665443 4443
No 308
>PF15086 UPF0542: Uncharacterised protein family UPF0542
Probab=38.27 E-value=1.5e+02 Score=23.33 Aligned_cols=22 Identities=32% Similarity=0.419 Sum_probs=12.9
Q ss_pred HHHHHHHhhhhhhhhHHhHHhh
Q 025511 39 LILVCLCTSFLFLLSFSLLFDM 60 (251)
Q Consensus 39 ~~~~~~~~~~~~~~~~~~~~~~ 60 (251)
+.-|.||.+-+|++|-.+..-+
T Consensus 23 l~~vll~LtPlfiisa~lSwkL 44 (74)
T PF15086_consen 23 LTTVLLILTPLFIISAVLSWKL 44 (74)
T ss_pred HHHHHHHHhHHHHHHHHHHHHH
Confidence 4455666666677665555444
No 309
>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=38.09 E-value=92 Score=24.23 Aligned_cols=41 Identities=17% Similarity=0.361 Sum_probs=35.2
Q ss_pred HHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcc
Q 025511 146 DFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLS 187 (251)
Q Consensus 146 ~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LT 187 (251)
.++..+..+ ++.||+|-..+|++-..+.=-+..|.+.|-|+
T Consensus 9 ~IL~~ls~~-c~TLeeL~ekTgi~k~~LlV~LsrL~k~GiI~ 49 (72)
T PF05584_consen 9 KILIILSKR-CCTLEELEEKTGISKNTLLVYLSRLAKRGIIE 49 (72)
T ss_pred HHHHHHHhc-cCCHHHHHHHHCCCHHHHHHHHHHHHHCCCee
Confidence 345555555 99999999999999999999999999999875
No 310
>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=38.07 E-value=1.3e+02 Score=24.32 Aligned_cols=64 Identities=17% Similarity=0.246 Sum_probs=49.4
Q ss_pred chHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHH--HHHhcCCccHHHHHhhc
Q 025511 158 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVAD--YIKRQGRVSISHLASKS 226 (251)
Q Consensus 158 ~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~--fI~qrGRVSisELa~~s 226 (251)
.+.++|..+|+++.- |.--+..|-|.....+.|.|=|-|++++..+.. +.+.-| +|++++.+.-
T Consensus 2 ~I~e~a~~~gvs~~t----lR~Ye~~Gll~~~~r~~~g~R~Y~~~~l~~l~~I~~lr~~G-~sL~eI~~~l 67 (126)
T cd04785 2 SIGELARRTGVNVET----IRYYESIGLLPEPARTAGGYRLYGAAHVERLRFIRRARDLG-FSLEEIRALL 67 (126)
T ss_pred CHHHHHHHHCcCHHH----HHHHHHCCCCCCCCcCCCCccccCHHHHHHHHHHHHHHHCC-CCHHHHHHHH
Confidence 467899999997644 667899999998777778888899999987653 445556 8988877653
No 311
>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=38.05 E-value=1.6e+02 Score=24.61 Aligned_cols=65 Identities=14% Similarity=0.253 Sum_probs=47.0
Q ss_pred chHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHH--HHHHhcCCccHHHHHhhccc
Q 025511 158 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVA--DYIKRQGRVSISHLASKSNQ 228 (251)
Q Consensus 158 ~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA--~fI~qrGRVSisELa~~sN~ 228 (251)
.+.++|..+|+++. -|.--+..|.|...-++ |.|=+-|++.+..+. ...++-| +|++++....+.
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----ALHFYESKGLITSIRNS-GNQRRYKRDVLRRVAVIKAAQRVG-IPLATIGEALAV 69 (142)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHCCCCCCccCC-CCCEEECHHHHHHHHHHHHHHHcC-CCHHHHHHHHHh
Confidence 47899999999754 46778889999985554 445666788876553 4445567 898888876654
No 312
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=37.24 E-value=66 Score=26.58 Aligned_cols=40 Identities=20% Similarity=0.243 Sum_probs=28.1
Q ss_pred cchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEc
Q 025511 157 IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYIS 200 (251)
Q Consensus 157 V~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS 200 (251)
+...+||...|++.+-+-.-+++|.++|-|. -.|+.|.|.
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 5668999999996555444488999998664 334445554
No 313
>PLN03086 PRLI-interacting factor K; Provisional
Probab=37.19 E-value=70 Score=33.15 Aligned_cols=20 Identities=20% Similarity=0.459 Sum_probs=11.9
Q ss_pred ceeee---CCCceEEEcHHHHHHH
Q 025511 187 SGVMD---DRGKYIYISQAEMKAV 207 (251)
Q Consensus 187 TGViD---DRGKFIYIS~EEm~aV 207 (251)
.||++ +-|. ||+++-=|+.+
T Consensus 141 ~GVlEF~A~EG~-v~lP~wm~~~L 163 (567)
T PLN03086 141 SGVLEFTAEEGS-VGLPPHVWSNL 163 (567)
T ss_pred EEEEEEEcCCCe-EEcCHHHHhhc
Confidence 46665 4443 77776666655
No 314
>CHL00088 apcB allophycocyanin beta subunit
Probab=37.11 E-value=16 Score=31.63 Aligned_cols=39 Identities=23% Similarity=0.472 Sum_probs=30.8
Q ss_pred eCCCceEEEcHHHHHHHHHHHHhc-CCccHH-HHHhhcccccc
Q 025511 191 DDRGKYIYISQAEMKAVADYIKRQ-GRVSIS-HLASKSNQFID 231 (251)
Q Consensus 191 DDRGKFIYIS~EEm~aVA~fI~qr-GRVSis-ELa~~sN~lI~ 231 (251)
|++|+| +|..||+.+..|+++- -|+++. -|.++++.+|+
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 7999999999999876 677764 47777776664
No 315
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=36.93 E-value=65 Score=22.34 Aligned_cols=35 Identities=11% Similarity=0.162 Sum_probs=27.5
Q ss_pred HHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHH
Q 025511 147 FVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLE 181 (251)
Q Consensus 147 FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Le 181 (251)
|+-..+.+.-+...+||..||++..-|-+.+....
T Consensus 10 ll~L~~LR~~~~~~~La~~FgIs~stvsri~~~~~ 44 (53)
T PF13613_consen 10 LLTLMYLRLNLTFQDLAYRFGISQSTVSRIFHEWI 44 (53)
T ss_pred HHHHHHHHcCCcHhHHhhheeecHHHHHHHHHHHH
Confidence 55567788889999999999998777766665543
No 316
>PF02841 GBP_C: Guanylate-binding protein, C-terminal domain; InterPro: IPR003191 Guanylate-binding protein is a GTPase that is induced by interferon (IFN)-gamma. GTPases induced by IFN-gamma are key to the protective immunity against microbial and viral pathogens. These GTPases are classified into three groups: the small 47-kd GTPases, the Mx proteins, and the large 65- to 67-kd GTPases. Guanylate-binding proteins (GBP) fall into the last class. In humans, there are seven GBPs (hGBP1-7) []. Structurally, hGBP1 consists of two domains: a compact globular N-terminal domain harbouring the GTPase function (IPR015894 from INTERPRO), and an alpha-helical finger-like C-terminal domain. Human GBP1 is secreted from cells without the need of a leader peptide, and has been shown to exhibit antiviral activity against Vesicular stomatitis virus and Encephalomyocarditis virus, as well as being able to regulate the inhibition of proliferation and invasion of endothelial cells in response to IFN-gamma [].; GO: 0003924 GTPase activity, 0005525 GTP binding; PDB: 1DG3_A 2D4H_A 2B8W_B 2B92_A 2BC9_A 1F5N_A.
Probab=36.78 E-value=3.4e+02 Score=24.95 Aligned_cols=37 Identities=19% Similarity=0.376 Sum_probs=28.5
Q ss_pred CccchhhhhhhHhhhHhhhhhcccccccccccchhHH
Q 025511 2 GIFSNRVILKTYIFDIHRVLEGYESSTRKDTRANSLL 38 (251)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 38 (251)
|.|+...-...|+=+..+++..|....+|...+..+|
T Consensus 142 ~~~~~~gg~~~~~~~~~~~~~~Y~~~p~Kg~ka~evL 178 (297)
T PF02841_consen 142 GCYSKPGGYQLFLKELDELEKEYEQEPGKGVKAEEVL 178 (297)
T ss_dssp TTTSSTTHHHHHHHHHHHHHHHHHHSS---TTHHHHH
T ss_pred CCCCCCCCHHHHHHHHHHHHHHHhhcCCCCccHHHHH
Confidence 6677666678899999999999999999998887765
No 317
>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=36.70 E-value=58 Score=28.72 Aligned_cols=112 Identities=20% Similarity=0.247 Sum_probs=72.2
Q ss_pred HHHhhhccceeccCCccc------hhcccCchhHHHHHHHHHH----hcC-ccchHhHHhHc--------CCChHHHHHH
Q 025511 116 EFEKWKGEFSIDAEGTTE------NEVQDGDRDLLADFVEYIK----KHK-CIPLEDLAAEF--------KLRTQECINR 176 (251)
Q Consensus 116 EY~KwK~~f~VEeeG~~~------~e~ee~sq~lL~~FI~YIK----~~K-VV~LEDLAa~F--------gLrTqdvI~R 176 (251)
+|..+=..++|+.--+.. ....+=..++-.++++++- .+- ++.|.||=..| -++++|+..-
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 677777777776322111 0011112444445555542 222 89999986655 3689999999
Q ss_pred HHHHHhcCCcceeeeCC-CceEEEc-H-HHH----HHHHHHH--HhcCCccHHHHHhhcc
Q 025511 177 ITSLENMGRLSGVMDDR-GKYIYIS-Q-AEM----KAVADYI--KRQGRVSISHLASKSN 227 (251)
Q Consensus 177 Iq~Lea~G~LTGViDDR-GKFIYIS-~-EEm----~aVA~fI--~qrGRVSisELa~~sN 227 (251)
++.|...|.=..|+.=. |+.+-.| | .++ ..|-.++ ...|.||..+|+...|
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 99999999877777644 6554444 4 477 7788888 8889999999999877
No 318
>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=36.68 E-value=2e+02 Score=23.27 Aligned_cols=59 Identities=27% Similarity=0.442 Sum_probs=38.3
Q ss_pred chhHHHHHHHHHHh------cCccchHhHHhHcCCChHHHHHHHHH-HHhcCCccee-eeCCCceEEEc
Q 025511 140 DRDLLADFVEYIKK------HKCIPLEDLAAEFKLRTQECINRITS-LENMGRLSGV-MDDRGKYIYIS 200 (251)
Q Consensus 140 sq~lL~~FI~YIK~------~KVV~LEDLAa~FgLrTqdvI~RIq~-Lea~G~LTGV-iDDRGKFIYIS 200 (251)
+.+.|.+++.-|.+ +|-...+++++.|+-+ ++.++.+.. |.+.| |+.+ ++..|-+|.++
T Consensus 25 n~~~L~~~l~~vsdP~s~~Ygk~Lt~~e~~~~~~p~-~~~v~~V~~wL~~~G-~~~~~~~~~~~~i~~~ 91 (143)
T PF09286_consen 25 NLDALEQYLAEVSDPGSPNYGKYLTPEEFAALFAPS-PEDVAAVKSWLKSHG-LTVVEVSANGDWITVS 91 (143)
T ss_dssp THHHHHHHHHHHHTTTSTTTT----HHHHHHHHS---HHHHHHHHHHHHHCT--EEEEEETTTTEEEEE
T ss_pred CHHHHHHHHHhCcCCCCcccccCCCHHHHHHHHCCC-HHHHHHHHHHHHHcC-CceeEEeCCCCEEEEE
Confidence 35567777777755 7999999999999975 555666655 77777 5444 58899999875
No 319
>TIGR01144 ATP_synt_b ATP synthase, F0 subunit b. This model describes the F1/F0 ATP synthase b subunit in bacteria only. Scoring just below the trusted cutoff are the N-terminal domains of Mycobacterial b/delta fusion proteins and a subunit from an archaeon, Methanosarcina barkeri, in which the ATP synthase homolog differs in architecture and is not experimentally confirmed. This model helps resolve b from the related b' subunit. Within the family is an example from a sodium-translocating rather than proton-translocating ATP synthase.
Probab=36.58 E-value=2.3e+02 Score=22.93 Aligned_cols=17 Identities=18% Similarity=0.559 Sum_probs=10.2
Q ss_pred HHHHHHHHhhhhhhhhH
Q 025511 38 LLILVCLCTSFLFLLSF 54 (251)
Q Consensus 38 ~~~~~~~~~~~~~~~~~ 54 (251)
++||+.+..-|+|-|-.
T Consensus 5 Flil~~il~~~~~~pi~ 21 (147)
T TIGR01144 5 FILLVWFCMKYVWPPLA 21 (147)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 45666666666666643
No 320
>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=36.47 E-value=98 Score=22.75 Aligned_cols=39 Identities=15% Similarity=0.132 Sum_probs=26.4
Q ss_pred cCCChHHHHHHHHHHHhcCCcceeeeCCCceE-EEcHHHHHH
Q 025511 166 FKLRTQECINRITSLENMGRLSGVMDDRGKYI-YISQAEMKA 206 (251)
Q Consensus 166 FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFI-YIS~EEm~a 206 (251)
.+.+..++.+++.+ ..-....|+|+.|+|+ +||...+..
T Consensus 8 ~~~~l~~a~~~~~~--~~~~~~~Vvd~~g~~~G~vt~~dl~~ 47 (114)
T cd04619 8 VNATLQRAAKILGE--PGIDLVVVCDPHGKLAGVLTKTDVVR 47 (114)
T ss_pred CCCcHHHHHHHHHh--cCCCEEEEECCCCCEEEEEehHHHHH
Confidence 34566667666522 2234557889999998 788888764
No 321
>KOG1425 consensus Microfibrillar-associated protein MFAP1 [Cytoskeleton]
Probab=36.44 E-value=1e+02 Score=30.98 Aligned_cols=23 Identities=26% Similarity=0.375 Sum_probs=13.8
Q ss_pred HHHHHHHhcCCcceeeeCCCceE
Q 025511 175 NRITSLENMGRLSGVMDDRGKYI 197 (251)
Q Consensus 175 ~RIq~Lea~G~LTGViDDRGKFI 197 (251)
.|-+.|.+++..+-=--+.|||=
T Consensus 304 ERr~~lrknpkv~tnk~~Kgkyk 326 (430)
T KOG1425|consen 304 ERRAELRKNPKVSTNKAKKGKYK 326 (430)
T ss_pred HHHHHHhhCcccccccccchhHH
Confidence 36677777776554444556653
No 322
>PHA03033 hypothetical protein; Provisional
Probab=36.39 E-value=50 Score=28.62 Aligned_cols=44 Identities=23% Similarity=0.312 Sum_probs=34.7
Q ss_pred HHHHHHHHhcCCcce---eeeCCCceEE--EcHHHHHHHHHHHHhcCCc
Q 025511 174 INRITSLENMGRLSG---VMDDRGKYIY--ISQAEMKAVADYIKRQGRV 217 (251)
Q Consensus 174 I~RIq~Lea~G~LTG---ViDDRGKFIY--IS~EEm~aVA~fI~qrGRV 217 (251)
-+.|.+|.+++.-+| |+-+.|+||| ||.+=++...+-|+-+-.+
T Consensus 45 yg~V~eLk~Qkk~~GeVAvLk~d~RyIYYLITKdyie~~v~~~ni~r~l 93 (142)
T PHA03033 45 YNSIKELKKQKKKKGEVAYIYKNNKYIIYIIIADYIEDIVDDINILRAL 93 (142)
T ss_pred hCCHHHHHhhccCCCeEEEEecCCEEEEEEEeHHHHHHHHHHHHHHHHH
Confidence 456999999999998 5668999999 8888888777777654433
No 323
>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=36.29 E-value=1.1e+02 Score=28.25 Aligned_cols=52 Identities=13% Similarity=0.204 Sum_probs=44.2
Q ss_pred chHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHH
Q 025511 158 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVAD 209 (251)
Q Consensus 158 ~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~ 209 (251)
.|-++...||++..-+---+..|.++|.|+..-..|.+|-+||+.-...+..
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 4556889999999999999999999999999877777999999987654443
No 324
>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=36.25 E-value=64 Score=24.83 Aligned_cols=55 Identities=15% Similarity=0.266 Sum_probs=39.9
Q ss_pred HHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHH
Q 025511 151 IKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYI 211 (251)
Q Consensus 151 IK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI 211 (251)
++..+|+..+|||.-+|..+-.+-..++.=... +.+..-|+.++.+|+..+..-.
T Consensus 7 ~rg~rV~t~~~lA~~yg~~~~~i~~~~~rN~~r------F~eg~~~f~L~~~e~~~~~~~~ 61 (88)
T PF10543_consen 7 YRGQRVMTDEDLAELYGVETKTINRNFKRNKDR------FIEGKDYFQLTGEELKELKSQL 61 (88)
T ss_pred EcCEEEEEHHHHHHHhCcCHHHHHHHHHHHHHh------CCCCCcEEEecchhhhhhhhhh
Confidence 356789999999999999887665555543321 3345567889999999876543
No 325
>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=36.20 E-value=1.5e+02 Score=23.60 Aligned_cols=65 Identities=12% Similarity=0.174 Sum_probs=49.5
Q ss_pred chHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHh--cCCccHHHHHhhccc
Q 025511 158 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKR--QGRVSISHLASKSNQ 228 (251)
Q Consensus 158 ~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~q--rGRVSisELa~~sN~ 228 (251)
.+.|+|..+|+++.- |.--+..|.|..+-++ |.|=|-|++++..+. +|+. .--+|++++....+.
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 467999999997643 6677888999998764 789999999998875 4432 235799988876654
No 326
>PRK05066 arginine repressor; Provisional
Probab=36.16 E-value=1.2e+02 Score=26.02 Aligned_cols=54 Identities=20% Similarity=0.335 Sum_probs=39.3
Q ss_pred HHHHHHhcCccchHhHHh---HcCCC--hHHHHHH-HHHHHhcCCcceeeeCCCceEEEcHHHH
Q 025511 147 FVEYIKKHKCIPLEDLAA---EFKLR--TQECINR-ITSLENMGRLSGVMDDRGKYIYISQAEM 204 (251)
Q Consensus 147 FI~YIK~~KVV~LEDLAa---~FgLr--TqdvI~R-Iq~Lea~G~LTGViDDRGKFIYIS~EEm 204 (251)
.-.-|..++|-.=+||.. +-|+. ||-+|+| |++| |- .=|-+..|+|+|.-|.+.
T Consensus 14 I~~iI~~~~I~tQeeL~~~L~~~Gi~~vTQATiSRDikeL---~l-vKv~~~~G~~~Y~l~~~~ 73 (156)
T PRK05066 14 FKALLKEEKFGSQGEIVTALQEQGFDNINQSKVSRMLTKF---GA-VRTRNAKMEMVYCLPAEL 73 (156)
T ss_pred HHHHHhhCCCCCHHHHHHHHHHCCCCeecHHHHHHHHHHc---CC-EEeeCCCCCEEEEeCCCC
Confidence 334577888887777654 34888 9999998 5544 43 448899999999876644
No 327
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=35.85 E-value=87 Score=25.48 Aligned_cols=63 Identities=10% Similarity=0.257 Sum_probs=46.6
Q ss_pred HhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEE-EcHHHHHHHHHHHHhcC
Q 025511 152 KKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIY-ISQAEMKAVADYIKRQG 215 (251)
Q Consensus 152 K~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIY-IS~EEm~aVA~fI~qrG 215 (251)
.....+...+||..+|++..=+-.-++.|...|-|..+=--.|-|.- -.|+++ .+.+-+.--+
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 34457889999999999999999999999999988877555555644 455543 4555555444
No 328
>TIGR01339 phycocy_beta phycocyanin, beta subunit. This model excludes the closely related phycoerythrocyanin beta subunit.
Probab=35.27 E-value=18 Score=31.91 Aligned_cols=39 Identities=18% Similarity=0.481 Sum_probs=31.5
Q ss_pred eCCCceEEEcHHHHHHHHHHHHh-cCCccHH-HHHhhcccccc
Q 025511 191 DDRGKYIYISQAEMKAVADYIKR-QGRVSIS-HLASKSNQFID 231 (251)
Q Consensus 191 DDRGKFIYIS~EEm~aVA~fI~q-rGRVSis-ELa~~sN~lI~ 231 (251)
|+.|+| +|..||+++..|++. .-|+.+. -|.++++.+++
T Consensus 11 D~~gRy--l~~~eL~~l~~~~~~~~~Rl~aa~~L~~na~~IV~ 51 (170)
T TIGR01339 11 DARGEF--ISSSQIDALSKLVADGNKRSDAVSRITNNASTIVT 51 (170)
T ss_pred HhccCC--CCHHHHHHHHHHHHhhHHHHHHHHHHHHhHHHHHH
Confidence 678886 799999999999998 5788874 57777777664
No 329
>KOG2587 consensus RNA polymerase III (C) subunit [Transcription]
Probab=35.21 E-value=1.7e+02 Score=30.46 Aligned_cols=73 Identities=18% Similarity=0.329 Sum_probs=59.6
Q ss_pred HhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCC---------------------ceEEEcHHHHH----H
Q 025511 152 KKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRG---------------------KYIYISQAEMK----A 206 (251)
Q Consensus 152 K~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRG---------------------KFIYIS~EEm~----a 206 (251)
+......+.=++..=|++..-|-+-+=.|...|.++=+.+.++ ||+||+.+++. +
T Consensus 30 r~G~lss~~~~~~~t~i~~~kVk~aL~sLiQh~~V~y~~~~~~~g~vt~Y~~~~~ei~hilry~r~~~i~~~~~~q~~~s 109 (551)
T KOG2587|consen 30 RTGRLSSLRVIAKDTGISLDKVKKALVSLIQHNCVSYQVHTRNSGKVTTYEAQCSEILHILRYPRYIYITKTLYSQTAES 109 (551)
T ss_pred HcCCcchhHHHHhhcCCChHHHHHHHHHHHHhcceEEEEecCCCCceEEEEehhhHHHHHHhcccceeeHHHHhhhHHHH
Confidence 3334444667888889999999999999999999999888775 99999999986 5
Q ss_pred HHHHHHhcCCccHHHHHh
Q 025511 207 VADYIKRQGRVSISHLAS 224 (251)
Q Consensus 207 VA~fI~qrGRVSisELa~ 224 (251)
|++++-..||.++++..+
T Consensus 110 Iv~~Lls~GrLTv~e~i~ 127 (551)
T KOG2587|consen 110 IVEELLSNGRLTVSEVIK 127 (551)
T ss_pred HHHHHHhcCceeHHHHHH
Confidence 667778899999987654
No 330
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=35.19 E-value=93 Score=21.21 Aligned_cols=38 Identities=5% Similarity=0.073 Sum_probs=28.9
Q ss_pred hhHHHHHHHHHHhcCccchHhHHhHcCC-ChHHHHHHHHH
Q 025511 141 RDLLADFVEYIKKHKCIPLEDLAAEFKL-RTQECINRITS 179 (251)
Q Consensus 141 q~lL~~FI~YIK~~KVV~LEDLAa~FgL-rTqdvI~RIq~ 179 (251)
...+...+.||..+ -..++|||..+|+ +..-.....+.
T Consensus 36 ~~r~~~a~~~l~~~-~~~~~~ia~~~g~~s~~~f~r~Fk~ 74 (84)
T smart00342 36 DRRLERARRLLRDT-DLSVTEIALRVGFSSQSYFSRAFKK 74 (84)
T ss_pred HHHHHHHHHHHHcC-CCCHHHHHHHhCCCChHHHHHHHHH
Confidence 34578889999887 6789999999999 66655555444
No 331
>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=35.04 E-value=1.6e+02 Score=20.75 Aligned_cols=61 Identities=15% Similarity=0.230 Sum_probs=40.5
Q ss_pred chHhHHhHcCCChHHHHHHHHHHHhc-CCcceeeeCCCceEEEcHHHHHHHHHH--HHhcCCccHHHHHh
Q 025511 158 PLEDLAAEFKLRTQECINRITSLENM-GRLSGVMDDRGKYIYISQAEMKAVADY--IKRQGRVSISHLAS 224 (251)
Q Consensus 158 ~LEDLAa~FgLrTqdvI~RIq~Lea~-G~LTGViDDRGKFIYIS~EEm~aVA~f--I~qrGRVSisELa~ 224 (251)
.+.++|..+|+++.- |...+.. |.+...-++ |-+=+.|++++..+..- .++ .-+|++++..
T Consensus 2 ~i~e~A~~~gVs~~t----lr~ye~~~gl~~~~r~~-~g~R~yt~~di~~l~~i~~l~~-~g~~l~~i~~ 65 (68)
T cd04763 2 TIGEVALLTGIKPHV----LRAWEREFGLLKPQRSD-GGHRLFNDADIDRILEIKRWID-NGVQVSKVKK 65 (68)
T ss_pred CHHHHHHHHCcCHHH----HHHHHHhcCCCCCCcCC-CCCcccCHHHHHHHHHHHHHHH-cCCCHHHHHH
Confidence 467899999997765 4455666 666555444 55567899998877542 222 5577777665
No 332
>COG3064 TolA Membrane protein involved in colicin uptake [Cell envelope biogenesis, outer membrane]
Probab=34.82 E-value=3.1e+02 Score=27.27 Aligned_cols=8 Identities=13% Similarity=0.248 Sum_probs=3.0
Q ss_pred cccccchh
Q 025511 29 RKDTRANS 36 (251)
Q Consensus 29 ~~~~~~~~ 36 (251)
++|.-.++
T Consensus 7 qn~k~~~A 14 (387)
T COG3064 7 QNDKLKRA 14 (387)
T ss_pred ccccchhH
Confidence 33333333
No 333
>PF13182 DUF4007: Protein of unknown function (DUF4007)
Probab=34.50 E-value=82 Score=29.22 Aligned_cols=61 Identities=23% Similarity=0.457 Sum_probs=49.7
Q ss_pred hhHHHHHHHHH----HhcCccchHhHH-------hHcCCChHHHHHHHHHHHhc-CCcceeeeCCC-ceEEEcHH
Q 025511 141 RDLLADFVEYI----KKHKCIPLEDLA-------AEFKLRTQECINRITSLENM-GRLSGVMDDRG-KYIYISQA 202 (251)
Q Consensus 141 q~lL~~FI~YI----K~~KVV~LEDLA-------a~FgLrTqdvI~RIq~Lea~-G~LTGViDDRG-KFIYIS~E 202 (251)
.-++-..++|. ...+.+.+++|+ .-|+|+..++++++..|++. |.|+ +.|.-| +=||+.+.
T Consensus 201 ~i~~YaL~~~~~~~~~~~~sis~~~L~~~~~sPGriF~L~~~~l~~~L~~l~~~~g~i~-~~~TaGl~qv~~~~~ 274 (286)
T PF13182_consen 201 EIFLYALLDFAERESPGRNSISFDELLNEPGSPGRIFKLDEESLAERLEQLEEIYGFIS-WSDTAGLDQVYLKDE 274 (286)
T ss_pred HHHHHHHHHHHHHhCCCCcEEEHHHHhcCCCCcceEeccCHHHHHHHHHHHHhhcCcEE-EEEcCCCeEEEeccc
Confidence 34466666766 578899999995 57999999999999999999 7665 888888 78888774
No 334
>PF01988 VIT1: VIT family; InterPro: IPR008217 Proteins containing this entry have no known function and are predicted to be integral membrane proteins. They include the Ccc1 protein from Saccharomyces cerevisiae (Baker's yeast) (P47818 from SWISSPROT) that may have a role in regulating calcium levels [].
Probab=34.14 E-value=2.6e+02 Score=24.52 Aligned_cols=32 Identities=19% Similarity=0.207 Sum_probs=17.9
Q ss_pred hccceeccCCccchhcccCchhHHHHHHHHHH
Q 025511 121 KGEFSIDAEGTTENEVQDGDRDLLADFVEYIK 152 (251)
Q Consensus 121 K~~f~VEeeG~~~~e~ee~sq~lL~~FI~YIK 152 (251)
...+..+|-|...++...--.+.+.-|+-|+-
T Consensus 113 ~~~m~~ee~g~~~~~~~~p~~~al~~~~sf~l 144 (213)
T PF01988_consen 113 LDFMMREELGLSPEEEESPWKAALATFLSFIL 144 (213)
T ss_pred HHHHHhhhccCCccccchHHHHHHHHHHHHHH
Confidence 44556667776652222223556777777763
No 335
>PRK13502 transcriptional activator RhaR; Provisional
Probab=33.97 E-value=1.6e+02 Score=25.79 Aligned_cols=76 Identities=11% Similarity=0.162 Sum_probs=49.2
Q ss_pred hhHHHHHHHHHHhc--CccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHhcCCcc
Q 025511 141 RDLLADFVEYIKKH--KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRVS 218 (251)
Q Consensus 141 q~lL~~FI~YIK~~--KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~qrGRVS 218 (251)
...+..+++||..+ .-+.+++||..+|++..-....+++--...-. =||..-=|......+ ..+..|
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 34688999998653 23678999999999988777666653211000 033444455444444 457889
Q ss_pred HHHHHhhcc
Q 025511 219 ISHLASKSN 227 (251)
Q Consensus 219 isELa~~sN 227 (251)
|+|+|..|.
T Consensus 244 I~eIA~~~G 252 (282)
T PRK13502 244 ISEISMQCG 252 (282)
T ss_pred HHHHHHHcC
Confidence 999998775
No 336
>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=33.92 E-value=93 Score=22.10 Aligned_cols=42 Identities=19% Similarity=0.329 Sum_probs=35.9
Q ss_pred HHHHHHHhcCccchHhHHhHc----CCChHHHHHHHHHHHhcCCcc
Q 025511 146 DFVEYIKKHKCIPLEDLAAEF----KLRTQECINRITSLENMGRLS 187 (251)
Q Consensus 146 ~FI~YIK~~KVV~LEDLAa~F----gLrTqdvI~RIq~Lea~G~LT 187 (251)
.|..+++.+.-..+.+|+.+| ++.....+.-|..|.+.+.|.
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 588888888889999999888 999999999999999998874
No 337
>PRK12704 phosphodiesterase; Provisional
Probab=33.89 E-value=5.2e+02 Score=26.26 Aligned_cols=11 Identities=18% Similarity=0.084 Sum_probs=5.6
Q ss_pred cCCChHHHHHH
Q 025511 166 FKLRTQECINR 176 (251)
Q Consensus 166 FgLrTqdvI~R 176 (251)
=||+.+++-+.
T Consensus 148 a~lt~~ea~~~ 158 (520)
T PRK12704 148 SGLTAEEAKEI 158 (520)
T ss_pred hCCCHHHHHHH
Confidence 35555555544
No 338
>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=33.77 E-value=1.6e+02 Score=22.13 Aligned_cols=49 Identities=16% Similarity=0.232 Sum_probs=44.5
Q ss_pred chhHHHHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcce
Q 025511 140 DRDLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSG 188 (251)
Q Consensus 140 sq~lL~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTG 188 (251)
.+.++.+-++|+...+-+...-|=.+|++--.-+-.-|..|++.|-++.
T Consensus 3 ~D~ly~~a~~~V~~~~~~S~S~lQR~~~IGynrAariid~lE~~GiV~p 51 (63)
T smart00843 3 EDELYDEAVELVIETQKASTSLLQRRLRIGYNRAARLIDQLEEEGIVGP 51 (63)
T ss_pred ccHHHHHHHHHHHHhCCCChHHHHHHHhcchhHHHHHHHHHHHCcCCCC
Confidence 3568889999999999999999999999999999999999999998876
No 339
>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=33.69 E-value=67 Score=26.17 Aligned_cols=31 Identities=26% Similarity=0.440 Sum_probs=26.3
Q ss_pred CcceeeeCCCceEEE------cHHHHHHHHHHHHhcC
Q 025511 185 RLSGVMDDRGKYIYI------SQAEMKAVADYIKRQG 215 (251)
Q Consensus 185 ~LTGViDDRGKFIYI------S~EEm~aVA~fI~qrG 215 (251)
-|-|+.|+.|+++|| |++++.++.++++...
T Consensus 20 LlLg~~~~~g~l~yvG~vtGf~~~~~~~L~~~l~~l~ 56 (122)
T cd07970 20 LLLGLYDDGGRLRHVGRTSPLAAAERRELAELLEPAR 56 (122)
T ss_pred EEEEEECCCCCEEEEEEECCCCHHHHHHHHHHHHHhh
Confidence 367889998999997 8999999999888764
No 340
>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=33.56 E-value=82 Score=27.23 Aligned_cols=73 Identities=14% Similarity=0.131 Sum_probs=57.6
Q ss_pred hhHHHHHHHHHHhcCccchHhHHhHcC--CChHHHHHHHHHHHhcCC-cceeeeCCCceEEEcHHHHHHHHHHHHhcCC
Q 025511 141 RDLLADFVEYIKKHKCIPLEDLAAEFK--LRTQECINRITSLENMGR-LSGVMDDRGKYIYISQAEMKAVADYIKRQGR 216 (251)
Q Consensus 141 q~lL~~FI~YIK~~KVV~LEDLAa~Fg--LrTqdvI~RIq~Lea~G~-LTGViDDRGKFIYIS~EEm~aVA~fI~qrGR 216 (251)
-+.+...+.|+|...+-+.=.+..-|+ ...+.+.+.++.+.+.|- ...+.|.-| +.+|+++..+.+.++++..
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 344667788888887665555666677 888999999999999875 556778877 4899999999999998754
No 341
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=33.53 E-value=50 Score=24.44 Aligned_cols=28 Identities=46% Similarity=0.617 Sum_probs=19.6
Q ss_pred EcHHHHHHHHHHHHhc----CCccHHHHHhhcc
Q 025511 199 ISQAEMKAVADYIKRQ----GRVSISHLASKSN 227 (251)
Q Consensus 199 IS~EEm~aVA~fI~qr----GRVSisELa~~sN 227 (251)
.|+.| ..||+||..+ ...|+.+||+.|+
T Consensus 14 ls~~e-~~Ia~yil~~~~~~~~~si~elA~~~~ 45 (77)
T PF01418_consen 14 LSPTE-KKIADYILENPDEIAFMSISELAEKAG 45 (77)
T ss_dssp S-HHH-HHHHHHHHH-HHHHCT--HHHHHHHCT
T ss_pred CCHHH-HHHHHHHHhCHHHHHHccHHHHHHHcC
Confidence 46776 6699999876 5788999999887
No 342
>PF11932 DUF3450: Protein of unknown function (DUF3450); InterPro: IPR016866 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. However, they are found in an operon along with components of a TonB transport system (typified by Vibrio cholerae TonB2 [], and are predicted to be localized to the periplasmic space. Caution: the low-complexity nature of these sequences produces spurious BLAST hits to chromosome segregation ATPases (which are much longer in length and contain canonical Walker motifs). Accordingly, some members are misidentified as such.
Probab=33.51 E-value=3.5e+02 Score=24.16 Aligned_cols=19 Identities=11% Similarity=0.195 Sum_probs=9.6
Q ss_pred HhHHhHcCCChHHHHHHHH
Q 025511 160 EDLAAEFKLRTQECINRIT 178 (251)
Q Consensus 160 EDLAa~FgLrTqdvI~RIq 178 (251)
.++=..-++++.+=..||-
T Consensus 137 ~~~l~~~dv~~~ek~r~vl 155 (251)
T PF11932_consen 137 RAMLDDADVSLAEKFRRVL 155 (251)
T ss_pred HHhhhccCCCHHHHHHHHH
Confidence 3344444566655555553
No 343
>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=33.51 E-value=28 Score=29.78 Aligned_cols=82 Identities=18% Similarity=0.345 Sum_probs=52.3
Q ss_pred hhHHHHHHHHHHhcCccchHhHHhHc---CCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHhcCCc
Q 025511 141 RDLLADFVEYIKKHKCIPLEDLAAEF---KLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRV 217 (251)
Q Consensus 141 q~lL~~FI~YIK~~KVV~LEDLAa~F---gLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~qrGRV 217 (251)
++-+++|++.|-..+ +.+|+.++ .-..+.+++-+++-+-......+ .+..|+.++-+|+++.| |
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 445788888887777 34444444 33445555544443322222222 35578899999999887 7
Q ss_pred cHHHHHhhcccccccccc
Q 025511 218 SISHLASKSNQFIDLETK 235 (251)
Q Consensus 218 SisELa~~sN~lI~L~p~ 235 (251)
.+..+...-|.++.+.|.
T Consensus 72 dv~~~i~~i~~~l~~~~~ 89 (179)
T PF06757_consen 72 DVYYYINQINDLLGLPPL 89 (179)
T ss_pred CHHHHHHHHHHHHcCCcC
Confidence 788888888888887765
No 344
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=33.44 E-value=59 Score=25.99 Aligned_cols=52 Identities=29% Similarity=0.314 Sum_probs=39.9
Q ss_pred HHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEc
Q 025511 146 DFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYIS 200 (251)
Q Consensus 146 ~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS 200 (251)
..+.|++..-+=.---+|..++++.++|...+..|+..|-|.=|- |+.|.=|
T Consensus 11 ~IL~hl~~~~~Dy~k~ia~~l~~~~~~v~~~l~~Le~~GLler~~---g~~iK~~ 62 (92)
T PF10007_consen 11 KILQHLKKAGPDYAKSIARRLKIPLEEVREALEKLEEMGLLERVE---GKTIKRS 62 (92)
T ss_pred HHHHHHHHHCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEec---Ccccchh
Confidence 455566665555555689999999999999999999999987664 6655444
No 345
>PRK09836 DNA-binding transcriptional activator CusR; Provisional
Probab=33.19 E-value=58 Score=26.53 Aligned_cols=34 Identities=26% Similarity=0.421 Sum_probs=30.5
Q ss_pred CCceEEEcHHHHHHHHHHHHhcCCc-cHHHHHhhc
Q 025511 193 RGKYIYISQAEMKAVADYIKRQGRV-SISHLASKS 226 (251)
Q Consensus 193 RGKFIYIS~EEm~aVA~fI~qrGRV-SisELa~~s 226 (251)
+|+-|.+|+.|+.-+.-++...|+| |..+|.+..
T Consensus 145 ~~~~i~Lt~~E~~ll~~l~~~~g~~~sr~~l~~~~ 179 (227)
T PRK09836 145 SGTRITLTSKEFTLLEFFLRHQGEVLPRSLIASQV 179 (227)
T ss_pred CCEEEecCHHHHHHHHHHHhCCCeeEcHHHHHHHH
Confidence 5889999999999999999999995 788888875
No 346
>KOG3878 consensus Protein involved in maintenance of Golgi structure and ER-Golgi transport [Intracellular trafficking, secretion, and vesicular transport]
Probab=33.06 E-value=1.2e+02 Score=30.47 Aligned_cols=32 Identities=16% Similarity=0.158 Sum_probs=12.5
Q ss_pred hhHHHHHHHHhhhhHHHHHHHHHHchHHHHHHH
Q 025511 62 DLKADEAARESRQSKQDRYTEMRRRKDEEREAR 94 (251)
Q Consensus 62 ~Reaee~~RE~Rk~~e~~~ee~rrkkeeere~e 94 (251)
.|.+.+.+.+.|...++ ++..+.++.+.|+..
T Consensus 131 ~kde~lkE~e~r~~ee~-~e~~~lQe~~qr~l~ 162 (469)
T KOG3878|consen 131 DKDETLKEKELRLMEEK-KEARELQENAQRELL 162 (469)
T ss_pred hhhhHHHHHHHHHHHhh-hcchhHHHHHHHHHH
Confidence 34444444444433333 233333444444433
No 347
>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=32.57 E-value=55 Score=22.97 Aligned_cols=25 Identities=28% Similarity=0.355 Sum_probs=19.1
Q ss_pred HHhcCCcceeeeCCCceEEEcHHHH
Q 025511 180 LENMGRLSGVMDDRGKYIYISQAEM 204 (251)
Q Consensus 180 Lea~G~LTGViDDRGKFIYIS~EEm 204 (251)
|.+......|+|..|+|+|+++.=.
T Consensus 1 l~~~p~~i~v~D~~~~i~~~N~~~~ 25 (110)
T PF08448_consen 1 LDSSPDGIFVIDPDGRIVYANQAAA 25 (110)
T ss_dssp HHHCSSEEEEEETTSBEEEE-HHHH
T ss_pred CCCCCceeEEECCCCEEEEEHHHHH
Confidence 4556677889999999999998733
No 348
>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=32.24 E-value=2.3e+02 Score=21.65 Aligned_cols=52 Identities=15% Similarity=0.236 Sum_probs=41.6
Q ss_pred HHHHHh-cCccchHhHHhHc-----CCChHHHHHHHHHHHhcCCcceeeeCCCceEEE
Q 025511 148 VEYIKK-HKCIPLEDLAAEF-----KLRTQECINRITSLENMGRLSGVMDDRGKYIYI 199 (251)
Q Consensus 148 I~YIK~-~KVV~LEDLAa~F-----gLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYI 199 (251)
++++.. .+-+..+||.... +++..-|-+-|+.|.+.|.|.=+-.+.|++-|-
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 688888999999999999999998888888884
No 349
>PRK09978 DNA-binding transcriptional regulator GadX; Provisional
Probab=32.20 E-value=1.2e+02 Score=28.27 Aligned_cols=75 Identities=12% Similarity=0.148 Sum_probs=54.3
Q ss_pred hhHHHHHHHHHHhc--CccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHhcCCcc
Q 025511 141 RDLLADFVEYIKKH--KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRVS 218 (251)
Q Consensus 141 q~lL~~FI~YIK~~--KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~qrGRVS 218 (251)
...+...++||..+ .-..++|||.++|+++.-.....+. .|. .+ .=||..-=|...+..+.. +..|
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---EET--SY------SQLLTECRMQRALQLIVI-HGFS 208 (274)
T ss_pred HHHHHHHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHh---cCC--CH------HHHHHHHHHHHHHHHHHc-CCCC
Confidence 35578899999765 5679999999999999987777764 241 11 125666667777777764 5689
Q ss_pred HHHHHhhcc
Q 025511 219 ISHLASKSN 227 (251)
Q Consensus 219 isELa~~sN 227 (251)
|+++|..|.
T Consensus 209 I~eIA~~~G 217 (274)
T PRK09978 209 IKRVAVSCG 217 (274)
T ss_pred HHHHHHHhC
Confidence 999888764
No 350
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=32.04 E-value=3.3e+02 Score=27.24 Aligned_cols=35 Identities=11% Similarity=0.221 Sum_probs=28.0
Q ss_pred HHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHh
Q 025511 147 FVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLEN 182 (251)
Q Consensus 147 FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea 182 (251)
.+++++ ..-+...+||..||+++.-+.+-|+.|..
T Consensus 9 iL~~L~-~~~~t~~~LA~~l~VS~RTIr~dI~~in~ 43 (584)
T PRK09863 9 IVDLLE-QQDRSGGELAQQLGVSRRTIVRDIAYINF 43 (584)
T ss_pred HHHHHH-cCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 444554 46789999999999999999998887743
No 351
>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=31.99 E-value=1.1e+02 Score=23.04 Aligned_cols=51 Identities=12% Similarity=0.223 Sum_probs=37.6
Q ss_pred HHHhcCccchHhHHhHc-CCChHHHHHHHHHHHhcCCcceeeeCC-C-ceEE-EcH
Q 025511 150 YIKKHKCIPLEDLAAEF-KLRTQECINRITSLENMGRLSGVMDDR-G-KYIY-ISQ 201 (251)
Q Consensus 150 YIK~~KVV~LEDLAa~F-gLrTqdvI~RIq~Lea~G~LTGViDDR-G-KFIY-IS~ 201 (251)
.+.. ...-..||.... |+++...-+|+++|++.|-|+=..+.. + +.-| +|+
T Consensus 13 ~l~~-g~~rf~el~~~l~~is~~~L~~~L~~L~~~GLv~r~~~~~~p~~v~Y~LT~ 67 (90)
T PF01638_consen 13 ALFQ-GPMRFSELQRRLPGISPKVLSQRLKELEEAGLVERRVYPEVPPRVEYSLTE 67 (90)
T ss_dssp HHTT-SSEEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSSSEEEEEE-H
T ss_pred HHHh-CCCcHHHHHHhcchhHHHHHHHHHHHHHHcchhhcccccCCCCCCccCCCc
Confidence 3434 566788999999 999999999999999999998877642 2 3334 555
No 352
>KOG3654 consensus Uncharacterized CH domain protein [Cytoskeleton]
Probab=31.94 E-value=1.8e+02 Score=30.68 Aligned_cols=36 Identities=33% Similarity=0.476 Sum_probs=17.9
Q ss_pred HhhhhHHHHHHHHHHchHHHHH--HHHHHHHHHHHHHH
Q 025511 71 ESRQSKQDRYTEMRRRKDEERE--ARESALEEEAKAQK 106 (251)
Q Consensus 71 E~Rk~~e~~~ee~rrkkeeere--~eE~~~eEeer~~~ 106 (251)
|.|+++|.+..|...+++|-|+ ++++...|+++.++
T Consensus 406 ear~rkqqleae~e~kreearrkaeeer~~keee~arr 443 (708)
T KOG3654|consen 406 EARRRKQQLEAEKEQKREEARRKAEEERAPKEEEVARR 443 (708)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhHhhhcchhhhhhHH
Confidence 3455555555555455555443 34444455555554
No 353
>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=31.80 E-value=1.3e+02 Score=23.21 Aligned_cols=35 Identities=17% Similarity=0.098 Sum_probs=28.4
Q ss_pred hcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcc
Q 025511 153 KHKCIPLEDLAAEFKLRTQECINRITSLENMGRLS 187 (251)
Q Consensus 153 ~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LT 187 (251)
...-+.-.+||...|++.+-|-.-|..|++.|-|.
T Consensus 44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~ 78 (95)
T TIGR01610 44 KQDRVTATVIAELTGLSRTHVSDAIKSLARRRIIF 78 (95)
T ss_pred cCCccCHHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence 45666788999999997775444599999999987
No 354
>COG3343 RpoE DNA-directed RNA polymerase, delta subunit [Transcription]
Probab=31.76 E-value=49 Score=29.71 Aligned_cols=59 Identities=8% Similarity=0.232 Sum_probs=44.1
Q ss_pred hHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHhcCCccHHHHHhhccccc
Q 025511 159 LEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRVSISHLASKSNQFI 230 (251)
Q Consensus 159 LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~qrGRVSisELa~~sN~lI 230 (251)
+.++++++|++-+++-+||-.+=.+ +...|+|||+....|. -|-+.++-++-..++.++
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 4568899999999999999776543 3457999999988774 456667777766666544
No 355
>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=31.74 E-value=1.4e+02 Score=23.43 Aligned_cols=52 Identities=21% Similarity=0.348 Sum_probs=36.5
Q ss_pred hhHHHHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceE
Q 025511 141 RDLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYI 197 (251)
Q Consensus 141 q~lL~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFI 197 (251)
..++.-.+..+-.-+=|..++||...|.+.+++..-+..+- .=..|+.|+-|
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 45667777888899999999999999999999988777652 23567777654
No 356
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=31.70 E-value=56 Score=27.92 Aligned_cols=21 Identities=24% Similarity=0.665 Sum_probs=17.8
Q ss_pred HHHHHHHHhcCCccHHHHHhh
Q 025511 205 KAVADYIKRQGRVSISHLASK 225 (251)
Q Consensus 205 ~aVA~fI~qrGRVSisELa~~ 225 (251)
..|-.|++++||+++.+++..
T Consensus 15 ~rIvElVRe~GRiTi~ql~~~ 35 (127)
T PF06163_consen 15 ARIVELVREHGRITIKQLVAK 35 (127)
T ss_pred HHHHHHHHHcCCccHHHHHHH
Confidence 457789999999999998764
No 357
>PLN03086 PRLI-interacting factor K; Provisional
Probab=31.57 E-value=2.2e+02 Score=29.62 Aligned_cols=25 Identities=16% Similarity=0.235 Sum_probs=15.2
Q ss_pred CCceEEEcHHHHHHHHHHHHhcCCccHHHHH
Q 025511 193 RGKYIYISQAEMKAVADYIKRQGRVSISHLA 223 (251)
Q Consensus 193 RGKFIYIS~EEm~aVA~fI~qrGRVSisELa 223 (251)
.|+.+|.. |=.|+..-|.|-+..+.
T Consensus 135 ~~~~th~G------VlEF~A~EG~v~lP~wm 159 (567)
T PLN03086 135 SQKTTHSG------VLEFTAEEGSVGLPPHV 159 (567)
T ss_pred CCcEEEEE------EEEEEcCCCeEEcCHHH
Confidence 46777765 34466666777765443
No 358
>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=31.48 E-value=1e+02 Score=31.87 Aligned_cols=52 Identities=33% Similarity=0.519 Sum_probs=39.8
Q ss_pred HHHHHHH--hcCccchHhHHhHcCCCh----HHHHHHHHHHHhcCCcceeeeCCCceEEE
Q 025511 146 DFVEYIK--KHKCIPLEDLAAEFKLRT----QECINRITSLENMGRLSGVMDDRGKYIYI 199 (251)
Q Consensus 146 ~FI~YIK--~~KVV~LEDLAa~FgLrT----qdvI~RIq~Lea~G~LTGViDDRGKFIYI 199 (251)
..++|++ ..+-+...+|+..||++. ...-..|..|+.+|.|. .+.+|+|...
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 3667776 458899999999999974 34778999999999985 4555666443
No 359
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=31.39 E-value=3.7e+02 Score=27.29 Aligned_cols=52 Identities=23% Similarity=0.454 Sum_probs=29.8
Q ss_pred HHHHHhcCCcceeeeCCCceEEEcH-----HHHHHHH-HHHHhcCCcc---HHHHHhhccc
Q 025511 177 ITSLENMGRLSGVMDDRGKYIYISQ-----AEMKAVA-DYIKRQGRVS---ISHLASKSNQ 228 (251)
Q Consensus 177 Iq~Lea~G~LTGViDDRGKFIYIS~-----EEm~aVA-~fI~qrGRVS---isELa~~sN~ 228 (251)
|..|+.---+.=+|||----|-||- -|+...| .-+-.-||++ |.+++..+.+
T Consensus 227 ir~~e~~tgvd~iiddtp~~v~ls~fdp~rreia~~~l~~li~dgrihp~riee~~~~~~~ 287 (514)
T TIGR03319 227 IRALETLTGVDLIIDDTPEAVILSGFDPVRREIARMALEKLIQDGRIHPARIEEMVEKATK 287 (514)
T ss_pred HHHHHHHhCceEEEcCCCCeEEecCCchHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHH
Confidence 4566554444446888877777774 2443333 2234468887 4566666554
No 360
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=31.24 E-value=51 Score=29.41 Aligned_cols=58 Identities=14% Similarity=0.186 Sum_probs=43.1
Q ss_pred hhHHHHHHHHHHhcCcc------chHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcH
Q 025511 141 RDLLADFVEYIKKHKCI------PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQ 201 (251)
Q Consensus 141 q~lL~~FI~YIK~~KVV------~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~ 201 (251)
+..+.....+|-+...- .=-+||..||++-..+-+-|+.|++.|.|.- -+|+=+||.+
T Consensus 13 ~~v~~~i~~~I~~g~~~~G~~LP~EreLae~fgVSR~~vREAl~~L~a~Glve~---r~G~Gt~V~~ 76 (241)
T COG2186 13 DEVAEQIGALIVSGELPPGDRLPSERELAERFGVSRTVVREALKRLEAKGLVEI---RQGSGTFVRP 76 (241)
T ss_pred HHHHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCcHHHHHHHHHHHHCCCeee---cCCCceEecC
Confidence 45567777788766544 3567999999999999999999999876532 2466666654
No 361
>COG5340 Predicted transcriptional regulator [Transcription]
Probab=31.19 E-value=67 Score=30.44 Aligned_cols=69 Identities=23% Similarity=0.388 Sum_probs=53.3
Q ss_pred HHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEc-----HHHHHH----HHHHHHhcCCccHH
Q 025511 150 YIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYIS-----QAEMKA----VADYIKRQGRVSIS 220 (251)
Q Consensus 150 YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS-----~EEm~a----VA~fI~qrGRVSis 220 (251)
-+|.+|++.++|+|.--|++..-+..-.-.|++-|.|--| -||+|.-|- ..++.. .++..-+.|-++..
T Consensus 24 aae~hkiiTirdvae~~ev~~n~lr~lasrLekkG~LeRi--~rG~YlI~~lpage~~~~t~he~~~~S~~~~~gyIay~ 101 (269)
T COG5340 24 AAEGHKIITIRDVAETLEVAPNTLRELASRLEKKGWLERI--LRGRYLIIPLPAGEEAVYTTHEYLIASHVAEPGYIAYY 101 (269)
T ss_pred HHHhCceEEeHHhhhhccCCHHHHHHHHhhhhhcchhhhh--cCccEEEeecCCCcccceeehhHHHHHHHcccchhhHH
Confidence 4789999999999999999999999999999999988665 378887653 112222 56666777877763
No 362
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=31.14 E-value=2.2e+02 Score=23.57 Aligned_cols=65 Identities=11% Similarity=0.194 Sum_probs=49.3
Q ss_pred chHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHH--HHHhcCCccHHHHHhhcc
Q 025511 158 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVAD--YIKRQGRVSISHLASKSN 227 (251)
Q Consensus 158 ~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~--fI~qrGRVSisELa~~sN 227 (251)
.+.++|..+|+++.- |.--+..|-|.....+.|.|=|-|++.+..+.. ..+.- -+|++++....+
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 467999999997654 556688899999877777788899999987753 33333 468888887654
No 363
>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=31.10 E-value=79 Score=22.15 Aligned_cols=32 Identities=22% Similarity=0.396 Sum_probs=27.7
Q ss_pred CceEEEcHHHHHHHHHHHHhcCC-ccHHHHHhh
Q 025511 194 GKYIYISQAEMKAVADYIKRQGR-VSISHLASK 225 (251)
Q Consensus 194 GKFIYIS~EEm~aVA~fI~qrGR-VSisELa~~ 225 (251)
|+=|-+|+.|+.-++-++...|+ ||..+|.+.
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 55688999999999999999999 588888874
No 364
>PRK05638 threonine synthase; Validated
Probab=31.04 E-value=1.6e+02 Score=28.52 Aligned_cols=64 Identities=13% Similarity=0.252 Sum_probs=47.5
Q ss_pred HHHHHHHhcCccchHhHHhHcC--CChHHHHHHHHHHHhcCCcceeee-CCCceEEEcHHHHHHHHHH
Q 025511 146 DFVEYIKKHKCIPLEDLAAEFK--LRTQECINRITSLENMGRLSGVMD-DRGKYIYISQAEMKAVADY 210 (251)
Q Consensus 146 ~FI~YIK~~KVV~LEDLAa~Fg--LrTqdvI~RIq~Lea~G~LTGViD-DRGKFIYIS~EEm~aVA~f 210 (251)
..+.+++.+ -...-||+..++ ++..-+-..++.|++.|.|+.-.. -|-+|-+||+.-...+..|
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 345566655 478999999998 888888999999999999987533 2444555888777665543
No 365
>COG3646 Uncharacterized phage-encoded protein [Function unknown]
Probab=30.94 E-value=58 Score=28.92 Aligned_cols=53 Identities=17% Similarity=0.161 Sum_probs=43.1
Q ss_pred HHHHHHhcC--ccchHhHHhHcCCChHHHHHHHHHHHhcCC------------cceeeeCCCceEEE
Q 025511 147 FVEYIKKHK--CIPLEDLAAEFKLRTQECINRITSLENMGR------------LSGVMDDRGKYIYI 199 (251)
Q Consensus 147 FI~YIK~~K--VV~LEDLAa~FgLrTqdvI~RIq~Lea~G~------------LTGViDDRGKFIYI 199 (251)
++.+|..++ ++.--++|--||-+..++..-|+.|-.++. =++-+|..||++|.
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 577899999 888889999999999999999999998883 13345566777764
No 366
>PRK13877 conjugal transfer relaxosome component TraJ; Provisional
Probab=30.80 E-value=74 Score=26.26 Aligned_cols=30 Identities=10% Similarity=0.107 Sum_probs=25.9
Q ss_pred eEEEcHHHHHHHHHHHHhcCCccHHHHHhhc
Q 025511 196 YIYISQAEMKAVADYIKRQGRVSISHLASKS 226 (251)
Q Consensus 196 FIYIS~EEm~aVA~fI~qrGRVSisELa~~s 226 (251)
-+|+||+|...+-.=-++-|- |+++..+.|
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 888887765
No 367
>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=30.55 E-value=1.1e+02 Score=23.10 Aligned_cols=59 Identities=17% Similarity=0.273 Sum_probs=42.9
Q ss_pred HHHHHHHHHhcC----ccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHH
Q 025511 144 LADFVEYIKKHK----CIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQA 202 (251)
Q Consensus 144 L~~FI~YIK~~K----VV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~E 202 (251)
++-|=+|+..+- +-.|=++...||++.+-+-.-+-.|-++|.|...-+.|--|--+|+.
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 344445654432 44566789999999999999999999999999988888777777764
No 368
>KOG2072 consensus Translation initiation factor 3, subunit a (eIF-3a) [Translation, ribosomal structure and biogenesis]
Probab=30.42 E-value=2e+02 Score=31.78 Aligned_cols=20 Identities=35% Similarity=0.617 Sum_probs=11.8
Q ss_pred HHHHhcCCcceeeeCCCceE
Q 025511 178 TSLENMGRLSGVMDDRGKYI 197 (251)
Q Consensus 178 q~Lea~G~LTGViDDRGKFI 197 (251)
..+...|++.-|.||+-+|.
T Consensus 740 ~~vk~k~~l~rm~~d~~~f~ 759 (988)
T KOG2072|consen 740 SAVKDKKRLSRMYDDRDKFK 759 (988)
T ss_pred HHHHHHHHHHHHhhhHHHHH
Confidence 34445566666666666653
No 369
>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=30.25 E-value=1.6e+02 Score=22.78 Aligned_cols=47 Identities=17% Similarity=0.272 Sum_probs=37.0
Q ss_pred cCCChHHHHHHHHHHHhcCCccee--eeC---CCceEEEcHHHHHHHHHHHH
Q 025511 166 FKLRTQECINRITSLENMGRLSGV--MDD---RGKYIYISQAEMKAVADYIK 212 (251)
Q Consensus 166 FgLrTqdvI~RIq~Lea~G~LTGV--iDD---RGKFIYIS~EEm~aVA~fI~ 212 (251)
++++..-+-.-+..|+++|-|+.. -++ |-|+..||+.--+.++....
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 467777888899999999999995 332 34899999998777776654
No 370
>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=30.11 E-value=1.2e+02 Score=28.54 Aligned_cols=55 Identities=5% Similarity=0.018 Sum_probs=44.7
Q ss_pred CccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHh
Q 025511 155 KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKR 213 (251)
Q Consensus 155 KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~q 213 (251)
....+.++|..+|+++ .+ |...+..|.+.++-.+.|.+-+-|++++..+...+..
T Consensus 32 ~~~~i~eva~~~gv~~-~t---lr~~e~~~~~~~~~r~~~g~r~yt~~di~~l~~~~~~ 86 (387)
T TIGR03453 32 RKFTSGEVAKLLGVSD-SY---LRQLSLEGKGPEPETLSNGRRSYTLEQINELRRHLAQ 86 (387)
T ss_pred ccCCHHHHHHHHCcCH-HH---HHHHHHcCCCCCCCcCCCCceeeCHHHHHHHHHHHHh
Confidence 4578999999999954 34 4448999999988777777889999999999887754
No 371
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=30.00 E-value=3.1e+02 Score=26.54 Aligned_cols=8 Identities=13% Similarity=0.343 Sum_probs=4.4
Q ss_pred hhhhhhHH
Q 025511 48 FLFLLSFS 55 (251)
Q Consensus 48 ~~~~~~~~ 55 (251)
.+|+|...
T Consensus 105 ii~nL~~~ 112 (309)
T TIGR00570 105 IVYNLTNN 112 (309)
T ss_pred HHHHhhcC
Confidence 45666544
No 372
>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=29.90 E-value=98 Score=22.10 Aligned_cols=56 Identities=14% Similarity=0.258 Sum_probs=31.0
Q ss_pred HHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHhcCCccHHHHHhhcc
Q 025511 162 LAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRVSISHLASKSN 227 (251)
Q Consensus 162 LAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~qrGRVSisELa~~sN 227 (251)
||..+|++....-..++......- .=|+..-=+..+...|.+.+..|+++++..|.
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 466666666665555555432211 11455555667777776667788888877664
No 373
>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=29.81 E-value=80 Score=25.38 Aligned_cols=29 Identities=14% Similarity=0.368 Sum_probs=24.5
Q ss_pred ceeeeCC-CceEEE-------cHHHHHHHHHHHHhcC
Q 025511 187 SGVMDDR-GKYIYI-------SQAEMKAVADYIKRQG 215 (251)
Q Consensus 187 TGViDDR-GKFIYI-------S~EEm~aVA~fI~qrG 215 (251)
-|+.|+. |+|+|| |+++++++.++++...
T Consensus 26 lg~~d~~~g~l~~vg~vgtG~~~~~~~~l~~~l~~~~ 62 (122)
T cd07972 26 LAVRDEETGELVPVGKVATGLTDEELEELTERLRELI 62 (122)
T ss_pred EEEEcCCCCeEEEEEEEccCCCHHHHHHHHHHhhhhh
Confidence 5899987 899995 7899999999888754
No 374
>CHL00019 atpF ATP synthase CF0 B subunit
Probab=29.12 E-value=3.7e+02 Score=23.00 Aligned_cols=78 Identities=15% Similarity=0.083 Sum_probs=0.0
Q ss_pred HHHHHHHHhhhhhhhhHHhH------HhhhhhHHHHHHHHhhhhHHHHHHHHHHchHHHHHHHHHHHHHHHHHHHHHHHH
Q 025511 38 LLILVCLCTSFLFLLSFSLL------FDMFDLKADEAARESRQSKQDRYTEMRRRKDEEREARESALEEEAKAQKAREEE 111 (251)
Q Consensus 38 ~~~~~~~~~~~~~~~~~~~~------~~~~~Reaee~~RE~Rk~~e~~~ee~rrkkeeere~eE~~~eEeer~~~eeeer 111 (251)
++||+.+..-|+|.|--..+ +..-..+|++...+......+.......-+.+..+..+..+.+.++........
T Consensus 34 flill~lL~~fl~kPI~~~l~~R~~~I~~~l~~Ae~~~~eA~~~~~e~e~~L~~A~~ea~~ii~~A~~~ae~~~~~il~~ 113 (184)
T CHL00019 34 LSVVLGVLIYFGKGVLSDLLDNRKQTILNTIRNSEERREEAIEKLEKARARLRQAELEADEIRVNGYSEIEREKENLINQ 113 (184)
T ss_pred HHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_pred HHHH
Q 025511 112 AAAF 115 (251)
Q Consensus 112 rE~E 115 (251)
...+
T Consensus 114 A~~e 117 (184)
T CHL00019 114 AKED 117 (184)
T ss_pred HHHH
No 375
>PRK08476 F0F1 ATP synthase subunit B'; Validated
Probab=29.00 E-value=3.3e+02 Score=22.50 Aligned_cols=15 Identities=27% Similarity=0.536 Sum_probs=8.1
Q ss_pred HHHHHHHhhhhhhhh
Q 025511 39 LILVCLCTSFLFLLS 53 (251)
Q Consensus 39 ~~~~~~~~~~~~~~~ 53 (251)
+||+.++.-|+|-|-
T Consensus 18 lil~~~l~kfl~kPi 32 (141)
T PRK08476 18 LLLIVILNSWLYKPL 32 (141)
T ss_pred HHHHHHHHHHHHHHH
Confidence 444555555666554
No 376
>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=28.82 E-value=1.1e+02 Score=27.48 Aligned_cols=94 Identities=19% Similarity=0.331 Sum_probs=57.3
Q ss_pred hhHHHHHHHHHHhcCc---cchHhHHhHcCCChHHHHHHHHHHHhcCCcceeee------CCCceEEEcHHHHHHHHHHH
Q 025511 141 RDLLADFVEYIKKHKC---IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMD------DRGKYIYISQAEMKAVADYI 211 (251)
Q Consensus 141 q~lL~~FI~YIK~~KV---V~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViD------DRGKFIYIS~EEm~aVA~fI 211 (251)
.-||..|-.+++.-+. ..+++....|+|.-.-+++||+ .|.-..|-+ +.|. .+.-=.+++..||
T Consensus 33 ~kLl~Qyk~~~~~~~~~~~~~le~F~~~y~l~cp~A~~Rl~----~G~P~Tie~~~~~~~~~~~---~ak~Vae~t~~FI 105 (188)
T PF03997_consen 33 NKLLNQYKTILKQLKDDEFPDLEEFMKKYNLDCPAALERLR----EGVPATIEHRISSSSDKGN---SAKLVAEATQNFI 105 (188)
T ss_dssp HHHHHHHHHHHTSTTHHHHHHHHHHHHHTTS-HHHHHHHHH----CTSS--------------C---HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcccccCCCHHHHHHHhcccCChHHHHHH----cCCCCchhhhcccccCCch---HHHHHHHHhChhh
Confidence 3457777666766655 6789999999999999999997 787776665 3332 3344456677777
Q ss_pred H----------hcCCcc--HHHHHhhcccccccccccchhhh
Q 025511 212 K----------RQGRVS--ISHLASKSNQFIDLETKAQFVED 241 (251)
Q Consensus 212 ~----------qrGRVS--isELa~~sN~lI~L~p~~~~~~~ 241 (251)
- -.+-+. ++||...=|++=.+.|.-....+
T Consensus 106 T~mDaLKLn~~a~DqLhPlL~dL~~slnr~~~~~~dfe~r~k 147 (188)
T PF03997_consen 106 TLMDALKLNYRAKDQLHPLLSDLMQSLNRVTDLPPDFEGRSK 147 (188)
T ss_dssp HHHHHHHTT--BHHHHHHHHHHHHHHHHHCTTS-TT-CCHHH
T ss_pred hhhHHHhccchhHhhHhhHHHHHHHHHhccCCCCCCCccHHH
Confidence 2 333333 47888888888776654444433
No 377
>KOG1363 consensus Predicted regulator of the ubiquitin pathway (contains UAS and UBX domains) [Signal transduction mechanisms]
Probab=28.72 E-value=2.3e+02 Score=28.66 Aligned_cols=10 Identities=20% Similarity=0.504 Sum_probs=5.3
Q ss_pred HHHHHHHHHh
Q 025511 144 LADFVEYIKK 153 (251)
Q Consensus 144 L~~FI~YIK~ 153 (251)
++..++|+-.
T Consensus 406 ~q~l~~~v~~ 415 (460)
T KOG1363|consen 406 LQILYDYVDS 415 (460)
T ss_pred hhHHHHHHHh
Confidence 4555666543
No 378
>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=28.68 E-value=96 Score=22.13 Aligned_cols=38 Identities=21% Similarity=0.362 Sum_probs=24.7
Q ss_pred cceeeeCCCceE-EEcHHHHHHHHHHHHhc---CCccHHHHHhhc
Q 025511 186 LSGVMDDRGKYI-YISQAEMKAVADYIKRQ---GRVSISHLASKS 226 (251)
Q Consensus 186 LTGViDDRGKFI-YIS~EEm~aVA~fI~qr---GRVSisELa~~s 226 (251)
...|+|+.|+|+ +||...+... +.+. +..++.+++...
T Consensus 26 ~~~v~~~~~~~~G~v~~~~l~~~---~~~~~~~~~~~v~~~~~~~ 67 (114)
T cd04613 26 NFPVVDDDGRLVGIVSLDDIREI---LFDPSLYDLVVASDIMTKP 67 (114)
T ss_pred ceeEECCCCCEEEEEEHHHHHHH---HhcccccccEEHHHhccCC
Confidence 467889999998 8998887643 3322 224566666443
No 379
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=28.62 E-value=47 Score=21.98 Aligned_cols=33 Identities=15% Similarity=0.310 Sum_probs=16.5
Q ss_pred ccchHhHHhHcCCChHHHHHHHHHHHhcCCccee
Q 025511 156 CIPLEDLAAEFKLRTQECINRITSLENMGRLSGV 189 (251)
Q Consensus 156 VV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGV 189 (251)
=....++|..||++.+-|-+-++...+.| +.|+
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 45778999999998777777666666666 5554
No 380
>PF04277 OAD_gamma: Oxaloacetate decarboxylase, gamma chain ; InterPro: IPR005899 This family comprises distantly related, low complexity, hydrophobic small subunits of several related sodium ion-pumping decarboxylases. These include oxaloacetate decarboxylase gamma subunit and methylmalonyl-CoA decarboxylase delta subunit [].; GO: 0008948 oxaloacetate decarboxylase activity, 0015081 sodium ion transmembrane transporter activity, 0071436 sodium ion export, 0016020 membrane
Probab=28.55 E-value=86 Score=23.05 Aligned_cols=30 Identities=17% Similarity=0.402 Sum_probs=24.4
Q ss_pred hhHHHHHHHHHhhhhhhhhHHhHHhhhhhH
Q 025511 35 NSLLLILVCLCTSFLFLLSFSLLFDMFDLK 64 (251)
Q Consensus 35 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~Re 64 (251)
+++.+.++++.+-|+|+.-.+.++-.+.+=
T Consensus 3 ~gl~i~i~Gm~iVF~~L~lL~~~i~l~~~~ 32 (79)
T PF04277_consen 3 EGLQIMIIGMGIVFLVLILLILVISLMSKL 32 (79)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 678888899999999888888877777655
No 381
>PRK07718 fliL flagellar basal body-associated protein FliL; Reviewed
Probab=28.54 E-value=35 Score=28.42 Aligned_cols=48 Identities=13% Similarity=0.156 Sum_probs=39.5
Q ss_pred hHHHHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceee
Q 025511 142 DLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVM 190 (251)
Q Consensus 142 ~lL~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGVi 190 (251)
..-+.++.|+...+.--|...+..-.| -+++.+||+.....|.+.+|.
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 456789999999998888777777777 578999999999999888763
No 382
>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=28.48 E-value=2.8e+02 Score=22.51 Aligned_cols=65 Identities=14% Similarity=0.213 Sum_probs=47.8
Q ss_pred chHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHH--HHHHhcCCccHHHHHhhcc
Q 025511 158 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVA--DYIKRQGRVSISHLASKSN 227 (251)
Q Consensus 158 ~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA--~fI~qrGRVSisELa~~sN 227 (251)
.+.++|..+|+++.- |.--++.|-|...-++.|.|=|-|++.+..+. .+.++-| +|++|+...-+
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 367899999997653 45668999999987765777788888888763 3344445 89888666443
No 383
>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=28.47 E-value=86 Score=23.94 Aligned_cols=30 Identities=27% Similarity=0.562 Sum_probs=23.4
Q ss_pred cceeeeCC-CceEEE-------cHHHHHHHHHHHHhcC
Q 025511 186 LSGVMDDR-GKYIYI-------SQAEMKAVADYIKRQG 215 (251)
Q Consensus 186 LTGViDDR-GKFIYI-------S~EEm~aVA~fI~qrG 215 (251)
|-|+.|+. |+|+|| |++++..+-..+....
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 57999997 999997 6788888877777544
No 384
>COG5301 Phage-related tail fibre protein [General function prediction only]
Probab=28.46 E-value=33 Score=35.41 Aligned_cols=14 Identities=36% Similarity=0.672 Sum_probs=13.1
Q ss_pred ceeeeCCCceEEEc
Q 025511 187 SGVMDDRGKYIYIS 200 (251)
Q Consensus 187 TGViDDRGKFIYIS 200 (251)
.|++|+.|+||||+
T Consensus 91 vGlfDadG~liavg 104 (587)
T COG5301 91 VGLFDADGKLIAVG 104 (587)
T ss_pred eeeecCCCCEEEEc
Confidence 69999999999996
No 385
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=28.26 E-value=34 Score=28.48 Aligned_cols=25 Identities=16% Similarity=0.364 Sum_probs=22.8
Q ss_pred CceEEEcHHHHHHHHHHHHhcCCcc
Q 025511 194 GKYIYISQAEMKAVADYIKRQGRVS 218 (251)
Q Consensus 194 GKFIYIS~EEm~aVA~fI~qrGRVS 218 (251)
++|-++|+|+++=|-.||+.+|.+.
T Consensus 29 ~~~~~L~~E~~~Fi~~Fi~~rGnlK 53 (113)
T PF09862_consen 29 PWFARLSPEQLEFIKLFIKNRGNLK 53 (113)
T ss_pred chhhcCCHHHHHHHHHHHHhcCCHH
Confidence 7899999999999999999999643
No 386
>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=28.17 E-value=2.3e+02 Score=20.33 Aligned_cols=57 Identities=11% Similarity=0.159 Sum_probs=31.7
Q ss_pred CCChHHHHHHHHHHHhcCCcceeeeCCCceE-EEcHHHHHHHHHHHHhcCCccHHHHHhh
Q 025511 167 KLRTQECINRITSLENMGRLSGVMDDRGKYI-YISQAEMKAVADYIKRQGRVSISHLASK 225 (251)
Q Consensus 167 gLrTqdvI~RIq~Lea~G~LTGViDDRGKFI-YIS~EEm~aVA~fI~qrGRVSisELa~~ 225 (251)
+.+..++++++. ........|.|+.|+|+ +||...+.....=-......++.++...
T Consensus 9 ~~~~~~~~~~~~--~~~~~~~~vvd~~~~~~G~v~~~dl~~~~~~~~~~~~~~i~~~~~~ 66 (113)
T cd04615 9 NTDIARAVAEMY--TSGSRALPVVDDKKRLVGIITRYDVLSYALESEELKDAKVREVMNS 66 (113)
T ss_pred CCcHHHHHHHHH--HcCCceEeEEcCCCCEEEEEEHHHHHHhhhhhhhhcCCcHHHhccC
Confidence 344556666543 22223456889899998 7899888653210111133456666643
No 387
>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=28.10 E-value=1.4e+02 Score=27.37 Aligned_cols=53 Identities=13% Similarity=0.164 Sum_probs=42.5
Q ss_pred cCCChHHHHHHHHHHHhcCCcceeee--CCCceEEEcHHHHHHHHHHHHhc--CCcc
Q 025511 166 FKLRTQECINRITSLENMGRLSGVMD--DRGKYIYISQAEMKAVADYIKRQ--GRVS 218 (251)
Q Consensus 166 FgLrTqdvI~RIq~Lea~G~LTGViD--DRGKFIYIS~EEm~aVA~fI~qr--GRVS 218 (251)
..+..+....-|+.|.+.|.++||+= .-|-|-++|.+|...+.+...+. |||.
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 45667777888899999998899754 57999999999999998877654 6654
No 388
>PF14880 COX14: Cytochrome oxidase c assembly
Probab=27.97 E-value=1.4e+02 Score=21.64 Aligned_cols=26 Identities=23% Similarity=0.145 Sum_probs=16.8
Q ss_pred cchhHHHHHHHHHhhhhhhhhHHhHH
Q 025511 33 RANSLLLILVCLCTSFLFLLSFSLLF 58 (251)
Q Consensus 33 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 (251)
|.-.+-||.++++.+.++..+..+.+
T Consensus 15 R~tV~~Lig~T~~~g~~~~~~~y~~~ 40 (59)
T PF14880_consen 15 RTTVLGLIGFTVYGGGLTVYTVYSYF 40 (59)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34466777788877777766654443
No 389
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=27.95 E-value=4.4e+02 Score=23.60 Aligned_cols=88 Identities=17% Similarity=0.297 Sum_probs=67.2
Q ss_pred HHHHHHHhcCc-cchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeC-CCceEEEcHHHHHHHHHHHHhcCCcc-----
Q 025511 146 DFVEYIKKHKC-IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDD-RGKYIYISQAEMKAVADYIKRQGRVS----- 218 (251)
Q Consensus 146 ~FI~YIK~~KV-V~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDD-RGKFIYIS~EEm~aVA~fI~qrGRVS----- 218 (251)
..++++....- +.+.|||...|++..-+-.-++.|...|-+. -|+ .|+| ++++.=+.-=+.|.....=++
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 35666665555 6899999999999999999999999999875 566 4555 699987777777777655444
Q ss_pred HHHHHhhccccccccccc
Q 025511 219 ISHLASKSNQFIDLETKA 236 (251)
Q Consensus 219 isELa~~sN~lI~L~p~~ 236 (251)
+.+|+...+...+|.--+
T Consensus 85 l~~L~~~tgetv~L~v~d 102 (246)
T COG1414 85 LEELAEETGETVHLSVLD 102 (246)
T ss_pred HHHHHHHhCCcEEEEEEe
Confidence 367888888777776544
No 390
>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=27.85 E-value=87 Score=23.23 Aligned_cols=44 Identities=20% Similarity=0.322 Sum_probs=34.4
Q ss_pred HHHHHHhcC--ccchHhHHhHcCCChHHHHHHHHHHHhcCCcceee
Q 025511 147 FVEYIKKHK--CIPLEDLAAEFKLRTQECINRITSLENMGRLSGVM 190 (251)
Q Consensus 147 FI~YIK~~K--VV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGVi 190 (251)
++..|-.++ =+.--||+..||+..-.+--+++.|+..|-|+..-
T Consensus 7 ~Le~I~rsR~~Gi~q~~L~~~~~~D~r~i~~~~k~L~~~gLI~k~~ 52 (75)
T PF04182_consen 7 LLERIARSRYNGITQSDLSKLLGIDPRSIFYRLKKLEKKGLIVKQS 52 (75)
T ss_pred HHHHHHhcCCCCEehhHHHHHhCCCchHHHHHHHHHHHCCCEEEEE
Confidence 445554333 24556899999999999999999999999998754
No 391
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=27.63 E-value=4e+02 Score=23.76 Aligned_cols=86 Identities=12% Similarity=0.081 Sum_probs=56.9
Q ss_pred HHHHHHhcC-ccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHhcCCc-----cHH
Q 025511 147 FVEYIKKHK-CIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRV-----SIS 220 (251)
Q Consensus 147 FI~YIK~~K-VV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~qrGRV-----Sis 220 (251)
.++++..+. -+.+.|||..+|++..-+-.-++.|++.|-|.=.-| .|+| .+++.=+.--..+.....-+ .+.
T Consensus 16 iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~~~g~v~~~~~-~~~Y-~Lg~~~~~l~~~~~~~~~l~~~a~p~l~ 93 (263)
T PRK09834 16 VLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQEEGYVRRSAS-DDSF-RLTLKVRQLSEGFRDEQWISALAAPLLG 93 (263)
T ss_pred HHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecC-CCcE-EEcHHHHHHHHhhhccccHHHHHHHHHH
Confidence 445555544 488999999999999999999999999999874333 3444 56765443222233222222 246
Q ss_pred HHHhhccccccccc
Q 025511 221 HLASKSNQFIDLET 234 (251)
Q Consensus 221 ELa~~sN~lI~L~p 234 (251)
+|+..++.-..|.-
T Consensus 94 ~La~~t~etv~L~v 107 (263)
T PRK09834 94 DLLRRVVWPTDLTT 107 (263)
T ss_pred HHHHHhCCceeEEE
Confidence 78877777666654
No 392
>CHL00090 apcD allophycocyanin gamma subunit
Probab=27.56 E-value=33 Score=29.70 Aligned_cols=39 Identities=28% Similarity=0.556 Sum_probs=29.3
Q ss_pred eCCCceEEEcHHHHHHHHHHHHhc-CCccHH-HHHhhcccccc
Q 025511 191 DDRGKYIYISQAEMKAVADYIKRQ-GRVSIS-HLASKSNQFID 231 (251)
Q Consensus 191 DDRGKFIYIS~EEm~aVA~fI~qr-GRVSis-ELa~~sN~lI~ 231 (251)
|+.|+| .|..||+.+..|++.- =|+++. -|..+++.+++
T Consensus 12 D~~gRy--ls~~EL~~l~~~~~~~~~Rl~aa~~l~~na~~IV~ 52 (161)
T CHL00090 12 DDELRY--PTIGELESIQDYLKTGEKRIRIATILRDNEKEIIQ 52 (161)
T ss_pred hhccCC--CCHHHHHHHHHHHHhHHHHhHHHHHHHHHHHHHHH
Confidence 667775 7999999999999876 567764 46666666554
No 393
>PRK09174 F0F1 ATP synthase subunit B'; Validated
Probab=27.52 E-value=4.4e+02 Score=23.43 Aligned_cols=6 Identities=0% Similarity=0.218 Sum_probs=2.4
Q ss_pred HHhhhh
Q 025511 57 LFDMFD 62 (251)
Q Consensus 57 ~~~~~~ 62 (251)
+-.+++
T Consensus 78 I~~vLe 83 (204)
T PRK09174 78 IGGIIE 83 (204)
T ss_pred HHHHHH
Confidence 334443
No 394
>PRK15466 carboxysome structural protein EutK; Provisional
Probab=27.48 E-value=63 Score=28.79 Aligned_cols=34 Identities=21% Similarity=0.305 Sum_probs=29.9
Q ss_pred cCccchHhHHhHcCCChHHHHHHHHHHHhcCCcc
Q 025511 154 HKCIPLEDLAAEFKLRTQECINRITSLENMGRLS 187 (251)
Q Consensus 154 ~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LT 187 (251)
+.=....++|+|||.+.+...+-+..|-.+|.|-
T Consensus 122 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 155 (166)
T PRK15466 122 RQGMTAGEVAAHFGWPLEKARNALEQLFSAGTLR 155 (166)
T ss_pred HccccHHHHHHHhCCcHHHHHHHHHHHHhccchh
Confidence 3456778999999999999999999999999873
No 395
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=27.41 E-value=4.7e+02 Score=25.35 Aligned_cols=11 Identities=0% Similarity=0.178 Sum_probs=4.2
Q ss_pred hhHHHHHHHHh
Q 025511 62 DLKADEAARES 72 (251)
Q Consensus 62 ~Reaee~~RE~ 72 (251)
+++....-..+
T Consensus 126 ~~~n~~~I~~n 136 (309)
T TIGR00570 126 QKENKDVIQKN 136 (309)
T ss_pred HHHhHHHHHHH
Confidence 33433333333
No 396
>PRK13460 F0F1 ATP synthase subunit B; Provisional
Probab=27.27 E-value=3.8e+02 Score=22.64 Aligned_cols=14 Identities=7% Similarity=0.432 Sum_probs=7.2
Q ss_pred hhhHHhHHhhhhhH
Q 025511 51 LLSFSLLFDMFDLK 64 (251)
Q Consensus 51 ~~~~~~~~~~~~Re 64 (251)
.+-|..+.++++..
T Consensus 35 ~~~~kpi~~~l~~R 48 (173)
T PRK13460 35 KFAWDVILKALDER 48 (173)
T ss_pred HHhHHHHHHHHHHH
Confidence 34444566666543
No 397
>PF14056 DUF4250: Domain of unknown function (DUF4250)
Probab=27.13 E-value=1.7e+02 Score=21.57 Aligned_cols=38 Identities=16% Similarity=0.392 Sum_probs=31.5
Q ss_pred hHHHHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHH
Q 025511 142 DLLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITS 179 (251)
Q Consensus 142 ~lL~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~ 179 (251)
..|-.|||-=-.--.-.|++|+..+++..+++++|+..
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 45667888665667789999999999999999998865
No 398
>PF00502 Phycobilisome: Phycobilisome protein; InterPro: IPR012128 Cyanobacteria and red algae harvest light through water-soluble complexes, called phycobilisomes, which are attached to the outer face of the thylakoid membrane []. These complexes are capable of transferring the absorbed energy to the photosynthetic reaction centre with greater than 95% efficiency. Phycobilisomes contain various photosynthetic light harvesting proteins known as biliproteins, and linker proteins which help assemble the structure. The two main structural elements of the complex are a core located near the photosynthetic reaction centre, and rods attached to this core. Allophycocyanin is the major component of the core, while the rods contain phycocyanins, phycoerythrins and linker proteins. The rod biliproteins harvest photons, with the excitation energy being passed through the rods into the allophycocyanin in the core. Other core biliproteins subsequently pass this energy to chlorophyll within the thylakoid membrane. This entry represents the alpha and beta subunits found in biliproteins from cyanobacteria and red algae. Structural studies indicate that the basic structural unit of most biliproteins is a heterodimer composed of these alpha and beta subunits [, , , ]. The full protein is a ring-like trimer assembly of these heterodimers. Each subunit of the heterodimer has eight helices and binds chromophores through thioester bonds formed at particular cysteine residues. These chromophores, also known as bilins, are open-chain tetrapyrroles whose number and type vary with the particular biliprotein eg R-phyocerythrin binds five phycoerythrobilins per heterodimer, while allophycocyanin binds two phycocyanobilins per heterodimer.; GO: 0015979 photosynthesis, 0030089 phycobilisome; PDB: 2VML_I 2VJR_A 1KTP_B 3L0F_B 1JBO_B 3KVS_B 1PHN_B 3BRP_B 2C7K_B 2C7L_B ....
Probab=27.09 E-value=23 Score=29.91 Aligned_cols=39 Identities=26% Similarity=0.636 Sum_probs=27.5
Q ss_pred eCCCceEEEcHHHHHHHHHHHHhc-CCccH-HHHHhhcccccc
Q 025511 191 DDRGKYIYISQAEMKAVADYIKRQ-GRVSI-SHLASKSNQFID 231 (251)
Q Consensus 191 DDRGKFIYIS~EEm~aVA~fI~qr-GRVSi-sELa~~sN~lI~ 231 (251)
|+.|+| +|+.||+++..|+..- =|+.+ .-|....+.+|+
T Consensus 8 D~egRy--ls~~EL~~l~~~~~~~~~Rl~aa~~L~~~a~~IV~ 48 (157)
T PF00502_consen 8 DAEGRY--LSDGELQALKGYFQSANARLEAAEKLRDNASEIVD 48 (157)
T ss_dssp HHTTSE--CEHHHHHHHHHHHHTHHHHHHHHHHHHHTHHHHHH
T ss_pred HhcCCC--CCHHHHHHHHHHHHhHHHHHHHHHHHHHhHHHHHH
Confidence 667775 7999999999998753 46665 455555555543
No 399
>COG3753 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.90 E-value=68 Score=27.98 Aligned_cols=24 Identities=25% Similarity=0.320 Sum_probs=21.0
Q ss_pred chHhHHhHcCCChHHHHHHHHHHH
Q 025511 158 PLEDLAAEFKLRTQECINRITSLE 181 (251)
Q Consensus 158 ~LEDLAa~FgLrTqdvI~RIq~Le 181 (251)
.|.+||.++|+.++++++++-+..
T Consensus 92 ~l~~la~~~Gld~~El~~~Ls~~L 115 (143)
T COG3753 92 TLSQLAQKTGLDEQELLKQLSEQL 115 (143)
T ss_pred HHHHHHHHhCCCHHHHHHHHHHHh
Confidence 578999999999999999987653
No 400
>PRK11517 transcriptional regulatory protein YedW; Provisional
Probab=26.74 E-value=2.7e+02 Score=22.33 Aligned_cols=35 Identities=17% Similarity=0.204 Sum_probs=29.7
Q ss_pred CCCceEEEcHHHHHHHHHHHHhcCCc-cHHHHHhhc
Q 025511 192 DRGKYIYISQAEMKAVADYIKRQGRV-SISHLASKS 226 (251)
Q Consensus 192 DRGKFIYIS~EEm~aVA~fI~qrGRV-SisELa~~s 226 (251)
..|+.+-+|+.|++-+.-++...|+| |-.+|...-
T Consensus 141 ~~~~~~~Lt~~E~~il~~l~~~~g~~~s~~~i~~~~ 176 (223)
T PRK11517 141 RDNISITLTRKEFQLLWLLASRAGEIIPRTVIASEI 176 (223)
T ss_pred ECCEEEeCCHHHHHHHHHHHhCCCccCCHHHHHHHh
Confidence 35899999999999999999999985 667777763
No 401
>TIGR00964 secE_bact preprotein translocase, SecE subunit, bacterial. This model represents exclusively the bacterial (and some organellar) SecE protein. SecE is part of the core heterotrimer, SecYEG, of the Sec preprotein translocase system. Other components are the ATPase SecA, a cytosolic chaperone SecB, and an accessory complex of SecDF and YajC.
Probab=26.74 E-value=77 Score=22.48 Aligned_cols=38 Identities=13% Similarity=0.286 Sum_probs=25.6
Q ss_pred hHhhhHhhhhhcccccccccccchhHHHHHHHHHhhhh
Q 025511 12 TYIFDIHRVLEGYESSTRKDTRANSLLLILVCLCTSFL 49 (251)
Q Consensus 12 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 49 (251)
.|+-|+-.-+..-.=.||+++..+++..++++++.+.+
T Consensus 3 ~f~~~~~~ElkkV~WPt~~e~~~~t~~Vi~~~~~~~~~ 40 (55)
T TIGR00964 3 KFFKEVKAELKKVVWPSRKELITYTIVVIVFVIFFSLF 40 (55)
T ss_pred hHHHHHHHHHhcCcCcCHHHHHhHHHHHHHHHHHHHHH
Confidence 45555544444445678999999998888777665543
No 402
>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]
Probab=26.62 E-value=2.4e+02 Score=20.71 Aligned_cols=73 Identities=22% Similarity=0.327 Sum_probs=48.3
Q ss_pred HHHHHHHHHhcCc--cchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHhcCCccHHH
Q 025511 144 LADFVEYIKKHKC--IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRVSISH 221 (251)
Q Consensus 144 L~~FI~YIK~~KV--V~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~qrGRVSisE 221 (251)
+...+.||..+-- ..+++||..+|++..-+-.+.+........ -||..-=|+. |..+-..|.-+|++
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 3378888887433 679999999999998888887765433222 3444444444 44444556668888
Q ss_pred HHhhcc
Q 025511 222 LASKSN 227 (251)
Q Consensus 222 La~~sN 227 (251)
+|..|.
T Consensus 91 iA~~~G 96 (127)
T COG2207 91 IALRLG 96 (127)
T ss_pred HHHHhC
Confidence 877664
No 403
>PRK06582 coproporphyrinogen III oxidase; Provisional
Probab=26.62 E-value=1.7e+02 Score=28.09 Aligned_cols=49 Identities=14% Similarity=0.348 Sum_probs=37.8
Q ss_pred HHhcCccchHhHHhHcCCChHHHH--HHHHHHHhcCCcceeeeCCCceEEEcHHHH
Q 025511 151 IKKHKCIPLEDLAAEFKLRTQECI--NRITSLENMGRLSGVMDDRGKYIYISQAEM 204 (251)
Q Consensus 151 IK~~KVV~LEDLAa~FgLrTqdvI--~RIq~Lea~G~LTGViDDRGKFIYIS~EEm 204 (251)
+..+.=|.+.++...||+...+.. +.|+.|.+.|.+.- + + -|++|+.-+
T Consensus 328 LR~~~Gl~~~~~~~~~g~~~~~~~~~~~l~~l~~~gll~~--~--~-~l~lT~~G~ 378 (390)
T PRK06582 328 LRLSKGINISTLEQKLNTKLENILDMNNLKHYQALDLIRL--D--E-NIYLTDKGL 378 (390)
T ss_pred HHhhCCCCHHHHHHHHCcCHHHhhhHHHHHHHHHCCCEEE--C--C-EEEECcchh
Confidence 456667888889999999887754 78999999998772 4 2 399998644
No 404
>PF13904 DUF4207: Domain of unknown function (DUF4207)
Probab=26.34 E-value=3.2e+02 Score=25.10 Aligned_cols=10 Identities=30% Similarity=0.664 Sum_probs=5.5
Q ss_pred HHHHHhhhcc
Q 025511 114 AFEFEKWKGE 123 (251)
Q Consensus 114 ~EEY~KwK~~ 123 (251)
..-|.+|-..
T Consensus 223 e~A~~~Wl~~ 232 (264)
T PF13904_consen 223 EEAFQKWLKN 232 (264)
T ss_pred HHHHHHHHHH
Confidence 3556666543
No 405
>PF13025 DUF3886: Protein of unknown function (DUF3886)
Probab=26.28 E-value=2.2e+02 Score=22.01 Aligned_cols=7 Identities=14% Similarity=0.112 Sum_probs=2.9
Q ss_pred HhhhhhH
Q 025511 58 FDMFDLK 64 (251)
Q Consensus 58 ~~~~~Re 64 (251)
-|++.-.
T Consensus 11 kD~L~~d 17 (70)
T PF13025_consen 11 KDQLNED 17 (70)
T ss_pred HHHHHHH
Confidence 3444433
No 406
>PF00430 ATP-synt_B: ATP synthase B/B' CF(0); InterPro: IPR002146 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. F-ATPases (also known as F1F0-ATPase, or H(+)-transporting two-sector ATPase) (3.6.3.14 from EC) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria (A-G, F6, F8). Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis []. These ATPases can also work in reverse to hydrolyse ATP to create a proton gradient. This entry represents subunits B and B' from the F0 complex in F-ATPases found in chloroplasts and in bacterial plasma membranes. The B subunits are part of the peripheral stalk that links the F1 and F0 complexes together, and which acts as a stator to prevent certain subunits from rotating with the central rotary element. The peripheral stalk differs in subunit composition between mitochondrial, chloroplast and bacterial F-ATPases. In bacterial and chloroplast F-ATPases, the peripheral stalk is composed of one copy of the delta subunit (homologous to OSCP in mitochondria), and two copies of subunit B in bacteria, or one copy each of subunits B and B' in chloroplasts and photosynthetic bacteria []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0015078 hydrogen ion transmembrane transporter activity, 0015986 ATP synthesis coupled proton transport, 0045263 proton-transporting ATP synthase complex, coupling factor F(o); PDB: 1L2P_A 2KHK_A 1B9U_A.
Probab=26.09 E-value=3.2e+02 Score=21.25 Aligned_cols=18 Identities=33% Similarity=0.429 Sum_probs=10.3
Q ss_pred HHHHHHHHhhhhhhhhHH
Q 025511 38 LLILVCLCTSFLFLLSFS 55 (251)
Q Consensus 38 ~~~~~~~~~~~~~~~~~~ 55 (251)
++||+.++.-|+|-|-..
T Consensus 9 Flil~~~l~~~~~~pi~~ 26 (132)
T PF00430_consen 9 FLILFFLLNKFLYKPIKK 26 (132)
T ss_dssp HHHHHHHHHHHTHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 455566666666665443
No 407
>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=26.03 E-value=2e+02 Score=21.28 Aligned_cols=47 Identities=26% Similarity=0.458 Sum_probs=32.8
Q ss_pred hHHHHHHHHHHh--cCccchHhHHhHc---CCChH--HHHHHHHHHHhcCCcce
Q 025511 142 DLLADFVEYIKK--HKCIPLEDLAAEF---KLRTQ--ECINRITSLENMGRLSG 188 (251)
Q Consensus 142 ~lL~~FI~YIK~--~KVV~LEDLAa~F---gLrTq--dvI~RIq~Lea~G~LTG 188 (251)
.+-+.||.++.. .+.+.+.++|..+ +.+|+ =+-|-++=|++-|-|+=
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 23344455666665543
No 408
>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=25.59 E-value=3.3e+02 Score=21.48 Aligned_cols=65 Identities=12% Similarity=0.122 Sum_probs=48.4
Q ss_pred chHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHH--HHHhcCCccHHHHHhhccc
Q 025511 158 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVAD--YIKRQGRVSISHLASKSNQ 228 (251)
Q Consensus 158 ~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~--fI~qrGRVSisELa~~sN~ 228 (251)
.+.++|..+|+++.- |.--++.|-|..+-++. .|=|-|++.+..+.. +.++ --+|++++....+.
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 66778899999987665 677889999888643 3344 44788888776554
No 409
>PF10107 Endonuc_Holl: Endonuclease related to archaeal Holliday junction resolvase; InterPro: IPR019287 This domain is found in various predicted bacterial endonucleases which are distantly related to archaeal Holliday junction resolvases.
Probab=25.46 E-value=4.8e+02 Score=23.14 Aligned_cols=15 Identities=27% Similarity=0.240 Sum_probs=7.0
Q ss_pred hhhHHHHHHHHhhhh
Q 025511 61 FDLKADEAARESRQS 75 (251)
Q Consensus 61 ~~Reaee~~RE~Rk~ 75 (251)
++..++.+++.....
T Consensus 16 l~~~~~~~a~~~fe~ 30 (156)
T PF10107_consen 16 LQGKIERRARELFEQ 30 (156)
T ss_pred HHHHHHHHHHHHHHH
Confidence 444555555444433
No 410
>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=25.45 E-value=1.2e+02 Score=26.12 Aligned_cols=45 Identities=16% Similarity=0.282 Sum_probs=36.0
Q ss_pred ccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHH
Q 025511 156 CIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAE 203 (251)
Q Consensus 156 VV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EE 203 (251)
++...+||.++|++.+-+..-|+.|++.|-|.=+ ..|-| +|.|.-
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 3456789999999999999999999999988654 44654 478764
No 411
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=25.44 E-value=1.4e+02 Score=27.07 Aligned_cols=77 Identities=16% Similarity=0.354 Sum_probs=51.8
Q ss_pred chhHHHHHHHHHHhc--CccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHhcCCc
Q 025511 140 DRDLLADFVEYIKKH--KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRV 217 (251)
Q Consensus 140 sq~lL~~FI~YIK~~--KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~qrGRV 217 (251)
....+..+++||..+ .-+.+++||.++|++..-.-.+.+......- .=||..-=|......+.. +..
T Consensus 216 ~~~~~~~~~~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~~~g~s~----------~~~~~~~Rl~~A~~lL~~-~~~ 284 (322)
T PRK09393 216 ESDRLGPLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAATGMTP----------AEWLLRERLARARDLLES-SAL 284 (322)
T ss_pred chHHHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCH----------HHHHHHHHHHHHHHHHHc-CCC
Confidence 346789999999886 4688999999999999888888876542100 002333334444444444 567
Q ss_pred cHHHHHhhcc
Q 025511 218 SISHLASKSN 227 (251)
Q Consensus 218 SisELa~~sN 227 (251)
|+++++..|.
T Consensus 285 ~i~~IA~~~G 294 (322)
T PRK09393 285 SIDQIAERAG 294 (322)
T ss_pred CHHHHHHHhC
Confidence 8888877663
No 412
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=25.18 E-value=1.1e+02 Score=23.68 Aligned_cols=37 Identities=11% Similarity=0.197 Sum_probs=28.2
Q ss_pred CCCceEE-EcHHHHH-HHHHHHHhcCCccHHHHHhhccc
Q 025511 192 DRGKYIY-ISQAEMK-AVADYIKRQGRVSISHLASKSNQ 228 (251)
Q Consensus 192 DRGKFIY-IS~EEm~-aVA~fI~qrGRVSisELa~~sN~ 228 (251)
+.|.|++ +|-+||- .++.|+.+.|.++-.++...-.+
T Consensus 34 ~~G~Ft~~~t~eemie~~~~~~~~~~~~~~~~a~~~~~~ 72 (81)
T PF12674_consen 34 QNGEFTQDITMEEMIEFCVPFMDEFNGMTPEEARKMMPR 72 (81)
T ss_pred cCCceeecCCHHHHHHHHHHHHHHhCCCCHHHHHHHHHH
Confidence 4699999 9998875 56789999998777666554433
No 413
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=24.93 E-value=2.5e+02 Score=26.10 Aligned_cols=57 Identities=14% Similarity=0.204 Sum_probs=45.9
Q ss_pred HHHHHHHHHHhcC-ccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEE
Q 025511 143 LLADFVEYIKKHK-CIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYI 199 (251)
Q Consensus 143 lL~~FI~YIK~~K-VV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYI 199 (251)
..++-++||+.+. .+.-.||....|++-.-+=.++++||+.|-|-=.=-.|+.+|-+
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 3578999999887 48899999999999999999999999999775444445555444
No 414
>PF13274 DUF4065: Protein of unknown function (DUF4065)
Probab=24.72 E-value=1.1e+02 Score=22.83 Aligned_cols=82 Identities=15% Similarity=0.055 Sum_probs=53.5
Q ss_pred HHHHHHHhcC-ccchHhHHhHcCCChHHHHHHHHHHHhcCCcc---------eeeeCCCceEEEcHHHHHHHHHHHHhcC
Q 025511 146 DFVEYIKKHK-CIPLEDLAAEFKLRTQECINRITSLENMGRLS---------GVMDDRGKYIYISQAEMKAVADYIKRQG 215 (251)
Q Consensus 146 ~FI~YIK~~K-VV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LT---------GViDDRGKFIYIS~EEm~aVA~fI~qrG 215 (251)
++..+.+..+ +....=.|-.+|==..++-+.++.+...+... +..+ ......+|+++.+.+-.-|+.-|
T Consensus 9 ~~~~~~~~g~~l~~~~~~a~~yGPv~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~i~~V~~~~~ 87 (108)
T PF13274_consen 9 DGYYLKKYGKPLFGDDFEAWKYGPVPSDVYDDLKNNGEISIEEFETTYEPIIKYKD-KFDLEELSEEEKEIIDEVINKYG 87 (108)
T ss_pred HHHHHHHhCCCCccchhhhhcCCCcCHHHHHHHHccCCcccccccccccccccccc-ccccccCCHHHHHHHHHHHHHHc
Confidence 3333444443 33344467777776777766666543332211 1111 15667999999999999999999
Q ss_pred CccHHHHHhhccc
Q 025511 216 RVSISHLASKSNQ 228 (251)
Q Consensus 216 RVSisELa~~sN~ 228 (251)
..|-.+|.+.|++
T Consensus 88 ~~s~~~L~~~sH~ 100 (108)
T PF13274_consen 88 DKSAWELSELSHK 100 (108)
T ss_pred CCCHHHHHHHHcC
Confidence 9999999998873
No 415
>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=24.45 E-value=2.5e+02 Score=20.29 Aligned_cols=64 Identities=17% Similarity=0.342 Sum_probs=34.3
Q ss_pred cCCChHHHHHHHHHHHhcC--CcceeeeCCCceE-EEcHHHHHHHHHHHHhcCCccHHHHHhhccccccccc
Q 025511 166 FKLRTQECINRITSLENMG--RLSGVMDDRGKYI-YISQAEMKAVADYIKRQGRVSISHLASKSNQFIDLET 234 (251)
Q Consensus 166 FgLrTqdvI~RIq~Lea~G--~LTGViDDRGKFI-YIS~EEm~aVA~fI~qrGRVSisELa~~sN~lI~L~p 234 (251)
-+.+..++++.+. ..+ ...-|+|+.|+++ +||...+.... .......+++++.......+.+.|
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 3455566665542 222 2345679999998 67888765432 122234456666654333334444
No 416
>TIGR01338 phycocy_alpha phycocyanin, alpha subunit. This model excludes the closely related phycoerythrocyanin alpha subunit.
Probab=24.32 E-value=39 Score=29.55 Aligned_cols=40 Identities=20% Similarity=0.474 Sum_probs=30.9
Q ss_pred eCCCceEEEcHHHHHHHHHHHHhc-CCccH-HHHHhhccccccc
Q 025511 191 DDRGKYIYISQAEMKAVADYIKRQ-GRVSI-SHLASKSNQFIDL 232 (251)
Q Consensus 191 DDRGKFIYIS~EEm~aVA~fI~qr-GRVSi-sELa~~sN~lI~L 232 (251)
|++|+| +|..|++++..|+++- =|+.+ .-|++.++.+++=
T Consensus 12 D~qgRy--ls~~eL~~l~~~~~~g~~RL~aa~~Lt~na~~IV~~ 53 (161)
T TIGR01338 12 DSQGRF--LSNGELQSIFGRFQRATASLEAAKSLTSNAQRLISG 53 (161)
T ss_pred HhccCC--CCHHHHHHHHHHHHchHHHHHHHHHHHhhHHHHHHH
Confidence 788987 6899999999999875 56665 4577777777653
No 417
>CHL00171 cpcB phycocyanin beta subunit; Reviewed
Probab=24.26 E-value=36 Score=29.94 Aligned_cols=40 Identities=15% Similarity=0.464 Sum_probs=29.9
Q ss_pred eeCCCceEEEcHHHHHHHHHHHHhc-CCccHH-HHHhhcccccc
Q 025511 190 MDDRGKYIYISQAEMKAVADYIKRQ-GRVSIS-HLASKSNQFID 231 (251)
Q Consensus 190 iDDRGKFIYIS~EEm~aVA~fI~qr-GRVSis-ELa~~sN~lI~ 231 (251)
-|.+|+| +|..||+++..|++.- =|+++. -|..+++.+|+
T Consensus 12 AD~~gRy--ls~~EL~~l~~~~~~~~~Rl~aa~~L~~na~~IV~ 53 (172)
T CHL00171 12 ADARGEF--LSNTQLDALSKMVAEGNKRLDAVNKINANASTIVT 53 (172)
T ss_pred HhhccCC--CCHHHHHHHHHHHHhHHHHHHHHHHHHHhHHHHHH
Confidence 3667885 7999999999999875 566653 47777666654
No 418
>COG4741 Predicted secreted endonuclease distantly related to archaeal Holliday junction resolvase [Nucleotide transport and metabolism]
Probab=24.23 E-value=5.3e+02 Score=23.23 Aligned_cols=20 Identities=25% Similarity=0.275 Sum_probs=10.5
Q ss_pred HhhhhhHHHHHHHHhhhhHH
Q 025511 58 FDMFDLKADEAARESRQSKQ 77 (251)
Q Consensus 58 ~~~~~Reaee~~RE~Rk~~e 77 (251)
+-.+++.-+..+|+-...++
T Consensus 24 Ir~lq~~~e~k~~~l~e~l~ 43 (175)
T COG4741 24 IRSLQGKVESKARELEETLQ 43 (175)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 44566666555555444433
No 419
>PF11845 DUF3365: Protein of unknown function (DUF3365); InterPro: IPR021796 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 198 to 657 amino acids in length.
Probab=24.04 E-value=2.1e+02 Score=23.74 Aligned_cols=41 Identities=10% Similarity=0.215 Sum_probs=26.1
Q ss_pred HHHHHHhcC--C---ccee-eeCCCceEEEcHHHHHHHHHHHHhcCCcc
Q 025511 176 RITSLENMG--R---LSGV-MDDRGKYIYISQAEMKAVADYIKRQGRVS 218 (251)
Q Consensus 176 RIq~Lea~G--~---LTGV-iDDRGKFIYIS~EEm~aVA~fI~qrGRVS 218 (251)
-|+.+.+.. . ...+ +|+...|.|..|--+ -...+..+|-++
T Consensus 111 ~L~~f~~~~~~e~~~~~~~~~~g~~~~ry~~pi~~--~~~CL~CHg~~~ 157 (188)
T PF11845_consen 111 ALEQFEKNPEDEYFEYVEVEINGKPYFRYARPIRV--EESCLSCHGDPD 157 (188)
T ss_pred HHHHHHhCCCcCcceeeeeccCCCceEEEEeehhc--chHHHHccCCcc
Confidence 345555555 2 3333 567899999999555 556788888443
No 420
>KOG0687 consensus 26S proteasome regulatory complex, subunit RPN7/PSMD6 [Posttranslational modification, protein turnover, chaperones]
Probab=24.04 E-value=83 Score=31.30 Aligned_cols=66 Identities=18% Similarity=0.245 Sum_probs=47.0
Q ss_pred HHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEE-cHHHHHHHHHHHHhcCC
Q 025511 151 IKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYI-SQAEMKAVADYIKRQGR 216 (251)
Q Consensus 151 IK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYI-S~EEm~aVA~fI~qrGR 216 (251)
+.+=|.+.|+-.|..||++..=+=+-+-.+.+.|+|.-+||-=+--|-. +|++=++.-+-.-+.|-
T Consensus 312 LESYrsl~l~~MA~aFgVSVefiDreL~rFI~~grL~ckIDrVnGVVEtNrpD~KN~qyq~vikqGd 378 (393)
T KOG0687|consen 312 LESYRSLTLESMAKAFGVSVEFIDRELGRFIAAGRLHCKIDRVNGVVETNRPDEKNAQYQAVIKQGD 378 (393)
T ss_pred HHHHHHHHHHHHHHHhCchHHHHHhHHHHhhccCceeeeeecccceeecCCccccchHHHHHHhhhH
Confidence 3566789999999999998766666799999999999999974444444 35554444333333443
No 421
>CHL00089 apcF allophycocyanin beta 18 subunit
Probab=23.87 E-value=40 Score=29.62 Aligned_cols=39 Identities=21% Similarity=0.493 Sum_probs=29.5
Q ss_pred eCCCceEEEcHHHHHHHHHHHHhc-CCccHH-HHHhhcccccc
Q 025511 191 DDRGKYIYISQAEMKAVADYIKRQ-GRVSIS-HLASKSNQFID 231 (251)
Q Consensus 191 DDRGKFIYIS~EEm~aVA~fI~qr-GRVSis-ELa~~sN~lI~ 231 (251)
|+.|+| +|..||+.+..|+++- -|++.. -|..+++.+|+
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 788886 7999999999999875 567764 46666655553
No 422
>CHL00086 apcA allophycocyanin alpha subunit
Probab=23.77 E-value=40 Score=29.24 Aligned_cols=39 Identities=18% Similarity=0.483 Sum_probs=29.5
Q ss_pred eCCCceEEEcHHHHHHHHHHHHhc-CCccHH-HHHhhcccccc
Q 025511 191 DDRGKYIYISQAEMKAVADYIKRQ-GRVSIS-HLASKSNQFID 231 (251)
Q Consensus 191 DDRGKFIYIS~EEm~aVA~fI~qr-GRVSis-ELa~~sN~lI~ 231 (251)
|..|+| +|..||+++..|++.- -|++.. -|..+++.+|+
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 667875 7999999999999886 477764 46666665554
No 423
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=23.76 E-value=2.5e+02 Score=24.69 Aligned_cols=74 Identities=18% Similarity=0.244 Sum_probs=54.2
Q ss_pred hhHHHHHHHHHHhc--Cc-cchHhHHhHcCCChHHHHHHHHHHHhcCC-cceeeeCCCceEEEcHHHHHHHHHHHHhc-C
Q 025511 141 RDLLADFVEYIKKH--KC-IPLEDLAAEFKLRTQECINRITSLENMGR-LSGVMDDRGKYIYISQAEMKAVADYIKRQ-G 215 (251)
Q Consensus 141 q~lL~~FI~YIK~~--KV-V~LEDLAa~FgLrTqdvI~RIq~Lea~G~-LTGViDDRGKFIYIS~EEm~aVA~fI~qr-G 215 (251)
...+...++||..+ .- +.+++||..+|++.--+..-.++ .|. +.. ||..-=|+....-+... .
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 45688999999877 32 78999999999997766655553 232 222 67778888888888332 3
Q ss_pred CccHHHHHhhc
Q 025511 216 RVSISHLASKS 226 (251)
Q Consensus 216 RVSisELa~~s 226 (251)
..||+++|..|
T Consensus 264 ~~sI~eIA~~~ 274 (302)
T PRK09685 264 DEKITSIAYKW 274 (302)
T ss_pred CCCHHHHHHHh
Confidence 57999999876
No 424
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=23.71 E-value=3.9e+02 Score=21.46 Aligned_cols=13 Identities=23% Similarity=0.403 Sum_probs=5.1
Q ss_pred HHHHHHhhhhhhh
Q 025511 40 ILVCLCTSFLFLL 52 (251)
Q Consensus 40 ~~~~~~~~~~~~~ 52 (251)
+++++...|.|.+
T Consensus 7 vll~ll~~l~y~l 19 (105)
T PRK00888 7 LLLALLVWLQYSL 19 (105)
T ss_pred HHHHHHHHHHHHH
Confidence 3333333444433
No 425
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=23.67 E-value=7.8e+02 Score=24.99 Aligned_cols=18 Identities=17% Similarity=0.132 Sum_probs=11.0
Q ss_pred hHHhHcCCChHHHHHHHH
Q 025511 161 DLAAEFKLRTQECINRIT 178 (251)
Q Consensus 161 DLAa~FgLrTqdvI~RIq 178 (251)
.|..-=||+.+++-+.|-
T Consensus 137 ~le~~a~lt~~eak~~l~ 154 (514)
T TIGR03319 137 ELERISGLTQEEAKEILL 154 (514)
T ss_pred HHHHHhCCCHHHHHHHHH
Confidence 444445777777776543
No 426
>PRK13500 transcriptional activator RhaR; Provisional
Probab=23.43 E-value=1.6e+02 Score=26.85 Aligned_cols=71 Identities=14% Similarity=0.279 Sum_probs=50.4
Q ss_pred hhHHHHHHHHHHhc--CccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHH-----HHHHHHHh
Q 025511 141 RDLLADFVEYIKKH--KCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMK-----AVADYIKR 213 (251)
Q Consensus 141 q~lL~~FI~YIK~~--KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~-----aVA~fI~q 213 (251)
...+..+++||..+ .-+.+++||..+|++..-.-...++- || .|+-++- .-|..+-.
T Consensus 205 ~~~l~~i~~yI~~~~~e~isl~~lA~~~~iS~~~L~r~FK~~------tG----------~T~~~yi~~~RL~~A~~LL~ 268 (312)
T PRK13500 205 ETLLDKLITRLAASLKSPFALDKFCDEASCSERVLRQQFRQQ------TG----------MTINQYLRQVRVCHAQYLLQ 268 (312)
T ss_pred HHHHHHHHHHHHHcccCCCCHHHHHHHHCcCHHHHHHHHHHH------HC----------cCHHHHHHHHHHHHHHHHHH
Confidence 45789999999885 45899999999999888777766653 22 3443332 22444455
Q ss_pred cCCccHHHHHhhcc
Q 025511 214 QGRVSISHLASKSN 227 (251)
Q Consensus 214 rGRVSisELa~~sN 227 (251)
.+..||+|+|..|.
T Consensus 269 ~t~~sI~eIA~~~G 282 (312)
T PRK13500 269 HSRLLISDISTECG 282 (312)
T ss_pred cCCCCHHHHHHHhC
Confidence 67889999998774
No 427
>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=23.30 E-value=70 Score=27.85 Aligned_cols=54 Identities=13% Similarity=0.271 Sum_probs=33.9
Q ss_pred HHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHH-HHHHHHHHhcCCccH
Q 025511 145 ADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEM-KAVADYIKRQGRVSI 219 (251)
Q Consensus 145 ~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm-~aVA~fI~qrGRVSi 219 (251)
..|..|++...++..++++..++..+.+ -..++|+++++ -.+++.+..--|.++
T Consensus 80 ~~f~~~l~~~~L~t~~ev~~~l~~~~~~---------------------~~~~~v~~~dYL~Gl~DltGEL~R~ai 134 (200)
T PF01997_consen 80 ISFYHYLETGRLLTPEEVGEILGFSEDD---------------------EDRFHVTPEDYLLGLADLTGELMRYAI 134 (200)
T ss_dssp HHHHHHHHHSSS--HHHHHHHCTCBSST---------------------SCSSB--HHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHcCCCCCCHHHHHHHHhhcccc---------------------ccceecCHHHHHHHHHHHHHHHHHHHH
Confidence 4477799999999999999999987655 44456666663 455555544444443
No 428
>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=22.99 E-value=3.8e+02 Score=21.54 Aligned_cols=64 Identities=14% Similarity=0.169 Sum_probs=46.7
Q ss_pred chHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHH--HHHhcCCccHHHHHhhc
Q 025511 158 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVAD--YIKRQGRVSISHLASKS 226 (251)
Q Consensus 158 ~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~--fI~qrGRVSisELa~~s 226 (251)
.+.++|..+|+++. -|.--+..|.|...-.+.|.|=|-|++++..+.. +.++-| +|++++.+.-
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 46789999999754 3567788899986655556677889999987643 444556 7888877643
No 429
>smart00434 TOP4c DNA Topoisomerase IV. Bacterial DNA topoisomerase IV, GyrA, ParC
Probab=22.88 E-value=71 Score=31.68 Aligned_cols=35 Identities=23% Similarity=0.532 Sum_probs=28.5
Q ss_pred cchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCC
Q 025511 157 IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDR 193 (251)
Q Consensus 157 V~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDR 193 (251)
+.+.+|- +|..|++.++.|.+|...|.|.|++|++
T Consensus 235 ivItElP--~~~~~~~~~e~I~~lv~~~ki~~i~~~~ 269 (445)
T smart00434 235 IVITELP--YQVNKAKLIEKIAELVKDKKIEGIIDVR 269 (445)
T ss_pred EEEEeCC--CcccHHHHHHHHHHHHhcCCCCcceehh
Confidence 3444443 5788999999999999999999999865
No 430
>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=22.78 E-value=3.6e+02 Score=21.65 Aligned_cols=65 Identities=17% Similarity=0.212 Sum_probs=49.2
Q ss_pred chHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHH--HHHhcCCccHHHHHhhcc
Q 025511 158 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVAD--YIKRQGRVSISHLASKSN 227 (251)
Q Consensus 158 ~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~--fI~qrGRVSisELa~~sN 227 (251)
.+.++|..+|+++. -|.--+..|-|...-.+.|-|=|-|++.+..|.. ..++-| +|++++.+..+
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 4668899999998766666788889999988763 334446 78888776544
No 431
>PHA02679 ORF091 IMV membrane protein; Provisional
Probab=22.71 E-value=55 Score=24.30 Aligned_cols=19 Identities=5% Similarity=0.289 Sum_probs=15.4
Q ss_pred HHHHHHHHhhhhhhhhHHh
Q 025511 38 LLILVCLCTSFLFLLSFSL 56 (251)
Q Consensus 38 ~~~~~~~~~~~~~~~~~~~ 56 (251)
++++.|+|.+.+.|..+|.
T Consensus 8 ~iL~~i~~~al~~N~~lS~ 26 (53)
T PHA02679 8 AVLVLIFCAALAANFYMPP 26 (53)
T ss_pred HHHHHHHHHHHHHHeeeCc
Confidence 6778899999998887764
No 432
>PF12668 DUF3791: Protein of unknown function (DUF3791); InterPro: IPR024269 This entry represents proteins of unknown function.
Probab=22.68 E-value=77 Score=22.82 Aligned_cols=22 Identities=18% Similarity=0.357 Sum_probs=19.7
Q ss_pred chHhHHhHcCCChHHHHHHHHH
Q 025511 158 PLEDLAAEFKLRTQECINRITS 179 (251)
Q Consensus 158 ~LEDLAa~FgLrTqdvI~RIq~ 179 (251)
.++.+|.++|++..++.+++.+
T Consensus 7 ~Ie~~A~~~~~s~~ea~~~~~~ 28 (62)
T PF12668_consen 7 CIEEFAKKLNISGEEAYNYFKR 28 (62)
T ss_pred HHHHHHHHHCcCHHHHHHHHHH
Confidence 5899999999999999998774
No 433
>KOG0388 consensus SNF2 family DNA-dependent ATPase [Replication, recombination and repair]
Probab=22.25 E-value=3.9e+02 Score=29.74 Aligned_cols=23 Identities=26% Similarity=0.609 Sum_probs=16.1
Q ss_pred hhhHhhhhhcccccccccccchh
Q 025511 14 IFDIHRVLEGYESSTRKDTRANS 36 (251)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~~~~~~ 36 (251)
|--.||++-+|.|..-.+.|.-|
T Consensus 358 i~k~~riiqq~q~~rstnakk~s 380 (1185)
T KOG0388|consen 358 IRKVHRIIQQYQSARSTNAKKTS 380 (1185)
T ss_pred HHHHHHHHHHHHHHhhhhhHHHH
Confidence 45578999999986655555544
No 434
>PF14163 SieB: Superinfection exclusion protein B
Probab=22.18 E-value=2.4e+02 Score=23.24 Aligned_cols=26 Identities=12% Similarity=0.285 Sum_probs=17.8
Q ss_pred hHHHHHHHHHhhhhhhhhHHhHHhhh
Q 025511 36 SLLLILVCLCTSFLFLLSFSLLFDMF 61 (251)
Q Consensus 36 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 61 (251)
..+.+.+.+|+||+....++..++-+
T Consensus 34 ~~i~~~fl~s~s~li~~~~~~~~~~~ 59 (151)
T PF14163_consen 34 PWIGLIFLFSVSYLIAQLLSFIYKEA 59 (151)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45566666788888887777775443
No 435
>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=22.08 E-value=3.8e+02 Score=20.80 Aligned_cols=54 Identities=15% Similarity=0.281 Sum_probs=38.5
Q ss_pred HHHHHHhc-CccchHhHHhHc-----CCChHHHHHHHHHHHhcCCcceeeeCCCceEEEc
Q 025511 147 FVEYIKKH-KCIPLEDLAAEF-----KLRTQECINRITSLENMGRLSGVMDDRGKYIYIS 200 (251)
Q Consensus 147 FI~YIK~~-KVV~LEDLAa~F-----gLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS 200 (251)
.+++|+.. +-+..++|-..+ +++..-|-+-|..|.+.|.|.-+-.+.|...|-.
T Consensus 13 Il~~l~~~~~~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~~~~~~~~~~Y~~ 72 (120)
T PF01475_consen 13 ILELLKESPEHLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRKIEFGDGESRYEL 72 (120)
T ss_dssp HHHHHHHHSSSEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEETTSEEEEEE
T ss_pred HHHHHHcCCCCCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEEEEcCCCcceEee
Confidence 45566554 466666665544 6777788999999999999999988877666643
No 436
>PRK13696 hypothetical protein; Provisional
Probab=21.90 E-value=1.5e+02 Score=22.56 Aligned_cols=27 Identities=26% Similarity=0.261 Sum_probs=23.5
Q ss_pred ceEEEcHHHHHHHHHHHHhcCCccHHHHHh
Q 025511 195 KYIYISQAEMKAVADYIKRQGRVSISHLAS 224 (251)
Q Consensus 195 KFIYIS~EEm~aVA~fI~qrGRVSisELa~ 224 (251)
|=|-||++.++.+. ..+|..|.+|+..
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 67899999999999 6778899998875
No 437
>PF00584 SecE: SecE/Sec61-gamma subunits of protein translocation complex; InterPro: IPR001901 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component []. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecCY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. The chaperone protein SecB [] is a highly acidic homotetrameric protein that exists as a "dimer of dimers" in the bacterial cytoplasm. SecB maintains preproteins in an unfolded state after translation, and targets these to the peripheral membrane protein ATPase SecA for secretion []. SecE, part of the main SecYEG translocase complex, is ~106 residues in length, and spans the inner membrane of the Gram-negative bacterial envelope. Together with SecY and SecG, SecE forms a multimeric channel through which preproteins are translocated, using both proton motive forces and ATP-driven secretion. The latter is mediated by SecA. In eukaryotes, the evolutionary related protein sec61-gamma plays a role in protein translocation through the endoplasmic reticulum; it is part of a trimeric complex that also consist of sec61-alpha and beta []. Both secE and sec61-gamma are small proteins of about 60 to 90 amino acids that contain a single transmembrane region at their C-terminal extremity (Escherichia coli secE is an exception, in that it possess an extra N-terminal segment of 60 residues that contains two additional transmembrane domains) [].; GO: 0006605 protein targeting, 0006886 intracellular protein transport, 0016020 membrane; PDB: 3J01_B 2WW9_B 2WWA_B 3DL8_C 2WWB_B 3DIN_G 2ZJS_E 2ZQP_E.
Probab=21.80 E-value=86 Score=21.99 Aligned_cols=39 Identities=10% Similarity=0.347 Sum_probs=26.4
Q ss_pred hhHhhhHhhhhhcccccccccccchhHHHHHHHHHhhhh
Q 025511 11 KTYIFDIHRVLEGYESSTRKDTRANSLLLILVCLCTSFL 49 (251)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 49 (251)
+.|+-++-.-+.--.=+|++++..+++..++++++.+.+
T Consensus 3 ~~f~~~~~~Elkkv~WP~~~e~~~~t~~Vl~~~~i~~~~ 41 (57)
T PF00584_consen 3 KNFFREVKKELKKVTWPSRKELLKSTIIVLVFVIIFGLF 41 (57)
T ss_dssp HHHHHCHHHHHHHHHCCCTHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 345555555555556678999998888877776665543
No 438
>PF10183 ESSS: ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) ; InterPro: IPR019329 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This entry represents the ESSS subunit from mitochondrial NADH:ubiquinone oxidoreductase (complex I). It carries mitochondrial import sequences [].
Probab=21.74 E-value=1.2e+02 Score=24.23 Aligned_cols=28 Identities=14% Similarity=-0.078 Sum_probs=14.9
Q ss_pred HHHHHhhhhhhhhHHhHHhhhhhHHHHHH
Q 025511 41 LVCLCTSFLFLLSFSLLFDMFDLKADEAA 69 (251)
Q Consensus 41 ~~~~~~~~~~~~~~~~~~~~~~Reaee~~ 69 (251)
+|++++.+.|.|-.+. -+-+.|||..+.
T Consensus 71 ~v~~~~~~~y~PD~~i-~~WA~rEA~~rl 98 (105)
T PF10183_consen 71 LVFGGVFLAYKPDTSI-QTWARREAYRRL 98 (105)
T ss_pred HHHHHHHHHcCCCCCH-HHHHHHHHHHHH
Confidence 3344444445555544 666777765543
No 439
>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=21.73 E-value=3.1e+02 Score=20.74 Aligned_cols=70 Identities=14% Similarity=0.207 Sum_probs=46.3
Q ss_pred HHHHHHHHh---cCccchHhHHhHcCCChHHHHH-HHHHHHhcCCcceeeeC----CCceEEEcHHHHHHHHHHHHhcC
Q 025511 145 ADFVEYIKK---HKCIPLEDLAAEFKLRTQECIN-RITSLENMGRLSGVMDD----RGKYIYISQAEMKAVADYIKRQG 215 (251)
Q Consensus 145 ~~FI~YIK~---~KVV~LEDLAa~FgLrTqdvI~-RIq~Lea~G~LTGViDD----RGKFIYIS~EEm~aVA~fI~qrG 215 (251)
..+++.+.. ...-.+=.|+...|+|..|++. +..++...+... .+.. ....|.|+++=...+..++...+
T Consensus 3 ~~l~~~~~~~~~~~~~~~~~l~~~tG~R~~Ei~~l~~~~~~~~~~~~-~i~~~K~~~~~~i~i~~~~~~~l~~~~~~~~ 80 (164)
T cd00397 3 ERLLAAAEASTPERLYLALLLLLATGLRISELCALRWSDIDLDKRVI-HITGTKTKKERTVPLSEEALKLLKEYLKKRR 80 (164)
T ss_pred HHHHHHhhhccccHHHHHHHHHHHhCCCHHHHhCCchhhhccccCEE-EEecCCCCCeeEEecCHHHHHHHHHHHHHhc
Confidence 455666665 5555666688889999999988 455565543111 2222 23689999988888888877654
No 440
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=21.70 E-value=4.4e+02 Score=21.35 Aligned_cols=62 Identities=16% Similarity=0.293 Sum_probs=41.9
Q ss_pred HHHHHHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHHhcCCccHHHH
Q 025511 143 LLADFVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIKRQGRVSISHL 222 (251)
Q Consensus 143 lL~~FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~qrGRVSisEL 222 (251)
+...+...++.+. +..+|||..-|++ +..|.+|. +|+. .+|.+-+.++|+++ .|++.+|
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 3445555555444 4688999999985 56666654 4555 68999999999987 4555555
Q ss_pred Hhh
Q 025511 223 ASK 225 (251)
Q Consensus 223 a~~ 225 (251)
...
T Consensus 65 ~~~ 67 (120)
T PRK13890 65 LES 67 (120)
T ss_pred hcc
Confidence 433
No 441
>COG5187 RPN7 26S proteasome regulatory complex component, contains PCI domain [Posttranslational modification, protein turnover, chaperones]
Probab=21.49 E-value=1.2e+02 Score=30.19 Aligned_cols=68 Identities=19% Similarity=0.230 Sum_probs=48.7
Q ss_pred HhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeC-CCceEEEcHHHHHHHHHHHHhcCCccH
Q 025511 152 KKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDD-RGKYIYISQAEMKAVADYIKRQGRVSI 219 (251)
Q Consensus 152 K~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDD-RGKFIYIS~EEm~aVA~fI~qrGRVSi 219 (251)
.+-|...|+-.|+.||+++.=+=+-+-+..-+|+|.-|||- .|----=+|+|-++=-+-+-+.|-+=+
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 45567899999999999988777789999999999999996 454333456765444444444454433
No 442
>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=21.44 E-value=44 Score=29.10 Aligned_cols=39 Identities=21% Similarity=0.392 Sum_probs=29.0
Q ss_pred eCCCceEEEcHHHHHHHHHHHHhc-CCccHH-HHHhhcccccc
Q 025511 191 DDRGKYIYISQAEMKAVADYIKRQ-GRVSIS-HLASKSNQFID 231 (251)
Q Consensus 191 DDRGKFIYIS~EEm~aVA~fI~qr-GRVSis-ELa~~sN~lI~ 231 (251)
|++|+| +|..||+.+..|++.- =|++.. -|..+++.+++
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 46666666554
No 443
>PRK04280 arginine repressor; Provisional
Probab=21.43 E-value=2.2e+02 Score=24.21 Aligned_cols=56 Identities=23% Similarity=0.306 Sum_probs=39.7
Q ss_pred HHHHHHHHhcCccchHhHHhHc---CCC-hHHHHHH-HHHHHhcCCcceeeeCCCceEEEcHHHH
Q 025511 145 ADFVEYIKKHKCIPLEDLAAEF---KLR-TQECINR-ITSLENMGRLSGVMDDRGKYIYISQAEM 204 (251)
Q Consensus 145 ~~FI~YIK~~KVV~LEDLAa~F---gLr-TqdvI~R-Iq~Lea~G~LTGViDDRGKFIYIS~EEm 204 (251)
.....-|+.+.|-.=+||+... |+. ||-+|+| |++| |- .=|-|..|+|.|.-|.+.
T Consensus 7 ~~I~~iI~~~~I~tQeeL~~~L~~~Gi~vTQATiSRDikeL---~l-vKv~~~~G~~~Y~lp~~~ 67 (148)
T PRK04280 7 IKIREIITNNEIETQDELVDRLREEGFNVTQATVSRDIKEL---HL-VKVPLPDGRYKYSLPADQ 67 (148)
T ss_pred HHHHHHHHhCCCCCHHHHHHHHHHcCCCeehHHHHHHHHHc---CC-EEeecCCCcEEEeecccc
Confidence 3445567888888888876542 443 7999998 5544 44 348899999999987764
No 444
>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=21.36 E-value=2.2e+02 Score=19.82 Aligned_cols=44 Identities=16% Similarity=0.301 Sum_probs=31.0
Q ss_pred chHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHH
Q 025511 158 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQA 202 (251)
Q Consensus 158 ~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~E 202 (251)
.+...|..+|++..-+-.+|+.||..=-.. +++-.|+-+-+|+.
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 778899999999999999999999753222 34443444666653
No 445
>COG4125 Predicted membrane protein [Function unknown]
Probab=21.35 E-value=92 Score=27.35 Aligned_cols=24 Identities=33% Similarity=0.290 Sum_probs=19.6
Q ss_pred HHHHHHHHhhhhhhhhHHhHHhhh
Q 025511 38 LLILVCLCTSFLFLLSFSLLFDMF 61 (251)
Q Consensus 38 ~~~~~~~~~~~~~~~~~~~~~~~~ 61 (251)
-+++..+|-.|+||.+|-.++-..
T Consensus 116 g~~lffl~Ytf~fNwaYD~l~~~~ 139 (149)
T COG4125 116 GLILFFLPYTFLFNWAYDRLRPRP 139 (149)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhcc
Confidence 467888999999999998887544
No 446
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=21.33 E-value=2.7e+02 Score=24.45 Aligned_cols=61 Identities=11% Similarity=0.228 Sum_probs=40.2
Q ss_pred chHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHHHH-hc-CCccHHHHHh
Q 025511 158 PLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADYIK-RQ-GRVSISHLAS 224 (251)
Q Consensus 158 ~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~fI~-qr-GRVSisELa~ 224 (251)
.+.++|..+|+++.-+... ...|.|...-|+.|.++ .|++.+. .-.||+ .+ -=+|+.++..
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 KTPFVAKKLGVSPKTVQRW----VKQLNLPCEKNEYGHYI-FTEEDLQ-LLEYVKSQIEEGQNMQDTQK 64 (175)
T ss_pred CHHHHHHHHCcCHHHHHHH----HHcCCCCCCcCCCCCEE-ECHHHHH-HHHHHHHHHHcCCCHHHHHH
Confidence 4678999999977654443 34788876566677666 4888885 445554 22 3467777755
No 447
>PF10882 bPH_5: Bacterial PH domain; InterPro: IPR020482 This entry contains membrane proteins with no known function.
Probab=21.20 E-value=92 Score=23.52 Aligned_cols=21 Identities=19% Similarity=0.279 Sum_probs=18.1
Q ss_pred ceEEEcHHHHHHHHHHHHhcC
Q 025511 195 KYIYISQAEMKAVADYIKRQG 215 (251)
Q Consensus 195 KFIYIS~EEm~aVA~fI~qrG 215 (251)
+-++|||+..+.+.+.+++|.
T Consensus 80 ~~y~isp~~~~~fi~~l~~r~ 100 (100)
T PF10882_consen 80 KTYVISPEDPEEFIEALKKRA 100 (100)
T ss_pred ceEEEcCCCHHHHHHHHHhcC
Confidence 666799999999999999874
No 448
>CHL00170 cpcA phycocyanin alpha subunit; Reviewed
Probab=21.00 E-value=49 Score=29.03 Aligned_cols=39 Identities=26% Similarity=0.559 Sum_probs=29.8
Q ss_pred eCCCceEEEcHHHHHHHHHHHHhc-CCccH-HHHHhhcccccc
Q 025511 191 DDRGKYIYISQAEMKAVADYIKRQ-GRVSI-SHLASKSNQFID 231 (251)
Q Consensus 191 DDRGKFIYIS~EEm~aVA~fI~qr-GRVSi-sELa~~sN~lI~ 231 (251)
|++|+| +|..|++++..|+++- -|+.+ .-|+.+++.+++
T Consensus 13 D~qgRy--ls~~eL~~l~~~~~~g~~RL~aa~~Lt~nA~~IV~ 53 (162)
T CHL00170 13 DSQGRF--LSNGELQACNGRFQRAAASLEAARSLTSNAQRLID 53 (162)
T ss_pred HhccCC--CCHHHHHHHHHHHhccHHHHHHHHHHHhhHHHHHH
Confidence 778887 6899999999999864 56665 357777766665
No 449
>KOG2784 consensus Phenylalanyl-tRNA synthetase, beta subunit [Translation, ribosomal structure and biogenesis]
Probab=20.94 E-value=2.2e+02 Score=28.92 Aligned_cols=77 Identities=26% Similarity=0.354 Sum_probs=55.8
Q ss_pred HHHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHH----------HHHHhcCC
Q 025511 147 FVEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVA----------DYIKRQGR 216 (251)
Q Consensus 147 FI~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA----------~fI~qrGR 216 (251)
.+..++..-=+.--+||+.|+.-.|.++.-|++|.+.|.|+- -+.-.+.|.=-.|=..+| .+|-.-|
T Consensus 8 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 8 ILEKLQESDEVDSSDLAAPFNEDHQQVVGALKSLQAGGVIEV--KDVETKTYELTAEGEEIAREGSHEALVFESIPEEG- 84 (483)
T ss_pred HHHHHHhccCCChhhhcCchhhhhHHHHHHHHHHhhcCceEE--EeeeeEEEeeChhHHHHHhcCCcceeeeeccCccc-
Confidence 445555555577789999999999999999999999555442 245566665444444444 4677788
Q ss_pred ccHHHHHhhc
Q 025511 217 VSISHLASKS 226 (251)
Q Consensus 217 VSisELa~~s 226 (251)
++++||.+..
T Consensus 85 l~~~el~~k~ 94 (483)
T KOG2784|consen 85 LAIAELMKKL 94 (483)
T ss_pred cCHHHHHhhh
Confidence 8999998776
No 450
>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=20.92 E-value=2.7e+02 Score=21.00 Aligned_cols=51 Identities=12% Similarity=0.103 Sum_probs=42.0
Q ss_pred HHHHHhcCccchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEE
Q 025511 148 VEYIKKHKCIPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIY 198 (251)
Q Consensus 148 I~YIK~~KVV~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIY 198 (251)
-+++..++-..+.+|+..-|++..++---|==|-.+|.|.---.++--||+
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 356667888999999999999999999999999999999766666655554
No 451
>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=20.85 E-value=2.4e+02 Score=20.17 Aligned_cols=38 Identities=11% Similarity=0.140 Sum_probs=25.3
Q ss_pred HcCCChHHHHHHHHHHHhcC-CcceeeeCCCceE-EEcHHHHH
Q 025511 165 EFKLRTQECINRITSLENMG-RLSGVMDDRGKYI-YISQAEMK 205 (251)
Q Consensus 165 ~FgLrTqdvI~RIq~Lea~G-~LTGViDDRGKFI-YIS~EEm~ 205 (251)
..+.+..++++.+. +.+ ....|+|+.|+|+ +||...+.
T Consensus 7 ~~~~~~~~~~~~~~---~~~~~~~~v~d~~~~~~G~v~~~~l~ 46 (112)
T cd04624 7 DPDTSIREAAKLMA---EENVGSVVVVDPDERPIGIVTERDIV 46 (112)
T ss_pred CCCCcHHHHHHHHH---HcCCCEEEEECCCCCEEEEeeHHHHH
Confidence 34556677776653 233 3456789889998 78888874
No 452
>PF06269 DUF1029: Protein of unknown function (DUF1029); InterPro: IPR009372 This entry is represented by Vaccinia virus, A14.5L; it is a family of uncharacterised viral proteins.
Probab=20.79 E-value=63 Score=24.00 Aligned_cols=19 Identities=26% Similarity=0.522 Sum_probs=15.5
Q ss_pred HHHHHHHHhhhhhhhhHHh
Q 025511 38 LLILVCLCTSFLFLLSFSL 56 (251)
Q Consensus 38 ~~~~~~~~~~~~~~~~~~~ 56 (251)
++++.|+|.+.++|..+|.
T Consensus 8 ~iL~~i~~~al~~N~~~S~ 26 (53)
T PF06269_consen 8 LILLGIICAALLANFKMSS 26 (53)
T ss_pred HHHHHHHHHHHHHHeeecc
Confidence 5677899999999987765
No 453
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=20.78 E-value=90 Score=26.73 Aligned_cols=32 Identities=25% Similarity=0.277 Sum_probs=25.4
Q ss_pred HhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCc
Q 025511 160 EDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGK 195 (251)
Q Consensus 160 EDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGK 195 (251)
-=||.++||+.. +++.|.+.|.|.|..+-.||
T Consensus 107 ~lLa~~L~lSrs----~l~~l~~~G~I~~~~~~~~~ 138 (142)
T PF06353_consen 107 RLLARQLGLSRS----RLKRLIEQGLIRSDPDKSKK 138 (142)
T ss_pred HHHHHHhCcCHH----HHHHHHHCCCEEecCccchh
Confidence 348899999864 68999999999998776443
No 454
>PRK13428 F0F1 ATP synthase subunit delta; Provisional
Probab=20.60 E-value=8.3e+02 Score=24.16 Aligned_cols=19 Identities=0% Similarity=0.099 Sum_probs=9.9
Q ss_pred hhhhhhhhHHhHHhhhhhH
Q 025511 46 TSFLFLLSFSLLFDMFDLK 64 (251)
Q Consensus 46 ~~~~~~~~~~~~~~~~~Re 64 (251)
..+++-.-|..+..+++..
T Consensus 15 ~~lL~kfl~~Pi~~~l~~R 33 (445)
T PRK13428 15 VFLVWRFVVPPVRRLMAAR 33 (445)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3334444555566666544
No 455
>PTZ00399 cysteinyl-tRNA-synthetase; Provisional
Probab=20.59 E-value=2.4e+02 Score=29.46 Aligned_cols=8 Identities=0% Similarity=0.206 Sum_probs=5.2
Q ss_pred HHHHhhhc
Q 025511 115 FEFEKWKG 122 (251)
Q Consensus 115 EEY~KwK~ 122 (251)
.+|.+|-.
T Consensus 602 ~~ys~~De 609 (651)
T PTZ00399 602 DKYSAFDE 609 (651)
T ss_pred cccCcccc
Confidence 45777765
No 456
>PRK11173 two-component response regulator; Provisional
Probab=20.53 E-value=1.8e+02 Score=24.04 Aligned_cols=35 Identities=20% Similarity=0.410 Sum_probs=29.7
Q ss_pred CCCceEEEcHHHHHHHHHHHHhcCCc-cHHHHHhhc
Q 025511 192 DRGKYIYISQAEMKAVADYIKRQGRV-SISHLASKS 226 (251)
Q Consensus 192 DRGKFIYIS~EEm~aVA~fI~qrGRV-SisELa~~s 226 (251)
-.|+-|.+|+.|+.-+.-|+...|+| |..+|...-
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 457
>PF14348 DUF4400: Domain of unknown function (DUF4400)
Probab=20.51 E-value=66 Score=27.80 Aligned_cols=38 Identities=26% Similarity=0.200 Sum_probs=27.1
Q ss_pred hHhhhhhcccccccccccchhHHHHHHHHHhhhhhhhh
Q 025511 16 DIHRVLEGYESSTRKDTRANSLLLILVCLCTSFLFLLS 53 (251)
Q Consensus 16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 53 (251)
||.|--=||+|+..-..-..++..+++..|..++++|.
T Consensus 134 ~iRr~~~g~eSp~~~h~a~~~~~~~~~~~~~lyL~lP~ 171 (198)
T PF14348_consen 134 DIRRFGFGRESPFVYHHAKRSVIPLLILPWVLYLSLPF 171 (198)
T ss_pred HHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHccc
Confidence 67777779999988766556666666666677777664
No 458
>PF02731 SKIP_SNW: SKIP/SNW domain; InterPro: IPR004015 SKIP (SKI-interacting protein) is an essential spliceosomal component and transcriptional coregulator, which may provide regulatory coupling of transcription initiation and splicing []. SKIP was identified in a yeast 2-hybrid screen, where it was shown to interact with both the cellular and viral forms of SKI through the highly conserved region on SKIP known as the SNW domain []. SKIP is now known to interact with a number of other proteins as well. SKIP potentiates the activity of important transcription factors, such as vitamin D receptor, CBF1 (RBP-Jkappa), Smad2/3, and MyoD. It works with Ski in overcoming pRb-mediated cell cycle arrest, and it is targeted by the viral transactivators EBNA2 and E7 []. This entry represents the SNW domain.; GO: 0000398 nuclear mRNA splicing, via spliceosome, 0005681 spliceosomal complex
Probab=20.48 E-value=4e+02 Score=23.56 Aligned_cols=25 Identities=28% Similarity=0.243 Sum_probs=15.3
Q ss_pred hhhhHHhHHhhhhhHHHHHHHHhhhh
Q 025511 50 FLLSFSLLFDMFDLKADEAARESRQS 75 (251)
Q Consensus 50 ~~~~~~~~~~~~~Reaee~~RE~Rk~ 75 (251)
.|-.|+.|-+-+. .|+..+|++=+.
T Consensus 103 INd~Fa~LseAL~-~Ad~~aReev~~ 127 (158)
T PF02731_consen 103 INDKFAKLSEALY-IADRKAREEVRQ 127 (158)
T ss_pred ccHHHHHHHHHHH-HHHHHHHHHHHH
Confidence 4667887766554 466666665433
No 459
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=20.43 E-value=2.8e+02 Score=23.67 Aligned_cols=66 Identities=9% Similarity=0.238 Sum_probs=56.1
Q ss_pred cchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeC--CCceEEEcHHHHHHHHHHHHhcCCccHHHHHhh
Q 025511 157 IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDD--RGKYIYISQAEMKAVADYIKRQGRVSISHLASK 225 (251)
Q Consensus 157 V~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDD--RGKFIYIS~EEm~aVA~fI~qrGRVSisELa~~ 225 (251)
....++|..||++-.-+.+=|+.....|.+ .... .|+==.+|+++++-+...++.+- .++.+++..
T Consensus 22 ~S~re~Ak~~gvs~sTvy~wv~r~~e~G~~--l~~~~~~GrP~kl~~~q~~~l~e~~~~k~-wTl~~~~~~ 89 (138)
T COG3415 22 LSCREAAKRFGVSISTVYRWVRRYRETGLD--LPPKPRKGRPRKLSEEQLEILLERLREKD-WTLKELVEE 89 (138)
T ss_pred ccHHHHHHHhCccHHHHHHHHHHhcccccc--ccCccCCCCCcccCHHHHHHHHHHHhccc-chHHHHHHH
Confidence 346789999999999999999999999998 4443 68888999999999999999888 877776543
No 460
>PRK10265 chaperone-modulator protein CbpM; Provisional
Probab=20.33 E-value=1.4e+02 Score=23.57 Aligned_cols=49 Identities=6% Similarity=0.165 Sum_probs=35.9
Q ss_pred cchHhHHhHcCCChHHHHHHHHHHHhcCCcceeeeCCCceEEEcHHHHHHHHHH
Q 025511 157 IPLEDLAAEFKLRTQECINRITSLENMGRLSGVMDDRGKYIYISQAEMKAVADY 210 (251)
Q Consensus 157 V~LEDLAa~FgLrTqdvI~RIq~Lea~G~LTGViDDRGKFIYIS~EEm~aVA~f 210 (251)
+.++||+...|+..+. |.+|.+.|-|....++.|.|.|-+ ..+..+-..
T Consensus 8 lt~~Elc~~~gi~~~~----l~eLve~GlIep~~~~~~~~~F~~-~~l~r~~~a 56 (101)
T PRK10265 8 FTITEFCLHTGVSEEE----LNEIVGLGVIEPREIQETTWVFDD-HAAIVVQRA 56 (101)
T ss_pred eeHHHHHHHHCcCHHH----HHHHHHCCCeecCCCCcccceECH-HHHHHHHHH
Confidence 6789999999997765 567888999988777778888754 334433333
No 461
>COG1695 Predicted transcriptional regulators [Transcription]
Probab=20.32 E-value=3e+02 Score=21.94 Aligned_cols=49 Identities=16% Similarity=0.285 Sum_probs=40.4
Q ss_pred CCChHHHHHHHHHHHhcCCcceeeeCC-C----ceEEEcHHHHHHHHHHHHhcC
Q 025511 167 KLRTQECINRITSLENMGRLSGVMDDR-G----KYIYISQAEMKAVADYIKRQG 215 (251)
Q Consensus 167 gLrTqdvI~RIq~Lea~G~LTGViDDR-G----KFIYIS~EEm~aVA~fI~qrG 215 (251)
..+..-+---+..|+++|-|++...+. | ||--||+.-.+.++.+.+.-+
T Consensus 41 ~~s~gtiYp~L~~Le~~Gli~~~~~~~~~g~~rk~Y~lTe~G~~~l~~~~~~~~ 94 (138)
T COG1695 41 EPSPGTIYPLLKRLEKEGLIESRWEESGGGPPRKYYRLTEKGKEELAELREEWG 94 (138)
T ss_pred cCCCCcHHHHHHHHHHCCCeEEEecccCCCCCceEEEECHHHHHHHHHHHHHHH
Confidence 356667778899999999999997765 3 899999999999998875543
No 462
>CHL00183 petJ cytochrome c553; Provisional
Probab=20.30 E-value=76 Score=24.51 Aligned_cols=17 Identities=29% Similarity=0.579 Sum_probs=15.2
Q ss_pred EEcHHHHHHHHHHHHhc
Q 025511 198 YISQAEMKAVADYIKRQ 214 (251)
Q Consensus 198 YIS~EEm~aVA~fI~qr 214 (251)
-+|++|+.+|+.||...
T Consensus 87 ~Ls~~ei~~i~aYi~~~ 103 (108)
T CHL00183 87 RLSDEDIEDVANYVLSQ 103 (108)
T ss_pred CCCHHHHHHHHHHHHHh
Confidence 38999999999999865
No 463
>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=20.11 E-value=1.4e+02 Score=26.86 Aligned_cols=25 Identities=24% Similarity=0.531 Sum_probs=20.7
Q ss_pred ccchHhHHhHcCCChHHHHHHHHHH
Q 025511 156 CIPLEDLAAEFKLRTQECINRITSL 180 (251)
Q Consensus 156 VV~LEDLAa~FgLrTqdvI~RIq~L 180 (251)
.+.++|||..-|++.+|+|.-++.|
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 6899999999999999998877665
No 464
>PF05262 Borrelia_P83: Borrelia P83/100 protein; InterPro: IPR007926 This family consists of several Borrelia P83/P100 antigen proteins.
Probab=20.11 E-value=2.8e+02 Score=28.39 Aligned_cols=15 Identities=33% Similarity=0.461 Sum_probs=9.4
Q ss_pred hHHhhhhhHHHHHHH
Q 025511 56 LLFDMFDLKADEAAR 70 (251)
Q Consensus 56 ~~~~~~~Reaee~~R 70 (251)
.++|.-.|+++++..
T Consensus 199 ~m~D~KEreaeea~k 213 (489)
T PF05262_consen 199 DMVDIKEREAEEAAK 213 (489)
T ss_pred hhHHHHHHHhHHHHH
Confidence 456777777655553
Done!